title: single cell RNA seq of human nasal epithelial tissue 4

description: single-cell RNA-seq


title: Pcgf4-/-Pcgf2fl_Input_UNT_rep2

status: Public on May 23 2022

type: SRA

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description: input for CDK8 ChIPs in Pcgf4-/-Pcgf2 flfl

library_source: genomic

data_processing:
For cChIP-seq, Bowtie2 was used to align paired-end reads to the concatenated mouse and spike-in genome sequences (mm10+dm6 for native cChIP-seq for histone modifications; mm10+hg19 for cross-linked cChIP-seq) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads were discarded, and PCR duplicates were removed with Sambamba.
For visualization of cChIP-seq, the data were internally calibrated using dm6 or hg19 spike-in as described previously (Fursova et al. 2019). Briefly, uniquely aligned mm10 reads were randomly subsampled based on the total number of spike-in (dm6 or hg19) reads in each sample. To account for variations in the spike-in cell mixing, we used the ratio of spike-in/mouse total read counts in the corresponding Input samples to correct the subsampling factors. After normalisation, read coverages across genomic regions of interest were compared for individual biological replicates using multiBamSummary and plotCorrelation from deepTools. For each experimental condition, biological replicates correlated well (Pearson correlation coefficient > 0.9) and were merged for downstream analysis.
Genome_build: mm10; dm6; hg19
Supplementary_files_format_and_content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

molecule: genomic DNA

organism:
Homo sapiens
Mus musculus

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control,Pcgf4-/-Pcgf2 fl/fl, Input

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. HEK293T celles were grown in EC-10 medium (DMEM supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.4 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For cross-linked ChIP, 50x10^6 ES cells were fixed for 45min with with 2mM DSG (ThermoFisher scientific) in PBS and 12.5 min with 1% formaldehyde (methanol-free, ThermoFisher scientific). Reactions were quenched by the addition of glycine to a final concentration of 125 µM and the fixed cells were washed in ice-cold 1xPBS and snap frozen in liquid nitrogen. 50x10^6 HEK293T cells were fixed as above, snap frozen in 2x106 aliquots, and stored at -80°C until further use. For calibrated ChIPseq, 2x10^6 HEK293T cells were resuspended in 1ml ice-cold lysis buffer (50mM HEPES pH 7.9, 140mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) and added to 50x10^6 fixed ESCs, resuspended in 9ml lysis buffer. The cell suspension was incubated for 10 min at 4°C. The released nuclei were then washed (10mM Tris-HCl pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) for 10 min at 4°C. The chromatin pellet was resuspended in 1mL of ice-cold sonication buffer (10mM Tris-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 25 min using a BioRuptor Pico sonicator (Diagenode), shearing genomic DNA to produce fragments between 300bp and 1kb. Following sonication, Triton X-100 was added to a final concentration of 1%. Two hundred and fifty µg chromatin diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1mM EDTA, 20mM Tris-HCl (pH 8.0), 150mM NaCl) was used per IP. Three reactions were set up per condition to allow for maximal DNA recovery suitable for library preparation. Chromatin was precleared with protein A Dynabeads blocked with 0.2 mg/ml BSA and 50 µg/ml yeast tRNA and incubated with the respective antibodies overnight at 4°C. Antibody-bound chromatin was purified using blocked protein A Dynabeads for 3 hours at 4°C. ChIP washes were performed as described in Farcas et al 2012. ChIP DNA was eluted in ChIP elution buffer (1% SDS, 100mM NaHCO3) and reversed cross-linked overnight at 65°C with 200mM NaCl and RNase A (Sigma). The reverse cross-linked samples were treated with 20 μg/ml Proteinase K and purified using ChIP DNA Clean and Concentrator kit (Zymo research). The three reactions per condition were pooled at this stage. For each sample, corresponding Input DNA was also reverse cross-linked and purified. The efficiency of the ChIP experiments was confirmed by quantitative PCR. Prior to library preparation, 5-10ng ChIP material was diluted to 50ul in TLE buffer (10mM Tris-HCl pH8.0, 0.1mM EDTA) and sonicated with Bioruptor Pico sonicator for 17 min (30 sec on/off). The antibodies used for ChIPseq experiments were rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories, 2.5μl), rabbit monoclonal anti-RING1B (5694, Cell signaling, 3 μl), rabbit polyclonal anti-PCGF2 (sc-10744, Santa Cruz, 3ul), rabbit monoclonal anti-T7-Tag (D9E1X) (13246, Cell signaling, 3ul). The antibodies used for ChIP-qPCR for TetO targeting experiments were rabbit polyclonal anti-FS2 (produced in house, 59, 3ul), polyclonal anti-MED12 (A300-774A, Bethyl laboratories, 3ul), polyclonal anti-MED1 (A300-793A, Bethyl laboratories, 3ul), polyclonal anti-CCNC (A301-989A, Bethyl laboratories, 3ul). For native ChIP, 50x10^6 ESCs were mixed with 20x10^6 SG4 Drosophila cells and washed with 1x PBS prior to chromatin isolation. Nuclei were released in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40), washed and resuspended in 1ml ice cold digestion buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 1x cOmplete protease inhibitor cocktail (Roche)). Chromatin was digested with 200mM MNase (ThermoFisher scientific) for 5 min at 37°C and the reaction was stopped by the addition of 4mM EDTA pH 8.0. The samples were centrifuged at 1500g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300μl of nucleosome release buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 0.2mM EDTA, 1x protease inhibitor cocktail (Roche)) at 4°C for 1 h, passed five times through a 27G needle using a 1mL syringe, and spun at 1500g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. Digestion to mostly mononucleosomes was confirmed on a 1.5% agarose gel. The prepared native chromatin was aliquot, snap frozen in liquid nitrogen and stored at -80°C until further use. ChIPs were performed as described in Fursova et al 2019, using 5ul of H3K27me3 antibody prepared in-house.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate or quadruplicate on Illumina NextSeq 500 platform.

treatment_protocol: Med13/13lfl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 96 hours. Pcgf4-/-/Pcgf2fl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 72 hours. For RA differentiation, ESCs were treated with 1µM retinoic acid (Sigma-Aldrich) for 48h.

tag: cell line

value: Pcgf4-/-Pcgf2 flfl

tag: strain

tag: treatment

value: untreated

tag: treatment time

tag: additional treatment

tag: additional treatment time

tag: replicate

tag: spike-in reference organism

value: Homo sapiens

tag: spike-in cell line

tag: type of chip

value: cross-linked

tag: ChIP

tag: antibody

value: rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories)


title: Med1313lfl-MED14-T7_RA_TAM_Input_rep2

description: input for T7 ChIPs in RA-treated Med13:Med13lflfl Med14-T7

organism: Mus musculus

source_name: Mouse embryonic stem cells treated with retinoic acid for 48h, Med13/13l flfl with endogenously tagged Med14-T7, tamoxifen treated, T7 ChIPseq

value: Med13;Med13l flfl Med14-T7

value: tamoxifen

value: retinoic acid

value: Input


title: Med1313lfl-MED14-T7_RA_TAM_Input_rep1


title: single cell RNA seq of human nasal epithelial tissue 3

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

country: USA

institute: Case Western Reserve University

description: single-cell RNA-seq

library_source: transcriptomic

data_processing:
Single cell RNA-seq matrices were generated using Cell Ranger 3.1.0
Genome_build: hg19 genome v1.0
Supplementary_files_format_and_content: 10X genomics CellRanger output: UMI count expression values for each gene (rows) in each cell (columns)

molecule: polyA RNA

organism: Homo sapiens

source_name: human nasal epithelial tissue

growth_protocol: Primary human airway epithelial cells from nasal brushings were expanded at 37 °C on irradiated 3T3 murine fibroblast feeder cells with growth media (F-12/DMEM [3:1] supplemented with 5% heat-inactivated FBS, 25 ng/mL hydrocortisone, 1 mg/mL insulin, 12.5 ng/mL EGF, 8.6 ng/mL cholera toxin, and 24 μg/mL Adenine) with ROCK inhibitor (RI, Y27632 at 16 μg/mL), antibiotics (50 µg/mL gentamicin, 0.25 µg/mL amphotericin B, 100 U/ml Penicillin, and 100 μg /ml Streptomycin), and cryopreserved upon initial passaging (P1). For ALI culture NHE cell stocks (P1) were expanded on collagen-coated culture dishes in AW#2 medium (F12/DMEM [1:1], supplemented with 2% Ultroser G, penicillin/streptomycin, gentamicin, and fungizone). Harvested cells were seeded (P2) onto collagen-coated 12 mm inserts (Costar 3801) in AW#2 with RI at 4 × 105 cells per insert. Media was replaced with AW #2 without RI 24 hours after seeding and cultures expanded for 3-4 days until confluent, when apical media was removed for mucociliary differentiation. Basolateral medium was exchanged for fresh AW#2 medium every other day. After six weeks, the ALI cultures were differentiated into polarized epithelia. Primary bronchial epithelial cells were Passage 1 (P1) obtained from the University of North Carolina at Chapel Hill. Cells were grown on collagen-coated plastic in bronchial epithelial growth medium (Lonza). Passage 2 primary HBE cells were used for air-liquid interface (ALI) cultures.

extract_protocol:
A total of 2500–3000 cells were used for scRNA-seq using the 10X Genomics Chromium system.
Single cell libraries were prepared using the Chromium Single Cell 3ʹ Library kit

treatment_protocol: The cultures were first digested with 0.25% trypsin and 1 mM EDTA at 37°C for 5 min, and then further digested to single cells using Accutase at 37°C for 10 min.

tag: disease

value: cystic fibrosis


title: Huh7_shVDAC1 rep1

type: RNA

city: Nantong

first: Yu

last: Zhang

address: Xisi road 20th

country: China

institute: Affiliated hospital of Nantong University

description: Gene expression data from shVDAC1 in Huh7

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Huh7 cells were incubated in Dulbecco’s modified eagle medium containing 10% fetal bovine serum and cultured in a humidified incubator at 37°C and 5% CO2.

