title: HAECs, siSOX13, OS, 3 [siSOX13OS3]

city: ATLANTA

first: Catherine

last: Demos

state: GA

address: 5310 Sloan Square NE

institute: Emory University

data_processing:
R version 4.1.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GRCh38/hg38 using standard R pipeline
Read count extraction and normalization were performed in R pipeline
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: Human Aortic Endothelial Cells

growth_protocol: HAECs were maintained in complete medium (MCDB 131, 10% FBS, 1% Pen-Strep, 1% L-glutamine, 1% ECGS, 15 ng/mL IGF-1, 1 mg/mL hydrocortisone, 50 mg/mL ascorbic acid, 5 ng/mL VEGF, 5 ng/mL EGF, 5 ng/mL FGF)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).  400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNAseq were performed by Novogene using the polyA enrichment library preparation procedure.

treatment_protocol: HAEcs were transfected with dsiRNA (IDT) using Oligofectamine transfection protcol. 24h later, the medie was exchanged for fresh medium and the cells were subjected to LS or OS for 24h by cone-and-plate viscometer.

value: Human Aortic Endothelial Cells

value: siSOX13, Oscillatory Shear


title: HAECs, siSOX13, OS, 2 [siSOX13OS2]

status: Public on Sep 27 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: Subj_1 baseline [S1]

city: BALTIMORE

first: Luigi

last: Ferrucci

state: MD

address: 251 BAYVIEW BLVD.

department: Translational Gerontology Branch

institute: National Institute on Aging, National Institutes of Health

description: 31 totalRNA-Seq samples were pooled and sequenced on 2 lanes of a NovaSeq 6000 S4 XP run using Illumina(R) Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing.

data_processing:
Reads were trimmed using Cutadapt (v. 1.18) to remove sequencing adapters.
Reads were aligned to human reference genome hg38 using STAR (v. 2.7.0f)
Expression levels were quantified using RSEM (v. 1.3.0) with GENCODE annotation (v. 21)
Assembly: hg38
Supplementary files format and content: RSEM raw counts as tab-delimited file for 58,381 genes (rows) and 31 samples (columns).

source_name: skeletal muscle

extract_protocol:
In each participant, a vastus lateralis muscle biopsy (∼150 mg) was collected using a Weil–Blakesley conchotome at ∼2 cm from the motor point. Two ml of lidocaine (2%) were injected in the area of the sampling and a small incision of muscle and fascia was performed. Muscle samples were frozen in liquid nitrogen and stored at −80°C. RNA was extracted from the muscle tissues by REPROCELL (USA) using a Norgen Animal Tissue RNA Purification Kit #257 (Norgen Biotek Corp, Ontario, CA).
RNA-Seq was performed at the Frederick National Laboratory for Cancer Research Sequencing Facility, NIH.  The libraries were made using the TruSeq Stranded Total RNA Library Prep protocol from Illumina.

tag: tissue

value: skeletal muscle

tag: subject

value: baseline


title: B23

city: Amsterdam

first: Niels

last: Verstegen

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research

library_source: transcriptomic single cell

data_processing: The quality of the retrieved sequencing data was assessed using FastQC (Andrews, 2010). Reads were pseudo-aligned to the human transcriptome (gencode version v27) using kallisto (Bray et al., 2016). Quantification of gene expression was obtained by gene-level summarization of transcripts abundance using the R package tximport (Soneson et al., 2015), without any scaling (countsFromAbundance option set to “no”). Counts were then normalized using the Transcript per Million (TPM) method (Li et al., 2010) with the following approach: a) gene length scaling, b) removal of all immunoglobulins genes and pseudogenes, and c) sequencing depth scaling (Figure1—figure supplement 1a). Removal of immunoglobulin genes at this stage prevented the artificial skewing of other genes expressed in the antibody-secreting cell clusters, due to the high content of immunoglobulins RNA present in this cell type. The scaled TPM matrix was used for downstream analysis.

source_name: differentiated human B cells starting from naive, scRNAseq

extract_protocol:
CD40L-expressing 3T3 cells were harvested, irradiated with 30 Gy, and 1 × 104 CD40L-expressing 3T3 cells were seeded in B cell medium (RPMI 1640 (Gibco) without phenol red containing 5% FCS, 100 U/ml penicillin, 100 μg/ml streptomycin, 2mM L-glutamine, 50 μM β-mercaptoethanol and 20 μg/ml human apotransferrin (Sigma Aldrich; depleted for human IgG with protein G sepharose)) in 96-well flat-bottom plates (NUNC) to allow adherence overnight. The next day, 2.5 × 104 human naive (CD19+CD27-IgG-IgD+) B cells were sorted on a FACS Aria and activated using the irradiated CD40L-expressing 3T3 cells in the presence of IL-4 (100 ng/ml; Cellgenix) for six days.  After six days, activated B cells were collected and co-cultured with 1 × 104 CD40L-expressing 3T3 cells or 1 × 104 WT together with CD40L-expressing 3T3 cells (ratio 9:1) that were irradiated and seeded one day in advance (as described above), together with IL-4 (100 ng/ml) and IL-21 (50 ng/ml; Invitrogen) for five days.
Sorted cells were processed using the Smart-seq2 protocol (Picelli et al., 2014) adjusted for 384-well plates. In short, 384-well plates containing single cells were thawed and cells were lysed and mRNA denatured by incubating the plates at 95°C for 3 minutes and put back on ice. Subsequently, 2.7 μl of first-strand cDNA reagent mix, containing 1x First-strand buffer, 5 mM DTT, 1 M betaine, 14 mM MgCl2, 5 U RNase inhibitor, 25 U Superscript II Reverse Transcriptase, and 1 μM Template-Switching oligonucleotides in nuclease-free water, was added to each well. Plates were incubated at 42°C for 90 minutes, 70°C for 15 minutes, and kept on hold at 4°C. Afterward, 7.5 μl of the pre-amplification mix, consisting of 1x KAPA HiFi HotStart Readymix and 0.12 μM ISPCR primers in nuclease-free water, was added to each well. Plates were then incubated as followed: 98°C for 3 minutes, 23 cycles of 98°C for 20 seconds; 67°C for 15 seconds; and 72°C for 6 minutes, then at 72°C for 5 minutes and kept on hold at 4°C. Purification of the resulting cDNA was performed using SeraMag SpeedBeads containing 19% w/v PEG 8,000 and a 1:0.8 ratio of cDNA/beads was used for cDNA precipitation. Purified cDNA was eluted in 14 μl of nuclease-free water. The quality of cDNA was randomly checked in 5% of the wells using the Tapestation High-Sensitivity D5000 assay. For the tagmentation reaction, 0.5 μl of 50-150 pg cDNA was mixed with a 1.5 μl Tagmentation mix containing 1x Tagment DNA buffer and Amplicon Tagment mix (Nextera XT DNA sample preparation kit). Plates were incubated at 55°C for 8 minutes and kept on hold at 4°C. 0.5 μl Neutralize Tagment buffer was added and incubated at room temperature for 5 minutes to inactivate Tn5. PCR amplification of adapter-ligated cDNA fragments was performed in a final volume of 5 μl containing the two index primers (Nextera XT Index kit) in a 1:5 dilution and Nextera PCR master mix. Plates were then incubated as followed: 72°C for 3 minutes, 95°C for 30 seconds, then 14-15 cycles of 95°C for 10 seconds; 55°C for 30 seconds; and 72°C for 30 seconds, then 72°C for 5 minutes and kept on hold at 4°C. 384 wells (the entire plate, including negative controls) were pooled in a single 2 ml tube (Eppendorf). Purification of cDNA was performed by adding 400 μl of cDNA in a 1:1 ratio with SeraMag SpeedBeads in 19% w/v PEG 8,000 in a 1.5 ml LoBind tube. Beads were washed with 1 ml of 80% ethanol. Purified cDNA was eluted in 200 μl of nuclease-free water. The concentration of the library was measured by Qubit according to the manufacturer’s instructions. The size distribution of the library was measured using the Tapestation High-Sensitivity D1000 or D5000 assay. The cDNA library pool was stored at -20°C until ready for sequencing.   cDNA library pool was diluted to 2 nM and prepared for sequencing using the NextSeq 500 High Output Kit v2 (75 cycles) according to the manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq 500 instrument.

value: Cultured naive B cells

value: Peripheral blood

tag: condition

value: CD40L and IL-4/IL-21 stimulated

tag: time point

value: 11 days cultured


title: B24


title: FBC for colon GF 1-2, colon PM 1-2, colon CR 1-2, colon EcN 1-2, colon kif 1-2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
TotalSeq C1-10
10x lane of 10 individually hashed colon samples. 2 Germfree biol reps, 2 GF + P. magnus biol reps, 2 GF + C. ramosum biol reps, 2 GF + E. coli Nissl biol reps, 2 GF + E. coli kifCD biol reps.

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 and hash libraries were processed using cite-seq-count
Data analsysis was performed using Seurat v3 pipeline. Low-quality cells were defined as those with less than 700 or more than 3000 unique genes, or those with >10% mitochondrial gene reads and were removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Colon

extract_protocol:
Lymphocytes were prepared by either digestion with collagenase and dispase (intestine) or mechanical disruption (MLNs, spleen), followed by staining with floursecent antibodies, hashing with Totalseq-C antibodies against MHCI and CD45,  and flow sorting CD4 T cells into RPMI/2%FCS
Libraries were prepared according to the 10x 5' (samples 1-22) and 10x5'v2 (samples 23-42) GEX, TCR, and FBC protocols

value: Colon

tag: cell line

value: CD4+ T cells

tag: strain

tag: genotype

tag: Sex

value: Male

value: None, P. magnus, C. ramosum, E. coli Nissl, E. coli kifCD


title: GEX for colon GF 1-2, colon PM 1-2, colon CR 1-2, colon EcN 1-2, colon kif 1-2


title: TCR for colon GF 1-2, colon PM 1-2, colon CR 1-2, colon EcN 1-2, colon kif 1-2


title: B22


title: HAECs, siSOX13, OS, 1 [siSOX13OS1]


title: HAECs, siSOX13, LS, 4 [siSOX13LS4]

value: siSOX13, Laminar Shear


title: B20


title: HUH7 CTRL-1

city: Worcester

first: Meghan

middle: E

last: Spears

address: 364 Plantation St, LRB

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
aligned to the reference genome assembly hg38 with star/2.5.3a (Dobin et al., 2013)
annotated with gencode.v29.primary_assembly (Harrow et al., 2012)
Aligned exon reads with mapping quality higher than 20 were counted toward gene expression with featureCounts_2.0.0 (Liao et al., 2014) with default settings except the following parameters ‘-Q 20 --minOverlap 1 --fracOverlap 0 -p -B -C’
Normalized expression values were calculated using the Transcripts Per Million (TPM) method.
Genome_build: hg38
Supplementary_files_format_and_content: Excel, normalized expression values in TPM

source_name: Cancer cell line

growth_protocol: Cells were grown adhered to tissue culture plates at 37°C, under 5% CO2 and atmospheric oxygen. Cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100units/ml penicillin-streptomycin, and 2mM L-glutamine.

extract_protocol: Total RNA was extracted from each sample using the RNeasy Kit for total RNA isolation (Qiagen #74104).

treatment_protocol: Cells were transduced with lentivirus containing lentiCRISPR v2 containing either a control non-targeting guide (CTRL) or a guide targeting KDSR (KDSR g1). Cells were selected with puromycin for 5 days and collected for RNA extraction at day 8 (HUH7 and DLD1) or day 10 (NCIH838) after lentiviral infection.

