title: HULC_1.5h_rep2_ATACseq

description:
Library name: HU90-2
HULC_1.5h_REP2.mLb.clN.sorted.bam


title: HULC_2h_rep2_ATACseq

status: Public on Apr 01 2026

type: SRA

city: Boulder

first: Mingfeng

last: Liu

state: CO

address: 709 Mohawk Dr

country: USA

institute: University of Colorado

description:
Library name: HU120-2
HULC_2h_REP2.mLb.clN.sorted.bam

library_source: genomic

data_processing:
Quality control, read mapping, and quantification were performed using nf-core/atacseq v2.1.2.
Assembly: The cleaned reads were aligned to the GRCh38.p13 human reference genome with the GENCODE v38 genome annotation file. Reads located in the ENCODE hg38 blacklist v2 region were removed.
Supplementary files format and content: .csv, consensus peaks raw counts of all samples
Supplementary files format and content: .bigWig, merged replicate ATAC-seq tracks of each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: hiPSCs

extract_protocol:
All steps from nuclei isolation through library preparation were performed by Novogene Co., Ltd. using their standardized, optimized ATAC-seq workflow.
The final ATAC-seq libraries were quantified, quality-controlled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end, 150 bp) by Novogene Co., Ltd.

tag: cell line

value: hiPSCs


title: C+ 2

city: Montreal

first: Anna

middle: K

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

country: Canada

institute: McGill University

description:
Library name: CWTM-2
CpG location, BETA, methylated count, unmethylated count

data_processing:
Genpipes V4.4.5 methylation sequencing pipeline was used for alignment  and methylation calls https://genpipes.readthedocs.io/en/genpipes-v4.6.1/
Assembly: mm10
Supplementary files format and content: tab-deliminated file containing beta, methylation counts and unmethylated counts for each Sample

organism: Mus musculus

source_name: liver

extract_protocol:
DNA was extracted using standard proteinase K/phenol/chloroform protocol
Library preparation for Illumina, WGBS bisulfite, low throughput (< 48 samples), Lucigen

tag: tissue

value: liver

tag: developmental stage

value: 10-11 weeks old

tag: strain

value: ICR

tag: genotype

value: wild type

tag: Sex

value: M


title: HULC_1.5h_rep3_ATACseq

description:
Library name: HU90-3
HULC_1.5h_REP3.mLb.clN.sorted.bam


title: C+ 3

description:
Library name: CWTM-3
CpG location, BETA, methylated count, unmethylated count


title: scMultiomic ATAC-Seq of LPS,1-DD

city: Houston

first: Zhao

last: Zheng

state: TX

address: 1901 East Rd

department: Genomic Medicine

institute: md anderson cancer center

description:
Library name: scATAC_1-DD
scATAC_1-DD

library_source: genomic single cell

data_processing:
1. Alignment and quantification using Cell Ranger ARC count to generate gene expression feature-barcode matrices and ATAC fragments.
2. Reference genome: GRCh38/hg38 (report exact reference package used by Cell Ranger ARC).
3. QC filtering based on RNA (genes/UMIs/mitochondrial fraction) and ATAC (TSS enrichment/fragments in peaks/nucleosome signal) metrics; doublets removed if applicable.
4. Downstream analysis performed in Seurat/Signac/ArchR: normalization, PCA/LSI, clustering, UMAP visualization, and optional peak calling/motif analysis.
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

source_name: primary de-differentiated liposarcoma

extract_protocol:
Nuclei were isolated from tissue/cell suspension using a detergent-based lysis buffer on ice following the Chromium Single Cell Multiome ATAC + Gene Expression nuclei isolation guidelines. Nuclei were filtered, washed, counted, and adjusted to the recommended input concentration. Nuclei integrity was confirmed by microscopy.
Single-nucleus multiome libraries were prepared using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression kit following the manufacturer protocol. Nuclei were partitioned into GEMs for barcoding; RNA was reverse transcribed and ATAC DNA was tagmented and barcoded. Gene Expression and ATAC libraries were amplified, indexed, QC’d, and sequenced on an Illumina platform with recommended read structure.

tag: cell type

value: primary de-differentiated liposarcoma

value: DD


title: C+/+ 10

description:
Library name: CWTF-10
CpG location, BETA, methylated count, unmethylated count

value: F


title: C+ 1

description:
Library name: CWTM-1
CpG location, BETA, methylated count, unmethylated count


title: C+/+ 9

description:
Library name: CWTF-9
CpG location, BETA, methylated count, unmethylated count


title: HULC_1h_rep3_ATACseq

description:
Library name: HU60-3
HULC_1h_REP3.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS, 11-WD

description:
Library name: scRNA_11-WD
scRNA_11-WD

library_source: transcriptomic single cell

molecule: polyA RNA

source_name: primary well-differentiated liposarcoma

value: primary well-differentiated liposarcoma

value: WD


title: HULC_1h_rep1_ATACseq

description:
Library name: HU60-1
HULC_1h_REP1.mLb.clN.sorted.bam


title: HULC_1.5h_rep1_ATACseq

description:
Library name: HU90-1
HULC_1.5h_REP1.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS, 12-WD

description:
Library name: scRNA_12-WD
scRNA_12-WD


title: HULC_0.5h_rep2_ATACseq

description:
Library name: HU30-2
HULC_0.5h_REP2.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS, 10-DD

description:
Library name: scRNA_10-DD
scRNA_10-DD


title: scMultiomic RNA-Seq of LPS, 9-WD-A

description:
Library name: scRNA_9-WD-A
scRNA_9-WD-A


title: scMultiomic RNA-Seq of LPS, 9-WD-B

description:
Library name: scRNA_9-WD-B
scRNA_9-WD-B


title: HULC_0.5h_rep3_ATACseq

description:
Library name: HU30-3
HULC_0.5h_REP3.mLb.clN.sorted.bam


title: C+/+ 8

description:
Library name: CWTF-8
CpG location, BETA, methylated count, unmethylated count


title: C+/+ 6

description:
Library name: CWTF-6
CpG location, BETA, methylated count, unmethylated count


title: HULC_0h_rep3_ATACseq

description:
Library name: HU0-3
HULC_0h_REP3.mLb.clN.sorted.bam


title: C+/+ 7

description:
Library name: CWTF-7
CpG location, BETA, methylated count, unmethylated count


title: HULC_1h_rep2_ATACseq

description:
Library name: HU60-2
HULC_1h_REP2.mLb.clN.sorted.bam


title: HULC_0h_rep2_ATACseq

description:
Library name: HU0-2
HULC_0h_REP2.mLb.clN.sorted.bam


title: HULC_0.5h_rep1_ATACseq

description:
Library name: HU30-1
HULC_0.5h_REP1.mLb.clN.sorted.bam


title: C- 15

description:
Library name: CKM-15
CpG location, BETA, methylated count, unmethylated count

value: hemizygous Kdm5c mutant


title: scMultiomic RNA-Seq of LPS, 8-DD-8

description:
Library name: scRNA_8-DD-B
scRNA_8-DD-B


title: HEIH_2.5h_rep2_ATACseq

description:
Library name: HIC3230-2
HEIH_2.5h_REP2.mLb.clN.sorted.bam


title: HEIH_2.5h_rep1_ATACseq

description:
Library name: HIC3230-1
HEIH_2.5h_REP1.mLb.clN.sorted.bam


title: HULC_0h_rep1_ATACseq

description:
Library name: HU0-1
HULC_0h_REP1.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS, 7-WD-B

description:
Library name: scRNA_7-WD-B
scRNA_7-WD-B


title: scMultiomic RNA-Seq of LPS, 6-WD-B

description:
Library name: scRNA_6-WD-B
scRNA_6-WD-B


title: HEIH_2.5h_rep3_ATACseq

description:
Library name: HIC3230-3
HEIH_2.5h_REP3.mLb.clN.sorted.bam


title: C- 14

description:
Library name: CKM-14
CpG location, BETA, methylated count, unmethylated count


title: HEIH_2h_rep1_ATACseq

description:
Library name: HIC32h-1
HEIH_2h_REP1.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS, 6-WD-A

description:
Library name: scRNA_6-WD-A
scRNA_6-WD-A


title: HEIH_1.5h_rep3_ATACseq

description:
Library name: HIC3130-3
HEIH_1.5h_REP3.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS, 7-WD-A

description:
Library name: scRNA_7-WD-A
scRNA_7-WD-A


title: HEIH_2h_rep2_ATACseq

description:
Library name: HIC32h-2
HEIH_2h_REP2.mLb.clN.sorted.bam


title: C- 13

description:
Library name: CKM-13
CpG location, BETA, methylated count, unmethylated count


title: HEIH_1.5h_rep2_ATACseq

description:
Library name: HIC3130-2
HEIH_1.5h_REP2.mLb.clN.sorted.bam


title: HEIH_2h_rep3_ATACseq

description:
Library name: HIC32h-3
HEIH_2h_REP3.mLb.clN.sorted.bam


title: C- 12

description:
Library name: CKM-12
CpG location, BETA, methylated count, unmethylated count


title: C+/- 20

description:
Library name: CHF-20
CpG location, BETA, methylated count, unmethylated count

value: het Kdm5c mutant


title: HEIH_1h_rep3_ATACseq

description:
Library name: HIC31h-3
HEIH_1h_REP3.mLb.clN.sorted.bam


title: C+/- 19

description:
Library name: CHF-19
CpG location, BETA, methylated count, unmethylated count


title: HEIH_0.5h_rep2_ATACseq

description:
Library name: HIC330-2
HEIH_0.5h_REP2.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS, 5-WD-B

description:
Library name: scRNA_5-WD-B
scRNA_5-WD-B


title: HEIH_1.5h_rep1_ATACseq

description:
Library name: HIC3130-1
HEIH_1.5h_REP1.mLb.clN.sorted.bam


title: C- 11

description:
Library name: CKM-11
CpG location, BETA, methylated count, unmethylated count


title: C+/- 17

description:
Library name: CHF-17
CpG location, BETA, methylated count, unmethylated count


title: HEIH_0h_rep2_ATACseq

description:
Library name: HIC30h-2
HEIH_0h_REP2.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS,4-DD-A

description:
Library name: scRNA_4-DD-A
scRNA_4-DD-A


title: scMultiomic RNA-Seq of LPS, 5-WD-A

description:
Library name: scRNA_5-WD-A
scRNA_5-WD-A


title: HEIH_1h_rep2_ATACseq

description:
Library name: HIC31h-2
HEIH_1h_REP2.mLb.clN.sorted.bam


title: HEIH_1h_rep1_ATACseq

description:
Library name: HIC31h-1
HEIH_1h_REP1.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS, 4-WD

description:
Library name: scRNA_4-WD
scRNA_4-WD


title: HEIH_0.5h_rep3_ATACseq

description:
Library name: HIC330-3
HEIH_0.5h_REP3.mLb.clN.sorted.bam


title: NG3

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

country: China

institute: xiamen university

description: Library name: sample6

library_source: transcriptomic

data_processing:
trim-galore;subjunc and featurecount
Assembly: mm10
Supplementary files format and content: gene_expression.xls

molecule: total RNA

source_name: Bone marrow

extract_protocol:
Total RNA was extracted using either the Micro RNA extraction kit(Magen, R4125).
RNA libraries for RNA-seq were prepared using the Stranded mRNA Prep.

value: Bone marrow

value: Neutrophils

tag: treatment

value: Ctrl microvesicles


title: NG2

description: Library name: sample5


title: C+/- 18

description:
Library name: CHF-18
CpG location, BETA, methylated count, unmethylated count


title: scMultiomic RNA-Seq of LPS, 4-DD-B

description:
Library name: scRNA_4-DD-B
scRNA_4-DD-B


title: NG1

description: Library name: sample4


title: HEIH_0h_rep1_ATACseq

description:
Library name: HIC30h-1
HEIH_0h_REP1.mLb.clN.sorted.bam


title: siMSR1-ANGPTL3-2

city: Shanghai

last: Zhao

state: Shanghai

address: 399  Wanyuan Road

institute: Children’s Hospital of Fudan  University

description:
Library name: Sample 11
si_A3_2

data_processing:
The raw reads were trimmed and the clean reads were aligned to reference genome by the HISAT2 software tool.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each samples

source_name: BMDMs

extract_protocol:
Total RNA from BMDMs was isolated using TRIzol™ (Invitrogen, USA) and RNA quality and concentration were determined by the ND-2000 (NanoDrop Technologies).
RNA sequencing libraries were prepared by Novogene Co., Ltd. (China) according to the manufacturer’s instructions.