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

treatment_protocol: In the KD group, Huh7 cells were infected with lentivirus to knock down VDAC1. In NC group，the normal cell group did not do any processing.

tag: cell type

value: Human hepatoma cell line

tag: genotype/variation

value: VDAC1 knockdown


title: Pcgf4-/-Pcgf2fl_Input_UNT_rep1


title: Huh7_Normal cell rep3

description: Gene expression data from Huh7

source_name: Huh7_Normal cell

value: normal control (NC)


title: Huh7_shVDAC1 rep2


title: Med1313lfl-MED14-T7_RA_TAM_Input_rep3


title: Med1313lfl-MED14-T7_RA_UNT_Input_rep2

description: input for T7 and CDK8 ChIPs in RA-treated Med13:Med13lflfl Med14-T7

source_name: Mouse embryonic stem cells treated with retinoic acid for 48h, Med13/13l flfl with endogenously tagged Med14-T7, untreated control, T7 ChIPseq


title: single cell RNA seq of human nasal epithelial tissue 2

description: single-cell RNA-seq

value: healthy donor


title: Huh7_Normal cell rep2

description: Gene expression data from Huh7


title: Med1313lfl-MED14-T7_RA_UNT_Input_rep1


title: Huh7_shVDAC1 rep3


title: Pcgf4-/-Pcgf2fl_CDK8_TAM_rep2

description: mESC_Pcgf2fl_XChIP_TAM_CDK8_mm10.UniqMapped_downsampled_MERGED_MACS2.bw.bw

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen treated,Pcgf4-/-Pcgf2 fl/fl, CDK8 ChIP-seq


title: Pcgf4-/-Pcgf2fl_CDK8_TAM_rep3


title: single cell RNA seq of human nasal epithelial tissue 1

description: single-cell RNA-seq


title: single cell RNA seq of human bronchial epithelial tissue 2

description: single-cell RNA-seq

source_name: human bronchial epithelial tissue


title: single cell RNA seq of human bronchial epithelial tissue 1

description: single-cell RNA-seq


title: Med1313lfl-MED14-T7_ESC_TAM_Input_rep3

description: input for T7 ChIPs in Med13:Med13lflfl Med14-T7

source_name: Mouse embryonic stem cells, Med13/13l flfl with endogenously tagged Med14-T7, tamoxifen treated, T7 ChIPseq


title: Med1313lfl-MED14-T7_RA_UNT_Input_rep3


title: Med1313lfl-MED14-T7_ESC_TAM_Input_rep2


title: Huh7_Normal cell rep1

description: Gene expression data from Huh7


title: Huh7_Normal cell_rep3

description: Gene expression data from shSMPLD3A in Huh7

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

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2100, Affymetrix).

treatment_protocol: In the KD group, Huh7 cells were infected with lentivirus to knock down SMPDL3A. In NC group，the normal cell group did not do any processing.

value: SMPDL3A knockdown


title: NGS19_K360_Dim_LBA_Hum12_S7

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

country: France

institute: PhyMedExp INSERM U1046

data_processing:
Library strategy: scRNA-Seq
The Cell Ranger (v3.0.2) application (10x Genomics) was then used to demultiplex the BCL files into FASTQ files (cellranger mkfastq), to perform alignment (to Cell Ranger human genome references 3.0.0 GRCh38/Ensembl93), filtering, UMI counting and to produce gene—barcode matrices (cellranger count).
Filtered matrix files were used for further scRNAseq analyses with R Bioconductor (3.12) and Seurat (3.2.1).
Filtered matrices containing cell IDs and feature names in each sample were used to build a Seurat object. We performed a quality control by filtering out the cells with less than 200 detected genes, the genes detected in less than 3 cells and the cells exhibiting more than 20% of mitochondrial genes. Gene counts in each sample was normalized separately by default method “LogNormalize” with scale factor 10000 and log-transformation. Two thousands of highly variable features were identified with the “vst” method.
After merge cells from all samples, the contaminated cells were removed based on the expression of specific genes. Four clusters were identified in the remained cell using FindClusters functionand the differentially expressed genes were calculated using FindMarkers function (Seurat package).
Genome_build: GRCh38
Supplementary_files_format_and_content: Text counts table: counts of genes for all cells in each sample
Supplementary_files_format_and_content: Rds R-object: Seurat object containing gene expression and cell metatdata for all cells for each sample
Supplementary_files_format_and_content: Text normalized expression: normalized gene expression for all filtered cells merged from all samples
Supplementary_files_format_and_content: Text metadata table: metadata for all filtered cells merged from all samples.

source_name: Bronchoalveolar lavage fluid (BALF) cells

extract_protocol:
For each sample, approximately 5000 cells were suspended in PBS with 0.04% BSA and loaded into the Chromium Controller, in which they were partitioned, their polyA RNAs captured and barcoded using Chromium Single Cell 3' Gel Bead Kit v2 (10X Genomics).
The cDNA were amplified and libraries compatible with Illumina sequencers were generated using Chromium Single Cell 3' Gel Bead Kit v2 (10X Genomics). The libraries were sequenced on an Illumina NovaSeq sequencer on an SP100 cell flow (read1: 28 cycles; index: 8 cycles; read2: 80 cycles) at a depth of 50 000 reads per cell.

tag: tissue

tag: patient age

tag: patient sex

value: M

tag: patient status

value: COPD

tag: disease state


title: NGS19_K359_Dim_LBA_Hum11_S6

value: Bronchoalveolar lavage fluid (BALF) cells

value: No fumer


title: Pcgf4-/-Pcgf2fl_CDK8_TAM_rep1

tag: cell line

value: Pcgf4-/-Pcgf2 flfl

tag: strain

tag: treatment

tag: treatment time

value: Homo sapiens


title: Med1313lfl-MED14-T7_ESC_TAM_Input_rep1

tag: additional treatment

tag: additional treatment time

tag: replicate

value: cross-linked


title: Huh7_Normal cell_rep1


title: Pcgf4-/-Pcgf2fl_CDK8_UNT_rep1

description: mESC_Pcgf2fl_XChIP_UNT_CDK8_mm10.UniqMapped_downsampled_MERGED_MACS2.bw.bw

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, Pcgf4-/-Pcgf2 fl/fl, CDK8 ChIP-seq

value: untreated

tag: spike-in reference organism

tag: spike-in cell line

tag: type of chip

tag: ChIP

value: rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories)


title: Med1313lfl_TAM_Input_rep3

description: input for CDK8, RING1B, and PCGF2 ChIPs in Med13:Med13lflfl

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen treated, Med13/13l fl/fl Input for ChIP

value: Med13;Med13l flfl

value: tamoxifen

tag: antibody


title: Huh7_shSMPDL3A_rep3

description: Gene expression data from Huh7

tag: cell type

tag: genotype/variation


title: Pcgf4-/-Pcgf2fl_CDK8_UNT_rep3


title: Huh7_Normal cell_rep2


title: Med1313lfl-MED14-T7_ESC_UNT_Input_rep3

source_name: Mouse embryonic stem cells, Med13/13l flfl with endogenously tagged Med14-T7, untreated control, T7 ChIPseq

value: Med13;Med13l flfl Med14-T7

value: Input


title: Med1313lfl-MED14-T7_ESC_UNT_Input_rep2


title: Med1313lfl_TAM_Input_rep2


title: NGS19_J263_Dim_LBA_Hum9_S3

tag: tissue

tag: patient age

tag: patient sex

value: Fumer


title: Huh7_shSMPDL3A_rep1

description: Gene expression data from Huh7

tag: cell line

value: Human hepatoma cell line

value: normal control (NC)


title: Pcgf4-/-Pcgf2fl_CDK8_UNT_rep2

tag: strain


title: Huh7_shSMPDL3A_rep2

description: Gene expression data from Huh7


title: Med1313lfl_TAM_Input_rep1

tag: treatment


title: NGS19_J264_Dim_LBA_Hum10_S4

tag: patient status

value: Healthy no smoker

tag: disease state


title: Med1313lfl-MED14-T7_ESC_UNT_Input_rep1

tag: treatment time

tag: additional treatment

tag: additional treatment time


title: NGS19_J142_Dim_LBA_Hum8_S4

value: M


title: Med1313lfl-MED14-T7_RA_UNT_CDK8_rep3

description: Med13fl_RA_UNT_CDK8_mm10_spikeinnormalised.MERGEDrep13_downsampled.MACS2.bw

source_name: Mouse embryonic stem cells treated with retinoic acid for 48h, Med13/13l flfl with endogenously tagged Med14-T7, untreated control, CDK8 ChIPseq

value: retinoic acid

tag: replicate


title: NGS19_J141_Dim_LBA_Hum7_S3

value: Bronchoalveolar lavage fluid (BALF) cells

value: Healthy smoker


title: Med1313lfl_UNT_Input_rep1

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, Med13/13l fl/fl Input for ChIP

