title: ChIP-seq from HEK293 (ENCLB574JQX)

description:
https://www.encodeproject.org/experiments/ENCSR413ABE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZFP2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR413ABE
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB574JQX
size range: 450-650

tag: description

value: embryonic

value: Michael Snyder, Stanford

value: ENCBS801SRT at ENCODE; https://www.encodeproject.org/ENCBS801SRT/


title: C1-1

status: Public on Jan 04 2017

type: SRA

city: Townsville

first: Aurelie

last: Moya

state: QLD

address: James Cook drive

department: ARC Centre of Excellence for Coral Reefs Studies

country: Australia

institute: James Cook University

description: Pteropods exposed 3 days to pH 8.1

library_source: transcriptomic

data_processing:
The reads from all the H. inflatus samples were trimmed from low quality regions and sequencing adaptors using libngs (https://github.com/sylvainforet/libngs) with a minimum quality of 20 and a minimum size of 75 bp.
The trimmed reads were then assembled using Trinity (Grabherr et al., 2011).
The sequences of the resulting assembly were clustered using cdhit-est (Fu et al., 2012) with a similarity threshold of 90% and a word size of 8 bp.
The multi-modal GC profile of this initial assembly is suggestive of contamination (Fig. S1a), probably originating from the Isochrysis galbana culture provided to the animals. In order to remove these potential contaminants, the transcripts were blasted against a database containing the NCBI refseq proteins augmented with sequences from the molluscs Biomphalaria glabrata (https://www.vectorbase.org/organisms/biomphalaria-glabrata) and Lymnea stagnalis (Sadamoto et al., 2012).
Sequences were then classified as putative H. inflatus sequences if they satisfied the following criteria: e-value less than 1e-10, a minimum bit-score of at least 100, and a delta bit-score of at least 100. Here delta bit-score refers to the difference between the best mollusc hit and the best non-mollusc hit.
Protein-coding sequences were predicted using Transdecoder (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875132/) and annotated using Blast2GO (Conesa et al., 2005).
The reads were mapped back to the assembled transcripts using Bowtie2 (Langmead & Salzberg, 2012).
Differential gene expression was inferred using EdgeR (Robinson et al., 2010) using a FDR threshold of 5%.
Genome_build: Heliconoides_inflatus.fasta
Supplementary_files_format_and_content: Txt - edgeR results

molecule: total RNA

organism: Heliconoides inflatus

source_name: Shelled pteropods_pH8.1

growth_protocol: Heliconoides inflatus individuals were collected in the Bay of Villefranche-sur-mer (43˚40’ N, 7˚18’ E) between 16th and 29th February 2012. Sampling was undertaken using very slow oblique tows of 2-4 min in duration at up to 100 m depth with a 57 cm diameter WP2 plankton net (200 µm mesh size). Plankton samples were immediately transported to the Laboratoire d’Océanographie de Villefranche. Using a tweezer, H. inflatus individuals where transferred to filtered seawater medium (pore size 0.2 µm).

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen) according to the manufacturer instructions. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrophotometer and denaturing gel electrophoresis using standard methods (Sambrook & Russel, 2001). Before being shipped on dry-ice to the Macrogen sequencing facilities in Seoul, South Korea, each RNA sample was precipitated in ethanol and sodium acetate (2x and 0.1x sample volume, respectively), and stored at -80 °C.
Library construction was performed by Macrogen (South Korea). The libraries were sequenced using the Illumina HiSeq2000 platform, producing an average of 63 million sequence reads (100 bp paired-end) per sample.

treatment_protocol: Individuals were exposed for 3 d to pH conditions maintained using a pH-stat system (IKS Karlsbard) that bubbled filtered seawater (pore size 0.2 µm) with either ambient air (control, pHT 8.1) or CO2 (treatment, pHT 7.9); pH was calibrated on the total scale using Tris/HCl and 2-aminopyridine/HCl buffer solutions with a salinity of 38.0. Three replicates were set up for each pH condition.Total alkalinity (AT), pHT, and dissolved inorganic carbon (CT) were measured at the start and end of the incubations. At the end of the 3-d incubations, the H. inflatus individuals from each of the three replicates were collected from the experimental jars by filtering the water over a 200 µm mesh. Specimens were rinsed with 0.45 µm filtered seawater, immediately snap-frozen in liquid nitrogen and stored at -80 °C until further treatment.

tag: exposed to

value: pH 8.1 for 3 days

tag: tissue

value: whole pteropods


title: eCLIP from K562 (ENCLB874IKE)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR258QKO/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against XRCC6
experiment encode accession: ENCSR258QKO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR687HHB
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB874IKE
size range: 175-300

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

organism: Homo sapiens

source_name: Homo sapiens K562 immortalized cell line

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

tag: line

value: immortalized cell line

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: female

tag: age

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

tag: passage number

tag: lab

value: Gene Yeo, UCSD

tag: link

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

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: eCLIP from HepG2 (ENCLB568XBD)

description:
https://www.encodeproject.org/experiments/ENCSR257OYO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against NCBP2
experiment encode accession: ENCSR257OYO
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB568XBD
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: Control

value: child

value: 15 year

value: male

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


title: PolyA RNA-seq WT KLA6h

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description: Sample 61

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.

molecule: polyA RNA

organism: Mus musculus

source_name: bone marrow derived macrophages

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: genotype/variation

value: Srebp1 WT

tag: cell type

value: bone marrow derived macrophages

tag: treated with

value: KLA for 6 hours


title: PolyA RNA-seq WT KLA24h

description: Sample 62

value: KLA for 24 hours


title: eCLIP from HepG2 (ENCLB950HQF)

description:
https://www.encodeproject.org/experiments/ENCSR247PDK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against XRN2
experiment encode accession: ENCSR247PDK
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB950HQF
size range: 175-300

