title: DAD7

description: Library name: SAMPLE 7


title: Midostaurin post-treatment

status: Public on Nov 13 2025

type: SRA

city: Helsinki

first: Li

last: Shen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: Midostaurin post-treatment
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Cell quality control was performed using Seurat v4.0.4 (https://satijalab.org/seurat/)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files for cell annotation and matrix for UMI counts

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Cells were resuspended in PBS + 0.04% BSA buffer.
Libraries were generated with 10x Genomics’ Chromium Next GEM Single Cell 3' Kit v3.1, Chromium Next GEM Chip G Single Cell Kit, and Dual Index Kit TT Set A according to the manufacturer’s instructions.

tag: tissue

value: peripheral blood

tag: cell line

tag: cell type

value: acute myeloid leukemia

tag: genotype

value: midostaurin


title: DAD1

city: Wuhan

first: Yifei

last: Wang

address: Baofeng street

country: China

institute: Huazhong University of Science and Technology

description: Library name: SAMPLE 1

library_source: transcriptomic

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000  platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Assembly: the reference genome  using HISAT2
Supplementary files format and content: FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count

source_name: blood

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: blood

value: mononuclear cell

tag: condition

value: DAD


title: Midostaurin pre-treatment

description:
Library name: Midostaurin pre-treatment
10x Genomics

value: pre-treatment


title: RNA-seq of B7H3-CAR T cells from healthy human donor 3, no TGFb

city: Stanford

first: Yiyun

last: Chen

state: California

address: 265 Campus Dr Room G2105

department: Stanford Cancer Institute

country: USA

institute: Stanford University

description: Library name: B7H3_noTGFb_Donor3

data_processing:
Bulk RNAseq was performed by Novogene using the NovaSeq platform. The raw RNA sequencing data was mapped to human reference genome hg38 using the STAR aligner, and genes annotated in Gencode v36 was quantified using featurecounts in the subread package.
Assembly: hg38
Supplementary files format and content: count and TPM matrices

source_name: T cells

extract_protocol:
CAR T cells were derived from the plate-bound stimulation assay described above and collected after ~20 hours of incubation. Cells were counted to ensure a maximum number of 500000 per sample.
Next, cell pellets were obtained after centrifugation and processed using the Qiagen RNeasy Micro kit and following the manufacturer’s protocol.

value: T cells

tag: treatment

value: no TGFb


title: Quizartinib post-treatment

description:
Library name: Quizartinib post-treatment
10x Genomics

value: quizartinib


title: Quizartinib pre-treatment

description:
Library name: Quizartinib pre-treatment
10x Genomics


title: Control post-treatment

description:
Library name: Control post-treatment
10x Genomics

value: DMSO


title: Control pre-treatment

description:
Library name: Control pre-treatment
10x Genomics


title: NAD3

description: Library name: SAMPLE 11

value: NAD


title: GFP-progerin,+Dox 6 days, R2, cell.line

city: Bethesda

first: Sandra

last: Vidak

state: MD

address: 9000 Rockville Pike

institute: NIH

description: Library name: Dox6dpt2

data_processing:
Basecalls were performed using bcl2fastq v2.20 for NovaSeq 6000 S4 output.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt 1.18 with parameter options --nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35
Trimmed sequence reads were mapped to hg38 genome using STAR 2.7.0f combined with the GENCODE_30 annotation
Raw tag counts were obtained using featureCounts in subread 2.0.3 with parameter options:-s 2 -t exon -g gene_name --countReadPairs
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts of all samples

source_name: TetON GFP-progerin

growth_protocol: Primary human fibroblasts were grown in high glucose DMEM containing 15% fetal bovine serum (FBS), 1% GlutaMAX and 1% Penicillin-Streptomycin  at 37 °C in 5% CO2. hTERT-immortalized TetON GFP-progerin doxycycline inducible dermal fibroblast cell lines were grown in high glucose DMEM containing 15% fetal bovine serum (FBS), 1% GlutaMAX and 1% Penicillin-Streptomycin  at 37 °C in 5% CO2.

extract_protocol:
RNA was extracted using NucleoSpin RNA Kit (Takara Bio) according to manufacturer instructions.
Libraries were constructed according to the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

treatment_protocol: hTERT-immortalized TetON GFP-progerin doxycycline inducible dermal fibroblast cell line was induced for 6 days with 1ug/ul doxycycline.

value: TetON GFP-progerin

value: Immortalized fibroblasts

value: GFP-progerin


title: GFP-progerin,+Dox 6 days, R1, cell.line

description: Library name: Dox6dpt1


title: GFP-progerin, -Dox, R3, cell.line

description: Library name: noDoxUpt3

value: -Dox


title: GFP-progerin, -Dox, R2, cell.line

description: Library name: noDoxUpt2


title: GFP-progerin,+Dox 6 days, R3, cell.line

description: Library name: Dox6dpt3


title: GFP-progerin, -Dox, R1, cell.line

description: Library name: noDoxUpt1


title: AG10578, R3, Coriell

description: Library name: HGPS20pt3

value: Primary fibroblasts

value: HGPS

tag: biomaterial provider


title: AG10578, R2, Coriell

description: Library name: HGPS20pt2


title: AG11572, R2, Coriell

description: Library name: HGPS19pt2


title: AG11572, R3, Coriell

description: Library name: HGPS19pt3


title: AG11572, R1, Coriell

description: Library name: HGPS19pt1


title: AG10578, R1, Coriell

description: Library name: HGPS20pt1


title: AG11498, R3, Coriell

description: Library name: HGPS18pt3


title: AG11498, R2, Coriell

description: Library name: HGPS18pt2


title: AG08466, R3, Coriell

description: Library name: HGPS17pt3


title: AG08466, R2, Coriell

description: Library name: HGPS17pt2


title: AG06917, R3, Coriell

description: Library name: HGPS16pt3


title: AG06917, R2, Coriell

description: Library name: HGPS16pt2


title: AG06917, R1, Coriell

description: Library name: HGPS16pt1


title: AG11498, R1, Coriell

description: Library name: HGPS18pt1


title: AG06297, R2, Coriell

description: Library name: HGPS15pt2


title: AG06297, R3, Coriell

description: Library name: HGPS15pt3


title: AG06297, R1, Coriell

description: Library name: HGPS15pt1


title: GM01972D, R2, Coriell

description: Library name: HGPS14pt2


title: GM01972D, R3, Coriell

description: Library name: HGPS14pt3


title: GM01972D, R1, Coriell

description: Library name: HGPS14pt1


title: GM01178, R3, Coriell

description: Library name: HGPS13pt3


title: GM01178, R2, Coriell

description: Library name: HGPS13pt2


title: GM01178, R1, Coriell

description: Library name: HGPS13pt1


title: HGADFN271, R2, PRF

description: Library name: HGPS11pt2


title: HGADFN271, R1, PRF

description: Library name: HGPS11pt1


title: HGADFN367, R3, PRF

description: Library name: HGPS12pt3


title: HGADFN188, R3, PRF

description: Library name: HGPS10pt3


title: HGADFN188, R1, PRF

description: Library name: HGPS10pt1


title: HGADFN367, R2, PRF

description: Library name: HGPS12pt2


title: HGADFN178, R1, PRF

description: Library name: HGPS9pt1


title: HGADFN271, R3, PRF

description: Library name: HGPS11pt3


title: HGADFN178, R3, PRF

description: Library name: HGPS9pt3


title: HGADFN169, R3, PRF

description: Library name: HGPS8pt3


title: HGADFN178, R2, PRF

description: Library name: HGPS9pt2


title: HGADFN169, R1, PRF

description: Library name: HGPS8pt1


title: HGADFN167, R2, PRF

description: Library name: HGPS7pt2


title: AG08466, R1, Coriell

description: Library name: HGPS17pt1


title: HGADFN167, R1, PRF

description: Library name: HGPS7pt1


title: HGADFN169, R2, PRF

description: Library name: HGPS8pt2


title: HGADFN164, R3, PRF

description: Library name: HGPS6pt3


title: HGADFN167, R3, PRF

description: Library name: HGPS7pt3


title: HGADFN164, R2, PRF

description: Library name: HGPS6pt2


title: HGADFN143, R3, PRF

description: Library name: HGPS5pt3


title: HGADFN164, R1, PRF

description: Library name: HGPS6pt1


title: HGADFN143, R2, PRF

description: Library name: HGPS5pt2


title: HGADFN143, R1, PRF

description: Library name: HGPS5pt1


title: HGADFN155, R3, PRF

description: Library name: HGPS4pt3


title: HGADFN127, R3, PRF

description: Library name: HGPS3pt3


title: HGADFN155, R1, PRF

description: Library name: HGPS4pt1


title: HGADFN155, R2, PRF

description: Library name: HGPS4pt2


title: HGADFN367, R1, PRF

description: Library name: HGPS12pt1


title: HGADFN188, R2, PRF

description: Library name: HGPS10pt2


title: HGADFN127, R2, PRF

description: Library name: HGPS3pt2


title: HGADFN127, R1, PRF

description: Library name: HGPS3pt1


title: HGADFN122, R3, PRF

description: Library name: HGPS2pt3


title: HGADFN122, R1, PRF

description: Library name: HGPS2pt1


title: HGADFN003, R3, PRF

description: Library name: HGPS1pt3


title: HGADFN003, R2, PRF

description: Library name: HGPS1pt2


title: AG09860, R2, Coriell

description: Library name: WT10pt2

value: WT


title: HGADFN003, R1, PRF

description: Library name: HGPS1pt1


title: AG09860, R3, Coriell

description: Library name: WT10pt3


title: AG09860, R1, Coriell

description: Library name: WT10pt1


title: HGADFN122, R2, PRF

description: Library name: HGPS2pt2


title: AG08470, R2, Coriell

description: Library name: WT9pt2


title: AG08470, R3, Coriell

description: Library name: WT9pt3


title: GM02036, R2, Coriell

description: Library name: WT8pt2


title: GM02036, R3, Coriell

description: Library name: WT8pt3


title: GM02036, R1, Coriell

description: Library name: WT8pt1


title: HGMDFN718, R3, PRF

description: Library name: WT6pt3


title: GM00038, R1, Coriell

description: Library name: WT7pt1


title: HGMDFN718, R2, PRF

description: Library name: WT6pt2


title: HGMDFN718, R1, PRF

description: Library name: WT6pt1


title: HGMDFN369, R2, PRF

description: Library name: WT4pt2


title: HGMDFN369, R1, PRF

description: Library name: WT4pt1


title: HGMDFN368, R3, PRF

description: Library name: WT3pt3


title: HGMDFN369, R3, PRF

description: Library name: WT4pt3


title: HGMDFN368, R2, PRF

description: Library name: WT3pt2


title: HGMDFN717, R1, PRF

description: Library name: WT5pt1


title: GM00038, R3, Coriell

description: Library name: WT7pt3


title: GM00038, R2, Coriell

description: Library name: WT7pt2


title: HGMDFN717, R2, PRF

description: Library name: WT5pt2


title: HGMDFN368, R1, PRF

description: Library name: WT3pt1


title: HGMDFN168, R3, PRF

description: Library name: WT2pt3


title: HGMDFN168, R1, PRF

description: Library name: WT2pt1


title: HGMDFN090, R3, PRF

description: Library name: WT1pt3


title: HGMDFN090, R2, PRF

description: Library name: WT1pt2


title: AG08470, R1, Coriell

description: Library name: WT9pt1


title: HGMDFN090, R1, PRF

description: Library name: WT1pt1


title: s94-nonemphysematous-copd

city: Houston

first: Francesca

last: POlVERINO

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: UA 26

data_processing:
Fastq data was processed using CellRanger v8 (10xGenomics)
Assembly: Human reference (GRCh38) - 2024-A
Supplementary files format and content: Hierarchical Data Format (HDF5 or H5) containing count matrix, features/genes, cell-barcodes

source_name: Lung

extract_protocol:
Cryopreserved lung samples were used for preparation of single cell RNA sequencing library construction. RNA extraction was performed following recommended protocol of the Chromium Next GEM Single Cell 5’ Reagent Kits v2, R2-only (10xGenomics)
Library construction was performed following recommended protocol of the Chromium Next GEM Single Cell 5’ Reagent Kits v2, R2-only (10xGenomics)

