title: patient#1 pre-Neosporin

description:
Gene expression data from unwounded human popliteal fossae.
patient#1 pre-Neosporin


title: patient#1 pre-vaseline

status: Public on Apr 01 2021

type: RNA

city: Baltimore

first: Luis

last: Garza

state: Maryland

address: 1551 Orleans Street

department: Dermatology

country: USA

institute: Johns Hopkins University

description:
Gene expression data from unwounded human popliteal fossae.
patient#1 pre-vaseline

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform. RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
Clariom_S_Human.r1.pgf
Clariom_S_Human.na36.mm10.transcript.csv

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Skin before treatment

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix GeneChip 3' IVT Plus Kit per manufacturer's instructions.

growth_protocol: 4-mm punch biopsies, microbiome swabs, and clinical photographs of bilateral popliteal fossae (PF). were obtained from participants under the above IRB protocol. Participants were asked to avoid washing 24 hours prior to sample collection and to use scent-free, non-antibacterial soap for the duration of the study. Samples were collected at two visits spanning an average of 15 days, including at a baseline visit prior to intervention (Day 0) and at a follow-up visit following secondary intention to obtain post-treatment samples (Day 15). A total of 12 skin biopsies were obtained from 3 individuals at identical anatomical sites across 2 time points. For tissue collection, 1% lidocaine with epinephrine was administered, and 4mm full-thickness punch biopsies were obtained from the center PF.

extract_protocol: Total RNA was isolated from cells using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: For the left PF, the wound was washed with Hibiclens (Molnlycke, 57516), and Neosporin was applied (Johnson & Johnson); for the right PF, Vaseline (Unilever) was applied. Both sites were occluded with bandages, and participants were asked to rebandage left and right PF daily with Neosporin and Vaseline, respectively, until wound closure to evaluate the changes in gene expressions.

tag: individual

tag: tissue

value: Popliteal fossa

tag: treatment

value: Untreated


title: breast tumour 10C

city: Dunedin

first: Anita

last: Dunbier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization.

source_name: breast tumour

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: mRNA from tumour biopsies taken 16 weeks after commencement of anastrazole treatement were extracted with an RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: Sex

value: female

tag: timepoint

value: 16 weeks

value: breast tumor

tag: patient

tag: age

tag: size

tag: grade

tag: nodal status

tag: her2 status

tag: pgr status pre_treatment

tag: response

value: Stable/No Response


title: Input-rep2

type: SRA

city: wuhan

first: Haojian

last: Zhang

state: Hubei

address: Donghu Rd

department: Medical Research Institute

country: China

institute: Wuhan university

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to Hg19 whole transcriptome using hisat v2.1.0 with default parameters
bigWig files were generated using Deeptools v2.0 bamCoverage with parameters --binSize 10 --normalizeUsingRPKM
Peak were called from macs2(version 2.2.7.1) with q-value <= 0.05
Genome_build: Hg19
Supplementary_files_format_and_content: .bigWig files for each sample

molecule: polyA RNA

growth_protocol: DMEM with 10% FBS, 100 IU ml−1 penicillin and 100μg ml−1 streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent.mRNA are isolated，fragmented and Ybx1-specific antibodies are used to immunoprecipitate RNA. Ybx1 binding RNA is reverse-transcribed to cDNA through first strand synthesis and second strand synthesis
Illumina TruSeq DNA Sample Prep Kit (Cat#15026486) was used with DNA for the construction of sequencing libraries. Libraries were prepared for sequencing using Illumina protocols.

treatment_protocol: Flag-Ybx1 were overexpressed in 293T

tag: cell line

tag: genotype

value: Flag-YBX1 overexpression

tag: rip antibody


title: Input-rep1


title: breast tumour 103C


title: H1694 CRISPR rep2

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline
RNA-seq sequencing quality was checked by running FastQC and TrimGalore was used for dapter and quality trimming. RNA-seq reads were mapped against hg38 using STAR aligner.
Differential gene expression analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files of normalized abundance measurements include baseMean, lfcSE, stat etc.

source_name: Small cell lung cancer cell line

growth_protocol: Cells were grown in medium recommended by the supplier.

extract_protocol:
Total RNA was extracted from cells using the RNeasy kit (Qiagen, Germantown, MD). On-column DNase treatment was given following the procedure provided by the manufacturer.
Strand-specific library was prepared using Illumina TruSeq stranded RNA library prep kit (Illumina, San Diego, CA) according to manufacturer’s protocols.

value: HEPACAM2 knockdown

tag: supplier

value: ATCC


title: a10: EGFR-KO_Kidney_SD

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

country: Germany

institute: Martin Luther University - Halle-Wittenberg

data_processing:
Alignment (HISAT2 2.1.0)
Counting (featureCounts - 2.0.0)
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing raw counts obtained after Counting with featureCounts

organism: Mus musculus

source_name: Kidney from mouse with endothelial cells-EGFR KO

growth_protocol: Mice were kept at constant temperature of 22±2°C, relative humidity of 30–60%, under a 12/12 h light-dark cycle with ad libitum access to water and standard chow. Recently, we generated and described an inducible knock out for EGFR in VSMC via the Cre/loxP system by mating EGFRflox/flox C57BL/6 mice (originally provided by Maria Sibilia, Vienna, Austria) with the B6.Cg-Tg(Tek-cre)1Ywa/J mouse (Cre-Recombinase under control of the Tie2-promotor, purchased from JAX, first described by Dr. Masashi Yanagisawa, Southwestern Medical School)

extract_protocol:
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
mRNA were enriched using oligo(dT) beads and then fragmented randomly by adding fragmentation buffer. cDNA synthesis is done with random hexamers primers and is followed by second strand synthesis after sequencing adaptor ligation. Double-stranded cDNA libraries are then subjected to size selection (250-300bp) and PCR enrichment. Libraries were pooled before clustering on flowcell for sequencing.

treatment_protocol: Mice received 1:1 HFD:SD for seven days at an everage age of 5 weeks, at 6 weeks of age chow was changed to HFD alone for 18 weeks. Afterwards mice were anaesthetized with isofluran, sacrificed in deep narcosis by cervical dislocation. Aortas were freed of adjacent fat and connective tissue, both organs were snap frozen in liquid nitrogen.

tag: organ

value: Kidney

value: EGFR KO

value: SD


title: H1694 CRISPR rep3


title: YBX1-Flag-IP-rep1

value: FLAG (M2, F3165, Sigma-Aldrich)


title: breast tumour 120C

tag: tissue

value: Partial Response


title: a9: EGFR-KO_Kidney_SD

tag: treatment


title: a3: EGFR-KO_Kidney_HFD

value: HFD


title: breast tumour 20C

tag: Sex


title: a4: EGFR-KO_Kidney_HFD


title: breast tumour 132C

tag: timepoint


title: Co-culture P. oleovorans 2

city: Berlin

first: Lisa

middle: Lotte

last: Lemoine

address: Max-Dohrnstraße 8-10

institute: German Federal Institute for Risk Assessment

description: RNA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Hybridization was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) using standard protocol for Affymetrix Clariom S.

scan_protocol: Array scanning was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) according to the manufacturer's instruction (Affymetrix).

data_processing: Raw data were processed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Further analyzing was done using Transcriptome Analysis Console (TAC) Software 4.0.

source_name: Co-culture P. oleovorans

label_protocol: Labelling was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) using standard protocol for Affymetrix Clariom S.

growth_protocol: EpiDermFT™ tissues (MatTek, Ashland, MA) were cultivated in 2.5 ml maintenance medium (EPI-100-MM-ABF, MatTek). Skin models were allowed to recover by incubation at 37 °C and 5 % CO2 overnight, followed by the respective treatments.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 15 µl of the respective bacteria suspension was topically applied. Similar amounts of solvent were applied in control experiments. Medium was refreshed daily. Tissue samples were maintained at 37 °C in a humidified atmosphere of 5 % CO2 for 8 days.

value: EpiDermFT™ (MatTek) skin tissue

tag: protocol

value: Co-culture with skin isolate P. oleovorans


title: Co-culture M. luteus 2

source_name: Co-culture M. luteus

value: Co-culture with skin isolate M. luteus


title: Co-culture M. luteus 3


title: a7: EGFR-KO_Kidney_SD


title: Co-culture P. oleovorans 3


title: Co-culture P. oleovorans 1


title: breast tumour 38C

tag: patient

tag: age


title: a6: EGFR-KO_Kidney_SD


title: a1: EGFR-KO_Kidney_HFD


title: a5: EGFR-KO_Kidney_HFD


title: H1694 CRISPR rep1


title: H1694 Cont rep3

value: WT


title: DMS454 CRISPR rep2

value: Sigma


title: a8: EGFR-KO_Kidney_SD


title: a2: EGFR-KO_Kidney_HFD


title: Control 1

source_name: Control

value: Control


title: DMS454 CRISPR rep3


title: H1694 Cont rep2


title: R-20: EGFR-KO_Aorta_HFD

source_name: Aorta from mouse with endothelial cells-EGFR KO

value: Aorta


title: H1694 Cont rep1


title: Control 2


title: C1.F1.pool__X__C1.F1.22

city: São Paulo

first: Maira

last: Marins Dourado

state: São Paulo

address: Avenida Professor Lineu Prestes, 748, bloco 9, sala 951

country: Brazil

institute: Institute of Chemistry, University of São Paulo

description: Comparison between RNA Leaf 1 C1F122  time point sample and RNA pool sample

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

organism: Saccharum officinarum

label_protocol: CyScribe Post-Labelling Kit Protocol - GE Healthcare

extract_protocol: Modified Trizol method

value: Leaf

tag: variety


title: R-18: EGFR-KO_Aorta_HFD


title: breast tumour 185C

value: female

value: 16 weeks

value: breast tumor

tag: size

tag: grade

tag: nodal status

value: Stable/No Response


title: DMS454 Cont rep3


title: Control 3


title: DMS454 CRISPR rep1

value: HEPACAM2 knockdown


title: DMS454 Cont rep1


title: DMS454 Cont rep2


title: R-16: EGFR-KO_Aorta_HFD

value: EGFR KO


title: R-17: EGFR-KO_Aorta_HFD


title: H1299 OE rep3

source_name: Lung cancer cell line

value: HEPACAM2 overexpressed

value: ATCC


title: R-19: EGFR-KO_Aorta_HFD

value: HFD


title: R-13: EGFR-KO_Aorta_SD

value: SD


title: C1.F1.pool__X__C1.F1.16

description: Comparison between RNA Leaf 1 C1F116  time point sample and RNA pool sample


title: R-15: EGFR-KO_Aorta_SD


title: C1.F1.pool__X__C1.F1.20

description: Comparison between RNA Leaf 1 C1F120  time point sample and RNA pool sample


title: Co-culture M. luteus 1

value: EpiDermFT™ (MatTek) skin tissue


title: C1.F1.pool__X__C1.F1.14

description: Comparison between RNA Leaf 1 C1F114  time point sample and RNA pool sample


title: H1299 OE rep1


title: soybean_9_DAF_pod_tachinagaha

city: Fukuoka

first: Yushi

last: Ishibashi

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Department of Bioresource Sciences

country: Japan

institute: Kyushu University, Faculty of Agriculture

description: Gene expression in pod at 9 day after flowering in Tachinagaha.

