title: untreated_REFORC_crosslinking_rep2

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min, cells were fixed with paraformaldehyde before lysis, rep2
untreated_crosslinking_REFORC.narrowPeak

data_processing:
For analysis of REFORC data acquired under crosslinking conditions, the raw reads were trimmed with Fastp version 0.20.1 (parameters: --trim_poly_g --poly_g_min_len 6 --trim_poly_x --poly_x_min_len 6 --cut_front --cut_tail --cut_window_size 4 --qualified_quality_phred 15 --low_complexity_filter --complexity_threshold 30 --length_required 4). For analysis of data acquired via REFORC without crosslinking, the raw reads were trimmed with Trim-galore version 0.6.10 (parameters: -q 20  --phred33 --length 20 --stringency 4).
For analysis of REFORC data acquired under crosslinking conditions, the cleaned reads were aligned to the genome with STAR version 2.7.10b (parameters: --outFilterMismatchNmax 10 --outFilterMatchNminutes 10 --seedSearchLmax 10 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0), we removed the reads near the rDNA loci on chromosome 21 as nonspecific signals. For analysis of data acquired via REFORC without crosslinking, the cleaned reads were aligned to the genome with HISAT2 version 2.2.1 (parameters: --dta-cufflinks --un-conc).
The duplicated reads were removed with Sambamba version 0.8.2, and mapped reads were sorted with SAMtools version 1.17 and converted to generate bigWig files via the bamCoverage function of deepTools version 3.5.1 (parameters: --normalizeUsing CPM).
For peak calling, the untreated group and mock group were used as controls to obtain HU group-specific peaks with MACS2 version 2.1.0.20150731 for analysis of data acquired via REFORC with crosslinking or with Piranha for analysis of data acquired via REFORC version 1.2.1 without crosslinking. The false discovery rate (FDR) cutoff was set as 0.2 in MACS2. In Piranha, the parameters were set as follows: -s -p 0.05 -b 20 -l -n -i 20.
Assembly: hg38
Supplementary files format and content: bigWig, BED, narrowPeak

molecule: nuclear RNA

growth_protocol: HeLa cells and DDX39A/DDX39B knockout cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, and incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
The cells were harvested by scraping, washed twice with prechilled PBS and then fixed or collected directly without fixation for further processing. When fixation was performed, the cells were subjected to crosslinking at room temperature for 10 minutes with 1% paraformaldehyde diluted in PBS, and the reaction was then quenched with 0.125 M glycine. The cells were then washed twice with prechilled DEPC-treated PBS and subsequently permeabilized with DEPC-treated PBS containing 0.25% Triton X-100 and 80 U/Ml RNase inhibitor (Biosharp, BL780B) on a rotator at room temperature for 30 minutes. After centrifugation, the cell pellets were washed once with DEPC-treated PBS. Then, fresh click reaction mixture (in DEPC-treated PBS with sequential addition and mixture of 25 μM biotin-PEG3-azide, 100 mM sodium ascorbate, 100 mM CuSO4 and 80 U/mL RNase inhibitor) was added to the pellets, which were incubated on a rotator at room temperature for 2 hours. The cell pellets were then washed once with DEPC-treated PBS and lysed on ice in lysis buffer (DEPC-treated double-distilled water (ddH2O) containing 1% SDS, 50 mM Tris-HCl (pH 8.0), and 80 U/mL RNase inhibitor) for 10 minutes. A noncontact ultrasonic disruptor (Covaris M220 focused ultrasonicator) was subsequently used to sonicate the pellets for 3 minutes to obtain smeared DNA‒RNA fragments of 100-300 bp. After sonication, the samples were centrifuged at 15000 rpm at 4°C for 10 minutes, after which the supernatant was collected. The supernatant was diluted with an equal volume of DEPC-treated PBS supplemented with cocktail and RNase inhibitor. Two hundred microliters of streptavidin beads (GE) was added to each group, and the mixtures were incubated on a rotator at 4°C for 14-16 hours. The beads were washed with DEPC-treated PBS four times. Two hundred microliters of NT2 buffer (DEPC-treated ddH2O containing 50 mM HEPES (pH 7.5), 150 mM KCl, 1 mM MgCl2, 0.05% NP-40 and 80 U of RNase inhibitor) was added to the beads in each group, which were incubated at 95°C for 5 minutes and then immediately placed on ice for 2 minutes. The beads were treated with 10 U of RQ1 RNase-Free DNase I (Promega, M6101) and 80 U of RNase inhibitor and incubated in a Thermo Mixer-Heat with rotation at 1200 rpm at 37°C for 2 hours. For the RNase H treatment group, 25 U of RNase H (NEB, M0297S) was added, and the mixture was incubated with rotation at 1200 rpm at 37°C for 1 h before DNase I treatment. Finally, 500 μL of TRIzol was added to the bead mixture, which was incubated at room temperature for 5 minutes and centrifuged at 15000 rpm for 5 minutes. Phenol–chloroform was added to the supernatant for extraction. Then, 10 μL of glycogen (20 mg/mL), 40 μL of NaCl (5 M), and a 5x volume of ethanol was added to the RNA-containing supernatant, which was mixed and incubated at -20°C overnight. The next day, the mixture was centrifuged at 15000 rpm for 30 minutes at 4°C. We then washed the RNA pellet once with 75% ethanol. Finally, we resuspended the pellet in 12 μL of DEPC-treated water to prepare the sample for sequencing.
We used rRNA probes for rRNA cleanup. The RNA samples (no more than 2 μg) were mixed with 1 μL of rRNA probes (1 μM) and 2 μL of probe hybridization buffer (750 mM Tris-HCl, pH 8.0; 750 mM NaCl) and incubated at 95°C for 2 minutes, cooled to 22°C at a rate of 0.1°C/s and incubated at 22°C for 5 minutes. Then, 2 μL of Thermostable RNase H (NEB, M0523S), 2 μL of 10x RNase H buffer and 1 μL of ddH2O were added to the mixture, which was incubated at 50°C for 30 minutes. The RNA samples were further incubated with 2.5 μL of DNase I (NEB, M0303S), 2.5 μL of 10x DNase I buffer and 4.5 μL of ddH2O at 37°C for 30 minutes. After cleaning the rRNA, we constructed strand-specific cDNA libraries with the Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (Yeasen) according to the instructions. However, we did not further fragment RNA with the reagent provided in the kit because the RNA was fragmented during sonication. The cDNA libraries were sequenced by Novogene on an Illumina platform.

treatment_protocol: First, the cells were synchronized by a double thymidine block. The cells were treated with 2 mM thymidine for 18 h, the block was released for 9 h, and the cells were then treated again with thymidine for 18 h. This process allowed the cells to be synchronized at the G1/S boundary, and the block was released for 1 h. Then, the cells were incubated with preheated 20 μM EdU for 10 min in a 37°C incubator. For the untreated group, cells were collected directly; for the HU group, cells were further treated with 4 mM HU for 1 h without EdU washout.

value: HeLa cell line


title: Cas13d gRNA amplicon of Homo sapiens: Essentiality HEK293FT_D0_R1

status: Public on Dec 18 2024

type: SRA

city: New York

first: Sydney

last: Hart

state: New York

address: 101 AVENUE OF THE AMERICAS NEW YORK, NY

country: USA

institute: New York Genome Center

description:
Library name: Essentiality_HEK293FT_D0_R1
EssHEK_D0_R1

library_source: genomic

data_processing:
We processed reads from pooled Cas13d screens following established pipelines4: First, reads were de-multiplexed based on Illumina i7 barcodes present in PCR2 reverse primers and custom in-read i5 barcodes, allowing for one mismatch. Reads were trimmed to the expected gRNA length by identifying known anchor sequences relative to the guide sequence. Reads were trimmed using Cutadapt (v.1.13)19 with the following parameters: -g CTGGTCGGGGTTTGAAAC -e 0.2 -O 5 --discard-untrimmed and -a TTTTTGAATTCGCTAGCT -e 0.1 -O 5 --minimum-length 15 --discard-untrimmed.
We aligned processed reads to the designed crRNA reference using bowtie (v.1.1.2)20 and allowed for up to three mismatches (parameters: -v 1 -m 3 –best -q) for Screen 1 and Screen 3. For Screen 2 (HDAC1 and HDAC2 titration), processed reads were collapsed (FASTX-Toolkit) to count perfect duplicates followed by exact string-match intersection with the reference such that only perfectly matching and unique alignments were kept. The raw gRNA counts were normalized using a median of ratio method21 and batch corrected for biological replicates using combat from the SVA R package (v.3.34.0)22 . Nonreproducible technical outliers were removed by pair-wise linear regression for each sample, collecting residuals, and taking the median value for individual gRNAs across each time point.
Assembly: GRCh38
Supplementary files format and content: comma-separated values files include raw counts for each sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: human embryonic kidney cells

growth_protocol: HEK293FT (Thermo R70007) and A375 (ATCC CRL-1619) cells were cultured in D10 medium, which is Dulbecco’s Modified Eagle Medium (DMEM) with high glucose and stabilized L-glutamine (Caisson DML23) supplemented with 10% fetal bovine serum (Sigma 14009C). HAP1 (Horizon C631) cells were cultured in I10 medium: Iscove’s Modified Dulbecco’s Medium (IMDM) with L-glutamine (Caisson IML02) supplemented with 10% fetal bovine serum. All cells were incubated at 37 °C with 5% carbon dioxide.

extract_protocol:
Genomic DNA was isolated from cell pellets via a modified salting out procedure. For that, 12 ml of NK Lysis Buffer (50 mM Tris, 50 mM EDTA, 1% SDS, pH 8) and 60 µl of 20 mg/ml Proteinase K (QIAGEN 19131) were added to 80 million cells and incubated at 55 °C overnight. The next day, 6 µl of 100 mg/ml RNase A (A.G. Scientific R-2000) was added to the lysed sample, which was then inverted 25 times and incubated at 37 °C for 30 min. Samples were cooled on ice before addition of 4 ml of pre-chilled 7.5M ammonium acetate (Sigma A1542) to precipitate proteins. After adding ammonium acetate, the samples were vortexed and centrifuged at 4,000 × g for 10 minutes. After the spin, 12 ml isopropanol was added to the collected supernatant, inverted 50 times and centrifuged at 4,000 × g for 10 minutes. The supernatant was discarded, 12 ml of freshly prepared 70% ethanol was added, the tube was inverted 10 times, and then centrifuged at 4,000 × g for 10 minutes. The supernatant was discarded, and remaining ethanol was removed. After air drying for 30 minutes, 500 µl of 0.2× TE buffer (Sigma 93283) was added, the tube was incubated at 65 °C for 1 hour and at room temperature overnight to fully resuspend the DNA. The next day, the gDNA samples were vortexed briefly. The gDNA concentration was measured using a Nanodrop (Thermo).
We amplified gRNA cassettes from the genomic DNA using a two-step PCR protocol (PCR1 and PCR2). PCR1 was performed to amplify a region containing the crRNA cassette in the lentiviral genomic integrant using TaqB polymerase (Enzymatics P7250L). We performed an appropriate amount of PCR1 reactions for each gDNA sample based on library size (Screen 1: 40 reactions; Screen 2: 20 reactions; Screen 3: 48 reactions) using 10 μg gDNA per 100 μl PCR1 reaction (10 cycles). We then combined PCR1 products for the same sample together before PCR2, which was done to incorporate Illumina adaptors using Q5 polymerase (NEB M0491). We performed an appropriate number of PCR2 reactions for each sample (Screen 1: 16 reactions; Screen 2: 8 reactions; Screen 3: 24 reactions) using 5 μl unpurified PCR1 product per 50 μl reaction (18 cycles). The resulting amplicons from PCR2 (~270 bp) were pooled and then purified using SPRI beads (Beckman B23317) or gel extracted using a QiaQuick Gel Extraction kit (Qiagen 28704).