value: liver

tag: disease

value: hepatocellular carcinoma

value: CRISPR non-targeting guide


title: HAECs, siSOX13, LS, 2 [siSOX13LS2]


title: B2


title: HAECs, siSOX13, LS, 3 [siSOX13LS3]


title: HAECs, siSOX13, OS, 4 [siSOX13OS4]


title: B19


title: RNA-TSC-1

city: Wuhan

first: Wu

last: Linhui

state: Hubei

address: No.1 Shizishan Street

department: College of Animal Science and Veterinary Medicine

country: China

institute: Huazhong Agricultural University

data_processing:
RNA-seq: Reads of RNA-seq were mapped to the mm10 genome with STAR[51] using the ENCODE standard options. Gene expression levels were quantified by Stringtie using the refFlat database[52] from the UCSC genome browser.  Differentially expressed genes follow this criteria: fold change > 2, FDR < 0.05 in knockdown sample for upregulated genes, fold change < 0.5, FDR < 0.05 and in control sample for downregulated genes.GO enrichment analyses of differentially expressed genes was used in DAVID.  ChIP-seq: Reads were trimmed using TrimGlare and then mapped to the mm10 genome using Bowtie2 (v4.4.7) with parameters '-X 2000'. Multi-mapped and unmapped and low-quality reads were removed using samtools (v1.11) (10.1093/bioinformatics/btp352) and PCR duplicates were removed using the MarkDuplicates command from Picard tools (v2.6.0). ChIP-Seq peaks were called using MACS2 (v2.2.6) (10.1186/gb-2008-9-9-r137) with '-q 0.01' parameters. Annotation was performed using ChIPseeker version 1.22.1 (10.1093/bioinformatics/btv145).  ATAC-seq: Raw files (fastq format) processed through the ATAC-seq pipeline published by ENCODE. Briefly, reads were trimmed, filtered, and aligned to mm10. All unmapped reads, reads with low mapping quality (MAPQ < 30) and PCR duplicates were removed. MACS2 was used to call peaks for each individual sample with the "-nomodel" and "--shift -100 --extsize 200" parameters. The bam files of the replicates were then merged together using Samtools. Peak files were merged using Bedops (v2.4.38) (10.1093/bioinformatics/bts277) merge to obtain a consensus set of peaks across samples. The number of reads that fell into the peaks was obtained using bedtools multicov (v2.27.0) (10.1093/bioinformatics/btq033). Then we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) by custom scripts. Limma was used for determining hyper and hypo-accessible peaks across different samples using default parameters. Peaks were called as hyper or hypo-accessible using abs( log2 fold change ) > 0.5 and adjusted P < 0.05. For each sample, the Pearson correlation between replicates was calculated using the peaks that had an RPKM > 5 in at least one of the replicates.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: bigWig(except for Input sample)

molecule: polyA RNA

source_name: mouse trophoblast stem cells

growth_protocol: Trophoblast stem cells were cultured in 70% feeder condition medium + 30% TS medium (RPMI1640 + 20% FBS + 0.1M 2-mercaptoethanol + 2 mM glutamine + 1 mM sodium pyruvate + 100× Pen/Strep) + 25 ng/ml Fgf4 (Peprotech) + 1 μg/ml heparin (Sigma) on mitomycin C treated mouse embryonic fibroblasts (MEFs). For partially differentiated medium, we removed Fgf4 from TSCs maintained culture medium.

extract_protocol:
RNA-seq: Total RNA was extracted from cells by Trizol (Invitrogen, 15596-018), and 1 μg total RNA was reverse transcribed to obtain cDNA with cDNA Synthesis Kit (Vazyme, R212-01) according to the manufacturer’s protocol.   ChIP-seq: For ChIP-seq, TSCs were crosslinked with 1% formaldehyde for 10 min, and quenched by 2 mL of 125 mM glycine for 5 min rotation at room temperature. Cells were washed 3 times with cold PBS. After centrifugation, cell pellets were lysed in buffer (50 mM HEPES-KOH, 140 mM NaCl, 1 mM EDTA, pH 8.0, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 50 mM Tris-HCl, pH 8.0) for 10 min at 4℃. Chromatin was sonicated to 100-500 bp for the subsequent experiments.   ATAC-seq: ATAC-seq was performed as previously report[50]. In brief, a total of 50,000 cells were washed once with 50 µl of cold PBS and resuspended in 50 µl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After centrifugation at 4℃, suspension of nuclei diluted to 5 ng/µl in the elution buffer (10 mM Tris buffer, pH 8) and followed by the addition of 50 µl transposition reaction mix of DNA Library Prep Kit V2 for Illumina (Vazyme, TD501).
RNA-seq: Total RNA was extracted from TSCs by Trizol and RNA-Seq library were generated using RNA Library Prep Kit for Illumina® (NEB, E7530L) according to the manufacturer’s recommendations.    ChIP-seq: The samples were pre-incubated with protein A/G Dynabeads (Life Technologies, 10015D) and the beads were then removed. Subsequently, the sample was added with 8 mg of Klf5(Sigma, 09-822) or H3K27ac antibody and rotated overnight at 4℃. Beads were washed four times with a Wash buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% glycerol, 0.5% Triton X-100, 0.01% SDS), eluted and reverse crosslinked. Paired-end 125 bp sequencing was performed on Illumina Hiseq X-Ten.   ATAC-seq: The reaction mix was gently mixed and incubated at 55℃ for 10 min. ATAC-seq library was amplified in 9 cycles. Libraries were purified using Qiagen PCR Cleanup Kit according to the manufacturer’s instructions. Library concentrations were measured by KAPA Library Quantification Kit (KAPA Biosystems, KK4824) according to the manufacturer's instructions and checked by gel electrophoresis. Lastly, ATAC libraries were sequenced on Illumina Hiseq X-Ten.

value: TSCs

value: mouse trophoblast stem cells


title: RNA-TSC-3


title: B16


title: B3


title: B18


title: RNA-TSC-2


title: RNA-Klf5_KD-3

value: Klf5-KD TSCs.


title: B15


title: B13


title: B14


title: HAECs, siSOX13, LS, 1 [siSOX13LS1]

value: Human Aortic Endothelial Cells


title: B21


title: B10


title: B11


title: RNA-Klf5_KD-2


title: HAECs, siControl, OS, 3 [siNCOS3]

value: siControl, Oscillatory Shear


title: HAECs, siControl, LS, 4 [siNCLS4]

value: siControl, Laminar Shear


title: A6

value: Cultured naive B cells

value: Peripheral blood


title: A9

value: CD40L and IL-4/IL-21 stimulated

value: 11 days cultured


title: A7


title: RNA-Klf5_KD-1


title: HAECs, siControl, OS, 2 [siNCOS2]


title: ChIP-TSC-P300-2

library_source: genomic

molecule: genomic DNA

tag: antibody


title: A4


title: B1


title: HAECs, siControl, OS, 1 [siNCOS1]


title: ChIP-TSC-P300-1


title: ChIP-TSC-H3K27ac-2


title: A24


title: B12


title: ChIP-TSC-H3K27ac-1


title: A3


title: HAECs, siControl, LS, 3 [siNCLS3]


title: ChIP-Klf5_KD-P300-2


title: A23


title: A22


title: ChIP-Klf5_KD-P300-1


title: HAECs, siControl, OS, 4 [siNCOS4]


title: A5


title: A21


title: B17


title: ChIP-Klf5_KD-H3K27ac-2


title: A2


title: P95H SRSF2_sh60 #3 (K562 SRSF2P95H/+/+; RUNX1 KD-sh60 #3)

city: San Diego

first: Dong-Er

last: Zhang

state: California

address: 3855 Health Sciences Dr

department: Pathology

institute: UCSD

description:
DEG.AvsF_double_+geneclass.xls
AvsF_Double_AS.005005.xlsx

data_processing:
Mouse LK and K562 reads were aligned to GRCm38 and GRCh38 references genomes, respectively, using STAR software package.
Differential Gene Expression analysis was conducted for Mouse LK and K562 using DESeq2 package in R. For K562, DEGs were defined by FC > 2, FC < 0.5, and adjusted p < 0.05. In Mouse LK, DEGs were defined by FC > 1.5 or FC < 0.667, and adjusted p-value < 0.05.
rMATs was used to identify alternative splicing. In K562, altered splice events were identified, requiring at least 5% inclusion ration (-cstat) with FDR < 0.05. In mouse LK cells, altered splicing events were identified requiring > 5% inclusion ratio and FDR < 0.01.
Assembly: GRCm38, GRCh38
Supplementary files format and content: Differentially expressed genes (DEG) from DESeq2 analysis between indicated samples (WT vs P95H, etc.) for both Murine LK cells and K562
Supplementary files format and content: Alternative splice events from rMATs analysis of RNA-seq data between indicated samples (WT vs RUNX1 KD, etc.) for both Murine LK and K562

source_name: K562 chronic myelogenous leukemia

extract_protocol:
Total RNA was extracted from mouse LK cells and K562 cells using the Trizol Reagent. Mouse LK cells (Lin- c-Kit+) were flow sorted from bone marrow.
PolyA-selected RNA was purified using Illumina TruSeq RNA Sample Preparation Kit according to manufacturer's protocol.

value: chronic myelogenous leukemia

value: K562 SRSF2P95H/+/+; RUNX1 KD-sh60


title: P95H SRSF2_shCtrl #3 (K562 SRSF2P95H/+/+; shRNA-Ctrl #3)

description:
DEG.AvsD_P95H_+geneclass.xls
AvsD_P95H_AS.005005.xlsx

value: K562 SRSF2P95H/+/+; shRNA-Ctrl


title: A19


title: HAECs, siControl, LS, 2 [siNCLS2]


title: ChIP-Klf5_KD-H3K27ac-1


title: WT SRSF2_sh60 #3 (K562 SRSF2+/+/+; RUNX1 KD-sh60 #3)

description:
DEG.AvsC_RUNX1 KD_+geneclass.xls
AvsC_RUNX1 KD_AS.005005.xlsx


title: ChIP-Klf5-2


title: ChIP-Klf5-1


title: A14


title: A15


title: A16


title: A18


title: P95H SRSF2_sh60 #2 (K562 SRSF2P95H/+/+; RUNX1 KD-sh60 #2)


title: A12


title: A13


title: A11


title: ChIP-input-2


title: HAECs, siControl, LS, 1 [siNCLS1]


title: WT SRSF2_shCtrl #3 (K562 SRSF2+/+/+; shRNA-Ctrl #3)

value: K562 SRSF2+/+/+; shRNA-Ctrl


title: A20


title: A10


title: WT SRSF2_sh60 #2 (K562 SRSF2+/+/+; RUNX1 KD-sh60 #2)


title: P95H SRSF2_shCtrl #2 (K562 SRSF2P95H/+/+; shRNA-Ctrl #2)


title: A1


title: A8


title: NCIH1693, 200nM USP1I-38

first: Tianshu

last: Feng

address: 201 Brookline Ave Suite 901

institute: Tango Therapeutics

data_processing:
In-house customized pipeline for mapping and counting for sgRNAs
Assembly: GrCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample
Library strategy: DNA sequencing

source_name: Lung

growth_protocol: MDA-MB-436 and NCIH1693 cells were grown in RPMI-1640 with 10% FBS and 1% PenStrep

extract_protocol:
Genomic DNA was extracted with QIAamp Blood Maxi Kit (QIAGEN, 51194)
sgRNA sequences were amplified, purified with Kapa Pure Beads (Roche, KK8802) and sequenced on Illumina NextSeq500 systems

treatment_protocol: Cells were treated for 14 days with DMSO, 50 nM USP1i (I-138) or 5 days on, 5 days off with 200 nM USP1i (I-138)

value: Lung

value: Cell line

value: BRCA1/2 WT


title: NCIH1693, 50nM USP1I-38


title: ATAC-TSC-1

description: ATAC-TSC.bw

value: TSCs


title: ChIP-input-1

value: mouse trophoblast stem cells


title: P95H SRSF2_sh60 #1 (K562 SRSF2P95H/+/+; RUNX1 KD-sh60 #1)


title: ATAC-Klf5_KD-2

value: Klf5-KD TSCs.