value: BMDMs

value: MSR1 knockdown

value: treated with ANGPTL3-enriched supernatants


title: scMultiomic RNA-Seq of LPS,3-DD-B

description:
Library name: scRNA_3-DD-B
scRNA_3-DD-B


title: C+/- 16

description:
Library name: CHF-16
CpG location, BETA, methylated count, unmethylated count

value: liver

value: 10-11 weeks old


title: HAGLR_2.5h_rep3_ATACseq

description:
Library name: HAG150_3_QKDO240001119-1A_22J5G2LT4_L6
HAGLR_2.5h_REP3.mLb.clN.sorted.bam

value: hiPSCs


title: HEIH_0.5h_rep1_ATACseq

description:
Library name: HIC330-1
HEIH_0.5h_REP1.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS,2-WD-A

description:
Library name: scRNA_2-WD-A
scRNA_2-WD-A


title: HAGLR_2.5h_rep2_ATACseq

description:
Library name: HAG150_2_QKDO240001118-1A_22J5G2LT4_L6
HAGLR_2.5h_REP2.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS, 3-DD-A

description:
Library name: scRNA_3-DD-A
scRNA_3-DD-A


title: KDNG3

description: Library name: sample3

value: Ezrin KD microvesicles


title: siMSR1-ANGPTL3-3

description:
Library name: Sample 12
si_A3_3


title: scMultiomic RNA-Seq of LPS,2-WD-B

description:
Library name: scRNA_2-WD-B
scRNA_2-WD-B


title: siMSR1-ANGPTL3-1

description:
Library name: Sample 10
si_A3_1


title: NC-ANGPTL3-2

description:
Library name: Sample 8
NC_A3_2

value: WT


title: HAGLR_2h_rep3_ATACseq

description:
Library name: HAG120_3_QKDO240001116-1A_22J5G2LT4_L6
HAGLR_2h_REP3.mLb.clN.sorted.bam


title: HAGLR_2.5h_rep1_ATACseq

description:
Library name: HAG150_1_QKDO240001117-1A_22J5G2LT4_L6
HAGLR_2.5h_REP1.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LPS,1-DD

description:
Library name: scRNA_1-DD
scRNA_1-DD

value: primary de-differentiated liposarcoma

value: DD


title: NC-ANGPTL3-3

description:
Library name: Sample 9
NC_A3_3


title: EKD_Glc_IEVs

description:
Library name: sample3
Well-Paired-Seq

data_processing:
trim-galore;dynamicEX
Assembly: mm10
Supplementary files format and content: counts.csv.gz

source_name: liver cancer

extract_protocol:
NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (for Illumina®)(Cat. No.:N259-YH01)
After quality inspection, cell concentration of the single-cell suspensions was adjusted to 200 cells/μL, and then single cell capture and library construction were performed according to the instructions of the DECODER single cell 3‘ kit v1.0（Dynamic Biosystems, 2203106, 2203206, 2203306, 2203406）.
The cDNA library was constructed with the v1.0 protocol of DECODER Single cell 3 'kit by Dynamic Biosystems (Suzhou, China). The library was quantitatively examined after fragmentation, adaptor ligation and sample index PCR.

value: liver cancer

value: Hepa 1-6

value: Ezrin KD


title: HAGLR_1.5h_rep3_ATACseq

description:
Library name: HAG90_3_QKDO240001113-1A_22J5G2LT4_L6
HAGLR_1.5h_REP3.mLb.clN.sorted.bam


title: KDNG2

description: Library name: sample2


title: scMultiomic RNA-Seq of LPS,1-WD

description:
Library name: scRNA_1-WD
scRNA_1-WD

value: primary well-differentiated liposarcoma

value: WD


title: NC-ANGPTL3-1

description:
Library name: Sample 7
NC_A3_1


title: HAGLR_2h_rep2_ATACseq

description:
Library name: HAG120_2_QKDO240001115-1A_22J5G2LT4_L6
HAGLR_2h_REP2.mLb.clN.sorted.bam


title: KDNG1

description: Library name: sample1

value: Bone marrow

value: Neutrophils


title: HAGLR_2h_rep1_ATACseq

description:
Library name: HAG120_1_QKDO240001114-1A_22J5G2LT4_L6
HAGLR_2h_REP1.mLb.clN.sorted.bam


title: Glc_IEVs

description:
Library name: sample2
Well-Paired-Seq


title: scMultiomic ATAC-Seq of LMS, 18_411 (Batch3)

description:
Library name: scATAC_18_411
scATAC_18_411

source_name: uterine leiomyosarcoma tumor cells

value: uterine leiomyosarcoma tumor cells

value: Uterine

tag: time

value: Grade 3


title: IEVs

description:
Library name: sample1
Well-Paired-Seq

value: IEVs


title: HAGLR_1.5h_rep2_ATACseq

description:
Library name: HAG90_2_QKDO240001112-1A_22J5G2LT4_L6
HAGLR_1.5h_REP2.mLb.clN.sorted.bam


title: HAGLR_1.5h_rep1_ATACseq

description:
Library name: HAG90_1_QKDO240001111-1A_22J5G2LT4_L6
HAGLR_1.5h_REP1.mLb.clN.sorted.bam


title: siMSR1-CON-3

description:
Library name: Sample 6
si_kong_3

value: BMDMs

value: MSR1 knockdown

value: treated with control supernatants


title: scMultiomic ATAC-Seq of LMS, 17_494 (Batch3)

description:
Library name: scATAC_17_494
scATAC_17_494


title: scMultiomic ATAC-Seq of LMS, 13_085 (Batch3)

description:
Library name: scATAC_13_085
scATAC_13_085


title: HAGLR_1h_rep3_ATACseq

description:
Library name: HAG60_3_QKDO240001110-1A_22J5G2LT4_L6
HAGLR_1h_REP3.mLb.clN.sorted.bam

value: hiPSCs


title: AAV6-αSMA-shThbs2-3

city: Beijing

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

data_processing:
Illumina HiSeq2500: Clean reads were obtained by Perl script.
Illumina HiSeq2500: Clean reads were mapped to the mouse reference genome GRCm38 using Bowtie2 and HISAT algorithms.
Illumina HiSeq2500: Gene expression levels were measured using FPKM values by Cufflinks software.
DNBSEQ-T7: SOAPnuke (V2.1.0) was used to filter the sequencing data.
DNBSEQ-T7: HISAT2 (V2.1.0) was used to compare clean reads with the reference genome, and Bowtie2 (V2.3.5) was used to align the quality controlled sequence to the reference transcription sequence.
DNBSEQ-T7: FPKM conversion was performed as reported by Nat Biotechnol, 2010,28(5):511-515.
Assembly: GRCm38
Supplementary files format and content: Excel file includes FPKM values for AAV-CMV-shThbs2-NC mice.xlsx
Supplementary files format and content: Excel file includes FPKM values for AAV-αSMA-shThbs2-NC mice.xlsx

extract_protocol:
Illumina HiSeq2500: Poly(A) mRNAs were enriched using magnetic oligo (dT) beads (Invitrogen, Carlsbad, CA), followed by RNA-seq library preparation using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs, Hitchin, UK) according to the manufacturer’s instructions.
DNBSEQ-T7: Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis and purified using AMPure XP Beads. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end cDNA repair. The cDNA fragments obtained from previous steps were amplified by PCR, and products were purified by Ampure XP Bead, get the final library.

value: liver


title: AAV6-αSMA-shThbs2-4

description: Excel file includes FPKM values for AAV-αSMA-shThbs2-NC mice.xlsx


title: siMSR1-CON-2

description:
Library name: Sample 5
si_kong_2


title: NC-CON-3

description:
Library name: Sample 3
NC_kong_3

value: WT


title: scMultiomic ATAC-Seq of LMS, 1311956_7 (Batch2)

description:
Library name: scATAC_1311956_7
scATAC_1311956_7

source_name: retroperitoneal leiomyosarcoma tumor cells

value: RP/Vascular


title: siMSR1-CON-1

description:
Library name: Sample 4
si_kong_1


title: NC-CON-2

description:
Library name: Sample 2
NC_kong_2


title: HAGLR_1h_rep2_ATACseq

description:
Library name: HAG60_2_QKDO240001109-1A_22J5G2LT4_L6
HAGLR_1h_REP2.mLb.clN.sorted.bam


title: NC-CON-1

description:
Library name: Sample 1
NC_kong_1


title: scMultiomic ATAC-Seq of LMS, 18_049 (Batch3)

description:
Library name: scATAC_18_049
scATAC_18_049


title: HAGLR_0.5h_rep3_ATACseq

description:
Library name: HAG30_3_QKDO240001107-1A_22J5G2LT4_L6
HAGLR_0.5h_REP3.mLb.clN.sorted.bam


title: HAGLR_1h_rep1_ATACseq

description:
Library name: HAG60_1_QKDO240001108-1A_22J5G2LT4_L6
HAGLR_1h_REP1.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LMS, 1424298_3 (Batch2)

description:
Library name: scATAC_1424298_3
scATAC_1424298_3

source_name: extremity leiomyosarcoma tumor cells

value: extremity leiomyosarcoma tumor cells

value: Extremity


title: tdTom+ cells of young K14cre;Wwoxfl/fl;p53fl/fl epidrmis, bio rep3

city: Jerusalem

first: Rami

last: Aqeilan

address: Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

description: Library name: DKO100_3

data_processing:
BCL files (machine output) were converted to fastq files for bioinformatics analysis.
For library quality control, Trim-Galore (v0.4.1) wrapper tool was applied to raw fastq files, trimming low-quality bases (Q > 20), residual adapters, and filtering out short reads (L > 20).
File assessment before and after quality control was performed using FastQC (v0.11.5).
Fastq files were mapped to mouse transcriptome with salmon tool v0.13.1.
Differential gene expression was analyzed with R package (v1.16.1) and analyzed using DESeq2 (v1.28.1).
Assembly: mm39
Supplementary files format and content: Tab-deliminated text file includes raw counts for each sample.

source_name: epidermis (skin)

growth_protocol: After genotyping, the mice were tracked weekly for spontanouse cSCC formation and collected immediately when tumor detected. For the young mice epidermis, 100–120-day old mice were used. For old mice epidermis 400+ days old mice were used. Cell dissociation protocol: Epidermis dissociation protocol-JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols. https://app.jove.com/pdf/50311/cell-population-analyses-during-skin-carcinogenesis. cSCC dissociation protocol- Fontenete, S. & Perez-Moreno, M. Isolation of cancer stem cells from squamous cell carcinoma. Methods Mol. Biol. 1879, 407–414 (2019). Cell sort: Cells were sorted for tdTomato+ cells by Sony SH800 cell sorter.

extract_protocol:
After sorting RNA was extracted via Rneasy plus mini kit for RNA isolation (Qiagen; 74134). 5g RNA was used for RNA-seq.
For library preparation, 5 ng of RNA from each sample was processed using the SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara).

value: epidermis (skin)

value: Keratinocyte


title: scMultiomic ATAC-Seq of LMS, 1109587_2 (Batch2)

description:
Library name: scATAC_1109587_2
scATAC_1109587_2

value: retroperitoneal leiomyosarcoma tumor cells

value: Grade 2


title: AAV6-αSMA-NC-3


title: HAGLR_0.5h_rep2_ATACseq

description:
Library name: HAG30_2_QKDO240001106-1A_22J5G2LT4_L6
HAGLR_0.5h_REP2.mLb.clN.sorted.bam


title: tdTom+ cells of young K14cre;Wwoxfl/fl;p53fl/fl epidrmis, bio rep2

description: Library name: DKO100_2


title: OCP_3

city: Xinxiang

first: dongfang

last: Zhang

state: Henan

address: 46 East Jianshe Rd

institute: Henan Normal University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36) (parameter- ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE)
Clean Reads were further treated with UMI_soft (in-house) to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co., Ltd.）
The de-duplicated consensus sequences were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow-derived macrophages

growth_protocol: bone marrow-derived macrophages were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

treatment_protocol: Osteoclast precursors differentiation was induced by treatment of 3-day bone marrow-derived macrophages  with 20 ng/ml of macrophage colony-stimulating factor (M-CSF, R&D Systems Inc.) and 10 ng/ml of nuclear factor-κB ligand (RANKL, R&D Systems Inc.)  and osteoclast differentiation was induced by treatment of 6-day bone marrow-derived macrophages  with 20 ng/ml M-CSF and 10 ng/ml RANKL.

