title: WT-2

description: ribosome protected RNA


title: H3K27me3_WT_rep2

status: Public on Jan 05 2017

type: SRA

city: Göttingen, Niedersachsen

first: Steven

middle: A

last: Johnsen

state: Niedersachsen

address: Robert Koch Strasse 40

department: Clinic for General, Visceral and Pediatric Surgery

country: Germany

institute: University Medical Center Göttingen

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 1.0.0
peaks were called using MACS version 1.0.0 with the following setting: Effective Genome Size (Mouse (mm9)), Tag size (25), Bandwidth (300), Pvalue (0.00001), Shift size (125).
Coverage was determined by normalizing the filtered reads per hundred million
bigwig files were generated using Wig/BedGraph-to-bigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated from wig files using Wig/BedGraph-to-bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

growth_protocol: Primary MEFs were cultured in high-glucose GlutaMAX™-DMEM (Invitrogen) supplemented with 10% FBS Superior (Biochrom), 1% penicillin–streptomycin (Sigma-Aldrich), and 1% non-essential amino acids (Invitrogen) at 37°C, 5% CO2.

extract_protocol:
Cells were crosslinked with 1% Formaldehyde for 10  minutes and quenched with 1.25 M Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.

treatment_protocol: For RNF40 knockout, MEFs were passaged into GlutaMAX™-DMEM supplemented with 250nM of 4-hydroxitamoxifen (4-OHT) for 5 days, and then cultured for 3 days without 4-OHT.

tag: genotype

tag: passages

tag: chip antibody

value: H3K27me3 (Diagenode, pAb-195-050)


title: 8m2

city: Shanghai

first: Cheng

last: Yang

address: 227 Chongqing South Road, Luwan District

country: China

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using EasyAlign version 3.2.
Peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg19
Supplementary_files_format_and_content: wig files

organism: Homo sapiens

source_name: Memory CD8+ T cells, triggered through CD3/CD28 signaling for 4 hr

growth_protocol: Freshly sorted naive and memory CD8 T cells were cultured in R10 medium (RPMI 1640 + 10% fetal bovine serum + 100 U/mL Penicillin/Streptomycin) (GIBCO) at a cell concentration of 2×106 /mL in 96-U-bottom plates.

extract_protocol:
Histone-DNA complexes were isolated with a p300-specific antibody
Libraries were prepared according to Illumina's instructions accompanying the TruSeq_DNA_SamplePrep Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells stimulated with anti-CD3 and anti-CD28 mAbs coupled magnetic beads (Invitrogen) at a cell-bead ratio of 1:1 for 0 or 4 hr, after that, cells were washed twice with PBS, then suspended with PBS supplemented with formaldehyde (final concentration of 1%), and incubated at 37℃ for 10 min.

tag: tissue

value: Peripheral Blood

tag: cell type

value: Memory CD8+ T cells

tag: cell markers

value: anti-p300 (Santa Cruz, #sc-585X)


title: 8m1

source_name: Memory CD8+ T cells at rest


title: 8n2

source_name: Naïve CD8+ T cells, triggered through CD3/CD28 signaling for 4 hr

value: Naive CD8+ T cells


title: 8n1

source_name: Naïve CD8+ T cells at rest


title: mapkkk5_mock_rep3

city: Kyoto

first: Akira

last: Mine

state: Kyoto

address: Kitashirakawaoiwake-cho

department: Graduate School of Agriculture

country: Japan

institute: Kyoto university

description: replicate 3

library_source: transcriptomic

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the Arabidopsis genome using splice-aware read aligner TopHat (version 2.0.10) with the parameters -p 10 -a 10 -g 10 --library-type fr-firststrand -G TAIR10_GFF3_genes.gff and transformed into a count per gene per library by using HTSeq (version 0.6.1) with the parameters -s reverse -f bam -t exon.
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were sterilized and germinated in MGRL medium containing 0.2% agarose and 1% sucrose. Seedlings were grown for 8 days in a 16 hours light/ 8 hours dark cycle at 22°C (light) or 20°C (dark).

extract_protocol:
Total RNAs were extracted using TRIzol (Invitrogen), followed by Dnase I (Roche) treatment.
RNA libraries were prepared from 1 μg of total RNA. Poly A enrichment and library preparation were performed with NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: The seedlings were pre-incubated in liquid MGRL medium for 3 hours and then treated with 40 μM chitin.

tag: treatment

value: mock


title: mapkkk5_chitin_rep3

description: replicate 3

value: chitin


title: WT rep1

city: Kansas City

first: Agne

last: Kozlovskaja-Gumbriene

state: MO

country: USA

institute: Stowers Institute for Medical Research

data_processing:
Illumina CASAVA-1.8.2 software used for basecalling.
Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters -p 8 --transcriptome-index -G -o --no-coverage-search
The fragments per kilobase of transcript per million mapped reads (FPKM) values were generated using Cufflinks version 2.2.1 with parameters -p 4 -g -o.
Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters -m intersection-nonempty -s no -f bam.
Genome_build: danRer10 from UCSC
Supplementary_files_format_and_content: Two tab-delimited text files: one includes raw counts of sequencing reads for each Sample, one includes FPKM values for each Sample.

organism: Danio rerio

source_name: dissociated embryo tails

growth_protocol: Zebrafish embryos were raised for 36 hours post fertizilation in the 28.5C incubator.

extract_protocol:
Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2302) was used with 13 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Zebrafish embryos positive for GFP were selected.

