title: RHB280217, tumorsphere sample, biological replicate 3

city: Singapore

first: Reshma

last: Taneja

address: National University of Singapore Dept of Physiology, Blk MD9 Level 2, 2 Medical Drive,

department: Physiology

country: Singapore

institute: National University of Singapore

description: Library name: RHB280217_TS3

data_processing:
Raw image data file from sequencing was transformed to Sequenced Reads by CASAVA base recognition (Base Calling).
Bcl2fastq was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR v2.5 with parameters mismatch=2. STAR used the method of Maximal Mappable Prefix (MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis between two condition/groups (three biological replicates per condition) was performed using the DESeq2 R package (v2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: raw gene counts in Excel sheet(.xls) format

source_name: Patient Derived Xenograft cells

growth_protocol: Rh30 and Rh41 alveolar rhabdomyosarcoma (ARMS) cell lines, provided by Peter Houghton and Rosella Rota, were cultured in RPMI-1640 medium (Hyclone, Cytiva, #SH30027.01) supplemented with 10% fetal bovine serum (FBS) (HyClone, Cytiva, #SH30071.03) and 1% penicillin-streptomycin (Gibco, #15140-122) under standard conditions (37 °C, 5% CO₂). Normal human skeletal muscle myoblasts (HSMMs; ZenBio, #SKB-F) were cultured in Skeletal Muscle Cell Growth Medium (ZenBio, #SKM-M), containing DMEM, FBS, BSA, fetuin, hEGF, dexamethasone, insulin, penicillin, streptomycin, and amphotericin B.  Mycoplasma contamination was routinely monitored. PDX tumor samples were obtained from the VIVA-KKH Pediatric Solid Tumor Research Laboratory. Tumors were excised, mechanically dissociated, and resuspended in Matrigel (Corning, #354234) (2:1) before implantation into NOD SCID mice. Tumor-bearing mice were euthanized when tumor size exceeded 15 mm. PDX-derived TICs were cultured in NB medium supplemented with B27, EGF (20 ng/mL), FGF (40 ng/mL), Glutmax (Gibco, #35050061).

extract_protocol:
Total RNA was extracted from adherent and tumorsphere-derived Rh30, Rh41, and RHB280217 samples using the RNeasy Mini Kit (Qiagen), followed by quality assessment with an Agilent 2100 Bioanalyzer
RNA libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit and sequenced on an Illumina NovaSeq 6000 platform, generating 150-bp paired-end reads

treatment_protocol: For tumorsphere assays, ARMS cells were dissociated and seeded at 10,000 cells/mL in ultra-low attachment plates with serum-free Neurobasal medium (Gibco, #21103049) supplemented with B27 (Gibco, #17504044), EGF (40 ng/mL, Gibco, #PHG0311), FGF (80 ng/mL, Gibco, #13256-029), and insulin (50 µg/mL, Sigma-Aldrich, #I9278). Tumorspheres (>50 µm) were quantified after 72 hours. RHB280217 cells were maintained under low-attachment conditions for tumorsphere formation and passaged enzymatically using Accutase (Innovative Cell Technologies, #AT104)

value: Patient Derived Xenograft cells

value: Alveolar Rhabdomyosarcoma cells

value: FP-RMS

value: Tumorsphere cells

value: 26 February 2025


title: RHB280217, tumorsphere sample, biological replicate 2

status: Public on Aug 20 2025

type: SRA

description: Library name: RHB280217_TS2

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: batch


title: RHB280217, tumorsphere sample, biological replicate 4

description: Library name: RHB280217_TS4


title: RHB280217, adherent sample, biological replicate 2

description: Library name: RHB280217_AD2

value: Adherent cells


title: Rh41, tumorshere sameple, biological replicate 3

description: Library name: Rh41_TS3

source_name: Cell line

value: Cell line

value: 15 February 2022


title: Rh41, tumorshere sameple, biological replicate 2

description: Library name: Rh41_TS2


title: RHB280217, adherent sample, biological replicate 3

description: Library name: RHB280217_AD3


title: RHB280217, adherent sample, biological replicate 1

description: Library name: RHB280217_AD1


title: Rh41, adherent sample, biological replicate 1

description: Library name: Rh41_AD1


title: Rh41, adherent sample, biological replicate 3

description: Library name: Rh41_AD3


title: RHB280217, adherent sample, biological replicate 4

description: Library name: RHB280217_AD4


title: Rh30, tumorsphere sample, biological replicate 1

description: Library name: Rh30_TS1

value: 12 November 2021


title: Rh30, tumorsphere sample, biological replicate 2

description: Library name: Rh30_TS2


title: Rh41, tumorshere sameple, biological replicate 1

description: Library name: Rh41_TS1


title: Rh30, adherent sample, biological replicate 3

description: Library name: Rh30_AD3


title: Rh30, adherent sample, biological replicate 2

description: Library name: Rh30_AD2


title: Rh30, tumorsphere sample, biological replicate 4

description: Library name: Rh30_TS4


title: Rh30, adherent sample, biological replicate 4

description: Library name: Rh30_AD4


title: Rh41, adherent sample, biological replicate 2

description: Library name: Rh41_AD2


title: Astrocyte, BD LR3, wo Li, rep1

city: Daejeon

first: Dayeon

last: Kim

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

description:
Library name: Sample 6-1
L3_wo_1

data_processing:
The sequenced reads were mapped to the human genome (hg38/GRCh38) using STAR 2.7.9.
The mapped reads were annotated and quantified using RSEM.
DESeq2 was used for normalization and differential analysis.
Assembly: hg38/GRCh38
Supplementary files format and content: csv file includes TPM values

source_name: Astrocyte

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) following the munufacturer's instructions.
RNA libraries for RNA-seq were prepared using NEBNext ultra II directional RNA library prep kit according to manufacturer’s instructions.

value: Astrocyte

value: wo Li


title: Astrocyte, BD LR3, with Li, rep2

description:
Library name: Sample 5-2
L3_with_2

value: with Li


title: Astrocyte, BD LR2, wo Li, rep2

description:
Library name: Sample 4-2
L2_wo_2


title: Rh30, tumorsphere sample, biological replicate 3

description: Library name: Rh30_TS3


title: Astrocyte, BD LR3, with Li, rep1

description:
Library name: Sample 5-1
L3_with_1


title: Rh30, adherent sample, biological replicate 1

description: Library name: Rh30_AD1


title: RHB280217, tumorsphere sample, biological replicate 1

description: Library name: RHB280217_TS1


title: Astrocyte, BD LR2, with Li, rep2

description:
Library name: Sample 3-2
L2_with_2


title: Astrocyte, BD LR1, wo Li, rep2

description:
Library name: Sample 2-2
L1_wo_2


title: Astrocyte, BD LR1, with Li, rep1

description:
Library name: Sample 1-1
L1_with_1


title: Astrocyte, BD LR2, with Li, rep1

description:
Library name: Sample 3-1
L2_with_1


title: Astrocyte, BD LR2, wo Li, rep1

description:
Library name: Sample 4-1
L2_wo_1


title: shAURKB rep1

city: Shanghai

first: Yuyi

last: Li

address: Zhizao ju road

country: China

institute: Shanghai Jiaotong University School of Medicine

description:
Library name: Sample4
Column name in processed_data.xlsx:FPKM_shAURKB1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchmark (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchmark (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchmark
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: RKO

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).  1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  VAHTS Universal V5 RNA-seq Library Prep Kit following manufacturer's protocols.

value: RKO

value: colorectal cancer cell

value: AURKB knockdown


title: Astrocyte, BD LR1, with Li, rep2

description:
Library name: Sample 1-2
L1_with_2


title: shAURKB rep2

description:
Library name: Sample5
Column name in processed_data.xlsx:FPKM_shAURKB2


title: shNC rep3

description:
Library name: Sample3
Column name in processed_data.xlsx:FPKM_shNC3

value: WT


title: shAURKB rep3

description:
Library name: Sample6
Column name in processed_data.xlsx:FPKM_shAURKB3


title: shNC rep2

description:
Library name: Sample2
Column name in processed_data.xlsx:FPKM_shNC2


title: Astrocyte, BD LR1, wo Li, rep1

description:
Library name: Sample 2-1
L1_wo_1


title: Astrocyte, BD LR3, wo Li, rep2

description:
Library name: Sample 6-2
L3_wo_2


title: Control 2

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Library name: pLKO2

data_processing:
Libraries were sequenced by the Illumina Novaseq 6000 using SP mode 100 cycles kit (Illumina)
Mapping of sequences to the genome was performed by the UTAP pipeline (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154)
Reads were trimmed using cutadapt (DOI:10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
The remaining reads were mapped to the genome (hg38) using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
Assembly: hg38
Supplementary files format and content: Matrix table with gene counts for every gene and every sample

growth_protocol: Cells were maintained in RPMI medium supplemented with 10% FBS, 1% Penicillin-Streptomycin solution.

extract_protocol:
RNA was extracted using TRI reagent (Sigma), following standard extraction protocol.
RNAseq libraries were constructed by applying a bulk adaptation of the MARS‐seq protocol (Jaitin et al. 2014 Science.343:776-9).

treatment_protocol: Cells were infeted with pLKO vector harboring shPNKP to induce PNKP knock-down, or empty pLKO as control.

value: Breast Cancer

value: pLKO (empty vector)


title: Control 3

description: Library name: pLKO3


title: S8_SpT

city: Houston

first: Moran

last: Amit

address: 1515 Holcombe Blvd

department: Head & Neck Surgery

country: USA

institute: University of Texas - MD Anderson Cancer Center

description: Library name: S8_SpT

data_processing:
The raw spatial sequencing data were processed using the 10X Genomics Space Ranger pipeline. The spaceranger (version 1.3.0) mkfastq pipeline was used to convert Illumina sequencer’s binary base call (BCL) files into FASTQ format. Samples were then run through the spaceranger count pipeline, which performs alignment, tissue detection, fiducial detection, and barcode/unique molecular identifier counting.
Reference sequence alignment of human samples was performed with the GRCh38 Reference 2020-A (June 23, 2020).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of genes
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: cutaneous squamous cell carcinoma FFPE tissue samples

extract_protocol:
FFPE clinical trial samples were serially sectioned, and one section was H&E stained, and another unstained section was processed for spatial transcriptome analyses using the Visium (10X Genomics). FFPE samples were initially tested for RNA quality with a DV200 > 50% (Agilent). The samples were cut at 5 μM thickness onto four 6.5 mm × 6.5 mm capture areas with 5,000 oligo-barcoded spots of Visium spatial slides. The slides then were deparaffinized and stained by H&E with immediate imaging on EVOS7000 imaging system (Thermo Fisher) and then processed for a full spatial transcriptomic (ST) experiment; cDNA amplification, library preparation, quantification and purity check were performed according to the manufacturer’s instructions (10x Genomics, Visium Spatial).
Spatial transscriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction


title: shPNKP 1

description: Library name: PNKPKD4

value: shPNKP


title: shPNKP 3

description: Library name: PNKPKD6


title: shPNKP 2

description: Library name: PNKPKD5


title: S7_SpT

description: Library name: S7_SpT

value: cutaneous squamous cell carcinoma FFPE tissue samples


title: Control 1

description: Library name: pLKO1


title: S6_SpT

description: Library name: S6_SpT


title: S5_SpT

description: Library name: S5_SpT


title: S4_SpT

description: Library name: S4_SpT


title: S11_SpT

description: Library name: S11_SpT


title: Motor_IC8_3

description: Library name: Motor_IC8_3

data_processing:
The raw sequencing data (FASTQ files) were imported into QIAGEN CLC Genomics Workbench 20.0.4. Initial quality control of the sequencing reads was performed using the built-in tools, including the "Quality Control" function, to evaluate read quality metrics. Low-quality reads and contaminants were trimmed or filtered out.
The cleaned sequencing reads were mapped to the GRCh38.p14 reference genome using the "Map Reads to Reference" tool in the CLC Genomics Workbench.
Gene expression levels were quantified using the "Count Features" tool. This step involved counting the number of reads mapped to each gene based on the annotation file corresponding to the reference genome. The output generated a count table indicating the raw read counts for each gene across all samples.
Assembly: GRCh38
Supplementary files format and content: counts_matrix.txt contains a count table indicating the raw read counts for each gene across all samples.

