title: RAMPAGE from stomach (ENCLB282ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGW/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal stomach tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGW
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFI
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB282ZZZ
size range: >200

source_name: Homo sapiens stomach tissue male fetal (36 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3d60d15c-986a-446f-9bcc-28f8aaab9c93/@@download/attachment/SID78003.pdf

value: stomach

value: tissue

value: Human fetal stomach

value: 36 week

value: male

value: ENCBS074RNA at ENCODE; https://www.encodeproject.org/ENCBS074RNA/

value: Derived from ENCODE donor ENCDO071AAA; https://www.encodeproject.org/ENCDO071AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244248-50


title: RAMPAGE from temporal lobe (ENCLB284ZZZ)

status: Public on Nov 08 2016

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR000AGX/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal temporal lobe tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGX
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFJ
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB284ZZZ
size range: >200

library_source: transcriptomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens temporal lobe tissue female fetal (24 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/091dee54-7b3e-4e10-a50a-aafe138452a9/@@download/attachment/SID78255.pdf

value: temporal lobe

tag: description

value: Human fetal temporal lobe

tag: biosample encode accession

tag: age

value: 24 week

tag: dev stage

value: fetal

tag: Sex

value: female

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS076RNA at ENCODE; https://www.encodeproject.org/ENCBS076RNA/

value: Derived from ENCODE donor ENCDO067AAA; https://www.encodeproject.org/ENCDO067AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244078-50


title: SGE_143

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

institute: Arizona State University

data_processing:
Following sequencing, we trimmed Illumina adapter sequence from the ends of the reads using Trim Galore! (v0.2.7), mapped trimmed reads to the rhesus macaque genome (MacaM v7; Zimin et al. PMID 25319552) using the STAR 2-pass method, and collated the number of reads that mapped uniquely to each annotated MacaM gene (v7.6.8) using HTSeq-count (v0.6.1) with the option “intersection-nonempty”.
We first filtered out genes that were very lowly or not detectably expressed in our samples by removing any gene with a median RPKM ≤ 2 in that cell type.
We normalized the resulting read count matrix using the function voom from the R package limma. We then modeled the normalized expression values as a function of the sample donor’s social group membership. Controlling for the identity of the group removes biological variation related to differences in group dynamics, and most technical batch effects related to sample collection and processing. The residuals of the model relating normalized expression to social group identity as our primary outcome measure in all subsequent analyses.
Genome_build: MacaM
Supplementary_files_format_and_content: [.txt] abundance measurements

molecule: polyA RNA

organism: Macaca mulatta

source_name: peripheral blood mononuclear cells

growth_protocol: we drew 12-20 mL of blood from each female, purified the PBMC fraction using density gradient centrifugation, and performed fluorescent activated cell sortingto purify 5 PBMC populations. We sorted cell types as follows: classical monocytes (CD3-/CD20-/HLA-DR+/CD14+), natural killer cells (CD3-/CD20-/HLA-DR-/CD16+), B cells (CD3-/CD20+/HLA-DR+), helper T cells (CD3+/CD8-/CD4+), cytotoxic T cells (CD3+/CD8+/CD4-)

extract_protocol:
Purified cells were immediately pelleted, lysed, and frozen at -80°C until DNA and RNA extraction using the Qiagen AllPrep extraction kit.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra RNA Library Prep Kit. Briefly, we purified the poly-adenylated mRNA from 200 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. The mRNA was then reverse transcribed into cDNA, ligated to Illumina adapters, size-selected for a median size of ~350 bp, and amplified via PCR for 13 cycles. We tagged each sample with a unique molecular barcode and pooled 10-12 samples per Illumina HiSeq 2500 lane of single-end 100 bp sequencing.

tag: cell type

value: monocyte (CD3-/CD20-/HLADR+/CD14+)

tag: sample date

tag: study phase

value: phase 1

tag: study group


title: SGE_141

value: helper T (CD3+/CD4+/CD8-)


title: SGE_142

value: cytotoxic T (CD3+/CD4-/CD8+)


title: SGE_150


title: RAMPAGE from spinal cord (ENCLB279ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGV/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal spinal cord tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFH
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB279ZZZ
size range: >200

source_name: Homo sapiens spinal cord tissue male fetal (22 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d3d91918-3c3e-41d5-aebd-ef3604cdd856/@@download/attachment/SID78252.pdf

value: spinal cord

value: tissue

value: Human fetal spinal cord

value: 22 week

value: male

tag: health state

value: unknown

value: ENCBS071RNA at ENCODE; https://www.encodeproject.org/ENCBS071RNA/

value: Derived from ENCODE donor ENCDO065AAA; https://www.encodeproject.org/ENCDO065AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244234-10


title: SGE_138


title: RAMPAGE from stomach (ENCLB281ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGW/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal stomach tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGW
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFI
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB281ZZZ
size range: >200

source_name: Homo sapiens stomach tissue female fetal (40 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2b2d660f-86b1-4e66-83f6-b70cfe6eca2d/@@download/attachment/SID78002.pdf

value: stomach

value: Human fetal stomach

value: 40 week

value: fetal

value: female

value: Thomas Gingeras, CSHL

value: ENCBS073RNA at ENCODE; https://www.encodeproject.org/ENCBS073RNA/

value: Derived from ENCODE donor ENCDO066AAA; https://www.encodeproject.org/ENCDO066AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244248-50


title: SGE_139

value: phase 1


title: RAMPAGE from skeletal muscle tissue (ENCLB276ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGT/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal skeletal muscle tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGT
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFF
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB276ZZZ
size range: >200

source_name: Homo sapiens skeletal muscle tissue male fetal (22 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/00d735fd-6d27-4d73-8d9f-973485234215/@@download/attachment/SID78242.pdf

value: skeletal muscle tissue

value: tissue

value: Human fetal skeletal muscle Tissue

value: ENCBS068RNA at ENCODE; https://www.encodeproject.org/ENCBS068RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244171-50


title: SGE_130


title: SGE_136

value: helper T (CD3+/CD4+/CD8-)


title: RAMPAGE from skeletal muscle tissue (ENCLB275ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal skeletal muscle tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGT
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFF
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB275ZZZ
size range: >200

source_name: Homo sapiens skeletal muscle tissue female fetal (19 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a33de33d-5f2c-4faa-a817-c0e6dd401f05/@@download/attachment/SID78241.pdf

value: 19 week

value: ENCBS067RNA at ENCODE; https://www.encodeproject.org/ENCBS067RNA/

value: Derived from ENCODE donor ENCDO070AAA; https://www.encodeproject.org/ENCDO070AAA/


title: RAMPAGE from skin of body (ENCLB278ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGU/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal skin tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGU
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFG
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB278ZZZ
size range: >200

source_name: Homo sapiens skin of body tissue female fetal (24 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c6dfd476-2244-4932-8fef-870186c88f42/@@download/attachment/SID78244.pdf

value: skin of body

value: Human fetal skin of body

value: 24 week

value: ENCBS070RNA at ENCODE; https://www.encodeproject.org/ENCBS070RNA/

value: Derived from ENCODE donor ENCDO067AAA; https://www.encodeproject.org/ENCDO067AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244218-50


title: RAMPAGE from skin of body (ENCLB277ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal skin tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGU
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFG
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB277ZZZ
size range: >200

source_name: Homo sapiens skin of body tissue male fetal (22 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/1efcfddf-6999-4b32-b7dc-57f9bae8df27/@@download/attachment/SID78243.pdf

