title: inguinal white adipose tissue, Medium-term obesity regression, biological replicate 6, mouse SMA_3701

description:
Library name: B417
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3701; Medium-term obesity regression; biological replicate 6.
iWAT_raw_counts.tsv

value: Medium-term obesity regression


title: inguinal white adipose tissue, Medium-term obesity regression, biological replicate 5, mouse SMA_3700

status: Public on Jul 17 2026

type: SRA

city: Odense M

first: Blagoy

last: Blagoev

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
Library name: B416
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3700; Medium-term obesity regression; biological replicate 5.
iWAT_raw_counts.tsv

library_source: transcriptomic

data_processing:
The count matrix was imported into R (v4.2.2; RStudio v2023.06.1) and normalized for library size and sequencing depth, followed by log2 transformation using DESeq2 (v1.38.3). Transcripts with an average normalized log2 count <1 or containing NA values in any sample were removed prior to analysis. Differential gene expression analysis was performed using DESeq2 (v1.38.3).
Assembly: Illumina). Raw reads were aligned to the mouse genome (mm10) using STAR (v2.4.1c). Exonic peak detection was performed using iRNA (v1.1).
Supplementary files format and content: Processed data consist of tab-delimited gene expression count matrices (raw counts) generated from RNA-seq data for eWAT and iWAT samples. Differential expression results are also procided as comma-separated value (CSV) files generated using DESeq2.

molecule: polyA RNA

organism: Mus musculus

source_name: inguinal white adipose tissue

extract_protocol:
Unless otherwise stated, all steps were performed on ice. Tissues were homogenized at room temperature in 500 µL TRI Reagent® (Sigma-Aldrich, T9424) and six 1.4 mm ceramic beads (OMNI International, 19-645) per 80 mg tissue using the mouse liver program on a FastPrep-24TM 5G (MP Biomedicals). Homogenates were centrifuged at 10,000 x g for 10 min at 4 °C, and the infranatant was transferred to a new DNA LoBind tube (Eppendorf), avoiding the lipid layer and debris pellet. 0.2 volumes of chloroform (Acros Organics, 383770025) were added, samples were mixed by inversion, incubated at room temperature for 5 min, and centrifuged at 10,000 x g for 10 min at 4 °C. The aqueous phase was transferred to a new DNA LoBind tube. 0.6 volumes of isopropanol (VWR Chemicals, 20880.320) were added, samples were mized by inversion, incubated at -20 °C for 1 hr, and centrifuged at 12,000 x g for 15 min at 4 °C. The supernatant was removed, and the pellet was washed with 1mL 70% ethanol (VWR Chemicals, 20824.365) prepared in DEPC-treated water (Sigma-Aldrich, D5758), followed by centrifugation at 12,000 x g for 10 min at 4 °C.
Illumina libraries were prepared using poly(A) enrichment according to the manufacturer’s instructions and sequenced with paired-end reads on a NovaSeq 6000 (Illumina).

tag: tissue

value: inguinal white adipose tissue

tag: genotype

tag: treatment


title: inguinal white adipose tissue, Short-term lean control, biological replicate 2, mouse SMA_3763

description:
Library name: B405
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3763; Short-term lean control; biological replicate 2.
iWAT_raw_counts.tsv

value: Short-term lean control


title: inguinal white adipose tissue, Medium-term obesity regression, biological replicate 4, mouse SMA_3699

description:
Library name: B415
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3699; Medium-term obesity regression; biological replicate 4.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Medium-term obesity regression, biological replicate 3, mouse SMA_3767

description:
Library name: B409
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3767; Medium-term obesity regression; biological replicate 3.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Diet-induced obesity, biological replicate 4, mouse SMA_3693

description:
Library name: B413
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3693; Diet-induced obesity; biological replicate 4.
iWAT_raw_counts.tsv

value: Diet-induced obesity


title: inguinal white adipose tissue, Diet-induced obesity, biological replicate 5, mouse SMA_3695

description:
Library name: B414
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3695; Diet-induced obesity; biological replicate 5.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Medium-term obesity regression, biological replicate 2, mouse SMA_3766

description:
Library name: B408
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3766; Medium-term obesity regression; biological replicate 2.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Medium-term lean control, biological replicate 6, mouse SMA_3707

description:
Library name: B420
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3707; Medium-term lean control; biological replicate 6.
iWAT_raw_counts.tsv

value: Medium-term lean control


title: inguinal white adipose tissue, Medium-term obesity regression, biological replicate 1, mouse SMA_3765

description:
Library name: B407
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3765; Medium-term obesity regression; biological replicate 1.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Medium-term lean control, biological replicate 5, mouse SMA_3706

description:
Library name: B419
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3706; Medium-term lean control; biological replicate 5.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Medium-term lean control, biological replicate 3, mouse SMA_3755

description:
Library name: B400
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3755; Medium-term lean control; biological replicate 3.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Medium-term lean control, biological replicate 4, mouse SMA_3705

description:
Library name: B418
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3705; Medium-term lean control; biological replicate 4.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Medium-term lean control, biological replicate 2, mouse SMA_3754

description:
Library name: B399
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3754; Medium-term lean control; biological replicate 2.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Medium-term lean control, biological replicate 1, mouse SMA_3753

description:
Library name: B398
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3753; Medium-term lean control; biological replicate 1.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Long-term obesity regression, biological replicate 6, mouse SMA_3725

description:
Library name: B432
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3725; Long-term obesity regression; biological replicate 6.
iWAT_raw_counts.tsv

value: Long-term obesity regression


title: inguinal white adipose tissue, Long-term obesity regression, biological replicate 5, mouse SMA_3724

description:
Library name: B431
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3724; Long-term obesity regression; biological replicate 5.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Long-term obesity regression, biological replicate 4, mouse SMA_3723

description:
Library name: B430
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3723; Long-term obesity regression; biological replicate 4.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Long-term obesity regression, biological replicate 2, mouse SMA_3748

description:
Library name: B393
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3748; Long-term obesity regression; biological replicate 2.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Long-term obesity regression, biological replicate 3, mouse SMA_3749

description:
Library name: B394
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3749; Long-term obesity regression; biological replicate 3.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Long-term obesity regression, biological replicate 1, mouse SMA_3747

description:
Library name: B392
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3747; Long-term obesity regression; biological replicate 1.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Long-term lean control, biological replicate 5, mouse SMA_3709

description:
Library name: B422
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3709; Long-term lean control; biological replicate 5.
iWAT_raw_counts.tsv

value: Long-term lean control


title: inguinal white adipose tissue, Long-term lean control, biological replicate 3, mouse SMA_3758

description:
Library name: B403
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3758; Long-term lean control; biological replicate 3.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Long-term lean control, biological replicate 2, mouse SMA_3757

description:
Library name: B402
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3757; Long-term lean control; biological replicate 2.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Long-term lean control, biological replicate 4, mouse SMA_3708

description:
Library name: B421
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3708; Long-term lean control; biological replicate 4.
iWAT_raw_counts.tsv


title: inguinal white adipose tissue, Long-term lean control, biological replicate 6, mouse SMA_3710

description:
Library name: B423
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3710; Long-term lean control; biological replicate 6.
iWAT_raw_counts.tsv


title: epididymal white adipose tissue, Diet-induced obesity, biological replicate 3, mouse SMA_3752

description:
Library name: B444
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3752; Diet-induced obesity; biological replicate 3.
eWAT_raw_counts.tsv

source_name: epididymal white adipose tissue

value: epididymal white adipose tissue


title: epididymal white adipose tissue, Diet-induced obesity, biological replicate 4, mouse SMA_3693

description:
Library name: B460
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3693; Diet-induced obesity; biological replicate 4.
eWAT_raw_counts.tsv


title: inguinal white adipose tissue, Long-term lean control, biological replicate 1, mouse SMA_3756

description:
Library name: B401
Bulk RNA sequencing of inguinal white adipose tissue from male mouse SMA_3756; Long-term lean control; biological replicate 1.
iWAT_raw_counts.tsv


title: epididymal white adipose tissue, Diet-induced obesity, biological replicate 5, mouse SMA_3695

description:
Library name: B461
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3695; Diet-induced obesity; biological replicate 5.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Diet-induced obesity, biological replicate 1, mouse SMA_3750

description:
Library name: B442
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3750; Diet-induced obesity; biological replicate 1.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Diet-induced obesity, biological replicate 2, mouse SMA_3751

description:
Library name: B443
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3751; Diet-induced obesity; biological replicate 2.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Lean control at obesity time point, biological replicate 6, mouse SMA_3728

description:
Library name: B482
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3728; Lean control at obesity time point; biological replicate 6.
eWAT_raw_counts.tsv

value: Lean control at obesity time point


title: epididymal white adipose tissue, Lean control at obesity time point, biological replicate 4, mouse SMA_3726

description:
Library name: B480
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3726; Lean control at obesity time point; biological replicate 4.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Lean control at obesity time point, biological replicate 5, mouse SMA_3727

description:
Library name: B481
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3727; Lean control at obesity time point; biological replicate 5.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Lean control at obesity time point, biological replicate 3, mouse SMA_3785

description:
Library name: B459
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3785; Lean control at obesity time point; biological replicate 3.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Lean control at obesity time point, biological replicate 2, mouse SMA_3784

description:
Library name: B458
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3784; Lean control at obesity time point; biological replicate 2.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Lean control at obesity time point, biological replicate 1, mouse SMA_3783

description:
Library name: B457
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3783; Lean control at obesity time point; biological replicate 1.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term obesity regression, biological replicate 6, mouse SMA_3713

description:
Library name: B473
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3713; Short-term obesity regression; biological replicate 6.
eWAT_raw_counts.tsv

value: Short-term obesity regression


title: epididymal white adipose tissue, Short-term obesity regression, biological replicate 5, mouse SMA_3712

description:
Library name: B472
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3712; Short-term obesity regression; biological replicate 5.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term obesity regression, biological replicate 4, mouse SMA_3711

description:
Library name: B471
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3711; Short-term obesity regression; biological replicate 4.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term lean control, biological replicate 6, mouse SMA_3719

description:
Library name: B476
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3719; Short-term lean control; biological replicate 6.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term obesity regression, biological replicate 1, mouse SMA_3744

description:
Library name: B436
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3744; Short-term obesity regression; biological replicate 1.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term obesity regression, biological replicate 3, mouse SMA_3746

description:
Library name: B438
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3746; Short-term obesity regression; biological replicate 3.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term obesity regression, biological replicate 2, mouse SMA_3745

description:
Library name: B437
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3745; Short-term obesity regression; biological replicate 2.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term lean control, biological replicate 5, mouse SMA_3718