source_name: Motor neurons cocultured with IC8 human squamous cell carcinoma cells

growth_protocol: Neurons were plated on laminin-coated (Life Technologies, Cat# 23017015) round glass coverslips set in 12-well plates. Two hours after plating, the wells were flooded with 1 mL of warm (37°C) Ham’s F12 culture medium (Sigma-Aldrich) supplemented with 10% EV-depleted fetal bovine serum (Gibco, Thermo Fisher Scientific) and 1% penicillin/streptomycin and incubated at 37°C in 5% CO2 and 95% air. The carcinoma cells were plated (1:10 neuron: cancer cells ratio), and cultures were grown in RPMI 1640 medium containing 10% EV-depleted fetal bovine serum in 37°C and 5% CO2 incubation conditions, for 72 hours, with or without anti-PD1 antibody (Cemiplimab, 1000ug/ml,  or RMP1-14, 100ug/ml, InVivoMAb Antibodies, BioXCell, for human and murine, respectively), before neuron sorting and RNA extraction.

extract_protocol:
RNA was isolated from tumor samples using total RNA was extracted using the RecoverALL™ Total Nucleic Acid Isolation kit (Ambion) according to the manufacturer’s instructions.
RNA libraries were prepared and sequenced at the University of Houston Sequencing and Editing Core as per standard protocols. Enrichment for mRNA from total RNA was performed by coding region-specific biotinylated capture probes, which were selected using streptavidin magnetic beads. mRNA-enriched libraries were prepared using a QIAseq Stranded Total RNA Kit (QIAGEN) with 200 ng of input RNA.

treatment_protocol: see above


title: Motor_IC8_2

description: Library name: Motor_IC8_2

value: Motor neurons cocultured with IC8 human squamous cell carcinoma cells


title: shNC rep1

description:
Library name: Sample1
Column name in processed_data.xlsx:FPKM_shNC1


title: S15_SpT

description: Library name: S15_SpT


title: S1_SpT

description: Library name: S1_SpT


title: Motor_3

description: Library name: Motor_3

source_name: Monoculture of motor neurons

value: Monoculture of motor neurons


title: Motor_IC8_1

description: Library name: Motor_IC8_1


title: HEK_2

description: Library name: HEK_2

source_name: Monoculture of normal keratinocytes (HEK)


title: IC8_3

description: Library name: IC8_3

source_name: Monoculture of IC8 human squamous cell carcinoma cells


title: S9_SpT

description: Library name: S9_SpT


title: IC8_2

description: Library name: IC8_2

value: Monoculture of IC8 human squamous cell carcinoma cells


title: Motor_1

description: Library name: Motor_1


title: HEK_3

description: Library name: HEK_3

value: Monoculture of normal keratinocytes (HEK)


title: DRG_HEK_3

description: Library name: DRG_HEK_3

source_name: Dorsal root ganglia (DRG) neurons co-cultured with normal keratinocytes (HEK)


title: HEK_1

description: Library name: HEK_1


title: DRG_IC8_5

description: Library name: DRG_IC8_5

source_name: Dorsal root ganglia (DRG) neurons cocultured with IC8 human squamous cell carcinoma cells


title: DRG_HEK_2

description: Library name: DRG_HEK_2

value: Dorsal root ganglia (DRG) neurons co-cultured with normal keratinocytes (HEK)


title: DRG_IC8_4

description: Library name: DRG_IC8_4

value: Dorsal root ganglia (DRG) neurons cocultured with IC8 human squamous cell carcinoma cells


title: DRG_HEK_1

description: Library name: DRG_HEK_1


title: DRG_Cem_6

description: Library name: DRG_Cem_6

source_name: Monoculture of dorsal root ganglia (DRG) neurons treated with anti-PD-1


title: DRG_IC8_6

description: Library name: DRG_IC8_6


title: S3_SpT

description: Library name: S3_SpT


title: DRG_Cem_4

description: Library name: DRG_Cem_4

value: Monoculture of dorsal root ganglia (DRG) neurons treated with anti-PD-1


title: DRG_Cem_5

description: Library name: DRG_Cem_5


title: S10_SpT

description: Library name: S10_SpT


title: DRG_6

description: Library name: DRG_6

source_name: Monoculture of human dorsal root ganglia (DRG) neurons


title: DRG_4

description: Library name: DRG_4

value: Monoculture of human dorsal root ganglia (DRG) neurons


title: IC8_1

description: Library name: IC8_1


title: DRG_5

description: Library name: DRG_5


title: P9445_RNA55962

description: Library name: P9445_RNA55962

data_processing:
The paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Illumina universal adapters were trimmed from the reads using cutadapt 1.18 and read quality was checked again using FastQC 0.11.8
The trimmed reads were aligned to the Gencode GRCh38 human reference genome using STAR 2.7.0f
The BAM file with mapped reads for each sample was sorted and then used as an input for featureCounts (Subread 1.6.3) in order to generate read count data on gene/feature level (parameters: -p -t exon -g gene_id -s 2)
Genes/features were annotated using the GTF file from Gencode human GRCh38 reference
Assembly: Human GRCh38
Supplementary files format and content: Read count data generated by featureCounts (Subread 1.6.3) for each sample

extract_protocol:
The RNA extraction was performed with Mag-Bind® FFPE DNA/RNA 96 Kit (Omega Bio-Tek) following the manufacturer’s protocol. Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA).
Libraries were constructed with KAPA™ RNA HyperPrep with RiboErase (Roche, Indiana, USA) and performed based on the manufacturer’s recommendations.

value: Pre-treatment

tag: response

value: Non-responders


title: P9445_RNA66983

description: Library name: P9445_RNA66983

value: Post-treatment


title: P8860_RNA59223

description: Library name: P8860_RNA59223

value: Responders


title: P8674_RNA53159

description: Library name: P8674_RNA53159


title: P9445_RNA14363

description: Library name: P9445_RNA14363


title: P8485_RNA70944

description: Library name: P8485_RNA70944


title: P8485_RNA18487

description: Library name: P8485_RNA18487


title: P8485_RNA15819

description: Library name: P8485_RNA15819


title: P8294_RNA74374

description: Library name: P8294_RNA74374


title: P8362_RNA49996

description: Library name: P8362_RNA49996


title: P8088_RNA51412

description: Library name: P8088_RNA51412


title: P8485_RNA96265

description: Library name: P8485_RNA96265


title: P8011_RNA38999

description: Library name: P8011_RNA38999


title: P8073_RNA89714

description: Library name: P8073_RNA89714


title: P8011_RNA92097

description: Library name: P8011_RNA92097


title: P7982_RNA68251

description: Library name: P7982_RNA68251


title: P7396_RNA93981

description: Library name: P7396_RNA93981


title: P7669_RNA25860

description: Library name: P7669_RNA25860


title: P7396_RNA54891

description: Library name: P7396_RNA54891


title: P7043_RNA91214

description: Library name: P7043_RNA91214


title: P7043_RNA98766

description: Library name: P7043_RNA98766


title: P7669_RNA15993

description: Library name: P7669_RNA15993


title: P7043_RNA80779

description: Library name: P7043_RNA80779


title: P7043_RNA78744

description: Library name: P7043_RNA78744


title: P6365_RNA58601

description: Library name: P6365_RNA58601


title: P5956_RNA55274

description: Library name: P5956_RNA55274


title: P8658_RNA67816

description: Library name: P8658_RNA67816


title: P5956_RNA82505

description: Library name: P5956_RNA82505


title: P8485_RNA75819

description: Library name: P8485_RNA75819


title: P6365_RNA30271

description: Library name: P6365_RNA30271


title: P5828_RNA65889

description: Library name: P5828_RNA65889


title: P5828_RNA63630

description: Library name: P5828_RNA63630


title: P4418_RNA17603

description: Library name: P4418_RNA17603


title: P5665_RNA57331

description: Library name: P5665_RNA57331


title: P4272_RNA95536

description: Library name: P4272_RNA95536


title: P3707_RNA12078

description: Library name: P3707_RNA12078


title: P3707_RNA19295

description: Library name: P3707_RNA19295


title: P3112_RNA35212

description: Library name: P3112_RNA35212


title: P2819_RNA62595

description: Library name: P2819_RNA62595


title: P3112_RNA79212

description: Library name: P3112_RNA79212


title: P2482_RNA14420

description: Library name: P2482_RNA14420


title: P3123_RNA59780

description: Library name: P3123_RNA59780


title: P2482_RNA46246

description: Library name: P2482_RNA46246


title: P2687_RNA81791

description: Library name: P2687_RNA81791


title: P2000_RNA62515

description: Library name: P2000_RNA62515


title: P2060_RNA75355

description: Library name: P2060_RNA75355


title: P2060_RNA80265

description: Library name: P2060_RNA80265


title: P2060_RNA77171

description: Library name: P2060_RNA77171


title: P2060_RNA57508

description: Library name: P2060_RNA57508


title: P5828_RNA71762

description: Library name: P5828_RNA71762


title: P2000_RNA50452

description: Library name: P2000_RNA50452


title: P1854_RNA97318

description: Library name: P1854_RNA97318


title: P2000_RNA53397

description: Library name: P2000_RNA53397


title: P1854_RNA42170

description: Library name: P1854_RNA42170


title: P4272_RNA28803

description: Library name: P4272_RNA28803


title: P1854_RNA31645

description: Library name: P1854_RNA31645


title: Aging mice, exoWT treatment, 3 months, rep1

city: Guangzhou

first: Shixiang

middle: Clover

last: Wang

state: Guangdong

address: Guanzhou street

institute: Guangzhou national labratory

description:
Library name: Sample 67
Aging_WT_rep1
raw_count_aging.csv

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low- quality sequence, then mapped to reference genome using Hisat2(v2.0.5). For HE cells, human hepatic organoids and primary hepatocytes, reads were aligned against the GRCH38 human reference genome, while for mouse livers, reads were aligned against the mm10 mouse reference genome. Reads numbers mapped to each gene was calculated using featureCounts (v1.5.0-p3).
Assembly: For HE cells, human hepatic organoids and primary hepatocytes, reads were aligned against the GRCH38 human reference genome, while for mouse livers, reads were aligned against the mm10 mouse reference genome.
Supplementary files format and content: CSV files containing raw read count values (integer counts) for each gene across all samples. Each file includes a header row with sample identifiers and the first column listing gene IDs or gene symbols.

