title: Exp1_halfparS25_Rep3

source_name: bacterial cell


title: MRC5_VA cells, + UV, 3 h recovery, RNAPII-Ser2P, ChIP

status: Public on Aug 03 2023

type: SRA

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

country: China

institute: Guangzhou medical university

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NovaSeq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v3.36, discarding reads left with < 20bp.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragment, renormalized and reformatted in the bigWig file format.
Peaks were called using MACS v1.4.2 with the significance cut-off q-value <=0.01.
bigWig files were generated usign the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MRC5_VA cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were harvested by trypsin-treatment and fixed with 1% formaldehyde for 15 min. After quenching and cell lysis, nuclear lysate was sheared by sonication, fragmented chromatin was extracted.
1 ng of ChIPed DNA and input samples were used for standard ChIP-Seq library preparation by using NEBNext Ultra DNA Library prep kit (NEB, E7103) and sequenced under Illumina NovaSeq 6000 system, resulting in the production of 150 bp paired-end reads.

treatment_protocol: UV-C irradiated (10 J/m2) followed by recovery for the indicated time intervals prior to cell extraction.

tag: cell line

tag: cell type

value: human fibroblast cells

tag: genotype

value: WT

tag: treatment

value: UV-C irradiated 10J/m2

tag: chip antibody

value: CTD Ser2P (Millipore, 04-1571)


title: SNF2hKO, mESC, +m, biorep1, techrep4

city: San Francisco

first: Megan

last: Ostrowski

state: CA

address: 1700 Owens

country: USA

institute: Gladstone Institutes

description: SNF2h knockout and wild-type re-expression mouse embryonic stem cells were gifted from Dirk Schübeler Laboratory

data_processing:
Library strategy: SAMOSA
Demultiplexing BAM files using Lima
Generating circular concensus sequences (CCS) using ccs
Aligning CCS to mm10 using pbmm2 (in vivo samples only)
Aligning subreads to nonanucleosomal molecule reference (in vitro samples only)
Genome_build: mm10
Supplementary_files_format_and_content: pickle

organism: Mus musculus

source_name: murine embryonic stem cells (in vivo)

growth_protocol: mESCs were thawed and grown for two passages onto CF-1 Irradiated mouse embryonic feeder cells. mESCs were MEF depleted at least two times prior to experimentation. mESCs were grown on 0.2% gelatin plates and maintained with 1X KnockOut DMEM supplemented with 10% Fetal Bovine Serum, 1% 100X GlutaMAX, 1% 100X MEM Non-Essential Amino Acids, 7.82 mM 2-Mercaptoethanol, and 1X Leukemia Inhibitory Factor.

extract_protocol:
Chromatin was purified with 10uL RNaseA at RT for 10 minutes (in vivo samples only), 10uL Proteinase K (20mg/mL) and 10uL 10% SDS at 65°C for a minimum of 2 hours up to overnight). DNA was extracted with Phenol-Chloroform and ethanol precipitation.
Library preparation included DNA damage repair, end repair, blunt-end SMRTbell® ligation, Exonuclease treatment, and Ampure PB cleanup according to manufacturer’s instruction. Library quality was assessed with Agilent Bioanalyzer High Sensitivity DNA kit or Agilent Tapestation D5000 Assay.
OTHER: PacBio SMRTbell® library preparation

treatment_protocol:
Isolated mESC nuclei were methylated (10uL EcoGII per 1e6 nuclei) with non-specific adenine methyltransferase EcoGII (New England Biolabs, HC stock 2.5e4U/mL) at 37°C for 30 minutes, supplemented with SAM to 6.25mM (NEB) after 15 minutes.
Isolated nuclei (methylated or unmethylated) were digested with Micrococcal Nuclease (Sigma) at 1U per 50e6 nuclei at varying conditions (see characteristics above). MNase-digested nuclei were treated with 300ug/mL of Lysolethicin (L-α-Lysophosphatidylcholine from bovine brain, Sigma) for nuclear lysis and liberation of chromatin fibres.

tag: snf2h remodeling turnover conditions

tag: snf2h remodeling atp/adp conditions

tag: histone

value: dna ratio:N/A

tag: mnase digestion temperature

tag: mnase digestion duration

value: 60 min

tag: ecogii methylation

value: EcoGII Methylated


title: wcon_GLKD_pA_ee_new

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description: total RNA (polyA selected) from MTD-Gal4 control KD

library_source: transcriptomic

data_processing:
reads were prepared by removal of the adaptor sequences and base-clipping to keep nucleotides 6-50
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using STAR (2.7.10b) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster genome using STAR (2.7.10b)
reads mapping to rRNA, tRNA, mitoRNA were excluded
gene expression was quantified using Salmon (1.5.1) on Flybase r6.40 transcripts with transoposon sequences added and normalization by the GeTMM method implemented in edgeR (3.34)
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: gene expression table showing GeTMM expression values

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol:
25˚C, 12h dark/light, ovary dissection into 1x PBS on ice, snap frozen in Trizol
parents were kept in cages at 25˚C, 12h dark/light, embryos collected on applejuice agar plates, bleached, rinsed with water and 1xPBS 0.05% x-100 Triton, snap frozen in Trizol

extract_protocol:
RNA was extracted using Trizol
Libraries were prepared using a NEBNext Ultra Directional library prep kit (NEB) or NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

tag: tissue

value: embryo

value: 0-1 hour old


title: CTCF_DNA_9uM_SNF2h_75min_techrep3

description: Nonanucleosome DNA in a plasmid was purified by Gigaprep, isolated via restriction enzyme sites, and purified with Sephacryl S1000 super fine gel filtration.

data_processing:
Demultiplexing subreads BAM files with lima (v2.6.0)
Generating circular concensus sequences (CCS) using ccs
Aligning subreads to nonanucleosomal molecule reference
Assembly: mm10
Supplementary files format and content: *_full.pickle: Python pickle files containing IPD measurements for each base in the forward and reverse strands per CCS read
Library strategy: SAMOSA

organism: unidentified plasmid

source_name: CTCF site 1 from Mus Musculus amplified, gibson cloned, isolated, and histone assembled

growth_protocol: N/A (in vitro samples)

extract_protocol:
CTCF site 1 was purified using a GigaPrep kit (Qiagen), restriction enzyme digested, and purified by size exclusion chromatography. Chromatin was assembled using salt gradient dialysis
Library preparation included DNA damage repair, end repair, blunt-end SMRTbell® ligation, Exonuclease treatment, and Ampure PB cleanup according to manufacturer’s instruction. Library quality was assessed with Agilent Bioanalyzer High Sensitivity DNA kit or Agilent Tapestation D5000 Assay.
PacBio SMRTbell® library preparation

treatment_protocol:
N/A (in vitro samples)
N/A (in vitro samples)

tag: remodeler

tag: remodeler concentration

value: 9 uM

tag: remodeling turnover_conditions

value: single-turnover

tag: remodeling time

value: Long

tag: remodeling atp/adp_conditions

value: plus ATP

tag: sample type

value: in vitro (plasmid insert)


title: E14, mESC, +m, biorep1, techrep3

description: E14 mESCs were gifted from Elphege Nora Laboratory at UCSF


title: MRC5_VA cells, no UV, Input

tag: cell line

tag: cell type

value: no treatment


title: MRC5_VA cells, + UV, 12 h recovery, RNAPII-Ser5P, ChIP

tag: genotype

tag: treatment

value: CTD Ser5P (Millipore, 04-1572)


title: wcon_GLKD_pA_ee_old


title: Exp1_WT_Rep1

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description:
RNAseq_WT_halfparS25_raw_counts.csv
Exp1_halfparS25_vs_WT_gene_expression_changes_All.csv

data_processing:
base calling: bcl2fastq v2.20 (Illumina)
Sequencing data were quality-checked and filtered using FASTP version 0.22.0.
Reads were mapped to P. aeruginosa PAO11161 genome (CP032126) using Bowtie2 version 2.2.5 using default settings.
The number of reads mapping to individual genes was counted using FeatureCounts v 2.0.3 (with the -s2 option).
Differential expression analysis was conducted using edgeR ver 3.40.2.
Assembly: CP032126
Supplementary files format and content: Raw counts of sequencing (FeatureCounts output summarized for all samples) (RNAseq_WT_halfparS25_raw_counts.csv).
Supplementary files format and content: A table with DE data for all genes and normalized abundance measurements (EdgeR output, separately for the two experiments) (Exp1_halfparS25_vs_WT_gene_expression_changes_All.csv and Exp2_halfparS25_vs_WT_gene_expression_changes_All.csv).

molecule: total RNA

organism: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa PAO1161 (WT) as well as half-parS25 strains were grown overnight in LB broth (DifcoTM L Broth, Lennox, BD), diluted 1:200 in fresh medium and cells were harvested at logarithmic phase of growth (OD 600nm of 0.5). Culturing was performed in 20ml of medium in 100ml flask, closed with a cotton plug with shaking 200 rpm, at  37oC.

extract_protocol:
Total RNA was isolated from three independent replicates of each strain. 2 ml of cultures which reached optical density 0.4-0.6 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
rRNA was depleted using Ribo-Zero rRNA Removal Kit (Bacteria) (MRZMB126, Illumina) according to manufacturer instructions. Libraries were prepared according to instructions accompanying the NEBNext Ultra DirectionalRNA Library Prep Kit for Illumina (NEB, E7420). Libraries were sequenced using standard Illumina protocols.

tag: strain

value: PAO1161 leu-

tag: growth phase

value: LB 37oC log phase of culture growth

value: bacterial cell


title: CTCF_DNA_9uM_SNF2h_15min_techrep3

value: Standard

tag: histone


title: Exp2_WT_Rep1

description:
RNAseq_WT_halfparS25_raw_counts.csv
Exp2_halfparS25_vs_WT_gene_expression_changes_All.csv

value: WT


title: CTCF_DNA_2uM_ACF_75min_techrep3

value: ACF

value: 2 uM

value: dna ratio:N/A


title: SNF2hKO, mESC, +m, biorep1, techrep3

tag: snf2h remodeling turnover conditions

tag: snf2h remodeling atp/adp conditions

tag: mnase digestion temperature

value: 60 min

value: EcoGII Methylated


title: Methylated_array_10:1_techrep3

description: Nonanucleosome DNA in a plasmid was purified by Gigaprep, isolated via restriction enzyme sites, and purified with Sephacryl S1000 super fine gel filtration. Histone octamers (Luger et al., 1999) were assembled onto purified DNA via salt gradient dialysis.

value: unremodeled

value: dna ratio:10:1 ratio

tag: ecogii methylation


title: Exp2_WT_Rep2


title: SNF2hWTAB, mESC, +m, biorep1, techrep3

tag: mnase digestion duration


title: spnE30_GLKD_pA_ee_old

description: total RNA (polyA selected) from MTD-Gal4 spindle-E-sh KD

tag: tissue

value: embryo

value: 0-1 hour old

value: MTD-GAL4/w1118;MTD-GAL4/+; MTD-GAL4/spn-E sh parents


title: MRC5_VA cells, + UV, 3 h recovery, RNAPII-Ser5P, ChIP

value: human fibroblast cells

value: UV-C irradiated 10J/m2

tag: chip antibody


title: MRC5_VA cells, + UV, 12 h recovery, RNAPII-Ser2P, ChIP

value: CTD Ser2P (Millipore, 04-1571)


title: intramuscular adipocytes, NC-4

city: chengdu

first: Yinggui

state: sichuan

address: 2-31, Jingwenyuan, South District, Airport Campus, Southwest University for Nationalities, Chengdu, Sichuan

institute: Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province

description:
The sample-4 of negative control
nc4

data_processing:
fastp
Sequence readswere trimmed for adaptor sequnce/low-quality sequence using fastp
Trimmed sequnence reads wrere mapped to ARS1 using hisat2 samtools
The transcript was assembled using htseq-count.
Assembly: ARS1
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Capra hircus

source_name: goat intramuscular preadipocyte

growth_protocol: Goat intramuscular precursor adipocytes were cultured using DMEM medium (containing 10% fetal bovine serum, 1% double antibody) at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using 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 is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are 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 library was 300±50 bp.

treatment_protocol: The negative control groups was treated with negative control interfering RNA (NC) and the experimental groups treated with interfering RNA that silences CPT1B gene (si-CPT1B).