value: bone marrow-derived macrophages

value: osteoclast precursors differentiation


title: OCP_2


title: scMultiomic ATAC-Seq of LMS, 989922_9 (Batch2)

description:
Library name: scATAC_989922_9
scATAC_989922_9


title: OCP_1


title: HAGLR_0.5h_rep1_ATACseq

description:
Library name: HAG30_1_QKDO240001105-1A_22J5G2LT4_L4
HAGLR_0.5h_REP1.mLb.clN.sorted.bam


title: tdTom+ cells of young K14cre;Wwoxfl/fl;p53fl/fl epidrmis, bio rep1

description: Library name: DKO100_1


title: tdTom+ cells of young K14cre;p53fl/fl epidrmis, bio rep3

description: Library name: PKO100_3


title: scMultiomic ATAC-Seq of LMS, 986219_11 (Batch2)

description:
Library name: scATAC_986219_11
scATAC_986219_11

value: Grade 3


title: HAGLR_0h_rep3_ATACseq

description:
Library name: HAG0_3_QKDO240001104-1A_22J5G2LT4_L4
HAGLR_0h_REP3.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LMS, 890688_1 (Batch2)

description:
Library name: scATAC_890688_1
scATAC_890688_1


title: OC_2

value: osteoclasts differentiation


title: HAGLR_0h_rep2_ATACseq

description:
Library name: HAG0_2_QKDO240001103-1A_22J5G2LT4_L4
HAGLR_0h_REP2.mLb.clN.sorted.bam


title: tdTom+ cells of young K14cre;p53fl/fl epidrmis, bio rep1

description: Library name: PKO100_1


title: AAV6-αSMA-NC-4


title: OC_1


title: OC_3


title: scMultiomic ATAC-Seq of LMS, 1007170_8 (Batch2)

description:
Library name: scATAC_1007170_8
scATAC_1007170_8


title: tdTom+ cells of young K14cre;p53fl/fl epidrmis, bio rep2

description: Library name: PKO100_2


title: scMultiomic ATAC-Seq of LMS, 133209_6 (Batch2)

description:
Library name: scATAC_133209_6
scATAC_133209_6


title: HAGLR_0h_rep1_ATACseq

description:
Library name: HAG0_1_QKDO240001102-1A_22J5G2LT4_L4
HAGLR_0h_REP1.mLb.clN.sorted.bam


title: FENDRR-2.5h_rep1_ATACseq

description:
Library name: F230_1
FENDRR.2.5h_REP1.mLb.clN.sorted.bam


title: scMultiomic ATAC-Seq of LMS, 1532950_8 (Batch1)

description:
Library name: scATAC_1532950_8
scATAC_1532950_8


title: FENDRR-2.5h_rep3_ATACseq

description:
Library name: F230_3
FENDRR.2.5h_REP3.mLb.clN.sorted.bam


title: Background Cntrl Infected

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

description: Library name: A16

data_processing:
Raw sequence data were processed using the nf-core RNA-Seq pipeline (version 3.14.0). Reads were aligned to the GRCm39.primary_assembly.genome reference genome combined with the sequences for the viruses using the STAR aligner and gene quantification was performed against the GENCODE GRCm39 primary assembly annotation with RSEM to obtain gene expression counts.
Assembly: GRCm39
Supplementary files format and content: tab delimited text file that includes counts for each gene and sample
Supplementary files format and content: tab delimited text file that includes TPM for each gene and sample

source_name: brain

growth_protocol: Hippocampi were isolated from ArcP/P , ActbM/M , or ArcP/P ; ActbM/M  double homozygous mice on post-natal day 0 (P0), and both sexes were used and combined. Hippocampal tissue was digested with 0.25% trypsin for 15 minutes at 37℃, triturated and plated onto Poly-D-Lysine (Sigma) coated 6 well plates for APEX experiments or glass bottom Mattek dishes for imaging experiments.

extract_protocol:
RNA was extracted from TRIzol Reagent (Invitrogen) as per the manufacturer’s instructions, using 10µg RNAse free Glycogen (Thermo Scientific) as a carrier.
Biotinylated RNA enrichment was performed similar to as described in stress granule APEX-seq1 All enrichment buffers were made fresh from RNAse free ingredients whenever possible and all washes occurred on a magnetic rack. Briefly: 10µl of Dynabeads MyOne Streptavidin C1 beads(ThermoFisher) per sample was washed three times with 1mM MgCl2, 0.25% sodium deoxycholate, 1x PBS wash buffer. Beads were then washed once and blocked for 30 minutes in 5x Denhardt’s reagent, 150 µg/mL Poly IC, 1mM MgCl2, 1x PBS, 0.25% sodium deoxycholate, 1:100 Ribolock RNAse inhibitor blocking buffer. Block was removed and RNA samples were added along with fresh blocking buffer. Samples were incubated on a slow rocking nutator at RT for 1.5hrs ensuring sample mixing. Beads were washed twice with 6M urea, 0.1% SDS, 1x PBS. Beads were washed once with 2% SDS, 1x PBS. Beads were washed once with 750 mM NaCl, 0.25% sodium deoxycholate, 0.1 % SDS, 1x PBS. Beads were washed once with 150mM NaCl, 0.25% sodium deoxycholate, 0.1 % SDS, 1x PBS. RNA was eluted from the beads with 300uL TRIzol and purified with the Direct-Zol RNA direct-zol RNA microprep kit (Zymogen). RNA was not quantified after pulldown, it was frozen at -80C or immediately processed for first strand cDNA synthesis using the Smartseq v4 mRNA Library prep kit (Takara) with maximum RNA input volume.       .

value: brain

value: neuron

value: Actb:24xMBS and Arc:24xPBS

value: MCP virus infected

tag: batch


title: scMultiomic ATAC-Seq of LMS,107168_9 (Batch1)

description:
Library name: scATAC_107168_9
scATAC_107168_9


title: FENDRR-2h_rep3_ATACseq

description:
Library name: F2_3
FENDRR.2h_REP3.mLb.clN.sorted.bam

value: hiPSCs


title: Background Cntrl Uninfected

description: Library name: A17

value: uninfected


title: scMultiomic ATAC-Seq of LMS, 1242796_12 (Batch1)

description:
Library name: scATAC_1242796_12
scATAC_1242796_12

value: RP/Vascular


title: FENDRR-2.5h_rep2_ATACseq

description:
Library name: F230_2
FENDRR.2.5h_REP2.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LMS, 18_411 (Batch3)

description:
Library name: scRNA_18_411
scRNA_18_411

value: uterine leiomyosarcoma tumor cells

value: Uterine


title: tdTom+ cells of young K14cre;Wwoxfl/fl epidrmis, bio rep2

description: Library name: WKO100_2

value: epidermis (skin)

value: Wwoxfl/fl


title: scMultiomic RNA-Seq of LMS, 18_049 (Batch3)

description:
Library name: scRNA_18_049
scRNA_18_049


title: scMultiomic ATAC-Seq of LMS, 768869_7 (Batch1)

description:
Library name: scATAC_768869_7
scATAC_768869_7

value: retroperitoneal leiomyosarcoma tumor cells


title: tdTom+ cells of young K14cre;Wwoxfl/fl epidrmis, bio rep1

description: Library name: WKO100_1

value: Keratinocyte


title: tdTom+ cells of young Wild-type epidrmis, bio rep1

description: Library name: WT100_1

value: WT


title: Actin Cntrl

description: Library name: A12

value: PCP virus infected


title: scMultiomic RNA-Seq of LMS, 17_494 (Batch3)

description:
Library name: scRNA_17_494
scRNA_17_494

value: Grade 3


title: Arc Rep. 2

description: Library name: A15


title: tdTom+ cells of cSCC from K14cre;Wwoxfl/fl;p53fl/fl mice, bio rep3

description: Library name: DKOscc_3

source_name: cSCC (skin tumor)

value: cSCC (skin tumor)

value: cSCC


title: tdTom+ cells of young K14cre;Wwoxfl/fl epidrmis, bio rep3

description: Library name: WKO100_3


title: tdTom+ cells of young Wild-type epidrmis, bio rep3

description: Library name: WT100_3


title: Arc Rep. 1

description: Library name: A14

value: brain

value: neuron


title: Actin Rep. 2

description: Library name: A13

value: MCP virus infected


title: Actin Rep. 1

description: Library name: A9

value: Actb:24xMBS and Arc:24xPBS


title: scMultiomic RNA-Seq of LMS, 1424298_3 (Batch2)

description:
Library name: scRNA_1424298_3
scRNA_1424298_3

value: extremity leiomyosarcoma tumor cells

value: Extremity


title: tdTom+ cells of cSCC from K14cre;Wwoxfl/fl;p53fl/fl mice, bio rep1

description: Library name: DKOscc_1


title: scMultiomic RNA-Seq of LMS, 1311956_7 (Batch2)

description:
Library name: scRNA_1311956_7
scRNA_1311956_7

value: RP/Vascular


title: tdTom+ cells of young Wild-type epidrmis, bio rep2

description: Library name: WT100_2


title: FENDRR-1.5h_rep2_ATACseq

description:
Library name: F130_2
FENDRR.1.5h_REP2.mLb.clN.sorted.bam

value: hiPSCs


title: FENDRR-1.5h_rep1_ATACseq

description:
Library name: F130_1
FENDRR.1.5h_REP1.mLb.clN.sorted.bam


title: FENDRR-2h_rep1_ATACseq

description:
Library name: F2_1
FENDRR.2h_REP1.mLb.clN.sorted.bam


title: FENDRR-2h_rep2_ATACseq

description:
Library name: F2_2
FENDRR.2h_REP2.mLb.clN.sorted.bam


title: FENDRR-1h_rep3_ATACseq

description:
Library name: F1_3
FENDRR.1h_REP3.mLb.clN.sorted.bam


title: Beta-PRLRKO PRL treated islets

city: Baltimore

first: Nelmari

last: Ruiz Otero

email: nelmari634@gmail.com, nruizot1@jhu.edu

state: MD

address: 5501 Hopkins Bayview Circle Allergy & Immunology Center Bayview Campus Lab 2A10

institute: Johns Hopkins University

description:
Library name: PRL-B1
10X Genomics

data_processing:
The Single Cell & Transcriptomics Core (SCTC, Johns Hopkins University, School of Medicine, Baltimore, MD) aid in the pre-processing of the cells using the 10X Genomics Cell Ranger ATAC pipeline.
Assembly: mm10
Supplementary files format and content: Sample.fragments.tsv.gz contains all high-confidence fragments passing quality filtering and Sample.fragments.tsv.gz.tbi is the index file generated using tabix to allow rapid genomic coordinate-based access to the compressed fragments.tsv.gz file
Supplementary files format and content: BED format files and HDF5 files

source_name: Pancreatic islets

extract_protocol:
Single cell suspensions were obtained after incubating islets in 0.05% trypsin-EDTA (Invitrogen, #25300054) at 37C with gentle trituration using a P1000 pipette for 10 minutes. Digestion was interrupted using FBS and cells were immediately filtered using a 40um cell strainer. After a PBS wash, cells were resuspended in 0.04% BSA in PBS 1X. Cell viability and concentration were quantified using Cell Countess II (Thermo Fisher Scientific).
After nuclei extraction, transposition, GEM generation and library preparation was prepared according to the manufacturer’s instructions using Chromium Next GEM Single Cell ATAC Kit (10X Genomics, #1000406), Chromium Next GEM Chip H Single Cell Kit (10X Genomics, #1000162), Single Index Kit N Set A, (10X Genomics, #1000212) and the Chromium Controller (10X Genomics Model GCG-SR-1). The Single Cell & Transcriptomics Core (SCTC, Johns Hopkins University, School of Medicine, Baltimore, MD) assessed the quality of the constructed library, performed Illumina sequencing using the NovaSeq X.

treatment_protocol: Isolated islets were cultured in RPMI-1640 (Thermo Fisher Scientific, # 22400089) supplemented with 10% FBS and 2% penicillin-streptomycin overnight at 37C in a humid chamber to allow for recovery. Islets were treated with DMSO (control) or 500ng/mL of recombinant mouse prolactin (Bio-Techne, # 1445-PL-050) for 24 hours.

value: Pancreatic islets

value: Mixed

value: Rip-Cre; Prlrf/f (beta-PrlrKO)

value: Prolactin (500ng/mL-24hours)


title: tdTom+ cells of cSCC from K14cre;p53fl/fl mice, bio rep2

description: Library name: PKOscc_2


title: Wild type Prolactin treated islets 2

description:
Library name: PRL-A4
10X Genomics

value: Wild Type (C57B6)


title: FENDRR-1.5h_rep3_ATACseq

description:
Library name: F130_3
FENDRR.1.5h_REP3.mLb.clN.sorted.bam


title: Arc Cntrl

description: Library name: A11


title: tdTom+ cells of cSCC from K14cre;Wwoxfl/fl;p53fl/fl mice, bio rep2

description: Library name: DKOscc_2


title: scMultiomic RNA-Seq of LMS, 13_085 (Batch3)

description:
Library name: scRNA_13_085
scRNA_13_085

value: uterine leiomyosarcoma tumor cells

value: Uterine


title: Uninfected Cntrl

description: Library name: A8

value: uninfected


title: tdTom+ cells of cSCC from K14cre;p53fl/fl mice, bio rep3

description: Library name: PKOscc_3

value: cSCC (skin tumor)

value: cSCC


title: FENDRR-1h_rep1_ATACseq

description:
Library name: F1_1
FENDRR.1h_REP1.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LMS, 1109587_2 (Batch2)

description:
Library name: scRNA_1109587_2
scRNA_1109587_2

value: retroperitoneal leiomyosarcoma tumor cells

value: Grade 2


title: tdTom+ cells of cSCC from K14cre;p53fl/fl mice, bio rep1

description: Library name: PKOscc_1


title: scMultiomic RNA-Seq of LMS, 1007170_8 (Batch2)

description:
Library name: scRNA_1007170_8
scRNA_1007170_8

value: Grade 3


title: FENDRR-0.5h_rep1_ATACseq

description:
Library name: F30_1
FENDRR.0.5h_REP1.mLb.clN.sorted.bam


title: FENDRR-0.5h_rep3_ATACseq

description:
Library name: F30_3
FENDRR.0.5h_REP3.mLb.clN.sorted.bam


title: FENDRR-1h_rep2_ATACseq

description:
Library name: F1_2
FENDRR.1h_REP2.mLb.clN.sorted.bam


title: Beta-PRLRKO DMSO treated islets

description:
Library name: Ctrl-B1
10X Genomics

value: DMSO


title: KOCD451_FO_M11

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: LUF7174A23

data_processing:
Alignment of paired-end raw reads was done with the nf-core rnaseq pipeline v3.6 using the star rsem aligner option and the ENSEMBL GRCm39 release 105 transcriptome.
Downstream processing was conducted using the R-package DESeq2
Assembly: GRCm39
Supplementary files format and content: tab delimited read count file

source_name: spleen

growth_protocol: Mixed bone marrow chimeras were generated by reconstitution of sub-lethally-irradiated Rag1-/- mice with bone marrow from Tnfrsf13b-/- or Tnfrsf13b+/+ littermates (CD45.2+; C57BL/6NCrl) mixed 50:50 with bone marrow from wildtype CD45.1+ mice (B6.SJL-Ptprca Pepcb/BoyJ). Spleens were harvested from chimeras (KO:WT and WT:WT) at 13 weeks post-reconstitution. CD45.2+ and CD45.1+ marginal zone (CD1dhiIgMhiCD93-B220+CD19+) and follicular (CD1dmedIgM+CD93-B220+CD19+) B cells were isolated via FACS.

