title: intact Hi-C from left lung (ENCLB168JFX)

description:
https://www.encodeproject.org/experiments/ENCSR305GRJ/
***************
biological replicate number: 1
technical replicate number: 2
description: w76 left lung intact dnase hic
experiment encode accession: ENCSR305GRJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB168JFX
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

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

value: left lung

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

value: adult

value: 40 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS196NEQ at ENCODE; https://www.encodeproject.org/ENCBS196NEQ/

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


title: RNA-seq pMN day4 progenitors rep3

status: Public on Jul 24 2023

type: SRA

city: Aurora

first: Elena

last: Abarinov

state: Colorado

address: 1775 Aurora Ct

country: USA

institute: University of Colorado at Denver

description:
RNAseq_FPKM.txt
RNAseq_readcounts.txt
RNAseq_SigGenes.txt

library_source: transcriptomic

data_processing:
RNA-seq: Reads were mapped to the mouse genome (mm10) using the RNA-seq alignment algorithm in the STAR (Spliced Transcripts Alignment to a Reference) software package (version 2.3.1) (Dobin et al., 2013).
RNA-seq: To estimate the relative abundances of transcripts, Cufflinks software was used (version 2.2.1) (Trapnell et al., 2013). FPKM values (Fragments Per Kilobase of exon per Million fragments mapped) were calculated per individual gene.
RNA-seq: Differential RNA expression across cohorts was assessed using EdgeR (version 3.20.9) and limma (version 3.34.9) software (Phipson et al., 2016; Ritchie et al., 2015; Robinson et al., 2010). Specifically, raw counts of all replicate samples in the pMN, iNkx2.2, and iTNmut groups were analyzed together, and all genes which did not have a count of 10 in at least two samples were excluded and considered to be not expressed. Read counts in each replicate were normalized to their new respective library size, and the data were normalized using the trimmed mean of M-values (TMM) method with the calcNormFactors function (Robinson and Oshlack, 2010).
RNA-seq: Significant differences were then determined in EdgeR/limma through linear modeling with precision weights (Law et al., 2014) and were based on adjusted p-values obtained through Benjamini and Hochberg’s method to control false discovery rate set at 5% (Benjamini and Hochberg, 1995).
Supplementary_files_format_and_content: RNA-seq: raw readcount text file used as input into EdgeR/limma
Supplementary_files_format_and_content: RNA-seq: test file of results of EdgeR/limma analysis
Supplementary_files_format_and_content: RNA-seq: text file of abundance measurements (FPKM values)
ChIP-seq: All sequencing data sets were aligned using Bowtie (version 0.12.7) (Langmead et al., 2009) to the mm10 genome assembly.
ChIP-seq: Peak calling of Sox2, Flag, Grg, Med1, and p300 was carried out using the GEM algorithm (Guo et al., 2012) with multi-condition settings to simultaneously identify all regions enriched over background in pMN, iNkx2.2, and iTNmut progenitors. Peak calling of H3K27ac, H3K4me1, H3K27me3, and HDAC2 was performed with the MACS software (“--- broad”; version2.0.9) (Zhang et al., 2008).
ChIP-seq: Read-count intensity was obtained within +/- 500bp of all GEM identified peaks and +/- 1kb around the midpoints of all MACS-defined regions. Read counts of individual replicates were then normalized to their respective sequencing library size, and only loci above a given threshold in both replicates (when n = 2) were used for subsequent analysis.
ChIP-seq: GEM peaks were then further processed as follows. After filtering out very low-occupied regions, each ChIP-seq dataset (e.g. Grg) contained loci that were bound in at least one of the three cell types (e.g. iNkx2.2, iTNmut, and pMN progenitors). If multiple ChIP-seq peaks resided within 500bp of each other in a given cell type, they were merged into one peak using Bedtools (version 2.17.0) (Quinlan, 2010). The locus with the highest read density (+/- 100bp) was identified using Tidyverse (version 1.2.1) (Wickham H., 2019) and utilized as the center of the occupied region. Read counts for all replicates across the three cell types were obtained within +/- 500bp from the center of all merged peaks as defined above, regardless of their cell-type origin. These datasets were then imported into the EdgeR (version 3.20.9) and limma (version 3.34.9) software packages (Phipson et al., 2016; Ritchie et al., 2015; Robinson et al., 2010) to globally identify all significantly altered occupancy regions among pMN, iNkx2.2, and iTNmut progenitors for ChIP-seq datasets with an n = 2. Read counts in each replicate were normalized to their new respective library size and additionally quantile normalized to account for variations in ChIP-seq quality using the voom function (Hansen et al., 2012; Law et al., 2014). Significant differences in occupancy were then determined through linear modeling with precision weights (Law et al., 2014) and were based on adjusted p-values obtained through Benjamini and Hochberg’s method to control false discovery rate set at 5% (Benjamini and Hochberg, 1995).
ChIP-seq: MACS-defined peaks were similarly processed. After filtering out very low-occupied regions, the remaining peaks in each individual replicate were merged into one peak if they resided within 1kb of each other. Peaks that overlapped with each other in both replicates were then further merged into one peak to create the dataset for each cell type (e.g. pMN H3K27ac) and the midpoint of the newly merged peak was defined as the center. To globally identify all differential occupancy loci as described above for GEM-defined regions, peaks that overlapped among the three cell types (e.g. H3K27ac sites overlapping in pMN, iNkx2.2, iTNmut) were merged into one peak and the midpoint of the newly merged peak was defined as the center. These shared peaks and the remaining cell-type specific peaks were combined into one dataset, and read counts for all replicates across the three cell types were obtained within +/- 1kb from the center of the peaks regardless of their cell-type origin (e.g. pMN H3K27ac ChIP-seq signal was recorded at not only pMN-specific and shared coordinates but also iNkx2.2- and iTNmut-specific loci). These datasets were then further analyzed in EdgeR (version 3.20.9) and limma (version 3.34.9) software packages (Phipson et al., 2016; Ritchie et al., 2015; Robinson et al., 2010), as described above for GEM-identified loci.
ChIP-seq: Final readcounts for all peaks of each ChIP-seq were converted to counts per million (CPM), quantile-normalized, and log2 transformed (logCPM). These logCPM values were then extracted to calculate significant differences in occupancy at specific regions (e.g. subsets of enhancers bound by Nkx2.2). Significance was determined using the Mann-Whitney test or the Kruskal-Wallis test with Dunn's post hoc analysis.
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: peak text files generated by GEM or MACS software
Supplementary_files_format_and_content: ChIP-seq: raw readcount text files for peaks used as input into EdgeR/limma software and to make logCPM files
Supplementary_files_format_and_content: ChIP-seq: text file of results of EdgeR/limma analysis
Supplementary_files_format_and_content: ChIP-seq: logCPM text files for all peaks used in EdgeR/limma analysis

molecule: total RNA

organism: Mus musculus

source_name: motor neuron progenitor cells

growth_protocol: Motor neuron differentiation of ESCs was performed as previously described (Rhee et al., 2016; Tan et al., 2016), with slight modifications. Briefly, ESCs were trypsinized (Thermo Fisher Scientific, SC25300054) and seeded at 5 x 105 cells in 12mL of medium (Advanced DMEM/F12:Neurobasal (1:1) Medium; Thermo Fisher Scientific, 12634-010, 21103-049) supplemented with 10% Knockout Serum Replacement (Thermo Fisher Scientific, 10828-028), 2 mM Glutamax (Invitrogen, 35050061), and 0.1 mM b-mercaptoethanol (Sigma-Aldrich, M3148) to initiate formation of embryoid bodies (day0). Embryoid bodies were split 1:4 on day2 of differentiation, and patterning was induced by supplementing fresh media with 1μM all-trans retinoic acid (RA, Sigma, R2625) and 0.5μM Smoothened agonist of hedgehog signaling (SAG, EMD Millipore, 566660). Doxycycline (DOX; Thermo Fisher Scientific, NC0424034) was added to the cultures at 1μg/mL on late day3 of differentiation for 24hrs. DAPT (Selleck, S2215) was added to the culture medium at 5μM on early day4 (~12hrs after DOX addition). DOX was washed on late day4 by replacing medium in both treated and control conditions. Fresh RA, SAG, and DAPT were re-added to this medium. On day5, the medium was again replaced, and only DAPT was re-added to the cultures. Embryoid bodies were collected on day4 (~16hrs post DOX induction) and day6 for analysis. For ChIP experiments, the same conditions were used but scaled to seed 4 x 106 cells on day0, and 1X Penicillin-Streptomycin (Thermo Fisher Scientific, 15140-122) was maintained in the cultures throughout the differentiation. DAPT was not added to cells collected on day4.

