title: Exp_Fgfr2bflox_AECI_rep2

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: 2 Âµg of the labeled cDNA were subjected to hybridization. The cDNA was not fragmented before hybridization. Hybridization was performed following the Agilent protocol at 65Â°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 Âµm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Primary isolated cells, FACS-isolated AECI cells from E18.5 lungs

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2Âµg amplified cDNA was Cy-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

extract_protocol: QIAgen microRNeasy mini kit

treatment_protocol: Pregnant females carrying embryos with the experimental genotype were injected with tamoxifen at E14.5 and E15.5. Lungs were harvested at E18.5, single cell suspensions performed, and cells prepared for FACS-based cell sorting. Another set of pregnant females were used to obtain embryos with the control genotype, and control samples were prepared in an identical manner to experimental samples. The RNA of sorted cells was then isolated for gene array.

tag: tissue


title: Ctl_AECII_rep2

status: Public on Jun 01 2021

type: RNA

molecule: total RNA

organism: Mus musculus

source_name: Primary isolated cells, FACS-isolated AECII cells from E18.5 lungs


title: T6.WGBS.NBL

type: SRA

city: Shenzhen,Guangdong Province,China

first: Yayan

last: Feng

state: --- Select a state ---

address: No. 7 pengfei road, dapeng new district, shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: genomic

data_processing:
Raw sequencing reads with more than 30% ‘N’s in over 10% of the sequences or smaller than 30 bp were discarded
Clean reads were aligned to the corresponding reference genome using BSMAP (v2.73) with a of maximal four mismatches and gap size up to 2 nucleotides
Methylation level of each cytosine was calculated as the number of reads ascertained methylated to the total number of reads for each covered CpG sites.
To accurately investigate the methylation levels in each sample, we used CpG sites with a minimal 5× sequencing depth per strand.
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: cout, bed format

molecule: genomic DNA

organism: Trichinella sp. T6

extract_protocol:
DNA was extracted using the phenol chloroform extraction method
Genomic DNA extracted from three life stages of all Trichinella species were selected for libraries construction of WGBS. Briefly, approx. two to five micrograms of gDNA were first fragmented by Covaris to an average size of ~200-300 bp. End-repair, A-tailing and ligation were conducted as the Illumina PE genomic DNA sample prep kit protocol, except that ligation was performed using methylated cytosine PE adapters provided by Illumina previously. Ligation products were purified and bisulfited converted using the EZ DNA Methylation-Gold KitTM (ZYMO) according to the manufacturer’s instructions. The libraries were sequenced using Illumina HiSeq 2,500 platform.

tag: tag

value: Newborn larvae


title: IMR-90_Control_rep2

city: Rochester

first: Daniel

middle: J.

last: Tschumperlin

state: MN

address: 200 First St SW, AL 4-184

department: Physiology and Biomedical Engineering

country: USA

institute: Mayo Clinic

description: Gene expression data from IMR-90 control cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on 3. GeneChip PrimeView Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Homo sapiens

source_name: IMR-90 cells, control treatments, rep2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: IMR-90 cells (ATCC) were maintained in EMEM (ATCC) containing 10% FBS, 10,000 U/mL of penicillin, 10,000 μg/mL of streptomycin, and 25 μg/mL of amphotericin B in a humidified 37 °C, 5% CO2 incubator.

extract_protocol: RNA was extracted and isolated using a RNAeasy micro kit (Qiagen) according to manufacturer’s instructions containing at least 200 ng of purified RNA per sample.

treatment_protocol: IMR-90 cells were treated with TGFβ1 (2 ng/ml)  and transfected with siRNA (ON-TARGETplus SMARTpool; Dharmacon) targeting YAP and TAZ alone or in combination, or scrambled control for 72 hours, using Lipofectamine® RNAiMAX (Invitrogen).

tag: sample type

value: cultured cells

tag: cell line


title: T6.WGBS.ML

value: Muscle larvae


title: 25FP

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Quality control (QC) of FASTQ files was performed using FastQC Toolkit (v0.11.5) [http://www.bioinformatics.babraham.ac.uk/projects/fastqc]
Paired-end reads were aligned against Dp_genome_v3
the reference genome of Danaus plexippus [Zhan and Reppert 2013] using HISAT2 (v2.0.5) [Kim et al. 2015]
The latest version of monarch GTF (OGS2.0) consisting of 15130 expressed gene models was downloaded from MonarchBase [http://monarchbase.umassmed.edu/geneset.html] for gene expression quantification
The paired-end reads mapped to the genome assembly were summarized using featureCounts (v1.5.2) [Liao et al. 2014]
Differential expression analysis at the gene-level was carried out using limma-voom [Law et al. 2014] open source R packages.
Trimmed mean of M-values (TMM) normalization [Robinson and Oshlack 2010] was carried out to determine normalization factors for all samples.
Genome_build: Dp_genome_v3 the reference genome of Danaus plexippus [Zhan and Reppert 2013]
Supplementary_files_format_and_content: TEXT - Raw Gene Counts

organism: Danaus plexippus

source_name: proboscis

growth_protocol: The monarch butterflies were caught in the field.

extract_protocol:
The frozen tissue was thawed, and then total RNA was harvested using Trizol reagent following Qiagen RNeasy protocol. RNA concentration and RNA IQ (integrity and quality) score were determined using a Qubit 4 Fluorometer (Thermo Fischer).
Illumina TruSeq Stranded mRNAseq Prep Kit was used with 100 ng of total RNA for the construction of sequencing libraries, following the manufactor's protocols.

treatment_protocol: The caught monarch butterflies were sex-identified and dissected to separate and collect antennae, legs and proboscis tissues. The collected tissues were stored at -80C until RNA isolation.

tag: animal id

tag: batch

tag: developmental stage

value: adult

tag: Sex

value: female

tag: female state

value: gravid


title: SF8 IL6 24h

city: Madrid

first: Manuel

middle: J

last: Del Rey

address: Avda Córdoba s/n

department: Grupo de Enfermedades Inflamatorias y Autoinmunes

country: Spain

institute: Instituto de Investigación Hospital 12 de Octubre

hyb_protocol: Following fragmentation the labelled ds-cDNA was hybridized in Affymetrix GeneChip® PrimeView™ Human Gene Expression Array platform containing 49395 probesets

scan_protocol: GeneChip were scanned with GeneChip® Scanner 3000 7G (GCS 3000 7G)

data_processing: The microarray data analysis was performed by using Expression Console and Transcriptome Analysis Console (TAC) softwares

source_name: Synovial fibroblast 8 IL6/IL6R (20ng/ml each) 24h

label_protocol: 10ng of RNA was used to synthesize biotinylated double-stranded cDNA (ds-cDNA) by using GeneChip 3’ IVT Pico Reagent Kit

growth_protocol: Synovial fibroblasts cultures in DMEM 10%FBS were established by explant growth of small arthroscopic biopsy fragments of synovial tissues obtained from the knee of patients without previous joint disease at elective arthroscopy for minor traumatic lesions.