treatment_protocol: Cas13d-expressing cells were transduced with the library lentivirus through separate infection replicates by spinfection at 1000 rpm for 1 hour at 37 °C, followed by overnight incubation. After 24 hours, new media with 1 μg/ml puromycin (Invivogen ant-pr-1) was added. Puromycin selection was completed within 48 hours for all cell lines. Following puromycin selection, RfxCas13d or HfCas13d expression was induced by replenishing the growth medium containing 1 μg/ml puromycin, 5 μg/ml blasticidin and 1 μg/ml doxycycline. Cells were passaged every 2 to 4 days and split as needed, ensuring a guide representation of >1,000×. Samples with a guide abundance of 1,000-fold were harvested at day 0 and 14 days post-Cas13d induction.

tag: tissue

value: human embryonic kidney cells

tag: cell line

tag: cell type

value: embryonic kidney cells

tag: genotype

tag: treatment

value: doxycycline induction

tag: batch

value: Input Day 0


title: control, R12565

city: New York City

first: Michael

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Raw RNA sequences were aligned to the hg38 reference genome from Ensembl via the STAR algorithm.
Quality control checks, including assessments of GC content, duplication rates, gene body coverage, and library complexity, were carried out using RSeQC30 and Picard tools (https://broadinstitute.github.io/picard/). Gene expression levels were quantified with featureCounts and the resulting expression matrix was curated to retain genes present in at least one-third of our sample set. This matrix was then normalized through the VOOM method.
Assembly: hg38
Supplementary files format and content: Raw count data were generated with featureCounts and are provided as a separate matrix.

molecule: total RNA

source_name: DLPFC

extract_protocol:
Total RNA was extracted from all tissue samples using AllPrep DNA/RNA Mini Kit (Qiagen Cat No./ID: 80204).
Paired-end strand-specific sequencing libraries were prepared from 300ng total RNA using the TruSeq Stranded Total RNA Library Preparation kit with Ribo-Zero Gold ribosomal RNA depletion which removes rRNA and mtRNA. The libraries were then sequenced on an Illumina HiSeq 3000 at the Promega Sequencing Facility, producing a median of 46.9 million reads per sample.

value: DLPFC

value: Postmortem brain tissue

tag: Sex

value: F

tag: group/disease

value: control

tag: rin


title: HU_RNaseH_REFORC_crosslinking

city: Beijing

first: Jiadong

last: Wang

address: 38 College Road, Haidian District

department: Department of Radiation Medicine

country: China

institute: Peking University Health Science Center

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, cells were fixed with paraformaldehyde before lysis, and the beads were treated with RNase H (NEB, M0297S) at 37°C for 1 h,  without replicate
HU_vs_untreated_crosslinking_REFORC.narrowPeak

source_name: HeLa cell line

value: Wild type


title: untreated_REFORC_crosslinking_rep1

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min, cells were fixed with paraformaldehyde before lysis, rep1
untreated_crosslinking_REFORC.narrowPeak


title: High fidelity Cas13d gRNA amplicon of Homo sapiens: HAP1_D14_R3

description:
Library name: HfCas13d_HAP1_D14_R3
Hf_D14_R3

source_name: chronic myelogenous leukemia

value: chronic myelogenous leukemia

value: cancer cells

value: High-fidelity Cas13d

value: Fitness Screen Day 14


title: 28-09-0001-4_post_12

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the University of California Santa Cruz (UCSC) Human genome assembly version 38.91, using STAR v.2.4.2a. Duplicate filtering, QC and metrics analysis was performed using the Picard 1.134 family of tools[ref]. For quality control, samples were kept that had human aligned counts > 250,0001 million mapped reads and median coefficient of variation (CV) coverage < 0.956. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1.20.8 in at least 23 samples and further filtered for only protein coding genes. Normalized counts were transformed to log2 counts per million mapped reads along with observations level weights using voomWithQualityWeights from the limma R package version 3.5.1.(Ritchie ME et al. Nucleic Acids Res. 2015;20;43(7):e47) Sequencing was performed in 3 sample batches and a batch correction was done using limma removeBatcheffects.
Differentially expressed genes were then coassociated into modules using weighted gene correlation network analysis (WGCNA)
Assembly: GRCh38
Supplementary files format and content: csv file voom normalized counts

source_name: nasal lavage sample

extract_protocol:
Total RNA was isolated from pre- and post NAC nasal lavage samples.  Cell pellets were collected in RNAprotect Saliva Reagent (Qiagen) with extraction using the RNeasy MinElute spin column (Qiagen) following the manufacturer’s protocol. Total RNA was isolated from nasal cell pellets in RNAprotect Saliva Reagent (Qiagen). Samples were centrifuged for 10 minutes at 10,000g, supernatant was removed, and the cell pellet was resuspended in 350μl RLT Buffer + 1% beta mercaptoethanol. The sample was vortexed for 1-2 seconds, sonicated for 30 seconds, spun through a Qiashredder column (Qiagen) and then extracted using the RNeasy MinElute spin column (Qiagen) following the manufacturer’s protocol. RNA quality was assessed using RNA electrophoresis (Agilent) and NanoDrop 1000 (NanoDrop Products, Thermo Fisher Scientific).
Sequencing libraries were constructed from total RNA using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina)

tag: participant id

value: Female

value: Placebo

tag: age

tag: month

tag: nac

value: post

tag: tnss

tag: tsneez

tag: dose

tag: pct reads

tag: median cv

value: nasal lavage sample


title: control, R12541

tag: tissue


title: HU_REFORC_crosslinking_rep2

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, cells were fixed with paraformaldehyde before lysis, rep2
HU_vs_untreated_crosslinking_REFORC.narrowPeak

tag: cell line

value: HeLa cell line


title: 28-09-0001-4_pre_12

value: pre


title: High fidelity Cas13d gRNA amplicon of Homo sapiens: HAP1_D14_R2

description:
Library name: HfCas13d_HAP1_D14_R2
Hf_D14_R2

tag: cell type

tag: genotype

value: doxycycline induction


title: HU_REFORC_crosslinking_rep1

description: HeLa, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, cells were fixed with paraformaldehyde before lysis, rep1

tag: treatment


title: 28-05-0001-0_post_0

tag: Sex

value: SCIT

tag: batch


title: control, R12525

value: DLPFC

value: M

tag: group/disease

tag: rin


title: High fidelity Cas13d gRNA amplicon of Homo sapiens: HAP1_D14_R1

description:
Library name: HfCas13d_HAP1_D14_R1
Hf_D14_R1


title: control, R12522

value: Postmortem brain tissue

value: F


title: 28-03-0004-8_post_0

tag: participant id

value: Male

tag: age


title: High fidelity Cas13d gRNA amplicon of Homo sapiens: HAP1_D0_R3

description:
Library name: HfCas13d_HAP1_D0_R3
Hf_D0_R3

value: chronic myelogenous leukemia

value: Input Day 0


title: mock_REFORC

description:
HeLa,  treated with 4 mM HU for 1 h and without EdU labeled, without replicate
WT_HU_vs_untreated_REFORC.peak.bed

value: Wild type


title: Cas13d gRNA amplicon of Homo sapiens: Dual Titration A375_D0_R1

description:
Library name: DualTitration_A375_D0_R1
Dual_D0_R1

source_name: malignant melanoma skin cells

value: malignant melanoma skin cells

value: cancer cells


title: mock_REFORC_crosslinking

description:
HeLa,  treated with 4 mM HU for 1 h and without EdU labeled, cells were fixed with paraformaldehyde before lysis, without replicate
untreated_crosslinking_REFORC.narrowPeak


title: 28-03-0004-8_pre_0

value: Placebo

tag: month

tag: nac


title: WT_untreated_REFORC_rep2

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min, rep2
WT_HU_vs_untreated_REFORC.peak.bed


title: High fidelity Cas13d gRNA amplicon of Homo sapiens: HAP1_D0_R2

description:
Library name: HfCas13d_HAP1_D0_R2
Hf_D0_R2

value: High-fidelity Cas13d


title: High fidelity Cas13d gRNA amplicon of Homo sapiens: HAP1_D0_R1

description:
Library name: HfCas13d_HAP1_D0_R1
Hf_D0_R1


title: 28-03-0002-6_pre_0

value: Female

tag: tnss

tag: tsneez

value: nasal lavage sample


title: WT_HU_REFORC_rep2

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, rep2
WT_HU_vs_untreated_REFORC.peak.bed

value: HeLa cell line


title: control, R12510

value: control


title: control, R12481


title: 28-03-0003-7_post_0

value: SCIT

value: post

tag: dose

tag: pct reads


title: WT_untreated_REFORC_rep1

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min, rep1
WT_HU_vs_untreated_REFORC.peak.bed


title: control, R12443

tag: tissue

value: DLPFC

value: M


title: sample4(d16)_CD8_lung_TCR

city: Paris

first: Sebastien

last: Mella

address: 28 rue du Dr Roux

department: Immunology

country: France

institute: Institut Pasteur

data_processing:
Chromium Single Cell 5p RNA library v1
Illumina sequencing system
Cell Ranger 3.1.0, mkfastq (bcl2fastq v2.20.0) to generate fastq files from .bcl
Cell Ranger 3.1.0, count  to make the count matrix from fastq files
Assembly: GRCh38-3.0.0
Supplementary files format and content: CellrRanger output; count matrix in .h5 format
Supplementary files format and content: CellRanger output: TCR information in comma-delimited format
Library strategy: scTCR-seq

source_name: Lung

extract_protocol:
Fresh renal tumors were collected in Hank’s Balanced Salt Solution (HBSS). After being mechanically dissociated with a scalpel, they were digested with DNAse I (30IU/mL, Roche) and Collagenase D (1mg/mL, Roche) at 37°C for one hour. Primary cells were then isolated by successive filtration on a 70μm Falcon cell strainer (BD Falcon) and a 20μm Falcon cell strainer (BD Falcon) and counted on a Malassez chamber.Cells were then stained with a fixable viability stain FVS 520 (eBioscience), an anti-CD8a labeled with APC fluorophore (Biolegend) and an anti-NKP46 labeled with BV421 (Biolegend) in order to eliminate natural killer cells from the analysis during the cell sorting.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

value: CD8+T cells


title: 28-03-0003-7_pre_0

value: Male

value: pre

tag: median cv


title: control, R12447

tag: cell type

value: Postmortem brain tissue

value: F


title: WT_HU_REFORC_rep1

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, rep1
WT_HU_vs_untreated_REFORC.peak.bed

tag: cell line

tag: genotype

value: Wild type


title: sample4(d16)_CD8_lung_GEX

library_source: transcriptomic single cell

data_processing:
Chromium Single Cell 5p RNA library v1
Illumina sequencing system
Cell Ranger 3.1.0, mkfastq (bcl2fastq v2.20.0) to generate fastq files from .bcl
Cell Ranger 3.1.0, count  to make the count matrix from fastq files
Assembly: GRCh38-3.0.0
Supplementary files format and content: CellrRanger output; count matrix in .h5 format
Supplementary files format and content: CellRanger output: TCR information in comma-delimited format


title: DDX39BKO_untreated_REFORC_rep2

description:
HeLa,DDX39B knockout, incubated with 20 μM EdU at 37°C for 10 min, rep2
DDX39BKO_HU_vs_untreated_REFORC.peak.bed

value: DDX39B knockout

tag: treatment


title: 28-09-0002-0_pre_12

tag: Sex

value: Placebo

tag: batch


title: 28-06-0014-3_post_0


title: control, R12408

tag: group/disease

tag: rin


title: DDX39BKO_untreated_REFORC_rep1

description:
HeLa,DDX39B knockout, incubated with 20 μM EdU at 37°C for 10 min, rep1
DDX39BKO_HU_vs_untreated_REFORC.peak.bed


