title: ChIP-seq from HEK293 (ENCLB908DRS)

description:
https://www.encodeproject.org/experiments/ENCSR363XBR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF488 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR363XBR
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: ENCLB908DRS
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF488 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF488 under the control of a CMV promoter.

value: embryonic

value: female

value: unknown

value: ENCBS066RVK at ENCODE; https://www.encodeproject.org/ENCBS066RVK/


title: eCLIP from HepG2 (ENCLB123MRC)

status: Public on Jan 04 2017

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR373ODC/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against SMNDC1
experiment encode accession: ENCSR373ODC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR388VKV
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB123MRC
size range: 175-300

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

tag: antibody

tag: line

value: immortalized cell line

tag: biosample encode accession

tag: dev stage

value: child

tag: age

value: 15 year

tag: Sex

value: male

tag: passage number

tag: lab

value: Gene Yeo, UCSD

tag: health state

value: hepatocellular carcinoma

tag: link

value: ENCBS859FFE at ENCODE; https://www.encodeproject.org/ENCBS859FFE/

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 K562 (ENCLB611KDW)

description:
https://www.encodeproject.org/experiments/ENCSR369LPC/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-PTRF tagged K562 cell line.
experiment encode accession: ENCSR369LPC
assay title: ChIP-seq
encode release date: 2015-12-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB611KDW
size range: 450-650

library_source: genomic

molecule: genomic DNA

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

value: Control

tag: description

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

value: adult

value: 53 year

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS544EAP at ENCODE; https://www.encodeproject.org/ENCBS544EAP/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW38; http://web.expasy.org/cellosaurus/CVCL_AW38


title: LXR ChIP-seq KLA6h

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 8

data_processing:
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer, Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
For ChIP-Seq (single end reads), reads were aligned to the mm9 genome (NCBI37) using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.
For RNA-Seq samples (single end reads), reads were aligned to the mm9 genome (NCBI37) using default parameter for RNA-Star. Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, then perform analyses as indicated in the study.
For ChIP-Seq, Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, and perform other analyses in the study. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped. UCSC Genome Browser BigWig or BigWig hub text files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), peak text files (ChIP-Seq peak data, using default HOMER parameters), and expression text files (RNA-Seq expression data, using default HOMER parameters).  All genomic coordinates are relative to mm9  (NCBI37) mouse assembly.

organism: Mus musculus

growth_protocol:
Peritoneal thioglycollate-elicited macrophages (TGEMs): Primary cells were isolated from 6-8 week-old C57Bl/6 (Harlan Laboratories) male mice. Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3-4 days following peritoneal injection of 2.5 ml thioglycollate. Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 1 – 24 hours. For LXR experiments cells were treated with 1uM GW3965 or 20uM Desmosterol for 24 hours.
Bone marrow derived macrophages (BMDMs): Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 1 – 24 hours. For LXR experiments cells were treated with 1uM GW3965 or 20uM Desmosterol for 24 hours.

extract_protocol:
ChIP-Seq: Sequencing libraries were prepared from collected DNA by blunting, A-tailing, adapter ligation as previously described (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 12-15 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2000 (Illumina) for 51 cycles.
RNA-Seq: Sequencing libraries were prepared from polyA enriched mRNA, either as previously described (Kaikkonen M.U. et al. Molecular Cell 51, 310-325 (2013)), or as follows. Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Invitrogen), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primer (Invitrogen), 0.5 µL of Oligo dT primer (Invitrogen), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for three minutes. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.2 µL of Superscript III (Invitrogen) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads according to manufacture’s instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 1 hour. The resulting dUTP-marked dsDNA was purified using 28 µL of Sera-Mag Speedbeads (Thermo Fisher Scientific), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation as previously described (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 9-14 cycles, size selected by gel extraction, quantified Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on either a Genome Analyzer II (Illumina) or Hi-Seq 2000 (Illumina) for 51 cycles.

tag: strain background

tag: cell type

tag: treated with

value: KLA for 6 hours

tag: chip antibody

value: LXR (Santa Cruz sc-1000X, Lot:I0310, Abcam ab-41902, lot:GR9889-3, Active Motif 61177, lot:29111001)


title: LXR ChIP-seq KLA1h

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 7

value: none (control)


title: Nucleoplasm RNA-Seq

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
library strategy: NP-Seq
Adapter trimming with Cutadapt v. 1.8.3 in paired end mode with the following parameters: -A GATCGTCGGACTGTAGAACTCTGAAC -a TGGAATTCTCGGGTGCCAAGG --minimum-length 10
Alignment with Tophat v. 2.0.13 and the parameters -g 1 -r 3000 --no-coverage-search to hg19
Extraction of properly paired, properly mapped reads (samflags 0x63, 0x93, 0x53, 0xA3) with SAMtools v. 1.2
For mNET-Seq profiles only the most 3’ nucleotide of the second read was used with the strandedness of the first read
BigWig files were generated from the above bedgraph files through the bedGraphToBigWig tool (Kent et al., 2002).
Data was visualized with Bedtools v. 2.23.0 (genomeCoverageBed).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: Nucleoplasm RNA-Seq

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum.

extract_protocol:
Nascent RNAs were prufied from Pol II IP products of solubilized chromatin.
Libraries were prepared acooding to the protocols of Trueseq small RNA sequencing preparation kit (Illumina) for mNET-seq; Ultra directional RNA sequencing preparation kit (NEB) for chrRNA and Np RNA-seq.

treatment_protocol:
1% Empigen was aded IP buffer and IP washing buffer.
siRNAs were transfected for 60-72 hrs accroding to RNAiMAX reagent protocol.

tag: cell line

value: HeLa

tag: genotype/variation

value: Nucleoplasm fraction

tag: molecule subtype

value: Nucleoplasmic RNA


title: pA+ Nucleoplam RNA-Seq rep2

source_name: pA+ Nucleoplam RNA-Seq

value: polyA+ fraction, Nucleoplasm


title: ChIP-seq from K562 (ENCLB778WXY)

description:
https://www.encodeproject.org/experiments/ENCSR385AHH/
***************
biological replicate number: 3
technical replicate number: 1
description: ZNF24 ChIP-seq on human K562
experiment encode accession: ENCSR385AHH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-04-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB778WXY
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

tag: antibody

tag: line

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: female

value: Michael Snyder, Stanford

value: ENCBS994WPS at ENCODE; https://www.encodeproject.org/ENCBS994WPS/

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: LXR ChIP-seq GW3965

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 6


title: ChIP-seq from HEK293 (ENCLB883NEN)

description:
https://www.encodeproject.org/experiments/ENCSR361UQO/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZNF707 tagged human HEK293 cells.
experiment encode accession: ENCSR361UQO
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB883NEN
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF707 fusion protein

value: Control

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF707 under the control of a CMV promoter.

tag: biosample encode accession

tag: dev stage

value: embryonic

value: unknown

value: ENCBS402FLP at ENCODE; https://www.encodeproject.org/ENCBS402FLP/

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


title: pA- Nucleoplasm RNA-Seq rep2

source_name: pA- Nucleoplasm RNA-Seq

value: HeLa

value: polyA- fraction, Nucleoplasm


title: ChIP-seq from HEK293 (ENCLB692LRV)

description:
https://www.encodeproject.org/experiments/ENCSR363XBR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF488 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR363XBR
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: ENCLB692LRV
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF488 under the control of a CMV promoter.