value: goat intramuscular preadipocyte


title: intramuscular adipocytes, NC-3

description:
The sample-3 of negative control
nc3


title: SNF2hKO, mESC, +m, biorep2, techrep2


title: Exp1_halfparS25_Rep1

value: PAO1161 leu-

value: LB 37oC log phase of culture growth

value: bacterial cell


title: SNF2hWTAB, mESC, +m, biorep2, techrep2


title: intramuscular adipocytes, NC-1

description:
The sample-1 of negative control
nc1

value: WT


title: CTCF_15:1_9uM_SNF2h_15min_techrep3

tag: remodeler

tag: remodeler concentration

value: 9 uM

tag: remodeling turnover_conditions

value: single-turnover

tag: remodeling time

value: Standard

value: plus ATP

value: dna ratio:15:1 ratio

value: in vitro (plasmid insert)


title: SNF2hKO, mESC, +m, biorep2, techrep3

value: dna ratio:N/A

value: 60 min

value: EcoGII Methylated


title: Exp1_WT_Rep3

tag: cell type


title: MRC5_VA cells, no UV, RNAPII-Ser2P, ChIP

tag: cell line

value: human fibroblast cells

tag: genotype

value: no treatment


title: SNF2hKO, mESC, +m, biorep3, techrep3

value: 45 min


title: SNF2hWTAB, mESC, +m, biorep1, techrep2


title: CTCF_DNA_2uM_ACF_15min_techrep3

value: ACF

value: 2 uM

tag: remodeling atp/adp_conditions

tag: sample type


title: intramuscular adipocytes, si-CPT1B-3

description:
The sample-3 of knockdown CPT1B
si3

value: goat intramuscular preadipocyte

value: Knockdown of CPT1B gene


title: MRC5_VA cells, no UV, RNAPII-Ser5P, ChIP

value: WT

tag: treatment

value: CTD Ser5P (Millipore, 04-1572)


title: E14, mESC, +m, biorep3, techrep3

tag: snf2h remodeling turnover conditions

tag: histone


title: LacZ - D2d - Input

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

data_processing:
Data analysis was carried out using the web tool https://usegalaxy.org/. Briefly, Bowtie2 [http://bowtie-bio.sourceforge.net/] was used for fastq files alignments and, for peak detection, MACS software [http://liulab.dfci.harvard.edu/MACS/] with default parameters. The Integrative Genomics Viewer (IGV) [http://www.broadinstitute.org/igv] was used for a graphic illustration of ChIP-Seq peaks and ENCODE data (http://genome.ucsc.edu/ENCODE/) for information on chromatin organization. Raw data files from ChIP-seq assays were aligned to the GRCh38 reference genome with Bowtie2. MACS2 software was used for peak detection, with a q-value cutoff of 0.05. Peaks were annotated and merged with the annotatePeaks.pl and mergepeaks.pl functions, available within the HOMER software.
Assembly: GRCh38
Supplementary files format and content: BigWig files

source_name: A375 melanoma cell line

growth_protocol: All melanoma cell lines and patient-derived primary melanoma cells were maintained in Roswell Park Memorial Institute (RPMI) medium (Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (Thermo Fisher Scientific).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes at RT, followed by quenching with glycine (final concentration 125 mM). After washing with ice-cold PBS, cells were collected through centrifugation (400g). For the analysis of total lamin A/C chromatin binding, cells were lysed and chromatin was prepared using the Chromatin EasyShear Kit - High SDS (Diagenode; Cat# C01020012), and sonicated using an E220 focused ultrasonicator (Covaris). The ChIP reaction was performed using the iDeal ChIP-seq kit (Diagenode, Cat# C01010055). Samples were pre-cleared using the beads provided in the kit and incubated overnight at 4°C with 5ug of anti-Androgen Receptor, PG-21, Cat. No. 06-680 (Sigma). Antibody-chromatin complexes were pulled down using protein A-coated magnetic beads. Elution was performed as per the manufacturer's instructions and chromatin was quantified using the Qubit Fluorometric Quantification Kit (Thermo Scientific). For library preparation, 10 ng of DNA was utilized with the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina. Subsequently, sequencing was performed at the Novegene facility using the Novaseq 6000 platform.
For library preparation, 10 ng of DNA was utilized with the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina.

treatment_protocol: A375 melanoma cells were treated with Dabrafenib (0.5uM) versus vehicle (DMSO) control for 48h.

value: Dabrafenib

tag: transfection

value: control


title: CTCF_15:1_320nM_SNF2h_75min_biolrep1_techrep3

value: stoichiometric

value: Long

value: plus ATP

tag: ecogii methylation


title: LacZ - control - AR

value: 5ug of anti-Androgen Receptor, PG-21, Cat. No. 06-680 (Sigma)


title: Exp1_WT_Rep2

tag: strain

value: PAO1161 leu-

tag: growth phase

value: LB 37oC log phase of culture growth

value: bacterial cell


title: intramuscular adipocytes, NC-2

description:
The sample-2 of negative control
nc2


title: CTCF_15:1_9uM_SNF2h_75min_biolrep2_techrep3

value: 9 uM

value: single-turnover

value: dna ratio:15:1 ratio

value: EcoGII Methylated

value: in vitro (plasmid insert)


title: SNF2hKO, mESC, +m, biorep1, techrep2

tag: snf2h remodeling atp/adp conditions

value: dna ratio:N/A

tag: mnase digestion temperature

tag: mnase digestion duration

value: 60 min


title: intramuscular adipocytes, si-CPT1B-4

description:
The sample-4 of knockdown CPT1B
si4

value: goat intramuscular preadipocyte

value: Knockdown of CPT1B gene


title: Snf2hWTAB, mESC, +m, biorep3, techrep3

value: 45 min


title: CTCF_15:1_9uM_SNF2h_75min_biolrep1_techrep3

tag: remodeler

tag: remodeler concentration

tag: remodeling turnover_conditions


title: LacZ - control - Input

tag: cell line

value: control

tag: chip antibody


title: CTCF_15:1_320nM_SNF2h_15min_biolrep1_techrep3

value: stoichiometric

tag: remodeling time

value: Standard

tag: remodeling atp/adp_conditions


title: E14, mESC, +m, biorep3, techrep2


title: E14, mESC, +m2, biorep2, techrep2


title: CTCF_15:1_320nM_SNF2h_75min_biolrep2_techrep3

value: Long

value: plus ATP

tag: sample type


title: LacZ - D2d - AR

tag: treatment

value: Dabrafenib

value: 5ug of anti-Androgen Receptor, PG-21, Cat. No. 06-680 (Sigma)


title: Snf2hWTAB, mESC, +m, biorep3, techrep2

tag: snf2h remodeling turnover conditions

tag: histone


title: AR overexpression - control - AR

tag: transfection

value: AR OE


title: AR overexpression - control - Input


title: Endometrium_EST-33-G2-EPST85

city: Paterna

first: Raul

last: Pérez-Moraga

state: Valencia

address: Rda. de Narcís Monturiol, 11, Bloque C

country: Spain

institute: Carlos Simon Foundation, INCLIVA Health Research Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Processing of scRNA-seq data was conducted with the CellRanger software suite (version 3.1.0). Raw reads were demultiplexed using the mkfastq wrapper command of bcl2fastq (Illumina). The libraries were mapped using GRCh38-3.0.0 as a reference provided by 10x Genomics. The count gene expression matrices per cell were computed per sample using the counts pipeline (with --expect-cells parameter set to default), which performs the steps of read alignment (with STAR mapping tool), UMI counting, calling of cell barcodes, and filtering of empty droplets based on a simple. Processed samples were merged and saved into h5ad objects
Raw/Filter count matrix file format 1): matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices 2): features.tsv.gz contains feature information that corresponds to the row index of matrix.mtx.gz 3): barcodes.tsv.gz contains cellular barcodes that correspond to column indices of matrix.mtx.gz.
oThe filter count matrix was obtained by the CellRanger count pipeline output
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content: h5ad single-cell object with barcode metadata
Supplementary files format and content: tar archive with raw count matrix data (MTX, TSV)

source_name: Endometrium

extract_protocol:
A two-stage dissociation protocol separated endometrial biopsies into stromal fibroblasts and epithelial enriched single-cell suspensions. Before dissociation, tissue was rinsed with PBS in a petri dish to remove blood and mucus, and excess PBS was removed after rinsing. The tissue was minced into small pieces and dissociated with 3 ml collagenase mix (Collagenase V, Sigma), RPMI+10% fetal bovine serum, and DNaseI (Sigma) at 37ºC under continuous shaking at 175 rpm for 25 min in a 15 mL Falcon tube in a horizontal position. This primary enzymatic step mostly dissociates stromal fibroblasts into single cells while leaving epithelial glands and lumen mostly undigested. The contents were transferred to a 50 mL tube in RPMI media and filtered with a 100 mm cell strainer. The tissue remaining on the filter was used for the epithelial enrichment cell isolation by resuspending and incubating in 10 ml Trypsin mix (Trypsin -EDTA (0.25%) phenol and DNaseI) for 10 min.    The resulting two contents were transferred to 50 mL tubes with 20 mL RPMI, filtered with a 100 mm cell strainer, centrifuged, and then resuspended in 1 mL RPMI. Dead cells were removed using the MACS dead cell removal kit (Miltenyi Biotec). Live-cell suspensions were loaded into a Chromium Next GEM Chip G (10X Genomics) to obtain cDNA from individual cells.    Mean cells obtained in stromal and epithelial enriched suspensions were 2.38x106 (5x105-6.4x106) and 1.25x106 (2x105-5.3x106), respectively. Viability of stromal cells was 67.44% (31-87%) and 39.5% (20-80%) for epithelial cells.
Total RNA was extracted using the RNeasy Micro Kit with on-column DNase treatment (Qiagen) following the manufacturer's instructions. RNA was resuspended in 14 μl of RNase-free water, and purity and concentration determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher). For cDNA synthesis, 500-1000 ng of total RNA was reverse transcribed following the manufacturer's instructions(Thermo Fisher).    10x-Genomics v3 libraries were prepared as per the manufacturer's instructions. Libraries were sequenced, aiming at a minimum coverage of 50,000 raw reads per cell, on an Illumina NovaSeq 6000 S2v1.5 300 cycles at a mean 40x coverage (paired-end; read 1: 26 cycles; i7 index: 8 cycles, i5 index: 0 cycles; read 2: 98 cycles)

treatment_protocol: BMDSC mobilization was performed using granulocyte-CSF (G-CSF) injection at 10 mcgr/kg. CD133+ cells were collected through peripheral blood apheresis and subsequently isolated. Patients were excluded if they did not reach the minimal requirements for mobilized cells (at least 30 million cells with a purity above 70% and viability >50%), presented an unstable medical condition, or refused a central venous catheter when required. Finally, isolated CD133+ cells were delivered into the spiral arterioles of the patient using a minimal invasive radiology intervention through the left brachial artery, reaching each uterine artery using a microcatheter

tag: biospy origin

value: Epithelium/Stroma

tag: seurat id

tag: tissue

value: Endometrium

tag: treatment stage

value: WOI Control

tag: patient

tag: menstrual day_cycle


title: CTCF_15:1_320nM_SNF2h_15min_biolrep2_techrep3

tag: remodeler

tag: remodeler concentration

value: dna ratio:15:1 ratio

tag: ecogii methylation

value: EcoGII Methylated

value: in vitro (plasmid insert)


title: NSCLC4_PBMC_TIL_GEX

city: Pittsburgh

first: Feng

last: Shan

state: Pennsylvania

address: Ford Building, 5051 Centre Ave

institute: University of Pittsburgh

description: GEX

data_processing:
scRNA-seq
CellRanger (10X Genomics, version 3.1.0) pipeline to generate gene/barcode matrices.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-separated files and matrix file

source_name: PBMC and TIL from NSCLC patients

extract_protocol:
Single-cell suspensions from tonsil tissues and tumors were generated by mechanical disruption followed by enzymatic digestion in serum-free Roswell Park Memorial Institute media (RPMI). After initial isolation from tissue, cells were passed through a 100 μm filter and spun down to yield single-cell suspensions. Cells were stained and sorted for live CD4+ Tconv (CD4+CD25-CD127high) and Tregs (CD4+CD25highCD127low) by fluorescence-activated cell sorting (FACS) on the Sony MA900 at the Hillman Cancer Center Cytometry Facility.
Immediately following sorting, Tconv and Tregs were centrifuged for 5 min at 500 xg and were resuspended in PBS with 0.04% BSA. Cells were then counted using the Cellometer Auto2000 (Nexcelom) and loaded into the 10X Controller (10X Genomics) targeting a recovery of 2000 cells per sample. The RNA capture, barcoding, cDNA and library preparation were performed according to the manufacturer’s recommendations (single cell 3' v2).

