title: 10nM siRNA HNRNPH1 knockdown, rep3 (HNRNPH_KD_10000pM_rep3)

description: Library name: HNRNPH_KD_10000pM_rep3

data_processing:
Trimming: all reads trimmed to 100 bp, custom bash script
Quality control: FastQC (v0.11.5)
Mapping: STAR (v2.5.4b) with non-default parameters: --outFilterMismatchNmax 5 --outSJfilterReads Unique --genomeDir STARindex_Gencode_release25_GRCh38.p7 --sjdbGTFfile gencode.v25.annotation.gtf --sjdbOverhang 99 --outSAMunmapped Within --outStd SAM --runThreadN 4 --readFilesCommand zcat
Filter/remove secondary hits: Samtools (v1.5) with parameters: samtools view -F 256
Counts per gene: Subread (v1.5.1) with non-default parameters: featureCounts --donotsort -s 2 -a gencode.v25.annotation.gtf -T 4 (defaults used for -t exon -g gene_id)
Assembly: GRCh38.p7
Supplementary files format and content: tab-delimited text file of read counts per gene per sample

growth_protocol: MCF7 cells were maintained in RPMI medium (Life technologies) supplemented with 10% fetal bovine serum (FBS, Life technologies), 1% glutamine (Life technologies), 1% penicilline-streptomycine (Life technologies)  and 10 µg/mL insuline (sigma) in humidified atmosphere with 5% CO2 and 37°C

extract_protocol:
For RNA extraction, cells were washed twice with ice cold 1x PBS and collected on ice. For total RNA isolation the RNeasy Plus Mini Kit (Qiagen) was used following the manufacturer’s instructions.
NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol (Part # 15031047 Rev. E). Libraries were prepared with a starting amount of 1000ng (samples 1-12) or 363ng (samples 13-36) and amplified in 10 PCR cycles (samples -12) or 11 PCR cycles (samples 13-36). Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). The samples 1-12 were pooled in equimolar ratio and sequenced on 2 NextSeq 500 Highoutput Flowcells, SR for 1x 159 cycles plus 1x 7 cycles for the index read. The samples 13-36 were pooled in equimolar ratio and sequenced on 3 NextSeq 500 Highoutput FC, for 1x 159 cycles plus 7 cycles for the index read.

treatment_protocol: For transfection, the MCF7 cells were plated in 6-well cell culture plates. For the HNRNPH overexpression (OE) samples, increasing amounts of the HNRNPH1 overexpression plasmid (PMID: 30120239) were transfected using 5 µL Lipofectamine 2000 (Invitrogen). Empty vector served as control. For the HNRNPH knockdown (KD) samples, the HNRNPH1 knockdown was performed using increasing concentrations of an siRNA targeting HNRNPH1 (5′-GGAGCUGGCUUUGAGAGGA[dT][dT]-3′, Sigma-Aldrich; PMID: 21512137). The siRNA was transfected with 5 µL Lipofectamine RNAiMAX (Invitrogen). A non-targeting control siRNA (5′-UGGUUUACAUGUCGACUAA[dT][dT]-3′, Sigma-Aldrich) served as control. All samples were harvested 48 h after transfection to isolate RNA.

value: epithelial cell

value: HNRNPH1 knockdown


title: DOGMA-plex GEX library 6

status: Public on Apr 14 2026

type: SRA

city: San Francisco

first: Romain

last: Lopez

state: California

address: 1396 Sanchez St

country: USA

institute: New York University

description:
Library name: DOGMA-plex GEX library 6
RNA

library_source: transcriptomic single cell

data_processing:
Fastqs were generated using CellRanger-arc mkfastq v1.2.0
Sequencing reads were aligned using CellRanger-arc or cellranger count for the hg38 reference genome
For ADT, HTO and CT count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Assembly: hg38
Supplementary files format and content: Per-barcode count abundance for the protein and viral barcode count data including the scRNA and scMultiome singlecell QC metrics; barcoded accessible chromatin fragments and transcripts per library

molecule: total RNA

organism: Homo sapiens

source_name: primary T cells

extract_protocol:
Digitonin lysis for DOGMA-seq and standard 10x Genomics protocol for scRNA-seq
DOGMA-seq libraries were constructed according to previously described protocols (Mimitou et al, 2021). icCITE-seq libraries were constructed as described previously (Chen et al., 2025) and CITE tags were prepared as described in CITE-seq protocols (Stoeckius et al, 2017). Viral barcodes were amplified by two rounds of DialOut PCR adapted from Perturb-CITE-seq (Frangieh et al., 2021).

tag: cell type

value: primary T cells


title: 5nM siRNA HNRNPH1 knockdown, rep3 (HNRNPH_KD_5000pM_rep3)

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

country: Germany

institute: Würzburg University

description: Library name: HNRNPH_KD_5000pM_rep3

library_source: transcriptomic

molecule: polyA RNA

tag: cell line

tag: genotype


title: 1nM siRNA HNRNPH1 knockdown, rep3 (HNRNPH_KD_1000pM_rep3)

description: Library name: HNRNPH_KD_1000pM_rep3


title: 1-month, substantia nigra, wild-type replicate 4

city: Cambridge

first: Sameer

last: Aryal

state: Massachusetts

address: 75 Ames St

institute: Broad Institute of MIT and Harvard

description:
Library name: P28-SN-WT4
1-mo_SN_WT_4

data_processing:
Reads were aligned to Gencode M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: Gencode M25 / GRCm38.p6
Supplementary files format and content: Comma-separated text files that includes raw counts (estimated by RSEM) for each sample.

organism: Mus musculus

source_name: Brain

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Srrm2 +/- mutant mice and wild-type littermates. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
Libraries were prepared using Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.

tag: tissue

value: Brain

value: Wild-type


title: 1-month, substantia nigra, wild-type replicate 5

description:
Library name: P28-SN-WT5
1-mo_SN_WT_5


title: Gout7

city: Guangzhou

first: Huan

last: Dong

state: Guangdong

address: No. 58, Zhongshan Road, Yuexiu District, Guangzhou

country: China

institute: Sun Yat-sen University First Affiliated Hospital

description:
Library name: Sample7
T7

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequencing quality are examined by FastQC (pass Illumina quality filter),  and reads were trimmed 5 ,3-adaptor bases by cutadapt.
The expression profiling of tRF & tiRNA  were calculated based on counts of reads mapped.
Reads were aligned allowing for 1 mismatch only to the mature tRNA sequences,  then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
Differential expression analysis of tRF&tiRNAs between groups was performed using edgeR. For differentially expressed tRF&tiRNAs were screened with the significant threshold to 1.5-fold difference, p-value ≤ 0.05 and the mean CPM within the group ≥ 1
Assembly: GRCh38
Supplementary files format and content: the CPM value of detected tRF&tiRNA for each sample

source_name: Serum

growth_protocol: Venous blood samples obtained after overnight fasting were aseptically processed(centrifugation at 1000 × g for 10 min at 4 °C) to obtain serum, which was then stored at −80 °C. Serum samples were collected from 10 gout patients and 10 HCs.

extract_protocol:
Serum RNA was extracted using TRIzol LS reagent (Cat#10296028, Invitrogen, USA) according to the manufacturer’s protocol. Briefly, 0.25 ml serum was added to a 1.5 ml tube mixed with 0.75 ml TRIzol LS reagent and swirled. The mixtures were incubated on ice for 2 h with occasional vortexing to ensure the serum was completely cracked. Then, 0.2 ml chloroform was added to the mixtures, vortexed, and incubated at room temperature for 10 min. The samples were centrifuged at 12,000×g for 15 min at 4 °C. Next, the aqueous phase was collected into a tube filled with an equal volume of isopropanol. Then, the mixtures were gently mixed with 1.5 μl glycogen (Cat#10901393001, Roche, Switzerland) and refrigerated at −80 °C for at least 30 min to precipitate RNA. The mixture was centrifuged at 12,000×g for 30 min at 4 °C, and the pellet was washed with 75% cold ethanol twice. Finally, the RNA pellet was dissolved in 10 μl of RNase-free water after being dried and stored at −80 °C.
Total RNA samples were first pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3-aminoacyl (charged) deacylation to 3-OH for 3-adaptor ligation, 3-cP(2,3-cyclic phosphate) removal to 3-OH for 3-adaptor ligation, 5-OH(hydroxyl group) phosphorylation to 5-P for 5-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Then pretreated total RNA was used to prepare the sequencing library in the following steps: 1) 3-adapter ligation; 2) 5-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of 134∼160bp PCR amplified fragments (corresponding to 14∼40nt small RNA size range). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as sequencing clusters and sequenced for 50 cycles on Illumina NextSeq 500 system per the manufacturer sinstructions.

value: Serum

tag: gender

value: male

tag: age

tag: sua(μmol/l)

tag: ast(u/l)

tag: alt(u/l)

tag: crea(μmol/l)

tag: crp(mg/l)


title: 0.5nM siRNA HNRNPH1 knockdown, rep3 (HNRNPH_KD_500pM_rep3)

description: Library name: HNRNPH_KD_500pM_rep3


title: DOGMA-plex GEX library 4

description:
Library name: DOGMA-plex GEX library 4
RNA


title: DOGMA-plex GEX library 5

description:
Library name: DOGMA-plex GEX library 5
RNA


title: 0.25nM siRNA HNRNPH1 knockdown, rep3 (HNRNPH_KD_250pM_rep3)

description: Library name: HNRNPH_KD_250pM_rep3


title: 0.05nM siRNA HNRNPH1 knockdown, rep3 (HNRNPH_KD_50pM_rep3)

description: Library name: HNRNPH_KD_50pM_rep3


title: 1-month, substantia nigra, wild-type replicate 3

description:
Library name: P28-SN-WT3
1-mo_SN_WT_3


title: 0.1nM siRNA HNRNPH1 knockdown, rep3 (HNRNPH_KD_100pM_rep3)

description: Library name: HNRNPH_KD_100pM_rep3


title: DOGMA-plex GEX library 3

description:
Library name: DOGMA-plex GEX library 3
RNA


title: 1-month, substantia nigra, heterozygous replicate 5

description:
Library name: P28-SN-HT5
1-mo_SN_HET_5

value: Srrm2 +/-


title: 0.25nM siRNA HNRNPH1 knockdown, rep2 (HNRNPH_KD_250pM_rep2)

description: Library name: HNRNPH_KD_250pM_rep2


title: 0.5nM siRNA HNRNPH1 knockdown, rep2 (HNRNPH_KD_500pM_rep2)

description: Library name: HNRNPH_KD_500pM_rep2


title: DOGMA-plex ATAC library 28

description:
Library name: DOGMA-plex ATAC library 28
ATAC

library_source: genomic

molecule: genomic DNA


title: DOGMA-plex ATAC library 27

description:
Library name: DOGMA-plex ATAC library 27
ATAC


title: 10nM siRNA HNRNPH1 knockdown, rep1 (HNRNPH_KD_10000pM_rep1)

description: Library name: HNRNPH_KD_10000pM_rep1


title: 1-month, substantia nigra, wild-type replicate 2

description:
Library name: P28-SN-WT2
1-mo_SN_WT_2


title: siRNA knockdown Ctrl, rep3 (HNRNPH_KD_Ctrl_rep3)

description: Library name: HNRNPH_KD_Ctrl_rep3

value: WT


title: 1-month, substantia nigra, heterozygous replicate 1

description:
Library name: P28-SN-HT1
1-mo_SN_HET_1


title: 1-month, substantia nigra, wild-type replicate 1

description:
Library name: P28-SN-WT1
1-mo_SN_WT_1


title: 5nM siRNA HNRNPH1 knockdown, rep1 (HNRNPH_KD_5000pM_rep1)

description: Library name: HNRNPH_KD_5000pM_rep1


title: 0.5nM siRNA HNRNPH1 knockdown, rep1 (HNRNPH_KD_500pM_rep1)

description: Library name: HNRNPH_KD_500pM_rep1


title: 1nM siRNA HNRNPH1 knockdown, rep1 (HNRNPH_KD_1000pM_rep1)

