title: delta lexA/delta sulA M9/rdm/glu input replicate 3

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description: Input

data_processing:
Adapter removal using the common Illumina TruSeq adapter sequences with cutadapt 1.8.1.
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed.
Surviving DNA reads with proper paired-end alignments were quantified using an in-house pipeline in which each read contributes a total signal of weight 1, divided over the length of the read. Further processing is described in detail in the accompanying paper.
RNA reads were subject to quantitation using kallisto v0.43 and differential expression calling using sleuth 0.30.0.
Genome_build: E. coli U00096.3
Supplementary_files_format_and_content: Important: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript. Ipod_vs_inp.gr files – Raw IPOD occupancy traces prior to ChIP subtraction, given as a log_2 ratio of extracted to input. The .gr file extension refers to a simple graph type, where the first column indicates a genomic position and the second a corresponding signal chip_vs_inp.gr files – RNA polymerase occupancy given as a log_2 ratio of extracted to input rzlog10p.gr files – ChIP-subtracted IPODHR occupancy, z-scored and then used to calculate enrichment p values as described in the text Abundance.tsv files – kallisto output giving (among other information) gene names and tpm estimates. See the kallisto documentation for details of the file format.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Cultured cells

growth_protocol: Cells were grown to exponential phase (OD600=0.2) in M9/rdm/glu rich defined medium.

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, a 50 microliter input sample was diluted 1:9 in elution buffer (50 mM Tris, pH 8.0; 10 mM EDTA; 1% SDS) and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50o C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext DNA kit, but with a spin column replacing the first bead cleanup.

treatment_protocol: Cells were treated for 10 minutes with rifampicin, then crosslinked for 5 minutes with 1% formaldehyde, prior to quenching with excess glycine. The resulting pellets are washed with PBS and frozen.

value: delta lexA / delta sulA

tag: media

value: MOPS rich defined medium + glucose

tag: time of harvest

value: logarithmic phase


title: delta lexA/delta sulA M9/rdm/glu chip replicate 2

status: Public on Jun 15 2021

type: SRA

country: USA

description:
DlexA_m9_rdm_glu_rzlog10p_chipsub.gr.gz
DlexA_m9_rdm_glu_chip_vs_inp_lograt.gr.gz

library_source: genomic

molecule: genomic DNA

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the digested lysates were mixed 1:1 with 2x IP buffer (200 mM Tris, pH 8.0; 600 mM NaCl; 4% Triton X-100; 2x Roche Complete EDTA-free protease inhibitors), and then kept on ice for no more than a few hours prior to antibody addition. We added 10 microliters of purified anti-E. Coli RNA polymerase antibody (Neoclone WP023), and incubated overnight with rocking at 4 C. Near the end of the incubation period, we resuspended an aliquot of 50 microliters of protein G dynabeads (Invitrogen) and equilibrated the protein G beads with 1x IP buffer lacking protease inhibitors. The bead aliquot was added to the antibody-lysate mixture, and then incubated 2 hours with rocking at 4o C. The bead-antibody-target complexes were subsequently subjected to the following series of washes, with 1 mL used per wash. All washes were at room temperature, and involved manual resuspension of the beads in the new wash buffer followed by immediate re-separation: 1x Wash buffer A (100 mM Tris, pH 8.0; 250 mM LiCl; 2% Triton X-100; 1 mM EDTA); 1x Wash buffer B (100 mM Tris, pH 8.0; 500 mM NaCl; 1% Triton X-100; 0.1% sodium deoxycholate; 1 mM EDTA); 1x Wash buffer C (10 mM Tris, pH 8.0; 500 mM NaCl; 1% Triton X-100; 1 mM EDTA); 1x TE (10 mM Tris, pH 8.0; 1 mM EDTA). The antigens were subsequently eluted by adding 500 microliters of elution buffer (composition described above) and incubating 30 minutes at 65 C, with vigorous vortexing every 5-10 minutes, the protein G beads removed, and the remaining supernatant reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext DNA kit, but with a spin column replacing the first bead cleanup.

tag: genotype


title: 1074NEC

city: NEW HAVEN

first: Oluwabunmi

last: Olaloye

state: CT

address: 1435 STATE ST, APT 301

department: Pediatrics

institute: Yale University

library_source: transcriptomic

data_processing:
Cell Ranger 4.0.0 pipeline was. Used to align reads and generate a count matrix
R package Seurat 4.0 to select cells with mitochondria reads >25%, samples where genes were <200 or >7000 were filtered out
Data normalized using the "LogNormalize" to log-transform the data and cells integrated to minimize batch effect
Data from 1074 excluded from analysis given inadequate cell number. Monocytes in cluster 3 from all files in initial run re-clustered to generate analysis of CD14+ CD16+ CD163+ monocytes.
Genome_build: cannonical gene expression
Supplementary_files_format_and_content: R data from Seurat sample

molecule: total RNA

organism: Homo sapiens

source_name: Preterm small intestine

extract_protocol:
Fresh intestinal tissue was cryopreserved per published protocol in freezing media (Fetal Bovine Serum + 10% Dimethyl sulfoxide). Samples were thawed and single cell suspensions made with dissociation on gentleMACS Octo Dissociator with heaters (Miltenyi Biotec). Live cells selected for using a live/dead kit.
#' GEM libraries were used from 10X kit from Medgenome

tag: gestational age

value: 31 weeks

tag: Sex

value: M

tag: diagnosis

value: necrotizing enterocolitis

tag: tissue

value: Preterm small intestine


title: 1109NEC

value: 39 weeks

value: F


title: SAMPLE 16: HC5

status: Public on Jun 16 2021

type: genomic

city: Beijing

first: Xuan

last: Luo

address: Dongcheng district

country: China

institute: Peking Union Medical College Hospital

hyb_protocol: Samples were processed for array hybridization using Illumina provided array reagents.

scan_protocol: performed on the illumina iScan system following the manufacturer’s procedure.