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (G. max (Soybean) Oligo Microarray 4x44K ; 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 all samples were normalized by the quantile algorithm with the Bioconductor.

organism: Glycine max

source_name: 9 DAF, pod

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

growth_protocol: Seeds of soybean (Glycine max (L.) Merr.) ‘Tachinagaha’ (Tc), ‘Iyodaizu’ (Iy) were grown at Kyushu University (33°37′N, 130°25′E). Tc has large pods and Iy has small pods. Three seeds per pot were sown in 1/5000-a Wagner pots supplied with 5 g/pot of compound fertilizer (N:P:K, 3:10:10) and 5 g/pot of magnesium lime.

extract_protocol: Total RNA was isolated from tissues using SDS–phenol–LiCl method.

treatment_protocol: When the development stage is V1, soybean plant was made one plant per pot. After flowering, each flower was labeled. In 9 days after flowering (DAF), pods were sampled.

tag: cultivar

value: Tachinagaha

value: pod

tag: time point

value: 9 DAF


title: R-14: EGFR-KO_Aorta_SD

tag: genotype


title: H1299 OE rep2

tag: cell line


title: R-11: EGFR-KO_Aorta_SD


title: soybean_9_DAF_pod_iyodaizu

description: Gene expression in pod at 9 day after flowering in Iyodaizu.

value: Iyodaizu


title: H1299 Cont rep3

value: WT

tag: supplier


title: C1.F1.pool__X__C1.F1.18

description: Comparison between RNA Leaf 1 C1F118  time point sample and RNA pool sample

value: Leaf


title: C1.F1.pool__X__C1.F1.10

description: Comparison between RNA Leaf 1 C1F110  time point sample and RNA pool sample


title: C1.F1.pool__X__C1.F1.08

description: Comparison between RNA Leaf 1 C1F108 time point sample and RNA pool sample


title: soybean_66_DAF_pedicel

description: Gene expression in pedicel at 66 day after flowering.

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (G. max (Soybean) Oligo Microarray 4x44K; Agilent Technologies) according to the manufacturer's instructions.

source_name: 66 DAF, pedicel

growth_protocol: Soybean (Glycine max L. Merrill) cv. Fukuyutaka was used as the plant material. Paddy soil mixed with 5 g compound fertilizer (N: P: K = 3:10:10) and 5 g magnesium lime was packed in a 1/5000a Wagner pot before sowing. Three seed were sown in a pot on 19 July 2012 at Kyushu University, Japan (33.63° N, 130.42° E).

treatment_protocol: When the development stage is V1, soybean plant was made one plant per pot. After flowering, each flower was labeled. In 51, 56, 61, 66, 71, 76 and 81 days after flowering (DAF), pedicel was sampled.

value: Fukuyutaka

value: pedicel

value: 66 DAF


title: R-10: WT_Aorta_HFD

source_name: Aorta from mouse with endothelial cells-EGFR WT

tag: organ

value: Aorta


title: R-12: EGFR-KO_Aorta_SD


title: H1299 Cont rep1


title: H1299 Cont rep2


title: R-9: WT_Aorta_HFD


title: C1.F1.pool__X__C1.F1.04

description: Comparison between RNA Leaf 1 C1F104  time point sample and RNA pool sample

tag: tissue


title: 5-HT neurons (group S; differentiation day 30), Biological Rep1

city: Bongmyeongdong

first: Vincencius

last: Vidyawan

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

description: Gene expression data from 5-HT neuron derived from hESC (H9)

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)
DATA Preprocessing (logarithm, normalization, boxplot, correlation)

label: Biotin

source_name: non-patterned neurons derived from hESC (H9)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: To initiate differentiation, the maintenance medium was replaced with knockout serum replacement (KSR) medium containing knockout DMEM (Gibco), 15% KSR (Gibco), 1:100 of minimum essential medium non-essential amino acid (MEM NEAA; Gibco), and 1:100 Pen Strep Glutamine (PSG; Gibco). KSR was supplemented with 200 nM LDN193189 (STEMCELL Technologies, Vancouver, BC, Canada) and 10 μM SB431542 (Tocris; “day 0”). To support neuronal differentiation, the medium was switched at day 11 into NB/B27 medium containing Neurobasal (NB; Gibco) medium, 1:50 B27 supplement (Gibco), and 1:100 PSG, supplemented with 20 ng/ml BDNF (Peprotech, London, UK). At day 20, cells were passaged at a 1:2 ratio onto freshly prepared Matrigel-coated dishes. During the first 20 days of differentiation, the medium was changed on a daily basis; after that, the medium was changed every 2 or 3 days

extract_protocol: Total RNA was isolated using TRIZOL (Life Technology), and RNA quality was checked by OD 260/280 ratio and analyzed by Agilent 2100 Bioanalyzer

treatment_protocol: From day 1, 2 μM of each purmorphamine (Tocris) and RA (Sigma, St Louis, MO) were given until day 6 and 13, respectively, except for certain experiments where RA was given at various lengths, times, or concentrations to optimize the RA treatment

tag: cell source

value: Human blastocyst, Female

tag: cell type

value: 5-HT neuron derived from hESC (H9)


title: C1.F1.pool__X__C1.F1.06

description: Comparison between RNA Leaf 1 C1F106  time point sample and RNA pool sample


title: 5-HT neurons (group S; differentiation day 30), Biological Rep3


title: R-8: WT_Aorta_HFD

tag: treatment


title: soybean_51_DAF_pedicel

description: Gene expression in pedicel at 51 day after flowering.

source_name: 51 DAF, pedicel

value: 51 DAF


title: A549 OE rep3

value: HEPACAM2 overexpressed

value: ATCC


title: 5-HT neurons (group S; differentiation day 30), Biological Rep2


title: A549 OE rep2


title: A549 OE rep1


title: Non-patterned neurons (group N; differentiation day 25), Biological Rep 3

description: Gene expression data from Non-Patterned neuron derived from hESC (H9)

source_name: 5-HT neurons  neurons derived from hESC (H9)


title: C1.F1.pool__X__C1.F1.12

description: Comparison between RNA Leaf 1 C1F112  time point sample and RNA pool sample


title: Non-patterned neurons (group N; differentiation day 25), Biological Rep 2

value: Non-Patterned neuron derived from hESC (H9)


title: A549 Cont rep3


title: R-5: WT_Aorta_SD

value: SD


title: R-6: WT_Aorta_HFD

value: HFD


title: A549 Cont rep1


title: C1.F1.pool__X__C1.F1.02

description: Comparison between RNA Leaf 1 C1F102  time point sample and RNA pool sample


title: C1.F1.20_X_C1.F1.pool

description: Comparison between RNA Leaf 1 C1F120 time point sample and RNA pool sample


title: C1.F1.pool__X__C1.F1.00

description: Comparison between RNA Leaf 1 C1F100 time point sample and RNA pool sample


title: C1.F1.22_X_C1.F1.pool

description: Comparison between RNA Leaf 1 C1F122 time point sample and RNA pool sample


title: Non-patterned neurons (group N; differentiation day 25), Biological Rep 1


title: R-4: WT_Aorta_SD


title: Gene UMUC3_BCG-resistant_2

city: Rochester

first: Taichi

last: Mizushima

state: NY

address: 601 Elmwood

institute: University of Rochester

hyb_protocol: standard Affymetrix protocol

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: RMA

source_name: UMUC3; Bladder cancer cell line

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was isolated from UMUC3 and its subline with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of RNase inhibitor in the lysis buffer.

tag: treament

value: BCG-resistant


title: C1.F1.18_X_C1.F1.pool


title: Undifferentiatied hESC (group E), Biological Rep2

description: Gene expression data from hESC (H9)

source_name: Embryonic Stem Cell, H9 (WA09) line

value: hESC (H9)


title: R-3: WT_Aorta_SD


title: Undifferentiatied hESC (group E), Biological Rep1

description: Gene expression data from hESC (H9)


title: C1.F1.16_X_C1.F1.pool

description: Comparison between RNA Leaf 1 C1F116 time point sample and RNA pool sample


title: C1.F1.14_X_C1.F1.pool

description: Comparison between RNA Leaf 1 C1F114  time point sample and RNA pool sample


title: Gene UMUC3_BCG-resistant_1


title: A549 Cont rep2


title: Gene UMUC3-AR-konck-down_2

value: AR-konck down


title: R-2: WT_Aorta_SD

value: WT


title: E0771 IL-26 24hr

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: E0771 cells were grown in RPMI1640 supplemented with 10% FBS. Cells were cultured at 37°C  in a humidified 5 % CO2 incubator.