tag: strain

value: dissociated embryo tails

tag: age

value: 36 hours post fertilization

value: wild type


title: HepG2 cells expressing ATP7B H1069Q and treated with JNK Inhibitor, biological rep1

status: Public on Jan 04 2017

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

description:
Adeno ATP7BH1069Q_JNKInh_1
Gene expression data from cells infected with adenovirus expressing ATP7B H1069Q -GFP and treated with 1uM SP600125 (Sigma Aldrich)
cell line derived from the liver tissue of a Caucasian American male

data_processing:
Reads were aligned and assigned to Human Gencode release 19 transcripts and genes by using RSEM version 1.2.19 with standard parameters (Li & Dewey, 2011).
Genome_build: Human Gencode release 19
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each Sample

source_name: HepG2 cells expressing ATP7B H1069Q and treated with JNKInhibitor

growth_protocol: The cells were grown for 72 hours at 37°C in 5% CO2

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).
Total RNA (500 ng) from each sample was prepared using TruSeq RNA sample prep reagents (Illumina, San Diego, CA, USA) according to manufacturer's instructions
The amplified fragmented cDNA of ∼200 bp in size were sequenced in paired-end mode using the HiSeq 2000 (Illumina) with a read length of 2×100 bp

treatment_protocol: The cells, after 24 hour of plating, were infected with adenovirus. The cells infected were grown for 48 hours. Cells were treated with 1uM JNKinhibitor (SP600125, Sigma Aldrich) or 5uM p38inhibitor (SB202190, Sigma Aldrich) for 24 hours. After the treatment, the cells were scraped with a lysis buffer (Qiagen)

tag: cell line

value: HepG2 hepatocellular carcinoma cell line

tag: gender

value: male

tag: genotype/variation

value: overexpressing ATP7B H1069Q

tag: agent

value: JNK Inhibitor


title: HepG2 cells expressing ATP7B WT, biological rep3

description:
Adeno ATP7BWT3
Gene expression data from cells infected with adenovirus expressing ATP7B wt -GFP
cell line derived from the liver tissue of a Caucasian American male

source_name: HepG2 cells expressing ATP7B WT

value: overexpressing ATP7B WT


title: HepG2 cells expressing ATP7B H1069Q and treated with p38 MAPK Inhibitor, biological rep1

description:
Adeno ATP7BH1069Q_p38Inh_1
Gene expression data from cells infected with adenovirus expressing ATP7B H1069Q -GFP and treated with 5uM SP202190 (Sigma Aldrich)
cell line derived from the liver tissue of a Caucasian American male

value: p38 MAPK Inhibitor


title: HepG2 cells expressing ATP7B H1069Q and treated with JNK Inhibitor, biological rep2

description:
Adeno ATP7BH1069Q_JNKInh_2
Gene expression data from cells infected with adenovirus expressing ATP7B H1069Q -GFP and treated with 1uM SP600125 (Sigma Aldrich)
cell line derived from the liver tissue of a Caucasian American male


title: HepG2 cells expressing ATP7B H1069Q and treated with p38 MAPK Inhibitor, biological rep3

description:
Adeno ATP7BH1069Q_p38Inh_3
Gene expression data from cells infected with adenovirus expressing ATP7B H1069Q -GFP and treated with 5uM SP202190 (Sigma Aldrich)
cell line derived from the liver tissue of a Caucasian American male


title: HepG2 cells expressing ATP7B H1069Q and treated with JNK Inhibitor, biological rep3

description:
Adeno ATP7BH1069Q_JNKInh_3
Gene expression data from cells infected with adenovirus expressing ATP7B H1069Q -GFP and treated with 1uM SP600125 (Sigma Aldrich)
cell line derived from the liver tissue of a Caucasian American male


title: HepG2 cells expressing ATP7B H1069Q and treated with p38 MAPK Inhibitor, biological rep2

description:
Adeno ATP7BH1069Q_p38Inh_2
Gene expression data from cells infected with adenovirus expressing ATP7B H1069Q -GFP and treated with 5uM SP202190 (Sigma Aldrich)
cell line derived from the liver tissue of a Caucasian American male


title: HepG2 cells expressing ATP7B WT, biological rep2

description:
Adeno ATP7BWT2
Gene expression data from cells infected with adenovirus expressing ATP7B wt -GFP
cell line derived from the liver tissue of a Caucasian American male


title: HepG2 cells expressing ATP7B H1069Q, biological rep2

description:
Adeno ATP7BH1069Q_2
Gene expression data from cells infected with adenovirus expressing ATP7B H1069Q -GFP
cell line derived from the liver tissue of a Caucasian American male

source_name: HepG2 cells expressing ATP7B H1069Q


title: HepG2 cells expressing ATP7B WT, biological rep1

description:
Adeno ATP7BWT1
Gene expression data from cells infected with adenovirus expressing ATP7B wt -GFP
cell line derived from the liver tissue of a Caucasian American male


title: D. ana male 2

city: Stanford

first: Jin Billy

last: Li

state: California

address: 300 Pasteur Drive. Alway M303

department: Genetics

institute: Stanford University

data_processing:
Primer sequences were trimmed off paired or single-end sequencing reads before mapping using Tophat.
RNA editing levels were calculated as the fraction of G reads at each site. Only sites covered by 50 reads were used
Genome_build: dm3/droSim1/droYak2/droAna2/dp3/droVir3
Supplementary_files_format_and_content: Processed data files are tab-delineated with a header line and include editing levels of different Drosophila strains and species.

organism: Drosophila ananassae

source_name: male whole body

growth_protocol: Whole bodies of adult male and female flies aged 5 days old were collected.

extract_protocol:
Total RNA was extracted using the Rneasy Kit (Qiagen). After DNase I treatment, 3 ug of total RNA was used to synthesize the cDNA using iScript Advanced cDNA Synthesis Kit (Bio-Rad). cDNA was purified using the MinElute PCR Purification Kit (Qiagen)
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.
microfluidic multiplex PCR (mmPCR-seq) or targeted sequencing

tag: developmental stage

value: 5 day old adult

tag: replicate

tag: library strategy

value: mmPCR-seq


title: D. ana male 1


title: D. ana female 2

source_name: female whole body


title: D. pse male 2

organism: Drosophila pseudoobscura


title: D. ana female 1


title: D. pse female 2


title: D. pse female 1


title: D. pse male 1


title: glc0.05_1h_3

city: Tianjin

first: Bang

last: Wang

address: 32 Xi Qi Dao, Tianjin Airport Economic Area

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

description: Sample 5

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

organism: Neurospora crassa OR74A

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

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

tag: growth condition

value: 1×Vogel’s salts with 2% (w/v) sucrose for 16 h pregrowth, then transferred to 1×Vogel’s salts with  0.05% glucose induced for 1 h

