title: H3K27ac_olig2_WTSgshKO_8mo_input

city: La Jolla

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

description: ChIP-seq

data_processing:
FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert reads aligning to a single genomic location into “tag directories” for subsequent analysis using the command makeTagDirectory (Heinz et al., 2010). To annotate H3K27ac signal around ATAC-seq peaks, the parameter -size 800 was used with the annotatePeaks command. To annotate MITF/TFE tags around ATAC-seq peaks, the parameter -size 200 was used. DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal with > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text. For TFE3-bound promoter and enhancer analyses, promoters were defined as ±500 bp from the TSS and enhancers as outside this region, both having a minimum of ≥16 normalized merged tags for H3K27ac and ≥64 normalized tags for TFE3 IDR peaks. To identify motifs enriched in differential peak regions over background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. Background sequences were comprised of random GC-matched genomic sequences.
Assembly: mm10
Supplementary files format and content: Tab-separated text file that contains the H3K27ac-annotated ATAC IDR peaks for microglia. Microglia ATAC-Seq IDR peak regions were annotated with normalized tag counts from H3K27Ac ChIP-seq data. Peak annotation with H3K27ac tag directories was performed with HOMER annotatePeaks command with option -size 800. All genomic coordinates are relative to mm10 mouse assembly.
Supplementary files format and content: Tab-separated text file that contains the H3K27ac-annotated ATAC IDR peaks for neurons. Neuron ATAC-Seq IDR peak regions were annotated with normalized tag counts from H3K27Ac ChIP-seq data. Peak annotation with H3K27ac tag directories was performed with HOMER annotatePeaks command with option -size 800. All genomic coordinates are relative to mm10 mouse assembly.
Supplementary files format and content: Tab-separated text file that contains the H3K27ac-annotated ATAC IDR peaks for oligodendrocytes. Oligodendrocyte ATAC-Seq IDR peak regions were annotated with normalized tag counts from H3K27Ac ChIP-seq data. Peak annotation with H3K27ac tag directories was performed with HOMER annotatePeaks command with option -size 800. All genomic coordinates are relative to mm10 mouse assembly.
Supplementary files format and content: Tab-separated text file that contains MITF/TFE tag-annotated ATAC IDR peaks for microglia. Microglia ATAC-Seq IDR peak regions were annotated with normalized tag counts from merged MITF/TFE ChIP-seq data. Peak annotation with merged MITF/TFE tag directories was performed with HOMER annotatePeaks command with option -size 200. All genomic coordinates are relative to mm10 mouse assembly.
Supplementary files format and content: Tab-separated text file that contains MITF/TFE-annotated ATAC IDR peaks for oligodendrocytes. Oligodendrocyte ATAC-Seq IDR peak regions were annotated with normalized tag counts from merged MITF/TFE ChIP-seq data. Peak annotation with merged MITF/TFE tag directories was performed with HOMER annotatePeaks command with option -size 200. All genomic coordinates are relative to mm10 mouse assembly.

extract_protocol:
Brain nuclei were isolated as previously described (Nott et al., 2019,2021), with initial homogenization and crosslinking performed with either 1% formaldehyde in Dulbecco’s PBS for 10 minutes (H3K27ac) or 2mM DSG (Proteochem) in Dulbecco’s PBS for 30 minutes then 1% formaldehyde for 10 minutes (TF ChIP) at room temperature. Nuclei were stained overnight with PU.1-PE (Cell Signaling 81886S), OLIG2-AF488 (Abcam 225099), or NEUN-AF488 (Millipore MAB 377X). Nuclei were stained with DAPI (BioLegend 422801) the next day then sorted with a Beckman Coulter MoFlo Astrios EQ or BD Influx Cell Sorter. Nuclei were sorted as DAPI positive singlets, additionally with microglia as PU.1+/OLIG2-/NEUN-/DAPI+, neurons as PU.1-/OLIG2-/NEUN+/DAPI+, and oligodendrocytes as PU.1-/OLIG2+/NEUN-/DAPI+. Chromatin immunoprecipitation sequencing was performed as previously described (Heinz et al, 2010, Texari et al, 2021). For H3K27ac ChIP-seq, ~500,000 fixed nuclei were quickly thawed on ice and resuspended in ice-cold LB3 buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and 1x protease inhibitor cocktail. Nuclei / chromatin was sheared by sonication using the PIXUL Multi-Sample Sonicator (Active Motif) in low bind 96 well plates following the manufacturer’s instructions. Samples were sonicated with the following settings: Pulse (N): 50, PRF [kHz]: 1.00, Process time: 60 min, Burst Rate [Hz]: 20.00. Samples were pulse spun to 600xg at 4°C in the 96-well plate, transferred to low-bind tubes, and chromatin was recovered by retaining the supernatant following a spin at 21,000xg at 4°C for 10 minutes. The supernatant was then diluted 1.1-fold with ice-cold 10% Triton X-100. Two percent of the lysate was kept as ChIP input control. 10 μL of Dynabead Protein A and 10 μL of Protein G were added per sample, in addition to 2 μg of a specific antibody for H3K27ac (Active Motif 39685). The samples were rotated overnight at 4°C and were washed as follows the next day: 3x with Wash Buffer I (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) + 1x protease inhibitor cocktail, 3x with Wash Buffer III (10 mM Tris-HCl pH 7.5, 250 mM LiCl, 1% Triton X-100, 1 mM EDTA, 0.7% Sodium Deoxycholate) + 1x protease inhibitor cocktail, 2x with TET (0.2% Tween-20/TE) + 1/3x protease inhibitor cocktail, and 1x with IDTET (0.2% Tween-20, 10 mM Tris pH 8, 0.1 mM EDTA). Samples were finally resuspended in 25 μL TT buffer (10 mM Tris pH 8 + 0.05% Tween 20) prior to on-bead library preparation. For MITF, TFEB, and TFE3 ChIP-seq, one million nuclei were thawed on ice and resuspended in ice-cold RLNR1 buffer (20mM Tris HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 1% NP-40, 0,1% SDS, 0.5 mM DTT) + 1x protease inhibitor cocktail/PMSF. Nuclei / chromatin was sheared and recovered with the same method employed for H3K27ac. 10 μL of Dynabead Protein A and 10 μL of Protein G beads per sample were then coupled to either 2 μg of MITF antibody (ActiveMotif, 91201), 2 μg each of two TFEB antibodies (Abcam ab2636, Cell Signaling CST 37785 (D2O7D), or 2 μg each of two TFE3 antibodies (Abcam ab93808, Millipore  Sigma HPA023881). Bead/antibody complexes were added to each sample and rotated overnight at 4°C. The samples were washed with the following buffers: 2x RLNR1 + PIC/PMSF/DTT buffer, 3x LWB-RCNR1 buffer (10 mM Tris HCl pH 7.5, 1 mM EDTA, 0.7% sodium deoxycholate, 1% NP-40, 250 mM LiCl) + PIC/PMSF, 2x TET buffer, 1x IDTET buffer, and then resuspended in 25 μL TT for on-bead library preparation.
Sequencing libraries for ChIP and input samples were prepared with NEBNext Ultra II DNA library prep kit (NEB, E7645) reagents according to the manufacturer’s protocol on beads suspended in 25 μL TT (10 mM Tris/HCl pH 7.5, 0.05% Tween-20), with reagent volumes reduced by half. DNA was eluted and crosslinks reversed by adding 4 μL 10% SDS, 4.5 μL 5 M NaCl, 3 μL EDTA, 4 μL EGTA, 1 μL proteinase K (20 mg/ml), 16 μL water, incubating for 1 h at 55°C, then 30 minutes to overnight at 65°C. DNA was purified using 2 μL of SpeedBeads (Cytiva GE45152105050250) in a 20% PEG8000 / 1.5M NaCl solution to final concentration of 12% PEG, then eluted with 25 μL TT. DNA contained in the eluate was then amplified for 12-14 cycles in 25 μL PCR reactions using NEBNext High-Fidelity Q5 2X PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. Resulting libraries were size selected by gel excision to 200-500 bp, purified, and single or paired-end sequenced using an Illumina NovaSeq instrument.

tag: strain

value: Olig2+ nuclei


title: HEK293T pSG5-miR-129 2

status: Public on Aug 13 2026

type: SRA

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

library_source: transcriptomic

data_processing:
Sample primary processing was performed with miRMaster (Fehlmann et al., Nucleic Acids Res, 2021) using standard parameters. Mapping to the genome was performed allowing up to 5 mulit-mapping hits with Bowtie. One mismatch was allowed for the quantification of isomiRs.  As output, miRMaster generated a list with the expression of 80,668 RNAs from 10 RNA classes. The data were normalized to expression in one million reads and further processed with R (R 4.0.4 GUI 1.74 Catalina build (7936)). To limit the effect of low-abundance miRNAs, we considered miRNA isoforms as expressed if at least five in 10 million mapped miRNA reads were found for at least three independent samples.
Supplementary files format and content: Reads per million mapped miRNA normalzed counts for each sample and human miRNA from miRBase v22.

molecule: total RNA

organism: Homo sapiens

growth_protocol: The cell lines HEK293T (ACC 635), SH-SY5Y (ACC 209) and HeLa (ACC 57) were purchased from the German collection of microorganisms and cell cultures (DSMZ). The authenticity of the cell lines was confirmed by STR fingerprinting by the supplier. Cell lines were cultivated in DMEM (Life Technologies, Darmstadt, Germany) supplemented with penicillin (100 U/ml), streptomycin (100 µg/ml) and either 10% [v/v] FCS for 293T and HeLa cells or 20% [v/v] FCS for SH-SY5Y cells. Lund human mesencephalic (LUHMES) cells were purchased from the American Type Culture Collection (ATCC; CRL-2927). The cells were cultured as previously described by Scholz et al. We performed one passage for all cell lines after purchasing them and cryo-conserved them. All cell lines are from female. All cell lines were subcultured two times a week for no more than three months after the start of the culture.

extract_protocol:
0, 4, 8, 24, 48 h after transfections for miR-7 and 48 h for miRNAs miR-34a, -129, -133b, 873, cells were lysed by QIAzol Lysis Reagent (Qiagen, Hilden, Germany), and total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Library preparation for small RNA sequencing was performed using the MGIEasy Small RNA Library Prep Kit according to the manufacturer’s recommendations. In detail, after 3’ and 5’ adapter ligation, RNAs were reverse transcribed and PCR amplified (21 cycles). PCR products were purified using 6% TBE gels, excising only the 110 bp band corresponding to the PCR product of miRNAs. Subsequently, twelve samples were pooled equimolar into one library, and the library was further circularized and purified. Circularized libraries were sent to BGI Hong Kong for sequencing using the standard MPS protocol as described previously (Li et al., Nucleic Acids Res, 2021).