title: NCIH1693, DMSO

value: DMSO


title: ATAC-TSC-2

description: ATAC-TSC.bw


title: MDA-MB-436, 200nM USP1I-38

source_name: Breast

value: Breast

value: BRCA1/2 Mut


title: MDA-MB-436, 50nM USP1I-38


title: WT SRSF2_sh60 #1 (K562 SRSF2+/+/+; RUNX1 KD-sh60 #1)


title: MDA-MB-436, DMSO


title: P95H SRSF2_shCtrl #1 (K562 SRSF2P95H/+/+; shRNA Ctrl #1)

value: K562 SRSF2P95H/+/+; shRNA Ctrl


title: WT SRSF2_shCtrl #2 (K562 SRSF2+/+/+; shRNA-Ctrl #2)


title: MED1-siR #1

city: La Jolla

first: John

last: Shyy

state: CA

address: 9500 Gilman Dr

institute: UC San Diego

data_processing:
Processing the raw RNA-seq reads by FASTX-Toolkit to obtain a high-quality base.
Reads were mapped and splice junctions were annotated to the UCSC human hg38 reference genome by using TopHat2
Then the annotated transcripts were assembled and abundances were estimated and normalized by using Cufflinks.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: PAEC

extract_protocol:
PAECs were transfected with MED1 siRNA or control siRNA (40 nM, Qiagen) for 48 hr and total RNA was extracted with Trizol (Invitrogen).
RNA libraries were prepared by using the NEBNex Ultra RNA Library Pre Kit (Illumina) following the manufacturer’s protocols.

value: PAEC

value: Endothelial cells

value: MED1 knockdown

value: MED1 siRNA


title: WT SRSF2_shCtrl #1 (K562 SRSF2+/+/+; shRNA-Ctrl #1)

value: chronic myelogenous leukemia


title: set2_3_shMyoX

city: Turku

first: Emilia

last: Peuhu

address: Medisiina D5, Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of turku

description:
set2_mouse3_shMyoX
shMyoX_4

data_processing:
The base calling was done using bcl2fastq (v. 2.17)
Read alignment was done using Star (v. 2.5.2b) to mm10 mouse genome reference
Read alignment was done using Star (v. 2.5.2b) to hg38 human genome reference
The human reads were filtered out with XenofilteR (v.0.99.0)
Genewise read counts were calculated using subreads package (v. 1.5.1)
Genome_build: mouse genome mm10 and human genome hg38
Supplementary_files_format_and_content: Processed data file RawData.csv is tab delimited text file containing the genewise read counts for each sample. Reads mapped to the human genome are filtered out with XenofilteR tool.

source_name: tumor

growth_protocol: 100 000 shCTRL- or shMYO10 LifeAct-mRFP MCF10DCIS.com cells were injected s.c. (100 µl volume; 50% Matrigel, 50% PBS) at the flank of 6-7 -week-old virgin female NOD.scid mice (Envigo). Tumor tissue samples were collected 25 days post tumor inoculation from two independent experiments.

extract_protocol:
RNA was isolated using Qiagen RNeasy Plus Mini kit.
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide

treatment_protocol: Tumors were dissected, one half of each tumor was immersed in RNAlater lysis buffer (Sigma Aldrich), and stored at -80C until RNA extraction.

tag: growth condition

value: xenograft in NOD.scid mouse

tag: disease state

value: breast cancer

value: Myosin-X gene silenced


title: MED1-siR #2


title: ATAC-Klf5_KD-1


title: MED1-siR #3


title: set2_1_shCtrl

description:
set2_mouse1_shCtrl
shCtrl_4

value: control


title: Ctrl-siR #2

value: Control

value: Control siRNA


title: PC3_siFOXA1_R3

city: Candiolo

first: Matteo

last: Cereda

country: Italy

institute: Italian Institute for Genomic Medicine

data_processing:
Basecalling performed by Illumina NovaSeq6000 and Illumina NextSeq500 for PC3 and VCaP, respectively.
RNA sequencing reads were aligned to the human genome reference GENCODE GRCh37 version 28 using STAR (v. 2.7.3a) in two-pass mode (--peOverlapNbasesMin=40 and --peOverlapMMp=0.8).
Gene level read counts were estimated using featureCounts (Subread v. 2.0.0) with -p, -B and -s 2 parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: One tab-delimited text file for each sample obtained with featureCounts including gene raw counts.

source_name: PC3 (CRL-1435, ATCC)

growth_protocol: PC3 (CRL-1435, ATCC) and VCaP (CRL-2876, ATCC) cells were obtained from ATCC and their identities were confirmed by Short Tandem Repeat (STR) profiling (DDC Medical). Cells were incubated at 37oC, 5% CO2 in a humidified incubator. Cells were maintained at sub-confluency in RPMI-1640 medium (21875-034, Gibco), for PC3, and DMEM (41966-029, Gibco), for VCaP, both containing 2 mM L-glutamine, supplemented with 10% foetal calf serum (FCS) (Gibco), 100 units/ml penicillin and 100 µg/ml streptomycin (15140-122, Gibco) and regularly tested for the presence of mycoplasma.

extract_protocol:
After 72 hours siRNA treatment, cells were washed 3x in PBS and then lysed in TriReagent (AM9738, Invitrogen) and RNA extracted by phase separation using 1-bromo-3-chloropropane. To exclude genomic contamination, total RNA was treated with DNase I and cleared with RNA Clean and Concentrator (Zymo Research).
RNAs were quantified using the Qubit Fluorometric Quantitation (Thermo Fisher Scientific). RNA quality was determined using the RNA 6000 Nano kit on a Bioanalyzer (Agilent Technologies). RNA samples with an RNA integrity number >7 were selected for library preparation. RNA-seq libraries were generated from 1 µg of RNA using TruSeq stranded mRNA (Illumina) or TruSeq total RNA (Illumina), for PC3 and VCaP, respectively, according to manufacturer’s recommendations.

treatment_protocol: PC3 and VCaP cells were transfected with 20nM and 40nM, respectively, non-targeting (NSI) or FOXA1 targeting siRNA with RNAiMax (13778-075, Thermo Fisher Scientific) according to the manufacturers’ instructions.

value: Prostate Cancer Cell Line

tag: sirna


title: set2_30_shMyoX

description:
set2_mouse30_shMyoX
shMyoX_3


title: A17

value: Cultured naive B cells

value: Peripheral blood

value: CD40L and IL-4/IL-21 stimulated

value: 11 days cultured


title: PC3_siFOXA1_R2


title: Ctrl-siR #1


title: WGBSseq_hek293_qko_mbd

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 2.4.1 (NextSeq 500) and bcl2fastq2 v2.17 or lllumina RTA 3.4.5 (NovaSeq 6000) and bcl2fastq2 v2.20 was used for basecalling and demultiplexing.
Assembly: hg19 and mm10
Supplementary files format and content: Human (single-end) or mouse (paired-end) WGBS-seq reads were aligned to hg19 or mm10, respectively, using qAlign from the QuasR package with default parameters (with bisulfite = ”dir”). Number of total and methylated counts for Cs in the CpG context (genome-wide) were calculated using the qMeth function from QuasR.

growth_protocol: HA36 mouse ES cells (mixed 129-C57Bl/6 strain) were maintained in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), 1x GlutaMax (ThermoScientific) and 1x Non-essential amino acids (Gibco), 0.001% beta-mercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). HEK293 cells were cultured in Dulbecco’s Modified Eagle Medium (Invitrogen), supplemented with 10 % Fetal Calf Serum (Invitrogen) and 2 mM L-Glutamine (ThermoScientific).

extract_protocol:
Nuclei of neurons (day 8) were isolated as in Grand et al.(Grand et al. 2021) and sorted by flow cytometry (BD FACS Aria III). Genomic DNA was isolated (QIAamp DNA Micro Kit, catalog number 56304) from  mouse ES cells or sorted nuclei of neurons and 1 ug was fragmented (Covaris S220) to an average size of ~ 300 bp. HEK293 genomic DNA was isolated with QIAamp DNA mini kit (Qiagen catalog number 51306) and fragmented with Covaris S220.
Libraries of mouse DNA were prepared according to manufacturer's instructions: Adapter ligation was performed using NEBNext Ultra II DNA Library Prep Kit (catalog number E7645L) with methylated adapters (NEBNext, catalog number E7535S), bisulfite treated (EZ DNA Methylation-Gold™ Kit, Zymo catalog number D5006) and indexed (NEBNext® Multiplex Oligos for Illumina) using 11 cycles in the PCR reaction (KAPA HiFi HotStart Uracil+ ReadyMix, Roche catalog number 07959052001). For HEK293 DNA, 500 ng of fragmented DNA were used for library preparation (NEBNext Ultra DNA Library Prep Kit, NEB catalog number E7370) with methylated adapters (NEBNext, NEB catalog number E7535S) and bisulfite treated with EZ DNA methylation-lightning Kit (Zymo Research catalog number D5046). Final PCR amplification was performed using KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (Roche catalog number 07959052001) with 12 cycles of amplification.

treatment_protocol: For HA36 ES cells containing the pTRE-Ngn2 construct differentiation was carried out by inducing expression of NGN2 with doxycycline as previously described (Thoma et al., 2012) with modifications. In brief, cells were plated on poly-D-lysine/laminin coated plates and treated with DMEM/F12 with Glutamax (LifeTech, 31331-028) containing 1x B27 without VitaminA (LifeTech #12587-010), 1x N2 supplement (LifeTech #17502-048), 10 ng/ml hEGF (LifeTech, PHG0315), 10 ng/ml hFGF (LifeTech, CTP0261) and 1 μg/mL doxycycline (Sigma, D989) for three days with no media change. At day three after doxycycline induction, medium was exchanged to Neurobasal-Medium (LifeTech, 21103-049) supplemented with 1x B27 with Vitamin A (LifeTech, 17504-044) , 1x N2 (LifeTech #17502-048) and 10ng/ml BDNF (PeproTech, 450-02), 10ng/ml GDNF (PeproTech, 450-10) and 10ng/ml NT-3 (PeproTech, 450-03). Every second day half of the media was replaced with fresh media.

value: embryonic kidney cells

value: MBD quadruple knock-out

value: kidney; Embryo


title: set2_10_shCtrl

description:
set2_mouse10_shCtrl
shCtrl_3


title: set1_3_R_shCtrl

description:
set1_mouse3_right flank_shCtrl
shCtrl_2


title: set1_10_R_shCtrl

description:
set1_mouse10_right flank_shCtrl
shCtrl_1


title: WGBSseq_hek293_wt

value: wild-type


title: PC3_NSI_R2

value: NSI


title: set1_3_L_shMyoX

description:
set1_mouse3_left flank_shMyoX
shMyoX_2


title: PC3_NSI_R1


title: PC3_siFOXA1_R1


title: set1_10_L_shMyoX

description:
set1_mouse10_left flank_shMyoX
shMyoX_1


title: Ctrl-siR #3

value: PAEC

value: Endothelial cells


title: PC3_NSI_R3


title: RNA-Seq OCILY19_AZA

city: Seoul

first: Junshik

last: Hong

state: Seoul

address: 101 Daehak-ro, Jongno-gu

department: Department of Internal Medicine

country: South Korea

institute: Seoul National University

data_processing:
Trim adaptors and low quality regions
Map reads using bwa
Sort bam file
Count reads mapped to ERVs
Map reads using tophat2
Counts reads mapped to genes
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw erv counts for every erv and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Diffuse large B_cell lymphoma  cell lines

growth_protocol: DLBCL cell lines were cultured according to DSMZ and ATCC user manuals.