description:
Library name: B475
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3718; Short-term lean control; biological replicate 5.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term lean control, biological replicate 4, mouse SMA_3717

description:
Library name: B474
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3717; Short-term lean control; biological replicate 4.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term lean control, biological replicate 3, mouse SMA_3764

description:
Library name: B453
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3764; Short-term lean control; biological replicate 3.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term lean control, biological replicate 2, mouse SMA_3763

description:
Library name: B452
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3763; Short-term lean control; biological replicate 2.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Short-term lean control, biological replicate 1, mouse SMA_3762

description:
Library name: B451
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3762; Short-term lean control; biological replicate 1.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term obesity regression, biological replicate 6, mouse SMA_3701

description:
Library name: B464
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3701; Medium-term obesity regression; biological replicate 6.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term obesity regression, biological replicate 5, mouse SMA_3700

description:
Library name: B463
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3700; Medium-term obesity regression; biological replicate 5.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term obesity regression, biological replicate 4, mouse SMA_3699

description:
Library name: B462
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3699; Medium-term obesity regression; biological replicate 4.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term obesity regression, biological replicate 1, mouse SMA_3765

description:
Library name: B454
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3765; Medium-term obesity regression; biological replicate 1.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term obesity regression, biological replicate 3, mouse SMA_3767

description:
Library name: B456
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3767; Medium-term obesity regression; biological replicate 3.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term obesity regression, biological replicate 2, mouse SMA_3766

description:
Library name: B455
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3766; Medium-term obesity regression; biological replicate 2.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term lean control, biological replicate 6, mouse SMA_3707

description:
Library name: B467
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3707; Medium-term lean control; biological replicate 6.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term lean control, biological replicate 5, mouse SMA_3706

description:
Library name: B466
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3706; Medium-term lean control; biological replicate 5.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term lean control, biological replicate 4, mouse SMA_3705

description:
Library name: B465
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3705; Medium-term lean control; biological replicate 4.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term lean control, biological replicate 3, mouse SMA_3755

description:
Library name: B447
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3755; Medium-term lean control; biological replicate 3.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term lean control, biological replicate 2, mouse SMA_3754

description:
Library name: B446
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3754; Medium-term lean control; biological replicate 2.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Medium-term lean control, biological replicate 1, mouse SMA_3753

description:
Library name: B445
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3753; Medium-term lean control; biological replicate 1.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term obesity regression, biological replicate 6, mouse SMA_3725

description:
Library name: B479
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3725; Long-term obesity regression; biological replicate 6.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term obesity regression, biological replicate 5, mouse SMA_3724

description:
Library name: B478
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3724; Long-term obesity regression; biological replicate 5.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term obesity regression, biological replicate 4, mouse SMA_3723

description:
Library name: B477
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3723; Long-term obesity regression; biological replicate 4.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term obesity regression, biological replicate 3, mouse SMA_3749

description:
Library name: B441
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3749; Long-term obesity regression; biological replicate 3.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term obesity regression, biological replicate 2, mouse SMA_3748

description:
Library name: B440
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3748; Long-term obesity regression; biological replicate 2.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term lean control, biological replicate 5, mouse SMA_3709

description:
Library name: B469
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3709; Long-term lean control; biological replicate 5.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term obesity regression, biological replicate 1, mouse SMA_3747

description:
Library name: B439
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3747; Long-term obesity regression; biological replicate 1.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term lean control, biological replicate 6, mouse SMA_3710

description:
Library name: B470
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3710; Long-term lean control; biological replicate 6.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term lean control, biological replicate 4, mouse SMA_3708

description:
Library name: B468
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3708; Long-term lean control; biological replicate 4.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term lean control, biological replicate 2, mouse SMA_3757

description:
Library name: B449
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3757; Long-term lean control; biological replicate 2.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term lean control, biological replicate 3, mouse SMA_3758

description:
Library name: B450
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3758; Long-term lean control; biological replicate 3.
eWAT_raw_counts.tsv


title: epididymal white adipose tissue, Long-term lean control, biological replicate 1, mouse SMA_3756

description:
Library name: B448
Bulk RNA sequencing of epididymal white adipose tissue from male mouse SMA_3756; Long-term lean control; biological replicate 1.
eWAT_raw_counts.tsv


title: Colon_TNBS_Vehicle_rep10

city: Suzhou

first: zhong

last: huiting

address: Building B, Phase 3, Suzhou BioBay, Suzhou Industrial Park

country: China

institute: Allianthera bio-pharmaceutical Co., Ltd CN

description: Library name: Vehicle-380

data_processing:
Quality Control: Raw reads in FASTQ format were processed using Cutadapt (v1.9.1) to remove adapter sequences and low-quality bases (phred cutoff: 20, error rate: 0.1, adapter overlap: 1 bp, minimum length: 75, proportion of N: 0.1) to obtain high-quality clean data.  Alignment: Clean reads were aligned to the mouse reference genome using HISAT2 (v2.2.1). Reference genome sequences and gene model annotation files were downloaded from UCSC, NCBI, or ENSEMBL.  Expression analysis: Gene-level expression counts were quantified using HTSeq (v0.6.1) based on the reference gene annotation file.  Normalization: FPKM values were calculated for each gene.  Differential expression analysis: Differential expression analysis was performed using the DESeq2 Bioconductor package (based on the negative binomial distribution), with an adjusted p-value ≤ 0.05 considered statistically significant.
Assembly: Mus_musculus_GRCm39.107_Ensembl
Supplementary files format and content: Tab-delimited text file containing FPKM and raw count values for all samples. Rows represent genes. Columns include gene_id, exonic gene size, count, FPKM, genomic coordinates (Chr, Start, End, Strand), gene symbol, gene description, GO terms (Biological Process, Cellular Component, Molecular Function), KO (KEGG Orthology), and KEGG pathway annotations.

source_name: colon

extract_protocol:
Total RNA was extracted from colon tissues using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA concentration and purity were measured using a NanoDrop 2000 spectrophotometer, and RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: colon

value: BALBC

value: TNBS

tag: batch


title: Colon_TNBS_Vehicle_rep7

description: Library name: Vehicle-344


title: Colon_TNBS_Vehicle_rep9

description: Library name: Vehicle-357


title: Colon_TNBS_Vehicle_rep8

description: Library name: Vehicle-354


title: Colon_TNBS_Vehicle_rep5

description: Library name: Vehicle-321


title: Colon_TNBS_Vehicle_rep6

description: Library name: Vehicle-331


title: Colon_TNBS_Vehicle_rep3

description: Library name: Vehicle-290


title: Colon_TNBS_Vehicle_rep4

description: Library name: Vehicle-308


title: Colon_Sham_rep10

description: Library name: Sham-384

value: Sham


title: Colon_TNBS_Vehicle_rep2

description: Library name: Vehicle-289


title: Colon_TNBS_Vehicle_rep1

description: Library name: Vehicle-271


title: Exp1_organoid_severelyperturbed_rep2

status: Public on Jul 18 2026

city: Carlsbad

first: Tom

last: Chen

state: CA

address: 6155 Corte Del Cedro

department: R&D

country: USA

institute: Universal Sequencing Technology Corp.

description:
AmpliDrop
230602_06_GM516S6_Exp1_org_severely_perturbed_rep2

library_source: transcriptomic single cell

data_processing:
Sequencing reads were processed with AmpliDrop software v1.0. Cell calling and data processing was generated with Cell Ranger v5.1
Within AmpliDrop software analysis, after bcl files been converted to fastq files, the pipeline generated three types of fastq files: cDNA reads, been called as "R1"; sample index reads, with 8 nucleotides, been called as "I1"; and barcode reads, with 20 nucleotides, been called as "I2", in which six nucleotides at positions of 4, 5, 10, 11, 16, and 17 were used as code. The pipeline was then demultiplexing the samples based on the sample index combined with the code used. However, the sample index and code sequences were not saved after demultiplexing. To evaluate the fastq quality, the pipeline ran the fastqc tool on each set of fastq files for the demultiplexed sample. After the barcodes were error collected and the cDNA reads were trimmed with the potential adapter sequences and poly-A nucleotides, the pipeline ran a merging algorithm to merge the barcodes that were located in the same droplet. At the end of the pipeline, the fastq files were converted into 10X Genomic cellranger compatible format.
Assembly: hg38 and mm10
Supplementary files format and content: _barcodes.tsv.gz contains all cellular barcodes, tab separated text file, gzipped; _features.tsv.gz contains feature annotations, tab separated text file, gzipped, column1: feature id, column2: feature name, and column3: type of feature, i.e., "Gene Expression"; _matrix.mtx.gz contains UMI counts in each gene and in each cellular barcode, with mtx format, gzipped.

organism: Homo sapiens

source_name: brain cells

growth_protocol: All cell lines were grown in an incubator at 37C and 5% CO2 with media conditions as suggested by ATCC (293T, NIH-3T3, MCF7, HCT-116, and Jurkat) or Sigma (A2780 and A2780cis) supplemented with pen/strep antibiotics. Cells were generally grown close to confluency at the moment of collecting the cells. The WT83 clone6 of human induced-pluripotent stem cells (hiPSCs), derived from a typically developing Caucasian male 29,72, were grown on growth factor-reduced Matrigel, coated 6-cm dishes in mTeSR Plus without antibiotics. For propagation, cells were dissociated with Versene, EDTA, or Relers. To generate forebrain organoids, we followed a semi-guided protocol with a few modifications. Human iPSCs were grown in mTeSR Plus to a confluency of approximately 70% in a 6-cm plate and dissociated with a 1:1 mix of accutase/DPBS. Approximately, three million hiPSCs with a viability >95% were transferred into ultra-low attachment 6-well plates with mTeSR plus media supplemented with the SMAD inhibitors SB-431542 and Dorsomorphin, and the Rho-associated proteinase kinase (ROCK) inhibitor (RI) Y-27632. Plates were placed on orbital shaker. Alternatively, 2 million hiPSCs were transferred to a well of AggreWell-800 plate, pre-coated with Anti-Adherent Solution in mTeSR plus supplemented with RI. The AggreWell plate was centrifugated and transferred to incubator overnight. The following day, embryoid bodies (EB) were transferred to a well of 6-well plate changing the media to fresh mTsERplus supplemented with SB and Dorsomorphin as described above. Regular media and factors changes to complete generation of forebrain organoids were performed in M2 medium composed of Neurobasal supplemented with 1% Glutamax, 1% MEM non-essential amino acids solution, NEAA, and 1x B27 performing half/medium changes every two days for the first month or twice a week after.

