title: male_right atrium_18 months_1541569

description: Library name: 1541569


title: LPMI467_ATAC

status: Public on Mar 05 2026

type: SRA

city: Houston

first: Haopeng

last: Yang

state: TX

address: 7455 Fannin ST

department: Lymphoma and Myeloma

country: USA

institute: The University of Texas MD Anderson Cancer Center

description: Library name: LPMI467_ATAC

library_source: genomic

data_processing:
RNA-seq data were processed using an in-house computational pipeline. Raw reads were trimmed with Trimmomatic, and both pre- and post-trimming quality metrics were assessed using FastQC. Trimmed reads were aligned to the human reference genome (hg38) using STAR in 2-pass mode. To remove contaminating mouse reads, trimmed reads were filtered using XenoFilteR. Only samples with at least 20 million uniquely mapped reads were retained for downstream analyses. Gene-level quantification was performed with HTSeq using the following parameters: -m union -f bam -i gene_id -s reverse -t exon --additional-attr=gene_name. The resulting DESeqDataSet was filtered to retain genes with a minimum of 10 total reads across all samples. Transcripts per million reads (TPM) values were calculated for expression normalization. For gene set enrichment analyses, normalized counts were evaluated using curated B-cell lymphoma gene sets and the SignatureDB database (https://lymphochip.nih.gov/signaturedb/).
Technical replicates for each ATAC-seq sample were merged prior to quality control assessment with FastQC. Adapter sequences were removed from paired-end FASTQ files through Trimmomatic trimming, followed by alignment to the hg19 human reference genome using the Burrows-Wheeler Aligner (BWA). Post-alignment processing included coordinate-based sorting and filtering to exclude reads mapping to mitochondrial DNA and blacklisted genomic regions via Samtools. PCR duplicates were marked and removed using Picard Tools' MarkDuplicates command. Deduplicated BAM files were then processed with XenoFilteR to remove contaminating mouse reads. The processed BAM files, having completed alignment, sorting, and filtering, served as input for subsequent analyses. For track visualization purposes, BAM files were transformed into BigWig format through deepTools' bamCoverage function, incorporating Tn5 transposase insertion site correction. Peak calling was performed on Tn5-adjusted insertion sites using MACS2 with the following parameters: -g hs (genome size), -q 0.05 (q-value threshold), -f BAMPE (paired-end BAM format), and -B (bedGraph output). Genomic tracks were visualized using pyGenomeTracks version 3.9.
Assembly: RNA-seq: hg38; ATAC-seq: hg19
Supplementary files format and content: txt files with raw count for RNA-seq; bigwig files for ATAC-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: PDX tumor

extract_protocol:
For RNA-seq library prepration, PDX tumors were homogenized, and total RNA was extracted using the AllPrep DNA/RNA Kit (Qiagen, 80204) and quantified with the Qubit High Sensitivity RNA Kit (Life Technologies, Q32852). One microgram of RNA was used to generate sequencing libraries. For ATAC-seq library prepration, viably cryopreserved PDX tumor cells were thawed and processed using the Dead Cell Removal Kit to eliminate non-viable cells. Fifty thousand live tumor cells were washed in ATAC-seq resuspension buffer, resuspended in 50 μL of ATAC-seq resuspension buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, and incubated on ice for 3 min. Following lysis, nuclei were washed with cold ATAC-seq resuspension buffer containing 0.1% Tween-20 (without NP-40 or digitonin), then resuspended in 50 μL of transposition mixture and incubated at 37 °C for 30 min in a thermomixer at 1000 rpm. Fragmented DNA was purified using the Zymo DNA Clean & Concentrator-5 kit (Zymo, D4024).
For RNA-seq library prepration, one microgram of RNA was used to generate sequencing libraries with the KAPA HyperPrep RNA Kit with RiboErase (Roche, KK8560), using 8 cycles of PCR amplification according to the manufacturer’s instructions. For ATAC-seq library prepration, libraries were prepared with the KAPA HyperPrep Kit (Roche, KK8502) using 10 cycles of PCR amplification. Both RNA-seq and ATAC-seq libraries were assessed on a TapeStation 4200 (Agilent, G2991BA), quantified with the Qubit High Sensitivity dsDNA Kit (Life Technologies, Q32854), multiplexed, and sequenced on an Illumina NovaSeq 6000 using a 100-10-10-100 bp read configuration.

tag: tissue

value: PDX tumor


title: mixed_leukaemia_BM_LMPP_4

city: Edinburgh

first: Alasdair

last: Duguid

address: 5 Little France Drive

department: Institute for Regeneration and Repair

country: United Kingdom

institute: University of Edinburgh

description:
Library name: mixed_leukaemia_BM_LMPP_4
10-1-10-B; normalised_count_data_130b.csv

library_source: transcriptomic

data_processing:
The Cogent NGS Analysis Pipeline v2.0 (TaKaRa) in the command line was used for data preprocessing. SummarizedExperiment objects containing count matrices were created using the GenomicAlignments package and the aligned BAM files. SummarizedExperiment objects were transformed into DESeqDataSet objects, prefiltered, normalised and a results table created using the DESeq2 package.
Assembly: GRCm39
Supplementary files format and content: FASTQ format files containing raw sequencing reads for each sample.
Supplementary files format and content: normalized gene expression values

molecule: total RNA

organism: Mus musculus

source_name: BM

extract_protocol:
RNA was extracted from freshly sorted leukaemia propagating cells and haematopoietic stem and progenitor cells harvesed from the bone marrow and central nervous system of mice that developed terminal leukaemia and controls using the Quick-RNA Microprep Kit (Zymo, R1050).
cDNA library preparation was performed using SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian (TaKaRa, 634487).

value: BM

tag: disease state

value: leukaemia

tag: cell type

value: LMPP

tag: genotype

value: miR-130b overexpressing Kmt2a-AFF1+

tag: mouse id


title: male_left atrium_27 months_1541576

city: Tarrytown

first: Kun

last: Xiong

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

description: Library name: 1541576

data_processing:
Sequencing reads were processed with ArrayStudio (11.7.4) RNA-seq pipeline to quantify gene expression levels
Assembly: Rn7
Supplementary files format and content: Tab-separated raw counts

organism: Rattus norvegicus

source_name: left atrium

extract_protocol:
Rats were anesthetized with 3.5% isoflurane and sacrificed by exsanguination and thoracotomy. Organs were removed, tissues were dissected on ice, preserved in RNAlater® solution (Thermo Fisher Scientific) and stored at -80℃ until further processing. RNA was extracted using MagMax-96 total RNA isolation kit (Termo Fisher). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies), and the integrity was assessed using Fragment Analyzer (Agilent).
Strand-specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen). RNA-seq libraries were sequenced at 100 million reads using Illumina Novo-Seq 6000 platforms in paired-end mode to a length of 2×76 bp base-pairs

tag: strain

value: Sprague Dawley

value: left atrium

tag: Sex

value: male

tag: age

value: 27 months


title: mixed_leukaemia_CNS_LMPP_4

description:
Library name: mixed_leukaemia_CNS_LMPP_4
10-1-10-C; normalised_count_data_130b.csv

source_name: CNS

value: CNS


title: mixed_leukaemia_CNS_LK_3

description:
Library name: mixed_leukaemia_CNS_LK_3
8-2-4-C; normalised_count_data_130b.csv

value: LK/CLP


title: male_cerebellum_27 months_1377531

description: Library name: 1377531

data_processing:
Sequencing reads were processed with ArrayStudio (11.7.4) RNA-seq pipeline to quantify gene expression levels
Assembly: mm10
Supplementary files format and content: Tab-separated raw counts

source_name: cerebellum

extract_protocol:
Mice were sacrificed by CO2 asphyxiation. Organs were removed, tissues were dissected on ice, preserved in RNAlater® solution (Thermo Fisher Scientific) and stored at -80℃ until further processing. RNA was extracted using MagMax-96 total RNA isolation kit (Termo Fisher). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies), and the integrity was assessed using Fragment Analyzer (Agilent).
Strand-specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen). RNA-seq libraries were sequenced at 100 million reads using Illumina Novo-Seq 6000 platforms in paired-end mode to a length of 2×76 bp base-pairs

value: cerebellum


title: snRNA-seq library from donor A.5

city: New Haven

first: Marcello

last: DiStasio

state: CT

address: 300 George St. Rm. 353D Rm. 353D

department: Pathology

institute: Yale School of Medicine

description:
Library name: A_5_snRNAseq
Single-nucleus RNA sequencing library from human choroid plexus; Paired-end sequencing (Read 1: 28 bp, Read 2: 91 bp) on an Illumina NovaSeq 6000.

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were converted to FASTQ files and processed using the 10x Genomics Cell Ranger pipeline. Reads were aligned to the human reference genome (GRCh38), and gene–barcode count matrices were generated according to standard 10x Genomics workflows for single-nucleus RNA sequencing.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Processed data files consist of filtered gene–barcode expression matrices generated by the 10x Genomics Cell Ranger pipeline. For each sample, the processed data include a sparse count matrix in Matrix Market format (matrix.mtx.gz) along with corresponding feature annotation (features.tsv.gz) and barcode identifiers (barcodes.tsv.gz). Matrices contain UMI counts for genes detected in high-quality nuclei after Cell Ranger filtering.

source_name: choroid plexus

extract_protocol:
Nuclei were isolated from frozen retinal tissue on ice using the Nuclei EZ Prep Kit (NUC-101, Sigma-Aldrich) with minor modifications. All steps were performed on ice or at 4 °C. Tissue was dounce-homogenized (25 strokes with loose pestle A followed by 25 strokes with tight pestle B) in 2 mL EZ Lysis Buffer using a KIMBLE Dounce Tissue Grinder. The homogenate was transferred to a 15 mL tube, supplemented with an additional 2 mL EZ Lysis Buffer, incubated on ice for 5 min, and centrifuged at 500 × g for 5 min at 4 °C. The supernatant was discarded, and the nuclei pellet was resuspended in 4 mL EZ Lysis Buffer, incubated on ice for 5 min, and centrifuged again at 500 × g for 5 min at 4 °C. Nuclei were washed in 4 mL ice-cold Nuclei Suspension Buffer (1× PBS containing 0.01% BSA and 0.1% RNase inhibitor), resuspended in 1 mL Nuclei EZ Storage Buffer, and filtered through a 40 µm nylon cell strainer. Nuclei were counted using trypan blue exclusion with a hemocytometer prior to library preparation.
RNA libraries of barcoded single nuclei were generated using the 10x Genomics Chromium Next GEM Single Cell 3′ Library & Gel Bead Kit according to the manufacturer’s instructions. Briefly, isolated nuclei were loaded onto the Chromium Controller, where individual nuclei were partitioned into Gel Beads-in-Emulsion (GEMs) for barcoding. Within each GEM, reverse transcription was performed to generate barcoded cDNA molecules containing unique cell barcodes and unique molecular identifiers (UMIs). Following GEM cleanup and cDNA amplification, sequencing libraries were constructed through fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR. Final libraries were quantified and assessed for quality prior to sequencing.

value: choroid plexus


title: mixed_leukaemia_CNS_LK_2

description:
Library name: mixed_leukaemia_CNS_LK_2
7-1-11-C; normalised_count_data_130b.csv


title: snRNA-seq library from donor YA.1

description:
Library name: YA_1_snRNAseq
Single-nucleus RNA sequencing library from human choroid plexus; Paired-end sequencing (Read 1: 28 bp, Read 2: 91 bp) on an Illumina NovaSeq 6000.

value: female


title: LPMI466_ATAC

description: Library name: LPMI466_ATAC


title: male_right atrium_18 months_1541567

description: Library name: 1541567

source_name: right atrium

value: right atrium

value: 18 months


title: Endothelial enriched PyMT-M

first: Luis

last: Becerra Dominguez

address: 1 Baylor Plz

department: Breast Cancer

institute: Baylor College of Medicine

description: Library name: PyMT-M

data_processing:
Barcoded processing and gene counting were performed with 10x Genomics Cell Ranger v8.0.0.
Assembly: mm39
Supplementary files format and content: tab-separated value files for counts matrices, barcodes, and genes

source_name: Breast tissue

extract_protocol:
Mammary tumors were harvested from female C57BL/6 mice, minced, and enzymatically digested with 1.5 mM collagenase I and 1 μg/mL DNase I at 37°C for 1 hour with rotation. Digested tissue was passed through a 70 μm strainer, washed with PBS containing 2% FBS, and live cells were subjected to endothelial magnetic enrichment and subsequently isolated by sorting prior to pooling, single-cell library preparation and downstream analysis.
Single-cell suspensions were processed using the 10x Genomics Chromium Single Cell 3′ Gene Expression platform (v3.1 chemistry) according to the manufacturer’s instructions. Libraries were prepared from sorted live cells, amplified, and sequenced on Illumina X platform at BCM RNA Profiling Core.

