title: ChIP-seq from HepG2 (ENCLB758NLY)

description:
https://www.encodeproject.org/experiments/ENCSR219NRT/
***************
biological replicate number: 3
technical replicate number: 1
description: GTF2F1 ChIP-seq on human HepG2
experiment encode accession: ENCSR219NRT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB758NLY
size range: 150-350

source_name: Homo sapiens HepG2 immortalized cell line

value: Hepatocellular carcinoma

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS522AAA at ENCODE; https://www.encodeproject.org/ENCBS522AAA/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: 14317A_2_treat_24rs

status: Public on Jan 04 2017

type: SRA

city: Zhengzhou city

first: Juan

last: Li

state: Henan

address: kexue road

department: college of public health

country: China

institute: Zhengzhou University

description: Index: TGACCA

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
  A Perl program was used to filter off low quality sequences from raw sequencing data. Then, the remaining high quality reads of a sample were mapped by bowtie software (version 0.12.8) to the Rat genome downloaded from Ensembl  with the default parameter.
Peaks were called using MACS(Model-based Analysis for ChIP-Seq) using the parameter:-f BOWTIE -w –S.
Wig files were generated using Integrative Genomics Viewer(v2.3.18); the normalized read counts were used to measure level of methylated peaks to allow for comparison between experiments. Transcripts Reads Number Per Million (TPM) method was used to normalize the read counts. The formula is: TPM=1000000*（The Transcript Mapped Reads) / (Total Mapped Reads).
Genome_build: rn5
Supplementary_files_format_and_content: wig files

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Lung

growth_protocol: Lung fibroblasts were isolated from SPF male SD rats. Briefly, lung tissue was separated from the main airways of adult SD rats under sterile conditions. The explants were minced, washed 3 times with D-Hank’s solution, and disaggregated with crude bovine pancreatic trypsin. The resulting cell population was resuspended in DMEM (Olarbio Science and Technology, Beijing, China) containing 10% heat-inactivated fetal calf serum at 37˚C and 5% CO2. Rat macrophages (AMs) were collected from the SD rats by bronchoalveolar lavage (BAL). Tracheas were cannulated and BAL was performed with 5 ml cold sterile D-Hank's solution. After counted the cell number, the cells were incubated at 37˚C for 2 hours at 5% CO2 and then refresh new medium.

extract_protocol:
Genomic DNA was isolated using the DNeasy Kit (Qiagen, CA) according to the manufacturer’s protocols.
Libraries were prepared according to the manufacturer’s protocol, the fragmented DNA were end-repaired, A-tailed, ligated adapter and purified using Agencourt AMPure XP kit. 0.4µg DNA was used for subsequent MeDIP enrichment. Briefly, immunoprecipitation was carried out at 37˚C for 0.5 hr to 1 hr. After amplification and purification, we performed agarose gel electrophoresis and excised bands from the gel to produce libraries with insert sizes of ~125bp, then quantified these libraries using KAPA DNA Reagent and Kits (KAPA Biosystem). The total libraries randomly arranged in 8 lanes were sequenced by the Next Generation Sequencing.

treatment_protocol: The co-culture was established of AMs and fibroblasts. Seeding fibroblasts into six-well plates and incubated for one or two days until approximately 60% confluence was achieved. AMs were seeding into the inserts and placed the insert into the six-well dish and then exposed to 100µg/ml SiO2 for 0-, 24-, and 48 hours after overnight culture.

tag: cell type

value: fibroblast

tag: passage

tag: strain

value: SD

tag: co-culture

value: Yes

tag: sio2 treatment

tag: treatment time

value: 24 hours


title: ChIP-seq from HepG2 (ENCLB213FHF)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR219NRT/
***************
biological replicate number: 2
technical replicate number: 1
description: GTF2F1 ChIP-seq on human HepG2
experiment encode accession: ENCSR219NRT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB213FHF
size range: 150-350

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

organism: Homo sapiens

tag: antibody

tag: line

value: immortalized cell line

tag: description

tag: biosample encode accession

tag: dev stage

value: child

tag: age

tag: Sex

tag: lab

value: Michael Snyder, Stanford

tag: health state

tag: link

value: ENCBS523AAA at ENCODE; https://www.encodeproject.org/ENCBS523AAA/


title: ChIP-seq from HEK293 (ENCLB326OMD)

description:
https://www.encodeproject.org/experiments/ENCSR228PGT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF292 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR228PGT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB326OMD
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF292 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF292 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: ENCBS829KGK at ENCODE; https://www.encodeproject.org/ENCBS829KGK/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from HeLa-S3 (ENCLB092IEW)

description:
https://www.encodeproject.org/experiments/ENCSR219MKK/
***************
biological replicate number: 1
technical replicate number: 1
description: DEK ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR219MKK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR580ECR
encode release date: 2016-04-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB092IEW
size range: 150-350

source_name: Homo sapiens HeLa-S3 immortalized cell line

value: DEK

value: adult

value: 31 year

value: cervical adenocarcinoma

value: ENCBS812AOY at ENCODE; https://www.encodeproject.org/ENCBS812AOY/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058


title: ChIP-seq from K562 (ENCLB806EAG)

description:
https://www.encodeproject.org/experiments/ENCSR376WCJ/
***************
biological replicate number: 1
technical replicate number: 1
description: IRF2 ChIP-seq on human K562
experiment encode accession: ENCSR376WCJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB806EAG
size range: 150-350

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS594GNK at ENCODE; https://www.encodeproject.org/ENCBS594GNK/

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

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


title: ChIP-seq from HEK293 (ENCLB130VTD)

description:
https://www.encodeproject.org/experiments/ENCSR223TAV/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-PRDM10 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR223TAV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB130VTD
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-PRDM10 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-PRDM10 under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS154XJI at ENCODE; https://www.encodeproject.org/ENCBS154XJI/


title: ChIP-seq from HEK293 (ENCLB753VDZ)

description:
https://www.encodeproject.org/experiments/ENCSR223TAV/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-PRDM10 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR223TAV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB753VDZ
size range: 450-650

value: female

value: ENCBS002NWR at ENCODE; https://www.encodeproject.org/ENCBS002NWR/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: eCLIP from K562 (ENCLB313ZNN)

description:
https://www.encodeproject.org/experiments/ENCSR218NAB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against TNRC6A
experiment encode accession: ENCSR218NAB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR800LOQ
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB313ZNN
size range: 175-300

library_source: transcriptomic

molecule: total RNA

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/dde0b669-0909-4f8b-946d-3cb9f35a6c52/@@download/attachment/eCLIP_analysisSOP_v1.P.pdf
general protocol: https://www.encodeproject.org/documents/842f7424-5396-424a-a1a3-3f18707c3222/@@download/attachment/eCLIP_SOP_v1.P_110915.pdf
extraction method: see document

value: adult

tag: passage number

value: Gene Yeo, UCSD

value: ENCBS489LOC at ENCODE; https://www.encodeproject.org/ENCBS489LOC/

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: ChIP-seq from MCF-7 (ENCLB877GNU)

description:
https://www.encodeproject.org/experiments/ENCSR231ENE/
***************
biological replicate number: 2
technical replicate number: 1
description: ARID3A ChIP-seq on human MCF-7
experiment encode accession: ENCSR231ENE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB877GNU
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS183ZAS at ENCODE; https://www.encodeproject.org/ENCBS183ZAS/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: ChIP-seq from IMR-90 (ENCLB427MQL)

description:
https://www.encodeproject.org/experiments/ENCSR197WGI/
***************
biological replicate number: 3
technical replicate number: 1
description: NFE2L2 ChIP-seq on human IMR90
experiment encode accession: ENCSR197WGI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR970FKL
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB427MQL
size range: 150-350

source_name: Homo sapiens IMR-90 primary cell female fetal (16 weeks)

value: primary cell

value: Fetal lung fibroblasts

value: fetal

value: 16 week

value: ENCBS048GPK at ENCODE; https://www.encodeproject.org/ENCBS048GPK/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/

value: ENCODE dbxrefs Cellosaurus CVCL_0347; http://web.expasy.org/cellosaurus/CVCL_0347