treatment_protocol: Sequence inserts representing miRNA precursor sequences with additional nucleotides up- and downstream of the precursor sequence for mir-129 and mir-873 were either synthesized by Eurofins Genomics (Ebersberg, Germany) or PCR amplified using sequence-specific primers with human genomic DNA as a template and subsequently cloned into the expression plasmid pSG5 (Agilent Technologies, Santa Clara, California) using EcoR I and BamH I restriction sites. The expression plasmid pSG5-miR-129 harbors nucleotides 128207756-128208053[+] of human chromosome 7 (GRCh38/hg38) and pSG5-miR-873 nucleotides 28888786-28889058[-] of human chromosome 9 (GRCh38/hg38). Cloned sequences of miRNA expression plasmids were verified by Sanger sequencing. Cloning of the pSG5-miR-133b, pSG5-miR-34a and pSG5-miR-7 expression vectors was described previously (Alles et al., Nucleic Acids Res, 2019; Hart et al., Oncotarget, 2016; Kern et al., Nucleic Acids Res, 2021).  For ectopic expression of the respective miRNAs for NGS of miR-transfected HEK293T and HeLa cells, 4x105 cells were seeded out in 6-well plates. Twenty-four hours later, the cells were transfected with the respective DNA amounts (0.5 µg, 1 µg, 2 µg for miR-7, 2 µg for mir-34a, -129, -133b, 873) using PolyFect transfection reagent (Qiagen, Hilden, Germany). For the transfection of the different amounts of mir-7 (0.5 µg, 1 µg) in HEK293T cells, the pSG5-miR-7 expression plasmids were supplemented with the respective amount of pSG5 empty vector to achieve equal amounts of transfected DNA in all samples. For ectopic expression of the respective miRNAs of miR-transfected SH-SY5Y (4,5x105 cells/well) and 4x105 LUHMES (4x105 cells/well) cells for NGS, cells were seeded out in 6-well plates. Twenty-four hours later, the cells were transfected with 2 µg of the respective expression plasmids for mir-7, mir-34a, mir-129, mir-133b, mir-873 or the pSG5-empty vector using Lipofectamine™ 2000 transfection reagent (Invitrogen, Karlsbad, USA). All experiments were conducted 3 times.

tag: cell line

tag: Sex

value: Female

tag: plasmid

tag: concentration

tag: time

value: 48 hr


title: H3K27ac_olig2_SgshKO_8mo_rep2

state: CA

country: USA

description: ChIP-seq

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Brain

tag: tissue

value: Brain

tag: cell type

tag: genotype

value: SgshKO

tag: chip antibody

value: ActiveMotif #39685


title: SUDHL4 - BMS158_1.25 - D1 - rep3

city: Summit

first: Junfei

last: Zhao

state: NJ

address: 556 Morris Ave

institute: Bristol Myers Squibb

description: Library name: 7357-CH-0099

data_processing:
We used featureCounts 2.0.6 to count the number of reads on gene level.
Assembly: GRCh38
Supplementary files format and content: readcount on gene level

source_name: cell line

extract_protocol:
Cells for RNAseq were prepared according to instructions from Discovery Life Sciences.
Five million cells per sample were collected, washed, fixed, and stored at -80 C prior to shipping to Discovery Life Sciences where downstream RNAseq was carried out.

value: cell line

tag: treatment

tag: batch


title: MW26

city: Little Rock

first: ryan

last: allen

state: Arkansas

address: 4301 W. Markham St

department: Physiology and Cell Biology

institute: University of Arkansas for Medical Sciences

description:
Library name: MW26_S26_L001_R1_001.fastq.gz
DMW_24

data_processing:
Bioinformatic processing was performed using the TIGER data analysis pipeline (v20220205), previously described in Allen and Zhao et al. 2018 (Journal of Extracellular Vesicles).
Cutadapt v4.5
Alignment with Bowtie1
spcount (https://github.com/shengqh/spcount)
Assembly: GENCODE GRCm38.p6
Supplementary files format and content: .txt files are all normalized by reads per million (RPM) of total reads

source_name: Biofluid

growth_protocol: Mice were transduced with AAV-GFP or AAV-PCSK9-D377Y and fed a chow-diet or western-diet, respectively, for 14 weeks.

extract_protocol:
Plasma was fractionated by size exclusion chromatography on two Superose-6 Increase columns in tandem. Fractions corresponding with APOB were pooled concentrated by ultrafiltration to ~100 uL. Total RNA was then extracted using Trizol LS and purified with Zymo RNA Clean and Concentrate spin columns.
Approximately 15% of the extracted total RNA was aliquoted for small RNA sequencing using the randomized splint ligation method previously developed by New England Biolabs, Inc54. Briefly, 7 microliters of isolated RNA were ligated to 0.25 pmol of annealed 3’ splint adapter using 200 units of T4 RNA Ligase, truncated KQ (New England Biolabs). The ligation reaction was then treated with 2.5U of lambda exonuclease (New England Biolabs) and 25U of 5’ deadenylase (New England Biolabs), followed by 5U of Uracil-DNA Glycosylase (New England Biolabs) and 20U of Endonuclease IV (New England Biolabs). Ligation of 0.5 pmol of 5’ splinted adapter was performed using 20U of truncated T4 RNA Ligase 2 (New England Biolabs). Reverse transcription of adapter-ligated RNA was performed using Protoscript II (New England Biolabs), and cDNA were purified using CleanNGS DNA Cleanup Magnetic Beads (Bulldog Bio) according to manufacturer instructions. Individual libraries were then amplified by PCR using NEB Next 2X High-Fidelity PCR Master mix (New England Biolabs). Following PCR amplification, individual libraries were size-selected (136-196 bp product) using pre-cast 3% agarose gel cassettes with a Pippin Prep (Sage Sciences) and quantified on a Qubit 4 Fluorometer (Invitrogen) with the Qubit 1X dsDNA HS Assay (Invitrogen).

treatment_protocol: Mice received a surgical unicortical defect in the right femur that was inoculated with PBS (Sham) or 1x10^6 CFU of USA300 LAC methicillin-resistant Staphylococcus aureus (MRSA)

value: Biofluid

value: LDL

value: lipoprotein

value: AAV-PCSK9/Western Diet

value: MRSA


title: HEK293T pSG5-miR-133b 2


title: SUDHL4 - BMS158_1.25 - D1 - rep2

description: Library name: 7357-CH-0098


title: HEK293T pSG5-miR-873 2


title: H3K27ac_olig2_SgshKO_8mo_rep1

description: ChIP-seq


title: MW25

description:
Library name: MW25_S25_L001_R1_001.fastq.gz
DMW_23


title: SUDHL4 - BMS158_1.25 - D1 - rep1

description: Library name: 7357-CH-0097


title: H3K27ac_olig2_WT_8mo_rep2

description: ChIP-seq

value: WT


title: SW24

description:
Library name: SW24_S24_L001_R1_001.fastq.gz
CSW_22

value: Sham


title: HEK293T pSG5-miR-873 1


title: H3K27ac_olig2_WT_8mo_rep1

description: ChIP-seq


title: SUDHL4 - DMSO - D1 - rep3

description: Library name: 7357-CH-0096

value: DMSO


title: SW23

description:
Library name: SW23_S23_L001_R1_001.fastq.gz
CSW_21


title: HEK293T pSG5-miR-133b 1


title: SUDHL4 - DMSO - D1 - rep2

description: Library name: 7357-CH-0095


title: H3K27ac_neun_WTSgshKO_8mo_input

description: ChIP-seq

value: NeuN+ nuclei


title: HEK293T pSG5-miR-129 1


title: SW22

description:
Library name: SW22_S22_L001_R1_001.fastq.gz
CSW_20


title: SUDHL4 - DMSO - D1 - rep1

description: Library name: 7357-CH-0094


title: H3K27ac_neun_SgshKO_8mo_rep2

description: ChIP-seq


title: SW21

description:
Library name: SW21_S21_L001_R1_001.fastq.gz
CSW_19


title: HEK293T pSG5-miR-34a 1


title: ChIP_INPUT-dTAG-43

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: Library name: ChIP_INPUT-dTAG-43

data_processing:
ChIP-seq samples normalized by spike-in were mapped against a synthetic genome constituted by the human and the fruit fly chromosomes (hg38 + dm3) using Bowtie (PubMed ID 19261174) with the option -m 1 to discard reads that did not map uniquely to one region.
Peak detection was performed with MACS (PubMed ID 18798982). ChIP-seq profiles were produced with SeqCode (PubMed ID 34599234): samples with spike-in were normalized by the total number of reads mapped on the fruit fly.
Assembly: hg38
Supplementary files format and content: Genome-wide profiles in Bedgraph format
Supplementary files format and content: Peaks in BED format

extract_protocol:
Cells were crosslinked in 1% formaldehyde for Pol II ChIPs. For TANGO6-Flag ChIPs a double-crosslinking was used, first with ChIP Crosslink Gold (Diagenode, C01019027) followed by the regular formaldehyde crosslinking. For chromatin preparation cell pellets were incubated in Swelling buffer [25 mM HEPES-KOH pH 7.9; 1.5 mM MgCl2; 10 mM KCl; 0.1% NP-40], centrifuged to recover the nuclei. Nuclei pellets were lysed in sonication buffer [50 mM HEPES-KOH pH 7.9; 140 mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% Na-deoxycholate; 0.1% SDS] and sonicated to generate 100-500 bp chromatin fragment. ChIP experiments were performed by incubating ON the chromatin plus the specific antibodies in sonication buffer, followed by immunoprecipitation using Dynabeads protein A/G. After successive washes, ChIPed chromatin was eluted from the beads, de-crosslinked and DNA was purified.
Libraries were prepared according to Illumina instructions.

tag: antibody


title: H3K27ac_neun_SgshKO_8mo_rep1

description: ChIP-seq


title: SW20

description:
Library name: SW20_S20_L001_R1_001.fastq.gz
CSW_18


title: HEK293T pSG5-miR-7 1


title: ChIP_INPUT-DMSO-43

description: Library name: ChIP_INPUT-DMSO-43


title: H3K27ac_neun_WT_8mo_rep2

description: ChIP-seq


title: SW19

description:
Library name: SW19_S19_L001_R1_001.fastq.gz
CSW_17


title: ChIP_INPUT-dTAG-37

description: Library name: ChIP_INPUT-dTAG-37


title: H3K27ac_neun_WT_8mo_rep1

description: ChIP-seq


title: SW18

description:
Library name: SW18_S18_L001_R1_001.fastq.gz
CSW_16


title: HEK293T pSG5 1


title: 293T 48h pSG5-miR-7 1µg 3


title: 4 hr sporulation media, gim3∆ cells

city: Berkeley

first: Naohiro

last: Kuwayama

address: 628 Barker Hall

institute: UC Berkeley

description:
Library name: Sample 2
4 hr sporulation media, gim3∆ cells, footprints

library_source: other

data_processing:
Adaptor sequences were trimmed with fastx_clipper, and reads aligning to rRNA were removed with bowtie2 (Langmead and Salzberg, 2012)
Remaining reads were aligned to the Saccharomyces cerevisiae SK1 reference genome using STAR (Dobin et al., 2013)
Only uniquely mapping reads (MAPQ ≥ 50) were retained, followed by sorting and indexing with samtools (Li et al., 2009).
Read periodicity and A-site offsets were determined with fp-framing, and gene-level ribosome occupancy was quantified using fp-count. Strand-specific wiggle files were generated with wiggle-track for downstream visualization. Visualization was performed using Integrative Genomics Viewer (Robinson, 2011).
Assembly: sk1_revised_100331 (fasta and gtf files published in Brar et. al, Science, 2012)
Supplementary files format and content: Processed data include an Excel (.xlsx) file containing gene-level RPKM values and wiggle (.wig) files generated for visualization of ribosome profiling signals.
Library strategy: Ribo-Seq

molecule: other

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Vegetative: Strains were grown in YEPD(2%) at 30C, with shaking. Meiotic: Strains were grown in YEPD(2%) at 22C for 24 hours, then BYTA for 16 hours, then cells were washed one time with water and resuspended in sporulation media.