tag: condition

value: NSCLC

value: PBMC and TIL

tag: cell line

value: Primary cells

tag: cell type

value: Sorted CD45+

tag: genotype

value: Wild Type


title: Endometrium_EST-32-G2-EPST84

description: 10x Genomics


title: SCLC1_TIL

description: GEX

source_name: TIL from SCLC patients

value: SCLC

value: TIL


title: intramuscular adipocytes, si-CPT1B-1

description:
The sample-1 of knockdown CPT1B
si1

value: goat intramuscular preadipocyte

value: Knockdown of CPT1B gene


title: E14, mESC, +m, biorep1, techrep2

tag: snf2h remodeling atp/adp conditions

value: dna ratio:N/A

tag: mnase digestion temperature

tag: mnase digestion duration

value: 60 min


title: CTCF_15:1_320nM_ACF_75min_biolrep2_techrep3

value: ACF

tag: remodeling turnover_conditions

value: stoichiometric

tag: remodeling time

value: Long

tag: remodeling atp/adp_conditions

value: plus ATP

tag: histone

tag: sample type


title: SNF2hKO, mESC, +m, biorep3, techrep2

tag: snf2h remodeling turnover conditions

value: 45 min

value: EcoGII Methylated


title: Endometrium_EST-29-G2-EPST81

description: 10x Genomics

tag: biospy origin

value: Epithelium/Stroma

tag: seurat id

tag: tissue

value: Endometrium

tag: treatment stage

value: WOI Control

tag: patient

tag: menstrual day_cycle


title: intramuscular adipocytes, si-CPT1B-2

description:
The sample-2 of knockdown CPT1B
si2

tag: cell type


title: SCLC1_PBMC

description: GEX

source_name: PBL from SCLC patients

tag: condition

value: PBL

tag: cell line

value: Primary cells

value: Sorted CD45+

tag: genotype


title: NSCLC3_PBMC_TIL_GEX

description: GEX

value: NSCLC

value: PBMC and TIL

value: Wild Type


title: Endometrium_EST-41-G2-EPST109

description: 10x Genomics


title: NSCLC4_CITEseq

description: Cell hashing

library_source: other

molecule: protein

source_name: PBL and TIL from NSCLC patients

value: PBL and TIL


title: Endometrium_EST-31-G2-EPST83

description: 10x Genomics


title: CTCF_15:1_2uM_ACF_75min_biolrep2_techrep3

tag: remodeler

tag: remodeler concentration

value: 2 uM

value: single-turnover

value: dna ratio:15:1 ratio

tag: ecogii methylation

value: in vitro (plasmid insert)


title: CTCF_15:1_320nM_ACF_15min_biolrep1_techrep3

value: ACF

tag: remodeling turnover_conditions

value: stoichiometric

tag: remodeling time

value: Standard

tag: remodeling atp/adp_conditions

value: plus ATP


title: CTCF_15:1_320nM_ACF_15min_biolrep2_techrep3

tag: histone

value: EcoGII Methylated

tag: sample type


title: SNF2h, ATPasemutAB, -m, biorep2

tag: snf2h remodeling turnover conditions

tag: snf2h remodeling atp/adp conditions

value: dna ratio:N/A

tag: mnase digestion temperature

tag: mnase digestion duration

value: 60 min

value: Unmethylated


title: SNF2h, ATPasemutAB, -m, biorep1


title: NSCLC3_CITEseq

description: Cell hashing

tag: tissue

value: Primary cells

value: Sorted CD45+


title: Endometrium_EST-21-G2-EPST65

description: 10x Genomics

tag: biospy origin

value: Epithelium/Stroma

tag: seurat id

value: Endometrium

tag: treatment stage

value: WOI Control

tag: patient

tag: menstrual day_cycle


title: SNF2hKO, mESC, +m, biorep3, techrep1

value: 45 min


title: NSCLC2_TIL

description: GEX

source_name: TIL from NSCLC patients

tag: condition

value: NSCLC

value: TIL

tag: cell line

tag: cell type

tag: genotype

value: Wild Type


title: Organoids_CO-14_Control

description: 10x Genomics

data_processing:
Processing of scRNA-seq data was conducted with the CellRanger software suite (version 3.1.0). Raw reads were demultiplexed using the mkfastq wrapper command of bcl2fastq (Illumina). The libraries were mapped using GRCh38-3.0.0 as a reference provided by 10x Genomics. The count gene expression matrices per cell were computed per sample using the counts pipeline (with --expect-cells parameter set to default), which performs the steps of read alignment (with STAR mapping tool), UMI counting, calling of cell barcodes, and filtering of empty droplets based on a sample. Finally, Cellbender was used to filter out the ambient RNA. Processed samples were merged and saved into h5ad objects.
Raw count matrix file format 1): matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices 2): features.tsv.gz contains feature information that corresponds to the row index of matrix.mtx.gz 3): barcodes.tsv.gz contains cellular barcodes that correspond to column indices of matrix.mtx.gz.
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content: h5ad single-cell object with barcode metadata
Supplementary files format and content: h5 files with filtered count matrix data from Cellbender output
Supplementary files format and content: Zip archive with raw count matrix data (MTX, TSV)

extract_protocol:
Organoids were generated from AS patients’ endometrium pre- and post-treatment and from healthy control endometrium. After enzymatic dissociation of the endometrial biopsies, epithelial and stromal cells were obtained (in the same tube), and total cell numbers were counted. After centrifugation at 300 g, the pellet was resuspended in 70% Matrigel and 30% DMEM/F12 (Thermo Fisher Scientific, 11330032) and supplemented with the ROCK inhibitor Y-27632 (1/500). The suspension was cultured in 20-µl droplets containing 25,000 cells, deposited in prewarmed 48-well plates, and allowed to form a gel at 37ºC and 5% CO2 before adding culture medium. Organoid culture medium was prepared as previously described. Matrigel droplets were cultured for 14-16 days in the first passage (P0) with medium changes every two days. Organoids were then grown for seven days before the following passage, with media changes every two days. Organoids were recovered for passaging by liquifying the Matrigel droplets with ice-cold DMEM/F12 (without any growth factors, serum, or enzymes), followed by repeated pipetting to ensure maximum recovery. Organoids were then dissociated by incubation with TrypLE supplemented with Y-27632 (1/1000) and mechanically triturated. The resulting cell suspension was centrifuged at 300 g, and the pellets were resuspended in 70% Matrigel and 30% DMEM/F12 supplemented with Y-27632 and placed as droplets in 48-well plates. Two passages (till P2) were performed to remove the contaminating stromal cells from the epithelial organoids before scRNA-seq analysis.  Once P2 was reached and after 2 days of culture at passage 2, organoids were treated with E2 [10 nM] for two days, and with E2 [10 nM] + MPA [1 uM] + cAMP [0,25 mM]+ XAV 939 [10 uM] for 4 additional days. After treatment, organoids were dissociated for single-cell transcriptomic analysis following the same protocol described for passaging but with an additional cell counting step to use the exact number of cells that requires the protocol for single-cell transcriptomics
Total RNA was extracted using the RNeasy Micro Kit with on-column DNase treatment (Qiagen) following the manufacturer's instructions. RNA was resuspended in 14 μl of RNase-free water, and purity and concentration determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher). For cDNA synthesis, 500-1000 ng of total RNA was reverse transcribed following the manufacturer's instructions(Thermo Fisher).    10x-Genomics v3 libraries were prepared as per the manufacturer's instructions. Libraries were sequenced, aiming at a minimum coverage of 50,000 raw reads per cell, on an Illumina NovaSeq 6000 S2v1.5 300 cycles at a mean 40x coverage (paired-end; read 1: 26 cycles; i7 index: 8 cycles, i5 index: 0 cycles; read 2: 98 cycles)

value: Epithelial organoids

value: Control


title: CTCF_15:1_320nM_ACF_75min_biolrep1_techrep3

tag: remodeler

value: ACF

tag: remodeler concentration

tag: remodeling turnover_conditions

value: stoichiometric

tag: remodeling time

value: Long

tag: remodeling atp/adp_conditions

value: dna ratio:15:1 ratio

tag: ecogii methylation

value: in vitro (plasmid insert)


title: Snf2hWTAB, mESC, +m, biorep3, techrep1

tag: snf2h remodeling turnover conditions

tag: snf2h remodeling atp/adp conditions

tag: histone

value: dna ratio:N/A

tag: mnase digestion temperature

tag: mnase digestion duration

value: EcoGII Methylated


title: CTCF_15:1_2uM_ACF_75min_biolrep1_techrep3

value: 2 uM

value: single-turnover

value: plus ATP

tag: sample type


title: CTCF_15:1_2uM_ACF_15min_biolrep2_techrep3

value: Standard


title: NSCLC2_PBMC

description: GEX

source_name: PBL from NSCLC patients

tag: tissue

value: PBL

value: Primary cells

value: Sorted CD45+


title: Organoids_CO-9_Control

description: 10x Genomics

growth_protocol: Organoids were generated from AS patients’ endometrium pre- and post-treatment and from healthy control endometrium. After enzymatic dissociation of the endometrial biopsies, epithelial and stromal cells were obtained (in the same tube), and total cell numbers were counted. After centrifugation at 300 g, the pellet was resuspended in 70% Matrigel and 30% DMEM/F12 (Thermo Fisher Scientific, 11330032) and supplemented with the ROCK inhibitor Y-27632 (1/500). The suspension was cultured in 20-µl droplets containing 25,000 cells, deposited in prewarmed 48-well plates, and allowed to form a gel at 37ºC and 5% CO2 before adding culture medium. Organoid culture medium was prepared as previously described. Matrigel droplets were cultured for 14-16 days in the first passage (P0) with medium changes every two days. Organoids were then grown for seven days before the following passage, with media changes every two days.

tag: biospy origin

tag: seurat id

value: Endometrium

tag: treatment stage


title: CTCF_15:1_2uM_ACF_15min_biolrep1_techrep3


title: E14, mESC, +m, biorep3, techrep1

value: 45 min


title: Organoids_CO-8_Control

description: 10x Genomics

value: Epithelial organoids

value: Control


title: NSCLC1_TIL

description: GEX

tag: condition

value: NSCLC

value: TIL

tag: cell line

tag: cell type

tag: genotype

value: Wild Type


title: E14, mESC, gDNA, +m

value: 60 min


title: Organoids_1-15_AS-Pre

description: 10x Genomics

value: AS-Pre


title: NSCLC1_PBMC

description: GEX


title: E14, mESC, +m2, biorep2, techrep1

value: dna ratio:N/A

value: EcoGII Methylated


title: CTCF_10:1_9uM_SNF2h_75min_biolrep2_techrep3

tag: remodeler

tag: remodeler concentration

value: 9 uM

tag: remodeling turnover_conditions

value: single-turnover

tag: remodeling time

value: Long

value: dna ratio:10:1 ratio

value: in vitro (plasmid insert)


title: CTCF_10:1_9uM_SNF2h_75min_biolrep1_techrep3

tag: remodeling atp/adp_conditions

value: plus ATP

value: dna ratio:15:1 ratio

tag: ecogii methylation


title: E14, mESC, +m, biorep1, techrep1

tag: snf2h remodeling turnover conditions

tag: snf2h remodeling atp/adp conditions

tag: histone

tag: mnase digestion temperature


title: Organoids_1-13_AS-Pre

description: 10x Genomics

tag: biospy origin

tag: tissue

value: Endometrium


title: Mel_TPF115_PBL

description: GEX

source_name: PBL from melanoma patients

value: melanoma

value: PBL

value: Primary cells

value: Sorted CD45+


title: CTCF_10:1_9uM_SNF2h_15min_techrep3

value: Standard

tag: sample type


title: CTCF_10:1_320nM_SNF2h_75min_biolrep2_techrep3

value: stoichiometric


title: E14, mESC, -m, biorep2

tag: mnase digestion duration

value: 60 min

value: Unmethylated


title: Mel_TPF115_TIL

description: GEX

source_name: TIL from melanoma patients

tag: condition

value: TIL

tag: cell line

value: Wild Type


title: Mel_TP290_TIL

description: GEX

tag: cell type

tag: genotype


title: Mel_TP290_PBL

description: GEX


title: CTCF_10:1_320nM_SNF2h_75min_biolrep1_techrep3

tag: remodeler

tag: remodeler concentration

value: EcoGII Methylated


title: SNF2hWTAB, mESC, -m, biorep2

value: dna ratio:N/A


title: Mel_178953_TIL

description: GEX


title: CTCF_10:1_320nM_SNF2h_15min_biolrep2_techrep3

tag: remodeling turnover_conditions

tag: remodeling time

value: dna ratio:10:1 ratio


title: E14, mESC, -m, biorep1

tag: ecogii methylation


title: CTCF_10:1_320nM_SNF2h_15min_biolrep1_techrep3

tag: remodeling atp/adp_conditions

value: in vitro (plasmid insert)