extract_protocol: Cell pellets were harvested and treated with RLT buffer and RNA isolated with Qiagen RNeasy Mini kit following the standard protocol.

treatment_protocol: E0771 cells were treated with IL-26 (30 ng/ml) or media alone for 6 hr or 24 hr.

value: breast carcinoma cell line E0771

value: IL-26 (30 ng/ml) for 24hr


title: C1.F1.12_X_C1.F1.pool

value: Leaf


title: R-1: WT_Aorta_SD


title: Hip_CFA_rep2

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

institute: Hirosaki University Graduate School of Medicine

description: Hip CFA 2

hyb_protocol: Fragmented and biotin-labeled single-strand cDNA (5.5 μg each) hybridized on GeneChip® MTA 1.0 for 16 h at 45°C with rotation at 60 rpm using GeneChip® Hybridization Oven 645.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Expression Console version 1.4.1 (Affymetrix) using default settings for background correction, normalization and summarization. CHP files include RMA values.

source_name: hippocampus, CFA, replicate 2

label_protocol: Fragmented single-strand cDNA were subjected to 3' terminal labeling with biotin using GeneChip® WT PLUS Reagent Kit in accordance with manufacturer's protocol.

growth_protocol: Mice were housed in plastic cages containing wood chips and covered with a wire lid. The cages were kept at 23±2 °C under a 12 h light/dark cycle (lights on at 8:00). The diet were standard laboratory food and water ad libitum. Male mice of 12 weeks old were used in this study.

extract_protocol:
Two days after CFA injection, the mice were deeply anesthetized with a medetomidine-midazolam-butorphanol combination and were transcardially perfused with cold PBS. The brains were then quickly removed and cut into coronal slices with brain matrix. The hippocampus and anterior cingulate cortex (ACC) were punched out from the coronoal slices and preserved in RNAlater (Ambion) solution according to the manufacturer's instructions and were stored at -80℃ for further processing.
Total RNA was extracted from each source using RNeasy Lipid Tissue Mini Kit (QIAGEN) according to the manufacturer's protocol. 100 ng of total RNA was subsequently carried out to First-strand cDNA synthesis using GeneChip® WT PLUS Reagent Kit (Affymetrix).

treatment_protocol: To induce chronic inflammatory pain, 10 μl of 50% CFA was injected subcutaneously into the dorsal surface of the left hindpaw.

tag: strain

value: hippocampus

tag: Sex

value: male

value: 12 weeks

value: CFA


title: Hip_CFA_rep3

description: Hip CFA 3

source_name: hippocampus, CFA, replicate 3

tag: age


title: Undifferentiatied hESC (group E), Biological Rep3

description: Gene expression data from hESC (H9)

value: Human blastocyst, Female


title: G3_miRNA-seq

city: Nanjing

first: Chen

last: Jishuang

state: Jiangsu

address: NO.30 Puzhu Road(S)

department: College of Biotechnology and Pharmaceutical Engineering

institute: Nanjing Tech University

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then detected miRNA using miRDeep2 v2_0_0_8; mapper.pl with parameters -d -c -i -j -l 18 -m,miRDeep2.pl with default parameter
miRNA expression were calcuated using quantifier.pl from miRDeep2 v2_0_0_8 with parameters, then differential analysis using R package Ballgown
Genome_build: Rnor_6.0

organism: Rattus norvegicus

source_name: femur bone of hyperlipidemic rats

growth_protocol: Wistar rats in the experimental group and the control group were fed a high-fat diet and a normal diet for eight weeks, respectively.

extract_protocol:
The bone around the implant was dissected with a margin of 1 mm and the surrounding muscle tissues were thoroughly removed.Then the remaining bone specimens were grinded into powder while submerged in liquid nitrogen and total RNA was isolated with QIAGEN miRNeasy Mini Kit (QIAGEN, USA).
Small RNA sequencing libraries were prepared from the abovementioned total RNA using TruSeq Small RNA Sample Prep Kit (Illumina, USA). Briefly, the RNA fragments were ligated to 5'- and 3’-adapters using T4 RNA Ligase 1 and 2, respectively, before being reverse-transcribed with miScriptII RT-Kit (Qiagen, Germany) and then amplified. The resultant cDNA fragments were electrophoresized on a 4% agarose gel. Bands between 140 and 160 bp were excised and the DNA was extracted by MinElute Gel Extraction Kit (Qiagen, Germany). Library constructs were then sequenced on the HiSeq4000 Illumina platform (Illumina, USA) to generate 50-bp single-end reads.

treatment_protocol: Titanium root-form implants was inserted into both femoral shafts of each rat.

value: Wistar

tag: gender

value: femur bone

tag: developmental stage

value: 12-13 weeks after birth


title: Hip_CFA_rep1

description: Hip CFA 1

source_name: hippocampus, CFA, replicate 1


title: Hip_cont_rep3

description: Hip cont 3

source_name: hippocampus, control, replicate 3

value: control


title: G4_miRNA-seq


title: G2_miRNA-seq


title: Hip_cont_rep2

description: Hip cont 2

source_name: hippocampus, control, replicate 2


title: C1.F1.10_X_C1.F1.pool

tag: variety


title: Gene UMUC3_Control_2

value: Control


title: C1.F1.08_X_C1.F1.pool

description: Comparison between RNA Leaf 1 C1F108  time point sample and RNA pool sample


title: C1.F1.00_X_C1.F1.pool

value: leaf


title: C1.F1.04_X_C1.F1.pool


title: G1_miRNA-seq


title: Hip_cont_rep1

description: Hip cont 1

source_name: hippocampus, control, replicate 1


title: C1.F1.06_X_C1.F1.pool

description: Comparison between RNA Leaf 1 C1F106 time point sample and RNA pool sample


title: E0771 IL-26 6hr

value: IL-26 (30 ng/ml) for 6hr


title: E0771 Vehicle 6hr

value: Vehicle for 6hr


title: Skov3_GA_24hr_3

city: Shiraoka

first: Ayako

last: Otani

state: Saitama

address: 1470 Shiraoka

department: Medical Materials group

institute: Nissan Chemical Industries

description: Gene expression data from Skov3 cells which were isolated from cultured Skov3 cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G system.

data_processing: The data were analyzed with Affimetrix Expression Console Softwere ver.1.3.0 using RMA-Sketch (RMA-Gene-Default) algorithm.

source_name: Skov3 cells_with_GA-017

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

growth_protocol: Skov3 cells were cultured under 3D condition with McCoy's 5A medium supplemented with 15% FBS, 30 ng/mL EGF, and 0.015% FP001(gellan gum).

extract_protocol: Extraction of total RNA was performed with Quiagen RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: DMSO or 10uM GA-017 was added into culture medium and cultured for 24 hours.

tag: culture method

value: 3D cell culture


title: C1.F1.02_X_C1.F1.pool

description: Comparison between RNA Leaf 1 C1F102 time point sample and RNA pool sample


title: Skov3_Ctrl_24hr_2

source_name: Skov3 cells_control


title: Skov3_GA_24hr_2


title: ACC_CFA_rep3

description: ACC CFA 3

source_name: anterior cingulate cortex, CFA, replicate 3

value: anterior cingulate cortex


title: P4_miRNA-seq

source_name: femur bone of normal rats


title: Skov3_GA_24hr_1


title: Mouse_Tg _BAT_AP_rep2

city: Tokushima

first: Masato

last: Miyake

state: Tokushima

address: 3-18-15 Kuramoto

department: Institute of Advanced Medical Sciences

institute: Tokushima university

description: Gene expression of maP2::Fv2E-PERK mouse BAT injected with AP

hyb_protocol: 1.65ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60ﾂｰC for 30 minutes in a reaction volume of 55 ul containing 1x Agilent Fragmentation buffer and 2x Agilent Blocking Agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-028005 Whole Mouse Genome Oligo Microarrays for 17.5 hours at 65ﾂｰC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ﾂｰC GE Wash buffer 2 (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities. Global normalization has been conducted using Subio software. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: TG BAT, AP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the Low Input Quick Amp Labeling Kit (One-Color) (Agilent) according to the manufacturer's instructions, followed by RNeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: Adipose tissue were snap frozen in liquid nitrogen. Total RNA was extracted using the conventional acid guanidinium thiocyanate phenol-chloroform (AGPC) procedure and cleaned up using the RNeasy MinElute Cleanup Kit according to manufacturer's instructions (QIAGEN Valencia, CA).

treatment_protocol: In mice, AP20187 (1 ng/g) or vehicle (4% ethanol, 10% PEG-400, 1.75% Tween-20 in water) was intraperitoneally injected and brown adipose tissue were collected after 12 h.

value: Brown adipose tissue (BAT)


title: Skov3_Ctrl_24hr_1


title: ACC_CFA_rep2

description: ACC CFA 2

source_name: anterior cingulate cortex, CFA, replicate 2


title: P3_miRNA-seq


title: Skov3_Ctrl_24hr_3


title: ACC_CFA_rep1

description: ACC CFA 1

source_name: anterior cingulate cortex, CFA, replicate 1


title: P1_miRNA-seq


title: P2_miRNA-seq


title: G4_RNA-seq

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed fo adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to genome Rnor_6.0 using HISAT2 v2.1.0 with parameters --dta -x -q --rna-strandness
Reads Per Kilobase of transcript per Million (FPKM) were calculated using StringTie v1.3.3b with default paramters, then differential analysis using R package Ballgown
Genome_build: Rnor_6.0

extract_protocol:
The bone around the implant was dissected with a margin of 1 mm and the surrounding muscle tissues were thoroughly removed.Then the remaining bone specimens were grinded into powder while submerged in liquid nitrogen and total RNA was isolated with QIAGEN miRNeasy Mini Kit (QIAGEN, USA).
Approximately 3 µg of total RNA were used to construct cDNA library. Briefly, the sample was first subjected to ribosomal RNA depletion through Ribo-Zero rRNA Removal Kit (Human/ Mouse/Rat) (Epicentre, USA) according to the manufacturer’s protocol and then fragmented in Fragmentation Buffer (Thermo Fisher Scientific, USA). The resultant RNA fragments were reverse-transcribed to construct the cDNA library via the previously described dUTP method[23]. The amount of library DNA and the size distribution of the inserted fragments were determined by Qubit 2.0 RNA Broad Range Assay Kit (Invitrogen, USA) and on a 2100 Bioanalyzer (Agilent, USA), respectively. Library was subsequently sequenced on a HiSeq 4000 platform (Illumina, USA) that produced 150-bp paired-end reads.