extract_protocol:
RNA was extracted using Trizol Reagent (Life Technologies, SC: 15596-018) in combination with RNeasy Mini Kit (Qiagen, 74104).
RNA libraries were prepared for sequencing using Illumina Trueseq RNA Prep Kit.

treatment_protocol: Selected samples were treated with doxycycline (DOX) for 14-16hrs prior to collection. See SAMPLES section.

tag: cell type

value: ES-derived motor neuron progenitors

tag: cell line

value: mES iNkx2.2

tag: treatment

value: untreated

tag: differentiation stage


title: intact Hi-C from left lung (ENCLB484IAT)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR305GRJ/
***************
biological replicate number: 1
technical replicate number: 1
description: w76 left lung intact dnase hic
experiment encode accession: ENCSR305GRJ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB484IAT
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

value: tissue

tag: biosample encode accession

tag: encode accession

tag: Sex

value: male

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

tag: link


title: RNA-seq iNkx2.2 day4 progenitors rep1

value: treated with DOX for 14-16hrs


title: intact Hi-C from activated CD4-positive, alpha-beta T cell (ENCLB978ZBF)

description:
https://www.encodeproject.org/experiments/ENCSR421CGL/
***************
biological replicate number: 2
technical replicate number: 2
description: LP6 CD4+ T Cells activated intact Hi-C
experiment encode accession: ENCSR421CGL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB978ZBF
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 36 hours

value: primary cell

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:36; duration_units:hour;

value: ENCBS949CQQ at ENCODE; https://www.encodeproject.org/ENCBS949CQQ/

value: derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: intact Hi-C from activated CD4-positive, alpha-beta T cell (ENCLB898BNW)

description:
https://www.encodeproject.org/experiments/ENCSR421CGL/
***************
biological replicate number: 2
technical replicate number: 1
description: LP6 CD4+ T Cells activated intact Hi-C
experiment encode accession: ENCSR421CGL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB898BNW
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: adult


title: RNA-seq pMN day4 progenitors rep2


title: ChIP-seq Nkx2.2-Flag iNkx2.2 day4 progenitors rep2

description:
Nkx2.2-Flag_GEM_events.txt
Nkx2.2_logCPM.txt
RawCounts_Nkx2.2-Flag.txt
SigNkx2.2.txt

extract_protocol:
40-50 million cells were fixed in 1% formaldehyde. Lysates were clarified from sonicated nuclei, and FLAG-DNA complexes were isolated with antibody.
Purified DNA fragments were processed according to the Illumina/Solexa standard sequencing protocol.

tag: chip antibody

value: mouse anti Flag (Sigma-Aldrich, F1804)


title: intact Hi-C from activated CD4-positive, alpha-beta T cell (ENCLB050GOB)

description:
https://www.encodeproject.org/experiments/ENCSR421CGL/
***************
biological replicate number: 2
technical replicate number: 4
description: LP6 CD4+ T Cells activated intact Hi-C
experiment encode accession: ENCSR421CGL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB050GOB
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1300000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: ChIP-seq Sox2 iNkx2.2 progenitors rep1

description:
Sox2_GEM_events.txt
Sox2_logCPM.txt
RawCounts_Sox2.txt

extract_protocol:
40-50 million cells were fixed in 1% formaldehyde. Lysates were clarified from sonicated nuclei, and Sox2-DNA complexes were isolated with antibody.
Purified DNA fragments were processed according to the Illumina/Solexa standard sequencing protocol.

value: goat anti Sox2 (R&D systems, AF2018-SP)


title: intact Hi-C from activated CD8-positive, alpha-beta T cell (ENCLB562JYM)

description:
https://www.encodeproject.org/experiments/ENCSR351NAI/
***************
biological replicate number: 1
technical replicate number: 2
description: CD8+ activated intact Hi-C
experiment encode accession: ENCSR351NAI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB562JYM
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 500000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 36 hours

value: 21 year

value: ENCBS544JLP at ENCODE; https://www.encodeproject.org/ENCBS544JLP/

value: derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: intact Hi-C from activated CD8-positive, alpha-beta T cell (ENCLB571PTU)

description:
https://www.encodeproject.org/experiments/ENCSR351NAI/
***************
biological replicate number: 1
technical replicate number: 5
description: CD8+ activated intact Hi-C
experiment encode accession: ENCSR351NAI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB571PTU
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 500000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: synovium, Control, rep2

city: Guangzhou

first: Yan

last: Yan

state: Guangdong province

address: yanjiang west road No.107

department: orthopaedic surgery

country: China

institute: No. 107, Yanjiang West Road, Yuexiu District, Guangzhou, Guangdong Province

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: synovium

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: tissue

value: synovium

value: healthy control

tag: genotype

value: WT


title: synovium, Control, rep3

tag: cell type


title: synovium, Frozen shoulder, rep4

value: individual with frozen shoulder


title: intact Hi-C from activated CD8-positive, alpha-beta T cell (ENCLB713NAQ)

description:
https://www.encodeproject.org/experiments/ENCSR351NAI/
***************
biological replicate number: 1
technical replicate number: 6
description: CD8+ activated intact Hi-C
experiment encode accession: ENCSR351NAI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB713NAQ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 500000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: primary cell

value: male


title: intact Hi-C from activated CD8-positive, alpha-beta T cell (ENCLB047FMS)

description:
https://www.encodeproject.org/experiments/ENCSR351NAI/
***************
biological replicate number: 1
technical replicate number: 3
description: CD8+ activated intact Hi-C
experiment encode accession: ENCSR351NAI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB047FMS
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 500000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: Yijun Ruan, JAX


title: synovium, Frozen shoulder, rep3


title: intact Hi-C from activated CD8-positive, alpha-beta T cell (ENCLB073VSD)

description:
https://www.encodeproject.org/experiments/ENCSR351NAI/
***************
biological replicate number: 1
technical replicate number: 1
description: CD8+ activated intact Hi-C
experiment encode accession: ENCSR351NAI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB073VSD
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 500000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: AllCells


title: synovial fibroblast, siCD36, Day2, rep3

growth_protocol: Synovial fibroblasts were maintained in high-glucose DMEM containing 10% FBS in humidified atmosphere with 5% Co2 at 37C

treatment_protocol: Synovial fibroblasts were seeded in 6-well plates (1.5 * 10^5 cells/well) and transfected with 20 µM siRNA, or negative controls via Lipofectamine 3000 (Thermo Fisher Scientific, USA) according to the manufacturer's instructions. After 48 h, cells were harvested to quantify the mRNA or protein expression.