value: 22 week

value: fetal

value: male

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS069RNA at ENCODE; https://www.encodeproject.org/ENCBS069RNA/

value: Derived from ENCODE donor ENCDO065AAA; https://www.encodeproject.org/ENCDO065AAA/


title: RAMPAGE from thyroid gland (ENCLB286ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGY/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal thyroid gland tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGY
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFK
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB286ZZZ
size range: >200

source_name: Homo sapiens thyroid gland tissue female fetal (40 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/14518b6b-327e-4513-b532-0f2ca9de5749/@@download/attachment/SID78257.pdf

value: thyroid gland

value: tissue

value: Human fetal thyroid gland

value: 40 week

value: female

value: ENCBS078RNA at ENCODE; https://www.encodeproject.org/ENCBS078RNA/

value: Derived from ENCODE donor ENCDO066AAA; https://www.encodeproject.org/ENCDO066AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244265-10


title: SGE_145

value: phase 1


title: RAMPAGE from occipital lobe (ENCLB271ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal occipital lobe tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGR
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFD
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB271ZZZ
size range: >200

source_name: Homo sapiens occipital lobe tissue female fetal (20 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6c4bd181-c59c-4c81-91cc-f6d3f54713d2/@@download/attachment/SID78264.pdf

value: occipital lobe

value: Human fetal occipital lobe

value: 20 week

value: ENCBS063RNA at ENCODE; https://www.encodeproject.org/ENCBS063RNA/

value: Derived from ENCODE donor ENCDO064AAA; https://www.encodeproject.org/ENCDO064AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244062-50


title: RAMPAGE from parietal lobe (ENCLB273ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal parietal lobe tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGS
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFE
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB273ZZZ
size range: >200

source_name: Homo sapiens parietal lobe tissue male fetal (22 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/44bc41d3-a534-43a3-999c-195dd5af696e/@@download/attachment/SID78266.pdf

value: parietal lobe

value: Human fetal parietal lobe

value: 22 week

value: fetal

value: male

value: unknown

value: Thomas Gingeras, CSHL

value: ENCBS065RNA at ENCODE; https://www.encodeproject.org/ENCBS065RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244066-50


title: SGE_129


title: SGE_128

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: RAMPAGE from parietal lobe (ENCLB274ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGS/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal parietal lobe tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGS
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFE
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB274ZZZ
size range: >200

source_name: Homo sapiens parietal lobe tissue female fetal (24 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0537bf48-bb09-43b1-91ea-474408c3e5aa/@@download/attachment/SID78267.pdf

value: tissue

value: 24 week

value: female

value: ENCBS066RNA at ENCODE; https://www.encodeproject.org/ENCBS066RNA/

value: Derived from ENCODE donor ENCDO067AAA; https://www.encodeproject.org/ENCDO067AAA/


title: RAMPAGE from occipital lobe (ENCLB272ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGR/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal occipital lobe tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGR
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFD
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB272ZZZ
size range: >200

source_name: Homo sapiens occipital lobe tissue male fetal (22 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/994b0084-d677-468f-9f1e-2e9dedd1d8ed/@@download/attachment/SID78265.pdf

value: occipital lobe

value: Human fetal occipital lobe

value: ENCBS064RNA at ENCODE; https://www.encodeproject.org/ENCBS064RNA/

value: Derived from ENCODE donor ENCDO065AAA; https://www.encodeproject.org/ENCDO065AAA/


title: SGE_127

value: cytotoxic T (CD3+/CD4-/CD8+)

value: phase 1


title: RAMPAGE from spinal cord (ENCLB280ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGV/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal spinal cord tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGV
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFH
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB280ZZZ
size range: >200

source_name: Homo sapiens spinal cord tissue female fetal (24 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/02199ec1-c2b3-46b7-8f88-8b09f4935bb1/@@download/attachment/SID78253.pdf

value: spinal cord

value: Human fetal spinal cord

value: fetal

value: ENCBS072RNA at ENCODE; https://www.encodeproject.org/ENCBS072RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244234-10


title: SGE_126

value: helper T (CD3+/CD4+/CD8-)


title: RAMPAGE from lung (ENCLB269ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal lung tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGQ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFC
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB269ZZZ
size range: >200

source_name: Homo sapiens lung tissue female fetal (20 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ad710ee2-47a1-41d9-ade6-08371d9dd2fa/@@download/attachment/SID78262.pdf

value: lung

value: tissue

value: Human fetal lung

value: 20 week

value: Thomas Gingeras, CSHL

value: ENCBS061RNA at ENCODE; https://www.encodeproject.org/ENCBS061RNA/

value: Derived from ENCODE donor ENCDO064AAA; https://www.encodeproject.org/ENCDO064AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244152-50


title: SGE_125

value: VBB


title: SGE_137

value: cytotoxic T (CD3+/CD4-/CD8+)


title: RAMPAGE from liver (ENCLB267ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal liver tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGP
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFB
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB267ZZZ
size range: >200

source_name: Homo sapiens liver tissue female fetal (20 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/346a8939-6e67-4a19-b248-7a1824e15701/@@download/attachment/SID78260.pdf

value: liver

value: Human fetal liver

value: female

value: ENCBS059RNA at ENCODE; https://www.encodeproject.org/ENCBS059RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244149-50


title: SGE_124

value: phase 1


title: RAMPAGE from liver (ENCLB268ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGP/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal liver tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGP
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFB
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB268ZZZ
size range: >200

source_name: Homo sapiens liver tissue male fetal (22 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/144c8098-9d28-4c57-830b-de3a0ca6ed5d/@@download/attachment/SID78261.pdf

value: 22 week

value: fetal

value: male

value: unknown

value: ENCBS060RNA at ENCODE; https://www.encodeproject.org/ENCBS060RNA/

value: Derived from ENCODE donor ENCDO065AAA; https://www.encodeproject.org/ENCDO065AAA/


title: SGE_123

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: SGE_122


title: SGE_121

value: helper T (CD3+/CD4+/CD8-)


title: SGE_120


title: SGE_118


title: RAMPAGE from heart (ENCLB264ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGN/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal heart tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGN
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEZ
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB264ZZZ
size range: >200

source_name: Homo sapiens heart tissue female fetal (19 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e3edcbdf-0ea1-4191-bf8f-16298b20cb1e/@@download/attachment/SID77990.pdf

value: heart

value: tissue

value: Human fetal heart

value: 19 week

value: Thomas Gingeras, CSHL

value: ENCBS056RNA at ENCODE; https://www.encodeproject.org/ENCBS056RNA/

value: Derived from ENCODE donor ENCDO070AAA; https://www.encodeproject.org/ENCDO070AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244122-50


title: RAMPAGE from metanephros (ENCLB265ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal kidney tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGO
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFA
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB265ZZZ
size range: >200

source_name: Homo sapiens metanephros tissue female fetal (20 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b1ed3a23-3401-49e2-ad43-528eaeff37ff/@@download/attachment/SID77991.pdf

value: metanephros

value: Human fetal kidney

value: 20 week

value: female

value: ENCBS057RNA at ENCODE; https://www.encodeproject.org/ENCBS057RNA/

value: Derived from ENCODE donor ENCDO064AAA; https://www.encodeproject.org/ENCDO064AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244142-10


title: SGE_119

source_name: peripheral blood mononuclear cells

extract_protocol:
Purified cells were immediately pelleted, lysed, and frozen at -80°C until DNA and RNA extraction using the Qiagen AllPrep extraction kit.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra RNA Library Prep Kit. Briefly, we purified the poly-adenylated mRNA from 200 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. The mRNA was then reverse transcribed into cDNA, ligated to Illumina adapters, size-selected for a median size of ~350 bp, and amplified via PCR for 13 cycles. We tagged each sample with a unique molecular barcode and pooled 10-12 samples per Illumina HiSeq 2500 lane of single-end 100 bp sequencing.