organism: Mus musculus

source_name: liver

extract_protocol:
Treated cell lines, organoids and mice livers were collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the library construction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: WT

value: Aging mice, exoWT treatment, 3 months


title: Aging mice, exoWT treatment, 3 months, rep3

description:
Library name: Sample 69
Aging_WT_rep3
raw_count_aging.csv


title: Aging mice, exoWT treatment, 6 months, rep2

description:
Library name: Sample 71
Aging_WR_rep2
raw_count_aging.csv

value: Aging mice, exoWT treatment, 6 months


title: Aging mice, exoWT treatment, 6 months, rep3

description:
Library name: Sample 72
Aging_WR_rep3
raw_count_aging.csv


title: Aging mice, exoWT treatment, 6 months, rep1

description:
Library name: Sample 70
Aging_WR_rep1
raw_count_aging.csv


title: Aging mice, 18 months, rep3

description:
Library name: Sample 66
Aging_old_rep3
raw_count_aging.csv

value: Aging mice, 18 months


title: Aging mice, exoWT treatment, 3 months, rep2

description:
Library name: Sample 68
Aging_WT_rep2
raw_count_aging.csv


title: P3544_RNA80675

description: Library name: P3544_RNA80675

value: cutaneous squamous cell carcinoma FFPE tissue samples


title: P3544_RNA74317

description: Library name: P3544_RNA74317


title: P1848_RNA97899

description: Library name: P1848_RNA97899


title: P3123_RNA62690

description: Library name: P3123_RNA62690


title: Aging mice, 18 months, rep2

description:
Library name: Sample 65
Aging_old_rep2
raw_count_aging.csv


title: P1604_RNA37864

description: Library name: P1604_RNA37864


title: P1848_RNA24407

description: Library name: P1848_RNA24407


title: Aging mice, 18 months, rep1

description:
Library name: Sample 64
Aging_old_rep1
raw_count_aging.csv


title: P1848_RNA44698

description: Library name: P1848_RNA44698


title: P1604_RNA36583

description: Library name: P1604_RNA36583


title: P1381_RNA73526

description: Library name: P1381_RNA73526


title: CCl4 treated mice, exoWNT3A/RSPO1 treatment, 6 months, rep3

description:
Library name: Sample 60
CCl4_WR_6w_rep3
raw_count_CCl4.csv


title: Young control mice for aging mice, 3 months, rep2

description:
Library name: Sample 62
Aging_Young_rep2
raw_count_aging.csv


title: P1333_RNA87287

description: Library name: P1333_RNA87287


title: P1604_RNA19882

description: Library name: P1604_RNA19882


title: CCl4 treated mice, exoWT treatment, 6 months, rep3

description:
Library name: Sample 57
CCl4_WT_6w_rep3
raw_count_CCl4.csv


title: P1244_RNA87818

description: Library name: P1244_RNA87818


title: Young control mice for aging mice, 3 months, rep3

description:
Library name: Sample 63
Aging_Young_rep3
raw_count_aging.csv


title: CCl4 treated mice, exoWNT3A/RSPO1 treatment, 6 months, rep1

description:
Library name: Sample 58
CCl4_WR_6w_rep1
raw_count_CCl4.csv


title: P1381_RNA84045

description: Library name: P1381_RNA84045


title: CCl4 treated mice, exoWNT3A/RSPO1 treatment, 3 months, rep3

description:
Library name: Sample 54
CCl4_WR_3w_rep3
raw_count_CCl4.csv


title: P1244_RNA25952

description: Library name: P1244_RNA25952


title: CCl4 treated mice, exoWT treatment, 6 months, rep2

description:
Library name: Sample 56
CCl4_WT_6w_rep2
raw_count_CCl4.csv


title: P1178_RNA73171

description: Library name: P1178_RNA73171


title: CCl4 treated mice, exoWNT3A/RSPO1 treatment, 6 months, rep2

description:
Library name: Sample 59
CCl4_WR_6w_rep2
raw_count_CCl4.csv


title: CCl4 treated mice, exoWT treatment, 6 months, rep1

description:
Library name: Sample 55
CCl4_WT_6w_rep1
raw_count_CCl4.csv


title: P1244_RNA16996

description: Library name: P1244_RNA16996


title: CCl4 treated mice, exoWNT3A/RSPO1 treatment, 3 months, rep2

description:
Library name: Sample 53
CCl4_WR_3w_rep2
raw_count_CCl4.csv


title: P1178_RNA58443

description: Library name: P1178_RNA58443


title: CCl4 treated mice, exoWNT3A/RSPO1 treatment, 3 months, rep1

description:
Library name: Sample 52
CCl4_WR_3w_rep1
raw_count_CCl4.csv


title: CCl4 treated mice, exoWT treatment, 3 months, rep3

description:
Library name: Sample 51
CCl4_WT_3w_rep3
raw_count_CCl4.csv


title: P1175_RNA99644

description: Library name: P1175_RNA99644


title: CCl4 treated mice, exoWT treatment, 3 months, rep2

description:
Library name: Sample 50
CCl4_WT_3w_rep2
raw_count_CCl4.csv


title: Young control mice for aging mice, 3 months, rep1

description:
Library name: Sample 61
Aging_Young_rep1
raw_count_aging.csv


title: P1178_RNA25160

description: Library name: P1178_RNA25160


title: CCl4 treated mice, exoWT treatment, 3 months, rep1

description:
Library name: Sample 49
CCl4_WT_3w_rep1
raw_count_CCl4.csv


title: P1175_RNA54968

description: Library name: P1175_RNA54968


title: P1134_RNA37737

description: Library name: P1134_RNA37737


title: CCl4 treated mice, 6 months, rep3

description:
Library name: Sample 48
CCl4_CCl4_rep3
raw_count_CCl4.csv

value: CCl4 treated mice, 6 months


title: P1244_RNA61590

description: Library name: P1244_RNA61590


title: P1065_RNA64053

description: Library name: P1065_RNA64053


title: P1134_RNA29443

description: Library name: P1134_RNA29443


title: P1065_RNA22107

description: Library name: P1065_RNA22107


title: Oil treated control mice for CCl4 treatment, 6 months, rep3

description:
Library name: Sample 45
CCl4_Oil_rep3
raw_count_CCl4.csv


title: Oil treated control mice for CCl4 treatment, 6 months, rep2

description:
Library name: Sample 44
CCl4_Oil_rep2
raw_count_CCl4.csv


title: CCl4 treated mice, 6 months, rep1

description:
Library name: Sample 46
CCl4_CCl4_rep1
raw_count_CCl4.csv


title: Oil treated control mice for CCl4 treatment, 6 months, rep1

description:
Library name: Sample 43
CCl4_Oil_rep1
raw_count_CCl4.csv


title: P1065_RNA10143

description: Library name: P1065_RNA10143


title: APAP-treated mice, day 3, exoWNT3A/RSPO1 treatment, rep3

description:
Library name: Sample 42
APAP_exoWR_rep3
raw_count_APAP.csv


title: Human MuSC ASC-24h G4 bio rep1

city: Hong Kong

first: Feng

last: Yang

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

institute: The Chinese University of Hong Kong

description:
Library name: hASC-24h_G4
Human MuSC ASC G4 bio rep1

library_source: genomic

data_processing:
The raw data was first pre-processed by initial quality assessment, adapters trimming, and low-quality filtering and then mapped to the mouse reference genome (mm10) using Bowtie2, and only the non-redundant reads were kept.
The peaks (sites) were identified using MACS2. During the peak calling, the cutoff was set to p value euqals to 0.001 or q value equals to 0.05, for G4, H3K4me3, and MAX CUT&RUN-Seq experiment.
Assembly: mm10 or hg38
Supplementary files format and content: Bigwig,narrowPeak

molecule: genomic DNA

source_name: skeletal muscle

growth_protocol: Freshly isolated muscle stem cells were cultured in growth medium (F10 medium containing 20% FBS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% P/S). To induce differentiation, after cultured for 72h the cell medium was altered to differentiation medium (F10 with 2% HS and 1% P/S) under the same culture environment.

extract_protocol:
Skeletal muscle tissue from mouse hindlimb and forelimb muscles were dissected, gently minced with blades and digested with Collagenase II (1000U/ml) in Ham’s F10 for 90 minutes in a shaking water bath at 37°C. Digested tissue was then washed twice with rinsing media (10% HS, in Ham’s F-10) and centrifuged at 700 xg at 4°C for 5 minutes. Second digestion was performed by adding Collagenase II (1000U/ml) and Dispase (11U/ml) in rinsing media and incubated in shaking water bath at 37°C for 30 minutes. Digested tissue was passed through a 20-gauge needle for 12 times and filtered through a 40 μm filter followed by spinning at 700 xg for 5 min at 4°C. For mouse muscles, MuSCs were then sorted out by FACS Aria Fusion (BD) and collected as GFP+ groups. For human muscles, cells were stained with antibodies and FITC-(CD45-, CD31-, CD34-) APC+(CD29+) PE-CY7+ (CD56+) cells were sorted out as human MuSCs. Isolated satellite cells were immediately collected or were cultured in Ham’s F10 supplemented with 20% FBS and bFGF (0.025 μg/ml) (growth medium) for other assays. CUT&RUN protocol is referred to CUT&RUN assay kit (Cell Signaling Technology, 86652,).
For DNA library construction, a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S) was used according to the manufacturer’s instructions.

value: skeletal muscle

value: human primary muscle stem cell

value: 24h-cultured activated muscle stem cell


title: human_ASC_24h_RNA

description:
Library name: hASC_24h_RNA
Human MuSC ASC bio rep1

data_processing:
The adapter and low-quality sequences were trimmed from 3' to 5' ends for each read, and the reads shorter than 50 bp were discarded. The clean reads were aligned to the mouse (mm10) or human (hg38) reference genome with Hista2. Next, we used Cufflinks to quantify the gene expression. Genes were identified as DEGs if the absolute log2foldchange of expression level is greater than 0.5 and the adjusted p-value is <0.05 between two stages/conditions by DESeq2.
Assembly: mm10 or hg38
Supplementary files format and content: Bigwig

molecule: polyA RNA

growth_protocol: Freshly isolated muscle stem cells were cultured in F10 medium containing 20% FBS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% P/S.

extract_protocol:
RNAs were extracted by Trizol reagent referred to it's protocal (Ambion, 15596)
Total RNAs were subject to polyA selection (Ambion, 61006) followed by library preparation using NEBNext Ultra II RNA Library Preparation Kit (NEB, E7770S).