title: Blood, ParticipantH, 05.00h

city: Cologne

first: Annica

last: Gosch

address: Melatengürtel 60-62

department: Forensic Genetics

country: Germany

institute: Institute of Legal Medicine Cologne

data_processing:
FastQC v0.11.9 was used to analyze the quality score of the RNASeq sequencing reads.
Poor-quality and adapter bases were trimmed from the sequencing reads by the Trim Galore pipeline (v0.6.7) [--min_trimmed_reads = 10000 i.e. Minimum number of trimmed reads below which samples are removed from further processing]
Filtered high quality paired end reads were aligned against the reference genome (GRCh38) using STAR method v2.6.1d (--min_mapped_reads : 5 ; )
Gene counts were estimated with featureCounts v1.5.2 (default parameters) (--featurecounts_feature_type : 'exon' attribute within the GTF file)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw read counts for genes in each sample

source_name: whole blood

growth_protocol: Blood samples were obtained from ten healthy volunteers (five males, five females; median age: 26.5 years, range: 19-31 years). Donors with any known conditions or reporting to take medication potentially effecting regular sleep-wake cycles were excluded from the study (Exclusion criteria: Irregular sleep-wake-rhythms (e.g. jet-lag, shift-work), diagnosed sleeping disorders, extreme chronotypes (scores of ≤30 or ≥70 in the German version of the Horne-Östberg-Morningness-Eveningness-Questionnaire D-MEQ, pregnancy or lactation, diseases of inner organs or the hematopoietic system (current or within the last five years), use of medication such as hormone preparations (excl. birth control pills), immunosuppressants, antidepressants and blood thinners (current or within the last year)).  Collection was performed at eight specified time points (8.00h, 11.00h, 14.00h, 17.00h, 20.00h, 23.00h, 02.00h, 05.00h) over the course of an entire day. Donors refrained from sleeping, intake of alcohol and other drugs for a minimum of 24h prior to the collection of the first sample as well as on the entire day of sample collection, but otherwise pursued regular every-day activities. Donors self-collected blood samples via fingerprick, with 28G SafetyLancets (MyLife, Ningbo Medsun Medical Co., Zhenhai, Ningbo, China, Ref. 7100031) and untreated “neutral” Minivettes (Sarstedt, Nürmbrecht, Germany, Cat. No. 17.2111.100) to ensure collection of homogenous samples volumes of 100 µl.

extract_protocol:
Total RNA was extracted using the “Preserved Blood RNA Purification Kit I (for use with Tempus Blood RNA tubes)” (Norgen, Thorold, Canada, Cat. No. 43400) according to a modified version of the manufacturer’s instructions in which the amount of Tempus Blood RNA Tube Diluent was downscaled to a sample volume of 100 µl blood and 200 µl Tempus™ RNA Blood stabilization solution. The RNA was finally eluted in a volume of 30 µl Elution Solution and residual genomic DNA was removed by treatment with the TURBO DNAse free kit (Thermo Fisher Scientific, Massachussets, USA, Cat. No. AM1907).
Library preparation including rRNA removal was performed applying the Stranded total RNA with RiboZero Plus protocol (Illumina, California, USA, Cat. No.: 20037135).
ssRNA-seq (stranded RNA-seq)

treatment_protocol: Blood samples were immediately added to 200 µl Tempus™ RNA Blood stabilization solution (Thermo Fisher Scientific, Massachussets, USA, Cat. No. 4342792) and stored frozen until further processing

value: whole blood

tag: sampling time

tag: participant

value: H

tag: Sex

value: Male

tag: age


title: CTCF_10:1_320nM_ACF_75min_biolrep2_techrep3

value: ACF

value: Long

value: plus ATP

tag: histone


title: Blood, ParticipantJ, 05.00h

tag: tissue

value: J

value: Female


title: Blood, ParticipantI, 05.00h

value: I


title: Mel_178953_PBL

description: GEX

value: melanoma

value: PBL

value: Primary cells

value: Sorted CD45+


title: SNF2hWTAB, mESC, -m, biorep1

tag: snf2h remodeling turnover conditions

tag: snf2h remodeling atp/adp conditions

tag: mnase digestion temperature

tag: mnase digestion duration

value: 60 min

value: Unmethylated


title: Organoids_1-14_AS-Pre

description: 10x Genomics

tag: biospy origin

value: Epithelial organoids

tag: seurat id

value: Endometrium

tag: treatment stage

value: AS-Pre


title: Blood, ParticipantG, 05.00h

value: whole blood

value: G


title: Mel_198_PBL

description: GEX

tag: condition

tag: cell line

tag: cell type

tag: genotype

value: Wild Type


title: Blood, ParticipantF, 05.00h

tag: sampling time

value: F


title: Blood, ParticipantE, 05.00h

tag: participant

value: E


title: SNF2hWTAB, mESC, +m, biorep1, techrep1

value: dna ratio:N/A

tag: ecogii methylation

value: EcoGII Methylated


title: Mel_198_TIL

description: GEX

value: TIL


title: SNF2hKO, mESC, -m, biorep2


title: CTCF_10:1_320nM_ACF_75min_biolrep1_techrep3

tag: remodeler

value: ACF

tag: remodeler concentration

tag: remodeling turnover_conditions

value: stoichiometric

tag: remodeling time

value: Long

tag: remodeling atp/adp_conditions

value: plus ATP

value: dna ratio:10:1 ratio

tag: sample type

value: in vitro (plasmid insert)


title: CTCF_10:1_320nM_ACF_15min_biolrep2_techrep3

value: Standard

tag: histone


title: tonsil tissue-SE-GEX

description: GEX

source_name: tonsil from Tonsilitis patients

value: Tonsilitis

tag: tissue

value: tonsil

value: Primary cells

value: Sorted CD4 Tconv and Tregs


title: SNF2hKO, mESC, -m, biorep1

tag: snf2h remodeling turnover conditions

tag: snf2h remodeling atp/adp conditions

tag: mnase digestion temperature

tag: mnase digestion duration

value: 60 min

value: Unmethylated


title: CTCF_10:1_320nM_ACF_15min_biolrep1_techrep3


title: tonsil tissue-RC-GEX

description: GEX

tag: condition

tag: cell line

tag: cell type

value: Wild Type


title: Blood, ParticipantD, 05.00h

value: whole blood

tag: sampling time

tag: participant

value: D

tag: Sex

value: Male

tag: age


title: Blood, ParticipantC, 05.00h

value: C

value: Female


title: CTCF_10:1_2uM_ACF_75min_biolrep2_techrep3

tag: remodeler

value: ACF

tag: remodeler concentration

value: 2 uM

tag: remodeling turnover_conditions

value: single-turnover

value: Long

tag: ecogii methylation

value: EcoGII Methylated


title: SNF2hKO, mESC, +m, biorep2, techrep1

tag: histone

value: dna ratio:N/A


title: SNF2hKO, mESC, +m, biorep1, techrep1


title: tonsil tissue-JA-GEX

description: GEX

value: Tonsilitis

tag: tissue

value: tonsil

tag: genotype


title: CTCF_10:1_2uM_ACF_75min_biolrep1_techrep3

tag: remodeling time

tag: remodeling atp/adp_conditions

value: plus ATP

value: dna ratio:10:1 ratio

tag: sample type

value: in vitro (plasmid insert)


title: SNF2hWTAB, mESC, +m, biorep2, techrep1

tag: snf2h remodeling turnover conditions

tag: snf2h remodeling atp/adp conditions

tag: mnase digestion temperature

tag: mnase digestion duration

value: 60 min


title: Blood, ParticipantA, 05.00h

value: whole blood

tag: sampling time

tag: participant

value: A


title: Blood, ParticipantB, 05.00h

value: B

tag: Sex

value: Male

tag: age


title: tonsil tissue-JA-CITEseq

description: Cell hashing

tag: condition

tag: cell line

value: Primary cells

tag: cell type

value: Sorted CD4 Tconv and Tregs

value: Wild Type


title: Blood, ParticipantI, 02.00h

value: I

value: Female


title: Methylated_array_15:1_techrep2

tag: remodeler

tag: remodeler concentration

tag: remodeling turnover_conditions

value: unremodeled

tag: histone

value: dna ratio:15:1 ratio

tag: ecogii methylation

value: EcoGII Methylated


title: CTCF_10:1_2uM_ACF_15min_biolrep2_techrep3

value: ACF

value: 2 uM

value: single-turnover

tag: remodeling time

value: Standard

tag: remodeling atp/adp_conditions

tag: sample type


title: tonsil tissue-KD-GEX

description: GEX

value: Tonsilitis

tag: tissue

value: tonsil

tag: genotype


title: Blood, ParticipantJ, 02.00h

value: whole blood

tag: sampling time

value: J


title: tonsil tissue-TS-GEX

description: GEX


title: CTCF_10:1_2uM_ACF_15min_biolrep1_techrep3

value: plus ATP

value: dna ratio:10:1 ratio

value: in vitro (plasmid insert)


title: tonsil tissue-TS-CITEseq

description: Cell hashing

value: Primary cells

value: Sorted CD4 Tconv and Tregs

value: Wild Type


title: Blood, ParticipantH, 02.00h

tag: participant

value: H

value: Male


title: Human Tregs, scrambled ctrl, rep5

data_processing:
Read alignment with STAR
R package DESeq2 (1.40.1) was used for downstream bulk RNA-seq analysis.
The batch effects between donors were corrected by ComBat-seq (v3.36.0)
Genes were filtered as not expressed if their read count less than 10. Differential gene analysis was done by DESeq function in DESeq2 (1.40.1).
Log2 fold changes were added into the analysis by lfcShrink function in DESeq2
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Cord blood PBMC

extract_protocol:
CRISPR edited Tregs and scrambled controls were double sorted (purity >99.5%) directly into individual wells of a 96-well plate containing 2μl lysis buffer (0.2% Triton X-100 with RNase inhibitor at 2Uμl −1). The plate was spun down at 2,000 xg for 2min and reverse transcription was then performed.
Sequencing libraries were prepared from 1ng cDNA using the Nextera XT DNA Library Prep kit (Illumina FC-131-1096), following the manufacturer’s instructions. cDNA Libraries were quantified by the KAPA library quantification kit (KAPA KK4854) and size (peak at ~400bp) was verified on a TapeStation1000.

value: Cord blood PBMC

value: Regulatory T cells

tag: treatment

value: TCR stimulation


title: Human Tregs, scrambled ctrl, rep6


title: CTCF_DNA_9uM_SNF2h_75min_techrep2

value: 9 uM

value: single-turnover

value: Long

value: dna ratio:N/A

value: EcoGII Methylated


title: Methylated_array_10:1_techrep2

value: unremodeled


title: Blood, ParticipantE, 02.00h

value: whole blood

value: E

tag: Sex

value: Female

tag: age


title: Human Tregs, scrambled ctrl, rep4

tag: cell line

value: Primary cells


title: CTCF_DNA_9uM_SNF2h_15min_techrep2

value: Standard

value: plus ATP

value: in vitro (plasmid insert)


title: Human Tregs, scrambled ctrl, rep3

tag: cell type

value: Wild Type


title: Blood, ParticipantD, 02.00h

value: D

value: Male


title: CTCF_DNA_2uM_ACF_15min_techrep2

tag: remodeler

value: ACF

value: 2 uM


title: Blood, ParticipantC, 02.00h

value: C


title: Blood, ParticipantG, 02.00h

value: G


title: Human Tregs, scrambled ctrl, rep1

value: Cord blood PBMC

value: Regulatory T cells

value: TCR stimulation


title: Human Tregs, scrambled ctrl, rep2


title: Blood, ParticipantB, 02.00h

value: whole blood

value: B


title: CTCF_15:1_9uM_SNF2h_75min_biolrep2_techrep2

tag: remodeler concentration

value: 9 uM

value: single-turnover

value: Long

value: dna ratio:15:1 ratio

value: EcoGII Methylated


title: CTCF_15:1_9uM_SNF2h_75min_biolrep1_techrep2

tag: remodeling turnover_conditions

value: plus ATP

value: in vitro (plasmid insert)


title: Blood, ParticipantA, 02.00h

value: A

value: Male


title: Blood, ParticipantF, 02.00h

value: F

value: Female


title: Human Tregs, BATF KO, rep6

value: Primary cells

value: BATF KO


title: CTCF_DNA_2uM_ACF_75min_techrep2

value: ACF

value: 2 uM

tag: histone

value: dna ratio:N/A


title: Blood, ParticipantJ, 23.00h

value: whole blood

value: J


title: BRAF resistant WM9 melanoma cells

type: RNA

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Arrays were scanned on GS300 scanner (Thermo Fisher Scientific) with AGCC Scan Control Software.