title: ACC_cont_rep3

description: ACC cont 3

source_name: anterior cingulate cortex, control, replicate 3


title: ACC_cont_rep1

description: ACC cont 1

source_name: anterior cingulate cortex, control, replicate 1


title: Mouse_Tg _BAT_vehicle_rep1

description: Gene expression of maP2::Fv2E-PERK mouse BAT injected with vehicle

source_name: TG BAT, vehicle


title: G2_RNA-seq


title: G1_RNA-seq


title: P4_RNA-seq


title: Mature_spherule_CDS_2

city: La Jolla

first: Theo

middle: N

last: Kirkland

state: CA

address: 9500 Gilman Drive

institute: UCSD

data_processing:
transcripts mapped and  quantified with kallisto
count tables from Kallisto imported to DESeq2
DESEq2 run with output filtered for more than 5 counts in both samples and an adjusted p value < 0.05 (Benjamini-Hochberg)
Genome_build: ASM14933v2
Supplementary_files_format_and_content: est_counts

organism: Coccidioides immitis RS

growth_protocol: To grow mycelia, arthroconidia were washed 2 times with glucose-yeast extract (GYE) media and 2×10^6 spores/ml were incubated in 250 ml flat-bottom Erlenmeyer flasks (Corning) in 50 ml GYE media. Four flasks were cultured in a 30°C incubator without shaking for 5 days.  To grow spherules  arthroconidia were inoculated at 4×10^6 arthroconidia/ml into a 250 ml baffled Erlenmeyer flask containing 50 ml of modified Converse media. Eight identical flasks were set up and grown on a shaker at 160 rpm, in 14% CO2 at 42°C. Four flasks were harvested 2 days after inoculation and the remaining four flasks after 8 days. The spherules did not rupture and release endospores within that time in this culture system.

extract_protocol:
Mycelia and spherules were stored in QIAzol (Qiagen) at -70°C. Samples were added to 2 ml ZR BashingBead lysis tube with 0.5 mm beads (Zymoresearch) and tubes arranged in a pre-cooled Tissuelyzer II adapter (Qiagen) and disrupted by shaking at 50 Hz for 25 min. Total RNA was purified from mycelia and spherule samples (2 replicates / condition) using chloroform extraction and isopropanol precipitation and quantified using a Qubit 3.0 Fluorometer (Invitrogen)
Strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Yeast Ribo-Zero rRNA Removal Kit (Illumina) and using the TruSeq Stranded total RNA-Seq kit (Illumina).

tag: developmental stage/tissue

value: Mature Spherules

tag: molecule subtype

value: rRNA-depleted RNA


title: Young_Spherule_CDS_Transposons_2


title: Mouse_Tg _BAT_vehicle_rep2

value: male


title: P3_RNA-seq


title: Gene UMUC3_AR-konck-down_1

source_name: UMUC3; Bladder cancer cell line

value: AR-konck down


title: Mouse_Tg _BAT_AP_rep1


title: Young_Spherule_CDS_Transposons_1


title: P2_RNA-seq


title: ACC_cont_rep2

description: ACC cont 2

source_name: anterior cingulate cortex, control, replicate 2

value: 12 weeks


title: Mycelia_CDS_Transposons_2

value: Mycelia


title: P1_RNA-seq

value: Wistar


title: Mycelia_CDS_Transposons_1


title: eWAT_high fat diet_rep5

city: Kanazawa

first: Mayumi

last: Nagashimada

address: 5-11-80 Kodatsuno

institute: Kanazawa University

description: Gene expression data from epididymal white adipose tissue after 8 weeks feeding of high fat diet

hyb_protocol: Fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner 3000; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing:
Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method.
Programmatic identifier: GeneChip.CallGEBaseCall.1
Algorithm: ExpressionStat 5.0

source_name: eWAT_high fat diet

label_protocol: Double-stranded cDNA was synthesized from the total RNA of each mouse using the One-Cycle cDNA Synthesis Kit (Affymetrix Japan KK, Tokyo, Japan) with a T7-(dT)24 primer. Biotin-labeled cRNA was then synthesized using an IVT Labeling Kit (Affymetrix). The biotin-labeled cRNA was further purified and fragmented using the Sample Cleanup Module (Affymetrix).

growth_protocol: Mice were housed in colony cages with a 12-hour light/12-hour dark cycle and allowed food and water at libitum.

extract_protocol: The mice were killed and epididymal white adipose tissues (eWAT) were immediately removed and weighted.  A large portion of each eWAT was snap-frozen in liquid nitrogen. Total RNA was isolated from frozen eWAT using an mRNA Miniprep Kit (Roche, Basel, Switzerland) according to the manufacturer’s instructions.

treatment_protocol: Eight-week old male C57BL/6J mice were fed for 8 weeks on a normal chow (CRF-1; Charles River Laboratories) or high-fat diet consisting of 60% fat (Research Diets).

value: high fat diet for 8 weeks

value: epididymal white adipose tissue (eWAT)


title: Mature_spherule_CDS_1


title: E0771 Vehicle 24hr

tag: cell line

value: breast carcinoma cell line E0771

value: Vehicle for 24hr


title: eWAT_high fat diet_rep3


title: normoxia_1hr_Pol2_input_biorep1

status: Public on Mar 31 2021

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

country: United Kingdom

institute: Genomic Services QIAGEN

library_source: genomic

data_processing:
POl2-ChIP-seq and G4-ChIP-seq Fastq files were trimmed from adapters using cutadapt (-m 10 -q 20 -O 3 -a CTGTCTCTTATACACATCT) and aligned to a the human genome hg38 with bwa-mem. Bam files were generated from the alignment with samtools view. Duplicated reads were marked and removed using picard MarkDuplicates (ver: 2.20.3).Peak calling was performed with macs2 over input (ver. 2.1.2) with fdr 0.05 (default). For G4-ChIP-seq, regions confirmed across 2 out of 3 tecnical replicates have been assigned to each biological replicate. Regions shared by 2 out of 3 biological replicates have been elected as consensus of the cell type and multiIntersectBed was used for this.
ATAC-seq: fastq files were trimmed from adapters with cutadapt ( -a AGATCGGAAGAGC -A AGATCGGAAGAG) and aligned to hg38 with bwa-mem for paired-end (-M -t 12 $read1 $read2). Mapped reads have been filtered using samtools view (-Sb -F780 -q 10 -L )  to keep only mapped and properly paired reds. Those reads have been then used to identify accessible reagions using macs2 wih default options. Regions identified in 2 out 3 biolofical replicates have used as consensus each experimental condition.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak: narrowPeak regions obtained with macs2 default options
bed: consensus representing genomic regions observed in 2/3 of the experiments available (if 3 replicates: 2 out of 3; if 12 replicates : 8 out of 12; f 6 replicates: 4 out of 6)
10uM_TPL_2hr.confirmed.4out6.bed: G4 regions observed upon TPL in 4 out of 6 replicates;  1uM_pyPDS_2hr_hypoxia_whole_cell_ATACseq.multi2.bed: atac regions observed upon 1uM_pyPDS_2hr_hypoxia in 2 out of 3 replicates;  1uM_pyPDS_2hr_normoxia_whole_cell_ATACseq.multi2.bed: atac regions observed upon 1uM_pyPDS_2hr_normoxia in 2 out of 3 replicates;  DRB_1hr.confirmed.8out12.bed: G4 regions observed upon DRB in 8 or 12 replicates;  DMSO_control_2hr_hypoxia_whole_cell_ATACseq.multi2.bed: atac regions observed upon DMSO_2hr_hypoxia in 2 out of 3 replicates;  DMSO_control_2hr_normoxia_whole_cell_ATACseq.multi2.bed: atac regions observed upon DMSO_2hr_normoxia in 2 out of 3 replicates;  hypoxia_1hr_wholeK562_fragment_1hr.multi2.bed: atac regions observed in hyoxia in 2 out of 3 replicates;  hypoxia.bio2.bed: G4 regions observed in 2 biological replicates  noDRB.confirmed.8out12.bed: G4 regions observed in the control (for DRB)  normoxia_1hr_wholeK562_fragment.multi2.bed: atac regions observed in normoxia  normoxia.bio2.bed: G4 regions observed in normoxia  noTPL.confirmed.8out12.bed: G4 regions observed in the control (for TPL)  normoxia.multi3.bed: pol2 regions observed in normoxia  in 3 biological replicates;  hypoxia.multi3.bed: pol2 regions observed upon hypoxia in 3 biological replicates;  1uM_pyPDS_2hr_hypoxia_Pol2.multi3.bed: pol2 regions observed upon 1uM_pyPDS_2hr_hypoxia in 3 biological replicates;  DMSO_control_2hr_hypoxia_Pol2.multi3.bed: pol2 regions observed upon DMSO_control_2hr_hypoxia in 3 biological replicates;  1uM_pyPDS_2hr_normoxia_Pol2.multi3.bed: pol2 regions observed upon 1uM_pyPDS_2hr_normoxia  in 3 biological replicates;  DMSO_control_2hr_normoxia_Pol2.multi3.bed: pol2 regions observed upon DMSO_control_2hr_normoxia in 3 biological replicates.