value: mycelia


title: glc10.0_1h_1

description: Sample 11

value: 1×Vogel’s salts with 2% (w/v) sucrose for 16 h pregrowth, then transferred to 1×Vogel’s salts with  10.0% glucose induced for 1 h


title: glc0.05_1h_2

description: Sample 4


title: glc0.05_2h

description: Sample 6

value: 1×Vogel’s salts with 2% (w/v) sucrose for 16 h pregrowth, then transferred to 1×Vogel’s salts with  0.05% glucose induced for 2 h


title: glc10.0_1h_2

description: Sample 12


title: glc2.0_1h_1

description: Sample 9

value: 1×Vogel’s salts with 2% (w/v) sucrose for 16 h pregrowth, then transferred to 1×Vogel’s salts with  2.0% glucose induced for 1 h


title: glc2.0_1h_2

description: Sample 10


title: HepG2 cells expressing ATP7B H1069Q, biological rep3

description:
Adeno ATP7BH1069Q_3
Gene expression data from cells infected with adenovirus expressing ATP7B H1069Q -GFP
cell line derived from the liver tissue of a Caucasian American male


title: glc0.5_1h_2

description: Sample 8

value: 1×Vogel’s salts with 2% (w/v) sucrose for 16 h pregrowth, then transferred to 1×Vogel’s salts with  0.5% glucose induced for 2 h


title: HepG2 cells expressing ATP7B H1069Q, biological rep1

description:
Adeno ATP7BH1069Q_1
Gene expression data from cells infected with adenovirus expressing ATP7B H1069Q -GFP
cell line derived from the liver tissue of a Caucasian American male


title: glc0.05_1h_1

description: Sample 3


title: noCarbon_1h_1

description: Sample 1

value: 1×Vogel’s salts with 2% (w/v) sucrose for 16 h  pregrowth, then transferred to carbon-free 1×Vogel’s salts induced for 1 h


title: noCarbon_1h_2

description: Sample 2


title: polyA RNA-seq KLA12h

city: La Jolla

first: Nathanael

middle: Judge

last: Spann

state: CA

address: 9500 Gilman Drive CMMW 219A

department: Cellular and Molecular Medicine

institute: UCSD

description: Sample 57

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

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: treated with

value: KLA for 12 hours


title: polyA RNA-seq KLA24h

description: Sample 58

value: KLA for 24 hours


title: ChIP-seq from HEK293 (ENCLB100XVY) -2

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR537CWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-SP7 tagged human HEK293 cells.
experiment encode accession: ENCSR537CWQ
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB100XVY
size range: 450-650

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

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-SP7 fusion protein

tag: antibody

value: Control

tag: line

value: immortalized cell line

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-SP7 under the control of a CMV promoter.

tag: biosample encode accession

tag: dev stage

value: embryonic

value: unknown

tag: Sex

value: female

tag: lab

value: Michael Snyder, Stanford

tag: health state

tag: link

value: ENCBS387JTD at ENCODE; https://www.encodeproject.org/ENCBS387JTD/

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


title: ChIP-seq from HEK293 (ENCLB529UQM) -2

description:
https://www.encodeproject.org/experiments/ENCSR499OOH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZNF18 tagged human HEK293 cells.
experiment encode accession: ENCSR499OOH
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB529UQM
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF18 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF18 under the control of a CMV promoter.

tag: age

value: ENCBS867IQP at ENCODE; https://www.encodeproject.org/ENCBS867IQP/


title: polyA RNA-seq KLA6h

description: Sample 56

tag: cell type

value: KLA for 6 hours


title: polyA RNA-seq KLA1h

description: Sample 55

value: KLA for 1 hours


title: polyA RNA-seq 1-12h noTx

description: Sample 54

value: none (control)


title: ChIP-seq from HEK293 (ENCLB760OCM)

description:
https://www.encodeproject.org/experiments/ENCSR398UVH/
***************
biological replicate number: 1
technical replicate number: 1
description: Input ChIP-seq on eGFP-ZSCAN5A tagged human HEK293 cells.
experiment encode accession: ENCSR398UVH
assay title: ChIP-seq
encode release date: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB760OCM
size range: 450-650

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

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

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


title: glc0.5_1h_1

description: Sample 7

tag: genotype/variation

value: wild type

value: 1×Vogel’s salts with 2% (w/v) sucrose for 16 h pregrowth, then transferred to 1×Vogel’s salts with  0.5% glucose induced for 1 h

value: mycelia


title: ChIP-seq from K562 (ENCLB717XNT)

description:
https://www.encodeproject.org/experiments/ENCSR998AJK/
***************
biological replicate number: 2
technical replicate number: 1
description: NRF1 ChIP-seq on human K562
experiment encode accession: ENCSR998AJK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB717XNT
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS293ZDP at ENCODE; https://www.encodeproject.org/ENCBS293ZDP/

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

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

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


title: ChIP-seq from K562 (ENCLB029MXN)

description:
https://www.encodeproject.org/experiments/ENCSR998AJK/
***************
biological replicate number: 1
technical replicate number: 1
description: NRF1 ChIP-seq on human K562
experiment encode accession: ENCSR998AJK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB029MXN
size range: 450-650

value: female

value: Michael Snyder, Stanford

value: ENCBS232KKV at ENCODE; https://www.encodeproject.org/ENCBS232KKV/


title: ChIP-seq from HEK293 (ENCLB548ICK)

description:
https://www.encodeproject.org/experiments/ENCSR996FYT/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF202 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR996FYT
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: ENCLB548ICK
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF202 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF202 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS684ULW at ENCODE; https://www.encodeproject.org/ENCBS684ULW/