value: Lung

tag: subject group

value: patients with nonemphysematous COPD

tag: subject identity

tag: lab id

value: UA 26

tag: steroidstype

value: ICS

tag: smoke

value: Never

tag: gold

value: GOLD 2

tag: age

tag: Sex

value: F

tag: copd

value: COPD

tag: quitdate

tag: steroids

value: TRUE

tag: lobe

value: RUL

tag: lobe emphysema_severity_laa%

tag: lobe emphysema

value: NE-COPD

tag: packyear


title: s90-nonemphysematous-copd

description: Library name: UA 53

tag: tissue

value: UA 53

value: Current

value: M

value: FALSE

value: LLL


title: s83-nonemphysematous-copd

description: Library name: UA 28

value: UA 28


title: s57-nonemphysematous-copd

description: Library name: UA 94

value: Lung

value: UA 94

value: ICS+OCS


title: s62-nonemphysematous-copd

description: Library name: UA 5

value: patients with nonemphysematous COPD

value: UA 5


title: s4-nonemphysematous-copd

description: Library name: UA 38

value: UA 38

value: Former

value: GOLD 2

value: RLL


title: s88-nonemphysematous-copd

description: Library name: UA 50

value: UA 50

value: GOLD 1

value: F

value: COPD

value: RUL


title: HGMDFN717, R3, PRF

description: Library name: WT5pt3

tag: cell line

tag: cell type

value: Primary fibroblasts

tag: genotype

value: WT


title: s60-nonemphysematous-copd

description: Library name: UA 95

tag: subject group

tag: subject identity

tag: lab id

value: UA 95

value: FALSE

value: NE-COPD


title: s59-nonemphysematous-copd

description: Library name: UA 44/102

value: Lung

tag: steroidstype

tag: smoke

tag: gold


title: s95-nonemphysematous-copd

description: Library name: UA 37

value: patients with nonemphysematous COPD

value: UA 37

value: Current

value: GOLD 0

tag: age

tag: Sex

value: M

tag: copd


title: s49-nonemphysematous-copd

description: Library name: UA 72

value: UA 72

tag: quitdate

tag: steroids

tag: lobe


title: HGMDFN168, R2, PRF

description: Library name: WT2pt2


title: s7-nonemphysematous-copd

description: Library name: UA 44

value: UA 44

value: Former

tag: lobe emphysema_severity_laa%

tag: lobe emphysema

tag: packyear


title: s51-nonemphysematous-copd

description: Library name: UA 70

tag: tissue

value: UA 70

value: LLL


title: s73-nonemphysematous-copd

description: Library name: UA 58

value: UA 58

value: COPD

value: LUL


title: s52-nonemphysematous-copd

description: Library name: UA 73

value: UA 73

value: OCS

value: GOLD 1

value: RLL


title: s85-control

description: Library name: UA 32

value: Lung

value: patients with no history of COPD

value: UA 32

value: Control

value: F

value: FALSE


title: s58-nonemphysematous-copd

description: Library name: UA 100

value: patients with nonemphysematous COPD

value: GOLD 2

value: M

value: NE-COPD


title: s55-nonemphysematous-copd

description: Library name: UA 96

value: UA 96

value: Former


title: s87-control

description: Library name: UA 36

value: UA 36

value: Current

value: RUL


title: s84-control

description: Library name: UA 30

value: UA 30

value: Never

value: LLL


title: s71-control

description: Library name: UA 39

value: Lung

value: patients with no history of COPD

value: UA 39

value: LUL


title: s8-nonemphysematous-copd

description: Library name: UA 48

value: UA 48

value: COPD

value: FALSE


title: s75-control

description: Library name: UA 42

value: UA 42

value: Control

value: M

value: RLL


title: s82-control

description: Library name: UA 27

value: UA 27

value: Former


title: s56-nonemphysematous-copd

description: Library name: UA 90

value: patients with nonemphysematous COPD

value: UA 90

value: Current

value: GOLD 2

value: F

value: RUL

value: NE-COPD


title: s68-control

description: Library name: UA 60

value: Lung

value: patients with no history of COPD

value: UA 60


title: s5-nonemphysematous-copd

description: Library name: UA 41

value: UA 41

value: GOLD 0

value: COPD

value: FALSE


title: s72-control

description: Library name: UA 56

value: UA 56

value: Never

value: Control

value: LLL


title: s66-nonemphysematous-copd

description: Library name: UA 64

value: patients with nonemphysematous COPD

value: UA 64

value: Former

value: M

value: LUL


title: s64-control

description: Library name: UA 66

value: UA 66

value: Current

value: F

value: RUL


title: s65-control

description: Library name: UA 65

value: Lung

value: patients with no history of COPD

value: UA 65


title: s70-control

description: Library name: UA 35

value: UA 35

value: FALSE


title: s63-control

description: Library name: UA 61

value: UA 61

value: RLL


title: s6-control

description: Library name: UA 43

value: UA 43

value: Control

value: RML


title: s53-control

description: Library name: UA 74

value: UA 74

value: Former


title: s50-control

description: Library name: UA 69

value: UA 69


title: s22-control

description: Library name: DNAZ 4 RML

value: DNAZ 4 RML

value: Never

value: M


title: s89-control

description: Library name: Ua 51

value: Ua 51

value: ICS

value: F

value: TRUE

value: LUL


title: s91-control

description: Library name: UA 59

value: Lung

value: patients with no history of COPD

value: UA 59

value: OCS

value: FALSE

value: RUL


title: s20-control

description: Library name: DNAZ 7 LLL

value: DNAZ 7 LLL

value: Control

value: LLL


title: s92-nonemphysematous-copd

description: Library name: UA 46

value: patients with nonemphysematous COPD

value: UA 46

value: Former

value: GOLD 0

value: COPD

value: NE-COPD


title: s19-control

description: Library name: DNAZ 6 LUL

value: DNAZ 6 LUL

value: Never

value: M


title: s18-control

description: Library name: DNAZ 5 LUL

value: Lung

value: patients with no history of COPD

value: DNAZ 5 LUL

value: ICS

value: F

value: LUL


title: s69-control

description: Library name: UA 16

value: UA 16

value: Control

value: FALSE

value: RUL


title: s16-control

description: Library name: DNAZ 2 LUL

value: DNAZ 2 LUL


title: s13-control

description: Library name: DNAZ 4 RLL

value: DNAZ 4 RLL

value: RLL


title: s14-control

description: Library name: DNAZ 6 LLL

value: DNAZ 6 LLL

value: LLL


title: s12-control

description: Library name: DNAZ 1 LLL

value: DNAZ 1 LLL

value: Never


title: s93-emphysematous-copd

description: Library name: COPD 10 LLL

value: Lung

value: patients with emphysematous COPD

value: COPD 10 LLL

value: Former

value: GOLD 4

value: M

value: COPD

value: TRUE

value: E-COPD


title: s9-emphysematous-copd

description: Library name: COPD 4 RUL

value: COPD 4 RUL

value: OCS

value: FALSE

value: RUL


title: s79-emphysematous-copd

description: Library name: COPD8 LLL

value: COPD8 LLL

value: ICS

value: November


title: s81-emphysematous-copd

description: Library name: COPD7 LUL

value: COPD7 LUL

value: ICS+OCS

value: F

value: LUL


title: s78-emphysematous-copd

description: Library name: COPD 6 LLL

value: Lung

value: patients with emphysematous COPD

value: COPD 6 LLL

value: Former

value: LLL


title: s76-emphysematous-copd

description: Library name: COPD 2 RUL

value: COPD 2 RUL

value: GOLD 4

value: M

value: COPD

value: TRUE

value: E-COPD


title: s3-emphysematous-copd

description: Library name: COPD 3 RUL

value: COPD 3 RUL

value: RUL


title: s23-emphysematous-copd

description: Library name: COPD 5 RLL

value: COPD 5 RLL

value: ICS

value: RLL


title: s2-emphysematous-copd

description: Library name: COPD 8 LUL

value: COPD 8 LUL

value: November

value: LUL


title: s11-emphysematous-copd

description: Library name: COPD 10 LUL

value: Lung

value: patients with emphysematous COPD

value: COPD 10 LUL


title: s10-emphysematous-copd

description: Library name: COPD 6 LUL

value: COPD 6 LUL

value: Former

value: F

value: FALSE


title: s21-control

description: Library name: DNAZ 1 LUL

value: patients with no history of COPD

value: DNAZ 1 LUL

value: Never

value: Control

value: M


title: s74-emphysematous-copd

description: Library name: UA 45

value: UA 45

value: GOLD 1

value: COPD

value: E-COPD


title: Rv1, control, SMARCA1, rep2

city: Baltimore

first: Jianfei

last: Qi

address: 655W baltimore street

department: Biochemistry and Molecular Biology

institute: University of Maryland

description: Library name: Rv1-pLKO.1-SMARCA1-rep2

library_source: genomic

data_processing:
Quality of CUT&RUN ChIP-seq read were checked with fastqc
Reads were trimmed from 3' end until the final base had a quality score > 28, using trimgalore v0.6.6
Reads were aligned to the UCSC human hg19 reference genome and E. coli K12, MG1655 reference genome using Bowtie2 v2.3.5.1. If one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant (--dovetail)
Samples were normalized compare do total reads counts, and BAM files were processed (remove duplicates, sorting, and indexing) using samtools v1.10 and Picard v2.23.9
Processed Bam files were normalized with spike-in normalization method and formatted in the bigWig and bedgraph file format, using Deeptools v3.5.0
Assembly: Peaks were called uing MACS2 bdgpeakcall v2.2.6 with the significance cut-off p-value <=0.01 and reproducible peaks were generaged from two replicated peaks using IDR v2.0.4.2
Supplementary files format and content: hg19, K12 MG1655
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

growth_protocol: Cells were maintained in RPMI 1640 media supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were incubated at 37C and 5% CO2.

extract_protocol:
Cell nuclei were extracted using nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1 % Triton X-100, 20% glycerol, 1X protease cocktail) and incubated with ConA Beads to absorb nuclei to beads for 10 min at RT. The nuclei-beads were placed in magnet and the supernatant was removed. Antibody buffer and 0.5 μg antibody was added to each sample and incubate overnight at 4°C. After washing the nuclei-beads, 2.5 μl of pAG-NMase was added and incubated for 10 min at RT. After washing, 1 μl of Chromatin Digest additive was added and incubate for 2 hrs at 4°C. Then, stop buffer and 0.5 ng of Spike-in DNA were added and incubate for 10 min at 37 °C. We purified DNA from this using DNA purification kit (EpiCypher).
Using 5 ng of purified CUT&RUN-enriched DNA, we prepared sequencing library using library prep kit for illumine sequencing (E7645, NEB). The library was purified with 1.0 X AMPure beads (Beckman) and library fragment size was checked with Agilent Bioanalyzer.

tag: cell line

tag: cell type

value: Human prostate cancer cell line

tag: genotype

value: WT

tag: treatment

value: shControl

tag: chip antibody

value: SMARCA1 (EpiCypher, 13-2005)


title: s61-emphysematous-copd

description: Library name: Ua 104

value: Lung

tag: subject group

value: patients with emphysematous COPD

tag: subject identity

tag: lab id

tag: steroidstype

value: ICS

tag: smoke

value: TRUE

value: LUL


title: Rv1, control, SMARCA1, rep1

description: Library name: Rv1-pLKO.1-SMARCA1-rep1


title: s17-control

description: Library name: DNAZ 4 RUL

value: patients with no history of COPD

value: DNAZ 4 RUL

tag: gold

tag: age

tag: Sex

tag: copd

tag: quitdate

value: FALSE

value: RUL


title: rotavirus infection, 16hr, hypoxia, rep 3

city: Gainesville

first: Sorin

middle: Ophelie

last: Jacobs

state: Florida

address: 1200 Newell Dr. ARB R2-273

department: Molecular Genetics and Microbiology

institute: University of Florida

description:
Library name: H_rota16h_3
H_r16_3

data_processing:
use HISAT2 to accomplish the mapping, alignment by Novogene
Assembly: GRCh38/hg38
Supplementary files format and content: gene_count_GEO.csv contains raw counts for each gene across all samples
Supplementary files format and content: gene_fpkm_GEO.csv contains fpkm for each gene across all samples

source_name: Colon carcinoma cell line

growth_protocol: Human T84 colon carcinoma cells (ATCC, CCL-248) were maintained in DMEM:F12 1:1 media (Corning, 10-092-CV) supplemented with 10% fetal bovine serum (FBS) (Summerlin Scientific, SS100), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco, 15140-122), and plasmocin prophylactic (Invivogen, ant-mpp) at 37°C, 5% CO2. Hypoxia exposure was 1% O2 for 24hr prior to infection.