extract_protocol:
Cells were flash frozen and mixermilled at -80 together with ribosome profiling lysis buffer, extract was clarified with a low and high speed spin, all as described in Ingolia et. al, Science, 2009.
Ribosome profiling was performed as in (Hollerer et al., 2021; Powers and Brar, 2021)

value: Saccharomyces cerevisiae

value: gim3 deletion


title: ChIP_INPUT-DMSO-37

description: Library name: ChIP_INPUT-DMSO-37


title: 293T 48h pSG5-miR-7 1µg 2

value: Female


title: SW17

description:
Library name: SW17_S17_L001_R1_001.fastq.gz
CSW_15


title: 4 hr sporulation media, WT cells

description:
Library name: Sample 1
4 hr sporulation media, WT cells, footprints


title: MC16

description:
Library name: MC16_S16_L001_R1_001.fastq.gz
BMC_14

value: AAV-GFP/Chow Diet


title: ChIP_RPB1-dTAG-43

description: Library name: ChIP_RPB1-dTAG-43

value: anti-Rpb1 NTD (D8L4Y) Rabbit mAb, Cell Signaling #14958


title: 293T 48h pSG5-miR-7 1µg 1

value: 48 hr


title: ChIP_RPB1-DMSO-43

description: Library name: ChIP_RPB1-DMSO-43


title: mTSC, Trpv2 KO_chir_3

city: Leuven

first: Katrien

last: De Clercq

address: Herestraat 49, box 611

country: Belgium

institute: KU Leuven

description: Library name: S128

data_processing:
Reads were aligned against the mouse GENCODE gene set release M27 (tissues) or M28 (Cells)  using the STAR aligner (v2.7.10b) and gene and isoform expression levels were estimated using the RSEM (v1.3.1) software package (tissues) or Salmon (v1.10.3) package (cells)
Assembly: GENCODE M27 (GRCm39) (tissues) or GENCODE M28 (GRCm39) (cells)
Supplementary files format and content: Sxxx.genes.results: RSEM 1.3.1 output file; tab-delimited expression estimates (expected count, TPM, FPKM)
Supplementary files format and content: Sxxx.quant.sf: SALMON 1.10.3 quantification output file; tab-delimited expression estimates (TPM, number of reads)

source_name: placenta

extract_protocol:
Cells: RNeasy mini kit, Tissues: TriPure Isolation Reagent
cells: Illumina Stranded mRNA prep; Tissues: Illumina Trueq Stranded mRNA prep

value: placenta

tag: group

value: mTSC

value: mouse trophoblast stem cells

value: KO

value: CHIR differentiation


title: MC15

description:
Library name: MC15_S15_L001_R1_001.fastq.gz
BMC_13

value: Biofluid

value: LDL

value: lipoprotein


title: ChIP_RPB1-dTAG-37

description: Library name: ChIP_RPB1-dTAG-37


title: MC13

description:
Library name: MC13_S13_L001_R1_001.fastq.gz
BMC_12

value: MRSA


title: mTSC, Trpv2 KO_chir_2

description: Library name: S123


title: ChIP_RPB1-DMSO-37

description: Library name: ChIP_RPB1-DMSO-37


title: mTSC, Trpv2 KO_chir_1

description: Library name: S118


title: MC12

description:
Library name: MC12_S12_L001_R1_001.fastq.gz
BMC_11


title: 293T 48h pSG5-miR-7 0.5µg 2


title: 293T 48h pSG5-miR-7 0.5µg 1


title: ChIP_Ser5P_siT6

description: Library name: ChIP_Ser5P_siT6

value: RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody, abcam, ab5131


title: 293T 48h pSG5-miR-7 0.5µg 3


title: mTSC, Scrambled_chir_3

description: Library name: S108

value: Scrambled


title: MC11

description:
Library name: MC11_S11_L001_R1_001.fastq.gz
BMC_10


title: CRISPR KO non-targeting  guide control, replicate 2

city: Gent

first: Igor

last: Fijalkowski

address: Sint-Pietersnieuwstraat 33

institute: Ugent

description: Library name: shRNA_CTR_Rep2

data_processing:
Sequencing data was mapped to the reference genome (GRCh38.105 assembly) using STAR (version STAR/2.7.11b)
Differential expression analysis was performed with DESeq2 (version 1.42.1)
Assembly: GRCh38.105 assembly
Supplementary files format and content: Tab-separated file of raw read counts per gene as outputed by feature count function of STAR.

molecule: polyA RNA

source_name: Blood

extract_protocol:
RNA was extracted from 5M JURKAT cells according to the manufacturer's protocol of the RNeasy kit (QIAGEN)
For RNA-seq library construction of total RNA obtained from transduced JURKAT cell line, the Watchmaker total mRNA library preparation kit (7BK0001-096, Watchmaker Genomics, Boulder, CO, USA) was used following the manufacturer’s protocol.

value: Blood

value: JURKAT

value: T-ALL

value: CRISPR KO non-targeting  guide control


title: ChIP_Ser5P_siCT

description: Library name: ChIP_Ser5P_siCT


title: MC10

description:
Library name: MC10_S10_L001_R1_001.fastq.gz
BMC_9

value: AAV-GFP/Chow Diet


title: mTSC, Scrambled_6

description: Library name: S103

value: TSC


title: CRISPR KO non-targeting  guide control, replicate 1

description: Library name: shRNA_CTR_Rep1


title: ChIP_Ser2P_siT6

description: Library name: ChIP_Ser2P_siT6

value: Phospho-Rpb1 CTD (Ser2) Cell Signaling #13499


title: mTSC, Scrambled_chir_2

description: Library name: S101

value: placenta

value: mTSC


title: CRISPR KO of KSR2, guide 2, replicate 3

description: Library name: KSR_KO2_Rep3

value: CRISPR KO of KSR2, guide 2


title: MC9

description:
Library name: MC9_S9_L001_R1_001.fastq.gz
BMC_8


title: mTSC, Scrambled_5

description: Library name: S96

value: mouse trophoblast stem cells


title: ChIP_Ser2P_siCT

description: Library name: ChIP_Ser2P_siCT


title: SC7

description:
Library name: SC7_S7_L001_R1_001.fastq.gz
ASC_7

value: Biofluid

value: Sham


title: CRISPR KO of KSR2, guide 2, replicate 2

description: Library name: KSR_KO2_Rep2


title: INPUTforsiT6

description: Library name: INPUTforsiT6

data_processing:
ChIP-seq samples were mapped against the hg38 human genome assembly using Bowtie (PubMed ID 19261174) with the option -m 1 to discard those reads that could not be uniquely mapped to just one region. ChIP-seq samples normalized by spike-in were mapped against a synthetic genome constituted by the human and the fruit fly chromosomes (hg38 + dm3) using Bowtie (PubMed ID 19261174) with the option -m 1 to discard reads that did not map uniquely to one region.
Peak detection was performed with MACS (PubMed ID 18798982). ChIP-seq profiles were produced with SeqCode (PubMed ID 34599234): samples without spike-in were normalized by the total number of reads mapped on human; samples with spike-in were normalized by the total number of reads mapped on the fruit fly.
Assembly: hg38
Supplementary files format and content: Genome-wide profiles in BedGraph format
Supplementary files format and content: Peaks in BED format

extract_protocol:
ChIP experiments were carried out adapting with modifications a standard protocol in the lab (PubMed ID 34473698)
Libraries were prepared according to Illumina instructions.

value: KD


title: mTSC, Scrambled_chir_1

description: Library name: S94

value: CHIR differentiation


title: CRISPR KO of KSR2, guide 2, replicate 1

description: Library name: KSR_KO2_Rep1


title: INPUTforsiCt

description: Library name: INPUTforsiCt

value: CT


title: mTSC, Scrambled_4

description: Library name: S91

value: Scrambled


title: SC5

description:
Library name: SC5_S5_L001_R1_001.fastq.gz
ASC_5

value: LDL

value: lipoprotein


title: CRISPR KO of KSR2, guide 1, replicate 3

description: Library name: KSR_KO1_Rep3

value: Blood

value: JURKAT

value: T-ALL

value: CRISPR KO of KSR2, guide 1


title: SC6

description:
Library name: SC6_S6_L001_R1_001.fastq.gz
ASC_6

value: AAV-GFP/Chow Diet


title: RPB2_siT6

description: Library name: RPB2_siT6


title: mTSC, Scrambled_diff_3

description: Library name: S57

value: placenta

value: standard differentiation


title: SC4

description:
Library name: SC4_S4_L001_R1_001.fastq.gz
ASC_4


title: SUDHL4 - BMS158_2.5 - D2 - rep1

description: Library name: 7357-CH-0160

value: cell line


title: RPB2_siCt

description: Library name: RPB2_siCt


title: mTSC, Scrambled_3

description: Library name: S56

value: mTSC

value: mouse trophoblast stem cells

value: TSC


title: CRISPR KO of KSR2, guide 1, replicate 1

description: Library name: KSR_KO1_Rep1


title: RPB1-NTD_siT6

description: Library name: RPB1-NTD_siT6

value: KD

value: anti-Rpb1 NTD (D8L4Y) Rabbit mAb, Cell Signaling #14958


title: KSRi KSR2 inhibition, replicate 3

description: Library name: KSRi_Rep3

value: KSRi (APS-2-79)


title: SC2

description:
Library name: SC2_S2_L001_R1_001.fastq.gz
ASC_2

value: Biofluid

value: Sham


title: mTSC, Scrambled_diff_2

description: Library name: S55

value: Scrambled


title: RPB1-NTD_siCt

description: Library name: RPB1-NTD_siCt

value: CT


title: mTSC, Scrambled_2

description: Library name: S54


title: KSRi KSR2 inhibition, replicate 2

description: Library name: KSRi_Rep2

value: Blood

value: JURKAT


title: SC1

description:
Library name: SC1_S1_L001_R1_001.fastq.gz
ASC_1

value: LDL

value: lipoprotein


title: INPUTforTANGO6_43

description: Library name: INPUTforTANGO6_43


title: KPB25Luv_aCD19_CD40ag_7Day_Mouse_Tumor_scRNAseq

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files were processed through 10x Genomics Cell Ranger pipeline version 6.1.1
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Tumor

extract_protocol:
Whole mammary tumors were extracted from the mouse and placed into ice cold PBS. The tumors were then cut into 2mm pieces and then placed into digestion buffer provided by Miltenyi's mouse tumor dissasociating kit. The tumor tissue was then incubated on a Miltenyi's octo dissascoiater to obtain a single cell suspension of the tumor tissue. The resulting suspension is then centrifuged at 300xG for 5 minutes. Supernatent was then removed and cells were resuspended in RPMI. Cells were then strained through a 70um cell strainer. Cells were then centrifuged at 300xG for 5 minutes. Supernatant were then removed and cells resupended in suspension buffer (PBS, 2% FBS).
Library was constructed according to 10x Genomics protocol from their single cell 5' v2 kit.