extract_protocol:
The treated DLBCL cell lines were collected, and RNA was harvested using Trizol reagent. NEBNext ultra II Directional RNA-seq kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three consecutive days low dose (0.3 μM) 5-azacytidine or PBS

value: AZA

tag: cisplatin sensitivity

tag: dlbcl subtype

value: GCB


title: cko, rep3

city: Shanghai

first: Yan

middle: Feng

last: Liu

state: State...

address: No.160 Pu Jian Road, Pudong New Area

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Illumina Novaseq 6000 PE150 used for sequencing
Paired-end clean reads were aligned to the reference genome using HISAT2 (v2.1.0).
Differential expression analysis of two groups was performed using the DESeq R package
Assembly: Genome_build: GRCh38
Supplementary files format and content: All.HTSeq.ReadsCount.xls.xlsx and All.FPKM.xls includes ReadsCount and FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was harvested using Trizol reagent (Invitrogen, 15596018) and mRNA was enriched by Oligo(dT) beads .
The enriched mRNA was fragmented into short fragments using the fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA fragments were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then these cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were then size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq 6000

value: liver


title: RNA-Seq OCILY19_PBS_rep3

value: PBS


title: SK-N-BE(2)C cells, sgSNHG1 rep2 (ChIP-seq)

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Adaptor trimming by cutadapt
Alignment by BWA-mem
Merge two replicated samples and then peak calling with MASC2 (-f BAMPE -g hs -p 0.000001 --nomodel --extsize 200 --keep-dup all)
Assembly: GRCh38
Supplementary files format and content: BED format file contains the peak locations together with peak summit, p-value, and q-value.

growth_protocol: Human neuroblastoma cell lines SK-N-BE(2)C cells were routinely generated by re-plating day 4 (typically 1 × 106 cells into a 10 cm dish) and cultured in Dulbecco's Modified Eagle's Medium with 10% fetal bovine serum. Cells were grown at 37°C in an atmosphere of 5% CO2.

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to the previous work (Durbin AD et al. Nature Genetic 2018, 50(9):1240-1246)
Libraries were constructed according to the Illumina manufacturers

treatment_protocol: On the day of transfection, cells were optimal at 80% confluency. Constructs carried Cas9 and dual sgRNAs and pSurrogate reporters were introduced into cells by co-transfection using Lipofectamine 3000 transfection reagent (Invitrogen) according to the manufactures’ protocol. At 16-24 hours post-transfection, the culture medium was replaced with fresh medium containing puromycin to remove non-transfected cells. After 3-7 days puromycin selection, single cell clones were isolated by fluorescence cell sorting into 96-well plates and incubated for 1-2 weeks. The sorted clones were then expanded and cultured in 10 cm dish.

value: SNHG1 gRNA

tag: cell type

value: neuroblastoma

value: SNHG1 knockout

tag: chip antibody


title: AM20026_02_Prox1-cKO

data_processing:
Reads were aligned to the mm10 genome assembly using BWA-MEM.
peaks were called using MACS2
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Indicated cells were lysed and nuclei were extracted.
Genomic libraries were prepared according to ATAC-Seq Kit (Active Motif. 53150) for tagmentation and PCR amplification.

tag: tissue


title: AM20026_01_WT


title: SK-N-BE(2)C cells, sgSNHG1 rep1 (ChIP-seq)

tag: treatment


title: RNA-Seq OCILY19_PBS_rep2


title: RNA-Seq OCILY19_PBS_rep1


title: SK-N-BE(2)C cells, Control rep2 (ChIP-seq)

value: non-targeting control gRNA

value: wildtype


title: WT, rep3


title: cko, rep1


title: SK-N-BE(2)C cells, sgSNHG1 rep1 (ATAC-seq)

data_processing:
Adaptor sequences were removed using cutadapt and clean reads were aligned to the human genome GRCh38 using Burrows-Wheeler Alignment tool (BWA). The duplicated reads were marked by GATK-Picard. Aligned reads that were improperly paired, had multiple hits, mapped to mitochondria or ENCODE blacklisted regions, or were duplicates were removed from further analysis and the position of aligned reads were shifted +4 and –5 bp for the positive and negative strands using alignmentSieve from deepTools. Peaks were called using MACS2 with parameters -f BAMPE –keep-dup all and annotated by ChIPSeeker.
Assembly: GRCh38
Supplementary files format and content: BED format file contains the peak locations together with peak summit, p-value, and q-value.

extract_protocol:
Cells were trypsinized using a cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Following lysis, nuclei were centrifuged at 500 × g for 10 min. To avoid losing cells during the experiment preparation, we used a fixed-angle centrifuge. After nuclei preparation, a Tn5 transposition reaction was performed using a Nextera Kit (Illumina, San Diego, CA, USA), according to the manufacturer’s protocol. Directly following transposition, DNA was purified using a MinElute Kit (QIAGEN, Hilden, Germany).
Llibrary amplification was performed using a NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, Ipswich, MA, USA) with SYBR Green I dye (Invitrogen, Waltham, MA, USA) and Nextera PCR primers Ad1 and Ad2. The amplified libraries were purified using a PCR purification kit (QIAGEN) and quality control was performed using the 2200 Tapestation (Agilent, Santa Clara, CA, USA).


title: SK-N-BE(2)C cells, Control rep2 (ATAC-seq)


title: RNA-Seq TOLEDO_AZA


title: SK-N-BE(2)C cells, Control rep1 (ATAC-seq)


title: SK-N-BE(2)C cells, Control rep1 (ChIP-seq)


title: RNA-Seq OCILY3_AZA

value: ABC


title: cko, rep2


title: VCaP_siFOXA1_R2

source_name: VCaP (CRL-2876, ATCC)

value: VCaP

value: Prostate Cancer Cell Line


title: VCaP_siFOXA1_R1


title: WT, rep2


title: WT, rep1


title: RNA-Seq TOLEDO_PBS


title: VCaP_siFOXA1_R3


title: SK-N-BE(2)C cells, sgSNHG1 rep2 (ATAC-seq)


title: VCaP_NSI_R3


title: VCaP_NSI_R2


title: RNA-Seq OCILY3_PBS


title: VCaP_NSI_R1


title: cKO, mNK2, rep3

city: Cambridge

first: Rahul

last: Roychoudhuri

address: Tennis Court Road

department: Department of Pathology

country: United Kingdom

institute: University of Cambridge

data_processing:
Fastq files were analysed using Fastqc, trimmed and aligned to Mm9 genome using the STAR aligner v 2.5.0
Read counts for each gene were generated using the --quantMode GeneCounts option in the STAR aligner v 2.5.0
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Spleens of conditional knockout or control animals (CI0146)

extract_protocol:
Cells were stored in RNAlater (Ambion/Sigma) and total RNA purified using Qiagen Rneasy Plus Mini kit. RNA quality was assessed using bioanalyser analysis
Libraries were generated using the Clontech SMARTer protocols following the manufacturer's instructions

value: Spleen

value: NK cells

value: cKO (Bach2flox/flox Ncr1Cre)


title: cKO, mNK1, rep3


title: MBD-Seq OCILY19_AZA

data_processing:
Trim adaptors and low quality regions
Map reads using Bowtie2
The coverage was calculated using deepTools: bamCoverage -b reads.bam -o coverage.bw
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file for each Sample

extract_protocol:
The treated DLBCL cell lines were collected, and gDNA was harvested using QIAamp DNA mini kit. NEB Methylated DNA Enrichment Kit and NEB Ultra DNA Library kit were used for the construction of sequencing libraries.
DNA libraries were prepared for sequencing using standard Illumina protocols


title: MBD-Seq OCILY19_PBS


title: RNA-Seq SUDHL8_PBS_rep3


title: MBD-Seq TOLEDO_AZA


title: cKO, iNK, rep3


title: MBD-Seq TOLEDO_PBS


title: RNA-Seq SUDHL8_PBS_rep1


title: MBD-Seq OCILY3_PBS


title: cWT, mNK2, rep3

value: cWT (Ncr1Cre)


title: MBD-Seq OCILY3_AZA


title: MBD-Seq SUDHL8_AZA


title: cKO, NK, rep3


title: MBD-Seq SUDHL8_PBS


title: 601_Xl_MPE_XL_(20220324_TB_601_MPE_XLnuc_Xlink_cntrl_20220317)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Widom 601 3-copy array with 40-bp linkers

data_processing:
Library strategy:  MPE-seq
Genome_build: Genome_601x3.fasta
1. We used cutadapt 2.9 with parameters "--nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters off 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the trimmed reads to the reference sequence (Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 3. We extracted properly paired reads from the alignments with bedtools bamtobed  to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  4. We used bedtools genomecov to make a normalized count bigwig file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bigwig).

organism: synthetic construct

source_name: MPE-seq of 601 with Xenopus laevis histones, cross-linked

extract_protocol:
MPE-extraction_TB2021.pdf
viral DNA

tag: description

value: DNA from MPE-digested chromatin


title: MBD-Seq SUDHL2_AZA

value: AZA


title: cWT, mNK1, rep3


title: RNA-Seq SUDHL2_AZA


title: RNA-Seq SUDHL2_PBS


title: 601_Xl_MPE_(20220324_TB_601_MPE_XLnuc_noXlink_cntrl_20220317)

source_name: MPE-seq of 601 with Xenopus laevis histones


title: RNA-Seq OCILY1_AZA

value: GCB


title: cWT, iNK, rep3


title: 601_Xl_MNase_XL_(20220324_TB_601_Mnase_XLnuc_Xlink_cntrl_20220317)

data_processing:
Genome_build: Genome_601x3.fasta
1. We used cutadapt 2.9 with parameters "--nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters off 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the trimmed reads to the reference sequence (Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 3. We extracted properly paired reads from the alignments with bedtools bamtobed  to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  4. We used bedtools genomecov to make a normalized count bigwig file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bigwig).

source_name: MNase-seq of 601 with Xenopus laevis histones, cross-linked

extract_protocol:
MNase-extraction_TB2021.pdf
viral DNA

value: DNA from MNase-digested chromatin


title: MBD-Seq OCILY1_AZA


title: RNA-Seq SUDHL8_AZA


title: 601_Xl_MNase_(20220324_TB_601_Mnase_XLnuc_noXlink_cntrl_20220317)

source_name: MNase-seq of 601 with Xenopus laevis histones


title: RNA-Seq SUDHL8_PBS_rep2

value: PBS


title: D9-CHIR

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

description: Mix-QY-Qip151-C-d9-ATCATTCC_BKDL190807198-1a-A81

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Raw reads were trimmed with TrimGalore (v.0.6.4)
Reads were aligned to  hg38 ensembl v101 transcriptome using rsem (v1.3.1) and bowtie2 (v2.4.1) (—bowtie2—bowtie2-sensitivity-level very_sensitive— no-bam-output—estimate-rspd).
The gene expression level was calculated by using  RSEM
The gene expression was normalized using EDAseq on a basis of GC-content. RNA-seq data was expressed in units of GC-normalized tag counts.
Genome_build: hg38

source_name: UiPSM Day9-CHIR

growth_protocol: Specific culture media for each cell type

extract_protocol:
Purified total RNA was capture with magnetic bead with oligo-polyA, interrupt and reverse-transcribed into cDNA using the VAHTSTM mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme), purified using VAHTS DNA Clean Beads (N411, Vazyme).
cDNAs ligated adapters and amplified libraries using the amplification mix (NR611, Vazyme). Finally, sequencing the cDNAs library to obtain 150bp paired-end reads.