description: Library name: HNRNPH_KD_1000pM_rep1


title: 5nM siRNA HNRNPH1 knockdown, rep2 (HNRNPH_KD_5000pM_rep2)

description: Library name: HNRNPH_KD_5000pM_rep2


title: 0.25nM siRNA HNRNPH1 knockdown, rep1 (HNRNPH_KD_250pM_rep1)

description: Library name: HNRNPH_KD_250pM_rep1


title: 1-month, prefrontal cortex, wild-type replicate 5

description:
Library name: P28-PFC-WT5
1-mo_PFC_WT_5


title: 10nM siRNA HNRNPH1 knockdown, rep2 (HNRNPH_KD_10000pM_rep2)

description: Library name: HNRNPH_KD_10000pM_rep2


title: Gout1

description:
Library name: Sample1
T1


title: DOGMA-plex GEX library 1

description:
Library name: DOGMA-plex GEX library 1
RNA


title: 0.05nM siRNA HNRNPH1 knockdown, rep2 (HNRNPH_KD_50pM_rep2)

description: Library name: HNRNPH_KD_50pM_rep2


title: 1-month, substantia nigra, heterozygous replicate 4

description:
Library name: P28-SN-HT4
1-mo_SN_HET_4


title: 1-month, prefrontal cortex, wild-type replicate 4

description:
Library name: P28-PFC-WT4
1-mo_PFC_WT_4


title: DOGMA-plex ATAC library 24

description:
Library name: DOGMA-plex ATAC library 24
ATAC


title: 0.1nM siRNA HNRNPH1 knockdown, rep1 (HNRNPH_KD_100pM_rep1)

description: Library name: HNRNPH_KD_100pM_rep1


title: 1-month, substantia nigra, heterozygous replicate 2

description:
Library name: P28-SN-HT2
1-mo_SN_HET_2


title: 0.05nM siRNA HNRNPH1 knockdown, rep1 (HNRNPH_KD_50pM_rep1)

description: Library name: HNRNPH_KD_50pM_rep1


title: siRNA knockdown Ctrl, rep1 (HNRNPH_KD_Ctrl_rep1)

description: Library name: HNRNPH_KD_Ctrl_rep1


title: 1-month, prefrontal cortex, wild-type replicate 3

description:
Library name: P28-PFC-WT3
1-mo_PFC_WT_3


title: 2500ng HNRNPH1 overexpression vector, rep3 (HNRNPH_OE_2500ng_rep3)

description: Library name: HNRNPH_OE_2500ng_rep3

value: HNRNPH1 overexpression


title: DOGMA-plex GEX library 2

description:
Library name: DOGMA-plex GEX library 2
RNA


title: 1-month, prefrontal cortex, wild-type replicate 2

description:
Library name: P28-PFC-WT2
1-mo_PFC_WT_2


title: DOGMA-plex ATAC library 23

description:
Library name: DOGMA-plex ATAC library 23
ATAC


title: 1000ng HNRNPH1 overexpression vector, rep3 (HNRNPH_OE_1000ng_rep3)

description: Library name: HNRNPH_OE_1000ng_rep3


title: overexpression Ctrl, empty vector, rep3 (HNRNPH_OE_Ctrl_rep3)

description: Library name: HNRNPH_OE_Ctrl_rep3


title: 2500ng HNRNPH1 overexpression vector, rep2 (HNRNPH_OE_2500ng_rep2)

description: Library name: HNRNPH_OE_2500ng_rep2


title: 600ng HNRNPH1 overexpression vector, rep3 (HNRNPH_OE_600ng_rep3)

description: Library name: HNRNPH_OE_600ng_rep3


title: DOGMA-plex ATAC library 21

description:
Library name: DOGMA-plex ATAC library 21
ATAC


title: DOGMA-plex ATAC library 22

description:
Library name: DOGMA-plex ATAC library 22
ATAC


title: 1-month, prefrontal cortex, wild-type replicate 1

description:
Library name: P28-PFC-WT1
1-mo_PFC_WT_1


title: 1000ng HNRNPH1 overexpression vector, rep2 (HNRNPH_OE_1000ng_rep2)

description: Library name: HNRNPH_OE_1000ng_rep2


title: 1-month, prefrontal cortex, heterozygous replicate 5

description:
Library name: P28-PFC-HT5
1-mo_PFC_HET_5


title: DOGMA-plex ATAC library 20

description:
Library name: DOGMA-plex ATAC library 20
ATAC


title: DOGMA-plex ATAC library 19

description:
Library name: DOGMA-plex ATAC library 19
ATAC


title: 1-month, substantia nigra, heterozygous replicate 3

description:
Library name: P28-SN-HT3
1-mo_SN_HET_3


title: DOGMA-plex ATAC library 25

description:
Library name: DOGMA-plex ATAC library 25
ATAC


title: 1-month, prefrontal cortex, heterozygous replicate 4

description:
Library name: P28-PFC-HT4
1-mo_PFC_HET_4


title: overexpression Ctrl, empty vector, rep2 (HNRNPH_OE_Ctrl_rep2)

description: Library name: HNRNPH_OE_Ctrl_rep2


title: 2500ng HNRNPH1 overexpression vector, rep1 (HNRNPH_OE_2500ng_rep1)

description: Library name: HNRNPH_OE_2500ng_rep1


title: DOGMA-plex ATAC library 18

description:
Library name: DOGMA-plex ATAC library 18
ATAC


title: siRNA knockdown Ctrl, rep2 (HNRNPH_KD_Ctrl_rep2)

description: Library name: HNRNPH_KD_Ctrl_rep2


title: 1000ng HNRNPH1 overexpression vector, rep1 (HNRNPH_OE_1000ng_rep1)

description: Library name: HNRNPH_OE_1000ng_rep1


title: 1-month, prefrontal cortex, heterozygous replicate 3

description:
Library name: P28-PFC-HT3
1-mo_PFC_HET_3


title: 600ng HNRNPH1 overexpression vector, rep1 (HNRNPH_OE_600ng_rep1)

description: Library name: HNRNPH_OE_600ng_rep1


title: 600ng HNRNPH1 overexpression vector, rep2 (HNRNPH_OE_600ng_rep2)

description: Library name: HNRNPH_OE_600ng_rep2


title: overexpression Ctrl, empty vector, rep1 (HNRNPH_OE_Ctrl_rep1)

description: Library name: HNRNPH_OE_Ctrl_rep1


title: iCLIP, MCF7, HNRNPH immunoprecipitation, rep7

description: Library name: hnRNPH_sample7_H_4

data_processing:
Quality control: FastQC (v0.11.5)
Adapter trimming (min. read length of 30 bp includes 15 bp barcode and UMI regions plus 15 bp sequence insert): Flexbar (v3.0.0) with non-default parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 30 --length-dist
Barcode trimming (first 15 bp of read and quality string + their attachment to read name + removal of empty space characters and "/" in the read names): custom bash script
Mapping: STAR (v2.5.4b) with non-default parameters: --genomeDir STARindex_Gencode_release25_GRCh38.p7 --sjdbGTFfile gencode.v25.chr_patch_hapl_scaff.annotation.gtf --sjdbOverhang 76 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 4000000000
Mark duplicates: bamUtil (v1.0.13): bam dedup
Duplicate removal: custom Perl script to remove reads mapped to the same position and having the same UMIs as another read
BAM to BED shifting one base upstream to strand-wise bedgraph: bedtools (v2.25.0): bamToBed -i SAMPLE.duprm.bam | awk '{if ($6=="-") printf "%s\t%s\t%s\t-1\n",$1,$3,$3+1; else printf "%s\t%s\t%s\t1\n",$1,$2-1,$2;}' | sort -k1,1 -k2,2n | uniq -c | awk '{printf "%s\t%s\t%s\t%s\n",$2,$3,$4,$1*$5;}' > SAMPLE.duprm.bedgraph; custom Perl script to remove shifted counts beyond chromosome ends; cat SAMPLE.duprm.bedgraph | awk -v bgplus="SAMPLE.duprm.plus.bedgraph" -v bgminus="SAMPLE.duprm.minus.bedgraph" '{if ($4>0) print $0 > bgplus; else print $0 > bgminus;}'
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v365)
Crosslink events (bigWig) from the 7 iCLIP replicates were summed per genomic position separately for plus and minus strands
Peak calling: PureCLIP (v1.3.1) on merged BAM files (merge of replicates 1-3 and 4-7)
Binding site identification: Merged crosslink events were used together with significant crosslink positions reported by PureCLIP to define 5 nt wide HNRNPH binding sites. Significant crosslink positions with a distance of ≤ 3 nt were combined into regions, and regions shorter than 2 nt were removed. Next, a two-strep procedure was applied. First, the position with the highest number of crosslink events was determined for each region, extended by 2 nt up- and downstream and stored as 5 nt binding site. Second, the 5 nt of the binding sites along with the 4 nt up- and downstream were excised from the regions, creating up to two new regions. These  steps were iteratively repeated until no regions were left. In a final cleanup step, binding sites whose center was not a significant crosslink position or the position with the highest number of crosslink events were removed, as well as binding sites with less than 3 positions with crosslink events.
Assembly: GRCh38.p7
Supplementary files format and content: HNRNPH_iCLIP_crosslink_events_merged_plus.bw, HNRNPH_iCLIP_crosslink_events_merged_minus.bw: HNRNPH crosslink events  (merge of all replicates), separately for each strand
Supplementary files format and content: HNRNPH_binding_sites.bed: all identified HNRNPH binding sites (5 nt width)
Library strategy: iCLIP

extract_protocol:
The RNA was extracted from the cells using immunoprecipitation of HNRNPH. MCF7 cells were UV-crosslinked at 254 nm with 150 mJ/cm2 and lysed. After RNA digestion using RNase I, the protein-RNA complexes were immunoprecipitated using Protein G Dynabeads with 5 µg HNRNPH antibody (Abcam #10374) per replicate.
For iCLIP2, the protocol from a previous publication was used (PMID: 31610236). Briefly, after protein-RNA complex extraction using the HNRNPH antibody, the RNA was 3' end dephosphorylated and subsequently ligated with a pre-adenylated L3-App linker. Then, the 5’ end was radioactively labelled and the protein-RNA complexes were separated using an SDS-PAGE. After transfer to a nitrocellulose membrane and exposure to a Fuji film, the protein-RNA complexes were isolated. RNA was eluted using proteinase K treatment, phenol-chloroform extraction and ethanol precipitation. Using an RT primer against the L3-App linker, the RNA was reversely transcribed to cDNA. After MyONE Silane bead clean up to purify the cDNA, the 5’ linker was ligated to the cDNA. The cDNA was pre-amplified using a 6-cycle PCR and size-selected with ProNex beads. For the final library preparation, the samples were PCR-amplified using 10 cycles, which was followed by a second size selection using ProNex beads. The samples were quality checked and profiled on a High Sensitivity D1000 ScreenTape using TapeStation 2200 (Agilent). After quantification with the Qubit dsDNA HS Assay Kit (Life technologies) the samples were pooled in an equimolar ratio, Sequencing was performed on a NextSeq 500 High Output Flowcell.