value: Tumor

value: Cancer Cell Line

value: Brca 1 Null/ P53 Null


title: mTSC, Scrambled_diff_1

description: Library name: S53

value: placenta

value: mTSC

value: standard differentiation


title: KSRi KSR2 inhibition, replicate 1

description: Library name: KSRi_Rep1

value: T-ALL


title: mTSC, Scrambled_1

description: Library name: S52

value: mouse trophoblast stem cells

value: TSC


title: INPUTforTANGO6_37

description: Library name: INPUTforTANGO6_37


title: KPB25luv Nontreated TDLN M422

data_processing:
To quantify virus count, we processed the raw sequencing reads with the following two main steps. Step1: raw sequenced reads were quality-tested using FASTQC (v0.11.8) and mapped to the mm10 mouse genome using the STAR aligner (v2.5.3a) with parameters “--outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM Unsorted --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outSAMstrandField intronMotif --outFilterMultimapNmax 1080”. The transcriptome bam files were then sorted by read name, following raw gene count quantification using Salmon “quant” command with default parameters. Step 2: The unmapped reads to mm10 genome were remapped to our custom constructed virus genome using STAR with parameters “--outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNmax 4 --outFilterMultimapNmax 52 --quantMode GeneCounts”. The virus read counts were summarized with custom java script
Assembly: mm10
Supplementary files format and content: viral_counts.tsv
Supplementary files format and content: salmon_tpm.tsv
Supplementary files format and content: salmon_counts.tsv

source_name: Lyhmph Node

extract_protocol:
Whole mammary tumors and draining lymphnodes were extracted from the mice and flash frozened in liquid N2. Frozen tissues were then placed in Trizol and mechanically disrubted until homogenized. Once homogenized chloroform was added and the solution was spun to create a phase seperation gradient. The aqueous phase was then extracted and subsequently ran through the RNeasy mini kit protocol by Qiagen in order to isolate total RNA from animal tissues.
RNA libraries for RNA-seq was prepared by using TruSeq Stranded mRNA Library Prep kit and following manufacturer protocols

value: Lyhmph Node

value: Cancer Cell

value: Nontreated


title: ChIP_FLAG-TANGO6_43

description: Library name: ChIP_FLAG-TANGO6_43

value: CT

value: Anti-FLAG M2 Mouse mAb, Sigma #F1804


title: DMSO, control, replicate 3

description: Library name: DMSO_Rep3

value: Blood

value: JURKAT

value: DMSO


title: mTSC, Trpv2 KO_diff_3

description: Library name: S51

value: KO


title: DMSO, control, replicate 2

description: Library name: DMSO_Rep2


title: KPB25luv Nontreated TDLN M420


title: ChIP_FLAG-TANGO6_37

description: Library name: ChIP_FLAG-TANGO6_37


title: KPB25luv Nontreated TDLN M418


title: mTSC, Trpv2 KO_diff_2

description: Library name: S49


title: DMSO, control, replicate 1

description: Library name: DMSO_Rep1


title: T11 Apobec CD40ag Tumor 102519 32L

description: 200302_UNC18-D00493_0645_ACE7MTANXX_GGTACCTT-AAGACGTC_S4_L002_R1

value: Tumor

value: T11 Apobec

value: P53 Null

value: CD40 Agonist


title: RNA_KD_R3_6101

data_processing:
The RNA-seq samples were mapped against the hg38 mouse genome assembly using TopHat(Trapnell et al., 2009) with the option –g 1 to discard those reads that could not be uniquely mapped in just one region.
DESeq2(Love et al., 2014) was run to quantify the expression of every annotated transcript using the RefSeq(O’Leary et al., 2016) catalogue of exons and to identify each set of differentially expressed genes.
Assembly: hg38
Supplementary files format and content: RPKMs calculated by DESeq2 (columns ordered by samples CTR1,CTR2,CTR3,KD1,KD2,KD3

extract_protocol:
RNA extraction was performed using the RNeasy kit (Qiagen, 74134) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina instructions.

value: KD


title: mTSC, Trpv2 KO_diff_1

description: Library name: S47

value: placenta

value: mTSC

value: standard differentiation


title: RNA_KD_R2_6100


title: KPB25luv Nontreated TDLN M408

value: Lyhmph Node

value: Brca 1 Null/ P53 Null


title: 3D7 PfDBSP ChIP DNA

city: Pune

first: Devatrisha

last: Purkayastha

state: Maharashtra

address: Dr Homi Bhabha Road, Pashan,

country: India

institute: Indian Institute of Science Education and Research

description: Library name: PfDBSP (ChIP)

data_processing:
The files were demultiplexed using bcl2fastq.
Trimming and quality control (QC) of the raw data was done using Trim Galore.
The trimmed data was aligned against the P. falciparum reference genome (PlasmoDB_v66, retrieved from plasmodb.org ) using Bowtie2.
The aligned files were sorted using samtools which gave bam output files. The peaks were called using MACS2, using the input files as control.
The normalized bedgraph files were loaded on IGV (Integrative Genomes Browser) to visualize the enrichment pattern. For the mean tag density and gene body profile seqMINER was used.
Assembly: PlasmoDB_v66
Supplementary files format and content: PfDBSP_inputnormalized.bdg

organism: Plasmodium falciparum

growth_protocol: Plasmodium falciparum 3D7 strain was cultured in O+ erythrocytes and RPMI-1640 media supplemented with 0.5% Albumax II, and 40mg/L hypoxanthine  under mixed gas conditions (5% CO2, 5% O2, 90% N2) at 37 °C. Parasite was maintained at 4% hematocrit and synchronised at ring stage by treatment with 5% sorbitol.

extract_protocol:
Cells were crosslinked with 1% formaldehyde and quenched with 2mM Glycine. The samples were lysed, chromatin was sheared by sonication, and pulled down using respective antibodies.
The sequencing library was prepared using the NEB Ultra II DNA kit (E7645), following the manufacturer's instructions. The prepared library was estimated for the average size using Agilent bioanalyzer or tapestation and for the amount using Qubit fluorometer. A final amount of 1.3 pM library was loaded from the multiplexed pool of all libraries.

value: Plasmodium falciparum

value: anti-PfDBSP

tag: Stage

value: mid trophozoite (30-34 hrs)


title: KPB25luv CD40ag TDLN M411

value: Cancer Cell


title: T11 Apobec CD40ag Tumor 102519 46B

description: 200302_UNC18-D00493_0645_ACE7MTANXX_TGCGGCGT-CCTCGGTA_S8_L003_R1


title: RNA_KD_R1_6099


title: Input DNA

description: Library name: PfDBSP (Input)


title: KPB25luv CD40ag TDLN M407


title: T11 Apobec CD40ag Tumor 102519 43R

description: 200302_UNC18-D00493_0645_ACE7MTANXX_ATGAGGCC-GTTAATTG_S7_L002_R1


title: SC3

description:
Library name: SC3_S3_L001_R1_001.fastq.gz
ASC_3

value: Biofluid

value: LDL

value: lipoprotein

value: AAV-GFP/Chow Diet

value: Sham


title: RNA_CTR_R3_6098

value: CTR


title: KPB25luv CD40ag TDLN M406

value: CD40 Agonist


title: RNA_CTR_R2_6097


title: T11 Apobec CD40ag Tumor 102519 45N

description: 200302_UNC18-D00493_0645_ACE7MTANXX_GCAGAATT-ACCGGCCA_S6_L002_R1

value: Tumor

value: T11 Apobec

value: P53 Null


title: HepG2 cell,sh-NSUN6

city: Hefei

first: Fan

last: Wenhu

address: 81 Meishan Road, Hefei, Anhui 230032, China

country: China

institute: Anhui Medical University

description: Library name: Sample2

data_processing:
The reduced RNA were used as input for RNA sequencing library preparation utilizing some components of the KCTM Digital mRNA Library Prep Kit (Seqhealth Tech. Co., Ltd., Wuhan, China), according to the manufacturer’s instructions. The kit eliminates duplication bias and errors in PCR and sequencing steps, by using unique molecular identifier (UID) of 12 random bases to label the cDNA molecules. The library PCR products corresponding to fragments ranging from 200 to 500 base pairs were enriched and sequenced on a DNBSEQ-T7 (MGI) with PE150 mode.
Assembly: Compare methylation levels between KD and Ctrl samples to identify NSUN6-dependent M5c sites.
Supplementary files format and content: xlsx file including gene and methylation levels

source_name: HepG2 cell

growth_protocol: Culture KD and Ctrl HepG2 stable cell lines in DMEM with 10% FBS at 37°C and 5% CO₂ until approximately 80% confluency.

extract_protocol:
Total RNA was isolated from the specified biological materials using TRIzol Reagent (Thermo Scientific, cat. #15596026) following the manufacturer's recommended protocol. Subsequent to RNA extraction, genomic DNA was removed by treating the samples with DNase I (NEB, cat. #M0303L) to eliminate potential DNA contamination. The purity of the extracted RNA was assessed by measuring the A260/A280 ratio using a Nanodrop TM OneC spectrophotometer (Thermo Scientific). The integrity of the RNA was verified using the LabChip GX Touch system (Revvity). The concentration of the qualified RNA was then determined using a Qubit 3.0 fluorometer with the QubitTM RNA Broad Range Assay kit (Thermo Scientific, #Q10210)  Polyadenylated RNA enrichment was conducted using VAHTS mRNA Capture Beads (Vazyme, China, cat. #N401) from the total RNA, following the manufacturer's prescribed protocol. The polyA+RNA was chemically fragmented into approximately 200-nucleotide-long fragments by treatment with 20 mM ZnCl2 at 95℃ for 5-7 minutes. Bisulfite treatment was performed using the EZ RNA Methylation™ Kit (Zymo Research, cat. #R5002) after a certain proportion of negative control(human 28S rRNA) were added.
Reverse transcribe bisulfite-treated RNA into cDNA using random primers.Amplify cDNA and add sequencing adapters to prepare libraries.

treatment_protocol: Clone NSUN6 shRNA into pLKO.1-puro vector.Transfect HEK293T with shRNA, psPAX2, and pMD2.G plasmids using Lipofectamine 2000.Collect lentivirus at 48-72h, filter, and infect HepG2 cells with polybrene.