molecule: genomic DNA

source_name: cultured K562 cells

growth_protocol:
K562 cells were cultured in RPMI 1640 supplemented with 10% of fetal bovine serum (FBS), and were incubated at 37°C in 5% CO2 unless stated otherwise.
K562 cells profiling by G4-ChIP-seq upon DRB, TPL; K562 cells profiling by G4-ChIP-seq, Pol2-ChIP-seq and Atac-seq upon pyPDS, Hypoxia, Hypoxia plus pyPDS or DMSO, Normoxia plus pyPDS or DMSO.U2OS cells (ATCC, HTB-96) were cultured in DMEM (Thermo Fisher, 41966-029) supplemented with 10% of FBS

extract_protocol:
Cell nuclei were extracted and  sonicated. G4 containing DNA and RNA Pol II-DNA complexes were respectively isolated with BG4 antibody and RNA Pol II antibody. For ATAC-seq, washed cells were directly incubated with transposase Tn5 for library preparation.
For G4 ChIP libraries and ATAC libraries, DNA was tagmented and the library was prepared using Nextera library preparation kit (20034197) by following the manufacturer instruction. The library was amplified using Nextera index primers (Illumina, FC-121-1030). For RNA Pol II ChIP-seq, library was prepared by using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645).

treatment_protocol: For hypoxia treatment, cells were incubated at 1% O2, 5% CO2 and 37°C. DRB, triptolide and pyPDS were dissolved in DMSO at a final concentration of 100 µM, 10 µM and 1 µM respectively. For pyPDS stabilisation in hypoxia, cells were exposed to 1% O2 following 1-hour pyPDS treatment.

value: K562 cells

tag: chip antibody

value: normoxia (21% O2 and 5% CO2) for 1 hr


title: normoxia_1hr_G4_ChIP_input.bio3


title: normoxia_1hr_Pol2_input_biorep2


title: normoxia_1hr_Pol2_input_biorep4


title: eWAT_high fat diet_rep2


title: normoxia_1hr_Pol2_input_biorep3


title: eWAT_high fat diet_rep4


title: normoxia_1hr_G4_ChIP_input.bio2


title: eWAT_normal chow diet_rep5

description: Gene expression data from epididymal white adipose tissue after 8 weeks feeding of normal chow diet

source_name: eWAT_normal chow diet

value: normal chow diet for 8 weeks


title: G3_RNA-seq

source_name: femur bone of hyperlipidemic rats

value: femur bone

value: 12-13 weeks after birth


title: no_TPL_1hr_input.bio4

value: treated with DMSO (0.1% v/v) for 1 hr


title: no_TPL_1hr_input.bio2


title: no_TPL_1hr_input.bio1


title: normoxia_1hr_Pol2_input_biorep5


title: no_TPL_1hr_input.bio3


title: no_DRB_1hr_input.bio4


title: no_DRB_1hr_input.bio1


title: normoxia_1hr_G4_ChIP_input.bio1


title: eWAT_normal chow diet_rep3


title: no_DRB_1hr_input.bio3


title: hypoxia_1hr_Pol2_input_biorep4

value: hypoxia (1% O2, 5% CO2) for 1 hr


title: hypoxia_1hr_Pol2_input_biorep3


title: eWAT_normal chow diet_rep1


title: hypoxia_1hr_G4_ChIP_input.bio3


title: hypoxia_1hr_Pol2_input_biorep1


title: hypoxia_1hr_G4_ChIP_input.bio2


title: eWAT_normal chow diet_rep4


title: 100uM_DRB_1hr_input.bio2

value: treated with DRB (100uM) for 1 hr


title: 100uM_DRB_1hr_input.bio3


title: R-7: WT_Aorta_HFD

source_name: Aorta from mouse with endothelial cells-EGFR WT

tag: organ

value: Aorta

tag: genotype

value: WT

value: HFD


title: hypoxia_1hr_Pol2_input_biorep2


title: hypoxia_1hr_G4_ChIP_input.bio1


title: DMSO_control_2hr_normoxia_Pol2_input_biorep2

value: normoxia 21% O2 for 1 hr following 1 hr DMSO (0.1% v/v) treatment


title: DMSO_control_2hr_hypoxia_Pol2_input_biorep5

value: treated in 1% O2 for 1 hr following 1 hr DMSO (0.1% v/v) treatment


title: DMSO_control_2hr_normoxia_Pol2_input_biorep1


title: eWAT_high fat diet_rep1

value: male

value: high fat diet for 8 weeks

tag: tissue


title: DMSO_control_2hr_normoxia_Pol2_input_biorep4


title: eWAT_normal chow diet_rep2

value: epididymal white adipose tissue (eWAT)


title: DMSO_control_2hr_hypoxia_Pol2_input_biorep3


title: DMSO_control_2hr_normoxia_Pol2_input_biorep5


title: DMSO_control_2hr_hypoxia_Pol2_input_biorep2


title: DMSO_control_2hr_normoxia_Pol2_input_biorep3


title: DMSO_control_2hr_hypoxia_Pol2_input_biorep4


title: no_DRB_1hr_input.bio2


title: DMSO_control_2hr_hypoxia_Pol2_input_biorep1


title: 1uM_pyPDS_2hr_normoxia_Pol2_input_biorep5

value: normoxia 21% O2 for 1 hr following 1 hr pyPDS (1uM) treatment


title: 1uM_pyPDS_2hr_normoxia_Pol2_input_biorep3

value: K562 cells


title: 1uM_pyPDS_2hr_normoxia_Pol2_input_biorep4


title: 1uM_pyPDS_2hr_normoxia_Pol2_input_biorep2


title: 1uM_pyPDS_2hr_normoxia_Pol2_input_biorep1


title: 1uM_pyPDS_2hr_hypoxia_Pol2_input_biorep5

value: treated in 1% O2 for 1 hr following 1 hr pyPDS (1uM) treatment


title: 1uM_pyPDS_2hr_hypoxia_Pol2_input_biorep3


title: 1uM_pyPDS_2hr_hypoxia_Pol2_input_biorep4


title: hypoxia_1hr_Pol2_input_biorep5


title: 10uM_TPL_2hr_input.bio2

value: treated with TPL (10uM) for 2 hr


title: 10uM_TPL_2hr_input.bio1


title: normoxia_1hr_whole_cell_ATACseq_biorep3

value: normoxia (21% O2 and 5% CO2) for 1 hr


title: 1uM_pyPDS_2hr_hypoxia_Pol2_input_biorep2


title: normoxia_1hr_Pol2_ChIP_biorep5

value: RNA Pol II (Abcam, ab817)