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-186.aspx


title: UCD4 E2+P4 replicate 3 input

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

data_processing:
ChIPseq reads were processed with cutadapt (https://code.google.com/p/cutadapt/) to remove 3’ adaptor sequences and 3’ bases with QUAL < 13.
Trimmed reads were aligned to the human genome (grch37/hg19 build) using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Peaks were called on aligned reads using HOMER-IDR (https://github.com/karmel/homer-idr), an implementation of the Irreproducible Discovery Rate (IDR) framework (https://sites.google.com/site/anshulkundaje/projects/idr) using the HOMER peak caller (http://homer.salk.edu/homer/index.html).
Genome_build: hg19
Supplementary_files_format_and_content: BED file with HOMER-IDR peak calls for all four experimental groups (IgG control).

source_name: Breast tumor xenograft

growth_protocol: Xenografts were grown in NOD/SCID/Il2rgnull mice

extract_protocol:
Tissue was pulverized and crosslinked. Lysates were produced from sonicated nuclei and ER or PR were isolated with antibody.
Libraries were prepared at the University of Colorado Denver Genomics and Microarray Core facility using the NuGEN Ovation Ultralow Library System v2 .

treatment_protocol: Chronic E2/E2+P4 treatment upon transplant

tag: xenograft

tag: treatment

value: estrogen plus progesterone

tag: chip antibody

value: input


title: ChIP-seq from HEK293 (ENCLB443YBZ)

description:
https://www.encodeproject.org/experiments/ENCSR217WRC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TSHZ1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR217WRC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB443YBZ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-TSHZ1 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-TSHZ1 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS429FXL at ENCODE; https://www.encodeproject.org/ENCBS429FXL/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: eCLIP from K562 (ENCLB674YBJ)

description:
https://www.encodeproject.org/experiments/ENCSR218NAB/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against TNRC6A
experiment encode accession: ENCSR218NAB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR800LOQ
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB674YBJ
size range: 175-300

value: immortalized cell line

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS931MQO at ENCODE; https://www.encodeproject.org/ENCBS931MQO/

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/HB-8065.aspx


title: ChIP-seq from HeLa-S3 (ENCLB051HUK)

description:
https://www.encodeproject.org/experiments/ENCSR219MKK/
***************
biological replicate number: 2
technical replicate number: 1
description: DEK ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR219MKK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR580ECR
encode release date: 2016-04-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB051HUK
size range: 150-350

value: DEK

value: 31 year

value: cervical adenocarcinoma

value: ENCBS529RSF at ENCODE; https://www.encodeproject.org/ENCBS529RSF/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058


title: ChIP-seq from K562 (ENCLB583AAU)

description:
https://www.encodeproject.org/experiments/ENCSR189PYJ/
***************
biological replicate number: 1
technical replicate number: 1
description: SMAD2 ChIP-seq on human K562
experiment encode accession: ENCSR189PYJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB583AAU
size range: 150-350

value: Leukemia, 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. - ATCC

value: female

value: Michael Snyder, Stanford

value: ENCBS489ZOH at ENCODE; https://www.encodeproject.org/ENCBS489ZOH/

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


title: UCD4 E2+P4 replicate 3 ER ChIP

value: estrogen plus progesterone

value: ER (sc-543X, Santa Cruz Biotechnology), lot# F1215


title: UCD4 E2+P4 replicate 2 PR ChIP

value: PR (sc-7208X, Santa Cruz Biotechnology), lot# H1415


title: ChIP-seq from K562 (ENCLB009VYH)

description:
https://www.encodeproject.org/experiments/ENCSR189PYJ/
***************
biological replicate number: 2
technical replicate number: 1
description: SMAD2 ChIP-seq on human K562
experiment encode accession: ENCSR189PYJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB009VYH
size range: 150-350

value: immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS207UAM at ENCODE; https://www.encodeproject.org/ENCBS207UAM/

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


title: ChIP-seq from HEK293 (ENCLB733OPG)

description:
https://www.encodeproject.org/experiments/ENCSR217WRC/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TSHZ1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR217WRC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB733OPG
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-TSHZ1 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS351LOZ at ENCODE; https://www.encodeproject.org/ENCBS351LOZ/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from MCF-7 (ENCLB336TVW)

description:
https://www.encodeproject.org/experiments/ENCSR217LRF/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human MCF-7
experiment encode accession: ENCSR217LRF
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB336TVW
size range: 450-650

value: Control

value: Mammary gland, adenocarcinoma. (PMID:4357757)

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: ENCBS034XKZ at ENCODE; https://www.encodeproject.org/ENCBS034XKZ/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-22.aspx


title: UCD4 E2+P4 replicate 3 PR ChIP

value: estrogen plus progesterone

value: PR (sc-7208X, Santa Cruz Biotechnology), lot# H1415


title: UCD4 E2+P4 replicate 3 IgG ChIP

value: IgG (sc-2027, Santa Cruz Biotechnology), lot # H2615


title: ChIP-seq from MCF-7 (ENCLB678IDC)

description:
https://www.encodeproject.org/experiments/ENCSR217LRF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human MCF-7
experiment encode accession: ENCSR217LRF
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB678IDC
size range: 450-650

value: immortalized cell line

value: adult

value: ENCBS216AOQ at ENCODE; https://www.encodeproject.org/ENCBS216AOQ/


title: UCD4 E2+P4 replicate 2 ER ChIP

value: ER (sc-543X, Santa Cruz Biotechnology), lot# F1215


title: eCLIP from K562 (ENCLB208FLO)

description:
https://www.encodeproject.org/experiments/ENCSR224QWC/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against FXR2
experiment encode accession: ENCSR224QWC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR411IMJ
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB208FLO
size range: 175-300

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS333OTT at ENCODE; https://www.encodeproject.org/ENCBS333OTT/

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: ChIP-seq from HepG2 (ENCLB385BLP)

description:
https://www.encodeproject.org/experiments/ENCSR157CAU/
***************
biological replicate number: 3
technical replicate number: 1
description: ZKSCAN1 ChIP-seq on human HepG2
experiment encode accession: ENCSR157CAU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB385BLP
size range: 150-350

value: Hepatocellular carcinoma

value: child

value: 15 year

value: male

value: Michael Snyder, Stanford

value: hepatocellular carcinoma

value: ENCBS523AAA at ENCODE; https://www.encodeproject.org/ENCBS523AAA/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: UCD4 E2+P4 replicate 2 IgG ChIP

value: estrogen plus progesterone

value: IgG (sc-2027, Santa Cruz Biotechnology), lot # H2615


title: ChIP-seq from HEK293 (ENCLB876EXL)

description:
https://www.encodeproject.org/experiments/ENCSR217HTK/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ATF2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR217HTK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB876EXL
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ATF2 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ATF2 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: ENCBS818PXJ at ENCODE; https://www.encodeproject.org/ENCBS818PXJ/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: UCD4 E2+P4 replicate 1 IgG ChIP