value: Breast tissue

tag: cell line

value: PyMT-M

value: Endothelial


title: Endothelial enriched PyMT-N

description: Library name: PyMT-N

value: PyMT-N


title: male_cerebellum_27 months_1377535

description: Library name: 1377535


title: male_left atrium_27 months_1541573

description: Library name: 1541573


title: HTO associated to XCRS1-POOL-SCG85

city: San Francisco

first: Tristan

last: Courau

state: CA

address: 513 Parnassu Ave

institute: UCSF

description: Library name: XCRS1-POOL-SCM85

data_processing:
Detailed protocols can be found here https://www.biorxiv.org/content/10.1101/2025.07.01.661217v1 and in subsequent publications. All scRNAseq procedures were done according to 10X genomic's V3 3' SOPs.
Assembly: mm10
Supplementary files format and content: We provide a processed RDS file containing cells analyzed for and used in https://www.biorxiv.org/content/10.1101/2025.07.01.661217v1 and https://quipi.org/app/quipi_humu

molecule: polyA RNA

source_name: Primary tumor

extract_protocol:
Detailed protocols can be found here https://www.biorxiv.org/content/10.1101/2025.07.01.661217v1 and in subsequent publications. All scRNAseq procedures were done according to 10X genomic's V3 3' SOPs.
Detailed protocols can be found here https://www.biorxiv.org/content/10.1101/2025.07.01.661217v1 and in subsequent publications. All scRNAseq procedures were done according to 10X genomic's V3 3' SOPs.

value: Primary tumor

value: Multiple

tag: library type

value: TotalSeq-A anti-mouse HTO


title: mixed_leukaemia_BM_LK_2

description:
Library name: mixed_leukaemia_BM_LK_2
7-1-11-B; normalised_count_data_130b.csv

value: BM

value: leukaemia

value: miR-130b overexpressing Kmt2a-AFF1+


title: LPMI386_ATAC

description: Library name: LPMI386_ATAC

value: PDX tumor


title: HTO associated to XCRS1-POOL-SCG79

description: Library name: XCRS1-POOL-SCM79

value: RENCA


title: female_cerebellum_24 months_1377537

description: Library name: 1377537

value: cerebellum

value: 24 months


title: HTO associated to XCRS1-POOL-SCG78

description: Library name: XCRS1-POOL-SCM78


title: mixed_leukaemia_CNS_LK_1

description:
Library name: mixed_leukaemia_CNS_LK_1
6-2-4-C; normalised_count_data_130b.csv

value: CNS

value: LK/CLP


title: male_right atrium_18 months_1541562

description: Library name: 1541562

value: Sprague Dawley

value: right atrium

value: male

value: 18 months


title: male_right atrium_27 months_1541571

description: Library name: 1541571

value: 27 months


title: male_right atrium_18 months_1541561

description: Library name: 1541561


title: snRNA-seq library from donor A.2

description:
Library name: A_2_snRNAseq
Single-nucleus RNA sequencing library from human choroid plexus; Paired-end sequencing (Read 1: 28 bp, Read 2: 91 bp) on an Illumina NovaSeq 6000.

value: choroid plexus

value: female


title: mixed_leukaemia_BM_LK_1

description:
Library name: mixed_leukaemia_BM_LK_1
6-2-4-B; normalised_count_data_130b.csv


title: male_cerebellum_27 months_1377533

description: Library name: 1377533


title: mixed_leukaemia_BM_HSC_4

description:
Library name: mixed_leukaemia_BM_HSC_4
10-1-3-B; normalised_count_data_130b.csv

value: HSC/MPP


title: snRNA-seq library from donor A.1

description:
Library name: A_1_snRNAseq
Single-nucleus RNA sequencing library from human choroid plexus; Paired-end sequencing (Read 1: 28 bp, Read 2: 91 bp) on an Illumina NovaSeq 6000.


title: HTO associated to XCRS1-POOL-SCG72

description: Library name: XCRS1-POOL-SCM72

value: Primary tumor

value: Multiple

value: TotalSeq-A anti-mouse HTO


title: male_right atrium_18 months_1541559

description: Library name: 1541559


title: female_cerebellum_27 months_1377532

description: Library name: 1377532


title: HTO associated to XCRS1-POOL-SCG66

description: Library name: XCRS1-POOL-SCM66


title: male_right atrium_18 months_1541568

description: Library name: 1541568


title: mixed_leukaemia_CNS_LMPP_3

description:
Library name: mixed_leukaemia_CNS_LMPP_3
8-2-10-C; normalised_count_data_130b.csv

value: leukaemia

value: LMPP

value: miR-130b overexpressing Kmt2a-AFF1+


title: mixed_leukaemia_CNS_HSC_2

description:
Library name: mixed_leukaemia_CNS_HSC_2
7-2-0-C; normalised_count_data_130b.csv


title: mixed_leukaemia_BM_LMPP_3

description:
Library name: mixed_leukaemia_BM_LMPP_3
8-2-10-B; normalised_count_data_130b.csv

value: BM


title: LPMI431_ATAC

description: Library name: LPMI431_ATAC

value: PDX tumor


title: male_right ventricle_18 months_1541556

description: Library name: 1541556

source_name: right ventricle

value: right ventricle


title: LPMI406_ATAC

description: Library name: LPMI406_ATAC


title: mixed_leukaemia_CNS_LMPP_2

description:
Library name: mixed_leukaemia_CNS_LMPP_2
8-2-0-C; normalised_count_data_130b.csv

value: CNS


title: male_right ventricle_18 months_1541555

description: Library name: 1541555

value: Sprague Dawley


title: HTO associated to XCRS1-POOL-SCG60

description: Library name: XCRS1-POOL-SCM60


title: mixed_leukaemia_BM_HSC_2

description:
Library name: mixed_leukaemia_BM_HSC_2
7-2-0-B; normalised_count_data_130b.csv


title: male_right atrium_18 months_1541565

description: Library name: 1541565

value: right atrium

value: male


title: male_right atrium_18 months_1541566

description: Library name: 1541566

value: 18 months


title: LPMI396_ATAC

description: Library name: LPMI396_ATAC


title: male_right atrium_18 months_1541564

description: Library name: 1541564


title: HTO associated to XCRS1-POOL-SCG84

description: Library name: XCRS1-POOL-SCM84


title: male_right atrium_18 months_1541563

description: Library name: 1541563


title: mixed_leukaemia_CNS_LMPP_1

description:
Library name: mixed_leukaemia_CNS_LMPP_1
7-1-10-C; normalised_count_data_130b.csv


title: LPMIRT15_RNA

description: Library name: LPMIRT15_RNA


title: LPMI329_ATAC

description: Library name: LPMI329_ATAC


title: HTO associated to XCRS1-POOL-SCG55

description: Library name: XCRS1-POOL-SCM55

value: LLC


title: mixed_leukaemia_BM_LMPP_1

description:
Library name: mixed_leukaemia_BM_LMPP_1
7-1-10-B; normalised_count_data_130b.csv


title: mixed_leukaemia_BM_LMPP_2

description:
Library name: mixed_leukaemia_BM_LMPP_2
8-2-0-B; normalised_count_data_130b.csv


title: LPMI300_ATAC

description: Library name: LPMI300_ATAC


title: male_right ventricle_18 months_1541554

description: Library name: 1541554


title: mixed_leukaemia_BM_HSC_1

description:
Library name: mixed_leukaemia_BM_HSC_1
6-2-0-B; normalised_count_data_130b.csv


title: male_right ventricle_18 months_1541553

description: Library name: 1541553


title: LPMIC029_RNA

description: Library name: LPMIC029_RNA


title: mixed_leukaemia_CNS_HSC_4

description:
Library name: mixed_leukaemia_CNS_HSC_4
10-1-3-C; normalised_count_data_130b.csv


title: A40_Male5

city: London

first: Nazif

last: Alic

address: Gower St

institute: UCL

data_processing:
Read quality was assessed with FastQC and transcript abundance was estimated with Salmon against the fasta file containing all Drosophila transcripts (Flybase, r6.55). Data was imported into R with RStudio, using tximport package and differential expression assessed with DESeq2 and ihw packages.
Assembly: Drosophila melanogaster genome release dmel_r6.55 from Flybase.
Supplementary files format and content: .xlsx

organism: Drosophila melanogaster

source_name: Gut

growth_protocol: Fly stocks were maintained and experiment was conducted at 25oC, 60% humidity and 12h:12h light/dark cycle on a yeast/sugar/agar (SYA) food medium. All the crosses were performed in cages containing grape juice, agar and live yeast. We used mid-gut specific gene-switch driver TIGS to induce CrebB. RU486 (Sigma, dissolved in ethanol) was added to a final concentration of 200µM to SYA food to induce the driver. As control (RU486minus), ethanol (solvent) was added to the SYA food.

extract_protocol:
For RNA extraction, eight mid-guts were dissected from gut-induced CrebB (TIGS>CrebB- plusRU486) flies, non-induced CrebB (TIGS>CrebB- minusRU486) flies, driver alone (TIGS only- plusRU486) and driver alone (TIGS only- minus RU486) flies at indicated times in ice-cold PBS and placed into ice-cold TRIzol (Thermo Fisher Scientific, 15596026). Five experimental replicates were performed and RNA samples were preserved in -80oC freezer prior to extraction by TRIzol/choloroform method as per manufacturer’s instructions and quantified by NanoDrop 2000c spectrophotometer.
For RNA sequencing, library preparation (Illumina, strand-specific RNA-seq with PolyA selection) and sequencing (Illumina NovaSeq 2 x 150 bp sequencing) were performed by Azenta Life Sciences (GENEWIZ UK Ltd., Essex, UK).
2x150 bp sequencing

value: Male

value: Gut

value: TIGS only

tag: treatment


title: HTO associated to XCRS1-POOL-SCG73

description: Library name: XCRS1-POOL-SCM73

value: Primary tumor

value: Multiple


title: HTO associated to XCRS1-POOL-SCG54

description: Library name: XCRS1-POOL-SCM54

value: TotalSeq-A anti-mouse HTO


title: A39_Male5

treatment_protocol: RU486 (Sigma, dissolved in ethanol) was added to a final concentration of 200µM to SYA food to induce the driver. As control (RU486minus), ethanol (solvent) was added to the SYA food.