title: normoxia_1hr_G4_ChIP_rep2.bio3


title: normoxia_1hr_Pol2_ChIP_biorep2


title: normoxia_1hr_G4_ChIP_rep3.bio3


title: normoxia_1hr_G4_ChIP_rep3.bio2


title: normoxia_1hr_G4_ChIP_rep2.bio2


title: normoxia_1hr_G4_ChIP_rep1.bio3


title: normoxia_1hr_G4_ChIP_rep1.bio2


title: normoxia_1hr_G4_ChIP_rep2.bio1


title: no_DRB_1hr_rep3.bio1

value: treated with DMSO (0.1% v/v) for 1 hr


title: no_DRB_1hr_rep1.bio1


title: no_DRB_1hr_rep2.bio1


title: normoxia_1hr_whole_cell_ATACseq_biorep2


title: no_DRB_1hr_rep1.bio4


title: no_DRB_1hr_rep3.bio4


title: normoxia_1hr_G4_ChIP_rep1.bio1


title: normoxia_1hr_whole_cell_ATACseq_biorep1


title: normoxia_1hr_Pol2_ChIP_biorep4


title: 1uM_pyPDS_2hr_hypoxia_Pol2_input_biorep1


title: no_DRB_1hr_rep1.bio3


title: normoxia_1hr_Pol2_ChIP_biorep3


title: no_DRB_1hr_rep3.bio3


title: no_DRB_1hr_rep3.bio2


title: no_DRB_1hr_rep2.bio2


title: normoxia_1hr_Pol2_ChIP_biorep1


title: no_TPL_1hr_rep3.bio2


title: normoxia_1hr_G4_ChIP_rep3.bio1


title: no_DRB_1hr_rep1.bio2


title: no_TPL_1hr_rep2.bio1


title: 100uM_DRB_1hr_input.bio4


title: no_TPL_1hr_rep2.bio4


title: 100uM_DRB_1hr_input.bio1


title: no_TPL_1hr_rep3.bio4


title: no_DRB_1hr_rep2.bio4


title: no_DRB_1hr_rep2.bio3


title: no_TPL_1hr_rep3.bio3


title: no_TPL_1hr_rep2.bio3


title: no_TPL_1hr_rep1.bio3


title: hypoxia_1hr_whole_cell_ATACseq_biorep2

value: hypoxia (1% O2, 5% CO2) for 1 hr


title: hypoxia_1hr_Pol2_ChIP_biorep5


title: hypoxia_1hr_whole_cell_ATACseq_biorep3


title: hypoxia_1hr_whole_cell_ATACseq_biorep1


title: hypoxia_1hr_Pol2_ChIP_biorep3


title: hypoxia_1hr_Pol2_ChIP_biorep2


title: hypoxia_1hr_Pol2_ChIP_biorep1


title: hypoxia_1hr_G4_ChIP_rep2.bio3


title: hypoxia_1hr_G4_ChIP_rep3.bio3


title: hypoxia_1hr_G4_ChIP_rep1.bio3


title: hypoxia_1hr_G4_ChIP_rep3.bio2


title: no_TPL_1hr_rep1.bio1


title: hypoxia_1hr_G4_ChIP_rep1.bio2


title: hypoxia_1hr_G4_ChIP_rep3.bio1


title: no_TPL_1hr_rep1.bio2


title: no_TPL_1hr_rep2.bio2


title: hypoxia_1hr_G4_ChIP_rep2.bio1


title: hypoxia_1hr_G4_ChIP_rep1.bio1


title: hypoxia_1hr_Pol2_ChIP_biorep4


title: 100uM_DRB_1hr_rep3.bio3

value: treated with DRB (100uM) for 1 hr


title: 100uM_DRB_1hr_rep1.bio4


title: 100uM_DRB_1hr_rep2.bio4


title: no_TPL_1hr_rep3.bio1


title: no_TPL_1hr_rep1.bio4


title: 100uM_DRB_1hr_rep3.bio4


title: 100uM_DRB_1hr_rep2.bio3


title: 100uM_DRB_1hr_rep3.bio2


title: 100uM_DRB_1hr_rep1.bio3


title: 100uM_DRB_1hr_rep2.bio2


title: 100uM_DRB_1hr_rep3.bio1


title: hypoxia_1hr_G4_ChIP_rep2.bio2


title: 100uM_DRB_1hr_rep2.bio1


title: 100uM_DRB_1hr_rep1.bio1


title: DMSO_control_2hr_normoxia_whole_cell_ATACseq_biorep3


title: DMSO_control_2hr_normoxia_whole_cell_ATACseq_biorep2


title: DMSO_control_2hr_normoxia_Pol2_ChIP_biorep3


title: 100uM_DRB_1hr_rep1.bio2


title: DMSO_control_2hr_normoxia_whole_cell_ATACseq_biorep1


title: DMSO_control_2hr_normoxia_Pol2_ChIP_biorep5


title: DMSO_control_2hr_normoxia_Pol2_ChIP_biorep4


title: DMSO_control_2hr_normoxia_Pol2_ChIP_biorep1


title: DMSO_control_2hr_normoxia_Pol2_ChIP_biorep2


title: DMSO_control_2hr_hypoxia_whole_cell_ATACseq_biorep3


title: DMSO_control_2hr_hypoxia_whole_cell_ATACseq_biorep1


title: DMSO_control_2hr_hypoxia_Pol2_ChIP_biorep5


title: DMSO_control_2hr_hypoxia_whole_cell_ATACseq_biorep2


title: DMSO_control_2hr_hypoxia_Pol2_ChIP_biorep3


title: 1uM_pyPDS_2hr_normoxia_whole_cell_ATACseq_biorep1


title: 1uM_pyPDS_2hr_normoxia_whole_cell_ATACseq_biorep3


title: 1uM_pyPDS_2hr_normoxia_Pol2_ChIP_biorep5


title: DMSO_control_2hr_hypoxia_Pol2_ChIP_biorep1


title: 1uM_pyPDS_2hr_normoxia_Pol2_ChIP_biorep4


title: 1uM_pyPDS_2hr_hypoxia_whole_cell_ATACseq_biorep3


title: 1uM_pyPDS_2hr_hypoxia_whole_cell_ATACseq_biorep2


title: 1uM_pyPDS_2hr_normoxia_Pol2_ChIP_biorep3


title: DMSO_control_2hr_hypoxia_Pol2_ChIP_biorep2


title: 1uM_pyPDS_2hr_normoxia_Pol2_ChIP_biorep2


title: 1uM_pyPDS_2hr_normoxia_Pol2_ChIP_biorep1


title: 1uM_pyPDS_2hr_hypoxia_Pol2_ChIP_biorep5


title: 1uM_pyPDS_2hr_hypoxia_whole_cell_ATACseq_biorep1


title: 1uM_pyPDS_2hr_hypoxia_Pol2_ChIP_biorep2


title: DMSO_control_2hr_hypoxia_Pol2_ChIP_biorep4


title: 10uM_TPL_2hr_rep1.bio1


title: 10uM_TPL_2hr_rep3.bio2


title: 10uM_TPL_2hr_rep3.bio1


title: 10uM_TPL_2hr_rep1.bio2


title: 1uM_pyPDS_2hr_hypoxia_Pol2_ChIP_biorep3


title: 10uM_TPL_2hr_rep2.bio1


title: 1uM_pyPDS_2hr_hypoxia_Pol2_ChIP_biorep4


title: 1uM_pyPDS_2hr_normoxia_whole_cell_ATACseq_biorep2


title: 1uM_pyPDS_2hr_hypoxia_Pol2_ChIP_biorep1


title: 10uM_TPL_2hr_rep2.bio2


title: CD8+_T-cells_patient_N15_TIGIT-

city: Bethesda

first: Jana

last: Blazkova

address: 9000 Rockville Pike

institute: NIH

hyb_protocol: Six μg of labeled cRNA was hybridized to Affymetrix Human Genome WT Array Strip at 48°C for 20 hours. The arrays were washed using the GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips.

scan_protocol: Raw CEL files were obtained from the GeneAtlas Software and were normalized by Robust Multiarray Average (RMA)

data_processing: The normalized expression values were batch corrected for array prep and array ID. Differential expression was performed on batch corrected expression values using the Linear Models for Microarray Analysis (LIMMA) package.

source_name: CD8+ T-cells TIGIT-

label_protocol: 100 ng of total RNA was amplified and labeled using GeneChip Whole Transcript (WT) PLUS Reagent Kit (Affymetrix), according to manufacturer’s instructions.

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from whole blood and leukapheresed products by Ficoll-Hypaque density gradient centrifugation.

extract_protocol: Total RNA from TIGIT+ and TIGIT-CD8+ T cells were isolated using an RNeasy Mini kit (Qiagen) according to manufacturer’s specifications.

treatment_protocol: CD8+ T cells were isolated using a negative cell separation technique (StemCell Technologies). TIGIT+ and TIGIT- cells were further enriched using TIGIT-PE antibody (eBioscience) and anti-PE magnetic beads (StemCell Technologies).

tag: cell type

value: CD8+ T-cells

tag: expression

value: TIGIT-

tag: hiv status

value: healthy


title: CD8+_T-cells_patient_V02_TIGIT+

source_name: CD8+ T-cells TIGIT+

value: TIGIT+

value: viremic


title: CD8+_T-cells_patient_V04_TIGIT-


title: CD8+_T-cells_patient_V03_TIGIT+


title: CD8+_T-cells_patient_V02_TIGIT-


title: CD8+_T-cells_patient_V06_TIGIT+


title: CD8+_T-cells_patient_V05_TIGIT-


title: CD8+_T-cells_patient_N14_TIGIT+


title: CD8+_T-cells_patient_V06_TIGIT-


title: CD8+_T-cells_patient_N15_TIGIT+


title: CD8+_T-cells_patient_V05_TIGIT+


title: CD8+_T-cells_patient_N13_TIGIT+


title: CD8+_T-cells_patient_N12_TIGIT+


title: CD8+_T-cells_patient_N09_TIGIT+


title: CD8+_T-cells_patient_N13_TIGIT-


title: CD8+_T-cells_patient_N10_TIGIT+


title: CD8+_T-cells_patient_V03_TIGIT-


title: CD8+_T-cells_patient_N12_TIGIT-


title: CD8+_T-cells_patient_V01_TIGIT-


title: CD8+_T-cells_patient_N10_TIGIT-


title: CD8+_T-cells_patient_V04_TIGIT+


title: CD8+_T-cells_patient_N08_TIGIT-


title: CD8+_T-cells_patient_V01_TIGIT+


title: CD8+_T-cells_patient_N11_TIGIT+


title: CD8+_T-cells_patient_N07_TIGIT+


title: CD8+_T-cells_patient_N07_TIGIT-


title: CD8+_T-cells_patient_N08_TIGIT+


title: CD8+_T-cells_patient_N14_TIGIT-


title: CD8+_T-cells_patient_N06_TIGIT+


title: CD8+_T-cells_patient_N02_TIGIT+


title: CD8+_T-cells_patient_N04_TIGIT-


title: CD8+_T-cells_patient_N05_TIGIT+


title: CD8+_T-cells_patient_N09_TIGIT-


title: CD8+_T-cells_patient_A08_TIGIT+

value: aviremic


title: CD8+_T-cells_patient_N06_TIGIT-


title: CD8+_T-cells_patient_N03_TIGIT-


title: CD8+_T-cells_patient_A04_TIGIT-


title: CD8+_T-cells_patient_A06_TIGIT+


title: CD8+_T-cells_patient_A07_TIGIT+


title: CD8+_T-cells_patient_N03_TIGIT+


title: CD8+_T-cells_patient_N01_TIGIT+


title: CD8+_T-cells_patient_A06_TIGIT-


title: CD8+_T-cells_patient_A08_TIGIT-


title: CD8+_T-cells_patient_N05_TIGIT-


title: CD8+_T-cells_patient_N01_TIGIT-


title: CD8+_T-cells_patient_A01_TIGIT+


title: CD8+_T-cells_patient_A03_TIGIT-


title: CD8+_T-cells_patient_A03_TIGIT+


title: CD8+_T-cells_patient_A02_TIGIT+


title: CD8+_T-cells_patient_A04_TIGIT+


title: CD8+_T-cells_patient_A05_TIGIT+


title: CD8+_T-cells_patient_A05_TIGIT-


title: CD8+_T-cells_patient_N02_TIGIT-


title: CD8+_T-cells_patient_A07_TIGIT-


title: CD8+_T-cells_patient_N04_TIGIT+


title: CD8+_T-cells_patient_A01_TIGIT-


title: CD8+_T-cells_patient_A02_TIGIT-


title: Control ChIP-seq from brain (ENCLB286WOU)

status: Public on Mar 30 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR688WUZ/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR688WUZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB286WOU
size range: 200-600