value: synovial fibroblst

value: CD36 knock down

tag: time


title: intact Hi-C from Calu3 (ENCLB212OUE)

description:
https://www.encodeproject.org/experiments/ENCSR118AQZ/
***************
biological replicate number: 1
technical replicate number: 3
description: Calu3 intact Hi-C
experiment encode accession: ENCSR118AQZ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB212OUE
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1185000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens Calu3 cell line

tag: line

value: cell line

value: Lung adenocarcinoma

value: 25 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS151RPO at ENCODE; https://www.encodeproject.org/ENCBS151RPO/

value: derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: synovial fibroblast, siCD36. Day2, rep2

value: synovium

tag: treatment


title: synovium, Control, rep1

value: healthy control


title: intact Hi-C from activated CD4-positive, alpha-beta T cell (ENCLB541PRC)

description:
https://www.encodeproject.org/experiments/ENCSR421CGL/
***************
biological replicate number: 2
technical replicate number: 3
description: LP6 CD4+ T Cells activated intact Hi-C
experiment encode accession: ENCSR421CGL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB541PRC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: biosample encode accession

value: adult

value: 20 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:36; duration_units:hour;

value: ENCBS949CQQ at ENCODE; https://www.encodeproject.org/ENCBS949CQQ/

value: derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: intact Hi-C from activated CD8-positive, alpha-beta T cell (ENCLB082PJY)

description:
https://www.encodeproject.org/experiments/ENCSR351NAI/
***************
biological replicate number: 1
technical replicate number: 4
description: CD8+ activated intact Hi-C
experiment encode accession: ENCSR351NAI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB082PJY
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 500000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: primary cell

tag: encode accession

value: male

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS544JLP at ENCODE; https://www.encodeproject.org/ENCBS544JLP/

value: derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: synovium, Control, rep4

value: WT


title: intact Hi-C from Calu3 (ENCLB373FOD)

description:
https://www.encodeproject.org/experiments/ENCSR118AQZ/
***************
biological replicate number: 1
technical replicate number: 4
description: Calu3 intact Hi-C
experiment encode accession: ENCSR118AQZ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB373FOD
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1185000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

tag: Sex

value: Lung adenocarcinoma

value: 25 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS151RPO at ENCODE; https://www.encodeproject.org/ENCBS151RPO/


title: intact Hi-C from Calu3 (ENCLB408QHM)

description:
https://www.encodeproject.org/experiments/ENCSR118AQZ/
***************
biological replicate number: 1
technical replicate number: 2
description: Calu3 intact Hi-C
experiment encode accession: ENCSR118AQZ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB408QHM
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1185000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: health state

value: adult

value: derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: intact Hi-C from Calu3 (ENCLB021PNY)

description:
https://www.encodeproject.org/experiments/ENCSR118AQZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Calu3 intact Hi-C
experiment encode accession: ENCSR118AQZ
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB021PNY
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1185000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: dev stage


title: synovium, Frozen shoulder, rep1

value: synovium

value: individual with frozen shoulder


title: intact Hi-C from heart left ventricle (ENCLB404CRZ)

description:
https://www.encodeproject.org/experiments/ENCSR210LEF/
***************
biological replicate number: 1
technical replicate number: 1
description: w76 heart left ventricle intact dnase hic
experiment encode accession: ENCSR210LEF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB404CRZ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

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

value: heart left ventricle

value: tissue

value: male

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

tag: age

value: 40 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS334QAD at ENCODE; https://www.encodeproject.org/ENCBS334QAD/

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


title: synovial fibroblast, siControl, Day2, rep2

value: synovial fibroblst

value: WT

value: siControl


title: synovial fibroblast, siControl, Day2, rep1


title: RNA-seq pMN day4 progenitors rep1

description:
RNAseq_FPKM.txt
RNAseq_readcounts.txt
RNAseq_SigGenes.txt

value: ES-derived motor neuron progenitors

tag: cell line

value: mES iNkx2.2

value: untreated

tag: differentiation stage


title: synovial fibroblast, siControl, Day2, rep3

value: synovium


title: intact Hi-C from right cardiac atrium (ENCLB548QIK)

description:
https://www.encodeproject.org/experiments/ENCSR168PIR/
***************
biological replicate number: 1
technical replicate number: 1
description: W72 right cardiac atrium intact HIC
experiment encode accession: ENCSR168PIR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB548QIK
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (46 years) right cardiac atrium tissue, preserved by flash-freezing

value: right cardiac atrium

value: female

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

value: adult

value: 46 year

tag: lab

tag: source

tag: link

value: ENCBS783VFC at ENCODE; https://www.encodeproject.org/ENCBS783VFC/

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


title: CVB_iEC_SORL1_KO_Rep3

city: Boston

first: Richard

middle: VanDyke

last: Pearse

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Womens Hospital

data_processing:
fastq files were trimmed using trimmomatic in paired-end mode removing base calls 3'-5' with phred33 scores <25
pseudo-aligned sequences to human transcriptome (GRCh38 cDNA+ncRNA) using Kallisto (0.43.1) program running 100 bootstrap iterations
TPM normalized matrix compiled and output using Sleuth (0.30.1) package in Rstudio
Assembly: GRCh38
Supplementary files format and content: comma separated values for TPM normalized counts

molecule: polyA RNA

source_name: CVB

extract_protocol:
RNA was extracted from 500,000 cells using the Invitrogen Purelink RNA mini kit and QC'd using an Agilent Tapestation.
Library was generated by Genewiz using 10ugs input for the polyA selection library synthesis pipeline.

value: CVB

value: iEC


title: synovium, Frozen shoulder, rep2

tag: tissue

value: individual with frozen shoulder


title: CVB_iEC_SORL1_KO_Rep1

tag: genotype


title: CVB_iEC_SORL1_KO_Rep2

tag: cell type


title: intact Hi-C from left colon (ENCLB628RVQ)

description:
https://www.encodeproject.org/experiments/ENCSR298UUL/
***************
biological replicate number: 1
technical replicate number: 3
description: W73 left colon intact HIC
experiment encode accession: ENCSR298UUL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB628RVQ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (59 years) left colon tissue, preserved by flash-freezing

value: left colon

value: tissue

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS592JPI at ENCODE; https://www.encodeproject.org/ENCBS592JPI/

value: derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: intact Hi-C from left colon (ENCLB583RVC)

description:
https://www.encodeproject.org/experiments/ENCSR298UUL/
***************
biological replicate number: 1
technical replicate number: 1
description: W73 left colon intact HIC
experiment encode accession: ENCSR298UUL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB583RVC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 9
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: female


title: CVB_iEC_SORL1_WT_Rep3


title: synovial fibroblast, siCD36, Day2, rep1

value: synovium

value: synovial fibroblst

value: CD36 knock down

tag: time


title: intact Hi-C from left colon (ENCLB354WEW)

description:
https://www.encodeproject.org/experiments/ENCSR298UUL/
***************
biological replicate number: 1
technical replicate number: 2
description: W73 left colon intact HIC
experiment encode accession: ENCSR298UUL
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB354WEW
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: adult


title: CVB_iMGL_SORL1_KO_Rep4

value: iMGL


title: intact Hi-C from heart left ventricle (ENCLB779MAN)

description:
https://www.encodeproject.org/experiments/ENCSR348KEP/
***************
biological replicate number: 1
technical replicate number: 1
description: uw65-heart-left-ventricle intact HiC
experiment encode accession: ENCSR348KEP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB779MAN
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 7
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (73 years) heart left ventricle tissue

value: heart left ventricle

value: male

value: ischemic (EF 35%, LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: 73 year

value: Shin Lin

value: ENCBS096GES at ENCODE; https://www.encodeproject.org/ENCBS096GES/

value: derived from ENCODE donor ENCDO804CLC; https://www.encodeproject.org/ENCDO804CLC/


title: intact Hi-C from OCI-LY7 (ENCLB586LZA)

description:
https://www.encodeproject.org/experiments/ENCSR088BOG/
***************
biological replicate number: 1
technical replicate number: 3
description: OCI-LY7 intact Hi-C
experiment encode accession: ENCSR088BOG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB586LZA
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens OCI-LY7 cell line

tag: line

value: cell line

value: B cell lymphoma

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS852CMI at ENCODE; https://www.encodeproject.org/ENCBS852CMI/

value: derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: CVB_iMGL_SORL1_KO_Rep3

value: CVB


title: CVB_iEC_SORL1_WT_Rep1

value: iEC


title: CVB_iMGL_SORL1_KO_Rep2

value: iMGL


title: intact Hi-C from right cardiac atrium (ENCLB229LOS)

description:
https://www.encodeproject.org/experiments/ENCSR168PIR/
***************
biological replicate number: 1
technical replicate number: 2
description: W72 right cardiac atrium intact HIC
experiment encode accession: ENCSR168PIR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB229LOS
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: right cardiac atrium

value: tissue

value: female

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

value: adult

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS783VFC at ENCODE; https://www.encodeproject.org/ENCBS783VFC/