title: UCD4 E2+P4 replicate 1 PR ChIP

value: PR (sc-7208X, Santa Cruz Biotechnology), lot# H1415


title: UCD4 E2+P4 replicate 2 input

value: input


title: ChIP-seq from HepG2 (ENCLB784GTR)

description:
https://www.encodeproject.org/experiments/ENCSR157CAU/
***************
biological replicate number: 1
technical replicate number: 1
description: ZKSCAN1 ChIP-seq on human HepG2
experiment encode accession: ENCSR157CAU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB784GTR
size range: 150-350

value: child

value: 15 year

value: male

value: Michael Snyder, Stanford

value: ENCBS546FZO at ENCODE; https://www.encodeproject.org/ENCBS546FZO/


title: ChIP-seq from HEK293 (ENCLB364PGJ)

description:
https://www.encodeproject.org/experiments/ENCSR217HTK/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ATF2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR217HTK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB364PGJ
size range: 450-650

value: ENCBS268PXW at ENCODE; https://www.encodeproject.org/ENCBS268PXW/


title: ChIP-seq from K562 (ENCLB502JVC)

description:
https://www.encodeproject.org/experiments/ENCSR213VUI/
***************
biological replicate number: 1
technical replicate number: 1
description: TRIM25 ChIP-seq on human K562
experiment encode accession: ENCSR213VUI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB502JVC
size range: 450-650

value: Leukemia, 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. - ATCC

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS207UAM at ENCODE; https://www.encodeproject.org/ENCBS207UAM/

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: ChIP-seq from HeLa-S3 (ENCLB694OHW)

description:
https://www.encodeproject.org/experiments/ENCSR140DSL/
***************
biological replicate number: 3
technical replicate number: 1
description: MAFF ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR140DSL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR580ECR
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB694OHW
size range: 150-350

value: MAFF

value: immortalized cell line

value: 31 year

value: female

value: cervical adenocarcinoma

value: ENCBS899VUW at ENCODE; https://www.encodeproject.org/ENCBS899VUW/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058


title: UCD4 E2+P4 replicate 1 input

value: estrogen plus progesterone

value: input


title: UCD4 E2+P4 replicate 1 ER ChIP

value: ER (sc-543X, Santa Cruz Biotechnology), lot# F1215


title: ChIP-seq from HeLa-S3 (ENCLB748YJS)

description:
https://www.encodeproject.org/experiments/ENCSR140DSL/
***************
biological replicate number: 2
technical replicate number: 1
description: MAFF ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR140DSL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR580ECR
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB748YJS
size range: 150-350

value: adult

value: Michael Snyder, Stanford

value: ENCBS658BKJ at ENCODE; https://www.encodeproject.org/ENCBS658BKJ/


title: ChIP-seq from K562 (ENCLB609TDY)

description:
https://www.encodeproject.org/experiments/ENCSR213VUI/
***************
biological replicate number: 2
technical replicate number: 1
description: TRIM25 ChIP-seq on human K562
experiment encode accession: ENCSR213VUI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB609TDY
size range: 450-650

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS837GDT at ENCODE; https://www.encodeproject.org/ENCBS837GDT/

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


title: ChIP-seq from K562 (ENCLB680YFS)

description:
https://www.encodeproject.org/experiments/ENCSR138FUZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RING1 ChIP-seq on human K562
experiment encode accession: ENCSR138FUZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB680YFS
size range: 150-350

value: immortalized cell line

value: Leukemia, 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. - ATCC

value: ENCBS207UAM at ENCODE; https://www.encodeproject.org/ENCBS207UAM/

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: ChIP-seq from K562 (ENCLB365UJY)

description:
https://www.encodeproject.org/experiments/ENCSR124BJR/
***************
biological replicate number: 2
technical replicate number: 1
description: ETV6 ChIP-seq on human K562
experiment encode accession: ENCSR124BJR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB365UJY
size range: 150-350

value: female

value: ENCBS534MHY at ENCODE; https://www.encodeproject.org/ENCBS534MHY/


title: ChIP-seq from K562 (ENCLB107GJJ)

description:
https://www.encodeproject.org/experiments/ENCSR138FUZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RING1 ChIP-seq on human K562
experiment encode accession: ENCSR138FUZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB107GJJ
size range: 150-350

value: ENCBS489ZOH at ENCODE; https://www.encodeproject.org/ENCBS489ZOH/


title: ChIP-seq from K562 (ENCLB247PDR)

description:
https://www.encodeproject.org/experiments/ENCSR124BJR/
***************
biological replicate number: 1
technical replicate number: 1
description: ETV6 ChIP-seq on human K562
experiment encode accession: ENCSR124BJR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB247PDR
size range: 150-350


title: eCLIP from K562 (ENCLB161TSJ)

description:
https://www.encodeproject.org/experiments/ENCSR212ILN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against HNRNPM
experiment encode accession: ENCSR212ILN
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB161TSJ
size range: 175-300

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/dde0b669-0909-4f8b-946d-3cb9f35a6c52/@@download/attachment/eCLIP_analysisSOP_v1.P.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fa2a3246-6039-46ba-b960-17fe06e7876a/@@download/attachment/CLIP_SOP_v1.0.pdf

value: Control

value: Gene Yeo, UCSD

value: ENCBS270GGH at ENCODE; https://www.encodeproject.org/ENCBS270GGH/


title: UCD4 E2 replicate 3 input

value: estrogen

value: input


title: ChIP-seq from IMR-90 (ENCLB802DMN)

description:
https://www.encodeproject.org/experiments/ENCSR197WGI/
***************
biological replicate number: 2
technical replicate number: 1
description: NFE2L2 ChIP-seq on human IMR90
experiment encode accession: ENCSR197WGI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR970FKL
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB802DMN
size range: 150-350

value: primary cell

value: fetal

value: 16 week

value: Michael Snyder, Stanford

value: unknown

value: ENCBS486FIC at ENCODE; https://www.encodeproject.org/ENCBS486FIC/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/

value: ENCODE dbxrefs Cellosaurus CVCL_0347; http://web.expasy.org/cellosaurus/CVCL_0347


title: UCD4 E2 replicate 3 PR ChIP

value: PR (sc-7208X, Santa Cruz Biotechnology), lot# H1415


title: UCD4 E2 replicate 3 ER ChIP

value: ER (sc-543X, Santa Cruz Biotechnology), lot# F1215


title: 2J_YFV_cap_ntr2_lvp_96hrs_rep1

city: Blacksburg

first: Kevin

last: Myles

state: VA

address: Fralin Life Science Institute 360 West Campus Drive

institute: Virginia Tech

data_processing:
Basecalls performed using CASAVA version 1.4
Randomly 25 million sequences were selected for analysis form each library using in house perl script
Mosquito ncRNAs were taken out using bowtie v12.7 (-q -t -p 8 -v 3 -k 1 -m 1)
Recombinat SINV viral small RNAs were removed using bowtie v12.7 (-q -t -p 8 -v 1 -k 1 -B 1 --best)
Mosquito miRNAs, Transposable elements, and endosiRNAs were removed using bowtie v12.7 (-q -t -p 8 -v 1 -k 1 -B 1 --best)
Individual counts for each small RNA class was totaled using in house perl scripts
Libraries were normalized using edgeR, using counts from viRNAs, miRNAs, TE, and endosiRNAs
Supplementary_files_format_and_content: Processed counts were pasted into excel spreadsheet

organism: Aedes aegypti

source_name: whole body

growth_protocol: Mosquito were reared in environmental chambers with a light cycle of 14:10 (day:night) and humidity of 80%.