extract_protocol:
Cell pellets were lysed after FACS in Buffer RLT (QIAGEN) with 1:100 beta-mercaptoethanol then frozen until processing. Lysates were homogenised using QIAshredder spin columns then RNA was extracted using the RNeasy Mini or Micro kit (QIAGEN) with DNase digestion on a QIAcube Connect, all according to the manufacturer’s instructions.
cDNA libraries were generated using the Watchmaker RNA Library Prep Kit with Polaris Depletion of rRNA and globin transcripts according to the manufacturer’s instructions.

value: spleen

value: Follicular B cells

value: KO:WT chimera


title: scMultiomic RNA-Seq of LMS, 986219_11 (Batch2)

description:
Library name: scRNA_986219_11
scRNA_986219_11

value: RP/Vascular


title: scMultiomic RNA-Seq of LMS, 989922_9 (Batch2)

description:
Library name: scRNA_989922_9
scRNA_989922_9


title: FENDRR-0.5h_rep2_ATACseq

description:
Library name: F30_2
FENDRR.0.5h_REP2.mLb.clN.sorted.bam

value: hiPSCs


title: tdTom+ cells of old Wild-type epidrmis, bio rep2

description: Library name: WTold_2

value: epidermis (skin)

value: Keratinocyte

value: WT


title: Wild type DMSO treated islet 2

description:
Library name: Ctrl-A4
10X Genomics

value: Pancreatic islets

value: Mixed

value: Wild Type (C57B6)


title: scMultiomic RNA-Seq of LMS, 890688_1 (Batch2)

description:
Library name: scRNA_890688_1
scRNA_890688_1

value: extremity leiomyosarcoma tumor cells

value: Extremity


title: tdTom+ cells of old Wild-type epidrmis, bio rep1

description: Library name: WTold_1


title: scMultiomic RNA-Seq of LMS, 1532950_8 (Batch1)

description:
Library name: scRNA_1532950_8
scRNA_1532950_8


title: KOCD451_FO_M10

description: Library name: LUF7174A22


title: FENDRR-0h_rep3_ATACseq

description:
Library name: F0_3
FENDRR.0h_REP3.mLb.clN.sorted.bam


title: KOCD451_FO_M12

description: Library name: LUF7174A24


title: Wild type Prolactin treated islets 1

description:
Library name: PRL_A3
10X Genomics

value: Prolactin (500ng/mL-24hours)


title: KOCD451_FO_M4

description: Library name: LUF7174A16


title: Uninfected5

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: E5

data_processing:
Adaptor sequences and low quality reads removed
Mapped to M musculus genome (version GRCm39)
DEG determined using DESeq2
Assembly: GRCm39
Supplementary files format and content: excel file with count data and gene symbol for each sample

source_name: Liver

extract_protocol:
total RNA was extracted using mRNAeasy kits (Qiagen)
standard Illumina

value: Liver


title: FENDRR-0h_rep2_ATACseq

description:
Library name: F0_2
FENDRR.0h_REP2.mLb.clN.sorted.bam

source_name: hiPSCs


title: scMultiomic RNA-Seq of LMS, 133209_6 (Batch2)

description:
Library name: scRNA_133209_6
scRNA_133209_6

value: retroperitoneal leiomyosarcoma tumor cells

value: Grade 3


title: Uninfected4

description: Library name: E4


title: Wild type DMSO treated islet 1

description:
Library name: Ctrl_A3
10X Genomics

value: DMSO


title: FENDRR-0h_rep1_ATACseq

description:
Library name: F0_1
FENDRR.0h_REP1.mLb.clN.sorted.bam


title: DMSO control tumor-infiltrating lymphocytes, donor 189

city: New Haven

first: Katrine

last: Madsen

state: CT

address: 300 George St.

department: CMCO

institute: Yale School of Medicine

description: Library name: Sample_TIL_189_DMSO_135_058

data_processing:
Quality assessment was performed using FastQC and RNA-SeQC (version 2.4.2).
Reads were aligned to the human reference genome (GRCh38.p10) using STAR (version 2.7.10a) with two-pass mapping.
PCR duplicates were marked using Picard MarkDuplicates (version 2.27.1).
Gene and transcript abundance was quantified using RSEM (version 1.3.1).
Gene-level expected counts and TPM values were aggregated across samples into project-level matrices.
Assembly: GRCh38.p10 (NCBI accession GCA_000001405.25)
Supplementary files format and content: Project_Knm32_2.gene_reads.gct.gz — tab-delimited matrix of gene-level read counts for all samples.
Supplementary files format and content: Project_Knm32_2.gene_tpm.gct.gz — tab-delimited matrix of gene-level TPM values for all samples.

source_name: kidney tumor

growth_protocol: Primary human pan T cells were isolated by negative selection from PBMCs obtained from healthy donors or ccRCC patients, or from ccRCC tumor specimens as tumor-infiltrating T cells. T cells were activated with anti-CD3/CD28 Dynabeads and cultured under hypoxic conditions (1% O₂).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen). DNase treatment and library preparation were performed by the Yale Center for Genome Analysis.
Poly(A)-selected libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit at the Yale Center for Genome Analysis. Samples were sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads (~25 million reads per sample)

treatment_protocol: T cells were treated with belzutifan (2 μM) or DMSO vehicle control for five days under hypoxic conditions (1% O₂).

value: kidney tumor

value: tumor-infiltrating T cells


title: Uninfected3

description: Library name: E3


title: DANCR_2.5h_rep3_ATACseq

description:
Library name: D230_3
DANCR_2.5h_REP3.mLb.clN.sorted.bam


title: scMultiomic RNA-Seq of LMS, 1242796_12 (Batch1)

description:
Library name: scRNA_1242796_12
scRNA_1242796_12

value: RP/Vascular


title: scMultiomic RNA-Seq of LMS, 768869_7 (Batch1)

description:
Library name: scRNA_768869_7
scRNA_768869_7


title: Uninfected2

description: Library name: E2


title: DANCR_2.5h_rep2_ATACseq

description:
Library name: D230_2
DANCR_2.5h_REP2.mLb.clN.sorted.bam

value: hiPSCs


title: KOCD451_MZ_M12

description: Library name: LUF7174A48

value: spleen

value: Marginal Zone B cells

value: KO:WT chimera


title: KOCD451_FO_M5

description: Library name: LUF7174A17

value: Follicular B cells


title: DMSO control tumor-infiltrating lymphocytes, donor 184

description: Library name: Sample_TIL_184_DMSO_147_046

value: WT


title: scMultiomic RNA-Seq of LMS, 107168_9 (Batch 1)

description:
Library name: scRNA_107168_9
scRNA_107168_9


title: DANCR_2h_rep2_ATACseq

description:
Library name: D2_2
DANCR_2h_REP2.mLb.clN.sorted.bam


title: KOCD451_MZ_M10

description: Library name: LUF7174A46


title: DANCR_2h_rep3_ATACseq

description:
Library name: D2_3
DANCR_2h_REP3.mLb.clN.sorted.bam


title: KOCD451_FO_M6

description: Library name: LUF7174A18


title: HighTemp5

description: Library name: D5


title: Uninfected1

description: Library name: E1


title: DANCR_1.5h_rep3_ATACseq

description:
Library name: D130_3
DANCR_1.5h_REP3.mLb.clN.sorted.bam


title: Belzutifan-treated tumor-infiltrating lymphocytes, donor 189

description: Library name: Sample_TIL_189_Belzutifan_158_035

value: belzutifan 2uM 5 days


title: HighTemp1

description: Library name: D1


title: HighTemp4

description: Library name: D4


title: KOCD451_MZ_M11

description: Library name: LUF7174A35


title: KOCD451_MZ_M5

description: Library name: LUF7174A41


title: HighTemp2

description: Library name: D2


title: DANCR_1.5h_rep2_ATACseq

description:
Library name: D130_2
DANCR_1.5h_REP2.mLb.clN.sorted.bam


title: HighTemp3

description: Library name: D3


title: DANCR_2h_rep1_ATACseq

description:
Library name: D2_1
DANCR_2h_REP1.mLb.clN.sorted.bam


title: KOCD451_MZ_M6

description: Library name: LUF7174A42


title: Belzutifan-treated tumor-infiltrating lymphocytes, donor 184

description: Library name: Sample_TIL_184_Belzutifan_170_023


title: KOCD451_MZ_M4

description: Library name: LUF7174A40


title: Belzutifan-treated tumor-infiltrating lymphocytes, donor 181

description: Library name: Sample_TIL_181_Belzutifan_182_011


title: DMSO control tumor-infiltrating lymphocytes, donor 181

description: Library name: Sample_TIL_181_DMSO_159_034


title: Belzutifan-treated tumor-infiltrating lymphocytes, donor 177

description: Library name: Sample_TIL_177_Belzutifan_099_094


title: Control5

description: Library name: C5


title: DMSO control tumor-infiltrating lymphocytes, donor 169

description: Library name: Sample_TIL_169_DMSO_171_022


title: KOCD452_FO_M10

description: Library name: LUF7174A10

value: TACI KO CD45.2+


title: DANCR_1.5h_rep1_ATACseq

description:
Library name: D130_1
DANCR_1.5h_REP1.mLb.clN.sorted.bam


title: Control4

description: Library name: C4


title: DANCR_1h_rep2_ATACseq

description:
Library name: D1_2
DANCR_1h_REP2.mLb.clN.sorted.bam


title: DANCR_1h_rep3_ATACseq

description:
Library name: D1_3
DANCR_1h_REP3.mLb.clN.sorted.bam


title: KOCD452_FO_M4

description: Library name: LUF7174A4


title: Belzutifan-treated tumor-infiltrating lymphocytes, donor 169

description: Library name: Sample_TIL_169_Belzutifan_111_082


title: DANCR_2.5h_rep1_ATACseq

description:
Library name: D230_1
DANCR_2.5h_REP1.mLb.clN.sorted.bam


title: Control2

description: Library name: C2


title: KOCD452_FO_M12

description: Library name: LUF7174A12


title: Control3

description: Library name: C3


title: DANCR_1h_rep1_ATACseq

description:
Library name: D1_1
DANCR_1h_REP1.mLb.clN.sorted.bam


title: Belzutifan-treated tumor-infiltrating lymphocytes, donor 158

description: Library name: Sample_TIL_158_Belzutifan_123_070


title: DANCR_0.5h_rep3_ATACseq

description:
Library name: D30_3_CKDL250005757-1A_22MKY2LT4_L2
DANCR_0.5h_REP3.mLb.clN.sorted.bam


title: Control1

description: Library name: C1


title: SSM2;TP53fl/fl rep3

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

description:
Library name: 1037
20643R_rpkm.csv
20643X26

data_processing:
Read alignment was accomplished with the STAR (2.7.11) against the mm10 version of the mouse genome [PMID: 23104886].
Assembly: mm10
Supplementary files format and content: csv, gene rpkm for each sample

source_name: mouse tumor

extract_protocol:
RNA was extracted with Zymo Direct-zolTM RNA Miniprep kit.
Total RNA samples (5-500 ng) were hybridized with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) to substantially diminish rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized and pooled in preparation for Illumina sequence analysis.