value: HepG2 cell

value: Liver cancer cells

value: NSUN6 knock down


title: HepG2 cell,sh-NC,

description: Library name: Sample1

value: WT


title: KPB25luv CD40ag TDLN M405

value: Lyhmph Node

value: Brca 1 Null/ P53 Null


title: RNA_CTR_R1_6096


title: Act34-Swab1

status: Public on Aug 12 2026

city: Chicago

first: Jason

middle: M

last: Wood

state: IL

address: 900 S Ashland Ave rm 1057

department: Research Informatics Core

institute: University of Illinois at Chicago

description: Library name: UW360A

data_processing:
A custom FASTA database was generated containing all of the coding sequences (CDS) from reference genome GAS ATCC 12344 and CDS from HG316453.2, NC_002737.2, NC_006086.1, NC_007296.2, NC_008021.1, NC_008022.1, and NC_008024.1 that could not be found in the ATCC strain using BWA MEM v0.7.17 (49). Raw RNA-seq reads were aligned to this custom database using BWA MEM. The expression level of gene features (CDS regions from the reference) were quantitated using FeatureCounts v2.0.3 (55) as raw read counts of the stranded libraries. Differential analysis of quantitated gene features as compared with treatment (acute vs carrier) or sampling method (liquid vs swab) was performed using the software package edgeR (56, 57) on raw sequence counts. Prior to analysis, the data were filtered to remove any features that had less than 5 total counts summed across all samples. Data were normalized as counts per million and an additional normalization factor was computed using the trimmed mean of M-values (TMM) algorithm. Statistical tests were performed using the “exactTest” function in edgeR. Adjusted p-values (q-values) were calculated using the Benjamini-Hochberg false discovery rate (FDR) correction. Significant gene features were determined based on an FDR threshold of 0.05 (5%).
Assembly: Custom database, see above.
Supplementary files format and content: Tab delimited text file containing the counts for each gene (CDS) in the custom reference database for each sample.

molecule: cytoplasmic RNA

organism: Streptococcus pyogenes

source_name: Oropharyngeal swab

growth_protocol: For liquid samples, overnight cultures of GAS strains were grown in THY medium. In the morning, cultures were diluted 1:10 in fresh THY medium and grown at 37 °C static until the OD600 reached 0.4-0.6. Cells were then spun down and resuspended in 500 µL DNA/RNA Shield (Zymo) before storage at -80 °C until extraction. Swab samples were processed directly from -80C flash frozen swabs.

extract_protocol:
For liquid samples, pellets were resuspended in 200 µL lysis solution (TRIzol Max Bacterial Enhancement Reagent (ThermoFisher 16122012) which had been pre-heated to 95 °C mixed with 1 mg/mL lysozyme and 50 U/mL mutanolysin) and moved to a MagMAX prime bead beating tube (ThermoFisher A58155). For swabs, 500 µL DNA/RNA Shield was added to frozen swabs and then vortexed for 30-60 seconds. The tubes containing the swabs were then sonicated in a sonicator bath for 5 minutes to help with removing adherent cells. Following sonication, swabs were again vortexed for 30-60 seconds  and then the tubes were spun down for 5 minutes at 4 °C. The supernatant and swab were removed and the resulting pellet resuspended in 200 µL lysis solution and moved to MagMAX bead beating tubes as above. All samples were placed in an OMNI Bead Ruptor 12 (Omni International, 19-050A) and beat twice for 4 minutes each with a 30 second break in between. The mixtures were then incubated at 37 °C for 30 minutes to allow additional enzymatic lysis and then incubated at 95 °C for 5 minutes. RNA was then collected using the TRIzol Max Bacterial RNA Isolation kit (ThermoFisher 16096-040) per manufacturer’s instructions including the phase separation and RNA precipitation steps. RNA pellets were air dried and resuspended in 45 µL DEPC-treated water. The Turbo DNA-free kit (ThermoFisher AM1907) was used per manufacturer’s instructions to remove any remaining DNA in the sample. The final RNA quantity and quality were measured on a NanoDrop One. Depletion of eurkaryotic RNA was done on the RNA from the swab samples using the MICROEnrich kit (ThermoFisher AM1901) per manufacturer’s instructions. The final precipitation step was skipped and the samples were taken immediately into the MICROBExpress kit protocol (ThermoFisher AM1905) per manufacturer’s instructions to remove bacterial rRNA. For liquid cultures, bacterial rRNA was removed using the same MICROBExpress kit using 2-10 µg starting RNA in 15 µL or less volume.
RNA-seq libraries for samples sequenced on the Novaseq X: Libraries were prepared in house using the NEB Next Ultra II Directional RNA library prep kit (NEB E7765) per the manufacturer’s protocol for purified mRNA. mRNA input amounts ranged from 1-100 ng total. Briefly, rRNA depleted RNA in was first fragmented at 94°C for 10 minutes with random primers. First and then second strand cDNA was synthesized, followed by cDNA purification using SPRIselect beads. Ends were prepped and NEBNext adaptors were ligated to cDNA strands. Samples were again purified using SPRIselect beads, followed by PCR enrichment of adaptor ligated DNA using unique indexed forward and reverse primers. Samples were purified once more using SPRIselect beads, and library quality was analyzed using a NanoDrop, Qubit and Tapestation.  RNA-seq libraries for samples sequenced on the HiSeq 2500 were prepared in house using the Kapa Stranded RNASeq Library Preparation kit (KK8400) per manufacturers instructions for purified mRNA with input range of 10-100 ng total. RNA was fragmented at 94°C for 6 minutes with random primers. Illumina adapters were ligated and library quality analyzed using NanoDrop, Qubit, and Tapestation.

value: Oropharyngeal swab


title: Act31-Swab1

description: Library name: UW273A


title: T11 Apobec CD40ag Tumor 102519 36B

description: 200302_UNC18-D00493_0645_ACE7MTANXX_AACGTTCC-GGAGTACT_S5_L002_R1

value: Cancer Cell


title: Act6-Swab1

description: Library name: UW232


title: Car4-Swab3

description: Library name: UW265H


title: Car5-Swab3

description: Library name: UW267H


title: Car3-Swab3

description: Library name: UW255H


title: Car5-Swab1

description: Library name: UW267A


title: Car4-Swab1

description: Library name: UW265A


title: db/db+renin+VEFB1 Rep5, 2 weeks

city: St. Louis

first: Haojia

last: Wu

state: MO

address: 4523 Clayton Ave, MSB Rm 820

institute: Washington University in St Louis

description:
Library name: F3059
10X Genomics

data_processing:
Illumina data were demultiplexed and the resulting fastq files were processed by the 10X Genomics cellranger pipeline (version 6.0.1). Reads were mapped to mouse genome mm10. Both exonic and intronic reads were incorporated in the final molecule counts.
Assembly: mm10
Supplementary files format and content: The hdf5 files contain the count matrix generated by CellRanger for each sample.

molecule: nuclear RNA

source_name: Kidney

extract_protocol:
Single nucleus were isolated using a protocol developed from our lab (dx.doi.org/10.17504/protocols.io.nahdab6).
Single nucleus suspensions at a concentration of 1000 nuclei/ul were loaded into the Chromium Controller as per manufacturer instructions, which target 10,000 nuclei per sample. 12 PCR cycles were used for cDNA synthesis. Each library was sequenced using an Illumina NovaSeq instrument, 8 samples per S4 lane, with one 150 bp read located near the 3′ end of the mRNA.

treatment_protocol: Mice were received isotype control and VGFB1 (3 or 10 mg/kg, SC). Terminal samples were collected 48 hours and 2 weeks after treatment inception

value: female

value: Kidney

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

tag: treatment timepoint

value: 2 weeks


title: db/db+renin+VEFB1 Rep4, 2 weeks

description:
Library name: E3058
10X Genomics


title: db/db+renin+VEFB1 Rep3, 2 weeks

description:
Library name: O3057
10X Genomics


title: db/db+renin+VEFB1 Rep2, 2 weeks

description:
Library name: N3056
10X Genomics


title: db/db+renin+VEFB1 Rep1, 2 weeks

description:
Library name: D3055
10X Genomics


title: db/db+renin+VEFB1 Rep5, 2 days

description:
Library name: F3054
10X Genomics

value: 2 days


title: db/db+renin+VEFB1 Rep3, 2 days

description:
Library name: H3052
10X Genomics


title: db/db+renin+VEFB1 Rep4, 2 days

description:
Library name: E3053
10X Genomics


title: db/db+renin+VEFB1 Rep1, 2 days

description:
Library name: C3050
10X Genomics


title: db/db+renin+VEFB1 Rep2, 2 days

description:
Library name: G3051
10X Genomics


title: db/db+renin+Mscb20 Rep3, 2 weeks

description:
Library name: M3047
10X Genomics


title: db/db+renin+Mscb20 Rep4, 2 weeks

description:
Library name: C3048
10X Genomics


title: db/db+renin+Mscb20 Rep2, 2 weeks

description:
Library name: L3046
10X Genomics


title: db/db+renin+Mscb20 Rep5, 2 weeks

description:
Library name: D3049
10X Genomics


title: db/db+renin+Mscb20 Rep1, 2 weeks

description:
Library name: C3045
10X Genomics


title: db/db+renin+Mscb20 Rep5, 2 days

description:
Library name: D3044
10X Genomics


title: db/db+renin+Mscb20 Rep4, 2 days

description:
Library name: C3043
10X Genomics


title: db/db+renin+Mscb20 Rep3, 2 days

description:
Library name: F3042
10X Genomics


title: db/db+renin+Mscb20 Rep2, 2 days

description:
Library name: E3041
10X Genomics


title: db/db+renin+Mscb20 Rep1, 2 days

description:
Library name: J3040
10X Genomics


title: Lung tissue from PBS-treated mouse, single-cell RNA-seq

city: Chengdu

first: Zhnag

last: Xinyue

address: No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan 610041, PR China.

institute: Sichuan University

description: Library name: PBS

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline (10× Genomics) with default parameters. Reads were aligned to the mouse reference genome mm10. Gene expression counts were quantified and used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz (UMI count matrix).

source_name: lung

extract_protocol:
Total RNA was extracted from lung tissues using a commercial RNA isolation kit (e.g., RNeasy Mini Kit, Qiagen) according to the manufacturer's instructions.
Single‑cell libraries were constructed using the 10× Genomics Chromium platform following the manufacturer's standard protocol. Single cells were partitioned into nanoliter‑scale gel beads‑in‑emulsion (GEMs) using the Chromium Controller, and cDNA was generated and amplified.

value: lung

value: PBS


title: Lung tissue from 1V209-Cho-Lip-treated mouse, single-cell RNA-seq

description: Library name: LC_1V


title: Mouse liver RNA-seq control H2

city: guangzhou

first: ran

last: ding

state: guangdong

address: School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, China.

institute: South china university of technology

description:
Library name: H2
Liver tissue RNA-seq from control mouse H2.

data_processing:
Raw sequencing reads were quality-checked and adaptor sequences and low-quality reads removed.
Clean paired-end reads were aligned to the Mus musculus reference genome (GRCm38/mm10).
Gene-level read counts were quantified.
Gene expression levels were normalized and reported as FPKM.
Differential expression analysis was performed between ethanol-exposed and control groups using R-based statistical methods.
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: GSE_processed_liver_RNAseq_FPKM_matrix.txt

source_name: liver

growth_protocol: Male C57BL/6J mice aged 6–8 weeks were maintained under standard laboratory conditions with free access to food and water.

extract_protocol:
Total RNA was extracted from liver tissue using TRIzol reagent following the manufacturer’s instructions. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer.
RNA-seq libraries were constructed using standard protocols and sequenced on Illumina NovaSeq 6000, paired-end 150 bp.