extract_protocol:
Total RNA was isolated with Tri RT (Molecular Research Center) from adult female mosquitoes 96 h after infection.
Small RNAs (18 to 35-nt) were recovered by PAGE separation, and libraries prepared with the Truseq small RNA sample prep kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Two day old mosquitoes were injected with 0.5 μl (106 pfu/ml) of recombinant SINV, and monitored daily for survival.

tag: genotype/variation

value: recombinate SINV expressing a non-translatalbe version of YFV-capsid


title: UCD4 E2 replicate 2 IgG ChIP

value: IgG (sc-2027, Santa Cruz Biotechnology), lot # H2615


title: ChIP-seq from K562 (ENCLB395VPY)

description:
https://www.encodeproject.org/experiments/ENCSR209YCR/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF740 tagged K562 cell line.
experiment encode accession: ENCSR209YCR
assay title: ChIP-seq
encode release date: 2016-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB395VPY

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ZNF740 fusion protein

value: Control

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF740

value: adult

value: 53 year

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS928AAC at ENCODE; https://www.encodeproject.org/ENCBS928AAC/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA08; http://web.expasy.org/cellosaurus/CVCL_HA08


title: 2J_YFV_cap_ntr2_lvp_96hrs_rep3


title: ChIP-seq from HEK293 (ENCLB195JBS)

description:
https://www.encodeproject.org/experiments/ENCSR210MET/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF391 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR210MET
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB195JBS
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF391 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF391 under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS076BVM at ENCODE; https://www.encodeproject.org/ENCBS076BVM/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: 2J_YFV_cap_lvp_96hrs_rep3

value: recombinate SINV expressing YFV capsid


title: ChIP-seq from HEK293 (ENCLB215KOR)

description:
https://www.encodeproject.org/experiments/ENCSR210MET/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF391 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR210MET
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB215KOR
size range: 450-650

value: immortalized cell line

value: ENCBS813VRX at ENCODE; https://www.encodeproject.org/ENCBS813VRX/


title: 2J_YFV_cap_ntr2_lvp_96hrs_rep2

value: recombinate SINV expressing a non-translatalbe version of YFV-capsid


title: UCD4 E2 replicate 2 PR ChIP

value: estrogen

value: PR (sc-7208X, Santa Cruz Biotechnology), lot# H1415


title: ChIP-seq from HEK293 (ENCLB307YFV)

description:
https://www.encodeproject.org/experiments/ENCSR211PZO/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-GLI4 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR211PZO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB307YFV
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-GLI4 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-GLI4 under the control of a CMV promoter.

value: female

value: ENCBS966YJO at ENCODE; https://www.encodeproject.org/ENCBS966YJO/


title: UCD4 E2 replicate 3 IgG ChIP

value: IgG (sc-2027, Santa Cruz Biotechnology), lot # H2615


title: UCD4 E2 replicate 1 IgG ChIP


title: eCLIP from HepG2 (ENCLB940UVB)

description:
https://www.encodeproject.org/experiments/ENCSR205ZCE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against IGF2BP1
experiment encode accession: ENCSR205ZCE
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB940UVB
size range: 175-300

value: Control

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

value: ENCBS040EJF at ENCODE; https://www.encodeproject.org/ENCBS040EJF/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: UCD4 E2 replicate 2 ER ChIP

value: ER (sc-543X, Santa Cruz Biotechnology), lot# F1215


title: 2J_YFV_cap_lvp_96hrs_rep1

value: recombinate SINV expressing YFV capsid


title: ChIP-seq from GM12878 (ENCLB927CUY)

description:
https://www.encodeproject.org/experiments/ENCSR205SKQ/
***************
biological replicate number: 2
technical replicate number: 1
description: YBX1 ChIP-seq on human GM12878
experiment encode accession: ENCSR205SKQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2016-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB927CUY
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

value: immortalized cell line

value: adult

value: unknown

value: Michael Snyder, Stanford

value: ENCBS339VHO at ENCODE; https://www.encodeproject.org/ENCBS339VHO/

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

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


title: UCD4 E2 replicate 2 input

value: estrogen

value: input


title: UCD4 E2 replicate 1 ER ChIP


title: UCD4 E2 replicate 1 PR ChIP

value: PR (sc-7208X, Santa Cruz Biotechnology), lot# H1415


title: ibm11_Col_1st

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

description: ibm1-1 mutant 1st generation

data_processing:
The raw reads were trimmed using Trimmomatic (Bolger et al, 2014 Bioinformatics) in order to remove adapter sequences. Reads with an average quality value of at least 15 in a window of 4 nucleotides were trimmed from both ends. After trimming, reads shorter than 16 bases were discarded.
The remaining sequences were aligned using Bismark (Krueger et al. 2011, Bioinformatics) against the Arabidopsis thaliana genome TAIR10 version or the PacBio Ler-0 genome assembly (http://www.pacb.com/uncategorized/new-data-release-arabidopsis-assembly/) for Col-0 ibm1 or Ler-0 ibm1 mutant, respectively. Duplicated reads were collapsed into one read.
Chloroplast sequences were used to estimate the bisulfite conversion.
Genome_build: Arabidopsis thaliana Col-0: TAIR10; Ler-0: PacBio assembly (http://www.pacb.com/uncategorized/new-data-release-arabidopsis-assembly/)
Supplementary_files_format_and_content: For each genotype, the CX_Report generated by Bismark is reported (Krueger et al. 2011, Bioinformatics).

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Plants were grown in plates under long-day conditions (21°C, 16 h light, 8 h dark)

extract_protocol:
Genomic DNA was extracted using the Plant DNeasy kit (Qiagen) following the manufacturer's instructions.
Libraries were constructed starting from 150 ng of genomic DNA, using the EZ-DNA Methylation-Gold Kit (Zymo Research), following by DNA library preparation with the TruSeq DNA methylation kit (Illumina), according to manufacturer's instructions.

tag: ecotype

tag: tissue

value: rosette leaves

value: 3 weeks


title: siRNA RNA-seq from K562 (ENCLB789IED)

description:
https://www.encodeproject.org/experiments/ENCSR205BWT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting BRCA1.
experiment encode accession: ENCSR205BWT
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR401RKW, ENCSR608CVU
encode release date: 2016-10-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB789IED
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting BRCA1

tag: antibody

value: K562 cells treated with a siRNA knockdown against BRCA1, used in RNA-seq experiments.