extract_protocol:
RNA extraction was performed using the RNeasy minikit (Qiagen, 74104) as per manufacturer’s instructions
Library construction by Novogene. Briefly, mRNA was isolated from RNA samples using poly-T oligo-attached magnetic beads. Library preparation used random hexamer primers, followed by the second strand cDNA synthesis using dTTP.

treatment_protocol: T84 cells were placed into normoxic (20% O2) or hypoxic (1% O2) conditions, and either treated with poly I:C (1ug per well) or infected with rotavirus (at MOI 0.25 as measure in MA104 cells). For each condition, cells were seeded in 24-well plates with four replicates. Mock, poly I:C, and rotavirus infected samples were harvested at 8 hours, with an addition timepoint harvested for rotavirus at 16 hours.

value: Colon carcinoma cell line

value: Intestinal epithelial cell

tag: oxygen level

value: hypoxia

value: rotavirus


title: rotavirus infection, 16hr, hypoxia, rep 4

description:
Library name: H_rota16h_4
H_r16_4

tag: tissue


title: s15-control

description: Library name: DNAZ 7 RLL

value: DNAZ 7 RLL

value: Never

value: Control

value: F

tag: steroids

tag: lobe

value: RLL

tag: lobe emphysema_severity_laa%

tag: lobe emphysema

tag: packyear


title: rotavirus infection, 8hr, hypoxia, rep 4

description:
Library name: H_rota8h_4
H_r8_4

tag: cell line

tag: cell type

tag: treatment


title: rotavirus infection, 16hr, hypoxia, rep 1

description:
Library name: H_rota16h_1
H_r16_1


title: rotavirus infection, 8hr, hypoxia, rep 3

description:
Library name: H_rota8h_3
H_r8_3


title: polyI:C transfection, 8hr, hypoxia, rep 4

description:
Library name: H_polyIC_4
H_p_4


title: polyI:C transfection, 8hr, hypoxia, rep 2

description:
Library name: H_polyIC_2
H_p_2


title: s77-emphysematous-copd

description: Library name: COPD 4 LLL

value: Lung

tag: subject group

value: patients with emphysematous COPD

tag: subject identity

tag: lab id

value: COPD 4 LLL

tag: steroidstype

value: OCS

value: Former

value: GOLD 4

value: M

value: COPD

value: LLL

value: E-COPD


title: rotavirus infection, 8hr, hypoxia, rep 1

description:
Library name: H_rota8h_1
H_r8_1

value: Colon carcinoma cell line

value: Intestinal epithelial cell

value: hypoxia


title: rotavirus infection, 8hr, hypoxia, rep 2

description:
Library name: H_rota8h_2
H_r8_2

value: rotavirus


title: polyI:C transfection, 8hr, hypoxia, rep 3

description:
Library name: H_polyIC_3
H_p_3


title: polyI:C transfection, 8hr, hypoxia, rep 1

description:
Library name: H_polyIC_1
H_p_1


title: rotavirus infection, 16hr, normoxia, rep 4

description:
Library name: N_rota16h_4
N_r16_4

value: normoxia


title: mock, hypoxia, rep 3

description:
Library name: H_mock_3
H_m_3

value: mock


title: rotavirus infection, 16hr, normoxia, rep 2

description:
Library name: N_rota16h_2
N_r16_2


title: rotavirus infection, 16hr, normoxia, rep 3

description:
Library name: N_rota16h_3
N_r16_3


title: s1-emphysematous-copd

description: Library name: COPD 2 LUL

value: COPD 2 LUL

value: ICS

tag: smoke

tag: gold

tag: age

tag: Sex

value: TRUE

value: LUL


title: mock, hypoxia, rep 1

description:
Library name: H_mock_1
H_m_1

tag: tissue

tag: oxygen level


title: rotavirus infection, 16hr, normoxia, rep 1

description:
Library name: N_rota16h_1
N_r16_1


title: s80-emphysematous-copd

description: Library name: COPD1 LUL

value: Lung

value: patients with emphysematous COPD

value: COPD1 LUL

value: GOLD 2

tag: copd

tag: quitdate

tag: steroids

tag: lobe


title: rotavirus infection, 8hr, normoxia, rep 4

description:
Library name: N_rota8h_4
N_r8_4

tag: cell line


title: rotavirus infection, 16hr, hypoxia, rep 2

description:
Library name: H_rota16h_2
H_r16_2

tag: cell type


title: rotavirus infection, 8hr, normoxia, rep 3

description:
Library name: N_rota8h_3
N_r8_3

tag: treatment


title: rotavirus infection, 8hr, normoxia, rep 2

description:
Library name: N_rota8h_2
N_r8_2


title: polyI:C transfection, 8hr, normoxia, rep 4

description:
Library name: N_polyIC_4
N_p_4


title: rotavirus infection, 8hr, normoxia, rep 1

description:
Library name: N_rota8h_1
N_r8_1


title: polyI:C transfection, 8hr, normoxia, rep 3

description:
Library name: N_polyIC_3
N_p_3


title: polyI:C transfection, 8hr, normoxia, rep 2

description:
Library name: N_polyIC_2
N_p_2


title: polyI:C transfection, 8hr, normoxia, rep 1

description:
Library name: N_polyIC_1
N_p_1


title: mock, hypoxia, rep 2

description:
Library name: H_mock_2
H_m_2


title: mock, hypoxia, rep 4

description:
Library name: H_mock_4
H_m_4


title: mock, normoxia, rep 1

description:
Library name: N_mock_1
N_m_1


title: mock, normoxia, rep 4

description:
Library name: N_mock_4
N_m_4


title: mock, normoxia, rep 2

description:
Library name: N_mock_2
N_m_2


title: mock, normoxia, rep 3

description:
Library name: N_mock_3
N_m_3


title: A549_siBAP18_2

city: Shenyang

first: Qilin

last: Hu

state: Liaoning

address: No. 155 Nanjing North Street

institute: The First Hospital of China Medical University

description:
Library name: sample 5
target BAP18 siRNA group, replicate biosample 2

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

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

treatment_protocol: A549 cells were collected 48 hours after siRNA transfection for RNA extraction and transcriptome sequencing. The experimental group was transfected with siRNA targeting BAP18, while the control group was transfected with non-specific siRNA. Each group had three biological replicates.


title: A549_siBAP18_3

description:
Library name: sample 6
target BAP18 siRNA group, replicate biosample 3


title: A549_siCtrl_2

description:
Library name: sample 2
untarget siRNA group, replicate biosample 2


title: A549_siBAP18_1

description:
Library name: sample 4
target BAP18 siRNA group, replicate biosample 1


title: Lung, LPS, rep3

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

description: Library name: TW12

data_processing:
Sample demultiplexing, alignment to the reference genome (GRCm39) and calculating count matrices were performed by the ScaleRNA pipeline v.1.3.2 (https://github.com/ScaleBio/ScaleRna). The default parameters were used, apart from the minCellRatio parameter, which was set to 100. The library structure used was the libV1.
Assembly: GRCm39
Supplementary files format and content: Each sample has a file with features (genes), barcodes detected and matrix.mtx containing counts per gene and per cell barcode

organism: Mus musculus

extract_protocol:
Obtained lung homogenates were first filtered through 70 µm and subsequently 40 µm cell strainers, and centrifuged for 10 min, 300 xg at 4˚C. Erythrocytes were lysed with RBC lysis solution for 15 min at 4˚C. Cells were then prepared according to ScaleBioTM fixation protocol.
ScaleBio™ Single Cell RNA Sequencing Kit v1.1

treatment_protocol: Mice were anesthetized and 20 µg of LPS in a volume of 30 µL was administered intranasally on day 0. Control mice received 30 µL of sterile PBS. 6h, 24h and 48h after, mice were anesthetized and received 40 µL of isolithocholic acid (isoLCA) [200 µg/Kg body weight (bw)] resuspended in sterile PBS via intranasal instillation. Control mice received identical volume of PBS with vehicle. On day 4, mice were sacrificed with a lethal dose of pentobarbital and 0.75 mL of dispase II was injected intratracheally, followed by intratracheal injection of 0.5 mL 1% low melting agarose. Lungs were then covered with ice for 5 min, removed and placed in a 15 mL Falcon tube with 2 mL of dispase II and incubated for 1h at RT with gentle agitation (350 RPM). Then, the lungs were mechanically disrupted using forceps in DMEM supplemented with DNAse I.

tag: gender

value: male

value: 8 weeks

tag: strain

value: LPS

tag: batch


title: A549_siCtrl_3

description:
Library name: sample 3
untarget siRNA group, replicate biosample 3


title: A549_siCtrl_1

description:
Library name: sample 1
untarget siRNA group, replicate biosample 1


title: Lung, LPS, rep2

description: Library name: TW11


title: BRD4S-1

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

description: Library name: FLAG2-1

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic Genome Analysis Core (GAC) using the pipeline Cassava 1.7.
Raw sequencing reads were aligned to the human reference genome (GRCh38) using BWA-MEM (version 0.7.13-r1126) with the following command:: bwa mem -v 3 -k 19 -t 4 ./hg38_V43_gencode/genome.fa R1.fq.gz R2.fq.gz
Peak calling was performed using MACS2 with the following command: macs2 callpeak -t sample.bam  -g hs -f BAMPE -n sample_peak -q 0.1 --keep-dup all
Reproducible peaks (between two replicates) were called using the IDR algorithem with IDR cutoff 0.05
Assembly: GRCh38
Supplementary files format and content: Standard ENCODE narrowPeak format (https://genome.ucsc.edu/FAQ/FAQformat.html#format12).
Library strategy: CUT&Tag

source_name: ovarian cancer

growth_protocol: RPMI-1640，10% FBS，1% P/S

extract_protocol:
CUT&Tag assay was performed as described previously with modifications (Hatice et al., 2019 ). Briefly, 100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). 10 μL Concanavalin A coated magnetic beads (Bangs Laboratories) were added per sample and incubated at RT for 10 min. Remove unbound supernatant and resuspended bead-bound cells with Primary Antibody Buﬀer (Mix 8 ul 0.5 M EDTA and 6.7 ul 30% BSA with 2 mL Dig-wash buffer) and a 1:50 dilution of primary antibody incubated on a rotating platform overnight at 4℃. The primary antibody was removed using magnet stand. Sencondary antibody (Goat Anti-Mouse IgG H&L (Cat. No. N270) or Goat Anti-Rabbit IgG H&L (Cat. No. N269)）was diluted 1:100 in dig wash buffer and cells were incubated at RT for 60 min. Cells were washed using the magnet stand three times in dig wash buffer. A 1:100 dilution of pA-Tn5 adapter complex was prepared in dig-300 buffer (0.01% Digitonin; 20 mM HEPES pH 7.5; 300 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail) and incubated with cells at RT for 1 h. Cells were washed three times for 5 min in 1 mL dig-300 buffer. Then cells were resuspended in tagmentation buffer (10 mM MgCl2 in dig-300 buffer) and incubated at 37 °C for 1 h. DNA was purified using Tagment DNA Extract Beads.
To amplify libraries, 21 μL DNA was mixed with 2 μL of a universal i5 and auniquely barcoded i7 primer. A volume of 25 μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. libraried clean-up was performed XP beads (Beckman Counter).