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


title: ChIP-seq from HEK293 (ENCLB301ZOD)

description:
https://www.encodeproject.org/experiments/ENCSR996FYT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF202 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR996FYT
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: ENCLB301ZOD
size range: 450-650

value: immortalized cell line

value: ENCBS963BCC at ENCODE; https://www.encodeproject.org/ENCBS963BCC/


title: ChIP-seq from K562 (ENCLB596BXN)

description:
https://www.encodeproject.org/experiments/ENCSR991ELG/
***************
biological replicate number: 1
technical replicate number: 1
description: SP1 ChIP-seq on human K562
experiment encode accession: ENCSR991ELG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB596BXN
size range: 450-650

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: adult

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


title: eCLIP from HepG2 (ENCLB177QDR)

description:
https://www.encodeproject.org/experiments/ENCSR993OLA/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against IGF2BP3
experiment encode accession: ENCSR993OLA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR077KVG
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB177QDR
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

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

value: child

value: 15 year

value: male

tag: passage number

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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

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 24h noTx

description: Sample 53

value: none (control)


title: ChIP-seq from K562 (ENCLB545UPC)

description:
https://www.encodeproject.org/experiments/ENCSR990AZC/
***************
biological replicate number: 1
technical replicate number: 1
description: MCM3 ChIP-seq on human K562
experiment encode accession: ENCSR990AZC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB545UPC
size range: 450-650

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

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

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

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

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


title: ChIP-seq from K562 (ENCLB040HMX)

description:
https://www.encodeproject.org/experiments/ENCSR991ELG/
***************
biological replicate number: 2
technical replicate number: 1
description: SP1 ChIP-seq on human K562
experiment encode accession: ENCSR991ELG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB040HMX
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: ENCBS232KKV at ENCODE; https://www.encodeproject.org/ENCBS232KKV/


title: eCLIP from HepG2 (ENCLB742AYH)

description:
https://www.encodeproject.org/experiments/ENCSR989VIY/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against SRSF1
experiment encode accession: ENCSR989VIY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR499ZCU
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB742AYH
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: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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


title: ChIP-seq from K562 (ENCLB362HCT)

description:
https://www.encodeproject.org/experiments/ENCSR990AZC/
***************
biological replicate number: 2
technical replicate number: 1
description: MCM3 ChIP-seq on human K562
experiment encode accession: ENCSR990AZC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB362HCT
size range: 450-650

value: 53 year

value: female

value: ENCBS398HUM at ENCODE; https://www.encodeproject.org/ENCBS398HUM/


title: ChIP-seq from K562 (ENCLB946ZIV)

description:
https://www.encodeproject.org/experiments/ENCSR987PBI/
***************
biological replicate number: 2
technical replicate number: 1
description: DNMT1 ChIP-seq on human K562
experiment encode accession: ENCSR987PBI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB946ZIV
size range: 450-650

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)


title: ChIP-seq from K562 (ENCLB111IXN)

description:
https://www.encodeproject.org/experiments/ENCSR987PBI/
***************
biological replicate number: 1
technical replicate number: 1
description: DNMT1 ChIP-seq on human K562
experiment encode accession: ENCSR987PBI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB111IXN
size range: 450-650

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

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

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


title: eCLIP from HepG2 (ENCLB948MQK)

description:
https://www.encodeproject.org/experiments/ENCSR987NYS/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against FAM120A
experiment encode accession: ENCSR987NYS
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR839KAX
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB948MQK
size range: 175-300

value: immortalized cell line

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: eCLIP from HepG2 (ENCLB770EDJ)

description:
https://www.encodeproject.org/experiments/ENCSR989VIY/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against SRSF1
experiment encode accession: ENCSR989VIY
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR499ZCU
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB770EDJ
size range: 175-300

value: child

value: 15 year

value: male

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


title: eCLIP from HepG2 (ENCLB132ATR)

description:
https://www.encodeproject.org/experiments/ENCSR993OLA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against IGF2BP3
experiment encode accession: ENCSR993OLA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR077KVG
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB132ATR
size range: 175-300

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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


title: ChIP-seq from HEK293 (ENCLB032CPO)

description:
https://www.encodeproject.org/experiments/ENCSR977HTH/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF18 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR977HTH
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: ENCLB032CPO
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF18 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS511ASG at ENCODE; https://www.encodeproject.org/ENCBS511ASG/

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


title: ChIP-seq from HEK293 (ENCLB725VAD)

description:
https://www.encodeproject.org/experiments/ENCSR984MDV/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF24 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR984MDV
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: ENCLB725VAD
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF24 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF24 under the control of a CMV promoter.

value: ENCBS417ONA at ENCODE; https://www.encodeproject.org/ENCBS417ONA/


title: eCLIP from K562 (ENCLB289NPV)

description:
https://www.encodeproject.org/experiments/ENCSR981WKN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against PTBP1
experiment encode accession: ENCSR981WKN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR445FZX
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB289NPV
size range: 175-300

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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 (ENCLB467VKY)

description:
https://www.encodeproject.org/experiments/ENCSR978JXM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SAFB2
experiment encode accession: ENCSR978JXM
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB467VKY
size range: 175-300

value: Control

value: Gene Yeo, UCSD

value: ENCBS257HMY at ENCODE; https://www.encodeproject.org/ENCBS257HMY/

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


title: ChIP-seq from HEK293 (ENCLB727PNF)

description:
https://www.encodeproject.org/experiments/ENCSR984MDV/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF24 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR984MDV
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: ENCLB727PNF
size range: 450-650

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS386RAW at ENCODE; https://www.encodeproject.org/ENCBS386RAW/


title: ChIP-seq from MCF-7 (ENCLB263NPG)

description:
https://www.encodeproject.org/experiments/ENCSR986XYK/
***************
biological replicate number: 1
technical replicate number: 1
description: PKNOX1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR986XYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB263NPG
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS637YEV at ENCODE; https://www.encodeproject.org/ENCBS637YEV/

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


title: eCLIP from HepG2 (ENCLB180GIG)

description:
https://www.encodeproject.org/experiments/ENCSR987FTF/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against RBFOX2
experiment encode accession: ENCSR987FTF
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR799EKA
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB180GIG
size range: 175-300