data_processing: The array data (.IDAT files) was analyzed using ChAMP package in R for deriving the methylation level .

label: Cy5 and Cy3

source_name: Monocyte

label_protocol: performed using Zymo-Research EZ DNA Methylation kits.

extract_protocol: genomic DNA was extracted and purified from Monocyte samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: normal

tag: gender

value: female

value: Monocyte


title: delta lexA/delta sulA M9/rdm/glu chip replicate 1


title: delta lexA/delta sulA M9/rdm/glu input replicate 2

description: Input

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, a 50 microliter input sample was diluted 1:9 in elution buffer (50 mM Tris, pH 8.0; 10 mM EDTA; 1% SDS) and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50o C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
Illumina TruSeq kit, but with a spin column replacing the first bead cleanup.


title: SAMPLE 10: SS10

value: pSS


title: 1127Neontal

source_name: Neonatal small intestine

value: 37 weeks

value: meconium ileus

value: Neonatal small intestine


title: LK0824 cell line grown without CAF in 2D

type: RNA

city: Linköping

first: Emilia

last: Wiechec

address: Sandbäcksgatan 7

department: Biomedical and Clinical Sciences

country: Sweden

institute: Linköping University

description: Gene expression data; RMA expression value derived from TAC software

hyb_protocol: Hybridization was done according to the GeneChip® WT Hy-bridization User Manual for use with the Ambion® WT Expression Kit (Affymetrix). A total of 5.5 µg of sscDNA was fragmented and hybridized on a Human Exon 1.0 ST Array.

scan_protocol: Hybridized arrays were scanned with an Affymetrix GeneChip® 3000 fluorescent scanner.

data_processing: Raw intensity CEL files generated by the GeneChip Command Console were imported into Transcriptome Analysis Console (TAC) and CHP files were generated for gene level analysis using the RMA summarization method.

label: biotin

source_name: cell culture without CAF

label_protocol: Labeling was done according to the GeneChip® WT Terminal La-beling  User Manual for use with the Ambion® WT Expression Kit (Affymetrix). The starting amount of total RNA was 100 ng. 15 µg of cRNA was used for single-stranded cDNA-synthesis (sscDNA).

growth_protocol: Tumor cells and CAFs were co-cultured in 2D in cell culture flasks. Tumor cell and CAF numbers were adjusted to that an approximate ratio of 3:1 was achieved by the end of co-culture

extract_protocol: Total RNA extraction was performed using the RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol:
Tumor cells were separated from CAFs by magnetic activated cell sorting (MACS).
Gene expression data from HNSCC cell lines grown with or without CAFs in 2D

value: HNSCC cell line (tongue)

tag: age


title: A485_replicate 2

city: Gainesville

first: Daiqing

last: Liao

state: Florida

address: 2033 Mowry Road

department: Anatomy and Cell Biology

institute: University of Florida

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Human Transcriptome Array 2.0 and scanned at the University of Florida Interdisciplinary Center for Biotechnology Research.

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

data_processing: For data analysis, we performed differential expression (DE) analysis using R package limma to compare the DMSO group and the A-485 group. Limma utilizes linear model approach to identify differentially expressed genes and employs empirical Bayesian methods to stabilize the variance estimation. Differentially expressed genes with p-value < 0.05 and fold change (FC) ≥ 1.25 or ≤ -1.25 were identified

label_protocol: All microarray sample preparation reactions used the  Ambion® WT Expression Kit, combined with the GeneChip WT Terminal Labeling and  Controls Kit (Affymetrix)

growth_protocol: MCF-7 cells were grown at 37 °ºC with 5% CO2 in a humidified atmosphere. MCF-7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM with 4.5 g/L glucose, L-glutamine and sodium pyruvate, Corning) supplemented with 10% bovine calf serum (HyClone, GE Healthcare Bio-Sciences), penicillin (10 units/ml), and streptomycin (10 µg/ml) (designated as complete media).

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer instructions.

treatment_protocol: MCF-7 cells were treated with A-485 at 3 µM or DMSO control for 24 hours in complete media.

tag: drug treatment

tag: cancer type

value: ER+ breast cancer


title: 1102_Fetal

source_name: Fetal small intestine

value: 21 weeks

value: Fetal small intestine


title: 1100A_Fetal

value: not determined


title: Mint-ChIP-seq from H9 (ENCLB518ERI)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR998ZMN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9
experiment encode accession: ENCSR998ZMN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB518ERI
fragmentation methods: none

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

source_name: Homo sapiens H9 cell line

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: health state

value: healthy

tag: dev stage

value: embryonic

value: 5 day

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Joseph Bonventre

tag: passage number

tag: link

value: ENCBS965ZIX at ENCODE; https://www.encodeproject.org/ENCBS965ZIX/

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


title: Mint-ChIP-seq from H9 (ENCLB366SHQ)

description:
https://www.encodeproject.org/experiments/ENCSR998ZMN/
***************
biological replicate number: 2
technical replicate number: 3
description: H3K27ac Mint-ChIP-seq on human H9
experiment encode accession: ENCSR998ZMN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB366SHQ
fragmentation methods: none

tag: Sex

value: female


title: Mint-ChIP-seq from H9 (ENCLB989TUA)

description:
https://www.encodeproject.org/experiments/ENCSR998ZMN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9
experiment encode accession: ENCSR998ZMN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB989TUA
fragmentation methods: none

value: ENCBS877WZR at ENCODE; https://www.encodeproject.org/ENCBS877WZR/


title: Mint-ChIP-seq from H9 (ENCLB918PNB)

description:
https://www.encodeproject.org/experiments/ENCSR998ZMN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9
experiment encode accession: ENCSR998ZMN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB918PNB
fragmentation methods: none


title: 1164Neonatal

tag: gestational age

value: 36 weeks

value: F

tag: diagnosis

value: gastroschisis


title: SAMPLE 13: HC2

tag: disease state

value: normal

tag: tissue

value: Monocyte


title: Mint-ChIP-seq from H9 (ENCLB599IZH)

description:
https://www.encodeproject.org/experiments/ENCSR998ZMN/
***************
biological replicate number: 2
technical replicate number: 4
description: H3K27ac Mint-ChIP-seq on human H9
experiment encode accession: ENCSR998ZMN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB599IZH
fragmentation methods: none

tag: age


title: SAMPLE 9: SS9

value: pSS

tag: gender


title: SAMPLE 14: HC3


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB690VDE)

description:
https://www.encodeproject.org/experiments/ENCSR989YNV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR989YNV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR881SIP
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB690VDE
fragmentation methods: none