value: ovarian cancer

value: Epithelial cell

tag: genotype

value: BRD4 short isoform (BRD4S)


title: Lung, LPS, rep1

description: Library name: TW8


title: BRD4S-2

description: Library name: FLAG2-2


title: Lung, LPS + isoLCA, rep2

description: Library name: TW9

value: LPS + isoLCA


title: Lung, LPS + isoLCA, rep1

description: Library name: TW7


title: BRD4L-1

description: Library name: FLAG1-1

value: BRD4 full length (BRD4L)


title: Lung, isoLCA, rep3

description: Library name: TW6

value: isoLCA


title: Control rep 3

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Control rep 3 E005820

library_source: other

data_processing:
library strategy: Massively Parallel Reporter Assay (MPRA)
Oligo-barcode association: Paired-end, 150bp reads were first quality filtered using Trimmomatic (v0.38) (flags: PE -phred33, LEADING:25, TRAILING:25, MINLEN:80). Read 1 was separated into the 20bp barcode region and the oligo-matching region. The trimmed oligo-matching regions of Read 1 and Read 2 were mapped back to the synthesized oligo sequences using Bowtie2 (v2.3.4.1) (flags: -X 250, -very-sensitive, -p 16). Barcodes were then associated with the oligo sequences using the read ID. Only uniquely mapped barcodes were used for downstream analysis.
Barcode counting: Single-end 150bp reads were first quality filtered using Trimmomatic (v0.38) (flags: PE -phred33, LEADING:3, TRAILING:3, MINLEN:70). Each read was then separated into the 20bp barcode region and the constant region. The trimmed constant regions of the reads were mapped back to the constant region within the eGFP 3′ UTR using Bowtie2 (v2.3.4.1) (flags: -very-sensitive, -p 16). Only reads with Levenshtein distance of 4 or less within the constant region and perfect matches to the two bases directly adjacent to the barcode were kept. Barcodes were then associated with the retained reads using the read ID. All barcodes were summarized at the oligo level.
Assembly: hg38
Supplementary files format and content: for BC-seq libraries: tab-delimited txt file containing oligo summaries for each sample
Supplementary files format and content: tab-delimited txt file containing barcode counts for each sample

molecule: other

growth_protocol: The GM12878, MS-1, and MS-2 cell lines were grown in RPMI medium supplemented with 10% FBS, 100ug/ml normocin, and 1X antibiotic-antimycotic

extract_protocol:
Total RNA was extracted by the RNeasy Midi Kit following the manufacturer’s instruction. Extracted RNA was subjected to DNase treatment. eGFP mRNA enrichment and elution were performed using biotinylated probes as in Lu et al (PMID: 33712590), and the mRNA was reverse transcribed to cDNA using SuperScript™ IV First-Strand Synthesis System with gene specific primer MPRA_v3_Amp2Sc_R, following the manufacturer’s instruction.
We assembled the MPRA libraries as in Lu et al  (PMID: 33712590) and Shook et al  (PMID: 38183988)

treatment_protocol: After transfection, cells were recovered in pre-warmed DMEM medium supplemented only with 10% FBS for 24hrs. Cells were then collected for preparation of the sequencing library for barcode counting.


title: Lung, isoLCA, rep1

description: Library name: TW4


title: Lung, isoLCA, rep2

description: Library name: TW5


title: Control rep 2

description: Library name: Control rep 2 E005819


title: Control rep 1

description: Library name: Control rep 1 E005818


title: Barcode library

description: Library name: Barocde library E005202


title: Lung, Non treated, rep2

description: Library name: TW2

value: Non treated


title: Lung, Non treated, rep1

description: Library name: TW1


title: HDF_shZNF469_2

city: Bangkok

first: Thammachanok

last: Boonto

address: 254 Phaya Thai Rd, Khwaeng Wang Mai, Pathum Wan

department: Biochemistry

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

description: Library name: Sample 5

data_processing:
Clean data with high quality, each sample had a Q-score no less than Q30, was obtained by filtering Raw data, which removes adapter sequence and reads with low quality. HISAT2 and StringTie was applied to assemble the mapped reads. To investigate differentially expressed genes and pathways, we applied GSEA software (UC San Diego and Broad Institute) and conducted enrichment analysis using GO and KEGG databases.
Assembly: Homo_sapiens.GRCh38.p14.genome.fa.
Supplementary files format and content: tab-delimited text file includes raw counts and TPM values for each Sample

source_name: skin

growth_protocol: Human dermal fibroblasts (CRL-2076) was acquired from The American Type Culture Collection (ATCC) and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM; #30-2005) supplemented with fetal bovine serum (FBS), Primocin (InvivoGen), 1% Antibiotic-Antimycotic, and GlutaMAXTM (Thermo Fisher Scientific) at 37°C with 5% CO2.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepare using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer’s recommendations.

value: skin

value: fibroblast

value: ZNF469 knockdown


title: Tibialis Anterior, Young Dex treatment, 6

city: Tallahassee

first: Cynthia

last: Vied

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

description: Library name: YDN6

data_processing:
Libraries were demultiplexed, adapters trimmed, and trimmed reads were aligned to the mouse genome (UCSC mm10) using Illumina Dragen RNA v4.1.23 by the core facility.
Differential expression analysis of count tables was performed using the default settings of DESeq2 version 1.30.1 (Benjamini-Hochberg FDR correction).
Assembly: UCSC mm10
Supplementary files format and content: Microsoft Excel Worksheet (.xlsx). Contains normalized counts by Dragen RNA.

source_name: Skeletal muscle

growth_protocol: Male C57BL/6 mice were housed in a temperature- (25℃) and light- (12 h light/12 h dark) controlled environment within the vivarium at Florida State University and were provided standard 5001 rodent chow (LabDiet, St. Louis, MO) and water ad libitum until the day of testing. Animals were euthanized by cardiectomy while under deep isoflurane anesthesia.

extract_protocol:
RNA was isolated using Zymo RNA Miniprep kit . 300 nanoograms of total RNA was used for construction of sequencing libraries.
A cDNA library was prepared for each sample using the the NEBNext PolyA mRNA and Ultra II RNA library kit for Illumina. Libraries were barcoded for multiplexing with NEBNext Multiplex Oligos for Illumina unique dual index Primer Pairs. The multiplexed sample was quantified with qPCR (Kapa Biosystems) specific for Illumina sequencing primers and the average fragment size was determined with a Tapestation D1000 high sensitivity (Agilent Technologies). The pooled sample was sequenced, with paired-end, 150 base reads on an Illumina NovaSeq X Plus located in the Translational Science Laboratory at the College of Medicine, Florida State University.  The pooled data were demultiplexed into individual sample data.

treatment_protocol: Young (4months) and aged (24months) mice were each randomized into 2 groups of equal body weight. One group from each age was given daily subcutaneous injections of saline while the other group from each age was given daily subcutaneous injections of dexamethasone (1mg/kg/day). Injections were administered for 7 days. On the final day, mice were given a final injection and the tibialis anterior muscle was harvested 6.5 hr later under deep isoflurane (3%) anesthesia, snap-frozen in liquid nitrogen, and stored at -80°C until analysis.

value: Skeletal muscle

value: Tibialis Anterior

value: Daily dexamethasone injection


title: HDF_shZNF469_3

description: Library name: Sample 6


title: Tibialis Anterior, Young Dex treatment, 5

description: Library name: YDN5


title: Tibialis Anterior, Young Dex treatment, 3

description: Library name: YDN3


title: Lung, LPS + isoLCA, rep3

description: Library name: TW10

value: Lung


title: Tibialis Anterior, Young Dex treatment, 4

description: Library name: YDN4


title: snRNA_age12

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

description: Library name: snRNA_age12

data_processing:
The raw single-cell BCR sequencing data were processed with subcommand vdj in 10× Genomics software CellRanger (version: 6.1.2), in which process the sequencing data were aligned into the mouse reference VDJ database (GRCm38).
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: "barcodes.tsv" files include snRNA-seq barcode information, "features.tsv" files include snRNA-seq gene features and "matrix.mtx" files include snRNA-seq gene expression. "tissue.gef" files include scStereo-seq data.

molecule: cytoplasmic RNA

source_name: ovary

extract_protocol:
BD Vacutainer K2 EDTA tube (10ml) were used for blood collection. We obtained peripheral venous blood samples by venipunction from six participants. And then used Ficoll density gradient centrifugation (TBD, China) to separate PBMCs. We pre-added 4 mL Ficoll to each 15 mL centrifuge tube. For each participant, equal volumes of blood were carefully layered onto Ficoll and centrifuged at 800 g and RT for 25 min (3 acceleration and 1 brake). After centrifugation, we collected PBMCs with pipette into a 15-ml tube, and diluted up to 15 ml with pre-warmed PBS (TBD, China). After centrifuging for 10 min, at 250 g and RT, PBMC were resuspended in 2 mL Red Blood Cell Lysis Buffer (Solarbio, China). After incubating the cells on ice for 10 min, 8 mL PBS was added, gently mixed, and centrifuged at 4℃ 300 g for 10 min. We resuspended the centrifuged cells in 10ml of pre-prepared washing buffer (1× PBS with 0.04% BSA). The cleaning step was performed at 250 g and 4℃ for 10 min. The second time the cells were resuspended by the cleaning buffer and counted with the Dual Fluorescence Cell Counter (LunaTM fl). After centrifugation, the cells were resuspended in the cell cryopreservation system recommended by 10× Genomics. With about 2×106 cells per milliliter, one-milliliter aliquots were gradually frozen in a freezing box over the course of 24 h at -80℃ before being kept in a vapor-phase liquid nitrogen tank.
The cells were first thawed according to the 10× Genomics protocol (Demonstrated Protocol, CG00039). The thawed cells were then stained with trypan blue and placed under a light microscope to observe the cell state and background. The cells were counted using the Dual Fluorescence Cell Counter (LunaTM fl), and subsequent procedures were performed after confirming that the survival rate was not less than 90%. The ChromiumTM Single cell 5’ Reagent Kit, Chromium Single Cell Human BCR Amplification Kit, and Chromium Single Cell Human TCR Amplification Kit of the Chromium platform (10× Genomics, California, USA) were used to create the scRNA-seq and paired single-cell BCR and TCR libraries in accordance with the Chromium Single Cell 5’ Reagent Kits User Guide (v2 Chemistry Dual Index). On the Illumina HiSeq X Ten platform, generated scRNA-seq libraries were sequenced. The preprocessing of the PE150 Illumina sequencing reads was done using the 10× Genomics software CellRanger (version: 6.1.2).