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

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

value: brain

value: organoid

tag: biosample encode accession

value: female

tag: health state

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: Control ChIP-seq from brain (ENCLB131GSV)

description:
https://www.encodeproject.org/experiments/ENCSR688WUZ/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR688WUZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB131GSV
size range: 200-600

tag: Sex

tag: age

value: ENCBS678HIV at ENCODE; https://www.encodeproject.org/ENCBS678HIV/


title: Control ChIP-seq from brain (ENCLB529VBZ)

description:
https://www.encodeproject.org/experiments/ENCSR688WUZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR688WUZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB529VBZ
size range: 200-600


title: Control ChIP-seq from H9 (ENCLB610NNP)

description:
https://www.encodeproject.org/experiments/ENCSR686HII/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on H9 originated from H9
experiment encode accession: ENCSR686HII
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB610NNP
size range: 200-600

source_name: Homo sapiens H9 cell line originated from H9

tag: line

value: cell line

tag: description

value: WA09 ES cells

value: SESCC

value: ENCBS713BMM at ENCODE; https://www.encodeproject.org/ENCBS713BMM/


title: Control ChIP-seq from H9 (ENCLB903EKO)

description:
https://www.encodeproject.org/experiments/ENCSR686HII/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on H9 originated from H9
experiment encode accession: ENCSR686HII
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB903EKO
size range: 200-600

value: healthy

value: ENCBS654ADT at ENCODE; https://www.encodeproject.org/ENCBS654ADT/


title: Control ChIP-seq from left lung (ENCLB722KHC)

description:
https://www.encodeproject.org/experiments/ENCSR650AIN/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on left lung female child (16 years)
experiment encode accession: ENCSR650AIN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB722KHC
size range: 200-600

source_name: Homo sapiens female child (16 years) left lung tissue, preserved by flash-freezing

value: left lung

value: tissue

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS742MOS at ENCODE; https://www.encodeproject.org/ENCBS742MOS/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: Control ChIP-seq from left lung (ENCLB212MYP)

description:
https://www.encodeproject.org/experiments/ENCSR650AIN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on left lung female child (16 years)
experiment encode accession: ENCSR650AIN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB212MYP
size range: 200-600

value: female


title: Control ChIP-seq from brain (ENCLB009ZZL)

description:
https://www.encodeproject.org/experiments/ENCSR688WUZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR688WUZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB009ZZL
size range: 200-600

value: brain

value: organoid

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS678HIV at ENCODE; https://www.encodeproject.org/ENCBS678HIV/

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


title: Control ChIP-seq from K562 (ENCLB478HTR)

description:
https://www.encodeproject.org/experiments/ENCSR589YUZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR589YUZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-26
lab: Richard Myers, HAIB
library encode accession: ENCLB478HTR
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS874WOY at ENCODE; https://www.encodeproject.org/ENCBS874WOY/

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


title: Control ChIP-seq from nephron (ENCLB502KVF)

description:
https://www.encodeproject.org/experiments/ENCSR959CIX/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on nephron female embryo (5 days)
experiment encode accession: ENCSR959CIX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB502KVF
size range: 200-600

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

value: nephron

value: female

value: healthy

value: Joseph Bonventre

value: ENCBS047TRT at ENCODE; https://www.encodeproject.org/ENCBS047TRT/


title: Control ChIP-seq from nephron (ENCLB186ODZ)

description:
https://www.encodeproject.org/experiments/ENCSR959CIX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on nephron female embryo (5 days)
experiment encode accession: ENCSR959CIX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB186ODZ
size range: 200-600

value: organoid

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad


title: TF ChIP-seq from heart left ventricle (ENCLB057WHT)

description:
https://www.encodeproject.org/experiments/ENCSR565HBN/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on heart left ventricle female adult (46 years)
experiment encode accession: ENCSR565HBN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR403VPZ
encode release date: 2020-09-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB057WHT
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (46 years) heart left ventricle tissue, preserved by flash-freezing

tag: antibody

value: CTCF

value: heart left ventricle

value: tissue

value: DM:no; HTN:no; CAD:no

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS273XUE at ENCODE; https://www.encodeproject.org/ENCBS273XUE/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: Control ChIP-seq from type B pancreatic cell (ENCLB677ZSM)

description:
https://www.encodeproject.org/experiments/ENCSR394CIG/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR394CIG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB677ZSM
size range: 200-600

source_name: Homo sapiens female embryo (5 days) type B pancreatic in vitro differentiated cells originated from type B pancreatic cell

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

value: female

value: SESCC

value: ENCBS779FCS at ENCODE; https://www.encodeproject.org/ENCBS779FCS/

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


title: Control ChIP-seq from type B pancreatic cell (ENCLB523UHU)

description:
https://www.encodeproject.org/experiments/ENCSR394CIG/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR394CIG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB523UHU
size range: 200-600

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad


title: Control ChIP-seq from K562 (ENCLB781XHA)

description:
https://www.encodeproject.org/experiments/ENCSR606GRT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR606GRT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: Yijun Ruan, JAX
library encode accession: ENCLB781XHA

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Yijun Ruan, JAX

value: ATCC

value: ENCBS772XSD at ENCODE; https://www.encodeproject.org/ENCBS772XSD/

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


title: TF ChIP-seq from heart left ventricle (ENCLB321ILR)

description:
https://www.encodeproject.org/experiments/ENCSR565HBN/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on heart left ventricle female adult (46 years)
experiment encode accession: ENCSR565HBN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR403VPZ
encode release date: 2020-09-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB321ILR
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: heart left ventricle

value: tissue

value: DM:no; HTN:no; CAD:no

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS273XUE at ENCODE; https://www.encodeproject.org/ENCBS273XUE/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: Control ChIP-seq from A549 (ENCLB513LFR)

description:
https://www.encodeproject.org/experiments/ENCSR663DVJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR663DVJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB513LFR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting PRDM1

value: cell line

value: male

value: 58 year

value: Michael Snyder

value: ENCBS798LHW at ENCODE; https://www.encodeproject.org/ENCBS798LHW/

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


title: Control ChIP-seq from brain (ENCLB830HDI)

description:
https://www.encodeproject.org/experiments/ENCSR553CWR/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR553CWR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB830HDI
size range: 200-600

value: brain

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS022EUB at ENCODE; https://www.encodeproject.org/ENCBS022EUB/

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


title: Control ChIP-seq from type B pancreatic cell (ENCLB113UQS)

description:
https://www.encodeproject.org/experiments/ENCSR394CIG/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR394CIG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB113UQS
size range: 200-600

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

value: SESCC

value: ENCBS251SEQ at ENCODE; https://www.encodeproject.org/ENCBS251SEQ/


title: Control ChIP-seq from brain (ENCLB697COI)

description:
https://www.encodeproject.org/experiments/ENCSR553CWR/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR553CWR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB697COI
size range: 200-600


title: Control ChIP-seq from brain (ENCLB871ZDY)

description:
https://www.encodeproject.org/experiments/ENCSR553CWR/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR553CWR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB871ZDY
size range: 200-600

value: ENCBS534HJQ at ENCODE; https://www.encodeproject.org/ENCBS534HJQ/


title: Control ChIP-seq from K562 (ENCLB074MFD)

description:
https://www.encodeproject.org/experiments/ENCSR653VRZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR653VRZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB074MFD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting BCL6

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS929LYE at ENCODE; https://www.encodeproject.org/ENCBS929LYE/

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


title: Control ChIP-seq from brain (ENCLB307ATK)

description:
https://www.encodeproject.org/experiments/ENCSR553CWR/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR553CWR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB307ATK
size range: 200-600

value: brain

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta


title: Control ChIP-seq from H9 (ENCLB624GRZ)

description:
https://www.encodeproject.org/experiments/ENCSR686HII/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on H9 originated from H9
experiment encode accession: ENCSR686HII
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB624GRZ
size range: 200-600

value: WA09 ES cells

value: SESCC

value: ENCBS654ADT at ENCODE; https://www.encodeproject.org/ENCBS654ADT/

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


title: TF ChIP-seq from heart left ventricle (ENCLB469TFP)

description:
https://www.encodeproject.org/experiments/ENCSR355PMV/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on heart left ventricle male adult (40 years)
experiment encode accession: ENCSR355PMV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR945LPX
encode release date: 2020-09-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB469TFP
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (40 years) heart left ventricle tissue, preserved by flash-freezing

value: CTCF

value: heart left ventricle

value: tissue

value: male

value: DM:no; HTN:yes; CAD:no

value: adult

value: 40 year

value: Yiing Lin, MD, PhD

value: ENCBS649GUV at ENCODE; https://www.encodeproject.org/ENCBS649GUV/

value: Derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/


title: TF ChIP-seq from heart left ventricle (ENCLB232PXP)

description:
https://www.encodeproject.org/experiments/ENCSR355PMV/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on heart left ventricle male adult (40 years)
experiment encode accession: ENCSR355PMV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR945LPX
encode release date: 2020-09-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB232PXP
fragmentation methods: sonication (generic)
size range: 200-600

value: Michael Snyder, Stanford


title: Control ChIP-seq from A549 (ENCLB691RYU)

description:
https://www.encodeproject.org/experiments/ENCSR650VIH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR650VIH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB691RYU
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line

value: cell line

value: 58 year

value: ATCC

value: ENCBS405WCD at ENCODE; https://www.encodeproject.org/ENCBS405WCD/

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


title: Control ChIP-seq from H9 (ENCLB129TYA)

description:
https://www.encodeproject.org/experiments/ENCSR686HII/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on H9 originated from H9
experiment encode accession: ENCSR686HII
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB129TYA
size range: 200-600

value: WA09 ES cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS713BMM at ENCODE; https://www.encodeproject.org/ENCBS713BMM/