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell

value: primary cell

tag: description

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: unknown

value: David Hafler

value: ENCBS135XFB at ENCODE; https://www.encodeproject.org/ENCBS135XFB/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB147CJO)

description:
https://www.encodeproject.org/experiments/ENCSR989YNV/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR989YNV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR881SIP
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB147CJO
fragmentation methods: none

tag: antibody

value: healthy

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from brain (ENCLB249IWL)

description:
https://www.encodeproject.org/experiments/ENCSR988RUI/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR988RUI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR577JQZ
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB249IWL
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) brain organoid, 90 days post differentiation

value: brain

value: organoid

value: female

value: embryonic

value: 5 day

value: Paola Arlotta

value: ENCBS140WFQ at ENCODE; https://www.encodeproject.org/ENCBS140WFQ/

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


title: Mint-ChIP-seq from brain (ENCLB326ZDC)

description:
https://www.encodeproject.org/experiments/ENCSR988RUI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR988RUI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR577JQZ
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB326ZDC
fragmentation methods: none

value: ENCBS069IXO at ENCODE; https://www.encodeproject.org/ENCBS069IXO/


title: Mint-ChIP-seq from brain (ENCLB911NDN)

description:
https://www.encodeproject.org/experiments/ENCSR988RUI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR988RUI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR577JQZ
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB911NDN
fragmentation methods: none


title: LK0942 cell line grown with CAF in 2D

source_name: cell co-culture with CAF

value: HNSCC cell line (larynx)


title: delta lexA/delta sulA M9/rdm/glu IPOD replicate 2

description:
DlexA_m9_rdm_glu_rzlog10p_chipsub.gr.gz
DlexA_m9_rdm_glu_ipod_vs_inp_lograt.gr.gz

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
Illumina TruSeq DNA prep kit, with spin column cleanups replaced with Zymo spin columns.

tag: genotype

value: delta lexA / delta sulA

tag: media

value: MOPS rich defined medium + glucose

tag: time of harvest

value: logarithmic phase


title: SAMPLE 12: HC1

value: normal

value: Monocyte


title: SAMPLE 8: SS8

value: pSS


title: SAMPLE 5: SS5


title: Mint-ChIP-seq from brain (ENCLB282EHZ)

description:
https://www.encodeproject.org/experiments/ENCSR988RUI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR988RUI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR577JQZ
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB282EHZ
fragmentation methods: none

tag: biosample encode accession

tag: health state

value: healthy

tag: dev stage

value: Bradley Bernstein, Broad


title: SAMPLE 11: SS11


title: SAMPLE 15: HC4


title: SAMPLE 6: SS6

value: male


title: Mint-ChIP-seq from brain (ENCLB587NXI)

description:
https://www.encodeproject.org/experiments/ENCSR988RUI/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR988RUI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR577JQZ
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB587NXI
fragmentation methods: none

value: brain

value: organoid

value: female

tag: lab

tag: source

value: ENCBS277HZS at ENCODE; https://www.encodeproject.org/ENCBS277HZS/


title: SAMPLE 3: SS3


title: Mint-ChIP-seq from brain (ENCLB616ESR)

description:
https://www.encodeproject.org/experiments/ENCSR988RUI/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR988RUI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR577JQZ
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB616ESR
fragmentation methods: none

tag: Sex

value: embryonic

value: 5 day

value: Paola Arlotta

tag: link


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB158ULF)

description:
https://www.encodeproject.org/experiments/ENCSR898VJE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR898VJE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR127UUU
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB158ULF
fragmentation methods: none

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell with multiple sclerosis

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS437FZY at ENCODE; https://www.encodeproject.org/ENCBS437FZY/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: SAMPLE 7: SS7

value: pSS

value: Monocyte


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB759VVE)

description:
https://www.encodeproject.org/experiments/ENCSR898VJE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR898VJE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR127UUU
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB759VVE
fragmentation methods: none

value: Bradley Bernstein, Broad


title: SAMPLE 2: SS2

value: female


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB095XTI)

description:
https://www.encodeproject.org/experiments/ENCSR884ROQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR884ROQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR749PSE
encode release date: 2020-09-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB095XTI
fragmentation methods: none

source_name: Homo sapiens CD8-positive, alpha-beta memory T primary cell

value: CD8-positive, alpha-beta memory T cell

value: healthy

value: ENCBS020LPJ at ENCODE; https://www.encodeproject.org/ENCBS020LPJ/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB057DRH)

description:
https://www.encodeproject.org/experiments/ENCSR985RAJ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR985RAJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR867UMZ
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB057DRH
fragmentation methods: none

source_name: Homo sapiens CD14-positive monocyte primary cell with multiple sclerosis, preserved by cryopreservation

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: ENCBS522LRV at ENCODE; https://www.encodeproject.org/ENCBS522LRV/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: Mint-ChIP-seq from naive B cell (ENCLB036IEW)

description:
https://www.encodeproject.org/experiments/ENCSR987OPY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR987OPY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR707UVZ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB036IEW

source_name: Homo sapiens naive B primary cell with multiple sclerosis

value: naive B cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: ENCBS049BNE at ENCODE; https://www.encodeproject.org/ENCBS049BNE/