value: mouse tumor

value: mouse  express SS18::SSX2 gene combine with conditional knockout of Trp53


title: KOCD452_FO_M11

description: Library name: LUF7174A11


title: KOCD452_FO_M5

description: Library name: LUF7174A5


title: DANCR_0.5h_rep2_ATACseq

description:
Library name: D30_2_CKDL250005756-1A_22MKY2LT4_L2
DANCR_0.5h_REP2.mLb.clN.sorted.bam


title: DMSO control pan T cells from PBMCs, donor 189

description: Library name: Sample_PBMC_189_DMSO_184_009

source_name: peripheral blood

value: peripheral blood

value: pan T cells


title: DMSO control tumor-infiltrating lymphocytes, donor 158

description: Library name: Sample_TIL_158_DMSO_183_010


title: DANCR_0h_rep3_ATACseq

description:
Library name: D0_3_CKDL250005754-1A_22MKY2LT4_L2
DANCR_0h_REP3.mLb.clN.sorted.bam


title: KOCD452_FO_M6

description: Library name: LUF7174A6


title: KOCD452_MZ_M11

description: Library name: LUF7174A47


title: Belzutifan-treated pan T cells from PBMCs, donor 189

description: Library name: Sample_PBMC_189_Belzutifan_100_093


title: SSM2;TP53fl/fl rep2

description:
Library name: 530
20643R_rpkm.csv
20643X25


title: SSM2;TP53fl/fl rep1

description:
Library name: 527
20643R_rpkm.csv
20643X24


title: KOCD452_MZ_M10

description: Library name: LUF7174A34


title: KOCD452_MZ_M12

description: Library name: LUF7174A36


title: SSM2 rep3

description:
Library name: 1032
20643R_rpkm.csv
20643X19

value: mouse  express SS18::SSX2 gene


title: DMSO control pan T cells from PBMCs, donor 181

description: Library name: Sample_PBMC_181_DMSO_114_079

value: DMSO


title: SSM2 rep2

description:
Library name: 1035
20643R_rpkm.csv
20643X18


title: DANCR_0h_rep2_ATACseq

description:
Library name: D0_2_CKDL250005753-1A_22MKY2LT4_L2
DANCR_0h_REP2.mLb.clN.sorted.bam


title: DMSO control pan T cells from PBMCs, donor 184

description: Library name: Sample_PBMC_184_DMSO_102_091


title: DANCR_0h_rep1_ATACseq

description:
Library name: D0_1_CKDL250005752-1A_22MKY2LT4_L2
DANCR_0h_REP1.mLb.clN.sorted.bam


title: SSM2 rep1

description:
Library name: 1043
20643R_rpkm.csv
20643X17


title: DANCR_0.5h_rep1_ATACseq

description:
Library name: D30_2
DANCR_0.5h_REP1.mLb.clN.sorted.bam


title: Belzutifan-treated pan T cells from PBMCs, donor 181

description: Library name: Sample_PBMC_181_Belzutifan_124_069


title: CRNDE_2.5h_rep3_ATACseq

description:
Library name: CR150-3
CRNDE_2.5h_REP3.mLb.clN.sorted.bam


title: Belzutifan-treated pan T cells from PBMCs, donor 184

description: Library name: Sample_PBMC_184_Belzutifan_112_081


title: DMSO control pan T cells from PBMCs, donor 177

description: Library name: Sample_PBMC_177_DMSO_126_067


title: KOCD452_MZ_M5

description: Library name: LUF7174A29


title: KOCD452_MZ_M6

description: Library name: LUF7174A30


title: CRNDE_2.5h_rep2_ATACseq

description:
Library name: CR150-2
CRNDE_2.5h_REP2.mLb.clN.sorted.bam


title: KOCD452_MZ_M4

description: Library name: LUF7174A28


title: Panobinostat rep3

description:
Library name: Pano_1920
20219R_rpkm.csv
20219X14


title: Vehicle rep3

description:
Library name: veh_1911
20219R_rpkm.csv
20219X16


title: CRNDE_2.5h_rep1_ATACseq

description:
Library name: CR150-1
CRNDE_2.5h_REP1.mLb.clN.sorted.bam


title: Belzutifan-treated pan T cells from PBMCs, donor 177

description: Library name: Sample_PBMC_177_Belzutifan_136_057


title: CRNDE_2h_rep3_ATACseq

description:
Library name: CR120-3
CRNDE_2h_REP3.mLb.clN.sorted.bam


title: WTCD451_FO_M2

description: Library name: LUF7174A14

value: WT:WT chimera


title: HDM201 rep3

description:
Library name: HDM201_1915
20219R_rpkm.csv
20219X13


title: HDM201 rep2

description:
Library name: HDM201_1914
20219R_rpkm.csv
20219X11


title: WTCD451_FO_M1

description: Library name: LUF7174A13


title: DMSO control pan T cells from PBMCs, donor 161

description: Library name: Sample_PBMC_161_DMSO_150_043


title: WTCD451_FO_M7

description: Library name: LUF7174A19


title: DMSO control pan T cells from PBMCs, donor 169

description: Library name: Sample_PBMC_169_DMSO_138_055


title: CRNDE_1.5h_rep3_ATACseq

description:
Library name: CR90-3
CRNDE_1.5h_REP3.mLb.clN.sorted.bam


title: Panobinostat rep2

description:
Library name: Pano_1919
20219R_rpkm.csv
20219X10


title: HDM201 rep1

description:
Library name: HDM201_1930
20219R_rpkm.csv
20219X6


title: Belzutifan-treated pan T cells from PBMCs, donor 161

description: Library name: Sample_PBMC_161_Belzutifan_160_033


title: CRNDE_2h_rep2_ATACseq

description:
Library name: CR120-2
CRNDE_2h_REP2.mLb.clN.sorted.bam


title: CRNDE_2h_rep1_ATACseq

description:
Library name: CR120-1
CRNDE_2h_REP1.mLb.clN.sorted.bam


title: WTCD451_FO_M3

description: Library name: LUF7174A15


title: DMSO control pan T cells from PBMCs, donor 158

description: Library name: Sample_PBMC_158_DMSO_162_031


title: Belzutifan-treated pan T cells from PBMCs, donor 169

description: Library name: Sample_PBMC_169_Belzutifan_148_045


title: CRNDE_1.5h_rep2_ATACseq

description:
Library name: CR90-2
CRNDE_1.5h_REP2.mLb.clN.sorted.bam


title: Belzutifan-treated pan T cells from PBMCs, donor 158

description: Library name: Sample_PBMC_158_Belzutifan_172_021


title: WTCD451_FO_M8

description: Library name: LUF7174A20


title: Panobinostat rep1

description:
Library name: Pano_1913
20219R_rpkm.csv
20219X7


title: CRNDE_1h_rep3_ATACseq

description:
Library name: CR60-3
CRNDE_1h_REP3.mLb.clN.sorted.bam


title: WTCD451_MZ_M1

description: Library name: LUF7174A37


title: Combination rep3

description:
Library name: comb_1642
20219R_rpkm.csv
20219X3


title: Belzutifan-treated pan T cells, healthy donor HD-48

description: Library name: Sample_HD_48_Belzutifan_174_019


title: WTCD451_FO_M9

description: Library name: LUF7174A21


title: Combination rep2

description:
Library name: comb_1459
20219R_rpkm.csv
20219X2


title: Vehicle rep2

description:
Library name: veh_1644
20219R_rpkm.csv
20219X5


title: CRNDE_1.5h_rep1_ATACseq

description:
Library name: CR90-1
CRNDE_1.5h_REP1.mLb.clN.sorted.bam


title: Vehicle rep1

description:
Library name: veh_1643
20219R_rpkm.csv
20219X4


title: CRNDE_0.5h_rep3_ATACseq

description:
Library name: CR30-3
CRNDE_0.5h_REP3.mLb.clN.sorted.bam


title: WTCD451_MZ_M9

description: Library name: LUF7174A45


title: Belzutifan-treated pan T cells, healthy donor HD-44

description: Library name: Sample_HD_44_Belzutifan_103_090


title: CRNDE_0.5h_rep1_ATACseq

description:
Library name: CR30-1
CRNDE_0.5h_REP1.mLb.clN.sorted.bam


title: DMSO control pan T cells, healthy donor HD-48

description: Library name: Sample_HD_48_DMSO_139_054


title: Group 1

city: New York

first: Jennifer

middle: C

last: Chan

state: New York

address: 1470 Madison Ave 9-201

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 16
NEBNext Ultra II DNA Library Prep Kit for Illumina

data_processing:
Alignment using bowtie2 to the appropriate genome (mm10 or hg19)
Filtered using samtools (MAPQ>30)
Deduplicated using picard
Normalized for ecoli spike in
Bigwig files generated using deeptools bamCoverage and scaled based on ecoli spike in normalization factor
Assembly: mm10
Supplementary files format and content: bigwig files
Library strategy: CUT&Run

source_name: Brain

extract_protocol:
Nuclei isolation using lysis buffer, 40um filtering, followed by overnight incubation with antibody indicated. Following Mnase cleavage in calcium buffer, reaction was stopped and DNA was purified using the Zymo ChIP DNA Clean and Concentrator Kit.
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Brain

tag: region

value: dHpc

tag: group

value: Control RE

tag: virus

tag: antibody

value: IgG


title: DMSO control pan T cells, healthy donor HD-38

description: Library name: Sample_HD_38_DMSO_175_018


title: CRNDE_0h_rep3_ATACseq

description:
Library name: CR0-3
CRNDE_0h_REP3.mLb.clN.sorted.bam

value: hiPSCs


title: WTCD451_MZ_M2

description: Library name: LUF7174A38

value: spleen

value: Marginal Zone B cells


title: WTCD452_FO_M2

description: Library name: LUF7174A2

value: Follicular B cells

value: TACI WT CD45.2+


title: CRNDE_1h_rep2_ATACseq

description:
Library name: CR60-2
CRNDE_1h_REP2.mLb.clN.sorted.bam


title: WTCD451_MZ_M3

description: Library name: LUF7174A39


title: CRNDE_0h_rep2_ATACseq

description:
Library name: CR0-2
CRNDE_0h_REP2.mLb.clN.sorted.bam


title: DMSO control pan T cells, healthy donor HD-46

description: Library name: Sample_HD_46_DMSO_151_042

value: WT


title: CRNDE_0h_rep1_ATACseq

description:
Library name: CR0-1
CRNDE_0h_REP1.mLb.clN.sorted.bam


title: CRNDE_1h_rep1_ATACseq

description:
Library name: CR60-1
CRNDE_1h_REP1.mLb.clN.sorted.bam


title: Combination rep1

description:
Library name: comb_1460
20219R_rpkm.csv
20219X1

value: mouse tumor


title: Belzutifan-treated pan T cells, healthy donor HD-46

description: Library name: Sample_HD_46_Belzutifan_186_007

value: belzutifan 2uM 5 days


title: Belzutifan-treated pan T cells, healthy donor HD-36

description: Library name: Sample_HD_36_Belzutifan_127_066

value: peripheral blood


title: WTCD451_MZ_M7

description: Library name: LUF7174A43


title: WTCD451_MZ_M8

description: Library name: LUF7174A44


title: 941

description:
Library name: Sample 13
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: CRNDE_0.5h_rep2_ATACseq

description:
Library name: CR30-2
CRNDE_0.5h_REP2.mLb.clN.sorted.bam


title: DMSO control pan T cells, healthy donor HD-44

description: Library name: Sample_HD_44_DMSO_163_030

value: pan T cells


title: Group 2

description:
Library name: Sample 17
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Stress RE


title: BANCR_2.5h_rep2_ATACseq

description:
Library name: BA150-2
BANCR_2.5h_REP2.mLb.clN.sorted.bam


title: WTCD452_FO_M9

description: Library name: LUF7174A9


title: Group 3

description:
Library name: Sample 18
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: WTCD452_FO_M7

description: Library name: LUF7174A7


title: WTCD452_FO_M1

description: Library name: LUF7174A1


title: 946

description:
Library name: Sample 15
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: WTCD452_FO_M3

description: Library name: LUF7174A3


title: Belzutifan-treated pan T cells, healthy donor HD-38

description: Library name: Sample_HD_38_Belzutifan_115_078


title: 945

description:
Library name: Sample 14
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: BANCR_2.5h_rep3_ATACseq

description:
Library name: BA150-3
BANCR_2.5h_REP3.mLb.clN.sorted.bam


title: Non-targeting control, donor LRS-43

description: Library name: Sample_LRS_43_NT_290_287

data_processing:
Quality assessment was performed using FastQC and RNA-SeQC (version 2.4.2).
Reads were aligned to the human reference genome (GRCh38.p10) using STAR (version 2.7.10a) with two-pass mapping.
PCR duplicates were marked using Picard MarkDuplicates (version 2.27.1).
Gene and transcript abundance was quantified using RSEM (version 1.3.1).
Gene-level expected counts and TPM values were aggregated across samples into project-level matrices.
Assembly: GRCh38.p10 (NCBI accession GCA_000001405.25)
Supplementary files format and content: Project_Knm32.rsem_genes_expected_count.txt.gz — tab-delimited matrix of RSEM gene-level expected counts for all samples.
Supplementary files format and content: Project_Knm32.rsem_genes_tpm.txt.gz — tab-delimited matrix of RSEM gene-level TPM values for all samples.

source_name: Peripheral blood

growth_protocol: Primary human pan T cells were isolated by negative selection from PBMCs obtained from healthy donors. T cells were activated with anti-CD3/CD28 Dynabeads and cultured under hypoxic conditions (1% O₂) to stabilize hypoxia-inducible factors prior to genetic perturbation.