data_processing:
.CEL files were summarized using RMA function in the R package oligo with background correction and quantile normalization. Gene IDs were mapped using the Chip-annotation package clariomdhumantranscriptcluster.db and differential expression analysis was performed with limma, using the formula ~treatment + cell_line . The cutoffs for the new signatures (BRAF and “extended”) were FC > 1.5, and  adj-p < 0.1
Clariom_D_Human.r1.pgf
Clariom_D_Human.na36.hg38.transcript.csv

label: biotin

source_name: WM9 melanoma cell line

label_protocol: Standard Affymetrix protocol

growth_protocol: All melanoma cell lines and patient-derived primary melanoma cells were maintained in Roswell Park Memorial Institute (RPMI) medium (Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (Thermo Fisher Scientific). Five different BRAF resistant (BR) melanoma cell lines were established from the parental (P) cells (A375, M121224, M160915, UACC903  and WM9) by continuous culturing in Dabrafenib for a period of 4 weeks, with weekly multistep increases in concentration from 0.5 to 3uM.

extract_protocol: RNA was extracted using Direct-zol RNA MiniPrep kit (Zymo Research) coupled with DNase treatment. RNA quality was verified by Bioanalyzer (Agilent Technologies).

treatment_protocol: Five different BRAF resistant (BR) melanoma cell lines (A375, M121224, M160915, UACC903  and WM9) were cultured in Dabrafenib for a period of 4 weeks, with weekly multistep increases in concentration from 0.5 to 3uM. Drug-containing media was replnished every 48-72h

tag: phenotype

value: BR


title: Parental WM9 melanoma cells

value: P


title: Parental UACC903 melanoma cells

source_name: UACC903 melanoma cell line


title: CTCF_15:1_9uM_SNF2h_15min_techrep2

source_name: CTCF site 1 from Mus Musculus amplified, gibson cloned, isolated, and histone assembled

value: 9 uM

value: single-turnover

tag: remodeling time

value: Standard

value: dna ratio:15:1 ratio

tag: ecogii methylation


title: Human Tregs, BATF KO, rep5

value: Cord blood PBMC

value: Regulatory T cells

value: TCR stimulation


title: Parental M160915 melanoma cells

source_name: M160915 melanoma cell line


title: CTCF_15:1_320nM_SNF2h_75min_biolrep2_techrep2

value: stoichiometric

value: Long

tag: remodeling atp/adp_conditions

value: plus ATP

value: EcoGII Methylated

tag: sample type

value: in vitro (plasmid insert)


title: BRAF resistant M121224 melanoma cells

source_name: M121224 melanoma cell line


title: Parental M121224 melanoma cells


title: BRAF resistant A375 melanoma cells

source_name: A375 melanoma cell line


title: BRAF resistant M160915 melanoma cells


title: Blood, ParticipantI, 23.00h

tag: tissue

value: I

value: Female


title: Human Tregs, BATF KO, rep4

value: Primary cells

tag: genotype

value: BATF KO


title: Blood, ParticipantH, 23.00h

value: whole blood

tag: sampling time

tag: participant

value: H

value: Male


title: Blood, ParticipantG, 23.00h

value: G

tag: Sex


title: CTCF_15:1_320nM_SNF2h_15min_biolrep2_techrep2

value: Standard

value: dna ratio:15:1 ratio


title: CTCF_15:1_320nM_SNF2h_75min_biolrep1_techrep2


title: BRAF resistant UACC903 melanoma cells

value: BR


title: Human Tregs, BATF KO, rep2

value: Cord blood PBMC

value: Regulatory T cells

tag: treatment

value: TCR stimulation


title: Human Tregs, BATF KO, rep3

tag: cell line


title: CTCF_15:1_320nM_SNF2h_15min_biolrep1_techrep2

value: stoichiometric

value: plus ATP


title: Blood, ParticipantF, 23.00h

value: F

tag: age


title: WM9_LacZ_DMSO

hyb_protocol: Affymetrix protocol

data_processing: .CEL files were summarized using RMA function in the R package oligo with background correction and quantile normalization. Gene IDs were mapped using the Chip-annotation package clariomdhumantranscriptcluster.db and differential expression analysis was performed with limma, using the formula ~treatment + cell_line . The cutoffs for the new signatures (BRAF and “extended”) were FC > 1.5, and  adj-p < 0.1

source_name: WM9 melanoma cell line; LacZ + DMSO

label_protocol: Affymetrix protocol

growth_protocol: Human melanoma A375, M14 and WM9 cell lines were cultured in RPMI (RPMI1640 with L-glutamine; Corning) supplemented with 10% fetal bovine serum (FBS; Sigma Aldrich).  For transduction, cells were treated with ARoe or LacZ lentiviruses overnight. Transduced cells were selected using blasticidin.

treatment_protocol: ARoe and LacZ melanoma cells were treated with 500nM Dabrafenib or with a vehicle control (DMSO) 48h prior to RNA extraction.

tag: gender

value: male

tag: group

value: LacZ + DMSO

value: WM9 melanoma cell line


title: WM9_LacZ_Dabrafenib

source_name: WM9 melanoma cell line; LacZ + Dabrafenib

value: LacZ + Dabrafenib


title: Human Tregs, BATF KO, rep1

value: Primary cells

tag: cell type

value: BATF KO


title: Parental A375 melanoma cells

value: P


title: Blood, ParticipantE, 23.00h

value: whole blood

value: E

value: Female


title: Ginkgetin, replicate3,scRNA-Seq

city: Wuhan

first: Chaoyang

address: Jiefang Avenue #1277

institute: Wuhan Union Hospital

description: 10X Genomics

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 deletion 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 files include raw counts for each Sample

source_name: liver tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for scRNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver tissue

value: treated with ginkgetin


title: CTCF_15:1_320nM_ACF_75min_biolrep1_techrep2

tag: remodeler

value: ACF

tag: remodeler concentration

tag: remodeling turnover_conditions

value: Long

tag: histone

value: dna ratio:15:1 ratio

value: EcoGII Methylated

value: in vitro (plasmid insert)


title: CTCF_15:1_320nM_ACF_15min_biolrep2_techrep2

value: stoichiometric

tag: remodeling time

value: Standard

tag: remodeling atp/adp_conditions

value: plus ATP

tag: ecogii methylation


title: WM9_ARoe_DMSO

source_name: WM9 melanoma cell line; AR overexpression + DMSO

value: male

value: AR overexpression + DMSO

value: WM9 melanoma cell line


title: WM9_ARoe_Dabrafenib

source_name: WM9 melanoma cell line; AR overexpression + Dabrafenib

value: AR overexpression + Dabrafenib


title: CTCF_15:1_320nM_ACF_15min_biolrep1_techrep2

tag: sample type


title: M14_LacZ_DMSO

source_name: M14 melanoma cell line; LacZ + DMSO

value: LacZ + DMSO

value: M14 melanoma cell line


title: Ginkgetin, replicate1,scRNA-Seq

description: 10X Genomics

tag: tissue


title: Control, replicate3,scRNA-Seq

description: 10X Genomics

value: treated with vehicle


title: Blood, ParticipantB, 23.00h

value: whole blood

tag: sampling time

tag: participant

value: B

value: Male


title: Blood, ParticipantC, 23.00h

value: C

tag: Sex

value: Female


title: CTCF_15:1_2uM_ACF_75min_biolrep1_techrep2

value: ACF

value: 2 uM

value: single-turnover

value: Long

value: dna ratio:15:1 ratio

value: EcoGII Methylated


title: CTCF_15:1_320nM_ACF_75min_biolrep2_techrep2

value: stoichiometric

value: plus ATP

value: in vitro (plasmid insert)


title: Control, replicate2,scRNA-Seq

description: 10X Genomics

value: liver tissue

tag: treatment


title: Blood, ParticipantD, 23.00h

value: D

tag: age


title: Blood, ParticipantI, 20.00h

value: I


title: CTCF_15:1_2uM_ACF_75min_biolrep2_techrep2


title: M14_LacZ_Dabrafenib

source_name: M14 melanoma cell line; LacZ + Dabrafenib

tag: gender

value: male

value: LacZ + Dabrafenib

tag: cell line

value: M14 melanoma cell line


title: M14_ARoe_DMSO

source_name: M14 melanoma cell line; AR overexpression + DMSO

tag: group

value: AR overexpression + DMSO


title: Blood, ParticipantJ, 20.00h

source_name: whole blood

value: whole blood

value: J

value: Female


title: Control, replicate1,scRNA-Seq

description: 10X Genomics

value: treated with vehicle


title: LSK, FLT3-ITD/ITD Llgl1+/+ Cre-, Rep2

city: Hannover

first: Tina

middle: M.

last: Schnoeder

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

description: alternative name for the analysis: 236_ITD_b1

data_processing:
Batch effect was corrected using the FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre- samples (= sample271.fq.gz; sample236.fq.gz; AS-311282-LR-41637_R1.fastq.gz; AS-311280-LR-41637_R1.fastq.gz)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39
Trimmed sequence reads were aligned to the UCSC mm10 genome using STAR v2.7.10a
Read count extraction was performed using featureCounts v2.0.1
Normalization and differential gene expression analysis were performed using the DESeq2 R package
Assembly: mm10
Supplementary files format and content: abundance data in tab-delimited matrix table (.txt) and Excel formats

source_name: BM

growth_protocol:
Cells were obtained from isolated BM cells sorted for LSK (Lin- Sca-1+ cKit+) cells from FLT3-ITD/ITD; Llgl1-/-; Mx1-Cre+,  FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre- and FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre+ animals (FLT3-ITD animals from gifted from Prof. Benjamin L. Ebert (Harvard Medical School, Boston, MA, USA) conferring to the Lee et al., 2007 animal model; Mx1-Cre-recombinase was obtained from Jackson Laboratories (Strain 03556); Llgl1-flox/flox animals are described in Klezovitch et al., 2004)
Samples were processed at different timepoints (TP) TP1: sample271.fq.gz; sample236.fq.gz; sample270.fq.gz; sample273.fq.gz; sample274.fq.gz  and TP2: AS-311281-LR-41637_R1.fastq.gz; AS-311276-LR-41636_R1.fastq.gz; AS-311278-LR-41636_R1.fastq.gz; AS-311282-LR-41637_R1.fastq.gz; AS-311280-LR-41637_R1.fastq.gz

extract_protocol:
RNA isolation was perfomed using Arcturus PicoPuroe RNA Isolation Kit (Thermo Fisher Scienficif) or TRIzol (Thermo Fisher Scientific) according to the manufacturer's instruction.
RNA libraries for RNA-seq were prepared for TP1 using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's instruction, assessed for size and quantified using the 2100 Bioanalyzer (Agilent Technologies) and Kapa Library Quantification Kit (Illumina) prior to sequencing on the Illumina NextSeq500 platform (75bp single end) and TP2 using SmarTer Ultra Low Input RNA v4 (Takara Bio) and NEBNext ChIP-Seq Library Prep Kit for Illumina (New England Biolabs) following manufacturer's instruction, prior to sequencing on the Illumina HiSeq2000 platform (51bp single end).