tag: antibody

value: HNRNPH (abcam #10374)


title: 1-month, prefrontal cortex, heterozygous replicate 1

description:
Library name: P28-PFC-HT1
1-mo_PFC_HET_1


title: DOGMA-plex ATAC library 17

description:
Library name: DOGMA-plex ATAC library 17
ATAC


title: DOGMA-plex ATAC library 14

description:
Library name: DOGMA-plex ATAC library 14
ATAC


title: iCLIP, MCF7, HNRNPH immunoprecipitation, rep5

description: Library name: hnRNPH_sample5_H_2


title: DOGMA-plex ATAC library 15

description:
Library name: DOGMA-plex ATAC library 15
ATAC


title: iCLIP, MCF7, HNRNPH immunoprecipitation, rep3

description: Library name: hnRNPH_sample3_KT_3


title: DOGMA-plex ATAC library 16

description:
Library name: DOGMA-plex ATAC library 16
ATAC


title: iCLIP, MCF7, HNRNPH immunoprecipitation, rep6

description: Library name: hnRNPH_sample6_H_3


title: iCLIP, MCF7, HNRNPH immunoprecipitation, rep4

description: Library name: hnRNPH_sample4_H_1


title: 1-month, hippocampus, wild-type replicate 5

description:
Library name: P28-HP-WT5
1-mo_HP_WT_5


title: HOS cells, CIN85 knockdown replicate 3

city: Brno

first: Lucia

last: Knopfova

address: Kamenice 5

department: Department of Experimental Biology

country: Czech Republic

institute: Faculty of Science, Masaryk University

description:
Library name: siCIN85_3
siCIN85_3

data_processing:
Quality check of raw paired-end fastq reads was carried out by FastQC.
The Illumina adapters clipping and quality trimming of raw fastq reads were performed using cutadapt v4.3 with settings --quality-base=33 -q 0,20 -m 35 -M 250. Trimmed RNA-Seq reads were mapped to the reference genome using STAR v2.7.3a as a splice-aware short read aligner and default parameters except for --outFilterMismatchNoverLmax 0.1 and --twopassMode Basic.
Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, mapped regions, read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using several tools – namely, RSeQC v4.0.0, Picard toolkit v2.25.6, and Qualimap v.2.2.2. All statistics were processed by MultiQC v1.10.1.
Mapped read counts were obtain using featureCounts from the Subread package v2.0.
Assembly: Homo sapiens genome (GRCh38) with Ensembl annotation (release 95)
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: HOS

extract_protocol:
Total RNA was isolated using GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich).
Library preparation was performed withLexogen QuantSeq 3’ FWD Library Preparation Kit with UMI Second strand module according to the manufacturers reccommendations.

value: HOS

value: osteosarcoma cell line

value: CIN85 knockdown


title: 1-month, hippocampus, wild-type replicate 3

description:
Library name: P28-HP-WT3
1-mo_HP_WT_3


title: DOGMA-plex ATAC library 13

description:
Library name: DOGMA-plex ATAC library 13
ATAC


title: DOGMA-plex ATAC library 12

description:
Library name: DOGMA-plex ATAC library 12
ATAC


title: iCLIP, MCF7, HNRNPH immunoprecipitation, rep1

description: Library name: hnRNPH_sample1_HH_2


title: iCLIP, MCF7, HNRNPH immunoprecipitation, rep2

description: Library name: hnRNPH_sample2_KT_2


title: 1-month, prefrontal cortex, heterozygous replicate 2

description:
Library name: P28-PFC-HT2
1-mo_PFC_HET_2


title: HOS cells, CIN85 knockdown replicate 2

description:
Library name: siCIN85_2
siCIN85_2


title: 1-month, hippocampus, wild-type replicate 4

description:
Library name: P28-HP-WT4
1-mo_HP_WT_4


title: HOS cells, non-targeting siRNA control replicate 3

description:
Library name: siNeg_3
siNeg_3

value: non-targeting siRNA control


title: HOS cells, non-targeting siRNA control replicate 2

description:
Library name: siNeg_2
siNeg_2


title: 1nM siRNA HNRNPH1 knockdown, rep2 (HNRNPH_KD_1000pM_rep2)

description: Library name: HNRNPH_KD_1000pM_rep2


title: 1-month, hippocampus, wild-type replicate 1

description:
Library name: P28-HP-WT1
1-mo_HP_WT_1


title: HOS cells, CIN85 knockdown replicate 1

description:
Library name: siCIN85_1
siCIN85_1


title: HOS cells, CIN85 overexpression replicate 3

description:
Library name: upCIN85_3
upCIN85_3

value: CIN85 overexpression


title: DOGMA-plex ATAC library 26

description:
Library name: DOGMA-plex ATAC library 26
ATAC


title: DOGMA-plex ATAC library 10

description:
Library name: DOGMA-plex ATAC library 10
ATAC


title: 0.1nM siRNA HNRNPH1 knockdown, rep2 (HNRNPH_KD_100pM_rep2)

description: Library name: HNRNPH_KD_100pM_rep2


title: 1-month, hippocampus, wild-type replicate 2

description:
Library name: P28-HP-WT2
1-mo_HP_WT_2


title: HOS cells, non-targeting siRNA control replicate 1

description:
Library name: siNeg_1
siNeg_1


title: HOS cells, CIN85 overexpression replicate 1

description:
Library name: upCIN85_1
upCIN85_1


title: HOS cells, mock-transfected control replicate 3

description:
Library name: Mock_3
Mock_3

value: mock-transfected control


title: 1-month, hippocampus, heterozygous replicate 4

description:
Library name: P28-HP-HT4
1-mo_HP_HET_4


title: HOS cells, mock-transfected control replicate 2

description:
Library name: Mock_2
Mock_2


title: HOS cells, CIN85 overexpression replicate 2

description:
Library name: upCIN85_2
upCIN85_2


title: DOGMA-plex ATAC library 9

description:
Library name: DOGMA-plex ATAC library 9
ATAC


title: DOGMA-plex ATAC library 11

description:
Library name: DOGMA-plex ATAC library 11
ATAC


title: DNase-seq_FB_BRG1_WT_rep2

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

description: Library name: DNase-seq_FB_BRG1_WT_rep2

data_processing:
All bioinformatics analyses were performed using mouse (mm10) and human (hg38) reference genomes annotated by GENCODE (M21 and V30, respectively) (Frankish, et al., 2019).  DNase-seq were processed from raw reads into reads-per-million (RPM)-normalized bigWig tracks following established pipelines (Cao, et al., 2023; Cui, et al., 2023). Briefly, sequencing reads were mapped using Bowtie2 (v2.3.5) (Langmead and Salzberg, 2012), retaining only non-redundant reads with MAPQ ≥ 10 for downstream analyses. Peak calling was performed using the cLoops2 callPeaks module (Cao, et al., 2022) with pooled replicates and assay-specific parameters: DNase-seq (-eps 75,150 -minPts 10,20 -sen). Genome-browser-style visualizations were generated using the cLoops2 plotting module (5), and averaged tracks from biological replicates were produced using the bigwigCompare function from deepTools2 (Ramirez, et al., 2016).
Assembly: mm10
Supplementary files format and content: BigWig files containing signals normalized as reads per million (RPM)

organism:
Homo sapiens
Mus musculus

extract_protocol:
The GATA3-fl/fl-CreERT mice were treated with or without tamoxifen for 3 days. To sort DN3 T cells, single cell suspension was prepared from thymus and CD4/CD8 T cells were labeled with unlabeled anti-CD4 and anti-CD8 antibody. BioMag Goat anti-rat IgG beads from QIAGEN were added and bead-bound CD4/CD8 T cells were removed. The remaining cells were stained with linage markers (anti-CD4, CD8a, TCR gamma/delta, CD19, B220, Gr-1, CD11b, CD11c, Nk1.1 and Ter119) and anti-CD3, CD44, CD25. DN3 T subset were sorted as linage-CD3-CD44-CD25+.     The primary fibroblasts were isolated from mice ear in WT and BRG1-AID mice. In brief, the ear was cut into 1 ~ 3 mm pieces, incubated with 0.25% trypsin–EDTA solution for 30 min at 37 °C, neutralized by culture medium with FBS and then plated on 6 well plate with coverslip on it. Fibroblasts will migrate from tissues during the 3 ~ 5-day culture period. After reaching the appropriate confluence, tissues will be removed and primary fibroblasts will be passaged and maintained in DMEM medium (high glucose) containing 10% fetal bovine serum.  For plasmid transfection in fibroblasts, 20 μg plasmid DNA was used for each 10 cm dish using a combination of two commercial reagents, Lipofectamine LTX (Cat. No. 15338100) and FuGENE HD (Cat. No. E2311) with the ratio of 1:1. The auxin was added 24 h later after transfection and incubated for 8 ~ 10 h. Then, the live fibroblasts were sorted for further experiments.
DNase-seq assays were performed as described previously. Briefly, 10,000 cells from each group were collected by FACS sorting and fixed in 1% formaldehyde for 10min at RT. The fixation was stopped by glycine and washed twice by PBS buffer. DNase I was added to each sample and incubated at 37 °C for 1 min. Reactions were stopped by adding stop buffer (10 mM Tris-HCl, 10 mM NaCl, 0.1% SDS, 10 mM EDTA) containing 1 μl of 20 mg/ml proteinase K. Samples were incubated at 65 °C overnight, and DNAs were purified by using MinElute reaction cleanup kit following the manufacturer’s protocol. DNase-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. For fibroblasts, equal amount of human 293T cells were added as spike in before DNase treatment.

value: Fibroblast

tag: treatment

value: BRG1 AID


title: DOGMA-plex ATAC library 8

description:
Library name: DOGMA-plex ATAC library 8
ATAC

value: primary T cells


title: HOS cells, mock-transfected control replicate 1

description:
Library name: Mock_1
Mock_1


title: 1-month, hippocampus, heterozygous replicate 2

description:
Library name: P28-HP-HT2
1-mo_HP_HET_2

value: Brain


title: DOGMA-plex ATAC library 7

description:
Library name: DOGMA-plex ATAC library 7
ATAC


title: DNase-seq_FB_BRG1_AID_rep1

description: Library name: DNase-seq_FB_BRG1_AID_rep1


title: 1-month, hippocampus, heterozygous replicate 3

description:
Library name: P28-HP-HT3
1-mo_HP_HET_3


title: icCITE-seq CT library H9

description:
Library name: icCITE-seq CT library H9
CT

data_processing:
Sequencing reads were aligned to hg38 reference genome using cellranger (v7.0.0).
Surface protein tag abundances and hashtag antibody barcode abundances were estimated using kallisto (v0.44.0), bustools (v0.39.3) and kite (v0.02) frameworks.
For ADT, HTO and CT count libraries, tag abundances were quantified per barcode using the kallisto/kite framework.
Quality filtering removed cells with <1 UMI in any modality, >8% mitochondrial UMIs, <1.5k RNA UMIs, <10 protein counts, or >100k RNA UMIs.
Assembly: hg38; mm10
Supplementary files format and content: Gene expression counts matrix, surface protein counts, intracellular protein counts, hashtag counts, and CellTag barcode counts per cell.

growth_protocol: CD4+ CD25- CD45RA+ naïve T cells were cultured in ImmunoCult™-XF T Cell Expansion Medium with penicillin/streptomycin and stimulated for 72 hours using plate-bound anti-CD3ε (10 µg/ml) and anti-CD28 (5 µg/ml) with 50 IU/mL IL-2.

extract_protocol:
Cells were processed using Chromium Next GEM Single Cell 3′ Kit v3.1 and 3′ Feature Barcode Kit according to manufacturer's recommendations.
CellTag libraries were enriched by two-step DialOut PCR. TotalSeq-A hashtag and surface antibody libraries were prepared per manufacturer's recommendations. Libraries were sequenced on Illumina NovaSeq6000.

treatment_protocol: Transduced cells were treated with compounds at specified concentrations for 72 hours in culture medium containing 50 IU/mL IL-2 and CD3/CD28 Dynabeads for activation. Cells were fixed and permeabilized using True-Phos Perm Buffer overnight at -20°C, followed by intracellular staining with TotalSeq-B antibodies.