value: ovary

tag: library

value: snRNA-seq


title: Lung, Non treated, rep3

description: Library name: TW3

value: male

value: 8 weeks


title: HDF_shControl_3

description: Library name: Sample 3

value: WT


title: Tibialis Anterior, Young Dex treatment, 2

description: Library name: YDN2


title: HDF_shControl_1

description: Library name: Sample 1


title: Tibialis Anterior, Young Dex treatment, 1

description: Library name: YDN1


title: BRD4L-2

description: Library name: FLAG1-2

value: ovarian cancer

value: Epithelial cell


title: Tibialis Anterior, Young Vehicle, 6

description: Library name: YVN6

value: Daily saline Injections


title: Tibialis Anterior, Young Vehicle, 5

description: Library name: YVN5


title: RNA-Seq, Rv1, FOXA1KD, rep1

description: Library name: Rv1-FOXA1-rep1

data_processing:
the sequenced reads with low quality or adaptor contamination were removed
Clear reads were mapped to the human reference genome (hg19) using Hisat2 v2.2.1 software
To count the reads numbers mapped to each gene, featureCounts v2.0.6 was used.
The fragments per kilobase of transcript per million mapped reads (FPKM) method was used to estimate expression levels.
Differential expression analysis was performed using the DESeq2 R package (1.42.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Rv1 cells were transduced with sh-Control, sh-BPTF, sh-SMARCA1, sh-SMARCA4, or sh-FOXA1 lentivirus for 48 hours. Total RNAs were extracted using a total RNA miniprep kit (Sigma-Aldrich, St. Louis, MO).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina

value: Human prostate cancer cell line

value: FOXA1 knock down


title: HDF_shControl_2

description: Library name: Sample 2

value: skin


title: RNA-Seq, Rv1, FOXA1KD, rep2

description: Library name: Rv1-FOXA1-rep2


title: RNA-Seq, Rv1, FOXA1KD, rep3

description: Library name: Rv1-FOXA1-rep3


title: Tibialis Anterior, Young Vehicle, 4

description: Library name: YVN4


title: Tibialis Anterior, Young Vehicle, 3

description: Library name: YVN3


title: RNA-Seq, Rv1, control, forFOXA1KD, rep3

description: Library name: Rv1-pLKO.1-forFOXA1KD-rep3


title: RNA-Seq, Rv1, control, forFOXA1KD, rep2

description: Library name: Rv1-pLKO.1-forFOXA1KD-rep2


title: RNA-Seq, Rv1, control, forFOXA1KD, rep1

description: Library name: Rv1-pLKO.1-forFOXA1KD-rep1


title: Tibialis Anterior, Young Vehicle, 2

description: Library name: YVN2


title: HDF_shZNF469_1

description: Library name: Sample 4

value: fibroblast


title: Tibialis Anterior, Young Vehicle, 1

description: Library name: YVN1


title: Tibialis Anterior, Aged Dex treatment, 6

description: Library name: ODN6


title: RNA-Seq, Rv1, SMARCA5KD, rep2

description: Library name: Rv1-SMARCA5-rep2

value: SMARCA5 knock down


title: RNA-Seq, Rv1, SMARCA5KD, rep3

description: Library name: Rv1-SMARCA5-rep3


title: Tibialis Anterior, Aged Dex treatment, 3

description: Library name: ODN3

value: Skeletal muscle


title: RNA-Seq, Rv1, SMARCA1KD, rep2

description: Library name: Rv1-SMARCA1-rep2

value: SMARCA1 knock down


title: Tibialis Anterior, Aged Dex treatment, 5

description: Library name: ODN5

value: Tibialis Anterior

value: Daily dexamethasone injection


title: Tibialis Anterior, Aged Dex treatment, 2

description: Library name: ODN2


title: RNA-Seq, Rv1, SMARCA1KD, rep1

description: Library name: Rv1-SMARCA1-rep1


title: RNA-Seq, Rv1, control, forSMARCA1.5KD, rep3

description: Library name: Rv1-pLKO.1-forSMARCA1.5KD-rep3


title: RNA-Seq, Rv1, SMARCA1KD, rep3

description: Library name: Rv1-SMARCA1-rep3


title: Tibialis Anterior, Aged vehicle, 5

description: Library name: OVN5


title: RNA-Seq, Rv1, SMARCA5KD, rep1

description: Library name: Rv1-SMARCA5-rep1


title: Tibialis Anterior, Aged vehicle, 6

description: Library name: OVN6


title: Tibialis Anterior, Aged Dex treatment, 1

description: Library name: ODN1


title: RNA-Seq, Rv1, control, forSMARCA1.5KD, rep2

description: Library name: Rv1-pLKO.1-forSMARCA1.5KD-rep2


title: Tibialis Anterior, Aged vehicle, 3

description: Library name: OVN3


title: RNA-Seq, Rv1, control, forSMARCA1.5KD, rep1

description: Library name: Rv1-pLKO.1-forSMARCA1.5KD-rep1


title: Tibialis Anterior, Aged vehicle, 1

description: Library name: OVN1


title: RNA-Seq, Rv1, BPTFKD, rep3

description: Library name: Rv1-BPTFKD-rep3

value: BPTF knock down


title: clsy4_EN_rep2, ncRNA-Seq

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

description: Library name: Sample4

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using UEA sRNA workbench. The sRNAs of appropriate size class(16-35nt) was chosen further.
The processed reads were aligned to the rice genome using Bowtie with one allowed mismatch.
Assembly: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Text delimited files showing the sequence and raw abundance of the sRNAs.

organism: Oryza sativa

source_name: Endosperm (20 days after anthesis)

growth_protocol: The plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius.

extract_protocol:
Total RNA from endosperm was extracted using Trizol (Invitrogen) reagent.
Size fractionation. adaptor_seq TGGAATTCTCGGGTGCCAAGG

treatment_protocol: WT and clsy4- knockdown lines were handled in the same manner.

value: Endosperm (20 days after anthesis)

tag: cultivar

value: Indica, Pusa Basmati1 (PB1)


title: Tibialis Anterior, Aged vehicle, 4

description: Library name: OVN4


title: ACC control, scRNAseq

city: New York

first: Andrea

last: Terceros

address: 1230 York ave

institute: The Rockefeller University

description:
Library name: ACC_control
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the seqc software (https://github.com/dpeerlab/seqc)
Assembly: mm10
Supplementary files format and content: csv file (cells along rows, genes along columns)

source_name: Brain

extract_protocol:
Briefly, mice were sacrificed within 40-60 minutes from behavioral testing, with an overdose of isoflurane, followed by transcardial perfusion with carbonated (95% O2, 5% CO2) Hanks' Balanced Salt Solution (HBSS) containing small-molecule cocktail consisting of 1 μM TTX (Sigma), 100 μM AP-V (Thermo Fisher Scientific), 5 μg actinomycin D (Sigma) per milliliter and 10 μM triptolide (Sigma) to optimize for preserving transcriptional state. Brains were removed, 500μm sections were collected, and the region of interest was dissected (ANT or ACC). The tissue was dissociated using papain (Worthington, cat. no. LS003124) dissolved in Hibernate A buffer (Fisher Scientific, cat. no. NC1787837) containing 1 μM TTX, 100 μM AP-V (Thermo Fisher Scientific), 5 μg actinomycin D (Sigma) per milliliter, 10 μM triptolide (Sigma), and 10 μg anisomycin (Sigma) per milliliter, and incubated for 25-30 min at 37C, followed by manual trituration using fire polished Pasteur pipettes and filtering through a 40μm cell strainer (Millipore Sigma, cat. no. BAH136800040). Cells were washed with a wash buffer (PBS + 1% BSA) and centrifuged at 500 g for 5 min, the supernatant was carefully removed, and cells were resuspended in ~500ul wash buffer and 10% DAPI.
Single cell RNA- sequencing was carried out with the Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, cat. no. 1000268). Manufacturer’s instructions were followed for downstream cDNA synthesis (12-14 PCR cycles) and library preparation.

value: Brain

value: All brain cell types

tag: age

value: 9-11 weeks old

value: male

tag: condition

value: control


title: RNA-Seq, Rv1, control, rep3

description: Library name: Rv1-pLKO.1-rep3

value: Human prostate cancer cell line

value: WT


title: RNA-Seq, Rv1, BPTFKD, rep1

description: Library name: Rv1-BPTFKD-rep1


title: clsy4_EN_rep1, ncRNA-Seq

description: Library name: Sample3

tag: tissue


title: RNA-Seq, Rv1, control, rep2

description: Library name: Rv1-pLKO.1-rep2


title: ACC Retrieval_day20_LR, scRNAseq

description:
Library name: ACC_Time_point_R20_LR
10x Genomics

tag: Sex

value: LR


title: RNA-Seq, Rv1, control, rep1

description: Library name: Rv1-pLKO.1-rep1


title: WT_EN_rep1, ncRNA-Seq

description: Library name: Sample1


title: Tibialis Anterior, Aged Dex treatment, 4

description: Library name: ODN4


title: clsy4-kd_Leaf_rep2

description: Library name: Sample6

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using cutadapt.
The reads were aligned to PCR templates as genome using Bismark and methylation extraction was done using Bismark protocol.
The methylation was calculated using the Bismark tool and cytosine coverage report was used to create the bedgraph files for methylation density.
Assembly: Custome genome built from Oryza sativa japonica nipponbare genome – IRGSP1 with the PCR amplicon regions as template.
Supplementary files format and content: Processed files contain  citosine report in text format which generated from Bismark alignment tool.

source_name: Leaf (60 days old)

extract_protocol:
Total DNA was extracted from the tissues using CTAB method.
Bisulfite convertion by EZ DNA Methylation-Gold Kit (Catalog no-D5005) as per manufacturer’s protocol. Adapters used: Read 1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA  and Read 2- AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT .
library constructed using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions.

treatment_protocol: WT tissues were handled in the same manner. Treated with Zymo bisulfite reagents

value: Leaf (60 days old)


title: clsy4-kd_Leaf_rep1

description: Library name: Sample5


title: WT_EN_rep2, ncRNA-Seq

description: Library name: Sample2


title: Rv1, control, H3K4me1, rep1

description: Library name: Rv1-pLKO.1-H3K4me1-rep1

data_processing:
Quality of CUT&RUN ChIP-seq read were checked with fastqc
Reads were trimmed from 3' end until the final base had a quality score > 28, using trimgalore v0.6.6
Reads were aligned to the UCSC human hg19 reference genome and E. coli K12, MG1655 reference genome using Bowtie2 v2.3.5.1. If one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant (--dovetail)
Samples were normalized compare do total reads counts, and BAM files were processed (remove duplicates, sorting, and indexing) using samtools v1.10 and Picard v2.23.9
Processed Bam files were normalized with spike-in normalization method and formatted in the bigWig and bedgraph file format, using Deeptools v3.5.0
Assembly: Peaks were called uing MACS2 bdgpeakcall v2.2.6 with the significance cut-off p-value <=0.01 and reproducible peaks were generaged from two replicated peaks using IDR v2.0.4.2
Supplementary files format and content: hg19, K12 MG1655
Supplementary files format and content: bigWig

value: shControl

tag: chip antibody

value: H3K4me1 (EpiCypher, 13-0040)


title: Rv1, control, H3K4me1, rep2

description: Library name: Rv1-pLKO.1-H3K4me1-rep2


title: ACC Retrieval_day20_HR, scRNAseq

description:
Library name: ACC_Time_point_R20_HR
10x Genomics

value: HR


title: ACC Retrieval_day15_LR, scRNAseq

description:
Library name: ACC_Time_point_R15_LR
10x Genomics


title: clsy3-kd_Leaf_rep2

description: Library name: Sample4


title: clsy3-kd_Leaf_rep1

description: Library name: Sample3


title: ACC Retrieval_day15_HR, scRNAseq

description:
Library name: ACC_Time_point_R15_HR
10x Genomics


title: Rv1, control, H3K27ac, rep2

description: Library name: Rv1-pLKO.1-H3K27ac-rep2

value: H3K27ac (EpiCypher, 13-0059)


title: WT_Leaf_rep1

description: Library name: Sample1


title: Tibialis Anterior, Aged vehicle, 2

description: Library name: OVN2

value: Skeletal muscle

value: Tibialis Anterior

value: Daily saline Injections


title: RNA-Seq, Rv1, BPTFKD, rep2

description: Library name: Rv1-BPTFKD-rep2

value: BPTF knock down


title: Rv1, control, H3K27ac, rep1

description: Library name: Rv1-pLKO.1-H3K27ac-rep1


title: clsy4-kd_Endosperm

description: Library name: Sample 1

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic.
The reads were aligned to genome using Bismark and methylation extraction was done using Bismark protocol.
The methylation was calculated using the Bismark tool and cytosine coverage report was used to create the bedgraph files for methylation density.
Assembly: Genome built from Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Genome-wide cytosine reports are the output file

extract_protocol:
Total DNA was extracted from the tissues using CTAB method.
The DNA samples were sheared by ultrasonication (Covaris) avarage 350bp. Bisulfite convertion by EZ DNA Methylation-Gold Kit (Catalog no-D5005) as per manufacturer’s protocol. Adapters used: Read 1-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and Read2- AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
xGen™ Methyl-Seq DNA Library Prep Kit (Catalog no. 10009860)

treatment_protocol: Endosperm tissues were handled in the same manner.

value: Endosperm (20 days after anthesis)

value: Indica, Pusa Basmati1 (PB1)


title: clsy4-kd_EN_rep2

description: Library name: Sample4

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic.
The processed reads were aligned to the rice genome using HISAT2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Assembly: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Text delimited files including FPKM for each sample.