tag: spike-in reference organism

tag: spike-in cell line

tag: type of chip


title: Med1313lfl-MED14-T7_RA_UNT_CDK8_rep2

tag: ChIP

tag: antibody


title: Med1313lfl_UNT_Input_rep3


title: NGS19_I679_Dim_LBA_Hum4_S6

tag: tissue

value: F

value: COPD


title: NGS19_J028_Dim_LBA_Hum5_S10

tag: patient age


title: Med1313lfl-MED14-T7_RA_TAM_T7_rep3

description: Med13fl_RA_TAM_MED14-T7_mm10_readcountnorm_MERGED_MACS2.bw.bw

value: cross-linked

value: rabbit monoclonal anti-T7-Tag (D9E1X) (13246, Cell signaling)


title: NGS19_I415_Dim_LBA_Hum3_S6

tag: patient sex

value: No fumer


title: Med1313lfl-MED14-T7_RA_TAM_T7_rep2

tag: cell line


title: Med1313lfl_TAM_PCGF2_rep2

description: MED1313Lfl_PCGF2_TAM_mm10_spikeinnormalised_MERGED_MACS2.bw

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen treated, Med13/13l fl/fl PCGF2 ChIP-seq

value: Med13;Med13l flfl

tag: strain

value: Homo sapiens

value: rabbit polyclonal anti-PCGF2 (sc-10744, Santa Cruz)


title: 29.copd.wa.ma_NGS19.K366

data_processing:
Sequence alignment with the human genome, sequence counting and quality control were performed using the nf-core/rnaseq pipeline. RNA-seq data were analyzed using R Bioconductor (3.5.1) and DESeq2 package (version 1.26.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: Text gene counts: counts of genes for each sample

source_name: Sorted AFhi CD206+ CD45+ macrophages from BALF

extract_protocol:
For bulk mRNA-sequencing (RNA-seq), CD14+ monocytes were isolated from the blood and AFlo and AFhi CD45+CD206+ cells were FACS-sorted from the BALF of the same patients. Total RNA was extracted and concentrated from the different samples with the RNA Clean & Concentrator 5 (Zymo Research). Possible DNA contaminant were removed with DNAse I. RNA quality and quantity were evaluated using a 2100 bioanalyzer (Agilent) and the Quant-iT™ RiboGreen™ RNA Assay Kit (ThermoFisher). The RNA Integrity Number (RIN) was greater than 7 for all samples.
One hundred nano-grams of RNA was used to generate the libraries using the Truseq stranded mRNA kit (Illumina). These libraries were sequenced on an Illumina Novaseq sequencer on a SP flow cell in single read 100 bp.

tag: cell type

tag: patient group


title: Med1313lfl-MED14-T7_RA_UNT_T7_rep3

description: Med13fl_RA_UNT_MED14-T7_mm10_readcountnorm_MERGED_MACS2.bw.bw

value: Med13;Med13l flfl Med14-T7

tag: treatment

value: untreated


title: 28.copd.wa.mono_NGS19.K365

source_name: Sorted CD14+ monocytes from blood

value: Sorted CD14+ monocytes from blood


title: Med1313lfl_TAM_PCGF2_rep3

value: tamoxifen

tag: treatment time


title: Med1313lfl_UNT_PCGF2_rep3

description: MED1313Lfl_PCGF2_UNT_mm10_spikeinnormalised_MERGED_MACS2.bw

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated contol, Med13/13l fl/fl PCGF2 ChIP-seq

tag: additional treatment


title: Med1313lfl_UNT_Input_rep2

tag: additional treatment time

value: Input


title: Med1313lfl-MED14-T7_RA_UNT_T7_rep1

tag: replicate


title: 30.copd.wa.mreg_NGS19.K367

source_name: Sorted AFlo CD206+ CD45+ macrophages from BALF


title: Med1313lfl_UNT_PCGF2_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, Med13/13l fl/fl PCGF2 ChIP-seq

tag: spike-in reference organism


title: Med1313lfl_UNT_PCGF2_rep1

tag: spike-in cell line


title: Med1313lfl-MED14-T7_RA_UNT_T7_rep2

tag: type of chip


title: Med1313lfll-MED14-T7_RA_UNT_CDK8_rep1

tag: ChIP

value: rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories)


title: Med1313lfl_TAM_RING1B_rep3

description: MED1313Lfl_RING1B_TAM_mm10_spikeinnormalised_MERGED_MACS2.bw

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen treated, Med13/13l fl/fl RING1B ChIP-seq

tag: antibody

value: rabbit monoclonal anti-RING1B (5694, Cell signaling)


title: 24.smoker.wb.mreg_NGS19.K329

value: Sorted AFlo CD206+ CD45+ macrophages from BALF

value: Smoker


title: 25.copd.hp.mono_NGS19.K362


title: Med1313lfl-MED14-T7_RA_TAM_T7_rep1

source_name: Mouse embryonic stem cells treated with retinoic acid for 48h, Med13/13l flfl with endogenously tagged Med14-T7, tamoxifen treated, T7 ChIPseq

value: retinoic acid


title: 27.copd.hp.mreg_NGS19.K364

value: COPD


title: Med1313lfll-MED14-T7_ESC_TAM_T7_rep3

description: Med13fl_ESC_TAM_MED14-T7_mm10_readcountnorm_MERGED_MACS2.bw.bw

value: cross-linked


title: 26.copd.hp.ma_NGS19.K363

value: Sorted AFhi CD206+ CD45+ macrophages from BALF


title: Med1313lfl-MED14-T7_ESC_UNT_T7_rep3

description: Med13fl_ESC_UNT_MED14-T7_mm10_readcountnorm_MERGED_MACS2.bw.bw

value: rabbit monoclonal anti-T7-Tag (D9E1X) (13246, Cell signaling)


title: Med1313lfl-MED14-T7_ESC_TAM_T7_rep2


title: Med1313lfl_TAM_PCGF2_rep1

value: Med13;Med13l flfl


title: Med1313lfl_UNT_RING1B_rep3

description: MED1313Lfl_RING1B_UNT_mm10_spikeinnormalised_MERGED_MACS2.bw

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, Med13/13l fl/fl RING1B ChIP-seq

value: Homo sapiens


title: 23.smoker.wb.ma_NGS19.K328


title: Med1313lfl-MED14-T7_ESC_TAM_T7_rep1


title: Med1313lfl_TAM_RING1B_rep1


title: Med1313lfl-MED14-T7_ESC_UNT_T7_rep2


title: Med1313lfl_UNT_RING1B_rep2


title: 22.smoker.wb.mono_NGS19.K327


title: 20.copd.gm.ma_NGS19.K325


title: Med1313lfl_UNT_RING1B_rep1


title: 19.copd.gm.mono_NGS19.K324


title: TetR-PCGF2_ES_rep3

description:
Atoh8_id4813071_MEL18-TetR_bg.bed_bg_sorted.bw
Atoh8_id4813071_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Col26a1_id4597268_MEL18-TetR_bg.bed_bg_sorted.bw
Col26a1_id4597268_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Dlgap2_id5403564_MEL18-TetR_bg.bed_bg_sorted.bw
Dlgap2_id5403564_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Dlk1_id1352504_MEL18-TetR_bg.bed_bg_sorted.bw
Dlk1_id1352504_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Fli1_id5763606_MEL18-TetR_bg.bed_bg_sorted.bw
Fli1_id5763606_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Gas6_id5401688_MEL18-TetR_bg.bed_bg_sorted.bw
Gas6_id5401688_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Igdcc3_id5844680_MEL18-TetR_bg.bed_bg_sorted.bw
Igdcc3_id5844680_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Kbtbd11_cgi_id5405786_MEL18-TetR_bg.bed_bg_sorted.bw
Kbtbd11_cgi_id5405786_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Kbtbd11_id5405755_MEL18-TetR_bg.bed_bg_sorted.bw
Kbtbd11_id5405755_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Kif26b_id440256_MEL18-TetR_bg.bed_bg_sorted.bw
Kif26b_id440256_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Mn1_id4534474_MEL18-TetR_bg.bed_bg_sorted.bw
Mn1_id4534474_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Rasa3_id5402095_MEL18-TetR_bg.bed_bg_sorted.bw
Rasa3_id5402095_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Samd14_id1023739_MEL18-TetR_bg.bed_bg_sorted.bw
Samd14_id1023739_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Sox1_id5399245_MEL18-TetR_bg.bed_bg_sorted.bw
Sox1_id5399245_MEL18-TetR_scores_bg.bed_bg_sorted.bw
Spry1_id3577811_MEL18-TetR_bg.bed_bg_sorted.bw
Spry1_id3577811_MEL18-TetR_scores_bg.bed_bg_sorted.bw
TetO.1_id5402489_MEL18-TetR_bg.bed_bg_sorted.bw
TetO.1_id5402489_MEL18-TetR_scores_bg.bed_bg_sorted.bw
TetO.2_id5402488_MEL18-TetR_bg.bed_bg_sorted.bw
TetO.2_id5402488_MEL18-TetR_scores_bg.bed_bg_sorted.bw

data_processing:
For CaptureC, paired-end reads were aligned and filtered for HiC artefacts using HiCUP (Wingett S, et al. (2015)) and Bowtie2 (Langmead and Salzberg, 2012) with fragment filter set to 100-800bp. Read counts of reads aligning to captured gene promoters and interaction scores (=significant interactions) were then called  by CHiCAGO (Cairns et al., 2016).
For visualisation of CaptureC data weighted pooled read counts from chicago data files were normalized to total read count aligning to captured gene promoters in the sample and further to the number of promoters in the respective capture experiment. Bigwig files were generated from these normalized read counts.
For comparative boxplot analysis interactions called by chicago (score >= 5) across all samples were aggregated and interactions with a distance of less than 4 DpnII fragments were merged to a single interaction peak. For each interaction peak we then quantified mean normalized read count and chicago score of all overlapping DpnII fragments.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files showing the genome coverage of normalized read counts for each sample and each promoter were generated from chicago data object.