treatment_protocol: For the acute ethanol-induced liver injury model, mice were fasted for 12 h and administered a single oral dose of 50% ethanol at 6 g/kg. Liver tissues were collected 24 h later. Control mice were maintained without ethanol.

value: liver

value: wild type

value: control

value: batch 1


title: Mouse liver RNA-seq control H1

description:
Library name: H1
Liver tissue RNA-seq from control mouse H1.


title: Mouse liver RNA-seq control H3

description:
Library name: H3
Liver tissue RNA-seq from control mouse H3.


title: Mouse liver RNA-seq ethanol A2

description:
Library name: A2
Liver tissue RNA-seq from acute ethanol-exposed mouse A2.

value: acute ethanol exposure


title: Mouse liver RNA-seq ethanol A3

description:
Library name: A3
Liver tissue RNA-seq from acute ethanol-exposed mouse A3.


title: Mouse liver RNA-seq ethanol A1

description:
Library name: A1
Liver tissue RNA-seq from acute ethanol-exposed mouse A1.


title: DOCA-salt, kidney, rep3

city: Shanghai

first: Chongjian

last: Wang

address: Ruijin 2nd Road

institute: Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University

description:
Library name: doca62
10× Genomics

data_processing:
The FASTQ files were processed and aligned to CRCm39 mouse reference genome using Cell Ranger software (version 9.0.0) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode. The UMI count matrix was then analyzed using Seurat (version 4.0.0) R package. To remove low-quality cells and likely multiplet captures, a set of criteria were conducted: Cells were filtered by (1) gene numbers (gene numbers < 170), (2) UMI (UMI <500), (3) percentage of mitochondrial RNA UMIs (proportion of UMIs mapped to mitochondrial genes > 50%) and (4) percentage of hemoglobin RNA UMIs (proportion of UMIs mapped to hemoglobin genes > 5%). The DoubletFinder package (version 2.0.3) was used to identify potential doublets. To obtain the normalized gene expression data, library size normalization was processed using the NormalizeData function. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor, and log-transformed the results. The highly variable genes were identified using the Seurat function FindVariableGenes (mean.function=FastExpMean, dispersion.function= FastLogVMR). Principal-component analysis (PCA) was performed to reduce the dimensionality with RunPCA function. Then, the RunHarmony function in harmony (version 1.0) R package was performed to remove the batch effects. Graph-based clustering was performed to cluster cells according to their gene expression profile with the FindClusters function. Cells were visualized using a 2-dimensional Uniform Manifold Approximation and Projection (UMAP) algorithm with the RunUMAP function. The FindAllMarkers function was used to identify marker genes of each cluster and selecte differentially expressed genes (DEGs). KEGG pathway enrichment analysis of DEGs were respectively performed using R (version 4.0.3) based on the hypergeometric distribution.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The freshly collected kidney tissue were washed twice with pre-cooled RPMI 1640 medium containing 0.04% BSA. The tissues were then mechanically dissociated into approximately 0.5 mm³ fragments using surgical scissors and transferred into freshly prepared enzymatic digestion solution. The digestion mixture contained RPMI 1640 (Conring, cat.no. 10-040-CVR), 0.04% BSA (MACS, cat.no. 1000076), and 0.2% collagenase II (Gibco, cat.no. 17101015). The samples were incubated at 37°C for 30-60 minutes with gentle inversion every 5-10 minutes. The digested cell suspension was filtered through a BD 40 μm cell strainer (Falcon, cat.no. 352340) 1-2 times. The filtrate was centrifuged at 300 × g for 5 minutes at 4°C. The cell pellet was resuspended in appropriate medium, mixed with an equal volume of red blood cell lysis buffer (Miltenyi, cat.no. 130-094-183), and incubated at 4°C for 10 minutes. After centrifugation at 300 × g for 5 minutes, the supernatant was discarded. The pellet was washed once with medium followed by another centrifugation at 300 × g for 5 minutes, and the final supernatant was removed.
The freshly prepared single-cell suspension was adjusted to a concentration of 700–1200 cells/μl. Library preparation and loading were performed following the manufacturer’s protocol for the 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (cat.no.PN-1000268). The constructed libraries were sequenced on the Illumina Nova 6000 PE150 platform for high-throughput sequencing.


title: DOCA-salt, kidney, rep2

description:
Library name: doca61
10× Genomics


title: Sham, kidney, rep3

description:
Library name: control68
10× Genomics


title: DOCA-salt, kidney, rep1

description:
Library name: doca59
10× Genomics


title: Sham, kidney, rep1

description:
Library name: control66
10× Genomics


title: Sham, kidney, rep2

description:
Library name: control67
10× Genomics


title: KL, ETBF, midproximal_rep2

city: Baltimore

first: Jessica

last: Queen

state: Maryland

address: 600 N. Wolfe St.

institute: Johns Hopkins

description: Library name: KL_MP_2

data_processing:
Paired-end fastq files were submitted to Salmon (v1.9) for gene level quantification using mouse transcriptome reference mm10 index (retrieved from refgenomes.databio.org). Raw counts per gene were aggregated across all samples and submitted for immune cell profiling using CIBERSORT (v1.0) against a mouse specific reference matrix. DESeq2 (v1.34) for normalization of gene counts and differential expression analysis at the gene level emphasizing FDR-adjusted P-values. Normalized counts were analyzed using principal components analysis (prcomp in R) with Z-score centering and scaling of gene features per dataset. Utilizing mouse associated hallmark gene sets from the R package msigdbr (v7.5.1), gene set enrichment analysis (GSEA) was performed using the fgsea (v1.20) R package.
Assembly: mm10
Supplementary files format and content: .tsv
Supplementary files format and content: raw count values

source_name: Midproximal colon

extract_protocol:
Flushed and sectioned colon regions were mechanically and enzymatically digested and separated into single cells using 0.1mg/mL DNAse1 (Sigma-Aldrich Cat. No.10 104 159 001) and 400U/mL Liberase (Sigma-Aldrich Cat. No. 05 401 119 001), and leukocytes were isolated using a Percoll gradient (GE Healthcare Life Science 17089102). CD45+ cells were enriched using the Miltenyi QuadroMACS Separator (Cat. No. 130-090-976), LS columns (Cat. No. 130-042-401), and CD45 microbeads (Cat. No. 130-052-301). Collected cells were lysed in lysis buffer containing 1% β-mercaptoethanol (BME) and stored at -80C until extraction was completed using the Invitrogen PureLink RNA micro kit (Cat. No. 12183016). RNA was quantified using the Invitrogen Qubit system and the Qubit high sensitivity RNA kit (Cat. No. Q32852).
Libraries were generated using NEB Next Ultra RNA Library Prep Kit for Illumina (NEB). Paired-end 150-bp sequencing was performed on an Illumina Novaseq 6000.

value: Midproximal colon

value: KL

value: ETBF


title: KL, ETBF, distal_rep3

description: Library name: KL_DIS_3

source_name: Distal colon

value: Distal colon


title: KL, ETBF, midproximal_rep3

description: Library name: KL_MP_3


title: KL, ETBF, distal_rep2

description: Library name: KL_DIS_2


title: KL, ETBF, distal_rep1

description: Library name: KL_DIS_1


title: BL, ETBF, midproximal_rep3

description: Library name: BL_MP_3

value: BL


title: BL, ETBF, midproximal_rep2

description: Library name: BL_MP_2


title: KL, ETBF, midproximal_rep1

description: Library name: KL_MP_1


title: BL, ETBF, midproximal_rep1

description: Library name: BL_MP_1


title: BL, ETBF, distal_rep3

description: Library name: BL_DIS_3


title: BL, ETBF, distal_rep2

description: Library name: BL_DIS_2


title: BL, ETBF, distal_rep1

description: Library name: BL_DIS_1


title: WT, ETBF, distal, rep8

description: Library name: TScol5

extract_protocol:
Colons were rapidly flushed and sectioned into distal and midproximal regions as described above, before being flash frozen in liquid nitrogen, and stored at -80C until RNA extraction. RNA was isolated with the Invitrogen PureLink RNA Mini kit (Cat. No. 12183020) and treated with an on-column PureLink DNase Kit (Cat. No. 12185010).
Libraries were generated using NEB Next Ultra RNA Library Prep Kit for Illumina (NEB). Paired-end 150-bp sequencing was performed on an Illumina Novaseq 6000.

value: WT


title: WT, ETBF, distal, rep7

description: Library name: TScol4


title: WT, ETBF, distal, rep5

description: Library name: TScol2


title: WT, ETBF, distal, rep6

description: Library name: TScol3


title: WT, ETBF, distal, rep4

description: Library name: TScol1


title: WT, ETBF, distal, rep3

description: Library name: WT_ETBFdis3


title: WT, ETBF, distal, rep2

description: Library name: WT_ETBFdis2


title: WT, ETBF, distal, rep1

description: Library name: WT_ETBFdis1


title: WT, sham, midproximal, rep2

description: Library name: WT_shamMP2

value: Sham


title: WT, sham, midproximal, rep1

description: Library name: WT_shamMP1


title: WT, sham, midproximal, rep3

description: Library name: WT_shamMP3


title: WT, sham, distal, rep3

description: Library name: WT_shamdis3


title: WT, sham, distal, rep1

description: Library name: WT_shamdis1


title: Min, ETBF, midproximal, rep2

description: Library name: Min_ETBFMP2

value: Min


title: WT, sham, distal, rep2

description: Library name: WT_shamdis2


title: Min, ETBF, midproximal, rep1

description: Library name: Min_ETBFMP1


title: Min, ETBF, midproximal, rep3

description: Library name: Min_ETBFMP3


title: Min, ETBF, distal, rep9

description: Library name: TScol17


title: Min, ETBF, distal, rep8

description: Library name: TScol16


title: Min, ETBF, distal, rep7

description: Library name: TScol15


title: Min, ETBF, distal, rep6

description: Library name: TScol14


title: Min, ETBF, distal, rep5

description: Library name: TScol13


title: Min, ETBF, distal, rep3

description: Library name: Min_ETBFdis3


title: Min, ETBF, distal, rep4

description: Library name: Min_ETBFdis4


title: Min, ETBF, distal, rep2

description: Library name: Min_ETBFdis2


title: Min, ETBF, distal, rep1

description: Library name: Min_ETBFdis1


title: Min, sham, midproximal, rep3

description: Library name: Min_shamMP3


title: Min, sham, midproximal, rep2

description: Library name: Min_shamMP2


title: Min, sham, midproximal, rep1

description: Library name: Min_shamMP1


title: Min, sham, distal, rep3

description: Library name: Min_shamdis3


title: Min, sham, distal, rep2

description: Library name: Min_shamdis2


title: Min, sham, distal, rep1

description: Library name: Min_shamdis1


title: KL, ETBF, distal, rep7

description: Library name: TScol11


title: KL, ETBF, distal, rep8

description: Library name: TScol12


title: KL, ETBF, distal, rep6

description: Library name: TScol10


title: KL, ETBF, distal, rep5

description: Library name: TScol9


title: KL, ETBF, distal, rep3

description: Library name: KL_ETBFdis3


title: KL, ETBF, distal, rep4

description: Library name: TScol8


title: KL, ETBF, distal, rep2

description: Library name: KL_ETBFdis2


title: KL, sham, midproximal, rep1

description: Library name: KL_shamMP1


title: KL, sham, midproximal, rep2

description: Library name: KL_shamMP2


title: KL, sham, distal, rep2

description: Library name: KL_shamdis2


title: KL, ETBF, distal, rep1

description: Library name: KL_ETBFdis1


title: KL, sham, distal, rep1

description: Library name: KL_shamdis1


title: BL, ETBF, distal, rep5

description: Library name: TScol7


title: BL, ETBF, distal, rep4

description: Library name: TScol6


title: BL, ETBF, distal, rep3

description: Library name: BL_ETBFdis3


title: BL, ETBF, distal, rep2

description: Library name: BL_ETBFdis2


title: BL, ETBF, distal, rep1

description: Library name: BL_ETBFdis1


title: BL, sham, midproximal, rep2

description: Library name: BL_shamMP2


title: BL, sham, distal, rep3

description: Library name: BL_shamdis3


title: BL, sham, midproximal, rep3

description: Library name: BL_shamMP3


title: BL, sham, distal, rep2

description: Library name: BL_shamdis2


title: BL, sham, distal, rep1

description: Library name: BL_shamdis1


title: BL, sham, midproximal, rep1

description: Library name: BL_shamMP1


title: LM-4T1-3

first: Rui

last: Zeng

address: Dong An Road

institute: Fudan University

description: Library name: Sample 6

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values file and matrix files