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Sherman Weissman, Yale

value: ENCBS279FHQ at ENCODE; https://www.encodeproject.org/ENCBS279FHQ/

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


title: UCD65 E2+MPA, replicate 3

data_processing:
Reads were aligned separately to the human genome (hg19) and mouse genome (mm10) using TopHat.
Reads successfully aligned to both mm10 and hg19 were removed from the hg19 alignments, leaving only human-specific reads.
Differential expression testing and normalized transcript abundance measurement was perfomed using cuffdiff.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: tab-delimited, normalized isoform abundance measurements from cuffdiff.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit at the University of Colorado Denver Genomics and Microarray Core facility.

treatment_protocol: Chronic E2/E2+MPA treatment upon transplant

value: estrogen+MPA


title: eCLIP from HepG2 (ENCLB673EEU)

description:
https://www.encodeproject.org/experiments/ENCSR202BFN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against U2AF2
experiment encode accession: ENCSR202BFN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR049GND
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB673EEU
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/dde0b669-0909-4f8b-946d-3cb9f35a6c52/@@download/attachment/eCLIP_analysisSOP_v1.P.pdf
general protocol: https://www.encodeproject.org/documents/842f7424-5396-424a-a1a3-3f18707c3222/@@download/attachment/eCLIP_SOP_v1.P_110915.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fa2a3246-6039-46ba-b960-17fe06e7876a/@@download/attachment/CLIP_SOP_v1.0.pdf

tag: line

value: immortalized cell line

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS836LJE at ENCODE; https://www.encodeproject.org/ENCBS836LJE/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: CCTO90-ORSI-26Oct2011

city: Corvallis

first: Richard

middle: C

last: Cronn

state: Oregon

address: 3200 SW Jefferson Way

department: Pacific Northwest Research Station

institute: USDA Forest Service

description: Douglas-fir annual transcriptome analysis

data_processing:
Base-calling and demultiplexing was performed using Casava v1.8 (Illumina Inc.).
Transcript read mapping: To quantify transcript abundance in diurnal and RNA-Seq samples, we mapped reads to the pan-transcriptome reference with bowtie2.2.3 (Langmead and Salzberg, 2012) using the following call:  bowtie2 --end-to-end -D 15 -R 2 -L 22 -i S,1,1.15. This allows 15 consecutive seed extension attempts before the aligner moved on (-D 15), a maximum of 2 attempts to re-seed reads with repetitive seeds (-R 2), and a 22 bp seed (-L 22) with zero allowed mismatches in this seed. The function to determine the interval between seed substrings during multi-seed alignment was set to f(x) = 1 + 1.15 * sqrt(x), where x is the read length (-i S,1,1.15) (based on the 101 bp read lengths this resulted in an interval of 13 bp).  Output from this step is provided as processed data file "filename2.gz"
Transcript filtering and normalization: Since many transcripts showed near-zero counts, we excluded transcripts showing median counts at or below 5 from analyses because they were essentially indistinguishable from background transcription. For transcripts meeting the median cut-off, counts were normalized using DESeq normalization (Anders and Huber, 2010; Bullard et al., 2010; Dillies et al., 2012).
Transcript count interpolation: For the Annual Expression study, five trees from two families were sampled at 16 time points (80 total samples). Thirteen samples were too low-quality and had to be dropped from the analysis. To obtain full coverage over the 16 sample time points-- two trees from family A (CCTO44, CCCTO90) and three from family B (CCTO43, CCTO46, CCTO89) were used.  Counts were median filtered by gene (retained if median>5 counts), and then normalized for library size using DESeq normalization. For cyclic expression analysis, normalized values were averaged and then analyzed by family. The 16 sample time points  were not quite evenly spaced, so new values at equally spaced time intervals were inferred using linear interpolation on the the family averages.  This was done individually for every gene in the table.
Genome_build: Douglas-fir pan-transcriptome reference v2.03 (TSA in submission)
Supplementary_files_format_and_content: tab-separated text files were generated using  bowtie 2.2.3; Counts represent the number of reads mapping to each transcript model
Supplementary_files_format_and_content: tab-separated text files were generated using DESeq; Counts represent the number of reads mapping to each transcript model, after the application of a normalization factor to correct for library size
Supplementary_files_format_and_content: tab-separated text files were generated using a custom R-script; Counts represent the interpolated DESeq-adjusted counts for each transcript model, where interpolations correct for uneven sample intervals.

molecule: polyA RNA

organism: Pseudotsuga menziesii

growth_protocol: Trees used for annual transcriptome analysis are a sample from a reciprocal translocation study (Harrington et al., 2010) that includes families from multiple geographic sources in the Pacific Northwestern region of North America. Sources were chosen to maximize climatic differences in geographic origin (temperature, precipitation), and differences in growth phenology determined for the same seed lots. Three source climate zones are represented: a cold/wet region (Washington Cascades high elevation; 47.3° N, -121.6° W, 950 m elevation); a cool/wet region (Washington Coast low elevation; 47.2° N, -123.9° W, 111 m elevation); and a warm/dry region (Oregon Siskiyou low elevation; 43.3° N, -123.1° W, 429 m elevation). Two-year old trees were planted in a warm/dry region similar to Oregon Siskiyou sources (J. Herbert Stone Nursery , Central Point, Oregon, USA; 42.3° N, -122.9° W, 390 m elevation) in November, 2009, and sampling of the 2010 cohort of needles was initiated on October 27, 2010 at approximately three week intervals until November, 2011 (16 samples points).  Needles were collected at approximately 12:00 pm (ZT = 04:20 to 06:30). Annual precipitation at the Central Point, OR garden site during our experiment was 460 mm, minimum air temperature was -8.0°C, and maximum air temperature was 37.5°C. Environmental data (sunrise; sunset; day length; cumulative weekly precipitation; mean minimum and maximum weekly temperature) was collected for this experiment.

extract_protocol:
Needles (8 – 12 per sample) were collected 2.5 - 5 cm basipetal of dormant branch apical buds from branches representing four cardinal directions. Needles were flash-frozen in liquid N2, followed by homogenization on dry ice (FastPrep-24 mill, matrix A; MP Biomedical, Solon, OH., USA). Ice-cold extraction buffer (1.5 mL of 3M LiCl/8M urea; 1% PVP K-60; 0.1M dithiothreitol; Tai et al., 2004) was added to ground tissue, homogenized, then centrifuged at 200g x 10 min., 4°C. The supernatant was incubated overnight at 4°C, and crude RNA was pelleted (20,000g x 30 min., 4°C) and cleaned using the ZR Plant RNA MiniPrep kit (Zymo Research, Irvine, CA., USA) and DNAse treatment (Turbo DNAse; New England Biolabs, Ipswich, MA., USA). RNA concentration was estimated using a Qubit fluorometer (Invitrogen, Carlsbad, CA., USA), and total RNA yield averaged 0.3 µg/mg tissue.
Indexed Illumina RNA-Seq libraries used 2 µg total RNA and TruSeq chemistry (Illumina Inc., San Diego, CA), modified for strand-specific sampling (Parkhomchuk et al., 2009). In this protocol, the first-strand synthesis reaction was desalted to remove unincorporated dNTPs using Sephadex G-25 (Sigma-Aldrich, St. Louis, MO., USA) filtration. Desalted products were reconstituted in dNTP-free second-strand synthesis buffer, second strand enzyme mix (New England Biolabs, Ipswich, MA., USA), and a dUTP/dNTP mixture (ThermoScientific, Waltham, MA., USA) to incorporate dUTP into the second strand. All other steps follow Illumina protocols, except that uracil-containing strands were degraded using a uracil-specific excision reagent mixture (37°C for 15 minutes; New England Biolabs) prior to PCR. Amplified libraries were quantified by fluorometry and pooled at equimolar 6-plex representation at 10 nM. Sequencing was performed at Oregon State University's Center for Genome Research and Biocomputing (Corvallis, OR., USA) using a HiSeq 2000 (Illumina Inc.) with version 3.0 chemistry.

tag: family-tag

value: Oregon Siskiyou low elevation


title: 2J_YFV_cap_lvp_96hrs_rep2

value: recombinate SINV expressing YFV capsid


title: ChIP-seq from GM12878 (ENCLB159YJL)

description:
https://www.encodeproject.org/experiments/ENCSR205SKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: YBX1 ChIP-seq on human GM12878
experiment encode accession: ENCSR205SKQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2016-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB159YJL
size range: 450-650

tag: biosample encode accession

value: adult

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS421UOG at ENCODE; https://www.encodeproject.org/ENCBS421UOG/