title: LPMI203_ATAC

description: Library name: LPMI203_ATAC


title: HTO associated to XCRS1-POOL-SCG48

description: Library name: XCRS1-POOL-SCM48


title: male_right ventricle_18 months_1541550

description: Library name: 1541550


title: male_right ventricle_18 months_1541548

description: Library name: 1541548


title: LPMI010_ATAC

description: Library name: LPMI010_ATAC


title: mixed_leukaemia_CNS_HSC_3

description:
Library name: mixed_leukaemia_CNS_HSC_3
8-2-1-C; normalised_count_data_130b.csv

value: leukaemia

value: HSC/MPP


title: LPMIC019_RNA

description: Library name: LPMIC019_RNA


title: A24_Male3


title: A23_Male3


title: male_right ventricle_18 months_1541558

description: Library name: 1541558


title: HTO associated to XCRS1-POOL-SCG67

description: Library name: XCRS1-POOL-SCM67


title: mixed_leukaemia_BM_HSC_3

description:
Library name: mixed_leukaemia_BM_HSC_3
8-2-1-B; normalised_count_data_130b.csv

value: BM

value: miR-130b overexpressing Kmt2a-AFF1+


title: LPMIC014_RNA

description: Library name: LPMIC014_RNA

value: PDX tumor


title: male_right ventricle_18 months_1541547

description: Library name: 1541547

value: right ventricle


title: male_right ventricle_18 months_1541557

description: Library name: 1541557

value: Sprague Dawley


title: HTO associated to XCRS1-POOL-SCG31

description: Library name: XCRS1-POOL-SCM31

value: RENCA


title: LPMIRT5_RNA

description: Library name: LPMIRT5_RNA


title: male_left ventricle_18 months_1541545

description: Library name: 1541545

source_name: left ventricle

value: left ventricle

value: male


title: SP1814_RNA

description: Library name: SP1814_RNA


title: A15_Male2


title: male_left ventricle_18 months_1541543

description: Library name: 1541543

value: 18 months


title: HTO associated to XCRS1-POOL-SCG22

description: Library name: XCRS1-POOL-SCM22


title: LPMIC012_RNA

description: Library name: LPMIC012_RNA


title: LPMIC013_RNA

description: Library name: LPMIC013_RNA


title: male_left ventricle_18 months_1541542

description: Library name: 1541542


title: A7_Male1

value: Male


title: LPMIC011_RNA

description: Library name: LPMIC011_RNA


title: HTO associated to XCRS1-POOL-SCG61

description: Library name: XCRS1-POOL-SCM61


title: A36_Female5

value: Female

value: Gut


title: LPMIRT17G6_RNA

description: Library name: LPMIRT17G6_RNA


title: mixed_leukaemia_CNS_HSC_1

description:
Library name: mixed_leukaemia_CNS_HSC_1
6-2-0-C; normalised_count_data_130b.csv

value: CNS


title: LPMIC007_RNA

description: Library name: LPMIC007_RNA


title: HTO associated to XCRS1-POOL-SCG49

description: Library name: XCRS1-POOL-SCM49

value: Primary tumor

value: Multiple


title: male_right ventricle_18 months_1541551

description: Library name: 1541551


title: male_left ventricle_18 months_1541539

description: Library name: 1541539


title: LPMIC022_RNA

description: Library name: LPMIC022_RNA


title: A32_Male4

value: TIGS only


title: LPMIC031_RNA

description: Library name: LPMIC031_RNA


title: LPMIC024_RNA

description: Library name: LPMIC024_RNA


title: HTO associated to XCRS1-POOL-SCG43

description: Library name: XCRS1-POOL-SCM43

value: TotalSeq-A anti-mouse HTO


title: HTO associated to XCRS1-POOL-SCG42

description: Library name: XCRS1-POOL-SCM42


title: LPMIC016_RNA

description: Library name: LPMIC016_RNA


title: HTO associated to XCRS1-POOL-SCG37

description: Library name: XCRS1-POOL-SCM37


title: A31_Male4


title: HTO associated to XCRS1-POOL-SCG15

description: Library name: XCRS1-POOL-SCM15

value: LLC


title: LPMIC006_RNA

description: Library name: LPMIC006_RNA


title: LPMIC015_RNA

description: Library name: LPMIC015_RNA


title: HTO associated to XCRS1-POOL-SCG36

description: Library name: XCRS1-POOL-SCM36


title: A28_Female4


title: male_left ventricle_18 months_1541546

description: Library name: 1541546


title: male_left ventricle_18 months_1541544

description: Library name: 1541544


title: A16_Male2


title: LPMIC004_RNA

description: Library name: LPMIC004_RNA


title: A27_Female4


title: HTO associated to XCRS1-POOL-SCG30

description: Library name: XCRS1-POOL-SCM30


title: A8_Male1


title: HTO associated to XCRS1-POOL-SCG10

description: Library name: XCRS1-POOL-SCM10


title: Enriched lymphoid cells from MMT-PyMT GEMM females tumors 2

description: Library name: XCRS1-MM97-SCPYMT2PTL1-SCG1

value: MMT-PyMT GEMM females

value: mRNA


title: male_left ventricle_18 months_1541535

description: Library name: 1541535


title: Enriched myeloid cells from MMT-PyMT GEMM females tumors 2

description: Library name: XCRS1-MM97-SCPYMT2PTM1-SCG1


title: Enriched myeloid cells from MMT-PyMT GEMM females tumors 1

description: Library name: XCRS1-MM91-SCPYMT1PTM1-SCG1


title: male_left ventricle_18 months_1541541

description: Library name: 1541541


title: LPMIC008_RNA

description: Library name: LPMIC008_RNA

value: PDX tumor


title: male_left atrium_18 months_1541534

description: Library name: 1541534

value: Sprague Dawley

value: left atrium


title: A11_Female2


title: LPMIC001_RNA

description: Library name: LPMIC001_RNA


title: A35_Female5


title: male_left ventricle_18 months_1541540

description: Library name: 1541540

value: left ventricle


title: A4_Female1


title: male_left ventricle_18 months_1541536

description: Library name: 1541536

value: male


title: LPMI809_RNA

description: Library name: LPMI809_RNA


title: Enriched myeloid cells from CT26 tumors

description: Library name: XCRS1-POOL-SCG85


title: male_left atrium_18 months_1541532

description: Library name: 1541532

value: 18 months


title: HTO associated to XCRS1-POOL-SCG16

description: Library name: XCRS1-POOL-SCM16


title: male_left ventricle_18 months_1541538

description: Library name: 1541538


title: HTO associated to XCRS1-POOL-SCG9

description: Library name: XCRS1-POOL-SCM9


title: LPMI734_RNA

description: Library name: LPMI734_RNA


title: A20_Female3


title: A37_Male5

value: Male

value: TIGS>CrebB


title: A30_Male4

value: Gut


title: male_left ventricle_18 months_1541537

description: Library name: 1541537


title: male_left atrium_18 months_1541530

description: Library name: 1541530


title: LPMIC003_RNA

description: Library name: LPMIC003_RNA


title: male_left atrium_18 months_1541528

description: Library name: 1541528


title: LPMI725_RNA

description: Library name: LPMI725_RNA


title: LPMIC002_RNA

description: Library name: LPMIC002_RNA


title: A19_Female3

value: Female


title: Enriched lymphoid cells from 4T1 tumors

description: Library name: XCRS1-POOL-SCG72

value: Primary tumor


title: A12_Female2


title: A22_Male3


title: Enriched lymphoid cells from B16-F10 tumors

description: Library name: XCRS1-POOL-SCG66

value: Multiple


title: male_left atrium_18 months_1541526

description: Library name: 1541526


title: LPMI815_RNA

description: Library name: LPMI815_RNA


title: male_left atrium_18 months_1541525

description: Library name: 1541525


title: LPMI580_RNA

description: Library name: LPMI580_RNA


title: Enriched lymphoid cells from MMT-PyMT GEMM females tumors 1

description: Library name: XCRS1-MM91-SCPYMT1PTL1-SCG1


title: LPMI612_RNA

description: Library name: LPMI612_RNA


title: male_left atrium_18 months_1541533

description: Library name: 1541533


title: A14_Male2


title: LPMI581_RNA

description: Library name: LPMI581_RNA


title: LPMI797_RNA

description: Library name: LPMI797_RNA


title: LPMI805_RNA

description: Library name: LPMI805_RNA


title: A3_Female1

value: TIGS only


title: Enriched lymphoid cells from CT26 tumors

description: Library name: XCRS1-POOL-SCG84


title: Enriched lymphoid cells from MC38 tumors

description: Library name: XCRS1-POOL-SCG60


title: Enriched myeloid cells from LLC tumors

description: Library name: XCRS1-POOL-SCG55


title: male_left atrium_18 months_1541523

description: Library name: 1541523


title: OT7

city: Shanghai

first: Yifan

last: Zhu

state: Shanghai

address: No.1678, Road Dongfang, Pudong district

country: China

institute: shanghai children’s medical center

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
FeatureCounts v1.5.0-p3 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.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.5) software was used to analysis the AS event.
PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.
WGCNA (Weighted correlation network analysis) was used to describe the gene association modes among different samples.
Assembly: Rnor_6.0.97
Supplementary files format and content: gene_expression.txt: Tab-delimited text file includes total RNA read counts and FPKM values.

source_name: cardiac tissue,the old donor heart(1year)

extract_protocol:
Myocardium of LV was rapidly removed from executed rat and flash frozen in liquid nitrogen, RNA was harvested using Trizol reagent. Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent)

value: LV myocardium

value: Sprague-Dawley

tag: time

value: postoperative Day 1

value: WT

tag: donor age

value: old (1 year)

value: heterotopic heart transplantation


title: LPMI556_RNA

description: Library name: LPMI556_RNA

value: PDX tumor


title: A13_Male2


title: A5_Male1


title: OT4


title: A21_Male3


title: male_left atrium_18 months_1541531

description: Library name: 1541531

value: Sprague Dawley

value: left atrium


title: LPMI495_RNA

description: Library name: LPMI495_RNA


title: A38_Male5


title: Enriched myeloid cells from RENCA tumors

description: Library name: XCRS1-POOL-SCG79

value: RENCA

value: mRNA


title: A34_Female5

value: TIGS>CrebB


title: Enriched myeloid cells from KPC-F/KPCY-C2 tumors

description: Library name: XCRS1-POOL-SCG49


title: A33_Female5

value: Gut


title: Enriched lymphoid cells from RENCA tumors

description: Library name: XCRS1-POOL-SCG78


title: OT3


title: LPMI478_RNA

description: Library name: LPMI478_RNA


title: Enriched lymphoid cells from KPC-F/KPCY-C2 tumors

description: Library name: XCRS1-POOL-SCG48


title: male_left atrium_18 months_1541529

description: Library name: 1541529

value: male

value: 18 months


title: Enriched myeloid cells from CT26 tumors XCRS1-POOL-SCG43

description: Library name: XCRS1-POOL-SCG43

value: Primary tumor

value: Multiple


title: WT13

source_name: cardiac tissue,the Young donor heart(10weeks)

value: LV myocardium

value: young (10 weeks)


title: Enriched myeloid cells from 4T1 tumors

description: Library name: XCRS1-POOL-SCG73


title: A25_Female4

value: Female


title: LPMI467_RNA

description: Library name: LPMI467_RNA


title: LPMI702_RNA

description: Library name: LPMI702_RNA


title: Enriched lymphoid cells from CT26 tumors XCRS1-POOL-SCG42

description: Library name: XCRS1-POOL-SCG42


title: A29_Male4

value: Male


title: Enriched myeloid cells from 4T1 tumors XCRS1-POOL-SCG37

description: Library name: XCRS1-POOL-SCG37


title: male_left atrium_18 months_1541527

description: Library name: 1541527


title: A18_Female3


title: Enriched myeloid cells from B16-F10 tumors

description: Library name: XCRS1-POOL-SCG67


title: LPMI462_RNA

description: Library name: LPMI462_RNA


title: Enriched lymphoid cells from 4T1 tumors from XCRS1-POOL-SCG36

description: Library name: XCRS1-POOL-SCG36


title: Enriched myeloid cells from MC38 tumors

description: Library name: XCRS1-POOL-SCG61


title: LPMI431_RNA

description: Library name: LPMI431_RNA


title: Enriched myeloid cells from RENCA tumors from XCRS1-POOL-SCG31

description: Library name: XCRS1-POOL-SCG31


title: LV myocardium, ChIP-seq, SP1, input

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <30 bp) and low quality reads using fastp (v0.20.0). Then FastQC was used to perform quality control.
Trimmed reads were aligned to the rat reference genome(Rnor_6.0.97 ) using Bowtie2 (v2.2.6) and saved with format of bam by SAMtools (v1.10).
Peaks were called using MACS2(v2.2.7.1) with the parameters by default. FDR cut-off of 0.05 was used to determine significant peaks. ChIPseeker R package was invoked to annotate nearest genes and genomic features to peaks. Differentially peaks were identified by DiffBind with a cut-off value of log2|fold- change|>1 and p-value <0.05. The clusterProfiler[10] was used to perform functional enrichment analysis for the annotated significant peaks based on Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG).
The clusterProfiler was used to perform functional enrichment analysis for the annotated significant peaks based on Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG).
HOMER(v4.11)  was utilized to search for sequence motif among significant peaks. E value cutoff of 0.05 was used to select significantly enriched motifs.
Assembly: Rnor_6.0.97
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: primary cardiomyoctes from LV myocardium

extract_protocol:
Cells were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine.
The fragmented chromatin fragments were pre-cleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti-sp1 antibodies. After reverse crosslinking, ChIP and input DNA fragments were end- repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adaptor ligation with the NEBNext Ultra Ligation Module (E7445, NEB). The DNA libraries were amplified for 15 cycles and sequenced using Illumina NovaSeq 6000 with paired-end 150 as the sequencing mode.