title: Human MuSC FISC G4 bio rep1

description:
Library name: hFISC_G4
Human MuSC FISC G4 bio rep1

value: freshly isolated muscle stem cell


title: APAP-treated mice, day 3, exoWNT3A/RSPO1 treatment, rep1

description:
Library name: Sample 40
APAP_exoWR_rep1
raw_count_APAP.csv


title: human_FISC_RNA

description:
Library name: hFISC_RNA
Human MuSC FISC bio rep1


title: APAP-treated mice, day 3, rep3

description:
Library name: Sample 36
APAP_APAP_rep3
raw_count_APAP.csv

value: APAP-treated mice, day 3


title: APAP-treated mice, day 3, exoWT treatment, rep1

description:
Library name: Sample 37
APAP_exoWT_rep1
raw_count_APAP.csv


title: APAP-treated mice, day 3, rep2

description:
Library name: Sample 35
APAP_APAP_rep2
raw_count_APAP.csv


title: APAP-treated mice, day 3, exoWNT3A/RSPO1 treatment, rep2

description:
Library name: Sample 41
APAP_exoWR_rep2
raw_count_APAP.csv


title: P1175_RNA62465

description: Library name: P1175_RNA62465


title: APAP-treated mice, day 3, rep1

description:
Library name: Sample 34
APAP_APAP_rep1
raw_count_APAP.csv


title: APAP-treated mice, day 3, exoWT treatment, rep2

description:
Library name: Sample 38
APAP_exoWT_rep2
raw_count_APAP.csv


title: Healthy control mice for APAP treatment, rep2

description:
Library name: Sample 32
APAP_Healthy_rep2
raw_count_APAP.csv

value: Healthy control mice for APAP treatment


title: Healthy control mice for APAP treatment, rep3

description:
Library name: Sample 33
APAP_Healthy_rep3
raw_count_APAP.csv


title: CCl4 treated mice, 6 months, rep2

description:
Library name: Sample 47
CCl4_CCl4_rep2
raw_count_CCl4.csv


title: Healthy control mice for APAP treatment, rep1

description:
Library name: Sample 31
APAP_Healthy_rep1
raw_count_APAP.csv


title: mESC,Ring1BKIflag,experiment,H2AZ2 knockdown,1

city: Richmond

first: Xiangyu

last: Shen

state: Virginia

address: 101N 5th street ,Apt1513,Richmond,VA2321, 1513

institute: Henan University

description: Library name: Ring1B_Z2KD_rep1

data_processing:
Raw sequencing data were uploaded. Processed data include bigwig of H2AZ1 CUT&Tag and Ring1B CUT&Tag
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed data include bigwig of H2AZ1 CUT&Tag and Ring1B CUT&Tag
Library strategy: CUT&Tag

growth_protocol: Mouse ESC lines were maintained in ESC medium, which consists of DMEM supplemented with 50 U/ml penicillin-streptomycin, 15% defined murine ESC FBS (R&D System, S10250), 1% GlutaMax (Gibco, 35050-061), 1 X non-essential amino acids (Corning, NY, MT-25-025-CI), 1 X nucleoside (Millipore, ES-008-D), 0.007% β-mercaptoethanol (Sigma, M3148), and 1,000 U/ml mLIF (Millipore, ESGRO) at 37oC in a humidified incubator with 5% CO2. ESCs were culture on 0.1% gelatin-coated plates or irradiated mouse embryonic fibroblasts (Fisherbrand, A34181)

extract_protocol:
Cells were washed with PBS and permeabilized using the reagents provided in the Vazyme CUT&Tag Assay Kit (Cat# TD904), following the manufacturer’s protocol. Primary antibody was incubated with the cells overnight at 4°C. After washing, cells were incubated with the secondary antibody according to the kit instructions.
Following tagmentation using the Vazyme CUT&Tag Assay Kit (Cat# TD904), DNA was purified and used for library construction with the Vazyme VAHTS Universal DNA Library Prep Kit for Illumina (Cat# TD202), according to the manufacturer’s protocol. Libraries were PCR-amplified with indexed primers, size-selected, and sequenced on an Illumina platform.

treatment_protocol: Cells were transfected with siRNA targeting H2AZ1, H2AZ2, or non-targeting control siRNA. After 48 hours, cells were harvested for CUT&Tag.

value: mESC


title: mESC,Ring1BKIflag,experiment,H2AZ2 knockdown,2

description: Library name: Ring1B_Z2KD_rep2


title: mESC,Ring1BKIflag,experiment,H2AZ1 knockdown,3

description: Library name: Ring1B_Z1KD_rep3


title: mESC,Ring1BKIflag,experiment,H2AZ2 knockdown,3

description: Library name: Ring1B_Z2KD_rep3


title: mESC,Ring1BKIflag,experiment,H2AZ1 knockdown,2

description: Library name: Ring1B_Z1KD_rep2


title: mESC,Ring1BKIflag,Negative control,3

description: Library name: Ring1B_NC_rep3


title: mESC,Ring1BKIflag,experiment,H2AZ1 knockdown,1

description: Library name: Ring1B_Z1KD_rep1


title: mESC,Ring1BKIflag,Negative control,1

description: Library name: Ring1B_NC_rep1


title: APAP-treated mice, day 3, exoWT treatment, rep3

description:
Library name: Sample 39
APAP_exoWT_rep3
raw_count_APAP.csv


title: mESC,Ring1BKIflag,Negative control,2

description: Library name: Ring1B_NC_rep2


title: mtDT, Family F, IPW-5371 + RT + anti-PD-L1  #3, d7

city: San Francisco

first: Mary Helen

last: Barcellos-Hoff

state: CA

address: 2340 Sutter Street

department: Radiation Oncology

institute: UCSF

description:
Library name: 15-A2304-13
Column name in fc_PE_counts.csv : 15.A2304.13.R1.001.fastq.gz.subread.BAM

data_processing:
Rsubread package (RRID: SCR_016945) Software R Package used for sequence aligment and counting in  R . The program includes assessment of sequence reads, read alignment, read summarization and is compatible with many major platforms including Illumina.
Assembly: Mus musculus GRCm38
Supplementary files format and content: excel files including counts for each sample

source_name: mammary carcinoma

growth_protocol: 8–10 week-old BALB/cJ female mice were transplanted orthotopically with F2 mammary tumor-derived transplants (mTDT) from family F. Mice were palpated three times a week until the tumor reached 2×2mm in size, and then daily on randomization into treatment groups when the tumor reached 65–100mm^3. Animals were sacrificed 7 days following  treatment and the tumors were collected and flash frozen in liquid nitrogen (LN2) until processed for RNA extraction.

extract_protocol:
Qiagen RNA Easy Kit and following standard Protocol and DNAase I cleanup protocol listed in the Appendix.  Approximately 15 ul and 1000ng of RNA was used
Samples were quantified using  Qubit 4 flurometer and quality was assessed using a 4200 TapeStation.  Any  samples with >10% DNA contamination were  treated with TURBO Dnase to remove DNA contamination. QIAGEN FastSelect rRNA HMR Kit was then used for rRNA depletion following manufacturer's protocol. RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations

treatment_protocol: Sham immunoglobulin G (IgG), anti-programmed death ligand (PD-L1), TGFβ inhibition (TGFβi) with small molecule IPW or single-dose radiation (RT) treatment, and dual and triple combinations. All agents were administered intraperitoneally (i.p.) 24 hours before irradiation at the indicated schedule for up to three 3 weeks. Anti-PD-L1 (Roche, Inc.) was administered once a week (10mg/kg, PD-L1 9708, 6E11), TGFβ small molecule inhibitor IPW-5371 (Innovation Pathways, Inc.; designated as IPW) was administered daily (20 mg/kg mg/kg), or IgG control antibody (Bio X Cell BP0083) three times per week (25 mg/kg). Tumors were irradiated with 10 Gy focally using a small animal radiation research platform (SARRP, XStrahl) and individualized plans  (Muriplan, XStrahl) based on arc beam computerized tomography.

value: mammary carcinoma

value: Trp53 null

value: 7 days post treatment


title: mtDT, Family F, RT #3, d7

description:
Library name: 12-A2304-26
Column name in fc_PE_counts.csv : 12.A2304.26.R1.001.fastq.gz.subread.BAM

value: RT


title: mtDT, Family F, RT #2, d7

description:
Library name: 11-A2304-7
Column name in fc_PE_counts.csv : 11.A2304.7.R1.001.fastq.gz.subread.BAM


title: mtDT, Family F, IPW-5371 + RT  #3, d7

description:
Library name: 8-A2301-63 (resub-8b)
Column name in fc_PE_counts.csv : resub.8b.R1.001.fastq.gz.subread.BAM

value: IPW+RT (Radiation)


title: mtDT, Family F, IPW-5371 + RT + anti-PD-L1  #1, d7

description:
Library name: 9-A2301-71
Column name in fc_PE_counts.csv : 9.A2301.71.R1.001.fastq.gz.subread.BAM


title: mtDT, Family F, IPW-5371 + RT  #2, d7

description:
Library name: 7-A2301-32
Column name in fc_PE_counts.csv : 7.A2301.32.R1.001.fastq.gz.subread.BAM


title: mtDT, Family F, IPW-5371  #1, d7

description:
Library name: 4-A2301-11
Column name in fc_PE_counts.csv : 4.A2301.11.R1.001.fastq.gz.subread.BAM

value: Control + IPW  (TGFbi)


title: mtDT, Family F, Sham #3, d7

description:
Library name: 3-A2301-30
Column name in fc_PE_counts.csv : 3.A2301.30.R1.001.fastq.gz.subread.BAM

value: Sham/Control


title: mtDT, Family F, IPW-5371 + RT + anti-PD-L1  #2, d7

description:
Library name: 14-A2304-3
Column name in fc_PE_counts.csv : 14.A2304.3.R1.001.fastq.gz.subread.BAM


title: mtDT, Family F, Sham #2, d7

description:
Library name: 2-A2301-29
Column name in fc_PE_counts.csv: 2.A2301.29.R1.001.fastq.gz.subread.BAM


title: mtDT, Family F, Sham #1, d7

description:
Library name: 1-A2301-14
Column name in fc_PE_counts.csv : 1.A2301.14.R1.001.fastq.gz.subread.BAM


title: IA1036

city: Chicago

first: Federico

last: Salas-Lucia

state: IL

department: Endocrinology Department

institute: University of Chicago

description:
Library name: IA1036
miRNA_raw_count.csv

library_source: other

data_processing:
Adaptor trimming performed with sRNAbench from SRNAtoolbox version 0.0.4, with adapter minimum length of 10, adapter sequence "TGGAATTCTCGGGTGCCAAGG", no recursive trimming, and 1 allowed mismatch in the adapter.
Read Mapping to known libraries of mouse miRNA was performed  using sRNAbench from SRNAtoolbox version 0.0.4. Wth mmu library as reference, species set for GRCm39, minimum read count of 2, number of mitmatches set to 1, seed = 19, hierarchical alignment type, isoMIR set to false.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include matrix with reads  mapped to mature miRNA from sense strand summarized by sRNAbench.