extract_protocol: Total RNA was harvested using TRI Reagent lysis buffer according to the manufacturer's instructions

treatment_protocol: SF lines from were stimulated for 24h with either TNFα (20ng/ml) or IL6 and sIL6R (20ng/ml each)

tag: donor

value: Healthy

value: Synovial membrane

tag: treatment


title: SF8 TNF 24h

source_name: Synovial fibroblast 8 TNFa (20ng/ml) 24h

value: TNF


title: Exp_Fgfr2bflox_AECII_rep2

value: Primary isolated cells, FACS-isolated AECII cells from E18.5 lungs


title: SF8 Control 24h

source_name: Synovial fibroblast 8 Control 24h

value: Control


title: Ctl_AECI_rep1

value: Primary isolated cells, FACS-isolated AECI cells from E18.5 lungs


title: 25FL

source_name: legs


title: IMR-90_Control_rep1

source_name: IMR-90 cells, control treatments, rep1


title: T6.WGBS.AD

value: Adult


title: Ctl_AECII_rep1


title: Exp_Fgfr2bflox_AECII_rep1


title: Exp_Fgfr2bflox_AECI_rep1


title: Ctl_AECI_rep2


title: SF7 TNF 24h

source_name: Synovial fibroblast 7 TNFa (20ng/ml) 24h


title: SF7 IL6 24h

source_name: Synovial fibroblast 7 IL6/IL6R (20ng/ml each) 24h


title: 25FA

source_name: antennae


title: T5.RNA-seq.NBL

data_processing:
SOAPnuke was used for trimming adapters and filtering on length and quality of the raw sequencing reads, with the following paramaters: -q 0.5 -d -Q 2 --sanger -l 20
Clean reads were mapped to respective reference genome using hisat2 with default settings
The levels of gene expression were quantified using Cufflinks (v2.2.1) with RPKM (reads per kilobase million).
Differentially expressed genes were estimated by Cuffdiff (v2.2.1) with default paramaters
Genes with a threshold false discovery rate (FDR) ≤ 0.05 and the absolute value of log2Ratio ≥ 1 or ≤ -1 were considered significantly differentially expressed
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: rpkm Bed format

molecule: polyA RNA

organism: Trichinella murrelli

source_name: T. murrelli

extract_protocol:
Total RNA of T. spiralis (Ad, NBL and ML) was purified using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions.
To degrade any possible DNA contamination, the total RNA samples were dissolved in diethylpyrocarbonate (DEPC)-treated water and treated with DNaseI. NanoDrop 2000 (Thermo Scientific CA, USA) was then used to assess the quantity and quality of the total mRNA enriched using oligo (dT) magnetic beads. Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform following the Illumina’s protocols.

tag: strain

tag: passages


title: 20MP

value: male


title: T5.RNA-seq.ML


title: 20ML


title: T5.RNA-seq.AD


title: 20MA


title: T5.WGBS.NBL


title: Mutant_AECII_rep2

source_name: Primary isolated cells, AECI and AECII

extract_protocol: miRNeasy Micro Kit

value: Primary isolated AECII cells


title: 18FP


title: 18FL


title: T5.WGBS.ML


title: WT_AECII_rep2


title: SF6 IL6 24h

source_name: Synovial fibroblast 6 IL6/IL6R (20ng/ml each) 24h


title: Mutant_AECII_rep1


title: SF6 Control 24h

source_name: Synovial fibroblast 6 Control 24h


title: SF6 TNF 24h

source_name: Synovial fibroblast 6 TNFa (20ng/ml) 24h


title: WT_AECI_rep2

value: Primary isolated AECI cells


title: 18FA


title: SF1 TNF 24h

source_name: Synovial fibroblast 1 TNFa (20ng/ml) 24h


title: SF7 Control 24h

source_name: Synovial fibroblast 7 Control 24h


title: Mutant_AECI_rep2


title: 15MP


title: Mutant_AECI_rep1


title: Unsort 6

city: Saint Louis

first: Charles

middle: K

last: Kaufman

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St. Louis

data_processing:
Demultiplex and trim reads with Cutadapt
Align reads to GRCz10/danRer10 using BWA-MEM
Remove duplicate reads with Picard tools
Index and filter for high quality reads with SAMtools
Identify peaks with MACS2 callpeak function
Genome_build: danRer10
Supplementary_files_format_and_content: bigwig files generated as above

organism: Danio rerio

source_name: Bulk melanoma tumor

extract_protocol:
Bulk melanoma tumors were removed with a razor, homogenized, and lysed to extract genomic DNA.
50,000 cells were tagmented with an Illumina Nextera kit and purified with a Qiagen MinElute Purification Kit. DNA was amplified with a 9x cycling protocol combined with bead purification of proper sized fragments.

value: Melanoma


title: T5.WGBS.AD


title: 15ML


title: 15MA


title: WT_AECII_rep1


title: Splenic B cells, normal, replicate 3

city: Yangzhou

first: fang

last: tian

state: Jiangsu

address: huai hai road 11

department: Institute of Translational Medicine

institute: Yangzhou university

description: Gene expression in uninfected mice

hyb_protocol: Cy3-labelled miRNA was incubated at 100°C for 5 minutes in a reaction volume of 45 µl containing 10x GE blocking agent and 2×Hi-RPM Hybridization Buffer following the manufacturers instructions. Then the hybridization sample was hybridized to Agilent Microarrays for 20 hours at 55 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 2 and 5 minute with 37 °C GE Wash buffer 3, then dried immediately by brief centrifugation.

scan_protocol: Agilent Feature Extraction (FE) software.10.7.1.1 (Agilent) analyzed the scanned images using default parameters to obtain background subtracted and spatially detrended processed signal intensities as the raw data.

data_processing: Raw data were normalized in a quantile algorithm with Genespring software (version 12.5; Agilent Technologies). Filtering on the standardized data for each sample at least one group of 100% labelled Detected probe left for further analysis.

source_name: Splenic B cells, normal

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100 ng RNA using miRNA complete Labeling and Hyb Kit according to the manufacturer's instructions, followed by Micro Bio-Spin 6 column purification.

extract_protocol: Small RNA was isolated using the mirVana™ miRNA Isolation Kit (Ambion, Austin, TX, USA) according to the manufacturer's instructions. RNA purity and quantity were assessed using the NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). The samples were used immediately or stored at −80 °C for future use.

treatment_protocol: At 13w post-infection, the infected mice and uninfected mice were sacrificed and single cell suspensions of splenocytes were prepared in PBS containing 1% fetal bovine serum (FBS) (Gibco, Grand Island, NY) and 1% EDTA. Red blood cells were lysed using ACK lysis buffer containing ammonium chloride (Beyotime Ltd, Shanghai, China). CD19+ B cells were enriched using anti-CD19 MicroBeads (Miltenyi Biotec) with a purity of 96%, which were then stored in TRIzol reagent for gene expression analysis.

tag: gender

tag: age

tag: cell type

value: Splenic B cells

tag: infection

value: control


title: Unsort 3

tag: tissue


title: Splenic B cells, normal, replicate 2

description: Gene expression in uninfected mice


title: 13MP

source_name: proboscis


title: E16.5_9hrs_Exp._rep4

hyb_protocol: Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

source_name: Organ homogenate, E16.5 lung

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: All mice used in this experiment come from our colony at the ZTL animal housing facility, and are maintained according to their standard housing procedures. Pregnant female mice were transferred to the Gaffkystraße animal facility on the day of doxycycline administration. After doxycycline treatment, the pregnant females were housed according to Gaffkystraße's standard housing protocol until their sacrifice 9hrs later.

extract_protocol: Lungs were harvested in PBS. The left lobe of each sample was lysed in QIAzol. Total RNA was isolated using the QIAgen miRNeasy Mini Kit according to manufacturer's instructions.

treatment_protocol: Pregnant females were injected intraperitonally with 0.0015mg doxycycline per gram mouse body weight. Females were sacrificed 9hrs post injection. Embryos were removed and placed in PBS on ice. Embryonic lungs were harvested under sterile conditions and processed for RNA isolation. Embryonic tissue was taken from each sample for genotyping.