extract_protocol:
Peripheral venous blood was drawn from voluntary donor using EDTA-treated tubes and LymphoprepTM and stored at 4°C. Cells were resuspended in 1x phosphate-buffered saline buffer solution (1xPBS) supplemented with 2% bovine serum albumin, BSA, and layered over 1.5 mL Lymphoprep Density Gradient Medium in a 15 mL conical tube, according to the manufacturer’s protocol.  The solution was centrifuged at 800xg for 20 min at room temperature without brake.  The mononuclear cell layer at the gradient interface was collected in a new tube and washed in PBS/2% FBS (10 mL total volume) and centrifuged at 120xg for 10 min at room temperature without brake.  The wash step was repeated two more times, and the cells were resuspended in PBS for sequencing library preparation.  The cells not used immediately were cryopreserved in 90% FBS/10% DMSO.
3' scRNA-seq (AmpliDrop technology); Dissociated cells (typically, >90-95% viable) in 0.1% BSA-supplemented 1x DPBS buffer were processed with AmpliDrop 3’ scRNA-seq kits following the manufacturer’s recommendations. Briefly, more than 200,000 cells were typically fixed at room temperature for 45 minutes and permeabilized for 10 minutes. For the RT and tagmentation reactions, we used 60,000 fixed and permeabilized cells. RT was conducted at 50°C for 10 minutes, and 10 cycles at 60°C for 30 sec and 50°C for 3 min, and tagmentation was conducted at 37°C for 15 minutes. Cell encapsulation was based on the following mixing protocol: 50 mixes of 170 µL at Speed 2 followed by 10 mixes of 170 µL at Speed 3. The emulsions were then moved to a thermocycler to run the following PCR/barcoding program: 72°C for 5 min, 98°C for 1 min, 26 cycles with 98°C for 15 sec, 61°C for 40 sec, and 72°C for 30 sec, and 5 cycles with 98°C for 15 sec, 50°C for 2 min, and 72°C for 40 sec, ending with 72°C for 2 min. After PCR/barcoding, the emulsions were dissolved, and the DNA was recovered from the solution  with the same volume of SPRI beads from MagBio genomics. The libraries were cleaned up with 80% ethanol for three times and finally eluted in 38 µL of 0.1x TE buffer, and half of this volume was used for indexing using Illumina adapters. Typically, we amplified the library with 9 to 12 cycles depending on the expected number of cell output (12 cycles for 1,000-2,000 cells and 9 cycles for 7,000-10,000 cells). The PCR indexing program is the following: 98°C for 30 sec, and 9-12 cycles with 98°C for 20 sec, 61°C for 30 sec, and 72°C for 30 sec, ending with 72°C for 2 min. After PCR, the library (40 µL) was diluted to 100 µL with TE buffer and cleaned up with 90 µL of SPRI beads. After washing with 80% ethanol twice, the library was eluted in 30 µL of 0.1x TE buffer. Libraries were then subject to quality control, sizing, and quantification using Agilent 4150 TapeStation system with High Sensitivity D1000 ScreenTape and Reagents.

treatment_protocol: No treatments were performed on cell lines. For seven-month-old organoids (Exp 1), mildly-perturbed conditions refer to a regimen of pipette aspiration with a wide-origfice 1mL tip and transfer of the organoids to a metal platform to mimic a mild physical manipulation of these multicellular structures. Severely-perturbed conditions refer to smashing the organoids to generate deformative compression to mimic a highly damaging physicial manipulation. Both treatments required maintaining the organoids for approximately 90 minutes outside the incubator. In the incubator, both sets of organoids were maintained withouth motion for 3 days. Non-perturbed organoids were maintained under orbital shaking all the time. For six-month-old organoids (Exp 2), everything was as in Exp1 but the non-perturbed group of organoids was also maintained 90 minutes outside the incubator. For two-month-old organoids (Exp3), one set was grown under orbital shaking always, while the other set was kept withouth motion for three days before library preparation.

value: brain cells

tag: cell line

value: hiPSC-derived forebrain organoids

tag: cell type

value: Human forebrain orgaboids derived from hiPSCs

value: WT

value: 7-month-old culture


title: Colon_Sham_rep9

description: Library name: Sham-383


title: Colon_Sham_rep8

description: Library name: Sham-381


title: Cell line MALME3M, CXXC1 siRNA, biological rep 1

city: Charlottesville

first: Mohammad

last: Fallahi-Sichani

state: Virginia

address: Box 800759, Health System

department: Biomedical Engineering

institute: University of Virginia

description: Library name: MALME3M_siCXXC1_Rep1

data_processing:
Raw FASTQ files were subjected to initial quality control using FastQC. Adapter sequences and low-quality bases were removed from paired-end reads using Trim Galore, with post-trimming quality assessment performed using FastQC. Trimmed reads were aligned to the human reference genome (GRCh38) using STAR (PMID: 23104886), with genome indices generated from the GENCODE v41 primary assembly FASTA and annotation files. STAR was run in paired-end mode to generate coordinate-sorted BAM files as well as transcriptome-aligned BAMs for downstream quantification. Alignment quality and read distribution metrics were assessed using Qualimap RNA-seq. Transcript- and gene-level expression quantification was performed using RSEM (PMID: 21816040) with a reference prepared from the same GENCODE v41 annotation, yielding expected counts and TPM values. Gene-level expected counts were compiled across all samples into a single expression matrix for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Gene-level read counts compiled across all samples into a single matrix (rows: genes, columns: experimental conditions)

molecule: total RNA

source_name: Skin

growth_protocol: SKMEL28 cells were grown in DMEM/F12 supplemented with 1% sodium pyruvate and 5% FBS. MALME3M, LOXIMVI, and UACC62 cells were grown in RPMI 1640 supplemented with 1% sodium pyruvate and 5% FBS. 100 U/mL Penicillin-Streptomycin (10,000 U/mL) and 0.5 mg/mL Plasmocin Prophylactic were present in all cell cultures. Cells were grown at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
At harvest, cells were washed once with PBS and lysed directly in the well using Buffer RLT (Qiagen). Lysates were homogenized using QIAshredder columns (Qiagen, catalog no. 79654), and total RNA was extracted using the RNeasy Mini Kit (Qiagen, catalog no. 74104) following the manufacturer’s protocol, including on-column DNase digestion (Qiagen RNase-Free DNase Set, catalog no. 79254). RNA integrity was assessed using the Agilent TapeStation (RNA ScreenTape), and all samples used for sequencing had RINe values > 9.
Bulk RNA sequencing libraries were prepared with assistance from the University of Virginia Genome Analysis and Technology Core (RRID: SCR_018883). Poly(A)+ RNA was isolated using the NEB mRNA Isolation Module, followed by library preparation using the NEBNext UltraExpress mRNA Library Prep Kit, according to the manufacturers’ instructions. Libraries were sequenced on an Illumina NextSeq 2000 platform using a P3-100 sequencing kit.

treatment_protocol: LOXIMVI, MALME3M, UACC62, and SKMEL28 cells were seeded in 6-well plates in biological triplicate and allowed to attach for 24 h prior to siRNA transfection. Cells were then treated with ON-TARGETplus siRNA SMARTpool targeting human CXXC1 (Horizon Discovery Biosciences; catalog no. L-014923-01-0005) or ON-TARGETplus Non-targeting siRNA #1 control (catalog no. D-001810-01-05) and cultured for 96 h post-transfection. siRNA transfections were performed using DharmaFECT transfection reagents (Horizon Discovery), including DharmaFECT 1 (catalog no. T-2001-02), DharmaFECT 2 (catalog no. T-2002-01), and DharmaFECT 3 (catalog no. T-2003-01), according to the manufacturer’s instructions.

value: Skin

value: Cutaneous melanoma

value: CXXC1 knockdown

value: CXXC1 siRNA (96 h)


title: Colon_Sham_rep6

description: Library name: Sham-378


title: Colon_Sham_rep5

description: Library name: Sham-377


title: Colon_Sham_rep7

description: Library name: Sham-379


title: Colon_Sham_rep3

description: Library name: Sham-375


title: Colon_Sham_rep2

description: Library name: Sham-374


title: Colon_Sham_rep4

description: Library name: Sham-376


title: Colon_TNBS_A1007_90mpk_rep10

description: Library name: A1007-90-369


title: Colon_Sham_rep1

description: Library name: Sham-373


title: HGC-27_1

city: Shanghai

first: Zewen

last: Chu

address: 1200 Cai Lun Road

institute: Shanghai University of Traditional Chinese Medicine

description: Library name: Sample 7

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCH38
Supplementary files format and content: tab-delimited xlsx files include FPKM values for each Sample

growth_protocol: Cells were cultured in RPMI-1640 medium (HyClone, Cat. No. SH30809.01, USA) supplemented with 10% fetal bovine serum (TransGen, Cat. No. FS301, China) and 1% penicillin–streptomycin solution (Beyotime, Cat. No. C0222, China). The cells were maintained in a humidified incubator at 37 °C with 5% CO₂.

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

treatment_protocol: The two gastric cancer cell lines were treated with betulonic acid at their respective 24-h IC50 concentrations and incubated for 24 h.