molecule: other

source_name: Blood plasma

extract_protocol:
RNAs was extracted using an RNA isolation kit (miRNeasy Serum/Plasma Kit (Qiagen, Venlo, Netherlands).
RNA libraries were prepared for sequencing using commercially available Illumina small RNA-Seq kits (San Diego, California, USA),

value: Blood plasma

tag: Sex

value: Female

tag: phenotype

value: WT


title: IA1035

description:
Library name: IA1035
miRNA_raw_count.csv


title: mtDT, Family F, IPW-5371  #2, d7

description:
Library name: 6-A2301-36
Column name in fc_PE_counts.csv : 6.A2301.36.R1.001.fastq.gz.subread.BAM


title: IA1034

description:
Library name: IA1034
miRNA_raw_count.csv

value: Male


title: IA1032

description:
Library name: IA1032
miRNA_raw_count.csv


title: IA1031

description:
Library name: IA1031
miRNA_raw_count.csv

value: E4FAD (5xFAD+/-; human APOE4+/+, C57BL/6 background)

value: CMB


title: IA1037

description:
Library name: IA1037
miRNA_raw_count.csv


title: IA1028

description:
Library name: IA1028
miRNA_raw_count.csv


title: mtdt Internal reference control

description:
Library name: 16-Mouse-Control
Column name in fc_PE_counts.csv : 16.Ms.Control.R1.001.fastq.gz.subread.BAM

value: internal reference control


title: IA1027

description:
Library name: IA1027
miRNA_raw_count.csv


title: mtDT, Family F, IPW-5371  #3, d7

description:
Library name: 13-A2301-38 (resub 13b)
Column name in fc_PE_counts.csv : resub.13b.R1.001.fastq.gz.subread.BAM


title: LSK_WT_Fixed_CUT&RUN

city: St. Louis

first: Jeffrey

middle: J

last: Bednarski

state: Missouri

address: 660 S. Euclid Ave.

department: Pediatrics

institute: Washington University School of Medicine

data_processing:
CUT&RUNTools 2.0 was used to align the ChIPseq reads to the mm10 reference genome, normalize signals and call peaks.
Motif enrichments were analyzed with HOMER2 using the findMotifsGenome.pl script.
Assembly: mm10
Supplementary files format and content: narrowPeak, bigWig
Library strategy: CUT&RUN

source_name: E17.5 fetal liver

extract_protocol:
50,000 E17.5 HSCs pooled from 24-26 embryos or 50,000 adult bone marrow Lineage-Sca+Kit+ cells pooled from 2-3 mice were sorted into IMDM with 10% FBS. CUT&RUN protocol was followed as in Jannsens and Henikoff using protocol option 1 with modifications.15–17 Optimal digitonin concentration for primary cells was determined by titration and cell visualization with trypan blue. For fixed samples, cells were incubated with 0.1% methanol-free formaldehyde for 2 minutes and fixation was quenched with 125 mM glycine before processing. Concanavalin A magnetic beads (Bangs Laboratories #BP531) were activated with binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Cells were washed once with wash buffer (20 mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, Roche Complete Protease Inhibitor EDTA-free) or cross-link wash buffer (xL wash buffer; wash buffer plus 1% Triton X-100 and 0.05% SDS) and incubated with ConA beads for 10 minutes at room temp to bind. Anti-BCLAF1 antibody (Bethyl Labs #A300-608A) was added at a 1:50 concentration in antibody buffer (wash buffer with 0.02% digitonin and 0.00008M EDTA) and incubated overnight on a nutator at 4˚C. Antibody buffer was then removed via magnet, and beads/cells were washed with dig-wash or xL dig-wash buffer (respective buffers with 0.02% digitonin). pAG-MNase (Epicypher #15-1016) was added at 1:20 concentration and incubated for 1 hour at 4˚C. Beads/cells were washed with dig-wash/xL buffer 2x and resuspended in dig-wash/xL buffer. pAG-MNase was activated by addition of 0.1 M CaCl2 and allowed to digest chromatin for 2 hours on ice. Digest was stopped by addition of 2X STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% digitonin, 100 µg/ml RNAse A, 50 µg/ml glycogen). Chromatin release standard option 1 was followed. Beads/cells were incubated for 30 minutes at 37˚C and cells were collected via magnet into new tubes for DNA extraction. DNA extraction was performed via 1 hour proteinase K digest at 50˚C and phenol/chloroform extraction with phase/lock tubes (Qiagen #129056). Reverse crosslinking for fixed samples was achieved by a longer overnight proteinase K digest prior to pheno/chloroform extraction.
DNA was library prepped using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645), Agencourt AMPure XP magnetic beads (Beckman Coulter #A63880), and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1; NEB #E7600) according to manufacturer’s instructions, with alterations to preserve small fragments.

value: E17.5 fetal liver

tag: chip antibody

value: BCLAF1 (Bethyl #A300-608A)

value: LSK

value: Fixed


title: LSK_WT_Native_CUT&RUN

value: Native


title: mtDT, Family F, RT #1, d7

description:
Library name: 10-A2304-1
Column name in fc_PE_counts.csv : 10.A2304.1.R1.001.fastq.gz.subread.BAM

value: mammary carcinoma

value: Trp53 null

value: 7 days post treatment


title: HSC_KO_CUT&RUN

value: HSC

value: KO


title: HSC_WT_CUT&RUN_2


title: HSC_WT_CUT&RUN_1


title: mtDT, Family F, IPW-5371 + RT  #1, d7

description:
Library name: 5-A2301-70
Column name in fc_PE_counts.csv : 5.A2301.70.R1.001.fastq.gz.subread.BAM

value: IPW+RT (Radiation)


title: MKL-1, JNJ-64619178, biol rep 4, PacBio Sequel IIe

city: Durham

first: Joseph

middle: L

last: Sevigny

state: NH

address: 35 Colovos Rd.

institute: Hubbard Center for Genome Studies

description:
Library name: FL.BioSample_8
IsoSeq

data_processing:
Starting with multiplexed HiFi reads produced from PacBio IsoSeq protocol.  Read Segementation was completed using skera with the kinnex8 segmentation adapters.
Demultiplexed using lima with the options '--ignore-biosamples --isoseq --peek-guess --overwrite-biosample-names' and the  IsoSeq primer sequences IsoSeq_v2_primers_12.fasta
Refinement of isoforms using isoseq3 refine and the option '--require-polya', clustering using isoseq cluster 2 with default settings, and isoseq collapse with the option '--do-not-collapse-5exons'
Read mapping using pbmm2 align  (minimap2) with the '--preset ISOSEQ' option.
Isofrom classification was completed using pigeon classify, filter, report, and prepare commands.
Assembly: GENCODE Human Release 39 (GRCh38.p13) Transcript sequences, gencode.v39.transcripts.fa.gz
Supplementary files format and content: Quantifications, including read counts and TPM for each isoform , are in the SQANTI3 *classifications.txt format described here. https://github.com/ConesaLab/SQANTI3/wiki/Understanding-the-output-of-SQANTI3-QC#glossary-of-classification-file-columns-classificationtxt

growth_protocol: MKL-1 cells were maintained in RPMI-1640 medium supplemented with 10% FBS, 1% GlutaMAX, and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen)
Strand-specific libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit, following the manufacturer's instructions. ≥400 ng of total RNA (measured by Qubit) was used. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis with dUTP instead of dTTP to maintain strand specificity. The strand-specific libraries then underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Size selection was performed using AMPure XP beads to isolate fragments of approximately 300 bp. Library quality was assessed using Qubit and real-time PCR for quantification and a Bioanalyzer for size distribution analysis. Equimolar amounts of each quantified library were pooled for sequencing on the Illumina NovaSeq X Plus Series platform, generating paired-end 150 bp reads with 18 GB of raw data per sample (60 million reads).

treatment_protocol: Cells were treated with DMSO or 12 nM JNJ-64619178 for 4 days

value: virus-positive Merkel cell carcinoma cells


title: MKL-1, JNJ-64619178, biol rep 2, PacBio Sequel IIe

description:
Library name: FL.BioSample_6
IsoSeq

value: WT


title: MKL-1, DMSO, biol rep 4, PacBio Sequel IIe

description:
Library name: FL.BioSample_4
IsoSeq

value: DMSO


title: MKL-1, JNJ-64619178, biol rep 3, PacBio Sequel IIe

description:
Library name: FL.BioSample_7
IsoSeq


title: MKL-1, DMSO, biol rep 1, PacBio Sequel IIe

description:
Library name: FL.BioSample_1
IsoSeq


title: MKL-1, JNJ-64619178, biol rep 1, PacBio Sequel IIe

description:
Library name: FL.BioSample_5
IsoSeq


title: IA1033

description:
Library name: IA1033
miRNA_raw_count.csv

value: Blood plasma

value: Male


title: mdtA mutant stationary phase 3

city: Montpellier

first: Anne

last: Lanois

address: 75 rue du Truel CC54

country: France

institute: INRA

data_processing:
BWA software (v.0.7.4)
SAMtools (v.0.1.12)
Bioconductor-GenomicFeatures package
Bioconductor-DESeq package
Assembly: https://mage.genoscope.cns.fr/microscope/genomic/overview.php?O_id=8
Supplementary files format and content: tab delimited text file includes raw counts for each sample

organism: Photorhabdus laumondii subsp. laumondii TTO1

source_name: bacterial strain

growth_protocol: culture phase in LB broth at 28°C  logarithmic phase (4 hours) or stationary culture phase (overnight culture)

extract_protocol:
RNEasy miniprep QIAGEN kit and depletion of rRNA with NEBNext® rRNA Depletion Kit (Bacteria)
Illumina TruSeq Stranded mRNA Sample Preparation kit

treatment_protocol: RNA Protect Bacteria reagent 5 min

value: bacterial strain

value: mdtA mutant

tag: growth phase

value: stationary phase


title: MKL-1, DMSO, biol rep 3, PacBio Sequel IIe

description:
Library name: FL.BioSample_3
IsoSeq


title: mdtA mutant stationary phase 1


title: mdtA mutant stationary phase 2


title: acrA mutant stationary phase 3

value: acrA mutant


title: IA1030

description:
Library name: IA1030
miRNA_raw_count.csv

value: Female

value: E4FAD (5xFAD+/-; human APOE4+/+, C57BL/6 background)

value: CMB


title: acrA mutant stationary phase2


title: IA1029

description:
Library name: IA1029
miRNA_raw_count.csv


title: acrA mutant stationary phase 1


title: Wild Type stationary phase 3


title: Wild Type stationary phase 1


title: Wild Type stationary phase 2


title: IA1026

description:
Library name: IA1026
miRNA_raw_count.csv


title: mdtA mutant exponential phase 3

value: exponential phase


title: mdtA mutant exponential phase 2


title: mdtA mutant exponential phase 1


title: acrA mutant exponential phase 1


title: acrA mutant exponential phase 3


title: acrA mutant exponential phase 2


title: Wild Type exponential phase 3


title: Wild Type exponential phase 2


title: Wild Type exponential phase 1


title: MKL-1, DMSO, biol rep 2, PacBio Sequel IIe

description:
Library name: FL.BioSample_2
IsoSeq


title: colon mucosa, UC FMT treatment, day 5, replicate 1

city: Kosice

first: Maria

last: Rynikova

address: Srobarova 2

country: Slovakia

institute: Pavol Jozef Safarik University in Kosice

description: Library name: FMT1

data_processing:
Data processing was performed by Novogene (cambridge, UK). Please inquire Novogene for further details.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstreamanalyses were based on the clean data with high quality.
Hisat2 (v 2.2.1) was used to map the reads to the reference genome (GRCh38.p13 (GCA_000001405.28))
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCh38.p13
Supplementary files format and content: csv file of FPKM values for each gene for each number. Additional information, such as gene full name, chromosome number, orientation, transcription factor family are also included in the file.