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB947RHK)

description:
https://www.encodeproject.org/experiments/ENCSR884ROQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR884ROQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR749PSE
encode release date: 2020-09-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB947RHK
fragmentation methods: none

value: unknown

value: David Hafler


title: SAMPLE 4: SS4

value: pSS

value: female

value: Monocyte


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB830YXK)

description:
https://www.encodeproject.org/experiments/ENCSR881AOK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR881AOK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR996DNY
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB830YXK
fragmentation methods: none
instrument models: Illumina HiSeq 2500,Illumina NovaSeq 6000

source_name: Homo sapiens CD8-positive, alpha-beta memory T primary cell, preserved by cryopreservation

value: CD8-positive, alpha-beta memory T cell

value: CD8+ memory CD3+ CD4- CD8+ CD45RA- CD45RO+

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS274KKV at ENCODE; https://www.encodeproject.org/ENCBS274KKV/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB786NSL)

description:
https://www.encodeproject.org/experiments/ENCSR881SIP/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR881SIP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB786NSL

value: ENCBS135XFB at ENCODE; https://www.encodeproject.org/ENCBS135XFB/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB047OKR)

description:
https://www.encodeproject.org/experiments/ENCSR881SIP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR881SIP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB047OKR

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017


title: Mint-ChIP-seq from naive B cell (ENCLB986QXV)

description:
https://www.encodeproject.org/experiments/ENCSR987OPY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR987OPY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR707UVZ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB986QXV

value: naive B cell

value: not collected

value: multiple sclerosis

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: Control Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB927JNA)

description:
https://www.encodeproject.org/experiments/ENCSR887UYJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR887UYJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB927JNA

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell, preserved by cryopreservation

value: CD4-positive, alpha-beta memory T cell

value: CD4+ memory cells from healthy donor

value: unknown

value: David Hafler

value: ENCBS963BXF at ENCODE; https://www.encodeproject.org/ENCBS963BXF/

value: Derived from ENCODE donor ENCDO258PRN; https://www.encodeproject.org/ENCDO258PRN/


title: Control Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB802AZK)

description:
https://www.encodeproject.org/experiments/ENCSR887UYJ/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR887UYJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB802AZK

value: healthy

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB677YEQ)

description:
https://www.encodeproject.org/experiments/ENCSR881AOK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR881AOK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR996DNY
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB677YEQ
fragmentation methods: none
instrument models: Illumina HiSeq 2500,Illumina NovaSeq 6000

value: CD8-positive, alpha-beta memory T cell

value: CD8+ memory CD3+ CD4- CD8+ CD45RA- CD45RO+

value: ENCBS274KKV at ENCODE; https://www.encodeproject.org/ENCBS274KKV/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB091FWE)

description:
https://www.encodeproject.org/experiments/ENCSR985RAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR985RAJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR867UMZ
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB091FWE
fragmentation methods: none

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

value: ENCBS522LRV at ENCODE; https://www.encodeproject.org/ENCBS522LRV/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: Mint-ChIP-seq from brain (ENCLB202ELU)

description:
https://www.encodeproject.org/experiments/ENCSR978LBY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR978LBY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB202ELU
fragmentation methods: none

source_name: Homo sapiens male adult (53 years) brain organoid, 90 days post differentiation

value: brain

value: organoid

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: male

value: adult

value: 53 year

value: Paola Arlotta

value: ENCBS291HMT at ENCODE; https://www.encodeproject.org/ENCBS291HMT/

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


title: Mint-ChIP-seq from brain (ENCLB352YAW)

description:
https://www.encodeproject.org/experiments/ENCSR978LBY/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR978LBY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB352YAW
fragmentation methods: none

value: Bradley Bernstein, Broad

value: ENCBS377FQM at ENCODE; https://www.encodeproject.org/ENCBS377FQM/


title: Mint-ChIP-seq from brain (ENCLB004FTN)

description:
https://www.encodeproject.org/experiments/ENCSR978LBY/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR978LBY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB004FTN
fragmentation methods: none

value: ENCBS524OMS at ENCODE; https://www.encodeproject.org/ENCBS524OMS/


title: SAMPLE 1: SS1

value: pSS

value: female

value: Monocyte


title: Mint-ChIP-seq from brain (ENCLB260EBF)

description:
https://www.encodeproject.org/experiments/ENCSR978LBY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR978LBY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB260EBF
fragmentation methods: none


title: Mint-ChIP-seq from brain (ENCLB831VHS)

description:
https://www.encodeproject.org/experiments/ENCSR978LBY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR978LBY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB831VHS
fragmentation methods: none


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB184DLB)

description:
https://www.encodeproject.org/experiments/ENCSR878YHM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR878YHM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR128CIX
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB184DLB

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell with multiple sclerosis

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS040CMJ at ENCODE; https://www.encodeproject.org/ENCBS040CMJ/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB676BVD)

description:
https://www.encodeproject.org/experiments/ENCSR878YHM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR878YHM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR128CIX
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB676BVD


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB644NMX)

description:
https://www.encodeproject.org/experiments/ENCSR869QEN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR869QEN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR749PSE
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB644NMX
fragmentation methods: none

value: CD8-positive, alpha-beta memory T cell

value: healthy

value: ENCBS020LPJ at ENCODE; https://www.encodeproject.org/ENCBS020LPJ/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Mint-ChIP-seq from immature natural killer cell (ENCLB690TYR)

description:
https://www.encodeproject.org/experiments/ENCSR977FMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR977FMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR242ARJ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB690TYR
fragmentation methods: none

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

value: Bradley Bernstein, Broad

value: ENCBS142IVK at ENCODE; https://www.encodeproject.org/ENCBS142IVK/


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB725OJQ)

description:
https://www.encodeproject.org/experiments/ENCSR869QEN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR869QEN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR749PSE
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB725OJQ
fragmentation methods: none


title: Mint-ChIP-seq from immature natural killer cell (ENCLB407VUS)

description:
https://www.encodeproject.org/experiments/ENCSR977FMZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR977FMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR242ARJ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB407VUS
fragmentation methods: none


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB303XQQ)

description:
https://www.encodeproject.org/experiments/ENCSR977EPS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR977EPS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283QZJ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB303XQQ
fragmentation methods: none