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fa2a3246-6039-46ba-b960-17fe06e7876a/@@download/attachment/CLIP_SOP_v1.0.pdf

value: immortalized cell line

value: Gene Yeo, UCSD

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


title: ChIP-seq from GM12878 (ENCLB603ZYH)

description:
https://www.encodeproject.org/experiments/ENCSR412QBS/
***************
biological replicate number: 2
technical replicate number: 1
description: TARDBP ChIP-seq on human GM12878
experiment encode accession: ENCSR412QBS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2016-04-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB603ZYH
size range: 450-650

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens GM12878 immortalized cell line

value: TARDBP

value: adult

value: female

value: unknown

value: Michael Snyder, Stanford

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

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

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


title: ChIP-seq from K562 (ENCLB447KRR)

description:
https://www.encodeproject.org/experiments/ENCSR412HJH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-MEF2D tagged K562 cell line.
experiment encode accession: ENCSR412HJH
assay title: ChIP-seq
encode release date: 2016-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB447KRR

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-MEF2D fusion protein

value: Control

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to MEF2D

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Kevin White, UChicago

value: ENCBS207FBE at ENCODE; https://www.encodeproject.org/ENCBS207FBE/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ89; http://web.expasy.org/cellosaurus/CVCL_GZ89


title: ChIP-seq from GM12878 (ENCLB993ETM)

description:
https://www.encodeproject.org/experiments/ENCSR412QBS/
***************
biological replicate number: 1
technical replicate number: 1
description: TARDBP ChIP-seq on human GM12878
experiment encode accession: ENCSR412QBS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2016-04-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB993ETM
size range: 450-650

value: immortalized cell line

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


title: PolyA RNA-seq WT noTx

description: Sample 59

value: Srebp1 WT

value: bone marrow derived macrophages

value: none (control)


title: eCLIP from K562 (ENCLB688NBO)

description:
https://www.encodeproject.org/experiments/ENCSR412NOW/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against HNRNPM
experiment encode accession: ENCSR412NOW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR212ILN
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB688NBO
size range: 175-300

value: HNRNPM

value: adult

value: female

value: Gene Yeo, UCSD

value: ENCBS123QRB at ENCODE; https://www.encodeproject.org/ENCBS123QRB/

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: eCLIP from K562 (ENCLB287JOM)

description:
https://www.encodeproject.org/experiments/ENCSR412NOW/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against HNRNPM
experiment encode accession: ENCSR412NOW
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR212ILN
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB287JOM
size range: 175-300

value: 53 year

value: chronic myelogenous leukemia (CML)

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


title: eCLIP from K562 (ENCLB789HGL)

description:
https://www.encodeproject.org/experiments/ENCSR238CLX/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against GEMIN5
experiment encode accession: ENCSR238CLX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR347MVO
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB789HGL
size range: 175-300

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/

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

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


title: polyA RNA-seq GW3965-18h

description: Sample 52

value: GW3965 (1uM) for 18 hours


title: eCLIP from K562 (ENCLB146KYP)

description:
https://www.encodeproject.org/experiments/ENCSR238CLX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against GEMIN5
experiment encode accession: ENCSR238CLX
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR347MVO
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB146KYP
size range: 175-300

value: immortalized cell line

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/


title: polyA RNA-seq noTx

description: Sample 50

value: none (control)


title: ChIP-seq from K562 (ENCLB922EBZ)

description:
https://www.encodeproject.org/experiments/ENCSR411UYA/
***************
biological replicate number: 1
technical replicate number: 1
description: MTA2 ChIP-seq on human K562
experiment encode accession: ENCSR411UYA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB922EBZ
size range: 450-650

value: Michael Snyder, Stanford

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


title: PolyA RNA-seq Srebf1-/- noTx

description: Sample 63

value: Srebp1 -/-

value: bone marrow derived macrophages


title: H4K5Ac ChIP-seq Srebf1-/- KLA24h

description:
formaldehyde cross-linked
Sample 49

value: KLA for 24 hours

tag: chip antibody

value: H4K5Ac (Vendor:Millipore, cat# 07-327, lot# 2524676)


title: polyA RNA-seq KLA-GW3965-18h

description: Sample 51

value: KLA,GW3965 (1uM) for 18 hours


title: ChIP-seq from K562 (ENCLB262OYC)

description:
https://www.encodeproject.org/experiments/ENCSR411UYA/
***************
biological replicate number: 2
technical replicate number: 1
description: MTA2 ChIP-seq on human K562
experiment encode accession: ENCSR411UYA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB262OYC
size range: 450-650

value: adult

value: 53 year

value: female

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

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


title: ChIP-seq from HEK293 (ENCLB556KVV)

description:
https://www.encodeproject.org/experiments/ENCSR224QDY/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF121 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR224QDY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB556KVV
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF121 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF121 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS258CDJ at ENCODE; https://www.encodeproject.org/ENCBS258CDJ/

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


title: ChIP-seq from HEK293 (ENCLB776GKQ)

description:
https://www.encodeproject.org/experiments/ENCSR224QDY/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF121 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR224QDY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB776GKQ
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

value: ENCBS557JBD at ENCODE; https://www.encodeproject.org/ENCBS557JBD/


title: eCLIP from K562 (ENCLB949LUH)

description:
https://www.encodeproject.org/experiments/ENCSR411IMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against FXR2
experiment encode accession: ENCSR411IMJ
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB949LUH
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
general protocol: https://www.encodeproject.org/documents/842f7424-5396-424a-a1a3-3f18707c3222/@@download/attachment/eCLIP_SOP_v1.P_110915.pdf
extraction method: see document

value: Control

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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

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

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


title: eCLIP from HepG2 (ENCLB584YTW)

description:
https://www.encodeproject.org/experiments/ENCSR214BZA/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against DDX59
experiment encode accession: ENCSR214BZA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR334OMC
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB584YTW
size range: 175-300

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS492SDY at ENCODE; https://www.encodeproject.org/ENCBS492SDY/

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: PolyA RNA-seq WT KLA1h

description: Sample 60

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 1 hours


title: H4K5Ac ChIP-seq Srebf1-/- KLA6h

description:
formaldehyde cross-linked
Sample 48

value: Srebp1 -/-

value: KLA for 6 hours

value: H4K5Ac (Vendor:Millipore, cat# 07-327, lot# 2524676)


title: ChIP-seq from K562 (ENCLB329LTQ)

description:
https://www.encodeproject.org/experiments/ENCSR410DWC/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-PYGO2 ChIP-seq on human K562
experiment encode accession: ENCSR410DWC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR298DKW
encode release date: 2016-01-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB329LTQ
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-PYGO2 fusion protein