value: Human gastric cancer cell HGC-27

value: untreated


title: Colon_TNBS_A1007_90mpk_rep8

description: Library name: A1007-90-361


title: Colon_TNBS_A1007_90mpk_rep9

description: Library name: A1007-90-366


title: Colon_TNBS_A1007_90mpk_rep5

description: Library name: A1007-90-319


title: Colon_TNBS_A1007_90mpk_rep4

description: Library name: A1007-90-312


title: Colon_TNBS_A1007_90mpk_rep7

description: Library name: A1007-90-325


title: AGS_BA_3

description: Library name: Sample 6

source_name: AGS

value: AGS

value: Human gastric cancer cell AGS

value: Betulonic acid-treated


title: Colon_TNBS_A1007_90mpk_rep6

description: Library name: A1007-90-323

value: colon

value: BALBC


title: Colon_TNBS_A1007_90mpk_rep3

description: Library name: A1007-90-309


title: Colon_TNBS_A1007_30mpk_rep10

description: Library name: A1007-30-363


title: Colon_TNBS_A1007_90mpk_rep1

description: Library name: A1007-90-247


title: Colon_TNBS_A1007_30mpk_rep8

description: Library name: A1007-30-318


title: Exp1_organoid_nonperturbed_rep1

description:
AmpliDrop
230602_01_GM516S1_Exp1_org_non_perturbed_rep1


title: Colon_TNBS_A1007_30mpk_rep7

description: Library name: A1007-30-304


title: Colon_TNBS_A1007_30mpk_rep6

description: Library name: A1007-30-272


title: Colon_TNBS_A1007_30mpk_rep9

description: Library name: A1007-30-342


title: Colon_TNBS_A1007_90mpk_rep2

description: Library name: A1007-90-296


title: Colon_TNBS_A1007_30mpk_rep4

description: Library name: A1007-30-262


title: Colon_TNBS_A1007_30mpk_rep3

description: Library name: A1007-30-254


title: Colon_TNBS_A1007_30mpk_rep2

description: Library name: A1007-30-250


title: Colon_TNBS_A1007_10mpk_rep10

description: Library name: A1007-10-346


title: Colon_TNBS_A1007_30mpk_rep1

description: Library name: A1007-30-235


title: Colon_TNBS_A1007_10mpk_rep9

description: Library name: A1007-10-330


title: Colon_TNBS_A1007_10mpk_rep7

description: Library name: A1007-10-298


title: Colon_TNBS_A1007_10mpk_rep8

description: Library name: A1007-10-315


title: Colon_TNBS_A1007_10mpk_rep2

description: Library name: A1007-10-259


title: Colon_TNBS_A1007_10mpk_rep6

description: Library name: A1007-10-295


title: Colon_TNBS_A1007_10mpk_rep5

description: Library name: A1007-10-282


title: Colon_TNBS_A1007_10mpk_rep3

description: Library name: A1007-10-265


title: Colon_TNBS_A1007_10mpk_rep4

description: Library name: A1007-10-276


title: MC38 Vehicle Deple 1

city: Houston

first: Rajasekaran

last: Mahalingam

state: TX

address: 6565 MD Anderson Blvd

department: Symptom Research

institute: University of Texas MD Anderson Cancer Center

description: Library name: Sample22

data_processing:
Raw seqeuning qualit assessed with FastQC, trimmed with Trimmomatic
Aligned to the mouse reference genome (mm10) using the STAR aligner
Gene-level quantification was performed with HTSeq-count
Differential gene expression analysis was performed using the DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimted text file raw counts for each sample

source_name: Schwann cells

extract_protocol:
RNA was extracted using Rneasy mini plus kit and poly-T oligo-attached magnetic beads were used to isolate mRNA from the total RNA
The library construction included end repair, A-tailing, adapter ligation, size selection, and PCR amplification, concluding with purification

value: Schwann cells

value: MC38 serum


title: Colon_TNBS_A1007_10mpk_rep1

description: Library name: A1007-10-242


title: MC38 Vehicle Deple 3

description: Library name: Sample24


title: MC38 Vehicle intact 2

description: Library name: Sample20


title: MC38 Vehicle intact 1

description: Library name: Sample19


title: BMDM Vehicle Deple 2

description: Library name: Sample17

source_name: Bone Marrow Derived Macrophages

value: Bone Marrow Derived Macrophages

value: Vehicle serum


title: BMDM Vehicle intact 3

description: Library name: Sample15


title: BMDM Vehicle Deple 1

description: Library name: Sample16


title: BMDM Vehicle intact 2

description: Library name: Sample14


title: BMDM Vehicle intact 1

description: Library name: Sample13


title: SC MC38 3

description: Library name: Sample12


title: SC  Vehicle 2

description: Library name: Sample8


title: SC MC38 1

description: Library name: Sample10


title: SC  Vehicle 3

description: Library name: Sample9


title: BMDM MC38 2

description: Library name: Sample5


title: BMDM  Vehicle 3

description: Library name: Sample3


title: BMDM MC38 3

description: Library name: Sample6


title: BMDM  Vehicle 1

description: Library name: Sample1


title: MDFB, IL-17A

city: San Diego

first: Kellen

last: Cavagnero

state: California

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

description: Library name: KC36_2

data_processing:
Alignment to reference genome using STAR
Raw counts table generated using FeatureCounts
Assembly: mm10
Supplementary files format and content: CSV files with raw counts values for each sample

source_name: skin

extract_protocol:
ThermoFisher PureLink RNA Kit
Illumina stranded mRNA

value: skin

value: MDFB

value: Fibroblast

value: Wild type


title: MDFB, Vehicle

description: Library name: KC36_1

value: Vehicle


title: SIF6

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: Library name: SIF6

data_processing:
Reads were aligned and quantified using a nf-core/rnaseq pipeline (v3.12.0), which includes adapter trimming (Nextera/ISML) performed using bclconvert (v3.9.3) and employs STAR for alignment and Salmon for transcript quantification against the mouse reference genome (mm10), using reverse-strand specificity and default parameters.
Raw counts were normalized using TMM normalization (edgeR v3.40.2) followed by voom transformation (limma v3.54.2). Low-expression genes (zero TPM or zero counts), non-protein coding genes, pseudogenes, predicted genes, and uncharacterized transcripts were removed, resulting in a final matrix of 19,193 protein-coding genes.
Assembly: mm10
Supplementary files format and content: We provide 2 text files that contain raw counts as quantified by Salmon (raw_counts.txt), and log2 normalized counts of retained genes after removing lowly expressed or non-protein coding genes (filtered_lognorm_counts.txt). Both text files contain Ensembl Gene Ids in the first column, and the subsequent columns contain the gene expression values per sample.

source_name: Small intestine (jejunum)

growth_protocol: C57BL/6 mice were maintained under specific pathogen-free conditions with ad libitum access to food and water on a 12 h light/dark cycle. Mice were used at 8–12 weeks of age. Animals received either FLASH or conventional (CONV) whole-abdominal irradiation at a dose of 15 Gy, or were left untreated as controls.

extract_protocol:
Whole jejunum tissue was harvested and homogenized. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions. RNA quantity and quality were assessed prior to library preparation.
Sequencing libraries were prepared from 250 ng total RNA using the Illumina Stranded mRNA Ligation (ISML) library preparation protocol (Illumina protocol 1000000124518 v03). Library concentration was measured using the Qubit dsDNA High Sensitivity assay, and fragment size distribution was assessed using an Agilent TapeStation 4200. Libraries were sequenced on an Illumina NovaSeq 6000 platform using single-end 100 bp reads.

treatment_protocol: Mice were subjected to a single fraction of 15 Gy whole-abdominal irradiation delivered either at ultra-high dose rate (FLASH) or conventional dose rate (CONV). Unirradiated mice served as controls. Whole jejunum tissue was collected 16 h after irradiation for RNA extraction and transcriptomic analysis.

value: Small intestine (jejunum)

value: Whole jejunum tissue

value: Flash radiotherapy


title: SIF4

description: Library name: SIF4


title: SIF2

description: Library name: SIF2


title: SIF1

description: Library name: SIF1


title: SIF5

description: Library name: SIF5


title: SIC7

description: Library name: SIC7

value: Conventional radiotherapy


title: SIC6

description: Library name: SIC6


title: SIC2

description: Library name: SIC2


title: SIC5

description: Library name: SIC5


title: SICtrol6

description: Library name: SICtrol6

value: No treatment


title: SIC3

description: Library name: SIC3


title: SICtrol5

description: Library name: SICtrol5


title: VIM2_mutant_2

city: Freising

first: Zhilin

last: Zhang

state: Bavaria

address: Emil-Ramann-Str. 4

department: School of Life Sciences

country: Germany

institute: Technical University of Munich

description:
Library name: Sample5
vim2 T-DNA insertion mutant (NASC ID: N664186), biological replicate 2

data_processing:
Reads trimmed with Trimmomatic (v0.38) with options "ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:1:true", "LEADING:3", "TRAILING:3", "SLIDINGWINDOW:4:15", "MINLEN:36"
Reads aligned with STAR (v2.7.6a) with options "--alignIntronMin 60", "--alignIntronMax 6000"
Counts gathered for features using HTSeq-count (v0.13.5) with options "--mode=union". The strandedness parameter was set to --stranded=reverse for Ler_Cvi_RIL samples, and to --stranded=no for overexpression (OX), mutant, and control samples.
Assembly: TAIR10 genome and Araport11 annotation
Supplementary files format and content: HTSeq count files (.txt) with the following columns: <locus> <read count>

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: Transgenic overexpression lines and mutant plants were grown under long-day conditions (16h light/8h dark) at 22C on soil. T1 plants were selected in the presence of 50 ug/ml kanamycin. RIL plants were grown on half-strength MS plates under long-day conditions (16h light/8h dark) at 25C for 7-9 days.

extract_protocol:
For VIM overexpression and mutant lines, total RNA was extracted from leaves of 4 to 12-week-old T1 plants with the Monarch Total RNA Miniprep Kit (N2010, NEB) and tested with Qubit RNA BR Assay (Q33223, Thermo Fisher). For Ler x Cvi RILs, total RNA was extracted from bulk seedlings following the TRIzol extraction method.
For VIM overexpression and mutant lines, library preparation and 150 bp paired-end sequencing were performed by Novogene on an Illumina NovaSeq X Plus platform. For Ler x Cvi RILs, libraries were constructed using the TruSeq Stranded mRNA Library Kit (No.20020594, Illumina) with a custom dual index workflow. Paired-end 150 bp sequencing was performed on an Illumina NovaSeq 6000 platform.

value: leaf tissue

value: Col-0; vim2 (NASC ID:N664186)


title: SICtrol4

description: Library name: SICtrol4


title: SICtrol3

description: Library name: SICtrol3


title: SICtrol1

description: Library name: SICtrol1


title: SICtrol2

description: Library name: SICtrol2


title: RIL4_G02_L02_3

description: Library name: Sample18

library_source: genomic

data_processing:
Run MethylStar pipeline (Shahryary et al., 2020), using TAIR10 as a reference.
Cytosine-level methylation states were called as either methylated (“M”), unmethylated (“U”) or intermediate methylated (“I”) using a three-state Hidden Markov Model (Taudt et al. 2018).
Assembly: A. thaliana(TAIR10)
Supplementary files format and content: Tab-delimited text files for methylome generated using METHimpute (Taudt et al. 2018)

molecule: genomic DNA

growth_protocol: The MAMP was grown in climate-controlled chambers for nine selfing generations (Long day conditions, 16-h-day lengths, 18 C).

extract_protocol:
Samples were collected from young above-ground tissue. Leaf tissue was flash frozen in liquid nitrogen and DNA was extracted using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA, USA) based on the manufacturer’s instructions.
MethylC-seq libraries were prepared based on the protocol described in Urich et al., (2015). Libraries were sequenced at Genewiz on a NovaSeq 6000 platform (Illumina) in a paired-end 150bp format.