tag: Sex

tag: age

value: ENCBS294FAI at ENCODE; https://www.encodeproject.org/ENCBS294FAI/


title: LXR ChIP-seq no treatment

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 5

value: none (control)

value: LXR (Santa Cruz sc-1000X, Lot:I0310, Abcam ab-41902, lot:GR9889-3, Active Motif 61177, lot:29111001)


title: pA- Nucleoplasm RNA-Seq rep1

value: Nucleoplasmic RNA


title: ChIP-seq from MCF-7 (ENCLB012TZO)

description:
https://www.encodeproject.org/experiments/ENCSR360JOC/
***************
biological replicate number: 1
technical replicate number: 1
description: CHD1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR360JOC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB012TZO
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

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

value: adult

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

tag: lab

value: Michael Snyder, Stanford

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

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: Srebp1 ChIP-seq  GW3965

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 3

value: GW3965 (1uM) for 18 hours


title: ChIP-seq from MCF-7 (ENCLB328XTR)

description:
https://www.encodeproject.org/experiments/ENCSR360JOC/
***************
biological replicate number: 3
technical replicate number: 1
description: CHD1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR360JOC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB328XTR
size range: 450-650

tag: health state

value: ENCBS616MBU at ENCODE; https://www.encodeproject.org/ENCBS616MBU/


title: S5P mNET-Seq siLuc 2 (Ctrl for siDICER1) rep2

data_processing:
library strategy: mNET-Seq
Adapter trimming with Cutadapt v. 1.8.3 in paired end mode with the following parameters: -A GATCGTCGGACTGTAGAACTCTGAAC -a TGGAATTCTCGGGTGCCAAGG --minimum-length 10
Alignment with Tophat v. 2.0.13 and the parameters -g 1 -r 3000 --no-coverage-search to hg19
Extraction of properly paired, properly mapped reads (samflags 0x63, 0x93, 0x53, 0xA3) with SAMtools v. 1.2
For mNET-Seq profiles only the most 3’ nucleotide of the second read was used with the strandedness of the first read
BigWig files were generated from the above bedgraph files through the bedGraphToBigWig tool (Kent et al., 2002).
Data was visualized with Bedtools v. 2.23.0 (genomeCoverageBed).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

value: HeLa

value: siLuc control for DICER1 KD, Ser5 phospho

value: Polymerase bound RNA


title: S5P mNET-Seq siDICER1 rep2

source_name: S5P mNET-Seq siDICER1

value: DICER1 KD, Ser5 phospho


title: ChIP-seq from HEK293 (ENCLB072EGE)

description:
https://www.encodeproject.org/experiments/ENCSR357QJR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZSCAN5A ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR357QJR
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: ENCLB072EGE
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZSCAN5A fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZSCAN5A under the control of a CMV promoter.

value: embryonic

value: unknown

tag: link

value: ENCBS190VSK at ENCODE; https://www.encodeproject.org/ENCBS190VSK/

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


title: Srebp1 ChIP-seq no treatment

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 1

value: none (control)


title: pA+ Nucleoplasm RNA-Seq rep1

source_name: pA+ Nucleoplasm RNA-Seq

value: polyA+ fraction, Nucleoplasm

value: Nucleoplasmic RNA


title: S5P mNET-Seq siDGCR8 rep2

source_name: S5P mNET-Seq siDGCR8

value: DGCR8 KD, Ser5 phospho


title: ChIP-seq from HEK293 (ENCLB047TUO)

description:
https://www.encodeproject.org/experiments/ENCSR357QJR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZSCAN5A ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR357QJR
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: ENCLB047TUO
size range: 450-650

tag: description

value: female

value: Michael Snyder, Stanford

value: ENCBS882KQI at ENCODE; https://www.encodeproject.org/ENCBS882KQI/


title: ChIP-seq from K562 (ENCLB371YXR)

description:
https://www.encodeproject.org/experiments/ENCSR352BJL/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF318 ChIP-seq on human K562
experiment encode accession: ENCSR352BJL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB371YXR
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: ENCBS994WPS at ENCODE; https://www.encodeproject.org/ENCBS994WPS/

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: Srebp1 ChIP-seq Desmosterol

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 2

tag: strain background

value: Desmosterol (20uM) for 18 hours


title: eCLIP from HepG2 (ENCLB068HLW)

description:
https://www.encodeproject.org/experiments/ENCSR354KAS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against HNRNPK
experiment encode accession: ENCSR354KAS
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB068HLW
size range: 175-300

value: Control

value: immortalized cell line

value: child

value: 15 year

value: male

tag: passage number

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS864WAF at ENCODE; https://www.encodeproject.org/ENCBS864WAF/

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: T4P mNET-Seq Empigen treated rep2

source_name: T4P mNET-Seq Empigen treated

value: HeLa

value: Empigen treated Thr4 phospho

value: Polymerase bound RNA


title: eCLIP from HepG2 (ENCLB318PMA)

description:
https://www.encodeproject.org/experiments/ENCSR351PVI/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against SLTM
experiment encode accession: ENCSR351PVI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR670UPZ
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB318PMA
size range: 175-300

value: SLTM

value: ENCBS547JWV at ENCODE; https://www.encodeproject.org/ENCBS547JWV/


title: ChIP-seq from K562 (ENCLB268TBX)

description:
https://www.encodeproject.org/experiments/ENCSR352BJL/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF318 ChIP-seq on human K562
experiment encode accession: ENCSR352BJL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB268TBX
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: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

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: Srebp1 ChIP-seq  KLA24h

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 4

tag: cell type

tag: treated with

value: KLA for 24 hours


title: T4P mNET-Seq (untreated) rep2

source_name: T4P mNET-Seq (untreated)

tag: cell line

value: Control:Empigen untreated Thr4 phospho


title: CV314_High

city: Chapel Hill

first: Bailey

last: Peck

state: NC

address: 120 Mason Farm Rd, 5100H Genetic Medicine Bldg

department: Genetics

institute: University of North Carolina at Chapel Hill

description: small RNA

data_processing:
Small RNA-seq data was aligned using methodology described in Baran-Gale et al. (PLOS ONE, 2012), with the following modification: only contigs with greater than one read alignment were passed into the to Shrimp alignment pipeline.
Reads were trimmed by cutAdapt to remove adaptor remnants. Trimmed reads of 14-41 nt are first mapped exactly (no mismatches) using Bowtie. Windows are determined using these mapped reads, and the unmapped reads, are realigned to these windows using SHRiMP2 with mismatches allowed (See Baran-Gale et al, 2012), these would be considered edits & isomiRs, and are named based on the canonical miRNA (miRbase).
Reads were normalized using Reads per Million Mapped to miRNAs (RPMMM). We pulled out miRNAs and isomiRs with at least 400 RPMMM in at least 1 sample for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Multiple sample Tab-delimited file with RPMMMs of all miRNAs & isomiRs (no expression threshold)

source_name: Intestinal Epithelial Cells

growth_protocol: Germfree animals were raised at the University of North Carolina's Gnotobiotic Core Facility. At 8-10 weeks of age, one littermate was transferred to the UNC MBRB Animal facility and conventionalized by oral gavage with fecal slurry prepared from fecal pellets collected from the conventionally raised Sox9-EGFP mouse colony. Following 2-week conventionalization, both animals were harvested for their jejunal IECs, and samples sorted using previously described methods (Van Landeghem et al., 2012). Animal studies were approved my our institutions IACUC (protocol 13-162).