title: 28-06-0014-3_pre_0

tag: participant id

tag: age


title: control, R12384


title: sample3(d8)_CD8_lung_GEX


title: DDX39BKO_HU_REFORC_rep2

description:
HeLa,DDX39B knockout, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, rep2
DDX39BKO_HU_vs_untreated_REFORC.peak.bed


title: 28-06-0004-4_post_0

value: Female

tag: month

tag: nac


title: DDX39BKO_HU_REFORC_rep1

description:
HeLa,DDX39B knockout, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, rep1
DDX39BKO_HU_vs_untreated_REFORC.peak.bed


title: control, R12368


title: control, R12381


title: sample2(d4)_CD8_lung_TCR


title: sample2(d4)_CD8_lung_GEX


title: control, R12362


title: DDX39AKO_untreated_REFORC_rep2

description:
HeLa,DDX39A knockout, incubated with 20 μM EdU at 37°C for 10 min, rep2
DDX39AKO_HU_vs_untreated_REFORC.peak.bed

value: DDX39A knockout


title: DDX39AKO_untreated_REFORC_rep1

description:
HeLa,DDX39A knockout, incubated with 20 μM EdU at 37°C for 10 min, rep1
DDX39AKO_HU_vs_untreated_REFORC.peak.bed

value: HeLa cell line


title: sample1(d3)_CD8_lung_GEX


title: sample1(d3)_CD8_lung_TCR


title: 28-06-0001-1_post_0

tag: tnss

tag: tsneez

value: nasal lavage sample


title: DDX39AKO_HU_RNaseH_REFORC

description:
HeLa,DDX39A knockout, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h and the beads were treated with RNase H (NEB, M0297S) at 37°C for 1 h,  without replicate
DDX39AKO_HU_vs_untreated_REFORC.peak.bed

value: incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h and then treated with 4 mM HU for 1 h, the beads were treated with RNase H (NEB, M0297S) at 37°C for 1 h


title: control, R12344

value: control


title: 28-06-0003-3_pre_0

tag: dose

tag: pct reads


title: 28-06-0003-3_post_0

value: post

tag: median cv

tag: tissue


title: fMPN3 [ATAC-seq]

city: paris

first: SARAVANAN

last: GANESAN

state: Paris

address: 1 Avenue Claude Vellefaux, 75010 Pa

institute: IRSL, Hopital Saint Louis

data_processing:
Read from ATAC-seq were mapped to the hg38 genome using bowtie2. Snaptools was used to generate binary count matrices in 5kb genomic bins. Clustering analysis was performed using SnapATAC for cells with greater than 1000 reads and percentage of reads in promoters greater than 20%.
Assembly: hg38
Supplementary files format and content: bigWig files

source_name: Bone marrow

growth_protocol: F-MPN MSCs and normal MSCs were expanded from the bone marrow biopsies from MPN patients and age-matched normal patients who underwent hip replacement surgery respectively. MSCs were cultured using MEM alpha medium (Life Technologies Inc.) with 10% fetal bovine serum (Life Technologies Inc.), 100 units/ml penicillin and 100 ug/ml streptomycin, L-Glutamine, β- mercaptoethanol (Life Technologies Inc.) in a humidified atmosphere with 5% CO2. Medium was changed every 3 days until the stroma is expanded. Stromal cells from passage 2 or 3 were used for the study. For osteoblast and adipocyte differentiation, the MSCs from passage 2 were used. The medium for osteoblast differentiation was MEM alpha (Life Technologies Inc.) supplemented with 10% FBS, pen-strep (1%), L-glutamine (1%), Dexamethasone (0.1uM), β-Glycerophosphate (10mM), Ascorbic acid (50uM).

extract_protocol: 50k viable nuclei were tagmented using Tn5 enzyme pre-loaded with next-gen sequencing adapters, followed by amplification of tagmented DNA using standard primers from the kit (Active -motif Inc, USA). The amplified libraries were subjected to sequencing using NextSeq500 (Illumina).

tag: diagnosis

value: myelofibrosis

tag: cell type

value: mesenchymal stromal cells (MSCs)


title: fMPN2 [ATAC-seq]


title: 28-06-0001-1_pre_0

tag: treatment

value: SCIT


title: DDX39AKO_HU_REFORC_rep2

description:
HeLa,DDX39A knockout, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, rep2
DDX39AKO_HU_vs_untreated_REFORC.peak.bed

tag: cell line

tag: genotype


title: DDX39AKO_HU_REFORC_rep1

description:
HeLa,DDX39A knockout, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, rep1
DDX39AKO_HU_vs_untreated_REFORC.peak.bed


title: control, R12347

value: DLPFC

tag: Sex

value: M

tag: group/disease


title: control, R12096

value: Postmortem brain tissue

tag: rin


title: 28-07-0005-7_post_0

tag: participant id

value: Male

tag: age

tag: batch


title: sample3(d8)_CD8_lung_TCR

value: Lung

value: CD8+T cells


title: 28-06-0004-4_pre_0

tag: month

tag: nac

value: pre

tag: tnss


title: fMPN1 [ATAC-seq]


title: HeLa, untreated, rep3

data_processing:
The raw data were trimmed using Trim-Galore version 0.6.10 (parameters: -q 20  --phred33 --length 20 --stringency 4).
The cleaned reads were alignment to the hg38 genome by HISAT2 version 2.2.1 (parameters: --dta-cufflinks --un-conc).
The count matrix was generated using featureCounts version 2.0.6.
Assembly: hg38
Supplementary files format and content: Text files includes raw counts for each sample

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, and incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent.
mRNA was isolated from total RNA using magnetic beads with poly-T oligo attached. Fragmentation was conducted by subjecting the RNA to elevated temperature in the presence of divalent cations and the First Strand Synthesis Reaction Buffer. First strand cDNA synthesis was performed using M-MuLV Reverse Transcriptase (RNase H-) and random hexamer primers. Subsequently, second strand cDNA synthesis was carried out using DNA Polymerase I and RNase H. Following adenylation of the 3' ends of DNA fragments, adaptors with hairpin loop structures were ligated to facilitate hybridization. The library was purified using the AMPure XP system. PCR was then performed using Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. Finally, the PCR products were purified.

treatment_protocol: untreated

value: Wild type

value: untreated


title: control, R12323

value: F


title: 28-07-0005-7_pre_0

value: Placebo

tag: tsneez

tag: dose

tag: pct reads

value: nasal lavage sample


title: control, R12087

tag: tissue

value: control


title: nMSC3 [ATAC-seq]

tag: diagnosis

value: normal control

tag: cell type


title: OCD, R12081

value: OCD


title: nMSC2 [ATAC-seq]

value: mesenchymal stromal cells (MSCs)


title: HeLa, untreated, rep1

tag: cell line

value: HeLa cell line

tag: treatment


title: OCD, R12066

value: DLPFC

tag: Sex


title: ED, R12062

tag: group/disease

value: ED


title: 28-07-0002-3_post_0

value: Female

value: SCIT

value: post

tag: median cv


title: mock_IP_EdUseq

description:
HeLa, treated with 4 mM HU for 1 h, IP
WT_untreated_EdUseq.narrowPeak

data_processing:
The raw reads were trimmed with Trim-galore version 0.6.10 (parameters: -q 20  --phred33 --length 20 --stringency 4).
The cleaned reads were aligned to the genome with HISAT2 version 2.2.1 (parameters: --dta-cufflinks --un-conc).
Duplicate reads were removed with Sambamba version 0.8.2, mapped reads were sorted with SAMtools version 1.17, and converted to generate bigWig files via the bamCoverage function of deepTools version 3.5.1 (parameters: --normalizeUsing CPM).
The called peaks and narrowPeak files were generated with MACS2 version 2.1.0.20150731 (parameters: -q 0.2).
Assembly: hg38
Supplementary files format and content: bigWig and narrowPeak files

growth_protocol: HeLa cells and DDX39A knockout cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, and incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
The cells were harvested by scraping, washed twice with prechilled PBS and then fixed with 90% methanol at 4°C overnight. The cells were then washed twice with PBS, permeabilized with PBS containing 0.25% Triton-X 100 on a rotator at room temperature for 30 minutes. After centrifugation, the cell pellets were washed once with PBS. Then, fresh click reaction mixture (PBS with sequential addition and mixture of 25 μM biotin-PEG3-azide, 100 mM sodium ascorbate, 100 mM CuSO4) was added to the pellets, which were incubated on a rotator at room temperature for 2 hours. The cell pellets were then washed once with PBS and lysed on ice in lysis buffer (double-distilled water (ddH2O) containing 1% SDS, 50 mM Tris-HCl (pH 8.0)) for 10 minutes. A noncontact ultrasonic disruptor (Covaris M220 focused ultrasonicator) was subsequently used to sonicate the pellets for 3 minutes to obtain smeared DNA fragments of 100-300 bp. After sonication, the samples were centrifuged at 15000 rpm at 4°C for 10 minutes, after which the supernatant was collected. Part of the supernatant was taken as the input sample, while the remaining portion was used as the immunoprecipitation (IP) fraction. 100 μL of streptavidin beads was added to the supernatant of each IP group, and the mixture was incubated on a rotator at room temperature for 2 hours. The beads were subsequently washed successively with the following solutions: lysis buffer, 1 M NaCl, lysis buffer, 1 M NaCl, lysis buffer, and TE buffer (1 mM EDTA, pH 8.0; and 10 mM Tris-HCl, pH 8.0). Then, 300 μL of 2% β-mercaptoethanol was added to the beads, and the mixture was incubated with rotation at room temperature for 1 hour. The samples were subsequently centrifuged at 15000 rpm for 2 minutes, the supernatants were collected and extracted with phenol-chloroform. Then, 10 μL of glycogen (20 mg/mL), 100 μL of ammonium acetate (7.5 M), 40 μL of NaCl (5 M), and a 5x volume of ethanol were added to each supernatant and mixed, and the mixtures were incubated at -20°C overnight. The next day, the samples were centrifuged at 15000 rpm for 30 minutes at 4°C. We washed each pellet once with 75% ethanol and then centrifuged the sample and removed the supernatant. Finally, we resuspended the pellet in nuclease-free water to prepare the sample for sequencing.
The purified DNA was used NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645L) for library preparation.

tag: genotype

value: treated with 4 mM HU for 1 h

tag: fraction

value: IP


title: WT_untreated_IP_EdUseq

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min, IP
WT_untreated_EdUseq.narrowPeak

value: Wild type


title: mice podocyte cells, KO_2

city: Nanjing

first: Yang

last: Chen

address: 639 Longmian Avenue

institute: Chinese Pharmaceutical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: renal podocyte

growth_protocol: Extraction and culture of primary mouse podocytes:  In brief, mice were anesthetized with isoflurane. Sequentially, 10 ml PBS, 2 ml Perfusion Solution 1 (50 μl/ml Dynabeads in PBS), and 2 ml Perfusion Solution 2 (50μl/ml Dynabeads, 1 mg/ml Collagenase, 0.5 mg/ml Pronase E and 50 U/ml DNase I in PBS) were perfused at a rate of 5 ml/min. The perfused kidneys were then cut into 1 mm3 sizes and transferred to a 2 ml centrifuge tube. Subsequently, 1 ml digestion solution (1 mg/ml Collagenase, 0.5 mg/ml Pronase E and 50 U/ml DNase I in PBS) was added to the tube, and centrifuged at 300 rpm for 5 minutes. The digestive solution was then passed through a size of 100 μm sieve and a magnetic field sequentially to obtain the glomeruli. Glomeruli were washed with 1 ml PBS containing 10% FBS and 3% Penicillin/Streptomycin for 5 times. Finally, glomeruli were resuspended and planted at a density of 300 glomeruli/10cm2 into type I collagen coated culture plates or culture flasks for further culture and experiment.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina  following the vendor's recommended protocol.