value: Organ homogenate, E16.5 lung


title: Unsort 2


title: Unsort 5


title: WT_AECI_rep1


title: 13ML

value: adult


title: E16.5_9hrs_Exp._rep5


title: 13MA


title: Splenic B cells, 13w infection, replicate 2

description: Gene expression at 13w post-infection with schistosoma japonicum

source_name: Splenic B cells, 13w infection

value: female

value: S. japonicum


title: Splenic B cells, 13w infection, replicate 3


title: Unsort 1


title: E16.5_9hrs_Exp._rep3


title: Splenic B cells, normal, replicate 1

description: Gene expression in uninfected mice


title: LNFP_D

status: Public on May 31 2021

city: Davis

first: saumya

last: wickramasibnghe

state: CA

address: One Shields AVE

department: Food Science and Technology

institute: University of California Davis

description:
DNase treated total RNA
ribo-depleted RNA

data_processing:
Demultiplexed sequence files were processed using the CLC-Bio Genomics Workbench (CLC Bio, Denmark). Reads were trimmed (maximum of 2 ambiguous base pairs) and deleted if the quality scores were below 0.5.
Edited reads were aligned to fasta files generated for Bifidobacterium pseudocatenulatum MP80 genome at IMG.
Reads Per Kilobase per Million mapped reads (RPKM) values were automatically calculated by CLC-Bio Genomics Workbench by using information on the gene length, total and unique gene reads aligning to a specific locus tag.
Genome_build: Bifidobacterium pseudocatenulatum MP80 genome at IMG.
Supplementary_files_format_and_content: *.txt: Matrix tables with raw gene counts and RPKM for every gene and every sample.

organism: Bifidobacterium pseudocatenulatum

growth_protocol: Bifidobacterium pseudocatenulatum MP80 inoculated into basal MRS media supplemented with 2% lactose, 2% 2'-FL or 2% LNFP1 in four biological replicates, sample collection at mid log phase.

extract_protocol:
Bacterial cells were immediately pelleted and resuspended in 1ml of RNAprotect Bacteria Reagent. Cells were pre-lysed lysozyme and mutanolysin. Then, Total RNA is extracted using the RNeasy mini kit (Qiagen Inc, Valencia). Total RNA samples were DNase treated twice. Ribosomal RNA depletion was carried using RiboMinus Transcriptome Isolation Kit, bacteria (Thermo Fisher, Waltham, MA) on 1 μg of total RNA.
Barcode indexed RNA-seq libraries were generated from 20 ng ribo-depleted RNA using the Kapa Hyper Stranded RNA-seq kit (KapaBiosystems, Cape Town, South Africa).

treatment_protocol: Treatment is MRS media supplemented with 2% 2'-FL or 2% LNFP1, control is MRA media supplemented with 2% lactose.

value: Grown on 2% LNFP1


title: E16.5_9hrs_Ctrl_rep2


title: SF1 Control 24h

source_name: Synovial fibroblast 1 Control 24h

value: Healthy

value: Synovial membrane


title: SF1 IL6 24h

source_name: Synovial fibroblast 1 IL6/IL6R (20ng/ml each) 24h


title: MeWo_Scr-shRNA

city: Fukuoka

first: Yuhui

last: Huang

address: Hakozaki 6-10-1

department: Department of Bioscience and Biotechnology

country: Japan

institute: Faculty of Agriculture, Kyushu University

description: Gene expression in Scr knockdown MeWo cells

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: Scr knockdown MeWo cells

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: MeWo

value: melanoma


title: E16.5_9hrs_Ctrl_rep1


title: E16.5_9hrs_Ctrl_rep3


title: LNFP_1


title: E16.5_9hrs_Exp._rep2


title: LNFP_B


title: MeWo_STARD3-shRNA

description: Gene expression in STARD3 knockdown MeWo cells

source_name: STARD3 knockdown MeWo cells


title: 2FL_D

value: Grown on 2% 2'-FL


title: 2FL_B


title: 2FL_A


title: Lac_D

value: Grown on 2% lactose


title: Splenic B cells, 13w infection, replicate 1


title: E16.5_9hrs_Exp._rep1


title: Lac_C


title: Lac_B


title: LNFP_C


title: Lac_A


title: HEK293T SON GO-CaRT Rep2

status: Public on May 28 2021

city: San Francisco

first: Tomasz

last: Nowakowski

state: Ca

institute: UCSF

data_processing:
Library strategy: GO-CaRT
150bp paired-end sequencing of GO-CaRT libraries was performed on the Illumina HiSeq 4000. Low quality reads and adaptors were removed with BBduk (http://jgi.doe.gov/data-and-tools/bb-tools/), and resulting reads were aligned to the mouse (UCSC mm10), macaque (USCS rheMac8) or human (UCSC hg38) genome using bowtie2 and the following settings: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700. Duplicate reads were removed with Picard tools

growth_protocol: Cells were cultured in DMEM with 10% FBS

extract_protocol:
75,000-100,000 acutely isolated cells from mouse, macaque, and human forebrain (or cultured 3T3 and HEK293T cells) were used for each experiment. Cells were resuspended in 500 mL ice cold Nuclei Isolation Buffer (NIB) (10 mM HEPES-KOH, Ph 7.9. 10 mM KCl, 0.1% NP40, 0.5 mM Spermidine and 1X Halt protease inhibitor cocktail) and incubated for 10 min in ice. Nuclear pellet was collected by centrifuging at 600xg for 3 min at 40C and again washed with 500 mL NIB. Nuclear pellet was collected by centrifugation at 600xg for 3 and resuspended in 100 mL of NIB. Successful nuclei isolation was confirmed by visual inspection under a phase contrast microscope. Next, 10 mL Concanavalin A lectin beads (Bio-Mag Plus) washed and resuspended in Binding Buffer (BiB) (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 1 mM CaCl2 and 1 mM MnCl2) were added to each sample and rotated for 10 min at room temperature. Nuclei bound Concanavalin A beads were pulled by placing the tubes on a magnetic stand to remove the supernatant. For LaminB GO-CaRT, anti LaminB1 antibody (Abcam# ab16048) was used and for SON GO-CaRT, anti-SON antibody (Atlas antibodies #HPA031755) was used at 1:100 dilution in Blocking Buffer (BlocB) (Wash buffer containing 2mM EDTA). Same steps were followed for histone marks using anti-H3K9me2 (Active Motif #39239, 1:100), anti-H3K9me3 (Abcam# ab8898; 1:100), anti-H3K27me3 (Cell signaling technologies #9733; 1:100). An IgG control was run in parallel for all experiments (Cell signaling technologies #2729; 1:100). To each sample 50 mL of BlocB containing primary antibody was added and incubated overnight on a rotator at 40C. Next day, samples were briefly spun and placed on magnetic stand to clear off the liquid. Samples were washed twice with 1mL Wash Buffer (WaB) (20 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 0.1% BSA, 0.5 mM Spermidine and 1X Halt protease inhibitor cocktail). At the end of two washing steps, Concanavalin A bound nuclei were resuspended in 50 mL of WaB and gently mixed. To each tube, 2.5 mL of pA-MNase (diluted 1:10 in WaB from 140 mg/mL stock) kindly provided by Steven Henikoff (Fred Hutchison Cancer Research Center) was added and rotated for 1 hour at 40C. Samples were briefly spun and placed on magnetic stand to remove the liquid. Samples were washed twice with 1mL WaB. At the end of two washing steps, Concanavalin A bound nuclei were resuspended in 100 mL of WaB and gently mixed. The tubes were placed in pre-chilled metal blocks sitting in ice. While gently vortexing, 2 mL of 100 mM CaCl2 was added to initiate MNase digestion and returned to pre-chilled metal blocks. Digestion was carried out for 30 min and stopped by adding 100 mL of 2XSTOP (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 mg/mL RNAseA, 40 mg/mL Glycogen and 10 pg/mL of heterologous DNA) while gently vortexing. To release pA-MNase cleaved fragments, samples were incubated at 370C for 15 min. DNA was extracted using Phenol: Chloroform extraction method. We considered the possibility that the pA-MNase cleaved DNA-protein complexes might be too large to diffuse out of the nucleus and enter the “soluble” fraction.  To test this, we recovered DNA from both soluble and total fractions (soluble + insoluble).  LaminB profiles were highly similar (Pearson= 0.94) between soluble and total fractions, indicating that DNA-protein complexes released by LaminB GO-CaRT can readily diffuse out of the nucleus.
Sequencing libraries were prepared from GO-CaRT DNA fragments using KAPA HyperPlus with amplification DNA library preparation kit (#KK8512) following manufacturer instructions. The library was amplified for 13-15 PCR cycles and larger DNA fragments were depleted by doing a 0.55X size selection using Agencourt AMPure XP beads (Beckman #A63881).