treatment_protocol: Extracted RNA using phenolic chloroform after pretreatment with Trizol

value: UiPSM

tag: time point

value: Day 9


title: MBD-Seq OCILY1_PBS


title: RNA-Seq OCILY1_PBS


title: cWT, NK, rep3


title: cKO, iNK, rep2


title: MBD-Seq SUDHL2_PBS


title: cKO, mNK1, rep2


title: 601_60_MPE_2_(20210818_TB_601_3A_60_MPE_20210730)

data_processing:
Library strategy:  MPE-seq
Genome_build: Genome_601x3.fasta
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (Drosophilia melanogaster dm6 or Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: MPE-seq of 601 60uM on 3-copy array

value: Widom 601 3-copy array with 40-bp linkers

tag: type

value: Linear DNA


title: D3-CHIR

description: Mix-QY-Qip151-C-d3-AGCACCTC_BKDL190807198-1a-A77

source_name: UiPSM Day3-CHIR

value: Day 3


title: 601_3B_MPE_(20210810_TB_601_3B_MPE_210730)

source_name: MPE-seq of 601 on 3-copy array replicate 2


title: 3D Non-balding dermal papilla cell_replicate A

city: London

last: Philipott

address: 4 Newark St

department: Center for Molecular Medicine Cologne

institute: Blizard Institute Barts and The London School of Medicine and Dentistry

data_processing:
Sequenced reads were aligned to the hg19 human genome (GRCh37) with STAR version 2.5.2a (default settings).
Transcripts were assembled with RSEM version 1.3.0.
DESeq2 was used to identify significant differential genes between samples (Benjamini-Hochberg-adjusted p-value (padj) ≤ 0.05).
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix table with raw gene count for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Dermal papilla cells derived from non-balding scalp

growth_protocol: BAB and BAN were plated in 6-well plates at seeding density of 1x10^5 cells/well, maintained for 48 hr in DMEM media (DMEM with High Glucose, 4.0 mM L-Glutamine (Cat no.: SH30022.02, Hyclone) supplemented with 10% (v/v) fetal bovine serum (Cat no.: 10082147, Life Technologies), 100 U/ml penicillin G, and 100 mg/ml streptomycin (Cat no.: P4333, Sigma-Alrich)) at 37°C in an atmosphere of 10% CO2 and 90% air.

extract_protocol:
Total RNA from BAB and BAN samples was isolated with RNeasy Mini kit and on-column DNase treatment. RNA samples of high integrity (RIN value ≥ 8) were used for RNA-seq library construction.
RNA-seq library construction and downstream analysis were carried out on technical triplicates. cDNA was generated from 30 ng of extracted RNA with SMARTer Ultra Low Input RNA for Illumina Sequencing (Cat no.: 634823, Clontech), followed by RNA-seq library construction with NEBNext DNA Library Prep Master Mix Set for Illumina (Cat no.: E6040, NEB). Constructed libraries were paired-end sequenced with Illumina HiSeq High Output v3.

treatment_protocol: BAB and BAN were conditioned in phenol red-free DMEM media for 24 hr, and treated with 10 nM DHT for 24 hr.

value: Dermal papilla

tag: phenotype

value: Non-balding

tag: culture format


title: 3D Balding dermal papilla cell_replicate C

source_name: Dermal papilla cells derived from balding scalp

value: Balding


title: D9-EPZ

description: Mix-QY-Qip151-E-d9-ATTGGCTC_BKDL190807198-1a-A82

source_name: UiPSM Day9-EPZ


title: 3D Non-balding dermal papilla cell_replicate C


title: D6-CHIR

description: Mix-QY-Qip151-C-d6-AGGCTAAC_BKDL190807198-1a-A79

source_name: UiPSM Day6-CHIR

value: Day 6


title: cWT, mNK2, rep2

value: Spleen

value: NK cells

tag: genotype


title: D6-EPZ

description: Mix-QY-Qip151-E-d6-ATAGCGAC_BKDL190807198-1a-A80

source_name: UiPSM Day6-EPZ


title: cKO, mNK2, rep2

value: cKO (Bach2flox/flox Ncr1Cre)


title: cWT, mNK1, rep2

value: cWT (Ncr1Cre)


title: 601_3A_MPE_(20210810_TB_601_3A_MPE_210730)

source_name: MPE-seq of 601 on 3-copy array replicate 1

value: DNA from MPE-digested chromatin


title: 3D Balding dermal papilla cell_replicate A


title: 601_3A_60_MNase_(20210810_TB_601_3A_60_Mnase_210730)

source_name: MNase-seq of 601 60uM on 3-copy array


title: D3-EPZ

description: Mix-QY-Qip151-E-d3-AGCCATGC_BKDL190807198-1a-A78

source_name: UiPSM Day3-EPZ


title: 601_60_MPE_1_(20210810_TB_601_3A_60_MPE_210730)


title: cWT, iNK, rep2

source_name: Spleens of conditional knockout or control animals (CI0146)


title: D9

description: Day9_QY-mix-TCTTCACA_BKDL190796859-1A-A63

source_name: UiPSM Day9


title: 601_3A_300_MNase_(20210810_TB_601_3A_300_Mnase_210730)

source_name: MNase-seq of 601 300uM on 3-copy array


city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

country: Japan

institute: University of Tokyo

description: RNA-seq, A clone of SAS cells (control sgRNA), replicate 2

data_processing:
Reference files of the human genome GRCh38 (NCBI build 38, Dec. 2013) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
RNA-seq reads were aligned and gene abundance in transcripts per million fragments (TPM) were estimated using Hisat2 (version 2.1.0. with default parameters) and Stringtie (version 2.0.4. parameters used: -A -e -G) (Pertea et al, Nat Protocols 2016 11:1650-1667) without de novo transcript assembly.
Genome_build: GRCh38
Supplementary_files_format_and_content: An Excel format file includes coverage, FPKM, and TPM values of genes for each Sample, which was generated by Stringtie.

source_name: human oral squamous carcinoma SAS

growth_protocol: The SAS human oral squamous carcinoma cell lines were obtained from the RIKEN BioResource Center Cell Bank. SAS cells bearing fluorescent ubiquitination-based cell cycle indicator (Fucci), SAS-Fucci cells, were previously established by Department of Oral Radiation Oncology (Tokyo Medical and Dental University) as described previously (Nojima et al, Exp Cell Res 2020). All cell lines were tested negative for mycoplasma contamination. All cell lines were maintained in humidified incubator at 37℃ with 5% CO2. All cell lines were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Nacalai Tesque) supplemented with 10% fetal bovine serum (FBS; Gibco), 100 units/mL penicillin, and 100 μg/mL streptomycin (Nacalai Tesque).

extract_protocol:
RNA was isolated using the RNeasy Plus (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using Dynabeads mRNA DIRECT Purification Kit and the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific).

treatment_protocol: SAS-Fucci cells were treated with 1 ng/ml of TGF-beta for 72h or left untreated.

tag: stable expression

value: Fucci (Fluorescent Ubiquitination-based Cell Cycle Indicator)

tag: cell cycle

value: unsorted

tag: stimulation


description: RNA-seq, A clone of SAS cells (KRTAP2-3 sgRNA), replicate 2


title: 601_300_MPE_2_(20210818_TB_601_3A_300_MPE_20210730)

source_name: MPE-seq of 601 300uM on 3-copy array


title: cWT, NK, rep2


title: D6

description: Day6_QY-mix-TCCGTCTA_BKDL190796859-1A-A62

source_name: UiPSM Day6


title: cKO, mNK2, rep1


title: cKO, mNK1, rep1


title: 601_300_MPE_1_(20210810_TB_601_3A_300_MPE_210730)


title: D3

description: Day3_QY-mix-TATCAGCA_BKDL190796859-1A-A61

source_name: UiPSM Day3


title: 601_12B_MPE_(20210810_TB_601_12B_MPE_210730)

source_name: MPE-seq of 601 on 12-copy array replicate 2

value: Widom 601 12-copy array with 40-bp linkers


description: RNA-seq, A clone of SAS cells (KRTAP2-3 sgRNA), replicate 1


title: UC

description: Day0_QY-mix-TAGGATGA_BKDL190796859-1A-A60

source_name: Urine Cell

value: Urine Cell


title: 3D Balding dermal papilla cell_replicate B


title: cKO, iNK, rep1


description: RNA-seq, A clone of SAS cells (control sgRNA), replicate 1


title: 601_12A_MPE_(20210810_TB_601_12A_MPE_210730)

source_name: MPE-seq of 601 on 12-copy array replicate 1


title: A S/G2/M phase fraction of SAS-Fucci cells, TGF-b treated, replicate 2

description: RNA-seq, S/G2/M phase fraction of SAS-Fucci cells, TGF-b treated, replicate 2

value: TGF-β (1 ng/ml) for 72 h


title: cKO, NK, rep1


title: PpARFC2, iOX, β-estradiol,Replicate-3

city: Nankang

first: Ooi-kock

last: Teh

state: Taipei

address: 128 Sec. 2, Academia Rd

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

description:
RPKM-Summary.txt
TMM-Normalization.txt
Column-G of both processed files

data_processing:
Firstly, we removed the reads mapped to rRNAs and get rawdata, then we filter the low  quality reads (More than 20% of the bases qualities are lower than 10), reads with  adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.  Then we map those clean reads onto reference genome(database), followed with novel  gene prediction, SNP & INDEL calling and gene splicing detection. Finally, we identify  DEGs (differentially expressed genes) between samples and do clustering analysis and  functional annotations.
1. Sequencing Reads Filtering-an internal software SOAPnuke  version： v1.5.2  parameters: -n 0.001 -l 20 -q 0.4 -A 0.25  2. Genome Mapping- HISAT2  Version: v2.0.4  Parameters: --phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000  3. Novel Transcript Prediction  StringTie:  Version: v1.0.4  Parameters: -f 0.3 -j 3 -c 5 -g 100 -s 10000 -p 8  Cufflinks:  Version: v2.2.1  Parameters: -p 12  CPC:  Version: v0.9-r2  Parameters: Default
4. Differentially Splicing Gene Detection  rMATS:  Version: v4.0.2  Parameters: -t paired --nthread 8 --tstat 4  5. Gene Expression Analysis  Bowtie2:  Version: v2.2.5  Parameters: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --nomixed --no-discordant -p 1 -k 200  RSEM:  Version: v1.2.12  Parameters: default
6. Circos Diagram  Circos:  Version: v0.69  7. Gene expression cluster analysis  cluster:  Version: v3.0  Parameters: -g 7 -e 7 -m a
8.DEG Detection  EBseq:  Parameters: Fold Change >= 2.00 and Posterior Probability of being Equivalent Expression(PPEE) <= 0.05  NOIseq:  Parameters: Fold Change >= 2.00 and Probability >= 0.8  PossionDis:  Parameters: Fold Change >= 2.00 and FDR <= 0.001
We use HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step using Physcomitrium patens as the reference genome
Assembly: Physcomitrium patens v3.3 (reference genome for Physcomitrium patens is available at https://phytozome-next.jgi.doe.gov/info/Ppatens_v3_3)
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample
tab-delimited text file include TMM normalized abundance measurements
Gene IDs can be verified from Phytozome (https://phytozome-next.jgi.doe.gov/)

organism: Physcomitrium patens

source_name: Protonemata

growth_protocol: 7-day-old protonemata were grown on BCDAT medium at 24C, 40% humidity and continuous white light