value: phase 1

value: VBB


title: RAMPAGE from metanephros (ENCLB266ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGO/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal kidney tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGO
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFA
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB266ZZZ
size range: >200

source_name: Homo sapiens metanephros tissue female fetal (24 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/db0521dc-d514-42d2-82db-2d4423393836/@@download/attachment/SID77992.pdf

value: 24 week

value: fetal

value: ENCBS058RNA at ENCODE; https://www.encodeproject.org/ENCBS058RNA/

value: Derived from ENCODE donor ENCDO067AAA; https://www.encodeproject.org/ENCDO067AAA/


title: RAMPAGE from frontal cortex (ENCLB261ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGM/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal frontal cortex tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGM
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEY
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB261ZZZ
size range: >200

source_name: Homo sapiens frontal cortex tissue female fetal (20 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0c495bce-106b-4d1e-88ce-e37a0ac282d2/@@download/attachment/SID78247.pdf

value: frontal cortex

value: tissue

value: Human fetal frontal cortex

value: Thomas Gingeras, CSHL

value: ENCBS053RNA at ENCODE; https://www.encodeproject.org/ENCBS053RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244051-50


title: RAMPAGE from lung (ENCLB270ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal lung tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGQ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AFC
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB270ZZZ
size range: >200

source_name: Homo sapiens lung tissue female fetal (24 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5db4d392-1ae0-429b-856c-69b983de00a7/@@download/attachment/SID78263.pdf

value: lung

value: Human fetal lung

value: ENCBS062RNA at ENCODE; https://www.encodeproject.org/ENCBS062RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244152-50


title: SGE_114


title: SGE_116

value: helper T (CD3+/CD4+/CD8-)


title: SGE_115

value: phase 1


title: RAMPAGE from cerebellum (ENCLB258ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGK/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal cerebellum tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGK
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEW
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB258ZZZ
size range: >200

source_name: Homo sapiens cerebellum tissue female fetal (19 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d79db0d8-54ff-4947-a6ab-1776dcd5797a/@@download/attachment/SID78240.pdf

value: cerebellum

value: Human fetal cerebellum

value: 19 week

value: female

value: ENCBS050RNA at ENCODE; https://www.encodeproject.org/ENCBS050RNA/

value: Derived from ENCODE donor ENCDO070AAA; https://www.encodeproject.org/ENCDO070AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244039-50


title: RAMPAGE from diencephalon (ENCLB259ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGL/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal diencephalon tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGL
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEX
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB259ZZZ
size range: >200

source_name: Homo sapiens diencephalon tissue female fetal (20 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5c46efcb-26ab-4d30-9476-01913c7a6f09/@@download/attachment/SID78245.pdf

value: diencephalon

value: tissue

value: Human fetal diencephalon

value: 20 week

value: fetal

value: ENCBS051RNA at ENCODE; https://www.encodeproject.org/ENCBS051RNA/

value: Derived from ENCODE donor ENCDO064AAA; https://www.encodeproject.org/ENCDO064AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244049-10


title: RAMPAGE from cerebellum (ENCLB257ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGK/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal cerebellum tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGK
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEW
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB257ZZZ
size range: >200

source_name: Homo sapiens cerebellum tissue female fetal (37 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/968bc8d2-58b6-43ad-9e0f-bebe670ae0f3/@@download/attachment/SID78239.pdf

value: 37 week

value: Thomas Gingeras, CSHL

value: ENCBS049RNA at ENCODE; https://www.encodeproject.org/ENCBS049RNA/

value: Derived from ENCODE donor ENCDO063AAA; https://www.encodeproject.org/ENCDO063AAA/


title: RAMPAGE from diencephalon (ENCLB260ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGL/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal diencephalon tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGL
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEX
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB260ZZZ
size range: >200

source_name: Homo sapiens diencephalon tissue male fetal (22 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/de3f6c18-5e01-496b-a19a-f030819fb4e6/@@download/attachment/SID78246.pdf

value: 22 week

value: male

value: unknown

value: ENCBS052RNA at ENCODE; https://www.encodeproject.org/ENCBS052RNA/

value: Derived from ENCODE donor ENCDO065AAA; https://www.encodeproject.org/ENCDO065AAA/


title: SGE_112

value: cytotoxic T (CD3+/CD4-/CD8+)

value: phase 1

value: VBB


title: RAMPAGE from urinary bladder (ENCLB255ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal urinary bladder tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGJ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEV
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB255ZZZ
size range: >200

source_name: Homo sapiens urinary bladder tissue female fetal (20 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6c1d727e-98b2-41ab-87e0-7809d5d62313/@@download/attachment/SID78237.pdf

value: urinary bladder

value: tissue

value: Human fetal urinary bladder

value: 20 week

value: female

value: ENCBS047RNA at ENCODE; https://www.encodeproject.org/ENCBS047RNA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244010-50


title: SGE_113

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: RAMPAGE from urinary bladder (ENCLB256ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGJ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal urinary bladder tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGJ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEV
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB256ZZZ
size range: >200

source_name: Homo sapiens urinary bladder tissue female fetal (24 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/70e11fdd-69aa-464f-a959-1e8337f96de9/@@download/attachment/SID78238.pdf

value: 24 week

value: fetal

value: Thomas Gingeras, CSHL

value: ENCBS048RNA at ENCODE; https://www.encodeproject.org/ENCBS048RNA/

value: Derived from ENCODE donor ENCDO067AAA; https://www.encodeproject.org/ENCDO067AAA/


title: RAMPAGE from K562 (ENCLB065ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AER/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line K562.  They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.
experiment encode accession: ENCSR000AER
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEL
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB065ZZZ
size range: >200

source_name: Homo sapiens K562 immortalized cell line

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
data sheet: https://www.encodeproject.org/documents/7ae25f97-ab0a-448b-b345-cfffd6368c90/@@download/attachment/AmbionMix1Concentrations.tsv, general protocol: https://www.encodeproject.org/documents/f48823fb-b40c-4fc1-aaf4-f783e094ec5c/@@download/attachment/K562_Long_Total_RAMPAGE_2x101_ENCLB065ZZZ_Ging.pdf, data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf

tag: line

value: immortalized cell line

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. ENCODE3 RNA-seq evaluation replicate 1.

value: 53 year

value: adult

tag: passage number

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS087RNA at ENCODE; https://www.encodeproject.org/ENCBS087RNA/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: SGE_111

value: helper T (CD3+/CD4+/CD8-)

value: phase 1

value: VBB


title: SGE_110


title: RAMPAGE from K562 (ENCLB066ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AER/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line K562.  They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.
experiment encode accession: ENCSR000AER
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEL
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB066ZZZ
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bb25cd8a-8c7c-4f88-939a-435f4b19d4ea/@@download/attachment/K562_Long_Total_RAMPAGE_2x101_ENCLB066ZZZ_Ging.pdf, data sheet: https://www.encodeproject.org/documents/7ae25f97-ab0a-448b-b345-cfffd6368c90/@@download/attachment/AmbionMix1Concentrations.tsv, data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. ENCODE3 RNA-seq evaluation replicate 2.