extract_protocol:
Sorted cells were lysed and RNA was extracted using Norgen Single cell and Total RNA isolation kits as per the manufacturer's instructions
Small RNA libraries were prepared at the University of Texas Health Sciences Center at San Antonio Genome Sequencing Facility. Libraries were prepared using an average of 50 ng of total RNA using the TriLink CleanTag Small RNA Ligation kit (TriLink Biotechnologies, San Diego, CA) and suggested library preparation method. Six to seven libraries were pooled per lane, and the small RNA sequencing was conducted at the Genome Sequencing Facility of Greehey Children's Cancer Research Institute at University of Texas Health Science Center at San Antonio single-end 50x on the HiSeq2000 platform.

treatment_protocol: Jejunal IECs were stained for Annexin-V, CD31, CD45, and by Sytox-blue. FACS was used to gete these populations out during sorting.

tag: strain

value: Sox9-EGFP on C57BL/6J background

value: Female

tag: tissue

value: jejunum

value: Intestinal Epithelial Cells

tag: condition

value: Conventionalized

tag: iec population

value: Sox9-EGFP High

tag: littermate pair

value: D

tag: sequence date

value: October 1, 2015

value: 11 weeks


title: GF315_NS

description:
small RNA
Processed data for this sample are not available due to read alignment failure.

tag: Sex

value: Germfree

value: Sox9-EGFP Non-sorted IECs


title: CV314_Low

description: small RNA

value: Sox9-EGFP Low

tag: age


title: CV314_Sublow

description: small RNA

value: Sox9-EGFP Sublow


title: GF315_Neg

description: small RNA

value: Sox9-EGFP Neg


title: Y1P mNET-Seq (untreated) rep2

source_name: Y1P mNET-Seq (untreated)

value: HeLa

tag: genotype/variation

value: Control:Empigen untreated Tyr1 phospho

tag: molecule subtype

value: Polymerase bound RNA


title: Y1P mNET-Seq Empigen treated rep2

source_name: Y1P mNET-Seq Empigen treated

value: Empigen treated Tyr1 phospho


title: ChIP-seq from HEK293 (ENCLB968TGA)

description:
https://www.encodeproject.org/experiments/ENCSR348ONY/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZFP41 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR348ONY
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: ENCLB968TGA
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZFP41 fusion protein

tag: antibody

tag: line

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZFP41 under the control of a CMV promoter.

tag: biosample encode accession

tag: dev stage

value: embryonic

value: unknown

value: female

tag: lab

value: Michael Snyder, Stanford

tag: health state

tag: link

value: ENCBS424AYE at ENCODE; https://www.encodeproject.org/ENCBS424AYE/

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


title: S5P mNET-Seq Empigen treated rep2

source_name: S5P mNET-Seq Empigen treated

tag: cell line

value: Empigen treated Ser5 phospho


title: ChIP-seq from HEK293 (ENCLB071FYL)

description:
https://www.encodeproject.org/experiments/ENCSR348ONY/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZFP41 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR348ONY
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: ENCLB071FYL
size range: 450-650

tag: description

value: ENCBS503YOP at ENCODE; https://www.encodeproject.org/ENCBS503YOP/


title: CV314_Neg

description: small RNA

tag: strain

value: Sox9-EGFP on C57BL/6J background

value: Female

tag: tissue

value: jejunum

tag: cell type

value: Intestinal Epithelial Cells

tag: condition

value: Conventionalized

value: D

value: October 1, 2015

value: 11 weeks


title: S5P mNET-Seq siLuc 1 (Ctrl for siDGCR8) rep2

source_name: S5P mNET-Seq siLuc 1 (Ctrl for siDGCR8)

value: HeLa

value: siLuc control for DGCR8 KD, Ser5 phospho

value: Polymerase bound RNA


title: eCLIP from K562 (ENCLB998OOV)

description:
https://www.encodeproject.org/experiments/ENCSR344EGD/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against RBM22
experiment encode accession: ENCSR344EGD
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB998OOV
size range: 175-300

value: Control

value: immortalized cell line

value: adult

value: 53 year

tag: Sex

value: female

tag: passage number

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: GF315_Low

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

value: Germfree

tag: iec population

value: Sox9-EGFP Low

tag: littermate pair

value: D

tag: sequence date

tag: age


title: GF315_Sublow

description: small RNA

value: Sox9-EGFP Sublow

value: October 1, 2015

value: 11 weeks


title: S2P mNET-Seq untreated rep2

source_name: S2P mNET-Seq untreated

value: HeLa

tag: genotype/variation

value: Control:Empigen untreated Ser2 phospho

tag: molecule subtype

value: Polymerase bound RNA


title: ChIP-seq from MCF-7 (ENCLB434ZBI)

description:
https://www.encodeproject.org/experiments/ENCSR348JOJ/
***************
biological replicate number: 2
technical replicate number: 1
description: MTA1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR348JOJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB434ZBI
size range: 450-650

tag: antibody

tag: line

value: immortalized cell line

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

tag: biosample encode accession

tag: dev stage

value: adult

value: 69 year

value: female

tag: lab

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

value: ENCBS536NWC at ENCODE; https://www.encodeproject.org/ENCBS536NWC/

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: S5P mNET-Seq untreated rep2

source_name: S5P mNET-Seq untreated

tag: cell line

value: Control:Empigen untreated Ser5 phospho


title: ChIP-seq from MCF-7 (ENCLB285GDH)

description:
https://www.encodeproject.org/experiments/ENCSR348JOJ/
***************
biological replicate number: 1
technical replicate number: 1
description: MTA1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR348JOJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB285GDH
size range: 450-650

tag: description

tag: health state

tag: link

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


title: CV304_Low

description: small RNA

tag: strain

value: Sox9-EGFP on C57BL/6J background

tag: Sex

value: Female

tag: tissue

value: jejunum

tag: cell type

value: Intestinal Epithelial Cells

tag: condition

value: Conventionalized

value: Sox9-EGFP Low

value: C

value: October 1, 2015

value: 10 weeks


title: GF315_High

description: small RNA

value: Germfree

tag: iec population

value: Sox9-EGFP High

tag: littermate pair

value: D

tag: sequence date

tag: age

value: 11 weeks


title: Total mNET-Seq siLuc rep2

source_name: Total mNET-Seq siLuc

value: HeLa

tag: genotype/variation

value: Total polymerase, siLuc control for EXOC3 KD

tag: molecule subtype

value: Polymerase bound RNA


title: CV304_Neg

description: small RNA

value: Sox9-EGFP Neg


title: ChIP-seq from K562 (ENCLB949BLX)

description:
https://www.encodeproject.org/experiments/ENCSR343ELW/
***************
biological replicate number: 4
technical replicate number: 1
description: LEF1 ChIP-seq on human K562
experiment encode accession: ENCSR343ELW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB949BLX
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

tag: antibody

tag: line

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

tag: biosample encode accession

tag: dev stage

value: adult

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS828OIW at ENCODE; https://www.encodeproject.org/ENCBS828OIW/