value: Sprague-Dawley

tag: chip antibody

value: none (inmput)

value: sham


title: LPMI550_RNA

description: Library name: LPMI550_RNA

value: PDX tumor


title: A6_Male1


title: male_left atrium_18 months_1541524

description: Library name: 1541524

value: Sprague Dawley

value: left atrium


title: LPMI530_RNA

description: Library name: LPMI530_RNA


title: A9_Female2


title: Enriched lymphoid cells from LLC tumors

description: Library name: XCRS1-POOL-SCG54

value: LLC

value: mRNA


title: PD-plug, 72h, DMSO, rep 2

city: Hangzhou

first: Hannah

middle: Rae

last: Thomas

state: Zhejiang

address: 866 Yuhangtang Road

department: Horticulture

institute: Zhejiang University

data_processing:
Library quality was accessed with Fastqc v0.11.8
Libraries were trimmed using Trim_galore v0.5.0 and Cutadapt v1.7
Libraries were aligned to the Arabidopsis genome using Hisat2 v2.1.0 or STAR 2.5.a in the case of mapping to the transgene, mCherry.
Libraries were converted to SAM and BAM files using Samtools v1.4.1.
Transcripts were assembled using Stringtie v1.3.3.
Raw read counts were extracted using the Stringtie python script, Deprep.py
Assembly: TAIR10 https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
Supplementary files format and content: tab-delimited csv file with includes raw counts for each sample from hisat aligner and STAR aligner

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Three  Arabidopsis thaliana lines, Columbia-0 wild-type, icals3m, and PD-plug, were grown on MS media (1% sucrose, 0.8% agar) for 5 weeks in 50mm diameter petri dishes at 10 h light at 22 °C.

extract_protocol:
Two leaves from four plants (either DMSO or estradiol treated) were harvested 12 h, 24 h, 48 h and 72 h post treatment. Three biological replicates for each genotype/treatment/time point were collected.
Leaves were flash frozen in liquid nitrogen. Leaf tissue was homogenised using a Genogrinder and each Eppendorf tube contained 2 steel ball bearings.
RNA was extracted from leaf tissue using the Qiagen Plant RNeasy mini kit.
Rigorous treatment with Turbo DNase was undertaken to remove genomic DNA contamination.
Libraries were constructed by Novogene Co., Ltd using Illumina NovaSeq 6000

treatment_protocol: Leaves were painted on both the abaxial and adaxial side with either 0.1% DMSO (mock treatment) or 20 µM β-Estradiol 17-acetate (estradiol treatment) containing 0.01% Silwet L-77 in ddH2O, using a fine paint brush

value: PD-plug

value: DMSO

value: leaves


title: PD-plug, 72h, DMSO, rep 3


title: PD-plug, 72h, DMSO, rep 1


title: Enriched myeloid cells from MC38 tumors XCRS1-POOL-SCG22

description: Library name: XCRS1-POOL-SCG22

value: Primary tumor


title: A10_Female2

value: Gut

value: TIGS>CrebB


title: HTO associated to XCRS1-POOL-SCG21

description: Library name: XCRS1-POOL-SCM21

value: Multiple

value: TotalSeq-A anti-mouse HTO


title: A1_Female1

value: Female


title: LPMI480_RNA

description: Library name: LPMI480_RNA


title: Enriched lymphoid cells from MC38 tumors XCRS1-POOL-SCG21

description: Library name: XCRS1-POOL-SCG21


title: WT15

value: LV myocardium

value: Sprague-Dawley

value: postoperative Day 1

value: WT

value: young (10 weeks)

value: heterotopic heart transplantation


title: A26_Female4


title: A2_Female1


title: TA_Male5

growth_protocol: Fly stocks were maintained and experiment was conducted at 25oC, 60% humidity and 12h:12h light/dark cycle on a yeast/sugar/agar (SYA) food medium. All the crosses were performed in cages containing grape juice, agar and live yeast. Tyramine (TA, Sigma-Aldrich, St. Louis, Mo) was dissolved in H2O and added to SYA food at the 100 µg/ml concentration. As control, vehicle alone equivalent to highest concentrations of TA was added.

extract_protocol:
For RNA extraction, eight mid-guts from Tyramine (TA: 100 µg/ml) or control food-fed flies were dissected at indicated times in ice-cold PBS and placed into ice-cold TRIzol (Thermo Fisher Scientific, 15596026). Five experimental replicates were performed and RNA samples were preserved in -80oC freezer prior to extraction by TRIzol/choloroform method as per manufacturer’s instructions and quantified by NanoDrop 2000c spectrophotometer.
For RNA sequencing, library preparation (Illumina, strand-specific RNA-seq with PolyA selection) and sequencing (Illumina NovaSeq 2 x 150 bp sequencing) were performed by Azenta Life Sciences (GENEWIZ UK Ltd., Essex, UK).

value: Male

value: wild-type

value: TA


title: Enriched lymphoid cells from RENCA tumors XCRS1-POOL-SCG30

description: Library name: XCRS1-POOL-SCG30

value: RENCA

value: mRNA


title: A17_Female3


title: PD-plug, 72h, estradiol, rep 3

value: PD-plug

value: estradiol

value: leaves


title: LPMI424_RNA

description: Library name: LPMI424_RNA

value: PDX tumor


title: LPMI466_RNA

description: Library name: LPMI466_RNA


title: LV myocardium, ChIP-seq, SP1, IP

value: primary cardiomyoctes from LV myocardium

value: male

value: anti-sp1 (proteintech, 21962-1-AP)

value: sham


title: PD-plug, 72h, estradiol, rep 2


title: LPMI414_RNA

description: Library name: LPMI414_RNA


title: control_Male5

treatment_protocol: Tyramine (TA, Sigma-Aldrich, St. Louis, Mo) was dissolved in H2O and added to SYA food at the 100 µg/ml concentration. As control, vehicle alone equivalent to highest concentrations of TA was added.

value: Gut

value: control


title: LPMI396_RNA

description: Library name: LPMI396_RNA


title: Enriched myeloid cells from LLC tumors XCRS1-POOL-SCG16

description: Library name: XCRS1-POOL-SCG16

value: Primary tumor

value: LLC

value: Multiple


title: LPMI406_RNA

description: Library name: LPMI406_RNA


title: LPMI411_RNA

description: Library name: LPMI411_RNA


title: LPMI408_RNA

description: Library name: LPMI408_RNA


title: LPMI395_RNA

description: Library name: LPMI395_RNA


title: WT3

value: LV myocardium

value: Sprague-Dawley

value: postoperative Day 1

value: WT

value: young (10 weeks)

value: heterotopic heart transplantation


title: PD-plug, 48h, DMSO, rep 3

value: PD-plug

value: DMSO

value: leaves


title: Enriched myeloid cells from B16-F10 tumors from  XCRS1-POOL-SCG10

description: Library name: XCRS1-POOL-SCG10

value: mRNA


title: Enriched lymphoid cells from B16-F10 tumors from XCRS1-POOL-SCG9

description: Library name: XCRS1-POOL-SCG9


title: PD-plug, 72h, estradiol, rep 1

value: estradiol


title: TA_Female5

value: Female

value: wild-type

value: TA


title: PD-plug, 48h, DMSO, rep 2


title: Enriched lymphoid cells from LLC tumors from XCRS1-POOL-SCG15

description: Library name: XCRS1-POOL-SCG15

value: Primary tumor


title: LPMI386_RNA

description: Library name: LPMI386_RNA

value: PDX tumor


title: control_Female5

value: Gut

value: control


title: LPMI374_RNA

description: Library name: LPMI374_RNA


title: PD-plug, 48h, DMSO, rep 1


title: PD-plug, 48h, estradiol, rep 3


title: TA_Male4

value: Male


title: TA_Female4


title: control_Female4


title: Rps19p53_dhet1_MO_GEX, Rps19p53dhet, replica_1

city: Memphis

first: Te

last: Ling

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

description:
Library name: Rps19p53_dhet1_MO_GEX
10X Genomics

data_processing:
3' single-cell RNA-seq libraries generated with the 10x Genomics platform were processed using 10x Genomics Cell Ranger Suite (V7.0.0) with --include-introns option, which aligned the data to mm10 reference genome, de-multiplexing and generate UMI count matrix files. Downstream analyses were performed in R(V4.0.5) using Seurat (V.4.3.1).  10x Genomics Cell Ranger ARC pipeline (V2.0.0) was used to process the Single Cell Mutliome ATAC+Gene Expression libraries. Key steps involve barcode correction, alignment to mm10 reference genome, identification of accessible chromatin peaks, and generation of count matrix for both RNA and ATAC modalities. Furthermore, Seurat (V4.3.0 ) and Signac (V1.13.0)  in R (V4.3.3)  were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: processed data is filtered features .h5 files and bed files for atac data

source_name: E13.5 fetal liver

extract_protocol:
To isolate total E13.5 fetal liver cells, livers from E13.5 embryos were harvested, and single-cell suspensions were prepared by gently pipetting cold 1× PBS supplemented with 10% FBS. Dead cells were removed before library preparation.
Libraries were prepared according to the manufacturer's instructions.