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


title: intact Hi-C from OCI-LY7 (ENCLB705OGW)

description:
https://www.encodeproject.org/experiments/ENCSR088BOG/
***************
biological replicate number: 1
technical replicate number: 4
description: OCI-LY7 intact Hi-C
experiment encode accession: ENCSR088BOG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB705OGW
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

value: male

value: B cell lymphoma

value: 48 year

value: Mats Ljungman, UMichigan


title: CVB_iMGL_SORL1_KO_Rep1

value: CVB


title: CVB_iMGL_SORL1_WT_Rep4

value: iMGL


title: intact Hi-C from OCI-LY7 (ENCLB668DZN)

description:
https://www.encodeproject.org/experiments/ENCSR088BOG/
***************
biological replicate number: 1
technical replicate number: 1
description: OCI-LY7 intact Hi-C
experiment encode accession: ENCSR088BOG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB668DZN
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: DSMZ

value: ENCBS852CMI at ENCODE; https://www.encodeproject.org/ENCBS852CMI/

value: derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: intact Hi-C from heart left ventricle (ENCLB905KGI)

description:
https://www.encodeproject.org/experiments/ENCSR210LEF/
***************
biological replicate number: 1
technical replicate number: 2
description: w76 heart left ventricle intact dnase hic
experiment encode accession: ENCSR210LEF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB905KGI
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: heart left ventricle

value: tissue

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

value: 40 year

value: ENCBS334QAD at ENCODE; https://www.encodeproject.org/ENCBS334QAD/

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


title: CVB_iMGL_SORL1_WT_Rep3


title: intact Hi-C from pancreas (ENCLB849BBU)

description:
https://www.encodeproject.org/experiments/ENCSR408HOG/
***************
biological replicate number: 1
technical replicate number: 1
description: w80-pancreas intact HiC
experiment encode accession: ENCSR408HOG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB849BBU
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (61 years) pancreas tissue, preserved by flash-freezing

value: pancreas

value: female

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS502NRJ at ENCODE; https://www.encodeproject.org/ENCBS502NRJ/

value: derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: CVB_iMGL_SORL1_WT_Rep1

value: CVB

value: iMGL


title: CVB_iMGL_SORL1_WT_Rep2


title: intact Hi-C from heart right ventricle (ENCLB457PJN)

description:
https://www.encodeproject.org/experiments/ENCSR297CCU/
***************
biological replicate number: 1
technical replicate number: 1
description: w72 heart right ventricle intact dnase hic
experiment encode accession: ENCSR297CCU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB457PJN
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

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

value: heart right ventricle

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

value: 46 year

value: ENCBS747YFV at ENCODE; https://www.encodeproject.org/ENCBS747YFV/

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


title: intact Hi-C from heart right ventricle (ENCLB788BST)

description:
https://www.encodeproject.org/experiments/ENCSR297CCU/
***************
biological replicate number: 1
technical replicate number: 2
description: w72 heart right ventricle intact dnase hic
experiment encode accession: ENCSR297CCU
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB788BST
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue


title: CVB_iEC_SORL1_WT_Rep2

value: iEC


title: CVB_iAst_SORL1_KO_Rep4

value: iAst


title: intact Hi-C from heart left ventricle (ENCLB181BGV)

description:
https://www.encodeproject.org/experiments/ENCSR348KEP/
***************
biological replicate number: 1
technical replicate number: 2
description: uw65-heart-left-ventricle intact HiC
experiment encode accession: ENCSR348KEP
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB181BGV
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 7
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: heart left ventricle

value: male

value: ischemic (EF 35%, LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: 73 year

value: Shin Lin

value: ENCBS096GES at ENCODE; https://www.encodeproject.org/ENCBS096GES/

value: derived from ENCODE donor ENCDO804CLC; https://www.encodeproject.org/ENCDO804CLC/


title: intact Hi-C from OCI-LY7 (ENCLB684EAH)

description:
https://www.encodeproject.org/experiments/ENCSR088BOG/
***************
biological replicate number: 1
technical replicate number: 2
description: OCI-LY7 intact Hi-C
experiment encode accession: ENCSR088BOG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB684EAH
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

value: B cell lymphoma

value: adult

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS852CMI at ENCODE; https://www.encodeproject.org/ENCBS852CMI/

value: derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: intact Hi-C from IMR-90 (ENCLB942MFB)

description:
https://www.encodeproject.org/experiments/ENCSR345VTI/
***************
biological replicate number: 1
technical replicate number: 2
description: IMR-90 intact Hi-C
experiment encode accession: ENCSR345VTI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB942MFB
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1600000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens IMR-90 cell line

value: female

value: unknown

value: embryonic

value: 16 week

value: ATCC

value: ENCBS299KRY at ENCODE; https://www.encodeproject.org/ENCBS299KRY/

value: derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: CVB_iAst_SORL1_KO_Rep2

value: CVB

value: iAst


title: intact Hi-C from IMR-90 (ENCLB931ZMF)

description:
https://www.encodeproject.org/experiments/ENCSR345VTI/
***************
biological replicate number: 2
technical replicate number: 1
description: IMR-90 intact Hi-C
experiment encode accession: ENCSR345VTI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB931ZMF
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

value: ENCBS785QWQ at ENCODE; https://www.encodeproject.org/ENCBS785QWQ/


title: CVB_iAst_SORL1_KO_Rep3


title: intact Hi-C from IMR-90 (ENCLB493FNH)

description:
https://www.encodeproject.org/experiments/ENCSR345VTI/
***************
biological replicate number: 2
technical replicate number: 2
description: IMR-90 intact Hi-C
experiment encode accession: ENCSR345VTI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB493FNH
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: CVB_iAst_SORL1_KO_Rep1


title: CVB_iAst_SORL1_WT_Rep4


title: CVB_iAst_SORL1_WT_Rep3


title: intact Hi-C from IMR-90 (ENCLB283QJD)

description:
https://www.encodeproject.org/experiments/ENCSR345VTI/
***************
biological replicate number: 1
technical replicate number: 3
description: IMR-90 intact Hi-C
experiment encode accession: ENCSR345VTI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB283QJD
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1600000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: CVB_iAst_SORL1_WT_Rep2


title: intact Hi-C from IMR-90 (ENCLB699AYD)

description:
https://www.encodeproject.org/experiments/ENCSR345VTI/
***************
biological replicate number: 2
technical replicate number: 3
description: IMR-90 intact Hi-C
experiment encode accession: ENCSR345VTI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB699AYD
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: intact Hi-C from IMR-90 (ENCLB625KVS)

description:
https://www.encodeproject.org/experiments/ENCSR345VTI/
***************
biological replicate number: 1
technical replicate number: 1
description: IMR-90 intact Hi-C
experiment encode accession: ENCSR345VTI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB625KVS
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1600000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: CVB_iAst_SORL1_WT_Rep1


title: intact Hi-C from pancreas (ENCLB250LEO)