source_name: Colon

extract_protocol:
Colon tissue samples (∼ 2 cm) were excised post-mortem, snap-frozen in liquid nitrogen and stored at -70°C. For RNA extraction, frozen tissues were transferred directly into gentleMACS™ M Tubes (Miltenyi Biotec, Bergisch Gladbach, Germany) containing TRI Reagent® (Molecular Research Center, Cincinnati, OH, USA) without allowing them to thaw. The tissues were homogenized using the gentleMACS™ Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany). Subsequently, mucosal RNA was isolated from the homogenized tissue using the Monarch® Total RNA Miniprep Kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. The concentration and purity of the isolated DNA and RNA samples were first assessed in-house using a spectrophotometer (NanoDrop™ One/OneC, Thermo Fisher Scientific, Waltham, MA, USA). The samples were then shipped on dry ice to Novogene Europe (Cambridge, UK) for library preparation, sequencing, data processing, and statistical analysis.
Library preparation was performed by Novogene (Cambridge, UK). Please inquire Novogene for further details.

treatment_protocol: UC was induced in mice in one of the following ways (based on the experimental group): 5% DSS in drinking water; UC FMT administered orally; 5% DSS in drinking water and simulatneous administration of UC FMT orally

value: Colon

value: Mucosal cells

value: UC FMT


title: proCTLA4-1

city: Beijing

first: Wenyan

address: Tsinghua Road

institute: Tsinghua

description: Library name: proCTLA4-1

library_source: transcriptomic single cell

data_processing:
The scRNA-seq data generated were aligned and quantified using the Cell Ranger Single-Cell toolkit (v.8.0.0) against the mm10 mouse reference genome. Preliminary filtered data generated from Cell Ranger were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

source_name: tumor

growth_protocol: C57B6/J mice were inoculated 5*105 MC38 tumor cells.

extract_protocol:
MC38 tumors were collected on days 17 post inoculation for scRNA-seq library preparation. Each group homogenized 5 samples for single scRNA-seq processing.Tumor tissues were dissected and enzymatically digested using the gentleMACS (Miltenyi) according to manufacturer’s instruction. Single-cell suspensions were stained with antibodies against 7AAD/CD45 for FACS sorting on a BD Melody instrument.
Sorted live CD45+ immune cells were loaded onto a GemCode Single-Cell Instrument (10x Genomics, Pleasanton, CA) by using Single Cell 3’ Library and Gel Bead Kit V4 (10x Genomics), and subsequent steps were performed according to manufacturer instructions. Single-cell RNA libraries were sequenced by an Illumina NovaSeq 6000 sequencer with 150 bp paired-end reads (performed by Analytical Bioscience Limited, Beijing).

treatment_protocol: Tumor-bearing mice were treated with PBS (CTR group) or 100 μg ADCC-enhanced mouse CTLA-4 antibody (CTLA-4 group) and equimolar ADCC-enhanced ProCTLA-4 antibody (ProCTLA-4 group) on days 11 and 14 post inoculation.

value: tumor


title: colon mucosa, UC FMT treatment, day 5, replicate 2

description: Library name: FMT2


title: CTLA4-1

description: Library name: CTLA4-1


title: colon mucosa, UC FMT treatment, day 5, replicate 3

description: Library name: FMT3


title: Trimetazidine Group5

city: Jinan

first: hu

last: ying

address: No. 16369, Jingshi Road

institute: Affiliated Hospital of Shandong University of Traditional Chinese Medicine

description: Library name: QM5

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome mm10 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample
Supplementary files format and content: Raw_gene_counts_matrix.txt

source_name: cardiac tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A total of 24 mice were randomly divided into four groups (n = 6 per group): blank group (KB), model group (M), Trimetazidine treatment group (QM), and LGZGD treatment group (LG). M, QM, and LG groups received intraperitoneal injections of doxorubicin at a dose of 2.5 mg/kg, three times per week for 2 weeks (a total of 6 injections), for a cumulative dose of 15 mg/kg. Successful model establishment was defined by a reduction of left ventricular ejection fraction by 10% from baseline, confirmed via echocardiography. Mice in the KB group were injected with an equal volume of saline. Starting on day 8, mice in the LG group were administered LGZGD (raw herbal material) via gastric gavage at a dose of 6.6 g/kg, while mice in the QM group received trimetazidine via gastric gavage at a dose of 2 mg/kg/day (equivalent to the clinical dosage). Mice in the KB and M groups were gavaged with an equal volume of distilled water. The treatment continued for two weeks. Body weight was measured before modeling, after modeling, and following drug administration.

value: cardiac tissue

value: Doxorubicin-Induced Modeling

value: Trimetazidine treatment group (QM)


title: colon mucosa, DSS and UC FMT treatment, day 5, replicate 1

description: Library name: COMB1

value: DSS and UC FMT


title: colon mucosa, control, day 0, replicate 2

description: Library name: C0_2

value: Control


title: colon mucosa, DSS and UC FMT treatment, day 5, replicate 4

description: Library name: COMB4


title: colon mucosa, DSS and UC FMT treatment, day 5, replicate 3

description: Library name: COMB3


title: colon mucosa, DSS treatment, day 5, replicate 2

description: Library name: DSS2

value: DSS


title: colon mucosa, control, day 0, replicate 3

description: Library name: C0_3


title: colon mucosa, DSS treatment, day 5, replicate 1

description: Library name: DSS1


title: Trimetazidine Group6

description: Library name: QM6

growth_protocol: A total of 24 mice were randomly divided into four groups (n = 6 per group): blank group (KB), model group (M), Trimetazidine treatment group (QM), and LGZGD treatment group (LG). M, QM, and LG groups received intraperitoneal injections of doxorubicin at a dose of 2.5 mg/kg, three times per week for 2 weeks (a total of 6 injections), for a cumulative dose of 15 mg/kg.


title: colon mucosa, control, day 0, replicate 1

description: Library name: C0_1


title: colon mucosa, DSS and UC FMT treatment, day 5, replicate 2

description: Library name: COMB2


title: colon mucosa, DSS treatment, day 5, replicate 3

description: Library name: DSS3


title: Trimetazidine Group4

description: Library name: QM4


title: Trimetazidine Group1

description: Library name: QM1


title: Trimetazidine Group2

description: Library name: QM2


title: Linggui Zhugan Decoction Group6

description: Library name: LG6

value: LGZGD treatment group (LG)


title: Linggui Zhugan Decoction Group5

description: Library name: LG5


title: Linggui Zhugan Decoction Group4

description: Library name: LG4


title: Linggui Zhugan Decoction Group3

description: Library name: LG3


title: Trimetazidine Group3

description: Library name: QM3


title: Linggui Zhugan Decoction Group2

description: Library name: LG2


title: colon mucosa, UC FMT treatment, day 5, replicate 4

description: Library name: FMT4


title: Linggui Zhugan Decoction Group1

description: Library name: LG1


title: Model Group6

description: Library name: M6

value: model group (M)


title: CTRL-1

description: Library name: CTRL-1


title: Model Group4

description: Library name: M4


title: Control Group4

description: Library name: KB4

value: saline injection for modeling

value: blank group (KB)


title: Control Group6

description: Library name: KB6


title: Model Group3

description: Library name: M3


title: Control Group5

description: Library name: KB5


title: Control Group3

description: Library name: KB3


title: Model Group2

description: Library name: M2


title: Model Group5

description: Library name: M5


title: Model Group1

description: Library name: M1


title: mESC_WT_NONO

city: WASHINGTON

first: Jia-Ray

last: Yu

state: DC

address: 7144 13th PL NW

institute: Virginia Tech

description: Library name: CH77_mESC_WT_NONO

data_processing:
Data was processed with the nf-core/chip-seq v2.1.0 pipeline, with default settings for 150bp reads.
Spike-in was performed by re-running the pipeline with dm6 genome, and dividing uniquely mapped paired hg38 reads by dm6 reads. The wild type sample’s ratio was set to 1, and mutant samples were calculated relative to the wild type. Coverage tracks were then generated using the bam_coverage function of deepTools, with the scaling factor manually set as calculated for each sample
Assembly: mm10, hg38
Supplementary files format and content: Supplementary_files_format_and_content:

source_name: Embryo

growth_protocol: 37 degree and 5% CO2 in humidified incubators.

extract_protocol:
crosslinked and sheared chromatin
NEBNext Ultra II

treatment_protocol: Spiked with equal amounts Drosophila chromatin for normalization

value: Embryo

value: E14Tg2a mESC

value: embryonic stem cell

value: WT

value: NONO


title: mESC_WT_NSD1

description: Library name: CH150_mESC_WT_NSD1


title: Control Group1

description: Library name: KB1


title: EGFPF1

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

description: Library name: 1

data_processing:
The single-cell sequence preprocessing was performed with the standard 10x Genomics Cell Ranger Single Cell Software Suite (v3.0.0). In brief, raw sequencing data were demultiplexed, aligned to the mouse genome mm10, and the reads aligned to each gene were counted. Cell filtration, normalization, clustering, and differential expression analyses were performed with standard Seurat package procedures (v.4.3).
SoupX was used to remove ambient RNA contamination.
Assembly: mm10
Supplementary files format and content: .tsv file of barcodes
Supplementary files format and content: .tsv file of genes
Supplementary files format and content: .mtx file of count matrices

source_name: cortical

growth_protocol: C57BL/6J wild-type mice were purchased from Jackson laboratory (Strain #000664, Bar Harbor, ME) and the colony was maintained at Mayo Clinic Jacksonville. Both male and female mice were received intraperitoneal injection of AAV- GFP or AAV-p16 (1.8 × 1011 GC in 100-120 µl saline/mouse) at the age of 2-3 months and subjected to experiments 1, 3, or 6 months after the administration. Mouse brains were harvested after intracardiac perfusion. All animal procedures were in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals and approved by the Institutional Animal Care and Use Committee (IACUC) at Mayo Clinic or the University of Miami.

extract_protocol:
Both male and female mice were used, 6 mice per group. Briefly, cortical samples were enzymatically digested with the Neural Tissue Dissociation kit (P; 130-092-628, Miltenyi Biotec), and myelin was removed with magnetic bead separation (Myelin Removal Beads II, 130-096-733, Miltenyi Biotec). After myelin removal and red blood cells were removed with Red Blood Cell Lysis Solution (130-094-183, Miltenyi Biotec). Microglia and debris were then removed by magnetic separation using anti-CD11b+ microbeads (130-093-634, Miltenyi Biotec), followed by a dead cell removal kit (130-090-101, Miltenyi Biotec). The final cell pellet was suspended in DPBS supplemented with 0.04% BSA. In all samples, more than 90% of the cells were viable based on Trypan Blue examination. Approximately 6,000 cells from one animal were loaded into each sample well on a chip and combined with gel beads containing barcoded oligonucleotides using a 10x Chromium Controller (10x Genomics).
Single-cell libraries were constructed according to the manufacturer’s instructions and were sequenced by an Illumina NovaSeq Sequencing System at an average depth of 50,000 reads per cell.