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to PYGO2

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Kevin White, UChicago

value: ENCBS203NBV at ENCODE; https://www.encodeproject.org/ENCBS203NBV/

value: ENCODE dbxrefs Cellosaurus CVCL_AW40; http://web.expasy.org/cellosaurus/CVCL_AW40


title: ChIP-seq from K562 (ENCLB851MSF)

description:
https://www.encodeproject.org/experiments/ENCSR410DWC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-PYGO2 ChIP-seq on human K562
experiment encode accession: ENCSR410DWC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR298DKW
encode release date: 2016-01-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB851MSF
size range: 450-650

value: ENCBS102NQC at ENCODE; https://www.encodeproject.org/ENCBS102NQC/

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


title: eCLIP from HepG2 (ENCLB794ZGT)

description:
https://www.encodeproject.org/experiments/ENCSR214BZA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against DDX59
experiment encode accession: ENCSR214BZA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR334OMC
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB794ZGT
size range: 175-300

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS881CIF at ENCODE; https://www.encodeproject.org/ENCBS881CIF/

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 K562 (ENCLB808KPU)

description:
https://www.encodeproject.org/experiments/ENCSR224SND/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against DHX30
experiment encode accession: ENCSR224SND
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB808KPU
size range: 175-300

value: Control

value: immortalized cell line

value: adult

value: female

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

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


title: ChIP-seq from GM12878 (ENCLB745AQU)

description:
https://www.encodeproject.org/experiments/ENCSR408JQO/
***************
biological replicate number: 2
technical replicate number: 1
description: IRF3 ChIP-seq on human GM12878
experiment encode accession: ENCSR408JQO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB745AQU
size range: 450-650

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

value: unknown

value: Michael Snyder, Stanford

value: ENCBS965YSG at ENCODE; https://www.encodeproject.org/ENCBS965YSG/

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 HEK293 (ENCLB432PLO)

description:
https://www.encodeproject.org/experiments/ENCSR417VWF/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZEB2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR417VWF
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: ENCLB432PLO
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZEB2 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZEB2 under the control of a CMV promoter.

value: embryonic

value: ENCBS665JKR at ENCODE; https://www.encodeproject.org/ENCBS665JKR/

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


title: ChIP-seq from K562 (ENCLB811RXM)

description:
https://www.encodeproject.org/experiments/ENCSR213HBY/
***************
biological replicate number: 2
technical replicate number: 1
description: TOE1 ChIP-seq on human K562
experiment encode accession: ENCSR213HBY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB811RXM
size range: 450-650

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS906KIP at ENCODE; https://www.encodeproject.org/ENCBS906KIP/

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


title: ChIP-seq from K562 (ENCLB963MXU)

description:
https://www.encodeproject.org/experiments/ENCSR213HBY/
***************
biological replicate number: 1
technical replicate number: 1
description: TOE1 ChIP-seq on human K562
experiment encode accession: ENCSR213HBY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB963MXU
size range: 450-650

value: immortalized cell line

value: adult

value: female

value: ENCBS320BUL at ENCODE; https://www.encodeproject.org/ENCBS320BUL/


title: ChIP-seq from K562 (ENCLB890AJD)

description:
https://www.encodeproject.org/experiments/ENCSR400FSM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-POLR2H ChIP-seq on human K562
experiment encode accession: ENCSR400FSM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR776RXA
encode release date: 2016-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB890AJD

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-POLR2H fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to POLR2H

value: Kevin White, UChicago

value: ENCBS188WMP at ENCODE; https://www.encodeproject.org/ENCBS188WMP/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ93; http://web.expasy.org/cellosaurus/CVCL_GZ93


title: ChIP-seq from GM12878 (ENCLB482QLA)

description:
https://www.encodeproject.org/experiments/ENCSR408JQO/
***************
biological replicate number: 1
technical replicate number: 1
description: IRF3 ChIP-seq on human GM12878
experiment encode accession: ENCSR408JQO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB482QLA
size range: 450-650

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

value: unknown

value: Michael Snyder, Stanford

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

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: H4K5Ac ChIP-seq WT KLA6h

description:
formaldehyde cross-linked
Sample 44

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 6 hours

value: H4K5Ac (Vendor:Millipore, cat# 07-327, lot# 2524676)


title: H4K5Ac ChIP-seq Srebf1-/- noTx

description:
formaldehyde cross-linked
Sample 46

value: Srebp1 -/-

value: none (control)


title: eCLIP from K562 (ENCLB101GWM)

description:
https://www.encodeproject.org/experiments/ENCSR207DWI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against DDX6
experiment encode accession: ENCSR207DWI
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB101GWM
size range: 175-300

value: Control

value: immortalized cell line

value: adult

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS505ILK at ENCODE; https://www.encodeproject.org/ENCBS505ILK/

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: eCLIP from K562 (ENCLB952UUA)

description:
https://www.encodeproject.org/experiments/ENCSR206RXT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against AKAP8L
experiment encode accession: ENCSR206RXT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR550SGC
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB952UUA
size range: 175-300

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


title: ChIP-seq from GM12878 (ENCLB522JER)

description:
https://www.encodeproject.org/experiments/ENCSR398JTO/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human GM12878
experiment encode accession: ENCSR398JTO
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB522JER
size range: 450-650

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

value: unknown

value: Michael Snyder, Stanford

value: ENCBS276RPG at ENCODE; https://www.encodeproject.org/ENCBS276RPG/

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 K562 (ENCLB223NVK)

description:
https://www.encodeproject.org/experiments/ENCSR400FSM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-POLR2H ChIP-seq on human K562
experiment encode accession: ENCSR400FSM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR776RXA
encode release date: 2016-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB223NVK