treatment_protocol: No treatment

value: renal podocyte

value: Kidney primitive extraction

value: SIRPa Knockout

value: No treatment


title: 28-07-0001-2_post_0

tag: participant id

value: Male

tag: age

tag: batch

value: nasal lavage sample


title: ED, R11988

value: Postmortem brain tissue

value: F

tag: rin


title: OCD, R11987

value: M

value: OCD


title: 28-09-0004-2_post_0

tag: month

tag: nac

tag: tnss

tag: tsneez


title: 28-09-0004-2_pre_0

value: pre

tag: dose

tag: pct reads

tag: tissue


title: mice podocyte cells, WT_3

tag: cell type

value: WT

tag: treatment


title: ED, R11891

value: DLPFC

tag: Sex

tag: group/disease

value: ED


title: WT_HU_input_EdUseq

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, input
WT_HU_EdUseq.narrowPeak

tag: cell line

value: HeLa cell line

tag: genotype

value: input


title: WT_HU_IP_EdUseq

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, IP
WT_HU_EdUseq.narrowPeak

value: Wild type

tag: fraction

value: IP


title: 28-09-0002-0_post_0

tag: participant id

value: Female

value: Placebo

tag: age

value: post

tag: median cv


title: 28-07-0006-8_post_0

value: Male

tag: month

tag: batch


title: ED, R11870

tag: rin


title: mice podocyte cells, WT_2

value: renal podocyte

value: Kidney primitive extraction

value: No treatment


title: HeLa, untreated, rep2

value: untreated


title: 28-09-0002-0_pre_0

tag: nac

tag: tnss

tag: tsneez

value: nasal lavage sample


title: DDX39AKO_HU_IP_EdUseq

description:
HeLa, DDX39A knockout, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, IP
DDX39AKO_HU_EdUseq.narrowPeak

value: DDX39A knockout


title: 28-07-0006-8_pre_0

value: pre

tag: dose

tag: pct reads

tag: tissue


title: ED, R11852

value: DLPFC

tag: cell type

value: Postmortem brain tissue

tag: Sex

value: M


title: nMSC1 [ATAC-seq]

tag: diagnosis

value: normal control

value: mesenchymal stromal cells (MSCs)


title: DDX39AKO_HU_input_EdUseq

description:
HeLa, DDX39A knockout, incubated with 20 μM EdU at 37°C for 10 min and then treated with 4 mM HU for 1 h, input
DDX39AKO_HU_EdUseq.narrowPeak

tag: cell line

value: HeLa cell line

tag: genotype

tag: treatment

value: input


title: mice podocyte cells, KO_3

value: SIRPa Knockout


title: WT_untreated_input_EdUseq

description:
HeLa, incubated with 20 μM EdU at 37°C for 10 min, input
WT_untreated_EdUseq.narrowPeak

value: Wild type

tag: fraction


title: 28-09-0001-4_post_0

tag: participant id

value: Female

value: Placebo

tag: age

value: post

tag: median cv


title: untreated_IP_gH2AX

description:
HeLa DDX39A-Tet-On cells, untreated, without replicate
untreated_gH2AX_ChIPseq.narrowPeak

growth_protocol: HeLa DDX39A-Tet-On stable cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, without doxycycline (DOX) treatment and incubated at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Cells were harvested by scraping, washed twice with prechilled PBS, and fixed with 1% formaldehyde at room temperature for 10 minutes, and the reaction was then quenched with 0.125 M glycine. After being washed once with PBS, the cells were lysed with buffer 1 (50 mM HEPES, pH 7.5; 140 mM NaCl; 1 mM EDTA, pH 8.0; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100) and buffer 2 (200 mM NaCl; 1 mM EDTA; 0.5 mM ethylene glycol-bis (β-aminoethyl ether)-N,N,N′,N′-tetraacetic acid (EGTA); 10 mM Tris-HCl, pH 8.0) at 4°C for 10 minutes. After centrifugation, the pellets were treated with lysis buffer (1% SDS, 10 mM EDTA, pH 8.0; 50 mM Tris-HCl, pH 8.0). All the above buffers contained 1 mM PMSF (Amresco), 0.6-2 μg/mL aprotinin (TargetMol) and 1× cocktail (CWBIO). The mixtures were subjected to sonication with a Covaris M220 focused ultrasonicator for 4 minutes to obtain smeared DNA fragments of 200-500 bp. After sonication, the samples were centrifuged at 15000 rpm, and the supernatants were diluted with an equal volume of NETN buffer (20 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1 mM EDTA (pH 8.0), and 0.5% NP-40). A portion of each sample was taken as input; 5 μg of anti-γH2AX (Millipore, 05-636) antibody was added to the remainder of each sample; and the samples were then incubated with rotation at 4°C overnight.  Protein G (Cytiva) beads were added to each sample, and the samples were incubated with rotation at 4°C for 2-3 hours. The beads were subsequently washed successively with the following buffers: one wash with low-salt buffer (0.1% SDS, 1% Triton X-100; 2 mM EDTA, pH 8.0; 20 mM Tris-HCl, pH 8.0; 150 mM NaCl); one wash with high-salt buffer (0.1% SDS, 1% Triton X-100; 2 mM EDTA, pH 8.0; 20 mM Tris-HCl, pH 8.0; 500 mM NaCl); one wash with LiCl buffer (10 mM Tris-HCl, pH 8.0; 1% sodium deoxycholate; 1% NP-40; 250 mM LiCl; 1 mM EDTA, pH 8.0); and two washes with TE buffer (10 mM Tris-HCl, pH 8.0; and 1 mM EDTA, pH 8.0). Then, the beads were incubated in 200 μL of elution buffer (10 mM Tris-HCl, 1% SDS, 1 mM EDTA) and incubated in a Thermo Mixer-Heat with vibration at 1200 rpm at 65°C overnight. Finally, the samples were incubated with 10 μg/mL RNase A at 37°C for 1 h and then with 20 μg/mL proteinase K at 55°C for 1 hour. The samples were extracted with phenol–chloroform. Then, 10 μL of glycogen (20 mg/mL), 100 μL of ammonium acetate (7.5 M), 40 μL of NaCl (5 M), and a 5x volume of ethanol were added to each supernatant and mixed, and the mixtures were incubated at -20°C overnight. The next day, the samples were centrifuged at 15000 rpm for 30 minutes at 4°C. We washed each pellet once with 75% ethanol and then centrifuged the sample and removed the supernatant. Finally, we resuspended the pellet in nuclease-free water to prepare the sample for sequencing.
The purified DNA was used NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645L) for library preparation.

treatment_protocol: First, the cells were synchronized by a double thymidine block. The cells were treated with 2 mM thymidine for 18 h, the block was released for 9 hours, and the cells were then treated again with thymidine for 18 hours. This process allowed the cells to be synchronized at the G1/S boundary, and the block was released for 1 hour. Cells were then treated with 4 mM HU and/or 100 μM DRB for 3 h.

value: DDX39A-Tet-On stable

value: without doxycycline (DOX) treatment

tag: chip antibody

value: γH2AX antibody


title: sig_neg, rep3

city: shang hai

first: yin

middle: shen

last: hui

address: xiangyin road 800

institute: Second military medical university

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed  for adaptor sequence, and masked low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2（version:2.0.4）
Fragments Per Kilobase of exon model per Million mapped reads(FPKM) were calculated  using Stringtie（version:1.3.0, MM（trimmed mean of M values）and perl.
Assembly: mm10
Supplementary files format and content: raw gene FPKM and counts for each gene and each sample

source_name: spleen

extract_protocol:
RNA was harvested using RNeasy Micro Kit-(QIAGEN).0.1-0.5 μg total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq® HT Kit following manufacturer's protocols.

value: spleen

value: primary cells

value: CD8+ T cells

value: Siglec-G-


title: control, R11632

value: DLPFC

value: Postmortem brain tissue

value: F

tag: group/disease

value: control

tag: rin


title: 28-09-0001-4_pre_0

tag: month

tag: nac

value: pre

tag: tnss

tag: tsneez

tag: batch

value: nasal lavage sample


title: mice podocyte cells, KO_1

tag: tissue

value: renal podocyte

tag: cell type

value: Kidney primitive extraction

value: SIRPa Knockout

value: No treatment


title: control, R11569

tag: Sex


title: sig_neg, rep2

tag: cell line

tag: genotype


title: control, R11558

value: M


title: untreated_input

description:
HeLa DDX39A-Tet-On cells, untreated, input
untreated_gH2AX_ChIPseq.narrowPeak

value: HeLa cell line

value: DDX39A-Tet-On stable

tag: treatment

value: without doxycycline (DOX) treatment


title: Donor75, Dynamic, day4

city: Amsterdam

first: Giulia

last: Iacono

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin

data_processing:
FASTQ quality control check (fastqc)
Genome Aligment (STAR)
Differentially express analysis (EdgeR)
Assembly: GRCh38(Ensembl 107)
Supplementary files format and content: Normalized readcounts (.csv)
Supplementary files format and content: Differentially expressed genes (.csv)

source_name: Blood

growth_protocol: PBMC were cultured to proerythroblasts in IMDM medium supplemented with EPO (2U/mL), human recombinant Stem Cell Factor (100ng/mL) and dexamethasone (1μM) at a density of 0.7-1.5 million/mL by dilution with fresh medium.

extract_protocol:
RNA was isolated from cell pellets using Trizol as indicated by the manufacturer's protocol (Invitrogen Technologies, CA, USA) and DNA remnants  removed by RNA clean up kits (Zymo Research, CA, USA).
RNA-Seq library was prepared for analysis according to the Illumina TruSeq stranded mRNA protocol (www.illumina.com).

treatment_protocol: To differentiate EBL to reticulocytes, cells were washed twice in PBS,  and resuspended in IMDM supplemented with EPO (10U/mL), 5% Omniplasma, holotransferrin (700μg/m), and heparin (5U/mL) at a desnsity of 1 million/mL and cultured in static (dish) and dynamic (orbital shaker) conditions.

value: Blood

value: Primary human erythroblasts

tag: group

value: Dynamic, day4

value: differentiation in static (dish culture)


title: sig_neg, rep1

value: spleen

value: primary cells

value: CD8+ T cells

value: Siglec-G-


title: IgG_IP_gH2AX

description:
HeLa DDX39A-Tet-On cells, untreated, incubated with mouse IgG, without replicate
HUDRB_gH2AX_ChIPseq.narrowPeak

value: mouse IgG


title: Donor75, Dynamic, day2

value: Dynamic, day2


title: sig_pos, rep3

value: Siglec-G+


title: control, R11544

value: DLPFC

value: Postmortem brain tissue

value: control


title: sig_pos, rep2


title: control, R11384

value: F


title: Donor75, static, day4

value: static, day4


title: mice podocyte cells, WT_1

value: renal podocyte

value: Kidney primitive extraction

value: WT

value: No treatment


title: Donor75, Dynamic, day1

value: Blood

value: Primary human erythroblasts

value: Dynamic, day1

value: differentiation in static (dish culture)


title: HUDRB_IP_gH2AX_rep1

description:
HeLa DDX39A-Tet-On cells, treated with 4 mM HU and 100 μM DRB for 3 h, rep1
HUDRB_gH2AX_ChIPseq.narrowPeak

value: HeLa cell line

value: DDX39A-Tet-On stable

value: treated with 4 mM HU and 100 μM DRB for 3 h without doxycycline (DOX) treatment

value: γH2AX antibody


title: HUDRB_input

description:
HeLa DDX39A-Tet-On cells, treated with 4 mM HU and 100 μM DRB for 3 h, input
HUDRB_gH2AX_ChIPseq.narrowPeak


title: sig_pos, rep1

value: spleen

value: primary cells

value: CD8+ T cells

value: Siglec-G+


title: OCD, R11382

value: DLPFC

value: Postmortem brain tissue

value: M

value: OCD


title: Donor75, static, day2

value: static, day2


title: OCD, R11380


title: WT_9h_Control2

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters。
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using Featurecounts
Assembly: mm10 (mouse)
Supplementary files format and content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: BMDM

growth_protocol: The mice were maintained under specific pathogen-free (SPF) conditions at the Center for New Drug Safety Evaluation and Research, China Pharmaceutical University.