source_name: Endosperm ( 20 days after anthesis)

extract_protocol:
Total RNA was isolated from Endosperm (20 days after anthesis). RNA was extracted using TRIzol method.
Libraries were prepared for sequencing using standard Illumina protocols. The kit used is NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L) and the adapter sequences are Read 1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and for read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: WT and clsy4 knockdown lines were handled in the same manner.

value: Endosperm ( 20 days after anthesis)


title: WT_EN_rep2

description: Library name: Sample2


title: ACC Retrieval_day2_LR, scRNAseq

description:
Library name: ACC_Time_point_R2_LR
10x Genomics

value: Brain

value: All brain cell types

value: 9-11 weeks old

value: male


title: clsy4-kd_EN_rep1

description: Library name: Sample3


title: WT_Leaf_rep2

description: Library name: Sample2


title: ACC Retrieval_day8_HR, scRNAseq

description:
Library name: ACC_Time_point_R8_HR
10x Genomics


title: WT_EN_rep1

description: Library name: Sample1


title: Rv1, FOXA1KD, AR, rep2

description: Library name: Rv1-FOXA1KD-AR-rep2

value: Human prostate cancer cell line

value: FOXA1 knock down

value: AR (EMD Millipore, 06-680)


title: Rv1, FOXA1KD, AR, rep1

description: Library name: Rv1-FOXA1KD-AR-rep1


title: ACC Retrieval_day2_HR, scRNAseq

description:
Library name: ACC_Time_point_R2_HR
10x Genomics


title: 12mo IgG

city: Philadelphia

first: Sean

last: Louzon

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: Sample 2

data_processing:
Fastq files were aligned with Bowtie2
NGS plot was used to generate metaplots
deepTools was used to generate bigwig files
MACS3 was used for peak-calling
Assembly: mm10
Supplementary files format and content: bigwig files generated by deepTools from bam files aligned by Bowtie2
Library strategy: CUT&Tag

source_name: cortex

extract_protocol:
Cortical tissue was mechanically homogenized in a sucrose solution and nuclei were isolated through a iodixanol gradient and ultracentrifugation. CUT&Tag was performed with anti-H2BE antibody (Millipore ABE1384).
Transposition reaction mix from Nextera Library Prep kit was used (Tagment DNA Enzyme 1 and Tagment DNA Buffer).

value: cortex

value: WT


title: Rv1, control, AR, forFOXA1KD, rep2

description: Library name: Rv1-pLKO.1-AR-forFOXA1KD-rep2

value: shControl


title: 3mo IgG

description: Library name: Sample 1


title: Rv1, control, AR, forFOXA1KD, rep1

description: Library name: Rv1-pLKO.1-AR-forFOXA1KD-rep1


title: ANT control, scRNAseq

description:
Library name: ANT_control
10x Genomics

value: control


title: Passaged bio rep 3

description: Library name: Sample 6

extract_protocol:
Primary cortical astrocytes were collected in wash buffer (Kaya-Okue et al. 2019) and CUT&Tag was performed with anti-E2F1 antibody (Invitrogen 32-1400).
Transposition reaction mix from Nextera Library Prep kit was used (Tagment DNA Enzyme 1 and Tagment DNA Buffer).

value: astrocytes

value: Passaged


title: ANT Retrieval_day15_LR, scRNAseq

description:
Library name: ANT_Time_point_R15_LR
10x Genomics

value: LR


title: Control bio rep 3

description: Library name: Sample 3


title: Passaged bio rep 1

description: Library name: Sample 4


title: Passaged bio rep 2

description: Library name: Sample 5


title: Control bio rep 2

description: Library name: Sample 2


title: ANT Retrieval_day15_HR, scRNAseq

description:
Library name: ANT_Time_point_R15_HR
10x Genomics

value: HR


title: Rv1, FOXA1KD, BPTF, rep2

description: Library name: Rv1-FOXA1KD-BPTF-rep2

extract_protocol:
Cell nuclei were extracted using nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1 % Triton X-100, 20% glycerol, 1X protease cocktail) and incubated with ConA Beads to absorb nuclei to beads for 10 min at RT. The nuclei-beads were placed in magnet and the supernatant was removed. Antibody buffer and 0.5 μg antibody was added to each sample and incubate overnight at 4°C. After washing the nuclei-beads, 2.5 μl of pAG-NMase was added and incubated for 10 min at RT. After washing, 1 μl of Chromatin Digest additive was added and incubate for 2 hrs at 4°C. Then, stop buffer and 0.5 ng of Spike-in DNA were added and incubate for 10 min at 37 °C. We purified DNA from this using DNA purification kit (EpiCypher).
Using 5 ng of purified CUT&RUN-enriched DNA, we prepared sequencing library using library prep kit for illumine sequencing (E7645, NEB). The library was purified with 1.0 X AMPure beads (Beckman) and library fragment size was checked with Agilent Bioanalyzer.

value: BPTF (EMD Millipore, ABE1966)


title: Rv1, FOXA1KD, BPTF, rep1

description: Library name: Rv1-FOXA1KD-BPTF-rep1


title: ANT Retrieval_day8_LR, scRNAseq

description:
Library name: ANT_Time_point_R8_LR
10x Genomics


title: Control bio rep 1

description: Library name: Sample 1


title: ACC Retrieval_day8_LR, scRNAseq

description:
Library name: ACC_Time_point_R8_LR
10x Genomics


title: 18mo bio rep 2

description: Library name: Sample 6


title: Rv1, control, BPTF, forFOXA1KD, rep2

description: Library name: Rv1-pLKO.1-BPTF-forFOXA1KD-rep2


title: ANT Retrieval_day8_HR, scRNAseq

description:
Library name: ANT_Time_point_R8_HR
10x Genomics


title: 12mo bio rep 2

description: Library name: Sample 4


title: Rv1, control, BPTF, forFOXA1KD, rep1

description: Library name: Rv1-pLKO.1-BPTF-forFOXA1KD-rep1


title: 18mo IgG

description: Library name: Sample 3


title: 18mo bio rep 1

description: Library name: Sample 5


title: ANT Retrieval_day2_LR, scRNAseq

description:
Library name: ANT_Time_point_R2_LR
10x Genomics


title: 12mo bio rep 1

description: Library name: Sample 3


title: 3mo bio rep 1

description: Library name: Sample 1


title: 3mo bio rep 2

description: Library name: Sample 2


title: Rv1, FOXA1KD, FOXA1, rep2

description: Library name: Rv1-FOXA1KD-FOXA1-rep2

value: FOXA1 (EpiCypher, 13-2001)


title: ANT Retrieval_day2_HR, scRNAseq

description:
Library name: ANT_Time_point_R2_HR
10x Genomics

value: Brain


title: DOT1L shRNA bio rep 3

first: Marissa

last: Maroni

data_processing:
Fastq files were aligned by Star
DESeq2 was used for differential gene expression analysis
Assembly: mm10
Supplementary files format and content: csv of DESeq output

molecule: polyA RNA

source_name: primary cortical neurons

extract_protocol:
Zymo Quick-RNA Minprep kits were used to isolate RNA
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library prep kit

value: primary cortical neurons

value: DOT1L shRNA


title: ANT Training_day6, scRNAseq

description:
Library name: ANT_Time_point_T6
10x Genomics

value: All brain cell types

value: 9-11 weeks old

value: male

value: training


title: Rv1, FOXA1KD, FOXA1, rep1

description: Library name: Rv1-FOXA1KD-FOXA1-rep1

value: Human prostate cancer cell line

value: FOXA1 knock down


title: DOT1L shRNA bio rep 1

value: WT


title: DOT1L shRNA bio rep 2


title: CLSY3OE_EN_rep2

description: Library name: Sample6

value: Endosperm (20 days after anthesis)

value: Indica, Pusa Basmati1 (PB1)


title: Ctrl Luciferase bio rep 3

value: Luciferase shRNA


title: Lung__Pos_2

city: Charlottesville

first: Arka

last: Sen Chaudhuri

state: VA

address: 345 Crispell Drive

department: Carter Immunology Center

institute: University of Virginia

description: Library name: Sequencing 12

data_processing:
Differentially expressed genes between each group were identified using DESeq2. For functional analysis, Gene Set Enrichment Analysis was performed to identify enriched gene sets from MSigDB.
Assembly: Mouse mm10
Supplementary files format and content: txt file include normalized expression values

extract_protocol:
After mRNA-S plus Ad5-S immunization, CD4+ T cells in the BAL, lung parenchyma, and draining lymph nodes in IL-21-VFP reporter mice were enriched with negative selection by using biotin-labeled CD8a, TER-119, and B220 antibody and streptavidin magnetic beads (Miltenyi Biotec) before surface markers staining. Live CD4+CD44+VFP+ and CD4+CD44+VFP- cells were sorted by Sony MA900 Cell Sorter and then resuspended in Trizol for RNA extraction. Two replicates of each cell subset were obtained.
RNA quality was assessed and sequenced using Illumina 2 x 150 platform provided by Admera Health. cDNA libraries construction, sequencing alignment to the mouse reference genome through services were provided by Admera Health.

value: Lung


title: Rv1, control, FOXA1, forFOXA1KD, rep2

description: Library name: Rv1-pLKO.1-FOXA1-forFOXA1KD-rep2

value: shControl


title: Rv1, control, FOXA1, forFOXA1KD, rep1

description: Library name: Rv1-pLKO.1-FOXA1-forFOXA1KD-rep1


title: Rv1, control, IgG, forARKD, forFOXA1KD

description: Library name: Rv1-pLKO.1-IgG-forARKD-FOXA1KD

value: IgG (EpiCypher, 13-0042)


title: ANT Training_day2, scRNAseq

description:
Library name: ANT_Time_point_T2
10x Genomics


title: CLSY3OE_EN_rep1

description: Library name: Sample5

value: Endosperm ( 20 days after anthesis)


title: SW480 cells, negative control vector, 48h-2

city: Daejon

first: Semi

last: Kim

address: 125 Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Library name: ZEB2neg_sw480-2

data_processing:
Reference genome indexing and read mapping of samples were performed using HISAT2 software.
StringTie was used to calculate genereated binary alignment map (BAM) files.
The FPKM of each samples were used to estimate the expression level of each gene.
Assembly: GRCh38
Supplementary files format and content: csv files include raw read counts for each Sample

growth_protocol: SW480 cells were maintained in RPMI1640 containing 10% FBS at 5% CO2 at 37oC.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen)
RNA libraries for RNA-seq were prepared using TruSeq Staranded Total RNA Library Prep Gold Kit according to the manufacturer's protocols

treatment_protocol: SW480 cells were transfected with negative control vector or ZEB2 expression vector for 48h.

value: epithelial, adenocarcinoma


title: Lung__Pos_1

description: Library name: Sequencing 11


title: Ctrl Luciferase bio rep 1

value: primary cortical neurons


title: SW480 cells, ZEB2, 48h-1

description: Library name: ZEB2_sw480-1

value: ZEB2 overexpression


title: Lung_Neg_1

description: Library name: Sequencing 9


title: Rv1, ARKD, AR, rep1

description: Library name: Rv1-ARKD-AR-rep1

value: AR knock down

value: shAR

value: AR (EMD Millipore, 06-680)


title: SW480 cells, ZEB2, 48h-2

description: Library name: ZEB2_sw480-2


title: eTK_HS, rep3

city: Taipei

first: Lavakau

last: Thalimaraw

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Institute of Plants and Microbial biology, Academia Sinica

description:
Library name: sample 18
Column name in counts_HS_Ath.txt: eTK-HS3

data_processing:
Raw sequences from Arabidopsis were first processed to remove adaptors using fastp (v0.24.0). The cleaned reads were then mapped to the reference genome (Araport11) using STAR (v2.7.9a) with default settings. Read count matrix were generated by featureCounts function from subread (v2.0.6).
Assembly: Arabidopsis genome Araport11
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: counts_HS_Ath.txt

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana wild type (Col-0) and knockout mutants (hsfa1a/hsfa1b/hsfa1d triple knockout) were grown on 1/2× MS + 1% sucrose medium (pH 5.5) with 1% agar under continuous light (90–100 µmol m⁻²s⁻¹) at 22°C.