value: Ler X Cvi RIL

tag: ril line

tag: generation

tag: lineage

tag: sublineage


title: jo1_mice_model_868_pbs_inj_lt_hs

city: Pittsburgh

first: Alyxzandria

last: Gaydosik

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

description: Library name: jo1_mice_model_868_pbs_inj_lt_hs

data_processing:
Aligner: STAR (version 2.7.8a) Genome: mm39
Filtering: Noise Reduction. Excluded genes with a maximum count <= 1.0 across all samples.
Normalization: TMM (Trimmed Mean of M-values).
Differential Analysis: limma-voom.
Assembly: GRCm39
Supplementary files format and content: normalized counts, txt file

source_name: muscle

extract_protocol:
Libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module
Libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs, ref. #E7760). Libraries were sequenced on Illumina NovaSeq 6000, NovaSeq X Plus, and NextSeq 2000 platforms.

treatment_protocol: Mice Treatment: 100 uL of affinity-purified, filter-sterilized recombinant HRS (3-5 mg/mL) was administered via bilateral intramuscular hamstring injection (50 ml/side) of 8-10 week old female C57BL/6 mice to induce myositis; control mice received PBS only.  Mice were sacrificed 14 days post-immunization for collection of muscle tissue

value: muscle

tag: mouse


description: Library name: mouse_861_mouse_immunized_with_ma_mbp_fusion_protein_2_3_mg_ml

value: HRS (3-5 mg/mL)


title: Rosa-Cre CD4+ and PD-1fl/fl Rosa-Cre CD4+

city: Hershey

first: Vonn

last: Walter

address: 500 University Drive

department: Public Health Sciences

institute: Penn State College of Medicine

description: Library name: H173-01

data_processing:
Samples were demultiplexed using BCL Convert software (Illumina). Adaptors were not trimmed during demultiplexing.
Sample analysis was performed using BD Rhapsody Sequence Analysis Pipeline version 2.2.1. The pipeline performed a number of steps including quality control analysis, barcode detection on the multiplexed samples, and read alignment to the mouse reference, RhapRef_Mouse_WTA_2023-02. The reference was obtained from the BD publicly available refences resources. The pipeline also performed differential expression analysis producing gene expression matrices and cell clustering visualizations. The pipeline was run with default settings with the addition of the "Sample Tags Version" set to mouse in order to process the multiplexed samples.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
10 Rosa-Cre and 10 PD-1lf/fl Rosa-Cre mice were infected with MuPyV (A2 strain) and given tamoxifen 8 to 12 days dpi. Mice were IV-labeled, brains resected, and lymphocytes isolated and stained with CD3, CD8, CD4, CD44 (all Biolegend), and Db LT359 tetramers (NIH Tetramer Core). After staining, cells were pooled per mouse strain and stored overnight in BD OMICS-Guard Sample Preservation Buffer (BD Biosciences). The next day, cells were sorted into CD3+ CD4+ CD44+ T cells and CD3+ CD8+ CD44+ Db LT359+ T cells using a BD FACSAria SORP (BD Biosciences). After sorting, cells were multiplexed by cell type and strain using the BD Ms Single-Cell Multiplexing Kit (BD Biosciences) per manufacturer’s instructions. Cells were loaded onto the BD RhapsodyTM Cartridge, and mRNA was hybridized onto BD Rhapsody™ Enhanced Cell Capture Beads. Beads were retrieved, and reverse transcription was performed as detailed in the BD Rhapsody™ Single-Cell Analysis System User Guide.
Libraries were prepared in the Penn State College of Medicine Genome Sciences core using BD Rhapsody™ System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag following the manufacturer's protocol with the suggested cycles of 12 and 11 for RPE PCR and Sample Tag PCR1, respectively. For indexing, 8 cycles for WTA and 6 for cycles for sample indexing were carried out. Final libraries were assessed for size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). The libraries were pooled and sequenced on Illumina NovaSeq 6000 (Illumina) to get on average of 35,000 reads per cell, paired end 71 bp (read 2) and 51 bp (read 1) reads, according to the manufacturer's instructions.

treatment_protocol: A2 MuPyV and tamoxifen 8 to 12 days post infection

value: Brain

tag: age

value: 8 to 12 weeks old

tag: Sex

value: female

value: CD4 T cells

value: Rosa-Cre

value: Intracerebral infection and tamoxifen


title: Rosa-Cre CD8+ and PD-1fl/fl Rosa-Cre CD8+

description: Library name: H173-02

value: CD8 T cells

value: PD-1fl/fl Rosa-Cre


title: jo1_mice_model_867_pbs_inj_lt_hs

description: Library name: jo1_mice_model_867_pbs_inj_lt_hs


title: jo1_mice_model_866_pbs_inj_rt_hs

description: Library name: jo1_mice_model_866_pbs_inj_rt_hs


title: jo1_mice_model_867_pbs_inj_rt_hs

description: Library name: jo1_mice_model_867_pbs_inj_rt_hs


title: jo1_mice_model_864_pbs_inj_rt_hs

description: Library name: jo1_mice_model_864_pbs_inj_rt_hs


title: jo1_mice_model_865_pbs_inj_rt_hs

description: Library name: jo1_mice_model_865_pbs_inj_rt_hs


title: jo1_mice_model_863_pbs_inj_rt_hs

description: Library name: jo1_mice_model_863_pbs_inj_rt_hs


title: jo1_mice_model_862_pbs_inj_rt_hs

description: Library name: jo1_mice_model_862_pbs_inj_rt_hs


title: jo1_mice_model_866_ma_inj_lt_hs

description: Library name: jo1_mice_model_866_ma_inj_lt_hs


title: jo1_mice_model_864_ma_inj_lt_hs

description: Library name: jo1_mice_model_864_ma_inj_lt_hs


title: jo1_mice_model_862_ma_inj_lt_hs

description: Library name: jo1_mice_model_862_ma_inj_lt_hs


title: MMTV_Pymt_Pri_Tumor_Rep2

city: Chicago

first: Nissim

last: Hay

state: IL

address: 900 South Ashland Ave

department: BMG

institute: University of Illinois Chicago

description:
Library name: W28
10x Genomics

data_processing:
CellRanger (v6.0.2; 10x Genomics) was used to map the scRNAseq data. In brief, CellRanger’s mkfastq module was used to preprocess/demultiplex the raw sequences in the FASTQ files and also convert the BCL files to FASTQ files. Then, CellRanger’s align module (using STAR aligner v2.7.10b) was used to align the reads to the murine reference genome (GRCm38/mm10). The feature-barcode matrices, which contain the quantified expression of each gene in each cell, was generated using CellRanger’s count module. This module identifies the cell barcodes and UMIs (unique molecular identifiers) within each BAM files and creates a new filtered BAM file, which only contains cell-associated reads. The filtered BAM file is used to generate a digital expression matrix (DEMs), which quantifies the number of UMIs that correspond to genes in each individual cell. Finally, CellRanger’s agger module was used to perform quality control of the mapped data. This involves combining the DEMS from multiple scRNAseq libraries to generates a normalized expression matrix, which is used for downstream analyses. Since neutrophils are poor in RNA and, therefore, have less UMIs per barcode, we ran CellRanger with the "force-cells" option to capture cells with lower UMIs and gene counts. We also included introns using the "include-introns" option since neutrophils are known to retain more introns during differntiation (10x Genomics; Technical Note CG000444).
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated files and matrix files

source_name: Tumor

growth_protocol: All animals will be housed in a pathogen-free animal facility at the University of Illinois at Chicago and fed a standard autoclaved diet ad libitum on a 12 hour light/dark schedule with two to five companions per cage.

extract_protocol:
Bone marrow cells were collected by flushing tibia and femur with complete RPMI media with 2mM EDTA, followed by RBC lysis and 3 washes with complete RPMI. Blood was collected via the vena cava, followed by RBC lysis and three washes with complete RPMI. Lungs and tumor cells were collected after digestion with the tissue dissociation kit from Miltenyi Biotec following manufacturer's recommended protocol and then treated with RBC lysis buffer followed by three washes with complete RPMI. Spleen was collected and minced in a dish with complete RPMI, treated with RBC lysis buffer, and washed three times with complete RPMI. Cells were strained with a 70uM filter.
Samples were processed for scRNAseq using the Chromium Single Cell Library and Gel bead kit v3; the manufacturer’s recommended protocol was followed (10x Genomics, CG000183_ChromiumSingleCell3__v3_UG_RevB).  Chromium’s Controller was used to make nanoliter-sized droplets that harbor uniquely barcoded beads called Gel Bead-InEMulsions or GEMs. After GEM generation, the mRNA was reverse-transcribed, and the resulting cDNA was amplified with 11 PCR cycles. The Chromium i7 Samples Index plate (10x Genomics) was utilized to PCR amplify the final library for 11 to 14 cycles. QC of the libraries was assessed using the High Sensitivity D5000 ScreenTape (TapeStation, Agilent Technologies). Finally, the libraries were sequenced using a NovaSeq 6000 SP flowcell (Illumina). The facilities at Illinois Urbana-Champaign conducted the sequencing.

value: Tumor

value: Unsorted single cells

value: Ert2Cre; MMTV-Pymt


title: Wildtype_Spleen_Rep1

description:
Library name: W29
10x Genomics

source_name: Spleen

value: Spleen


title: MMTV_Pymt_Lung_Rep3

description:
Library name: W26
10x Genomics

source_name: Lung

value: Lung


title: MMTV_Pymt_Spleen_Rep1

description:
Library name: W30
10x Genomics

source_name: Spleeen


title: Wildtype_Lung_Rep3

description:
Library name: W24
10x Genomics


title: MMTV_Pymt_Blood_Rep2

description:
Library name: W23
10x Genomics

source_name: Blood

value: Blood


title: Wildtype_Blood_Rep2

description:
Library name: W22
10x Genomics


title: MMTV_Pymt_Lung_Rep2

description:
Library name: W20
10x Genomics


title: MMTV_Pymt_anti_GCSF_BM_Rep1

description:
Library name: W14
10x Genomics

source_name: Bone Marrow

value: Bone Marrow

value: anti-G-CSF antibody


title: Wildtype_Lung_Rep2

description:
Library name: W19
10x Genomics


title: MMTV_Pymt_iso_BM_Rep1

description:
Library name: W13
10x Genomics

value: IgG Ctrl


title: GCSF_BM_Rep2

description:
Library name: W12
10x Genomics

value: Recombinant mouse G-CSF


title: NT_BM_Rep2

description:
Library name: W11
10x Genomics

value: 0.1% BSA/PBS


title: uninjected_BM_Rep1

description:
Library name: W10
10x Genomics

value: Naive


title: NT_BM_Rep1

description:
Library name: W7
10x Genomics


title: MMTV_Pymt_BM_Rep2

description:
Library name: W4
10x Genomics


title: Wildtype_BM_Rep2

description:
Library name: W3
10x Genomics


title: MMTV_BM_Pymt_Rep1

description:
Library name: W2
10x Genomics


title: Wildtype_BM_Rep1

description:
Library name: W1
10x Genomics


title: BMP2&RSPO2_3

city: Ann Arbor

first: Buchan

last: Jiang

state: Michigan

address: 109 Zina Pitcher Pl, Room 2013

department: Department of Orthopaedic Surgery

institute: University of Michigan

description:
Library name: Sample12
Column name in FPKMs_all_sample.csv: FPKM.BMP2_RSPO2_3

data_processing:
Base calling and demultiplexing were performed using Illumina sequencing software. Raw sequencing reads were processed as follows: Adapter trimming and removal of low-quality reads were performed using Cutadapt (v1.10). Quality control of reads was assessed using FastQC (v0.10.1). Clean reads were aligned to the mouse reference genome (Mus musculus) using HISAT2 (v2.0). Aligned reads were assembled into transcripts using StringTie (v1.3.4). Transcript expression levels were quantified as FPKM (Fragments Per Kilobase per Million mapped reads). Differential gene expression analysis was performed using edgeR package in R. Differentially expressed genes were defined using: fold change ≥ 1.5 or ≤ -1.5, and p-value < 0.05.
Assembly: Mus musculus genome assembly: GRCm38 (mm10) (Ensembl release 92)
Supplementary files format and content: Raw counts file: tab-delimited text file (.txt). Containing raw read counts for each gene across all samples.
Supplementary files format and content: FPKM expression file: comma-separated values (.csv). Containing normalized gene expression values (FPKM) for each gene in each sample.