value: female

value: ENCBS088RNA at ENCODE; https://www.encodeproject.org/ENCBS088RNA/


title: SGE_109


title: SGE_117

value: cytotoxic T (CD3+/CD4-/CD8+)


title: RAMPAGE from GM12878 (ENCLB048ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AEI/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line GM12878.  They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.
experiment encode accession: ENCSR000AEI
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEC
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB048ZZZ
size range: >200

source_name: Homo sapiens GM12878 immortalized cell line

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8c76fe62-298f-4664-83e8-2ffdeb9c83d6/@@download/attachment/GM12878_Long_Total_RAMPAGE_2x101_ENCLB048ZZZ_Ging.pdf, data sheet: https://www.encodeproject.org/documents/7ae25f97-ab0a-448b-b345-cfffd6368c90/@@download/attachment/AmbionMix1Concentrations.tsv, data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf

value: immortalized cell line

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: unknown

value: Ali Mortazavi, UCI

value: ENCBS090RNA at ENCODE; https://www.encodeproject.org/ENCBS090RNA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: RAMPAGE from GM12878 (ENCLB047ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AEI/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from independent growths of cell line GM12878.  They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.
experiment encode accession: ENCSR000AEI
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEC
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB047ZZZ
size range: >200

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/904c7685-a8c5-404e-b69d-6e5fdebda051/@@download/attachment/GM12878_Long_Total_RAMPAGE_2x101_ENCLB047ZZZ_Ging.pdf, data sheet: https://www.encodeproject.org/documents/7ae25f97-ab0a-448b-b345-cfffd6368c90/@@download/attachment/AmbionMix1Concentrations.tsv, data sheet: https://www.encodeproject.org/documents/28fef8e0-e171-450d-b66d-e3d199531cf2/@@download/attachment/Ambion-ERCC-Mix1.pdf

value: adult

value: ENCBS089RNA at ENCODE; https://www.encodeproject.org/ENCBS089RNA/


title: SGE_107


title: RAMPAGE from heart (ENCLB263ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal heart tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGN
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEZ
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB263ZZZ
size range: >200

source_name: Homo sapiens heart tissue female fetal (28 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4c6487cc-f604-402c-a815-e3e26eb81df0/@@download/attachment/SID77989.pdf

value: heart

value: tissue

value: Human fetal heart

value: 28 week

value: fetal

value: Thomas Gingeras, CSHL

value: ENCBS055RNA at ENCODE; https://www.encodeproject.org/ENCBS055RNA/

value: Derived from ENCODE donor ENCDO069AAA; https://www.encodeproject.org/ENCDO069AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244122-50


title: SGE_106

value: helper T (CD3+/CD4+/CD8-)

value: phase 1

value: VBB


title: KhES-1_day7_arm2, rep20

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: Single Cell RNA-seq data

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
The sequenced short reads were trimmed by Trimmomatic 0.3.3 and mapped to the human reference genome hg19 using TopHat 2.0.14 and Bowtie 2.2.5.
RPKM counts for each gene were obtained using the RPKMforgenes software.
Genome_build: The sequence reads were mapped to hg19 reference genes, downloaded on 25th April 2014
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Genename, Refseq, RPKM, and Rawcount columns (from left to right), and the expression level was represented by RPKM.

source_name: KhES-1 cells, day7 of differentiation on LM411-E8

growth_protocol: PSCs were maintained on SNL feeder cells in ES medium supplemented with 5 ng/mL of bFGF. PSC clumps were plated onto GFR-Matrigel-coated plates at a density of 2 clumps/cm2 and cultured in mTeSR1.

extract_protocol:
Single cells were sorted using FACS Aria Ⅱ, and dropped into 96-well plates. The cells were direcxtly lyzed using Reaction buffer of SMARTer Ultra Low Input RNA – HV kit (Clontech),
cDNA synthesis and amplificationof the cDNA were performed using SMARTer Ultra Low Input RNA kit according to manufacturer’s instruction. Sequencing libraries were constructed using Nextera XT DNA Sample Prep kit.

treatment_protocol: When the colonies grew up to a diameter of 750 μm, the medium was replaced with fresh mTeSR1 containing BMP4 (80 ng/mL). After three days, the cells were dissociated to the single-cell level using TrypLE Express for 20 minutes at 37℃ and subsequently plated onto a matrix-coated plate and cultured for an additional four days in Stempro34SFM containing VEGF (80 ng/mL). BD falcon non-coating tissue culture plates and dishes were used in this study. The following matrices were diluted with phosphate-buffered saline (PBS) (-) and used for dish coating at the indicated concentrations, unless otherwise described: LM411 (2 μg/cm2)and GFR-Matrigel (20 μg/cm2). The dishes and plates were coated for 2 hours at room temperature.

tag: tissue

value: differentiating embryonic stem cells

tag: differentiation day

value: day 7

tag: coating matrix


title: KhES-1_day7_arm2, rep19

description: Single Cell RNA-seq data


title: KhES-1_day7_arm2, rep17

description: Single Cell RNA-seq data


title: SGE_108

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: RAMPAGE from frontal cortex (ENCLB262ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AGM/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from human fetal frontal cortex tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000AGM
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR000AEY
encode release date: 2014-06-30
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB262ZZZ
size range: >200

source_name: Homo sapiens frontal cortex tissue male fetal (22 weeks)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/824e1af2-0b2a-4653-8ea4-e7e06425a7a0/@@download/attachment/SID78248.pdf

value: frontal cortex

tag: description

value: Human fetal frontal cortex

value: 22 week

value: male

value: unknown

value: ENCBS054RNA at ENCODE; https://www.encodeproject.org/ENCBS054RNA/

value: Derived from ENCODE donor ENCDO065AAA; https://www.encodeproject.org/ENCDO065AAA/

value: BioChain sample source; http://www.biochain.com/index.php/catalogsearch/advanced/result/?catalog_number=R1244051-50


title: KhES-1_day7_arm2, rep18

description: Single Cell RNA-seq data


title: SGE_105

extract_protocol:
Purified cells were immediately pelleted, lysed, and frozen at -80°C until DNA and RNA extraction using the Qiagen AllPrep extraction kit.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra RNA Library Prep Kit. Briefly, we purified the poly-adenylated mRNA from 200 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. The mRNA was then reverse transcribed into cDNA, ligated to Illumina adapters, size-selected for a median size of ~350 bp, and amplified via PCR for 13 cycles. We tagged each sample with a unique molecular barcode and pooled 10-12 samples per Illumina HiSeq 2500 lane of single-end 100 bp sequencing.