source_name: Mouse embryonic stem cells, CaptureC

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor.

extract_protocol:
CaptureC libraries were prepared as described previously (Hughes et al., Nature Genetics 2014). Briefly, 10 Million mouse ES cells were trypsinized, collected in 50ml falcon tubes in 9.3ml media and crosslinked with 1.25ml 16% formaldehyde for 10min at room temperature. Cells were quenched with 1.5M glycine, washed with PBS and lysed for 20 minutes at 4oC lysis buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40, supplemented with complete proteinase inhibitors) prior to snap freezing in 1ml lysis buffer at -80oC.
Lysates were then thawed on ice, pelleted and resuspended in 650µl 1x DpnII buffer (NEB). Three 1.5ml tubes with 200µl lysate each were treated in parallel with SDS (0.28% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off), quenched with trypsin (1.67% final concentration, 1hr, 37 oC, interval shaking 500rpm, 30sec on/30sec off) and subjected to a 24 hour digestion with 3x10µl DpnII (homemade, 37 oC, interval shaking 500rpm, 30sec on/30sec off). Each chromatin aliquot was independently ligated with 8 µl T4 Ligase (240 U) in a volume of 1440µl (20 hours, 16oC). Following this, the nuclei containing ligated chromatin were pelleted to remove any non-nuclear chromatin, reverse-crosslinked and the ligated DNA was phenol-chloroform purified. The sample was resupended in 300µl water and sonicated 13x (Pico Bioruptor, 30sec on, 30sec off) or until a fragment size of approximately 200bp was reached. Fragments were size selected using AmpureX beads (Beckman Coulter: A63881, selection ratios: 0.85x / 0.4x). 2x 1-5µg of DNA were adaptor ligated and indexed using the NEBNext DNA library Prep Reagent Set (New England Biolabs: E6040S/L) and NEBNext Multiplex Oligos for Illumina Primer sets 1 (New England: E7335S/L) and 2 (New England: E7500S/L). The libraries were amplified 7x using Herculase II Fusion Polymerase kit (Agilent: 600677). Libraries were hybridized in teh following way: Probes were designed using the online tool by the Hughes lab (CapSequm: http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi) to be either 120bp (Sox2) or 70bp long each, two probes for each promoter of interest. The probes were pooled at a 2.9nM each and the samples were multiplexed by mass prior to hybridization. Hybridization was carried out using the Nimblegen SeqCap system (Roche, Nimblegen SeqCap EZ HE-oligo kit A # 06777287001, Nimblegen SeqCap EZ HE-oligo kit B # 06777317001, Nimblegen SeqCap EZ Accessory kit v2 # 07145594001, Nimblegen SeqCap EZ Hybridisation and wash kit # 05634261001) according to Roche protocol for 72 hours followed by a 24 hours hybridization (double Capture). The captured libraries were sequenced on Illumina NextSeq.
CaptureC

treatment_protocol: To induce conditional removal of Med13 and Med13l in MED13/13lfl ESC line or Pcgf2 in Pcgf2fl ESC line, cells were treated with 800nM 4-hydroxytamoxifen (TAM) for 96 hours or 72 hours, respectively.

tag: genotype

tag: treatment agent

tag: treatment time point


title: 21.copd.gm.mreg_NGS19.K326


title: Med1313lfl_TAM_RING1B_rep2

tag: cell line


title: ChIP-Seq PTIP input

city: Nangjing

first: Ming

last: Fang

state: jiangsu

address: 2 Sipailou Road

institute: Southeast University

data_processing:
The clean reads were then subjected to further analysis based on the ChIP-seq pipeline, by the open source STAR, MACS2, BEDTools, and deepTools software suite, built in our lab. In brief, reads were mapped to the D. melanogaster genome (BDGP6, the fruit fly iGenome package, Ensemble build) using STAR (v 2.7.5a) and the peaks calling were performed by using MACS2 (v2.1.4) (parameters “--broad --broad-cutoff 0.1 -f BAMPE -g 1.2e8 -B --keep-dup all” and the bgdcmp function “-m FE”. BEDTools (v 2.29.2) (windowBed module with parameters: -l 50 -r 50) was used for genome arithmetic. The computeMatrix program within deepTools (with parameters: - scale regions -binsize 30, upstream 3000bp, downstream 3000bp) (v 3.4.3) calculates scores per genome region and prepares an intermediate file for plotHeatmap.
Assembly: BDGP6, the fruit fly iGenome package, Ensemble build
Supplementary files format and content: bigWig

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
PTIP ChIP was generated according to standard procedures. (Furlong, 2006. PMID: 17406543 DOI: 10.1038/nprot.2006.383 )
ChIP-Seq libraries were prepared using standard procedures developed by Furlong et al. (PMID: 17406543) with slightly modification.

tag: tissue

value: embryo

value: After egg lay 4-8H


title: AM05_auxin1hr_L3_ArimaHiC_col1007_rep2_JK14

city: New York

first: Ana

middle: Karina

last: Morao

state: New York

address: 29 Washington Place

department: Biology

institute: New York University

data_processing:
Basecalls were performed using CASAVA version 1.8.
Hi-C:  data was mapped to ce10 (WS220) reference genome using default parameters of the Juicer pipeline version 1.5.7 (Durand et al., 2016). For downstream analysis, inter_30.hic outputs from juicer pipeline were converted to h5 file to be used in HiCExplorer (version=3.5.1)(Ramirez et al., 2018; Wolff et al., 2018). Matrices of replicates were combined using hicSumMatrices. Each replicate or each summed matrix were normalized to match the depth of the smallest matrix in comparison using hicNormalize with the option --smallest. The replicate and summed matrices were ICE normalized using hicCorrectMatrix with the following parameters: --correction_method ICE, -t 1.7 5, --skipDiagonal, --chromosomes I II III IV V X.
Assembly: WS220
Supplementary files format and content: Hi-C:  hic matrix files

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C.

extract_protocol:
Hi-C: Crosslinked worms were resuspended in 20 ul of PBS per 50ul of worm pellet then dripped into liquid nitrogen containing mortar. The worms were grounded with pestle until fine powder. Grounded worms were crosslinked again in 2% formaldehyde using the TC buffer as described by the Arima Hi-C kit, which uses two 4-base cutters, DpnII and HinfI. The Arima manufacturer’s protocol was followed.
Hi-C:  Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.

treatment_protocol: Auxin treatment: synchronized L2/L3s were washed three times with M9 and split into two aliquots. Half of the worms were transferred to NGM plates containing 1mM of indole-3-acetic-acid (Fisher 87-51-4) prepared as in (Zhang et al., 2015). The other half were placed in normal NGM plates (no-auxin control) for the indicated time. Worms were then washed one time with M9 and processed accordingly to future application. For ChIP and Hi-C, L2/L3 worms were incubated in 2% formaldehyde for 30 minutes, followed by quenching with glycine, one wash with M9 and two washes with PBS, PMSF and protease inhibitors. For RNA-seq, worms were stored in Trizol.

tag: strain

value: AM05 (top-1::degron::GFP)

tag: developmental stage

value: auxin


title: 18.non_smoker.pk.mreg_NGS19.K323

tag: cell type

tag: patient group


title: ChIP-Seq PTIP

value: PTIP-FLAG

tag: treatment


title: TetR-PCGF2_ES_rep2


title: Med1313lfl_TAM_CDK8_rep3

description: mESC_MED13fl_TAM_CDK8_mm10.UniqMapped_downsampled_MERGED_MACS2.bw.bw

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen treated, Med13/13l fl/fl CDK8 ChIP-seq

value: tamoxifen

tag: treatment time

tag: additional treatment

tag: additional treatment time


title: TetR-PCGF2_ES_rep1

tag: replicate


title: Med1313lfl_TAM_CDK8_rep2

tag: spike-in reference organism

tag: spike-in cell line

tag: type of chip

value: rabbit polyclonal anti-CDK8 (A302-500A, Bethyl laboratories)


title: E.  coli, B strain, untreated, ABBS primer

city: Carlsbad

first: Benjamin

last: Delatte

state: CA

address: 1914 Palomar Oaks Way STE 150

department: Advanced Research

institute: Active Motif

description: dcm-

data_processing:
Raw reads (FastQ files) were aligned to human hg19 or E. coli K12 genomes using Bismark (https://github.com/FelixKrueger/Bismark) following the command line: $ bismark <genome path> -p 4 --parallel 6 -q --pbat -o <output folder> -1 read1.fastq.gz -2 read2.fastq.gz.
PCR duplicates were removed following these arguments: $ deduplicate_bismark -p --output_dir <output folder> -- bam <input bam file>
MAPQ filter of 20 was applied using samtools (https://github.com/samtools/samtools): $ samtools view -h -q 20 <input bam file> -o <output folder bam file>.
Methylated cytosines were extracted with Bismark Methylation Extractor following the following arguments: $ bismark_methylation_extractor --parallel 10 -p --no_overlap --ignore 7 -- ignore_r2 7 --ignore_3prime 5 --ignore_3prime_r2 5 -o <output folder> --report --bedGraph -- zero_based --cutoff 1 --CX --remove_spaces --cytosine_report --genome_folder <genome path> <input bam file>
bam files were sorted and indexed using samtools sort and samtools index
Bigwig coverage files were obtained with deeptools bamcoverage (https://github.com/deeptools/deepTools): $ bamCoverage -b <input bam file> -o <output folder bigwig file> --normalizeUsing RPKM --binSize 5 --numberOfProcessors 16
Genome_build: E. coli K12 or hg19
Supplementary_files_format_and_content: Bigwig (bw) files are RPKM-normalized
Supplementary_files_format_and_content: Methylation bedgraph files contain methylation percentages and coverage information