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: △2hgt; △cre-1_54h_2

city: Tianjin

first: Bang

last: Wang

address: 32 Xi Qi Dao, Tianjin Airport Economic Area

country: China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

description: Sample 32

data_processing:
Illumina HiSeq™ 2000/2500 used for sequencing
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 12) with Tophat.
The alignment results were stored in SAM format files for subsequent analysis.
The count of reads uniquely mapped to only one gene for each transcript were calculated by HTseq-count using SAM files and genome annotation as input.
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM).
Genome_build: GCA_000182925.2
Supplementary_files_format_and_content: tab-delimited text files including gene locus, reads, and length

organism: Neurospora crassa OR74A

source_name: △2hgt; △cre-1_54h

growth_protocol:
Sample 1-12: Conidia were innoculated at 10e6 conidia/mL into 1×Vogel’s salts with 2% (w/v) sucrose for 16 h-pregrowth and mycelia were then induced on an indicated glucose gradient for 1 or 2 hours.
Sample 13-32: Conidia were innoculated at 10e6 conidia/mL into 1×Vogel’s salts with 2% (w/v) Avicel grown for indicated hours

extract_protocol:
Mycelia were harvested through filtration and immediately frozen in liquid nitrogen.Total RNA from frozen sample was isolated with TRIzol reagent (Invitrogen) and further treated with DNase I (RNeasy Mini Kit, QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth condition

value: 1×Vogel’s salts with 2% (w/v) Avicel for 54 h growth

value: mycelia


title: ChIP-seq from K562 (ENCLB462YLN)

description:
https://www.encodeproject.org/experiments/ENCSR343ELW/
***************
biological replicate number: 3
technical replicate number: 1
description: LEF1 ChIP-seq on human K562
experiment encode accession: ENCSR343ELW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB462YLN
size range: 450-650

tag: description

tag: lab

tag: health state

tag: link

value: ENCBS994WPS at ENCODE; https://www.encodeproject.org/ENCBS994WPS/


title: Total mNET-Seq siEX3 rep2

source_name: Total mNET-Seq siEX3

tag: cell line

value: HeLa

value: Total polymerase, EXOC3 KD


title: S2P mNET-Seq Empigen treated rep2

source_name: S2P mNET-Seq Empigen treated

value: Empigen treated Ser2 phospho

value: Polymerase bound RNA


title: CV304_Sublow

description: small RNA

tag: strain

value: Sox9-EGFP on C57BL/6J background

tag: Sex

value: Female

tag: tissue

value: jejunum

tag: cell type

value: Intestinal Epithelial Cells

tag: condition

value: Conventionalized

value: Sox9-EGFP Sublow

value: C

value: October 1, 2015

value: 10 weeks


title: CV304_High

description: small RNA

tag: iec population

value: Sox9-EGFP High

tag: littermate pair

tag: sequence date

tag: age


title: eCLIP from HepG2 (ENCLB089KST)

description:
https://www.encodeproject.org/experiments/ENCSR339FUY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against PCBP2
experiment encode accession: ENCSR339FUY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR115GAA
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB089KST
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

tag: antibody

tag: line

value: immortalized cell line

tag: biosample encode accession

value: child

value: 15 year

value: male

tag: passage number

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS548DJV at ENCODE; https://www.encodeproject.org/ENCBS548DJV/

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: △2hgt; △cre-1_54h_1

description: Sample 31

tag: genotype/variation

tag: growth condition

value: 1×Vogel’s salts with 2% (w/v) Avicel for 54 h growth

value: mycelia


title: ChIP-seq from HepG2 (ENCLB579ANK)

description:
https://www.encodeproject.org/experiments/ENCSR337NWW/
***************
biological replicate number: 2
technical replicate number: 1
description: HDAC2 ChIP-seq on human HepG2
experiment encode accession: ENCSR337NWW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB579ANK
size range: 450-650

tag: description

value: Hepatocellular carcinoma

tag: dev stage

tag: lab

value: Michael Snyder, Stanford

tag: health state

tag: link

value: ENCBS716YFX at ENCODE; https://www.encodeproject.org/ENCBS716YFX/


title: GF305_NS

description: small RNA

tag: strain

value: Sox9-EGFP on C57BL/6J background

tag: Sex

value: Female

tag: tissue

value: jejunum

tag: cell type

value: Intestinal Epithelial Cells

value: Germfree

value: Sox9-EGFP Non-sorted IECs

value: C

value: October 1, 2015

value: 10 weeks


title: CV304_NS

description: small RNA

tag: condition

value: Conventionalized

tag: iec population

tag: littermate pair

tag: sequence date


title: △2hgt; △cre-1_40h_1

description: Sample 29

source_name: △2hgt; △cre-1_40h

value: 1×Vogel’s salts with 2% (w/v) Avicel for 40 h growth


title: eCLIP from HepG2 (ENCLB093OIS)

description:
https://www.encodeproject.org/experiments/ENCSR351PVI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against SLTM
experiment encode accession: ENCSR351PVI
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR670UPZ
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB093OIS
size range: 175-300

tag: antibody

value: SLTM

tag: line

value: immortalized cell line

tag: biosample encode accession

value: child

tag: age

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS537ADD at ENCODE; https://www.encodeproject.org/ENCBS537ADD/

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: △2hgt_72h_2

description: Sample 28

tag: genotype/variation

value: NCU010021 & NCU04963 deleted

tag: growth condition

value: 1×Vogel’s salts with 2% (w/v) Avicel for 72 h growth

value: mycelia


title: siRNA RNA-seq from K562 (ENCLB362JJO)

description:
https://www.encodeproject.org/experiments/ENCSR336ZWX/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting TAL1.
experiment encode accession: ENCSR336ZWX
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR641CMW, ENCSR074DIJ
encode release date: 2016-11-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB362JJO
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting TAL1

tag: description

value: K562 cells treated with a siRNA knockdown against TAL1, used in RNA-seq experiments.

tag: dev stage

value: adult

value: 53 year

value: female

tag: lab

value: Sherman Weissman, Yale

value: chronic myelogenous leukemia (CML)

value: ENCBS853UTT at ENCODE; https://www.encodeproject.org/ENCBS853UTT/

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


title: GF305_Neg

description: small RNA

tag: strain

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

value: Germfree

value: Sox9-EGFP Neg

value: C

value: October 1, 2015

value: 10 weeks


title: GF305_High

description: small RNA

tag: Sex

value: Sox9-EGFP High


title: GF305_Low

description: small RNA

tag: tissue

value: Sox9-EGFP Low


title: siRNA RNA-seq from K562 (ENCLB832BVB)

description:
https://www.encodeproject.org/experiments/ENCSR336ZWX/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting TAL1.
experiment encode accession: ENCSR336ZWX
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR641CMW, ENCSR074DIJ
encode release date: 2016-11-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB832BVB
size range: >200
spikeins used: /references/ENCSR866KGS/

value: immortalized cell line

value: K562 cells treated with a siRNA knockdown against TAL1, used in RNA-seq experiments.

value: adult

value: 53 year

tag: health state

tag: link

value: ENCBS490GOA at ENCODE; https://www.encodeproject.org/ENCBS490GOA/


title: GF271_Sublow

description: small RNA

tag: cell type

tag: condition

tag: iec population

value: Sox9-EGFP Sublow

value: B

value: September 1, 2015


title: △2hgt_72h_1

description: Sample 27

value: NCU010021 & NCU04963 deleted

value: 1×Vogel’s salts with 2% (w/v) Avicel for 72 h growth

value: mycelia


title: △2hgt_54h_2

description: Sample 26

value: 1×Vogel’s salts with 2% (w/v) Avicel for 54 h growth


title: eCLIP from HepG2 (ENCLB381KLL)

description:
https://www.encodeproject.org/experiments/ENCSR334QFR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against AUH
experiment encode accession: ENCSR334QFR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR821VMD
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB381KLL
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

tag: antibody

value: AUH

value: child

value: 15 year

value: male

tag: passage number

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS582KNJ at ENCODE; https://www.encodeproject.org/ENCBS582KNJ/