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

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


title: UCD4 E2 replicate 1 input

value: estrogen

value: input


title: eCLIP from K562 (ENCLB082BLN)

description:
https://www.encodeproject.org/experiments/ENCSR200SAU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against DDX42
experiment encode accession: ENCSR200SAU
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB082BLN
size range: 175-300

value: Control

value: immortalized cell line

tag: dev stage

value: 53 year

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS365DFQ at ENCODE; https://www.encodeproject.org/ENCBS365DFQ/

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: siRNA RNA-seq from K562 (ENCLB127VBO)

description:
https://www.encodeproject.org/experiments/ENCSR205BWT/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting BRCA1.
experiment encode accession: ENCSR205BWT
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR401RKW, ENCSR608CVU
encode release date: 2016-10-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB127VBO
size range: >200
spikeins used: /references/ENCSR866KGS/

tag: description

value: K562 cells treated with a siRNA knockdown against BRCA1, used in RNA-seq experiments.

value: adult

tag: age

value: Sherman Weissman, Yale

value: ENCBS475SOK at ENCODE; https://www.encodeproject.org/ENCBS475SOK/


title: UCD65 E2+MPA, replicate 2

value: estrogen+MPA


title: CCTO90-ORSI-17Aug2011

value: Oregon Siskiyou low elevation


title: UCD65 E2+MPA, replicate 1


title: CCTO90-ORSI-07Jul2011


title: CCTO90-ORSI-28Jul2011


title: ChIP-seq from MCF-7 (ENCLB761YGZ)

description:
https://www.encodeproject.org/experiments/ENCSR200CUA/
***************
biological replicate number: 2
technical replicate number: 1
description: HDGF ChIP-seq on human MCF-7
experiment encode accession: ENCSR200CUA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF, ENCSR594UCI
encode release date: 2016-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB761YGZ
size range: 450-650

value: HDGF

tag: Sex

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

tag: lab

value: Michael Snyder, Stanford

value: ENCBS308QKF at ENCODE; https://www.encodeproject.org/ENCBS308QKF/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031


title: ChIP-seq from MCF-7 (ENCLB212QXI)

description:
https://www.encodeproject.org/experiments/ENCSR200CUA/
***************
biological replicate number: 1
technical replicate number: 1
description: HDGF ChIP-seq on human MCF-7
experiment encode accession: ENCSR200CUA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF, ENCSR594UCI
encode release date: 2016-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB212QXI
size range: 450-650

value: immortalized cell line

tag: health state

tag: link

value: ENCBS957OEW at ENCODE; https://www.encodeproject.org/ENCBS957OEW/


title: CCTO90-ORSI-17Jun2011


title: UCD65 E2, replicate 2

tag: xenograft

value: estrogen


title: CCTO90-ORSI-06May2011


title: CCTO90-ORSI-07Oct2011


title: CCTO90-ORSI-07Apr2011


title: UCD65 E2, replicate 3

tag: treatment


title: UCD65 E2, replicate 1


title: CCTO90-ORSI-10Mar2011


title: ChIP-seq from K562 (ENCLB089NIL)

description:
https://www.encodeproject.org/experiments/ENCSR198KYG/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-TAF7 tagged K562 cell line.
experiment encode accession: ENCSR198KYG
assay title: ChIP-seq
encode release date: 2015-12-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB089NIL
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-TAF7 fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to TAF7

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Kevin White, UChicago

value: ENCBS350VSG at ENCODE; https://www.encodeproject.org/ENCBS350VSG/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW44; http://web.expasy.org/cellosaurus/CVCL_AW44


title: UCD4 E2+MPA, replicate 3

value: estrogen+MPA


title: eCLIP from HepG2 (ENCLB478DYX)

description:
https://www.encodeproject.org/experiments/ENCSR202BFN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against U2AF2
experiment encode accession: ENCSR202BFN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR049GND
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB478DYX
size range: 175-300

value: child

value: 15 year

value: male

tag: passage number

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS405FLI at ENCODE; https://www.encodeproject.org/ENCBS405FLI/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: ChIP-seq from MCF-7 (ENCLB133NHZ)

description:
https://www.encodeproject.org/experiments/ENCSR197DJH/
***************
biological replicate number: 2
technical replicate number: 1
description: SREBF1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR197DJH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB133NHZ
size range: 450-650

value: immortalized cell line

value: Mammary gland, adenocarcinoma. (PMID:4357757)

value: adult

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: ENCBS331EJR at ENCODE; https://www.encodeproject.org/ENCBS331EJR/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-22.aspx


title: ChIP-seq from HEK293 (ENCLB295BKB)

description:
https://www.encodeproject.org/experiments/ENCSR211PZO/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-GLI4 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR211PZO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB295BKB
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-GLI4 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS601JDX at ENCODE; https://www.encodeproject.org/ENCBS601JDX/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: CCTO90-ORSI-07Feb2011

value: Oregon Siskiyou low elevation


title: UCD4 E2+MPA, replicate 1

value: estrogen+MPA


title: ChIP-seq from MCF-7 (ENCLB496FAI)

description:
https://www.encodeproject.org/experiments/ENCSR197DJH/
***************
biological replicate number: 1
technical replicate number: 1
description: SREBF1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR197DJH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB496FAI
size range: 450-650

value: immortalized cell line

value: Mammary gland, adenocarcinoma. (PMID:4357757)

value: ENCBS168ISE at ENCODE; https://www.encodeproject.org/ENCBS168ISE/


title: CCTO90-ORSI-06Jan2011


title: CCTO90-ORSI-09Nov2010


title: ChIP-seq from K562 (ENCLB562GOJ)

description:
https://www.encodeproject.org/experiments/ENCSR197ALX/
***************
biological replicate number: 2
technical replicate number: 1
description: HDGF ChIP-seq on human K562
experiment encode accession: ENCSR197ALX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB562GOJ
size range: 450-650

value: HDGF

value: Leukemia, 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. - ATCC

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS118YJZ at ENCODE; https://www.encodeproject.org/ENCBS118YJZ/

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: CCTO90-ORSI-27Oct2010


title: ChIP-seq from K562 (ENCLB004BGH)

description:
https://www.encodeproject.org/experiments/ENCSR197ALX/
***************
biological replicate number: 1
technical replicate number: 1
description: HDGF ChIP-seq on human K562
experiment encode accession: ENCSR197ALX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB004BGH
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS839CNN at ENCODE; https://www.encodeproject.org/ENCBS839CNN/


title: eCLIP from K562 (ENCLB715HYH)

description:
https://www.encodeproject.org/experiments/ENCSR194AVW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against RBM27
experiment encode accession: ENCSR194AVW
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB715HYH
size range: 175-300

value: Control

value: Gene Yeo, UCSD

value: ENCBS931MQO at ENCODE; https://www.encodeproject.org/ENCBS931MQO/

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: UCD4 E2, replicate 3

value: estrogen


title: eCLIP from K562 (ENCLB739SVB)

description:
https://www.encodeproject.org/experiments/ENCSR197NFH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against KHDRBS1
experiment encode accession: ENCSR197NFH
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB739SVB
size range: 175-300

value: immortalized cell line

value: ENCBS831COV at ENCODE; https://www.encodeproject.org/ENCBS831COV/


title: ChIP-seq from HEK293 (ENCLB207BQK)

description:
https://www.encodeproject.org/experiments/ENCSR185FOY/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF341 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR185FOY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB207BQK
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF341 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF341 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS015PWI at ENCODE; https://www.encodeproject.org/ENCBS015PWI/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: CCTO89-ORSI-17Aug2011

value: Oregon Siskiyou low elevation


title: UCD4 E2, replicate 1


title: CCTO89-ORSI-28Jul2011


title: eCLIP from K562 (ENCLB550OFF)

description:
https://www.encodeproject.org/experiments/ENCSR989SMC/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against FTO
experiment encode accession: ENCSR989SMC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR575DKE
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB550OFF
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: FTO

value: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS517UIR at ENCODE; https://www.encodeproject.org/ENCBS517UIR/