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to POLR2H

value: adult

value: Kevin White, UChicago

value: ENCBS420IWT at ENCODE; https://www.encodeproject.org/ENCBS420IWT/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ93; http://web.expasy.org/cellosaurus/CVCL_GZ93


title: eCLIP from K562 (ENCLB288WMN)

description:
https://www.encodeproject.org/experiments/ENCSR206RXT/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against AKAP8L
experiment encode accession: ENCSR206RXT
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR550SGC
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB288WMN
size range: 175-300

value: 53 year

value: female

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/


title: H4K5Ac ChIP-seq WT KLA1h

description:
formaldehyde cross-linked
Sample 43

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 1 hours

value: H4K5Ac (Vendor:Millipore, cat# 07-327, lot# 2524676)


title: p65 ChIP-seq Srebf1-/- KLA24h

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 41

value: Srebp1 -/-

value: KLA for 24 hours

value: p65 (Vendor:Santa Cruz, cat# sc-372, lot# A0314)


title: eCLIP from K562 (ENCLB333CPS)

description:
https://www.encodeproject.org/experiments/ENCSR200DKE/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against MTPAP
experiment encode accession: ENCSR200DKE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR927XDB
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB333CPS
size range: 175-300

value: MTPAP

value: immortalized cell line

value: adult

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

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

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


title: H4K5Ac ChIP-seq WT noTx

description:
formaldehyde cross-linked
Sample 42

value: none (control)


title: H4K5Ac ChIP-seq Srebf1-/- KLA1h

description:
formaldehyde cross-linked
Sample 47


title: eCLIP from K562 (ENCLB326ZKU)

description:
https://www.encodeproject.org/experiments/ENCSR399CBP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against LIN28B
experiment encode accession: ENCSR399CBP
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB326ZKU
size range: 175-300

value: Control

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS081NLE at ENCODE; https://www.encodeproject.org/ENCBS081NLE/


title: eCLIP from K562 (ENCLB241IUV)

description:
https://www.encodeproject.org/experiments/ENCSR200DKE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against MTPAP
experiment encode accession: ENCSR200DKE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR927XDB
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB241IUV
size range: 175-300

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

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


title: H4K5Ac ChIP-seq WT KLA24h

description:
formaldehyde cross-linked
Sample 45

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 24 hours

value: H4K5Ac (Vendor:Millipore, cat# 07-327, lot# 2524676)


title: p65 ChIP-seq Srebf1-/- KLA6h

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 40

value: Srebp1 -/-

value: KLA for 6 hours

value: p65 (Vendor:Santa Cruz, cat# sc-372, lot# A0314)


title: p65 ChIP-seq Srebf1-/- noTx

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 38


title: p65 ChIP-seq Srebf1-/- KLA1h

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 39

value: KLA for 1 hours


title: ChIP-seq from K562 (ENCLB102PME)

description:
https://www.encodeproject.org/experiments/ENCSR395HWC/
***************
biological replicate number: 1
technical replicate number: 1
description: IKZF1 ChIP-seq on human K562
experiment encode accession: ENCSR395HWC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-04-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB102PME
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: adult

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: eCLIP from K562 (ENCLB452GBQ)

description:
https://www.encodeproject.org/experiments/ENCSR197INS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against PPIL4
experiment encode accession: ENCSR197INS
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR346IHS
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB452GBQ
size range: 175-300

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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


title: ChIP-seq from K562 (ENCLB877SBR)

description:
https://www.encodeproject.org/experiments/ENCSR395HWC/
***************
biological replicate number: 2
technical replicate number: 1
description: IKZF1 ChIP-seq on human K562
experiment encode accession: ENCSR395HWC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-04-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB877SBR
size range: 450-650

value: ENCBS048GNZ at ENCODE; https://www.encodeproject.org/ENCBS048GNZ/

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


title: p65 ChIP-seq WT KLA24h

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 37

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 24 hours

value: p65 (Vendor:Santa Cruz, cat# sc-372, lot# A0314)


title: eCLIP from K562 (ENCLB526REQ)

description:
https://www.encodeproject.org/experiments/ENCSR197INS/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against PPIL4
experiment encode accession: ENCSR197INS
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR346IHS
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB526REQ
size range: 175-300

value: immortalized cell line

value: adult

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


title: eCLIP from HepG2 (ENCLB381YSU)

description:
https://www.encodeproject.org/experiments/ENCSR197LHH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against DKC1
experiment encode accession: ENCSR197LHH
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB381YSU
size range: 175-300

value: Control

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

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

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

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


title: ChIP-seq from MCF-7 (ENCLB515SII)

description:
https://www.encodeproject.org/experiments/ENCSR391KQC/
***************
biological replicate number: 2
technical replicate number: 1
description: MTA3 ChIP-seq on human MCF-7
experiment encode accession: ENCSR391KQC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB515SII
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: ENCBS200IWR at ENCODE; https://www.encodeproject.org/ENCBS200IWR/

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

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


title: ChIP-seq from MCF-7 (ENCLB442SWD)

description:
https://www.encodeproject.org/experiments/ENCSR391KQC/
***************
biological replicate number: 1
technical replicate number: 1
description: MTA3 ChIP-seq on human MCF-7
experiment encode accession: ENCSR391KQC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB442SWD
size range: 450-650

value: immortalized cell line

value: adult

value: ENCBS547AXB at ENCODE; https://www.encodeproject.org/ENCBS547AXB/


title: ChIP-seq from MCF-7 (ENCLB203VJE)

description:
https://www.encodeproject.org/experiments/ENCSR391JII/
***************
biological replicate number: 3
technical replicate number: 1
description: RCOR1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR391JII
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB203VJE
size range: 450-650

value: ENCBS747ZRJ at ENCODE; https://www.encodeproject.org/ENCBS747ZRJ/


title: ChIP-seq from GM12878 (ENCLB793DEG)

description:
https://www.encodeproject.org/experiments/ENCSR398JTO/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human GM12878
experiment encode accession: ENCSR398JTO
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB793DEG
size range: 450-650

value: Control

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

value: unknown

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: eCLIP from K562 (ENCLB774LDT)

description:
https://www.encodeproject.org/experiments/ENCSR195IWB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against DDX24
experiment encode accession: ENCSR195IWB
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB774LDT
size range: 175-300