extract_protocol:
Total RNA was extracted using RNeasy Mini Kits (QIAGEN). About 1ug RNA was used to construct the library.
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligoattached  magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent  cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using  reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA  Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and  subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.  We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle  (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle  by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs  were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq  platform for the following data analysis study. For this step, the DNBseq platform combines the DNA  nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis

treatment_protocol: Induced with 1uM beta-estradiol or 0.01% DMSO for 16 hours

value: Protonemata

tag: cell line

value: PpARFC2 inducible overexpressor line

value: 16h on 1 µM β-estradiol


title: cWT, mNK2, rep1


title: PpARFC2, iOX, β-estradiol,Replicate-1

description:
RPKM-Summary.txt
TMM-Normalization.txt
Column-E of both processed files


title: A S/G2/M phase fraction of SAS-Fucci cells, TGF-b treated, replicate 1

description: RNA-seq, S/G2/M phase fraction of SAS-Fucci cells, TGF-b treated, replicate 1


title: cWT, mNK1, rep1


title: A G1 phase fraction of SAS-Fucci cells, TGF-b treated, replicate 1

description: RNA-seq, G1 phase fraction of SAS-Fucci cells, TGF-b treated, replicate 1


title: A G1 phase fraction of SAS-Fucci cells, TGF-b treated, replicate 2

description: RNA-seq, G1 phase fraction of SAS-Fucci cells, TGF-b treated, replicate 2


title: A S/G2/M phase fraction of SAS-Fucci cells, unstimulated, replicate 2

description: RNA-seq, S/G2/M phase fraction of SAS-Fucci cells, unstimulated, replicate 2


title: PpARFC2, iOX, DMSO,Replicate-2

description:
RPKM-Summary.txt
TMM-Normalization.txt
Column-D of both processed files

value: 16h on 0.01% DMSO


title: cKO, NK, rep2


title: PpARFC2, iOX, DMSO,Replicate-1

description:
RPKM-Summary.txt
TMM-Normalization.txt
Column-C of both processed files


title: T19_MPE_(20210810_TB_MV_T19_MPE_210730)

data_processing:
Library strategy:  MPE-seq
Genome_build: T19_genome.fasta
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (Drosophilia melanogaster dm6 or Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

organism: Marseillevirus marseillevirus

source_name: MPE-seq of T19

tag: strain

value: viral DNA


title: PpARFC2, iOX, β-estradiol,Replicate-2

description:
RPKM-Summary.txt
TMM-Normalization.txt
Column-F of both processed files


title: A S/G2/M phase fraction of SAS-Fucci cells, unstimulated, replicate 1

description: RNA-seq, S/G2/M phase fraction of SAS-Fucci cells, unstimulated, replicate 1


title: KO-CCL4-79

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

data_processing:
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: FPKM and count values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

treatment_protocol: Tgfbr2f/f mice and Tgfbr2HKO mice were intraperitoneally injected with 0.25 ml/kg CCl4 (diluted 1:3 (v/v) in olive oil) twice a week for 4 weeks.

value: liver

value: hepatocyte

tag: age

value: 12-week old

value: KO


title: KO-CCL4-75


title: A G1 phase fraction of SAS-Fucci cells, unstimulated, replicate 2

description: RNA-seq, G1 phase fraction of SAS-Fucci cells, unstimulated, replicate 2


title: Balding dermal papilla cell_replicate C

data_processing:
All sequenced reads were aligned to the Hg19 human genome with TopHat2.
Transcripts were assembled with Cufflinks 2.2.1.
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix table with quantile normalised fpkm for every gene and every sample

source_name: Dermal papilla cells derived from balding scalp

value: Balding DP cell

value: 10nM DHT, 24hr


title: T19_8th_MNase_(20210610_TB_Mv_20210526_1_8x)

data_processing:
Genome_build: T19_genome.fasta
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (Drosophilia melanogaster dm6 or Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: MNase-seq of T19 1/32nd MNase

value: DNA from MNase-digested chromatin


title: BMMCs-ionomycin activated-4hrs-rep2

type: RNA

city: Durham

first: Soman

middle: N

last: Abraham

state: North Carolina

address: 207 Research Drive

institute: Duke University

description: Gene expression data from BMMCs 4hr post activation with ionomycin

hyb_protocol: RNA was hybridized on GeneChip Mouse Transcriptome Array 1.0 and washed using the Affymetrix Fluidics Station 450 according to manufacturer's instructions.

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

data_processing: The data were analyzed in the R statistical program using the oligo package within the Bioconductor suite. Data were normalized using Robust Multiarray Analysis.

label: biotin

source_name: BMMCs, 4hrs post ionomycin treatment

label_protocol: RNA was labeled using the Affymatrix GeneChip Whole Transcriptome Terminal Labeling Kit following manufacturer's instructions.

growth_protocol: Bone marrow-derived mast cells (BMMCs) were obtained by flushing femurs from C57BL/6J mice. Cells were maintained in RPMI-1640 cell media supplemented to contain 10% heat-inactivated fetal bovine serum, 2 mM L-glutamine, 1 mM nonessential amino acids, 25 mM HEPES, 1 mM sodium pyruvate, 1X Antibioitic-Antimycotic, 5 ng/mL recombinant murine IL-3, and 5% stem cell factor-containing supernatant from CHO-KL cells (BMMC media).  Cells were matured for 6 weeks prior to study.

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit (Qiagen) and following manufacturer's instructions.

treatment_protocol: BMMCs were washed once in Tyrode's buffer (135 mM NaCl, 5 mM KCl, 1.3 mM CaCl2, 1 mM MgCl2, 5.5 mM glucose, 1% BSA, 20 mM HEPES, pH 7.4) and then resuspended in Tyrode's buffer containing 1 μg/mL ionomycin or Tyrode's buffer alone (naïve) for 1 hr at 37°C. Cells were then washed three times with Tyrode's buffer and resuspended in BMMC media for 3hrs.

value: Bone marrow derived mast cells

value: 4hr post activation with ionomycin


title: A G1 phase fraction of SAS-Fucci cells, unstimulated, replicate 1

description: RNA-seq, G1 phase fraction of SAS-Fucci cells, unstimulated, replicate 1

value: Fucci (Fluorescent Ubiquitination-based Cell Cycle Indicator)


title: KO-CCL4-72


title: T19_64th_MNase_(20210610_TB_Mv_20210526_1_64x)

source_name: MNase-seq of T19 1/256th MNase


title: BMMCs-ionomycin activated-4hrs-rep3


title: BMMCs-ionomycin activated-4hrs-rep1


title: cWT, NK, rep1

source_name: Spleens of conditional knockout or control animals (CI0146)

value: Spleen

value: NK cells

value: cWT (Ncr1Cre)


title: BMMCs-Naïve-rep3

description: Gene expression data from naïve BMMCs

source_name: BMMCs, Naïve

value: naïve


title: T19_no-MNase_(20210610_TB_Mv_20210526_0x)

source_name: MNase-seq of T19 no MNase


title: cWT, iNK, rep1


title: WT-CCL4-13

value: WT


title: BMMCs-Naïve-rep1

description: Gene expression data from naïve BMMCs


title: T19_5min_MNase_(20210506_TB_Mv_5min_0430)

source_name: MNase-seq of T19 5 min MNase


title: BMMCs-Naïve-rep2

description: Gene expression data from naïve BMMCs


title: WT-CCL4-12


title: GMP.13

city: Boston

first: Michael

middle: K.

last: Mansour

address: 55 Fruit Street

institute: Massachusetts General Hospital

data_processing:
Mapping was performed with BWA aligner (PMID:23104886) using mm9 reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: granulocyte monocyte progenitor

growth_protocol: GMPs were maintained in culture in the presence of stem cell factor and β-estradiol (0.5 µM) which permits nuclear translocation of the ER-HoxB8 fusion protein, resulting in the conditional immortalization of the GMP.

extract_protocol:
Naïve GMP and neutrophil paired clones were prepared for ATAC-seq as described by Buenrosto et al (2015). GMPs or neutrophils were brought to 5x105 cells/ml and incubated with transposition reaction mix (NEBNext High-Fidelity 2X PCR master mix, NEB) for 30 min. followed by PCR for 18 cycles. ATAC-seq samples were not size selected here. ATAC-seq sequencing was performed on Illumina HiSeq 2500 instrument, resulting in approximately 15-20 million of paired-end 50 bp reads per sample.
Reads were mapped to mm9 mouse reference genome using BWA. Fragments with both ends unambiguously mapped to the genome that were longer than 100 bp were used in further analysis.

treatment_protocol: Removal of beta-estradiol from the media restores differentiation of the GMP into mature neutrophils. To remove β-estradiol completely, GMPs were washed twice with phosphate-buffered saline prior to seeding cells in complete RPMI containing stem cell factor.

value: C57Bl/6 CD45.1-STEM

tag: media type

value: Plus beta-estradiol (0.5 microM)

tag: barcode

value: TGGATCTG


title: Non-balding dermal papilla cell_replicate C

source_name: Dermal papilla cells derived from non-balding scalp

tag: cell type

value: Non-balding DP cell


title: T19_4x_NP40_(20210920_TB_Mv_T19_0_4xMnase_TM2_NP40)

source_name: MNase-seq of T19 NP40

value: viral DNA


title: PMN.12

source_name: neutrophil

value: Minus beta-estradiol (4 days post wash)

value: ACCACTGT


title: Balding dermal papilla cell_replicate B

value: Balding DP cell

value: 10nM DHT, 24hr


title: PMN.13

value: CCGTTTGT


title: Non-balding dermal papilla cell_replicate B


title: Balding dermal papilla cell_replicate A


title: T19_4x_MNase_2_(20210810_TB_MV_T19_4x_Mnase_210730)

source_name: MNase-seq of T19

value: DNA from MNase-digested chromatin


title: Non-balding dermal papilla cell_replicate A


title: GMP.12

value: GTCGTGAT


title: T19_4x_MNase_1_(20210610_TB_Mv_20210526_4x)

source_name: MNase-seq of T19 1x MNase


title: WT-CCL4-11

tag: tissue

value: liver

value: hepatocyte

value: 12-week old


title: WT-NC-2

tag: treatment

value: NC


title: GMP.10

value: AAGAGGCA


title: WT-NC-1

value: WT


title: PMN.10

value: C57Bl/6 CD45.1-STEM

value: GTAGAGGA


title: GAS15_T_B1

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

description:
Sample_Barcode_Information.xlsx
Cells are named as GASXXX(Patient information)_C or T(Cancer or Tissue)_BXXX(Batch information)_scXXX(barcode informaltion)

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the hg19 human transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

source_name: Gastric tissue

extract_protocol:
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, a single cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene).