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell

value: ENCBS370LJB at ENCODE; https://www.encodeproject.org/ENCBS370LJB/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB982TTF)

description:
https://www.encodeproject.org/experiments/ENCSR868SVG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR868SVG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR887UYJ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB982TTF
fragmentation methods: none

value: CD4-positive, alpha-beta memory T cell

value: CD4+ memory cells from healthy donor

value: ENCBS963BXF at ENCODE; https://www.encodeproject.org/ENCBS963BXF/

value: Derived from ENCODE donor ENCDO258PRN; https://www.encodeproject.org/ENCDO258PRN/


title: Mint-ChIP-seq from brain (ENCLB341KYJ)

description:
https://www.encodeproject.org/experiments/ENCSR978LBY/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR978LBY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB341KYJ
fragmentation methods: none

value: brain

value: organoid

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: male

value: adult

value: 53 year

value: Paola Arlotta

value: ENCBS524OMS at ENCODE; https://www.encodeproject.org/ENCBS524OMS/

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB286NCI)

description:
https://www.encodeproject.org/experiments/ENCSR975WTH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR975WTH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR917PCR
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB286NCI
fragmentation methods: none
instrument models: Illumina HiSeq 2500,Illumina NovaSeq 6000

value: primary cell

value: CD4+ memory CD3+ CD4+ CD8- CD45RA- CD45RO+ nonTreg

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS802GRA at ENCODE; https://www.encodeproject.org/ENCBS802GRA/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: Control Mint-ChIP-seq from CD14-positive monocyte (ENCLB548XPU)

description:
https://www.encodeproject.org/experiments/ENCSR867UMZ/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR867UMZ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB548XPU

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: ENCBS522LRV at ENCODE; https://www.encodeproject.org/ENCBS522LRV/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: Control Mint-ChIP-seq from CD14-positive monocyte (ENCLB872NGP)

description:
https://www.encodeproject.org/experiments/ENCSR867UMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR867UMZ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB872NGP


title: Mint-ChIP-seq from nephron (ENCLB018FFN)

description:
https://www.encodeproject.org/experiments/ENCSR862INW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR862INW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801AJD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB018FFN
fragmentation methods: none

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

value: nephron

value: organoid

value: female

value: embryonic

value: 5 day

value: Joseph Bonventre

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

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


title: Mint-ChIP-seq from nephron (ENCLB581MHQ)

description:
https://www.encodeproject.org/experiments/ENCSR862INW/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR862INW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801AJD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB581MHQ
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) nephron organoid, 49 days post differentiation

value: healthy

value: ENCBS546COW at ENCODE; https://www.encodeproject.org/ENCBS546COW/


title: Mint-ChIP-seq from nephron (ENCLB189FCH)

description:
https://www.encodeproject.org/experiments/ENCSR862INW/
***************
biological replicate number: 1
technical replicate number: 4
description: H3K4me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR862INW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801AJD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB189FCH
fragmentation methods: none


title: Mint-ChIP-seq from nephron (ENCLB250WAQ)

description:
https://www.encodeproject.org/experiments/ENCSR862INW/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K4me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR862INW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801AJD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB250WAQ
fragmentation methods: none


title: Control Mint-ChIP-seq from H9 (ENCLB779ICF)

description:
https://www.encodeproject.org/experiments/ENCSR854TWQ/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human H9
experiment encode accession: ENCSR854TWQ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB779ICF

tag: line

value: cell line

tag: passage number

value: ENCBS877WZR at ENCODE; https://www.encodeproject.org/ENCBS877WZR/


title: Control Mint-ChIP-seq from H9 (ENCLB356MSF)

description:
https://www.encodeproject.org/experiments/ENCSR854TWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human H9
experiment encode accession: ENCSR854TWQ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB356MSF


title: Control Mint-ChIP-seq from H9 (ENCLB115DOL)

description:
https://www.encodeproject.org/experiments/ENCSR854TWQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control Mint-ChIP-seq on human H9
experiment encode accession: ENCSR854TWQ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB115DOL

value: ENCBS965ZIX at ENCODE; https://www.encodeproject.org/ENCBS965ZIX/


title: Control Mint-ChIP-seq from H9 (ENCLB368RGA)

description:
https://www.encodeproject.org/experiments/ENCSR854TWQ/
***************
biological replicate number: 2
technical replicate number: 2
description: Control Mint-ChIP-seq on human H9
experiment encode accession: ENCSR854TWQ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB368RGA


title: Control Mint-ChIP-seq from H9 (ENCLB180HYN)

description:
https://www.encodeproject.org/experiments/ENCSR854TWQ/
***************
biological replicate number: 2
technical replicate number: 4
description: Control Mint-ChIP-seq on human H9
experiment encode accession: ENCSR854TWQ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB180HYN


title: Mint-ChIP-seq from nephron (ENCLB131UUN)

description:
https://www.encodeproject.org/experiments/ENCSR852EKS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR852EKS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB131UUN
fragmentation methods: none

value: ENCBS165DBC at ENCODE; https://www.encodeproject.org/ENCBS165DBC/


title: Mint-ChIP-seq from nephron (ENCLB507SQS)

description:
https://www.encodeproject.org/experiments/ENCSR852EKS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR852EKS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB507SQS
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) nephron organoid, 35 days post differentiation

value: Bradley Bernstein, Broad

value: ENCBS391CFV at ENCODE; https://www.encodeproject.org/ENCBS391CFV/


title: Control Mint-ChIP-seq from H9 (ENCLB731RIS)

description:
https://www.encodeproject.org/experiments/ENCSR854TWQ/
***************
biological replicate number: 2
technical replicate number: 3
description: Control Mint-ChIP-seq on human H9
experiment encode accession: ENCSR854TWQ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB731RIS

source_name: Homo sapiens H9 cell line


title: Mint-ChIP-seq from nephron (ENCLB582TFH)

description:
https://www.encodeproject.org/experiments/ENCSR852EKS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR852EKS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB582TFH
fragmentation methods: none