title: 1-month, hippocampus, heterozygous replicate 5

description:
Library name: P28-HP-HT5
1-mo_HP_HET_5


title: 1-month, hippocampus, heterozygous replicate 1

description:
Library name: P28-HP-HT1
1-mo_HP_HET_1


title: DNase-seq_FB_BRG1_WT_rep1

description: Library name: DNase-seq_FB_BRG1_WT_rep1


title: 1-month, cerebellar vermis, wild-type replicate 4

description:
Library name: P28-CV-WT4
1-mo_CV_WT_4

value: Wild-type


title: DNase-seq_FB_BRG1_AID_rep2

description: Library name: DNase-seq_FB_BRG1_AID_rep2


title: DOGMA-plex ATAC library 5

description:
Library name: DOGMA-plex ATAC library 5
ATAC


title: DOGMA-plex ATAC library 4

description:
Library name: DOGMA-plex ATAC library 4
ATAC


title: icCITE-seq CT library F9

description:
Library name: icCITE-seq CT library F9
CT


title: DOGMA-plex ATAC library 3

description:
Library name: DOGMA-plex ATAC library 3
ATAC


title: icCITE-seq CT library G9

description:
Library name: icCITE-seq CT library G9
CT


title: DOGMA-plex ATAC library 6

description:
Library name: DOGMA-plex ATAC library 6
ATAC


title: 1-month, cerebellar vermis, wild-type replicate 5

description:
Library name: P28-CV-WT5
1-mo_CV_WT_5


title: icCITE-seq CT library E9

description:
Library name: icCITE-seq CT library E9
CT


title: 1-month, cerebellar vermis, wild-type replicate 3

description:
Library name: P28-CV-WT3
1-mo_CV_WT_3


title: icCITE-seq TSB library H9

description:
Library name: icCITE-seq TSB library H9
TSB


title: icCITE-seq CT library D9

description:
Library name: icCITE-seq CT library D9
CT


title: DOGMA-plex ATAC library 2

description:
Library name: DOGMA-plex ATAC library 2
ATAC


title: icCITE-seq TSB library G9

description:
Library name: icCITE-seq TSB library G9
TSB


title: 1-month, cerebellar vermis, wild-type replicate 2

description:
Library name: P28-CV-WT2
1-mo_CV_WT_2


title: DOGMA-plex ATAC library 1

description:
Library name: DOGMA-plex ATAC library 1
ATAC


title: icCITE-seq TSB library F9

description:
Library name: icCITE-seq TSB library F9
TSB


title: icCITE-seq TSB library E9

description:
Library name: icCITE-seq TSB library E9
TSB


title: 1-month, cerebellar vermis, wild-type replicate 1

description:
Library name: P28-CV-WT1
1-mo_CV_WT_1


title: 1-month, cerebellar vermis, heterozygous replicate 5

description:
Library name: P28-CV-HT5
1-mo_CV_HET_5


title: icCITE-seq HTO library H9

description:
Library name: icCITE-seq HTO library H9
HTO


title: icCITE-seq HTO library F9

description:
Library name: icCITE-seq HTO library F9
HTO


title: icCITE-seq HTO library G9

description:
Library name: icCITE-seq HTO library G9
HTO


title: 1-month, cerebellar vermis, heterozygous replicate 4

description:
Library name: P28-CV-HT4
1-mo_CV_HET_4


title: 1-month, cerebellar vermis, heterozygous replicate 3

description:
Library name: P28-CV-HT3
1-mo_CV_HET_3


title: icCITE-seq ADT library H9

description:
Library name: icCITE-seq ADT library H9
ADT


title: miRNA_ZY10

city: Hefei City

first: jing

last: wang

address: No. 81 Meishan Road

institute: Anhui Medical University

description: Library name: sample 19

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

source_name: Systemic Sclerosis Case Group, miRNA-Sseq, replicate biosample 4

extract_protocol:
RNA was extracted from blood cell using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: blood


title: miRNA_ZY3

description: Library name: sample 16

source_name: Systemic Sclerosis Case Group, miRNA-Sseq, replicate biosample 1


title: 1-month, cerebellar vermis, heterozygous replicate 2

description:
Library name: P28-CV-HT2
1-mo_CV_HET_2


title: miRNA_ZY8

description: Library name: sample 18

source_name: Systemic Sclerosis Case Group, miRNA-Sseq, replicate biosample 3


title: icCITE-seq HTO library D9

description:
Library name: icCITE-seq HTO library D9
HTO


title: icCITE-seq ADT library G9

description:
Library name: icCITE-seq ADT library G9
ADT


title: icCITE-seq ADT library E9

description:
Library name: icCITE-seq ADT library E9
ADT


title: icCITE-seq HTO library E9

description:
Library name: icCITE-seq HTO library E9
HTO


title: icCITE-seq ADT library F9

description:
Library name: icCITE-seq ADT library F9
ADT


title: icCITE-seq TSB library D9

description:
Library name: icCITE-seq TSB library D9
TSB


title: miRNA_ZY11

description: Library name: sample 20

source_name: Systemic Sclerosis Case Group, miRNA-Sseq, replicate biosample 5


title: miRNA_ZY4

description: Library name: sample 17

source_name: Systemic Sclerosis Case Group, miRNA-Sseq, replicate biosample 2


title: icCITE-seq RNA library G9

description:
Library name: icCITE-seq RNA library G9
RNA


title: 1-month, cerebellar vermis, heterozygous replicate 1

description:
Library name: P28-CV-HT1
1-mo_CV_HET_1


title: miRNA_D20

description: Library name: sample 15

source_name: Healthy Control Group, miRNA-Sseq, replicate biosample 5


title: icCITE-seq RNA library H9

description:
Library name: icCITE-seq RNA library H9
RNA


title: 1-month, cerebellar cortex, wild-type replicate 5

description:
Library name: P28-CC-WT5
1-mo_CC_WT_5


title: icCITE-seq RNA library F9

description:
Library name: icCITE-seq RNA library F9
RNA


title: 1-month, cerebellar cortex, wild-type replicate 4

description:
Library name: P28-CC-WT4
1-mo_CC_WT_4


title: icCITE-seq ADT library D9

description:
Library name: icCITE-seq ADT library D9
ADT


title: miRNA_D18

description: Library name: sample 14

source_name: Healthy Control Group, miRNA-Sseq, replicate biosample 4


title: miRNA_D16

description: Library name: sample 13

source_name: Healthy Control Group, miRNA-Sseq, replicate biosample 3


title: 1-month, cerebellar cortex, wild-type replicate 3

description:
Library name: P28-CC-WT3
1-mo_CC_WT_3


title: icCITE-seq RNA library E9

description:
Library name: icCITE-seq RNA library E9
RNA


title: Small RNA-Seq of Danio rerio: FACS-sorted non-neural crest cells at 28hpf

city: Rosario

first: Tomás

middle: José

last: Steeman

state: Santa Fe

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

description:
Library name: SRALIB06
Sample_A6

data_processing:
GRCz11 (Danio rerio genome assembly, Ensembl release 98)
Reads were aligned to the Danio rerio reference genome (GRCz11, Ensembl release 98) using Bowtie (Langmead et al., 2009)
Mapped reads were assigned to annotated miRNA genes using HTSeq-count (Putri et al., 2022)
Assembly: GRCz11 (Danio rerio genome assembly, Ensembl release 98)
Supplementary files format and content: The processed data files normCountA23.csv and normCountA56.csv are comma-separated tables containing DESeq2-normalized expression values for annotated Danio rerio miRNAs. Rows represent individual miRNAs (e.g., dre-miR-155), and columns represent samples (e.g., Sample_A2, Sample_A3). The values correspond to normalized counts based on DESeq2 size factor normalization. No log transformation or variance-stabilizing transformation was applied. The first column is labeled miRNA and contains gene names based on Ensembl annotation.

organism: Danio rerio

source_name: non-neural crest cells

growth_protocol: Zebrafish (Danio rerio) embryos were obtained from natural matings and maintained at 28.5°C in E3 medium under standard light/dark cycle conditions until the desired developmental stage was reached.

extract_protocol:
Total RNA was extracted using the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. Cells were collected by FACS and immediately lysed in QIAzol for RNA isolation.
Small RNA libraries were prepared using the Illumina TruSeq Small RNA Library Preparation Kit, following the manufacturer’s protocol. Libraries were indexed, pooled, and sequenced on an Illumina NextSeq 500 with single-end 75 bp reads.

value: non-neural crest cells


title: Small RNA-Seq of Danio rerio: FACS-sorted non-neural crest cells at 16 hpf

description:
Library name: SRALIB03
Sample_A3


title: miRNA_D11

description: Library name: sample 11

source_name: Healthy Control Group, miRNA-Sseq, replicate biosample 1


title: icCITE-seq RNA library D9

description:
Library name: icCITE-seq RNA library D9
RNA


title: ZY11

description: Library name: sample 10

source_name: Systemic Sclerosis Case Group, RNA-Sseq, replicate biosample 5


title: ZY10

description: Library name: sample 9

source_name: Systemic Sclerosis Case Group, RNA-Sseq, replicate biosample 4


title: Small RNA-Seq of Danio rerio: FACS-sorted neural crest cells at 28 hpf

description:
Library name: SRALIB05
Sample_A5

source_name: neural crest cells

value: neural crest cells


title: 1-month, cerebellar cortex, wild-type replicate 2

description:
Library name: P28-CC-WT2
1-mo_CC_WT_2


title: 1-month, cerebellar cortex, heterozygous replicate 4

description:
Library name: P28-CC-HT4
1-mo_CC_HET_4

value: Srrm2 +/-


title: Small RNA-Seq of Danio rerio: FACS-sorted neural crest cells at 16 hpf

description:
Library name: SRALIB02
Sample_A2


title: Liver, CDHFD, semaglutide, rep2

city: Toronto

first: Daniel

middle: J.

last: Drucker

address: 25 Orde Street, Rm 5-1034

country: Canada

institute: Mt. Sinai Hospital, Lunenfeld Tanenbaum Research Institute, University of Toronto

description: Library name: CDHFD_SEMA2

data_processing:
Raw reads were processed with Cell Ranger Multi (v9.0.1, 10x Genomics) on 10x Cloud using Next GEM Flex Gene Expression Multiplex chemistry and the mm10 (2020-A) reference transcriptome. Per sample .fastqs were generated with 10x BAM to FASTQ converter.
Filtered feature-barcode matrices were loaded into R (v4.5.0) in RStudio (2025.05.0+496) and analyzed with Seurat (v5.3.0). Cells were filtered using the following criteria: minimum 1,000 and maximum 100,000 UMI counts, 300-8,000 detected features, and <30% mitochondrial reads; genes detected in fewer than 3 cells were excluded.
Assembly: 10X mm10 (2020-A) reference
Supplementary files format and content: CellRanger-filtered feature-barcode matrices in HDF5 format

source_name: Liver

extract_protocol:
Mice were injected intraperitoneally with 5 IU heparin sodium 5 minutes prior to euthanasia. Livers were excised, washed in ice-cold cell-suspension buffer (PBS + 4% FBS), minced into ~1 mm pieces, and subjected to sequential enzymatic digestion at 37°C with dispase (2.4 U/mL; Gibco #17105-041), collagenase type IA (Sigma-Aldrich #C9891), and collagenase type II (Worthington #LS004176), each followed by mechanical dissociation. After each step, suspensions were centrifuged (400g, 5 min, 4°C) and resuspended in the next enzyme solution. Final suspensions were filtered through 40 µm strainers and red blood cells were lysed with 1x RBC Lysis buffer (BioLegend #420302) for 3 min at room temperature. Cell viability and total cell number were assessed prior to fixation and library preparation.
Following liver dissociation, cell viability and total cell number were assessed. For each sample, pooled cell suspensions were combined to obtain approximately 10 million cells. Cells were fixed using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit, 16 rxns (10x Genomics, PN-1000414). Libraries were prepared using the Chromium Fixed RNA Kit, Mouse Transcriptome (10x Genomics, PN-1000496) with the Chromium Next GEM Chip Q Single Cell Kit (16 rxns) according to the manufacturer's instructions.

treatment_protocol: Wild-type C57BL/6J mice were fed either a standard chow diet (STD; 18% kcal from fat, TD.88137, Envigo) or a choline-deficient high-fat diet (CDHFD; 45% kcal from fat, D05010402, Research Diets) to induce hepatic steatosis, inflammation, and fibrosis. Following dietary induction, mice were randomly allocated into groups with comparable body weight to receive daily subcutaneous injections of semaglutide or vehicle (saline). Semaglutide was administered at 10 µg/kg/day during week 1, 20 µg/kg/day during week 2, and 40 µg/kg/day thereafter. On the day of sacrifice, mice received their final semaglutide injection 2 hours prior to tissue collection.