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: eCLIP from HepG2 (ENCLB874ISY)

description:
https://www.encodeproject.org/experiments/ENCSR339FUY/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against PCBP2
experiment encode accession: ENCSR339FUY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR115GAA
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB874ISY
size range: 175-300

tag: line

value: immortalized cell line

tag: biosample encode accession

value: ENCBS859FFE at ENCODE; https://www.encodeproject.org/ENCBS859FFE/


title: ChIP-seq from HepG2 (ENCLB748XVS)

description:
https://www.encodeproject.org/experiments/ENCSR334KIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: SP1 ChIP-seq on human HepG2
experiment encode accession: ENCSR334KIQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB748XVS
size range: 450-650

value: Hepatocellular carcinoma

tag: age

value: Michael Snyder, Stanford

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


title: △2hgt_54h_1

description: Sample 25

tag: genotype/variation

value: NCU010021 & NCU04963 deleted

tag: growth condition

value: mycelia


title: eCLIP from HepG2 (ENCLB814JNF)

description:
https://www.encodeproject.org/experiments/ENCSR334QFR/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against AUH
experiment encode accession: ENCSR334QFR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR821VMD
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB814JNF
size range: 175-300

value: AUH

tag: dev stage

value: ENCBS985FRY at ENCODE; https://www.encodeproject.org/ENCBS985FRY/


title: △2hgt_40h_1

description: Sample 23

value: 1×Vogel’s salts with 2% (w/v) Avicel for 40 h growth


title: △2hgt_40h_2

description: Sample 24


title: ChIP-seq from HepG2 (ENCLB382UET)

description:
https://www.encodeproject.org/experiments/ENCSR334KIQ/
***************
biological replicate number: 2
technical replicate number: 1
description: SP1 ChIP-seq on human HepG2
experiment encode accession: ENCSR334KIQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB382UET
size range: 450-650

value: child

value: 15 year

value: male

tag: lab

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


title: GF271_Neg

description: small RNA

tag: strain

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

value: Germfree

value: Sox9-EGFP Neg

tag: littermate pair

value: B

tag: sequence date

value: September 1, 2015

value: 10 weeks


title: eCLIP from HepG2 (ENCLB013TIM)

description:
https://www.encodeproject.org/experiments/ENCSR333PZV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against TIA1
experiment encode accession: ENCSR333PZV
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB013TIM
size range: 175-300

value: Control

value: immortalized cell line

tag: Sex

value: Gene Yeo, UCSD

tag: health state

value: hepatocellular carcinoma

value: ENCBS751GYX at ENCODE; https://www.encodeproject.org/ENCBS751GYX/

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: GF271_Low

description: small RNA

value: Sox9-EGFP on C57BL/6J background

tag: tissue

tag: cell type

value: Sox9-EGFP Low


title: GF271_High

description: small RNA

value: Female

value: jejunum

tag: condition

tag: iec population

value: Sox9-EGFP High


title: △2hgt; △cre-1_40h_2

description: Sample 30

value: 1×Vogel’s salts with 2% (w/v) Avicel for 40 h growth

value: mycelia


title: GF271_NS

description: small RNA

value: Intestinal Epithelial Cells

value: Germfree

value: Sox9-EGFP Non-sorted IECs

value: B

value: September 1, 2015


title: GF244_Sublow

description: small RNA

value: Sox9-EGFP Sublow

value: A

value: 12 weeks


title: △cre-1_54h_1

description: Sample 21

value: NCU08807 deleted

value: 1×Vogel’s salts with 2% (w/v) Avicel for 54 h growth


title: H3K27Ac ChIP-seq Srebf1-/- KLA6h

description:
formaldehyde cross-linked
Sample 16

source_name: bone marrow derived macrophages

tag: strain background

value: Srebp1 -/-

value: bone marrow derived macrophages

tag: treated with

value: KLA for 6 hours

tag: chip antibody

value: H3K27Ac (Vendor:Abcam, cat# ab4729, lot# GR132150-Y)


title: ChIP-seq from HepG2 (ENCLB492HKP)

description:
https://www.encodeproject.org/experiments/ENCSR337NWW/
***************
biological replicate number: 1
technical replicate number: 1
description: HDAC2 ChIP-seq on human HepG2
experiment encode accession: ENCSR337NWW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB492HKP
size range: 450-650

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: Hepatocellular carcinoma

tag: biosample encode accession

value: child

tag: age

value: 15 year

value: male

value: Michael Snyder, Stanford

value: hepatocellular carcinoma

tag: link

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

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: △cre-1_54h_2

description: Sample 22

tag: genotype/variation

value: NCU08807 deleted

tag: growth condition

value: mycelia


title: △cre-1_40h_2

description: Sample 20

value: 1×Vogel’s salts with 2% (w/v) Avicel for 40 h growth


title: GF244_Neg

description: small RNA

source_name: Intestinal Epithelial Cells

tag: strain

value: Sox9-EGFP on C57BL/6J background

tag: Sex

value: Female

value: jejunum

value: Intestinal Epithelial Cells

value: Germfree

value: Sox9-EGFP Neg

tag: littermate pair

value: A

tag: sequence date

value: September 1, 2015

value: 12 weeks


title: GF244_NS

description: small RNA

tag: tissue

tag: cell type

tag: condition

value: Sox9-EGFP Non-sorted IECs


title: eCLIP from K562 (ENCLB105HGF)

description:
https://www.encodeproject.org/experiments/ENCSR331VNX/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against FMR1
experiment encode accession: ENCSR331VNX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR735MBZ
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB105HGF
size range: 175-300

value: immortalized cell line

tag: dev stage

value: adult

value: 53 year

value: female

tag: passage number

tag: lab

value: Gene Yeo, UCSD

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS993NMB at ENCODE; https://www.encodeproject.org/ENCBS993NMB/

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 GM12878 (ENCLB608UML)

description:
https://www.encodeproject.org/experiments/ENCSR332EYT/
***************
biological replicate number: 2
technical replicate number: 1
description: STAT1 ChIP-seq on human GM12878
experiment encode accession: ENCSR332EYT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB608UML
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

tag: antibody

tag: line

tag: description

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

value: unknown

value: Michael Snyder, Stanford

value: ENCBS594YOH at ENCODE; https://www.encodeproject.org/ENCBS594YOH/

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

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

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


title: ChIP-seq from GM12878 (ENCLB726PMJ)

description:
https://www.encodeproject.org/experiments/ENCSR332EYT/
***************
biological replicate number: 1
technical replicate number: 1
description: STAT1 ChIP-seq on human GM12878
experiment encode accession: ENCSR332EYT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB726PMJ
size range: 450-650

value: immortalized cell line

tag: biosample encode accession

tag: age

tag: link

value: ENCBS260WJQ at ENCODE; https://www.encodeproject.org/ENCBS260WJQ/


title: GF244_Low

description: small RNA

tag: strain

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

value: Germfree

tag: iec population

value: Sox9-EGFP Low

value: A

value: September 1, 2015

value: 12 weeks


title: wt_54h_2

description: Sample 16

tag: genotype/variation

value: wild type

tag: growth condition

value: 1×Vogel’s salts with 2% (w/v) Avicel for 54 h growth

value: mycelia


title: △cre-1_40h_1

description: Sample 19

value: NCU08807 deleted

value: 1×Vogel’s salts with 2% (w/v) Avicel for 40 h growth


title: GF244_High

description: small RNA

tag: Sex

tag: tissue

value: Sox9-EGFP High

tag: littermate pair

tag: sequence date


title: wt_72h_2

description: Sample 18

value: 1×Vogel’s salts with 2% (w/v) Avicel for 72 h growth

tag: cell type


title: eCLIP from K562 (ENCLB498TQP)

description:
https://www.encodeproject.org/experiments/ENCSR331VNX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against FMR1
experiment encode accession: ENCSR331VNX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR735MBZ
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB498TQP
size range: 175-300

value: immortalized cell line

tag: dev stage

value: adult

value: 53 year

value: female

tag: passage number

tag: lab

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS885HUO at ENCODE; https://www.encodeproject.org/ENCBS885HUO/