treatment_protocol: CRISPR/Cas9-mediated knockout of HIF1A or EPAS1 was performed using RNP electroporation. Synthetic crRNAs targeting HIF1A or EPAS1 were annealed to tracrRNA and complexed with recombinant Cas9 protein. Activated T cells (48 hours post-stimulation) were electroporated using the Lonza 4D-Nucleofector system (program EO-115) and recovered in CTS OpTmizer medium supplemented with IL-2. Non-targeting CRISPR controls and no-electroporation controls served as comparators. Edited T cells were maintained under hypoxic conditions (1% O₂) for five days post-electroporation.

value: Peripheral blood

value: Pan T cells


title: DMSO control pan T cells, healthy donor HD-36

description: Library name: Sample_HD_36_DMSO_187_006

value: DMSO


title: WTCD452_FO_M8

description: Library name: LUF7174A8

value: WT:WT chimera


title: 932

description:
Library name: Sample 10
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Brain

value: dHpc

value: Control RE


title: HIF2A knockout, donor LRS-43

description: Library name: Sample_LRS_43_HIF2a_KO_361_216

value: EPAS1 KO


title: 930

description:
Library name: Sample 9
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 939

description:
Library name: Sample 12
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: BANCR_2h_rep2_ATACseq

description:
Library name: BA120-2
BANCR_2h_REP2.mLb.clN.sorted.bam

data_processing:
Quality control, read mapping, and quantification were performed using nf-core/atacseq v2.1.2.
Assembly: The cleaned reads were aligned to the GRCh38.p13 human reference genome with the GENCODE v38 genome annotation file. Reads located in the ENCODE hg38 blacklist v2 region were removed.
Supplementary files format and content: .csv, consensus peaks raw counts of all samples
Supplementary files format and content: .bigWig, merged replicate ATAC-seq tracks of each sample

value: hiPSCs


title: Non-targeting control, donor LRS-42

description: Library name: Sample_LRS_42_NT_338_239


title: BANCR_1.5h_rep3_ATACseq

description:
Library name: BA90-3
BANCR_1.5h_REP3.mLb.clN.sorted.bam


title: WTCD452_MZ_M7

description: Library name: LUF7174A31

value: spleen

value: Marginal Zone B cells


title: WTCD452_MZ_M8

description: Library name: LUF7174A32

value: TACI WT CD45.2+


title: 937

description:
Library name: Sample 11
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: WT


title: 925

description:
Library name: Sample 7
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: No CRISPR control, donor LRS-43

description: Library name: Sample_LRS_43_NC_349_228


title: WTCD452_MZ_M1

description: Library name: LUF7174A25


title: BANCR_2.5h_rep1_ATACseq

description:
Library name: BA150-1
BANCR_2.5h_REP1.mLb.clN.sorted.bam


title: 922

description:
Library name: Sample 5
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: TFH scRNA-seq

city: shanghai

first: GuoFeng

last: Fang

address: No. 1630 Dongfang Road, Pudong New Area

department: Shanghai Institute of Immunotherapy Innovation, Renji Hospital

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: sgNTC_TFH_scRNA-seq
CD4+CD25–CD45.1+CXCR5+SLAM– TFH cells

data_processing:
The Cell Ranger software (v.7.1.0; 10x Genomics) was used to process the raw sequencing data from the Illumina HiSeq run1. The pipeline performed demultiplexing, aligned the reads to the mouse genome (mm10 2020-A, ENSEMBL GRCm38), processed the barcodes, and constructed gene-cell matrices. Downstream analysis was conducted using the Seurat R package (v5.1.0). Cells exhibiting low UMI counts (likely dead cells) or high UMI counts (possibly doublets or multiplets) were excluded from further analysis. Cells with a high percentage (>5%) of mitochondrial reads, indicative of potential dead cells, were also removed. Normalization of the expression data was performed using the NormalizeData function in Seurat, with the scale factor set to 10^4.
Assembly: mm10 2020-A, ENSEMBL GRCm38
Supplementary files format and content: file includes filtered_feature_bc_matrix

growth_protocol: C57BL/6 mice were intraperitoneally injected with 2 × 105 plaque-forming units (PFU) of the Armstrong strain of LCMV on day 0. Simultaneously, 2 × 105 wild-type SMARTA cells were intravenously injected. After 7 days, CD4+CD25–CD45.1+CXCR5+SLAM– TFH cells were sorted and used for scRNA-seq analysis.

extract_protocol:
polyA RNA
Sorted TFH cells were pooled by experimental group, centrifuged at 2,000 rpm for 5 minutes, and resuspended in 1× PBS containing 0.04% BSA at a concentration of 1 × 10⁶ cells/mL  to maintain cell viability and minimize aggregation. Single-cell libraries were prepared using the Chromium Single Cell 3' Library & Gel Bead Kit (v.3.1) from 10x Genomics. Briefly, single-cell suspensions were loaded onto the Chromium Controller to generate 10,000 single-cell gel beads in emulsion per sample, based on their cell counts. Each sample was loaded into a separate channel. The cDNA content of each sample after 12-cycle PCR amplification was quantified using a High-Sensitivity D5000 ScreenTape on a TapeStation (Agilent Technologies) to determine optimal library preparation cycles. Following quality control, libraries were normalized to 1.5 nM and loaded onto a NovaSeq 6000 system (Illumina) with a 2×150-bp paired-end configuration, employing the following sequencing cycle parameters: 151 cycles (Read1), 8 cycles (i7 index), 8 cycles (i5 index), and 151 cycles (Read2). An average of 300 million paired-end reads per sample was generated (approximately 20,000 reads per cell).

value: mouse spleen cell

value: sgNTC Tfh


title: BANCR_2h_rep3_ATACseq

description:
Library name: BA120-3
BANCR_2h_REP3.mLb.clN.sorted.bam

extract_protocol:
All steps from nuclei isolation through library preparation were performed by Novogene Co., Ltd. using their standardized, optimized ATAC-seq workflow.
The final ATAC-seq libraries were quantified, quality-controlled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end, 150 bp) by Novogene Co., Ltd.


title: Non-targeting control, donor LRS-38

description: Library name: Sample_LRS_38_NT_291_286


title: WTCD452_MZ_M3

description: Library name: LUF7174A27


title: WTCD452_MZ_M2

description: Library name: LUF7174A26


title: BANCR_2h_rep1_ATACseq

description:
Library name: BA120-1
BANCR_2h_REP1.mLb.clN.sorted.bam


title: BANCR_1h_rep3_ATACseq

description:
Library name: BA60-3
BANCR_1h_REP3.mLb.clN.sorted.bam


title: 927

description:
Library name: Sample 8
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: HIF1A knockout, donor LRS-43

description: Library name: Sample_LRS_43_HIF1a_KO_373_204

value: HIF1A KO


title: No CRISPR control, donor LRS-42

description: Library name: Sample_LRS_42_NC_302_275


title: 923

description:
Library name: Sample 6
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Stress RE


title: 915

description:
Library name: Sample 3
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: HIF2A knockout, donor LRS-42

description: Library name: Sample_LRS_42_HIF2a_KO_314_263

value: Peripheral blood


title: BANCR_1.5h_rep2_ATACseq

description:
Library name: BA90-2
BANCR_1.5h_REP2.mLb.clN.sorted.bam


title: BANCR_1h_rep1_ATACseq

description:
Library name: BA60-1
BANCR_1h_REP1.mLb.clN.sorted.bam


title: WTCD452_MZ_M9

description: Library name: LUF7174A33


title: WT_th1_01

description:
Library name: WT_th1_01
fvd-cd4+ametrine+ly6c+pd1-

data_processing:
Raw reads were processed using Trim Galore/Fastp, aligned with STAR/HISAT2, and quantified via FeatureCounts (v2.0.3).
Assembly: GRCm39/mm39
Supplementary files format and content: comma-delimited csv file includes raw counts for each Sample

growth_protocol: C57BL/6 mice were intraperitoneally injected with 2 × 105 plaque-forming units (PFU) of the Armstrong strain of LCMV on day 0. Simultaneously, 2 × 105 wild-type SMARTA cells were intravenously injected. After 7 days,  FVD–CD4+CD45.1+Ly6C–PD1+ TFH and FVD–CD4+CD45.1+Ly6C+PD1– TH1 cells were sorted and used for RNA-seq analysis.

extract_protocol:
polyA RNA
Cell samples were snap-frozen in liquid nitrogen, and total RNA was isolated using the RNeasy Mini Kit (Qiagen, 74104). RNA integrity was validated via Agilent 2100 Bioanalyzer (RIN ≥8). Libraries were size-selected (300–500 bp) and PCR-amplified, followed by sequencing on an Illumina NovaSeq 6000 with S4 flow cells (PE150).

value: WT Th1


title: BANCR_0.5h_rep3_ATACseq

description:
Library name: BA30-3
BANCR_0.5h_REP3.mLb.clN.sorted.bam


title: Non-targeting control, donor LRS-36

description: Library name: Sample_LRS_36_NT_339_238

value: Pan T cells


title: WT_tfh_03

description:
Library name: WT_tfh_03
fvd-cd4+ametrine+ly6c-pd1+

value: WT Tfh


title: HIF1A knockout, donor LRS-42

description: Library name: Sample_LRS_42_HIF1a_KO_326_251


title: BANCR_1.5h_rep1_ATACseq

description:
Library name: BA90-1
BANCR_1.5h_REP1.mLb.clN.sorted.bam


title: 921

description:
Library name: Sample 4
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: Brain


title: No CRISPR control, donor LRS-36

description: Library name: Sample_LRS_36_NC_303_274


title: WT_th1_03

description:
Library name: WT_th1_03
fvd-cd4+ametrine+ly6c+pd1-


title: HIF1A knockout, donor LRS-38

description: Library name: Sample_LRS_38_HIF1a_KO_374_203


title: No CRISPR control, donor LRS-38

description: Library name: Sample_LRS_38_NC_350_227


title: BANCR_1h_rep2_ATACseq

description:
Library name: BA60-2
BANCR_1h_REP2.mLb.clN.sorted.bam


title: 914

description:
Library name: Sample 2
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: dHpc


title: Control, Initial experiment 4

description: Library name: 134

data_processing:
Adaptor sequences and low quality reads removed
Mapped to M. musculus genome (GRCm39)
DEG determined using DESeq2
Assembly: GRCm39
Supplementary files format and content: excel file with count data and gene symbol for each sample

source_name: Caecum

extract_protocol:
RNA was extracted from caecum tissue using RNAeasy extraction kits (Qiagen)
standard Illumina

value: Caecum

value: Control, Initial experiment


title: HIF1A knockout, donor LRS-36

description: Library name: Sample_LRS_36_HIF1a_KO_327_250


title: HIF2A knockout, donor LRS-38

description: Library name: Sample_LRS-38_HIF2a_KO_362_215

value: EPAS1 KO


title: WT_th1_02

description:
Library name: WT_th1_02
fvd-cd4+ametrine+ly6c+pd1-

value: spleen


title: WT_tfh_01

description:
Library name: WT_tfh_01
fvd-cd4+ametrine+ly6c-pd1+


title: Control, Initial experiment 2

description: Library name: 132


title: K562 cells, no doxycycline induction, KMT2A antibody, rep3

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description: Library name: K562_noDOX_KMT2A_3

data_processing:
Paired-end reads were trimmed using Fastp with adapter detection and poly-G trimming.
Trimmed reads from K562 samples were aligned to the human genome (GRCh38/hg38) and trimmed reads from mouse Lin- samples were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”.
Duplicates were marked using the Sambamba “markdup” subcommand.
Peaks were called with GoPeaks using IgG samples as negative controls.
K562 CUT&RUN samples were sequenced across multiple batches. Samples from Batch 3 use an in-batch IgG control (K562_noDOX_IgG_3) for peak calling. K562 CUT&RUN samples from Batch 2 use the IgG control (K562_noDOX_IgG_1) from Batch 1 for peak calling. The IgG from Batch 2 yielded insufficient read depth to reliably model background signal and was therefore not used. The Batch 1 IgG sample used for peak calling was prepared using the same cell line and protocols as the experimental samples, allowing for consistent background estimation and peak calling when in-batch controls were not usable.
Mouse lineage-negative CUT&RUN samples were sequenced across multiple batches. Batch 1 samples (KAT7 and KMT2A samples) used the Batch 1 IgG control (mouse_batch1_LUC_IgG) for peak calling, which had similarly high read depth as the experimental samples in that batch, making it suitable for background modeling. Batches 2-3 used the Batch 4 IgG control (mouse_batch4_LUC_IgG) for peak calling. Batch 2 (sequenced on NovaSeq 6000) did not originally include an IgG control, and Batch 3 included an IgG control that had insufficient read depth and could not be used to reliably model background signal. The Batch 4 IgG control had read depth similar to samples in Batches 2-3, allowing for consistent background estimation and peak calling when in-batch controls were not usable.
Spike-in DNA from E. coli K-12 MG1655 was provided in the Epicypher CUT&RUN kit and used according to the manufacturer's protocols. To determine normalization factors for signal visualization, reads were aligned to host and E. coli reference genomes, and uniquely aligned reads were retained. Spike-in percentages were calculated as the proportion of reads mapping to E. coli relative to reads mapping to the host genome. Normalization factors were then calculated based on the relative spike-in percentages, scaled to the sample with the lowest spike-in recovery within each antibody target, consistent with Epicypher guidelines. Spike-in normalization was applied to the histone mark samples (H3K14ac, H3K23ac), as these samples had consistent spike-in recovery across replicates within each condition. BigWig coverage tracks for these samples were generated using spike-in derived scale factors with deepTools bamCoverage (--binSize 10 --smoothLength 50 --scaleFactor <sample-specific value>). Other antibody targets were not spike-in normalized due to variable spike-in recovery across replicates. For these samples, counts-per-million (CPM) normalized bigWig tracks were generated using deepTools bamCoverage with parameters “--binSize 10 --smoothLength 50 --normalizeUsing CPM”.
Assembly: GRCh38 (hg38) for samples from K562 cells, GRCm38 (mm10) for samples from mouse lineage-negative bone marrow cells
Supplementary files format and content: BigWig files include either spike-in normalized (for histone marks) or CPM-normalized (for other antibody targets) read signal for each sample.
Library strategy: CUT&Run

growth_protocol: K562 cells were grown in IMDM medium with 10% FBS, 2mM glutamine, 1x penicillin/streptomycin. Mouse lineage-negative (Lin-) bone marrow primary cells were grown in IMDM medium with 15% FBS, 2mM glutamine, 1x penicillin/streptomycin in the presence of SCF, IL6, and IL3.