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

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

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

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

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


title: ChIP-seq from MCF-7 (ENCLB054TEA)

description:
https://www.encodeproject.org/experiments/ENCSR391JII/
***************
biological replicate number: 4
technical replicate number: 1
description: RCOR1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR391JII
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB054TEA
size range: 450-650

value: immortalized cell line

value: adult

value: 69 year

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

value: ENCBS609QTY at ENCODE; https://www.encodeproject.org/ENCBS609QTY/

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

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


title: eCLIP from K562 (ENCLB160YSI)

description:
https://www.encodeproject.org/experiments/ENCSR196INN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against RBM15
experiment encode accession: ENCSR196INN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR454EER
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB160YSI
size range: 175-300

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


title: eCLIP from HepG2 (ENCLB439DNZ)

description:
https://www.encodeproject.org/experiments/ENCSR388VKV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against SMNDC1
experiment encode accession: ENCSR388VKV
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB439DNZ
size range: 175-300

value: Control

value: child

value: 15 year

value: male

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


title: H3K4me2 ChIP-seq Srebf1-/- KLA6h

description:
formaldehyde cross-linked
Sample 32

value: Srebp1 -/-

value: bone marrow derived macrophages

value: KLA for 6 hours

value: H3K4me2 (Vendor:Millipore, cat# 07030, lot#DAM1724042)


title: eCLIP from HepG2 (ENCLB565DNA)

description:
https://www.encodeproject.org/experiments/ENCSR192PUP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against LARP4
experiment encode accession: ENCSR192PUP
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB565DNA
size range: 175-300

value: immortalized cell line

value: Gene Yeo, UCSD

value: ENCBS881CIF at ENCODE; https://www.encodeproject.org/ENCBS881CIF/

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


title: eCLIP from K562 (ENCLB327TOV)

description:
https://www.encodeproject.org/experiments/ENCSR196INN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against RBM15
experiment encode accession: ENCSR196INN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR454EER
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB327TOV
size range: 175-300

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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: H3K4me2 ChIP-seq Srebf1-/- KLA24h

description:
formaldehyde cross-linked
Sample 33

value: KLA for 24 hours


title: ChIP-seq from GM12878 (ENCLB373YZX)

description:
https://www.encodeproject.org/experiments/ENCSR189YYK/
***************
biological replicate number: 2
technical replicate number: 1
description: ZBTB40 ChIP-seq on human GM12878
experiment encode accession: ENCSR189YYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB373YZX
size range: 450-650

value: unknown

value: Michael Snyder, Stanford

value: ENCBS488GLI at ENCODE; https://www.encodeproject.org/ENCBS488GLI/

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: H3K4me2 ChIP-seq Srebf1-/- KLA1h

description:
formaldehyde cross-linked
Sample 31

value: Srebp1 -/-

value: bone marrow derived macrophages

value: KLA for 1 hours

value: H3K4me2 (Vendor:Millipore, cat# 07030, lot#DAM1724042)


title: ChIP-seq from K562 (ENCLB464RQG)

description:
https://www.encodeproject.org/experiments/ENCSR388QZF/
***************
biological replicate number: 2
technical replicate number: 1
description: POLR2A ChIP-seq on human K562
experiment encode accession: ENCSR388QZF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB464RQG
size range: 450-650

value: immortalized cell line

value: adult

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


title: eCLIP from HepG2 (ENCLB327UQW)

description:
https://www.encodeproject.org/experiments/ENCSR182AEG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against AGGF1
experiment encode accession: ENCSR182AEG
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB327UQW
size range: 175-300

value: Control

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Gene Yeo, UCSD

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

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 GM12878 (ENCLB317MFR)

description:
https://www.encodeproject.org/experiments/ENCSR189YYK/
***************
biological replicate number: 1
technical replicate number: 1
description: ZBTB40 ChIP-seq on human GM12878
experiment encode accession: ENCSR189YYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB317MFR
size range: 450-650

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS681NDP at ENCODE; https://www.encodeproject.org/ENCBS681NDP/

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


title: eCLIP from K562 (ENCLB864BOZ)

description:
https://www.encodeproject.org/experiments/ENCSR180EJY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against DDX55
experiment encode accession: ENCSR180EJY
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB864BOZ
size range: 175-300

value: immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

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: H3K4me2 ChIP-seq WT KLA24h

description:
formaldehyde cross-linked
Sample 29

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 24 hours

value: H3K4me2 (Vendor:Millipore, cat# 07030, lot#DAM1724042)


title: eCLIP from HepG2 (ENCLB944HKY)

description:
https://www.encodeproject.org/experiments/ENCSR161TFX/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against UCHL5
experiment encode accession: ENCSR161TFX
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB944HKY
size range: 175-300

value: Control

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/

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 (ENCLB118ODS)

description:
https://www.encodeproject.org/experiments/ENCSR387UWP/
***************
biological replicate number: 2
technical replicate number: 1
description: HDAC1 ChIP-seq on human K562
experiment encode accession: ENCSR387UWP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB118ODS
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: adult

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

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

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


title: H3K4me2 ChIP-seq WT KLA1h

description:
formaldehyde cross-linked
Sample 27

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 1 hours

value: H3K4me2 (Vendor:Millipore, cat# 07030, lot#DAM1724042)


title: H3K4me2 ChIP-seq WT KLA6h

description:
formaldehyde cross-linked
Sample 28

value: KLA for 6 hours


title: eCLIP from K562 (ENCLB246GUQ)

description:
https://www.encodeproject.org/experiments/ENCSR387RGT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against IGF2BP2
experiment encode accession: ENCSR387RGT
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB246GUQ
size range: 175-300

value: Control

value: Gene Yeo, UCSD

value: ENCBS978JIM at ENCODE; https://www.encodeproject.org/ENCBS978JIM/

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

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


title: eCLIP from HepG2 (ENCLB372IFN)

description:
https://www.encodeproject.org/experiments/ENCSR151MPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against DHX30
experiment encode accession: ENCSR151MPZ
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-08-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB372IFN
size range: 175-300

value: immortalized cell line

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/

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 (ENCLB942RWU)

description:
https://www.encodeproject.org/experiments/ENCSR387UWP/
***************
biological replicate number: 1
technical replicate number: 1
description: HDAC1 ChIP-seq on human K562
experiment encode accession: ENCSR387UWP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB942RWU
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: ENCBS293ZDP at ENCODE; https://www.encodeproject.org/ENCBS293ZDP/