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

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

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

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


title: eCLIP from HepG2 (ENCLB696TLV)

description:
https://www.encodeproject.org/experiments/ENCSR987FTF/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against RBFOX2
experiment encode accession: ENCSR987FTF
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR799EKA
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB696TLV
size range: 175-300

value: Gene Yeo, UCSD

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

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


title: eCLIP from HepG2 (ENCLB232EMV)

description:
https://www.encodeproject.org/experiments/ENCSR987NYS/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against FAM120A
experiment encode accession: ENCSR987NYS
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR839KAX
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB232EMV
size range: 175-300

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


title: eCLIP from K562 (ENCLB497KNG)

description:
https://www.encodeproject.org/experiments/ENCSR981WKN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against PTBP1
experiment encode accession: ENCSR981WKN
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR445FZX
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB497KNG
size range: 175-300

value: adult

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

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

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

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


title: ChIP-seq from HEK293 (ENCLB043ZDC)

description:
https://www.encodeproject.org/experiments/ENCSR977HTH/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF18 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR977HTH
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: ENCLB043ZDC
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF18 under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS867IQP at ENCODE; https://www.encodeproject.org/ENCBS867IQP/

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


title: eCLIP from K562 (ENCLB379DOA)

description:
https://www.encodeproject.org/experiments/ENCSR977GTT/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against GNL3
experiment encode accession: ENCSR977GTT
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB379DOA
size range: 175-300

value: Control

value: Gene Yeo, UCSD

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


title: eCLIP from K562 (ENCLB795NJI)

description:
https://www.encodeproject.org/experiments/ENCSR975KIR/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against IGF2BP1
experiment encode accession: ENCSR975KIR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR125CLF
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB795NJI
size range: 175-300

value: adult

value: ENCBS301EZU at ENCODE; https://www.encodeproject.org/ENCBS301EZU/

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


title: ChIP-seq from MCF-7 (ENCLB698ZWU)

description:
https://www.encodeproject.org/experiments/ENCSR986XYK/
***************
biological replicate number: 2
technical replicate number: 1
description: PKNOX1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR986XYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB698ZWU
size range: 450-650

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

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

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


title: eCLIP from K562 (ENCLB736ETW)

description:
https://www.encodeproject.org/experiments/ENCSR970NKP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against Lin28B
experiment encode accession: ENCSR970NKP
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR399CBP
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB736ETW
size range: 175-300

value: immortalized cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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 (ENCLB089DKQ)

description:
https://www.encodeproject.org/experiments/ENCSR975KIR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against IGF2BP1
experiment encode accession: ENCSR975KIR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR125CLF
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB089DKQ
size range: 175-300

value: Gene Yeo, UCSD

value: ENCBS476AUA at ENCODE; https://www.encodeproject.org/ENCBS476AUA/


title: ChIP-seq from K562 (ENCLB390CHI)

description:
https://www.encodeproject.org/experiments/ENCSR970NKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: NR2F1 ChIP-seq on human K562
experiment encode accession: ENCSR970NKQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB390CHI
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: Michael Snyder, Stanford

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


title: ChIP-seq from K562 (ENCLB278RSF)

description:
https://www.encodeproject.org/experiments/ENCSR970NKQ/
***************
biological replicate number: 2
technical replicate number: 1
description: NR2F1 ChIP-seq on human K562
experiment encode accession: ENCSR970NKQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB278RSF
size range: 450-650

value: female

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

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


title: ChIP-seq from HEK293 (ENCLB441RRJ)

description:
https://www.encodeproject.org/experiments/ENCSR966PJJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-WT1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR966PJJ
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: ENCLB441RRJ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-WT1 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-WT1 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS927FFT at ENCODE; https://www.encodeproject.org/ENCBS927FFT/

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


title: ChIP-seq from HEK293 (ENCLB948OXM)

description:
https://www.encodeproject.org/experiments/ENCSR966ULI/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-PATZ1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR966ULI
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: ENCLB948OXM
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-PATZ1 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-PATZ1 under the control of a CMV promoter.

value: ENCBS186LSD at ENCODE; https://www.encodeproject.org/ENCBS186LSD/


title: eCLIP from K562 (ENCLB914PVV)

description:
https://www.encodeproject.org/experiments/ENCSR970NKP/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against Lin28B
experiment encode accession: ENCSR970NKP
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR399CBP
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB914PVV
size range: 175-300

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Gene Yeo, UCSD

value: ENCBS253VOZ at ENCODE; https://www.encodeproject.org/ENCBS253VOZ/

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 (ENCLB249RSO)

description:
https://www.encodeproject.org/experiments/ENCSR978IXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-DDX20 tagged K562 cell line.
experiment encode accession: ENCSR978IXJ
assay title: ChIP-seq
encode release date: 2016-02-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB249RSO
size range: 450-650

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

value: Control

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

value: adult

value: female

value: Kevin White, UChicago

value: ENCBS026JDH at ENCODE; https://www.encodeproject.org/ENCBS026JDH/

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


title: ChIP-seq from HEK293 (ENCLB320JQH)

description:
https://www.encodeproject.org/experiments/ENCSR966PJJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-WT1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR966PJJ
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: ENCLB320JQH
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-WT1 under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS740TWL at ENCODE; https://www.encodeproject.org/ENCBS740TWL/

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


title: ChIP-seq from K562 (ENCLB639AYO)

description:
https://www.encodeproject.org/experiments/ENCSR962GNR/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-KLF13 tagged K562 cell line.
experiment encode accession: ENCSR962GNR
assay title: ChIP-seq
encode release date: 2015-12-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB639AYO
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-KLF13 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to KLF13

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS703NZF at ENCODE; https://www.encodeproject.org/ENCBS703NZF/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW33; http://web.expasy.org/cellosaurus/CVCL_AW33


title: ChIP-seq from HEK293 (ENCLB516DXE)

description:
https://www.encodeproject.org/experiments/ENCSR966ULI/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-PATZ1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR966ULI
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: ENCLB516DXE
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-PATZ1 under the control of a CMV promoter.