value: normal

tag: gender

value: male


title: GAS15_T_B2


title: T19_4x_day4_NP40_(20210920_TB_Mv_T19_0_4xMnase_TM2_NP40_day4)

source_name: MNase-seq of T19 day 4 NP40

value: viral DNA


title: PMN.7

value: Minus beta-estradiol (4 days post wash)

value: CGAGGCTG


title: WT-NC-3

source_name: liver


title: GAS15_C_B2

source_name: Gastric cancer

value: tumor


title: GMP.7

value: Plus beta-estradiol (0.5 microM)

value: GCTACGCT


title: Skeletal Muscle, mdxD2-NSG, 8Wk, replicate 1

city: Los Angeles

first: Kholoud

last: Saleh

address: 615 Charles E. Young Dr. S., BSRB 257

department: MIMG

institute: UCLA

description: 10X Genomics

data_processing:
Read alignment and gene-expression quantification was performed using the CellRanger Count Pipeline (version 3.1.0, 10X Genomics).
The filtered feature bc metrices output from CellRanger was used to create Seurat object using Seurat package version 3.1.5 with minimal alterations from published workflow (Butler et al., 2018). For each sample separately violin plots of number of expressed genes and unique transcripts (nFeature_RNA and nCount_RNA) of each cell were generated and outliers with too high or too low nFeature or nCount were removed from analysis to exclude potential doublets or low quality cells. After performing quality control, data normalization, and scaling, detection of highly variable features was then carried out for each sample separately. Further downstream analysis was carried out by merging the Seurat objects and integrating all of the cells from the different mouse models using R-package Harmony with minimal alteration from published workflow (Korsunsky et al., 2019).
Assembly: mm10
Supplementary files format and content: 10X Genomics CellRanger V3.1.0 output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.z

source_name: Gastrocnemius Skeletal Muscle

extract_protocol:
Freshly isolated right gastrocnemius muscles from 8 weeks old male mice were washed in wash buffer (DMEM/F12, 10% FBS, 0.5% P/S and 0.1 Amphotericin B ) in petri dishes. The muscles were then finely chopped with scissors in digestion buffer at room temperature (DMEM/F12, 0.5% O/S, 5% FBS and 500 units/ml collagenase II). The petri dish with chopped muscle was then placed on a shaker at a 37 ˚C incubator for 20 minutes. The digested muscle was then washed with ice cold wash buffer and transferred to a 50 ml conical tube. After centrifugation for 5 minutes at 600 g the pellet was resuspended in second digestion buffer (DMEM/F12, 0.5% P/S, 5% FBS, 1.5 units/ml collagenase D and 2.4 units/ml dispase). The conical was then secured on a shaker at a 37 ˚C incubator for 15 minutes with intermittent trituration. Ice cold FACS buffer (PBS, 2% FBS, 0.5% P/S) was then added to stop the digestion. The digested muscle was then filtered through a 70 um filter and then a 40 um filter, and then centrifuged at 400 g for 5 minutes at 4 ˚C. The supernatant was then centrifuged at 600 g for 5 minutes at 4 ˚C and the pellets from each centrifugation round were combined and supernatant was discarded. The cells were counted before live cell sort.
Libraries were performed according to 10X Genomics Chromium™ Single Cell 3’ library construction protocol.

value: Gastrocnemius Skeletal Muscle

value: Mdx, Scid, Il2rgnull, Anxa6, Ltbp4

value: severly dystrophic

value: Not treated


title: Skeletal Muscle, mdxD2-NSG, 8Wk, replicate 2

description: 10X Genomics


title: Skeletal Muscle, mdx-NSG, 8Wk, replicate 2

description: 10X Genomics

value: Mdx, Scid, Il2rgnull

value: dystrophic


title: GMP.4

value: CTCTCTAC


title: T19_4x_7h_NP40_(20211006_TB_Mv_T19_7hNP40_Mnase_20210914)

source_name: MNase-seq of T19 7 hr NP40

value: DNA from MNase-digested chromatin


title: T19_4x_day1_NP40_(20210920_TB_Mv_T19_0_4xMnase_TM2_NP40_day1)

source_name: MNase-seq of T19 day 1 NP40


title: T19_4x_55m_NP40_(20211006_TB_Mv_T19_55mNP40_Mnase_20210914)

source_name: MNase-seq of T19 55 min NP40


title: T19_4x_7m_NP40_(20211006_TB_Mv_T19_7mNP40_Mnase_20210914)

source_name: MNase-seq of T19 7 min NP40


title: PMN.3

value: C57Bl/6 CD45.1-STEM

value: TAGGCATG


title: T19_4x_3h_NP40_(20211006_TB_Mv_T19_3hNP40_Mnase_20210914)

source_name: MNase-seq of T19 3 hr NP40


title: GAS14_T_B2

value: normal

value: male


title: Skeletal Muscle, mdx-NSG, 8Wk, replicate 1

description: 10X Genomics


title: GMP.3

value: GGACTCCT


title: GAS15_C_B3


title: T19_4x_3m_NP40_(20211006_TB_Mv_T19_3mNP40_Mnase_20210914)

source_name: MNase-seq of T19 3 min NP40

value: viral DNA


title: Skeletal Muscle, Wt-NSG, 8Wk, replicate 2

description: 10X Genomics

value: Scid , Il2rgnull

value: healthy


title: GAS14_T_B1


title: PMN.2

value: Minus beta-estradiol (4 days post wash)

value: TCCTGAGC


title: GAS14_C_B3

value: tumor


title: PMN.4

value: CAGAGAGG


title: GMP.2

source_name: granulocyte monocyte progenitor

value: Plus beta-estradiol (0.5 microM)

value: AGGCAGAA


title: GAS14_C_B2


title: T19_4x_2m_day4_NP40_(20210920_TB_Mv_T19_2_4xMnase_TM2_NP40_day4)

source_name: MNase-seq of T19 2 day 4 NP40


title: Skeletal Muscle, Wt-NSG, 8Wk, replicate 1

description: 10X Genomics

value: Gastrocnemius Skeletal Muscle

value: Not treated


title: T19_4x_2m_NP40_(20210920_TB_Mv_T19_2_4xMnase_TM2_NP40)

source_name: MNase-seq of T19 2 NP40

value: DNA from MNase-digested chromatin


title: GAS14_C_B1


title: T19_4x_2m_day1_NP40_(20210920_TB_Mv_T19_2_4xMnase_TM2_NP40_day1)

source_name: MNase-seq of T19 2 day 1 NP40


title: TCR for colon GF 5-6, colon CR 5-6, colon EcN 5-6, colon kif 5-6, colon SPF_HMS 1, colon SPF_Jax 2

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description:
TotalSeq C1-10
10x  lane of 10 indiviually hashed colon samples. 2 Germfree biol reps, 2 GF + C. ramosum biol reps, 2 GF + E. coli Nissl biol reps, 2 GF + E. coli kifCD biol reps, 1 SPF_HMS rep, 1 SPF_Jax rep

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 and hash libraries were processed using cite-seq-count
Data analsysis was performed using Seurat v3 pipeline. Low-quality cells were defined as those with less than 700 or more than 3000 unique genes, or those with >10% mitochondrial gene reads and were removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
Lymphocytes were prepared by either digestion with collagenase and dispase (intestine) or mechanical disruption (MLNs, spleen), followed by staining with floursecent antibodies, hashing with Totalseq-C antibodies against MHCI and CD45,  and flow sorting CD4 T cells into RPMI/2%FCS
Libraries were prepared according to the 10x 5' (samples 1-22) and 10x5'v2 (samples 23-42) GEX, TCR, and FBC protocols

value: Colon

value: CD4+ CD44+  T cells

tag: Sex

value: Male

value: None, C. ramosum, E. coli Nissl, E. coli kifCD


title: GMP.1

value: C57Bl/6 CD45.1-STEM

value: TAAGGCGA


title: Dm_NP40_MNase_2_(20210920_TB_Dm_4xMnase_NEW_TM2_day4)

description: MNase-seq of Drosophila NP40 day 2

data_processing:
Genome_build: UCSC dm6
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to the reference sequence for Drosophila melanogaster dm6. 2. We extracted properly paired reads from the alignments with bedtools bamtobed to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  3. We used bedtools genomecov to make a normalized count bigwig file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bigwig).

organism: Drosophila melanogaster

source_name: MNase-seq


title: PMN.1

source_name: neutrophil

value: CGTACTAG


title: Dm_NP40_MNase_3_(20210920_TB_Dm_S2_4xMnase_TM2_NP40)

description: MNase-seq of Drosophila NP40


title: T19_4x_20m_NP40_1_(20210920_TB_Mv_T19_20_4xMnase_TM2_NP40)

source_name: MNase-seq of T19 20 NP40

tag: type

value: viral DNA


title: T19_4x_20m_NP40_2_(20211006_TB_Mv_T19_20mNP40_Mnase_20210914)

source_name: MNase-seq of T19 20 min NP40


title: TCR for spleen GF 1-2, spleen Ecn 1-2, spleen kif 1-2, spleen CR 2-3, spleen SPF_HMS 2, spleen SPF_Jax 1

description:
TotalSeq C1-10
10x  lane of 10 indiviually hashed spleen samples. 2 Germfree biol reps, 2 GF + C. ramosum biol reps, 2 GF + E. coli Nissl biol reps, 2 GF + E. coli kifCD biol reps, 1 SPF_HMS rep, 1 SPF_Jax rep

source_name: Spleen

value: Spleen


title: GEX for spleen GF 1-2, spleen Ecn 1-2, spleen kif 1-2, spleen CR 2-3, spleen SPF_HMS 2, spleen SPF_Jax 1


title: FBC for colon GF 5-6, colon CR 5-6, colon EcN 5-6, colon kif 5-6, colon SPF_HMS 1, colon SPF_Jax 2


title: GAS15_C_B1

source_name: Gastric cancer

value: male


title: Dm_S2_1mM_MPE_(20210927_TB_S2_1uM_MPE)

data_processing:
Library strategy:  MPE-seq
Genome_build: UCSC dm6
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (Drosophilia melanogaster dm6 or Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: MPE-seq of Drosophila 1 uM H2O2

value: DNA from MPE-digested chromatin

value: Drosophila melanogaster S2 cell


title: PMN.13.r2

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: htseq_output

extract_protocol:
Clonal naïve GMP and neutrophil total RNA was extracted from cells at 5x106 cells/ml using the Qiagen RNeasy Plus Mini Kit (Qiagen) with DNaseI treatment (RNase free DNase Set, Qiagen). RNA quality was confirmed by RNA Tapestration and quantified with Qbit. All samples showed RNA quality of >7.5 and RNA-seq libraries were prepared.
Sequencing was performed on Illumina HiSeq 2500 instrument, resulting in approximately 30 million of 50 bp reads per sample. Sequencing reads were mapped in a splice-aware fashion to the mouse reference transcriptome (mm9 assembly) using STAR. Read counts over transcripts were calculated using HTSeq based on the Ensembl annotation for NCBI37/mm9 assembly.

value: Minus beta-estradiol (4 days post wash)

tag: replicate

value: replicate 2


title: T19_4x_18hr_NP40_(20211006_TB_Mv_T19_18hNP40_Mnase_20210914)

source_name: MNase-seq of T19 18 hr NP40


title: 8_100 μg/mL PM2.5 treated cells

city: Busan

first: Jong-Ho

last: Lee

address: 37 Nakdong-daero 550 Beon-gil

institute: Dong-A University

data_processing:
HISAT v2.1.0
StringTie
StringTie v2.1.3b
Supplementary files format and content: expression

source_name: in vitro cultured cells

extract_protocol:
Total RNA was isolated using QIAzol® (Qiagen, Valencia, CA, USA). Total RNA concentration was quantified using Quant-IT RiboGreen (Invitrogen, Waltham, MA, USA). The integrity of total RNA was determined using TapeStation RNA screentape (Agilent Technologies, Atlanta, GA, USA), and samples with RNA integrity numbers higher than 7 were used for library generation.
A library was generated with 1 µg of total RNA from each sample using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina Inc., San Diego, CA, USA). First-strand cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen).
Second-strand cDNA was synthesized using DNA polymerase I, RNase H, and dUTP. The cDNA samples were processed via end repair by adding a single “A” base and ligating the adapters. The library samples were analyzed using Illumina NovaSeq (Illumina Inc.).