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen) and prepared into cDNA library according to the standard Illumina RNA-seq instruction.
The cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq2500 by a 2X150 bp run.

treatment_protocol: Sting deficiency mice on a C57BL/6J background were generated through CRISPR-Cas9 technology

value: BMDM

value: C57BL/6J WT

value: Mock 9h


title: Donor75, static, day1

value: Blood

value: Primary human erythroblasts

value: static, day1

value: differentiation in static (dish culture)


title: HU_IP_gH2AX_rep2

description:
HeLa DDX39A-Tet-On cells, treated with 4 mM HU for 3 h, rep2
HU_gH2AX_ChIPseq.narrowPeak

value: HeLa cell line

value: DDX39A-Tet-On stable

value: treated with 4 mM HU for 3 h without doxycycline (DOX) treatment

value: γH2AX antibody


title: ED, R11371

value: F

value: ED


title: WT_9h_Control1


title: Donor72, Dynamic, day4

value: Dynamic, day4


title: ED, R11362

value: DLPFC

value: Postmortem brain tissue


title: WT_9h_32cgamp2

value: 3'2'-cGAMP 9h


title: Donor72, Dynamic, day2

value: Dynamic, day2


title: ED, R11317


title: HUDRB_IP_gH2AX_rep2

description:
HeLa DDX39A-Tet-On cells, treated with 4 mM HU and 100 μM DRB for 3 h, rep2
HUDRB_gH2AX_ChIPseq.narrowPeak

value: treated with 4 mM HU and 100 μM DRB for 3 h without doxycycline (DOX) treatment


title: CB49_50_90_pool, HTO-derived cDNA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
Hashtag oligonucleotide (HTO)
CB49_50_90_pool_5DE_genematrix.csv
features.tsv.gz

library_source: other

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.6.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: CB49_50_90_pool_5DE_genematrix.csv: comma-delimited text file including UMI counts for all cells detected
Supplementary files format and content: features.tsv.gz: gzipped tab-delimited text file consisted of features (gene and tag) information

molecule: protein

source_name: CD56-CD3-CD14-CD19- cord blood mononuclear cells

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits v2 User Guide.


title: ED, R11313


title: WT_9h_32cgamp1

value: BMDM

value: C57BL/6J WT


title: WT_9h_23cgamp2

value: 2'3'-cGAMP 9h


title: Donor72, Dynamic, day1

value: Blood

value: Primary human erythroblasts

value: Dynamic, day1


title: CB49_50_90_pool, mRNA-derived cDNA

description:
poly A RNA
CB49_50_90_pool_5DE_genematrix.csv
features.tsv.gz

value: CD56-CD3-CD14-CD19- cord blood mononuclear cells


title: Donor72, static, day4

value: static, day4

value: differentiation in static (dish culture)


title: Donor72, static, day2

value: static, day2


title: X2-5O5-2_L3_362X62

city: Guangzhou

first: Peng

last: Deng

address: Panyu

institute: SYSUCC

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by STAR instruction
RSEM were used for counting
R were used for visualization
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

growth_protocol: OVCAR5 cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
Total RNA was obtained from cells using RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: OVCAR5 cells were plated into 6-well plate 20 h before treated with control, olaparib,xl413 and combination treatment for 48 hour.

value: high grade serous ovarian cancer (HGSOC)


title: WT_9h_23cgamp1


title: ED, R10592

value: F

value: ED


title: ED, R10540

value: DLPFC

value: Postmortem brain tissue

value: M


title: ED, R11276


title: WT_3h_Control1

value: Mock 3h


title: WT_3h_Control2

value: BMDM


title: HU_IP_gH2AX_rep1

description:
HeLa DDX39A-Tet-On cells, treated with 4 mM HU for 3 h, rep1
HU_gH2AX_ChIPseq.narrowPeak

value: HeLa cell line

value: DDX39A-Tet-On stable

value: treated with 4 mM HU for 3 h without doxycycline (DOX) treatment

value: γH2AX antibody


title: Donor72, static, day1

value: Blood

value: Primary human erythroblasts

value: static, day1


title: X2-5O5-1_L3_361X61


title: X2-5-1_L3_357X57


title: OCD, R10537

value: OCD


title: Donor63, Dynamic, day2

value: Dynamic, day2

value: differentiation in static (dish culture)


title: HU_input

description:
HeLa DDX39A-Tet-On cells, treated with 4 mM HU for 3 h, input
HU_gH2AX_ChIPseq.narrowPeak


title: ED, R10526

value: F


title: X2-5-2_L3_358X58

value: high grade serous ovarian cancer (HGSOC)


title: WT_3h_32cgamp1

value: C57BL/6J WT

value: 3'2'-cGAMP 3h


title: O5-2_L3_360X60


title: Donor63, Dynamic, day1

value: Dynamic, day1


title: Donor63, static, day4

value: static, day4


title: espRKO_exp2_rep2

city: Quincy

last: Luna

state: Massachusetts

address: 7 Seaport Dr, 322

institute: UMass Chan Medical School

data_processing:
The reads were mapped to the H37Rv genome (Genbank accession NC_000962.2) using BWA (v0.7.12), and read counts for each ORF were tabulated
Differentially expressed genes were identified using the R package DeSeq
Assembly: NC_000962.2
Supplementary files format and content: tab delimited txt file shows RPKM values for all samples

organism: Mycobacterium tuberculosis

growth_protocol: Mycobacterium tuberculosis WT and ESX-1 mutant strains were grown to mid-log phase in complete 7H9 broth

extract_protocol:
RNA was extracted using RNA using Zymo Research Direct-zol RNA Miniprep Plus Kit. rRNA was depleted using  Illumina Ribo-Zero Plus rRNA Depletion Kit.
NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina was used according to the instructions

value: espR KO


title: O5-1_L3_359X59


title: WT_3h_23cgamp2

value: BMDM

value: 2'3'-cGAMP 3h


title: espRKO_exp2_rep3

value: espRKO


title: WT_3h_23cgamp1


title: espRKO_exp2_rep1


title: ctrl-2_L3_356X56


title: Donor63, static, day1


title: ctrl-1_L3_355X55


title: Patient 4 mechanical load biological replicate 4

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA)
Fastq files were trimmed for adapters.
Trimmed reads were mapped to the reference human genome hg38 using STAR aligner.
Mapped reads were further filtered and quantified to hg38-GENCODE genes- release 35
Differential expression was performed using Deseq2

source_name: Human growth plate

extract_protocol:
Total RNA is extracted from the growth plate samples by zymo quick RNA microprep kit  as per the manufacturers protocol
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014)

value: Human growth plate

value: mechanical load


title: Donor63, Dynamic, day4

value: Blood

value: Primary human erythroblasts

value: Dynamic, day4


title: STKO_9h_Control2

value: C57BL/6J Sting KO

value: Mock 9h


title: STKO_9h_32cgamp2

value: 3'2'-cGAMP 9h


title: espRins_exp2_rep2

value: espR ins mutant


title: WT_3h_32cgamp2

value: C57BL/6J WT


title: STKO_9h_Control1


title: Donor1, Dynamic, day4

value: differentiation in static (dish culture)


title: Patient 4 mechanical load biological replicate 3


title: espRins_exp2_rep3


title: Donor1, Dynamic, day2

value: Dynamic, day2


title: STKO_9h_32cgamp1


title: Patient 4 mechanical load biological replicate 2


title: WT_exp2_rep3

value: WT H37Rv


title: espRins_exp2_rep1


title: Donor1, Dynamic, day1

value: Dynamic, day1


title: STKO_9h_23cgamp2

value: BMDM

value: 2'3'-cGAMP 9h


title: Patient 4 mechanical load biological replicate 1


title: Donor1, static, day4

value: static, day4


title: Donor63, static, day2

value: static, day2


title: Patient 3 control biological replicate 4

value: Human growth plate

value: control


title: Donor1, static, day2

value: Blood

value: Primary human erythroblasts


title: STKO_9h_23cgamp1

value: C57BL/6J Sting KO


title: STKO_3h_Control2

value: Mock 3h


title: WT_exp2_rep1


title: Patient 3 control biological replicate 3


title: Donor1, static, day1

value: static, day1


title: espRins_exp1_rep3

value: espR ins mutant


title: STKO_3h_Control1


title: Patient 3 control biological replicate 2


title: espRins_exp1_rep2


title: CD34+ iPSC-HE, day4, GFI1B#3

first: Emile

last: van den Akker

institute: Sanquin Research Amsterdam

data_processing:
In the trimming, Illumina adapter and poly-A sequences were removed from the reads
The trimmed reads were then aligned using HISAT2 (Kim et al, 2019)
After the HISAT2 alignment, SAMTools (Li et al, 2009) was used to sort and merge the alignments from multiple flow cells.
Quantification was performed using HT-seq count (Anders et al, 2015) after first sorting the alignments on readname using SAMTools.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: hematopoietic

extract_protocol:
RNA was isolated using TRIzol RNA isolation reagents (ThermoFisher Scientific)
RNA-Seq library was prepared for analysis according to the Illumina TruSeq stranded mRNA protocol (www.illumina.com).

value: hematopoietic

value: iPSC-HE

value: WT


title: STKO_3h_32cgamp2

value: 3'2'-cGAMP 3h


title: Patient 3 control biological replicate 1


title: CD34+ iPSC-HE, day4, GFI1B#2


title: STKO_3h_32cgamp1


title: espRins_exp1_rep1


title: Patient 2 mechanical load biological replicate 3

value: mechanical load


title: STKO_3h_23cgamp2

value: BMDM

value: 2'3'-cGAMP 3h


title: CD34+ iPSC-HE, day4, GFI1B#1


title: Patient 2 mechanical load biological replicate 2


title: CD34+ iPSC-HE, day4, EV#3

value: EV


title: Patient 2 mechanical load biological replicate 1


title: WT_exp1_rep1

value: WT H37Rv


title: WT_exp2_rep2


title: STKO_3h_23cgamp1


title: WT_exp1_rep2


title: Patient 2 control biological replicate 3

value: Human growth plate


title: T30-4-3dpi-ChIP-seq_input_rep2

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

institute: Nanjing Agricultural University

data_processing:
Clean reads were aligned to P. sojae or P. infestans genome using bowtie2 v2.3.3.1 with parameter -N 1
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None or "bamCoverage"
Assembly: Psojae v1.1 and P. infestans(T30-4)
Supplementary files format and content: Bigwig files, scores represent enriched value(log2(fold-change))

organism: Phytophthora infestans

source_name: 3dpi Phytophthora infestans infected potato leaves

extract_protocol:
After antibody Immunoprecipitation, target DNA was eluted from Dynabeads and precipitated using ethanol followed by twice washes, finally the samples was dried and dissolved in 33 μl ddH2O
Qualified library for sequencing was prepared using the QIAquick PCR Purification Kit(Qiagen). Briefly, 10-300ng DNA was taken to do DNA-end repair(3'-dA overhang and ligation of methylated sequencing adaptors) followed by PCR amplication and size selection (usually 100-300bp, including adaptor sequencing).