title: E13 NesGFP PFC H3K9me2 GO-CaRT

source_name: Embryonic Mouse Telencephalon

value: Embryonic Mouse Telencephalon

value: Embryonic Day 13

value: (C57BL/6 x BALB/cBy)F1


title: HEK293T SON GO-CaRT Rep1


title: E13 Liver LaminB GO-CaRT Rep 2

source_name: Embryonic Mouse Liver

value: Embryonic Mouse Liver


title: E13 Lung LaminB GO-CaRT Rep 2

source_name: Embryonic Mouse Lung

value: Embryonic Mouse Lung


title: HEK293T LaminB GO-CaRT Rep2


title: E13 Lung LaminB GO-CaRT Rep 1


title: 2FL_C


title: E13 Liver LaminB GO-CaRT Rep 1


title: 3T3 MEFs LaminB GO-CaRT Total Rep 2

source_name: NIH/3T3 cells

value: NIH/3T3 cells


title: 3T3 MEFs H3K9me3 GO-CaRT Rep 1


title: 3T3 MEFs LaminB GO-CaRT Soluble Rep 1


title: 3T3 MEFs H3K27me3 GO-CaRT Soluble Rep 1


title: 3T3 MEFs LaminB GO-CaRT Total Rep 1


title: 3T3 MEFs H3K9me2 GO-CaRT Rep 1


title: SVZ-cNSCs LaminB GO-CaRT

growth_protocol: Following microdissection of the V-SVZ, cells were dissociated and cultured in proliferative medium (DMEM/F12 with Glutamax, 5% Fetal Bovine Serum, N2 supplement, 35 µg/mL bovine pituitary extract, 20 ng/mL EGF, 20 ng/mL FGF, antibiotic/antimycotic) for 3-4 passages. To allow for differentiation, cultures were switched to differentiation medium (DMEM/F12 with Glutamax, 2% Fetal Bovine Serum, N2 supplement, 35 µg/mL bovine pituitary extract, antibiotic/antimycotic) and cultured for 7 days.

value: Derived from postnatal day 7


title: ChIPseq_neurons_IgG_r2

status: Public on May 25 2021

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 1.18.64 (HiSeq 2500) or RTA 2.4.1 (MiSeq) and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. ChIP-seq samples were aligned to the mm10/hg19 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters, allowing only for uniquely mapping reads.
Genome_build: mm10/hg19
wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and setting shift to the inferred shifts (Methods). The scores in the wig file therefore represent the number of shifted alignments per 100bp window and per million reads in the library. Peaks were identified using MACS2 using default parameters, except for the option -g, which was set to the mappable genome size for mm10 and hg19 respectively. For the mouse samples, MACS2 was run using the IgG samples as a control, for the human samples, no control was used. Resulting peaks were then filtered for mappability, whereby only peaks that were at least 80% mappable were retained for further analysis. Mappability was defined as the fraction of all possible 50mers contained in a given region that were mappable using the same alignment parameters as used to map the ChIP-seq data. For all downstream analysis, only reproducible peaks, i.e. peaks that occured in all replicates, were used. Scores in the bed files correspond to log2 enrichment over IgG for mouse or log2 read counts for human samples.
Banp motif matches for mm10 and hg19 (PredictedBanpMotifs_withChIPsignal_mm10.csv, PredictedBanpMotifs_withChIPsignal_hg19.csv) were defined as matches to the Banp weight matrix with a log2-odds score (versus a uniform background) of at least 12.5 (Methods). ChIP signal was calculated in a 201 bp window centered on each motif. File columns described in file header.

source_name: Ngn2-induced neurons

growth_protocol: For neural differentiation, dishes were coated with sterile filtered (0.22μm) Poly-D-lysine hydrobromide (0.5mg/ml, Sigma, P-7886-100MG) diluted in Borate Buffer (50mM, pH 8.5) for 24 hours at 37oC, washed 3x with sterile water and coated for at least 2 hours with Laminin (6.65ug/ml, Sigma, L2020-1MG) in PBS at 37oC. Wild-type BANP-dTAG ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008), trypsinated and plated at a density of 2x106 per 10cm dish in proliferation medium supplemented with 1μg/ml Doxycycline for three days to generate neurons.

extract_protocol: Three 15 cm dishes per ChIP-seq replicate were seeded (6x106) for neural generation three days before the experiment. Chromatin Immunoprecipitation (ChIP) was carried out as previously described (Lienert, F. et al. Nat. Genet., 2011) with following modifications: (1) Neurons were washed once with PBS, collected in PBS and cross-linked in 10ml PBS with 1% Formaldehyde (Sigma, 252549-25ml) for 10 min at room temperature, (2) chromatin was sonicated for ~22 cycles of 20 sec. on and 40 sec. off using a Diagenode Bioruptor Pico, (3) 75-200ug of chromatin was used per IP, (4) protein A/G magnetic Dynabeads (Thermo Fisher Scientific) were used.

value: Ngn2-induced neurons

tag: genotype

value: Ngn2 insertion, dTag

tag: chip antibody

value: IgG


title: ChIPseq_neurons_IgG_r3


title: ChIPseq_ESC_Ngn2_uninduced_IgG_r3

source_name: embryonic stem cells

value: embryonic stem cells


title: ChIPseq_ESC_Ngn2_uninduced_IgG_r2


title: ChIPseq_neurons_Banp_r2

value: Banp


title: ChIPseq_ESC_Ngn2_uninduced_IgG_r1


title: ChIPseq_ESC_Ngn2_uninduced_Banp_r3


title: ChIPseq_neurons_Banp_r1


title: HEK293T LaminB GO-CaRT Rep1


title: ChIPseq_ESC_Ngn2_uninduced_Banp_r2


title: TF ChIP-seq from brain (ENCLB382ZFI)

status: Public on May 23 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR467EQP/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR467EQP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR688WUZ
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB382ZFI
fragmentation methods: sonication (generic)
size range: 200-600

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

source_name: Homo sapiens female embryo (5 days) brain organoid

tag: antibody

value: CTCF

value: brain

value: organoid

tag: biosample encode accession

value: female

tag: health state

value: healthy

tag: dev stage

value: embryonic

value: 5 day

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Paola Arlotta

tag: link

value: ENCBS141JNO at ENCODE; https://www.encodeproject.org/ENCBS141JNO/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: TF ChIP-seq from K562 (ENCLB456WMS)

description:
https://www.encodeproject.org/experiments/ENCSR967AVR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZBTB5 ChIP-seq on human K562
experiment encode accession: ENCSR967AVR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR502RHA, ENCSR328FYU
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB456WMS
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZBTB5

tag: line

value: cell line

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB5.

tag: Sex

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: chronic myelogenous leukemia (CML)

value: ENCBS562MDX at ENCODE; https://www.encodeproject.org/ENCBS562MDX/

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


title: TF ChIP-seq from HepG2 (ENCLB882ZAU)

description:
https://www.encodeproject.org/experiments/ENCSR944LSA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR944LSA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR020QUJ
encode release date: 2020-07-08
lab: Richard Myers, HAIB
library encode accession: ENCLB882ZAU
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting DBP

value: DBP

value: male

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS604NXD at ENCODE; https://www.encodeproject.org/ENCBS604NXD/