extract_protocol:
Cells were harvested following the EpiCypher CUT&RUN kit protocol (EpiCypher CUTANA 14-1048).
CUT&RUN libraries were prepared using the New England Biolabs NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: K562 cells were either induced with 250ng/mL of doxycycline or not induced with any doxycycline for 24 hours. For mouse lineage-negative (Lin-) CUT&RUN, lentivirus were generated by co-transfecting psPAX2 (Addgene: 12260), pMD2.G (Addgene: 12259), and pSMAL_Luciferase (control) or pSMAL_SETBP1D868N into LentiX cells (Takara) with Fugene 6 (Promega E2691), according to the manufacturer's instructions. Mouse lineage-negative bone marrow cells were lentivirally transduced with either a control (luciferase) or SETBP1D868N mutant and then GFP-sorted.

value: myeloid leukemia cell line

value: No doxycycline induction

tag: cutrun antibody

value: KMT2A (Cell Signaling Technology, 14689)

tag: genome assembly

value: GRCh38 (hg38)

tag: sequencing batch


title: 904

description:
Library name: Sample 1
NEBNext Ultra II DNA Library Prep Kit for Illumina

value: WT


title: BANCR_0h_rep1_ATACseq

city: Boulder

last: Liu

address: 709 Mohawk Dr

institute: University of Colorado

description:
Library name: BA0-1
BANCR_0h_REP1.mLb.clN.sorted.bam

tag: cell line

value: hiPSCs


title: Control, Initial experiment 6

description: Library name: 136

tag: tissue


title: BANCR_0.5h_rep2_ATACseq

description:
Library name: BA30-2
BANCR_0.5h_REP2.mLb.clN.sorted.bam


title: Control, Initial experiment 5

description: Library name: 135


title: K562 cells, no doxycycline induction, KMT2A antibody, rep2

description: Library name: K562_noDOX_KMT2A_2


title: WT_tfh_02

description:
Library name: WT_tfh_02
fvd-cd4+ametrine+ly6c-pd1+

value: mouse spleen cell


title: BANCR_0.5h_rep1_ATACseq

description:
Library name: BA30-1
BANCR_0.5h_REP1.mLb.clN.sorted.bam


title: BANCR_0h_rep3_ATACseq

description:
Library name: BA0-3
BANCR_0h_REP3.mLb.clN.sorted.bam


title: GFPb2_2.5h_rep1_ATACseq

description:
Library name: g150_1_QKDO240001001-1A_22HVHJLT4_L1
GFPb2_2.5h_REP1.mLb.clN.sorted.bam


title: 3'SL, Initial experiment 5

description: Library name: 129

value: 3'SL, Initial experiment


title: HIF2A knockout, donor LRS-36

description: Library name: Sample_LRS_36_HIF2a_KO_315_262

value: Peripheral blood


title: 3'SL, Initial experiment 4

description: Library name: 128


title: 1 week of refeeding after a 72 hour fast 2

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

description:
Library name: RNAseq_1Wk_Refeed_Hypo4
RNA-seq on mouse hypothalamus in different metabolic states
refeed_1h12h1wk_19727_20058_CountsEnsFeb2023.txt
1wkRFvsFed_EdgeR.txt

data_processing:
RNA-seq Aligned with HISAT2 with the parameter ‘-x’.
Gene expression counted with Rsubread::featureCounts.
EdgeR differential expression analysis.
Assembly: mm10
Supplementary files format and content: RNA-seq: EdgeR Output with CPM normalized counts, tab delimited.
Supplementary files format and content: rSubread gene-level counts, tab delimited.

source_name: Hypothalamus

extract_protocol:
Qiagen RNeasy kit.
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (human, mouse, rat).

treatment_protocol: Fed, fasted 24h, fasted 72 hours, 72 hours fasted with cold treatment (18C), 1h refed after 72h fast, 12h refed after 72h fast, 1 month refed after 72h fast.

value: Hypothalamus

value: Refed 1 week


title: Secondary-Inf-ILCs_S3

city: New Orleans

first: Ulrich

last: Femoe Membe

state: Louisiana

address: 1430 Tulane Avenue

department: Microbiology and Immunology

institute: Tulane University School of Medicine

description:
Library name: Sample 3
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Processed count matrix in Matrix Market format (mtx + TSVs)

source_name: lung

extract_protocol:
Lung tissue was dissected, mechanically dissociated, and enzymatically digested in DMEM containing Liberase, Dispase II, and DNase I at 37°C for 40 minutes with agitation. Cell suspensions were filtered, stimulated with Cell Activation Cocktail (with Brefeldin A), and stained for viability, surface, and intracellular markers using standard protocols. ILC2s (CD45⁺ CD90.2⁺ CD127⁺) were sorted by FACS with >85% viability and resuspended in PBS with 10% FBS at 700–1200 cells/μL. Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kit v3 per manufacturer’s instructions.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics), following the manufacturer’s protocol. Libraries were uniquely indexed with the Chromium Dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 system using a paired-end, dual-indexing run. Each library was sequenced to a target depth of 20,000 mean reads per cell.

value: lung

value: ILC2s from wild-type (WT) mice (C57BL/6 strain)

value: 8-12 weeks old


title: BANCR_0h_rep2_ATACseq

first: Mingfeng

description:
Library name: BA0-2
BANCR_0h_REP2.mLb.clN.sorted.bam


title: Primary-Inf-ILCs_S2

description:
Library name: Sample 2
10x Genomics


title: K562 cells, doxycycline-induced, KMT2A antibody, rep2

description: Library name: K562_DOX250ng_KMT2A_2

value: Doxycycline 250ng/mL induction for 24 hours


title: 1 week of refeeding after a 72 hour fast 4

description:
Library name: RNAseq_1WkRefeed_Hypo3
RNA-seq on mouse hypothalamus in different metabolic states
refeed_1h12h1wk_19727_20058_CountsEnsFeb2023.txt
1wkRFvsFed_EdgeR.txt


title: GFPb2_2h_rep3_ATACseq

description:
Library name: g120_3_QKDO240001000-1A_22HVHJLT4_L1
GFPb2_2h_REP3.mLb.clN.sorted.bam


title: GFPb2_2h_rep2_ATACseq

description:
Library name: g120_2_QKDO240000999-1A_22HVHJLT4_L1
GFPb2_2h_REP2.mLb.clN.sorted.bam


title: Control, Initial experiment 3

description: Library name: 133

value: Caecum

value: Control, Initial experiment


title: Primary-Inf-ILCs_S1

description:
Library name: Sample 1
10x Genomics


title: GFPb2_2.5h_rep3_ATACseq

description:
Library name: g150_3_QKDO240001003-1A_22HVHJLT4_L1
GFPb2_2.5h_REP3.mLb.clN.sorted.bam


title: Control, Initial experiment 1

description: Library name: 131


title: 12 hour Refed after 72h fast B6 Mouse Hypothalamus sample 1

description:
Library name: RNAseq_12hrRefeed_1
RNA-seq on mouse hypothalamus in different metabolic states
refeed_1h12h1wk_19727_20058_CountsEnsFeb2023.txt
12hrRFvs1wRF_EdgeR.txt

value: Refed 12 hours


title: 3'SL, Initial experiment 2

description: Library name: 126


title: 3'SL, Initial experiment 6

description: Library name: 130


title: OSCC_denovo_Sample8

city: Bengaluru

first: Sukeerthi

last: Dasharathy

state: Karnataka

address: FMC building, Ramaiah University of Applied Sciences, New BEL Road

department: Biotechnology

country: India

institute: Ramaiah University of Applied Sciences

description: Library name: Sample13

data_processing:
RNA sequence data were acquired utilizing the Illumina Novoseq platform.
Assembly: UCSC hg19
Supplementary files format and content: Tab-delimited text files containing gene-level normalized expression counts and differential gene expression analysis results generated using DESeq2.

source_name: Left buccal mucosa

extract_protocol:
Total RNA extraction from the chosen samples was conducted employing the Isol+Qiagen RNeasy Mini Kit in accordance with the manufacturer's protocol (Invitrogen).
RNA sequencing libraries were meticulously prepared utilizing the Illumina-compatible NEXTflex Rapid Directional RNA-Seq Kit (BIOO Scientific, Austin, Texas).

value: Left buccal mucosa

value: Denovo OSCC


title: 12 hour Refed after 72h fast B6 Mouse Hypothalamus sample 2

description:
Library name: RNAseq_12hrRefeed_2
RNA-seq on mouse hypothalamus in different metabolic states
refeed_1h12h1wk_19727_20058_CountsEnsFeb2023.txt
12hrRFvs1wRF_EdgeR.txt


title: K562 cells, no doxycycline induction, KMT2A antibody, rep1

description: Library name: K562_noDOX_KMT2A_1

value: myeloid leukemia cell line

value: No doxycycline induction

value: KMT2A (Cell Signaling Technology, 14689)

value: GRCh38 (hg38)


title: 3'SL, Initial experiment 1

description: Library name: 125

value: 3'SL, Initial experiment


title: GFPb2_2.5h_rep2_ATACseq

description:
Library name: g150_2_QKDO240001002-1A_22HVHJLT4_L1
GFPb2_2.5h_REP2.mLb.clN.sorted.bam

value: hiPSCs


title: Control diet, no infection 6

description: Library name: 30

value: Control diet, no infection


title: OSCC_denovo_Sample6

description: Library name: Sample11

source_name: Right buccal mucosa and alveolus

value: Right buccal mucosa and alveolus


title: 1 week of refeeding after a 72 hour fast 3

description:
Library name: RNAseq_1WkRefeed_Hypo2
RNA-seq on mouse hypothalamus in different metabolic states
refeed_1h12h1wk_19727_20058_CountsEnsFeb2023.txt
1wkRFvsFed_EdgeR.txt

value: Hypothalamus

value: WT

value: Refed 1 week


title: K562 cells, doxycycline-induced, KMT2A antibody, rep3

description: Library name: K562_DOX250ng_KMT2A_3

value: Doxycycline 250ng/mL induction for 24 hours


title: 1 week of refeeding after a 72 hour fast 1

description:
Library name: RNAseq_1WkRefeed_Hypo1
RNA-seq on mouse hypothalamus in different metabolic states
refeed_1h12h1wk_19727_20058_CountsEnsFeb2023.txt
1wkRFvsFed_EdgeR.txt


title: GFPb2_1.5h_rep1_ATACseq

description:
Library name: g90_1_QKDO240000995-1A_22HVHJLT4_L1
GFPb2_1.5h_REP1.mLb.clN.sorted.bam


title: 3'SL, Initial experiment 3

description: Library name: 127

value: Caecum


title: 24 hour fasted B6 Mouse Hypothalamus sample 2

description:
Library name: RNAseq_1CR2
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
Fedvs24hrFD_EdgeR.txt

value: 24h Fasted


title: GFPb2_1h_rep3_ATACseq

description:
Library name: g60_3_QKDO240000994-1A_22HVHJLT4_L1
GFPb2_1h_REP3.mLb.clN.sorted.bam


title: 24 hour fasted B6 Mouse Hypothalamus sample 1

description:
Library name: RNAseq_1CR1
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
Fedvs24hrFD_EdgeR.txt


title: OSCC_denovo_Sample5

description: Library name: Sample10

source_name: Right buccal mucosa

value: Right buccal mucosa


title: OSCC_denovo_Sample3

description: Library name: Sample8

source_name: Left buccal mucosa and alveolus

value: Left buccal mucosa and alveolus


title: Control diet, no infection 3

description: Library name: 27


title: K562 cells, doxycycline-induced, KMT2A antibody, rep1

description: Library name: K562_DOX250ng_KMT2A_1


title: Control diet, no infection 2

description: Library name: 26


title: OSCC_denovo_Sample2

description: Library name: Sample7

value: Denovo OSCC


title: Control diet, no infection 1

description: Library name: 25


title: 1 hour Refed after 72h fast B6 Mouse Hypothalamus sample 1

description:
Library name: RNAseq_1hrRefeed_1
RNA-seq on mouse hypothalamus in different metabolic states
refeed_1h12h1wk_19727_20058_CountsEnsFeb2023.txt
1hrRFvs12hrRF_EdgeR.txt