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

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


title: ChIP-seq from HEK293 (ENCLB416YOM)

description:
https://www.encodeproject.org/experiments/ENCSR185FOY/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF341 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR185FOY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB416YOM
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS020GOD at ENCODE; https://www.encodeproject.org/ENCBS020GOD/


title: CCTO89-ORSI-07Jul2011

description: Douglas-fir annual transcriptome analysis


title: ChIP-seq from MCF-7 (ENCLB508LER)

description:
https://www.encodeproject.org/experiments/ENCSR176EXN/
***************
biological replicate number: 2
technical replicate number: 1
description: JUN ChIP-seq on human MCF-7
experiment encode accession: ENCSR176EXN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB508LER
size range: 450-650

value: JUN

value: immortalized cell line

value: Mammary gland, adenocarcinoma. (PMID:4357757)

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS053YJT at ENCODE; https://www.encodeproject.org/ENCBS053YJT/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-22.aspx


title: ChIP-seq from MCF-7 (ENCLB720CSU)

description:
https://www.encodeproject.org/experiments/ENCSR176EXN/
***************
biological replicate number: 1
technical replicate number: 1
description: JUN ChIP-seq on human MCF-7
experiment encode accession: ENCSR176EXN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB720CSU
size range: 450-650

value: adult

value: ENCBS216AOQ at ENCODE; https://www.encodeproject.org/ENCBS216AOQ/


title: CCTO89-ORSI-17Jun2011

value: Oregon Siskiyou low elevation


title: UCD4 E2, replicate 2

value: estrogen


title: eCLIP from K562 (ENCLB541DIZ)

description:
https://www.encodeproject.org/experiments/ENCSR952UOL/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against LSM11
experiment encode accession: ENCSR952UOL
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB541DIZ
size range: 175-300

value: Control

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/

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

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: CCTO89-ORSI-06May2011


title: ChIP-seq from K562 (ENCLB425FBF)

description:
https://www.encodeproject.org/experiments/ENCSR175SZH/
***************
biological replicate number: 1
technical replicate number: 1
description: ZSCAN29 ChIP-seq on human K562
experiment encode accession: ENCSR175SZH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB425FBF
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

value: ENCBS721MSZ at ENCODE; https://www.encodeproject.org/ENCBS721MSZ/


title: ChIP-seq from K562 (ENCLB217HKQ)

description:
https://www.encodeproject.org/experiments/ENCSR175SZH/
***************
biological replicate number: 2
technical replicate number: 1
description: ZSCAN29 ChIP-seq on human K562
experiment encode accession: ENCSR175SZH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB217HKQ
size range: 450-650

value: ENCBS406RFF at ENCODE; https://www.encodeproject.org/ENCBS406RFF/

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


title: CCTO90-ORSI-30Nov2010


title: UCD4 E2+MPA, replicate 2

value: estrogen+MPA


title: ChIP-seq from K562 (ENCLB359ZTD)

description:
https://www.encodeproject.org/experiments/ENCSR173USI/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human K562
experiment encode accession: ENCSR173USI
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB359ZTD
size range: 450-650

value: Leukemia, 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. - ATCC

value: adult

value: ENCBS543YEP at ENCODE; https://www.encodeproject.org/ENCBS543YEP/

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


title: CCTO89-ORSI-07Apr2011

value: Oregon Siskiyou low elevation


title: CCTO89-ORSI-10Mar2011


title: RAMPAGE from breast epithelium (ENCLB781BJP)

description:
https://www.encodeproject.org/experiments/ENCSR909QWB/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human mammary gland tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR909QWB
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR434TEU
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB781BJP
size range: >200

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

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/cdac3020-75b2-4fd5-8834-5a9d5cff3002/@@download/attachment/296889.pdf

value: breast epithelium

value: tissue

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

value: 53 year

value: female

value: Thomas Gingeras, CSHL

value: ENCBS490RBH at ENCODE; https://www.encodeproject.org/ENCBS490RBH/

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


title: eCLIP from K562 (ENCLB689GWR)

description:
https://www.encodeproject.org/experiments/ENCSR887LPK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against EWSR1
experiment encode accession: ENCSR887LPK
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR067UKU
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB689GWR
size range: 175-300

value: immortalized cell line

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS489LOC at ENCODE; https://www.encodeproject.org/ENCBS489LOC/

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

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: ChIP-seq from K562 (ENCLB783NHP)

description:
https://www.encodeproject.org/experiments/ENCSR173USI/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human K562
experiment encode accession: ENCSR173USI
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB783NHP
size range: 450-650

value: Control

value: Leukemia, 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. - ATCC

value: adult

value: Michael Snyder, Stanford

value: ENCBS603CUX at ENCODE; https://www.encodeproject.org/ENCBS603CUX/

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


title: CCTO89-ORSI-23Feb2011

value: Oregon Siskiyou low elevation


title: ChIP-seq from HepG2 (ENCLB938PAU)

description:
https://www.encodeproject.org/experiments/ENCSR171FUX/
***************
biological replicate number: 2
technical replicate number: 1
description: FOXK2 ChIP-seq on human HepG2
experiment encode accession: ENCSR171FUX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR770GTP, ENCSR121CWV
encode release date: 2016-04-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB938PAU
size range: 450-650

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS541YFT at ENCODE; https://www.encodeproject.org/ENCBS541YFT/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: eCLIP from K562 (ENCLB959KMS)

description:
https://www.encodeproject.org/experiments/ENCSR887LPK/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against EWSR1
experiment encode accession: ENCSR887LPK
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR067UKU
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB959KMS
size range: 175-300

value: immortalized cell line

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/


title: CCTO89-ORSI-07Feb2011


title: ChIP-seq from HepG2 (ENCLB729WHK)

description:
https://www.encodeproject.org/experiments/ENCSR171FUX/
***************
biological replicate number: 1
technical replicate number: 1
description: FOXK2 ChIP-seq on human HepG2
experiment encode accession: ENCSR171FUX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR770GTP, ENCSR121CWV
encode release date: 2016-04-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB729WHK
size range: 450-650

value: Hepatocellular carcinoma

value: Michael Snyder, Stanford

value: ENCBS591PPP at ENCODE; https://www.encodeproject.org/ENCBS591PPP/

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: RAMPAGE from upper lobe of left lung (ENCLB632RGS)

description:
https://www.encodeproject.org/experiments/ENCSR790PBX/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human upper lobe of left lung tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR790PBX
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR406SAW
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB632RGS
size range: >200

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

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/2a534c05-61c0-4967-b827-4b90d6d3880f/@@download/attachment/296878.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.

value: adult

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: eCLIP from K562 (ENCLB152QMP)

description:
https://www.encodeproject.org/experiments/ENCSR989SMC/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against FTO
experiment encode accession: ENCSR989SMC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR575DKE
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB152QMP
size range: 175-300

value: FTO

value: immortalized cell line

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

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


title: eCLIP from K562 (ENCLB177FFM)

description:
https://www.encodeproject.org/experiments/ENCSR170XQH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against XRN2
experiment encode accession: ENCSR170XQH
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB177FFM
size range: 175-300

value: Control

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS263GNB at ENCODE; https://www.encodeproject.org/ENCBS263GNB/