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


title: TF ChIP-seq from SK-N-SH (ENCLB071DIN)

description:
https://www.encodeproject.org/experiments/ENCSR969AIM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-PATZ1 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR969AIM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR593IWN, ENCSR481DSF
encode release date: 2020-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB071DIN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting PATZ1 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: cell line

value: female

value: 4 year

value: ATCC

value: Metastatic neuroblastoma from bone marrow

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS568BOG at ENCODE; https://www.encodeproject.org/ENCBS568BOG/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: TF ChIP-seq from HepG2 (ENCLB295EVQ)

description:
https://www.encodeproject.org/experiments/ENCSR944LSA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR944LSA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR020QUJ
encode release date: 2020-07-08
lab: Richard Myers, HAIB
library encode accession: ENCLB295EVQ
fragmentation methods: sonication (generic)

value: DBP

value: male

tag: age

value: ENCBS250UWW at ENCODE; https://www.encodeproject.org/ENCBS250UWW/


title: TF ChIP-seq from SK-N-SH (ENCLB982UVI)

description:
https://www.encodeproject.org/experiments/ENCSR969AIM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-PATZ1 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR969AIM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR593IWN, ENCSR481DSF
encode release date: 2020-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB982UVI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: child

value: Michael Snyder, Stanford

value: ENCBS307WPO at ENCODE; https://www.encodeproject.org/ENCBS307WPO/


title: Histone ChIP-seq from WERI-Rb-1 (ENCLB810VIW)

description:
https://www.encodeproject.org/experiments/ENCSR967DBV/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on human WERI-Rb-1
experiment encode accession: ENCSR967DBV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR723FET
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB810VIW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WERI-Rb-1 cell line

value: retinoblastoma

value: 1 year

value: ENCBS161OJA at ENCODE; https://www.encodeproject.org/ENCBS161OJA/

value: Derived from ENCODE donor ENCDO000ADT; https://www.encodeproject.org/ENCDO000ADT/


title: ChIPseq_neurons_IgG_r1

tag: cell type

value: Ngn2-induced neurons

value: Ngn2 insertion, dTag

value: IgG


title: ChIPseq_ESC_Ngn2_uninduced_Banp_r1

value: embryonic stem cells

value: Banp


title: TF ChIP-seq from SK-N-SH (ENCLB006GMW)

description:
https://www.encodeproject.org/experiments/ENCSR949COJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ARNTL ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR949COJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR566WAB, ENCSR618JZG
encode release date: 2020-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB006GMW
size range: 450-650

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting ARNTL treated with 6uM all-trans-retinoic acid for 48 hours

value: ARNTL

value: SK-N-SH

value: cell line

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ARNTL.

value: female

value: 4 year

value: Michael Snyder

value: Metastatic neuroblastoma from bone marrow

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS992OPI at ENCODE; https://www.encodeproject.org/ENCBS992OPI/


title: TF ChIP-seq from K562 (ENCLB157YYR)

description:
https://www.encodeproject.org/experiments/ENCSR967AVR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZBTB5 ChIP-seq on human K562
experiment encode accession: ENCSR967AVR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR502RHA, ENCSR328FYU
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB157YYR
size range: 450-650

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB5.

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: chronic myelogenous leukemia (CML)

value: ENCBS119HSP at ENCODE; https://www.encodeproject.org/ENCBS119HSP/

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


title: Histone ChIP-seq from WERI-Rb-1 (ENCLB452JZV)

description:
https://www.encodeproject.org/experiments/ENCSR967DBV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on human WERI-Rb-1
experiment encode accession: ENCSR967DBV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR723FET
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB452JZV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: retinoblastoma

value: child

value: 1 year

value: ATCC

value: ENCBS176OOK at ENCODE; https://www.encodeproject.org/ENCBS176OOK/

value: Derived from ENCODE donor ENCDO000ADT; https://www.encodeproject.org/ENCDO000ADT/


title: TF ChIP-seq from A549 (ENCLB009BQI)

description:
https://www.encodeproject.org/experiments/ENCSR908AOO/
***************
biological replicate number: 1
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR908AOO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR212FST
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB009BQI
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 15 minutes

value: cell line

value: male

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:15; duration_units:minute;

value: ENCBS173GFE at ENCODE; https://www.encodeproject.org/ENCBS173GFE/

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


title: TF ChIP-seq from A549 (ENCLB786FTI)

description:
https://www.encodeproject.org/experiments/ENCSR908AOO/
***************
biological replicate number: 2
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR908AOO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR212FST
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB786FTI
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: ENCBS329VDX at ENCODE; https://www.encodeproject.org/ENCBS329VDX/


title: TF ChIP-seq from A549 (ENCLB787CWE)

description:
https://www.encodeproject.org/experiments/ENCSR908AOO/
***************
biological replicate number: 3
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR908AOO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR212FST
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB787CWE
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS865TFY at ENCODE; https://www.encodeproject.org/ENCBS865TFY/


title: TF ChIP-seq from A549 (ENCLB162DTJ)

description:
https://www.encodeproject.org/experiments/ENCSR886OEO/
***************
biological replicate number: 3
technical replicate number: 1
description: EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR886OEO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR814XCZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB162DTJ
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line

value: ENCBS520AXC at ENCODE; https://www.encodeproject.org/ENCBS520AXC/


title: ChIPseq_neurons_Banp_r3

value: Ngn2-induced neurons

value: Ngn2 insertion, dTag

value: Banp


title: TF ChIP-seq from SK-N-SH (ENCLB388CCB)

description:
https://www.encodeproject.org/experiments/ENCSR507BWM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-GLIS3 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR507BWM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR000SND, ENCSR823HRT
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB388CCB
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting GLIS3 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: female

value: child

value: 4 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: Metastatic neuroblastoma from bone marrow

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS071NZE at ENCODE; https://www.encodeproject.org/ENCBS071NZE/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: TF ChIP-seq from MCF-7 (ENCLB086QQS)

description:
https://www.encodeproject.org/experiments/ENCSR877UJB/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-ZNF227 ChIP-seq on human MCF-7
experiment encode accession: ENCSR877UJB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR349CUL, ENCSR734XLI
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB086QQS
size range: 450-650

source_name: Homo sapiens MCF-7 cell line genetically modified (insertion) using CRISPR targeting ZNF227

value: cell line

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF227.

value: adult

value: 69 year

value: Kevin White

value: breast cancer (adenocarcinoma)

value: ENCBS120PYB at ENCODE; https://www.encodeproject.org/ENCBS120PYB/

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


title: TF ChIP-seq from SK-N-SH (ENCLB664BHK)

description:
https://www.encodeproject.org/experiments/ENCSR507BWM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-GLIS3 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR507BWM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR000SND, ENCSR823HRT
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB664BHK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: SK-N-SH

value: female

value: ENCBS038REP at ENCODE; https://www.encodeproject.org/ENCBS038REP/


title: Histone ChIP-seq from A549 (ENCLB199OME)

description:
https://www.encodeproject.org/experiments/ENCSR480OHP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.
experiment encode accession: ENCSR480OHP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR344CSQ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB199OME
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 25 minutes

value: male

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:25; duration_units:minute;

value: ENCBS128BGV at ENCODE; https://www.encodeproject.org/ENCBS128BGV/

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


title: Histone ChIP-seq from A549 (ENCLB728GFT)

description:
https://www.encodeproject.org/experiments/ENCSR480OHP/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.
experiment encode accession: ENCSR480OHP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR344CSQ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB728GFT
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: ENCBS334AKK at ENCODE; https://www.encodeproject.org/ENCBS334AKK/


title: Histone ChIP-seq from A549 (ENCLB352VET)

description:
https://www.encodeproject.org/experiments/ENCSR480OHP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 25 mins.
experiment encode accession: ENCSR480OHP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR344CSQ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB352VET
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: ENCBS978CEM at ENCODE; https://www.encodeproject.org/ENCBS978CEM/


title: TF ChIP-seq from SK-N-SH (ENCLB340GTD)

description:
https://www.encodeproject.org/experiments/ENCSR474KBG/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-CSDC2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR474KBG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR850KFE, ENCSR823HRT
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB340GTD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting CSDC2 treated with 6uM all-trans-retinoic acid for 48 hours

value: child

value: 4 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: Metastatic neuroblastoma from bone marrow

