title: 68: RNA-seq

city: Le Kremlin-Bicêtre

first: Say

last: Viengchareun

state: Val de Marne

address: 63 rue gabriel peri

country: France

data_processing:
RNA library preparation were realized following manufacturer’s recommendations (Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Kit from Illumina). Final samples pooled library prep were sequenced on Nextseq 500 ILLUMINA with HighOutPut cartridge (2x400Millions of 75 bases reads), corresponding to 2x30Millions of reads per sample after demultiplexing.
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.10.11) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts
Supplementary files format and content: Matrix table with tpm gene counts

source_name: Kidney

extract_protocol:
Total RNA was extracted using NucleoSpin miRNA kit (Macherey Nagel) according to the manufacturer’s protocol
RNA library preparation were realized following manufacturer’s recommendations (Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Kit from Illumina)

value: Kidney

tag: age

value: Day 8

value: Untreated


title: 67: RNA-seq

status: Public on Feb 10 2025

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

value: WT

tag: treatment


title: 69: RNA-seq


title: QGP-1, butyrate,1, K9Ac

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

country: USA

institute: Mayo Clinic

description: Library name: Bub-1_K9Ac-2

library_source: genomic

data_processing:
Reads were mapped to a composite hg38+dm6 genome using BWA
Peak calling was performed using MACS2
Assembly: hg38 + dm6
Supplementary files format and content: bed files containing peak calls

molecule: genomic DNA

organism: Homo sapiens

source_name: Pancreas

growth_protocol: QGP-1 cells were all grown in DMEM/F12 (Gibco, Jenks, OK) with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco) at 37°C with 5% CO2 atmosphere.

extract_protocol:
QGP-1 cells were trypsinized, crosslinked to 1% formaldehyde for 10 min, and quenched with 125 mM glycine for 5 min at room temperature. After washing with TBS, cells were resuspended in cell lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. Lysates were washed with MNase digestion buffer (20 mM Tris-HCl, pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After resuspension in 200 μL fresh MNase digestion buffer containing proteinase inhibitor cocktail (Sigma), the lysates were incubated with 2000 units of MNase (New England Biolabs, Ipswich, MA) per 4 x 10^6 cells at 37°C for 20 min with continuous mixing in a thermal mixer. After adding 200 μL of sonication buffer (100 mM Tris-HCl, pH 8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 20 min (30 s on/30 s off) using Bioruptor Twin (UCD-400) (Diagenode, Denville, NJ) and centrifuged at 21,130 x g for 10 min. The supernatants were collected, and the chromatin amount was estimated by the Qubit assay (Invitrogen).
ChIP-Rx; The chromatin was then incubated with anti-H3K27ac antibody (Cell Signaling Technology, Danvers, MA) or in-house generated anti-H3K9ac antibody (EDL lot 1) on a rocker overnight. Protein G-magnetic beads (30 μL, Life Technologies) were added, and further incubated for 3 hrs. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl2 buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen, Germantown, MD) after the treatment of RNase A and proteinase K. The libraries were prepared from about 5 - 10 ng ChIP and input DNA using the ThruPLEX DNA-seq kit (TaKaRa, San Jose, CA). ChIP enrichment was validated by performing real-time PCR in library DNAs. The following primers were used: H3K27ac-positive control locus: SMARCA4-TSS-F: 5’-TTGGCGAAGCTGCGATCGGG-3’, SMARCA4-TSS-R: 5’-AGGGGACCGCTAATGCCCGT-3’; ACTB-TSS-F: 5’-CCTCATGGCCTTGTCACAC-3’, ACTB-TSS-R: 5’-GCCCTTTCTCACTGGTTCTCT-3’; H3K27ac-negative control locus: Ch19-intergenic-F: 5’-AGCTTGTCTTTCCCAAGTTTACTC-3’, Ch19-intergenic-R: 5’-TAGCTGTCGCACTTCAGAGGA-3’.

treatment_protocol: Cells in the cointrol group were maintained in fresh DMEM/F12 medium, while those in butyrate group were maintained in fresh DMEM/F12 containing 5 mM butyrate for 24h.

value: Pancreas

tag: cell line

tag: cell type

value: human pancreatic islet cell carcinoma cell line

value: 5 mM butyrate

tag: chip antibody


title: 7ST7

city: Planegg-Martinstied

first: Giacomo

last: Masserdotti

address: Groshaderner Strasse 9

department: ISF

country: Germany

institute: Helmholtz Zentrum

data_processing:
Sequencing reads were mapped to the GRCm38.101 reference genome using STAR software version 2.6.0a.
TPM expression values based on ENSEMBL annotation version GRCm38.92 were calculated with RSEM (1.3.0).
Assembly: mm10
Supplementary files format and content: txt file

molecule: polyA RNA

source_name: brain

growth_protocol: Transgenic mice were fed ad libitum

extract_protocol:
Single cells were sucked with an electrophysiological tip and transfer to tube for subsequent analysis.
SmartSeq2 + illumina protocols

treatment_protocol: Transgenic mice were injected with Mok-LV carrying the gRNA targeting Sox9 or Trps1 or both

value: brain

value: Astrocyte

tag: grna

tag: day

tag: batch


title: ChIP_untagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 2

city: Vancouver

first: LeAnn

last: Howe

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry and Molecular Biology

country: Canada

institute: University Of British Columbia

description:
no tag_2_ChIP
ChIP DNA from untagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 2

data_processing:
Sequence reads were trimmed for adapter sequences using cutadapt (http://cutadapt.readthedocs.io/en/stable/) and mapped to the Saccer3 genome build using BWA-MEM. Only reads mapped in proper pairs by BWA-MEM were used in subsequent analysis.
Data was converted to bigwig files of using  DeepTools in the Galaxy web platform. bamCoverage was used to analyze IP and input samples separately, while bamCompare was used to compare IP and input signal. Parameters used were: bin size = 5 bp, mapping quality threshold >= 25, paired-end read extension, duplicate reads removed. IP reads were first multiplied by a scaling factor (1000 / S. pombe IP reads). IP and input samples were normalized based on the relative number of reads mapping to the genome of the S. pombe spike-in. “IP/input” analyses are presented as the log2 of IP signal divided by input signal, in which IP reads were multiplied by a scaling factor (1000 / S. pombe IP reads). This value of 1000 was used an arbitrary scaling factor while dividing by S. pombe spike-in reads, similar to the use of scaling factors in previous work64. Input samples were multiplied by a scaling factor of (1 / S. pombe input reads).
Assembly: saccer3.fa
Supplementary files format and content: bigwig files of read count normalized to S. pombe spike-ins
Supplementary files format and content: log2 (ChIP/input) bigwig files normalized to S. pombe spike-ins

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to mid-log phase in SC-ura media at 30C before treatment with 1 µM estradiol for one hour.

extract_protocol:
Cells (450 million S.cerevisiae and 68 million Schizosaccharomyces pombe as spike-in) were resuspended in 0.6 mL of lysis buffer (50 mM Hepes-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) and lysed by bead beating before centrifugation, then resuspended in 1 mL. Samples were sonicated with a Covaris S220 focused-ultrasonicator (peak power 150 W for 7min with 30s cycling off/on, duty factor 14, 200 cycles/burst). One hundred microlitres of lysate was reserved as input and 750 uL was used for immunoprecipitation. Samples were precleared with protein G Dynabeads™ (ThermoFisher cat# 10003D) for 1 hour, incubated overnight anti-GFP antibody (Abcam cat# ab290), and incubated with protein G beads for 1 hour, all at 4°C. Beads were washed twice with lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 0.5 mM EDTA, 1% triton X-100, 0.1% sodium deoxycholate), twice with lysis buffer with 500 mM NaCl, and twice with LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.6% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), before 1 wash with TE (pH 8). Samples were eluted in elution buffer (TE pH 8, 1% sodium dodecyl sulfate, 150 mM NaCl, 5 mM dithiothreitol) three times by incubation at 65°C for ten minutes, with shaking.
DNA was end-repaired, A-tailed, and ligated to adapters before 17 cycles of PCR amplification with indexed primers. All DNA purification steps used Solid Phase Reversible Immobilization magnetic beads (Omega, M1378). Samples were pooled, gel-purified (200-600 bp fragments) and sequenced on an Illumina NextSeq.

treatment_protocol: Cells were cross-linked with 1% formaldehyde for 15 min, quenched with 300 mM glycine for 5 min, and frozen.

value: anti-GFP antibody (Abcam cat# ab290)

value: Mata his3D200 leu2D1 lys2-128d ura3-52 trp1D63 pMeCP2_E1


title: QGP-1, butyrate,1, K27Ac

description: Library name: Bub-1_K27Ac-3


title: 59: RNA-seq


title: 66: RNA-seq


title: ChIP_GFP-tagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 2

description:
WT_2_ChIP
ChIP DNA from GFP-tagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 2

value: Mata his3D200 leu2D1 lys2-128d ura3-52 trp1D63 pGFP-MeCP2_E1

value: Cells were grown to mid-log phase in SC-ura media at 30C before treatment with 1 µM estradiol for one hour


title: 7ST6


title: QGP-1, butyrate, 1, Input

description: Library name: Bub-1_Input-19

value: Input


title: ChIP_GFP-tagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 1

description:
WT_1_ChIP
ChIP DNA from GFP-tagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 1


title: Flp-In 293 Rbfox2 KO#7 F-Rbfox1(F125A) line, rep3

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description:
WT_FA_rMATs.xlsx
KO_FA_rMATs.xlsx

data_processing:
Sequencing reads were mapped to hg38 using star (--alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNmax 2)
splicing analysis were done by using rmats-turbo-4.1.2
Assembly: hg38
Supplementary files format and content: rMATs results

source_name: Flp-In 293 Rbfox2 KO#7 F-Rbfox1(F125A)

growth_protocol: DMEM 10% FBS

extract_protocol:
Trizol followed by Zymo RNA Clean and Concentrator
Libraries prepared by UNGC core via TruSeq Stranded mRNA (Poly-A)
RNA-seq  Paired end 2x100

treatment_protocol: Doxycyline for 48 hrs

value: Flp-In 293 Rbfox2 KO#7 F-Rbfox1(F125A)

value: Doxycycline


title: 55: RNA-seq


title: Input_GFP-tagged T158M MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 2

description:
T158M_2_input
Input DNA from GFP-tagged T158M MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 2

value: Mata his3D200 leu2D1 lys2-128d ura3-52 trp1D63 pGFP-MeCP2_E1_T158M


title: 7ST2


title: Flp-In 293 Rbfox2 KO#7 F-Rbfox1(F125A) line, rep2

description:
WT_FA_rMATs.xlsx
KO_FA_rMATs.xlsx


title: 32: RNA-seq

value: Kidney

value: Day 0


title: Flp-In 293 Rbfox2 KO#7 F-Rbfox1(F125A) line, rep1

description:
WT_FA_rMATs.xlsx
KO_FA_rMATs.xlsx


title: Input_GFP-tagged T158M MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 1

description:
T158M_1_input
Input DNA from GFP-tagged T158M MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 1


title: Flp-In 293 Rbfox2 KO#7 F-Rbfox1(WT) line, rep3

description:
WT_KO_rMATs.xlsx
WT_FA_rMATs.xlsx

source_name: Flp-In 293 Rbfox2 KO#7 F-Rbfox1(WT)

value: Flp-In 293 Rbfox2 KO#7 F-Rbfox1(WT)


title: 7ST1


title: 7ST4


title: 28: RNA-seq

value: WT

value: Untreated


title: Input_untagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 2

description:
no tag_2_input
Input DNA from untagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 2


title: 27: RNA-seq


title: RNA from S. cerevisiae cells with vector alone grown in  CSM-uracil and pulsed with 4-tU replicate 1

description: Library name: vector_1_RNA

data_processing:
Bioinformatic analysis was performed as previously described (Ridenour and Donczew 2024). Reads were processed with fastp and bbduk to trim adapter sequences and polyA tails. The trim package was applied so that subsequent steps used read positions 14-56 for analysis. Reads were then analyzed with the slamdunk, alleyoop, and multiqc packages. A minimum of 2x T>C conversions was used as the threshold for T>C reads in slamdunk analysis, and a minimum base quality of 26 was used for T>C calls.
Assembly: saccer3.fa
Supplementary files format and content: Slamdunk counts

extract_protocol:
RNA was extracted using hot acid phenol  and 10 µg of purified RNA was alkylated with fresh iodoacetamide.
RNA samples were subject to polyA capture, reverse transcription, and amplification according to the Illumina Stranded mRNA prep workflow.