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB450EAO)

description:
https://www.encodeproject.org/experiments/ENCSR977EPS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR977EPS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283QZJ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB450EAO
fragmentation methods: none

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: unknown

value: David Hafler

value: ENCBS370LJB at ENCODE; https://www.encodeproject.org/ENCBS370LJB/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Mint-ChIP-seq from nephron (ENCLB827JWX)

description:
https://www.encodeproject.org/experiments/ENCSR852EKS/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR852EKS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB827JWX
fragmentation methods: none

value: nephron

value: organoid

value: female

value: embryonic

value: 5 day

value: Joseph Bonventre


title: Mint-ChIP-seq from nephron (ENCLB852ZAX)

description:
https://www.encodeproject.org/experiments/ENCSR852EKS/
***************
biological replicate number: 1
technical replicate number: 4
description: H3K4me1 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR852EKS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB852ZAX
fragmentation methods: none

value: healthy

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB891BUO)

description:
https://www.encodeproject.org/experiments/ENCSR868SVG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR868SVG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR887UYJ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB891BUO
fragmentation methods: none

value: CD4-positive, alpha-beta memory T cell

value: CD4+ memory cells from healthy donor

value: Bradley Bernstein, Broad

value: ENCBS963BXF at ENCODE; https://www.encodeproject.org/ENCBS963BXF/

value: Derived from ENCODE donor ENCDO258PRN; https://www.encodeproject.org/ENCDO258PRN/


title: Mint-ChIP-seq from nephron (ENCLB475DDB)

description:
https://www.encodeproject.org/experiments/ENCSR862INW/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR862INW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801AJD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB475DDB
fragmentation methods: none

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


title: WGS from transverse colon (ENCLB388OQF)

description:
https://www.encodeproject.org/experiments/ENCSR961ZRM/
***************
biological replicate number: 1
technical replicate number: 2
description: The data contained in this experiment correspond to Illumina-based whole genome shotgun sequencing of EN-TEX donor ENCDO793LXB, a 53 year old female. There are two libraries: PCR-based (9-cycle, ENCLB388OQF) and PCR-free (ENCLB358DLU), both sequenced on multiple lanes to a combined depth of ~ 60X in PE125 format.
experiment encode accession: ENCSR961ZRM
assay title: WGS
assembly: GRCh38
encode release date: 2016-04-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB388OQF
fragmentation methods: see document

source_name: Homo sapiens transverse colon tissue female adult (53 years)

value: transverse colon

value: tissue

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: 53 year

value: Thomas Gingeras, CSHL

value: ENCBS974EYF at ENCODE; https://www.encodeproject.org/ENCBS974EYF/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Mint-ChIP-seq from nephron (ENCLB921LJG)

description:
https://www.encodeproject.org/experiments/ENCSR862INW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR862INW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801AJD
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB921LJG
fragmentation methods: none

value: nephron

value: organoid

value: female

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS546COW at ENCODE; https://www.encodeproject.org/ENCBS546COW/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB254HOX)

description:
https://www.encodeproject.org/experiments/ENCSR959VZU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR959VZU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR127UUU
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB254HOX
fragmentation methods: none

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS437FZY at ENCODE; https://www.encodeproject.org/ENCBS437FZY/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: WGS from transverse colon (ENCLB358DLU)

description:
https://www.encodeproject.org/experiments/ENCSR961ZRM/
***************
biological replicate number: 1
technical replicate number: 1
description: The data contained in this experiment correspond to Illumina-based whole genome shotgun sequencing of EN-TEX donor ENCDO793LXB, a 53 year old female. There are two libraries: PCR-based (9-cycle, ENCLB388OQF) and PCR-free (ENCLB358DLU), both sequenced on multiple lanes to a combined depth of ~ 60X in PE125 format.
experiment encode accession: ENCSR961ZRM
assay title: WGS
assembly: GRCh38
encode release date: 2016-04-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB358DLU
fragmentation methods: see document

value: transverse colon

value: tissue

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: adult

value: 53 year

value: Thomas Gingeras, CSHL

value: ENCBS974EYF at ENCODE; https://www.encodeproject.org/ENCBS974EYF/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Mint-ChIP-seq from nephron (ENCLB864EWL)

description:
https://www.encodeproject.org/experiments/ENCSR850MVW/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR850MVW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB864EWL
fragmentation methods: none

value: nephron

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS165DBC at ENCODE; https://www.encodeproject.org/ENCBS165DBC/

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


title: Mint-ChIP-seq from nephron (ENCLB209DSW)

description:
https://www.encodeproject.org/experiments/ENCSR850MVW/
***************
biological replicate number: 1
technical replicate number: 4
description: H3K9me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR850MVW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB209DSW
fragmentation methods: none

value: Bradley Bernstein, Broad

value: ENCBS391CFV at ENCODE; https://www.encodeproject.org/ENCBS391CFV/


title: Mint-ChIP-seq from nephron (ENCLB223UCV)

description:
https://www.encodeproject.org/experiments/ENCSR850MVW/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR850MVW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB223UCV
fragmentation methods: none


title: Mint-ChIP-seq from nephron (ENCLB766XHF)

description:
https://www.encodeproject.org/experiments/ENCSR850MVW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR850MVW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB766XHF
fragmentation methods: none


title: Mint-ChIP-seq from nephron (ENCLB179RNZ)

description:
https://www.encodeproject.org/experiments/ENCSR850MVW/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K9me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR850MVW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB179RNZ
fragmentation methods: none


title: Mint-ChIP-seq from nephron (ENCLB934CLF)

description:
https://www.encodeproject.org/experiments/ENCSR850MVW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR850MVW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB934CLF
fragmentation methods: none


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB856CAV)

description:
https://www.encodeproject.org/experiments/ENCSR954ZLD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR954ZLD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR344TLH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB856CAV
fragmentation methods: none