title: KhES-1_day7_arm2, rep16

description: Single Cell RNA-seq data


title: SGE_103


title: KhES-1_day7_arm2, rep15

description: Single Cell RNA-seq data


title: SGE_102

value: cytotoxic T (CD3+/CD4-/CD8+)


title: SGE_104


title: KhES-1_day7_arm2, rep13

description: Single Cell RNA-seq data


title: SGE_101


title: KhES-1_day7_arm2, rep11

description: Single Cell RNA-seq data


title: KhES-1_day7_arm2, rep14

description: Single Cell RNA-seq data


title: KhES-1_day7_arm2, rep12

description: Single Cell RNA-seq data


title: SGE_100

value: WXC


title: SGE_099


title: SGE_098


title: KhES-1_day7_arm2, rep9

description: Single Cell RNA-seq data


title: KhES-1_day7_arm2, rep10

description: Single Cell RNA-seq data


title: KhES-1_day7_arm2, rep8

description: Single Cell RNA-seq data


title: SGE_097


title: SGE_096


title: SGE_095


title: KhES-1_day7_arm2, rep6

description: Single Cell RNA-seq data


title: SGE_094


title: SGE_092


title: KhES-1_day7_arm2, rep3

description: Single Cell RNA-seq data


title: SGE_093


title: KhES-1_day7_arm2, rep4

description: Single Cell RNA-seq data


title: KhES-1_day7_arm2, rep5

description: Single Cell RNA-seq data


title: KhES-1_day7_arm2, rep2

description: Single Cell RNA-seq data


title: KhES-1_day7_arm1, rep19

description: Single Cell RNA-seq data

source_name: KhES-1 cells, day7 of differentiation on Matrigel

value: Matrigel


title: SGE_090


title: SGE_091

value: helper T (CD3+/CD4+/CD8-)


title: KhES-1_day7_arm1, rep18

description: Single Cell RNA-seq data


title: KhES-1_day7_arm2, rep1

description: Single Cell RNA-seq data


title: KhES-1_day7_arm1, rep17

description: Single Cell RNA-seq data


title: SGE_087

value: phase 1


title: SGE_086


title: SGE_088


title: SGE_089


title: KhES-1_day7_arm1, rep16

description: Single Cell RNA-seq data


title: SGE_085


title: KhES-1_day7_arm1, rep15

description: Single Cell RNA-seq data


title: SGE_084


title: KhES-1_day7_arm1, rep14

description: Single Cell RNA-seq data


title: KhES-1_day7_arm2, rep7

description: Single Cell RNA-seq data


title: KhES-1_day7_arm1, rep13

description: Single Cell RNA-seq data


title: SGE_082


title: SGE_083


title: KhES-1_day7_arm1, rep12

description: Single Cell RNA-seq data


title: SGE_081


title: SGE_080


title: KhES-1_day7_arm1, rep11

description: Single Cell RNA-seq data


title: KhES-1_day7_arm1, rep10

description: Single Cell RNA-seq data


title: SGE_079


title: KhES-1_day7_arm1, rep9

description: Single Cell RNA-seq data


title: KhES-1_day7_arm1, rep8

description: Single Cell RNA-seq data


title: SGE_077


title: KhES-1_day7_arm1, rep7

description: Single Cell RNA-seq data


title: KhES-1_day7_arm1, rep3

description: Single Cell RNA-seq data


title: SGE_076


title: SGE_072


title: KhES-1_day7_arm1, rep1

description: Single Cell RNA-seq data


title: KhES-1_day7_arm1, rep4

description: Single Cell RNA-seq data


title: KhES-1_day7_arm1, rep2

description: Single Cell RNA-seq data


title: SGE_071


title: SGE_074


title: SGE_068


title: SGE_069


title: KhES-1_day5_arm2, rep16

description: Single Cell RNA-seq data

source_name: KhES-1 cells, day5 of differentiation on LM411-E8

value: day 5


title: SGE_067

source_name: peripheral blood mononuclear cells


title: SGE_070


title: KhES-1_day5_arm2, rep17

description: Single Cell RNA-seq data

value: differentiating embryonic stem cells


title: KhES-1_day5_arm2, rep14

description: Single Cell RNA-seq data


title: KhES-1_day7_arm1, rep6

description: Single Cell RNA-seq data

value: day 7


title: SGE_078

value: monocyte (CD3-/CD20-/HLADR+/CD14+)