description:
https://www.encodeproject.org/experiments/ENCSR408HOG/
***************
biological replicate number: 1
technical replicate number: 2
description: w80-pancreas intact HiC
experiment encode accession: ENCSR408HOG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB250LEO
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: pancreas

value: tissue

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS502NRJ at ENCODE; https://www.encodeproject.org/ENCBS502NRJ/

value: derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: intact Hi-C from HCT116 (ENCLB469IDY)

description:
https://www.encodeproject.org/experiments/ENCSR087JOM/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-RAD21 auxin treated intact HIC
experiment encode accession: ENCSR087JOM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB469IDY
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS889FKV at ENCODE; https://www.encodeproject.org/ENCBS889FKV/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: intact Hi-C from HCT116 (ENCLB469IXC)

description:
https://www.encodeproject.org/experiments/ENCSR087JOM/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116-RAD21 auxin treated intact HIC
experiment encode accession: ENCSR087JOM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB469IXC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

tag: biosample encode accession


title: CVB_iN_SORL1_KO_Rep4

value: CVB

value: iN


title: intact Hi-C from HCT116 (ENCLB507LPQ)

description:
https://www.encodeproject.org/experiments/ENCSR087JOM/
***************
biological replicate number: 2
technical replicate number: 2
description: HCT116-RAD21 auxin treated intact HIC
experiment encode accession: ENCSR087JOM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB507LPQ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: encode accession

value: adult

value: ENCBS123WSE at ENCODE; https://www.encodeproject.org/ENCBS123WSE/


title: CVB_iN_SORL1_KO_Rep3


title: intact Hi-C from dorsolateral prefrontal cortex (ENCLB897FTU)

description:
https://www.encodeproject.org/experiments/ENCSR165UJN/
***************
biological replicate number: 1
technical replicate number: 2
description: rush brain midfrontal cortex healthy intact dnase hic
experiment encode accession: ENCSR165UJN
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB897FTU
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (78 years) dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

tag: Sex

value: 78 year

value: John Stamatoyannopoulos

value: ENCBS092NWA at ENCODE; https://www.encodeproject.org/ENCBS092NWA/

value: derived from ENCODE donor ENCDO623FPG; https://www.encodeproject.org/ENCDO623FPG/


title: CVB_iN_SORL1_KO_Rep2


title: intact Hi-C from HCT116 (ENCLB088SIL)

description:
https://www.encodeproject.org/experiments/ENCSR087JOM/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116-RAD21 auxin treated intact HIC
experiment encode accession: ENCSR087JOM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB088SIL
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: male

tag: health state

value: colorectal carcinoma

value: 48 year


title: intact Hi-C from HCT116 (ENCLB699JAH)

description:
https://www.encodeproject.org/experiments/ENCSR087JOM/
***************
biological replicate number: 2
technical replicate number: 1
description: HCT116-RAD21 auxin treated intact HIC
experiment encode accession: ENCSR087JOM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB699JAH
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: dev stage

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;


title: CVB_iN_SORL1_WT_Rep4


title: intact Hi-C from dorsolateral prefrontal cortex (ENCLB851ZDR)

description:
https://www.encodeproject.org/experiments/ENCSR165UJN/
***************
biological replicate number: 1
technical replicate number: 1
description: rush brain midfrontal cortex healthy intact dnase hic
experiment encode accession: ENCSR165UJN
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB851ZDR
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

tag: age


title: CVB_iN_SORL1_WT_Rep3

tag: cell line


title: CVB_iN_SORL1_KO_Rep1


title: intact Hi-C from activated naive CD4-positive, alpha-beta T cell (ENCLB177OMZ)

description:
https://www.encodeproject.org/experiments/ENCSR195ETV/
***************
biological replicate number: 1
technical replicate number: 2
description: naive CD4+ T cell, activated Day 2 intact mnase
experiment encode accession: ENCSR195ETV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB177OMZ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (43 years) activated naive CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 36 hours

value: primary cell

value: 43 year

value: Charles Lee

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:36; duration_units:hour;

value: ENCBS190INC at ENCODE; https://www.encodeproject.org/ENCBS190INC/

value: derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: CVB_IPSC_SORL1_KO_Rep3

value: CVB

value: IPSC


title: intact Hi-C from placenta (ENCLB031OLS)

description:
https://www.encodeproject.org/experiments/ENCSR395DZW/
***************
biological replicate number: 1
technical replicate number: 2
description: human placenta intact hi-c dnase
experiment encode accession: ENCSR395DZW
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB031OLS
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female embryo placenta tissue

value: placenta

value: tissue

value: female

value: embryonic

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS222TFY at ENCODE; https://www.encodeproject.org/ENCBS222TFY/

value: derived from ENCODE donor ENCDO818SNP; https://www.encodeproject.org/ENCDO818SNP/


title: intact Hi-C from activated naive CD4-positive, alpha-beta T cell (ENCLB556GLO)

description:
https://www.encodeproject.org/experiments/ENCSR195ETV/
***************
biological replicate number: 1
technical replicate number: 1
description: naive CD4+ T cell, activated Day 2 intact mnase
experiment encode accession: ENCSR195ETV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB556GLO
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: primary cell

value: male

value: adult


title: CVB_iN_SORL1_WT_Rep2

value: iN


title: CVB_iN_SORL1_WT_Rep1


title: intact Hi-C from placenta (ENCLB714FVM)

description:
https://www.encodeproject.org/experiments/ENCSR395DZW/
***************
biological replicate number: 1
technical replicate number: 1
description: human placenta intact hi-c dnase
experiment encode accession: ENCSR395DZW
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB714FVM
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: CVB_IPSC_SORL1_KO_Rep2


title: CVB_IPSC_SORL1_KO_Rep1


title: CVB_IPSC_SORL1_WT_Rep2


title: CVB_IPSC_SORL1_WT_Rep3


title: intact Hi-C from HCT116 (ENCLB496NNT)

description:
https://www.encodeproject.org/experiments/ENCSR343ELD/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116 MED14degron treated intact mnase
experiment encode accession: ENCSR343ELD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB496NNT
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS446YDY at ENCODE; https://www.encodeproject.org/ENCBS446YDY/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: intact Hi-C from HCT116 (ENCLB909CNC)

description:
https://www.encodeproject.org/experiments/ENCSR343ELD/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116 MED14degron treated intact mnase
experiment encode accession: ENCSR343ELD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB909CNC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: CVB_IPSC_SORL1_WT_Rep1

value: CVB

value: IPSC


title: intact Hi-C from ovary (ENCLB065ECZ)

description:
https://www.encodeproject.org/experiments/ENCSR181LJD/
***************
biological replicate number: 1
technical replicate number: 1
description: entex ovary intact dnase hic
experiment encode accession: ENCSR181LJD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB065ECZ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (53 years) ovary tissue

value: ovary

value: tissue

value: female

value: 53 year

value: Kristin Ardlie

value: ENCBS677KJL at ENCODE; https://www.encodeproject.org/ENCBS677KJL/

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


title: intact Hi-C from HCT116 (ENCLB484JRF)

description:
https://www.encodeproject.org/experiments/ENCSR086RCC/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116-CTCF-auxin untreated degon-intact
experiment encode accession: ENCSR086RCC
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB484JRF
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF

value: cell line

value: male

value: adult

value: ENCBS567HKI at ENCODE; https://www.encodeproject.org/ENCBS567HKI/


title: intact Hi-C from HCT116 (ENCLB849OKG)

description:
https://www.encodeproject.org/experiments/ENCSR343ELD/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116 MED14degron treated intact mnase
experiment encode accession: ENCSR343ELD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB849OKG
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki


title: intact Hi-C from ovary (ENCLB712SMZ)