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS377IYO at ENCODE; https://www.encodeproject.org/ENCBS377IYO/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: TF ChIP-seq from MCF-7 (ENCLB286PLW)

description:
https://www.encodeproject.org/experiments/ENCSR877UJB/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF227 ChIP-seq on human MCF-7
experiment encode accession: ENCSR877UJB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR349CUL, ENCSR734XLI
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB286PLW
size range: 450-650

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF227.

value: female

value: 69 year

value: Kevin White

value: breast cancer (adenocarcinoma)

value: ENCBS996JKE at ENCODE; https://www.encodeproject.org/ENCBS996JKE/

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


title: TF ChIP-seq from SK-N-SH (ENCLB663ZCN)

description:
https://www.encodeproject.org/experiments/ENCSR474KBG/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-CSDC2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR474KBG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR850KFE, ENCSR823HRT
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB663ZCN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: SK-N-SH

value: cell line

value: ENCBS948IUU at ENCODE; https://www.encodeproject.org/ENCBS948IUU/


title: TF ChIP-seq from SK-N-SH (ENCLB697BCX)

description:
https://www.encodeproject.org/experiments/ENCSR949COJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ARNTL ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR949COJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR566WAB, ENCSR618JZG
encode release date: 2020-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB697BCX
size range: 450-650

value: ARNTL

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ARNTL.

value: child

value: 4 year

value: ENCBS813UGC at ENCODE; https://www.encodeproject.org/ENCBS813UGC/


title: Histone ChIP-seq from A549 (ENCLB756VWU)

description:
https://www.encodeproject.org/experiments/ENCSR864KVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.
experiment encode accession: ENCSR864KVZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR324VMZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB756VWU
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 20 minutes

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:20; duration_units:minute;

value: ENCBS010CCH at ENCODE; https://www.encodeproject.org/ENCBS010CCH/

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


title: Histone ChIP-seq from A549 (ENCLB603HPF)

description:
https://www.encodeproject.org/experiments/ENCSR864KVZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.
experiment encode accession: ENCSR864KVZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR324VMZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB603HPF
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS331TBM at ENCODE; https://www.encodeproject.org/ENCBS331TBM/


title: TF ChIP-seq from MCF-7 (ENCLB750FJE)

description:
https://www.encodeproject.org/experiments/ENCSR860XVO/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF331 ChIP-seq on human MCF-7
experiment encode accession: ENCSR860XVO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR438BNB, ENCSR734XLI
encode release date: 2020-07-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB750FJE
size range: 450-650

source_name: Homo sapiens MCF-7 cell line genetically modified (insertion) using CRISPR targeting ZNF331

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF331.

value: female

value: 69 year

value: Michael Snyder, Stanford

value: Kevin White

value: breast cancer (adenocarcinoma)

value: ENCBS558SHQ at ENCODE; https://www.encodeproject.org/ENCBS558SHQ/

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


title: TF ChIP-seq from A549 (ENCLB401CGM)

description:
https://www.encodeproject.org/experiments/ENCSR471EKW/
***************
biological replicate number: 1
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.
experiment encode accession: ENCSR471EKW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR204GMP
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB401CGM
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 10 minutes

value: cell line

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:minute;

value: ENCBS301FPL at ENCODE; https://www.encodeproject.org/ENCBS301FPL/


title: TF ChIP-seq from A549 (ENCLB383WPJ)

description:
https://www.encodeproject.org/experiments/ENCSR471EKW/
***************
biological replicate number: 3
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.
experiment encode accession: ENCSR471EKW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR204GMP
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB383WPJ
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: ENCBS059GTH at ENCODE; https://www.encodeproject.org/ENCBS059GTH/


title: TF ChIP-seq from A549 (ENCLB558AVC)

description:
https://www.encodeproject.org/experiments/ENCSR857QEA/
***************
biological replicate number: 3
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.
experiment encode accession: ENCSR857QEA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR085WWL
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB558AVC
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 5 minutes

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:minute;

value: ENCBS396JKU at ENCODE; https://www.encodeproject.org/ENCBS396JKU/

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


title: TF ChIP-seq from A549 (ENCLB028CWV)

description:
https://www.encodeproject.org/experiments/ENCSR471EKW/
***************
biological replicate number: 2
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 mins.
experiment encode accession: ENCSR471EKW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR204GMP
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB028CWV
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS478CQR at ENCODE; https://www.encodeproject.org/ENCBS478CQR/


title: TF ChIP-seq from SK-N-SH (ENCLB832GIO)

description:
https://www.encodeproject.org/experiments/ENCSR837YGS/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF608 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR837YGS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR459TUR, ENCSR072QAK
encode release date: 2021-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB832GIO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting ZNF608 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: female

value: child

value: 4 year

value: Michael Snyder, Stanford

value: Metastatic neuroblastoma from bone marrow

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS816AOG at ENCODE; https://www.encodeproject.org/ENCBS816AOG/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: TF ChIP-seq from SK-N-SH (ENCLB656NZB)

description:
https://www.encodeproject.org/experiments/ENCSR837YGS/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF608 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR837YGS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR459TUR, ENCSR072QAK
encode release date: 2021-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB656NZB
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: ENCBS250QAL at ENCODE; https://www.encodeproject.org/ENCBS250QAL/


title: TF ChIP-seq from A549 (ENCLB625AUV)

description:
https://www.encodeproject.org/experiments/ENCSR458VTP/
***************
biological replicate number: 3
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.
experiment encode accession: ENCSR458VTP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR324VMZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB625AUV
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:20; duration_units:minute;

value: ENCBS145FXO at ENCODE; https://www.encodeproject.org/ENCBS145FXO/


title: TF ChIP-seq from A549 (ENCLB969QJX)

description:
https://www.encodeproject.org/experiments/ENCSR458VTP/
***************
biological replicate number: 1
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.
experiment encode accession: ENCSR458VTP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR324VMZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB969QJX
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS246FMQ at ENCODE; https://www.encodeproject.org/ENCBS246FMQ/

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


title: TF ChIP-seq from A549 (ENCLB656TLU)

description:
https://www.encodeproject.org/experiments/ENCSR458VTP/
***************
biological replicate number: 2
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.
experiment encode accession: ENCSR458VTP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR324VMZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB656TLU
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS686ZWW at ENCODE; https://www.encodeproject.org/ENCBS686ZWW/


title: TF ChIP-seq from A549 (ENCLB870BVG)

description:
https://www.encodeproject.org/experiments/ENCSR857QEA/
***************
biological replicate number: 1
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.
experiment encode accession: ENCSR857QEA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR085WWL
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB870BVG
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:minute;

value: ENCBS062PME at ENCODE; https://www.encodeproject.org/ENCBS062PME/


title: TF ChIP-seq from A549 (ENCLB041MYT)

description:
https://www.encodeproject.org/experiments/ENCSR886OEO/
***************
biological replicate number: 2
technical replicate number: 1
description: EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR886OEO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR814XCZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB041MYT
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS937BMQ at ENCODE; https://www.encodeproject.org/ENCBS937BMQ/


title: TF ChIP-seq from A549 (ENCLB025ERZ)

description:
https://www.encodeproject.org/experiments/ENCSR857QEA/
***************
biological replicate number: 2
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.
experiment encode accession: ENCSR857QEA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR085WWL
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB025ERZ
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS820SVQ at ENCODE; https://www.encodeproject.org/ENCBS820SVQ/


title: TF ChIP-seq from K562 (ENCLB651RPO)

description:
https://www.encodeproject.org/experiments/ENCSR426PTT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-FOXO4 ChIP-seq on human K562
experiment encode accession: ENCSR426PTT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR972WGP, ENCSR328FYU
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB651RPO
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting FOXO4