title: SGE_066


title: KhES-1_day5_arm2, rep13

description: Single Cell RNA-seq data


title: KhES-1_day5_arm2, rep12

description: Single Cell RNA-seq data


title: SGE_064


title: SGE_073


title: KhES-1_day7_arm1, rep5

description: Single Cell RNA-seq data


title: KhES-1_day5_arm2, rep11

description: Single Cell RNA-seq data


title: KhES-1_day5_arm2, rep10

description: Single Cell RNA-seq data


title: SGE_063


title: KhES-1_day5_arm2, rep7

description: Single Cell RNA-seq data


title: KhES-1_day5_arm2, rep8

description: Single Cell RNA-seq data


title: SGE_058


title: KhES-1_day5_arm2, rep9

description: Single Cell RNA-seq data


title: KhES-1_day5_arm2, rep6

description: Single Cell RNA-seq data


title: KhES-1_day5_arm2, rep4

description: Single Cell RNA-seq data


title: KhES-1_day5_arm2, rep3

description: Single Cell RNA-seq data


title: SGE_056


title: KhES-1_day5_arm2, rep2

description: Single Cell RNA-seq data


title: SGE_054


title: SGE_055


title: SGE_053


title: SGE_065


title: KhES-1_day5_arm1, rep21

description: Single Cell RNA-seq data

source_name: KhES-1 cells, day5 of differentiation on Matrigel


title: SGE_052


title: SGE_051


title: KhES-1_day5_arm1, rep20

description: Single Cell RNA-seq data


title: SGE_062


title: SGE_050


title: KhES-1_day5_arm1, rep19

description: Single Cell RNA-seq data


title: KhES-1_day5_arm1, rep18

description: Single Cell RNA-seq data


title: SGE_059


title: SGE_061


title: SGE_049


title: SGE_048


title: KhES-1_day5_arm1, rep17

description: Single Cell RNA-seq data


title: SGE_060


title: KhES-1_day5_arm2, rep5

description: Single Cell RNA-seq data


title: SGE_057


title: SGE_047


title: KhES-1_day5_arm1, rep16

description: Single Cell RNA-seq data


title: SGE_046


title: KhES-1_day5_arm2, rep1

description: Single Cell RNA-seq data


title: KhES-1_day5_arm1, rep14

description: Single Cell RNA-seq data


title: SGE_045


title: KhES-1_day5_arm1, rep12

description: Single Cell RNA-seq data


title: KhES-1_day5_arm1, rep15

description: Single Cell RNA-seq data


title: SGE_044


title: KhES-1_day5_arm1, rep13

description: Single Cell RNA-seq data


title: SGE_075


title: SGE_043


title: KhES-1_day5_arm1, rep11

description: Single Cell RNA-seq data


title: SGE_042


title: KhES-1_day5_arm1, rep10

description: Single Cell RNA-seq data


title: SGE_041


title: KhES-1_day5_arm1, rep9

description: Single Cell RNA-seq data


title: SGE_040


title: SGE_038


title: SGE_039


title: SGE_037


title: KhES-1_day5_arm1, rep6

description: Single Cell RNA-seq data


title: KhES-1_day5_arm1, rep5

description: Single Cell RNA-seq data


title: SGE_036


title: SGE_035


title: KhES-1_day5_arm1, rep3

description: Single Cell RNA-seq data


title: KhES-1_day5_arm1, rep2

description: Single Cell RNA-seq data


title: KhES-1_day5_arm1, rep4

description: Single Cell RNA-seq data


title: SGE_033


title: KhES-1_day5_arm1, rep1

description: Single Cell RNA-seq data


title: SGE_032


title: KhES-1_day3, rep9

description: Single Cell RNA-seq data

source_name: KhES-1 cells, day3 of differentiation

value: day 3


title: KhES-1_day3, rep7

description: Single Cell RNA-seq data


title: KhES-1_day3, rep8

description: Single Cell RNA-seq data


title: SGE_030


title: KhES-1_day3, rep6

description: Single Cell RNA-seq data


title: SGE_031


title: SGE_029


title: SGE_028


title: SGE_027


title: KhES-1_day3, rep5

description: Single Cell RNA-seq data


title: KhES-1_day5_arm1, rep8

description: Single Cell RNA-seq data


title: KhES-1_day3, rep4

description: Single Cell RNA-seq data


title: KhES-1_day5_arm1, rep7

description: Single Cell RNA-seq data


title: SGE_026


title: SGE_025


title: KhES-1_day3, rep2

description: Single Cell RNA-seq data


title: SGE_034


title: KhES-1_day3, rep1

description: Single Cell RNA-seq data


title: KhES-1_day3, rep3

description: Single Cell RNA-seq data


title: SGE_024


title: SGE_023


title: SGE_021


title: KhES-1_day0, rep6

description: Single Cell RNA-seq data

source_name: KhES-1 cells

value: undifferentiated embryonic stem cells

value: day 0


title: KhES-1_day0, rep5

description: Single Cell RNA-seq data


title: SGE_022


title: SGE_019


title: SGE_020


title: KhES-1_day0, rep4

description: Single Cell RNA-seq data


title: KhES-1_day0, rep3

description: Single Cell RNA-seq data


title: SGE_018


title: SGE_016


title: KhES-1_day0, rep2

description: Single Cell RNA-seq data


title: RNA-seq_HAEC, rep3

description: Bulk RNA-Seq data

source_name: HAEC

extract_protocol:
Total RNA was extracted using the RNeasy kit, and the quality was tested with a Bioanalyzer.
Ribosomal RNA was depleted by RiboZero Gold. libraries were prepared with the Illumina TruSeq Stranded Total RNA Sample Prep kit, according to manufacturer's instructions.

treatment_protocol: When the colonies grew up to a diameter of 750 μm, the medium was replaced with fresh mTeSR1 containing BMP4 (80 ng/mL). After three days, the cells were dissociated to the single-cell level using TrypLE Express for 20 minutes at 37℃ and subsequently plated onto a matrix-coated plate and cultured for an additional four days in Stempro34SFM containing VEGF (80 ng/mL). BD falcon non-coating tissue culture plates and dishes were used in this study. The following matrices were diluted with phosphate-buffered saline (PBS) (-) and used for dish coating at the indicated concentrations, unless otherwise described: GFR-Matrigel (20 μg/cm2) and LM411-E8 (0.4 μg/cm2). The dishes and plates were coated for 2 hours at room temperature.

value: Human Aortic Endothelial Cells (HAEC)


title: SGE_015


title: RNA-seq_HAEC, rep2

description: Bulk RNA-Seq data


title: SGE_017


title: RNA-seq_HAEC, rep1

description: Bulk RNA-Seq data


title: SGE_013


title: RNA-seq_HUVEC, rep2

description: Bulk RNA-Seq data

source_name: HUVEC

value: Human Umbilical Vein Endothelial Cells (HUVEC)


title: RNA-seq_HUVEC, rep3

description: Bulk RNA-Seq data


title: SGE_012


title: SGE_011


title: RNA-seq_KhES1_411E8, rep2

description: Bulk RNA-Seq data

source_name: ESC-derived endothelial progenitor cells by differentiation on Laminin411-E8-coated dish

value: embryonic stem cell-derived endothelial progenitor cells by differentiation on Laminin411-E8-coated dish


title: RNA-seq_HUVEC, rep1

description: Bulk RNA-Seq data


title: RNA-seq_KhES1_411E8, rep1

description: Bulk RNA-Seq data


title: RNA-seq_KhES1_411E8, rep3

description: Bulk RNA-Seq data


title: SGE_009


title: SGE_010


title: SGE_008


title: RNA-seq_KhES1_411, rep2

description: Bulk RNA-Seq data

source_name: ESC-derived endothelial progenitor cells by differentiation on Laminin411-coated dish

value: embryonic stem cell-derived endothelial progenitor cells by differentiation on Laminin411-coated dish


title: RNA-seq_KhES1_411, rep3

description: Bulk RNA-Seq data


title: RNA-seq_KhES1_411, rep1

description: Bulk RNA-Seq data


title: SGE_007


title: SGE_006


title: SGE_005


title: RNA-seq_KhES1_nc, rep3

description: Bulk RNA-Seq data

source_name: ESC-derived endothelial progenitor cells, control

value: embryonic stem cell-derived endothelial progenitor cells, control


title: SGE_004


title: KhES-1_day0, rep1

description: Single Cell RNA-seq data


title: RNA-seq_KhES1_nc, rep2

description: Bulk RNA-Seq data


title: SGE_003


title: SGE_014


title: SGE_002

value: cytotoxic T (CD3+/CD4-/CD8+)


title: RNA-seq_KhES1_nc, rep1

description: Bulk RNA-Seq data


title: RNA-seq_KhES1_undiff, rep3

description: Bulk RNA-Seq data

source_name: undifferentiated ES cells


title: RNA-seq_KhES1_undiff, rep1

description: Bulk RNA-Seq data


title: RNA-seq_KhES1_undiff, rep2

description: Bulk RNA-Seq data


title: AI_d22.plvx.3

city: Smithville

first: Collene

last: Jeter

state: TX

address: 1808 Park Rd 1C, Box 389

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads for AD_d12 samples were mapped to human genome (hg18) by TopHat (version 2.0.4), and the other samples were mapped by TopHat (version 2.0.7).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on March 9, 2012) was enumerated using htseq-count from HTSeq package (version 0.5.3p9).
Genome_build: hg18
Supplementary_files_format_and_content: Number of fragments in each gene and sample

source_name: LNCaP_pLVX_AI_day 22

growth_protocol: LNCaP prostate cancer cells were cultured in standard media (RPMI, 5% FBS) for AD conditions or RPMI + 5% charcoal-dextran stripped serum for AI conditions plus doxycycline for the indicated time frame.

extract_protocol:
RNA was extracted using RNeasy RNA-purification kit
cDNA libraries were constructed using NuGen’s Ovation RNA-Seq System

treatment_protocol: Doxycycline (500 ng/mL) for the indicated time frame.