description:
https://www.encodeproject.org/experiments/ENCSR181LJD/
***************
biological replicate number: 1
technical replicate number: 2
description: entex ovary intact dnase hic
experiment encode accession: ENCSR181LJD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB712SMZ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: intact Hi-C from HCT116 (ENCLB204RPR)

description:
https://www.encodeproject.org/experiments/ENCSR086RCC/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116-CTCF-auxin untreated degon-intact
experiment encode accession: ENCSR086RCC
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB204RPR
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: intact Hi-C from HCT116 (ENCLB127EZO)

description:
https://www.encodeproject.org/experiments/ENCSR086RCC/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116-CTCF-auxin untreated degon-intact
experiment encode accession: ENCSR086RCC
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB127EZO
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: intact Hi-C from HCT116 (ENCLB307SWY)

description:
https://www.encodeproject.org/experiments/ENCSR086RCC/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116-CTCF-auxin untreated degon-intact
experiment encode accession: ENCSR086RCC
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB307SWY
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics


title: intact Hi-C from ovary (ENCLB085QMG)

description:
https://www.encodeproject.org/experiments/ENCSR160XGG/
***************
biological replicate number: 1
technical replicate number: 1
description: w61-ovary intact hic dnase
experiment encode accession: ENCSR160XGG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB085QMG
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (41 years) ovary tissue, preserved by flash-freezing

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

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS941QPR at ENCODE; https://www.encodeproject.org/ENCBS941QPR/

value: derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: intact Hi-C from ovary (ENCLB709VWO)

description:
https://www.encodeproject.org/experiments/ENCSR160XGG/
***************
biological replicate number: 1
technical replicate number: 3
description: w61-ovary intact hic dnase
experiment encode accession: ENCSR160XGG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB709VWO
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: ovary

value: tissue

value: female


title: intact Hi-C from ovary (ENCLB393FHP)

description:
https://www.encodeproject.org/experiments/ENCSR160XGG/
***************
biological replicate number: 1
technical replicate number: 2
description: w61-ovary intact hic dnase
experiment encode accession: ENCSR160XGG
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB393FHP
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: intact Hi-C from lower lobe of left lung (ENCLB393OMX)

description:
https://www.encodeproject.org/experiments/ENCSR068FXF/
***************
biological replicate number: 1
technical replicate number: 1
description: w78 lower lobe of left lung intact dnase hic
experiment encode accession: ENCSR068FXF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB393OMX
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (60 years) lower lobe of left lung tissue, preserved by flash-freezing

value: lower lobe of left lung

value: male

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: 60 year

value: ENCBS366XTB at ENCODE; https://www.encodeproject.org/ENCBS366XTB/

value: derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: 3PPE cells derived from hESCs, siControl, Day9, rep3

first: Yingjie

last: Fu

address: No.381, Wushan Road, Tianhe District

institute: South China University of Technology

description:
Third pharyngeal pouch endoderm cells derived from human embryonic stem cells, siControl, Day9, rep3
siControl_C

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 length fraction: 0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: H9 line cells (WA09)

growth_protocol: H9 cells were cultured on gelatin-coated plates with a feeder layer of MEF for 5 days, then the cells were subjected for endodermal differentiation. At the first day, differentiation medium was X-VIVO 20 medium (Lonza) supplemented with 100 ng/ml Activin A (Peprotech), 50 ng/ml WNT3A (Peprotech) , 10 μM ROCK inhibitor Y-27632 (Selleck). The following day, the medium was changed to X-VIVO 20 (Lonza) medium containing 100 ng/ml Activin A, 0.5% B27 (Gibco). At day 4 after the differentiation, endodermal cells were dissociated with TrypLE (Gibco), and reseeded on Matrigel (Corning)-coated plates with DMEM-F12 medium (Gibco）, supplemented with 0.5% B27, 1 μM RA (Sigma), 10 μM SB431542 (MCE), 20 ng/ml BMP4 (Peprotech), 2.5μM IWP2 (Selleck). The medium was changed daily, and the differentiation lasted until day 9 for the induction of the endoderm of 3PP.

extract_protocol:
RNAs were extracted from cells of NC group or siRNA-HOXA3 group with triplicate for each group.100ng of total RNAs was used to prepare sequencing libraries using the Ligation Mediated Sequencing (LM-Seq) protocol and quantified with the Qubit fluorometer (ThermoFisher).
RNA libraties for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Small interfering RNAs (siRNAs) against HOXA3 were synthesized. At day 7 after the differentiation, when the cell density reached 70% – 80%, the differentiated cells were transduced with HOXA3 siRNA and negative control siRNA using Lipofectamine 3000, respectively. Six to eight hours after the transduction, the differentiation medium was replaced with opti-MEM medium, and cells were harvested at days 9 after the differentiation.

value: H9 line cells (WA09)

value: hESCs

tag: treatment

value: directed differentiation

tag: differentiated cell type

value: the third pharyngeal pouch endoderm cells

value: WT


title: 3PPE cells derived from hESCs, siHOXA3, Day9, rep2

description:
Third pharyngeal pouch endoderm cells derived from human embryonic stem cells, siHOXA3, Day9, rep2
siHOXA3_B

value: HOXA3 knockdown


title: 3PPE cells derived from hESCs, siHOXA3, Day9, rep1

description:
Third pharyngeal pouch endoderm cells derived from human embryonic stem cells, siHOXA3, Day9, rep1
siHOXA3_A


title: intact Hi-C from lower lobe of left lung (ENCLB476RRI)

description:
https://www.encodeproject.org/experiments/ENCSR068FXF/
***************
biological replicate number: 1
technical replicate number: 2
description: w78 lower lobe of left lung intact dnase hic
experiment encode accession: ENCSR068FXF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB476RRI
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 6
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: adult

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD


title: intact Hi-C from HCT116 (ENCLB772REC)

description:
https://www.encodeproject.org/experiments/ENCSR343ELD/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116 MED14degron treated intact mnase
experiment encode accession: ENCSR343ELD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB772REC
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

tag: link

value: ENCBS446YDY at ENCODE; https://www.encodeproject.org/ENCBS446YDY/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: 3PPE cells derived from hESCs, siControl, Day9, rep2

description:
Third pharyngeal pouch endoderm cells derived from human embryonic stem cells, siControl, Day9, rep2
siControl_B

value: H9 line cells (WA09)

tag: genotype


title: TDX T144

city: London

first: Aris

last: Aristodemou

state: London

address: St Mary's Campus, Norfolk Place, Rear Lodge Immunology

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

description:
150 bp PE
deseq2_norm_counts.tsv

data_processing:
Transcript counts obtained using Kallisto v0.46.2 (non-default parameters: --threads=30 --bias)
Differential expression analysis performed using DESeq2 v1.32.0
Assembly: Human genome GRCh38 / HTLV-1 genome AB153134
Supplementary files format and content: Kallisto transcript abundances (tab-separated values files)
Supplementary files format and content: DESeq2-normalised transcript counts for all samples excluding V4 T24 (tab-separated values file)

source_name: Blood

extract_protocol:
RNeasy Plus Micro (Qiagen, Cat. No. 74034)
Polyadenylated transcript enrichment and strand specific library preparation was completed using the NEBNext Ultra II kit (NEB)

tag: tissue

value: Blood

tag: cell type

value: CD4+ T cell


title: intact Hi-C from activated CD4-positive, alpha-beta memory T cell (ENCLB355OJD)

description:
https://www.encodeproject.org/experiments/ENCSR291EBI/
***************
biological replicate number: 1
technical replicate number: 2
description: Memory CD4+ T cell, activated Day 2 LP11 Intact mnase
experiment encode accession: ENCSR291EBI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB355OJD
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 36 hours

value: primary cell

value: male

value: 43 year

value: Charles Lee

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:36; duration_units:hour;

value: ENCBS266BPD at ENCODE; https://www.encodeproject.org/ENCBS266BPD/

value: derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: intact Hi-C from kidney (ENCLB739LWS)

description:
https://www.encodeproject.org/experiments/ENCSR044YKV/
***************
biological replicate number: 1
technical replicate number: 2
description: w71-kidney intact dnase hic
experiment encode accession: ENCSR044YKV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB739LWS
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (47 years) kidney tissue, preserved by flash-freezing

value: kidney

value: tissue

value: female

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

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS902FGR at ENCODE; https://www.encodeproject.org/ENCBS902FGR/

value: derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: intact Hi-C from gastrocnemius medialis (ENCLB626CBP)

description:
https://www.encodeproject.org/experiments/ENCSR136MVS/
***************
biological replicate number: 1
technical replicate number: 1
description: entex skeletal muscle gatsrocnemius medialis
experiment encode accession: ENCSR136MVS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB626CBP
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (53 years) gastrocnemius medialis tissue

value: gastrocnemius medialis

value: 53 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS743JXN at ENCODE; https://www.encodeproject.org/ENCBS743JXN/