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to FOXO4.

value: female

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: chronic myelogenous leukemia (CML)

value: ENCBS252AWA at ENCODE; https://www.encodeproject.org/ENCBS252AWA/

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


title: TF ChIP-seq from K562 (ENCLB858IFI)

description:
https://www.encodeproject.org/experiments/ENCSR426PTT/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-FOXO4 ChIP-seq on human K562
experiment encode accession: ENCSR426PTT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR972WGP, ENCSR328FYU
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB858IFI
size range: 450-650

value: cell line

value: adult

value: ENCBS223NLO at ENCODE; https://www.encodeproject.org/ENCBS223NLO/


title: Histone ChIP-seq from WERI-Rb-1 (ENCLB121GTZ)

description:
https://www.encodeproject.org/experiments/ENCSR371OZG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on human WERI-Rb-1
experiment encode accession: ENCSR371OZG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR723FET
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB121GTZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: retinoblastoma

value: child

value: 1 year

value: ATCC

value: ENCBS176OOK at ENCODE; https://www.encodeproject.org/ENCBS176OOK/

value: Derived from ENCODE donor ENCDO000ADT; https://www.encodeproject.org/ENCDO000ADT/


title: Histone ChIP-seq from WERI-Rb-1 (ENCLB736TSE)

description:
https://www.encodeproject.org/experiments/ENCSR371OZG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on human WERI-Rb-1
experiment encode accession: ENCSR371OZG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR723FET
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB736TSE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: ENCBS161OJA at ENCODE; https://www.encodeproject.org/ENCBS161OJA/


title: TF ChIP-seq from A549 (ENCLB702IEK)

description:
https://www.encodeproject.org/experiments/ENCSR355HLV/
***************
biological replicate number: 1
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR355HLV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR814XCZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB702IEK
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: 58 year

value: Tim Reddy, Duke

value: ENCBS919WJV at ENCODE; https://www.encodeproject.org/ENCBS919WJV/

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


title: TF ChIP-seq from foreskin keratinocyte (ENCLB578AIO)

description:
https://www.encodeproject.org/experiments/ENCSR817HTJ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR817HTJ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR631ESZ
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB578AIO

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell

value: CTCF

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 0.0

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: Healthy

tag: passage number

value: ENCBS538XZS at ENCODE; https://www.encodeproject.org/ENCBS538XZS/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: TF ChIP-seq from foreskin keratinocyte (ENCLB979SMZ)

description:
https://www.encodeproject.org/experiments/ENCSR817HTJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR817HTJ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR631ESZ
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB979SMZ

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, grown in 2D culture, day 0.0

value: ENCBS666IIR at ENCODE; https://www.encodeproject.org/ENCBS666IIR/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: TF ChIP-seq from A549 (ENCLB588SJH)

description:
https://www.encodeproject.org/experiments/ENCSR355HLV/
***************
biological replicate number: 2
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR355HLV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR814XCZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB588SJH
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: ENCBS149KNM at ENCODE; https://www.encodeproject.org/ENCBS149KNM/


title: TF ChIP-seq from A549 (ENCLB353GHS)

description:
https://www.encodeproject.org/experiments/ENCSR355HLV/
***************
biological replicate number: 3
technical replicate number: 1
description: GR ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR355HLV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR814XCZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB353GHS
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS054AGF at ENCODE; https://www.encodeproject.org/ENCBS054AGF/

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


title: Histone ChIP-seq from A549 (ENCLB997KWT)

description:
https://www.encodeproject.org/experiments/ENCSR325VCV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR325VCV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR212FST
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB997KWT
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:15; duration_units:minute;

value: ENCBS071SOD at ENCODE; https://www.encodeproject.org/ENCBS071SOD/


title: TF ChIP-seq from MCF-7 (ENCLB885LCV)

description:
https://www.encodeproject.org/experiments/ENCSR860XVO/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF331 ChIP-seq on human MCF-7
experiment encode accession: ENCSR860XVO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR438BNB, ENCSR734XLI
encode release date: 2020-07-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB885LCV
size range: 450-650

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF331.

value: female

value: 69 year

value: Michael Snyder, Stanford

value: Kevin White

value: breast cancer (adenocarcinoma)

value: ENCBS008SGA at ENCODE; https://www.encodeproject.org/ENCBS008SGA/

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


title: Histone ChIP-seq from A549 (ENCLB127NXZ)

description:
https://www.encodeproject.org/experiments/ENCSR864KVZ/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 20 mins.
experiment encode accession: ENCSR864KVZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR324VMZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB127NXZ
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: male

value: adult

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:20; duration_units:minute;

value: ENCBS026DZZ at ENCODE; https://www.encodeproject.org/ENCBS026DZZ/


title: Histone ChIP-seq from A549 (ENCLB956WRL)

description:
https://www.encodeproject.org/experiments/ENCSR325VCV/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR325VCV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR212FST
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB956WRL
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: ENCBS982NSX at ENCODE; https://www.encodeproject.org/ENCBS982NSX/


title: Histone ChIP-seq from A549 (ENCLB411VUU)

description:
https://www.encodeproject.org/experiments/ENCSR325VCV/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR325VCV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR212FST
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB411VUU
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:15; duration_units:minute;

value: ENCBS334UWV at ENCODE; https://www.encodeproject.org/ENCBS334UWV/

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


title: TF ChIP-seq from foreskin keratinocyte (ENCLB134JON)

description:
https://www.encodeproject.org/experiments/ENCSR812FNU/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR812FNU
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR335GGM
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB134JON

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 5.5 days

value: CTCF

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

value: Healthy

value: ENCBS389AUD at ENCODE; https://www.encodeproject.org/ENCBS389AUD/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: TF ChIP-seq from A549 (ENCLB053AQJ)

description:
https://www.encodeproject.org/experiments/ENCSR788VKG/
***************
biological replicate number: 2
technical replicate number: 1
description: EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR788VKG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR212FST
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB053AQJ
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: ENCBS889KBF at ENCODE; https://www.encodeproject.org/ENCBS889KBF/


title: Histone ChIP-seq from RWPE2 (ENCLB995QFS)

description:
https://www.encodeproject.org/experiments/ENCSR785DEU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on human RWPE2
experiment encode accession: ENCSR785DEU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR753IXW
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB995QFS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens RWPE2 cell line

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS017OST at ENCODE; https://www.encodeproject.org/ENCBS017OST/

value: Derived from ENCODE donor ENCDO135ZNV; https://www.encodeproject.org/ENCDO135ZNV/


title: TF ChIP-seq from SK-N-SH (ENCLB071HPY)

description:
https://www.encodeproject.org/experiments/ENCSR325QLX/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF8 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR325QLX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR995TTS, ENCSR618JZG
encode release date: 2020-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB071HPY
size range: 450-650

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting ZNF8 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF8.

value: female

value: child

value: 4 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: Metastatic neuroblastoma from bone marrow

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS422KTW at ENCODE; https://www.encodeproject.org/ENCBS422KTW/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: Histone ChIP-seq from RWPE2 (ENCLB077URQ)

description:
https://www.encodeproject.org/experiments/ENCSR297ONS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on human RWPE2
experiment encode accession: ENCSR297ONS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR753IXW
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB077URQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: male

value: ATCC


title: TF ChIP-seq from A549 (ENCLB092FBR)

description:
https://www.encodeproject.org/experiments/ENCSR788VKG/
***************
biological replicate number: 3
technical replicate number: 1
description: EP300 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 15 mins.
experiment encode accession: ENCSR788VKG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR212FST
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB092FBR
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:15; duration_units:minute;

value: ENCBS292ELQ at ENCODE; https://www.encodeproject.org/ENCBS292ELQ/

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


title: TF ChIP-seq from HepG2 (ENCLB271BQR)

description:
https://www.encodeproject.org/experiments/ENCSR288ZFV/
***************
biological replicate number: 2
technical replicate number: 1
description: HepG2 immortalized cell line stably expressing C-terminal eGFP-ATF4 fusion protein.
experiment encode accession: ENCSR288ZFV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR149IMO, ENCSR592WMK
encode release date: 2020-07-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB271BQR
size range: 450-650

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting ATF4

value: HepG2 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ATF4.