value: Liver

tag: strain

tag: strain number

tag: diet

value: CDFHD

value: WT

value: semaglutide


title: Human chondrocytes P6 Donor 4

city: Philadelphia

first: Ellen

last: Zhang

state: PA

address: 36th Street and Hamilton Walk

department: Orthopaedic Surgery

institute: University of Pennsylvania

description: Library name: D4_P6

data_processing:
Raw sequence reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic (v0.36).
Trimmed reads were aligned to the Homo sapiens GRCh38 reference genome (Ensembl) using STAR aligner (v2.5.2b).
Gene-level read counts were quantified using featureCounts (Subread package v1.5.2).
Differential expression analysis was conducted using the DESeq2 package in R. Differentially expressed genes (DEGs) were identified using a Benjamini-Hochberg adjusted p-value < 0.05 and an absolute log₂ fold-change > 1.0.
Assembly: GRCh38
Supplementary files format and content: CSV file contains TPM values for all genes across all 12 samples. Rows = Ensembl gene IDs (column A: ID) with gene symbols (column N: Gene.name); columns B-M = samples.

source_name: primary human articular chondrocyte

extract_protocol:
RNA was extracted using the Zymo Direct-zol RNA Miniprep kit according to the manufacturer's instructions.
Libraries were prepared via rRNA depletion

tag: donor

value: Donor 4

tag: passage

value: primary human articular chondrocyte


title: 1-month, cerebellar cortex, wild-type replicate 1

description:
Library name: P28-CC-WT1
1-mo_CC_WT_1

source_name: Brain


title: 1-month, cerebellar cortex, heterozygous replicate 5

description:
Library name: P28-CC-HT5
1-mo_CC_HET_5


title: Liver, CDHFD, semaglutide, rep1

description: Library name: CDHFD_SEMA1


title: Liver, CDHFD, rep1

description: Library name: CDHFD


title: Human chondrocytes P0 Donor 4

description: Library name: D4_P0

tag: cell type


title: Human chondrocytes P3 Donor 4

description: Library name: D4_P3


title: 1-month, cerebellar cortex, heterozygous replicate 3

description:
Library name: P28-CC-HT3
1-mo_CC_HET_3

tag: genotype


title: Liver, STD, rep1

description: Library name: STD

tag: tissue

value: STD


title: miRNA_D13

description: Library name: sample 12

source_name: Healthy Control Group, miRNA-Sseq, replicate biosample 2


title: ZY4

description: Library name: sample 7

source_name: Systemic Sclerosis Case Group, RNA-Sseq, replicate biosample 2


title: 1-month, cerebellar cortex, heterozygous replicate 2

description:
Library name: P28-CC-HT2
1-mo_CC_HET_2


title: CD8+ T cells, Control, untreat, rep3

city: Beijing

first: Zhidong

last: Gao

address: No.11 Xizhimen South Street

institute: Peking University People’s Hospital

description: Library name: sg-Int untreat 3

data_processing:
We applied the RNA-Seq immune analysis pipeline (RIMA) to analyze bulk RNA-Seq data. In brief, sequencing reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR v2.6.1d. Salmon v0.13.1 was utilized to map transcripts to genes and generate a gene count matrix.
Differentially expressed genes were identified using DESeq2 v1.34.0, with an adjusted P-value (FDR) threshold of <0.05 for determining significance. The replicates of RNA-Seq from each condition were considered as a covariate in DESeq2.
Assembly: mm10
Supplementary files format and content: txt file includes raw counts for each sample

source_name: CD8+ T cells

growth_protocol: Arid3b-KO or Control OT1 CD8+ T cells were cultured in complete RPMI-1640 medium (containing 10% fetal bovine serum, 1% penicillin/streptomycin, 1% non-essential amino acids, 20 mM HEPES, 1 mM sodium pyruvate, and 0.05 mM 2-mercaptoethanol) supplemented with 20 ng/mL IL-2.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA kit following manufacturer’s instructions.

treatment_protocol: Arid3b-KO or Control OT1 CD8+ T cells were co-cultured with or without CMT93-OVA cells for 4 hours.

value: CD8+ T cells

value: intergenic sequence knockout


title: Human chondrocytes P6 Donor 3

description: Library name: D3_P6

value: Donor 3


title: ZY3

description: Library name: sample 6

source_name: Systemic Sclerosis Case Group, RNA-Sseq, replicate biosample 1


title: CD8+ T cells, Control, untreat, rep2

description: Library name: sg-Int untreat 2


title: 1-month, cerebellar cortex, heterozygous replicate 1

description:
Library name: P28-CC-HT1
1-mo_CC_HET_1


title: D20

description: Library name: sample 5

source_name: Healthy Control Group, RNA-Sseq, replicate biosample 5


title: Human chondrocytes P0 Donor 3

description: Library name: D3_P0


title: CD8+ T cells, Control, untreat, rep1

description: Library name: sg-Int untreat 1


title: ZY8

description: Library name: sample 8

source_name: Systemic Sclerosis Case Group, RNA-Sseq, replicate biosample 3


title: Human chondrocytes P3 Donor 3

description: Library name: D3_P3


title: 3-month, thalamus, wild-type replicate 5

description:
Library name: 12w-TH-WT5
3-mo_TH_WT_5


title: D18

description: Library name: sample 4

source_name: Healthy Control Group, RNA-Sseq, replicate biosample 4


title: CD8+ T cells, Arid3b-KO, untreat, rep3

description: Library name: sg-Arid3b untreat 3

value: Arid3b knockout


title: Human chondrocytes P6 Donor 2

description: Library name: D2_P6

value: Donor 2


title: D16

description: Library name: sample 3

source_name: Healthy Control Group, RNA-Sseq, replicate biosample 3


title: Human chondrocytes P3 Donor 2

description: Library name: D2_P3


title: 3-month, thalamus, wild-type replicate 3

description:
Library name: 12w-TH-WT3
3-mo_TH_WT_3

value: Brain

value: Wild-type


title: D13

description: Library name: sample 2

source_name: Healthy Control Group, RNA-Sseq, replicate biosample 2

value: blood


title: CD8+ T cells, Arid3b-KO, untreat, rep1

description: Library name: sg-Arid3b untreat 1


title: CD8+ T cells, Arid3b-KO, untreat, rep2

description: Library name: sg-Arid3b untreat 2


title: 3-month, thalamus, wild-type replicate 2

description:
Library name: 12w-TH-WT2
3-mo_TH_WT_2


title: 3-month, thalamus, wild-type replicate 1

description:
Library name: 12w-TH-WT1
3-mo_TH_WT_1


title: Human chondrocytes P0 Donor 2

description: Library name: D2_P0


title: Human chondrocytes P6 Donor 1

description: Library name: D1_P6

value: Donor 1


title: D11

description: Library name: sample 1

source_name: Healthy Control Group, RNA-Sseq, replicate biosample 1


title: 3-month, thalamus, wild-type replicate 4

description:
Library name: 12w-TH-WT4
3-mo_TH_WT_4


title: CD8+ T cells,Control, co-cultured with CMT93-OVA cells, rep2

description: Library name: sg-Int treat 2

value: CD8+ T cells were co-cultured with CMT93-OVA cells for 4 hours.

tag: time

value: 4 hours


title: Human chondrocytes P3 Donor 1

description: Library name: D1_P3


title: SCWOPD, scRNAseq [SCWOPD-5]

city: Hangzhou

first: XINLE

last: ZOU

address: No 600 Dunyun Road

institute: WESTLAKE UNIVERSITY

data_processing:
The demultiplexing, barcoded processing,gene counting and aggregation were made using the Cell Ranger software v7.0.0(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The organoids were dissociated into single cells using the STEMdiff Cardiomyocyte Dissociation Kit (Stemcell Technologies, #05025). The cell suspension was then loaded into Chromium microfluidic chips for single-cell RNA sequencing.
The cell suspension was processed with 3’ (v2 or v3, depending on the project) chemistry and barcoded using a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was reverse-transcribed, and sequencing libraries were constructed using the Chromium Single Cell 3’ v2 (v2 or v3, depending on the project) reagent kit (10X Genomics), following the manufacturer’s instructions.

tag: cell line

value: without PD173074


title: 3-month, thalamus, heterozygous replicate 5

description:
Library name: 12w-TH-HT5
3-mo_TH_HET_5

value: Srrm2 +/-


title: CD8+ T cells,Control, co-cultured with CMT93-OVA cells, rep3

description: Library name: sg-Int treat 3


title: SCWOPD, scRNAseq [SCWOPD-4]


title: 3-month, thalamus, heterozygous replicate 4

description:
Library name: 12w-TH-HT4
3-mo_TH_HET_4


title: CD8+ T cells, Arid3b-KO, co-cultured with CMT93-OVA cells, rep3

description: Library name: sg-Arid3b treat 3


title: Human chondrocytes P0 Donor 1

description: Library name: D1_P0


title: 3-month, thalamus, heterozygous replicate 3

description:
Library name: 12w-TH-HT3
3-mo_TH_HET_3


title: CD8+ T cells, Arid3b-KO, co-cultured with CMT93-OVA cells, rep2

description: Library name: sg-Arid3b treat 2


title: SCWOPD, scRNAseq [SCWOPD-2]


title: 3-month, thalamus, heterozygous replicate 2

description:
Library name: 12w-TH-HT2
3-mo_TH_HET_2


title: Liver, Semaglutide, rep 8

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

description: Library name: 19599

data_processing:
Reads were aligned to the GRCm38 Ensembl Mus musculus genome and counted using STAR v.2.7.0f with default settings.
Assembly: GRCm38, ensembl release 96
Supplementary files format and content: Tab-delimited text file contaning raw counts from each sample

source_name: liver

extract_protocol:
cDNA libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on the NextSeq 500 (Illumina) with NextSeq 500/550 High Output Kit V2 (#75 CYS, Illumina)
RNA-seq

treatment_protocol: Liver tissue were collected and snap-frozen in liquid nitrogen. RNA was isolated using the NucleoSpin® kit (MACHEREY-NAGEL).

value: liver

value: Semaglutide


title: 3-month, thalamus, heterozygous replicate 1

description:
Library name: 12w-TH-HT1
3-mo_TH_HET_1


title: Liver, Lean chow vehicle, rep 8

description: Library name: 19592

value: Liver

value: Lean chow vehicle


title: 3-month, striatum, wild-type replicate 5

description:
Library name: 12w-ST-WT5
3-mo_ST_WT_5


title: Liver, Vehicle, rep 7

description: Library name: 19584

value: Vehicle


title: 3-month, striatum, wild-type replicate 4

description:
Library name: 12w-ST-WT4
3-mo_ST_WT_4


title: SCPD, scRNAseq [SCPD-2]

value: with PD173074


title: 2-month-old brain (n = 3),  sgsh wild type, sgsh overexpressing, rep1

city: Melbourne

first: Jan

last: Kaslin

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description: Library name: sgshOE_young_WTOE1

data_processing:
SOAPnuke was used for adaptor removal and low-quality read filtration, and genome mapping was performed with HISAT2 for SNP analysis and novel transcript detection. Clean reads were mapped to the reference genome using Bowtie2, and gene expression levels were calculated with RSEM.
Assembly: GRCz11 INSDC Assembly GCA_000002035.6, May 2017
Supplementary files format and content: TSV or tab-separated text files containing raw counts for each sample

growth_protocol: 24 hpf embryos and 5 dpf larvae were raised in E3 medium at 28.5 °C. Juvenile and adult zebrafish were raised in system water under standard housing conditions

extract_protocol:
Prior to total RNA extraction: - 24 hpf embryos were manually dechorionated in E3 medium, then transferred to Eppendorf tubes on ice. - 5 dpf larvae were euthanised by tricaine overdose, then immediately decapitated in ice-cold 1x PBS. Heads were collected into an Eppendorf tube on ice. - Adult zebrafish were euthanised in an ice-water slurry, then exsanguinated by tail resection on ice. Following exsanguination, whole brains were dissected from the neurocranium, rinsed in fresh ice-cold PBS, then transferred to an Eppendorf tube on ice.  Extraction method: Total RNA from all samples were harvested in TRIzol (Sigma) per the manufacturer's protocol.
Libraries for 150 bp paired-end RNA-sequencing were prepared by BGI using the DNBSEQ method.