value: E13.5 fetal liver

value: total fetal liver cells

tag: batch


title: control_Male4


title: PD-plug, 48h, estradiol, rep 2


title: Rps19p53_dhet2_MO_GEX, Rps19p53dhet, replica_2

description:
Library name: Rps19p53_dhet2_MO_GEX
10X Genomics


title: Rps19_het2_MO_GEX, Rps19het, replica 2

description:
Library name: Rps19_het2_MO_GEX
10X Genomics


title: PD-plug, 48h, estradiol, rep 1


title: TA_Male3


title: Rps19_het1_MO_GEX, Rps19het, replica 1

description:
Library name: Rps19_het1_MO_GEX
10X Genomics


title: LPMI343_RNA

description: Library name: LPMI343_RNA

source_name: PDX tumor


title: PD-plug, 24h, DMSO, rep 2


title: control_Male3


title: LPMI372_RNA

description: Library name: LPMI372_RNA


title: LPMI351_RNA

description: Library name: LPMI351_RNA


title: TA_Female3


title: LPMI331_RNA

description: Library name: LPMI331_RNA


title: PD-plug, 24h, DMSO, rep 1


title: Rps19_WT1_MO_GEX, WT, replica_1

description:
Library name: Rps19_WT1_MO_GEX
10X Genomics

value: WT


title: LPMI300_RNA

description: Library name: LPMI300_RNA


title: control_Female3


title: PD-plug, 24h, DMSO, rep 3


title: Rps19_WT2_MO_GEX, WT, replica_2

description:
Library name: Rps19_WT2_MO_GEX
10X Genomics


title: LPMI322_RNA

description: Library name: LPMI322_RNA


title: LPMI329_RNA

description: Library name: LPMI329_RNA


title: PD-plug, 24h, estradiol, rep 3


title: Rps19_WT2_MO_ATAC, WT, replica_2

description:
Library name: Rps19_WT2_MO_ATAC
10X Genomics

library_source: genomic single cell


title: Rps19p53_dhet2_MO_ATAC, Rps19p53dhet, replica_2

description:
Library name: Rps19p53_dhet2_MO_ATAC
10X Genomics


title: Rps19_het2_MO_ATAC, Rps19het, replica 2

description:
Library name: Rps19_het2_MO_ATAC
10X Genomics


title: TA_Male2


title: PD-plug, 12h, DMSO, rep 3


title: Rps19_WT1_MO_ATAC, WT, replica_1

description:
Library name: Rps19_WT1_MO_ATAC
10X Genomics


title: PD-plug, 24h, estradiol, rep 2


title: Rps19p53_dhet1_MO_ATAC, Rps19p53dhet, replica_1

description:
Library name: Rps19p53_dhet1_MO_ATAC
10X Genomics


title: Rps19_het1_MO_ATAC, Rps19het, replica 1

description:
Library name: Rps19_het1_MO_ATAC
10X Genomics


title: TA_Male1


title: LPMI204_RNA

description: Library name: LPMI204_RNA


title: control_Male2


title: control_Female2


title: TA_Female2


title: TA_Female1


title: PD-plug, 12h, estradiol, rep 3


title: LPMI195_RNA

description: Library name: LPMI195_RNA


title: PD-plug, 24h, estradiol, rep 1


title: Rps19p53_WT2_3p, WT, replica 2

description:
Library name: Rps19p53_WT2_3p
10X Genomics


title: PD-plug, 12h, estradiol, rep 2


title: LPMI251_RNA

description: Library name: LPMI251_RNA


title: PD-plug, 12h, DMSO, rep 1


title: Rps19p53_dhet2, Rps19p53dhet, replica_2

description:
Library name: Rps19p53_dhet2_3p
10X Genomics


title: PD-plug, 12h, DMSO, rep 2


title: Rps19p53_dhet1, Rps19p53dhet, replica_1

description:
Library name: Rps19p53_dhet1_3p
10X Genomics


title: LPMI203_RNA

description: Library name: LPMI203_RNA


title: LPMI242_RNA

description: Library name: LPMI242_RNA


title: control_Male1


title: PD-plug, 12h, estradiol, rep 1


title: icals3m, 72h, DMSO, rep 3


title: LPMI147_RNA

description: Library name: LPMI147_RNA


title: KPC PDAC tumor microenvironment, sample Z287

first: xiaozhen

last: zhang

address: 79 Qingchun Road

institute: The first affiliated hospital, zhejiang university school of medicine

description: Library name: Z287

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PDAC tumor cell

extract_protocol:
Single-cell suspensions were prepared from dissociated whole pancreatic tumors harvested from the KPC mouse model of pancreatic ductal adenocarcinoma (PDAC). Briefly, individual tumors were minced into small fragments and digested in RPMI 1640 medium supplemented with 1 mg/mL collagenase IV, 0.5 mg/mL Dispase II, and 40 U/mL DNase I at 37°C for 20-30 minutes with gentle agitation. The digested tissue was then passed through a 70-μm cell strainer and washed with PBS containing 0.04% BSA. Red blood cells were lysed using ACK lysis buffer. Cell viability and concentration were assessed using trypan blue staining on an automated cell counter. To remove dead cells and debris, the suspension was processed through a Miltenyi Biotec Dead Cell Removal Kit according to the manufacturer’s instructions. Finally, the live single-cell suspension was resuspended in PBS with 0.04% BSA for loading onto the 10x Genomics Chromium Controller to generate gel bead-in-emulsions (GEMs) for subsequent library construction.
Single-cell RNA-seq libraries were constructed in accordance with the manufacturer's instructions. In brief, the prepared live single-cell suspension was combined with master mix, partitioning oil and gel beads containing barcoded oligonucleotides. This mixture was then loaded onto a Chromium chip to generate gel bead-in-emulsions (GEMs). Within each GEM, the cells were lysed and the poly-adenylated mRNA was reverse transcribed into barcoded cDNA. This process incorporated a unique molecular identifier (UMI), a cell barcode and an Illumina R1 sequence. Following GEM breakage, the barcoded cDNA from all GEMs was pooled and purified using DynaBeads MyOne SILANE beads. This was then amplified by PCR to generate sufficient material. The amplified cDNA was then fragmented enzymatically, with Illumina adapter sequences and a sample index added during the end repair, A-tailing, adaptor ligation and PCR amplification steps. Final library fragments optimised for sequencing were selected to enrich for constructs of an appropriate length (200–700 bp). The quality of the library was assessed based on fragment size distribution and quantified prior to pooling and sequencing.

value: PDAC tumor cell


title: control_Female1


title: LPMI065_RNA

description: Library name: LPMI065_RNA


title: KPC PDAC tumor microenvironment, sample Z204

description: Library name: Z204


title: icals3m, 72h, DMSO, rep 2


title: LPMI014_RNA

description: Library name: LPMI014_RNA


title: Six2TGC, Replicate 2

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: Library name: JP1382

data_processing:
Sequencing reads were aligned to UCSC mouse genome mm10 using hisat2. Only uniquely mapped reads were retained for downstream analysis.
Differential gene analysis was performed using cuffdiff.
Assembly: mm10
Supplementary files format and content: Excel file containing cuffdiff differential analysis results and FPKM for each sample

source_name: kidney

extract_protocol:
Total RNA from FACS isolated cells were prepared using Single Cell RNA Purification Kit (Norgen). From total RNA, mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs) following manufacturer’s instructions. Fragmentation of RNA followed by reverse transcription and second strand cDNA synthesis was done using NEBNext RNA First Strand Synthesis Module (E7525L) and NEBNext RNA Second Strand Synthesis Module (E6111L) following manufacturer’s instructions.
The resulting double-stranded cDNA’s were further processed to DNA sequencing libraries using ThruPLEX DNA-seq 12S Kit (R400428, Clontech Laboratories). Libraries were size-selected by gel purification for an average size of 350bp.

value: kidney

value: mesenchymal nephron progenitors

value: Six2TGC transgenic

value: isolated by FACS


title: icals3m, 72h, DMSO, rep 1

value: DMSO

value: leaves


title: LPMI037_RNA

description: Library name: LPMI037_RNA


title: Rps19_het2_3p, Rps19het, replica 2

description:
Library name: Rps19_het2_3p
10X Genomics


title: KPC PDAC tumor microenvironment, sample A163_3

description: Library name: A163_3


title: LPMI010_RNA

description: Library name: LPMI010_RNA


title: LPMI011_RNA

description: Library name: LPMI011_RNA


title: Rps19p53_WT1_3p, WT, replica 1

description:
Library name: Rps19p53_WT1_3p
10X Genomics


title: LPMI020_RNA

description: Library name: LPMI020_RNA


title: Rpl5_het1_3p, Rps19het, replica 1

description:
Library name: Rpl5_het1_3p
10X Genomics


title: Rpl5_WT1_3p, WT, replica_1

description:
Library name: Rpl5_WT1_3p
10X Genomics


title: icals3m, 72h, estradiol, rep 3

value: estradiol


title: Rpl5_WT2_3p, WT, replica_2

description:
Library name: Rpl5_WT2_3p
10X Genomics


title: Transcriptome pool samples from brain of 6 months‑old mice (wild type and CSTB‑deficient)

city: Helsinki

first: Tarja

middle: Hannele

last: Joensuu

address: P.O. Box 63 (Haartmaninkatu 8)

country: Finland

institute: Folkhälsan Research Center/Medicum

description: Library name: Sample 4

data_processing:
FASTQ files were generated using Illumina's Bcl2fastq software.
Read quality was assessed using FastQC, and results summarized with MultiQC.
Reads were trimmed to remove 5′ adapters and 3′ poly-A tails, and low-quality sequences were removed using Trimmomatic.
Reads were tagged with sample-specific barcodes and unique molecular identifiers (UMIs).
Processed reads were aligned and annotated using Drop-seq tools with GENCODE mouse M24 (GRCm38.p6), and gene expression matrices were generated per sample.
Assembly: GRCm38.p6 (GENCODE M24).
Supplementary files format and content: Excel file with gene counts information for all samples. Gene_counts_all_samples.xlsx
Supplementary files format and content: Excel file with sample information. Sample_information.xlsx

source_name: brain

growth_protocol: Mice were housed under standard conditions with access to food and water ad libitum unless otherwise noted. Adult mice aged 1, 3, and 6 months were fasted for 12 hours followed by 2–4 hours of feeding prior to tissue collection. P14 mice remained with their mother until euthanasia.

extract_protocol:
Total RNA was extracted from frozen brain tissue using the RNeasy Plus Mini Kit (Qiagen), following the manufacturer’s protocol. Tissue was homogenized in RLT Plus buffer with 2-mercaptoethanol using a SpeedMill PLUS bead homogenizer. RNA integrity was assessed using Agilent Tapestation.
Libraries were prepared using a Drop-seq-based bulk RNA-seq protocol (as in Macosko et al., 2015 and Freitag et al., 2020). Sequencing-ready libraries were generated with sample-specific barcodes and unique molecular identifiers (UMIs) to enable multiplexing.

treatment_protocol: No experimental treatments were applied. Mice were euthanized using CO₂, and tissues were collected for transcriptomic analysis.

value: brain

value: cerebellum, hippocampus and cerebral cortex

value: wild type and CSTB-deficient

value: 6 months

value: male


title: icals3m, 72h, estradiol, rep 2


title: Rps19_WT2_3p, WT, replica_2

description:
Library name: Rps19_WT2_3p
10X Genomics


title: DFBL96177_RNA

description: Library name: DFBL96177_RNA

value: PDX tumor


title: Six2TGC, Replicate 1

description: Library name: JP1381


title: icals3m, 72h, estradiol, rep 1


title: DFBL74251_RNA

description: Library name: DFBL74251_RNA


title: Rps19_het1_3p, Rps19het, replica 1

description:
Library name: Rps19_het1_3p
10X Genomics

value: E13.5 fetal liver


title: Transcriptome pool samples from brain of 3 months‑old mice (wild type and CSTB‑deficient)

description: Library name: Sample 3

value: 3 months


title: Rpl5_het2_3p, Rps19het, replica 2

description:
Library name: Rpl5_het2_3p
10X Genomics

value: total fetal liver cells


title: icals3m, 48h, DMSO, rep 3


title: DFBL49659_RNA

description: Library name: DFBL49659_RNA


title: DFBL47933_RNA

description: Library name: DFBL47933_RNA


title: icals3m, 48h, estradiol, rep 3


title: icals3m, 48h, DMSO, rep 1


title: colonic crypts, p53koAA, biol rep1

city: Taipei

first: Yi-Ting

last: Lin

address: No. 1, Jen-Ai Road, 1st Section

department: Department of Pharmacology

country: Taiwan

institute: College of Medicine, National Taiwan University

description:
Library name: 10-p53koAA281
Column name in Fulltable.txt:10-p53koAA281

data_processing:
Raw RNA-seq reads were quality controlled and adapter-trimmed using fastp v0.20.0. Read quality before and after trimming was assessed using FastQC v0.11.9.
Clean reads were aligned to the reference genome using HISAT2 v2.1.0. Resulting SAM files were converted to BAM format using SAMtools v1.9 for efficient storage and downstream processing.
Gene-level read counts were calculated using featureCounts from subread v2.0.1, and results were exported as tab-delimited files with raw counts per gene.
Read counts were normalized to TPM (Transcripts Per Million) to account for gene length and sequencing depth.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited .tsv file includes raw read counts per gene for each sample.
Supplementary files format and content: .tsv files include TPM values per gene for each sample.

source_name: Intestine

extract_protocol:
Intestinal crypts were disaggregated by pre-cold PBS with 30 mM EDTA. Total RNAs were extracted by TriZol (Invitrogen) according to manufacturers’ recommendations. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TsruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following manufacturer's protocols.

value: Intestine

value: colonic crypts


title: icals3m, 48h, estradiol, rep 2


title: icals3m, 48h, estradiol, rep 1


title: BM63014_RNA

description: Library name: BM63014_RNA

extract_protocol:
For RNA-seq library prepration, PDX tumors were homogenized, and total RNA was extracted using the AllPrep DNA/RNA Kit (Qiagen, 80204) and quantified with the Qubit High Sensitivity RNA Kit (Life Technologies, Q32852). One microgram of RNA was used to generate sequencing libraries. For ATAC-seq library prepration, viably cryopreserved PDX tumor cells were thawed and processed using the Dead Cell Removal Kit to eliminate non-viable cells. Fifty thousand live tumor cells were washed in ATAC-seq resuspension buffer, resuspended in 50 μL of ATAC-seq resuspension buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, and incubated on ice for 3 min. Following lysis, nuclei were washed with cold ATAC-seq resuspension buffer containing 0.1% Tween-20 (without NP-40 or digitonin), then resuspended in 50 μL of transposition mixture and incubated at 37 °C for 30 min in a thermomixer at 1000 rpm. Fragmented DNA was purified using the Zymo DNA Clean & Concentrator-5 kit (Zymo, D4024).
For RNA-seq library prepration, one microgram of RNA was used to generate sequencing libraries with the KAPA HyperPrep RNA Kit with RiboErase (Roche, KK8560), using 8 cycles of PCR amplification according to the manufacturer’s instructions. For ATAC-seq library prepration, libraries were prepared with the KAPA HyperPrep Kit (Roche, KK8502) using 10 cycles of PCR amplification. Both RNA-seq and ATAC-seq libraries were assessed on a TapeStation 4200 (Agilent, G2991BA), quantified with the Qubit High Sensitivity dsDNA Kit (Life Technologies, Q32854), multiplexed, and sequenced on an Illumina NovaSeq 6000 using a 100-10-10-100 bp read configuration.