organism: Escherichia coli

source_name: Bacterial cells

growth_protocol: Escherichia coli K12 cells were acquired from Neb (#E4104), MA and two clones were obtained by streaking an E. coli suspension on a LB agar plate, and further cultured in liquid LB containing no antibiotics, at 37C. Optical density was measured at 600nm every twenty minutes until bacteria reached a plateau phase, then the culture was quickly placed on ice and spun on a Sorvall centrifuge at 7500 RPM / 4C for 10 minutes, then washed twice with ice cold 1x PBS and aliquots were snap frozen in liquid nitrogen and kept at -80C for further genomic DNA extraction.  K562 cells were grown in RPMI-1640 supplemented with L-glutamine, 10% FBS and 1X penicillin G + streptomycin, at 37C / 5% CO2. Cells were then trypsinized and counted with a haemocytometer while viability was assessed with Trypan Blue staining. The culture was quickly placed on ice and spun on a Sorvall centrifuge at 3000 RPM / 4C for 5 minutes, then washed twice with ice cold 1x PBS and aliquots were snap frozen in liquid nitrogen and kept at -80C for further genomic DNA extraction.

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, Germany) following the manufacturer’s protocol.
3μg of E. coli or 10μg of K562 genomic DNA spiked with 1% of unmethylated Lambda DNA was bisulfite-converted with Zymo Lightning kit (Zymo Research, CA) following the manufacturer’s  instructions, then eluted in 2x10μl of Tris-HCl 10mM pH8.0 (of note, desulfonation was performed for 20mins, on column). An additional 15-minute sonication was achieved using PIXUL Multisample sonicator (Active Motif, CA) with the default settings. DNA was heated at 95C for 3 minutes then placed on ice and quantification was done using Nanodrop (Thermo Fisher Scientific, MA) while profiles were measured with RNA TapeStation (Agilent, CA) to ensure for proper sonication. Bacterial non-converted DNA was sonicated for 30 minutes using PIXUL Multisample sonicator with the default settings and DNA was further heated at 95C for 3 minutes and stored at -80C.  Second strand synthesis was performed as follow: 100ng of genomic DNA was diluted in Neb 1x NEBuffer 2, supplemented with 0.25mM dNTPs and 6.5μM (K562 cells) or 0.65μM (E. coli K12 cells) ABBS primers (NNNNNSuperG) or WGBS primers (NNNNNN) in 29 μl, then heated at 94C for 2 minutes and rapidly placed on ice for 3-5 minutes. One microliter of Neb Klenow exo minus (5 units/μl) was added to the reaction that was gradually heated from 4C to 37C at a rate of 0.1C/second. Samples were then incubated for 30 minutes at 37C and purified with 45μl of Ampure XP beads (Beckman Coulter, CA). DNA was eluted in 20μl Tris-HCl 10mM pH8.0 supplemented with 0.05% Tween-20 and quantified with Qubit 2.0 dsDNA HS kit (Thermo Fisher Scientific, MA).  Double stranded library preparation was performed either with Neb NEBNext® UltraTM II DNA Library Prep Kit for Illumina or Active Motif Next Gen DNA Library Kit, following manufacturers’ recommendations, with the exception that libraries amplification was performed using KAPA HiFi HotStart Real-Time Library Amp Kit (Roche, Switzerland). After a final purification using 0.75 volumes of Ampure XP beads, libraries were resuspended in 12μl of Tris-HCl 10mM pH8.0 supplemented with 0.05% Tween-20 and quantified with Qubit 2.0 dsDNA HS kit while profiles were measured with HS dsDNA TapeStation to calculate molarity

treatment_protocol: No cell treatment was applied.

value: Mock

tag: primer used

value: ABBS

tag: library prep kit used

value: NEB


title: TetR-CDK8_ES_rep3

description:
Atoh8_id4813071_CDK8-TetR_bg.bed_bg_sorted.bw
Atoh8_id4813071_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Col26a1_id4597268_CDK8-TetR_bg.bed_bg_sorted.bw
Col26a1_id4597268_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Dlgap2_id5403564_CDK8-TetR_bg.bed_bg_sorted.bw
Dlgap2_id5403564_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Dlk1_id1352504_CDK8-TetR_bg.bed_bg_sorted.bw
Dlk1_id1352504_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Fli1_id5763606_CDK8-TetR_bg.bed_bg_sorted.bw
Fli1_id5763606_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Gas6_id5401688_CDK8-TetR_bg.bed_bg_sorted.bw
Gas6_id5401688_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Igdcc3_id5844680_CDK8-TetR_bg.bed_bg_sorted.bw
Igdcc3_id5844680_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Kbtbd11_cgi_id5405786_CDK8-TetR_bg.bed_bg_sorted.bw
Kbtbd11_cgi_id5405786_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Kbtbd11_id5405755_CDK8-TetR_bg.bed_bg_sorted.bw
Kbtbd11_id5405755_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Kif26b_id440256_CDK8-TetR_bg.bed_bg_sorted.bw
Kif26b_id440256_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Mn1_id4534474_CDK8-TetR_bg.bed_bg_sorted.bw
Mn1_id4534474_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Rasa3_id5402095_CDK8-TetR_bg.bed_bg_sorted.bw
Rasa3_id5402095_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Samd14_id1023739_CDK8-TetR_bg.bed_bg_sorted.bw
Samd14_id1023739_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Sox1_id5399245_CDK8-TetR_bg.bed_bg_sorted.bw
Sox1_id5399245_CDK8-TetR_scores_bg.bed_bg_sorted.bw
Spry1_id3577811_CDK8-TetR_bg.bed_bg_sorted.bw
Spry1_id3577811_CDK8-TetR_scores_bg.bed_bg_sorted.bw
TetO.1_id5402489_CDK8-TetR_bg.bed_bg_sorted.bw
TetO.1_id5402489_CDK8-TetR_scores_bg.bed_bg_sorted.bw
TetO.2_id5402488_CDK8-TetR_bg.bed_bg_sorted.bw
TetO.2_id5402488_CDK8-TetR_scores_bg.bed_bg_sorted.bw

tag: genotype

tag: treatment agent

tag: treatment time point


title: Med1313lfl_TAM_CDK8_rep1

tag: cell line

tag: strain

tag: ChIP

tag: antibody


title: Med1313lfl-MED14-T7_ESC_UNT_T7_rep1

source_name: Mouse embryonic stem cells, Med13/13l flfl with endogenously tagged Med14-T7, untreated control, T7 ChIPseq

value: Med13;Med13l flfl Med14-T7

tag: treatment

value: untreated


title: 17.non_smoker.pk.ma_NGS19.K322

tag: cell type

tag: patient group


title: 16.non_smoker.pk.mono_NGS19.K321

value: Sorted CD14+ monocytes from blood


title: E.  coli, B strain, untreated, WGBS primer

description: dcm-

value: WGBS


title: Med1313lfl_UNT_CDK8_rep3

description: mESC_MED13fl_UNT_CDK8_mm10.UniqMapped_downsampled_MERGED_MACS2.bw.bw

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, Med13/13l fl/fl CDK8 ChIP-seq

tag: treatment time

tag: additional treatment

tag: additional treatment time

value: cross-linked


title: TetR-CDK8_ES_rep2

tag: replicate


title: AM05_auxin1hr_L3_ArimaHiC_col1152_rep1_JK93

tag: developmental stage


title: Med1313lfl_UNT_CDK8_rep2

value: Med13;Med13l flfl

tag: spike-in reference organism

tag: spike-in cell line

tag: type of chip


title: E.  coli, K12 strain, clone 2, bisulfited, ABBS primer (A.M. library prep)

value: Bisulfite

tag: primer used

tag: library prep kit used

value: Active Motif


title: 15.non_smoker.ld.mreg_NGS19.K320

value: Sorted AFlo CD206+ CD45+ macrophages from BALF


title: Med1313lfl_UNT_CDK8_rep1

tag: cell line

value: Homo sapiens


title: TetR-CDK8_ES_rep1

tag: genotype

tag: strain

tag: treatment agent

tag: treatment time point


title: E.  coli, K12 strain, clone 1, bisulfited, ABBS primer (A.M. library prep)