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


title: eCLIP from HepG2 (ENCLB523ZOX)

description:
https://www.encodeproject.org/experiments/ENCSR391GLS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against CSTF2T
experiment encode accession: ENCSR391GLS
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB523ZOX
size range: 175-300

value: Control

value: immortalized cell line

value: Gene Yeo, UCSD

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


title: H3K4me2 ChIP-seq WT noTx

description:
formaldehyde cross-linked
Sample 26

value: Srebp1 WT

value: bone marrow derived macrophages

value: none (control)

value: H3K4me2 (Vendor:Millipore, cat# 07030, lot#DAM1724042)


title: ChIP-seq from K562 (ENCLB045WLS)

description:
https://www.encodeproject.org/experiments/ENCSR387MCX/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-IRF1 tagged K562 cell line.
experiment encode accession: ENCSR387MCX
assay title: ChIP-seq
encode release date: 2015-12-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB045WLS
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-IRF1 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to IRF1

value: Kevin White, UChicago

value: ENCBS329CYL at ENCODE; https://www.encodeproject.org/ENCBS329CYL/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW28; http://web.expasy.org/cellosaurus/CVCL_AW28


title: H3K4me2 ChIP-seq Srebf1-/- noTx

description:
formaldehyde cross-linked
Sample 30

value: Srebp1 -/-


title: ChIP-seq from HEK293T (ENCLB552KLV)

description:
https://www.encodeproject.org/experiments/ENCSR386FAB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human HEK293T
experiment encode accession: ENCSR386FAB
assay title: ChIP-seq
encode release date: 2016-11-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB552KLV
size range: 450-650

source_name: Homo sapiens HEK293T immortalized cell line

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS582KZL at ENCODE; https://www.encodeproject.org/ENCBS582KZL/

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


title: eCLIP from HepG2 (ENCLB696YVF)

description:
https://www.encodeproject.org/experiments/ENCSR141OIM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against DDX6
experiment encode accession: ENCSR141OIM
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR099KAK
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB696YVF
size range: 175-300

value: immortalized cell line

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/

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 (ENCLB040QQO)

description:
https://www.encodeproject.org/experiments/ENCSR388QZF/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human K562
experiment encode accession: ENCSR388QZF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB040QQO
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: ENCBS576ESJ at ENCODE; https://www.encodeproject.org/ENCBS576ESJ/

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

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


title: eCLIP from HepG2 (ENCLB489ZHO)

description:
https://www.encodeproject.org/experiments/ENCSR141OIM/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against DDX6
experiment encode accession: ENCSR141OIM
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR099KAK
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB489ZHO
size range: 175-300

value: immortalized cell line

value: ENCBS492SDY at ENCODE; https://www.encodeproject.org/ENCBS492SDY/


title: ChIP-seq from HEK293T (ENCLB939BXA)

description:
https://www.encodeproject.org/experiments/ENCSR386FAB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human HEK293T
experiment encode accession: ENCSR386FAB
assay title: ChIP-seq
encode release date: 2016-11-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB939BXA
size range: 450-650

value: Control

value: embryonic

value: female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS323RYE at ENCODE; https://www.encodeproject.org/ENCBS323RYE/

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


title: RNApol2 ChIP-seq Srebf1-/- KLA24h

description:
formaldehyde cross-linked
Sample 25

value: Srebp1 -/-

value: bone marrow derived macrophages

value: KLA for 24 hours

value: RNApol2 (Santa Cruz sc-899X, Lot# L1510, Abcam ab26721, lot:GR84088-1)


title: RNApol2 ChIP-seq Srebf1-/- noTx

description:
formaldehyde cross-linked
Sample 22

value: none (control)


title: eCLIP from HepG2 (ENCLB670XGP)

description:
https://www.encodeproject.org/experiments/ENCSR135VMS/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against LSM11
experiment encode accession: ENCSR135VMS
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR114XBO
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB670XGP
size range: 175-300

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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 (ENCLB400ICV)

description:
https://www.encodeproject.org/experiments/ENCSR135VMS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against LSM11
experiment encode accession: ENCSR135VMS
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR114XBO
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB400ICV
size range: 175-300

value: immortalized cell line

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/


title: ChIP-seq from K562 (ENCLB212UPD)

description:
https://www.encodeproject.org/experiments/ENCSR385AHH/
***************
biological replicate number: 2
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: ENCLB212UPD
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: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS953HJY at ENCODE; https://www.encodeproject.org/ENCBS953HJY/

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: RNApol2 ChIP-seq WT KLA24h

description:
formaldehyde cross-linked
Sample 21

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 24 hours

value: RNApol2 (Santa Cruz sc-899X, Lot# L1510, Abcam ab26721, lot:GR84088-1)


title: eCLIP from HepG2 (ENCLB092SNT)

description:
https://www.encodeproject.org/experiments/ENCSR130TOJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against QKI
experiment encode accession: ENCSR130TOJ
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB092SNT
size range: 175-300

value: Control

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

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 K562 (ENCLB354LPS)

description:
https://www.encodeproject.org/experiments/ENCSR133QEA/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SF3B1
experiment encode accession: ENCSR133QEA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR496UBM
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB354LPS
size range: 175-300

value: immortalized cell line

value: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

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

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


title: ChIP-seq from MCF-7 (ENCLB943QXQ)

description:
https://www.encodeproject.org/experiments/ENCSR382WLL/
***************
biological replicate number: 1
technical replicate number: 1
description: ELK1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR382WLL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-02-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB943QXQ
size range: 450-650