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


title: RAMPAGE from subcutaneous adipose tissue (ENCLB523CHX)

description:
https://www.encodeproject.org/experiments/ENCSR785OGK/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human adipose tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR785OGK
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR150QJY
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB523CHX
size range: >200

source_name: Homo sapiens subcutaneous adipose tissue female adult (51 year)

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/73ce802f-4eba-4dff-8d7a-9a6685341f8d/@@download/attachment/296891.pdf

value: subcutaneous adipose tissue

value: tissue

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

value: 51 year

value: ENCBS606FXX at ENCODE; https://www.encodeproject.org/ENCBS606FXX/

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


title: RAMPAGE from tibial nerve (ENCLB413BTB)

description:
https://www.encodeproject.org/experiments/ENCSR722NWC/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human tibial nerve tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR722NWC
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR796HLX
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB413BTB
size range: >200

source_name: Homo sapiens tibial nerve tissue male adult (37 years)

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/37604600-2d9f-467b-9124-40a21acb7c0a/@@download/attachment/296875.pdf

value: tibial nerve

value: Tibial nerve tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: adult

value: male

value: 37 year

value: Thomas Gingeras, CSHL

value: ENCBS986CBC at ENCODE; https://www.encodeproject.org/ENCBS986CBC/

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


title: RAMPAGE from body of pancreas (ENCLB710MRA)

description:
https://www.encodeproject.org/experiments/ENCSR918MVG/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human pancreas tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR918MVG
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR671IYC
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB710MRA
size range: >200

source_name: Homo sapiens body of pancreas tissue female adult (51 year)

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/f3ad20f0-3658-4ff2-b253-5ce5ab2ced0b/@@download/attachment/296880.pdf

value: body of pancreas

value: Pancreas tissue from received by the Gingeras lab to do RNA-Seq assay on from GTEx.

value: female

value: ENCBS389HVX at ENCODE; https://www.encodeproject.org/ENCBS389HVX/


title: CCTO89-ORSI-30Nov2010

description: Douglas-fir annual transcriptome analysis

value: Oregon Siskiyou low elevation


title: CCTO89-ORSI-27Oct2010


title: CCTO89-ORSI-09Nov2010


title: ChIP-seq from K562 (ENCLB683FVA)

description:
https://www.encodeproject.org/experiments/ENCSR167KBO/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF316 ChIP-seq on human K562
experiment encode accession: ENCSR167KBO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-11-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB683FVA
size range: 450-650

value: immortalized cell line

value: Leukemia, 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. - ATCC

value: 53 year

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS576ESJ at ENCODE; https://www.encodeproject.org/ENCBS576ESJ/

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

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


title: ChIP-seq from K562 (ENCLB825JJI)

description:
https://www.encodeproject.org/experiments/ENCSR167KBO/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF316 ChIP-seq on human K562
experiment encode accession: ENCSR167KBO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-11-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB825JJI
size range: 450-650

value: adult

value: ENCBS839CNN at ENCODE; https://www.encodeproject.org/ENCBS839CNN/

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


title: RAMPAGE from Peyer's patch (ENCLB603UNB)

description:
https://www.encodeproject.org/experiments/ENCSR713KWE/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human ileum tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR713KWE
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR802HPM
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB603UNB
size range: >200

source_name: Homo sapiens Peyer's patch tissue male adult (37 years)

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/041bb21d-adba-4273-9f4b-484710bacb57/@@download/attachment/296886.pdf

value: Peyer's patch

value: tissue

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

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS024TYX at ENCODE; https://www.encodeproject.org/ENCBS024TYX/

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


title: eCLIP from K562 (ENCLB189OUL)

description:
https://www.encodeproject.org/experiments/ENCSR687GJH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against TROVE2
experiment encode accession: ENCSR687GJH
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB189OUL
size range: 175-300

value: Control

value: immortalized cell line

value: female

value: 53 year

value: Gene Yeo, UCSD

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: CCTO46-ORSI-07Sep2011

value: Oregon Siskiyou low elevation


title: ChIP-seq from K562 (ENCLB326QJS)

description:
https://www.encodeproject.org/experiments/ENCSR167JBG/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-DIDO1 ChIP-seq on human K562
experiment encode accession: ENCSR167JBG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR724HDV
encode release date: 2016-03-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB326QJS
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-DIDO1 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to DIDO1

value: adult

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS454ZTQ at ENCODE; https://www.encodeproject.org/ENCBS454ZTQ/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW18; http://web.expasy.org/cellosaurus/CVCL_AW18


title: RAMPAGE from transverse colon (ENCLB216HHI)

description:
https://www.encodeproject.org/experiments/ENCSR688YRV/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human transverse colon tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR688YRV
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR653ZJF
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB216HHI
size range: >200

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

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/6c78da0c-6704-4672-ab26-11b00bc53360/@@download/attachment/296885.pdf

value: transverse colon

value: tissue

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

value: 37 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS767MGS at ENCODE; https://www.encodeproject.org/ENCBS767MGS/


title: CCTO46-ORSI-17Aug2011


title: CCTO46-ORSI-28Jul2011


title: ChIP-seq from K562 (ENCLB066KAL)

description:
https://www.encodeproject.org/experiments/ENCSR167JBG/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-DIDO1 ChIP-seq on human K562
experiment encode accession: ENCSR167JBG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR724HDV
encode release date: 2016-03-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB066KAL
size range: 450-650

value: immortalized cell line

value: female

value: 53 year

value: ENCBS197ROV at ENCODE; https://www.encodeproject.org/ENCBS197ROV/


title: CCTO46-ORSI-17Jun2011

value: Oregon Siskiyou low elevation


title: eCLIP from K562 (ENCLB175BHT)

description:
https://www.encodeproject.org/experiments/ENCSR661ICQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against PUM2
experiment encode accession: ENCSR661ICQ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR439GXW
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB175BHT
size range: 175-300

value: adult

value: Gene Yeo, UCSD

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/

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

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: eCLIP from HepG2 (ENCLB092TOO)

description:
https://www.encodeproject.org/experiments/ENCSR167OYL/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against SND1
experiment encode accession: ENCSR167OYL
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB092TOO
size range: 175-300

value: Control

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS861HMN at ENCODE; https://www.encodeproject.org/ENCBS861HMN/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: ChIP-seq from HEK293 (ENCLB558QMS)

description:
https://www.encodeproject.org/experiments/ENCSR162MTR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF346 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR162MTR
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB558QMS
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF346 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF346 under the control of a CMV promoter.

value: unknown

value: embryonic

value: Michael Snyder, Stanford

value: ENCBS960GJX at ENCODE; https://www.encodeproject.org/ENCBS960GJX/

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: CCTO89-ORSI-06Jan2011

value: Oregon Siskiyou low elevation


title: CCTO46-ORSI-06May2011


title: eCLIP from K562 (ENCLB877GLA)

description:
https://www.encodeproject.org/experiments/ENCSR658IQB/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SMNDC1
experiment encode accession: ENCSR658IQB
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR631CJA
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB877GLA
size range: 175-300

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS489LOC at ENCODE; https://www.encodeproject.org/ENCBS489LOC/

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

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


title: ChIP-seq from HEK293 (ENCLB380HJW)

description:
https://www.encodeproject.org/experiments/ENCSR162MTR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF346 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR162MTR
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB380HJW
size range: 450-650

value: ENCBS550ZUY at ENCODE; https://www.encodeproject.org/ENCBS550ZUY/