value: cortical

value: EGFP

value: F


title: mESC_NONO-KO_NSD1

description: Library name: CH151_mESC_NONO-KO_NSD1

value: NONO-KO


title: p16M7

description: Library name: 7

value: M


title: p16M5

description: Library name: 5


title: EGFPF8

description: Library name: 8


title: p16F12

description: Library name: 12


title: p16F3

description: Library name: 3


title: mESC_NSD1-KO_NONO

description: Library name: CH78_mESC_NSD1-KO_NONO


title: mESC_WT_H3K36me2

description: Library name: CH43_mESC_WT_H3K36me2_D0


title: p16F2

description: Library name: 2


title: NONO-KO+RA-D6_rep2

description: Library name: JR18

data_processing:
Sequencing reads were aligned to mm10 reference genome using STAR v2.7.6a. Gene-level quantification was carried out using featureCounts v2.0.0 to generate a raw counts matrix53. To calculate normalized expression levels, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were estimated using Cufflinks v1.46
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: mRNA read counts summarized over genes

source_name: embryonic

extract_protocol:
total RNA by PureLink RNA mini kit (ThermoFisher)
NEBNext Ultra II (NEB)

value: embryonic

value: mESC

value: Retinoic Acid


title: EGFPM9

description: Library name: 9


title: EGFPM6

description: Library name: 6


title: EGFPF11

description: Library name: 11


title: EGFPM4

description: Library name: 4


title: p16M10

description: Library name: 10


title: Control Group2

description: Library name: KB2

value: cardiac tissue


title: NONO-KO+RA-D3_rep2

description: Library name: JR16


title: NONO-KO_rep2

description: Library name: JR14


title: NONO-KO+RA-D6_rep1

description: Library name: JR17


title: NONO-KO_rep1

description: Library name: JR13


title: NSD1-KO+RA-D6_rep1

description: Library name: JR11


title: NSD1-KO+RA-D3_rep2

description: Library name: JR10


title: NSD1-KO+RA-D6_rep2

description: Library name: JR12


title: NSD1-KO+RA-D3_rep1

description: Library name: JR9


title: WT+RA-D6_rep2

description: Library name: JR6


title: NSD1-KO_rep1

description: Library name: JR7


title: NSD1-KO_rep2

description: Library name: JR8


title: WT_rep2

description: Library name: JR2


title: WT_rep1

description: Library name: JR1


title: DMSO group (Control)

city: Yinchuan

first: Hechun

last: Xia

state: Ningxia

address: No. 804 Shengli South Street, Xingqing District, Yinchuan City, Ningxia, People's Republic of China

institute: General Hospital of Ningxia Medical University

description: Library name: Sample1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
In gene expression processes, particular exons on pre-mRNA may be included in or excluded from the final, resulting in different versions of mature mRNA. In this case, multiple proteins with different structures and biological functions can be translated from these alternatively spliced mRNA originated from the same gene. The process described here is named alternative splicing. StringTie was applied to assemble the mapped reads generated by Hisat2. ASprofile was employed to predict alternative splicing events in each samples and sorting them into 12 types.
For the samples with biological replicates: Differential expression analysis of two conditions/groups was performed using the DESeq2. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.01 & Fold Change≥2 found by DESeq2 were assigned as differentially expressed. For the samples without biological replicates: Differential expression analysis of two samples was performed using the edgeR.The FDR < 0.01 & Fold Change ≥2 was set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of the differentially expressed genes (DEGs) was implemented by the clusterProfiler packages based Wallenius non-central hyper-geometric distribution（Young et al, 2010）,which can adjust for gene length bias in DEGs.KEGG (Kanehisa et al., 2008) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS (Mao et al., 2005)database and clusterProfiler software to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: primary microglia

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
Qualified RNA were processed for library construction. The procedures are described as follow: (1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer. (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp. (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

value: primary microglia


title: Control vector (Control)

description: Library name: Sample1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
In gene expression processes, particular exons on pre-mRNA may be included in or excluded from the final, resulting in different versions of mature mRNA. In this case, multiple proteins with different structures and biological functions can be translated from these alternatively spliced mRNA originated from the same gene. The process described here is named alternative splicing. StringTie was applied to assemble the mapped reads generated by Hisat2. ASprofile was employed to predict alternative splicing events in each samples and sorting them into 12 types.
For the samples with biological replicates: Differential expression analysis of two conditions/groups was performed using the DESeq2. DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.01 & Fold Change≥2 found by DESeq2 were assigned as differentially expressed. For the samples without biological replicates: Differential expression analysis of two samples was performed using the edgeR.The FDR < 0.01 & Fold Change ≥2 was set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of the differentially expressed genes (DEGs) was implemented by the clusterProfiler packages based Wallenius non-central hyper-geometric distribution（Young et al, 2010）,which can adjust for gene length bias in DEGs.KEGG (Kanehisa et al., 2008) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS (Mao et al., 2005)database and clusterProfiler software to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

value: Control vector (Control)


title: Per2-overexpression vector (Treat)

description: Library name: Sample2

value: Per2-overexpression vector (Treat)


title: WT+RA-D3_rep2

description: Library name: JR4


title: WT+RA-D3_rep1

description: Library name: JR3


title: SP3

city: Seoul

first: Jungeun

last: Ji

address: 145 Anam-ro

department: Department of Integrated Biomedical and Life Science

institute: Korea University

description: Library name: SP3

data_processing:
Read alignment and processing were performed using the Nextflow RNAseq pipeline.
Raw reads were trimmed with TrimGalore, aligned against the mouse reference genome GRCm38 using STAR, and quantified with Salmon.
Assembly: GRCm38
Supplementary files format and content: tsv file includes raw counts for each value

source_name: Hippocampus

growth_protocol: Male C57BL/6N mice were purchased from Orient Bio (South Korea) and used for experiments after at least 1 week of adaptation. Eight-to ten-week-old mice were used in the experiments. Mice were housed under a 12-hour light/dark cycle (lights on: 8:00-20:00) with food and water ad libitum. All experiments were approved by the Seoul National University Institutional Animal Care and Use Committee

extract_protocol:
Extraction protocol followed the Trizol tissue extraction protocol.
Library construction followed the Illumina, TruSeq stranded mRNA Library preparation kits protocol.

treatment_protocol: Substance P was dissolved in distilled water and stored at -20 °C before use. Substance P (10 μM, 100 μl) was injected subcutaneously (s.c.) for 14 consecutive days. The injection dosage was based on a previous study, and is known to induce neutrophil infiltration and mast cell degranulation in mouse skin. The same volume of saline was injected subcutaneously into control mice.

value: Hippocampus

tag: strain

value: male

value: Wild-type

value: substance P injected


title: SP2

description: Library name: SP2


title: SP1

description: Library name: SP1


title: sgPrdm12-1 CUT&Tag

city: shanghai

first: guolong

last: liu

address: No. 500, Dongchuan Road, Minhang District, Shanghai

institute: East China Normal University

description:
Library name: SAMPLES 4
sgPrdm12-1.read_cnt

data_processing:
Raw sequencing reads were adapter-trimmed using Trimmomatic and aligned to the GRCm39 (Mus musculus) reference genome using Bowtie2. PCR duplicates were removed and uniquely mapped reads were used for peak calling with MACS2. BigWig files were generated for visualization in IGV, and differential binding analysis was performed using DiffBind.
Assembly: GRCm39
Supplementary files format and content: excel files include read_cnt values for each Sample
Library strategy: CUT&Tag

source_name: spleen

growth_protocol: mouse CD8+ T cell medium (cRPMI: RPMI-1640 + 10% FBS + 2 mM L-Glutamine + 100 U/mL Pen/Strep (Thermo Fisher) + 49 nM β-mercaptoethanol (Cat#M6250-10ML, Sigma)) at 1×10^6 cells/mL

extract_protocol:
Nuclei were isolated from CD8+ T cells and incubated with an antibody specific for H3K9me3 (#AB8898, Abcam). After washing, cells were incubated with Protein A-Tn5 transposase complex for tagmentation. Tagmented DNA fragments were purified using a DNA purification kit (e.g., Qiagen MinElute PCR Purification Kit). Library amplification was performed using indexed Illumina-compatible primers followed by size selection and quality assessment on a Bioanalyzer. Final libraries were sequenced on an Illumina platform.
Libraries were constructed using the CUT&Tag method. Following antibody binding and Tn5-mediated tagmentation, DNA fragments were purified using a PCR purification kit (Qiagen MinElute). Purified DNA was amplified with Illumina-compatible indexed primers through limited-cycle PCR (typically 12–14 cycles). Amplified libraries were purified again to remove primer dimers and subjected to quality control using a Bioanalyzer High Sensitivity DNA chip. Final libraries were normalized and pooled for sequencing on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

treatment_protocol: Mouse CD8+T cells were electroporated using P3 Primary Cell Nucleofection Solution (Catalog No. V4XP-3032, Lonza) according to the manufacturer's instructions. Ribonucleoprotein (RNP) complexes were generated by mixing 300 pmol of sgRNA (sgNTC/sgPrdm12) synthesized by Synthego with 300 pmol of Cas9 protein and incubated for 10 minutes at room temperature prior to electroporation.

value: spleen

value: RNP


title: sgPrdm12-2 CUT&Tag

description:
Library name: SAMPLES 5
sgPrdm12-2.read_cnt


title: WT+RA-D6_rep1

description: Library name: JR5


title: NONO-KO+RA-D3_rep1

description: Library name: JR15


title: Vehicle2

description: Library name: Vehicle2

value: Control


title: Vehicle3

description: Library name: Vehicle3


title: Vehicle1

description: Library name: Vehicle1


title: sgNTC-2 CUT&Tag

description:
Library name: SAMPLES 3
sgNTC-2.read_cnt


title: sgPrdm12-1

description:
Library name: SAMPLES 3
sgPrdm12-1 read_cnt

data_processing:
Raw FASTQ files were processed by first trimming adapter sequences using Cutadapt. Quality-filtered reads were aligned to the GRCm38 reference genome using Bowtie2 with default parameters. PCR duplicates were removed using Picard. ATAC-seq peak calling was performed using MACS2 with a p-value threshold of 0.01. Differentially accessible regions between Prdm12-edited and control samples were identified using DiffBind. Motif enrichment analysis was conducted using HOMER to identify transcription factors associated with differential peaks. Functional annotation and pathway analysis were carried out using GREAT or ChIPseeker.
Assembly: GRCm38
Supplementary files format and content: excel files include read_cnt values for each Sample

extract_protocol:
CD8+ T cells were isolated from OTI:Cas9 mice using magnetic bead separation. Cells were cultured and edited with CRISPR-Cas9 ribonucleoprotein (RNP) targeting Prdm12. Following recovery, cells were harvested and washed with cold PBS. Nuclei were isolated by lysis in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were then used for transposition reaction using the Tn5 transposase from the Nextera™ DNA Library Prep Kit. Libraries were amplified by PCR, size-selected, and sequenced on an Illumina platform.
ATAC-seq libraries were constructed following the standard protocol (Buenrostro et al., 2013). Briefly, nuclei were isolated from approximately 50,000 CD8+ T cells per sample by resuspension in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Tagmentation was performed using Tn5 transposase from the Nextera™ DNA Library Prep Kit in a 50 μL reaction at 37°C for 30 minutes. Resulting fragments were purified using AMPure XP beads and amplified with Illumina-indexed primers through 8–12 cycles of PCR. Final libraries were validated using  Agilent TapeStation and sequenced on an Illumina platform (e.g., NovaSeq ).