title: Rps19_WT1_3p, WT, replica_1

description:
Library name: Rps19_WT1_3p
10X Genomics

value: WT


title: icals3m, 48h, DMSO, rep 2


title: icals3m, 24h, DMSO, rep 3


title: DFBL28030_RNA

description: Library name: DFBL28030_RNA


title: DFBL20954_RNA

description: Library name: DFBL20954_RNA


title: Transcriptome pool samples from brain of 1 month‑old mice (wild type and CSTB‑deficient)

description: Library name: Sample 2

value: 1 month


title: MC4R KO mouse, western diet, large intestine contents, sample 7

city: Fujisawa

first: Akira

last: Mitsui

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: DMPK & Safety Business Unit

country: Japan

institute: Axcelead Drug Discovery Partners, Inc.

description: Library name: Colon-27

data_processing:
Read sequences (39,000 – 60,000 paired-end reads) whose starting sequences perfectly matched the primer sequences used were extracted using the fastx_barcode_splitter tool from FASTX-Toolkit (ver. 0.0.14). When the primer sequences contained N-mix, this process was repeated, considering the number of Ns (six types on the forward side × six types on the reverse side = 36 types). The extracted reads were trimmed to remove primer sequences using fastx_trimmer from the FASTX-Toolkit. Sequences with a quality score <20 were removed using Sickle (ver. 1.33), and sequences shorter than 130 bases along with their paired sequences were discarded. Paired-end read merging was performed using FLASH script (ver. 1.2.11). After removing chimeric and noisy sequences using the DADA2 plugin in Qiime2 (ver. 2021.4), 23,000 – 35,000 amplicon sequence variants (ASVs) and their feature table were generated. Taxonomic classification was performed by assigning the ASV sequences against Greengenes database (ver. 13_8) using a feature classifier plugin.
Assembly: Greengenes database (ver. 13_8)
Supplementary files format and content: Microsoft Excel file includes ASV counts for each Sample
Library strategy: 16S rRNA-seq

source_name: large intestine contents

extract_protocol:
Approximately 100-200 mg of small intestine or large intestine contents from WD-fed or ND-fed MC4RKO and WT mice were freeze-dried using a VD-250R Freeze Dryer (TAITEC). The freeze-dried samples were homogenized at 1,500 rpm for 2 min using a multi-bead shocker (Yasui Kikai, Osaka, Japan). The DNA was extracted as follows: Lysis Solution F (Nippon Gene, Tokyo, Japan) was added to the crushed samples and incubated at 65 °C for 10 min. The samples were then centrifuged at 12,000 × g for 2 min, and the supernatant was collected. DNA was purified from the collected solution using the MPure-12 system and MPure Bacterial DNA Extraction Kit (MP Biomedicals, Tokyo, Japan). The concentration of the purified DNA was measured using Synergy LX (BioTek, Winooski, Vermont, USA) and QuantiFluor dsDNA System (Promega, Madison, WI, USA).
The concentration of the purified DNA was measured using Synergy LX (BioTek, Winooski, Vermont, USA) and QuantiFluor dsDNA System (Promega, Madison, WI, USA). The sequencing library was prepared using a 2-step tailed PCR method. In the first PCR, 16S region-specific primers were used to amplify the V3-V4 region: 341f_MIX:5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNCCTACGGGNGGCWGCAG-3' 805r_MIX:5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNGACTACHVGGGTATCTAATCC-3' Each 10 μL reaction contained 0.05 U/μL of RxTaq HS (Takara Bio, Shiga, Japan), 0.5 μM of each primer, and 1 ng of template DNA. The PCR conditions were as follows: initial denaturation at 94°C for 2 min; 30 cycles of 94°C for 30 s, 55°C for 30 s, and 72°C for 30 s; followed by a final extension at 72°C for 5 min. PCR products were cleaned using AMPure XP beads (Beckman Coulter, CA, USA) following the manufacturer’s protocol. A second PCR was performed using the following indexed primers: F:5’-AATGATACGGCGACCACCGAGATCTACAC-Index2 ACACTCTTTCCCTACACGACGC-3' R:5’-CAAGCAGAAGACGGCATACGAGAT-Index1 GTGACTGGAGTTCAGACGTGTG-3' In this step, cleaned amplicons from the first PCR served as templates in 10 μL reactions with 0.05 U/μL of RxTaq HS (Takara Bio) and 0.5 μM of each indexed primer. Amplification was conducted for 10 cycles under the same cycling conditions as the first PCR. The concentration of the library was measured using Synergy H1 (BioTek) and QuantiFluor dsDNA System. Library quality was assessed using a Fragment Analyzer and a dsDNA 915 Reagent Kit (Advanced Analytical Technologies, Orangeburg, NY, USA).

value: large intestine contents


title: MC4R KO mouse, western diet, large intestine contents, sample 4

description: Library name: Colon-24


title: MC4R KO mouse, western diet, large intestine contents, sample 5

description: Library name: Colon-25


title: colonic crypts, p53koAA, biol rep3

description:
Library name: 12-p53koAA109
Column name in Fulltable.txt:12-p53koAA109


title: colonic crypts, p53koWT, biol rep3

description:
Library name: 9-p53koWT282
Column name in Fulltable.txt:9-p53koWT282


title: colonic crypts, p53koWT, biol rep2

description:
Library name: 8-p53koWT278
Column name in Fulltable.txt:8-p53koWT278


title: MC4R KO mouse, western diet, large intestine contents, sample 8

description: Library name: Colon-28


title: icals3m, 24h, DMSO, rep 1

value: DMSO


title: colonic crypts, p53koAA, biol rep2

description:
Library name: 11-p53koAA282
Column name in Fulltable.txt:11-p53koAA282


title: colonic crypts, p53koWT, biol rep1

description:
Library name: 7-p53koWT127
Column name in Fulltable.txt:7-p53koWT127


title: DFBL13727_RNA

description: Library name: DFBL13727_RNA

data_processing:
RNA-seq data were processed using an in-house computational pipeline. Raw reads were trimmed with Trimmomatic, and both pre- and post-trimming quality metrics were assessed using FastQC. Trimmed reads were aligned to the human reference genome (hg38) using STAR in 2-pass mode. To remove contaminating mouse reads, trimmed reads were filtered using XenoFilteR. Only samples with at least 20 million uniquely mapped reads were retained for downstream analyses. Gene-level quantification was performed with HTSeq using the following parameters: -m union -f bam -i gene_id -s reverse -t exon --additional-attr=gene_name. The resulting DESeqDataSet was filtered to retain genes with a minimum of 10 total reads across all samples. Transcripts per million reads (TPM) values were calculated for expression normalization. For gene set enrichment analyses, normalized counts were evaluated using curated B-cell lymphoma gene sets and the SignatureDB database (https://lymphochip.nih.gov/signaturedb/).
Technical replicates for each ATAC-seq sample were merged prior to quality control assessment with FastQC. Adapter sequences were removed from paired-end FASTQ files through Trimmomatic trimming, followed by alignment to the hg19 human reference genome using the Burrows-Wheeler Aligner (BWA). Post-alignment processing included coordinate-based sorting and filtering to exclude reads mapping to mitochondrial DNA and blacklisted genomic regions via Samtools. PCR duplicates were marked and removed using Picard Tools' MarkDuplicates command. Deduplicated BAM files were then processed with XenoFilteR to remove contaminating mouse reads. The processed BAM files, having completed alignment, sorting, and filtering, served as input for subsequent analyses. For track visualization purposes, BAM files were transformed into BigWig format through deepTools' bamCoverage function, incorporating Tn5 transposase insertion site correction. Peak calling was performed on Tn5-adjusted insertion sites using MACS2 with the following parameters: -g hs (genome size), -q 0.05 (q-value threshold), -f BAMPE (paired-end BAM format), and -B (bedGraph output). Genomic tracks were visualized using pyGenomeTracks version 3.9.
Assembly: RNA-seq: hg38; ATAC-seq: hg19
Supplementary files format and content: txt files with raw count for RNA-seq; bigwig files for ATAC-seq


title: Transcriptome pool samples from brain of 14‑day‑old mice (wild type and CSTB‑deficient)

description: Library name: Sample 1

value: 14 days


title: MC4R KO mouse, western diet, large intestine contents, sample 6

description: Library name: Colon-26


title: BL010815_RNA

description: Library name: BL010815_RNA


title: DFBL31357_RNA

description: Library name: DFBL31357_RNA


title: MC4R KO mouse, western diet, large intestine contents, sample 1

description: Library name: Colon-21


title: Patient 11_TCR

city: Beijing

first: Yipeng

last: Zhang

address: Fuxing Road 22

institute: Chinese PLA gerneral hospital

description: Library name: Sample 11

data_processing:
Raw data processed by Cell Ranger mkfastq (v7.1.0). Reads aligned to GRCh38 (GENCODE v32) with STAR. Cells filtered (>500 genes/cell, <20% mitochondrial reads). Normalized via SCTransform (Seurat v5), batch-corrected with Harmony (v0.1.1). Clustering (Leiden, resolution=0.8) and annotation (SingleR v1.10.0). Differential expression by MAST (v1.24.0).
Assembly: GRCh38
Supplementary files format and content: sample_filtered_feature_bc_matrix (including barcodes.tsv, features.tsv and matrix.mtx)
Library strategy: TCR-Seq

source_name: CAR-T

extract_protocol:
CAR-T cells washed with PBS (Mg²+/Ca²+-free), centrifuged (300×g, 5 min), resuspended in PBS at 1×10^6 cells/mL for sequencing.
R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: CAR-T