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


title: TDX T120

description:
150 bp PE
deseq2_norm_counts.tsv

value: Blood

value: CD4+ T cell


title: TDX T96

description:
150 bp PE
deseq2_norm_counts.tsv


title: TDX T48

description:
150 bp PE
deseq2_norm_counts.tsv


title: intact Hi-C from activated CD4-positive, alpha-beta memory T cell (ENCLB646JLX)

description:
https://www.encodeproject.org/experiments/ENCSR291EBI/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD4+ T cell, activated Day 2 LP11 Intact mnase
experiment encode accession: ENCSR291EBI
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB646JLX
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: primary cell

value: male

value: 43 year

value: Charles Lee

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:36; duration_units:hour;

value: ENCBS266BPD at ENCODE; https://www.encodeproject.org/ENCBS266BPD/

value: derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: intact Hi-C from gastrocnemius medialis (ENCLB026KST)

description:
https://www.encodeproject.org/experiments/ENCSR136MVS/
***************
biological replicate number: 1
technical replicate number: 2
description: entex skeletal muscle gatsrocnemius medialis
experiment encode accession: ENCSR136MVS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB026KST
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

value: female

value: adult


title: 3PPE cells derived from hESCs, siHOXA3, Day9, rep3

description:
Third pharyngeal pouch endoderm cells derived from human embryonic stem cells, siHOXA3, Day9, rep3
siHOXA3_C

value: H9 line cells (WA09)

value: hESCs

value: directed differentiation

value: the third pharyngeal pouch endoderm cells

value: HOXA3 knockdown


title: TDX T24

description:
150 bp PE
deseq2_norm_counts.tsv

value: Blood

value: CD4+ T cell


title: HES T144

description:
150 bp PE
deseq2_norm_counts.tsv


title: TDX T0

description:
150 bp PE
deseq2_norm_counts.tsv


title: intact Hi-C from thyroid gland (ENCLB069POL)

description:
https://www.encodeproject.org/experiments/ENCSR043XTM/
***************
biological replicate number: 1
technical replicate number: 2
description: entex thyroid intact dnase hic
experiment encode accession: ENCSR043XTM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB069POL
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (53 years) thyroid gland tissue

value: thyroid gland

value: 53 year

value: Erez Aiden, Baylor

value: Ellen Gelfand

value: ENCBS111NAE at ENCODE; https://www.encodeproject.org/ENCBS111NAE/

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


title: intact Hi-C from thyroid gland (ENCLB585SGM)

description:
https://www.encodeproject.org/experiments/ENCSR043XTM/
***************
biological replicate number: 1
technical replicate number: 1
description: entex thyroid intact dnase hic
experiment encode accession: ENCSR043XTM
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB585SGM
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: intact Hi-C from HCT116 (ENCLB559ZWL)

description:
https://www.encodeproject.org/experiments/ENCSR129NAE/
***************
biological replicate number: 1
technical replicate number: 4
description: HCT116 CDk7 degron treated intact mnase
experiment encode accession: ENCSR129NAE
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB559ZWL
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

value: cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS515TQU at ENCODE; https://www.encodeproject.org/ENCBS515TQU/

value: derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: intact Hi-C from HCT116 (ENCLB969AIE)

description:
https://www.encodeproject.org/experiments/ENCSR129NAE/
***************
biological replicate number: 1
technical replicate number: 2
description: HCT116 CDk7 degron treated intact mnase
experiment encode accession: ENCSR129NAE
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB969AIE
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

value: adult

tag: treatments


title: intact Hi-C from HCT116 (ENCLB154WGD)

description:
https://www.encodeproject.org/experiments/ENCSR129NAE/
***************
biological replicate number: 1
technical replicate number: 3
description: HCT116 CDk7 degron treated intact mnase
experiment encode accession: ENCSR129NAE
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB154WGD
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: biosample encode accession


title: HES T120

description:
150 bp PE
deseq2_norm_counts.tsv

value: Blood


title: intact Hi-C from HCT116 (ENCLB949WDQ)

description:
https://www.encodeproject.org/experiments/ENCSR129NAE/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116 CDk7 degron treated intact mnase
experiment encode accession: ENCSR129NAE
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB949WDQ
fragmentation methods: chemical (micrococcal nuclease)
size range: 100-400
nucleic acid starting quantity: 1000000
nucleic acid starting quantity units: cells
instrument model: Ultima Genomics

tag: encode accession


title: 3PPE cells derived from hESCs, siControl, Day9, rep1

description:
Third pharyngeal pouch endoderm cells derived from human embryonic stem cells, siControl, Day9, rep1
siControl_A

value: H9 line cells (WA09)

value: hESCs

value: directed differentiation

value: the third pharyngeal pouch endoderm cells

value: WT


title: intact Hi-C from esophagus squamous epithelium (ENCLB272GWY)

description:
https://www.encodeproject.org/experiments/ENCSR015CVF/
***************
biological replicate number: 1
technical replicate number: 1
description: entex esophagus mucosa intact dnase hic
experiment encode accession: ENCSR015CVF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB272GWY
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (53 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: tissue

tag: Sex

value: female

value: 53 year

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS360XJT at ENCODE; https://www.encodeproject.org/ENCBS360XJT/


title: intact Hi-C from esophagus squamous epithelium (ENCLB620HRD)

description:
https://www.encodeproject.org/experiments/ENCSR015CVF/
***************
biological replicate number: 1
technical replicate number: 2
description: entex esophagus mucosa intact dnase hic
experiment encode accession: ENCSR015CVF
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB620HRD
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

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


title: intact Hi-C from kidney (ENCLB768ABW)

description:
https://www.encodeproject.org/experiments/ENCSR044YKV/
***************
biological replicate number: 1
technical replicate number: 1
description: w71-kidney intact dnase hic
experiment encode accession: ENCSR044YKV
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2022-11-08
lab: Erez Aiden, Baylor
library encode accession: ENCLB768ABW
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: kidney

tag: health state

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

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS902FGR at ENCODE; https://www.encodeproject.org/ENCBS902FGR/

value: derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: HES T0

description:
150 bp PE
deseq2_norm_counts.tsv

value: Blood

value: CD4+ T cell


title: intact Hi-C from sigmoid colon (ENCLB368MRQ)

description:
https://www.encodeproject.org/experiments/ENCSR123ZFD/
***************
biological replicate number: 1
technical replicate number: 1
description: entex sigmoid colon intact dnase hic
experiment encode accession: ENCSR123ZFD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB368MRQ
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