value: WT

tag: genetic modification

tag: developmental stage

value: 2 months


title: Liver, Lean chow vehicle, rep 7

description: Library name: 19583


title: SC_2D, scRNAseq [SC_2D-3]

value: 2D culture


title: 3-month, striatum, wild-type replicate 2

description:
Library name: 12w-ST-WT2
3-mo_ST_WT_2

value: Brain


title: Liver, Semaglutide, rep 6

description: Library name: 19581


title: 2-month-old brain (n = 3),  sgshΔex5-6 homozygous, sgsh overexpressing, rep3

description: Library name: sgshOE_young_MutOE3


title: 2-month-old brain (n = 3),  sgshΔex5-6 homozygous, sgsh overexpressing, rep2

description: Library name: sgshOE_young_MutOE2


title: SCWOPD, scRNAseq [SCWOPD-1]


title: 3-month, striatum, wild-type replicate 1

description:
Library name: 12w-ST-WT1
3-mo_ST_WT_1

value: Wild-type


title: SC_2D, scRNAseq [SC_2D-2]


title: Liver, Vehicle, rep 6

description: Library name: 19575


title: SC_2D, scRNAseq [SC_2D-1]


title: CD8+ T cells,Control, co-cultured with CMT93-OVA cells, rep1

description: Library name: sg-Int treat 1

value: CD8+ T cells

value: intergenic sequence knockout


title: SCWOPD, scRNAseq [SCWOPD-3]


title: Liver, Lean chow vehicle, rep 6

description: Library name: 19574


title: Liver, Vehicle, rep 8

description: Library name: 19593


title: 3-month, striatum, heterozygous replicate 4

description:
Library name: 12w-ST-HT4
3-mo_ST_HET_4


title: 2-month-old brain (n = 3),  sgsh wild type, rep3

description: Library name: sgshOE_young_WT3


title: CD8+ T cells, Arid3b-KO, co-cultured with CMT93-OVA cells, rep1

description: Library name: sg-Arid3b treat 1

value: Arid3b knockout

value: CD8+ T cells were co-cultured with CMT93-OVA cells for 4 hours.


title: Liver, Semaglutide, rep 5

description: Library name: 19572


title: SC without PD_Day25.5, rep1 [5scwoPDd25.5]

data_processing:
Quality assessment of the original FASTQ files using the FastQC(v0.12.1) tool to generate quality reports.
Use the Trimmomatic(v0.39.0) tool to remove low-quality sequences and splice sequences to improve comparison accuracy.
Processed reads were compared to the reference genome using the STAR(v2.7.10a) tool to generate sequenced BAM files.
Gene expression estimation was performed using the RSEM(v1.3.1) tool using the comparison results to generate an expression matrix.
The gene expression matrix and sample information were read in R(v4.3.3). Differential expression analysis was performed using the DESeq2(v1.42.1) software package and the results were output.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted using the RNA-easy Isolation Reagent (Vazyme, #701) according to manufacturer instructions
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® and index codes were added to attribute sequences to each sample.

value: without PD173074


title: SCPD, scRNAseq [SCPD-1]


title: 3-month, striatum, heterozygous replicate 3

description:
Library name: 12w-ST-HT3
3-mo_ST_HET_3

value: Srrm2 +/-


title: SC without PD_Day25.5, rep2 [6scwoPDd25.5]


title: 2-month-old brain (n = 3),  sgsh wild type, rep2

description: Library name: sgshOE_young_WT2


title: SCPD, scRNAseq [SCPD-3]


title: 3-month, striatum, heterozygous replicate 2

description:
Library name: 12w-ST-HT2
3-mo_ST_HET_2


title: Liver, Lean chow vehicle, rep 5

description: Library name: 19565


title: SC without PD_Day15.5, rep1 [5scwoPDd15.5]


title: 2-month-old brain (n = 3),  sgshΔex5-6 homozygous, rep3

description: Library name: sgshOE_young_Mut3


title: 3-month, striatum, heterozygous replicate 1

description:
Library name: 12w-ST-HT1
3-mo_ST_HET_1


title: SC without PD_Day15.5, rep2 [6scwoPDd15.5]


title: Liver, Semaglutide, rep 4

description: Library name: 19563


title: SC without PD_Day10.5, rep2 [6scwoPDd10.5]


title: 3-month, somatosensory cortex, wild-type replicate 5

description:
Library name: 12w-SSC-WT5
3-mo_SSC_WT_5


title: 2-month-old brain (n = 3),  sgshΔex5-6 homozygous, sgsh overexpressing, rep1

description: Library name: sgshOE_young_MutOE1


title: Liver, Vehicle, rep 5

description: Library name: 19566


title: 2-month-old brain (n = 3),  sgshΔex5-6 homozygous, rep1

description: Library name: sgshOE_young_Mut1


title: 2-month-old brain (n = 3),  sgsh wild type, sgsh overexpressing, rep3

description: Library name: sgshOE_young_WTOE3


title: Liver, Semaglutide, rep 7

description: Library name: 19590


title: 3-month, somatosensory cortex, wild-type replicate 4

description:
Library name: 12w-SSC-WT4
3-mo_SSC_WT_4


title: Liver, Lean chow vehicle, rep 4

description: Library name: 19556


title: 5 dpf larval head pool (n = 50), sgsh wild type, rep3

description: Library name: sgsh_5d_WT3

source_name: Head

value: Head

value: 5 dpf


title: SC without PD_Day6.5, rep2 [6scwoPDd6.5]


title: 2-month-old brain (n = 3),  sgsh wild type, sgsh overexpressing, rep2

description: Library name: sgshOE_young_WTOE2


title: Liver, Semaglutide, rep 3

description: Library name: 19554

value: Liver

value: Semaglutide


title: SC without PD_Day6.5, rep1 [5scwoPDd6.5]


title: SC without PD_Day10.5, rep1 [5scwoPDd10.5]


title: 3-month, striatum, wild-type replicate 3

description:
Library name: 12w-ST-WT3
3-mo_ST_WT_3


title: Liver, Vehicle, rep 3

description: Library name: 19548

value: Vehicle


title: 3-month, somatosensory cortex, wild-type replicate 2

description:
Library name: 12w-SSC-WT2
3-mo_SSC_WT_2


title: 5 dpf larval head pool (n = 50), sgsh wild type, rep2

description: Library name: sgsh_5d_WT2


title: SC without PD_Day3.5, rep1 [5scwoPDd3.5]


title: 3-month, striatum, heterozygous replicate 5

description:
Library name: 12w-ST-HT5
3-mo_ST_HET_5


title: 2-month-old brain (n = 3),  sgsh wild type, rep1

description: Library name: sgshOE_young_WT1


title: 3-month, somatosensory cortex, heterozygous replicate 5

description:
Library name: 12w-SSC-HT5
3-mo_SSC_HET_5


title: 5 dpf larval head pool (n = 50), sgshΔex5-6 homozygous, rep2

description: Library name: sgsh_5d_Mut2


title: Liver, Semaglutide, rep 2

description: Library name: 19545


title: SCPD_Day25.5, rep2 [6scPDd25.5]

value: with PD173074


title: Liver, Vehicle, rep 2

description: Library name: 19539


title: 5 dpf larval head pool (n = 50), sgshΔex5-6 homozygous, rep1

description: Library name: sgsh_5d_Mut1


title: SC without PD_Day3.5, rep2 [6scwoPDd3.5]


title: 3-month, somatosensory cortex, wild-type replicate 1

description:
Library name: 12w-SSC-WT1
3-mo_SSC_WT_1


title: Liver, Lean chow vehicle, rep 3

description: Library name: 19547

value: Lean chow vehicle


title: 3-month, somatosensory cortex, heterozygous replicate 3

description:
Library name: 12w-SSC-HT3
3-mo_SSC_HET_3


title: 2-month-old brain (n = 3),  sgshΔex5-6 homozygous, rep2

description: Library name: sgshOE_young_Mut2

value: 2 months


title: Liver, Semaglutide, rep 1

description: Library name: 19536


title: genomic DNA in HU120 in WT cells for time course

city: Montpellier

first: Mégane

last: Da Mota

address: 141 rue de la cardonille

country: France

institute: CNRS

data_processing:
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Assembly: sacCer3
Supplementary files format and content: Biwgiw files correspond to a ratio relative to Input or relative to G1 (gDNA)

organism: Saccharomyces cerevisiae

source_name: hydroxyurea 200mM fo 120min

growth_protocol: S. cerevisiae cells were grown in YPAD and released from alpha-factor arrest in the presence of 200 mM HU (hydroxyurea) for 60 min, or 90min or 120min

extract_protocol:
Yeast genomic DNA was prepared using standard protocol
For single-end experiment : Libraries were constructed using standard Illumina kits (TruSeq SBS Kit v3) and protocols Sequencer: HiSeq4000 or for paired-end experiments : the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Sequencer : NovaSeq 6000. Reads lenght: 50.

value: yeast cells


title: SCPD_Day15.5, rep1 [5scPDd15.5]


title: Liver, Vehicle, rep 4

description: Library name: 19557


title: 3-month, somatosensory cortex, heterozygous replicate 1

description:
Library name: 12w-SSC-HT1
3-mo_SSC_HET_1

value: Brain


title: genomic DNA in HU90 in WT cells for time course

source_name: hydroxyurea 200mM fo 90min

value: S + HU 90


title: Liver, Vehicle, rep 1

description: Library name: 19530

source_name: Liver


title: SCPD_Day10.5, rep2 [6scPDd10.5]


title: 3-month, somatosensory cortex, wild-type replicate 3

description:
Library name: 12w-SSC-WT3
3-mo_SSC_WT_3

value: Wild-type


title: genomic DNA in HU60 in WT cells for time course

source_name: hydroxyurea 200mM fo 60min

value: S + HU 60


title: 3-month, somatosensory cortex, heterozygous replicate 2

description:
Library name: 12w-SSC-HT2
3-mo_SSC_HET_2

source_name: Brain


title: 5 dpf larval head pool (n = 50), sgshΔex5-6 homozygous, rep3

description: Library name: sgsh_5d_Mut3


title: genomic DNA in G1 in WT cells for time course

source_name: alpha-factor synchronization


title: SCPD_Day6.5, rep1 [5scPDd6.5]


title: 3-month, substantia nigra, wild-type replicate 4

description:
Library name: 12w-SN-WT4
3-mo_SN_WT_4


title: 3-month, substantia nigra, wild-type replicate 3

description:
Library name: 12w-SN-WT3
3-mo_SN_WT_3


title: SCPD_Day10.5, rep1 [5scPDd10.5]


title: Liver, Lean chow vehicle, rep 1

description: Library name: 19529


title: 3-month, substantia nigra, heterozygous replicate 3

description:
Library name: 12w-SN-HT5
3-mo_SN_HET_5


title: Input Brn1-PK in HU120 in WT cells for time course


title: IP Brn1-PK in HU120 in WT cells for time course


title: Liver, DIO-MASH Vehicle 12 w, rep 10

description: Library name: 24075

treatment_protocol: Liver tissue were collected and snap-frozen in liquid nitrogen. RNA was isolated using the NucleoSpin® kit (MACHEREY-NAGEL) or the RNAdvance Tissue Kit (Beckman-Coulter

value: liver

value: DIO-MASH Vehicle


title: SCPD_Day3.5, rep2 [6scPDd3.5]


title: 3-month, substantia nigra, wild-type replicate 1

description:
Library name: 12w-SN-WT1
3-mo_SN_WT_1


title: Input Brn1-PK in HU90 in WT cells for time course


title: SCPD_Day3.5, rep1 [5scPDd3.5]