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: wt_72h_1

description: Sample 17

value: wild type


title: CV270_Sublow

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

tag: condition

value: Conventionalized

value: Sox9-EGFP Sublow

value: B

value: September 1, 2015

value: 10 weeks


title: eCLIP from HepG2 (ENCLB074UAQ)

description:
https://www.encodeproject.org/experiments/ENCSR331MIC/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against SF3A3
experiment encode accession: ENCSR331MIC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR859PUB
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB074UAQ
size range: 175-300

tag: antibody

tag: line

value: immortalized cell line

value: child

value: 15 year

value: male

tag: health state

value: hepatocellular carcinoma

value: ENCBS362ASG at ENCODE; https://www.encodeproject.org/ENCBS362ASG/

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: eCLIP from HepG2 (ENCLB772PSD)

description:
https://www.encodeproject.org/experiments/ENCSR331MIC/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against SF3A3
experiment encode accession: ENCSR331MIC
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR859PUB
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB772PSD
size range: 175-300

tag: biosample encode accession

tag: age

value: Gene Yeo, UCSD

tag: link

value: ENCBS308ZPA at ENCODE; https://www.encodeproject.org/ENCBS308ZPA/


title: CV270_NS

description: small RNA

tag: strain

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

tag: iec population

value: Sox9-EGFP Non-sorted IECs


title: wt_54h_1

description: Sample 15

tag: genotype/variation

value: wild type

tag: growth condition

value: 1×Vogel’s salts with 2% (w/v) Avicel for 54 h growth

value: mycelia


title: wt_40h_1

description: Sample 13

value: 1×Vogel’s salts with 2% (w/v) Avicel for 40 h growth


title: wt_40h_2

description: Sample 14


title: CV270_Neg

description: small RNA

tag: Sex

tag: tissue

value: Conventionalized

value: Sox9-EGFP Neg

tag: littermate pair

value: B

value: September 1, 2015

value: 10 weeks


title: ChIP-seq from K562 (ENCLB560AIC)

description:
https://www.encodeproject.org/experiments/ENCSR329YMD/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF24 tagged K562 cell line.
experiment encode accession: ENCSR329YMD
assay title: ChIP-seq
encode release date: 2015-12-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB560AIC
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ZNF24 fusion protein

value: Control

value: immortalized cell line

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF24

tag: dev stage

value: adult

value: 53 year

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS778QBL at ENCODE; https://www.encodeproject.org/ENCBS778QBL/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW47; http://web.expasy.org/cellosaurus/CVCL_AW47


title: ChIP-seq from HEK293 (ENCLB907WNW)

description:
https://www.encodeproject.org/experiments/ENCSR328SUD/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF335 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR328SUD
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: ENCLB907WNW
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF335 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF335 under the control of a CMV promoter.

value: embryonic

value: unknown

tag: lab

value: Michael Snyder, Stanford

value: ENCBS967MZW at ENCODE; https://www.encodeproject.org/ENCBS967MZW/

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


title: CV246_Sublow

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

tag: cell type

value: Intestinal Epithelial Cells

tag: condition

value: Conventionalized

value: Sox9-EGFP Sublow

value: A

tag: sequence date

value: September 1, 2015

value: 12 weeks


title: CV270_Low

description: small RNA

value: Sox9-EGFP Low

value: B

value: 10 weeks


title: CV270_High

description: small RNA

value: Sox9-EGFP High


title: ChIP-seq from K562 (ENCLB437YKX)

description:
https://www.encodeproject.org/experiments/ENCSR331BDJ/
***************
biological replicate number: 1
technical replicate number: 1
description: NKRF ChIP-seq on human K562
experiment encode accession: ENCSR331BDJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB437YKX
size range: 450-650

tag: antibody

value: NKRF

tag: line

value: immortalized cell line

value: adult

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS465MWC at ENCODE; https://www.encodeproject.org/ENCBS465MWC/

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: CV246_Neg

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

value: Intestinal Epithelial Cells

value: Conventionalized

value: Sox9-EGFP Neg

tag: age


title: ChIP-seq from HEK293 (ENCLB214OXD)

description:
https://www.encodeproject.org/experiments/ENCSR328SUD/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF335 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR328SUD
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: ENCLB214OXD
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF335 under the control of a CMV promoter.

tag: biosample encode accession

value: embryonic

value: unknown

value: Michael Snyder, Stanford

tag: link

value: ENCBS879KEF at ENCODE; https://www.encodeproject.org/ENCBS879KEF/

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


title: CV246_NS

description: small RNA

tag: strain

tag: iec population

value: Sox9-EGFP Non-sorted IECs

value: A

value: September 1, 2015

value: 12 weeks


title: eCLIP from HepG2 (ENCLB127BIF)

description:
https://www.encodeproject.org/experiments/ENCSR328LLU/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against U2AF1
experiment encode accession: ENCSR328LLU
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR941GJG
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB127BIF
size range: 175-300

value: immortalized cell line

value: child

tag: Sex

value: male

value: 15 year

value: hepatocellular carcinoma

tag: passage number

value: Gene Yeo, UCSD

value: ENCBS012DTZ at ENCODE; https://www.encodeproject.org/ENCBS012DTZ/

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: CV246_Low

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: Female

tag: tissue

value: jejunum

value: Intestinal Epithelial Cells

value: Conventionalized

value: Sox9-EGFP Low

tag: littermate pair


title: ChIP-seq from HEK293 (ENCLB518DEI)

description:
https://www.encodeproject.org/experiments/ENCSR324LTM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-OSR2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR324LTM
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: ENCLB518DEI
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-OSR2 fusion protein

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-OSR2 under the control of a CMV promoter.

tag: dev stage

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS927YCP at ENCODE; https://www.encodeproject.org/ENCBS927YCP/

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


title: ChIP-seq from K562 (ENCLB457YMV)

description:
https://www.encodeproject.org/experiments/ENCSR331BDJ/
***************
biological replicate number: 2
technical replicate number: 1
description: NKRF ChIP-seq on human K562
experiment encode accession: ENCSR331BDJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB457YMV
size range: 450-650

value: NKRF

value: immortalized cell line

value: adult

value: 53 year

tag: lab

value: chronic myelogenous leukemia (CML)

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

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 IMR-90 (ENCLB451LZP)

description:
https://www.encodeproject.org/experiments/ENCSR970FKL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human IMR-90
experiment encode accession: ENCSR970FKL
assay title: ChIP-seq
encode release date: 2016-08-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB451LZP
size range: 150-350