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell with multiple sclerosis, preserved by cryopreservation

value: primary cell

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS321BAK at ENCODE; https://www.encodeproject.org/ENCBS321BAK/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: Control Mint-ChIP-seq from CD14-positive monocyte (ENCLB925EEP)

description:
https://www.encodeproject.org/experiments/ENCSR958CUX/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR958CUX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB925EEP

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: ENCBS929PLQ at ENCODE; https://www.encodeproject.org/ENCBS929PLQ/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: Control Mint-ChIP-seq from CD14-positive monocyte (ENCLB125VZK)

description:
https://www.encodeproject.org/experiments/ENCSR958CUX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR958CUX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB125VZK


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB034LHS)

description:
https://www.encodeproject.org/experiments/ENCSR954ZLD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR954ZLD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR344TLH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB034LHS
fragmentation methods: none


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB357UVF)

description:
https://www.encodeproject.org/experiments/ENCSR848XJL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR848XJL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR243EIU
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB357UVF

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell with multiple sclerosis

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: ENCBS771DND at ENCODE; https://www.encodeproject.org/ENCBS771DND/


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB938JWT)

description:
https://www.encodeproject.org/experiments/ENCSR848XJL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR848XJL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR243EIU
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB938JWT


title: Mint-ChIP-seq from nephron (ENCLB039LDM)

description:
https://www.encodeproject.org/experiments/ENCSR852EKS/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K4me1 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR852EKS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB039LDM
fragmentation methods: none

value: nephron

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB156RSX)

description:
https://www.encodeproject.org/experiments/ENCSR959VZU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR959VZU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR127UUU
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB156RSX
fragmentation methods: none

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell with multiple sclerosis

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS437FZY at ENCODE; https://www.encodeproject.org/ENCBS437FZY/


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB096OMC)

description:
https://www.encodeproject.org/experiments/ENCSR845VVI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR845VVI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR881SIP
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB096OMC
fragmentation methods: none

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: ENCBS135XFB at ENCODE; https://www.encodeproject.org/ENCBS135XFB/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB754NFW)

description:
https://www.encodeproject.org/experiments/ENCSR845VVI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR845VVI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR881SIP
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB754NFW
fragmentation methods: none


title: Mint-ChIP-seq from brain (ENCLB439KSL)

description:
https://www.encodeproject.org/experiments/ENCSR844OQI/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR844OQI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB439KSL
fragmentation methods: none

source_name: Homo sapiens male adult (53 years) brain organoid, 180 days post differentiation

value: brain

value: organoid

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: male

value: adult

value: 53 year

value: Paola Arlotta

value: ENCBS412HPI at ENCODE; https://www.encodeproject.org/ENCBS412HPI/

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


title: Mint-ChIP-seq from brain (ENCLB602OJZ)

description:
https://www.encodeproject.org/experiments/ENCSR844OQI/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR844OQI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB602OJZ
fragmentation methods: none


title: Mint-ChIP-seq from brain (ENCLB442KLF)

description:
https://www.encodeproject.org/experiments/ENCSR844OQI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR844OQI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB442KLF
fragmentation methods: none

value: ENCBS344QAP at ENCODE; https://www.encodeproject.org/ENCBS344QAP/


title: Mint-ChIP-seq from brain (ENCLB741MAF)

description:
https://www.encodeproject.org/experiments/ENCSR844OQI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR844OQI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB741MAF
fragmentation methods: none

value: ENCBS252LAB at ENCODE; https://www.encodeproject.org/ENCBS252LAB/


title: Mint-ChIP-seq from brain (ENCLB648UEQ)

description:
https://www.encodeproject.org/experiments/ENCSR844OQI/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR844OQI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB648UEQ
fragmentation methods: none

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from brain (ENCLB530TTS)

description:
https://www.encodeproject.org/experiments/ENCSR844OQI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR844OQI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR106WDX
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB530TTS
fragmentation methods: none


title: Mint-ChIP-seq from naive B cell (ENCLB305VRM)

description:
https://www.encodeproject.org/experiments/ENCSR945JTU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR945JTU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR906UGW
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB305VRM

source_name: Homo sapiens naive B primary cell

value: naive B cell

value: primary cell

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS973SPF at ENCODE; https://www.encodeproject.org/ENCBS973SPF/


title: Mint-ChIP-seq from naive B cell (ENCLB689END)

description:
https://www.encodeproject.org/experiments/ENCSR945JTU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR945JTU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR906UGW
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB689END

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB987UEX)

description:
https://www.encodeproject.org/experiments/ENCSR943WLE/
***************
biological replicate number: 2
technical replicate number: 3
description: H3K36me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR943WLE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB987UEX
fragmentation methods: none

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

value: nephron progenitor cell

value: in vitro differentiated cells

value: H9 NPC (Day 8):Nephron progenitor cells derived from H9 ES cells

value: female

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS491YOI at ENCODE; https://www.encodeproject.org/ENCBS491YOI/

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


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB500LVC)

description:
https://www.encodeproject.org/experiments/ENCSR943WLE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR943WLE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB500LVC
fragmentation methods: none

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB564ZNZ)

description:
https://www.encodeproject.org/experiments/ENCSR943WLE/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR943WLE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB564ZNZ
fragmentation methods: none


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB013MSM)

description:
https://www.encodeproject.org/experiments/ENCSR943WLE/
***************
biological replicate number: 2
technical replicate number: 4
description: H3K36me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR943WLE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB013MSM
fragmentation methods: none


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB597XDQ)

description:
https://www.encodeproject.org/experiments/ENCSR943WLE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR943WLE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB597XDQ
fragmentation methods: none

value: ENCBS835ZTQ at ENCODE; https://www.encodeproject.org/ENCBS835ZTQ/


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB558MST)

description:
https://www.encodeproject.org/experiments/ENCSR943WLE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR943WLE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB558MST
fragmentation methods: none

value: healthy


title: Mint-ChIP-seq from immature natural killer cell (ENCLB932YUN)

description:
https://www.encodeproject.org/experiments/ENCSR835AVN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR835AVN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR242ARJ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB932YUN
fragmentation methods: none

value: immature natural killer cell

value: primary cell

value: not collected

value: unknown

value: ENCBS142IVK at ENCODE; https://www.encodeproject.org/ENCBS142IVK/


title: Mint-ChIP-seq from immature natural killer cell (ENCLB072CVP)

description:
https://www.encodeproject.org/experiments/ENCSR835AVN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR835AVN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR242ARJ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB072CVP
fragmentation methods: none