title: 3-month, substantia nigra, wild-type replicate 2

description:
Library name: 12w-SN-WT2
3-mo_SN_WT_2


title: IP Brn1-PK in HU90 in WT cells for time course


title: 3-month, substantia nigra, heterozygous replicate 2

description:
Library name: 12w-SN-HT3
3-mo_SN_HET_3


title: SCPD_Day6.5, rep2 [6scPDd6.5]


title: SCPD_Day15.5, rep2 [6scPDd15.5]


title: Liver, Lean chow vehicle, rep 2

description: Library name: 19538


title: 3-month, somatosensory cortex, heterozygous replicate 4

description:
Library name: 12w-SSC-HT4
3-mo_SSC_HET_4


title: 5 dpf larval head pool (n = 50), sgsh wild type, rep1

description: Library name: sgsh_5d_WT1

value: WT


title: SCPD_Day25.5, rep1 [5scPDd25.5]


title: Liver, DIO-MASH Vehicle 12 w, rep 9

description: Library name: 24071


title: Day1.5, rep2 [6scPDd1.5]

value: No treatment


title: 3-month, substantia nigra, heterozygous replicate 1

description:
Library name: 12w-SN-HT1
3-mo_SN_HET_1

value: Srrm2 +/-


title: Input Brn1-PK in HU60 in WT cells for time course


title: Liver, Chow Vehicle 12 w, rep 9

description: Library name: 24070

value: Chow Vehicle


title: IP Brn1-PK in HU60 in WT cells for time course


title: Liver, Semaglutide 12 w, rep 8

description: Library name: 24069


title: Day0, rep2 [6scD0]


title: Day1.5, rep1 [5scPDd1.5]


title: Liver, DIO-MASH Vehicle 12 w, rep 8

description: Library name: 24067


title: Human neutrophils sUA+LPS5

city: Munich

first: Qiubo

last: Li

institute: LMU Klinikum

description:
Library name: E7
raw_counts_2.txt

data_processing:
Data processing were prepared by BGI following the manufacturer’s protocol.
Filtered reads were aligned to the human GRCh38/hg38 reference genome (primary assemblies retrieved from Ensembl, version 113) using STAR (v2.7.10b) with paired-end mode and default parameters. Gene quantification was conducted using featureCounts (v2.0.1) against Ensembl v113 annotation of GRCh38/hg38, with recommended parameters according to official documentation.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Blood

extract_protocol:
Total RNA was extracted from human peripheral blood neutrophils using the RNA extraction kit (Qiagen, 254 Düsseldorf, Germany) according to the manufacturer’s protocol.
RNA libraries were prepared by BGI following the manufacturer’s protocol.

treatment_protocol: Neutrophils were stimulated with either LPS, soluble uric acid, fMLP, or combinations. Untreated cells served as controls.

value: Blood

value: primary cells

value: Neutrophils

value: Soluble uric acid+LPS5


title: 3-month, prefrontal cortex, wild-type replicate 5

description:
Library name: 12w-PFC-WT5
3-mo_PFC_WT_5

data_processing:
Reads were aligned to Gencode M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: Gencode M25 / GRCm38.p6
Supplementary files format and content: Comma-separated text files that includes raw counts (estimated by RSEM) for each sample.

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Srrm2 +/- mutant mice and wild-type littermates. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
Libraries were prepared using Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.


title: Human neutrophils sUA+LPS4

description:
Library name: D7
raw_counts_2.txt

value: Soluble uric acid+LPS4


title: Liver, Semaglutide 12 w, rep 9

description: Library name: 24073

value: Semaglutide


title: 3-month, prefrontal cortex, wild-type replicate 3

description:
Library name: 12w-PFC-WT3
3-mo_PFC_WT_3


title: Liver, Chow Vehicle 12 w, rep 8

description: Library name: 24066


title: Day0, rep1 [5scD0]


title: Human neutrophils sUA+LPS3

description:
Library name: C7
raw_counts_2.txt

value: Soluble uric acid+LPS3


title: Liver, Semaglutide 12 w, rep 7

description: Library name: 24065


title: T_CO3

first: Huayuan

last: Liu

state: Beijing

address: New Student Apartment Building, No. 17, South Panjiayuan, Chaoyang District, Beijing

institute: Chinese Academy of Medical Sciences Cancer Hospital

description: Library name: Sample12

data_processing:
Gene Set Enrichment Analysis:
Gene Set Enrichment Analysis (GSEA) is a computational approach to  determine if a pre-defined Gene Set can show a significant consistent  difference between two biological states. The genes were ranked  according to the degree of differential expression in the two samples,  and then the predefined Gene Set were tested to see if they were  enriched at the top or bottom of the list. Gene set enrichment analysis  can include subtle expression changes. We use the local version of the  GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO,  KEGG, Reactome, DO, DisGeNET data set were used for GSEA  independently
Assembly: GRh38
Supplementary files format and content: information on RNA modification sites identified in each sample, RNA counts, and standardized values.

source_name: CD4+T cell

extract_protocol:
RNAquantification andqualification ①RNAdegradation and contamination was monitored on 1% agarose gels. ② RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . ③RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Atotal amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µlUSER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

value: CD4+T cell

tag: sample group


title: Human neutrophils sUA+fMLP5

description:
Library name: E6
raw_counts_2.txt

value: Soluble uric acid+fMLP5


title: T_CO1

description: Library name: Sample10


title: Liver, DIO-MASH Vehicle 12 w, rep 7

description: Library name: 24063


title: Liver, Chow Vehicle 12 w, rep 10

description: Library name: 24074


title: 3-month, prefrontal cortex, heterozygous replicate 4

description:
Library name: 12w-PFC-HT4
3-mo_PFC_HET_4

value: Brain


title: Human neutrophils sUA+fMLP4

description:
Library name: D6
raw_counts_2.txt

value: Soluble uric acid+fMLP4


title: T_Single3

description: Library name: Sample9


title: 3-month, prefrontal cortex, heterozygous replicate 3

description:
Library name: 12w-PFC-HT3
3-mo_PFC_HET_3


title: 3-month, prefrontal cortex, heterozygous replicate 2

description:
Library name: 12w-PFC-HT2
3-mo_PFC_HET_2


title: 3-month, prefrontal cortex, heterozygous replicate 1

description:
Library name: 12w-PFC-HT1
3-mo_PFC_HET_1


title: S_CO3

description: Library name: Sample6


title: Liver, Chow Vehicle 12 w, rep 6

description: Library name: 24058

value: liver


title: Human neutrophils fMLP3

description:
Library name: C5
raw_counts_2.txt


title: Liver, Semaglutide 12 w, rep 5

description: Library name: 24057


title: Liver, Semaglutide 12 w, rep 10

description: Library name: 24077


title: Liver, Chow Vehicle 12 w, rep 7

description: Library name: 24062


title: Liver, DIO-MASH Vehicle 12 w, rep 5

description: Library name: 24055

value: DIO-MASH Vehicle


title: 3-month, prefrontal cortex, wild-type replicate 4

description:
Library name: 12w-PFC-WT4
3-mo_PFC_WT_4

value: Wild-type


title: Human neutrophils fMLP5

description:
Library name: E5
raw_counts_2.txt


title: S_CO2

description: Library name: Sample5


title: Human neutrophils LPS5

description:
Library name: F4
raw_counts_2.txt


title: Liver, DIO-MASH Vehicle 12 w, rep 6

description: Library name: 24059


title: 3-month, hippocampus, wild-type replicate 3

description:
Library name: 12w-HP-WT3
3-mo_HP_WT_3


title: T_CO2

description: Library name: Sample11


title: Human neutrophils fMLP4

description:
Library name: D5
raw_counts_2.txt


title: Human neutrophils LPS4

description:
Library name: E4
raw_counts_2.txt


title: S_Single3

description: Library name: Sample3


title: Liver, Chow Vehicle 12 w, rep 5

description: Library name: 24054


title: Human neutrophils LPS3

description:
Library name: D4
raw_counts_2.txt


title: S_Single2

description: Library name: Sample2


title: Liver, Semaglutide 12 w, rep 4

description: Library name: 24053


title: 3-month, hippocampus, wild-type replicate 4

description:
Library name: 12w-HP-WT4
3-mo_HP_WT_4


title: 3-month, hippocampus, wild-type replicate 2

description:
Library name: 12w-HP-WT2
3-mo_HP_WT_2


title: S_Single1

description: Library name: Sample1


title: Human neutrophils sUA+fMLP3

description:
Library name: C6
raw_counts_2.txt

value: Soluble uric acid+fMLP3


title: T_Single1

description: Library name: Sample7


title: Liver, Semaglutide 12 w, rep 6

description: Library name: 24061


title: Liver, Chow Vehicle 12 w, rep 4

description: Library name: 24050


title: 3-month, hippocampus, heterozygous replicate 5

description:
Library name: 12w-HP-HT5
3-mo_HP_HET_5

value: Srrm2 +/-


title: Villarino-18829-003_FB3

city: Maimi

first: Alejandro

last: Villarino

state: Florida

address: 1600 NW 10th Ave, Rosenstiel Medical Science Building (RMSB), Room 3152A

institute: University of Miami

description:
Library name: 6 s3_WT_S3KO_MigR1_rep1
STAT3_N647_Frontiers_GEO_scRNAseq_multi_tag_metadata.csv
Thy1.1_feature_reference.csv
Villarino-18829-003_barcodes.tsv.gz
Villarino-18829-003_features.tsv.gz
Villarino-18829-003_matrix.mtx.gz

library_source: other

data_processing:
bulk RNA-seq: FASTQ alignment with Tophat2
bulk RNA-seq: transcript assembly with cufflinks
bulk RNA-seq: Gene level read count data generated using htseq-count
scRNA-seq: FASTQ alignment, transcript assembly and gene-level counts matrix generated with cellRanger
scRNA-seq: multitagged cells selected using custom scrip and metadata assembled with Seurat
Assembly: bulk RNA-seq: mm10
Supplementary files format and content: bulk RNA-seq: Tab delimited text of RNA-seq gene-level expression count data
Supplementary files format and content: scRNA-seq: Tab delimited text of metadata for multi-tagged cells

molecule: protein

source_name: peripheral lymph nodes

growth_protocol: 20-100K viable, GFP+ cells were sorted and cultured, then lysed and stored in Trizol

extract_protocol:
Total RNA isolated from TRIzol by phenol/chloroform extraction, then mRNA enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module
For bulk RNA-seq, sequencing libraries were generated with NEBNext Ultra II Library Prep Kit for Illumina (E7645L, New England Biolabs). For scRNA-seq , sequencing libraries were generated with 10X Chromium Single Cell 3' V3 chemistry kit.