treatment_protocol: Cells were treated with 4-thiouracil for eight minutes and flash frozen.

value: Mata his3D200 leu2D1 lys2-128d ura3-52 trp1D63 pRS416

value: Cells were grown to mid-log phase in SC-ura media at 30C before treatment with 1 µM estradiol for four hours.  Cells were then treated with 4-thiouracil for 8 minutes


title: AG7_b3

value: brain

value: no-gRNA

value: Adult


title: Flp-In 293 Rbfox2 KO#7 F-Rbfox1(WT) line, rep2

description:
WT_KO_rMATs.xlsx
WT_FA_rMATs.xlsx


title: 22: RNA-seq


title: AG6_b3

value: Astrocyte


title: Input_GFP-tagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 2

description:
WT_2_input
Input DNA from GFP-tagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 2

value: Mata his3D200 leu2D1 lys2-128d ura3-52 trp1D63 pGFP-MeCP2_E1


title: Flp-In 293 Rbfox2 KO#7 F-Rbfox1(WT) line, rep1

description:
WT_KO_rMATs.xlsx
WT_FA_rMATs.xlsx


title: 21: RNA-seq


title: Input_GFP-tagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 1

description:
WT_1_input
Input DNA from GFP-tagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 1

value: Cells were grown to mid-log phase in SC-ura media at 30C before treatment with 1 µM estradiol for one hour


title: Input_untagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 1

description:
no tag_1_input
Input DNA from untagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 1

value: Mata his3D200 leu2D1 lys2-128d ura3-52 trp1D63 pMeCP2_E1


title: AG5_b3


title: 20: RNA-seq


title: 7ST3


title: ChIP_untagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil rep 1

description:
no tag_1_ChIP
ChIP DNA from untagged MeCP2 expressed from an estradiol-inducible promoter in S. cerevisiae grown in CSM-uracil replicate 1

value: anti-GFP antibody (Abcam cat# ab290)


title: Whole brain, chr17 T428del/+, chr14 TU/PK, rep3

city: Adelaide

first: Lachlan

last: Baer

address: North Terrace

country: Australia

institute: The University of Adelaide

description: Library name: S27_eofad_het

data_processing:
Raw reads were trimmed with fastp v0.23.4 with parameters: --detect_adapter_for_pe --qualified_quality_phred 20 --length_required 35 --trim_poly_g
Trimmed reads were aligned to GRCz11 Ensembl release 111 with STAR v2.7.11b with parameters: --sjdbOverhang 149 --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Aligned reads were summarised to the gene level using Subread featureCounts v2.0.6 with parameters: -p --countReadPairs --fracOverlap 1 --minOverlap 35
Assembly: GRCz11
Supplementary files format and content: Processed data contains gene-level counts as output by featureCounts in TSV format.

organism: Danio rerio

source_name: Whole brain

extract_protocol:
RNA was extracted from whole brain tissue using Qiagen RNeasy columns.
Stranded polyA libraries prepared according to the Nugen Universal Plus mRNA-seq protocol and included 13 cycles of amplification.

value: Whole brain

value: chr17 T428del/+; chr14 TU/PK


title: 69: miRNA-seq

data_processing:
Quality of raw data was evaluated with FastQC.
The quantification of miRNAs was carried out according to recommendations by Potla et al, 2021.
Assembly: mature miRNA sequences from miRBase (v22.1) Mus musculus
Supplementary files format and content: Matrix table with raw miRs counts

extract_protocol:
Total RNA including miRNAs and larrge RNAs was extracted using NucleoSpin miRNA kit (Macherey Nagel) according to the manufacturer’s protocol
SmallRNA library preparation were realized following manufacturer’s recommendations (QIAseq miRNA Library Kit Kit from QIAGEN)

value: Kidney

value: Day 8


title: Whole brain, chr17 W233fs/+, chr14 PK/PK, rep3

description: Library name: S26_fai_pk

value: chr17 W233fs/+; chr14 PK/PK


title: Flp-In 293 Rbfox2 KO#7 line, rep1

description:
WT_KO_rMATs.xlsx
KO_FA_rMATs.xlsx

source_name: Flp-In 293 Rbfox2 KO#7

value: Flp-In 293 Rbfox2 KO#7

value: Doxycycline


title: AG10_b3


title: Flp-In 293 Rbfox2 KO#7 line, rep2

description:
WT_KO_rMATs.xlsx
KO_FA_rMATs.xlsx


title: AG4_b3


title: AG2_b3


title: 68: miRNA-seq

value: WT

value: Untreated


title: 67: miRNA-seq


title: 24ctrl

value: brain

value: in-slice control


title: Rat, Placenta, ITE treated, Male fetus, Rep.13

city: Madison

first: chi

last: zhou

state: WI

address: 202 S. Park Street, PAB1, Meriter Hospital

department: Department of OB/Gyn

institute: University of Wisconsin-Madison

data_processing:
Illumina bcl2fastq v2.20.0.422
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output
Differential expression estimation with edgeR v3.28.0
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file includee RSEM values for all samples.

organism: Rattus norvegicus

source_name: Placenta

extract_protocol:
Total RNA samples were isolated from rat placentas using an RNeasy Mini Kit (Qiagen, Valencia, CA). The concentration and quality of each RNA sample were assessed using NanoDrop™ND-2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100-bioanalyzer (Agilent Technologies, Santa Clara, CA). Only RNA samples with high RNA integrity number (>8.5) were utilized in this study.
RNA libraries (one library per cell preparation) are generated using the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, California, USA) following the manufacturer’s instruction. In brief, 300ng total RNA of each sample is fragmented using divalent cations under elevated temperature, and purified. Double-stranded complementary DNAs (cDNAs) are synthesized using SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, California, USA) and random primers. The cDNAs are ligated to Illumina adapters and amplified in a Linker Mediated PCR reaction (LM-PCR) for 9 cycles using PhusionTM DNA Polymerase and Illumina's PE genomic DNA primer set followed by purification (Agencourt AMPure XP beads, Qiagen).

value: Placenta

tag: sex (fetal)

value: Male

value: ITE


title: 66: miRNA-seq


title: Rat, Placenta, ITE treated, Male fetus, Rep.12


title: Flp-In 293 Rbfox2 KO#7 line, rep3

description:
WT_KO_rMATs.xlsx
KO_FA_rMATs.xlsx


title: Whole brain, chr17 W233fs/+, chr14 TU/PK, rep3

description: Library name: S24_fai_het

value: chr17 W233fs/+; chr14 TU/PK


title: 59: miRNA-seq


title: 2517

value: Astrocyte


title: Whole brain, chr17 +/+, chr14 TU/PK, rep3

description: Library name: S23_wt_het

value: chr17 +/+; chr14 TU/PK


title: Rat, Placenta, ITE treated, Male fetus, Rep.10


title: Rat, Placenta, ITE treated, Male fetus, Rep.11


title: 2518


title: Whole brain, chr17 +/+, chr14 TU/PK, rep2

description: Library name: S22_wt_het

value: Whole brain


title: 55: miRNA-seq


title: Whole brain, chr17 +/+, chr14 PK/PK, rep3

description: Library name: S21_wt_pk

value: chr17 +/+; chr14 PK/PK


title: 2516


title: 32: miRNA-seq

value: Kidney

value: Day 0


title: Rat, Placenta, ITE treated, Male fetus, Rep.09


title: Whole brain, chr17 T428del/+, chr14 TU/TU, rep2

description: Library name: S20_eofad_tu

value: chr17 T428del/+; chr14 TU/TU


title: 2515


title: 28: miRNA-seq


title: Rat, Placenta, ITE treated, Male fetus, Rep.07


title: Whole brain, chr17 T428del/+, chr14 TU/TU, rep3

description: Library name: S25_eofad_tu


title: 2510


title: Whole brain, chr17 W233fs/+, chr14 TU/TU, rep3

description: Library name: S19_fai_tu

value: chr17 W233fs/+; chr14 TU/TU


title: 27: miRNA-seq


title: 2519


title: Rat, Placenta, ITE treated, Male fetus, Rep.06


title: Whole brain, chr17 W233fs/+, chr14 TU/PK, rep2

description: Library name: S18_fai_het


title: Whole brain, chr17 T428del/+, chr14 PK/PK, rep3

description: Library name: S17_eofad_pk

value: chr17 T428del/+; chr14 PK/PK


title: 2508


title: Rat, Placenta, ITE treated, Male fetus, Rep.05


title: 2506


title: 21: miRNA-seq

value: WT


title: 20: miRNA-seq

value: Untreated


title: Rat, Placenta, ITE treated, Male fetus, Rep.04


title: Whole brain, chr17 W233fs/+, chr14 TU/PK, rep1

description: Library name: S15_fai_het


title: Whole brain, chr17 W233fs/+, chr14 TU/TU, rep2

description: Library name: S16_fai_tu


title: 2410

value: brain

value: g-Control


title: Rat, Placenta, ITE treated, Male fetus, Rep.03

value: Placenta


title: EC_IL1a_2

city: Minato-ku

first: Yoshiki

last: Kuse

address: Shirokanedai 4-6-1

country: Japan

institute: The University of Tokyo

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary files format and content: Comma-delimited text files include RPM values for each sample.

source_name: Organoid-derived cell

extract_protocol:
Organoid dissociationwas done by adding collagenase, pronase, and DNase at 37°C for 40 minutes in a water bath. Pipetting was carried out every ten minutes. RNA was extracted with PureLink™ RNA Micro Scale Kit (Invitrogen, Waltham, Massachusetts, USA) was used for RNA extraction from sorted cells.
RNA libraries were prepared using total RNA with an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific).