tag: strain

tag: Stage


title: Heat at 49C, biol rep 5

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Sequencing: Purified dual-indexed sequence-libraries of each sample were equimolarly pooled and sequenced on Illumina MiSeq v2 300 Micro kit, paired end 150 reads (151-10-10-151)) at the VIB Nucleomics Core.
Preprocessing: Low-quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15. Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.40.0. With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina.
Mapping: The preprocessed reads were aligned with bowtie2 2.3.3.1 to the reference genome of escherichia coli k12 (GCA000005845.ASM584v2) using the following options ‘--rf ---seed 1 -L 12 -k 20 --local’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments.
Counting: The number of reads in the alignments that overlap with gene features was counted with featureCounts 1.5.3. Following parameters were chosen: -Q 0 -s 0 -t exon -g gene_id.
Assembly: E.coli GCA 000005845.ASM584v2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Escherichia coli

source_name: Escherichia coli k12

growth_protocol: For optimal growth conditions of E. coli in Mueller Hinton Broth (MHB), incubate the culture at 37°C with continuous shaking (around 200-250 rpm) to ensure aeration. Inoculate the broth with a fresh overnight culture to an initial optical density (OD600) of 0.05-0.1 and allow growth until the culture reaches mid-log phase (OD600 of 0.4-0.6).

extract_protocol:
The extraction protocol focuses on isolating RNA from the resuspended inclusion body pellet. Begin by preparing the RNA extraction setup using the Aurum Total RNA Mini Kit from Bio-Rad, following the manufacturer's instructions. Resuspend the final pellet in an appropriate volume of the lysis buffer provided in the kit, then add lysozyme and proteinase K to the mixture, which aids in breaking down cellular components. Allow the mixture to incubate at room temperature for 10 to 30 minutes, facilitating the lysis of aggregated proteins and cellular debris. After the incubation, proceed with the RNA purification steps outlined in the Aurum Total RNA Mini Kit. This usually involves mixing the lysate with a binding buffer and transferring it to a spin column designed to capture RNA while washing away impurities with a wash buffer. Finally, elute the purified RNA using RNase-free water, ensuring that all RNA is collected effectively.
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using the Bioanalyzer 2100 (Agilent).  For each sample, 100 ng of total RNA was used as input, using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Kit (protocol version: #1000000124514 v02 (April 2021)). Initially, abundant rRNA molecules are first depleted from total RNA by means of DNA probes which bind to the rRNA molecules; both are then enzymatically digested. RNA-specific magnetic beads were used to recover and purify the rRNA-depleted total RNA. The purified total RNA was fragmented and in a reverse transcription reaction using random primers and actinomycin D. RNA was converted into single-stranded cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using dUTP to achieve strand specificity. The cDNA fragments were extended with a single adenosine base to the 3' ends of the blunt-ended cDNA fragments after which pre-index anchors were ligated preparing the fragments for dual indexing. Anchor-ligated fragments were then purified using magnetic beads. Finally, enrichment PCR was carried out to enrich those DNA fragments that have anchor-ligated DNA fragments and to add indexes and primer sequences for cluster generation.

treatment_protocol: Bacteria were cultured either by exposing them to P33 at the minimum inhibitory concentration (MIC) or by heating them at 49°C for 1 hour while in the log phase of growth.

value: Escherichia coli k12

value: Heat at 49C


title: CD34+ iPSC-HE, day4, EV#1


title: Heat at 49C, biol rep 4


title: Patient 2 control biological replicate 2

value: control


title: T30-4-3dpi-ChIP-seq_input_rep1

value: 3dpi Phytophthora infestans infected potato leaves

tag: chip antibody


title: Heat at 49C, biol rep 3


title: Patient 2 control biological replicate 1


title: T30-4-3dpi-ChIP-seq_H3K36me3_rep2

value: H3K36me3(abcam, ab9050)


title: WT_exp1_rep3


title: Heat at 49C, biol rep 2


title: T30-4-3dpi-ChIP-seq_H3K36me3_rep1


title: T30-4-3dpi-ChIP-seq_H3K27me3_rep2


title: P33 peptin, biol rep 5

value: P33 peptin


title: Heat at 49C, biol rep 1


title: not_used(Tag05mm), HBV-replicate-6(Tag06mm),scRNAseq

first: Takahiro

last: Kodama

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

institute: Osaka university, Graduate School of Medicine

description: BD Rhapsody

data_processing:
The FASTQ files from the sequences were processed using the BD Rhapsody WTA Pipeline v1.10.1 (Becton Dickinson) in the Seven Bridges Platform.
Assembly: mm10(GRCm38)
Supplementary files format and content: matrix file

source_name: intrahepatic immune cells

extract_protocol:
Intrahepatic mononuclear cells (MNCs) were isolated from perfused livers using 10mL PBS followed by filtering through a 70 μM cell strainer and gradient centrifugation on Percoll (40% and 70% Percoll, #17089101; Cytiva). Mononuclear cells from spleens were also filtered through a 70 μM cell strainer (#352350; Corning, NY, USA) and resuspended in red blood cell (RBC) lysis buffer.
For scRNA-seq, we utilized the BD Rhapsody system (Becton Dickinson). MNCs were labelled with sample tags (Ms Single Cell Sample Multiplexing Kit), counted, and multiplexed. Cell capture and library preparation were performed using the BD Rhapsody Whole Transcriptome Analysis (WTA) Reagent Kit (Becton Dickinson) following the manufacturer’s protocol, and libraries were sequenced on MGI Tech DNBSEQ-G400RS.

value: intrahepatic immune cells


title: CD34+ iPSC-HE, day4, EV#2

value: hematopoietic


title: Patient 1 control biological replicate 3


title: FAH-replicate-4(Tag03mm), not_used(Tag04mm),scRNAseq

description: BD Rhapsody


title: co-cultured HLE with TAM-like macrophage

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: PBMos (1.5 × 105 cells/well) were seeded in 0.4 µm pore size upper inserts with 10 ng/mL recombinant human M-CSF and 1ng/mL recombinant human GM-CSF.   For M0 macorphage experiment: On day 6, the medium was removed and macrophages (M0) were washed three times with serum-free low-glucose DMEM. Several hours before the co-culture, HCC cells were seeded in 6-well plates at 2 ×105 cells/well and incubated at 37℃ with 5% CO2. After confirming the attachment of HCC cells on the lower plates, HCC cells were co-cultured with macrophages (M0) and mono-cultured without macrophages (M0) in serum-free low-glucose DMEM for two days.  For TAM-like macorphage experiment: On day 6, the medium was removed and macrophages (M0) were washed three times with serum-free low-glucose DMEM and incubeted with 50% HCC-conditioned medium for 24 hours. On day 7,  the medium was removed and macrophages (TAM-like) were washed three times with serum-free low-glucose DMEM. Several hours before the co-culture, HCC cells were seeded in 6-well plates at 2 ×105 cells/well and incubated at 37℃ with 5% CO2. After confirming the attachment of HCC cells on the lower plates, HCC cells were co-cultured with macrophages (TAM-like) and mono-cultured without macrophages (TAM-like) in serum-free low-glucose DMEM for two days.

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

value: CD14-positive monocytes (PBMos)

value: with TAM-like macrophage


title: Patient 1 control biological replicate 2


title: HBV-replicate-4(Tag01mm),HBV-replicate-5(Tag02mm),scRNAseq

description: BD Rhapsody


title: mono-cultured HLE

source_name: mono-cultured HLE


title: T30-4-3dpi-ChIP-seq_H3K4me3_rep2

value: WT

value: H3K4me3(abcam, ab8580)


title: P33 peptin, biol rep 3


title: HBV treated wit SA5-2(Tag11mm),HBV treated wit IFNa-2(Tag12mm),scRNAseq

description: BD Rhapsody


title: P33 peptin, biol rep 2


title: 24h_HTO

first: Michael

last: Gildea

address: 550 1st avenue

institute: NYU Langone Health

description: Hashtah-derived oligonucleotide (HTO)

data_processing:
*library strategy: CITE-seq
Cell Ranger (10x Genomics, v6.0.1) was used to performalignment (GRCh38, Ensembl 98), filtering, barcode counting and UMI counting of sequencing reads from fastq files
Assembly: GRCh38
Supplementary files format and content: Tab -separated values files and matrix files

source_name: whole blood

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from 500 ml whole human blood obtained from the New York Blood Center as described previously10. Briefly, whole blood was processed within 2h of receipt and centrifuged at 480 g for 10 min. at room temperature (RT). Plasma was collected and the cell fraction diluted 1:2 in PBS, then placed in Ficoll-Paque PLUS density gradient media (GE Healthcare Life Sciences, 17144003) and centrifuged at 1,250 g for 20 min. at RT. The PBMC layer was collected, washed twice in PBS and resuspended at 2–5×105 cells per ml in 50% vol/vol RPMI-1640 (Gibco, 11875093) 40% vol/vol FBS 10% dimethyl sulfoxide (Tocris Bioscience, 3176) for frozen storage at –80 °C or liquid N2. On experiment date, PBMCs were thawed and placed in RPMI-1640 supplemented with 10% vol/vol FBS and 100 μg ml−1 penicillin-streptomycin (Corning, MT30002CI) to acclimatize in a humidified incubator at 37 °C and 5% CO2 for 2h. Viable PBMCs were cultured at 5×105 cells per well of a 12-well plate coated with Dynabeads Human T-Activator CD3/CD28 (Gibco, 11161D) to activate T cells. Following acclimatization and activation, 1 μg ml−1 anti-PD-1 (SIM0003, Bio X Cell) or 20 μg ml−1 anti-CTLA4 (SIM0004, Bio X Cell) were added to the corresponding experimental wells for 4h or 24h. Next, samples were washed in phosphate-buffered saline (PBS; Corning, 1-031-CV), centrifuged for 5 min. at 300 g and placed in PBS supplemented with 1% vol/vol bovine serum albumin (BSA, Jackson ImmunoResearch, 149856) and 10 μg Anti-Fc Receptor Binding Inhibitor (Invitrogen, 14-9161-73) for 10 min at 4 °C to prevent nonspecific binding in later steps. Fc-blocked samples were incubated with 0.5 μg unique hashtag antibodies from the 3ʹ CellPlex Kit Set A (10x Genomics, PN-1000261), respectively, and stained with the TotalSeq™-B Human Universal Cocktail, V1.0 (BioLegend, 399904) according to the manufacturer’s instructions. Stained, viable cells were submitted to the Genome Technology Center at the NYU Grossman School of Medicine at NYU Langone Health (NYU GTC) for CITE-seq analysis following the Single Cell 3’ v2 workflow and using a 3' CellPlex Kit, Set A for multiplexing (10x Genomics, 1000261) through the cDNA amplification step. The transcriptome library was generated according to the protocol by Stoeckius M. et al.82 Separate PCRs were used to generate the CITE-seq antibody-derived tag (ADT) protein library (SI-PCR and RPI-x primers) and the hashtag Iibrary, respectively. Finally, the ADT and hashtag libraries were sequenced on an Illumina NovaSeq 6000 using the S4 200 cycle flow cell v1.5, also at the NYU GTC.

value: whole blood

value: immunce checkpoint inhibitors

tag: hto

tag: library type

value: HTO


title: Patient 1 mechanical load biological replicate 3

value: mechanical load


title: P33 peptin, biol rep 1


title: 24h_ADT

description: Antibody_derived oligonucleotid (ADT)

value: Peripheral blood mononuclear cells (PBMCs)

tag: adt

value: TotalSeq™-B Human Universal Cocktail, V1.0 (BioLegend, 399904)

value: ADT


title: Patient 1 mechanical load biological replicate 2

value: Human growth plate


title: HBV-replicate-PBMC1(Tag07mm), HBV-replicate-PBMC2(Tag08mm),scRNAseq

description: BD Rhapsody

source_name: PBMC

value: PBMC


title: BCSP, Mettl3cko, IP, 3 days, Rep2.