treatment_protocol: Mice were injected two times i.p.  with poly(I):poly(C) (pIpC) at 4 weeks of age to induce the Mx1-Cre-recombinase

value: BM

tag: cell type

value: LSK

tag: genotype

value: FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre-

value: pIpC


title: CTCF_15:1_2uM_ACF_15min_biolrep2_techrep2

tag: remodeler

value: ACF

tag: remodeler concentration

value: 2 uM

tag: remodeling turnover_conditions

value: single-turnover

value: Standard

value: plus ATP

value: dna ratio:15:1 ratio

value: EcoGII Methylated


title: A375_LacZ_DMSO

source_name: A375 melanoma cell line; LacZ + DMSO

value: female

value: LacZ + DMSO

value: A375 melanoma cell line


title: Ginkgetin, replicate2,scRNA-Seq

description: 10X Genomics

value: liver tissue

value: treated with ginkgetin


title: 72 hours post EBV lytic reactivation, Replicate 2 [S1]

city: Kolkata

first: Samaresh

last: Malik

state: West Bengal

address: Street-358, Action Area-1, Newtown

department: Institute of Health Sciences

country: India

institute: Presidency University

data_processing:
The filtered in reads are aligned to human genome (hg19) using two-step alignment method. Reads were aligned using STAR (v2.7.10) and Bowtie2 (v 2.5.0) using default parameters. Both Alignment data are merged using Picard (v2.18.2.1).
Using the encode gene annotations for human genome (hg19), aligned reads were counted for each gene. Using DESeq2 package from R, study for differential expression analysis was performed between control and treated samples.
Transcripts were classified as upregulated or downregulated based on their log2 fold change (log2FC), considering a significance level of p<0.05.
Assembly: hg19
Supplementary files format and content: Excel sheets containing DESeq2 output

extract_protocol:
RNA was extracted using the PureZOL™ RNA Isolation Reagent (Bio-Rad, USA).
A total of 5µg of RNA that passed quality control (QC) was utilized for library preparation employing the standard mRNA sample prep kit.

tag: time

value: 72 Hours

value: TPA/NaBu


title: M14_ARoe_Dabrafenib

source_name: M14 melanoma cell line; AR overexpression + Dabrafenib

value: male

value: AR overexpression + Dabrafenib

value: M14 melanoma cell line


title: CTCF_15:1_2uM_ACF_15min_biolrep1_techrep2

value: ACF

tag: remodeling time

tag: remodeling atp/adp_conditions

tag: histone

tag: ecogii methylation

value: in vitro (plasmid insert)


title: Blood, ParticipantH, 20.00h

tag: tissue

value: whole blood

tag: sampling time

tag: participant

value: H

value: Male


title: LSK, FLT3-ITD/ITD Llgl1+/+ Cre-, Rep1

description: alternative name for the analysis: 271_ITD_b1

value: BM

value: LSK

value: FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre-

tag: treatment

value: pIpC


title: 48 hours post EBV lytic reactivation, Replicate 2 [S1]

value: 48 Hours


title: CTCF_10:1_9uM_SNF2h_75min_biolrep2_techrep2

value: 9 uM

value: single-turnover

value: Long

value: plus ATP

value: dna ratio:10:1 ratio

value: EcoGII Methylated

tag: sample type


title: Blood, ParticipantG, 20.00h

value: G

tag: Sex

tag: age


title: LSK, FLT3-ITD/ITD Llgl1+/+ Mx1+, Rep3

description: alternative name for the analysis: 274_ITD_Cre_b1

tag: cell type

value: FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre+


title: Untreated, Control, Replicate 2 [S1]

value: 0 Hour

value: Untreated


title: A375_LacZ_Dabrafenib

source_name: A375 melanoma cell line; LacZ + Dabrafenib

tag: gender

value: female

tag: group

value: LacZ + Dabrafenib

tag: cell line

value: A375 melanoma cell line


title: CTCF_10:1_9uM_SNF2h_75min_biolrep1_techrep2

source_name: CTCF site 1 from Mus Musculus amplified, gibson cloned, isolated, and histone assembled

tag: remodeler

tag: remodeler concentration

tag: remodeling turnover_conditions

value: dna ratio:15:1 ratio

value: in vitro (plasmid insert)


title: A375_ARoe_Dabrafenib

source_name: A375 melanoma cell line; AR overexpression + Dabrafenib

value: AR overexpression + Dabrafenib


title: Blood, ParticipantF, 20.00h

value: whole blood

value: F

value: Female


title: A375_ARoe_DMSO

source_name: A375 melanoma cell line; AR overexpression + DMSO

value: AR overexpression + DMSO


title: Blood, ParticipantE, 20.00h

value: E


title: 48 hours post EBV lytic reactivation, Replicate 1 [A2]

tag: time

value: 48 Hours

value: TPA/NaBu


title: LSK, FLT3-ITD/ITD Llgl1+/+ Mx1+, Rep1

description: alternative name for the analysis: 270_ITD_Cre_b1

value: BM

value: LSK

tag: genotype

value: pIpC


title: 72 hours post EBV lytic reactivation, Replicate 1 [A3]

value: 72 Hours


title: LSK, FLT3-ITD/ITD Llgl1+/+ Mx1+, Rep2

description: alternative name for the analysis: 273_ITD_Cre_b1

value: FLT3-ITD/ITD; Llgl1+/+; Mx1-Cre+


title: Blood, ParticipantC, 20.00h

value: C


title: Blood, ParticipantD, 20.00h

value: D

value: Male


title: CTCF_10:1_320nM_SNF2h_75min_biolrep2_techrep2

value: stoichiometric

tag: remodeling time

value: Long

tag: remodeling atp/adp_conditions

value: plus ATP

tag: histone

value: dna ratio:10:1 ratio

tag: ecogii methylation

value: EcoGII Methylated

value: in vitro (plasmid insert)


title: Untreated, Control, Replicate 1 [A1]

value: 0 Hour

tag: treatment

value: Untreated


title: CTCF_10:1_320nM_SNF2h_75min_biolrep1_techrep2

tag: sample type


title: D0_4_RPF

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

institute: NIEHS

data_processing:
Base calling was done with the Illumina software bcl2fastq v2.20
Optical duplicates were removed using clumpify from the bbtools suite
Adapters were trimmed using bbduk from the bbtools suite
rRNA was removed using bbduk
Reads were filtered to within 20-50nt length (for RNA-Seq) or 26-34nt length (for RFP) using bbduk.
Reads were mapped using bbmap from the bbtools suite in ‘slow’ mode.
The differential translational engagement was determined with Xtail using read counts of RNA-seq and RFP libraries from D0 and D6 samples as input.
Assembly: mm10 assembly annotated with GENCODE vM23 genes
Supplementary files format and content: Table with differential translational efficiency between D0 and D6.
Library strategy: Ribo-seq

molecule: other

growth_protocol: Mouse embryonal carcinoma P19 cells (ATCC) were maintained in Dulbecco's modified Eagle's medium with 4,500 mg/L of glucose supplemented with 100 units/mL penicillin/streptomycin (Life Technologies) and 10% fetal bovine serum (FBS, Gemini Bio-Products).

extract_protocol:
Cell lysates from each sample were split to generate the RPF and RNA-seq libraries. Total RNA from the cell lysates used for the RNA-seq libraries preparation was extracted using Qiazol.
To generate the RPF libraries, the lysates were digested with Mnase. The lysates were run on a polyacrylamide-Urea gel, and fragments 20-40 nucleotides long were purified. The NEBnext library preparation kit for small RNAs was used to generate libraries from the purified RPFs fragments. Illumina RNA-seq libraries were generated from the total RNA extracted from the cell lysates.
Libraries were sequenced on a High Output Flow Cell by a NextSeq 500 sequencer (Illumina), utilizing a 51 bp single-end protocol.

treatment_protocol: To induce neuronal differentiation, 3x105 cells were seeded in poly-L-lysine-coated 6-well plates in the presence TaKaRa NDiff® 227 Medium and 500 nM retinoic acid. Media was changed daily up to 6 days after induction.

value: Embryonal carcinoma

value: WT

value: Undifferentiated


title: Blood, ParticipantB, 20.00h

tag: tissue

value: whole blood

tag: sampling time

tag: participant

value: B

tag: Sex


title: CTCF_10:1_320nM_SNF2h_15min_biolrep2_techrep2

value: Standard


title: NGS98965_OSC_siARMI_HQK

description: small RNAs from OSC cells with siArmitage KD

data_processing:
Reads have been prepared by first clipping of the 3' adaptor sequence (AGATCGGAAGAGCACACGTCT) and then trimming 4nt from the 5' and the 3' end to remove random nucleotides contained in the adaptors.
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: table with counts for each sequenced small-RNA in all of the libraries

source_name: OSCs

growth_protocol:
25˚C, 12h dark/light, ovary dissection into 1x PBS on ice, snap frozen
OSC culture according to Niki et al., PNAS, 2006

extract_protocol:
Libraries were prepared by ligation of 3' and 5' adaptors containing 4 random nucleotides at the ends to reduce ligation biases followed by reverse transcription and amplification by PCR.
Argonaute-bound sRNAs were isolated according to Grentzinger et al. (2020)

value: OSCs

value: siArmitage


title: NGS97373_OSC_siGFP_HQK

description: small RNAs from OSC cells with siGFP (control) KD

value: siGFP


title: Blood, ParticipantA, 20.00h

value: A

value: Male

tag: age


title: CTCF_10:1_320nM_SNF2h_15min_biolrep1_techrep2

value: stoichiometric

value: plus ATP


title: CTCF_10:1_9uM_SNF2h_15min_techrep2

value: 9 uM

value: single-turnover

value: dna ratio:10:1 ratio

value: EcoGII Methylated


title: D6_4_RPF

tag: cell line

tag: cell type

value: Embryonal carcinoma

value: Neuronal differentiation


title: D6_3_RPF

value: WT


title: D0_3_RPF

value: Undifferentiated


title: zucGD_SKD_pA_ee1_r2

description: total RNA (polyA selected) from traffic jam-Gal4 zucchini KD biological rep2

data_processing:
reads were prepared by removal of the adaptor sequences and base-clipping to keep nucleotides 6-50
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using STAR (2.7.10b) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster genome using STAR (2.7.10b)
reads mapping to rRNA, tRNA, mitoRNA were excluded
gene expression was quantified using Salmon (1.5.1) on Flybase r6.40 transcripts with transoposon sequences added and normalization by the GeTMM method implemented in edgeR (3.34)
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: gene expression table showing GeTMM expression values

source_name: embryo

value: embryo

value: 0-1 hour old

value: w/+;tj-GAL4/+;zucGD/+ parents


title: CTCF_10:1_320nM_ACF_75min_biolrep2_techrep2

data_processing:
Demultiplexing subreads BAM files with lima (v2.6.0)
Generating circular concensus sequences (CCS) using ccs
Aligning subreads to nonanucleosomal molecule reference
Assembly: mm10
Supplementary files format and content: *_full.pickle: Python pickle files containing IPD measurements for each base in the forward and reverse strands per CCS read
Library strategy: SAMOSA

tag: remodeler

value: ACF

tag: remodeler concentration

value: Long

value: in vitro (plasmid insert)


title: Blood, ParticipantJ, 17.00h

value: whole blood

value: J

value: Female


title: D6_2_RPF


title: Blood, ParticipantA, 23.00h

value: A

value: Male


title: Blood, ParticipantI, 17.00h

value: I


title: D6_1_RPF


title: D0_2_RPF


title: CTCF_10:1_320nM_ACF_15min_biolrep2_techrep2

tag: remodeling turnover_conditions

value: stoichiometric

value: Standard

value: plus ATP

value: dna ratio:10:1 ratio

value: EcoGII Methylated


title: vretGD_SKD_pA_ee1_r2

description: total RNA (polyA selected) from traffic jam-Gal4 vreteno KD biological rep2

value: embryo

tag: genotype

value: w/+;tj-GAL4/+;vretGD/+ parents


title: Blood, ParticipantH, 17.00h

value: H


title: vretGD_SKD_pA_ee1_r1

description: total RNA (polyA selected) from traffic jam-Gal4 vreteno KD biological rep1

value: 0-1 hour old


title: CTCF_10:1_320nM_ACF_15min_biolrep1_techrep2

value: ACF

tag: remodeling time


title: Blood, ParticipantE, 17.00h

value: E


title: zucGD_SKD_pA_ov_r1

description: total RNA (polyA selected) from traffic jam-Gal4 zucchini KD biological rep1

source_name: ovary

value: ovary

value: 4-6 days old


title: Blood, ParticipantF, 17.00h

value: whole blood

value: F

value: Female


title: CTCF_10:1_2uM_ACF_75min_biolrep2_techrep2

value: 2 uM

value: single-turnover

value: Long

tag: remodeling atp/adp_conditions

value: in vitro (plasmid insert)