growth_protocol: MC3T3-E1 subclone 14 pre-osteoblast cells were cultured in α-minimum essential medium (α-MEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂. For osteogenic differentiation, cells were cultured in osteogenic medium consisting of: α-MEM, 50 μg/mL ascorbic acid phosphate, 5 mM β-glycerophosphate. Cells were plated at appropriate density and allowed to attach overnight prior to treatment.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA concentration and purity were measured using NanoDrop spectrophotometer. RNA integrity was assessed using Agilent Technologies 2100 Bioanalyzer. Only RNA samples with high integrity (RIN ≥ 7.0) were used for library preparation.
Poly(A) RNA sequencing libraries were prepared using Illumina TruSeq Stranded mRNA Library Preparation Kit according to the manufacturer’s protocol. Briefly, Poly(A)+ RNA was purified from total RNA using oligo(dT) magnetic beads. Purified RNA was fragmented using divalent cations at elevated temperature. First-strand cDNA synthesis was performed using reverse transcriptase and random primers. Second-strand cDNA synthesis was performed to generate double-stranded cDNA. cDNA fragments underwent end repair, A-tailing, and ligation of sequencing adapters. Adapter-ligated fragments were PCR amplified to enrich the library. Library quality and fragment size distribution were assessed using Agilent Bioanalyzer High Sensitivity DNA chip. Libraries were sequenced using Illumina NovaSeq 6000 platform.

treatment_protocol: Cells were treated under osteogenic differentiation conditions for 5 days with: vehicle control, recombinant mouse RSPO2 protein (200ng/ml; R&D Systems), recombinant human/mouse BMP2 protein (100ng/ml; R&D Systems), or the combination of RSPO2 and BMP2. RSPO2 and BMP2 were added at concentrations previously determined to induce osteogenic differentiation and transcriptional responses. Media and growth factors were refreshed every 3–4 days during the treatment period. Cells were harvested for RNA extraction on day 5.

value: pre-osteoblasts

value: WT

value: osteogenic differentiation, recombinant BMP2 and recombinant RSPO2

value: Day 5


title: BMP2&RSPO2_2

description:
Library name: Sample11
Column name in FPKMs_all_sample.csv: FPKM.BMP2_RSPO2_2


title: BMP2&RSPO2_1

description:
Library name: Sample10
Column name in FPKMs_all_sample.csv: FPKM.BMP2_RSPO2_1


title: BMP2_3

description:
Library name: Sample9
Column name in FPKMs_all_sample.csv: FPKM.BMP2_3

value: osteogenic differentiation and recombinant BMP2


title: BMP2_2

description:
Library name: Sample8
Column name in FPKMs_all_sample.csv: FPKM.BMP2_2


title: BMP2_1

description:
Library name: Sample7
Column name in FPKMs_all_sample.csv: FPKM.BMP2_1


title: Wildtype_Blood_Rep1

description:
Library name: W17
10x Genomics


title: RSPO2_3

description:
Library name: Sample6
Column name in FPKMs_all_sample.csv: FPKM.RSPO2_3

value: osteogenic differentiation and recombinant RSPO2


title: RSPO2_2

description:
Library name: Sample5
Column name in FPKMs_all_sample.csv: FPKM.RSPO2_2


title: RSPO2_1

description:
Library name: Sample4
Column name in FPKMs_all_sample.csv: FPKM.RSPO2_1


title: Control_3

description:
Library name: Sample3
Column name in FPKMs_all_sample.csv: FPKM.CON_3

value: osteogenic differentiation


title: Control_2

description:
Library name: Sample2
Column name in FPKMs_all_sample.csv: FPKM.CON_2


title: eo771_BM_ortho_Rep1

description:
Library name: W9
10x Genomics

value: Unsorted single cells

value: orthotopic injection with E0771


title: GCSF_BM_Rep1

description:
Library name: W8
10x Genomics


title: Control_1

description:
Library name: Sample1
Column name in FPKMs_all_sample.csv: FPKM.CON_1


title: Chaf1a cko 3M rep 3

first: Yuan

last: Min

address: 1239 Siping Road

institute: Tongji university

description:
Library name: Chaf1a_140_cko
Column name in 3M_gene_count_matrix.csv: Chaf1a_140_cko

data_processing:
Raw sequencing reads were quality checked using FastQC.
Adapters and low-quality bases were trimmed with Trimmomatic.
Cleaned reads were aligned to the mouse reference genome (mm10) using Hisat2.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
Total RNA was extracted from cultured cardiomyocytes using TRIzol reagent (Invitrogen, 15596018).
Stranded RNA sequencing was performed using the KAPA Stranded RNA-Seq Kit with RiboErase (Illumina® Platforms, KR1151) according to the manufacturer’s protocol.

value: heart

value: cardiomyocytes

value: Chaf1a cko


title: Chaf1a cko 3M rep 2

description:
Library name: Chaf1a_137_cko
Column name in 3M_gene_count_matrix.csv: Chaf1a_137_cko


title: Ctrl 3M rep 3

description:
Library name: Chaf1a_141_WT
Column name in 3M_gene_count_matrix.csv: Chaf1a_141_WT


title: Ctrl 3M rep 2

description:
Library name: Chaf1a_134_WT
Column name in 3M_gene_count_matrix.csv: Chaf1a_134_WT


title: Colon_TNBS_A1007_30mpk_rep5

description: Library name: A1007-30-268

source_name: colon

value: colon

value: BALBC


title: Chaf1a cko 3M rep 1

description:
Library name: Chaf1a_133_cko
Column name in 3M_gene_count_matrix.csv: Chaf1a_133_cko


title: Ctrl 3M rep 1

description:
Library name: Chaf1a_131_WT
Column name in 3M_gene_count_matrix.csv: Chaf1a_131_WT


title: Tut4WT_Tut7WT_71e_LSK

city: Cambridge

first: Bertie

last: Gottgens

email: bg200@cam.ac.uk, nkw22@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description: Library name: SITTH7

data_processing:
sequenced using the Illumina NovaSeq instrument, obtaining at least 20,000 reads per cell in each run. 10x genomics reads were pre-processed using cellranger (version 3.1.0, reference genome and annotation version 3.0.0) with default settings
Assembly: Cellrange reference v3
Supplementary files format and content: .h5 files containing counts

source_name: bone marrow

extract_protocol:
Femur/tibia/hip bones were collected and crushed in 4 ml of 2% FCS/PBS (resuspension buffer). Harvested liquid was filtered  through a 50um filter. Cells were centrifuged (300g, 5min) and resuspended in 3ml of resuspension buffer. 5ml of cold Ammonium Chloride (StemCell Tech. cat. No 07800) was added and cells were incubated for 5 min, vortexed and incubated for 5 min. 7ml of resuspension buffer was added and cells were centrifuged and resuspended in 1000ul resuspension buffer, subjected to lineage depletion (EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit) and stained with: 7AAD, Lineage cocktail, EPCR, CD48, Sca1, c-Kit, CD150. (Lin-,Sca1+/cKit+) or (Lin-, Sca1+ OR cKit+) were sorted by flow cytometry into resuspension buffer
In brief, up to 20,000 LK or LSK cells were sorted per biological donor, centrifuged and resuspended in a volume of droplet buffer optimal for recovery of up to 10,000 cells and immediately processed with the 10x Genomics Single Cell 3’ v3 protocol following the manufacturer’s instructions. Libraries were sequenced using the Illumina NovaSeq instrument, obtaining at least 20,000 reads per cell in each run

value: bone marrow

value: LSK


title: Tut4WT_Tut7WT_71e_LK

description: Library name: SITTG7

value: Lin-, Kit+ OR Sca1+


title: VavCre_Tut4KO_Tut7KO_71d_LSK

description: Library name: SITTF7

value: Lin-, kit+. Sca1+

value: Tut4/7 KO


title: VavCre_Tut4KO_Tut7KO_71d_LK

description: Library name: SITTE7


title: MC38 Vehicle Deple 2

description: Library name: Sample23

value: Schwann cells

value: MC38 serum


title: Tut4WT_Tut7WT_71c_LK

description: Library name: SITTC7

value: WT


title: VavCre_Tut4KO_Tut7KO_KO_71b_LSK

description: Library name: SITTB7


title: Tut4WT_Tut7WT_71c_LSK

description: Library name: SITTD7


title: BMDM Vehicle Deple 3

description: Library name: Sample18

value: Bone Marrow Derived Macrophages

value: Vehicle serum


title: MC38 Vehicle intact 3

description: Library name: Sample21


title: VavCre_Tut4KO_Tut7KO_71b_LK

description: Library name: SITTA7


title: Chaf1a cko rep 3

description: Library name: Chaf1a cko rep 3


title: Chaf1a cko rep 2

description: Library name: Chaf1a cko rep 2


title: Chaf1a cko rep 1

description: Library name: Chaf1a cko rep 1


title: SC MC38 2

description: Library name: Sample11


title: Ctrl rep 3

description: Library name: Ctrl rep 3


title: Ctrl rep 2

description: Library name: Ctrl rep 2


title: Spp1KO/CX3CR1-GFP microglia, ONC, replicate 4

city: Boston

first: Tatjana

last: Jakobs

state: MA

address: 20 Staniford Street

department: Howe Laboratory of Ophthalmology

institute: Massachusetts Eye and Ear Infirmary

description: Library name: F4

data_processing:
STAR, DEseq2
Assembly: GRCm38
Supplementary files format and content: csv, raw counts for all samples

source_name: retina

growth_protocol: ex vivo, FACS isolated microglia

extract_protocol:
RNeasy plus mini kit (Qiagen)
SMARTER RNA-seq library preparation kit

treatment_protocol: IOP elevation was induced by the injection of microbeads into the anterior chamber. Optic nerve crush was performed about 2 mm behind the globe.