source_name: dura mater

extract_protocol:
The dura maters were dissected from the cranium, then were minced into small pieces and digested with 1 mL of 1 mg/mL Collagenase VIII (#C2139, Sigma) and 0.1 mg/mL of DNase I (#DN25, Sigma) in 5%-FBS DMEM in a water bath at 37°C for 20 minutes. The enzymes were neutralized with 5 mL 5%-FBS DMEM, and samples were filtered through a 40 μm cell strainer, followed by centrifugation at 400×g for 5 minutes at 4°C.
The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 5’ library & gel bead kit(10X Genomics, Pleasanton, CA). Briefly, cells were concentrated to approximately 1000 cells/uL and loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was used to construct 5’ gene expression libraries. For 5’ library construction, the amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors were enriched from the amplified cDNA followed by fragmentation, A-tailing, adaptor ligation and index PCR amplification. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent).

value: dura mater

tag: disease state

value: leptomeningeal metastasis


title: LM-4T1-2

description: Library name: Sample 5


title: LM-4T1-1

description: Library name: Sample 4


title: Nontumor-2

description: Library name: Sample 2

value: Nontumor


title: Nontumor-3

description: Library name: Sample 3


title: Nontumor-1

description: Library name: Sample 1


title: WT to WT

city: Stony Brook

first: Kehan

last: Ren

state: NY

address: 101 Nicolls Road

department: Medicine

institute: Stony Brook University

description: Library name: Sample 6

data_processing:
Demultiplexing, barcode processing, gene counting, and sample aggregation were performed using Cell Ranger v9.0.0 (10x Genomics) according to the manufacturer’s recommended pipeline.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values and matrix files

source_name: Bone marrow

extract_protocol:
Femurs were collected from euthanized mice and cleaned of surrounding soft tissue under sterile conditions. Bone marrow was flushed from each femur using sterile PBS containing 2% FBS and gently triturated to generate a single-cell suspension. The suspension was filtered through a 40-µm cell strainer to remove aggregates and debris. After centrifugation, the cell pellet was incubated in RBC lysis buffer to deplete red blood cells. Lysis was stopped by addition of excess PBS containing 2% FBS, followed by centrifugation and washing. The resulting nucleated bone marrow cells were resuspended in PBS containing 0.04% bovine serum albumin for downstream single-cell RNA-sequencing workflow. Cell concentration and viability were determined prior to loading onto the single-cell capture platform.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ v4 platform with polyA-based mRNA capture, following the manufacturer’s protocol. Briefly, single cells were encapsulated, barcoded, reverse transcribed, and processed for 3′ gene expression library generation prior to Illumina sequencing.

value: Bone marrow

tag: dataset

value: role of Gsdmd dataset

value: WT to WT


title: Tet2-/- to Gsdmd-/-

description: Library name: Sample 5

value: Tet2-/- to Gsdmd-/-


title: Tet2-/- to WT

description: Library name: Sample 4

value: Tet2-/- to WT


title: tibialis anterior, PRURDBA, PRURDBA_TibAnt

city: San Francisco

first: Brian

middle: T

last: Feeley

address: 1700 Owens St

department: Orthopedic Surgery

institute: University of California, San Francisco

description:
Library name: PRURDBA_TibAnt
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: Mouse (mm10) 2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: integrated metadata and matrix files

source_name: tibialis anterior

extract_protocol:
Mouse tissue samples were obtained from tissue harvest of PRURDBA and PRURD2 mice. All samples were transferred from the operating room on ice and stored in 30% FBS (fetal bovine serum, Gibco, #10437028) in Dulbecco's Modified Eagle Medium (DMEM) (Gibco, #11965084) until processing. Samples were then mechanically and enzymatically digested in 1 mg/ml collagenase III (Worthington Biochemical Corporation, #NC0021929) in DMEM with 10% FBS and 1% Penicillin/Streptomycin (Gibco, #15140122) at 37°C for 70 minutes with intermittent manual needle trituration with an 18-gauge needle. Digests were washed with PBS (Gibco, #10010023) and further digested with 0.25% trypsin-EDTA (Gibco, #25200056) at 37°C for 12–15 min. Suspensions were passed through 40 µm nylon mesh (Corning, #431750), erythrocytes were lysed with ACK lysing buffer (Quality Biological, #188-156-101) for 5–7 minutes on ice and washed in PBS with 2% FBS. Cells were then resuspended in 100 µl flow cytometry buffer (PBS with 2% FBS, 5 mM EDTA (Corning, #MT-46034CI), 2 mM HEPES (Quality Biological, #118-089-721)) per 1 gram of starting tissue weight. Cells were imeediately proceeded to flow cytometry in flow cytometry buffer with 1:1000 SYTOX orange (ThermoFisher, #S34861). After sorting, cells were resuspended in 0.04% BSA in PBS at 1000 cells per μl to prepare for scRNA-seq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: tibialis anterior

value: fibroadipogenic progenitors (FAPs)

value: PRURDBA


title: tibialis anterior, PRURD2, PRURD2_TibAnt

description:
Library name: PRURD2_TibAnt
10x Genomics


title: heart, PRURDBA, PRURDBA_Heart

description:
Library name: PRURDBA_Heart
10x Genomics

source_name: heart

value: heart


title: heart, PRURD2, PRURD2_Heart

description:
Library name: PRURD2_Heart
10x Genomics


title: diaphragm, PRURD2, PRURD2_Diaphragm

description:
Library name: PRURD2_Diaphragm
10x Genomics

source_name: diaphragm

value: diaphragm


title: diaphragm, PRURDBA, PRURDBA_Diaphragm

description:
Library name: PRURDBA_Diaphragm
10x Genomics


title: Lumbar motor neurons (L1-L3), SMA + SMN-C3, rep3

city: New York

first: Maria

middle: Jose

last: Carlini

department: Neurology

institute: Columbia University

description: Library name: ML015

data_processing:
Raw sequencing reads were quality assessed and processed at the Columbia Genome Center.
Reads were pseudoaligned to the mouse transcriptome (Ensembl GRCm38.p6) using kallisto (v0.44.0).
Transcript-level abundance estimates were summarized to gene-level counts.
Differential gene expression analysis was performed using DESeq2.
Default parameters were used unless otherwise specified.
Assembly: Ensembl GRCm38.p6 (mm10)
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for each sample.
Supplementary files format and content: Tab-delimited text file containing normalized expression values and differential expression results for each comparison.

source_name: spinal cord (lumbar L1-L3)

growth_protocol: All mouse work was performed in accordance with National Institutes of Health guidelines and approved by the Institutional Animal Care and Use Committee of Columbia University. SMNΔ7 (Smn−/−;SMN2;SMNΔ7) mice and WT littermates (Smn+/+;SMN2;SMNΔ7) on an FVB background were maintained on a 12-hour light/dark cycle with food and water provided ad libitum. Lumbar spinal cord tissue was collected at postnatal day 6 (P6). Equal proportions of male and female mice were used.

extract_protocol:
Lumbar (L1–L3) spinal motor neurons were isolated by laser-capture microdissection. Total RNA was extracted using the Absolutely RNA Nanoprep Kit (Agilent) with on-column DNase treatment according to the manufacturer’s instructions.
Low-input poly(A)-selected RNA sequencing libraries were prepared at the Columbia Genome Center using a polyadenylated RNA amplification and library preparation workflow. Libraries were sequenced on an Illumina NovaSeq 6000 platform (paired-end, 100 bp).

treatment_protocol: SMA mice were treated daily starting at P0 by intraperitoneal injection with either Pifithrin-α (2.2 mg/kg), MW150 (5 mg/kg), or SMN-C3 (3 mg/kg). Control WT and untreated SMA mice received vehicle.

value: spinal cord (lumbar L1-L3)

value: motor neuron


title: Lumbar motor neurons (L1-L3), SMA + SMN-C3, rep2

description: Library name: ML014


title: Lumbar motor neurons (L1-L3), SMA + SMN-C3, rep1

description: Library name: ML013


title: Lumbar motor neurons (L1-L3), SMA + Pifithrin-α, rep3

description: Library name: ML012

value: Pifithrin-α


title: Lumbar motor neurons (L1-L3), SMA + Pifithrin-α, rep2

description: Library name: ML011


title: CRISPR KO of KSR2, guide 1, replicate 2

description: Library name: KSR_KO1_Rep2

data_processing:
Sequencing data was mapped to the reference genome (GRCh38.105 assembly) using STAR (version STAR/2.7.11b)
Differential expression analysis was performed with DESeq2 (version 1.42.1)
Assembly: GRCh38.105 assembly
Supplementary files format and content: Tab-separated file of raw read counts per gene as outputed by feature count function of STAR.

extract_protocol:
RNA was extracted from 5M JURKAT cells according to the manufacturer's protocol of the RNeasy kit (QIAGEN)
For RNA-seq library construction of total RNA obtained from transduced JURKAT cell line, the Watchmaker total mRNA library preparation kit (7BK0001-096, Watchmaker Genomics, Boulder, CO, USA) was used following the manufacturer’s protocol.

value: Blood

tag: cell line

value: JURKAT

value: T-ALL

value: CRISPR KO of KSR2, guide 1


title: Lumbar motor neurons (L1-L3), SMA + Pifithrin-α, rep1

description: Library name: ML010


title: Lumbar motor neurons (L1-L3), SMA + MW150, rep3

description: Library name: ML009


title: Lumbar motor neurons (L1-L3), SMA + MW150, rep2

description: Library name: ML008


title: Lumbar motor neurons (L1-L3), SMA, rep3

description: Library name: ML006

value: Vehicle


title: Lumbar motor neurons (L1-L3), SMA + MW150, rep1

description: Library name: ML007


title: Lumbar motor neurons (L1-L3), SMA, rep2

description: Library name: ML005


title: Lumbar motor neurons (L1-L3), SMA, rep1

description: Library name: ML004


title: Lumbar motor neurons (L1-L3), WT, rep2

description: Library name: ML002


title: Lumbar motor neurons (L1-L3), WT, rep3

description: Library name: ML003


title: Lumbar motor neurons (L1-L3), WT, rep1

description: Library name: ML001


title: M4

city: xi'an

first: Lin

last: Sun

address: xincheng street,169

department: Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University

institute: Fourth Military Medical University

description:
Library name: M4
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Ensembl_release113
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.