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: David Hafler

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB740FWZ)

description:
https://www.encodeproject.org/experiments/ENCSR832UMM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR832UMM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR127UUU
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB740FWZ
fragmentation methods: none

value: CD4-positive, alpha-beta memory T cell

value: multiple sclerosis

value: ENCBS437FZY at ENCODE; https://www.encodeproject.org/ENCBS437FZY/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB697PWD)

description:
https://www.encodeproject.org/experiments/ENCSR832UMM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR832UMM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR127UUU
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB697PWD
fragmentation methods: none


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB170DRR)

description:
https://www.encodeproject.org/experiments/ENCSR832PIM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human IgD-negative memory B cell
experiment encode accession: ENCSR832PIM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR469VTN
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB170DRR
fragmentation methods: none

source_name: Homo sapiens IgD-negative memory B primary cell, preserved by cryopreservation

value: IgD-negative memory B cell

value: B memory CD3- CD14- CD19+ CD27+ IgD-

value: ENCBS677QPD at ENCODE; https://www.encodeproject.org/ENCBS677QPD/


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB206SOY)

description:
https://www.encodeproject.org/experiments/ENCSR832PIM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human IgD-negative memory B cell
experiment encode accession: ENCSR832PIM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR469VTN
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB206SOY
fragmentation methods: none

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from HFFc6 (ENCLB775VKS)

description:
https://www.encodeproject.org/experiments/ENCSR938NXC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR938NXC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR114FEG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB775VKS
fragmentation methods: none

source_name: Homo sapiens HFFc6 cell line, preserved by cryopreservation

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: ENCBS217PYK at ENCODE; https://www.encodeproject.org/ENCBS217PYK/

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


title: Mint-ChIP-seq from HFFc6 (ENCLB874EVU)

description:
https://www.encodeproject.org/experiments/ENCSR938NXC/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR938NXC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR114FEG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB874EVU
fragmentation methods: none


title: Mint-ChIP-seq from HFFc6 (ENCLB599FOD)

description:
https://www.encodeproject.org/experiments/ENCSR938NXC/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR938NXC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR114FEG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB599FOD
fragmentation methods: none

value: ENCBS794NUP at ENCODE; https://www.encodeproject.org/ENCBS794NUP/


title: Mint-ChIP-seq from GM23338 (ENCLB867XBE)

description:
https://www.encodeproject.org/experiments/ENCSR828GHL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR828GHL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB867XBE
fragmentation methods: none

source_name: Homo sapiens GM23338 cell line, preserved by cryopreservation

value: PGP1 iPSCs

value: adult

value: 53 year

value: George Church

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

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


title: Mint-ChIP-seq from GM23338 (ENCLB885ZWV)

description:
https://www.encodeproject.org/experiments/ENCSR828GHL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR828GHL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB885ZWV
fragmentation methods: none

value: cell line

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from immature natural killer cell (ENCLB939WCS)

description:
https://www.encodeproject.org/experiments/ENCSR825ZXY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR825ZXY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR242ARJ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB939WCS
fragmentation methods: none

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS142IVK at ENCODE; https://www.encodeproject.org/ENCBS142IVK/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Control Mint-ChIP-seq from brain (ENCLB977GRS)

description:
https://www.encodeproject.org/experiments/ENCSR824UQL/
***************
biological replicate number: 3
technical replicate number: 2
description: Control Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR824UQL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB977GRS

source_name: Homo sapiens female embryo (5 days) brain organoid, 30 days post differentiation

value: brain

value: organoid

value: female

value: embryonic

value: 5 day

value: Paola Arlotta

value: ENCBS001KQF at ENCODE; https://www.encodeproject.org/ENCBS001KQF/

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


title: Control Mint-ChIP-seq from brain (ENCLB353FLO)

description:
https://www.encodeproject.org/experiments/ENCSR824UQL/
***************
biological replicate number: 2
technical replicate number: 2
description: Control Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR824UQL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB353FLO

value: Bradley Bernstein, Broad

value: ENCBS337FMJ at ENCODE; https://www.encodeproject.org/ENCBS337FMJ/


title: Control Mint-ChIP-seq from brain (ENCLB010SUC)

description:
https://www.encodeproject.org/experiments/ENCSR824UQL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR824UQL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB010SUC

value: ENCBS219JHY at ENCODE; https://www.encodeproject.org/ENCBS219JHY/


title: Control Mint-ChIP-seq from brain (ENCLB278VHA)

description:
https://www.encodeproject.org/experiments/ENCSR824UQL/
***************
biological replicate number: 3
technical replicate number: 1
description: Control Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR824UQL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB278VHA


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB548ELO)

description:
https://www.encodeproject.org/experiments/ENCSR923EGO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human IgD-negative memory B cell
experiment encode accession: ENCSR923EGO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR808EUQ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB548ELO

source_name: Homo sapiens IgD-negative memory B primary cell with multiple sclerosis

value: IgD-negative memory B cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: ENCBS720RJK at ENCODE; https://www.encodeproject.org/ENCBS720RJK/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB863PSF)

description:
https://www.encodeproject.org/experiments/ENCSR923EGO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human IgD-negative memory B cell
experiment encode accession: ENCSR923EGO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR808EUQ
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB863PSF

value: unknown

value: David Hafler


title: Control Mint-ChIP-seq from brain (ENCLB949EGT)

description:
https://www.encodeproject.org/experiments/ENCSR824UQL/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR824UQL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB949EGT

value: brain

value: organoid

value: female

value: healthy

value: embryonic