value: Organoid-derived cell

value: hiPSC

value: EC


title: Rat, Placenta, ITE treated, Male fetus, Rep.08

value: Male

value: ITE


title: Rat, Placenta, ITE treated, Male fetus, Rep.02


title: 2409

value: Astrocyte


title: Whole brain, chr17 W233fs/+, chr14 PK/PK, rep2

description: Library name: S13_fai_pk

value: Whole brain

value: chr17 W233fs/+; chr14 PK/PK


title: HE_IL1a_2

value: HE


title: 2407


title: Rat, Placenta, ITE treated, Female fetus, Rep.08

value: Female


title: Whole brain, chr17 T428del/+, chr14 PK/PK, rep2

description: Library name: S12_eofad_pk


title: EC_cont_2

value: Control


title: 22: miRNA-seq

value: Kidney

value: Day 0


title: 2405


title: 2412


title: Whole brain, chr17 T428del/+, chr14 TU/TU, rep1

description: Library name: S11_eofad_tu

value: chr17 T428del/+; chr14 TU/TU


title: MC_cont_2

value: MC


title: 2401

value: brain

value: g-Control


title: 2403


title: Rat, Placenta, ITE treated, Female fetus, Rep.06

value: Placenta


title: Whole brain, chr17 T428del/+, chr14 PK/PK, rep1

description: Library name: S10_eofad_pk

value: chr17 T428del/+; chr14 PK/PK


title: Whole brain, chr17 +/+, chr14 PK/PK, rep2

description: Library name: S08_wt_pk

value: chr17 +/+; chr14 PK/PK


title: EC_IL1a_1

value: Organoid-derived cell

value: hiPSC

value: EC


title: Rat, Placenta, ITE treated, Female fetus, Rep.04

value: ITE


title: Whole brain, chr17 T428del/+, chr14 TU/PK, rep2

description: Library name: S14_eofad_het

value: Whole brain

value: chr17 T428del/+; chr14 TU/PK


title: Whole brain, chr17 W233fs/+, chr14 PK/PK, rep1

description: Library name: S07_fai_pk

value: chr17 W233fs/+; chr14 PK/PK


title: Rat, Placenta, ITE treated, Female fetus, Rep.05

value: Female


title: MC_IL1a_1


title: HE_cont_2

value: HE

value: Control


title: 2308

value: Astrocyte


title: MC_IL1a_2

value: MC


title: Rat, Placenta, ITE treated, Male fetus, Rep.01

value: Male


title: Rat, Placenta, ITE treated, Female fetus, Rep.03


title: 2307

value: brain

value: g-Control


title: 2306


title: Rat, Placenta, ITE treated, Female fetus, Rep.07

value: Placenta


title: HE_IL1a_1


title: Rat, Placenta, ITE treated, Female fetus, Rep.02


title: Whole brain, chr17 +/+, chr14 PK/PK, rep1

description: Library name: S06_wt_pk

value: chr17 +/+; chr14 PK/PK


title: Whole brain, chr17 +/+, chr14 TU/TU, rep3

description: Library name: S09_wt_tu

value: chr17 +/+; chr14 TU/TU


title: 2309


title: Rat, Placenta, ITE treated, Female fetus, Rep.01


title: 2305


title: Whole brain, chr17 T428del/+, chr14 TU/PK, rep1

description: Library name: S04_eofad_het


title: 2303


title: Whole brain, chr17 +/+, chr14 TU/TU, rep2

description: Library name: S05_wt_tu


title: Rat, Placenta, Control, Male fetus, Rep.16

value: Ctrl


title: EC_cont_1

value: Organoid-derived cell

value: hiPSC

value: EC


title: Whole brain, chr17 +/+, chr14 TU/PK, rep1

description: Library name: S03_wt_het

value: Whole brain

value: chr17 +/+; chr14 TU/PK


title: 2302


title: Rat, Placenta, Control, Male fetus, Rep.14


title: Whole brain, chr17 W233fs/+, chr14 TU/TU, rep1

description: Library name: S02_fai_tu

value: chr17 W233fs/+; chr14 TU/TU


title: 2301


title: Whole brain, chr17 +/+, chr14 TU/TU, rep1

description: Library name: S01_wt_tu


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), Input

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

institute: CHU Ste-Justine Research Center/Université de Montréal

description:
Input_INV
Input_mESC_INV_RPKM.bw

data_processing:
Raw reads were processed using a homemade pipeline including Trimmomatic v0.32 for quality trimming of raw reads and removal of sequencing adapters, Burrows-Wheeler Aligner v0.6.1 for read alignment to the mouse reference genome assembly GRCm38/mm10, the MergeSamFiles.jar and MarkDuplicates.jar scripts from Picard v1.70 for merging read set files of each sample and removing duplicate reads, respectively, and the View function from SAMtools v0.1.18 for filtering reads as to only retain those with a MAPQ score ≥ 15. Then, peak calling was performed using MACS2 v2.0.10 with Python v2.7.8, correcting background noise with input signals. Next, MACS2 outputs and BAM files converted to BED format (via the bamTobed function from BEDTools v2.27) were used in the profile_bins function from MAnorm2_utils v1.0.0. The profile_bins function allowed for genomic regions of MACS2 called peaks to be merged into a common set of histone-modified regions across all samples for each histone modification, computing normalized signal enrichment within each region. Finally, MAnorm2 v1.0.0 was employed for conducting differential analysis of enrichment signals between experimental conditions, providing a p-value and log2 fold change for each histone-modified region.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig files containing genome-wide RPKM values of histone modifications and inputs for each experimental condition; RPKM of histone modifications were averaged between experimental condition replicates.
Supplementary files format and content: BED files containing genomic coordinates and signal values of histone modification peaks versus inputs called with the MACS2 software and merged among experimental condition replicates.
Supplementary files format and content: BED files containing results from differential analyses between experimental conditions (INV and RES versus CTL) conducted with the MAnorm2 software for each histone modification.

source_name: R1 mESCs

growth_protocol: Dnmt1tet/tet mESCs were maintained on gelatin-coated plates, free of mouse embryonic fibroblast feeder cells, in mESC culture medium in humidified atmosphere with 5% CO2 at 37 °C. Cell culture plates were coated with 0.1% solution of gelatin (Sigma-Aldrich, G1890) in DPBS 1X (Corning, 21-031-CV), then placed in the incubator for 30 minutes after which excess gelatin was removed. Culture medium for mESCs consisted of DMEM (Corning, 10-013-CV) supplemented with 15% ES cell qualified fetal bovine serum (Thermo Fisher, 16141079), 1% 2-mercaptoethanol 100X (Sigma-Aldrich, ES-007-E), 1% non-essential amino acids 100X (Thermo Fisher, 11140050), 1% L-Glutamine 200 mM (Corning, 25-005-CI), 1% nucleosides 100X (Sigma-Aldrich, ES-008-D), 1% penicillin-streptomycin 100X (Corning, 30-002-CI) and 103 units/mL of recombinant mouse LIF protein (Sigma-Aldrich, ESG1107), which was stored at 4 °C for up to 1 week. Culture medium was changed every day and cell confluency was maintained below 80%. Trypsin-EDTA 0.25% (Thermo Fisher, 25200056) was used for passaging cell cultures, typically every other day.

extract_protocol:
Chromatin immunoprecipitation (ChIP) sequencing was performed in duplicates for each histone modification per experimental condition and one aliquot of non-immunoprecipitated chromatin (i.e. input) was sequenced per experimental condition. First, cells were fixed with a solution consisting of 13% formaldehyde (Sigma-Aldrich, 47608) in DPBS (Corning, 21-031-CV) for 10 minutes at room temperature with gentle rocking. Then, cell and nuclei lysis was performed, and chromatin was purified and sonicated using buffers and protocols from the IDeal ChIP-Seq Histone Kit (Diagenode, C01010051). Sonication was conducted with the Bioruptor® Pico sonication device (Diagenode, B01060010) for 15 cycles (30 seconds ON/ 30 seconds OFF) to obtain DNA fragments between 150-400bp. Next, chromatin was pre-cleared via incubation with protein G Dynabeads™ (Thermo Fisher, 10009D) for 1h at 4°C on a rotator, after which samples were placed on a magnetic rack and input aliquots were taken from the supernatant. Chromatin immunoprecipitation was then conducted as follows. Pre-cleared chromatin samples were incubated overnight at 4°C on a rotator with histone modification antibodies–either anti-H3K4me3 (Active Motif, 39159), anti-H3K27ac (Abcam, ab4729), anti-H3K4me1 (Cell signaling technology, 5326), anti-H3K27me3 (Sigma-Aldrich, 07-449) or anti-H3K9me3 (Abcam, ab8898)–in quantities recommended by the antibody manufacturer. Dynabeads™ were added to the chromatin-antibody mixtures and were incubated for an additional 2h at 4°C on a rotator. Protein A Dynabeads™ (Thermo Fisher, 10001D) or protein G Dynabeads™ (Thermo Fisher, 10009D) were used depending on the antibody source. Washing, elution, decrosslinking and DNA purification were then conducted using the IDeal ChIP-Seq Histone Kit (Diagenode, C01010051).
Libraries were prepared with the KAPA HyperPrep Kit (Roche, KK8502).

treatment_protocol: To inactivate Dnmt1, Dnmt1tet/tet mESCs were treated with 2 μg/mL doxycycline hyclate (Sigma-Aldrich, D9891), a tetracycline derivative, which was added to the culture medium for 6 days. Then, doxycycline treatment was stopped, and cells were maintained for 21 days. Samples were collected prior to doxycycline treatment (Dnmt1 control, CTL), immediately following doxycycline treatment (Dnmt1 inactive, INV), and after the 21-day period of recovery from doxycycline treatment (Dnmt1 rescue, RES).

value: R1 mESCs

value: Embryonic stem cell

value: Doxycycline (2 μg/mL) for 6 days


title: HE_cont_1

value: HE

value: Control


title: MC_cont_1

value: MC


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), Input

description:
Input_RES
Input_mESC_RES_RPKM.bw

value: Doxycycline (2 μg/mL) for 6 days, then recovery for 21 days


title: Rat, Placenta, Control, Male fetus, Rep.13

value: Placenta

value: Male


title: Rat, Placenta, Control, Male fetus, Rep.15


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), Input

description:
Input_CTL
Input_mESC_CTL_RPKM.bw

value: Untreated


title: Sample71

value: brain

value: Astrocyte


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 2, H3K9me3 ChIP-seq

description:
H3K9me3_RES-2
H3K9me3_mESC_RES_Merged_RPKM.bw
H3K9me3_mESC_RES_vs_Input_RES_Merged_Peaks.bed

value: H3K9me3 (Abcam, ab8898)


title: Sample70


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 1, H3K9me3 ChIP-seq

description:
H3K9me3_RES-1
H3K9me3_mESC_RES_Merged_RPKM.bw
H3K9me3_mESC_RES_vs_Input_RES_Merged_Peaks.bed


title: Sample69


title: Rat, Placenta, Control, Male fetus, Rep.11

value: Ctrl


title: 1098

type: RNA

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: Data were collected as NanoString RCC files and provided as an Excel spreadsheet. Sample-specific background was calculated by adding the average of all the negative controls to their standard deviation multiplied by two and then subtracting this value from the raw values for each gene. Biological normalization was performed to correct for differences in sample abundances. Quantile normalization was applied to the dataset and revealed homogenous distribution and comparability of our samples.