extract_protocol:
Plant samples were frozen in liquid nitrogen, and total RNA was extracted from seedlings using the RNeasy Plant Mini Kit (Qiagen).
RNA libraries were prepared for sequencing following standard NovaSeq protocols.

treatment_protocol: Arabidopsis thaliana seeds were grown in 1/2× MS + 1% sucrose medium  for seven days under continuous light, then exposed to heat stress at 37°C for 0 or 1 hour.

value: seedlings

value: eTK

value: hsfa1a/hsfa1b/hsfa1d, ko

value: HS


title: Rv1, control, AR, forARKD, rep2

description: Library name: Rv1-pLKO.1-AR-forARKD-rep2

value: Human prostate cancer cell line

value: WT


title: dLN_Pos_2

description: Library name: Sequencing 8

source_name: dLN

value: dLN


title: eTK_HS, rep2

description:
Library name: sample 17
Column name in counts_HS_Ath.txt: eTK-HS2


title: Rv1, ARKD, AR, rep2

description: Library name: Rv1-ARKD-AR-rep2


title: eTK_HS, rep1

description:
Library name: sample 16
Column name in counts_HS_Ath.txt: eTK-HS1


title: Rv1, control, AR, forARKD, rep1

description: Library name: Rv1-pLKO.1-AR-forARKD-rep1


title: Ctrl Luciferase bio rep 2

value: Luciferase shRNA


title: eTK_Cntr, rep6

description:
Library name: sample 15
Column name in counts_HS_Ath.txt: eTK-CK6

value: Cntr


title: eTK_Cntr, rep5

description:
Library name: sample 14
Column name in counts_HS_Ath.txt: eTK-CK5


title: Rv1, ARKD, BPTF, rep2

description: Library name: Rv1-ARKD-BPTF-rep2

value: BPTF (EMD Millipore, ABE1966)


title: eTK_Cntr, rep4

description:
Library name: sample 13
Column name in counts_HS_Ath.txt: eTK-CK4


title: dLN_Pos_1

description: Library name: Sequencing 7


title: eTK_Cntr, rep3

description:
Library name: sample 12
Column name in counts_HS_Ath.txt: eTK-CK3


title: dLN_Neg_2

description: Library name: Sequencing 6


title: Col-0_HS, rep3

description:
Library name: sample 9
Column name in counts_HS_Ath.txt: Col0-HS3

value: Col-0, wt


title: SW480 cells, negative control vector, 48h-1

description: Library name: ZEB2neg_sw480-1

value: epithelial, adenocarcinoma


title: Lung_Neg_2

description: Library name: Sequencing 10

value: Lung


title: eTK_Cntr, rep1

description:
Library name: sample 10
Column name in counts_HS_Ath.txt: eTK-CK1


title: Rv1, ARKD, BPTF, rep1

description: Library name: Rv1-ARKD-BPTF-rep1


title: Rv1, control, BPTF, forARKD, rep2

description: Library name: Rv1-pLKO.1-BPTF-forARKD-rep2

value: shControl


title: BAL_Pos_2

description: Library name: Sequencing 4

source_name: Bronchoalveolar lavage (BAL)

value: Bronchoalveolar lavage (BAL)


title: Col-0_HS, rep2

description:
Library name: sample 8
Column name in counts_HS_Ath.txt: Col0-HS2


title: Rv1, control, BPTF, forARKD, rep1

description: Library name: Rv1-pLKO.1-BPTF-forARKD-rep1


title: eTK_Cntr, rep2

description:
Library name: sample 11
Column name in counts_HS_Ath.txt: eTK-CK2


title: Col-0_HS, rep1

description:
Library name: sample 7
Column name in counts_HS_Ath.txt: Col0-HS1


title: Col-0_Cntr, rep6

description:
Library name: sample 6
Column name in counts_HS_Ath.txt: Col0-CK6


title: BAL_Pos_1

description: Library name: Sequencing 3


title: Rv1, control, IgG

description: Library name: Rv1-pLKO.1-IgG

value: IgG (EpiCypher, 13-0042)


title: Col-0_Cntr, rep5

description:
Library name: sample 5
Column name in counts_HS_Ath.txt: Col0-CK5


title: Col-0_Cntr, rep3

description:
Library name: sample 3
Column name in counts_HS_Ath.txt: Col0-CK3


title: BAL_Neg_2

description: Library name: Sequencing 2


title: Rv1, BPTFKD, FOXA1, rep2

description: Library name: Rv1-BPTFKD-FOXA1-rep2

value: BPTF knock down

value: shBPTF

value: FOXA1 (EpiCypher, 13-2001)


title: BAL_Neg_1

description: Library name: Sequencing 1


title: Col-0_Cntr, rep4

description:
Library name: sample 4
Column name in counts_HS_Ath.txt: Col0-CK4

value: seedlings


title: Col-0_Cntr, rep2

description:
Library name: sample 2
Column name in counts_HS_Ath.txt: Col0-CK2


title: Rv1, BPTFKD, FOXA1, rep1

description: Library name: Rv1-BPTFKD-FOXA1-rep1


title: Col-0_Cntr, rep1

description:
Library name: sample 1
Column name in counts_HS_Ath.txt: Col0-CK1


title: eTK_HS_ATAC, rep2

description:
Library name: sample 8
Column name in counts_HS_Ath_ATAC.txt: eTK-HS2

data_processing:
Raw ATAC-seq sequence data were trimmed to remove adapters and were quality-checked using fastp (v0.24.0) and FastQC (v0.11.9). Processed reads were aligned to the Arabidopsis reference genome (Araport11) with Bowtie2 (v2.4.4). Alignments with low quality (mapping quality < 2), those mapped to mitochondrial or chloroplast genomes, and PCR duplicates were identified and removed using Samtools view (v1.14). ATAC-seq peaks were identified across biological replicates with MACS2 (v2.2.7.1) using the following parameters: -f BAMPE -g 1.1e8 --cutoff-analysis --nomodel --shift -100 --extsize 200. Identified peaks were consolidated using BEDtools merge to generate a consensus peak list. ATAC-seq alignments were assigned and quantified at these peak regions using the featureCounts function from subread (v2.0.6). Bigwig coverage tracks for data visualization in the Integrated Genome Browser (IGV) were created from merged replicate BAM files using deepTools49 (v3.5.5) bamCoverage with a 10-bp bin size and Reads Per Kilobase Million (RPKM) normalization.
Assembly: Arabidopsis genome Araport11
Supplementary files format and content: Tab-delimited text file includes peak raw counts for each sample, Bigwig coverage tracks from merged replicate BAM files
Supplementary files format and content: counts_HS_Ath_ATAC.txt and all bigwig coverage tracks

growth_protocol: Arabidopsis thaliana wild type (Col0) and knockout mutants (hsfa1a/hsfa1b/hsfa1d triple knockout) were grown on 1/2× MS + 1% sucrose medium  (pH 5.5) with 1% agar under continuous light (90–100 µmol m⁻²s⁻¹) at 22°C.

extract_protocol:
Whole Arabidopsis thaliana seedlings (1.5 g) were finely chopped with a razor blade in 4 mL of ice-cold LB01 buffer (15 mM pH7.5 Tris , 2 mM EDTA, 0.5 mM spermine, 10mM KCl, 20mM NaCl, 0.2% Triton X-100, and cOmplete Protease Inhibitor Cocktail) for 2-5 minutes in a chilled petri dish, followed by 10 minutes of incubation at 4°C. The lysate was then filtered twice through a 40 µm filter and transferred to an ice-cold 15 mL tube. Nuclei were pelleted by centrifugation at 500 × g for 10 minutes at 4°C, and the supernatant was carefully removed. The pellet was gently resuspended in 2 mL of LB01 buffer and centrifuged again under the same condition. After removing the supernatant, the nuclei were resuspended in 1 mL of LB01 buffer in a 5 mL round-bottom tube and stained with 10 µg/mL DAPI. Flow cytometry was performed on a BD FACS Aria II using a 100 µm nozzle at a pressure below 20 psi. Sorting gates were set based on FSC and SSC to exclude debris and potential doublets. Baseline fluorescence was established by running unstained control samples before sorting DAPI-stained nuclei. 50,000 sorted nuclei were collected into 500 µL of LB01 buffer (without Triton X-100) in 1.5 mL Eppendorf tubes per sample.
The nuclei were pelleted by centrifugation at 1000 × g for 10 minutes at 4°C. The sorted nuclei were resuspended in a 50 µL tagmentation reaction mixture consisting of 25 µL of 2x TD buffer, 2.5 µL of TDE1 enzyme (Illumina Tagment DNA TDE1 Enzyme and Buffer Kits), and 22.5 µL of nuclease-free water. The reaction was incubated at 37°C for 30 minutes, followed by DNA purification with Zymo CHIP DNA Clean and Concentrator (Cat# D5205). The eluted DNA was amplified with dual-indexed Nextera primers using NEBNext 2x HiFi PCR Master Mix (New England Biolabs) for library construction. For library amplification, 10 µL of transposed DNA fragments were mixed with 25 µL of NEBNext 2x HiFi PCR Master Mix, 6.25 µL of 10 µM T5 primer, and 2.5 µL of nuclease-free water. The corresponding T7 primer (6.25 µL) was added, and PCR amplification was performed with the following conditions: 72°C for 5 minutes (initial denaturation), 98°C for 30 seconds, then 5 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. Additional cycles were optimized via qPCR using PowerSYBR™ Green Master Mix on 5 µL of the amplified library. Amplified libraries underwent dual size selection using a 1.2x SPRIselect magnetic bead ratio (Beckman Coulter). Library quality was assessed with a Bioanalyzer High Sensitivity DNA Analysis kit (Agilent).

value: eTK

value: hsfa1a/hsfa1b/hsfa1d, ko

value: HS


title: dLN_Neg_1

description: Library name: Sequencing 5

value: dLN


title: Rv1, control, FOXA1, rep2

description: Library name: Rv1-pLKO.1-FOXA1-rep2

value: Human prostate cancer cell line

value: WT


title: Mouse Parathyroid M MUT4

city: Bethesda

first: James

last: Iben

address: 10 CENTER DR

department: NICHD

institute: NIH

description:
Library name: MUT-4
FFPE Visium probe capture

data_processing:
RNA probe sequences were demultiplexed and aligned using 10x spaceranger software, generating spatially resolved count matricies
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: List of genes
Supplementary files format and content: matrix.mtx.gz: Market Matrix Exchange format matrix of gene counts
Supplementary files format and content: spatial_enrichment.csv: Normalized gene expression
Supplementary files format and content: tissue_hires_image.png: Hi-res image of the tissue
Supplementary files format and content: tissue_positions.csv: Coordinates of spatial barcodes on the tissue
Library strategy: Spatial Transcriptomics

source_name: Parathyroid

extract_protocol:
FFPE fixed tissue was sections and placed on Visium slides according to 10x manufacturer instructions
Spatial transcriptomics slide libraries were prepared using 10x FFPE Visium kits following manufacterer instructions

value: Parathyroid

value: Gcm2 variant p.Y392S


title: Mouse Parathyroid F MUT3

description:
Library name: MUT-3
FFPE Visium probe capture


title: Rv1, control, FOXA1, rep1

first: Jianfei

last: Qi

description: Library name: Rv1-pLKO.1-FOXA1-rep1


title: eTK_Cntr_ATAC, rep1

description:
Library name: sample 5
Column name in counts_HS_Ath_ATAC.txt: eTK-CK1

value: Cntr


title: Col-0_HS_ATAC, rep2

description:
Library name: sample 4
Column name in counts_HS_Ath_ATAC.txt: Col0-HS2

value: Col-0, wt


title: Mouse Parathyroid M WT4

description:
Library name: WT-4
FFPE Visium probe capture


title: Rv1, BPTFKD, AR, rep2

description: Library name: Rv1-BPTFKD-AR-rep2

value: AR (EMD Millipore, 06-680)


title: Col-0_Cntr_ATAC, rep2

description:
Library name: sample 2
Column name in counts_HS_Ath_ATAC.txt: Col0-CK2