tag: treatment


title: E.  coli, K12 strain, clone 2, bisulfited, ABBS primer


title: 14.non_smoker.ld.ma_NGS19.K319

tag: cell type

value: Sorted AFhi CD206+ CD45+ macrophages from BALF

tag: patient group


title: TetR-GFP_ES_rep3

description:
Atoh8_id4813071_GFP-TetR_bg.bed_bg_sorted.bw
Atoh8_id4813071_GFP-TetR_scores_bg.bed_bg_sorted.bw
Col26a1_id4597268_GFP-TetR_bg.bed_bg_sorted.bw
Col26a1_id4597268_GFP-TetR_scores_bg.bed_bg_sorted.bw
Dlgap2_id5403564_GFP-TetR_bg.bed_bg_sorted.bw
Dlgap2_id5403564_GFP-TetR_scores_bg.bed_bg_sorted.bw
Dlk1_id1352504_GFP-TetR_bg.bed_bg_sorted.bw
Dlk1_id1352504_GFP-TetR_scores_bg.bed_bg_sorted.bw
Fli1_id5763606_GFP-TetR_bg.bed_bg_sorted.bw
Fli1_id5763606_GFP-TetR_scores_bg.bed_bg_sorted.bw
Gas6_id5401688_GFP-TetR_bg.bed_bg_sorted.bw
Gas6_id5401688_GFP-TetR_scores_bg.bed_bg_sorted.bw
Igdcc3_id5844680_GFP-TetR_bg.bed_bg_sorted.bw
Igdcc3_id5844680_GFP-TetR_scores_bg.bed_bg_sorted.bw
Kbtbd11_cgi_id5405786_GFP-TetR_bg.bed_bg_sorted.bw
Kbtbd11_cgi_id5405786_GFP-TetR_scores_bg.bed_bg_sorted.bw
Kbtbd11_id5405755_GFP-TetR_bg.bed_bg_sorted.bw
Kbtbd11_id5405755_GFP-TetR_scores_bg.bed_bg_sorted.bw
Kif26b_id440256_GFP-TetR_bg.bed_bg_sorted.bw
Kif26b_id440256_GFP-TetR_scores_bg.bed_bg_sorted.bw
Mn1_id4534474_GFP-TetR_bg.bed_bg_sorted.bw
Mn1_id4534474_GFP-TetR_scores_bg.bed_bg_sorted.bw
Rasa3_id5402095_GFP-TetR_bg.bed_bg_sorted.bw
Rasa3_id5402095_GFP-TetR_scores_bg.bed_bg_sorted.bw
Samd14_id1023739_GFP-TetR_bg.bed_bg_sorted.bw
Samd14_id1023739_GFP-TetR_scores_bg.bed_bg_sorted.bw
Sox1_id5399245_GFP-TetR_bg.bed_bg_sorted.bw
Sox1_id5399245_GFP-TetR_scores_bg.bed_bg_sorted.bw
Spry1_id3577811_GFP-TetR_bg.bed_bg_sorted.bw
Spry1_id3577811_GFP-TetR_scores_bg.bed_bg_sorted.bw
TetO.1_id5402489_GFP-TetR_bg.bed_bg_sorted.bw
TetO.1_id5402489_GFP-TetR_scores_bg.bed_bg_sorted.bw
TetO.2_id5402488_GFP-TetR_bg.bed_bg_sorted.bw
TetO.2_id5402488_GFP-TetR_scores_bg.bed_bg_sorted.bw

value: TetR-GFP


title: 13.non_smoker.ld.mono_NGS19.K318


title: TetR-GFP_ES_rep2


title: Daoy sh-HHIP-AS1#2

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

country: Germany

institute: Universitätsklinikum des Saarlandes

description:
shRNA
sh5_Daoy_R1

data_processing:
Fastq files were imported into Partek Flow (Partek Incorporated, Missouri, USA).
Quality analysis and quality control were performed on all reads to assess read quality and to determine the amount of trimming required (both ends: 13 bases 5´and 1 base 3´).
Trimmed reads were aligned against the hg38 genome using the STAR v2.4.1d aligner. Unaligned reads were further processed using Bowtie 2 v2.2.5 aligner.
Aligned reads were combined before quantifying the expression against the ENSEMBL (release 84) database by the Partek Expectation-Maximization algorithm using the counts per million normalization.
Genes with missing values and with a mean expression less than one were filtered out
Genome_build: hg38
Supplementary_files_format_and_content: CPM

source_name: Cell line

extract_protocol:
RNA was isolated using Trizol (#15596-018, Thermo Scientific)
500 ng total RNA was processed using the TruSeq RNA Sample Preparation v2 Kit (low-throughput protocol; Illumina, San Diego, USA) to prepare the barcoded libraries.
Libraries were validated and quantified using DNA 1000 and high-sensitivity chips on a Bioanalyzer (Agilent, Böblingen, Germany); 7.5 pM denatured libraries were used as input into cBot (Illumina), followed by deep sequencing using HiSeq 2500 (Illumina) for 101 cycles, with an additional seven cycles for index reading.

tag: plasmid

value: shRNA 2


title: Daoy sh-HHIP-AS1#1

description:
shRNA
sh2_Daoy_R1

value: shRNA 1


title: E.  coli, K12 strain, clone 2, bisulfited, WGBS primer


title: E.  coli, K12 strain, clone 2, untreated, ABBS primer

value: Mock


title: Daoy scr

description:
Control
scr_Daoy_R1

value: Control shRNA


title: 12.smoker.ag.mreg_NGS19.K317

value: Smoker


title: 11.smoker.ag.ma_NGS19.K316


title: TetR-GFP_ES_rep1


title: E.  coli, K12 strain, clone 2, untreated, WGBS primer

value: NEB


title: CHLA-266 sh-HHIP-AS1#2

description:
shRNA
266_sh5_R1


title: Pcgf2fl_ES_UNT_rep3_CapC_set2 72

description:
Sox1_id5399245_Pcgf2fl-TAM_bg.bed_bg_sorted.bw
Sox1_id5399245_Pcgf2fl-TAM_scores_bg.bed_bg_sorted.bw

source_name: Mouse embryonic stem cells , tamoxifen-treated (72hr OHT), CaptureC

value: Pcgf4-/-Pcgf2 flfl

value: tamoxifen (OHT)

value: 72 hr


title: E.  coli, K12 strain, clone 1, bisulfited, ABBS primer

value: ABBS


title: Pcgf2fl_ES_UNT_rep1_CapC_set2 72


title: 9.smoker.lc.mreg_NGS19.K314


title: Pcgf2fl_ES_TAM_rep4_CapC_set1

description:
1500009L16Rik_id3612757_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
1700025G04Rik_id374871_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Acss1_id843594_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Adra2a_id5957139_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Aebp1_id3733088_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Angptl4_id5462755_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ankrd6_id1387983_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Aplp1_id2508467_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Arhgef5_id2164246_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Arl10_id4439192_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Asns_id2075943_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Atoh8_id2237664_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Atp5l_id3218128_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Bmp2_id801622_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Bmper_id3163373_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Bmpr1b_id1269235_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Bnc1_id2640302_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Cacna1g_id3953925_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Car10_id3950536_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Casp2_id2161600_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ccnd2_id2373647_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Cdh11_id3045509_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Cdh6_id4930340_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Chrna4_id918412_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Cilp2_id2963523_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ckap2_id2847141_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Col26a1_id2027715_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Col27a1_id1462980_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Col2a1_id5139783_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Col4a1_id2820333_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Cpeb1_id2639040_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Cpm_id3694436_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Cpped1_id5177048_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Cpt1a_id5832120_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Creg1_id407574_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Csgalnact1_id2960479_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ctdspl_id3399202_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ctnnal1_id1447659_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Cyp1b1_id5578722_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Dagla_id5850122_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Dlk1_id4283906_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Dlx2_id648162_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Dmbx1_id1596177_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Dok6_id5828730_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Dph2_id1601224_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Dus1l_id4018608_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ecel1_id210126_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Eef1g_id5846437_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Egflam_id4916567_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Emilin2_id5558325_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Eomes_id3398229_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ephb3_id5201786_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ercc5_id104061_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Esrrb.2_id4227073_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Evi5l_id2802851_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Fam101b_id3908213_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Fasn_id4018679_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Fgf9_id4743707_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Fkbp9_id2196958_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Fli1_id3186524_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Foxa1_id4156272_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Frg1_id2894123_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Frzb_id668932_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Fzd8_id5631876_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Gabra4_id1865325_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Gadd45b_id3605594_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Gata4_id4756170_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Gata5_id916656_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Gdpd5_id2683883_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Gfra1_id5967445_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hcrtr1_id1632351_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hmga2_id3701143_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hnf1b.2_id3928029_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hnf1b_id3928025_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxa1_id2185852_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxa3_id2185971_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxa4_id2185916_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxa9_id2186005_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxb1_id3958722_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxb2_id3958685_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxb3.2_id3958618_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxb3_id3958676_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxb4_id3958609_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxb5_id3958568_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxb8_id3958517_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxc4_id5152335_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxc6_id5152266_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxc8_id5152231_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hoxd10_id655429_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Hspa8_id3208123_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Igfbp5_id174464_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Insm1_id832241_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Irak3_id3700588_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Islr2_id3250762_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Kcna6_id2372653_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Kcng2_id5806153_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Kif26b_id440003_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Klf2_id2969645_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Klf4_id1444272_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Lamb1_id4092801_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Large_id2972265_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Lfng_id2036913_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Llph_id3700641_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Lmx1b_id556421_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Lonrf1_id2881524_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Lrrc7_id1308138_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mafb_id867967_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mapkapk3_id3370575_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mcm3_id47198_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Meis1_id3766806_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Meis2_id758692_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mex3d_id3604301_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mn1_id1964984_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mpped2.2_id735207_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mpped2_id735202_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mpzl2_id3218449_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mroh1_id5086983_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mrpl19_id2261989_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Mrps14_id394136_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Msx1_id1781690_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Nanog_id2362093_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ndufb4_id5241421_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Nell1_id2560157_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Nfkbid_id2508402_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Nkx2-1_id4153981_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Nkx2-2_id834429_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Nlgn1_id982921_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Npr1_id1141068_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Nptx1_id4015615_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Nr2f1_id4499066_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Nsg1_id1782491_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ntsr1_id917074_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Numbl_id2500220_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Nwd2_id1845589_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Obscn_id3866120_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Oscp1_id1622319_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Pag1_id939316_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Parp8_id4594499_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Pck2_id4737370_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Pde3a_id2409145_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Pdgfra.2_id1873763_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Phc1_id2361131_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Pim3_id5118011_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Pitx2.2_id1238233_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Pitx2_id1238260_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Polr2e_id3603475_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Pou3f1_id1618825_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Pros1_id5303530_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Prox1_id467249_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Pth1r_id3379572_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Rab11fip4_id3917225_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Rbm24_id4418859_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Rbm34_id3104232_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Rexo2_id3226797_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Rgl1_id376092_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Rgs10_id2757885_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Rhpn2_id2522257_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Robo2_id5330322_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
S100a10_id1149986_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sall2_id4729121_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sall4_id888383_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Scly_id220349_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sema4c_id85884_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sema6d_id778751_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sgpp1_id4201286_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Shisa9_id5177242_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sim2_id5376947_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Slc1a3_id4919615_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Slc1a4_id3770077_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Slc24a2_id1523523_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Slit2_id1807209_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Smim3_id5757976_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sncaip_id5739239_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Snrpd3_id3591800_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sorcs3_id5942915_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sox17_id4096_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sox2_id1003349_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sox4_id4376345_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sp5_id645627_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Sp8_id4307594_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Spns2_id3898838_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Spsb4_id3345334_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
St6galnac5_id1294639_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
St8sia2_id2620202_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Stat3_id3970125_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Stat5b_id3969874_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Susd4_id449923_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Syce1_id2788219_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Tbc1d20_id847836_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Tbc1d4_id4849184_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Tmco1_id411517_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Tmem132b_id1999387_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Tnrc6c_id4011171_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Tomm7_id1746923_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Trib2_id4053775_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Tshz1_id5814715_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Tubb5_id5468158_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ubash3b_id3208950_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Ufm1_id1050580_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Vash2_id469223_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Wbscr17_id2013666_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Zbtb16_id3227741_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Zfp493_id4472136_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Zfp503_id4652828_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Zfp521_id5643669_Pcgf2fl_TAM_bg.bed_bg_sorted.bw
Zfp770_id754414_Pcgf2fl_TAM_bg.bed_bg_sorted.bw