label: NanoString

source_name: Pancreatic ductal adenocarcinoma

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: RNA was isolated from FFPE tissue using Recover ALL kit (Ambion)

value: Breast

tag: status

value: human resected PDAC


title: Rat, Placenta, Control, Male fetus, Rep.10


title: Sample68


title: 1055


title: 1076


title: Sample67

value: g-Control


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 1, H3K9me3 ChIP-seq

description:
H3K9me3_INV-1
H3K9me3_mESC_INV_Merged_RPKM.bw
H3K9me3_mESC_INV_vs_Input_INV_Merged_Peaks.bed

value: R1 mESCs


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 2, H3K9me3 ChIP-seq

description:
H3K9me3_INV-2
H3K9me3_mESC_INV_Merged_RPKM.bw
H3K9me3_mESC_INV_vs_Input_INV_Merged_Peaks.bed

value: Embryonic stem cell


title: Rat, Placenta, Control, Male fetus, Rep.09


title: Rat, Placenta, Control, Male fetus, Rep.08


title: 1049


title: Rat, Placenta, Control, Male fetus, Rep.07


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 2, H3K9me3 ChIP-seq

description:
H3K9me3_CTL-2
H3K9me3_mESC_CTL_Merged_RPKM.bw
H3K9me3_mESC_CTL_vs_Input_CTL_Merged_Peaks.bed


title: Sample65


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 1, H3K9me3 ChIP-seq

description:
H3K9me3_CTL-1
H3K9me3_mESC_CTL_Merged_RPKM.bw
H3K9me3_mESC_CTL_vs_Input_CTL_Merged_Peaks.bed


title: Sample66


title: 1044


title: Rat, Placenta, Control, Male fetus, Rep.12


title: Sample64


title: 1037


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 2, H3K27me3 ChIP-seq

description:
H3K27me3_RES-2
H3K27me3_mESC_RES_Merged_RPKM.bw
H3K27me3_mESC_RES_vs_Input_RES_Merged_Peaks.bed

value: H3K27me3 (Sigma-Aldrich, 07-449)


title: Rat, Placenta, Control, Male fetus, Rep.05


title: Rat, Placenta, Control, Male fetus, Rep.06


title: 1023


title: 1034


title: Sample63


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 2, H3K27me3 ChIP-seq

description:
H3K27me3_INV-2
H3K27me3_mESC_INV_Merged_RPKM.bw
H3K27me3_mESC_INV_vs_Input_INV_Merged_Peaks.bed

value: Doxycycline (2 μg/mL) for 6 days


title: 1015


title: Rat, Placenta, Control, Male fetus, Rep.03


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 1, H3K27me3 ChIP-seq

description:
H3K27me3_RES-1
H3K27me3_mESC_RES_Merged_RPKM.bw
H3K27me3_mESC_RES_vs_Input_RES_Merged_Peaks.bed


title: Sample61


title: Rat, Placenta, Control, Male fetus, Rep.02


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 2, H3K27me3 ChIP-seq

description:
H3K27me3_CTL-2
H3K27me3_mESC_CTL_Merged_RPKM.bw
H3K27me3_mESC_CTL_vs_Input_CTL_Merged_Peaks.bed


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 1, H3K27me3 ChIP-seq

description:
H3K27me3_INV-1
H3K27me3_mESC_INV_Merged_RPKM.bw
H3K27me3_mESC_INV_vs_Input_INV_Merged_Peaks.bed


title: Sample60


title: Rat, Placenta, Control, Male fetus, Rep.01


title: 1009


title: Rat, Placenta, Control, Female fetus, Rep.12

value: Female


title: 1007


title: Sample59


title: Sample62


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 1, H3K27me3 ChIP-seq

description:
H3K27me3_CTL-1
H3K27me3_mESC_CTL_Merged_RPKM.bw
H3K27me3_mESC_CTL_vs_Input_CTL_Merged_Peaks.bed


title: Rat, Placenta, Control, Female fetus, Rep.13


title: Sample58


title: 1100


title: Sample56

value: no-gRNA

value: Adult


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 1, H3K4me1 ChIP-seq

description:
H3K4me1_RES-1
H3K4me1_mESC_RES_Merged_RPKM.bw
H3K4me1_mESC_RES_vs_Input_RES_Merged_Peaks.bed

value: Doxycycline (2 μg/mL) for 6 days, then recovery for 21 days

value: H3K4me1 (Cell signaling technology, 5326)


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 2, H3K4me1 ChIP-seq

description:
H3K4me1_RES-2
H3K4me1_mESC_RES_Merged_RPKM.bw
H3K4me1_mESC_RES_vs_Input_RES_Merged_Peaks.bed


title: Rat, Placenta, Control, Female fetus, Rep.11

value: Placenta


title: 1077


title: Sample49

value: brain


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 1, H3K4me1 ChIP-seq

description:
H3K4me1_INV-1
H3K4me1_mESC_INV_Merged_RPKM.bw
H3K4me1_mESC_INV_vs_Input_INV_Merged_Peaks.bed


title: Rat, Placenta, Control, Male fetus, Rep.04

value: Male


title: Rat, Placenta, Control, Female fetus, Rep.09


title: 1075


title: 1039


title: Sample48

value: Astrocyte


title: 1005


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 2, H3K4me1 ChIP-seq

description:
H3K4me1_CTL-2
H3K4me1_mESC_CTL_Merged_RPKM.bw
H3K4me1_mESC_CTL_vs_Input_CTL_Merged_Peaks.bed

value: Untreated


title: Rat, Placenta, Control, Female fetus, Rep.08

value: Ctrl


title: Sample47


title: 1089

value: Breast

value: human resected PDAC


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 1, H3K4me1 ChIP-seq

description:
H3K4me1_CTL-1
H3K4me1_mESC_CTL_Merged_RPKM.bw
H3K4me1_mESC_CTL_vs_Input_CTL_Merged_Peaks.bed

value: R1 mESCs


title: Rat, Placenta, Control, Female fetus, Rep.06


title: Rat, Placenta, Control, Female fetus, Rep.07


title: Sample45


title: Sample44


title: Rat, Placenta, Control, Female fetus, Rep.10


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 1, H3K27ac ChIP-seq

description:
H3K27ac_RES-1
H3K27ac_mESC_RES_Merged_RPKM.bw
H3K27ac_mESC_RES_vs_Input_RES_Merged_Peaks.bed

value: Embryonic stem cell

value: H3K27ac (Abcam, ab4729)


title: Rat, Placenta, Control, Female fetus, Rep.05


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 2, H3K27ac ChIP-seq

description:
H3K27ac_INV-2
H3K27ac_mESC_INV_Merged_RPKM.bw
H3K27ac_mESC_INV_vs_Input_INV_Merged_Peaks.bed

value: Doxycycline (2 μg/mL) for 6 days


title: 1035


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 2, H3K4me1 ChIP-seq

description:
H3K4me1_INV-2
H3K4me1_mESC_INV_Merged_RPKM.bw
H3K4me1_mESC_INV_vs_Input_INV_Merged_Peaks.bed


title: Sample40


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 1, H3K27ac ChIP-seq

description:
H3K27ac_INV-1
H3K27ac_mESC_INV_Merged_RPKM.bw
H3K27ac_mESC_INV_vs_Input_INV_Merged_Peaks.bed


title: Rat, Placenta, Control, Female fetus, Rep.04

value: Female


title: 1016


title: 1020


title: Rat, Placenta, Control, Female fetus, Rep.03


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 2, H3K27ac ChIP-seq

description:
H3K27ac_CTL-2
H3K27ac_mESC_CTL_Merged_RPKM.bw
H3K27ac_mESC_CTL_vs_Input_CTL_Merged_Peaks.bed


title: Sample39

value: no-gRNA


title: 1038


title: Rat, Placenta, Control, Female fetus, Rep.02


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 2, H3K27ac ChIP-seq

description:
H3K27ac_RES-2
H3K27ac_mESC_RES_Merged_RPKM.bw
H3K27ac_mESC_RES_vs_Input_RES_Merged_Peaks.bed


title: Sample36

value: Adult


title: Sample53


title: Rat, Placenta, Control, Female fetus, Rep.01


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 1, H3K27ac ChIP-seq

description:
H3K27ac_CTL-1
H3K27ac_mESC_CTL_Merged_RPKM.bw
H3K27ac_mESC_CTL_vs_Input_CTL_Merged_Peaks.bed


title: 1036


title: 1021


title: Sample41


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 2, H3K4me3 ChIP-seq

description:
H3K4me3_RES-2
H3K4me3_mESC_RES_Merged_RPKM.bw
H3K4me3_mESC_RES_vs_Input_RES_Merged_Peaks.bed

value: Doxycycline (2 μg/mL) for 6 days, then recovery for 21 days

value: H3K4me3 (Active Motif, 39160)


title: 1115


title: Sample33


title: IL-7Rlow rep 3 (RNA-seq)

city: Ulsan

first: Seonjun

last: Park

address: UNIST-gil 50, Ulju-gun, Ulsan

country: South Korea

institute: UNIST

description:
Library name: R6-L_S12
Il7r_low_3

data_processing:
Adapter sequences were trimmed by using Skewer (v0.2.2).
Alignment was conducted using STAR aligner (v2.7.10a) with the following option: --quantMode TranscriptomeSAM.
RSEM (v1.3.3) was used to quantify gene expression.
Downstream analysis was performed using DESeq2 (v1.38.3).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Spleen

extract_protocol:
Mouse splenocytes were harvested and enriched by CD4 T cell isolation kit (#130-104-454, Miltenyi Biotec) in negative selection. Then using the enriched CD4+ T cells, naive CD4 T cells (TCR-β+, CD4+, CD25-, CD62Lhi, CD44low, IL-7Rsup-hi or low) were sorted using FACS (ARIA Fusion, BD Bioscience). RNA was extracted using a Quick-RNATM MicroPrep kit (ZYMO RESEARCH). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Spleen

value: CD4 T cells


title: Dnmt1tet/tet mESCs, Dnmt1 rescue (RES), replicate 1, H3K4me3 ChIP-seq

description:
H3K4me3_RES-1
H3K4me3_mESC_RES_Merged_RPKM.bw
H3K4me3_mESC_RES_vs_Input_RES_Merged_Peaks.bed


title: 1108


title: 1090


title: Sample32

value: brain


title: 1002


title: IL-7Rlow rep 2 (RNA-seq)

description:
Library name: R4-L_S10
Il7r_low_2


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 2, H3K4me3 ChIP-seq

description:
H3K4me3_INV-2
H3K4me3_mESC_INV_Merged_RPKM.bw
H3K4me3_mESC_INV_vs_Input_INV_Merged_Peaks.bed


title: IL-7Rlow rep 1 (RNA-seq)

description:
Library name: R2-L_S8
Il7r_low_1


title: IL-7Rsup-hi rep 3 (RNA-seq)

description:
Library name: R5-H_S11
Il7r_high_3


title: IL-7Rsup-hi rep 2 (RNA-seq)

description:
Library name: R3-H_S9
Il7r_high_2


title: 1081


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 2, H3K4me3 ChIP-seq

description:
H3K4me3_CTL-2
H3K4me3_mESC_CTL_Merged_RPKM.bw
H3K4me3_mESC_CTL_vs_Input_CTL_Merged_Peaks.bed


title: Sample30

value: Astrocyte


title: Sample19


title: 1066


title: IL-7Rsup-hi rep 1 (RNA-seq)

description:
Library name: R1-H_S7
Il7r_high_1


title: 1059


title: Sample18


title: Sample35


title: VDJ-Tcell of Pool4 GEM5

city: Heidelberg

first: Alexandra

middle: M

last: Poos

address: Im Neuenheimer Feld 410

institute: University Hospital Heidelberg

description:
Library name: Po4C5_TCR
patient sample
10X Genomics

library_source: other

data_processing:
CellRanger multi (v7.0.0) was used for the alignment of demultiplexed libraries to reference genome GRCh38 (refdata-gex-GRCh38-2020-A) and the generation of the feature barcode matrices. For the TCR libraries, reference refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 was used. The count matrices were loaded into R (v4.2.2) by using the standard Seurat (v5.0.1) parameters. The feature_reference.csv file is similar for all pools and channels. The file Hashing_information.txt includes all information for sample identification.
Assembly: GRCh38
Supplementary files format and content: CellRanger output GEX+ADT: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output TCR: filtered_contig_annotations.csv
Library strategy: TCR-Seq