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS050IJL at ENCODE; https://www.encodeproject.org/ENCBS050IJL/

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


title: Histone ChIP-seq from RWPE2 (ENCLB253NYL)

description:
https://www.encodeproject.org/experiments/ENCSR784MON/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on human RWPE2
experiment encode accession: ENCSR784MON
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR753IXW
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB253NYL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS017OST at ENCODE; https://www.encodeproject.org/ENCBS017OST/

value: Derived from ENCODE donor ENCDO135ZNV; https://www.encodeproject.org/ENCDO135ZNV/


title: TF ChIP-seq from SK-N-SH (ENCLB698REB)

description:
https://www.encodeproject.org/experiments/ENCSR325QLX/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF8 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR325QLX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR995TTS, ENCSR618JZG
encode release date: 2020-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB698REB
size range: 450-650

value: SK-N-SH

value: cell line

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF8.

value: female

value: 4 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: Metastatic neuroblastoma from bone marrow

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS323PGI at ENCODE; https://www.encodeproject.org/ENCBS323PGI/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: TF ChIP-seq from SK-N-SH (ENCLB752BUU)

description:
https://www.encodeproject.org/experiments/ENCSR282NLQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TSHZ2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR282NLQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR823HRT, ENCSR358RZO
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB752BUU
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting TSHZ2 treated with 6uM all-trans-retinoic acid for 48 hours

value: child

value: ENCBS743KWD at ENCODE; https://www.encodeproject.org/ENCBS743KWD/


title: TF ChIP-seq from HepG2 (ENCLB420TKX)

description:
https://www.encodeproject.org/experiments/ENCSR288ZFV/
***************
biological replicate number: 1
technical replicate number: 1
description: HepG2 immortalized cell line stably expressing C-terminal eGFP-ATF4 fusion protein.
experiment encode accession: ENCSR288ZFV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR149IMO, ENCSR592WMK
encode release date: 2020-07-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB420TKX
size range: 450-650

value: HepG2 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ATF4.

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS039CPR at ENCODE; https://www.encodeproject.org/ENCBS039CPR/

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


title: Histone ChIP-seq from RWPE2 (ENCLB083WUC)

description:
https://www.encodeproject.org/experiments/ENCSR784MON/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on human RWPE2
experiment encode accession: ENCSR784MON
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR753IXW
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB083WUC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: unknown

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS314QIO at ENCODE; https://www.encodeproject.org/ENCBS314QIO/

value: Derived from ENCODE donor ENCDO135ZNV; https://www.encodeproject.org/ENCDO135ZNV/


title: TF ChIP-seq from SK-N-SH (ENCLB383ZDI)

description:
https://www.encodeproject.org/experiments/ENCSR282NLQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TSHZ2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR282NLQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR823HRT, ENCSR358RZO
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB383ZDI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: SK-N-SH

value: female

value: 4 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: Metastatic neuroblastoma from bone marrow

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS657ZAZ at ENCODE; https://www.encodeproject.org/ENCBS657ZAZ/


title: TF ChIP-seq from foreskin keratinocyte (ENCLB021PUV)

description:
https://www.encodeproject.org/experiments/ENCSR812FNU/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR812FNU
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR335GGM
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB021PUV

value: CTCF

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

value: male

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

value: Healthy

value: ENCBS135YLX at ENCODE; https://www.encodeproject.org/ENCBS135YLX/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: Histone ChIP-seq from A549 (ENCLB952KJF)

description:
https://www.encodeproject.org/experiments/ENCSR778NQS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR778NQS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR814XCZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB952KJF
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line

value: cell line

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: ENCBS192IRK at ENCODE; https://www.encodeproject.org/ENCBS192IRK/

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


title: Histone ChIP-seq from A549 (ENCLB837AFL)

description:
https://www.encodeproject.org/experiments/ENCSR778NQS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR778NQS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR814XCZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB837AFL
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS297OJC at ENCODE; https://www.encodeproject.org/ENCBS297OJC/


title: TF ChIP-seq from SK-N-SH (ENCLB324PMI)

description:
https://www.encodeproject.org/experiments/ENCSR754GYI/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-BNC2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR754GYI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR540RTZ, ENCSR042UCB
encode release date: 2020-08-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB324PMI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting BNC2 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: female

value: child

value: 4 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: Metastatic neuroblastoma from bone marrow

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS806SBR at ENCODE; https://www.encodeproject.org/ENCBS806SBR/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: TF ChIP-seq from SK-N-SH (ENCLB455IYY)

description:
https://www.encodeproject.org/experiments/ENCSR758GOA/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-CREB5 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR758GOA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR042UCB, ENCSR411AFQ
encode release date: 2020-08-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB455IYY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting CREB5 treated with 6uM all-trans-retinoic acid for 48 hours

value: cell line

value: ENCBS860TSU at ENCODE; https://www.encodeproject.org/ENCBS860TSU/


title: TF ChIP-seq from SK-N-SH (ENCLB125JAE)

description:
https://www.encodeproject.org/experiments/ENCSR754ALX/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF565 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR754ALX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR247NVH, ENCSR618JZG
encode release date: 2020-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB125JAE
size range: 450-650

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting ZNF565 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF565.

value: ENCBS779NHJ at ENCODE; https://www.encodeproject.org/ENCBS779NHJ/


title: TF ChIP-seq from SK-N-SH (ENCLB963NFG)

description:
https://www.encodeproject.org/experiments/ENCSR226NRS/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TOX2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR226NRS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR684GHA, ENCSR618JZG
encode release date: 2020-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB963NFG
size range: 450-650

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting TOX2 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to TOX2.

value: ENCBS462YCT at ENCODE; https://www.encodeproject.org/ENCBS462YCT/


title: TF ChIP-seq from SK-N-SH (ENCLB423WTK)

description:
https://www.encodeproject.org/experiments/ENCSR226NRS/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TOX2 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR226NRS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR684GHA, ENCSR618JZG
encode release date: 2020-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB423WTK
size range: 450-650

value: ENCBS996JXR at ENCODE; https://www.encodeproject.org/ENCBS996JXR/


title: Histone ChIP-seq from A549 (ENCLB760NIV)

description:
https://www.encodeproject.org/experiments/ENCSR734FLK/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 mins.
experiment encode accession: ENCSR734FLK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR085WWL
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB760NIV
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:minute;

value: ENCBS349MXJ at ENCODE; https://www.encodeproject.org/ENCBS349MXJ/

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


title: Histone ChIP-seq from A549 (ENCLB134JFM)

description:
https://www.encodeproject.org/experiments/ENCSR778NQS/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 mins.
experiment encode accession: ENCSR778NQS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR814XCZ
encode release date: 2017-10-19
lab: Tim Reddy, Duke
library encode accession: ENCLB134JFM
fragmentation methods: sonication (Bioruptor Twin)
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS431BEM at ENCODE; https://www.encodeproject.org/ENCBS431BEM/