value: female

value: ENCBS577WIH at ENCODE; https://www.encodeproject.org/ENCBS577WIH/


title: eCLIP from HepG2 (ENCLB189TRV)

description:
https://www.encodeproject.org/experiments/ENCSR961OKA/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against LARP7
experiment encode accession: ENCSR961OKA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR095SIV
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB189TRV
size range: 175-300

value: child

value: 15 year

value: male

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

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

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

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

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


title: ChIP-seq from K562 (ENCLB949IYC)

description:
https://www.encodeproject.org/experiments/ENCSR957LDM/
***************
biological replicate number: 1
technical replicate number: 1
description: TRIM24 ChIP-seq on human K562
experiment encode accession: ENCSR957LDM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB949IYC
size range: 450-650

value: immortalized cell line

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS783WYV at ENCODE; https://www.encodeproject.org/ENCBS783WYV/

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


title: eCLIP from HepG2 (ENCLB179JQJ)

description:
https://www.encodeproject.org/experiments/ENCSR961OKA/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against LARP7
experiment encode accession: ENCSR961OKA
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR095SIV
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB179JQJ
size range: 175-300

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


title: ChIP-seq from K562 (ENCLB887DPL)

description:
https://www.encodeproject.org/experiments/ENCSR957LDM/
***************
biological replicate number: 2
technical replicate number: 1
description: TRIM24 ChIP-seq on human K562
experiment encode accession: ENCSR957LDM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB887DPL
size range: 450-650

value: female

value: chronic myelogenous leukemia (CML)

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

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


title: eCLIP from K562 (ENCLB320EKU)

description:
https://www.encodeproject.org/experiments/ENCSR943ZKM/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against AUH
experiment encode accession: ENCSR943ZKM
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB320EKU
size range: 175-300

value: Control

value: Gene Yeo, UCSD

value: ENCBS119WDQ at ENCODE; https://www.encodeproject.org/ENCBS119WDQ/

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


title: eCLIP from HepG2 (ENCLB918YPI)

description:
https://www.encodeproject.org/experiments/ENCSR941GJG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against U2AF1
experiment encode accession: ENCSR941GJG
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB918YPI
size range: 175-300

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

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

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

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


title: eCLIP from K562 (ENCLB465FHS)

description:
https://www.encodeproject.org/experiments/ENCSR947JVR/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against DGCR8
experiment encode accession: ENCSR947JVR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR616BTD
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB465FHS
size range: 175-300

value: immortalized cell line

value: adult

value: 53 year

value: ENCBS253VOZ at ENCODE; https://www.encodeproject.org/ENCBS253VOZ/

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 (ENCLB762DOX)

description:
https://www.encodeproject.org/experiments/ENCSR943MHU/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against SAFB2
experiment encode accession: ENCSR943MHU
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR978JXM
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB762DOX
size range: 175-300

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS271WWU at ENCODE; https://www.encodeproject.org/ENCBS271WWU/

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


title: ChIP-seq from MCF-7 (ENCLB175BWY)

description:
https://www.encodeproject.org/experiments/ENCSR954WVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ESRRA ChIP-seq on human MCF-7
experiment encode accession: ENCSR954WVZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB175BWY
size range: 450-650

value: ESRRA

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: eCLIP from K562 (ENCLB892KXP)

description:
https://www.encodeproject.org/experiments/ENCSR950WBG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SLBP
experiment encode accession: ENCSR950WBG
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB892KXP
size range: 175-300

value: Control

value: immortalized cell line

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: ENCBS540UNM at ENCODE; https://www.encodeproject.org/ENCBS540UNM/

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


title: ChIP-seq from MCF-7 (ENCLB555FMS)

description:
https://www.encodeproject.org/experiments/ENCSR954WVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ESRRA ChIP-seq on human MCF-7
experiment encode accession: ENCSR954WVZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555FMS
size range: 450-650

value: female

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


title: eCLIP from K562 (ENCLB322AEY)

description:
https://www.encodeproject.org/experiments/ENCSR943MHU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against SAFB2
experiment encode accession: ENCSR943MHU
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR978JXM
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB322AEY
size range: 175-300

value: chronic myelogenous leukemia (CML)

value: ENCBS257HMY at ENCODE; https://www.encodeproject.org/ENCBS257HMY/

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

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


title: eCLIP from K562 (ENCLB991LAW)

description:
https://www.encodeproject.org/experiments/ENCSR947JVR/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against DGCR8
experiment encode accession: ENCSR947JVR
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR616BTD
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB991LAW
size range: 175-300

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

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


title: siRNA RNA-seq from K562 (ENCLB893NBR)

description:
https://www.encodeproject.org/experiments/ENCSR942MUW/
***************
biological replicate number: 1
technical replicate number: 1
description: Control siRNA against no target in K562 cells followed by RNA-seq.
experiment encode accession: ENCSR942MUW
assay title: siRNA RNA-seq
assembly: GRCh38
encode release date: 2016-11-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB893NBR
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting Non-specific target control

value: K562 cells treated with siRNA knockdown using a human non-targeting control.

value: Sherman Weissman, Yale

value: ENCBS644JMQ at ENCODE; https://www.encodeproject.org/ENCBS644JMQ/


title: ChIP-seq from GM12878 (ENCLB901VQJ)

description:
https://www.encodeproject.org/experiments/ENCSR936XTK/
***************
biological replicate number: 3
technical replicate number: 1
description: ZNF143 ChIP-seq on human GM12878
experiment encode accession: ENCSR936XTK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB901VQJ
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

value: immortalized cell line

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

value: unknown

value: Michael Snyder, Stanford

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

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

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

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


title: ChIP-seq from GM12878 (ENCLB842ZPU)

description:
https://www.encodeproject.org/experiments/ENCSR936XTK/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF143 ChIP-seq on human GM12878
experiment encode accession: ENCSR936XTK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB842ZPU
size range: 450-650

value: adult

value: female

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


title: ChIP-seq from K562 (ENCLB652PHI)

description:
https://www.encodeproject.org/experiments/ENCSR931HNY/
***************
biological replicate number: 2
technical replicate number: 1
description: NCOA1 ChIP-seq on human K562
experiment encode accession: ENCSR931HNY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB652PHI
size range: 450-650