title: Blood, ParticipantG, 17.00h

value: G

value: Male


title: arr2GD_SKD_pA_ee1_r2

description: total RNA (polyA selected) from traffic jam-Gal4 control KD (arr2) biological rep2

value: embryo

value: w/+;tj-GAL4/+;arr2GD/+ parents


title: D6_4_RNA

value: Embryonal carcinoma

value: WT

value: Neuronal differentiation


title: D0_1_RPF

value: Undifferentiated


title: arr2GD_SKD_pA_ee1_r1

description: total RNA (polyA selected) from traffic jam-Gal4 control KD (arr2) biological rep1

value: 0-1 hour old


title: D6_3_RNA


title: D0_3_RNA


title: Blood, ParticipantC, 17.00h

value: C


title: zucGD_SKD_pA_ov_r2

value: ovary

value: 4-6 days old


title: CTCF_10:1_2uM_ACF_75min_biolrep1_techrep2

value: ACF

value: plus ATP

tag: histone

value: dna ratio:10:1 ratio

value: EcoGII Methylated


title: CTCF_10:1_2uM_ACF_15min_biolrep1_techrep2

value: 2 uM

value: single-turnover

value: Standard

tag: ecogii methylation

value: in vitro (plasmid insert)


title: CTCF_10:1_2uM_ACF_15min_biolrep2_techrep2


title: vretGD_SKD_pA_ov_r2


title: Blood, ParticipantB, 17.00h

value: whole blood

value: B

value: Male


title: Methylated_array_15:1_techrep1

value: unremodeled

value: dna ratio:15:1 ratio


title: CTCF_10:1_320nM_ACF_75min_biolrep1_techrep2

value: stoichiometric

value: Long


title: D6_2_RNA

value: Embryonal carcinoma

value: WT

tag: treatment

value: Neuronal differentiation


title: zucGD_SKD_pA_ee1_r1

value: embryo

value: 0-1 hour old

value: w/+;tj-GAL4/+;zucGD/+ parents


title: Blood, ParticipantA, 17.00h

value: A


title: D6_1_RNA


title: arr2GD_SKD_pA_ov_r2

value: ovary

value: 4-6 days old


title: vretGD_SKD_pA_ov_r1


title: Blood, ParticipantD, 17.00h

value: D


title: D0_4_RNA

value: Undifferentiated


title: CTCF_DNA_9uM_SNF2h_75min_techrep1

description: Nonanucleosome DNA in a plasmid was purified by Gigaprep, isolated via restriction enzyme sites, and purified with Sephacryl S1000 super fine gel filtration.

value: 9 uM

value: single-turnover

value: plus ATP

value: dna ratio:N/A

value: EcoGII Methylated

tag: sample type

value: in vitro (plasmid insert)


title: D0_2_RNA

value: Embryonal carcinoma


title: Blood, ParticipantJ, 14.00h

tag: tissue

value: whole blood

value: J

value: Female


title: Blood, ParticipantI, 14.00h

tag: sampling time

value: I


title: CTCF_DNA_9uM_SNF2h_15min_techrep1

value: Standard


title: D0_1_RNA

value: WT


title: Blood, ParticipantG, 14.00h

tag: participant

value: G

value: Male


title: nows.28

city: Boston

first: Camron

middle: D

last: Bryant

state: MA

address: 140 The Fenway

department: Department of Pharmaceutical Sciences - Center for Drug Discovery

institute: Northeastern University

data_processing:
Reads were trimmed for quality using Trimmomatic
Reads were aligned to the mm10 mouse reference genome using STAR
featureCounts program was used to cout reads mapping to the exon feature
Assembly: mm10
Supplementary files format and content: text file including reads from each sample

source_name: Nucleus accumbens (brain)

extract_protocol:
RNA was extracted using Trizol (Qiagen), ethanol precipitation, filtering columns (Qiagen), and elution with sterile, double deionized water
poly-A selection

value: Nucleus accumbens (brain)

tag: Sex

tag: agent

value: Saline


title: CTCF_DNA_2uM_ACF_75min_techrep1

value: ACF

value: 2 uM

value: Long


title: Methylated_array_10:1_techrep1

value: unremodeled

value: dna ratio:10:1 ratio


title: arr2GD_SKD_pA_ov_r1

extract_protocol:
RNA was extracted using Trizol
Libraries were prepared using a NEBNext Ultra Directional library prep kit (NEB) or NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

value: ovary

tag: cell line

value: 4-6 days old


title: nows.26


title: Blood, ParticipantH, 14.00h

value: whole blood

value: H

tag: age


title: nows.25

value: Morphine


title: nows.24

value: Female


title: CTCF_DNA_2uM_ACF_15min_techrep1

extract_protocol:
CTCF site 1 was purified using a GigaPrep kit (Qiagen), restriction enzyme digested, and purified by size exclusion chromatography. Chromatin was assembled using salt gradient dialysis
Library preparation included DNA damage repair, end repair, blunt-end SMRTbell® ligation, Exonuclease treatment, and Ampure PB cleanup according to manufacturer’s instruction. Library quality was assessed with Agilent Bioanalyzer High Sensitivity DNA kit or Agilent Tapestation D5000 Assay.
PacBio SMRTbell® library preparation

tag: remodeler

value: single-turnover

value: Standard

value: plus ATP

value: dna ratio:N/A

value: EcoGII Methylated

value: in vitro (plasmid insert)


title: Blood, ParticipantE, 14.00h

value: E


title: CTCF_15:1_9uM_SNF2h_75min_biolrep1_techrep1

tag: remodeler concentration

value: 9 uM

value: dna ratio:15:1 ratio


title: pool_C_Single_Cell

city: Ottawa

first: Duncan

middle: J.

last: Stewart

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: 10x Genomics

data_processing:
Cellranger (v3.0.2) was used to identify 10X barcodes associated with lung cells and to count UMIs and genes using a custom reference transcriptome comprising the mm10 transcriptome plus the human HBEGF diptheria toxin receptor sequence.
A total of 48,347 cells were identified - mean reads per cell: 8,550; median UMIs per cell: 1,560; median genes per cell: 845.
MULTI-seq barcode sequence libraries were processed using the deMULTIplex R package to identify the samples barcode(s) associated with each cell barcode.
Cells with a high proportion (>30%) of mitochondrial transcripts  and those with low complexity (<200 detected genes) were removed from the analysis, and an additional round of doublet detection was performed to remove doublets that may have been missed during demultiplexing. A total of 21,665 cells were used for downstream analyses.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Filtered feature-barcode matrices in HDF5 format
Supplementary files format and content: Meta data exported from Seurat object for (a) all cells analysed, and (b) the endothelial cell subset of the dataset, with identity of endothelial sub-clusters. Metadata annotation includes MULTI-seq barcode annotation for each cell. CSV format.

source_name: Dissociated Lung

extract_protocol:
Animals were anaesthetized with ketamine (100 mg/kg) and xylazine (10 mg/kg) (i.p.) and given 10 mU/g heparin sodium (i.p.) (LEO Pharma Inc., Thornhill, ON, Canada). The inferior vena cava was exposed surgically and the animals were bled and then 25 U/mL heparin in 10 mLs of sterile 0.9% saline was flushed through lungs via pulmonary artery until they were cleared of all evidence of red blood cells. Lungs were rinsed in PBS, cut into smaller pieces and placed into gentleMACS C tubes TM (Miltenyi Biotech, Bergisch Gladbach, Germany) containing 2.5 mLs DPBS to which 2.5 mLs of digestion enzyme mix were added. This mix included 2500 U Collagenase I, 30 U Neutral Protease/Dispase (Wothington Biochem., Lakewood, NJ, USA), and 500 U Deoxyribonuclease (Sigma-Aldrich, Oakville, ON, Canada) in 1x Dulbecco’s PBS (Thermofischer Scientific, Burlington, ON, Canada), and was made fresh for each experiment and kept on ice. GentleMACS C tubes were placed into a temperature regulated gentleMACS Octo Dissociator TM (Miltenyi Biotech, Bergisch Gladbach, Germany) and underwent mechanical dissociation according to a custom mouse lung program at 37 ºC for 30 minutes. Dissociated tissue was passed through a pre-wetted 75 μm filter (Thermofischer Scientific, Burlington, ON, Canada), re-suspended with additional 5 mLs PBS and treated with 200 μLs 0.5M EDTA (Thermofischer Scientific, Burlington, ON, Canada). Pelleted cells were re-suspended in RBC-lysis buffer (Thermofischer Scientific, Burlington, ON, Canada) for 3 minutes at room temperature. Final cell pellet was re-suspended in 5 mLs PBS and cell counts and viability were performed using a Countess TM automated counter (Thermofischer Scientific, Burlington, ON, Canada).
Barcoding of individual biological samples was performed as described by McGinnis et.al.(2019). Dissociated lung cells (0.5e+6 cells per sample) were suspended in 150 μLs solution containing a 1:1 molar ratio (200nM) of anchor and barcode oligonucleotide containing a unique sequence for each of the 12 samples to be processed. Samples were incubated for 13 minutes at room temperature with gentle mixing every 3-5 minutes. Next, a co-anchor (200nM) was added to stabilize the barcodes within the cell membrane and incubated for additional 5 minutes. Cells were washed twice in PBS,  cell counts were measured using a Countess(TM) automated counter (Thermofischer Scientific, Burlington, ON, Canada), and viability was measured based on the ratio of cells staining with trypan blue (Thermofischer Scientific, Burlington, ON, Canada). An equal number of cells from each 12 barcodes was pooled and 1000 cells/μL were further processed through the 10x-Genomics pipeline. Only samples with viability > 85% were used. Three libraries were constructed from the twelve pooled samples using the 10X Genomics Single Cell 3’ RNA sequencing kit v3.

value: Dissociated Lung

tag: treatment/time point

value: pooled; control, treatment 3, 5 and 7 days


title: pool_B_Barcode

description: 10x Genomics


title: pool_B_Single_Cell

description: 10x Genomics


title: CTCF_15:1_9uM_SNF2h_15min_techrep1

tag: remodeling turnover_conditions


title: CTCF_15:1_9uM_SNF2h_75min_biolrep2_techrep1

tag: remodeling time

value: Long


title: pool_A_Barcode

description: 10x Genomics


title: nows.23

value: Nucleus accumbens (brain)


title: CTCF_15:1_320nM_SNF2h_75min_biolrep2_techrep1

value: stoichiometric

tag: remodeling atp/adp_conditions


title: nows.27


title: pool_C_Barcode

description: 10x Genomics


title: Blood, ParticipantF, 14.00h

value: whole blood

value: F


title: Blood, ParticipantC, 14.00h

value: C

value: Female


title: Blood, ParticipantB, 14.00h

value: B

value: Male


title: BM_MIC-LUC_110

city: Montreal

first: Heather

last: Melichar

state: Quebec

address: 5415 Boulevard de l'Assomption

department: Immunology-Oncology Unit

institute: Maisonneuve-Rosemont Hospital Research Center

data_processing:
Performed single-end RNA-seq using the Illumina NextSeq500 platform for 75 cycles
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88) using STAR version 2.5.1b.
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression , either in TPM or FPKM values, for these stranded RNA libraries.
Assembly: GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88)
Supplementary files format and content: excel files with FPKM values

source_name: Bone Marrow

extract_protocol:
Cells were sorted directly into TRIZOL reagent. Total RNA was extracted and used to generate transcriptome libraries.
Library was prepared using the KAPA mRNA Hyper Prep (poly-A Capture)

value: Bone Marrow

tag: genotype

value: WT

value: MIC-LUC


title: Blood, ParticipantA, 14.00h

value: A


title: pool_A_Single_Cell

description: 10x Genomics


title: CTCF_15:1_320nM_SNF2h_15min_biolrep2_techrep1

value: Standard

value: plus ATP

tag: histone

tag: ecogii methylation

value: EcoGII Methylated

value: in vitro (plasmid insert)


title: BM_MIC-LUC_106

tag: treatment


title: BM_MIC-LUC_102

tag: tissue


title: nows.18

value: Morphine


title: nows.19

value: Nucleus accumbens (brain)

