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Transcriptome project (Gingeras)

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This page had recently undergone a "make-over" to reflect the Human Year 5 data sets.


RNA Analysis Task Group

Use this link to get to the ENCODE RNA-group where you will find information about ongoing analysis. http://encodewiki.ucsc.edu/EncodeDCC/index.php/RNA.


The Sample/Data Matrix

This is Carrie's informal Google doc wherein you can follow production in "real-time" from the trenches. https://docs.google.com/spreadsheet/ccc?key=0AtSJnrlt4cvidFVrb1pjQjQtelZnZi1JM0VEam05Y3c&hl=en_US#gid=0

Year 1-4 Samples Year 1-4 Samples

Year 5 Samples Year 5 Samples

For year 5 we focused on getting subcompartment RNA-Seq data from the Tier 2.5 cell lines [A549, IMR90, SK-N-SH, MCF7]. We also have RNA-Seq data from clinical samples [CD14+, CD20+, CD34+]. In addition, we have done ribosomal-depleted Total RNA-Seq for 20 primary cell lines of divers tissue origins. The lionshare of these were done on biological replicates.

Some more details about the 20 primary cell lines can be found below. In general, (1) donor is male and (1) donor is female for each cell type. The cells were sent to us in RNAlater (a preservative). We isolated the RNA, separated into long and small and did rRNA-depletions.