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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

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


title: eCLIP from K562 (ENCLB657WFG)

description:
https://www.encodeproject.org/experiments/ENCSR930BZL/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against DDX3X
experiment encode accession: ENCSR930BZL
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR028CRL
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB657WFG
size range: 175-300

value: Gene Yeo, UCSD

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

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


title: ChIP-seq from K562 (ENCLB964OKL)

description:
https://www.encodeproject.org/experiments/ENCSR931HNY/
***************
biological replicate number: 1
technical replicate number: 1
description: NCOA1 ChIP-seq on human K562
experiment encode accession: ENCSR931HNY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB964OKL
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: ENCBS207UAM at ENCODE; https://www.encodeproject.org/ENCBS207UAM/

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


title: eCLIP from K562 (ENCLB780MPM)

description:
https://www.encodeproject.org/experiments/ENCSR930BZL/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against DDX3X
experiment encode accession: ENCSR930BZL
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR028CRL
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB780MPM
size range: 175-300

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


title: ChIP-seq from K562 (ENCLB592VTM)

description:
https://www.encodeproject.org/experiments/ENCSR948VFL/
***************
biological replicate number: 1
technical replicate number: 1
description: IKZF1 ChIP-seq on human K562
experiment encode accession: ENCSR948VFL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB592VTM
size range: 450-650

value: Michael Snyder, Stanford

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


title: ChIP-seq from K562 (ENCLB190FZE)

description:
https://www.encodeproject.org/experiments/ENCSR948VFL/
***************
biological replicate number: 2
technical replicate number: 1
description: IKZF1 ChIP-seq on human K562
experiment encode accession: ENCSR948VFL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB190FZE
size range: 450-650

value: adult

value: female

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


title: eCLIP from K562 (ENCLB115MCQ)

description:
https://www.encodeproject.org/experiments/ENCSR925TYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against SRSF1
experiment encode accession: ENCSR925TYQ
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB115MCQ
size range: 175-300

value: Control

value: 53 year

value: chronic myelogenous leukemia (CML)


title: ChIP-seq from HEK293 (ENCLB716AGX)

description:
https://www.encodeproject.org/experiments/ENCSR927UJQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZBTB1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR927UJQ
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: ENCLB716AGX
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZBTB1 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZBTB1 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS255RNI at ENCODE; https://www.encodeproject.org/ENCBS255RNI/

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


title: ChIP-seq from K562 (ENCLB838IQJ)

description:
https://www.encodeproject.org/experiments/ENCSR922MYB/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-NFE2L1 tagged K562 cell line.
experiment encode accession: ENCSR922MYB
assay title: ChIP-seq
encode release date: 2015-12-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB838IQJ
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-NFE2L1 fusion protein

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NFE2L1

value: Kevin White, UChicago

value: ENCBS670PDV at ENCODE; https://www.encodeproject.org/ENCBS670PDV/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW35; http://web.expasy.org/cellosaurus/CVCL_AW35


title: ChIP-seq from K562 (ENCLB656SZS)

description:
https://www.encodeproject.org/experiments/ENCSR926KTP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-IRF9 ChIP-seq on human K562
experiment encode accession: ENCSR926KTP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR709DHP
encode release date: 2016-01-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB656SZS
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-IRF9 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to IRF9

value: adult

value: ENCBS264ETB at ENCODE; https://www.encodeproject.org/ENCBS264ETB/

value: ENCODE dbxrefs Cellosaurus CVCL_AW29; http://web.expasy.org/cellosaurus/CVCL_AW29


title: ChIP-seq from K562 (ENCLB892HRZ)

description:
https://www.encodeproject.org/experiments/ENCSR926KTP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-IRF9 ChIP-seq on human K562
experiment encode accession: ENCSR926KTP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR709DHP
encode release date: 2016-01-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB892HRZ
size range: 450-650

value: 53 year

value: female

value: ENCBS951JJK at ENCODE; https://www.encodeproject.org/ENCBS951JJK/


title: eCLIP from K562 (ENCLB615MWL)

description:
https://www.encodeproject.org/experiments/ENCSR924OLO/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against TARDBP
experiment encode accession: ENCSR924OLO
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB615MWL
size range: 175-300

value: Control

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)

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

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

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


title: ChIP-seq from HEK293 (ENCLB400KJK)

description:
https://www.encodeproject.org/experiments/ENCSR924GRG/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZBTB49 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR924GRG
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: ENCLB400KJK
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZBTB49 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZBTB49 under the control of a CMV promoter.

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS652OCL at ENCODE; https://www.encodeproject.org/ENCBS652OCL/

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


title: ChIP-seq from HEK293 (ENCLB527NCI)

description:
https://www.encodeproject.org/experiments/ENCSR919CZU/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-EGR2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR919CZU
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: ENCLB527NCI
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-EGR2 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-EGR2 under the control of a CMV promoter.

value: ENCBS738RNR at ENCODE; https://www.encodeproject.org/ENCBS738RNR/


title: eCLIP from HepG2 (ENCLB870VMU)

description:
https://www.encodeproject.org/experiments/ENCSR919HSE/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on HepG2 against CSTF2T
experiment encode accession: ENCSR919HSE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR391GLS
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB870VMU
size range: 175-300

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

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

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

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


title: ChIP-seq from HEK293 (ENCLB453XUU)

description:
https://www.encodeproject.org/experiments/ENCSR919CZU/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-EGR2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR919CZU
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: ENCLB453XUU
size range: 450-650

value: female

value: ENCBS970WCY at ENCODE; https://www.encodeproject.org/ENCBS970WCY/


title: ChIP-seq from HEK293 (ENCLB055XCX)

description:
https://www.encodeproject.org/experiments/ENCSR927UJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZBTB1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR927UJQ
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: ENCLB055XCX
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZBTB1 under the control of a CMV promoter.