title: MC4R KO mouse, western diet, large intestine contents, sample 3

description: Library name: Colon-23


title: icals3m, 24h, DMSO, rep 2

value: leaves


title: MC4R KO mouse, western diet, large intestine contents, sample 2

description: Library name: Colon-22


title: colonic crypts, AA, biol rep3

description:
Library name: 6-p53AA154
Column name in Fulltable.txt:6-p53AA154

value: AA


title: icals3m, 24h, estradiol, rep 2

value: estradiol


title: colonic crypts, AA, biol rep1

description:
Library name: 4-p53AA130
Column name in Fulltable.txt:4-p53AA130


title: colonic crypts, WT, biol rep2

description:
Library name: 2-p53WT189
Column name in Fulltable.txt:2-p53WT189


title: Patient 10_TCR

description: Library name: Sample 10


title: Patient 09_TCR

description: Library name: Sample 9


title: icals3m, 12h, DMSO, rep 2


title: colonic crypts, AA, biol rep2

description:
Library name: 5-p53AA131
Column name in Fulltable.txt:5-p53AA131


title: MC4R KO mouse, normal diet, large intestine contents, sample 8

description: Library name: Colon-20


title: icals3m, 24h, estradiol, rep 1


title: icals3m, 12h, DMSO, rep 1


title: MC4R KO mouse, normal diet, large intestine contents, sample 5

description: Library name: Colon-17


title: MC4R KO mouse, normal diet, large intestine contents, sample 7

description: Library name: Colon-19


title: icals3m, 24h, estradiol, rep 3


title: Patient 07_TCR

description: Library name: Sample 7


title: Patient 08_TCR

description: Library name: Sample 8


title: MC4R KO mouse, normal diet, large intestine contents, sample 6

description: Library name: Colon-18


title: colonic crypts, WT, biol rep1

description:
Library name: 1-p53WT188
Column name in Fulltable.txt:1-p53WT188


title: MC4R KO mouse, normal diet, large intestine contents, sample 3

description: Library name: Colon-15


title: icals3m, 12h, DMSO, rep 3


title: colonic crypts, WT, biol rep3

description:
Library name: 3-p53WT190
Column name in Fulltable.txt:3-p53WT190


title: MC4R KO mouse, normal diet, large intestine contents, sample 4

description: Library name: Colon-16


title: icals3m, 12h, estradiol, rep 1


title: icals3m, 12h, estradiol, rep 3


title: S2 Genomics_Singulator100_Sample_1

city: Indianapolis

first: Holly

last: Kersey

state: Indiana

address: 320 West 15th Street | NB 103

department: Medical & Molecular Genetics

institute: Indiana University

description: Library name: S_1

data_processing:
Sequencing was performed on a NovaSeq 6000 (v1.5 S2; Illumina) with a 28-10-10-91 read setup to a mean sequencing depth 437.9 +/- 23.9 million reads per sample.
Processing of the sequencing data was performed with the Cell Ranger pipeline (v7.0.1, 10x Genomics) and aligned to GRCm 38 (cellranger reference genome: gex-mm10-2020-A).
The filtered feature-cell barcode matrices (including the hashtag count matrix) generated by CellRanger were loaded into SoupX (v1.6.2) in Rstudio (v1.4.1717) running R (v4.3.1)[37] . SoupX quantified ambient RNA using default parameters. Doublets were identified using DoubletFinder (v2.0.4)[38]. The data was then loaded into Seurat (v5.0.1)[55]. Data was normalized using SCTransform (v0.4.1)[40]. Nuclei were clustered using the first 35 principal components based on an Elbow Plot. Cluster marker genes were identified using the FindConservedMarkers function. Clusters were annotated using scMCA (v0.2.0), provided by the Mouse Cell Atlas, and with PanglaoDB[44, 45]. Cell type proportions were quantified with speckle (v0.0.3)[56]. Population homogeneity was estimated with ROGUE (v1.0)[46]. Mitochondrial-derived reads were identified by the "mt" prefix, and ribosomal reads were identified by the "Rp[sl]" prefix. Summary scoring was performed with UCell (v2.2.0)[49]
Assembly: mm10
Supplementary files format and content: Analysis: Cell Ranger outputs
Supplementary files format and content: Raw Feature Matrix: raw count matrix
Supplementary files format and content: Filtered Feature Matrix: filtered count matrix

source_name: Anterior Cortex

extract_protocol:
Centrifugation-based nuclei isolation Frozen anterior cortex tissue was added to a 2 mL tube with 1 mL of ice-cold EZ nuclei suspension buffer (Sigma, EZ PREP NUC-101). The tissue was dissociated with gentle, manual pipetting. The dissociated tissue was transferred into a 15 mL conical tube and an additional 6 mL of ice-cold EZ nuclei suspension buffer was added. The solution was incubated at 4oC for 10 minutes while rotating. After rotating, the sample was centrifuged at 500×g for 5 minutes at 4oC. The supernatant was removed, and the pellet was resuspended in 1 mL of ice-cold EZ nuclei suspension buffer with gentle pipetting. An additional 6 mL of EZ nuclei resuspension buffer was added. The solution was incubated at 4oC for 10 minutes while rotating. After rotating, the sample was centrifuged at 500×g for 5 minutes at 4oC. The supernatant was removed. 1 mL of Nuclei Wash and Resuspension buffer (NWR Buffer) (1x PBS, 2% Bovine Serum Albumin (BSA), and 2U/μl RNAse inhibitor (Millipore Sigma, 3335399001)) was added and mixed with gentle pipetting. An additional 6 mL of NWR Buffer was added. The sample was centrifuged at 500×g for 5 minutes at 4oC. This wash step with NWR Buffer was repeated four times. After the last wash, the nuclei were resuspended in 1mL NWR buffer then another 6 mL was added. A 70-μm and 30-μm cell strainer were pre-wet with LS Column Calibration Buffer (1x PBS, 0.5% BSA). The nuclei were filtered through the 70 μm strainer and then the 30 μm strainer to remove clumps. The remaining solution was centrifuged at 500×g for 5 minutes at 4oC. The supernatant was removed, and the pellet was resuspended in 1 mL of NWR Buffer. 500 μL of the resuspended nuclei were added to an Eppendorf tube containing 900 μL of Sucrose Cushion Buffer (Nuclei PURE 2M Sucrose Cushion Solution (Sigma, S9308), 10% Nuclei PURE Sucrose Cushion Buffer (Sigma, S9058)). The mixture was carefully pipetted together. In a separate Eppendorf Tube, 500 μL of Sucrose Cushion Buffer was added. To create the sucrose gradient, the 1400 μL of nuclei suspension in Sucrose Cushion Buffer was added carefully to the top of the Eppendorf tube containing 500 μL of Sucrose Cushion Buffer with no mixing. The sucrose gradient was centrifuged at 13,000×g for 45 minutes at 4oC. After centrifugation, the supernatant was almost completely removed, leaving approximately 100 μL in the tube. The pellet was resuspended in 1 mL of NWR Buffer with gently pipette mixing. The solution was filtered through a 40 μm cell strainer to remove any leftover debris. Column-based isolation Nuclei suspensions were prepared according to 10x Chromium Nuclei Isolation Kit instructions, with all steps performed on ice[42]. Frozen anterior cortex tissue was added to a pre-chilled Sample Dissociation Tube (10x Genomics, 2000564). 200 μL of Lysis Buffer (10x Genomics, 2000558) was added to the tube and the tissue was dissociated with a pestle. 300 μL of additional Lysis Buffer was added and the sample was incubated on ice for 10 minutes. The solution was then added to a Nuclei Isolation Column (10x Genomics, 2000562) in a Collection Tube (10x Genomics, 2000563). The column was centrifuged at 13,000×g for 20 seconds at 4oC. The flowthrough was quickly vortexed. The solution was then centrifuged at 500×g for 3 minutes at 4oC. The supernatant was removed, and the pellet was resuspended in 500 μL of Debris Removal Buffer (10x Genomics, 2000560). The suspension was centrifuged at 700×g for 10 minutes at 4oC. The supernatant was removed and resuspended in 1 mL of Wash and Resuspension Buffer (1x PBS, 10% BSA, 2.5% RNAse Inhibitor (10x Genomics, 2000565)), then centrifuged at 500×g for 5 minutes at 4oC. This wash step was repeated once more. The supernatant was removed, and the nuclei suspension was resuspended in 50 μL of Wash and Resuspension Buffer by gentle pipette mixing. Machine-assisted nuclei isolation Nuclei were isolated using the Singulator 100 System, with all steps performed on ice[43]. Before isolation, nuclei isolation cartridges (S2 Genomics, #100-063-287) were pre-cooled to -25°C, and the Singulator was pre-chilled to ensure optimal processing conditions. For each sample, the frozen anterior cortex was placed into a pre-cooled nuclei isolation cartridge along with 75 μL of RNAse inhibitor (Millipore Sigma, 3335399001). The sample was processed using the Standard Nuclei Isolation Protocol. The resulting 3 mL nuclei suspension was transferred to a 15 mL conical tube and centrifuged at 500×g for 5 minutes at 4°C to pellet the nuclei. The supernatant was aspirated, and the pellet was resuspended in 3 mL of 20% Nuclei Debris Removal Stock Solution (S2 Genomics, #100-253-628) in Nuclear Storage Reagent (S2 Genomics, #100-063-623). The suspension was centrifuged for 8 minutes at 700×g and 4°C with a decreased brake setting (3 out of 10, Sorvall Legend X1R Centrifuge (ThermoFisher)). The tubes were carefully removed without disturbing the gradient, and the gradient was aspirated from just below the meniscus using a P1000 pipette to remove myelin debris, which was visible as a haze or flake at the top. Finally, the nuclei were resuspended in 3 mL of resuspension buffer (2% BSA in Nuclear Storage Reagent).
Nuclei concentration and viability were quantified with trypan blue staining and observed with an EVOS XL Core microscope. All nuclei suspensions were processed by the 10x Chromium. Each nuclei suspension was counted and diluted to 1,000 nuclei per uL then loaded into a Single Cell Chip G and run on the Chromium Controller for GEM generation and barcoding. Sample processing and library preparation were performed according to the manufacturer’s instructions using the Chromium Next GEM Single Cell 3′ v3.1 dual index kit (10x Genomics) and SPRIselect paramagnetic bead-based chemistry (Beckman Coulter Life Sciences).  The cDNA and library quality were assessed using the 2100 Bioanalyzer and a High Sensitivity DNA kit (Agilent Technologies). The final library concentration was determined using a QuBit Fluorometer and the dsDNA HS assay kit (Thermo Fisher Scientific).

value: Anterior Cortex


title: Patient 06_TCR

description: Library name: Sample 6


title: S2 Genomics_Singulator100_Sample_2

description: Library name: S_2


title: MC4R KO mouse, normal diet, large intestine contents, sample 1

description: Library name: Colon-13


title: MC4R KO mouse, normal diet, large intestine contents, sample 2

description: Library name: Colon-14


title: Patient 03_TCR

description: Library name: Sample 3


title: Sucrose Gradient Centrifugation _Sample_2

description: Library name: Sucrose_2


title: Sucrose Gradient Centrifugation _Sample_1

description: Library name: Sucrose_1


title: Patient 05_TCR

description: Library name: Sample 5


title: Patient 02_TCR

description: Library name: Sample 2


title: icals3m, 12h, estradiol, rep 2


title: WT mouse, western diet, large intestine contents, sample 6

description: Library name: Colon-12


title: Col-0, 72h, DMSO, rep 3


title: Patient 04_TCR

description: Library name: Sample 4


title: 10x Chromium Nuclei Isolation Kit _Sample_2

description: Library name: 10x_kit_2


title: Patient 01_TCR

description: Library name: Sample 1


title: Col-0, 72h, DMSO, rep 2


title: 10x Chromium Nuclei Isolation Kit _Sample_1

description: Library name: 10x_kit_1


title: Col-0, 72h, DMSO, rep 1


title: WT mouse, western diet, large intestine contents, sample 5

description: Library name: Colon-11


title: Vsig4 KO,GEX

city: Hefei

first: xia

last: zhou

address: huang shan Road 443

institute: university of science and technology of china

description: 10x Genomics,GEX

data_processing:
The demultiplexing,barcoded processing,gene counting and aggregation were made using the Cell Ranger software7.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Liver tissues enriched for metastatic B16F10 melanomas were harvested from WT or Vsig4-/- mice, cut into small pieces and digested with 0.5 mg/mL collagenase IV (Sigma) and 5 U/mL DNase I (Sigma) for 20 mins at 37℃ under shaking. The cell suspension was filtered through a 70 µm cell strainer and centrifugated at 400g for 5 mins at 4℃, followed by lysis of red blood cell inn ACK buffer (Biolegend).DAPI-CD45+ singlets were sorted by FACS and further processed for scRNA-seq.
GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.Library was performed according to the manufacter’s instructions (single cell 5’ v1.1 protocol with feature barcoding and VDJ sequencing, 10x Genomics).

value: liver

value: cd45+ cells

value: VSIG4 KO

value: liver bearing metastatic B16F10 melanomas


title: Patient 09

description: Library name: Sample 9

data_processing:
Raw data processed by Cell Ranger mkfastq (v7.1.0). Reads aligned to GRCh38 (GENCODE v32) with STAR. Cells filtered (>500 genes/cell, <20% mitochondrial reads). Normalized via SCTransform (Seurat v5), batch-corrected with Harmony (v0.1.1). Clustering (Leiden, resolution=0.8) and annotation (SingleR v1.10.0). Differential expression by MAST (v1.24.0).
Assembly: GRCh38
Supplementary files format and content: sample_filtered_feature_bc_matrix (including barcodes.tsv, features.tsv and matrix.mtx)


title: Patient 10

description: Library name: Sample 10


title: WT,GEX

description: 10x Genomics,GEX


title: Col-0, 72h, estradiol, rep 3


title: WT mouse, western diet, large intestine contents, sample 2

description: Library name: Colon-8


title: Patient 11

description: Library name: Sample 11


title: Ensheathing Glia, Pink1 KO, Batch 3, Replicate 3

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description: Library name: Pink1 KO 3 Rep 3

data_processing:
FASTQ files were cleaned with fastp with default settings.Aligning and counting were carried out with STAR and the 4th 2020 FlyBase Drosophila melanogaster release (r6.35) with the –quantMode flag set as GeneCounts.
For differential gene expression testing we used DESeq2, where we fit a negative binomial model and carried out the Wald-test. We removed experimental batch as a covariate according to the design formula ∼date+genotype. All genes below a Benjamini-Hochberg corrected p-value of 0.05 were considered deregulated.
Assembly: FlyBase Drosophila melanogaster release (r6.35)
Supplementary files format and content: All_Samples_Combined_Counts.csv: Comma seperated value table for raw counts
Supplementary files format and content: Metadata.csv: Comma separated value table for sample metadata

source_name: Ensheathing Glia

growth_protocol: Fruit flies were maintained in an incubator at 25°C under a 12:12 light-dark cycle, and provided with a standard diet consisting of cornmeal and molasses. For experiments, only fly males were used. Flies were raised in parallel on the same batch of food, which was exchanged every three to four days and kept in only male population of similar density.