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

value: 69 year

value: breast cancer (adenocarcinoma)

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: RNApol2 ChIP-seq WT KLA1h

description:
formaldehyde cross-linked
Sample 19

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 1 hours

value: RNApol2 (Santa Cruz sc-899X, Lot# L1510, Abcam ab26721, lot:GR84088-1)


title: RNApol2 ChIP-seq WT KLA6h

description:
formaldehyde cross-linked
Sample 20

value: KLA for 6 hours


title: ChIP-seq from MCF-7 (ENCLB335GWF)

description:
https://www.encodeproject.org/experiments/ENCSR382WLL/
***************
biological replicate number: 3
technical replicate number: 1
description: ELK1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR382WLL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-02-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB335GWF
size range: 450-650

value: immortalized cell line

value: adult

value: female

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


title: RNApol2 ChIP-seq WT noTx

description:
formaldehyde cross-linked
Sample 18

value: none (control)


title: H3K27Ac ChIP-seq Srebf1-/- KLA24h

description:
formaldehyde cross-linked
Sample 17

value: Srebp1 -/-

value: KLA for 24 hours

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


title: ChIP-seq from HEK293 (ENCLB333RHS)

description:
https://www.encodeproject.org/experiments/ENCSR382GSF/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-INSM2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR382GSF
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: ENCLB333RHS
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-INSM2 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-INSM2 under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS748WVG at ENCODE; https://www.encodeproject.org/ENCBS748WVG/

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


title: RNApol2 ChIP-seq Srebf1-/- KLA6h

description:
formaldehyde cross-linked
Sample 24

value: bone marrow derived macrophages


title: RNApol2 ChIP-seq Srebf1-/- KLA1h

description:
formaldehyde cross-linked
Sample 23

value: KLA for 1 hours

value: RNApol2 (Santa Cruz sc-899X, Lot# L1510, Abcam ab26721, lot:GR84088-1)


title: ChIP-seq from K562 (ENCLB035HCQ)

description:
https://www.encodeproject.org/experiments/ENCSR382AIB/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-DDX20 ChIP-seq on human K562
experiment encode accession: ENCSR382AIB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR978IXJ
encode release date: 2016-02-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB035HCQ
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-DDX20 fusion protein

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to DDX20

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Kevin White, UChicago

value: ENCBS216ZMH at ENCODE; https://www.encodeproject.org/ENCBS216ZMH/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW17; http://web.expasy.org/cellosaurus/CVCL_AW17


title: ChIP-seq from HEK293 (ENCLB036GOJ)

description:
https://www.encodeproject.org/experiments/ENCSR382GSF/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-INSM2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR382GSF
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: ENCLB036GOJ
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-INSM2 under the control of a CMV promoter.

value: female

value: ENCBS121NOF at ENCODE; https://www.encodeproject.org/ENCBS121NOF/


title: ChIP-seq from HEK293 (ENCLB070UQM)

description:
https://www.encodeproject.org/experiments/ENCSR125DNC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF394 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR125DNC
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB070UQM
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF394 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF394 under the control of a CMV promoter.

value: unknown

value: embryonic

value: Michael Snyder, Stanford

value: ENCBS906WJT at ENCODE; https://www.encodeproject.org/ENCBS906WJT/


title: ChIP-seq from HEK293 (ENCLB582FEP)

description:
https://www.encodeproject.org/experiments/ENCSR125DNC/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF394 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR125DNC
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB582FEP
size range: 450-650

value: ENCBS890IKR at ENCODE; https://www.encodeproject.org/ENCBS890IKR/

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


title: ChIP-seq from K562 (ENCLB229IMX)

description:
https://www.encodeproject.org/experiments/ENCSR130HEG/
***************
biological replicate number: 2
technical replicate number: 1
description: COPS2 ChIP-seq on human K562
experiment encode accession: ENCSR130HEG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-09-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB229IMX
size range: 450-650

value: immortalized cell line

value: adult

value: ENCBS538DYC at ENCODE; https://www.encodeproject.org/ENCBS538DYC/


title: ChIP-seq from K562 (ENCLB481LNJ)

description:
https://www.encodeproject.org/experiments/ENCSR130HEG/
***************
biological replicate number: 1
technical replicate number: 1
description: COPS2 ChIP-seq on human K562
experiment encode accession: ENCSR130HEG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2016-09-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB481LNJ
size range: 450-650

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS357NWO at ENCODE; https://www.encodeproject.org/ENCBS357NWO/


title: eCLIP from K562 (ENCLB203AIU)

description:
https://www.encodeproject.org/experiments/ENCSR133QEA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SF3B1
experiment encode accession: ENCSR133QEA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR496UBM
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB203AIU
size range: 175-300

value: Gene Yeo, UCSD

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

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

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

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


title: ChIP-seq from K562 (ENCLB448FFW)

description:
https://www.encodeproject.org/experiments/ENCSR382AIB/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-DDX20 ChIP-seq on human K562
experiment encode accession: ENCSR382AIB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR978IXJ
encode release date: 2016-02-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB448FFW
size range: 450-650

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to DDX20

value: female

value: Kevin White, UChicago

value: ENCBS196WDN at ENCODE; https://www.encodeproject.org/ENCBS196WDN/

value: ENCODE dbxrefs Cellosaurus CVCL_AW17; http://web.expasy.org/cellosaurus/CVCL_AW17


title: eCLIP from K562 (ENCLB055QBA)

description:
https://www.encodeproject.org/experiments/ENCSR121GQH/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SERBP1
experiment encode accession: ENCSR121GQH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR752YLF
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB055QBA
size range: 175-300

value: ENCBS039CVO at ENCODE; https://www.encodeproject.org/ENCBS039CVO/


title: H3K27Ac ChIP-seq Srebf1-/- KLA1h

description:
formaldehyde cross-linked
Sample 15

value: Srebp1 -/-

value: bone marrow derived macrophages

value: KLA for 1 hours

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


title: ChIP-seq from HEK293 (ENCLB650ECO)

description:
https://www.encodeproject.org/experiments/ENCSR381VYR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZFP69B ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR381VYR
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: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB650ECO
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZFP69B fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZFP69B under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS114DPO at ENCODE; https://www.encodeproject.org/ENCBS114DPO/