city: Wuhan

first: weidong

last: liu

address: donghu street

institute: Wuhan University

description: Library name: IP-Mettl3cko-BCSP-Rep2

data_processing:
All input and IP samples’ raw sequencing data were preprocessed using fastp (v. 0.20.1), aligned with HISAT2 (v. 2.2.1) to GRCm38 reference genome, and generated read counts by featureCounts (v.2.0.1). For calculating the relative m6A level for each gene, we used the DESeq2 to compare the read counts of genes between IP samples and input samples on a transcriptome-wide scale. Based on the adjusted fold change (Wald statistic, fourth column of output of DESeq2) of each gene from the output of DESeq2, we further calculated the Z-score of adjusted fold change in each cell type, and this Z-score represents the relative m6A level. We identified high-confidence m6A-tagged mRNAs by setting up the cutoff line based on log2(fold change) > 1 and P value < 0.05
Assembly: mm10
Supplementary files format and content: txt

source_name: long bone

extract_protocol: SCs and other targets cells were sorted into TRIzol reagent (Takara) to extract RNA.

value: long bone

value: skeletal stem and progenitor cells

value: wild type

value: no treatment


title: BCSP, Mettl3cko, IP, 3 days, rep1

description: Library name: IP-Mettl3cko-BCSP-Rep1


title: LC_20230323_synovium

first: Kun

last: Lin

state: Guangdong

address: NO.261, Longxi Road, Liwan District

description:
Library name: Sample 2
10x Genomics

data_processing:
(1) Utilize the official analysis software Cell Ranger from 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) to perform data filtering, alignment, quantification, and cell recovery from the raw data, ultimately obtaining the gene expression matrix for each cell. (2) Subsequently, employ Seurat (https://satijalab.org/seurat/) for further cell filtering, normalization, classification of cellular subtypes, analysis of differentially expressed genes among various subtypes, and selection of Marker genes.
Assembly: human NCBI genome build 36
Supplementary files format and content: Tab-separated values files and matrix files

source_name: synovium

extract_protocol:
The specimens used in this study were obtained from the Third Affiliated Hospital of Guangzhou University of Chinese Medicine (PJ-XS-20241029-001). Patients were diagnosed with hemophilia A and confirmed with HA through MRI. Fresh synovial membranes were collected from their knees after TKA, immersed in tissue storage solution (130-100-008, MACS).  Additionally, specimens from patients with OA and RA were similarly diagnosed through medical history and imaging, and fresh synovial membranes was obtained during TKA.
The Chromium™ Single Cell 3' Solution is built on the GemCode technology microfluidics platform, which encapsulates gel beads with barcodes and primers along with individual cells in oil droplets to form GEMs (Gel Bead in Emulsion). GEM refers to the mixture of oil droplets containing barcoded Gel beads and cells, along with reaction reagents. The primers are composed of the full-length Illumina TruSeq Read 1 sequencing primer, a 16bp 10X Barcode sequence (used for cell identification), a 12bp unique molecular identifier (UMI) (used to distinguish different transcripts from the same cell and to remove PCR duplicates), and a 30 bp poly dT reverse transcription primer.The prepared cell suspension, 10X Barcode gel beads, and oil droplets are separately introduced into different channels (a total of 8 channels) of the Chromium Next GEM Chip G. The GEMs (Gel Bead in Emulsion) are formed through a microfluidic system. To achieve a single-cell reaction system, the concentration of the cell suspension is controlled between 700-1200 cells per microliter (µl). As a result, 90-99% of the GEMs do not contain any cells, while the majority of the remaining GEMs contain a single cell.Within the GEM (Gel Bead in Emulsion), the gel beads dissolve, and the cells lyse to release mRNA.  This mRNA is then reverse transcribed to produce barcoded cDNA for sequencing.  The liquid oil layer is disrupted, and cDNA amplification is carried out.  After purification, quality control is performed, and once the quality is confirmed, library construction is initiated.Enzymatic cutting is performed, followed by end-repairing of the fragments and the addition of an A-base overhang. Adapters are then ligated. The target-sized fragments are recovered using a size-selection kit, and the library is subjected to quality control and quantification.The constructed library structure, from 5' to 3', consists of: Illumina P5 adapter, P5 sequencing primer (black Read1 position), 16bp Barcode, 12bp Unique Molecular Identifier (UMI), poly(dT) random nucleotide (VN) sequence, inserted cDNA fragment, P7 sequencing primer (black Read2 position), sample Index (i7 index read), and Illumina P7 adapter. The可用 (yòng, which means 'available' or 'usable' in this context) sequence length for Read 1 is 28 base pairs (bp) (16bp Barcode + 12bp UMI), which is used to distinguish between cells and the different transcripts (mRNA) within each cell. The可用 (yòng) sequence length for Read 2 is 91 base pairs (bp), which is used to map to a reference genome to determine gene information.

value: synovium

value: Synovial cell


title: co-cultured HLE with M0

source_name: co-cultured HLE with M0

value: CD14-positive monocytes (PBMos)

value: with M0


title: pre-BCSP, Mettl3cko, IP, 3 days, Rep2.

description: Library name: IP-Mettl3cko-pre-BCSP-Rep2


title: T30-4-3dpi-ChIP-seq_H3K27me3_rep1

value: 3dpi Phytophthora infestans infected potato leaves

value: WT


title: 4h_HTO

city: New York

description: Hashtah-derived oligonucleotide (HTO)

value: whole blood

value: immunce checkpoint inhibitors

value: HTO


title: MPN6_S10_STARAligned.sortedByCoord.out.bam [RNA-seq]

last: GANESAN

data_processing:
Read from RNA-seq were mapped to the hg38 genome using STAR. The differentially expressed RNA was analyzed using DESeq with an FDR corrected p values < 0.05.
Assembly: hg38
Supplementary files format and content: All_human_gene_counts-2.txt: Tab-delimited text file containing feature counts for genes.

source_name: Bone marrow

extract_protocol:
The total RNA was extracted using Trizol by standard protocol.
Total RNA libraries were prepared using the Illumina TruSeq RNA kit as described by the manufacturer (Illumina). 1 microgram of total RNA was used from each sample for the library preparation. 5` and 3` RNA adaptors were ligated to the RNA and the ligated products were reverse transcribed using superscript II reverse transcriptase (Invitrogen). The size and integrity of each library were verified using the Bioanalyser (Agilent).

tag: diagnosis

value: myelofibrosis

value: mesenchymal stromal cells (MSCs)


title: FAH-replicate-4(Tag07mm),FAH-replicate-5(Tag08mm),scRNAseq

description: BD Rhapsody

value: intrahepatic immune cells


title: ZHC_synovium

institute: Guangzhou University of Chinese Medicine

description:
Library name: Sample 1
10x Genomics


title: P33 peptin, biol rep 4

value: Escherichia coli k12

value: P33 peptin


title: pre-BCSP, Mettl3cko, IP, 3 days, rep1

description: Library name: IP-Mettl3cko-pre-BCSP-Rep1

value: long bone

value: skeletal stem and progenitor cells


title: 24h_RNA

description: 10x Genomics

molecule: polyA RNA

value: Peripheral blood mononuclear cells (PBMCs)

value: mRNA


title: HBV-replicate-2(Tag05mm),HBV-replicate-3(Tag06mm),scRNAseq

description: BD Rhapsody


title: 4h_ADT

description: Antibody_derived oligonucleotid (ADT)

value: TotalSeq™-B Human Universal Cocktail, V1.0 (BioLegend, 399904)

value: ADT


title: Patient 1 control biological replicate 1

value: Human growth plate

value: control


title: MPN3_S7_STARAligned.sortedByCoord.out.bam [RNA-seq]

institute: IRSL, Hopital Saint Louis


title: HBV treated wit SA5(Tag03mm),HBV treated wit IFNa(Tag04mm),scRNAseq

description: BD Rhapsody


title: T30-4-3dpi-ChIP-seq_H3K4me3_rep1

value: 3dpi Phytophthora infestans infected potato leaves

value: WT

value: H3K4me3(abcam, ab8580)


title: HBV treated wit IFNa-2(Tag09mm),HBV treated wit SA5-2(Tag10mm),scRNAseq

description: BD Rhapsody


title: SSC, Mettl3cko, IP, 3 days, Rep2.

description: Library name: IP-Mettl3cko-SSC-Rep2

value: wild type

value: no treatment


title: SSC, Mettl3cko, IP, 3 days, rep1

description: Library name: IP-Mettl3cko-SSC-Rep1


title: 4h_RNA

description: polyA RNA

value: whole blood

value: immunce checkpoint inhibitors


title: FAH-replicate-1(Tag01mm), HBV-replicate-1(Tag02mm),scRNAseq

description: BD Rhapsody

value: intrahepatic immune cells


title: MPN2_S6_STARAligned.sortedByCoord.out.bam [RNA-seq]

value: myelofibrosis

value: mesenchymal stromal cells (MSCs)


title: NGFR-, rep3

city: Kanazawa

first: Shinichiro

last: Takashima

address: 13-1 Takara-machi

department: Cardiovascular Medicine

institute: Kanazawa University

data_processing:
Total RNA was isolated from ~10,000 cells of NGFR+, NGFR- MNCs, or unsorted MNCs (N = 3) and amplified to produce cDNA.
cDNA libraries for RNA sequencing were constructed using a SMART-Seq Stranded Kit (Takara Bio).
Libraries underwent sequencing to 660 million reads of 150 base-pair lengths and were paired-end using the NovaSeq6000 system (Illumina, San Diego, CA, USA).
The RNA-sequencing fragment count was normalized to fragments per kilobase of exon per million fragments mapped (FPKM).
The FPKM values were log2-transformed, and the relative abundance of transcripts was analyzed using Subio Platform ver. 1.24 and Subio Basic Plug-in (Subio, Tokyo, Japan).
Assembly: grch38
Supplementary files format and content: The excel file includes the processed signals that the FPKM signals were log2-transformed, normalized with the mean of unsorted MNCs.
Supplementary files format and content: The lists include extracted genes with expression levels five-fold higher (632 genes) or lower (327 genes) in NGFR+ MNCs compared to NGFR- MNCs with a P-value of 0.01 by a one-sample t-test.

extract_protocol:
RNA extraction was outsourced to Takara Bio Inc. The quality and the amount of the RNA was checked.
RNA libraries for RNA-weq were prepared using SMARTer Stranded RNA-seq Kit following manufacturers' protocols.

value: PBMC

value: NGFR-

tag: individual

value: healthy volunteer_3


title: BCSP, Mettl3cko, 3 days, Rep2.

description: Library name: Mettl3cko-BCSP-Rep2

value: long bone

value: skeletal stem and progenitor cells


title: MPN1_S5_STARAligned.sortedByCoord.out.bam [RNA-seq]

first: SARAVANAN

address: 1 Avenue Claude Vellefaux, 75010 Pa


title: ID8_OR_Combo_rep2

city: Aurora

first: Lily

last: Nguyen

state: CO

address: 1635 Aurora Ct

institute: UNIVERSITY OF COLORADO DENVER

description: ID8_OR_COMBO_2_S36_L002_R.sorted.uniq.bam

data_processing:
quality assessement using FastQC (v0.11.8) and MultiQC (v1.7)
adapter trimming using BBDuk/BBMap (v38.05)
genome alignment using using hisat2 (v2.1.0)
count tables were generated using featureCounts from the subread (v1.6.2) package with the GENCODE v34 annotation gtf to estimate counts at the gene level, over each exon (including -p to count fragments instead of reads for paired-end reads; -O to assign reads to their overlapping meta-features; -s 2 to specify reverse-strandedness; -t exon to specify the feature type; -g gene_id to specify the attribute type).
Assembly: mm10
Supplementary files format and content: count table

source_name: ovarian cancer cells

growth_protocol: Cell Culture- ID8 cell line was kindly gifted from Dr. Iain McNeish lab (Imperial College London). All cells were authenticated via STR at The University of Arizona Arizona Genetics Core (RRID:SCR_012429). All cells undergo monthly mycoplasma testing using Sigma LookOut Mycoplasma Detection kit (Cat. #MP0035) and are only culture up to 20 passages or two months. Cells are cultured in DMEM (Gibco, Cat. #11995-065) supplemented with 4% FBS, Penicillin Streptomycin and 1x ITS (Gibco Cat. #41400-045).