molecule: other

source_name: bone marrow

extract_protocol:
Cryopreserved samples were thawed at 37ºC, resuspended in 10 mL RPMI with 10% FCS, and centrifuged at 300 g for 5 min. The pellet was resuspended in 10 mL RPMI with 10% FCS. Cells were centrifuged at 300 g for 5 min, and the pellet resuspended in 50-100 µL PBS plus Calcein (0.1 µM 1:100 from 10µM diluted stock) and efluor-506 fixable viability dye (eBioscience, 1:1000). After 5 min at RT, 100-200 µL antibody master mix for FACS sorting (Table S3) were added. Individual samples were hashed by adding 0.1 µg TotalSeq of the respective anti-human Hashtag 1-4 and 6-9 (Biolegend). After 15 min at 4ºC, 5 mL FACS buffer (1 x DPBS, 5% FCS, 0.5 mM EDTA) was added and the tube centrifuged at 300 g for 5 min, and the pellet resuspended in 300 µL FACS buffer. Sorting was performed with a BD FACS Aria. Gating strategy is shown in Fig. S5A. For each cell population and sample, a maximum of 10,000 events (range=3500-10000 per population, CD90+CD34+ all cells) were sorted into 1.5 mL Protein low binding Eppendorf tubes prefilled with 150 µL Cell Staining Buffer (Biolegend). Sorted cells were pooled into batches, where paired samples from the same patient were in different batches. Each batch contained approx. 130,000 sorted cells, which were centrifuged at 300 g for 5 min and the pellet resuspended in 25 µL Cell Staining Buffer. Subsequently, 2.5 µL of Human TruStain FcX Blocking reagent (Biolegend) was added to the pooled cell suspension and incubated for 10 min at 4ºC. After adding 25 µL of reconstituted TotalSeq™-C antibody cocktail (Biolegend), cells were incubated for 30 min at 4ºC.Cells were washed 3x with 3.5 mL Cell Staining Buffer and resuspended in PBS and loaded onto three 10x GEMs (22,000-24,000 cells per GEM) per batch.
Immunoprofiling was performed according to the Chromium Next GEM Single Cell 5ʹ Reagent Kit v2 (Dual Index) user guide with feature barcode technology for cell surface protein & immune receptor mapping (10x Genomics; CG000330 Rev A). Generated gene expression (GEX) and protein (ADT) libraries were paired-end sequenced on the NovaSeq 6000 S4. Generated V(D)J libraries were paired-end sequenced on the NextSeq 550.

value: bone marrow

value: sorted T cells


title: Sample17


title: Hepatocyte organoids, RGF, Day 12, Yap KO, 3

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

data_processing:
Sequence alignment were performed using STAR aligner.
Paired reads were then counted using ‘featureCounts’ in The Subread software
Raw counts were normalized using the edgeR package
Assembly: mm10
Supplementary files format and content: Comma delimited file include normalized CPM values for each sample

source_name: liver

growth_protocol: The HOs were maintained in the original HO growth medium with growth factors (GFs) (+GF medium). The +GF medium for  HO culture contains Advanced DMEM/F12 with B27 minus vitamin A, 10mM HEPES, GlutaMAX™, and Penicillin-Streptomycin (Thermo Fisher Scientific), 15% RSPO1 conditioned medium (home-made), 3μm CHIR99021 (MCE), 50ng/ml EGF (Biolegend), 25ng/ml HGF (Biolegend), 50ng/ml FGF7 (Peprotech), 50ng/ml FGF10 (Biolegend), 1μM A83-01 (Sigma), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 10 mM Nicotinamide (Sigma), and 1mM N-acetylcysteine (Sigma). The HOs were switched to the maturation medium for HO maturation. The basal medium for human and mouse HO maturation is Growth factors removed (RGF) medium, which includes William's E Medium with B27 minus vitamin A, 10mM HEPES, GlutaMAXTM and Penicillin-Streptomycin (Thermo Fischer Scientific), 50μg/ml Primocin (InvivoGen), 15% RSPO1 conditioned medium (house-made), 3μM CHIR99021 (MCE), 1μM A83-01 (MCE), 5μM Rho Inhibitor γ-27632 (MCE), 10nM gastrin (Sigma), 2.5 mM Nicotinamide (Sigma), and 1.25 mM N-acetylcysteine (Sigma). Additional components were added to RGF medium for hepatic maturation of HOs. RGF +T3: 10nM Triiodothyronine(T3) in RGF medium;

extract_protocol:
Organoids were retrieved from BME using Cultrex Organoid Harvesting Solution and pelleted by centrifuge at 50g for 3 minutes. RNA was isolated from the organoid pellet using PureLinkTM RNA mini kit (Thermo fisher scientific) according to the manufacturer's instruction.
DNA was removed from RNA using RapidOut DNA Removal Kit (Thermo Fisher Scientific) according to the manufacturer's instruction. After measuring RNA quantity and quality by Agilent 2200 TapeStation, 400ng-1000ng RNA per sample reaction were used for mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using xGen™ RNA Library Prep Kit (IDT) according to the manufacturer's instruction.

treatment_protocol: AAV-TBG-Cre was mixed with fragmented HOs in BME at a concentration of 1x10^10 GC/ml during the passage before the maturation process. 200ng/ml Dox were added to the medium to induce YAP overexpression.

value: liver

value: Hepatocyte organoids

value: hepatocytes

value: YAP fl/fl

value: Yap knockout


title: 1056

value: Breast

value: human resected PDAC


title: Dnmt1tet/tet mESCs, Dnmt1 inactive (INV), replicate 1, H3K4me3 ChIP-seq

description:
H3K4me3_INV-1
H3K4me3_mESC_INV_Merged_RPKM.bw
H3K4me3_mESC_INV_vs_Input_INV_Merged_Peaks.bed

value: R1 mESCs

value: Embryonic stem cell

value: Doxycycline (2 μg/mL) for 6 days


title: 1042


title: VDJ-Tcell of Pool4 GEM6

description:
Library name: Po4C6_TCR
patient sample
10X Genomics


title: Sample15

value: no-gRNA

value: Adult


title: VDJ-Tcell of Pool4 GEM4

description:
Library name: Po4C4_TCR
patient sample
10X Genomics


title: Hepatocyte organoids, RGF, Day 12, Yap KO, 1


title: Hepatocyte organoids, RGF, Day 12, Yap KO, 2


title: Sample14


title: 1010


title: Sample29


title: F.n (time2)

city: Guangzhou

first: Tianhao

last: Zhang

state: Guangdong

address: No. 58, Zhongshan 2nd Road, Yuexiu District

department: Division of Gastrointestinal Surgery Center

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
Basecalls performed using CASAVA version 1.8
Thedemultiplexing,barcodeprocessing,genecountingweremadeusingthe STARsolo
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Tumor tissue

growth_protocol: A 15-cm culture dish was used to cultivate the mouse MFC and human MGC803 cell lines to construct a 615 and BALB/c mice subcutaneous tumor xenograft model at a density of 5 × 106 cells per mouse, with 6–8 mice per group. The cells were prepared before performing the animal experiments as follows. We injected 100 μl of the cell suspension into the right armpit/groin of nude mice using a 1-ml insulin injection needle, and the subcutaneous tumor formation in the mice was then observed. After 3–4 days, after the model was successfully constructed, the long and short diameters of the subcutaneous tumors were measured twice a week using a Vernier caliper.

extract_protocol:
samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 250 U/mL collagenase I (Worthington) for 45 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

treatment_protocol: These tumor tissues of mice were collected from two distinct time periods (time 1 and time 2) and subjected to sequencing analysis. Time point 1 corresponds to a tumor growth period of 10 days, while time point 2 represents a 19-day growth period, capturing the acute and chronic stages of tumor growth affected by F. nucleatum. The PBS group serves as the control group, while the F.n group functions as the experimental group.

value: Tumor tissue

value: MFC

value: Mouse Forestomach Carcinoma

value: Subcutaneous injection 5 × 106 cells with F.n infection per mouse


title: 1006


title: Dnmt1tet/tet mESCs, Dnmt1 control (CTL), replicate 1, H3K4me3 ChIP-seq

description:
H3K4me3_CTL-1
H3K4me3_mESC_CTL_Merged_RPKM.bw
H3K4me3_mESC_CTL_vs_Input_CTL_Merged_Peaks.bed

value: Untreated

value: H3K4me3 (Active Motif, 39160)


title: Sample12

value: brain

value: Astrocyte


title: Sample13


title: VDJ-Tcell of Pool3 GEM2

description:
Library name: Po3C2_TCR
patient sample
10X Genomics

value: bone marrow

value: sorted T cells


title: VDJ-Tcell of Pool3 GEM1

description:
Library name: Po3C1_TCR
patient sample
10X Genomics


title: 1001

value: Breast


title: F.n (time1)

description: BD Rhapsody


title: PBS (time2)

description: BD Rhapsody

value: Subcutaneous injection 5 × 106 cells per mouse


title: Sample11


title: 1109

value: human resected PDAC


title: VDJ-Tcell of Pool2 GEM5

description:
Library name: Po2C5_TCR
patient sample
10X Genomics


title: Sample8


title: PBS (time1)

description: BD Rhapsody


title: DLBCL relapse-4

city: CHANDIGARH

first: ashim

last: das

state: pgimer post office

address: research block A, pgimer, pgimer

country: India

institute: pgimer

data_processing:
Reads less than 17 bp were removed using Fastx
aligned to reference genome hg19 using Bowtie
Differentially expressing micro-RNA in the nonresponder cohort compared to complete response was found by Dseq. Counts of each sample were normalised by analysing dispersion for each micro-RNA separately
Genome_build: hg19
Supplementary_files_format_and_content: excel file of complete mi-RNA counts contain raw reads of each miRNA in each sample
Supplementary_files_format_and_content: excel file of differential counts contain differential reads in relapse and refracory cohort

source_name: LYMPH NODE BIOPSY

extract_protocol:
Total RNA was isolated using Recover all Total Nucleic acid Isolation Kit for FFPE (Cat# AM 1975). Ion Total RNA-Seq Kit v2 was used library preparation and sequencing was performed on Ion Torrent S5.
RNA libraries were prepared for sequencing using standard ION TORRENT protocol

treatment_protocol: samples were divided in responder and non responder cohort based on response to chemotherapy and follow up time

value: formalin fixed paraffin embedded lymph node biopsy

tag: group

value: relapse

tag: disease

value: Diffuse Large B cell Lymphoma


title: VDJ-Tcell of Pool2 GEM4

description:
Library name: Po2C4_TCR
patient sample
10X Genomics


title: DLBCL response-3

value: response


title: VDJ-Tcell of Pool3 GEM3

description:
Library name: Po3C3_TCR
patient sample
10X Genomics


title: VDJ-Tcell of Pool1 GEM3

description:
Library name: Po1C3_TCR
patient sample
10X Genomics


title: Sample6

value: no-gRNA

value: Adult


title: 1094


title: 1008


title: 1102


title: Sample5


title: DLBCL response-2


title: VDJ-Tcell of Pool1 GEM2

description:
Library name: Po1C2_TCR
patient sample
10X Genomics


title: 1093


title: 1085


title: VDJ-Tcell of Pool2 GEM6

description:
Library name: Po2C6_TCR
patient sample
10X Genomics


title: DLBCL relapse-3


title: VDJ-Tcell of Pool1 GEM1

description:
Library name: Po1C1_TCR
patient sample
10X Genomics


title: Sample3


title: Sample4


title: DLBCL refactory-3

value: refactory


title: 1074


title: Sample7


title: 1070


title: Sample1


title: DLBCL refactory-2


title: 1053


title: 1063


title: g-Sox9+Trps1

description: 10x Genomics, Visium Spatial Gene Expression, spaceranger v1.2.2

data_processing:
Data demultiplexing was performed using the Je tool v1.2
Alignment was performed using Space Ranger v1.2.2
Tissue_hires_image.png images of brain sections were acquired on a Carl Zeiss Axio Imager.M2m microscope
In all the samples, only one of the two coronal sections used had sufficient reads (possibly due to a technical artefact during tissue processing or sequencing). The spots corresponding to the tissue with good reads were subsetted and subsequent analysis was performed.
gRNA_injection.tiff  images of brain sections were acquired on a Carl Zeiss Axio Imager.M2m microscope. This was used to define the injection region.
Assembly: mm10
Supplementary files format and content: barcode.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5,: Tab-separated values files and matrix files
Supplementary files format and content: tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg: image files
Library strategy: Spatial transcriptomics

extract_protocol:
Mouse brains were embedded and snap frozen in an isopentane/liquid nitrogen bath.  Two coronal sections (10µm) of the dorsal brain area were collected in each capture area and the tissue was enzymatically permeabelized according to the Visium Spatial Gene Expression from 10x Genomics.
Library was performed according to the manufacter’s instructions (Visium Spatial Gene Expression , 10x Genomics).