title: E.  coli, K12 strain, clone 1, bisulfited, WGBS primer

value: WGBS


title: CHLA-266 scr

description:
Control
266_scr_R1


title: Pcgf2fl_ES_TAM_rep3_CapC_set1


title: 7.smoker.lc.mono_NGS19.K312

value: Sorted CD14+ monocytes from blood


title: Pcgf2fl_ES_UNT_rep3_CapC_set2

description:
Sox1_id5399245_Pcgf2fl-UNT_bg.bed_bg_sorted.bw
Sox1_id5399245_Pcgf2fl-UNT_scores_bg.bed_bg_sorted.bw

source_name: Mouse embryonic stem cells , untreated control, CaptureC

value: 0 hr


title: Pcgf2fl_ES_UNT_rep1_CapC_set2


title: 6.non_smoker.do.mreg_NGS19.K311

value: Sorted AFlo CD206+ CD45+ macrophages from BALF


title: Pcgf2fl_ES_TAM_rep1_CapC_set1


title: 5.non_smoker.do.ma_NGS19.K310

source_name: Sorted AFhi CD206+ CD45+ macrophages from BALF


title: 8.smoker.lc.ma_NGS19.K313


title: CHLA-266 sh-HHIP-AS1#1

description:
shRNA
266_sh2_R1


title: Pcgf2fl_ES_UNT_rep1_CapC_set1

description:
1500009L16Rik_id3612757_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
1700025G04Rik_id374871_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Acss1_id843594_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Adra2a_id5957139_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Aebp1_id3733088_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Angptl4_id5462755_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Ankrd6_id1387983_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Aplp1_id2508467_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Arhgef5_id2164246_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Arl10_id4439192_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Asns_id2075943_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Atoh8_id2237664_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Atp5l_id3218128_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Bmp2_id801622_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Bmper_id3163373_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Bmpr1b_id1269235_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Bnc1_id2640302_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Cacna1g_id3953925_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Car10_id3950536_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Casp2_id2161600_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Ccnd2_id2373647_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Cdh11_id3045509_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Cdh6_id4930340_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Chrna4_id918412_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Cilp2_id2963523_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Ckap2_id2847141_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Col26a1_id2027715_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Col27a1_id1462980_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Col2a1_id5139783_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Col4a1_id2820333_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Cpeb1_id2639040_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Cpm_id3694436_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Cpped1_id5177048_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Cpt1a_id5832120_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Creg1_id407574_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Csgalnact1_id2960479_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Ctdspl_id3399202_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Ctnnal1_id1447659_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Cyp1b1_id5578722_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Dagla_id5850122_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Dlk1_id4283906_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Dlx2_id648162_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Dmbx1_id1596177_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Dok6_id5828730_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Dph2_id1601224_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Dus1l_id4018608_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Ecel1_id210126_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Eef1g_id5846437_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Egflam_id4916567_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Ephb3_id5201786_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Fasn_id4018679_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Fgf9_id4743707_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Fkbp9_id2196958_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Fli1_id3186524_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Foxa1_id4156272_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Frg1_id2894123_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Frzb_id668932_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Fzd8_id5631876_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Gabra4_id1865325_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Gadd45b_id3605594_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Gata4_id4756170_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Gata5_id916656_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Gfra1_id5967445_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Hcrtr1_id1632351_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Hmga2_id3701143_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Hnf1b.2_id3928029_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Hnf1b_id3928025_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Hoxa3_id2185971_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Hoxa4_id2185916_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Hoxa9_id2186005_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Hoxb3_id3958676_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Irak3_id3700588_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Islr2_id3250762_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Klf2_id2969645_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Klf4_id1444272_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Lamb1_id4092801_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Lfng_id2036913_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Llph_id3700641_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Lonrf1_id2881524_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Lrrc7_id1308138_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Mafb_id867967_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Mcm3_id47198_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Meis1_id3766806_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Meis2_id758692_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Mex3d_id3604301_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Mn1_id1964984_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Mpped2.2_id735207_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Mpped2_id735202_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Mpzl2_id3218449_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Mroh1_id5086983_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Mrpl19_id2261989_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Mrps14_id394136_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Msx1_id1781690_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Nanog_id2362093_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Ndufb4_id5241421_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Nell1_id2560157_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Nfkbid_id2508402_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Npr1_id1141068_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Nr2f1_id4499066_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Nsg1_id1782491_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Ntsr1_id917074_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Nwd2_id1845589_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Obscn_id3866120_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Oscp1_id1622319_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Pag1_id939316_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Pck2_id4737370_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Pde3a_id2409145_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Pdgfra.2_id1873763_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Phc1_id2361131_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Pim3_id5118011_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Pitx2.2_id1238233_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Pitx2_id1238260_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Polr2e_id3603475_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Pou3f1_id1618825_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Pros1_id5303530_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Rbm24_id4418859_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Rbm34_id3104232_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Rexo2_id3226797_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Rgl1_id376092_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Rgs10_id2757885_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Rhpn2_id2522257_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Robo2_id5330322_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
S100a10_id1149986_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sall2_id4729121_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sall4_id888383_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Scly_id220349_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
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Sema6d_id778751_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sgpp1_id4201286_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Shisa9_id5177242_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sim2_id5376947_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Slc1a3_id4919615_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Slc1a4_id3770077_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Slc24a2_id1523523_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Slit2_id1807209_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Smim3_id5757976_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sncaip_id5739239_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Snrpd3_id3591800_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sorcs3_id5942915_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sox17_id4096_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sox2_id1003349_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sox4_id4376345_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sp5_id645627_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Sp8_id4307594_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Spns2_id3898838_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Spsb4_id3345334_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
St6galnac5_id1294639_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
St8sia2_id2620202_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Stat3_id3970125_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Stat5b_id3969874_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Susd4_id449923_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Syce1_id2788219_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Tbc1d20_id847836_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Tbc1d4_id4849184_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Tmco1_id411517_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Tmem132b_id1999387_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Tnrc6c_id4011171_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Tomm7_id1746923_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Trib2_id4053775_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Tshz1_id5814715_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Tubb5_id5468158_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Ubash3b_id3208950_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Ufm1_id1050580_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Vash2_id469223_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Wbscr17_id2013666_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Zbtb16_id3227741_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Zfp493_id4472136_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Zfp503_id4652828_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Zfp521_id5643669_Pcgf2fl_UNT_bg.bed_bg_sorted.bw
Zfp770_id754414_Pcgf2fl_UNT_bg.bed_bg_sorted.bw


title: 10.smoker.ag.mono_NGS19.K315

source_name: Sorted CD14+ monocytes from blood


title: Pcgf2fl_ES_UNT_rep3_CapC_set1


title: macrophage stimulated by RANKL and AnnexinA1 ANX_3

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

data_processing:
Illumina NovaSeq 6000
An average of 33 million reads (paired-end reads of 100 bp) per sample was mapped by alignment to the human genome (GRCh38) using STAR, gene expression level was quantified using RSEM, and differentially expressed genes (DEGs) were analyzed using DESeq2 Wald test (R software packages).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited test files include count, TPM and FPKM values for each Sample

source_name: human macrophage

growth_protocol: Human monocytes obtained from the blood of healthy donors (Asian, 3 males with ages of 30-45 years) were isolated by density gradient centrifugation (Ficoll-PaqueTM PLUS: GE Healthcare, Waukesha, WI, USA) followed by MACS Pan monocyte isolation kit (Miltenyi Biotec, Auburn, CA, USA) 36. Cells were suspended in growth medium containing minimum essential medium Eagle (MEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), a 5% penicillin/streptomycin solution, and 5% L-glutamine and cultured in a 37°C-humidified atmosphere containing 5% CO2 in a 75 cm2 flask for 3 h. Thereafter, the medium was discarded and adherent monocytes (CD14+) were cultured in growth medium supplemented with 25 ng/ml human recombinant macrophage colony-stimulating factor (MCSF; Peprotech, Japan). After 3 days of cultivation, the adherent cells were washed 3 times with ice-cold phosphate-buffered saline (PBS; Nacalai Tesque, Kyoto, Japan) and detached by treatment with a 1% trypsin-EDTA solution (GE Healthcare). Cells were washed with PBS (Nacalai), seeded on a 96-well plate (1 x 104) and cultured in growth medium supplemented with 25 ng/ml MCSF (Peprotech, Japan) with or without 50 ng/ml of one growth factors for 8 days.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions, and the integrity of samples was assessed by determining 28S/18S ribosomal RNA bands with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
High-quality libraries assayed by Bioanalyzer High sensitivity DNA kit (Agilent) were subjected to Illumina NovaSeq 6000 System (Illumina).