extract_protocol:
RNA was harvested using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1057). All lysates were frozen at -80°C prior to extraction, and all extracted RNA were stored at -80°C as single-use aliquots.
Sequencing libraries were prepared from RNA harvested from treatment or transfection replicates. Total RNA was extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research, Cat. #D4209). Ribosome depletion and library preparation was performed using the Qiagen Fast-select (Cat. #334375) and KAPA BioSystems mRNA HyperPrep Kit (Cat. #KK8581) according to the manufacturer’s protocols. Briefly, 500ng of RNA was used as input, and KAPA BioSystems single-index adapters were added at a final concentration of 1.5mM. Purified, adapter-ligated library was amplified for a total of 11 cycles following the manufacturer’s protocol. The final libraries were pooled and sequenced on an Illumina NovaSeq X (University of Colorado Genomics Core) as 150 bp paired-end reads.

treatment_protocol: Cells were treated with DMSO, olaparib, EZM8266, or olaparib + EZM8266 for 72 hours

value: ovarian cancer cells

value: olaparib-resistant


title: MPN12_S16_STARAligned.sortedByCoord.out.bam [RNA-seq]


title: NGFR-, rep2

value: healthy volunteer_2


title: BCSP, Mettl3cko, 3 days, rep1

description: Library name: Mettl3cko-BCSP-Rep1


title: NGFR-, rep1

value: healthy volunteer_1


title: ID8_OR_Combo_rep1

description: ID8_OR_COMBO_1_S35_L002_R.sorted.uniq.bam


title: MPN10_S14_STARAligned.sortedByCoord.out.bam [RNA-seq]


title: pre-BCSP, Mettl3cko, 3 days, Rep2.

description: Library name: Mettl3cko-pre-BCSP-Rep2


title: NGFR+, rep3

value: NGFR+


title: NGFR+, rep2


title: ID8_OR_EZM_rep2


title: nMSC4_S4_STARAligned.sortedByCoord.out.bam [RNA-seq]

value: normal control


title: MPN11_S15_STARAligned.sortedByCoord.out.bam [RNA-seq]


title: ID8_OR_EZM_rep1


title: SSC, Mettl3cko, 3 days, Rep2.

description: Library name: Mettl3cko-SSC-Rep2

value: wild type

value: no treatment


title: NGFR+, rep1


title: ID8_OR_Olap_rep1

description: ID8_OR_OLAP_1_S43_L002_R.sorted.uniq.bam

value: Olaparib


title: pre-BCSP, Mettl3cko, 3 days, rep1

description: Library name: Mettl3cko-pre-BCSP-Rep1


title: MNC_all, rep3


title: ID8_OR_DMSO_rep2

description: ID8_OR_DMSO_2_S42_L002_R.sorted.uniq.bam

value: DMSO


title: SSC, Mettl3cko, 3 days, rep1

description: Library name: Mettl3cko-SSC-Rep1


title: HEC, wild type, IP, 3 days, Rep2.

description: Library name: IP-WT-HEC-Rep2


title: MNC_all, rep2


title: nMSC3_S3_STARAligned.sortedByCoord.out.bam [RNA-seq]


title: ID8_OR_DMSO_rep1

description: ID8_OR_DMSO_1_S41_L002_R.sorted.uniq.bam


title: HEC, wild type, IP, 3 days, rep1

description: Library name: IP-WT-HEC-Rep1


title: nMSC1_S1_STARAligned.sortedByCoord.out.bam [RNA-seq]


title: MNC_all, rep1


title: MCF10A cells, siDAB2IP_Rep3

city: Chapel Hill

first: Albert

middle: S.

last: Baldwin

state: North Carolina

address: 450 West Drive, Room 21-211

department: Lineberger Comprehensive Cancer Center

institute: UNC at Chapel Hill

data_processing:
Mapping was performed using STAR v2.6.1d  - as described by Novogene Report
Quantification was performed using FeatureCounts v1.5.0-p3  - as described by Novogene Report
Differential Analysis was performed using DESeq2 v1.20.0 (padj<=0.05) & EdgeR v3.24.3 (padj<=0.005 and |log2(FoldChange)|>=1)  - as described by Novogene Report
Assembly: hg38
Supplementary files format and content: tab-delimited text file formatted as a Matrix Table including FPKM values for each Sample, tab-delimited text file formatted as a Matrix Table including read counts for each Sample

growth_protocol: MCF10A cells were cultured in DMEM/F12 medium supplemented with 5% horse serum, 10 ug/mL recombinant human insulin, 20 ng/mL recombinant epidermal growth factor, 100 ng/mL cholera toxin, 0.5 ug/mL hydrocortisone, and 1% penicillin/streptomycin. Cells were maintained at 37oC with 5% CO2

extract_protocol:
RNA was isolated using Quick-RNA kits, Zymo Research following manufacturer’s instructions
RNA-seq libraries were prepared by Novogene Corporation Inc., California.

treatment_protocol: MCF10A cells were transfected with siRNA against DAB2IP or non-targeting control pool. Post 48 hours of transfection, total RNA was isolated using Quick-RNA kits, Zymo Research following manufacturer’s instructions

value: Non-malignant breast epithelial cell line

value: DAB2IP knockdown

value: DAB2IP targeting siRNA


title: SD-AcPbKO-04

city: Spokane

first: Yiyong

last: Liu

address: 412 E Spokane Falls Blvd

institute: Washington State University

data_processing:
HiSeq Control Software (HCS v2.2.68) was used for base-calling.
bcl2fastq2 Conversion Software v2.20 was used to convert base-calling files to fastq files and to trim adaptors.
HISAT2 v2.2.1 was used for alignment
featureCounts (from Subrea v2.0.1) was used to quantify genes and transcripts.
DESeq2 v1.31.16 was used for differential gene expression analysis.
Assembly: UCSC mm10
Supplementary files format and content: comma-delimited text files including read counts in genes and differential gene expression

source_name: somatosensory cortex

growth_protocol: Male C57BL/6 and male IL1 receptor AcPb-/- mice were obtained from Jackson Laboratories, Bar Harbor, ME, as authorized by Amgen, Thousand Oaks, CA, and were bred for 5-7 generations at Washington State University. Subsequent homozygotic offspring, aged 2-3 months, were utilized in the experiments. All mice were genotyped from tail snips by Transnetyx (Cordova, TN).  Mice were maintained in plastic filter-top cages at 23-24° C under a 12:12 light-dark cycle (light onset = ZT0) and during recordings in sound-attenuated environmental chambers.  Food and water were available ad libitum.  All animal procedures were approved by the Washington State University Animal Care and Use Committee and conformed to National Institutes of Health guidelines.

extract_protocol:
Total RNA was extracted using QIAzol lysis reagent (QIAGEN) and purified with Rneasy Plus Universal Kit (QIAGEN).
Library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: We exposed both wild-type (WT) and AcPb-/- mice to sleep disruption (SD) from ZT20-4 using a gentle handling technique, with four mice in each group (SD-WT [n=4], SD-AcPb [n=4]). Control mice from both strains, consisting of three WT mice (CTL-WT [n=3]) and five AcPb-/- mice (CTL-AcPb-/- [n=5]), were left undisturbed before being euthanized at ZT4. Total RNA was extracted from somatosensory cortex tissues collected post-euthanasia from both WT and AcPb-/- mice for RNA sequencing.

value: somatosensory cortex

value: AcPb-/-

value: Sleep disruption (SD)


title: 6C3, wild type, IP, 3 days, Rep2.

description: Library name: IP-WT-6C3-Rep2

value: long bone

value: skeletal stem and progenitor cells


title: 6C3, wild type, IP, 3 days, rep1

description: Library name: IP-WT-6C3-Rep1


title: SD-AcPbKO-03


title: MCF10A cells, siControl_Rep3

value: WT

value: siControl


title: ID8_OR_Olap_rep2

description: ID8_OR_OLAP_2_S44_L002_R.sorted.uniq.bam

value: ovarian cancer cells

value: olaparib-resistant


title: BLSP, wild type, IP, 3 days, rep1

description: Library name: IP-WT-BLSP-Rep1


title: H139-0061-T1_S10_L001

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

institute: Erasmus MC

description:
Library name: H139-0061-T1_S10_L001
data_processed2.xlsx

data_processing:
NGS output was uploaded to the ARResT/Interrogate immunoprofiler. Samples with <20.000 junctioned reads, excluding spiked sequences, were regarded as QC-failed and discarded. Reads were converted to cell equivalents using the EuroClonality central in-tube quality control. Clonotypes were defined as sequences with identical TRBV and TRBJ gene usage, and 100% complementarity determining region 3 (CDR3) amino acid sequence identity. Unproductive TRB rearrangements were discarded. Clonotypes associated with <0.5 cell equivalents were regarded as likely spillover reads and discarded. Shared clonotypes were cross-referenced against the VDJdb T cell compendium.
Assembly: hg19
Supplementary files format and content: xslx file contained the QC-output of the Arrest/Interrogate immunoprofiler

extract_protocol:
DNA was extracted using a QIA-cube
TRB libraries were amplified from genomic DNA, using the EuroClonality two-step TRB assay, developed by the Euroclonality-NGS Working Group (manuscript in preparation), aiming for 1μg of PBMC DNA input per sample. After each PCR step, amplification success was checked using the D1000 DNA ScreenTape assay on a 4200 Agilent TapeStation (Agilent, Santa Clara, CA, USA) and libraries were purified using the AMPure XP kit (Beckman Coulter, Brae, CA, USA.

treatment_protocol: See methods section of HOVON-139 main publication

value: PBMC

value: Venetoclax/Obinutuzumab


title: H139-0060-T1_S9_L001

description:
Library name: H139-0060-T1_S9_L001
data_processed2.xlsx


title: nMSC2_S2_STARAligned.sortedByCoord.out.bam [RNA-seq]

city: paris

value: normal control

value: mesenchymal stromal cells (MSCs)


title: MCF10A cells, siControl_Rep2


title: SD-AcPbKO-01


title: THY, wild type, IP, 3 days, Rep2.

description: Library name: IP-WT-THY-Rep2

value: wild type

value: no treatment


title: MCF10A cells, siDAB2IP_Rep2

value: Non-malignant breast epithelial cell line

value: DAB2IP knockdown


title: BLSP, wild type, IP, 3 days, Rep2.

description: Library name: IP-WT-BLSP-Rep2


title: H139-0066-T1_S2_L001

description:
Library name: H139-0066-T1_S2_L001
data_processed2.xlsx


title: H139-0059-T1_S8_L001

description:
Library name: H139-0059-T1_S8_L001
data_processed2.xlsx


title: MCF10A cells, siDAB2IP_Rep1

value: DAB2IP targeting siRNA


title: CTL-AcPbKO-05

value: somatosensory cortex

value: AcPb-/-

value: Control


title: H139-0062-T1_S1_L001

description:
Library name: H139-0062-T1_S1_L001
data_processed2.xlsx


title: THY, wild type, IP, 3 days, rep1

description: Library name: IP-WT-THY-Rep1

value: long bone

value: skeletal stem and progenitor cells


title: MCF10A cells, siControl_Rep1

value: WT

value: siControl