treatment_protocol: The animals were injected with the Mok-LV  virus for CRISPR mediated deletion of Sox9, Trps1 (or control)

tag: strain

tag: Sex

value: male

value: 12-16 weeks old

tag: timepoint


title: DLBCL refactory-1


title: 1050


title: DLBCL relapse-2


title: g-Trps1

tag: age


title: DLBCL relapse-1

tag: tissue


title: 1022


title: 1013


title: g-Control

value: female


title: S1097_476-1-1207641920 Tail_experimental

status: Public on Feb 09 2025

type: genomic

city: Baltimore

first: Caitlin

last: Bowen

address: 1800 Orleans

institute: Johns Hopkins

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Genomic DNA extracted from tail was genotyped using GIGA-Muga Array (Illumina)

label: Cy5, Cy3

source_name: Tail

label_protocol: Standard Illumina Protocol

extract_protocol: Extraction of genomic DNA from fresh tissue was performed using phenol-chloroform extraction.

value: Male


title: S1097_471-1-1207641912 Tail_experimental

value: Female


title: S1097_470-1-1207641904 Tail_experimental


title: S1097_9971-1-1207641841 Tail_Control


title: S1097_490-1-1207641872 Tail_experimental


title: S1097_460-1-1207641896 Tail_experimental


title: Brain, HIE+EPO

city: Seongnam-si

first: KyuBum

last: Kwack

address: CHA BioComplex 335, Pangy-ro, Bundang-gu

department: BioMedical Science

institute: CHA University

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label: biotin

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: On day 7 of pregnancy, pups whose sex was randomly selected were initially anesthetized with 3-5% isoflurane and maintained with 1-2% isoflurane for surgery. Briefly, a midline cervical incision was made in the anterior neck. The right common carotid artery was dissected and permanently ligated with a 5-0 blue nylon. The operated pups were exposed to hypoxic conditions in 8% O2 and 92% N2. Following exposure, the pups were returned to the cages with the dams. Sham-operated pups received anesthesia, and the artery was exposed without ligation or hypoxia.

extract_protocol: The cellular RNA from pup brains was extracted with TRIzol (ThermoFisher scientific, USA).

treatment_protocol: At 7 days post-injury, the operated pups were randomly assigned into 5 groups (each group, n=8 to 10). UCB (3 ×10^7 /kg, intraperitoneal injection once at 7d post-injury), EPO (500 IU/kg, intraperitoneal injection for five consecutive days from 7d HIE), UCB+EPO (at the same dose and schedule as the other groups) were intraperitoneally administered, and PBS (five consecutive days from 7 d HIE) was injected as a control (HIE).

value: ICR

tag: developmental stage

value: neonate

value: HIE+EPO

value: brain


title: S1097_9991-1-1207641888 Tail_Control


title: S1097_488-1-1207641864 Tail_experimental


title: S1097_500-1-1207641880 Tail_experimental


title: Brain, HIE+UCB

tag: treatment

value: HIE+UCB


title: Brain, SHAM

value: SHAM


title: S1097_483-1-1207641833 Tail_experimental


title: S1097_455-1-1207390180 Tail_experimental


title: Brain, HIE+EPO+UCB

value: HIE+EPO+UCB


title: S1097_446-1-1207641919 Tail_experimental


title: S1097_445-1-1207641911 Tail_experimental


title: S1097_444-1-1207641903 Tail_experimental


title: g-Sox9


title: S1097_440-1-1207641887 Tail_experimental


title: Brain, HIE

value: HIE


title: S1097_441-1-1207641895 Tail_experimental


title: S1097_432-1-1207641863 Tail_experimental


title: S1097_436-1-1207641871 Tail_experimental


title: S1097_438-1-1207641879 Tail_experimental


title: S1097_431-1-1207641855 Tail_experimental


title: DLBCL response-1

value: formalin fixed paraffin embedded lymph node biopsy

value: response

value: Diffuse Large B cell Lymphoma


title: S1097_B61-1-1207641839 Tail_Control


title: S1097_430-1-1207641847 Tail_experimental


title: S1097_422-1-1207641918 Tail_experimental


title: S1097_SVE1-1-1207641894 Tail_Control


title: S1097_418-1-1207641886 Tail_experimental


title: S1097_412-1-1207641870 Tail_experimental


title: S1097_421-1-1207641910 Tail_experimental


title: S1097_420-1-1207641902 Tail_experimental


title: S1097_413-1-1207641878 Tail_experimental


title: S1097_400-1-1207641846 Tail_experimental


title: S1097_450-1-1207641832 Tail_experimental


title: S1097_401-1-1207641854 Tail_experimental


title: S1097_F11-1-1207641856 Tail_Control


title: S1097_427-1-1207641831 Tail_experimental


title: S1097_452-1-1207641840 Tail_experimental


title: S1097_393-1-1207641917 Tail_experimental


title: S1097_392-1-1207641909 Tail_experimental


title: S1097_399-1-1207641838 Tail_experimental


title: S1097_384-1-1207641901 Tail_experimental


title: S1097_382-1-1207641893 Tail_experimental


title: S1097_F12-1-1207641877 Tail_Control


title: S1097_9961-1-1207641869 Tail_Control


title: S1097_398-1-1207641830 Tail_experimental


title: S1097_377-1-1207641861 Tail_experimental


title: S1097_381-1-1207641885 Tail_experimental


title: 422-1-1207641918 Tail_Control


title: S1097_372-1-1207641845 Tail_experimental


title: S1097_368-1-1207641829 Tail_experimental


title: S1097_410-1-1207641862 Tail_experimental


title: S1097_367-1-1207641916 Tail_experimental


title: S1097_358-1-1207641892 Tail_experimental


title: S1097_353-1-1207641868 Tail_experimental


title: 129S6_SvEv1-1207579631 Tail_Control


title: S1097_365-1-1207641908 Tail_experimental


title: S1097_352-1-1207641852 Tail_experimental


title: S1097_355-1-1207641876 Tail_experimental


title: S1097_357-1-1207641884 Tail_experimental


title: S1097_347-1-1207641836 Tail_experimental

value: Unknown


title: S1097_345-1-1207641828 Tail_experimental


title: 8788_191 Tail_experimental


title: 7172_221 Tail_experimental


title: 7172_222 Tail_experimental


title: 9394_297 Tail_experimental


title: 9394_296 Tail_experimental


title: 7778_232 Tail_experimental


title: 109110_290 Tail_experimental


title: 109_335 Tail_experimental


title: 114_328 Tail_experimental


title: 6970_267 Tail_experimental


title: 109110_288 Tail_experimental


title: 6970_273 Tail_experimental


title: 107108_237 Tail_experimental


title: 8788_196 Tail_experimental


title: 107108_256 Tail_experimental


title: 85_187 Tail_experimental


title: 105_180 Tail_experimental


title: S1097_351-1-1207641844 Tail_experimental


title: S1097_9981-1-1207641837 Tail_Control


title: C57BL_6J-4 Tail_experimental


title: 105_175 Tail_experimental


title: 7576_172 Tail_experimental


title: 7576_168 Tail_experimental


title: 7576_167 Tail_experimental


title: 7576_160 Tail_experimental


title: 113_326 Tail_experimental


title: 9394_242 Tail_experimental


title: 79_152 Tail_experimental


title: 7576_166 Tail_experimental


title: 98_148 Tail_experimental


title: 8788_194 Tail_experimental


title: 79_150 Tail_experimental


title: 105_179 Tail_experimental


title: 7576_159 Tail_experimental


title: 86_133 Tail_experimental


title: 85_185 Tail_experimental


title: 86_139 Tail_experimental


title: 98_146 Tail_experimental


title: 98_147 Tail_experimental


title: 86_136 Tail_experimental


title: C57BL_6J-3 Tail_experimental


title: 98_144 Tail_experimental


title: 8182_131 Tail_experimental


title: 8182_130 Tail_experimental


title: 79_156 Tail_experimental


title: 86_137 Tail_experimental


title: 8182_125 Tail_experimental


title: 79_153 Tail_experimental


title: 8182_132 Tail_experimental


title: 8182_126 Tail_experimental


title: 117118_111 Tail_experimental


title: 8182_120 Tail_experimental


title: 101102_101 Tail_experimental


title: 117118_110 Tail_experimental


title: 8182_121 Tail_experimental


title: 8990_85 Tail_experimental


title: 97_118 Tail_experimental


title: 9192_62 Tail_experimental


title: 8182_123 Tail_experimental


title: 101102_104 Tail_experimental


title: 97_117 Tail_experimental


title: 8182_124 Tail_experimental


title: 8384_94 Tail_experimental


title: 80_68 Tail_experimental


title: 101102_98 Tail_experimental


title: 9192_61 Tail_experimental


title: 9192_63 Tail_experimental


title: 8990_80 Tail_experimental


title: 9192_58 Tail_experimental


title: 9192_59 Tail_experimental


title: 9192_51 Tail_experimental


title: 115116_35 Tail_experimental


title: 115116_32 Tail_experimental


title: 103014_38 Tail_experimental


title: 103014_48 Tail_experimental


title: 8990_79 Tail_experimental


title: 97_115 Tail_experimental


title: 115116_31 Tail_experimental


title: Pan02_Co68

city: Beijing

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

description:
Library name: Sample 1
10x Genomics

data_processing:
Raw sequencing data were aligned to the reference genome using Cell Ranger.
Dimensionality reduction, clustering, and differential gene expression analysis were performed using the Seurat R package
Cell annotation was facilitated by the SingleR R package.
Pseudotime analysis was conducted with the monocle 3 R package
cell-cell communication analysis was performed using the CellChat R package
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

growth_protocol: Grow Pan02 cells in appropriate cell culture medium until they reach near confluency.

extract_protocol:
Single-cell suspensions were prepared from Pan02 tumors, and total RNA was extracted using the 10x Genomics Chromium Single Cell 3' Reagent Kits, following the manufacturer's instructions.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: C57BL/6J wild-type (WT) mice were subcutaneously injected with 1 × 10⁶ Pan02 cells. Once tumors reached a predefined volume of [specify volume] mm³, mice were randomly assigned to treatment groups receiving DMXAA, Co68, or PBS (vehicle control) via the intraperitoneal route at a dose of 10 mg/kg every three days for two weeks. Tumor length and width were measured using calipers every three days; volume was calculated as 0.5 × length × width².  After two weeks, mice were euthanized according to approved IACUC protocols.  Tumors were harvested, and single-cell RNA sequencing (scRNA-seq) libraries were prepared and sequenced.