value: ENCBS221WVG at ENCODE; https://www.encodeproject.org/ENCBS221WVG/


title: ChIP-seq from MCF-7 (ENCLB296KZV)

description:
https://www.encodeproject.org/experiments/ENCSR912NMR/
***************
biological replicate number: 2
technical replicate number: 1
description: NONO ChIP-seq on human MCF-7
experiment encode accession: ENCSR912NMR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB296KZV
size range: 450-650

value: NONO

value: adult

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 HEK293 (ENCLB933CIQ)

description:
https://www.encodeproject.org/experiments/ENCSR909TSW/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF547 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR909TSW
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: ENCLB933CIQ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF547 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF547 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS145GQX at ENCODE; https://www.encodeproject.org/ENCBS145GQX/

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


title: ChIP-seq from HEK293 (ENCLB134VRF)

description:
https://www.encodeproject.org/experiments/ENCSR909HMT/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZEB1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR909HMT
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: ENCLB134VRF
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZEB1 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZEB1 under the control of a CMV promoter.

value: female

value: ENCBS073ZEX at ENCODE; https://www.encodeproject.org/ENCBS073ZEX/


title: ChIP-seq from HEK293 (ENCLB587KXK)

description:
https://www.encodeproject.org/experiments/ENCSR909HMT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZEB1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR909HMT
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: ENCLB587KXK
size range: 450-650

value: immortalized cell line

value: ENCBS472JNF at ENCODE; https://www.encodeproject.org/ENCBS472JNF/


title: ChIP-seq from K562 (ENCLB465YBO)

description:
https://www.encodeproject.org/experiments/ENCSR907MZR/
***************
biological replicate number: 1
technical replicate number: 1
description: TRIM24 ChIP-seq on human K562
experiment encode accession: ENCSR907MZR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB465YBO
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS783WYV at ENCODE; https://www.encodeproject.org/ENCBS783WYV/

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

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


title: eCLIP from K562 (ENCLB113XXI)

description:
https://www.encodeproject.org/experiments/ENCSR898ZCL/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against HNRNPA1
experiment encode accession: ENCSR898ZCL
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB113XXI
size range: 175-300

value: Control

value: Gene Yeo, UCSD

value: ENCBS205QYW at ENCODE; https://www.encodeproject.org/ENCBS205QYW/

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


title: ChIP-seq from K562 (ENCLB447SXG)

description:
https://www.encodeproject.org/experiments/ENCSR907MZR/
***************
biological replicate number: 2
technical replicate number: 1
description: TRIM24 ChIP-seq on human K562
experiment encode accession: ENCSR907MZR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB447SXG
size range: 450-650

value: Michael Snyder, Stanford

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


title: ChIP-seq from A549 (ENCLB327ZYR)

description:
https://www.encodeproject.org/experiments/ENCSR897MYK/
***************
biological replicate number: 2
technical replicate number: 1
description: SREBF1 ChIP-seq on human A549
experiment encode accession: ENCSR897MYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR610YRT, ENCSR871XML
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB327ZYR
size range: 450-650

source_name: Homo sapiens A549 immortalized cell line

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

value: male

value: 58 year

value: ENCBS100LYC at ENCODE; https://www.encodeproject.org/ENCBS100LYC/

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

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

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


title: ChIP-seq from MCF-7 (ENCLB653XWX)

description:
https://www.encodeproject.org/experiments/ENCSR899BKM/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF687 ChIP-seq on human MCF-7
experiment encode accession: ENCSR899BKM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB653XWX
size range: 450-650

value: immortalized cell line

value: adult

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: ENCBS912WOF at ENCODE; https://www.encodeproject.org/ENCBS912WOF/

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 A549 (ENCLB782WCF)

description:
https://www.encodeproject.org/experiments/ENCSR897MYK/
***************
biological replicate number: 3
technical replicate number: 1
description: SREBF1 ChIP-seq on human A549
experiment encode accession: ENCSR897MYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR610YRT, ENCSR871XML
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB782WCF
size range: 450-650

value: Michael Snyder, Stanford

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


title: ChIP-seq from MCF-7 (ENCLB669OLV)

description:
https://www.encodeproject.org/experiments/ENCSR899BKM/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF687 ChIP-seq on human MCF-7
experiment encode accession: ENCSR899BKM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB669OLV
size range: 450-650

value: ENCBS050QMU at ENCODE; https://www.encodeproject.org/ENCBS050QMU/


title: ChIP-seq from HEK293 (ENCLB876EJP)

description:
https://www.encodeproject.org/experiments/ENCSR896UBV/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-REST ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR896UBV
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: ENCLB876EJP
size range: 450-650

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

value: eGFP-REST

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

value: embryonic

value: unknown

value: ENCBS988LBI at ENCODE; https://www.encodeproject.org/ENCBS988LBI/

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


title: eCLIP from HepG2 (ENCLB109CUT)

description:
https://www.encodeproject.org/experiments/ENCSR919HSE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on HepG2 against CSTF2T
experiment encode accession: ENCSR919HSE
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR391GLS
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB109CUT
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell 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 K562 (ENCLB554TAC)

description:
https://www.encodeproject.org/experiments/ENCSR895HSJ/
***************
biological replicate number: 2
technical replicate number: 1
description: SMARCA5 ChIP-seq on human K562
experiment encode accession: ENCSR895HSJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB554TAC
size range: 450-650

value: adult

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS734NZL at ENCODE; https://www.encodeproject.org/ENCBS734NZL/

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

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


title: ChIP-seq from HEK293 (ENCLB439YDP)

description:
https://www.encodeproject.org/experiments/ENCSR896UBV/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-REST ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR896UBV
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: ENCLB439YDP
size range: 450-650

value: eGFP-REST

value: immortalized cell line

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

value: embryonic

value: unknown

value: ENCBS064MAI at ENCODE; https://www.encodeproject.org/ENCBS064MAI/

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