value: cardiomyocyte cell line

value: 100 μg/mL PM2.5 treatment

tag: tissue source

value: heart


title: T19_4x_20m_day4_NP40_(20210920_TB_Mv_T19_20_4xMnase_TM2_NP40_day4)

source_name: MNase-seq of T19 20 day 4 NP40

value: DNA from MNase-digested chromatin


title: Dm_NP40_MNase_1_(20210920_TB_Dm_4xMnase_NEW_TM2_day1)

description: MNase-seq of Drosophila NP40 day 1


title: T19_4x_20m_day1_NP40_(20210920_TB_Mv_T19_20_4xMnase_TM2_NP40_day1)

source_name: MNase-seq of T19 20 day 1 NP40


title: PMN.13.r1

value: replicate 1


title: PMN.12.r2


title: T19_4x_1m_NP40_(20211006_TB_Mv_T19_1mNP40_Mnase_20210914)

source_name: MNase-seq of T19 1 min NP40


title: 7_100 μg/mL PM2.5 treated cells


title: PMN.12.r1


title: Dm_S2_100mM_MPE_(20210927_TB_S2_100uM_MPE)

source_name: MPE-seq of Drosophila 100 uM H2O2


title: 9_100 μg/mL PM2.5 treated cells


title: Dm_8th-MNase_(20210611_TB_Dm_20210525_1_8x)

data_processing:
Genome_build: UCSC dm6
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (Drosophilia melanogaster dm6 or Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz).  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: MNase-seq of Drosophila 1/8th MNase


title: 5_10 μg/mL PM2.5 treated cells

value: 10 μg/mL PM2.5 treatment


title: PMN.7.r2


title: Dm_S2_10mM_MPE_(20210927_TB_S2_10uM_MPE)

source_name: MPE-seq of Drosophila 10 uM H2O2


title: FBC for spleen GF 1-2, spleen Ecn 1-2, spleen kif 1-2, spleen CR 2-3, spleen SPF_HMS 2, spleen SPF_Jax 1

value: CD4+ CD44+  T cells

tag: genotype

value: Male

value: None, C. ramosum, E. coli Nissl, E. coli kifCD


title: Dm_no-MNase_(20210611_TB_Dm_20210525_0x)

source_name: MNase-seq of Drosophila no MNase


title: GEX for colon GF 5-6, colon CR 5-6, colon EcN 5-6, colon kif 5-6, colon SPF_HMS 1, colon SPF_Jax 2

source_name: Colon

value: Colon


title: Dm_4x-MNase_(20210611_TB_Dm_20210525_4x)

source_name: MNase-seq of Drosophila 4x MNase


title: PMN.10.r2

source_name: neutrophil

value: C57Bl/6 CD45.1-STEM


title: T19_4th_MNase_(20210610_TB_Mv_20210526_1_4x)

source_name: MNase-seq of T19 1/16th MNase

value: viral DNA


title: T19_32th_MNase_(20210610_TB_Mv_20210526_1_32x)

source_name: MNase-seq of T19 1/128th MNase


title: Dm_S2_1000mM_MPE_(20210927_TB_S2_1000uM_MPE)

source_name: MPE-seq of Drosophila 1000 uM H2O2


title: PMN.4.r1


title: PMN.4.r2


title: T19_30min_MNase_(20210506_TB_Mv_20min_0430)

source_name: MNase-seq of T19 30 min MNase


title: 6_10 μg/mL PM2.5 treated cells


title: 4_10 μg/mL PM2.5 treated cells


title: 3_non-treated control cells


title: PMN.7.r1


title: T19_2x_MNase_(20210610_TB_Mv_20210526_2x)

source_name: MNase-seq of T19 1/2 MNase


title: PMN.3.r2


title: T19_1x_MNase_(20210610_TB_Mv_20210526_1x)

source_name: MNase-seq of T19 1/4th MNase


title: PMN.10.r1


title: 1_non-treated control cells

source_name: in vitro cultured cells


title: 2_non-treated control cells


title: Dm_2x-MNase_(20210611_TB_Dm_20210525_2x)

source_name: MNase-seq of Drosophila 2x MNase


title: T19_1mM_MPE_(20211006_TB_Mv_T19_1uM_MPE_2SCU_20210831)

source_name: MPE-seq of T19 1 uM H2O2


title: T19_1min_MNase_(20210506_TB_Mv_1min_0430)

source_name: MNase-seq of T19 1 min MNase


title: Dm_4th-MNase_(20210611_TB_Dm_20210525_1_4x)

source_name: MNase-seq of Drosophila 1/4th MNase


title: T19_2th_MNase_(20210610_TB_Mv_20210526_1_2x)

source_name: MNase-seq of T19 1/8 MNase


title: PMN.3.r1


title: Dm_1x_MNase_(20210611_TB_Dm_20210525_1x)

source_name: MNase-seq of Drosophila 1x MNase


title: Dm_2th-MNase_(20210611_TB_Dm_20210525_1_2x)

source_name: MNase-seq of Drosophila 1/2 MNase


title: Dm_32th-MNase_(20210611_TB_Dm_20210525_1_32x)

source_name: MNase-seq of Drosophila 1/32nd MNase


title: Dm_16th-MNase_(20210611_TB_Dm_20210525_1_16x)

source_name: MNase-seq of Drosophila 1/16th MNase


title: shHif_H3

city: Wuhu

first: Xiaopeng

last: Shen

address: 1 East Beijing Rd.

institute: Anhui Normal University

data_processing:
trim_galore
Hisat2
Stringtie
Assembly: GRCm38
Supplementary files format and content: csv files include read counts values for each Sample

source_name: Embryonic stem cells

extract_protocol:
Total RNA samples were extracted using the Total RNA Isolation Reagent (Biosharp).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cells

value: ESC

value: shHif-1a hypoxia


title: shHif_H2


title: T19_16th_MNase_(20210610_TB_Mv_20210526_1_16x)

source_name: MNase-seq of T19 1/64th MNase


title: PMN.1.r2

source_name: neutrophil

value: Minus beta-estradiol (4 days post wash)


title: PMN.2.r1


title: T19_15min_MNase_(20210506_TB_Mv_15min_0430)

source_name: MNase-seq of T19 15 min MNase


title: shHif_N3

value: shHif-1a normoxia


title: PMN.1.r1


title: 3D Non-balding dermal papilla cell_replicate B

data_processing:
Sequenced reads were aligned to the hg19 human genome (GRCh37) with STAR version 2.5.2a (default settings).
Transcripts were assembled with RSEM version 1.3.0.
DESeq2 was used to identify significant differential genes between samples (Benjamini-Hochberg-adjusted p-value (padj) ≤ 0.05).
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix table with raw gene count for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Dermal papilla cells derived from non-balding scalp

value: Dermal papilla

tag: phenotype

value: Non-balding

tag: culture format


title: PMN.2.r2

value: replicate 2


title: CTL (3C)

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

institute: IRCCS Casa Sollievo della Sofferenza

data_processing:
Basecalls were performed using Illumina's bcl2fastq tool
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.3.5.1. Using the following parameters : -q --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were called uing MACS v2.2.6 with the following parameters : --broad -p 1e-5 -f BAMPE –keep-dup all
bigWig files were generated using the bamCoverage package of deepTools.
Assembly: hg38
Supplementary files format and content: bigWig (except for CTL samples)
Library strategy: CUT&Tag

source_name: HUVEC

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVEC) were obtained from Thermo Fisher Scientific (Massachusetts, USA). Cells were cultured in Nunc EasYFlasks in Endothelial Cell Growth medium 2 (Promocell, Heidelberg, Germany).

extract_protocol:
Cells on the fourth day post-transfections were collected in 1.5mL tubes. Cut & Tag was performed according to the manufacturer’s protocol (Active Motif, California, USA). Briefly, cells were harvested and washed once using 1mL of 1x Wash buffer. In parallel, the Concanavalin A Beads were prepared. Each 500.000 cells, 20µL of the beads’ slurry were withdrawn and mixed with 1,6mL of 1x Binding buffer. Beads were harvested using a magnetic stand and washed twice with 1,5 mL of 1x Binding buffer. The pellet containing the cells previously harvested and the beads’ suspension were mixed in a 1.5 mL tube, rotating end-over-end for 10 minutes at room temperature. Cells were harvested by using a magnetic stand to clear and the supernatant was discarded. The pellet was resuspended in 50µL of Antibody Buffer and 1µL of Rabbit ab9108 Anti-6X His tag antibody (Abcam, Cambridge, United Kingdom) was added where needed. The mix was incubated overnight at 4oC with orbital mixing ensuring the liquid to stay together at the bottom of the tube. The Guinea Pig Anti-Rabbit Antibody secondary antibody was diluted 1:100 in Dig-Wash Buffer. The tubes were cleared using a magnetic stand and the liquid was discarded. 100µL of Guinea Pig Anti-Rabbit Antibody mix was added and tubes were incubated at room temperature for 60 minutes in an orbital rotator. Cells were cleared through a magnetic stand, and they were washed three times using 1mL of Dig-Wash Buffer. In parallel, the CUT&TAGTM Assembled pA-Tn5 Transposomes was diluted 1:100 with Dig-300 Buffer. For each immunoprecipitated samples, 100µL of CUT&TAGTM Assembled pA-Tn5 Transposomes was added, and the mix was placed on an orbital rotator for 60 minutes at room temperature. The cells were harvested using a magnetic stand and eventually washed three times using 1mL of Dig-300 buffer. In the following step each tube was supplemented with 125µL of Tagmentation Buffer and incubated at 37oC for 60 minutes. To isolate the DNA surrounding macroH2A1.1 and macroH2A1.2 deposition regions, the tagmentation was first stopped by addition of 4,2µL of 0,5M EDTA, 1,25µL of 10% SDS and 1,25µL of Proteinase K (10mg/mL) per each sample. The tubes were then vortexed at full speed and incubated for 60 minutes at 55oC to digest. The samples were cleared using a magnetic stand and 625µL of DNA Purification Buffer per each were added. The samples were transferred to DNA Purification Columns, centrifuged at 17000G for 1 minute. After the flow-through was discarded, 750µL of DNA Purification Wash Buffer was added to each sample, which was then centrifuged again at 17000G for 1 minute. The flow-through was discarded. To remove any DNA Purification Wash Buffer leftover, the empty columns were further centrifuged at 17000G for 2 minutes. To isolate the DNA, 35µL of DNA Purification Elution Buffer were added to each sample, which was then incubated at room temperature for 1 minute and eventually centrifuged at 17000G for 1 minute.
Library preparation for Cut & Tag samples was performed according to the manufacturer’s protocol (Active Motif, California, USA). Paired-end Illumina sequencing was obtained using Illumina Hiseq 2500 (Illumina, San Diego, CA,  USA), obtaining two FASTQ files for each of the two biological replicates of macroH2A1.1,  two for each of the three biological replicates of macroH2A1.2  and two for each of the three biological replicates of the control samples, for a total of 4.8, 8.1 and 7.2 million reads, respectively.

treatment_protocol: Cellular reprogramming was performed as already described (Giallongo et al. 2022). Briefly, cells were harvested using TrypLE express enzyme (Thermo Fisher Scientific, Massachusetts, USA) and transfected with Epi5 Episomal iPSC Reprogramming Kit (Thermo Fisher Scientific, Massachusetts, USA), using 10µL Neon Transfection System (Thermo Fisher Scientific, Massachusetts, USA). For this purpose, 10^5 living cells were resuspended in 10µL of R buffer and 1µL of the content of each vial from the reprogramming kit was added. Furthermore, 3mL of E buffer were added to the Neon transfection tube together with the vectors expressing macroH2A1.1-6His and macroH2A1.2-6His (Addgene, Massachusetts, USA), where needed [25]. Electroporation was performed using Pulse voltage 1400 V, Pulse Width 20 ms, Pulse number 2. Cells were seeded on 35mm Petri dishes coated by hESC-qualified MatriGel in endothelial medium, which was changed daily until day 4 post-transfection.

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: control

tag: chip antibody

value: ab9108 Anti-6X His tag antibody