tag: cell line

value: LNCaP

value: prostate cancer cells

tag: genotype/variation

value: expressing pLVX (empty vector)

tag: androgen status

value: androgen independent (AI)

tag: time course

value: day 22


title: AI_d22.plvx.2


title: AI_d22.plvx.1


title: AI_d22.NanogP8.2

source_name: LNCaP_NANOGP8_AI_day 22

value: NANOGP8 overexpression


title: AI_d22.NanogP8.3


title: AI_d22.NanogP8.1


title: AI_d07.plvx.2

source_name: LNCaP_pLVX_AI_day 7

value: day 7


title: AI_d07.plvx.1


title: AI_d07.NanogP8.2

source_name: LNCaP_NANOGP8_AI_day 7


title: AI_d07.NanogP8.1


title: AD_d12.NanogP8.2

source_name: LNCaP_NANOGP8_AD_day 12

value: androgen dependent (AD)

value: day 12


title: AI_d07.NanogP8.3


title: AI_d07.plvx.3


title: AD_d05.plvx.3

source_name: LNCaP_pLVX_AD_day 5

value: day 5


title: AD_d12.plvx.1

source_name: LNCaP_pLVX_AD_day 12


title: AD_d05.plvx.2


title: AD_d05.NanogP8.3

source_name: LNCaP_NANOGP8_AD_day 5


title: AD_d05.NanogP8.2


title: AD_d05.Nanog1.2

source_name: LNCaP_NANOG1_AD_day 5

value: NANOG1 overexpression


title: AD_d05.Nanog1.3


title: AD_d05.Nanog1.1


title: AD_d05.plvx.1


title: SGE_001

source_name: peripheral blood mononuclear cells

value: helper T (CD3+/CD4+/CD8-)

value: phase 1


title: KhES-1_day5_arm2, rep15

description: Single Cell RNA-seq data

source_name: KhES-1 cells, day5 of differentiation on LM411-E8

value: differentiating embryonic stem cells


title: small RNA-seq from upper lobe of left lung (ENCLB365RNP)

description:
https://www.encodeproject.org/experiments/ENCSR996VHB/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's upper lobe of left lung tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR996VHB
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB365RNP
size range: <200

source_name: Homo sapiens upper lobe of left lung tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0d91a57f-9a65-4237-8c66-4429f6917660/@@download/attachment/LID296637.pdf

value: upper lobe of left lung

value: tissue

value: Lung tissue obtained from GTEx for the Gingeras lab to conduct RNA-Seq assays on.

tag: biosample encode accession

tag: age

value: 54 year

tag: dev stage

value: adult

tag: Sex

value: male

tag: lab

value: Thomas Gingeras, CSHL

value: ENCBS271JIM at ENCODE; https://www.encodeproject.org/ENCBS271JIM/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: small RNA-seq from upper lobe of left lung (ENCLB072XZS)

description:
https://www.encodeproject.org/experiments/ENCSR961FIG/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's upper lobe of left lung tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR961FIG
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB072XZS
size range: <200

source_name: Homo sapiens upper lobe of left lung tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7feb0ace-54b1-4db7-a32d-df4c78297ae9/@@download/attachment/LID296639.pdf

value: 51 year

value: female

tag: link

value: ENCBS711XVO at ENCODE; https://www.encodeproject.org/ENCBS711XVO/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: small RNA-seq from sigmoid colon (ENCLB959UXM)

description:
https://www.encodeproject.org/experiments/ENCSR968DMR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's sigmoid colon tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR968DMR
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB959UXM
size range: <200

source_name: Homo sapiens sigmoid colon tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/91a6ad35-2968-43d0-8b8f-9581223b95ab/@@download/attachment/LID296504.pdf

value: sigmoid colon

value: Sigmoid colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: ENCBS894VJJ at ENCODE; https://www.encodeproject.org/ENCBS894VJJ/


title: AD_d12.NanogP8.1

value: LNCaP

tag: cell type

value: prostate cancer cells

value: NANOGP8 overexpression

value: androgen dependent (AD)

value: day 12


title: AD_d12.plvx.2

value: expressing pLVX (empty vector)


title: small RNA-seq from gastroesophageal sphincter (ENCLB942GFI)

description:
https://www.encodeproject.org/experiments/ENCSR998CRC/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's esophagogastric junction tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR998CRC
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB942GFI
size range: <200

source_name: Homo sapiens gastroesophageal sphincter tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/931dcec2-ffa4-4196-9fdb-12f664fa34ae/@@download/attachment/LID296542.pdf

value: gastroesophageal sphincter

value: tissue

value: Esophagogastric junction tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 53 year

value: adult

value: ENCBS616IQR at ENCODE; https://www.encodeproject.org/ENCBS616IQR/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: small RNA-seq from spleen (ENCLB156CLU)

description:
https://www.encodeproject.org/experiments/ENCSR917CQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's spleen tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR917CQJ
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB156CLU
size range: <200

source_name: Homo sapiens spleen tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0ffc0fbb-dfa3-434d-a750-61f30c485acf/@@download/attachment/LID296620.pdf

value: spleen

value: Spleen tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS297IUS at ENCODE; https://www.encodeproject.org/ENCBS297IUS/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: small RNA-seq from sigmoid colon (ENCLB595PHO)

description:
https://www.encodeproject.org/experiments/ENCSR880LXP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's sigmoid colon tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR880LXP
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB595PHO
size range: <200

source_name: Homo sapiens sigmoid colon tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2689493e-b8eb-4c3a-8081-f569dfe4f950/@@download/attachment/LID296503.pdf

value: sigmoid colon

value: Sigmoid colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: ENCBS516KIQ at ENCODE; https://www.encodeproject.org/ENCBS516KIQ/


title: small RNA-seq from sigmoid colon (ENCLB877OYA)

description:
https://www.encodeproject.org/experiments/ENCSR882DFF/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's sigmoid colon tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR882DFF
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB877OYA
size range: <200

source_name: Homo sapiens sigmoid colon tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0dfbb040-8d7a-44da-a8c0-9a5b471915fe/@@download/attachment/LID296506.pdf

value: 51 year

value: female

value: ENCBS214FDP at ENCODE; https://www.encodeproject.org/ENCBS214FDP/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: small RNA-seq from gastroesophageal sphincter (ENCLB742FOQ)

description:
https://www.encodeproject.org/experiments/ENCSR866ZSG/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's esophagogastric junction tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR866ZSG
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB742FOQ
size range: <200

source_name: Homo sapiens gastroesophageal sphincter tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/e976d2fc-7485-495b-9025-ab9e2cfebc16/@@download/attachment/LID296543.pdf

value: gastroesophageal sphincter

value: tissue

value: Esophagogastric junction tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: ENCBS874HID at ENCODE; https://www.encodeproject.org/ENCBS874HID/


title: AD_d05.NanogP8.1

value: LNCaP

value: prostate cancer cells

value: NANOGP8 overexpression

value: androgen dependent (AD)

value: day 5


title: small RNA-seq from upper lobe of left lung (ENCLB983DVP)

description:
https://www.encodeproject.org/experiments/ENCSR737NPO/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's upper lobe of left lung tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR737NPO
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB983DVP
size range: <200

source_name: Homo sapiens upper lobe of left lung tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/48436f3d-e804-4172-9e1d-4bba20b28d5e/@@download/attachment/LID296638.pdf

value: upper lobe of left lung

value: Lung tissue obtained from GTEx for the Gingeras lab to conduct RNA-Seq assays on.