extract_protocol:
Ten brains of flies 5 ± 1 days old were collected, with most of the laminae removed. Dissections were performed in ice-cold PBS that contained 5 μM Actinomycin D (Sigma) to inhibit changes in gene expression during tissue processing. For the dissociation of brain tissue, a mix of Dispase I (0.6 mg/ml) (Sigma), Collagenase I (30 mg/ml) (Thermo Fisher), Trypsin (0.5x) (Thermo Fisher), and 5 μM Actinomycin D was used. Immediately after dissociation, cells were sorted using a FACSAria Fusion (BD Biosciences) flow cytometer with a 100 µm nozzle at 20 psi. Live (DAPI-negative), GFP-positive cells were sorted into 96-well PCR plates at 300 cells per well (3 wells per genotype) using a 4-way purity mask.
3 ul of cell lysis buffer (0.1% Triton X-100, Sigma Aldrich; 1U/ul of RNase Inhibitor, RNase OUT, Thermo Fisher; 2.5 uM Oligo dT(25), IDT; and 2.5 mM dNTP, Promega) was aliquoted in triplicate to 96 well plates (4titude, Cat. No. 4TI-0960/C). Roughly 300 cells were sorted into the wells with lysis buffer and the plate was spun down at 2000xg for 1 min prior to storage at - 80*C. For the first strand synthesis, the Smart-Seq 2 plates were thawed to room temperature for a minute and subsequently spun down at 2000 xg for minute. The RNA denaturation is carried out at 72*C for 10 mins and then flash cooled on ice for 5 mins. First strand synthesis mix (1X SuperScript II first strand synthesis buffer, Thermo Fisher; 5 mM DTT, Thermo Fisher; 100 U SuperScript II reverse transcriptase enzyme, Thermo Fisher; 10 U RNAse OUT, Thermo Fisher; 1M Betaine, Sigma Aldrich; 6 mM MgCl2, Thermo Fisher; and 1 uM TSO, IDT Technologies) is added to the cell lysis mix to a total volume of 10 ul. The First strand synthesis reaction was carried out with following program: 42*C for 90 mins; 10 cycles of {50*C for 2 mins; 42*C for 2 mins}; 72*C for 15 mins; 4*C indefinite hold. PCR amplification of the first strand product was performed by adding 15 ul of the PCR mix to the first strand product (1X KAPA HiFi HotStart Ready Mix, Roche; and 0.1 uM of IS PCR primer, IDT Technologies). 22 cycles of the following PCR program was used to amplify the first strand product: 98*C for 3 mins; 22 cycles of {98*C for 20 secs; 67*C for 15 secs; 72*C for 6 mins}; 72*C for 5 mins; 4*C indefinite hold. 20 ul of Ampure XP was added to each well and mixed. Standard Ampure XP purification was carried out as per manufacturer’s recommendation and the cDNA library was eluted in 17.5 ul of Elution buffer. 17 ul of the eluted library was transfered to fresh 96 well plate (4titude, Cat. No. 4TI-0960/C). 5 ul of Tn5 tagmentation mix (1X Tagment DNA buffer, Illumina; ATM mix, Illumina and cDNA library 1 ng) was prepared for cDNA fragmentation. Tn5 tagmentation was performed with following program: 55*C for 10 mins; 4*C indefinite hold. Tagementation reaction was stopped by quenching the reaction with 1.25ul of NT buffer for 5 mins (Illumina). 1.25 ul of the i5 and i7 Illumina indexes were added to the plates. Finally 3.75 ul of NPM master mix was added to the plate and mixed well and put for the index PCR amplification: 72*C for 3 mins; 95*C for 30 secs; 12 cycles of {95*C for 10 secs; 55*C for 30 secs; 72*C for 30 secs}; 72*C for 5 mins, and 4*C indefinite hold. The indexed PCR products were pooled in a single tube, and 0.8X Ampure XP purification (Beckman Coulter) was carried out as per the manufacturer’s recommendation, and finally, the sequencing library was eluted in 35.5 μl of Elution buffer (Qiagen). SMART seq 2 libraries were sequenced on the NextSeq 500 (Illumina) sequencing platform. Sequencing was done as per the protocol recommendations: paired-end read of 76 bps (read 1), 76 bps (read 2), 8 bps (index 1) and 8 bps (index 2). For a targeted sequencing depth of ~30 million reads per sample.

value: Ensheathing Glia


title: WT mouse, western diet, large intestine contents, sample 1

description: Library name: Colon-7


title: WT mouse, western diet, large intestine contents, sample 3

description: Library name: Colon-9


title: Patient 08

description: Library name: Sample 8


title: Col-0, 48h, DMSO, rep 3


title: Ensheathing Glia, Pink1 KO, Batch 3, Replicate 1

description: Library name: Pink1 KO 3 Rep 1


title: Col-0, 72h, estradiol, rep 2


title: WT mouse, western diet, large intestine contents, sample 4

description: Library name: Colon-10


title: Ensheathing Glia, Pink1 KO, Batch 3, Replicate 2

description: Library name: Pink1 KO 3 Rep 2


title: Col-0, 48h, DMSO, rep 2


title: Col-0, 72h, estradiol, rep 1


title: WT mouse, normal diet, large intestine contents, sample 5

description: Library name: Colon-5


title: Patient 06

description: Library name: Sample 6


title: Patient 05

description: Library name: Sample 5


title: Col-0, 48h, DMSO, rep 1


title: WT mouse, normal diet, large intestine contents, sample 6

description: Library name: Colon-6


title: Ensheathing Glia, Pink1 KO, Batch 2, Replicate 1

description: Library name: Pink1 KO 2 Rep 1


title: Ensheathing Glia, Pink1 KO, Batch 2, Replicate 2

description: Library name: Pink1 KO 2 Rep 2


title: Patient 04

description: Library name: Sample 4


title: Patient 07

description: Library name: Sample 7


title: Col-0, 48h, estradiol, rep 1


title: Col-0, 24h, DMSO, rep 3


title: Ensheathing Glia, Pink1 KO, Batch 2, Replicate 3

description: Library name: Pink1 KO 2 Rep 3


title: MC4R KO mouse, western diet, small intestine contents, sample 8

description: Library name: Intestine-28

source_name: small intestine contents

value: small intestine contents


title: Patient 03

description: Library name: Sample 3


title: Ensheathing Glia, Pink1 KO, Batch 1, Replicate 3

description: Library name: Pink1 KO 1 Rep 3


title: MC4R KO mouse, western diet, small intestine contents, sample 7

description: Library name: Intestine-27


title: WT mouse, normal diet, large intestine contents, sample 2

description: Library name: Colon-2


title: Ensheathing Glia, Pink1 KO, Batch 1, Replicate 2

description: Library name: Pink1 KO 1 Rep 2


title: MC4R KO mouse, western diet, small intestine contents, sample 6

description: Library name: Intestine-26


title: Col-0, 24h, DMSO, rep 1


title: WT mouse, normal diet, large intestine contents, sample 4

description: Library name: Colon-4


title: Patient 01

description: Library name: Sample 1


title: Ensheathing Glia, Control, Batch 3, Replicate 1

description: Library name: Control 3 Rep 1


title: Ensheathing Glia, Control, Batch 3, Replicate 3

description: Library name: Control 3 Rep 3


title: Patient 02

description: Library name: Sample 2


title: WT mouse, normal diet, large intestine contents, sample 1

description: Library name: Colon-1


title: Col-0, 48h, estradiol, rep 3


title: WT mouse, normal diet, large intestine contents, sample 3

description: Library name: Colon-3


title: Col-0, 48h, estradiol, rep 2


title: Col-0, 24h, DMSO, rep 2


title: Ensheathing Glia, Control, Batch 3, Replicate 2

description: Library name: Control 3 Rep 2


title: Hep3B, IgG control ChIP

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

institute: Chang Gung Memorial Hospital

data_processing:
The data processing steps were performed in the Partek Flow ChIP-Seq toolkit, starting with ChIP-Seq data. Alignment was performed using the BWA tool, resulting in aligned reads. Next, the aligned reads were filtered to remove low-quality alignments, producing filtered reads. The MACS tool was then used for peak calling, generating peak files.
Assembly: hg38
Supplementary files format and content: bedGraph, narrowPeak (except for control sample)

source_name: cell line

growth_protocol: MEM, 10% fetal bovine serum, 1x non-essential amino acid 1 mM sodium pyruvate. Cells were cultured at 5% CO2 at 37⁰C.

extract_protocol:
The ChIP assay was performed with cut & run assay kit (Cell signaling, 86652) as manufacturer’s instruction.
The sequencing libraries were generated by  DNA library prep kit (Cell Signaling, 56795)

value: Liver cancer


title: Col-0, 24h, estradiol, rep 3


title: MC4R KO mouse, western diet, small intestine contents, sample 5

description: Library name: Intestine-25


title: Hep3B, STAT6, ChIP

tag: antibody

value: STAT6 ChIP antibody (cell signaling, 5397S)


title: Hep3B, SOX4, ChIP

value: SOX4 ChIP antibody (abnova, PAB14092)


title: MC4R KO mouse, western diet, small intestine contents, sample 4

description: Library name: Intestine-24


title: STAT6 si 2

description:
Hep3B_STAT6_si_transfected-2
raw_counts-2.txt

data_processing:
The data processing steps were performed in the Partek Flow RNA toolkit, starting with mRNA samples. Base trimming was performed to generate trimmed reads, followed by alignment using STAR, resulting in aligned reads. Pre-alignment quality control (Pre-alignment QA/QC) was conducted before the alignment. The aligned reads were then quantified to an annotation model, producing transcript counts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene level count values for each Sample

extract_protocol:
RNA was purified by TRIzol reagent
RNA-seq libraries were generated by illumina stranded mRNA prep (illumina, 20040534)

value: STAT6 knockdown


title: Col-0, 24h, estradiol, rep 2


title: Ensheathing Glia, Pink1 KO, Batch 1, Replicate 1

description: Library name: Pink1 KO 1 Rep 1


title: Ensheathing Glia, Control, Batch 2, Replicate 2

description: Library name: Control 2 Rep 2


title: Ensheathing Glia, Control, Batch 2, Replicate 3

description: Library name: Control 2 Rep 3


title: STAT6 si 1

description:
Hep3B_STAT6_si_transfected-1
raw_counts-2.txt


title: Col-0, 12h, DMSO, rep 3

value: DMSO


title: control si 1

description:
Hep3B_control_si_transfected-1
raw_counts-2.txt

value: WT


title: Col-0, 24h, estradiol, rep 1


title: control si 2

description:
Hep3B_control_si_transfected-2
raw_counts-2.txt


title: Ensheathing Glia, Control, Batch 2, Replicate 1

description: Library name: Control 2 Rep 1


title: MC4R KO mouse, western diet, small intestine contents, sample 2

description: Library name: Intestine-22


title: Ensheathing Glia, Control, Batch 1, Replicate 2

description: Library name: Control 1 Rep 2


title: MC4R KO mouse, western diet, small intestine contents, sample 1

description: Library name: Intestine-21


title: Col-0, 12h, DMSO, rep 2


title: MC4R KO mouse, normal diet, small intestine contents, sample 8

description: Library name: Intestine-20


title: Ensheathing Glia, Control, Batch 1, Replicate 3

description: Library name: Control 1 Rep 3