value: Refed 1 hour


title: OSCC_denovo_Sample7

description: Library name: Sample12

value: Left buccal mucosa


title: GFPb2_2h_rep1_ATACseq

description:
Library name: g120_1_QKDO240000998-1A_22HVHJLT4_L1
GFPb2_2h_REP1.mLb.clN.sorted.bam


title: GFPb2_1.5h_rep3_ATACseq

description:
Library name: g90_3_QKDO240000997-1A_22HVHJLT4_L1
GFPb2_1.5h_REP3.mLb.clN.sorted.bam


title: Control diet, Tm infection 6

description: Library name: 24

value: Control diet, Tm infection


title: 12 hour Refed after 72h fast B6 Mouse Hypothalamus sample 3

description:
Library name: RNAseq_12hrRefeed_3
RNA-seq on mouse hypothalamus in different metabolic states
refeed_1h12h1wk_19727_20058_CountsEnsFeb2023.txt
12hrRFvs1wRF_EdgeR.txt

value: Refed 12 hours


title: GFPb2_1.5h_rep2_ATACseq

description:
Library name: g90_2_QKDO240000996-1A_22HVHJLT4_L1
GFPb2_1.5h_REP2.mLb.clN.sorted.bam


title: Control diet, no infection 5

description: Library name: 29


title: OSCC_denovo_Sample1

description: Library name: Sample6

source_name: Left gingivobuccal sulcus

value: Left gingivobuccal sulcus


title: Control diet, Tm infection 5

description: Library name: 23


title: GFPb2_0.5h_rep1_ATACseq

description:
Library name: g30_1_QKDO240000989-1A_22HVHJLT4_L1
GFPb2_0.5h_REP1.mLb.clN.sorted.bam

value: hiPSCs


title: GFPb2_0.5h_rep3_ATACseq

description:
Library name: g30_3_QKDO240000991-1A_22HVHJLT4_L1
GFPb2_0.5h_REP3.mLb.clN.sorted.bam


title: 1 month Refed after 72h fast B6 Mouse Hypothalamus sample 2

description:
Library name: RNAseq_1Mo_RNA_2
RNA-seq on mouse hypothalamus in different metabolic states
Refed1mo_24442R_HypothalamusCountsEns_Sept2024.txt
1monthRFvsFed_EdgeR.txt

value: 1 month refed


title: GFPb2_1h_rep2_ATACseq

description:
Library name: g60_2_QKDO240000993-1A_22HVHJLT4_L1
GFPb2_1h_REP2.mLb.clN.sorted.bam


title: Control diet, no infection 4

description: Library name: 28

value: Control diet, no infection


title: OSCC_denovo_Sample4

description: Library name: Sample9

source_name: Right gigivobuccal sulcus

value: Right gigivobuccal sulcus


title: OSMF_OSCC_Sample3

description: Library name: Sample3

value: OSMF to OSCC


title: 1 month Refed after 72h fast B6 Mouse Hypothalamus sample 4

description:
Library name: RNAseq_1Mo_RNA_4
RNA-seq on mouse hypothalamus in different metabolic states
Refed1mo_24442R_HypothalamusCountsEns_Sept2024.txt
1monthRFvsFed_EdgeR.txt

value: Hypothalamus

value: WT


title: GFPb2_1h_rep1_ATACseq

description:
Library name: g60_1_QKDO240000992-1A_22HVHJLT4_L1
GFPb2_1h_REP1.mLb.clN.sorted.bam


title: 24 hour fasted B6 Mouse Hypothalamus sample 3

description:
Library name: RNAseq_1CR3
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
Fedvs24hrFD_EdgeR.txt


title: 1 hour Refed after 72h fast B6 Mouse Hypothalamus sample 2

description:
Library name: RNAseq_1hrRefeed_2
RNA-seq on mouse hypothalamus in different metabolic states
refeed_1h12h1wk_19727_20058_CountsEnsFeb2023.txt
1hrRFvs12hrRF_EdgeR.txt


title: GFPb2_0h_rep2_ATACseq

description:
Library name: g0_2_QKDO240000987-1A_22HVHJLT4_L1
GFPb2_0h_REP2.mLb.clN.sorted.bam


title: Control diet, Tm infection 2

description: Library name: 20

value: Caecum


title: GFPb2_0h_rep1_ATACseq

description:
Library name: g0_1_QKDO240000986-1A_22J7J5LT4_L4
GFPb2_0h_REP1.mLb.clN.sorted.bam


title: 1 hour Refed after 72h fast B6 Mouse Hypothalamus sample 3

description:
Library name: RNAseq_1hrRefeed_3
RNA-seq on mouse hypothalamus in different metabolic states
refeed_1h12h1wk_19727_20058_CountsEnsFeb2023.txt
1hrRFvs12hrRF_EdgeR.txt


title: GFPb2_0.5h_rep2_ATACseq

description:
Library name: g30_2_QKDO240000990-1A_22HVHJLT4_L1
GFPb2_0.5h_REP2.mLb.clN.sorted.bam


title: GFPb1_2.5h_rep3_ATACseq

description:
Library name: g150-3
GFPb1_2.5h_REP3.mLb.clN.sorted.bam


title: OSMF_OSCC_Sample4

description: Library name: Sample4


title: OSMF_OSCC_Sample5

description: Library name: Sample5


title: 3'SL, Tm infection 6

description: Library name: 12

value: 3'SL, Tm infection


title: OSMF_OSCC_Sample1

description: Library name: Sample1

source_name: Right lateral border of tongue

value: Right lateral border of tongue


title: Control diet, Tm infection 4

description: Library name: 22


title: GFPb2_0h_rep3_ATACseq

description:
Library name: g0_3_QKDO240000988-1A_22HVHJLT4_L1
GFPb2_0h_REP3.mLb.clN.sorted.bam


title: OSMF_OSCC_Sample2

description: Library name: Sample2

value: Right buccal mucosa


title: Control diet, Tm infection 3

description: Library name: 21


title: 3'SL, Tm infection 5

description: Library name: 11


title: 1 month Refed after 72h fast B6 Mouse Hypothalamus sample 1

description:
Library name: RNAseq_1Mo_RNA_1
RNA-seq on mouse hypothalamus in different metabolic states
Refed1mo_24442R_HypothalamusCountsEns_Sept2024.txt
1monthRFvsFed_EdgeR.txt


title: 1 month Refed after 72h fast B6 Mouse Hypothalamus sample 5

description:
Library name: RNAseq_1Mo_RNA_5
RNA-seq on mouse hypothalamus in different metabolic states
Refed1mo_24442R_HypothalamusCountsEns_Sept2024.txt
1monthRFvsFed_EdgeR.txt


title: Control diet, Tm infection 1

description: Library name: 19


title: 72 hour fasted B6 Mouse Hypothalamus sample 1

description:
Library name: RNAseq_3CR1
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
24hrFDvs72hrFD_EdgeR.txt


title: 72 hour fasted B6 Mouse Hypothalamus sample 2

description:
Library name: RNAseq_3CR2
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
24hrFDvs72hrFD_EdgeR.txt


title: HPR042

city: Denver

first: Evans

last: Fernandez

address: 1400 Jackson St.

institute: National Jewish

description:
Library name: HPR042
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files compressed with gzip
Supplementary files format and content: Integrated Seurat object

source_name: PBMC

extract_protocol:
Single-cell suspensions were prepared from peripheral blood mononuclear cell samples following standard dissociation and filtration protocols to obtain high-quality, viable cells. Cell viability was confirmed to be greater than 85% using trypan blue exclusion. The concentration of each sample was adjusted to approximately 1,500–2,000 cells/µL to achieve the recommended target of up to 5,000 cells per sample for on-chip multiplexing using the 10x Genomics Chromium platform. Prior to loading, samples were inspected under a microscope to ensure the absence of debris and cell aggregates.
Following the recovery of the Gel Beads-In-Emulsions, the emulsions were broken, and barcoded complementary deoxyribonucleic acid was purified and amplified using the 10x Genomics GEM-X Universal Library Construction Kit. For on-chip multiplexing, each reaction was limited to approximately 5,000 cells per sample, ensuring comparable cell input and ribonucleic acid content across all multiplexed samples. Libraries were dual-indexed, pooled, and sequenced on an Illumina NextSeq 2000. Sequencing depth was adjusted to achieve approximately 20,000 reads per cell, depending on experimental design and transcriptome complexity.

value: PBMC

tag: phenotype

value: HP

value: Male

tag: race

value: White

tag: ethnicity

value: NotHispanicOrLatino

tag: age


title: PLC-M0

city: Hefei,

first: Xu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

description:
Library name: sample1
RNA-seq

library_source: other

data_processing:
For mecciRNA identification, the clean data were filtered by bowtie2 (v 1.2.1) to remove reads mapped to rDNA. The left reads were mapped to the reference genome by bwa-men (v 0.7.17). The discontinuously mapped reads were extracted and mapped again to mitochondrial genome by bowtie (v 1.2.1). mecciRNA candidates were predicted by pepline mentioned in our article.
Assembly: hg38, mm10,
Supplementary files format and content: comma-separated value files include count values for each Sample

molecule: other

source_name: PLC

extract_protocol:
The Isolated mitochondria and whole cells were lysed in TRIzol reagent (Life Technologies). RNA from mitochondria and whole cells was extracted using TRIzol reagent according to the manufacturer’s instructions.
For total RNA and mitochondrial RNA sequencing, rRNA is removed from the total RNA sample using TruSeq Stranded Total RNA Library Prep Gold (Illumina), and sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommendations. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.

value: PLC

tag: cell type

value: human hepatocellular carcinoma cell line

tag: genotype


title: GFPb1_2.5h_rep2_ATACseq

state: CO

description:
Library name: g150-2
GFPb1_2.5h_REP2.mLb.clN.sorted.bam

source_name: hiPSCs

value: hiPSCs


title: HPR040

description:
Library name: HPR040
10x Genomics

tag: Sex

value: Female

value: HispanicOrLatino


title: GFPb1_2h_rep3_ATACseq

description:
Library name: g120-3
GFPb1_2h_REP3.mLb.clN.sorted.bam


title: 72 hour fasted B6 Mouse Hypothalamus sample 3

description:
Library name: RNAseq_3CR3
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
24hrFDvs72hrFD_EdgeR.txt

tag: treatment

tag: batch


title: 72 hour fasted + cold B6 Mouse Hypothalamus sample 2

description:
Library name: RNAseq_3CRC2
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
72hrFDvs72hrFD_cold_EdgeR.txt

value: 72h Fasted + Cold


title: GFPb1_2h_rep2_ATACseq

description:
Library name: g120-2
GFPb1_2h_REP2.mLb.clN.sorted.bam


title: HPR038

description:
Library name: HPR038
10x Genomics


title: 72 hour fasted + cold B6 Mouse Hypothalamus sample 1

description:
Library name: RNAseq_3CRC1
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
72hrFDvs72hrFD_cold_EdgeR.txt

value: Hypothalamus


title: 72 hour fasted + cold B6 Mouse Hypothalamus sample 3

description:
Library name: RNAseq_3CRC3
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
72hrFDvs72hrFD_cold_EdgeR.txt

value: WT


title: HPR039

description:
Library name: HPR039
10x Genomics


title: 3'SL, Tm infection 2

description: Library name: 8

value: Caecum


title: HPR037

description:
Library name: HPR037
10x Genomics


title: 3'SL, Tm infection 4

description: Library name: 10

value: 3'SL, Tm infection


title: Fed B6 mouse hypothalamus sample 1

description:
Library name: RNAseq_Ctrl1
RNA-seq on mouse hypothalamus in different metabolic states
HungryHypothalamusCountsEns001_Feb2023.txt
Fedvs24hrFD_EdgeR.txt

value: Fed


title: GFPb1_2h_rep1_ATACseq

description:
Library name: g120-1
GFPb1_2h_REP1.mLb.clN.sorted.bam


title: 3'SL, Tm infection 3

description: Library name: 9


title: HPR036

description:
Library name: HPR036
10x Genomics


title: 3'SL, Tm infection 1

description: Library name: 7


title: GFPb1_1.5h_rep2_ATACseq

description:
Library name: g90-2
GFPb1_1.5h_REP2.mLb.clN.sorted.bam


title: HPR035

description:
Library name: HPR035
10x Genomics


title: GFPb1_2.5h_rep1_ATACseq

description:
Library name: g150-1
GFPb1_2.5h_REP1.mLb.clN.sorted.bam


title: GFPb1_1.5h_rep3_ATACseq

description:
Library name: g90-3
GFPb1_1.5h_REP3.mLb.clN.sorted.bam


title: HPR034

description:
Library name: HPR034
10x Genomics