treatment_protocol: 20-100K viable cells were sorted and cultured with IL-27, then lysed and stored in Trizol

value: peripheral lymph nodes

value: lymphocytes

value: Viable GFP+ RV tranduced

value: Stat3+/+ (WT) and Stat3-/-


title: Human neutrophils LPS2

description:
Library name: C4
raw_counts_2.txt

value: Blood

value: primary cells

value: Neutrophils


title: 3-month, hippocampus, heterozygous replicate 4

description:
Library name: 12w-HP-HT4
3-mo_HP_HET_4


title: Liver, Semaglutide 12 w, rep 3

description: Library name: 24049

value: Semaglutide


title: Human neutrophils sUA4

description:
Library name: E3
raw_counts_2.txt

value: Soluble uric acid4


title: Villarino-18829-002_FB3

description:
Library name: 5 s2_WT_S3KO_MigR1_rep1
STAT3_N647_Frontiers_GEO_scRNAseq_multi_tag_metadata.csv
Thy1.1_feature_reference.csv
Villarino-18829-002_barcodes.tsv.gz
Villarino-18829-002_features.tsv.gz
Villarino-18829-002_matrix.mtx.gz


title: Human neutrophils sUA3

description:
Library name: D3
raw_counts_2.txt

value: Soluble uric acid3


title: 3-month, hippocampus, heterozygous replicate 3

description:
Library name: 12w-HP-HT3
3-mo_HP_HET_3

value: Brain


title: Liver, DIO-MASH Vehicle 12 w, rep 3

description: Library name: 24047


title: T_Single2

description: Library name: Sample8

value: CD4+T cell


title: Human neutrophils sUA2

description:
Library name: C3
raw_counts_2.txt

value: Soluble uric acid2


title: Villarino-18829-001_FB3

description:
Library name: 4 s1_WT_S3KO_MigR1_rep1
STAT3_N647_Frontiers_GEO_scRNAseq_multi_tag_metadata.csv
Thy1.1_feature_reference.csv
Villarino-18829-001_barcodes.tsv.gz
Villarino-18829-001_features.tsv.gz
Villarino-18829-001_matrix.mtx.gz


title: 3-month, hippocampus, wild-type replicate 1

description:
Library name: 12w-HP-WT1
3-mo_HP_WT_1


title: 3-month, prefrontal cortex, heterozygous replicate 5

description:
Library name: 12w-PFC-HT5
3-mo_PFC_HET_5


title: 3-month, hippocampus, wild-type replicate 5

description:
Library name: 12w-HP-WT5
3-mo_HP_WT_5


title: S_CO1

description: Library name: Sample4


title: Villarino-18829-003_GEX3

description:
Library name: 3 s3_WT_S3KO_MigR1_rep1
STAT3_N647_Frontiers_GEO_scRNAseq_multi_tag_metadata.csv
Thy1.1_feature_reference.csv
Villarino-18829-003_barcodes.tsv.gz
Villarino-18829-003_features.tsv.gz
Villarino-18829-003_matrix.mtx.gz


title: Human neutrophils medium5

description:
Library name: E2
raw_counts_2.txt


title: Liver, Semaglutide 12 w rep 2

description: Library name: 24045

value: liver


title: Villarino-18829-002_GEX3

description:
Library name: 2 s2_WT_S3KO_MigR1_rep1
STAT3_N647_Frontiers_GEO_scRNAseq_multi_tag_metadata.csv
Thy1.1_feature_reference.csv
Villarino-18829-002_barcodes.tsv.gz
Villarino-18829-002_features.tsv.gz
Villarino-18829-002_matrix.mtx.gz


title: 3-month, cerebellar vermis, wild-type replicate 5

description:
Library name: 12w-CV-WT5
3-mo_CV_WT_5

value: Wild-type


title: Villarino-18829-001_GEX3

description:
Library name: 1 s1_WT_S3KO_MigR1_rep1
STAT3_N647_Frontiers_GEO_scRNAseq_multi_tag_metadata.csv
Thy1.1_feature_reference.csv
Villarino-18829-001_barcodes.tsv.gz
Villarino-18829-001_features.tsv.gz
Villarino-18829-001_matrix.mtx.gz


title: Liver, Chow Vehicle 12 w, rep 2

description: Library name: 24042

value: Chow Vehicle


title: Human neutrophils medium3

description:
Library name: C2
raw_counts_2.txt


title: Human neutrophils sUA+fMLP1

description:
Library name: Sample 9
E4

value: Soluble uric acid+fMLP1


title: Human neutrophils sUA+fMLP2

description:
Library name: Sample 10
E5

value: Soluble uric acid+fMLP2


title: S3KO_CD8_N647D_rep1

description:
Library name: Villarino‐18253‐019_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt

source_name: pooled LN and spleen

value: pooled LN and spleen

value: CD8+ T cell

value: Viable CD8+ GFP+ RV tranduced


title: 3-month, prefrontal cortex, wild-type replicate 2

description:
Library name: 12w-PFC-WT2
3-mo_PFC_WT_2


title: 3-month, cerebellar vermis, wild-type replicate 1

description:
Library name: 12w-CV-WT1
3-mo_CV_WT_1


title: Liver, DIO-MASH Vehicle 12 w, rep 1

description: Library name: 24039

value: DIO-MASH Vehicle


title: Liver, Chow Vehicle 12 w, rep 1

description: Library name: 24038


title: S3KO_CD8_N647I_rep1

description:
Library name: Villarino‐18253‐018_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: Human neutrophils sUA+LPS1

description:
Library name: Sample 7
E2

value: Blood

value: primary cells

value: Soluble uric acid+LPS1


title: Liver, DIO-MASH Vehicle 12 w, rep 2

description: Library name: 24043


title: 3-month, cerebellar vermis, heterozygous replicate 5

description:
Library name: 12w-CV-HT5
3-mo_CV_HET_5

value: Srrm2 +/-


title: 3-month, hippocampus, heterozygous replicate 2

description:
Library name: 12w-HP-HT2
3-mo_HP_HET_2


title: S3KO_CD8_Y640F_rep2

description:
Library name: Villarino‐18253‐058_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: Liver, DIO-MASH Vehicle 12 w, rep 4

description: Library name: 24051


title: Human neutrophils sUA5

description:
Library name: F3
raw_counts_2.txt

value: Neutrophils

value: Soluble uric acid5


title: 3-month, cerebellar vermis, heterozygous replicate 4

description:
Library name: 12w-CV-HT4
3-mo_CV_HET_4

value: Brain


title: Liver, Semaglutide 24 w, rep 7

description: Library name: 16252

value: Liver

value: Semaglutide


title: 3-month, cerebellar vermis, wild-type replicate 2

description:
Library name: 12w-CV-WT2
3-mo_CV_WT_2

value: Wild-type


title: Liver, Semaglutide 24 w, rep 8

description: Library name: 16363


title: 3-month, hippocampus, heterozygous replicate 1

description:
Library name: 12w-HP-HT1
3-mo_HP_HET_1


title: Human neutrophils fMLP2

description:
Library name: Sample 6
D5


title: Human neutrophils fMLP1

description:
Library name: Sample 5
D4


title: S3KO_CD8_Y640F_rep1

description:
Library name: Villarino‐18253‐034_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: 3-month, cerebellar vermis, heterozygous replicate 3

description:
Library name: 12w-CV-HT3
3-mo_CV_HET_3


title: Human neutrophils LPS1

description:
Library name: Sample 4
D3


title: Liver, Chow Vehicle 24 w, rep 8

description: Library name: 16244

value: Chow Vehicle


title: S3KO_CD8_N647D_rep2

description:
Library name: Villarino‐18253‐062_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: S3KO_CD8_STAT3.203_rep1

description:
Library name: Villarino‐18253‐015_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: 3-month, cerebellar vermis, wild-type replicate 4

description:
Library name: 12w-CV-WT4
3-mo_CV_WT_4


title: 3-month, cerebellar vermis, wild-type replicate 3

description:
Library name: 12w-CV-WT3
3-mo_CV_WT_3


title: Human neutrophils sUA1

description:
Library name: Sample 3
C5

value: Soluble uric acid1


title: Liver, Semaglutide 12 w, rep 1

description: Library name: 24041

value: liver


title: S3KO_CD8_N647I_rep2

description:
Library name: Villarino‐18253‐061_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt

value: pooled LN and spleen


title: Human neutrophils sUA+LPS2

description:
Library name: Sample 8
E3

value: Soluble uric acid+LPS2


title: 3-month, cerebellar cortex, wild-type replicate 5

description:
Library name: 12w-CC-WT5
3-mo_CC_WT_5


title: Liver, DIO-MASH Vehicle 24 w, rep 6

description: Library name: 16241


title: Liver, Chow Vehicle 24 w, rep 7

description: Library name: 16234


title: 3-month, cerebellar cortex, wild-type replicate 4

description:
Library name: 12w-CC-WT4
3-mo_CC_WT_4


title: Human neutrophils medium1

description:
Library name: Sample 1
C2


title: Liver, Semaglutide 24 w, rep 6

description: Library name: 16232


title: S3KO_CD8_MigR1_rep2

description:
Library name: Villarino‐18253‐055_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt

value: CD8+ T cell

value: Viable CD8+ GFP+ RV tranduced


title: Liver, DIO-MASH Vehicle 24 w, rep 5

description: Library name: 16231

value: DIO-MASH Vehicle


title: Human neutrophils medium4

description:
Library name: D2
raw_counts_2.txt

value: Blood

value: primary cells


title: Liver, DIO-MASH Vehicle 24 w, rep 7

description: Library name: 16251


title: 3-month, cerebellar cortex, wild-type replicate 2

description:
Library name: 12w-CC-WT2
3-mo_CC_WT_2


title: S3KO_CD8_MigR1_rep1

description:
Library name: Villarino‐18253‐014_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: Liver, Chow Vehicle 12 w, rep 3

description: Library name: 24046


title: S3KO_CD8_STAT3.203_rep2

description:
Library name: Villarino‐18253‐056_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: MOLM-13 cells, parental bio rep 2

first: Keren

last: Peng

address: Guangzhou University Town, Panyu District

institute: Sun Yat-sen University

description: Library name: Sample 2

data_processing:
CASAVA Base calling, FASTQ, Trimmomatic, HISAT2, RSeQC, Qualimap, BEDTools
Raw image data files were converted into raw sequencing reads via base calling using CASAVA software.
The quality of the raw sequencing data was evaluated using FastQC. Subsequently, Trimmomatic was employed for quality trimming to obtain high-quality clean reads.
The clean reads were aligned to the reference genome using HISAT2, and mapping statistics were calculated. Based on the alignment results, RSeQC was utilized to analyze read duplication rates, insert size distributions, and other quality metrics.
Qualimap was employed to assess the uniformity of read distribution and the distribution of reads across genomic features. Additionally, BEDTools was used to calculate gene coverage and analyze the chromosomal distribution of the mapped reads.
Assembly: GRCH38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

organism: Homo

source_name: blood

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instruction.
RNA libraries were prepared using VAHTSTM mRNA-Seg V2 Library Prep Kit for Illumina following manufacturer's protocols.

value: blood

value: leukemia cells

value: WT

tag: group

value: parental


title: MOLM-13/AR cells, resistant, bio rep 1

description: Library name: Sample 3

value: resistant


title: 3-month, cerebellar cortex, wild-type replicate 1

first: Sameer

last: Aryal

institute: Broad Institute of MIT and Harvard

description:
Library name: 12w-CC-WT1
3-mo_CC_WT_1

value: Brain


title: 3-month, cerebellar vermis, heterozygous replicate 1

description:
Library name: 12w-CV-HT1
3-mo_CV_HET_1

value: Srrm2 +/-


title: S3KO_CD4_N647D_rep1

description:
Library name: Villarino‐18253‐002_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt

value: CD4+ T cell

value: Viable CD4+ GFP+ RV tranduced


title: S3KO_CD8_STAT3.203_rep3

description:
Library name: Villarino‐18253‐005_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: Liver, Semaglutide 24 w, rep 5

description: Library name: 16222

value: Liver

value: Semaglutide


title: S3KO_CD4_N647I_rep2

description:
Library name: Villarino‐18253‐044_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt

value: pooled LN and spleen


title: Human neutrophils medium2

description:
Library name: Sample 2
C3

value: Neutrophils


title: MOLM-13 cells, parental, bio rep 1

description: Library name: Sample 1


title: MOLM-13/AR cells, resistant, bio rep 2

description: Library name: Sample 4


title: Liver, Chow Vehicle 24 w, rep 5

description: Library name: 16214

value: Chow Vehicle


title: S3KO_CD4_N647I_rep1

description:
Library name: Villarino‐18253‐009_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: 3-month, cerebellar cortex, heterozygous replicate 5

description:
Library name: 12w-CC-HT5
3-mo_CC_HET_5


title: Liver, DIO-MASH Vehicle 24 w, rep 4

description: Library name: 16221

value: DIO-MASH Vehicle


title: S3KO_CD4_Y640F_rep1

description:
Library name: Villarino‐18253‐022_RNAseq
STAT3_N647_Frontiers_GEO_RNAseq_gene_counts.txt


title: 3-month, cerebellar cortex, heterozygous replicate 2

description:
Library name: 12w-CC-HT2
3-mo_CC_HET_2