title: IgG

description: Library name: SAMPLES 1


title: sgNTC-1 CUT&Tag

description:
Library name: SAMPLES 2
sgNTC-1.read_cnt


title: sgPrdm12-2

description:
Library name: SAMPLES 4
sgPrdm12-2 read_cnt


title: sgNTC-2

description:
Library name: SAMPLES 2
sgNTC-2 read_cnt


title: sgNTC-1

description:
Library name: SAMPLES 1
sgNTC-1 read_cnt


title: GF pancreas, AP, rep2

city: Nanchang

first: Yaoyu

last: Zou

state: Jiangxi

address: 17 Yong Waizheng Street, Donghu District

institute: The First Affiliated Hospital of Nanchang University

description:
Library name: GF_AP_rep2
10x Genomics

data_processing:
Step 1 – demultiplex & alignment: BCL files were demultiplexed and aligned to the mouse reference genome (GRCm39, Cell Ranger refdata-gex-mm10-2020-A) using Cell Ranger v7.0.1 (10x Genomics) with default parameters; filtered_feature_bc_matrix outputs were generated.
Step 2 – quality control: In Seurat v4.3.0, cells with < 200 detected genes, < 1 000 UMIs, log10(Genes/UMI) < 0.7, mitochondrial UMIs > 20 % or hemoglobin UMIs > 5 % were discarded. Doublets were predicted and removed using DoubletFinder v2.0.2.
Step 3 – normalisation & HVGs: Data were log-normalised (NormalizeData) and the 2 000 most variable genes identified (FindVariableFeatures).
Step 4 – dimensionality reduction & clustering: Scaled data (ScaleData) underwent PCA, and UMAP was computed on the top 30 PCs. Clusters were defined using the Louvain algorithm (resolution = 0.5) via FindNeighbors / FindClusters.
Step 5 – cell-type annotation: Cluster markers were identified with FindAllMarkers (Wilcoxon), and cell identities were assigned using SingleR v2.2.0 against the ImmGen mouse reference; acinar and immune subsets were confirmed with canonical markers.
Assembly: Mouse genome GRCm39 (Ensembl 109) / Cell Ranger reference “refdata-gex-mm10-2020-A
Supplementary files format and content: For each sample: filtered gene–barcode matrix (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz); combined Seurat object (seurat.rds) containing normalised counts, UMAP coordinates, cluster and cell-type metadata.
Supplementary files format and content: Integrated AnnData file (merged_anndata.h5ad) with expression matrix, dimensionality reductions and annotations; supplementary CSV of marker genes per cluster.

source_name: pancreas

growth_protocol: Male C57BL/6J mice (7–8 weeks) were maintained under germ-free (GF) or specific-pathogen-free (SPF) conditions in individually ventilated isolators at 22 ± 2 °C, 50–60 % humidity, 12 h light/dark cycle with autoclaved chow and sterile water ad libitum.

extract_protocol:
Fresh pancreas was minced (~0.5 mm³) in DMEM + 10 % FBS and digested at 37 °C for 60 min in DMEM containing 0.25 % trypsin and 1 mg ml⁻¹ collagenase I/II/IV with gentle agitation. The digest was filtered through a 100 µm strainer and centrifuged (300 g, 5 min). Red blood cells were removed with MACS RBC lysis buffer (4 °C, 10 min). Cells were washed, resuspended in PBS + 0.04 % BSA, and viability was assessed on a Luna counter; suspensions were adjusted to 700–1 200 cells µl⁻¹ for library preparation.
Single-cell libraries were generated using Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (10x Genomics, PN 1000268) following the manufacturer’s instructions, targeting 8 000 cells per sample. GEM generation, reverse transcription, cDNA amplification and indexing PCR were performed on a Chromium Controller. Finished libraries were quantified (Qubit dsDNA HS) and quality-checked (Agilent 2100). Sequencing was carried out on an Illumina NovaSeq 6000 (paired-end 2 × 150 bp).

treatment_protocol: Acute pancreatitis (AP) was induced by intraperitoneal injections of cerulein (100 µg kg⁻¹) administered hourly for 10 h. Control animals received sterile saline. Mice were euthanized 24 h after the final injection; GF or SPF status was preserved throughout the experiment.

value: pancreas

value: CD45+ immune cells;Acinal Cells

value: C57BL/6J WT

value: cerulein 100 µg kg-1 ×10, GF

value: NovaSeq run 1


title: mESC_NONO-KO_H3K36me2

description: Library name: CH46_mESC_NONO-KO_H3K36me2

value: Embryo

value: E14Tg2a mESC

value: embryonic

value: NONO-KO


title: SPF pancreas, AP, rep2

description:
Library name: SPF_AP_rep2
10x Genomics

value: cerulein 100 µg kg-1 ×10, SPF


title: 1600 μM iron and 1 μM RSL3 group (Treat)

description: Library name: Sample2

value: primary microglia


title: GF pancreas, AP, rep1

description:
Library name: GF_AP_rep1
10x Genomics


title: 20999X18 NMuMG Obese secretome Rep3

city: Salt Lake City

first: Keren

last: Hilgendorf

state: Utah

address: 15 N Medical Drive East Rm 4100

department: Biochemistry

institute: University of Utah

description:
Library name: Sample 30
20999R_raw_counts.txt

data_processing:
Mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 108
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR 2.7.9a in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Assembly: GRCm39
Supplementary files format and content: Feature count output files combined into a tab-delimited count matrix

source_name: NMuMG

growth_protocol: E0771, NMuMG, and SkBr3 cells were plated at subconfluency and allowed to grow for 36 hours, before treatment addition. E0771 and SkBr3 cells were grown in DMEM with 10% FBS. NMuMG cells were grown in DMEM with 10% FBS, 4.5 g/L glucose and 10 mcg/ml insulin.

extract_protocol:
The cells (E0771, NMuMG, and SkBr3) were washed once post treatment with PBS then collected in RLT-bME buffer. The RNA was isolated using Qiagen RNeasy kit.
RNA was sequenced using Illumina Sequencing with Agilent RNA ScreenTape Assay for QC and NovaSeq S4 Reagent Kit v1.5_150x150 bp Sequencing (2500 M read-pairs/lane). The library was prepped using NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA Isolation with adapter read 1 (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) and adapter read 2 (AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).

treatment_protocol: The treatments,  standard growth media, lean inguinal adipocyte secretome, or obese inguinal adipocyte secretome (50% secretome, 50% standard growth media) was added to the cells for 16 hours.

value: NMuMG

value: Breast Cancer

value: Obese Inguial Adipocyte Secretome


title: 20999X16 NMuMG Obese secretome Rep1

description:
Library name: Sample 28
20999R_raw_counts.txt


title: 20999X13 NMuMG Lean secretome Rep1

description:
Library name: Sample 25
20999R_raw_counts.txt

value: Lean Inguinal Adipocyte Secretome


title: 20999X14 NMuMG Lean secretome Rep2

description:
Library name: Sample 26
20999R_raw_counts.txt


title: Human pancreatic organoid donor #2

city: Cleveland

first: Katreya

last: Lovrenert

address: 10900 Euclid Avenue

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

description: Library name: AH852 Human pancreatic organoid donor #2

data_processing:
Raw files were trimmed using Sickle (Joshi NA, Fass JN. (2011). Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33)
Trimmed reads aligned to the hg19 genome using the BWA aligner (Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60).
Aligned reads were marked for duplicates using Picard and coverage tracks were generated using deepTools bamCoverage (Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016))
Assembly: hg19
Supplementary files format and content: hg19 aligned merged ATAC-seq of biological replicates

source_name: pancreatic organoid

growth_protocol: Cell lines were grown by standard protocols

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were constructed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exceptions: Final libraries were purified with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

treatment_protocol: 50,000 cells were isolated prior to lysing/transpostion

value: pancreatic organoid


title: 20999X11 NMuMG Control Rep2

description:
Library name: Sample 23
20999R_raw_counts.txt

value: Control


title: Human pancreatic organoid donor #1-1

description: Library name: AH850 Human pancreatic organoid donor #1-1


title: 20999X12 NMuMG Control Rep3

description:
Library name: Sample 24
20999R_raw_counts.txt


title: Erythroid-committed primary cells, SAMD1 KO, day 12, rep4

city: Omaha

first: Meg

middle: A

last: Schaefer

state: Nebraska

address: 985805 Nebraska Medical Center

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center

data_processing:
RNA-seq data was aligned to the human genome, hg38, using STAR (v2.7.10b).
Sorted BAM files were obtained using samtools (v1.16.1), and normalized reads based on reads per kilobase per million mapped reads (TPM) were obtained using stringtie (v2.2.0).
Differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: DESeq2 results; raw counts

source_name: Kit+ Erythroid-committed primary human cells

growth_protocol: CD34+ cells were cultured in serum free expansion media for 4 days containing a cocktail of recombinant human (rh) Flt-3, SCF, IL3, and IL-6, followed by an 8-day differentiation phase in IMDM containing 15% FBS, 500 μg/mL holotransferrin, 2 mM glutamine, 1.5% pen/strep, 1% BSA, 10 μg/mL rhinsulin, 1 μm dexamethasone, 1 μm β-estradiol, 5 ng/mL rhIL-3, 100 ng/mL rhSCF, and 6 U/mL EPO. Lentiviral infections with scramble and sgSAMD1 constructs were performed on day 2 of the differentiation phase by spinoculation. 48 hours after infection, infected cells were puromycin selected.

extract_protocol:
RNA was isolated by TRIzol extraction and purified with the Rneasy Plus Micro Kit (Qiagen).
RNA libraries were prepared using the Universal Plus mRNA-Seq with NuQuant kit.

tag: condition

value: SAMD1 knockout

tag: timepoint

value: Day 12


title: 20999X9 E0771 Obese secretome Rep3

description:
Library name: Sample 21
20999R_raw_counts.txt


title: 20999X10 NMuMG Control Rep1

description:
Library name: Sample 22
20999R_raw_counts.txt


title: Human pancreatic organoid donor #1-2

description: Library name: AH851 Human pancreatic organoid donor #1-2


description: Library name: AH849 Human pancreatic organoid donor 1 (d9) #2


title: Erythroid-committed primary cells, SAMD1 KO, day 12, rep1

value: Kit+ Erythroid-committed primary human cells


title: Erythroid-committed primary cells, scramble, day 12, rep3

value: Scramble


title: Erythroid-committed primary cells, SAMD1 KO, day 12, rep3


title: 20999X7 E0771 Obese secretome Rep1

description:
Library name: Sample 19
20999R_raw_counts.txt


title: Erythroid-committed primary cells, SAMD1 KO, day 12, rep2