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Cell Type Description Lineage Karyotype Sex Tissue URL for Ordering Term ID Submitting Lab (by PI) Protocol Approved|
Formatting Conventions: cell name "_" more specific details, donor ID, vendor ID, or lot ID (must be unique) non-redundant (leave out descriptions such as normal, human and sex), lower-case, comma separated phrases ectoderm, mesoderm, endoderm, inner cell mass or blank cancer or normal M, F or U general tissue source, lower-case "["website vendorName vendorID"]" (space-delimited, no quotes) "["ebiBrendaTissueWebsite BTO:termID"]" (space-delimited, no quotes) PI last name "["[pdfTitle verticalBarOrPipe cellName]"]" (space-delimited, no quotes) No
HSaVEC_9100101.15 Saphenous Vein Endothelial Cells normal M saphenous vein / thigh PromoCell BTO:0003275 Gingeras HSaVEC-094 Promo_Cell_Protocol.pdf Yes
HSaVEC_0022202.16 Saphenous Vein Endothelial Cells normal M saphenous vein / thigh PromoCell BTO:0003275 Gingeras HSaVEC-093 Promo_Cell_Protocol.pdf Yes
NHEM M2_7011001.2 Epidermal Melanocytes (adult) normal M skin / cheek PromoCell BTO:0000847 Gingeras NHEM M2-084 Promo_Cell_Protocol.pdf Yes
NHEM M2_7012303 Epidermal Melanocytes (adult) normal F skin / temple PromoCell BTO:0000847 Gingeras NHEM M2-083 Promo_Cell_Protocol.pdf Yes
NHEM.f M2_5071302.2 Epidermal Melanocytes (foreskin) normal M skin / foreskin PromoCell BTO:0000847 Gingeras NHEM.f M2-082 Promo_Cell_Protocol.pdf Yes
NHEM.f M2_6022001 Epidermal Melanocytes (foreskin) normal M skin / foreskin PromoCell BTO:0000847 Gingeras NHEM.f M2-081 Promo_Cell_Protocol.pdf Yes
HWP_0092205 Undifferentiated White Preadipocytes normal M subcutaneous adipose tissue / abdomen PromoCell BTO:0004042 Gingeras HWP-080 Promo_Cell_Protocol.pdf Yes
HWP_8120201.5 Undifferentiated White Preadipocytes normal F subcutaneous adipose tissue / upper arm PromoCell BTO:0004042 Gingeras HWP-079 Promo_Cell_Protocol.pdf Yes
hMNC-PB_0022330.9 Mononuclear Cells normal M peripheral blood-single donor PromoCell BTO:0001025 Gingeras hMNC-PB-078 Promo_Cell_Protocol.pdf Yes
hMNC-PB_0082430.9 Mononuclear Cells normal F peripheral blood-single donor PromoCell BTO:0001025 Gingeras hMNC-PB-077 Promo_Cell_Protocol.pdf Yes
hMNC-CB_9111701.6 Mononuclear Cells normal F umbilical cord blood-single donor PromoCell BTO:0004054 Gingeras hMNC-CB-076 Promo_Cell_Protocol.pdf Yes
hMNC-CB_8072802.6 Mononuclear Cells normal M umbilical cord blood-single donor PromoCell BTO:0004054 Gingeras hMNC-CB-075 Promo_Cell_Protocol.pdf Yes
HPIEpC_ 9012801.2 Placental Epithelial Cells normal F placenta / amniotic membrane PromoCell BTO:0001975 Gingeras HPIEpC-074 Promo_Cell_Protocol.pdf Yes
HPIEpC_9041503.2 Placental Epithelial Cells normal M placenta / amniotic membrane PromoCell BTO:0001975 Gingeras HPIEpC-073 Promo_Cell_Protocol.pdf Yes
HPC-PL_0032601.13 Undifferentiated Pericytes normal M placenta PromoCell BTO:0001975 Gingeras HPC-PL-072 Promo_Cell_Protocol.pdf Yes
HPC-PL_0101504.13 Undifferentiated Pericytes normal F placenta PromoCell BTO:0001975 Gingeras HPC-PL-071 Promo_Cell_Protocol.pdf Yes
hMSC-UC_0081101.7 Undifferentiated Mesenchymal Stem Cells normal F umbilical cord / matrix (Wharton´s Jelly) PromoCell BTO:0003298 Gingeras hMSC-UC-070 Promo_Cell_Protocol.pdf Yes
hMSC-UC_0052501.7 Undifferentiated Mesenchymal Stem Cells normal M umbilical cord / matrix (Wharton´s Jelly) PromoCell BTO:0003298 Gingeras hMSC-UC-069 Promo_Cell_Protocol.pdf Yes
hMSC-BM_0050602.11 Undifferentiated Mesenchymal Stem Cells normal M bone marrow / femoral head PromoCell BTO:0003298 Gingeras hMSC-BM-068 Promo_Cell_Protocol.pdf Yes
hMSC-BM_0051105.11 Undifferentiated Mesenchymal Stem Cells normal F bone marrow / femoral head PromoCell BTO:0003298 Gingeras hMSC-BM-067 Promo_Cell_Protocol.pdf Yes
hMSC-AT_9061601.12 Undifferentiated Mesenchymal Stem Cells normal F subcutaneous adipose tissue / abdomen PromoCell BTO:0003298 Gingeras hMSC-AT-066 Promo_Cell_Protocol.pdf Yes
hMSC-AT_0102604.12 Undifferentiated Mesenchymal Stem Cells normal F subcutaneous adipose tissue / abdomen PromoCell BTO:0003298 Gingeras hMSC-AT-065 Promo_Cell_Protocol.pdf Yes
HMEpC Mammary Epithelial Cells (placeholder, waiting on second lot/donor from PromoCell) normal F mammary gland PromoCell BTO:0002178 Gingeras HMEpC-064 Promo_Cell_Protocol.pdf Yes
HMEpC_6022801.3 Mammary Epithelial Cells normal F mammary gland PromoCell BTO:0002178 Gingeras HMEpC-063 Promo_Cell_Protocol.pdf Yes
HFDPC_0100503.2 Follicle Dermal Papilla Cells normal F skin / lateral scalp / brown PromoCell BTO:0001849 Gingeras HFDPC-062 Promo_Cell_Protocol.pdf Yes
HFDPC_0102703.3 Follicle Dermal Papilla Cells normal F skin / lateral scalp / blond PromoCell BTO:0001849 Gingeras HFDPC-061 Promo_Cell_Protocol.pdf Yes
HCH_8100808.2 Undifferentiated Chondrocytes normal M catilage / knee joint PromoCell BTO:0000249 Gingeras HCH-060 Promo_Cell_Protocol.pdf Yes
HCH_0011308.2P Undifferentiated Chondrocytes normal F catilage / knee joint PromoCell BTO:0000249 Gingeras HCH-059 Promo_Cell_Protocol.pdf Yes
HAoEC_8061102.1 Aortic Endothelial Cells normal M aorta / thoracic PromoCell BTO:0000394 Gingeras HAoEC-058 Promo_Cell_Protocol.pdf Yes
HAoEC_7071706.1 Aortic Endothelial Cells normal F aorta / - PromoCell BTO:0000394 Gingeras HAoEC-057 Promo_Cell_Protocol.pdf Yes
HAoAF_6090101.11 Aortic Adventitial Fibroblasts normal M aorta / tunica adventitia PromoCell BTO:0000135 Gingeras HAoAF-056 Promo_Cell_Protocol.pdf Yes
HAoAF_6111301.9 Aortic Adventitial Fibroblasts normal F aorta / tunica adventitia PromoCell BTO:0000135 Gingeras HAoAF-055 Promo_Cell_Protocol.pdf Yes
HOB_0090202.1 Undifferentiated Osteoblasts normal M cancellous bone / femoral head PromoCell BTO:0004324 Gingeras HOB-054 Promo_Cell_Protocol.pdf Yes
HOB_0091301 Undifferentiated Osteoblasts normal F cancellous bone / femoral head PromoCell BTO:0004324 Gingeras HOB-053 Promo_Cell_Protocol.pdf Yes
HVMF_6100401.3 Villous Mesenchymal Fibroblasts normal F placenta / villous tissue PromoCell BTO:0001975 Gingeras HVMF-052 Promo_Cell_Protocol.pdf Yes
HVMF_6091203.3 Villous Mesenchymal Fibroblasts normal M placenta / villous tissue PromoCell BTO:0001975 Gingeras HVMF-051 Promo_Cell_Protocol.pdf Yes
NHDF_0060801.3 Dermal Fibroblasts normal F skin / temple PromoCell BTO:0003185 Gingeras NHDF-050 Promo_Cell_Protocol.pdf Yes
NHDF_7071701.2 Dermal Fibroblasts normal F skin / breast PromoCell BTO:0003185 Gingeras NHDF-049 Promo_Cell_Protocol.pdf Yes
SkMC_9011302 Skeletal Muscle Cells normal F striated muscle / M. pectoralis PromoCell BTO:0002916 Gingeras SkMC-047 Promo_Cell_Protocol.pdf Yes
SkMC_8121902.17 Skeletal Muscle Cells normal M striated muscle / Mm. intercostales PromoCell BTO:0002916 Gingeras SkMC-048 Promo_Cell_Protocol.pdf Yes