title: Mouse Parathyroid F WT3

description:
Library name: WT-3
FFPE Visium probe capture


title: Rv1, BPTFKD, AR, rep1

description: Library name: Rv1-BPTFKD-AR-rep1


title: Co-l0_HS_ATAC, rep1

description:
Library name: sample 3
Column name in counts_HS_Ath_ATAC.txt: Col0-HS1


title: Col-0_Cntr_ATAC, rep1

description:
Library name: sample 1
Column name in counts_HS_Ath_ATAC.txt: Col0-CK1


title: TSSB71 (OMM2.5_siSETDB1)

city: Nice

first: Corine

last: Bertolotto

address: 151 route Saint-Antoine de Ginestière

country: France

institute: C3M - U1065 INSERM - CENTRE MEDITERRANEEN DE MEDECINE MOLECULAIRE

description: Library name: Sample10

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Assembly: hg38
Supplementary files format and content: excel file with number of reads

extract_protocol:
Trizol RNA extraction
P2699 : Total RNA-Seq libraries were generated from 400 ng of total RNA using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit and IDT for Illumina RNA UD Indexes, Ligation (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, abundant ribosomal RNAs were depleted by hybridization to specific DNA probes and enzymatic digestion. The depleted RNAs were purified and fragmented using divalent cations at 94oC for 2 minutes. After random hexamers annealing, fragmented RNAs were then reverse transcribed into first strand complementary DNA (cDNA). Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dTTP in place of dUTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 13 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

value: uveal melanoma


title: Mouse Parathyroid M MUT2

description:
Library name: MUT-2
FFPE Visium probe capture


title: Rv1, control, AR, rep2

city: Baltimore

address: 655W baltimore street

institute: University of Maryland

description: Library name: Rv1-pLKO.1-AR-rep2

value: shControl


title: TSSB70 (OMM2.5_siLuc)

description: Library name: Sample9


title: Mouse Parathyroid F MUT1

description:
Library name: MUT-1
FFPE Visium probe capture


title: TSSB67 (OMM1_siSETDB1)

description: Library name: Sample6


title: TSSB68 (OMM1.3_siLuc)

description: Library name: Sample7


title: Mouse Parathyroid M WT2

description:
Library name: WT-2
FFPE Visium probe capture


title: Rv1, control, AR, rep1

description: Library name: Rv1-pLKO.1-AR-rep1


title: Rv1, BPTFKD, BPTF, rep2

description: Library name: Rv1-BPTFKD-BPTF-rep2

value: BPTF knock down

value: BPTF (EMD Millipore, ABE1966)


title: TSSB66 (OMM1_siLuc)

description: Library name: Sample5


title: eTK_HS_ATAC, rep1

description:
Library name: sample 7
Column name in counts_HS_Ath_ATAC.txt: eTK-HS1


title: TSSB65 (MP65_siSETDB1)

description: Library name: Sample4


title: Mouse Parathyroid F WT1

description:
Library name: WT-1
FFPE Visium probe capture


title: Rv1, BPTFKD, BPTF, rep1

description: Library name: Rv1-BPTFKD-BPTF-rep1

value: shBPTF


title: eTK_Cntr_ATAC, rep2

description:
Library name: sample 6
Column name in counts_HS_Ath_ATAC.txt: eTK-CK2

value: seedlings


title: D3_D4_D5

first: Kang-Yu

last: Tai

address: Yonglin Biomedical Engineering Hall, No.49, Fanglan Rd.

department: Genome and Systems Biology Degree Program

institute: National Taiwan University

description: Library name: Zone_D

data_processing:
Space Ranger V3.1.2
Raw sequencing data were processed using Space Ranger V3.1.2 (10x Genomics) for read alignment, unique molecular identifier (UMI) counting, and spatial gene expression matrix generation.
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg
Supplementary files format and content: tissue_hires_image.png
Supplementary files format and content: tissue_lowres_image.png
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
Skin samples were fixed in 10% neutral-buffered formalin for 24 hours at room temperature, followed by sequential dehydration in graded ethanol (70%–100%), clearing in xylene, and embedding in paraffin. Paraffin blocks were sectioned at 10 µm thickness using a rotary microtome (Leica RM2235) and mounted onto Visium HD Spatial Gene Expression slides (10x Genomics) under RNase-free conditions.
For spatially resolved transcriptomic profiling, Visium HD Mouse WT Probes v2 (10x Genomics) was employed according to the manufacturer’s protocol.

treatment_protocol: Murine skin samples were collected from C57BL/6 mice from day 0 to day 5 after SDS treatment.

value: Skin


title: TSSB63 (MP46_siSETDB1)

description: Library name: Sample2


title: TSSB62 (MP46_siLuc)

description: Library name: Sample1


title: Rv1, control, BPTF, rep2

description: Library name: Rv1-pLKO.1-BPTF-rep2


title: D0_D1_D2

description: Library name: Zone_A


title: Multiome - ATAC - PH626_T

first: Alexandre

last: Gaspar-Maia

address: 200 First street SW

description:
Library name: Multiome - ATAC - PH626_T
PH626_T_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
Sequenced reads from the gene expression (GEX) and DNA accessibility (ATAC) droplet libraries were aligned and quantified using 10x Genomics Cell Ranger ARC v2.0.0. The reads were aligned to the pre-built human reference genome GRCh38 - v2020-A-2.0.0 (May 3, 2021) provided by 10X Genomics. After quality control, data from each sample was processed using Seurat v5.2.1 and Signac v1.14.0 functions. GEX and ATAC count matrices from each sample were merged independently using Seurat. GEX count matrix was log-normalized, scaled to mean 0 and variance 1, and dimensionality reduction was performed using PCA on the top 2000 highly variable genes. Uniform manifold approximation and projection (UMAP) for GEX was calculated using the top 50 principal components. Open chromatin peaks called per sample were merged using reduce function from GenomicRanges R package, then the ATAC fragment count matrix was recalculated using Signac. Merged peaks that were smaller than 20 base pairs or larger than 10000 base pairs were removed from analysis. The ATAC count matrix was normalized using Term Frequency - Inverse Document Frequency (TF-IDF) and dimensionality reduction performed using singular value decomposition (SVD) using only peaks with non-zero counts in at least 20 cells - together known as latent semantic indexing (LSI) that generates LSI components. The UMAP for ATAC was calculated using LSI components 2 to 50. Seurat’s weighted nearest neighbor (WNN) algorithm was used on principal components 1 to 50 (GEX) and LSI components 2 to 50 (ATAC) together to obtain a combined UMAP projection of both modalities. Cells with more than 20% of reads mapped to mitochondrial genes, those with less than 200 unique genes detected (GEX), those with less than 200 unique peaks detected (ATAC) and those with transcription start site (TSS) enrichment score (as calculated by Signac) less than 1 were removed for quality control.
Assembly: hg38
Supplementary files format and content: Cellranger output files: h5 files and ATAC fragments files (tsv)

source_name: Ovarian cancer in PDX

extract_protocol:
Fresh tumor tissue obtained from ovarian cancer patients after debulking surgery was transferred in a sterile 10 cm culture dish and finely minced using scissors in KRB buffer. The sample was centrifuged at 500 g for 5 mins at 4°C, and the supernatant was gently removed without disrupting the pellet. Washes were repeated until the supernatant appeared clear. After the last centrifugation, tissue was aliquoted in cryovials and frozen in liquid nitrogen. On the day of the experiment, frozen tissue was cut into small pieces without thawing and used for the nuclei isolations.
The nuclei isolation was performed based on the 10x genomics suggested protocol for Complex Tissues for Single Cell snATAC + snRNA. After mincing, a small piece of tissue the size of rice grain was transferred to a 2 mL microcentrifuge tube containing 300 μL of NP-40 Lysis Buffer and homogenized on ice using a pellet pestle. After adding 1 mL of NP-40 Lysis Buffer, the samples were incubated on ice for either 5 or 30 minutes. After incubation, the samples were strained using a 70 μm cell strainer, and the flow through was then centrifuged 500 g for 5 mins at 4°C. After centrifugation, the nuclei were permeabilized by resuspending in 100 μL of 0.1X Lysis Buffer and incubating on ice for 2 minutes. After adding 1 mL of Wash Buffer, the nuclei were centrifuged at 500 g for 5 mins at 4°C, and the pellet was resuspended in Diluted nuclei buffer. The nuclei concentration was assessed by PI staining using a Cellometer K2 cell counter. Between 1000 and 8000 nuclei per sample were subjected to transposase assays (exposing buffered nuclei to Tn5 transposase) before proceeding to single-cell partitioning into gel beads in emulsion, barcoding, and pre-amplification. ATAC library construction and cDNA, followed by GEX library construction, were done following established 10x Genomics protocols. The libraries concentration was measured using Qubit High Sensitivity assays (Thermo Fisher Scientific), and library profiles were assessed in a fragment analyzer (Advance Analytical) before sequencing. The snATAC and snRNA libraries were sequenced for 50bp paired end sequencing, PE50 and 100PE, respectively on a HiSeq 4000, NextSeq 2000 or NovaSeq X 1.5B instrument (Illumina) before demultiplexing and alignment to the reference genome (GRCh38/hg38).

value: Ovarian cancer in PDX

value: Chemotherapy treated

tag: library type

value: ATAC


title: Rv1, control, BPTF, rep1

description: Library name: Rv1-pLKO.1-BPTF-rep1

value: Human prostate cancer cell line


title: Multiome - ATAC - PH27_T

description:
Library name: Multiome - ATAC - PH27_T
PH27_T_filtered_feature_bc_matrix.h5


title: Multiome - ATAC - PH626_C

description:
Library name: Multiome - ATAC - PH626_C
PH626_C_filtered_feature_bc_matrix.h5

value: Untreated


title: Rv1, SMARCA1KD, rep2

description: Library name: Rv1-SMARCA1KD-rep2

data_processing:
Quality of ATAC-seq reads was checked using FastQC software
Trim Galore was used to remove adaptor sequences and reads were aligned to the human hg19 reference genome using Bowtie2 –very-sensitive option
SAM files were converted to BAM files, and mitochondrial reads and PCR duplicates were removed. BAM files were used either for peak calling with MACS2 callpeak or for generating RPGC-normalized bigwig files using Deeptools
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
Two biological replicates (1x105 living cells per replicate) were used for sample preparation, following the ATAC-seq kit manual (Active Motif). In brief, cell nuclei were extracted using ATAC lysis buffer and incubated with 50 μl of Tagmentation Master Mix at 37° C for 30 minutes in a thermomixer. The transposed DNA was purified with spin column.
we prepared sequencing library using Nextera index kit. The library was purified with double-sided SPRI beads and library fragment size was evaluated using an Agilent Bioanalyzer.

value: SMARCA1 knock down


title: SDS_D5-1+Topsym

description: Library name: SDS-5-1T

data_processing:
Galaxy version 23.1.rc1
Sequence reads were trimmed for adaptors by Trim Galore ( ver0.6.7)
Trimmed sequence were mapped to mm10 using HISAT2 (ver 2.2.1)
Raw counts were extracted by featureCounts (ver 2.0.3)
Normalized counts were performed by DESeq2 (ver 2.11.40.8)
Assembly: mm10
Supplementary files format and content: tab-delimited file contains raw counts for each sample
Supplementary files format and content: tab-delimited matrix file contains normalized counts for all sample

source_name: whole skin

growth_protocol: 7 week-age mice

extract_protocol:
RNeasy Micro Kit
Agilent SureSelect Strand-Specific RNA library Prep Cat#G9691B

treatment_protocol: Topical treatment as indicated for 4 days

value: whole skin


title: SDS_D5-2+Topsym

description: Library name: SDS-5-2T


title: Multiome - ATAC - PH235_T

description:
Library name: Multiome - ATAC - PH235_T
PH235_T_filtered_feature_bc_matrix.h5


title: TSSB69 (OMM1.3_siSETDB1)

description: Library name: Sample8


title: Multiome - ATAC - PH235_C

description:
Library name: Multiome - ATAC - PH235_C
PH235_C_filtered_feature_bc_matrix.h5


title: Rv1, SMARCA1KD, rep1

description: Library name: Rv1-SMARCA1KD-rep1