value: tumor

tag: cell line

value: cancer cell line Pan02

tag: genotype

value: WT


title: 129S6_SvEv1-1 Tail_experimental

value: Male


title: 99100_27 Tail_experimental

value: Female


title: Pan02_DMXAA

description:
Library name: Sample 2
10x Genomics

value: DMXAA


title: 99100_28 Tail_experimental


title: Pan02_Mock

description:
Library name: Sample 3
10x Genomics

value: PBS


title: 115116_30 Tail_experimental


title: DMD sample, 5 years old

city: Seoul

first: Murim

last: Choi

address: 103 Daehakro, Jongrogu

institute: Seoul National University

description: Library name: DMD_2

data_processing:
Generated FASTQ files were mapped to human (GRCh38/hg38 pre-mRNA genome) transcriptome references provided by 10x Genomics using Cell Ranger v6.0.0.
Assembly: GRCh38/hg38
Supplementary files format and content: tsv, mtx

source_name: quad

extract_protocol:
All muscle samples were processed and snRNA-seq data generated by GENINUS (Seoul, Republic of Korea). After the frozen tissue was homogenized and nuclei were counted, the nuclei were isolated using flow cytometry. Single-cell capture, barcoding and library preparation were performed following the 10x Genomics Single cell Chromium 3’ protocols (V3: CG000183).
cDNA library quality was determined using an Agilent Bioanalyzer. Paired-end 200 bp reads were generated on an Illumina NovaSeq6000.

value: quad

tag: cell type

value: muscle

value: no steroid


title: BMD sample, 13 years old

description: Library name: BMD_1


title: 99100_23 Tail_experimental


title: 99100_22 Tail_experimental


title: 99100_19 Tail_experimental


title: 129S6_SvEv1-2 Tail_experimental


title: DMD sample, 17 years old

description: Library name: DMD_1


title: Control sample, 10 years old

description: Library name: Normal_5

source_name: abdomen

value: abdomen


title: Control sample, 5 years old

description: Library name: Normal_4


title: BMD sample, 7 years old

description: Library name: BMD_3


title: 99100_24 Tail_experimental


title: BMD sample, 4 years old

description: Library name: BMD_2


title: Control sample 3 years old

description: Library name: Normal_3


title: Control sample, 16 years old

description: Library name: Normal_1


title: 99100_16 Tail_experimental


title: 4 Tail_Control


title: 111112_7 Tail_experimental


title: 111112_9 Tail_experimental


title: 8788_197 Tail_experimental


title: DMD sample 5 years old

description: Library name: DMD_3


title: Control sample, 3 years old

description: Library name: Normal_2


title: S1 Tail_Control


title: Bone marrow stem cells with 50 uM docosatrienoic acid treatment, replicate 1, RNA-seq

city: Shanghai

first: Haihan

last: Gao

address: Xuhui District

department: Department of Orthopaedic Surgery

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: S50_1

data_processing:
DESeq2 Version 1.24.0
Assembly: GRCm39
Supplementary files format and content: xlsx inculdes FPKM

source_name: Bone marrow stem cells

extract_protocol:
Total RNA was extracted through Trizol reagent.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacture's protocols.

value: Bone marrow stem cells

value: wild-type

value: 50 uM docosatrienoic acid


title: 7172_12 Tail_experimental


title: Bone marrow stem cells without docosatrienoic acid treatment, replicate 2, RNA-seq

description: Library name: CT_2


title: Bone marrow stem cells without docosatrienoic acid treatment, replicate 3, RNA-seq

description: Library name: CT_3


title: 99100_15 Tail_experimental


title: Bone marrow stem cells without docosatrienoic acid treatment, replicate 1, RNA-seq

description: Library name: CT_1


title: 99100_14 Tail_experimental


title: 3 Tail_Control


title: B1 Tail_Control


title: Bone marrow stem cells with 50 uM docosatrienoic acid treatment, replicate 2, RNA-seq

description: Library name: S50_2


title: Bone marrow stem cells with 50 uM docosatrienoic acid treatment, replicate 3, RNA-seq

description: Library name: S50_3


title: 2RTB0269, Resister, MtbNEG, 22h, BAL, scRNA-seq

city: Montréal

first: Monica

last: Dallmann-Sauer

state: Quebec

address: 1001 Bd Décarie

institute: McGill

description: scRNA-seq (10X Genomics)

data_processing:
Count function from Cell Ranger software v7.0.1 (10X Genomics, USA) was used for alignment to GRCh38 human genome and generation of feature-barcode matrices per library.
Assembly: GRCh38 human genome
Supplementary files format and content: Tab-separated files with barcode, features and count matrix (CellRanger count output)

source_name: Bronchoalveolar lavage

extract_protocol:
Bronchoalveolar lavage (BAL) were collected and cryopreserved in 10% dimethyl sulfoxide (MilliporeSigma, Massachusetts, USA) and 90% fetal bovine serum (Cytiva, Massachusetts, USA) and, by gradual cooling to − 80 °C in a Nalgene Mr Frosty™ container [Sigma Aldrich (Pty) Ltd, Gauteng, South Africa] with isopropanol for 24 h followed by long term preservation in liquid nitrogen. Cryopreserved BAL samples were set in culture following dropwise thawing protocol. Then, BAL cells were cultured with media (not challenged, MtbNEG) or media + Mtb strain H37Rv at MOI 6.5:1 (challenged, MtbINF) for 6 or 24h at 37°C, 5% CO2, and 95% relative humidity.
Single cell capture and library preparation was performed with Chromium Next GEM Single Cell 3ʹ Reagents Kit v3.1 (10X Genomics, USA). Cell suspensions were loaded on a Chromium Next GEM Chip G (10X Genomics, USA) together with gel bead from Chromium Next GEM Single Cell 3ʹ GEM Kit v3.1 and captured on Chromium Controller (10X Genomics, USA) with recovery target of 1×104 cells. One quarter of the total cDNA was used to generate sequencing libraries using Library Construction Kit (10X Genomics, USA) and barcoded using Dual Index plate TT set A (10X Genomics, USA). Obtained libraries were double sided size selected using SPRIselect beads (Beckman Coulter, USA) to enrich for fragments 300-800 base pairs long, centered at 450bp. Libraries were checked for quality with Bioanalyzer High Sensitivity DNA Kit (Agilent, USA).

value: Bronchoalveolar lavage

tag: subject

value: Resister

tag: years art

tag: art

tag: alcohol

value: No

tag: smoker

tag: rec drugs

tag: bal date

tag: culture date

tag: mtb challenged

tag: hours incubation

tag: condition

tag: seq batch

tag: percent bal_lymphocytes


title: 2RTB0269, Resister, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: tissue

tag: group

tag: Sex

tag: age


title: 2RTB0269, Resister, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: subject

value: Yes


title: 2RTB0269, Resister, MtbINF, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: years art


title: 336 Tail_experimental


title: 2RTB0253, Resister, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: art


title: 341 Tail_experimental


title: 338 Tail_experimental


title: 333 Tail_experimental


title: 2RTB0253, Resister, MtbNEG, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: alcohol


title: 330 Tail_experimental


title: 331 Tail_experimental


title: 325 Tail_experimental


title: 2RTB0215, LTBI, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

value: LTBI

value: Occasionally

tag: smoker


title: 2RTB0215, LTBI, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: rec drugs


title: 44194 Tail_experimental


title: 2RTB0215, LTBI, MtbNEG, 24h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: bal date


title: 2RTB0253, Resister, MtbINF, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: culture date


title: 2RTB0209, Resister, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: mtb challenged


title: 322 Tail_experimental

value: Male


title: 2RTB0209, Resister, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

value: Female

tag: hours incubation


title: C57BL_6J-2 Tail_Control


title: 319 Tail_experimental


title: 320 Tail_experimental


title: 2RTB0253, Resister, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: condition


title: 316 Tail_experimental


title: 334 Tail_experimental


title: 318 Tail_experimental


title: 2RTB0205, LTBI, MtbNEG, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: seq batch


title: 2RTB0209, Resister, MtbNEG, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: percent bal_lymphocytes


title: 315 Tail_experimental


title: 314 Tail_experimental


title: 2RTB0205, LTBI, MtbINF, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: tissue


title: 44193 Tail_experimental

tag: group


title: 2RTB0205, LTBI, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: Sex


title: 2RTB0196, LTBI, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: age


title: 312 Tail_experimental


title: 2RTB0196, LTBI, MtbNEG, 25h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: subject


title: 309 Tail_experimental


title: 308 Tail_experimental


title: 2RTB0196, LTBI, MtbINF, 25h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: years art


title: 2RTB0215, LTBI, MtbINF, 24h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: art


title: 2RTB0196, LTBI, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: alcohol


title: 2RTB0183, Resister, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: smoker


title: 2RTB0183, Resister, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: rec drugs


title: S2 Tail_Control


title: 300 Tail_experimental


title: 2RTB0209, Resister, MtbINF, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: bal date


title: 2RTB0183, Resister, MtbINF, 24h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: culture date


title: 2RTB0148, LTBI, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: mtb challenged


title: 2RTB0148, LTBI, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: hours incubation


title: 284 Tail_experimental


title: 293 Tail_experimental


title: 2RTB0148, LTBI, MtbNEG, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: condition


title: 283 Tail_experimental


title: 2RTB0113, LTBI, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: seq batch


title: 2RTB0113, LTBI, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: percent bal_lymphocytes


title: 2RTB0183, Resister, MtbNEG, 24h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: tissue


title: 280 Tail_experimental

tag: group


title: 2RTB0113, LTBI, MtbNEG, 24h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: Sex


title: 301 Tail_experimental


title: 2RTB0092, LTBI, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: age


title: 270 Tail_experimental


title: 2RTB0113, LTBI, MtbINF, 24h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: subject


title: 260 Tail_experimental


title: 304 Tail_experimental


title: 2RTB0092, LTBI, MtbINF, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: years art


title: 295 Tail_experimental


title: 271 Tail_experimental


title: 44191 Tail_experimental


title: 276 Tail_experimental


title: 2RTB0092, LTBI, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: art


title: 278 Tail_experimental


title: 259 Tail_experimental


title: 2RTB0058, Resister, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: alcohol


title: 252 Tail_experimental


title: 2RTB0062, Resister, MtbNEG, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: smoker


title: 2RTB0062, Resister, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: rec drugs


title: 2RTB0148, LTBI, MtbINF, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: bal date


title: 2RTB0062, Resister, MtbINF, 16h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: culture date


title: 2RTB0062, Resister, MtbNEG, 16h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: mtb challenged


title: 250 Tail_experimental


title: 257 Tail_experimental


title: 268 Tail_experimental


title: 253 Tail_experimental


title: 2RTB0058, Resister, MtbNEG, 23h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: hours incubation


title: 2RTB0058, Resister, MtbINF, 23h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: condition


title: 251 Tail_experimental


title: 2RTB0014, LTBI, MtbINF, 30h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: seq batch


title: 2RTB0058, Resister, MtbINF, 6h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: percent bal_lymphocytes


title: Omicron-infected HSPC 3, Humaized mouse bone marrow, 12 weeks

first: Dong hoon

last: Chae

address: Gwanak-ro 1

data_processing:
Differentially expressed genes were subjected to gene enrichment analysis with the R package clusterProfiler
GSEA v3.0
Trimmed DEGs were used for pathway analysis using QIAGEN's Ingenuity® Pathway Analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each example