treatment_protocol: Growth factors included human recombinant proteins of Receptor activator of nuclear factor kappa-Β ligand (RANKL),  AnxA1(R&D system) . The growth medium for the cultures was regularly replenished with fresh growth medium supplemented with each recombinant protein at 3-day intervals.

value: macrophage


title: macrophage stimulated by RANKL and AnnexinA1 ANX_2


title: Pcgf2fl_ES_UNT_rep4_CapC_set1


title: SUP brain tissue of  sham group replicate 3

city: Shenzhen

first: Li

last: Yudi

address: No. 1098 Xueyuan Avenue, 518060 Shenzhen, Guangdong, China.

institute: Shenzhen Hospital, Southern Medical University

description: Biological replicate 2 of 3. the brain tissue of sham group was collected

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Mouse circRNA Epitranscriptomic Arrays (8x15K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent Scanner G2505C scanner.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images

source_name: Cerebral cortex tissue  in mice

label_protocol: The “IP” and “Sup” RNAs were treated with RNase R, and then labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit

growth_protocol: C57BL/6J mice weighing 23–26 g were raised in an SPF laboratory, at room temperature of 24˚C, and were kept on a 12-hour dark/ light cycle.

extract_protocol: Total RNAs were immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. The RNA was extracted by acid phenol-chloroform and ethanol precipitated.

treatment_protocol: They were randomized to three groups: the 3d after MCAO, 7d after MCAO, and sham groups The 3d and 7d groups were sacrificed 3 and 7 days after the operation, respectively, and the sham group underwent the same surgical procedure without the MCAO. During surgery and recovery, the body temperatures of the mice were maintained at 37℃.

tag: tissue

value: Cerebral cortex tissue

tag: age

value: sham


title: macrophage stimulated by RANKL and AnnexinA1 ANX_1


title: MED13-13lfl_ES_TAM_rep2_CapC_set2

description:
Sox1_id5399245_Med13-TAM_bg.bed_bg_sorted.bw
Sox1_id5399245_Med13-TAM_scores_bg.bed_bg_sorted.bw

source_name: Mouse embryonic stem cells , tamoxifen-treated (96hr OHT), CaptureC

value: Med13;Med13l flfl

tag: replicate

value: 96 hr


title: SUP brain tissue of  sham group replicate 2


title: MED13-13lfl_ES_TAM_rep4_CapC_set2


title: E.  coli, K12 strain, clone 1, untreated, WGBS primer

value: Mock


title: E.  coli, K12 strain, clone 1, untreated, ABBS primer


title: SUP brain tissue of  sham group replicate 1

description: Biological replicate 1 of 3. the brain tissue of sham group was collected

source_name: Cerebral cortex tissue around infarction in mice


title: JE_RNA_MV411_dTAG13_24h_R2

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

data_processing:
Quality control tests for unmapped sequences were performed based on the FastQC v.0.11.5 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The spiked-in human reads were mapped to the GRCh37/hg19 human genome using STAR v2.7.3  with standard parameters  --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes NH HI NM MD AS XS --outReadsUnmapped Fastx --outSAMstrandField intronMotif --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBan IndelSoftclipSingleend.
The ERCC92 Mix1 Spike-in sequences were mapped using STAR v2.7.3 according to the standard ThermoFisher protocol https://www.thermofisher.com/order/catalog/product/4456740#/4456740.
Gene level reads were summarized by using the featureCounts v1.6.3 method implemented in the Subread v2.0.0 package (http://subread.sourceforge.net) ref FeatureCounts. The technical quality metrics of the spiked-in mapped reads   were investigated using the standard methods   implemented  in the  erccdashboard package. Additional quality control tests for the mapped reads and for replicate reproducibility were performed using SARTools v1.7.3.
Gene counts were normalized and used to quantify differential  genes between the experimental and control conditions using the DESeq2 v1.24.0 method implemented in Bioconductor v3.9. Genes with at least 10 reads across at least 3 samples were annotated  as "expressed".
Differentiability for the expressed genes  was assessed with DESeq2 based on the robust shrunken log2 fold change scores  and  the approximate posterior estimation for GLM coefficients  method for effect size. The cutoffs for differentially expressed genes were |fold change expression|>1.5 and adjusted p-value < 0.10.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file include gene level counts values for each sample.

source_name: MV4-11 treated with dTAG-13 IRF2BP2 degrader for 24h

extract_protocol:
MV4-11 and PDX 16-01 IRF2BP2 degrader vs. DMSO:  these experiments were performed in three technical replicates for each time point and condition. ERCC RNA spike-in mix was added to all samples following the manufacturer’s instructions (ThermoFischer, 4456740).  RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen).
PDX AML parental: these experiments were performed in a single replicate. RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen), except for PDX 2017-63 and PDX 2017-94 for which RNA was extracted using the mirVana miRNA Isolation Kit (Thermo Fisher, Grand Island, NY) with the total RNA extraction protocol.
MV4-11 and PDX 16-01 IRF2BP2 degrader vs. DMSO:   PolyA mRNA was isolated and libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer’s protocol. All samples were sequenced on a Illumina NovaSeq 6000 instrument with paired-end 150 bp reads to a depth of 40-60 million reads per sample.
PDX AML parental (except PDX 2017-63 and PDX 2017-94):  PolyA mRNA was isolated and libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer’s protocol. All samples were sequenced on a Illumina NovaSeq 6000 instrument with paired-end 150 bp reads to a depth of 40-60 million reads per sample.
PDX 2017-63 and PDX 2017-94 parental: NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for poly(A) RNA purification with 50 uL total RNA as input. SMARTer Apollo NGS library prep system (Takara, Mountain View, CA) was used for automated poly(A) RNA isolation. The library for RNA-Seq was prepared by using NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs, Ipswich, MA). Libraries at the final concentration of 15 pM were clustered onto a single read (SR) flow cell v3 using Illumina TruSeq SR Cluster kit v3 and sequenced to 51 bp using TruSeq SBS kit v3 on Illumina HiSeq system.

value: Acute Myeloid Leukemia

value: dTAG-13 IRF2BP2 degrader for 24h

tag: disease state


title: JE_RNA_MV411_dTAG13_24h_R3


title: 4.non_smoker.do.mono_NGS19.K309


title: JE_RNA_MV411_dTAG13_24h_R1


title: SUP brain tissue of 7d after MCAO group replicate 1

description: Biological replicate 1 of 3. At 7day after cerebral infarction operation, the brain tissue was collected

value: Cerebral cortex tissue around infarction

value: cerebral infarction operation


title: SUP brain tissue of 7d after MCAO group replicate 2


title: SUP brain tissue of 3d after MCAO group replicate 3

description: Biological replicate 3 of 3. At 3day after cerebral infarction operation, the brain tissue was collected


title: JE_RNA_MV411_DMSO_24h_R3

source_name: MV4-11 treated with DMSO for 24h

value: DMSO for 24h


title: MED13-13lfl_ES_TAM_rep4_CapC_set1

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Tmco1_id411517_Med13fl_TAM_bg.bed_bg_sorted.bw
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Zfp770_id754414_Med13fl_TAM_bg.bed_bg_sorted.bw

value: tamoxifen (OHT)


title: MED13-13lfl_ES_TAM_rep3_CapC_set1


title: SUP brain tissue of 3d after MCAO group replicate 1

description: Biological replicate 1 of 3. At 3day after cerebral infarction operation, the brain tissue was collected


title: MED13-13lfl_ES_TAM_rep2_CapC_set1


title: SUP brain tissue of 7d after MCAO group replicate 3


title: SUP brain tissue of 3d after MCAO group replicate 2

description: Biological replicate 2 of 3. At 3day after cerebral infarction operation, the brain tissue was collected


title: MED13-13lfl_ES_UNT_rep4_CapC_set2

description:
Sox1_id5399245_Med13-UNT_bg.bed_bg_sorted.bw
Sox1_id5399245_Med13-UNT_scores_bg.bed_bg_sorted.bw


title: MED13-13lfl_ES_UNT_rep2_CapC_set2


title: IP brain tissue of  sham group replicate 3

value: brain


title: JE_RNA_MV411_DMSO_24h_R2


title: JE_RNA_MV411_DMSO_24h_R1


title: JE_RNA_MV411_dTAG13_06h_R3

source_name: MV4-11 treated with dTAG-13 IRF2BP2 degrader for 6h

value: dTAG-13 IRF2BP2 degrader for 6h