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


title: Control ChIP-seq from HFFc6 (ENCLB784MTR)

description:
https://www.encodeproject.org/experiments/ENCSR542JNY/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on HFFc6
experiment encode accession: ENCSR542JNY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB784MTR
size range: 200-600

source_name: Homo sapiens HFFc6 cell line, preserved by flash-freezing

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: normal

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

tag: passage number

value: ENCBS502RLX at ENCODE; https://www.encodeproject.org/ENCBS502RLX/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: Control ChIP-seq from HFFc6 (ENCLB815PAK)

description:
https://www.encodeproject.org/experiments/ENCSR542JNY/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on HFFc6
experiment encode accession: ENCSR542JNY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB815PAK
size range: 200-600

value: cell line

value: ENCBS055WKO at ENCODE; https://www.encodeproject.org/ENCBS055WKO/


title: Control ChIP-seq from HFFc6 (ENCLB861VBX)

description:
https://www.encodeproject.org/experiments/ENCSR542JNY/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on HFFc6
experiment encode accession: ENCSR542JNY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB861VBX
size range: 200-600


title: Control ChIP-seq from type B pancreatic cell (ENCLB169ICO)

description:
https://www.encodeproject.org/experiments/ENCSR394CIG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR394CIG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB169ICO
size range: 200-600

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

value: female

value: healthy

value: embryonic

value: ENCBS251SEQ at ENCODE; https://www.encodeproject.org/ENCBS251SEQ/


title: Control ChIP-seq from A549 (ENCLB199PLE)

description:
https://www.encodeproject.org/experiments/ENCSR615QEB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR615QEB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB199PLE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting EHF

value: male

value: adult

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS289IQB at ENCODE; https://www.encodeproject.org/ENCBS289IQB/

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


title: Control ChIP-seq from K562 (ENCLB112JBZ)

description:
https://www.encodeproject.org/experiments/ENCSR616LTS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR616LTS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB112JBZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting PATZ1

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS578UOX at ENCODE; https://www.encodeproject.org/ENCBS578UOX/

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


title: Control ChIP-seq from GM23338 (ENCLB045FIM)

description:
https://www.encodeproject.org/experiments/ENCSR627BZD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human GM23338
experiment encode accession: ENCSR627BZD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB045FIM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens GM23338 cell line genetically modified (insertion) using CRISPR targeting ZNF114

value: cell line

value: ENCBS598WJH at ENCODE; https://www.encodeproject.org/ENCBS598WJH/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Control ChIP-seq from A549 (ENCLB375WSY)

description:
https://www.encodeproject.org/experiments/ENCSR641LIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR641LIQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB375WSY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting ATOH8

value: ENCBS179YEH at ENCODE; https://www.encodeproject.org/ENCBS179YEH/


title: Control ChIP-seq from HepG2 (ENCLB403PPD)

description:
https://www.encodeproject.org/experiments/ENCSR152QMD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR152QMD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: Yijun Ruan, JAX
library encode accession: ENCLB403PPD

source_name: Homo sapiens HepG2 cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Yijun Ruan, JAX

value: ENCBS967VYJ at ENCODE; https://www.encodeproject.org/ENCBS967VYJ/

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


title: Control ChIP-seq from neural crest cell (ENCLB478BRX)

description:
https://www.encodeproject.org/experiments/ENCSR318RRK/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on neural crest cell originated from neural crest cell
experiment encode accession: ENCSR318RRK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB478BRX
size range: 200-600

source_name: Homo sapiens female embryo (5 days) neural crest in vitro differentiated cells originated from neural crest cell

value: neural crest cell

value: in vitro differentiated cells

value: WA09 derived neural crest cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS417JEU at ENCODE; https://www.encodeproject.org/ENCBS417JEU/

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


title: Control ChIP-seq from neural crest cell (ENCLB251ENM)

description:
https://www.encodeproject.org/experiments/ENCSR318RRK/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on neural crest cell originated from neural crest cell
experiment encode accession: ENCSR318RRK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB251ENM
size range: 200-600


title: Control ChIP-seq from neural crest cell (ENCLB140BKQ)

description:
https://www.encodeproject.org/experiments/ENCSR318RRK/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on neural crest cell originated from neural crest cell
experiment encode accession: ENCSR318RRK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB140BKQ
size range: 200-600

value: ENCBS200JOD at ENCODE; https://www.encodeproject.org/ENCBS200JOD/


title: Control ChIP-seq from neural progenitor cell (ENCLB335RLT)

description:
https://www.encodeproject.org/experiments/ENCSR322GAX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on neural progenitor cell
experiment encode accession: ENCSR322GAX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB335RLT
size range: 200-600

source_name: Homo sapiens female embryo (5 days) neural progenitor in vitro differentiated cells

value: neural progenitor cell

value: rapid NPCs, NGN2 +patterning; these are a form of neural progenitor cell -- see more here:https://docs.google.com/document/d/1VDqqe1h1WrG4kDADTFBROGCJrrNvYw5IHCNyMTYUASw/edit#heading=h.gjdgxs

value: Kevin Eggan and Ralda Nehme

value: ENCBS959UMI at ENCODE; https://www.encodeproject.org/ENCBS959UMI/


title: Control ChIP-seq from K562 (ENCLB413DQE)

description:
https://www.encodeproject.org/experiments/ENCSR592PUP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR592PUP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB413DQE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting CREB5

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS798JQO at ENCODE; https://www.encodeproject.org/ENCBS798JQO/

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


title: Control ChIP-seq from neural progenitor cell (ENCLB510DQM)

description:
https://www.encodeproject.org/experiments/ENCSR322GAX/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on neural progenitor cell
experiment encode accession: ENCSR322GAX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB510DQM
size range: 200-600

value: in vitro differentiated cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad


title: Control ChIP-seq from neural crest cell (ENCLB022IXD)

description:
https://www.encodeproject.org/experiments/ENCSR318RRK/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on neural crest cell originated from neural crest cell
experiment encode accession: ENCSR318RRK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB022IXD
size range: 200-600

value: neural crest cell

value: WA09 derived neural crest cells

value: SESCC

value: ENCBS200JOD at ENCODE; https://www.encodeproject.org/ENCBS200JOD/

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


title: Control ChIP-seq from GM23338 (ENCLB471PXU)

description:
https://www.encodeproject.org/experiments/ENCSR866FCH/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on GM23338
experiment encode accession: ENCSR866FCH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB471PXU
size range: 200-600

source_name: Homo sapiens GM23338 cell line, preserved by cryopreservation

value: cell line

value: PGP1 iPSCs

value: male

value: adult

value: George Church

value: ENCBS155WDP at ENCODE; https://www.encodeproject.org/ENCBS155WDP/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Control ChIP-seq from GM23338 (ENCLB936HCF)

description:
https://www.encodeproject.org/experiments/ENCSR866FCH/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on GM23338
experiment encode accession: ENCSR866FCH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB936HCF
size range: 200-600

value: 53 year


title: Control ChIP-seq from K562 (ENCLB274GRP)

description:
https://www.encodeproject.org/experiments/ENCSR965AWP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR965AWP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB274GRP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting HIVEP1

value: female

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS488YPL at ENCODE; https://www.encodeproject.org/ENCBS488YPL/

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


title: Control ChIP-seq from K562 (ENCLB801QNN)

description:
https://www.encodeproject.org/experiments/ENCSR596VPT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR596VPT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB801QNN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF707

value: ENCBS455XSF at ENCODE; https://www.encodeproject.org/ENCBS455XSF/


title: Control ChIP-seq from A549 (ENCLB945IPJ)

description:
https://www.encodeproject.org/experiments/ENCSR957URO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR957URO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB945IPJ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting ZNF302

value: 58 year

value: Michael Snyder

value: ENCBS412UJZ at ENCODE; https://www.encodeproject.org/ENCBS412UJZ/

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


title: Control ChIP-seq from A549 (ENCLB229PNZ)

description:
https://www.encodeproject.org/experiments/ENCSR969KWE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR969KWE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB229PNZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: male

value: ENCBS351ZDP at ENCODE; https://www.encodeproject.org/ENCBS351ZDP/


title: Control ChIP-seq from mesothelial cell of epicardium (ENCLB428LXE)

description:
https://www.encodeproject.org/experiments/ENCSR333DCK/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on epicardium (mesothelium) cells originated from epicardium (mesothelium) cells
experiment encode accession: ENCSR333DCK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB428LXE
size range: 200-600

source_name: Homo sapiens female embryo (5 days) mesothelial of epicardium in vitro differentiated cells originated from mesothelial cell of epicardium

value: mesothelial cell of epicardium

value: in vitro differentiated cells

value: WA09 derived epicardium (mesothelium)

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS924VAR at ENCODE; https://www.encodeproject.org/ENCBS924VAR/

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


title: Control ChIP-seq from HEK293T (ENCLB280VQX)

description:
https://www.encodeproject.org/experiments/ENCSR128PFN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR128PFN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: Yijun Ruan, JAX
library encode accession: ENCLB280VQX

source_name: Homo sapiens HEK293T cell line

value: female

value: unknown

value: Yijun Ruan, JAX

value: Thermo Fisher

value: ENCBS853TQM at ENCODE; https://www.encodeproject.org/ENCBS853TQM/

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


title: Control ChIP-seq from mesothelial cell of epicardium (ENCLB213PYX)

description:
https://www.encodeproject.org/experiments/ENCSR333DCK/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on epicardium (mesothelium) cells originated from epicardium (mesothelium) cells
experiment encode accession: ENCSR333DCK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB213PYX
size range: 200-600


title: Control ChIP-seq from HFFc6 (ENCLB472HFK)

description:
https://www.encodeproject.org/experiments/ENCSR542JNY/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on HFFc6
experiment encode accession: ENCSR542JNY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB472HFK
size range: 200-600

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: normal

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: ENCBS502RLX at ENCODE; https://www.encodeproject.org/ENCBS502RLX/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: DNase-seq from RCC (ENCLB333SUQ)

description:
https://www.encodeproject.org/experiments/ENCSR337IRF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR337IRF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2018-05-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB333SUQ
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens RCC cell line

value: RCC

value: adult

value: 62 year

value: John Stamatoyannopoulos, UW

value: Unknown Source

value: ENCBS354GLT at ENCODE; https://www.encodeproject.org/ENCBS354GLT/

value: Derived from ENCODE donor ENCDO335XPZ; https://www.encodeproject.org/ENCDO335XPZ/