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


title: ChIP-seq from HEK293 (ENCLB821ZCY)

description:
https://www.encodeproject.org/experiments/ENCSR381VYR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZFP69B ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR381VYR
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: 2016-10-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB821ZCY
size range: 450-650

value: ENCBS386IWZ at ENCODE; https://www.encodeproject.org/ENCBS386IWZ/


title: H3K27Ac ChIP-seq WT KLA24h

description:
formaldehyde cross-linked
Sample 13

value: Srebp1 WT

value: KLA for 24 hours


title: ChIP-seq from HEK293 (ENCLB778HJE)

description:
https://www.encodeproject.org/experiments/ENCSR121EZR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF71 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR121EZR
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB778HJE
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF71 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF71 under the control of a CMV promoter.

value: female

value: ENCBS549SBY at ENCODE; https://www.encodeproject.org/ENCBS549SBY/


title: H3K27Ac ChIP-seq Srebf1-/- noTx

description:
formaldehyde cross-linked
Sample 14

value: Srebp1 -/-

value: none (control)


title: eCLIP from K562 (ENCLB537XZW)

description:
https://www.encodeproject.org/experiments/ENCSR121GQH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SERBP1
experiment encode accession: ENCSR121GQH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR752YLF
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB537XZW
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS175JIH at ENCODE; https://www.encodeproject.org/ENCBS175JIH/

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: eCLIP from HepG2 (ENCLB787ICJ)

description:
https://www.encodeproject.org/experiments/ENCSR114XBO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against LSM11
experiment encode accession: ENCSR114XBO
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB787ICJ
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

value: Control

value: immortalized cell line

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS621TAB at ENCODE; https://www.encodeproject.org/ENCBS621TAB/

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

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


title: H3K27Ac ChIP-seq WT noTx

description:
formaldehyde cross-linked
Sample 10

source_name: bone marrow derived macrophages

value: Srebp1 WT

value: bone marrow derived macrophages

value: none (control)

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


title: ChIP-seq from K562 (ENCLB959EQZ)

description:
https://www.encodeproject.org/experiments/ENCSR375CYS/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-NFE2 tagged K562 cell line.
experiment encode accession: ENCSR375CYS
assay title: ChIP-seq
encode release date: 2016-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB959EQZ

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-NFE2 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NFE2

value: adult

value: 53 year

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS903THP at ENCODE; https://www.encodeproject.org/ENCBS903THP/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ90; http://web.expasy.org/cellosaurus/CVCL_GZ90


title: LXR ChIP-seq KLA24h

description:
disuccinimidyl glutarate-formaldehyde cross-linked
Sample 9

value: KLA for 24 hours

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


title: eCLIP from K562 (ENCLB938TSS)

description:
https://www.encodeproject.org/experiments/ENCSR365NVO/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against TRA2A
experiment encode accession: ENCSR365NVO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR619RLC
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB938TSS
size range: 175-300

value: immortalized cell line

value: Gene Yeo, UCSD

value: ENCBS110VVJ at ENCODE; https://www.encodeproject.org/ENCBS110VVJ/

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: H3K27Ac ChIP-seq WT KLA6h

description:
formaldehyde cross-linked
Sample 12

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 6 hours

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


title: ChIP-seq from HEK293 (ENCLB423HYM)

description:
https://www.encodeproject.org/experiments/ENCSR106EBH/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF366 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR106EBH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB423HYM
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF366 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF366 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS594XEQ at ENCODE; https://www.encodeproject.org/ENCBS594XEQ/

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


title: Chromatin 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: Chr-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: Chromatin 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

value: Chromatin fraction

tag: molecule subtype

value: Chromatin RNA


title: eCLIP from HepG2 (ENCLB608PZK)

description:
https://www.encodeproject.org/experiments/ENCSR373ODC/
***************
biological replicate number: 1
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: ENCLB608PZK
size range: 175-300

tag: antibody

tag: line

value: immortalized cell line

value: child

value: 15 year

value: male

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: ChIP-seq from HEK293 (ENCLB962TWM)

description:
https://www.encodeproject.org/experiments/ENCSR106EBH/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF366 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR106EBH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB962TWM
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF366 under the control of a CMV promoter.

tag: biosample encode accession

tag: dev stage

value: embryonic

value: unknown

value: female

value: ENCBS384PIE at ENCODE; https://www.encodeproject.org/ENCBS384PIE/


title: eCLIP from K562 (ENCLB985UUR)

description:
https://www.encodeproject.org/experiments/ENCSR365NVO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against TRA2A
experiment encode accession: ENCSR365NVO
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR619RLC
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB985UUR
size range: 175-300

value: adult

tag: age

value: 53 year

tag: Sex

value: chronic myelogenous leukemia (CML)

value: ENCBS774KGY at ENCODE; https://www.encodeproject.org/ENCBS774KGY/

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: eCLIP from K562 (ENCLB470YIY)

description:
https://www.encodeproject.org/experiments/ENCSR119AFY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against FASTKD2
experiment encode accession: ENCSR119AFY
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB470YIY
size range: 175-300

value: Control

value: immortalized cell line

tag: health state

tag: passage number

value: Gene Yeo, UCSD

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


title: ChIP-seq from HEK293 (ENCLB896ANU)

description:
https://www.encodeproject.org/experiments/ENCSR121EZR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF71 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR121EZR
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB896ANU
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF71 under the control of a CMV promoter.

tag: lab

value: Michael Snyder, Stanford

tag: link

value: ENCBS592NTV at ENCODE; https://www.encodeproject.org/ENCBS592NTV/

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


title: H3K27Ac ChIP-seq WT KLA1h

description:
formaldehyde cross-linked
Sample 11

tag: strain background

tag: genotype/variation

value: Srebp1 WT

value: bone marrow derived macrophages

value: KLA for 1 hours

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