source_name: Humanized mouse bone marrow

growth_protocol: HSPCs were incubated with HSPC culture media consisted of X-VivoTM 10 serum-free hematopoietic cell medium containing hSCF 100 ng/ml, hFLT3-ligand 100 ng/ml, hTPO 100 ng/ml, hIL-3 20 ng/ml, hIL-6 20 ng/ml, and primocin 25 ug/ml

extract_protocol:
Total RNA was extracted and purified from PsV-infected HSPCs studied in vitro using the TRIzol reagent. 1.2ug of total RNA was used to construct sequencing library
Libraries were generated using the Illumina TruSeq strand mRNA sample preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

treatment_protocol:
To evaluate the effect of PsV, 50 ul aliquots of PsV were added to 10^5 HSPCs with 10 ug/ul polybrene. After PsV treatment for 24 hr, media was replaced with fresh HPSC culture media, and cells were incubated for an additional 7 days.
After PsV treatment for 24hr, HSPCs were washed and resuspended in saline (1 × 10^5 cells in 200 µl), and injected intravenously into the mice. At week 12, mouse were sacrificed

tag: tissue

value: Humanized mouse bone marrow

tag: treatment

value: Omciron Psuedovirus


title: 238 Tail_experimental

tag: Sex

tag: group


title: 2RTB0092, LTBI, MtbNEG, 22h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: subject

tag: age


title: 2RTB0014, LTBI, MtbNEG, 7h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: years art

tag: art


title: GFP-infected HSPC 3, Humaized mouse bone marrow, 12 weeks

value: GFP Pseudovirus


title: 249 Tail_experimental


title: 2RTB0014, LTBI, MtbINF, 7h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: alcohol

tag: smoker


title: Input_DNA

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

institute: National Centre for Biological Sciences - TIFR

data_processing:
Adapter was removed and low quality bases were trimmed.
The processed reads were aligned to the 188bp Widom601 nucleosome positioning sequence containing sequence (GGACCCTATCGCGAGCCAGGCCTGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCACATATATACATCCAGGCCTTGTGTCGCGAAATTCATA)
The alignment files are converted to coverage files using bam coverage tool of Deeptools with the 1bp bin size.
Assembly: 188bp Widom601 DNA custom made (GGACCCTATCGCGAGCCAGGCCTGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCACATATATACATCCAGGCCTTGTGTCGCGAAATTCATA)
Supplementary files format and content: bigwig

organism: synthetic construct

source_name: In vitro-made recombinant nucleosomes

growth_protocol: Not applicable

extract_protocol:
Total DNA was extracted after Mnase treatment using Phenol-chloroform extraction method.
The Mnase library was constructed using NEBNext® Ultra? II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions. The adapter sequence used is AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. For paired end reads, the adapters used were AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (mate1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (mate2). The sequencing was done in paired end mode in a Illumina platform.

treatment_protocol: Not applicable

tag: sample type

value: input DNA

tag: nucleosome


title: 2RTB0014, LTBI, MtbNEG, 30h, BAL, scRNA-seq

description: scRNA-seq (10X Genomics)

tag: rec drugs

tag: bal date

tag: culture date

tag: mtb challenged


title: 244 Tail_experimental


title: C57BL_6J-1207579674 Tail_Control


title: Omicron-infected HSPC 4, Humaized mouse bone marrow, 12 weeks


title: HSPC1, omicron PsV, 7 day

source_name: hematopoietic stem and progenitor cells

tag: cell type

value: hematopoietic stem and progenitor cells

value: Omicron Pseudovirus


title: 214 Tail_experimental


title: 299 Tail_experimental


title: Omicron-infected HSPC 2, Humaized mouse bone marrow, 12 weeks

tag: tissue


title: 240 Tail_experimental


title: Omicron-infected HSPC 1, Humaized mouse bone marrow, 12 weeks

tag: treatment


title: Variant_NCPs

value: In vitro-made recombinant nucleosomes

value: H4 variant nucleosomes


title: 229 Tail_experimental

tag: Sex


title: 228 Tail_experimental

tag: group


title: B2 Tail_Control


title: GFP-infected HSPC 2, Humaized mouse bone marrow, 12 weeks


title: GFP-infected HSPC 1, Humaized mouse bone marrow, 12 weeks


title: 225 Tail_experimental


title: 226 Tail_experimental


title: HSPC2, omicron PsV, 7 day


title: T71860, Input

first: Huichuan

last: Yu

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then, sequence quality was verified using fastp.
We used HISAT2 to map reads to the genome of Homo sapiens (Version: V90) with default parameters. Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software.
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit by perl scripts in house. Called peaks were annotated by intersection with gene architecture using ChIPseeker. Then, StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM.
Genome_build: GRCh38 (V90)
Supplementary_files_format_and_content: peak files (xlsx)

source_name: primary tumor tissue from colorectal cancer patients

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
Eluted m6A-containing fragments (IP) and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was ~100±50 bp. we performed the paired-end 2×150bp sequencing on an Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.
MeRIP-seq

tag: individual

tag: disease state

value: colorectal cancer

value: tumor

tag: rip antibody

value: male


title: T72190, Input

tag: age


title: 248 Tail_experimental


title: T61521, Input


title: HSPC2, GFP control, 7 day


title: HSPC1, GFP control, 7 day


title: GFP-infected HSPC 4, Humaized mouse bone marrow, 12 weeks


title: Canonical_NCPs

value: canonical H4 nucleosomes


title: CTB3-cr1 under cold stress for 1d_biological replicate 3

first: Li

last: Jin

address: College of Agronomy and Biotechnology, China Agricultural University, 100193, China

country: Netherlands

institute: China Agricultural University

description:
Library name: KO_1d_3
KO_1d_3_fpkm

data_processing:
The raw reads were first subjected to quality control using fastp (version 0.19.7) to remove low-quality sequences and adapters, resulting in high-quality clean reads. These reads were then aligned to the rice reference genome using HISAT2 and only uniquely mapped reads were retained for further analysis. Gene expression levels were quantified by normalizing the raw read counts to account for sequencing depth differences across samples. Differential expression analysis was performed using DESeq2, where differentially expressed genes (DEGs) were identified based on an absolute log2(fold change) > 1 and an FDR (padj) < 0.01.
Assembly: IRGSP - 1.0
Supplementary files format and content: csv file include raw counts for each Sample
Supplementary files format and content: csv file include FPKM values for each Sample

organism: Oryza sativa

source_name: rice panicle

extract_protocol:
RNA was harvested using RNAiso Plus (Takara, Kyoto, Japan). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Illumina, San Diego, CA, USA) and sequenced on the Illumina NovaSeq 6000 platform by Beijing Novogene Co., Ltd.

value: rice panicle

tag: genotype

value: CTB3 knockdown


title: 210 Tail_experimental


title: 258 Tail_experimental


title: T71040, Input

value: female


title: Nipponbare under cold stress for 1d_biological replicate 3

description:
Library name: Nip_1d_3
Nip_1d_3_fpkm

value: WT


title: 44192 Tail_experimental

value: Male


title: 198 Tail_experimental


title: 206 Tail_experimental


title: 205 Tail_experimental

value: Unknown


title: Nipponbare under cold stress for 1d_biological replicate 2

description:
Library name: Nip_1d_2
Nip_1d_2_fpkm


title: WT_sdlng_salt_Rep2

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic.
The processed reads were aligned to the rice genome (IRGSP1) using HISAT2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Assembly: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Tab delimited text files including FPKM for all the genes in the experimental samples.

source_name: 20d old Seedlings

growth_protocol: For collecting mature leaves, the plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius. For seedlings, seeds were germinated on half-strength Murashige-Skoog medium with 0.3% Phytagel. Germinated seedlings were kept in dark for 5 days and then grown in growth chamber with 16h light and 8h dark day-night cycles for 15 days

extract_protocol:
Total RNA was isolated from tissues mentioned. RNA was extracted using TRIzol reagent following manufaturer’s protocol.
Libraries were prepared for sequencing using standard Illumina protocols. The kit used is NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L) and the adapter sequences are Read 1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and for read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: WT and transgenic lines were handled in the same manner. For salt stress treatment, all conditions were followed exactly as described for seedlings growth except that media contained 120mM of sodium chloride.

tag: subspecies

value: Indica

tag: cultivar

value: Pusa Basmati 1 (PB1)

value: Seedlings

value: 20d old

value: salt


title: 203 Tail_experimental


title: Nipponbare under cold stress for 1d_biological replicate 1

description:
Library name: Nip_1d_1
Nip_1d_1_fpkm


title: T59903, Input


title: N73568, Input

source_name: tumor-adjacent normal tissue from colorectal cancer patients

value: normal


title: U2OS sh-VNGD

city: hefei

first: Ben

state: anhui

address: daoxiangcun

department: Division of Life Sciences and Medicine

institute: University of Science and Technology of China

data_processing:
Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke.
Cleaned reads were mapped to the reference genome of GRCh38.p13 using Bowtie2 (version: 2.2.5).
MACS2 (version: 2.1.2) was used to call peaks (open chromatin regions) and the chromatin accessibility was analyzed by Deeptools.
Genome_build: hg38
Supplementary_files_format_and_content: chromatin accessibility was analyzed by Deeptools.

source_name: U2OS cells

growth_protocol: DMEM medium with 10% FBS, 37℃，5%CO2

extract_protocol:
After harvest and washing with cold PBS, 50,000 cells were gently lysed in 50μl of cold lysis buffer before centrifugation to yield a nuclear pellet
nuclei were treated with the transposition reaction mix at 37°C for 30 min (Nextera Tn5 Transposase) before purification and elution into 10μl elution buffer (Buffer EB 10 mM Tris·Cl, pH 8.0; Qiagen MinElute PCR Purification Kit). Lastly, adapters were added prior to PCR-based library amplification. Library quality control was performed using gel electrophoresis and the libraries pooled at equimolar ratios with barcodes and sequenced on the BGISEQ-500 platform (BGI-Shenzhen, China).

treatment_protocol: sh-ctrl or shVNGD infect

tag: cell line

value: sh-VNGD


title: U2OS sh-ctrl

value: sh-ctrl


title: 102 Tail_experimental

value: Female


title: N71860, Input

value: colorectal cancer

value: male


title: 199 Tail_experimental


title: h4v_sdlng_salt_Rep2


title: CTB3-cr1 under cold stress for 1d_biological replicate 2

description:
Library name: KO_1d_2
KO_1d_2_fpkm

value: rice panicle


title: N71040, Input


title: D2mdx 7 weeks with GSK126 and steroid replicate 2

description: Library name: GPSP2

data_processing:
Generated FASTQ files were mapped to mouse (mm10) transcriptome references provided by 10x Genomics using Cell Ranger v6.0.0.
Assembly: mm10
Supplementary files format and content: tsv, mtx

source_name: hindlimb muscle

value: hindlimb muscle

value: muscle

value: GSK126, deflazacort


title: CTB3-cr1 under cold stress for 1d_biological replicate 1

description:
Library name: KO_1d_1
KO_1d_1_fpkm

value: CTB3 knockdown


title: T73568, Input

value: tumor

value: female


title: D2mdx 7 weeks with GSK126 and steroid replicate 1

description: Library name: GPSP1


title: 173 Tail_experimental

value: Male


title: T71040, IP

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)


title: N72190, Input


title: D2mdx 7 weeks

description: Library name: DMD7

value: no treatment


title: 169 Tail_experimental


title: WT_sdlng_salt_Rep1

value: Indica

value: Pusa Basmati 1 (PB1)

value: Seedlings

value: 20d old

value: salt

value: WT


title: N61521, Input

value: colorectal cancer

value: normal

value: male