value: retina

value: freshly isolated

value: microglia

value: opic nerve crush


title: Ctrl rep 1

description: Library name: Ctrl rep 1

value: heart

value: cardiomyocytes


title: BMDM MC38 1

description: Library name: Sample4


title: BMDM  Vehicle 2

description: Library name: Sample2


title: Spp1KO/CX3CR1-GFP microglia, ONC, replicate 3

description: Library name: F3


title: Spp1KO/CX3CR1-GFP microglia, ONC, replicate 2

description: Library name: F2


title: Spp1KO/CX3CR1-GFP microglia, ONC, replicate 1

description: Library name: F1


title: Spp1KO/CX3CR1-GFP microglia, high IOP, replicate 3

description: Library name: E3

value: IOP elevation


title: SIF9

description: Library name: SIF9

value: Small intestine (jejunum)

value: Whole jejunum tissue

value: Flash radiotherapy


title: SIF7

description: Library name: SIF7


title: Spp1KO/CX3CR1-GFP microglia, high IOP, replicate 4

description: Library name: E4


title: Spp1KO/CX3CR1-GFP microglia, high IOP, replicate 2

description: Library name: E2


title: Spp1KO/CX3CR1-GFP microglia, high IOP, replicate 1

description: Library name: E1


title: Spp1KO/CX3CR1-GFP microglia, control, replicate 4

description: Library name: D4


title: Spp1KO/CX3CR1-GFP microglia, control, replicate 3

description: Library name: D3


title: Spp1KO/CX3CR1-GFP microglia, control, replicate 2

description: Library name: D2


title: Spp1KO/CX3CR1-GFP microglia, control, replicate 1

description: Library name: D1


title: CX3CR1-GFP microglia, ONC, replicate 3

description: Library name: C3


title: CX3CR1-GFP microglia, ONC, replicate 1

description: Library name: C1


title: CX3CR1-GFP microglia, ONC, replicate 2

description: Library name: C2


title: CX3CR1-GFP microglia, high IOP, replicate 4

description: Library name: B4


title: CX3CR1-GFP microglia, high IOP, replicate 3

description: Library name: B3


title: CX3CR1-GFP microglia, high IOP, replicate 2

description: Library name: B2


title: CX3CR1-GFP microglia, high IOP, replicate 1

description: Library name: B1


title: CX3CR1-GFP microglia, control, replicate 3

description: Library name: A3


title: CX3CR1-GFP microglia, control, replicate 4

description: Library name: A4


title: CX3CR1-GFP microglia, control, replicate 1

description: Library name: A1


title: HFDcoixenolide4

city: Hangzhou

first: Chen

last: Kaidi

address: Binwen Road, Hangzhou, Zhejiang

institute: Zhejiang Chinese Medical University

description:
Library name: Sample13
one sample from murine PAAD tumor tissue

data_processing:
The single-cell suspensions dissociated from tumors (derived from P01-P34) were centrifuged and washed twice with 1xPBS, and then the single-cell pellets were re-suspended within 1xPBS supplemented with 0.04% BSA at a final concentration of 1x106 cells/mL. About 10 mL of cell suspensions (z10000 cells) were mixed with barcoded Single Cell 3ʹ v.3.1 Gel Beads and Partitioning Oil to generate nanoliter-scale Gel beads in EMulsion (GEMs). Next, the GEMs were subjected to reverse transcription PCR using a T100 Thermal Cycler (Bio-Rad) in a 125 mL volume (program: 53℃ for 45 min, 85℃ for 5 min, hold at 4℃) to obtain full-length cDNA with barcoding. After this, the first-strand cDNAs were incubated with Dynabeads Cleanup Mix to purify them from the PCR mix and then amplified using the Amplification Reaction Mix on a T100 Thermal Cycler (Bio-Rad) (program: 98℃ for 3 min, 98℃ for 15 seconds, 63 ℃ for 20 seconds, 72℃ for 1 min [step 2 to step 4 for total 12 of cycles], and hold at 4℃). Subsequently, the amplified cDNA was used to generate a single-cell 3ʹ gene expression dual index library using Chromium Next GEM Single Cell 3’ Library Kit v.3.1 (10x Genomics). Finally, the well-prepared single cell 3ʹ gene expression libraries were sequenced on an Illumina NovaSeq 6000 sequencer.
Assembly: GRCh38 (Ensembl version 92 annotation)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PAAD tumor

extract_protocol:
Cells were isolated from tumor tissues using GEXSCOPE Nuclear Extraction Buffer (adding RNase inhibitor and DTT before use, the final concentrations of the two are 0.2 U/µL, 1 mM, respectively). Single-cell suspensions at a concentration of 1 × 105 cells/mL in PBS were prepared.
Single-cell suspensions were loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPE protocol using GEXSCOPE Single-Cell RNA Library Kit (Singleron Biotechnologies), which included cell lysis, mRNA trapping, labeling cells (barcode) and mRNA (UMI), mRNA reverse transcription, cDNA amplification, and finally cDNA fragmentation.

value: PAAD tumor


title: CX3CR1-GFP microglia, control, replicate 2

description: Library name: A2


title: HFDcoixenolide3

description:
Library name: Sample12
one sample from murine PAAD tumor tissue


title: HFDcoixenolide1

description:
Library name: Sample10
one sample from murine PAAD tumor tissue


title: HFDcoixenolide2

description:
Library name: Sample11
one sample from murine PAAD tumor tissue


title: HFDCtrl2

description:
Library name: Sample8
one sample from murine PAAD tumor tissue


title: HFDCtrl3

description:
Library name: Sample9
one sample from murine PAAD tumor tissue


title: CDcoixenolide3

description:
Library name: Sample6
one sample from murine PAAD tumor tissue


title: HFDCtrl1

description:
Library name: Sample7
one sample from murine PAAD tumor tissue


title: CDcoixenolide2

description:
Library name: Sample5
one sample from murine PAAD tumor tissue


description: Library name: mouse_860_mouse_immunized_with_ma_mbp_fusion_protein_2_3_mg_ml

value: muscle

value: HRS (3-5 mg/mL)


title: CDcoixenolide1

description:
Library name: Sample4
one sample from murine PAAD tumor tissue


title: CDCtrl3

description:
Library name: Sample3
one sample from murine PAAD tumor tissue


title: CDCtrl2

description:
Library name: Sample2
one sample from murine PAAD tumor tissue


title: CDCtrl1

description:
Library name: Sample1
one sample from murine PAAD tumor tissue


title: Trem2 KO, 13 hours, replicate 5, Low-input protocol [HSA-000027399]

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

data_processing:
Data was processed using nf-core/rnaseq v3.11.2 (doi:https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewelset al., 2020) using Gencode M31 gene annotations. Because the QuantSeq data only captures 3' tags from transcripts, the following custom parameters were supplied: extra_star_align_args: '--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA' and extra_salmon_quant_args: '--noLengthCorrection'.
Assembly: GRCm39
Supplementary files format and content: File raw_and_normalized_counts.xlsx is a Microsoft Excel file with four worksheets: 1. sample information, 2. gene information, 3. raw count table, 4. normalized count table (log2 counts per million).

source_name: BMDM

growth_protocol: Animals were sacrificed and the femur and tibia bones were collected into cold HBSS (Gibco; Cat# 14175095). Bones from multiple mice (6 for WT only studies) were pooled for each individual biological replicate and sterilized with 70% isopropanol, washed three times with HBSS, and cracked in HBSS using a mortar and pestle. The cell suspension containing bone marrow cells was filtered through a 70mm strainer to remove cracked bone pieces and centrifuged at 300xg for 5 minutes. The supernatant was removed, and the pellet was resuspended in ACK Lysing Buffer (ThermoFisher; Cat# A1049201) for 2 minutes at room temperature to remove red blood cells. Then, BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] was added to stop the ACK lysis reaction. Cells were pelleted at 300xg for 5 minutes and the supernatant was discarded. Then, the cell pellet was resuspended in BMDM medium, counted, and plated onto 15cm non-tissue culture treated petri dishes at a density of 20 million cells/plate in BMDM medium containing murine M-CSF (Life Technologies; Cat# PMC2044) at 50ng/mL. Four days after seeding the cells, an additional 50ng/mL fresh M-CSF was added to each plate. On day 7, differentiated BMDMs were washed once with PBS and harvested in BMDM medium using a cell scraper. Cells were pelleted at 300xg for 5 minutes, resuspended in BMDM medium, and counted. Finally, cells were centrifuged at 300xg for 5 minutes, resuspended in Recovery Cell Culture Freezing Medium (Gibco; Cat# 12648010) at a density of 10 million cells/mL, and cryopreserved for later use.

extract_protocol:
RNA was harvested from cells using the RNeasy Micro Kit (Qiagen), following the manufacturer’s protocol. RNA integrity (RIN) and concentration were measured by High Sensitivity RNA Screen Tape Analysis (Agilent) on a 4200 TapeStation System (Agilent). Libraries were generated using the QuantSeq 3’ mRNA-seq Library Prep Kit FWB for Illumina (Lexogen A01173) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Library quantity and quality were assessed with TapeStation High Sensitivity D1000 Screen Tape (Agilent 5067-5592) using High Sensitivity D1000 reagents (Agilent 5067-5593). Libraries were pooled in equimolar ratios and sent to SeqMatic for sequencing on a NovaSeq S1 (75bp, single-end reads).
Libraries were generated using the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173) with the UMI second strand synthesis module in order to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Library quantity and quality were assessed with TapeStation High Sensitivity D1000 ScreenTape (Agilent 5067-5592) using High Sensitivity D1000 reagents (Agilent 5067-5593).

treatment_protocol: Differentiated BMDMs were thawed, counted, and seeded at 75k cells/well onto poly-D-lysine-coated plates in BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] with supplemental M-CSF (50ng/mL). Fresh BMDM medium was changed 24 hours after seeding of the cells.