value: 53 year

value: Thomas Gingeras, CSHL

value: ENCBS596PXT at ENCODE; https://www.encodeproject.org/ENCBS596PXT/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: small RNA-seq from sigmoid colon (ENCLB608HYG)

description:
https://www.encodeproject.org/experiments/ENCSR635SLB/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's sigmoid colon tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR635SLB
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB608HYG
size range: <200

source_name: Homo sapiens sigmoid colon tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/53b8d3f1-686e-41b2-b9f0-b0e9c2c66bbd/@@download/attachment/LID296505.pdf

value: sigmoid colon

value: Sigmoid colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: female

value: ENCBS581JIS at ENCODE; https://www.encodeproject.org/ENCBS581JIS/


title: small RNA-seq from Peyer's patch (ENCLB123FNE)

description:
https://www.encodeproject.org/experiments/ENCSR718AXQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's ileum tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR718AXQ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB123FNE
size range: <200

source_name: Homo sapiens Peyer's patch tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/87ff1ddb-1438-4ce2-9281-939ffd621289/@@download/attachment/LID296641.pdf

value: Peyer's patch

value: tissue

value: Small intestine aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: ENCBS231DCI at ENCODE; https://www.encodeproject.org/ENCBS231DCI/


title: small RNA-seq from vagina (ENCLB684PUB)

description:
https://www.encodeproject.org/experiments/ENCSR812JEU/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's vagina tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR812JEU
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB684PUB
size range: <200

source_name: Homo sapiens vagina tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5de70393-e112-45b2-9f0f-f29d8b898362/@@download/attachment/LID296659.pdf

value: vagina

value: Vagina aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: ENCBS158OEU at ENCODE; https://www.encodeproject.org/ENCBS158OEU/


title: small RNA-seq from adrenal gland (ENCLB415HSX)

description:
https://www.encodeproject.org/experiments/ENCSR612WDT/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's adrenal gland tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR612WDT
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB415HSX
size range: <200

source_name: Homo sapiens adrenal gland tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/d351b5e2-dc2d-4bb2-bdb9-b3c97270a8c6/@@download/attachment/LID296581.pdf

value: adrenal gland

value: Adrenal gland aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: ENCBS423TBO at ENCODE; https://www.encodeproject.org/ENCBS423TBO/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: small RNA-seq from testis (ENCLB304YPH)

description:
https://www.encodeproject.org/experiments/ENCSR626GVP/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's testis tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR626GVP
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB304YPH
size range: <200

source_name: Homo sapiens testis tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9b45a485-a010-4bbb-8948-7aae3bd3eef2/@@download/attachment/LID296656.pdf

value: testis

value: Testis aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS255MJZ at ENCODE; https://www.encodeproject.org/ENCBS255MJZ/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: small RNA-seq from right lobe of liver (ENCLB496AQV)

description:
https://www.encodeproject.org/experiments/ENCSR603XUX/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's right lobe of liver tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR603XUX
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB496AQV
size range: <200

source_name: Homo sapiens right lobe of liver tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/3d5badd5-026b-4268-a647-a18580432f8e/@@download/attachment/LID296635.pdf

value: right lobe of liver

value: tissue

value: Liver tissue from a 53 year old female received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: 53 year

value: adult

value: female

value: ENCBS796JPW at ENCODE; https://www.encodeproject.org/ENCBS796JPW/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: small RNA-seq from omental fat pad (ENCLB672RVD)

description:
https://www.encodeproject.org/experiments/ENCSR610GDH/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's adipose tissue tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR610GDH
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-06-13
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB672RVD
size range: <200

source_name: Homo sapiens omental fat pad tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ea450e34-b990-4954-a137-160f431ae7f2/@@download/attachment/LID296579.pdf

value: omental fat pad

value: Visceral adipose tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 37 year

value: ENCBS517FSZ at ENCODE; https://www.encodeproject.org/ENCBS517FSZ/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: small RNA-seq from gastroesophageal sphincter (ENCLB675VYM)

description:
https://www.encodeproject.org/experiments/ENCSR646HQQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's esophagogastric junction tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR646HQQ
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB675VYM
size range: <200

source_name: Homo sapiens gastroesophageal sphincter tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/483dbbe6-2839-45fd-aaea-124733205037/@@download/attachment/LID296540.pdf

value: gastroesophageal sphincter

value: Esophagogastric junction tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: male

value: ENCBS581RWW at ENCODE; https://www.encodeproject.org/ENCBS581RWW/


title: small RNA-seq from spleen (ENCLB451RLT)

description:
https://www.encodeproject.org/experiments/ENCSR587CPE/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 54 year old male's spleen tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR587CPE
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB451RLT
size range: <200

source_name: Homo sapiens spleen tissue male adult (54 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2b7e0715-ae70-4a42-b11c-e309471183b4/@@download/attachment/LID296621.pdf

value: spleen

value: Spleen tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: Thomas Gingeras, CSHL

value: ENCBS379XNT at ENCODE; https://www.encodeproject.org/ENCBS379XNT/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: small RNA-seq from stomach (ENCLB598NTG)

description:
https://www.encodeproject.org/experiments/ENCSR573RGL/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's stomach tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR573RGL
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB598NTG
size range: <200

source_name: Homo sapiens stomach tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f8ccc0b1-52d8-413d-891c-f0bc7e2d2cb5/@@download/attachment/LID296627.pdf

value: stomach

value: tissue

value: Stomach aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: adult

value: female

value: ENCBS038PAI at ENCODE; https://www.encodeproject.org/ENCBS038PAI/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: small RNA-seq from upper lobe of left lung (ENCLB483BRP)

description:
https://www.encodeproject.org/experiments/ENCSR539RDF/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 37 year old male's upper lobe of left lung tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR539RDF
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-08-05
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB483BRP
size range: <200

source_name: Homo sapiens upper lobe of left lung tissue male adult (37 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2319f3ec-e5c3-4b2e-a49d-77597115137c/@@download/attachment/LID296636.pdf

value: upper lobe of left lung

value: Lung tissue obtained from GTEx for the Gingeras lab to conduct RNA-Seq assays on.

value: 37 year

value: ENCBS320PNF at ENCODE; https://www.encodeproject.org/ENCBS320PNF/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: small RNA-seq from esophagus squamous epithelium (ENCLB911VYJ)

description:
https://www.encodeproject.org/experiments/ENCSR379GPS/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's esophagus mucosa tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR379GPS
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-05-23
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB911VYJ
size range: <200

source_name: Homo sapiens esophagus squamous epithelium tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/62934297-50b9-4959-a7ef-a1b38f83fac0/@@download/attachment/LID296584.pdf

value: esophagus squamous epithelium

value: Esophagus mucosa tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 53 year

value: ENCBS504VDB at ENCODE; https://www.encodeproject.org/ENCBS504VDB/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: small RNA-seq from esophagus squamous epithelium (ENCLB234JEI)

description:
https://www.encodeproject.org/experiments/ENCSR779BVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 51 year old female's esophagus mucosa tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR779BVZ
assay title: small RNA-seq
assembly: GRCh38, hg19
encode release date: 2016-06-13
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB234JEI
size range: <200

source_name: Homo sapiens esophagus squamous epithelium tissue female adult (51 year)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6c3d35b8-e749-4150-830f-4ceb2d444005/@@download/attachment/LID296585.pdf

value: tissue

value: Thomas Gingeras, CSHL

value: ENCBS842VSS at ENCODE; https://www.encodeproject.org/ENCBS842VSS/


title: small RNA-seq from spleen (ENCLB925SKX)

description:
https://www.encodeproject.org/experiments/ENCSR307FBN/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's spleen tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.
experiment encode accession: ENCSR307FBN
assay title: small RNA-seq
assembly: hg19, GRCh38
encode release date: 2016-05-03
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB925SKX
size range: <200

source_name: Homo sapiens spleen tissue female adult (53 years)

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0917531e-a3ca-4b40-80df-7650e6c123b2/@@download/attachment/LID296622.pdf

value: spleen

value: Spleen tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: ENCBS213OJV at ENCODE; https://www.encodeproject.org/ENCBS213OJV/