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

value: sigmoid colon

tag: dev stage

value: adult

value: ENCBS451ETF at ENCODE; https://www.encodeproject.org/ENCBS451ETF/


title: intact Hi-C from sigmoid colon (ENCLB970PUE)

description:
https://www.encodeproject.org/experiments/ENCSR123ZFD/
***************
biological replicate number: 1
technical replicate number: 2
description: entex sigmoid colon intact dnase hic
experiment encode accession: ENCSR123ZFD
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB970PUE
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

value: female

tag: age

value: 53 year


title: HES T24

description:
150 bp PE
deseq2_norm_counts.tsv


title: TCQ T120

description:
150 bp PE
deseq2_norm_counts.tsv


title: TCQ T96

description:
150 bp PE
deseq2_norm_counts.tsv


title: TCQ T48

description:
150 bp PE
deseq2_norm_counts.tsv


title: Liver-Sinusoidal-Endothelium-A-RNA-SEQ

city: Washington

first: Anton

last: Wellstein

state: DC

address: 3970 Reservoir Road, N.W.,

department: Oncology

institute: Georgetown University

data_processing:
iIllumina multiplex analysis -> fastq
hisat2 alignment -> BAM
featurecounts -> DE table
Rsubread/limma, EdgeR
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
sorted human cell populations from healthy adult donors were cryopreserved in liquid nitrogen, and total RNA was harvested using the Rneasy kit (qiagen). Sequencing results (fastq files) were provided by Novogene (Sacramento, CA) using Illumina Hiseq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: endothelial


title: intact Hi-C from uterus (ENCLB208RKD)

description:
https://www.encodeproject.org/experiments/ENCSR008CUR/
***************
biological replicate number: 1
technical replicate number: 2
description: entex uterus intact dnase hic
experiment encode accession: ENCSR008CUR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB208RKD
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (53 years) uterus tissue

value: uterus

value: Erez Aiden, Baylor

value: Kristin Ardlie

value: ENCBS957VHZ at ENCODE; https://www.encodeproject.org/ENCBS957VHZ/

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


title: intact Hi-C from body of pancreas (ENCLB770FLR)

description:
https://www.encodeproject.org/experiments/ENCSR121ALS/
***************
biological replicate number: 1
technical replicate number: 2
description: entex pancreas intact dnase hic
experiment encode accession: ENCSR121ALS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB770FLR
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

source_name: Homo sapiens female adult (53 years) body of pancreas tissue

value: body of pancreas

value: ENCBS591IIT at ENCODE; https://www.encodeproject.org/ENCBS591IIT/


title: intact Hi-C from body of pancreas (ENCLB452EPG)

description:
https://www.encodeproject.org/experiments/ENCSR121ALS/
***************
biological replicate number: 1
technical replicate number: 1
description: entex pancreas intact dnase hic
experiment encode accession: ENCSR121ALS
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-01-04
lab: Erez Aiden, Baylor
library encode accession: ENCLB452EPG
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics


title: Cardiopulmonary-Endothelium-HCAEC-C-RNA-SEQ

source_name: Heart

value: Heart


title: TCQ T0

description:
150 bp PE
deseq2_norm_counts.tsv

value: Blood

value: CD4+ T cell


title: V4 T120

description:
150 bp PE
deseq2_norm_counts.tsv

value: Uninfected


title: Cardiopulmonary-Endothelium-HPAEC-A-RNA-SEQ

source_name: Lungs

value: Lungs


title: V4 T144

description:
150 bp PE
deseq2_norm_counts.tsv


title: Cardiopulmonary-Endothelium-HCAEC-A-RNA-SEQ


title: V4 T96

description:
150 bp PE
deseq2_norm_counts.tsv


title: HES T96

description:
150 bp PE
deseq2_norm_counts.tsv


title: Cardiopulmonary-Endothelium-HCAEC-B-RNA-SEQ


title: HES T48

description:
150 bp PE
deseq2_norm_counts.tsv


title: V4 T48

description:
150 bp PE
deseq2_norm_counts.tsv


title: V4 T0

description:
150 bp PE
deseq2_norm_counts.tsv


title: V4 T24

description:
150 bp PE
NA


title: TCQ T144

description:
150 bp PE
deseq2_norm_counts.tsv


title: TCL T120

description:
150 bp PE
deseq2_norm_counts.tsv


title: TCL T144

description:
150 bp PE
deseq2_norm_counts.tsv


title: intact Hi-C from uterus (ENCLB435QIB)

description:
https://www.encodeproject.org/experiments/ENCSR008CUR/
***************
biological replicate number: 1
technical replicate number: 1
description: entex uterus intact dnase hic
experiment encode accession: ENCSR008CUR
assay title: intact Hi-C
assembly: GRCh38
encode release date: 2023-04-26
lab: Erez Aiden, Baylor
library encode accession: ENCLB435QIB
fragmentation methods: chemical (DNaseI)
size range: 100-400
nucleic acid starting quantity: 3
nucleic acid starting quantity units: mg
instrument model: Ultima Genomics

value: tissue

value: adult


title: TCQ T24

description:
150 bp PE
deseq2_norm_counts.tsv


title: TCL T48

description:
150 bp PE
deseq2_norm_counts.tsv


title: TCL T24

description:
150 bp PE
deseq2_norm_counts.tsv


title: TCL T0

description:
150 bp PE
deseq2_norm_counts.tsv


title: TCL T96

description:
150 bp PE
deseq2_norm_counts.tsv


title: HQL T48

description:
150 bp PE
deseq2_norm_counts.tsv


title: HQL T120

description:
150 bp PE
deseq2_norm_counts.tsv


title: HQL T144

description:
150 bp PE
deseq2_norm_counts.tsv


title: HQL T24

description:
150 bp PE
deseq2_norm_counts.tsv


title: V3 T144

description:
150 bp PE
deseq2_norm_counts.tsv


title: HQL T0

description:
150 bp PE
deseq2_norm_counts.tsv


title: Brain_sham_WT_rep2

type: RNA

city: Bunkyo-ku

first: Akari

last: Nakamura

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression of WT mice in the sham-operated brain tissue

hyb_protocol: According to the Agilent Gene Expression Hybridization Kit protocol, 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized on an Agilent Mouse GE 4x44K v2 Microarray  for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5 µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12.1.1.1) with set to default for all parameters.

source_name: Brain, sham, WT, replicate 2

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA extracted from brain tissue was purified using RNeasy Mini Kit (QIAGEN). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were subjected to transient brain ischemia (middle cerebral artery occlusion: MCAO) for 60 min.

tag: genetic background

value: Wild type

value: Brain

tag: gender

value: male


title: V3 T120

description:
150 bp PE
deseq2_norm_counts.tsv


title: V3 T96

description:
150 bp PE
deseq2_norm_counts.tsv


title: Brain_sham_KO_rep3

description: Gene expression of Pla2g2e-deficient mice in the sham-operated brain tissue

source_name: Brain, sham, KO, replicate 3


title: Brain_sham_KO_rep2

source_name: Brain, sham, KO, replicate 2


title: Brain_sham_WT_rep3

source_name: Brain, sham, WT, replicate 3


title: Brain_sham_KO_rep1

source_name: Brain, sham, KO, replicate 1


title: HQL T96

description:
150 bp PE
deseq2_norm_counts.tsv

source_name: Blood


title: Brain_day3_KO_rep1

description: Gene expression of Pla2g2e-deficient mice on the day 3 post-ischemic brains

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: Brain, day 3, Pla2g2e-KO, replicate 1

label_protocol: 100 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

value: Pla2g2e -/-


title: Brain_day3_WT_rep2

description: Gene expression of WT mice on the day 3 post-ischemic brains

source_name: Brain, day 3, WT, replicate 2


title: Brain_day3_KO_rep2

source_name: Brain, day 3, Pla2g2e-KO, replicate 2


title: Brain_day3_KO_rep3

source_name: Brain, day 3, Pla2g2e-KO, replicate 3


title: Brain_day3_WT_rep3

source_name: Brain, day 3, WT, replicate 3