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

value: Control

value: primary cell

value: Fetal lung fibroblasts

value: fetal

value: 16 week

value: ENCBS648SCY at ENCODE; https://www.encodeproject.org/ENCBS648SCY/

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: ChIP-seq from HEK293 (ENCLB145CQN)

description:
https://www.encodeproject.org/experiments/ENCSR324LTM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-OSR2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR324LTM
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: ENCLB145CQN
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-OSR2 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS582ZUH at ENCODE; https://www.encodeproject.org/ENCBS582ZUH/

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


title: ChIP-seq from HEK293 (ENCLB587FUA)

description:
https://www.encodeproject.org/experiments/ENCSR316OQD/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZNF655 tagged human HEK293 cells.
experiment encode accession: ENCSR316OQD
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB587FUA
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF655 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF655 under the control of a CMV promoter.

value: ENCBS659QAK at ENCODE; https://www.encodeproject.org/ENCBS659QAK/


title: eCLIP from HepG2 (ENCLB417ZXE)

description:
https://www.encodeproject.org/experiments/ENCSR328LLU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against U2AF1
experiment encode accession: ENCSR328LLU
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR941GJG
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB417ZXE
size range: 175-300

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

value: ENCBS357UNN at ENCODE; https://www.encodeproject.org/ENCBS357UNN/

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 A549 (ENCLB481CKC)

description:
https://www.encodeproject.org/experiments/ENCSR996DUT/
***************
biological replicate number: 2
technical replicate number: 1
description: JUN ChIP-seq on human A549
experiment encode accession: ENCSR996DUT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR949BZP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB481CKC
size range: 150-350

source_name: Homo sapiens A549 immortalized cell line

value: JUN

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma.

value: adult

value: 58 year

value: ENCBS007LES at ENCODE; https://www.encodeproject.org/ENCBS007LES/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-185.aspx


title: ChIP-seq from K562 (ENCLB962QOX)

description:
https://www.encodeproject.org/experiments/ENCSR322CFO/
***************
biological replicate number: 2
technical replicate number: 1
description: ZEB2 ChIP-seq on human K562
experiment encode accession: ENCSR322CFO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB962QOX
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: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

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

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 A549 (ENCLB747WRD)

description:
https://www.encodeproject.org/experiments/ENCSR996DUT/
***************
biological replicate number: 1
technical replicate number: 1
description: JUN ChIP-seq on human A549
experiment encode accession: ENCSR996DUT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR949BZP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB747WRD
size range: 150-350

value: JUN

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma.

value: adult

value: male

value: ENCBS159AAA at ENCODE; https://www.encodeproject.org/ENCBS159AAA/


title: eCLIP from HepG2 (ENCLB718NMZ)

description:
https://www.encodeproject.org/experiments/ENCSR314UMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against TRA2A
experiment encode accession: ENCSR314UMJ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR544CTM
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB718NMZ
size range: 175-300

value: child

value: 15 year

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS533IVT at ENCODE; https://www.encodeproject.org/ENCBS533IVT/

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 IMR-90 (ENCLB964RDZ)

description:
https://www.encodeproject.org/experiments/ENCSR957KYB/
***************
biological replicate number: 2
technical replicate number: 1
description: BHLHE40 ChIP-seq on human IMR90
experiment encode accession: ENCSR957KYB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR970FKL
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB964RDZ
size range: 150-350

value: primary cell

value: Fetal lung fibroblasts

value: fetal

value: female

value: 16 week

value: unknown

value: Michael Snyder, Stanford

value: ENCBS073JZM at ENCODE; https://www.encodeproject.org/ENCBS073JZM/

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: eCLIP from HepG2 (ENCLB690VOR)

description:
https://www.encodeproject.org/experiments/ENCSR314UMJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against TRA2A
experiment encode accession: ENCSR314UMJ
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR544CTM
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB690VOR
size range: 175-300

value: immortalized cell line

value: child

value: male

value: 15 year

value: Gene Yeo, UCSD

value: ENCBS015PAC at ENCODE; https://www.encodeproject.org/ENCBS015PAC/


title: ChIP-seq from IMR-90 (ENCLB546TSM)

description:
https://www.encodeproject.org/experiments/ENCSR957KYB/
***************
biological replicate number: 1
technical replicate number: 1
description: BHLHE40 ChIP-seq on human IMR90
experiment encode accession: ENCSR957KYB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR970FKL
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB546TSM
size range: 150-350

value: primary cell

value: ENCBS412SDE at ENCODE; https://www.encodeproject.org/ENCBS412SDE/


title: ChIP-seq from HEK293 (ENCLB839WDB)

description:
https://www.encodeproject.org/experiments/ENCSR311DYU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZNF800 tagged human HEK293 cells.
experiment encode accession: ENCSR311DYU
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB839WDB
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF800 fusion protein

value: Control

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF800 under the control of a CMV promoter.

value: embryonic

value: ENCBS512GBG at ENCODE; https://www.encodeproject.org/ENCBS512GBG/

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


title: ChIP-seq from A549 (ENCLB404QMH)

description:
https://www.encodeproject.org/experiments/ENCSR949BZP/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human A549
experiment encode accession: ENCSR949BZP
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB404QMH
size range: 150-350

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma.

value: adult

value: 58 year

value: Michael Snyder, Stanford

value: ENCBS848SUF at ENCODE; https://www.encodeproject.org/ENCBS848SUF/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-185.aspx


title: ChIP-seq from A549 (ENCLB504NHD)

description:
https://www.encodeproject.org/experiments/ENCSR949BZP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human A549
experiment encode accession: ENCSR949BZP
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB504NHD
size range: 150-350

value: immortalized cell line

value: male

value: ENCBS611JSC at ENCODE; https://www.encodeproject.org/ENCBS611JSC/


title: ChIP-seq from K562 (ENCLB710GIY)

description:
https://www.encodeproject.org/experiments/ENCSR314BBS/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-PTTG1 ChIP-seq on human K562
experiment encode accession: ENCSR314BBS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR085OAX
encode release date: 2016-03-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB710GIY
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-PTTG1 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to PTTG1

value: 53 year

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS430AYP at ENCODE; https://www.encodeproject.org/ENCBS430AYP/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW39; http://web.expasy.org/cellosaurus/CVCL_AW39


title: CV246_High

description: small RNA

value: Sox9-EGFP on C57BL/6J background

value: Female

value: jejunum

tag: cell type

value: Intestinal Epithelial Cells

tag: condition

value: Conventionalized

value: Sox9-EGFP High

value: A

value: September 1, 2015

value: 12 weeks


title: ChIP-seq from K562 (ENCLB636VQQ)

description:
https://www.encodeproject.org/experiments/ENCSR314BBS/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-PTTG1 ChIP-seq on human K562
experiment encode accession: ENCSR314BBS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR085OAX
encode release date: 2016-03-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB636VQQ
size range: 450-650

tag: antibody

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to PTTG1

value: adult

value: ENCBS473LEX at ENCODE; https://www.encodeproject.org/ENCBS473LEX/


title: eCLIP from K562 (ENCLB363MVI)

description:
https://www.encodeproject.org/experiments/ENCSR307YIW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against EIF4G2
experiment encode accession: ENCSR307YIW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR651NUF
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB363MVI
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

tag: line

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS533ETT at ENCODE; https://www.encodeproject.org/ENCBS533ETT/