value: Saline


title: BM_CG2-LUC_84


title: Blood, ParticipantH, 11.00h

value: whole blood

tag: sampling time

value: H


title: Blood, ParticipantI, 11.00h

tag: participant

value: I


title: BM_CG2-LUC_98


title: nows.17

tag: Sex


title: CTCF_15:1_320nM_ACF_15min_biolrep2_techrep1

value: ACF

value: stoichiometric

value: dna ratio:15:1 ratio

tag: sample type


title: CTCF_15:1_320nM_ACF_75min_biolrep1_techrep1

value: Long


title: CTCF_15:1_320nM_ACF_75min_biolrep2_techrep1


title: nows.22

value: Male

tag: agent


title: BM_CG2-LUC_71

value: Bone Marrow

value: WT


title: CTCF_15:1_320nM_SNF2h_75min_biolrep1_techrep1


title: BM_CG2-LUC_75


title: nows.16


title: nows.21


title: Blood, ParticipantG, 11.00h

value: G

tag: age


title: CTCF_15:1_320nM_ACF_15min_biolrep1_techrep1

tag: remodeler

value: Standard

value: plus ATP


title: Blood, ParticipantF, 11.00h

value: F

value: Female


title: BM_CG2-RAS_70


title: Blood, ParticipantJ, 11.00h

value: J


title: CTCF_15:1_320nM_SNF2h_15min_biolrep1_techrep1

tag: remodeler concentration

value: EcoGII Methylated

value: in vitro (plasmid insert)


title: Blood, ParticipantE, 11.00h

value: whole blood

value: E


title: nows.20

value: Nucleus accumbens (brain)

value: Morphine


title: CTCF_15:1_2uM_ACF_75min_biolrep1_techrep1

value: ACF

value: 2 uM

value: single-turnover

value: dna ratio:15:1 ratio


title: nows.14

value: Male

value: Saline


title: Blood, ParticipantD, 14.00h

value: D


title: BM_CG2-RAS_79

value: Bone Marrow

value: WT


title: BM_CG2-RAS_77


title: nows.13


title: Blood, ParticipantC, 11.00h

value: C

value: Female


title: CTCF_15:1_2uM_ACF_15min_biolrep2_techrep1

value: Standard

value: plus ATP

value: EcoGII Methylated


title: nows.12


title: Blood, ParticipantB, 11.00h

value: whole blood

value: B


title: FL_CG2-RAS_89

source_name: Fetal Liver

value: Fetal Liver


title: nows.11

value: Nucleus accumbens (brain)

value: Morphine


title: FL_CG2-RAS_88


title: nows.10


title: nows.15


title: Blood, ParticipantA, 11.00h

value: A


title: CTCF_15:1_2uM_ACF_75min_biolrep2_techrep1

value: ACF

value: 2 uM

value: single-turnover

value: Long

value: dna ratio:15:1 ratio

value: in vitro (plasmid insert)


title: Blood, ParticipantJ, 08.00h

value: J


title: CTCF_10:1_9uM_SNF2h_15min_techrep1

value: 9 uM

value: dna ratio:10:1 ratio


title: CTCF_10:1_9uM_SNF2h_75min_biolrep1_techrep1

value: plus ATP


title: nows.9

value: Male


title: Blood, ParticipantD, 11.00h

value: whole blood

value: D


title: FL_CG2-MGI_91

value: Fetal Liver

value: WT


title: FL_CG2-RAS_52


title: CTCF_10:1_9uM_SNF2h_75min_biolrep2_techrep1

value: EcoGII Methylated


title: nows.8

value: Nucleus accumbens (brain)

value: Saline


title: Blood, ParticipantH, 08.00h

value: H


title: Blood, ParticipantI, 08.00h

value: I

value: Female


title: nows.7

value: Morphine


title: FL_CG2-MGI_53


title: CTCF_15:1_2uM_ACF_15min_biolrep1_techrep1

value: ACF

value: 2 uM

value: single-turnover

value: Standard

value: dna ratio:15:1 ratio

value: in vitro (plasmid insert)


title: CTCF_10:1_320nM_SNF2h_75min_biolrep1_techrep1

value: stoichiometric

value: Long

value: plus ATP

value: dna ratio:10:1 ratio


title: CTCF_10:1_320nM_SNF2h_15min_biolrep2_techrep1

value: EcoGII Methylated


title: FL-CG2-MGI_46

value: Fetal Liver

value: WT


title: Blood, ParticipantG, 08.00h

value: whole blood

value: G

value: Male


title: nows.6

value: Nucleus accumbens (brain)

value: Female

value: Morphine


title: Blood, ParticipantF, 08.00h

value: F


title: nows.5

value: Saline


title: FL_MIC-RAS_90

value: MIC-RAS


title: CTCF_10:1_320nM_SNF2h_15min_biolrep1_techrep1

value: Standard

value: in vitro (plasmid insert)


title: FL_MIC-RAS_51


title: CTCF_10:1_320nM_ACF_75min_biolrep2_techrep1

value: ACF

value: stoichiometric

value: Long


title: nows.4


title: FL_MIC-RAS_42-43


title: Blood, ParticipantC, 08.00h

value: C


title: CTCF_10:1_320nM_SNF2h_75min_biolrep2_techrep1

value: plus ATP

value: dna ratio:10:1 ratio

value: EcoGII Methylated


title: CTCF_10:1_320nM_ACF_75min_biolrep1_techrep1


title: nows.3


title: nows.2


title: Blood, ParticipantD, 08.00h

value: whole blood

value: D


title: FL_MIC-MGI_92

value: Fetal Liver

value: WT

value: MIC-MGI


title: CTCF_10:1_320nM_ACF_15min_biolrep2_techrep1


title: Blood, ParticipantB, 08.00h

value: B

value: Male


title: nows.1

value: Nucleus accumbens (brain)

value: Saline


title: FL_MIC-MGI_54


title: CTCF_10:1_320nM_ACF_15min_biolrep1_techrep1

value: Standard

value: in vitro (plasmid insert)


title: 1703801_mouse_bone marrow_HMOX-1_KO

city: Tarrytown

first: Wei Keat

last: Lim

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron

description:
10x 5prime NextGEM v2
10x Chromium

data_processing:
CellRanger (v.6.1.1, 10X Genomics) with GRCh38 reference was performed on the processed cells to compute gene expression levels and to generate analysis-ready data.
We checked the quality of the data (Number of cells, mean reads per cell, median genes per cell, median UMI counts per cell, etc.) to filter out artifacts, empty droplets, and multiplets. In each sample, cells with the total number of molecules detected within a cell higher than 30,000 and lower than 1,000 were filtered out.
Then Python module Scanpy (v1.7.1) was used to normalize the data. The normalization was done as following: 1. Transformation of total counts so each cell sums to 10,000. 2. Log1p of the transformed counts. 3.Unit Scaling of the gene expression counts across all cells to ensure a mean of zero and a max value of 10.
Lastly, R Seurat package (v4.3.0.1) was utilized to generate UMAP plots and to run clustering. In each cluster, we identified markers based on differentially expressed genes, and cell types were given to the clusters based on the top markers. Cell type percentages were calculated by [the number of cells for the cell type x 100 / the total number of cells in the condition].
Assembly: GRCh38 & GRCm38
Supplementary files format and content: Tab-separated matrix files

source_name: bone marrow

extract_protocol:
The generation of knock-in mice encoding human SIRPa, human M-CSF, human CD47, and Rag2/IL-2Rg deletions were created by Velocigene technology. Mice were maintained on a sulfa diet (LabDiet, St. Louis, MO) in a MPF facility, and were intra-bred for about 5-10 generations. Mouse and human CD45+ cell fractions were collected from the tissues of human HSC-engrafted HMOX-1+/+ and HMOX-1-/- hSIRPa/hM-CSF/hCD47/Rag2-/-/IL-2Ryc-/- mice. Cells were isolated by positive magnetic enrichment using either mouse CD45 or human CD45 microbeads (Miltenyi).
Library was performed according to the manufacter's insturction (10x 5prime NextGEM v2)

value: bone marrow

tag: cell type

value: mCd45+ cells


title: CTCF_10:1_2uM_ACF_75min_biolrep2_techrep1

value: ACF

value: 2 uM

tag: remodeling turnover_conditions

value: single-turnover

value: Long


title: THP-1-derived macrophages, sgKEAP1, 8h, rep3

city: Washington

first: Xiaolong

last: Cheng

state: DC

address: 7144 13th Place NW

institute: Children's National

data_processing:
All bulk RNA-seq reads were trimmed using Trimmomatic software with the following parameters “ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36” (Version 0.36) and were further quality-filtered using fastq_quality_trimmer command in FASTX Toolkit (Version 0.0.13) with the minimum quality score 20 and minimum percent of 80% bases that has a quality score larger than this cutoff value.
The high-quality reads were mapped to the mm10 genome by HISAT2, a fast and sensitive spliced alignment program for mapping RNA-seq reads, with -dta paramenter; PCR duplicate reads were removed using Picard tools
The expression levels of genes and repeat sequences were independently calculated by StringTie (Version v1.3.4d) with -e -B -G parameters using Release M18 (GRCm38.p6) gene annotations downloaded from GENCODE data portal and annotated repeats (RepeatMasker) downloaded from the UCSC genome browser, respectively.
Differential expression analysis of genes in different samples was performed by DESeq2 using the reads count matrix produced from a python script “prepDE.py” provided in StringTie website (http://ccb.jhu.edu/software/stringtie/).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: THP-1 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme, NR612-02) according to the manufacturer’s protocol.

treatment_protocol: THP-1 cells were treated with PMA (50 ng/mL) for 48 h, then refreshed the medium or stimulated by LPS (50 ng/mL) plus IFN-γ (50 ng/mL) for 24 h.

tag: cell line

value: macrophage

value: KEAP1 knockout

value: LPS and IFN-γ stimulated for 8 h


title: FL_CG2_3

description:
DSP601
DSP601_genes_FPKM.annotated.xls
FL_CG2_48h_S8

data_processing:
Performed paired-end RNA-seq using the Illumina NextSeq500 platform for 150 cycles
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88) using STAR version 2.5.1b.
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression , either in TPM or FPKM values, for these stranded RNA libraries.
Assembly: GRCm38 (or mm10, gene annotation from Gencode version M13, based on Ensembl 88)
Supplementary files format and content: excel files with FPKM values

value: Fetal Liver

value: WT


title: CTCF_10:1_2uM_ACF_75min_biolrep1_techrep1

city: San Francisco

first: Megan

address: 1700 Owens

institute: Gladstone Institutes

description: Nonanucleosome DNA in a plasmid was purified by Gigaprep, isolated via restriction enzyme sites, and purified with Sephacryl S1000 super fine gel filtration. Histone octamers (Luger et al., 1999) were assembled onto purified DNA via salt gradient dialysis.

tag: remodeling time

tag: remodeling atp/adp_conditions

value: plus ATP

value: dna ratio:10:1 ratio

value: EcoGII Methylated


title: THP-1-derived macrophages, sgKEAP1, 8h, rep2

tag: genotype


title: FL_CG2_4

description:
DSP601
DSP601_genes_FPKM.annotated.xls
FL_CG2_Lin-Kit_S9


title: 1703797_mouse_spleen_HMOX-1_KO

description:
10x 5prime NextGEM v2
10x Chromium

source_name: spleen

value: spleen


title: 1703800_mouse_bone marrow_HMOX-1_WT

description:
10x 5prime NextGEM v2
10x Chromium


title: Blood, ParticipantE, 08.00h

data_processing:
FastQC v0.11.9 was used to analyze the quality score of the RNASeq sequencing reads.
Poor-quality and adapter bases were trimmed from the sequencing reads by the Trim Galore pipeline (v0.6.7) [--min_trimmed_reads = 10000 i.e. Minimum number of trimmed reads below which samples are removed from further processing]
Filtered high quality paired end reads were aligned against the reference genome (GRCh38) using STAR method v2.6.1d (--min_mapped_reads : 5 ; )
Gene counts were estimated with featureCounts v1.5.2 (default parameters) (--featurecounts_feature_type : 'exon' attribute within the GTF file)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw read counts for genes in each sample

source_name: whole blood

value: whole blood

value: E

value: Female


title: CTCF_10:1_2uM_ACF_15min_biolrep2_techrep1

value: Standard

tag: histone

tag: ecogii methylation

value: in vitro (plasmid insert)


title: FL_CG2_2

description:
DSP601
DSP601_genes_FPKM.annotated.xls
48h_CG2_n2_Lin-Kit_FL_S11

tag: tissue

tag: treatment


title: Blood, ParticipantA, 08.00h

tag: sampling time

tag: participant

value: A

value: Male