The RNA Dashboard where you can batch download files (.BAM, splice junctions, contigs, etc..) This links to the Guigo Lab Dashboard whereby the bolus of the RNA-Seq data (Human and Mouse) can be downloaded from. Often times, there will be data there that is not at the DCC/UCSC. For example, the mouse data that was generated by the different mouse groups was all independently mapped and submitted to the DCC using each groups internal pipeline. However, these data will be downloaded and all re-mapped using a common pipeline for integrative analysis. These would be considered "duplicate" files at the DCC and hence they are not re-submitted there. They can however, be downloaded from the below dashboard. http://genome.crg.es/~jlagarde/encode_RNA_dashboard/




Old Stuff:


Transcriptome Goals: The goals of the ENCODE Transcriptome group are to generate maps of human RNAs, a dynamic population. In order to capture part of the vast diversity of transcripts we are targeting distinct populations based on size, structure, cellular compartment and associated ribonucleoproteins and classifying them according to their above properties in ENCODE cell lines. A subset of classified transcripts will be validated using 5’ and 3’ RACE as well as cross-referenced to each other.

Our pipeline is as follow: The independent labs perform the Tiling Arrays, CAGE, PET and small RNA Seq from a collective RNA source supplied by the Gingeras lab and distributed Distribution. Aliquots of cells are sent to the Tenenbaum lab for phenotyping assays. Each lab then submits their datasets to Roderic Guigo's lab at the CRG. These data are then complied and (1) Compared against each other to validate that a subset of the data derived from a particular RNA type are reproducible using independent techniques (e.g. one would expect to see a higher correlation for exons between arrays and PET as opposed to arrays and CAGE). (2) Analyzed to identify transcripts that are distinct in our datasets, i.e.. compartment-specific (nuclear vs. cytoplasm), structure-specific (A+ vs. A-), technique-specific (CAGE vs. Array), and/or cell line-specific as well as loci that generate both long and small RNAs. RACE and RT-PCR are then used to complete the validation of the above candidates, where applicable/appropriate. The data are submitted to the DCC via the CRG.


Transcriptome Group Pages

Long RNA-Seq Gingeras Lab

Small RNA-Seq Hannon Lab

Long RNA-Seq Wold Lab

CAGE -RIKEN

RNAPET 18/16 GIS

RNAPET 27/27 GIS

RT-PCR/RACE