tag: replicate

value: BMDM

value: Trem2 KO

tag: timepoint

value: 13 hours

tag: protocol

value: Low-input

tag: rin


title: jo1_mice_model_868_pbs_inj_rt_hs

description: Library name: jo1_mice_model_868_pbs_inj_rt_hs

tag: tissue


title: Trem2 KO, 13 hours, replicate 4, Low-input protocol [HSA-000027398]

tag: genotype


title: Trem2 KO, 13 hours, replicate 2, Low-input protocol [HSA-000027396]


title: Trem2 KO, 13 hours, replicate 3, Low-input protocol [HSA-000027397]


title: Trem2 KO, 13 hours, replicate 1, Low-input protocol [HSA-000027395]


title: Grn KO, 13 hours, replicate 5, Regular protocol [HSA-000027394]

value: Grn KO

value: Regular


title: Grn KO, 13 hours, replicate 4, Low-input protocol [HSA-000027393]


title: Grn KO, 13 hours, replicate 3, Low-input protocol [HSA-000027392]


title: Grn KO, 13 hours, replicate 2, Regular protocol [HSA-000027391]


title: Grn KO, 13 hours, replicate 1, Regular protocol [HSA-000027390]


title: Ctsd KO, 13 hours, replicate 5, Regular protocol [HSA-000027384]

value: Ctsd KO


title: Ctsd KO, 13 hours, replicate 4, Low-input protocol [HSA-000027383]


title: Ctsd KO, 13 hours, replicate 2, Regular protocol [HSA-000027381]


title: Ctsd KO, 13 hours, replicate 1, Low-input protocol [HSA-000027380]


title: Pik3c3 KO, 13 hours, replicate 5, Low-input protocol [HSA-000027379]

value: Pik3c3 KO


title: jo1_mice_model_863_ma_inj_lt_hs

description: Library name: jo1_mice_model_863_ma_inj_lt_hs

tag: treatment


title: Pik3c3 KO, 13 hours, replicate 4, Low-input protocol [HSA-000027378]


title: jo1_mice_model_865_ma_inj_lt_hs

description: Library name: jo1_mice_model_865_ma_inj_lt_hs


title: Ctsd KO, 13 hours, replicate 3, Low-input protocol [HSA-000027382]


title: Pik3c3 KO, 13 hours, replicate 2, Regular protocol [HSA-000027376]


title: Npc1 KO, 13 hours, replicate 5, Low-input protocol [HSA-000027374]

value: Npc1 KO


title: Pik3c3 KO, 13 hours, replicate 1, Low-input protocol [HSA-000027375]


title: Pik3c3 KO, 13 hours, replicate 3, Low-input protocol [HSA-000027377]


title: Npc1 KO, 13 hours, replicate 4, Regular protocol [HSA-000027373]


title: Npc1 KO, 13 hours, replicate 3, Low-input protocol [HSA-000027372]


title: Npc1 KO, 13 hours, replicate 2, Low-input protocol [HSA-000027371]


title: Npc1 KO, 13 hours, replicate 1, Regular protocol [HSA-000027370]


title: Atp6v1a KO, 13 hours, replicate 5, Regular protocol [HSA-000027369]

value: Atp6v1a KO


title: Atp6v1a KO, 13 hours, replicate 4, Regular protocol [HSA-000027368]


title: MMTV_Pymt_Lung_Mets_Rep3

description:
Library name: W25
10x Genomics

value: Lung

value: Unsorted single cells

value: Ert2Cre; MMTV-Pymt

tag: batch


title: Atp6v1a KO, 13 hours, replicate 3, Low-input protocol [HSA-000027367]


title: Atp6v1a KO, 13 hours, replicate 2, Low-input protocol [HSA-000027366]


title: Atp6v1a KO, 13 hours, replicate 1, Low-input protocol [HSA-000027365]


title: Rosa26 KO, 13 hours, replicate 5, Low-input protocol [HSA-000027364]

value: Rosa26 KO


title: Rosa26 KO, 13 hours, replicate 4, Regular protocol [HSA-000027363]


title: Rosa26 KO, 13 hours, replicate 3, Regular protocol [HSA-000027362]


title: Rosa26 KO, 13 hours, replicate 2, Regular protocol [HSA-000027361]


title: Trem2 KO, 4 hours, replicate 4, Regular protocol [HSA-000027358]

value: 4 hours


title: Trem2 KO, 4 hours, replicate 5, Regular protocol [HSA-000027359]


title: Trem2 KO, 4 hours, replicate 3, Regular protocol [HSA-000027357]


title: Rosa26 KO, 13 hours, replicate 1, Regular protocol [HSA-000027360]


title: Trem2 KO, 4 hours, replicate 1, Low-input protocol [HSA-000027355]


title: Grn KO, 4 hours, replicate 5, Regular protocol [HSA-000027354]


title: Grn KO, 4 hours, replicate 3, Regular protocol [HSA-000027352]


title: Ctsd KO, 4 hours, replicate 5, Regular protocol [HSA-000027344]


title: Ctsd KO, 4 hours, replicate 3, Regular protocol [HSA-000027342]


title: Ctsd KO, 4 hours, replicate 1, Regular protocol [HSA-000027340]


title: Pik3c3 KO, 4 hours, replicate 5, Regular protocol [HSA-000027339]


title: Pik3c3 KO, 4 hours, replicate 3, Regular protocol [HSA-000027337]


title: Pik3c3 KO, 4 hours, replicate 4, Regular protocol [HSA-000027338]


title: Pik3c3 KO, 4 hours, replicate 2, Regular protocol [HSA-000027336]


title: Pik3c3 KO, 4 hours, replicate 1, Regular protocol [HSA-000027335]


title: Npc1 KO, 4 hours, replicate 5, Regular protocol [HSA-000027334]


title: Npc1 KO, 4 hours, replicate 4, Regular protocol [HSA-000027333]


title: Npc1 KO, 4 hours, replicate 2, Regular protocol [HSA-000027331]


title: Atp6v1a KO, 4 hours, replicate 5, Regular protocol [HSA-000027329]


title: Atp6v1a KO, 4 hours, replicate 4, Regular protocol [HSA-000027328]


title: Rosa26 KO, 4 hours, replicate 4, Regular protocol [HSA-000027323]


title: Rosa26 KO, 4 hours, replicate 5, Regular protocol [HSA-000027324]


title: Rosa26 KO, 4 hours, replicate 1, Regular protocol [HSA-000027320]


title: Rosa26 KO, 4 hours, replicate 2, Regular protocol [HSA-000027321]


title: Trem2 KO, BafA1, replicate 2 [HSA-000022469]

growth_protocol: Animals were sacrificed and the femur and tibia bones were collected into cold HBSS (Gibco; Cat# 14175095). Bones from multiple mice (3 for KO studies) were pooled for each individual biological replicate and sterilized with 70% isopropanol, washed three times with HBSS, and cracked in HBSS using a mortar and pestle. The cell suspension containing bone marrow cells was filtered through a 70mm strainer to remove cracked bone pieces and centrifuged at 300xg for 5 minutes. The supernatant was removed, and the pellet was resuspended in ACK Lysing Buffer (ThermoFisher; Cat# A1049201) for 2 minutes at room temperature to remove red blood cells. Then, BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] was added to stop the ACK lysis reaction. Cells were pelleted at 300xg for 5 minutes and the supernatant was discarded. Then, the cell pellet was resuspended in BMDM medium, counted, and plated onto 15cm non-tissue culture treated petri dishes at a density of 20 million cells/plate in BMDM medium containing murine M-CSF (Life Technologies; Cat# PMC2044) at 50ng/mL. Four days after seeding the cells, an additional 50ng/mL fresh M-CSF was added to each plate. On day 7, differentiated BMDMs were washed once with PBS and harvested in BMDM medium using a cell scraper. Cells were pelleted at 300xg for 5 minutes, resuspended in BMDM medium, and counted. Finally, cells were centrifuged at 300xg for 5 minutes, resuspended in Recovery Cell Culture Freezing Medium (Gibco; Cat# 12648010) at a density of 10 million cells/mL, and cryopreserved for later use. Differentiated BMDMs were thawed, counted, and seeded at 75k cells/well onto poly-D-lysine-coated plates in BMDM culture medium [RPMI-1640 (Gibco; Cat# 61870036), 10% HyClone FBS (Cytiva; Cat# SH30080.03), and penicillin-streptomycin (Gibco; Cat# 15140122)] with supplemental M-CSF (50ng/mL). Fresh BMDM medium was changed 24 hours after seeding of the cells.

treatment_protocol: Cells were treated with 25nM BafA1 or equal percentage of DMSO (vehicle) for 22h prior to RNA extraction.

tag: treatment dose

value: 25 nM

tag: treatment duration

value: 22 hours


title: Rosa26 KO, 4 hours, replicate 3, Regular protocol [HSA-000027322]

tag: cell type

value: BMDM


title: Trem2 KO, BafA1, replicate 3 [HSA-000022470]

value: Trem2 KO


title: CAF | P4C | C

first: Ian

last: Dryg

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: P4C

data_processing:
Raw paired-end FASTQ files were quantified using Salmon (v1.10.2), reads were quasi-mapped against the human GENCODE v45 reference annotation.
Assembly: GENCODE v45 (GRCh38.p13)
Supplementary files format and content: TPM plus 1, log2 transformed

source_name: Patient Derived

extract_protocol:
RNA was extracted using the commercially available RNeasy Mini Kit (Qiagen; 74104). RNA concentration was evaluated via NanoDrop spectrophotometer. Samples were diluted to the final concentration of 20ng/ul prior shipment to Novogene Corporation Inc. 2921 Stockton Blvd. Suite 1810 Sacramento CA 95817.
Human mRNA Sequencing (WOBI): 80 total RNA samples were subjected to Eukaryotic mRNA-seq on the NovaSeq 6000 (PE150) with poly-A capture and non-directional library.

tag: cell line

value: Patient Derived

value: Cancer Associated Fibroblast

value: Control


title: RIL18_G09_L02_1

description: Library name: Sample53

value: leaf tissue

value: Ler X Cvi RIL

tag: ril line

tag: generation

tag: lineage


title: Trem2 KO, BafA1, replicate 1 [HSA-000022468]


title: Trem2 KO, DMSO, replicate 3 [HSA-000022467]

value: DMSO

value: 0 nM


title: Trem2 KO, DMSO, replicate 2 [HSA-000022466]


title: Trem2 KO, DMSO, replicate 1 [HSA-000022465]


title: WT, BafA1, replicate 3 [HSA-000022464]

value: WT


title: WT, BafA1, replicate 1 [HSA-000022462]


title: WT, BafA1, replicate 2 [HSA-000022463]


title: WT, DMSO, replicate 1 [HSA-000022459]


title: WT, DMSO, replicate 2 [HSA-000022460]