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 HEK293 (ENCLB634EGE)

description:
https://www.encodeproject.org/experiments/ENCSR307CKC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF680 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR307CKC
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: ENCLB634EGE
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF680 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF680 under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

tag: health state

value: ENCBS789RTN at ENCODE; https://www.encodeproject.org/ENCBS789RTN/

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


title: eCLIP from K562 (ENCLB522LSP)

description:
https://www.encodeproject.org/experiments/ENCSR307YIW/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against EIF4G2
experiment encode accession: ENCSR307YIW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR651NUF
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB522LSP
size range: 175-300

value: immortalized cell line

tag: age

value: ENCBS502SUO at ENCODE; https://www.encodeproject.org/ENCBS502SUO/

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


title: ChIP-seq from K562 (ENCLB932WDR)

description:
https://www.encodeproject.org/experiments/ENCSR920BLG/
***************
biological replicate number: 1
technical replicate number: 1
description: SIN3A ChIP-seq on human K562
experiment encode accession: ENCSR920BLG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2016-03-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB932WDR
size range: 150-350

tag: biosample encode accession

value: adult

value: ENCBS383VKK at ENCODE; https://www.encodeproject.org/ENCBS383VKK/


title: ChIP-seq from K562 (ENCLB698ZHC)

description:
https://www.encodeproject.org/experiments/ENCSR920BLG/
***************
biological replicate number: 2
technical replicate number: 1
description: SIN3A ChIP-seq on human K562
experiment encode accession: ENCSR920BLG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2016-03-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB698ZHC
size range: 150-350

value: 53 year

value: female

tag: link

value: ENCBS486UBH at ENCODE; https://www.encodeproject.org/ENCBS486UBH/


title: ChIP-seq from K562 (ENCLB572FFJ)

description:
https://www.encodeproject.org/experiments/ENCSR322CFO/
***************
biological replicate number: 1
technical replicate number: 1
description: ZEB2 ChIP-seq on human K562
experiment encode accession: ENCSR322CFO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB572FFJ
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: chronic myelogenous leukemia (CML)

value: ENCBS994WPS at ENCODE; https://www.encodeproject.org/ENCBS994WPS/


title: ChIP-seq from K562 (ENCLB392IDM)

description:
https://www.encodeproject.org/experiments/ENCSR907JPB/
***************
biological replicate number: 1
technical replicate number: 1
description: ZMIZ1 ChIP-seq on human K562
experiment encode accession: ENCSR907JPB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2016-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB392IDM
size range: 150-350

value: ENCBS555MCX at ENCODE; https://www.encodeproject.org/ENCBS555MCX/

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


title: ChIP-seq from K562 (ENCLB941GGD)

description:
https://www.encodeproject.org/experiments/ENCSR302AWT/
***************
biological replicate number: 2
technical replicate number: 1
description: FOXK2 ChIP-seq on human K562
experiment encode accession: ENCSR302AWT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB941GGD
size range: 450-650

value: ENCBS850QNJ at ENCODE; https://www.encodeproject.org/ENCBS850QNJ/


title: ChIP-seq from K562 (ENCLB323UAT)

description:
https://www.encodeproject.org/experiments/ENCSR907JPB/
***************
biological replicate number: 2
technical replicate number: 1
description: ZMIZ1 ChIP-seq on human K562
experiment encode accession: ENCSR907JPB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2016-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB323UAT
size range: 150-350

value: Michael Snyder, Stanford

value: ENCBS361MEX at ENCODE; https://www.encodeproject.org/ENCBS361MEX/


title: ChIP-seq from K562 (ENCLB897EPQ)

description:
https://www.encodeproject.org/experiments/ENCSR888XZK/
***************
biological replicate number: 1
technical replicate number: 1
description: TCF4 ChIP-seq on human K562
experiment encode accession: ENCSR888XZK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB897EPQ
size range: 150-350

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

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


title: ChIP-seq from K562 (ENCLB993DGG)

description:
https://www.encodeproject.org/experiments/ENCSR302AWT/
***************
biological replicate number: 1
technical replicate number: 1
description: FOXK2 ChIP-seq on human K562
experiment encode accession: ENCSR302AWT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB993DGG
size range: 450-650

value: immortalized cell line

value: ENCBS697XFI at ENCODE; https://www.encodeproject.org/ENCBS697XFI/


title: ChIP-seq from IMR-90 (ENCLB262FRG)

description:
https://www.encodeproject.org/experiments/ENCSR970FKL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human IMR-90
experiment encode accession: ENCSR970FKL
assay title: ChIP-seq
encode release date: 2016-08-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB262FRG
size range: 150-350

value: Control

value: primary cell

value: fetal

value: 16 week

value: unknown

value: ENCBS981UBX at ENCODE; https://www.encodeproject.org/ENCBS981UBX/

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: ChIP-seq from K562 (ENCLB687QGX)

description:
https://www.encodeproject.org/experiments/ENCSR888XZK/
***************
biological replicate number: 2
technical replicate number: 1
description: TCF4 ChIP-seq on human K562
experiment encode accession: ENCSR888XZK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB687QGX
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: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS201LYR at ENCODE; https://www.encodeproject.org/ENCBS201LYR/

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


title: eCLIP from K562 (ENCLB556NWJ)

description:
https://www.encodeproject.org/experiments/ENCSR301UQM/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against GNL3
experiment encode accession: ENCSR301UQM
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR977GTT
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB556NWJ
size range: 175-300

value: immortalized cell line

value: Gene Yeo, UCSD

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

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 K562 (ENCLB024FXK)

description:
https://www.encodeproject.org/experiments/ENCSR301UQM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against GNL3
experiment encode accession: ENCSR301UQM
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR977GTT
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB024FXK
size range: 175-300

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


title: ChIP-seq from K562 (ENCLB229LKR)

description:
https://www.encodeproject.org/experiments/ENCSR298JCG/
***************
biological replicate number: 1
technical replicate number: 1
description: NCOR1 ChIP-seq on human K562
experiment encode accession: ENCSR298JCG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB229LKR
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS831ATS at ENCODE; https://www.encodeproject.org/ENCBS831ATS/


title: ChIP-seq from HeLa-S3 (ENCLB882SCY)

description:
https://www.encodeproject.org/experiments/ENCSR887MXT/
***************
biological replicate number: 1
technical replicate number: 1
description: ZHX1 ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR887MXT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR580ECR
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB882SCY
size range: 150-350

source_name: Homo sapiens HeLa-S3 immortalized cell line

value: 31 year

value: cervical adenocarcinoma

value: ENCBS450RLH at ENCODE; https://www.encodeproject.org/ENCBS450RLH/

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 GM12878 (ENCLB346YYW)

description:
https://www.encodeproject.org/experiments/ENCSR819ATC/
***************
biological replicate number: 1
technical replicate number: 1
description: MYB ChIP-seq on human GM12878
experiment encode accession: ENCSR819ATC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR553NUG
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB346YYW
size range: 150-350

value: MYB

value: adult

value: unknown

value: female

value: ENCBS595CWJ at ENCODE; https://www.encodeproject.org/ENCBS595CWJ/

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: ChIP-seq from K562 (ENCLB820QPG)

description:
https://www.encodeproject.org/experiments/ENCSR815ZDS/
***************
biological replicate number: 1
technical replicate number: 1
description: SREBF1 ChIP-seq on human K562
experiment encode accession: ENCSR815ZDS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR080EOT
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB820QPG
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: 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 K562 (ENCLB844VLU)

description:
https://www.encodeproject.org/experiments/ENCSR298JCG/
***************
biological replicate number: 2
technical replicate number: 1
description: NCOR1 ChIP-seq on human K562
experiment encode accession: ENCSR298JCG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB844VLU
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS344LIE at ENCODE; https://www.encodeproject.org/ENCBS344LIE/