title: M3

description:
Library name: M3
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: M1

description:
Library name: M1
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: M2

description:
Library name: M2
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: CT4

description:
Library name: CT4
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: PBS


title: CT2

description:
Library name: CT2
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: CT3

description:
Library name: CT3
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: CT1

description:
Library name: CT1
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: IECs, SETD2-VILKO-92

first: Jing

last: Feng

address: Zhizao ju road

department: Gastroenterology

institute: Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University

description: Library name: SETD2-VILKO-92

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13 HISAT2.1.0 mapping to reference genome
Assembly: mm10/Ensembl v101
Supplementary files format and content: csv file including raw counts for each sample

source_name: colon

extract_protocol:
Total RNA was isolated utilizing the Trizol reagent. Subsequently, we employed the Illumina TruSeq RNA Sample Prep Kit to construct sequencing libraries, starting with an initial input of 1 μg of total RNA and strictly adhering to the manufacturer's established protocols.
RNA-seq library was constructed by using NEBNext Ultra Ⅱ RNA Library Prep Kit for illumina.

value: colon

value: intestinal epithelial cells


title: IECs, SETD2-VILKO-91

description: Library name: SETD2-VILKO-91


title: IECs, SETD2-FF-111

description: Library name: SETD2-FF-111


title: E14.5 Cnot1 +/+ developing diaphragm replicate 3

city: Bar Harbor

first: Stephen

last: Murray

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Library name: Cnot1_WT_E145_3

data_processing:
RNA sequencing reads were batch processed using The Jackson Laboratory standard Nextflow RNAseq pipeline (https://github.com/TheJacksonLaboratory/jds-nf-workflows/wiki/RNA-Pipeline-ReadMe), aligning to the mm10 (GRCm38) mouse genome and gencode gene annotation release M25 (GRCm38.6). In brief, sequenced reads were trimmed with Trim Galore, aligned STAR and counts were quantified with Salmon and STRINGTIE. Differential gene and transcript analysis was performed with DESeq2, using standard parameters, on both gene and isoform counts from STAR.
Software versions: bioconductor-deseq2: 1.28.0; r-base: 4.0.3; picard: 3.0.0; salmon: 1.10.1; star: 2.7.9a; samtools: 1.16.1; stringtie: 2.2.1; cutadapt: '3.4'; trimgalore: 0.6.7; Nextflow: 23.04.0; nf-core/rnaseq: 3.11.1
Assembly: mm10 (GRCm38) mouse genome
Supplementary files format and content: Tab delimited files with raw counts for each sample, one for counts mapping to full genes and one for transcript isoform mapping
Supplementary files format and content: Tab delimited files with TPM normalized counts for each sample, one for counts mapping to full genes and one for transcript isoform mapping

source_name: Embryonic diaphragm

extract_protocol:
Total RNA was isolated from snap frozen diaphragms using the Qiagen miRNeasy micro RNA Isolation Kit (Qiagen). Tissues were homogenized in TRIzol (ThermoFisher) using a Pellet Pestle Motor (Kimbal). After the addition of chloroform, the RNA-containing aqueous layer was removed for RNA isolation according to the manufacturer’s protocol.
Stranded libraries were constructed using the KAPA RNA Hyper Prep Kit with RiboErase (HMR) (Roche Sequencing and Life Science), according to the manufacturer’s protocol.

value: Embryonic diaphragm

tag: age

value: WT


title: E14.5 Cnot1 +/+ developing diaphragm replicate 2

description: Library name: Cnot1_WT_E145_2


title: E14.5 Cnot1 +/+ developing diaphragm replicate 1

description: Library name: Cnot1_WT_E145_1


title: E13.5 Cnot1 +/+ developing diaphragm replicate 2

description: Library name: Cnot1_WT_E135_2


title: E13.5 Cnot1 +/+ developing diaphragm replicate 3

description: Library name: Cnot1_WT_E135_3


title: E13.5 Cnot1 +/+ developing diaphragm replicate 1

description: Library name: Cnot1_WT_E135_1


title: E14.5 Cnot1 R623W/R623W developing diaphragm replicate 1

description: Library name: Cnot1_Hom_E145_1

value: Cnot1 R623W/R623W


title: E14.5 Cnot1 R623W/R623W developing diaphragm replicate 2

description: Library name: Cnot1_Hom_E145_2


title: E14.5 Cnot1 R623W/R623W developing diaphragm replicate 3

description: Library name: Cnot1_Hom_E145_3


title: E13.5 Cnot1 R623W/R623W developing diaphragm replicate 3

description: Library name: Cnot1_Hom_E135_3


title: E13.5 Cnot1 R623W/R623W developing diaphragm replicate 2

description: Library name: Cnot1_Hom_E135_2


title: E14.5 Cnot1 R623W/+ developing diaphragm replicate 1

description: Library name: Cnot1_Het_E145_1

value: Cnot1 R623W/+


title: E13.5 Cnot1 R623W/+ developing diaphragm replicate 3

description: Library name: Cnot1_Het_E135_3


title: E14.5 Cnot1 R623W/+ developing diaphragm replicate 2

description: Library name: Cnot1_Het_E145_2


title: E13.5 Cnot1 R623W/+ developing diaphragm replicate 1

description: Library name: Cnot1_Het_E135_1


title: E13.5 Cnot1 R623W/+ developing diaphragm replicate 2

description: Library name: Cnot1_Het_E135_2


title: Control1_1

city: West Lafayette

first: Harish

last: Kothandaraman

state: IN

address: 201S South State St

department: Purdue Institute for Cancer Research

institute: Purdue University

description: Library name: Control1_Rep1

data_processing:
Reads were trimmed free of adapters and low quality bases using cutadapt (1.1.0); followed by mapping with HISAT (2.0) to the mouse genome. StringTie (1.3.4) was used to assemble the transcripts, and differential expression was performed with DESeq2 and edgeR.
Assembly: Mus musculus, release 101 from ENSEMBL
Supplementary files format and content: .txt file containing the gene expression counts

growth_protocol: Mice were maintained on low‑arsenic AIN‑76A purified chow and Milli‑Q water for two weeks prior to tumor implantation. Following implantation, animals were housed under standard conditions with ad libitum access to food and either 0 ppb or 300 ppb inorganic arsenic (iAs) in drinking water until tissue collection at 21 days post‑implantation.

extract_protocol:
Tumors were harvested 21 days post‑implantation, and left/right flank samples from each mouse were combined. Tumor tissue was preserved in RNAlater for up to seven days at 4 °C, then stored at −80 °C. For RNA extraction, 15–18 mg of tissue was homogenized in RLT buffer with β‑mercaptoethanol. RNA was isolated using the Qiagen RNeasy Mini Kit, and RNA integrity was verified with the Agilent 2100 Bioanalyzer (RIN > 7.0).
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: Mice were subcutaneously implanted in both flanks with 125,000 TC2Ras prostate cancer cells, either alone or mixed with 1% ASC‑GFP cells. After implantation, animals were exposed to either 0 ppb or 300 ppb iAs in drinking water for the duration of the 21‑day study, generating four treatment groups based on ASC presence and iAs exposure.

tag: sample group


title: Control1_2

description: Library name: Control1_Rep2


title: Control1_3

description: Library name: Control1_Rep3


title: ASC_3

description: Library name: ASC_Rep3

value: ASC


title: ASC_1

description: Library name: ASC_Rep1


title: ASC_2

description: Library name: ASC_Rep2


title: ASC300_3

description: Library name: ASC300_Rep3


title: ASC300_2

description: Library name: ASC300_Rep2


title: ASC300_1

description: Library name: ASC300_Rep1


title: A300_3

description: Library name: A300_Rep3


title: A300_2

description: Library name: A300_Rep2


title: A300_1

description: Library name: A300_Rep1


title: Mov10 Deletion, Day 23, replicate 3

city: Urbana

first: Stephanie

last: Ceman

state: Illinois

address: 506 S Mathews Ave

department: Cell and Developmental Biology

institute: University of Illinois Urbana-Champaign

description:
Library name: D23_3
Output from Salmon quant

data_processing:
Cutadapt (cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT)
Create decoy-aware transcriptome using Salmon-1.10.0 and transcript annotations from GENCODE—gencode.vM37.transcripts.fa.gz and GRCm39.primary_assembly.genome.fa.gz. Quantify the transcripts using salmon quant with -seqBias --gcBias --recoverOrphans --validateMappings flags.
Differential gene expression was performed in R using DESeq2 with default parameters.
Assembly: GRCm39
Supplementary files format and content: quant.sf files with transcript-level quantifications from Salmon

source_name: Whole brain

extract_protocol:
Whole brains were dissected on ice and flash frozen using liquid nitrogen. Tissues were kept at -80C before being shipped to Biostate.ai in dry ice for RNA extraction and sequencing.
NEBNext Poly(A) mRNA Magnetic Isolation Module

value: Whole brain

value: Mov10 Deletion

value: Day 23


title: Mov10 Deletion, Day 23, replicate 1

description:
Library name: D23_1
Output from Salmon quant


title: Mov10 Deletion, Day 14, replicate 3

description:
Library name: D14_3
Output from Salmon quant

value: Day 14


title: Mov10 Deletion, Day 14, replicate 2

description:
Library name: D14_2
Output from Salmon quant


title: Mov10 Deletion, Day 14, replicate 1

description:
Library name: D14_1
Output from Salmon quant


title: Mov10 Deletion, Day 7, replicate 3

description:
Library name: D7_3
Output from Salmon quant

value: Day 7


title: Mov10 Deletion, Day 7, replicate 2

description:
Library name: D7_2
Output from Salmon quant


title: Mov10 Deletion, Day 7, replicate 1

description:
Library name: D7_1
Output from Salmon quant


title: Mov10 Deletion, Day 0, replicate 3

description:
Library name: D0_3
Output from Salmon quant

value: Day 0


title: Mov10 Deletion, Day 0, replicate 2

description:
Library name: D0_2
Output from Salmon quant


title: 1952-2.TCR.SamplePool.rs116821

city: Beaverton

first: Benjamin

middle: N

last: Bimber

state: OR

address: 505 NW 185th Ave

description:
Library name: 116821
Fig5.seurat.rds
Fig5.counts.rds

data_processing:
CellRanger count
DropletUtils emptyDrops
Seurat Normalize/Scale/PCA
Assembly: GCA_003339765.3
Supplementary files format and content: Sparse count matrix (RDS file)
Supplementary files format and content: Seurat Object (RDS file)

organism: Macaca mulatta

source_name: PBMC

extract_protocol: 10x Genomics 5' VDJ scRNA-seq

value: PBMC