title: RAW264.7 cells,ALBL,3

city: Zhangjiagang

first: Cheng

last: Tang

state: Jiangsu

address: Zhugangxiang Road No.1

institute: Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine

description: Library name: Sample 6

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.2.1 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.2.1.
featureCounts v2.0.6-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.42.0).
Assembly: ensembl_107_mus_musculus_c57bl6nj_c57bl_6nj_v1_toplevel
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

growth_protocol: RAW264.7 macrophage cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using TRIzol (TIANGEN) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2（Cat.No.RK20306） for Illumina® following manufacturer's protocols.

treatment_protocol: Osteoclast differentitation was induced by treatment of 3-days post confluent cells(desighnated day,D0)with 50ng/mL RANKL(R&D SYSTEM)

value: Mouse Monocyte/Macrophage Cell Line

value: osteoclast differentiation

tag: condition

value: albiflorin intervention


title: pig endometrium1

status: Public on Jul 01 2026

type: SRA

city: Qingda

first: yadan

last: Jin

state: 山东Shandong

address: Qingdao

country: China

institute: Qingdao Agricultural University

description: Library name: Samples1

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support 10xgenomics. com/single-cel-gene-expression/software/pipelines/latestwhat- is-cel-range)
Assembly: 10mm
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Sus scrofa

source_name: endometrium

extract_protocol:
About 200 mg of endometrial tissue was clipped, washed twice with precooled phosphate-buffered saline (PBS) solution, placed in tissue protection solution (BioYou, 21903-10), and transferred to the laboratory on ice for follow-up treatment. After adding enzyme digestion solution (2 mg/mL collagenase II, 1 mg/mL dispersed protease, 30 μg/mL DNase I, 2.5 mM CaCl2, containing FBS 2% dissolved in basal medium), the samples were shaken in a 37 ℃ water bath shaker at 100 rpm/min for 20 min. The enzyme-digested suspension was filtered through a 30 µm cell filter and added to 15 mL PBS, centrifuged at 500 g for 5 min at 4 ℃. The supernatant was removed and the pellet resuspended with 1 ml of 0.04% BSA, added into 3 ml of 1X RBC to lyse erythrocytes, and left at room temperature for 5 min (the time can be adjusted according to the actual situation of erythrocyte lysis). The suspension was then washed twice with PBS and centrifuged at 4 ℃, 300 g for 5 min. The supernatant was removed and the pellet resuspended in 500 μl of 0.04% BSA. Cell parameters were then tested with a cell counter (CountessTM II FL Automated Cell Counter, Thermo Fisher Scientific, Waltham, MA, USA).
The 10X Genomics 3 'transcriptome uses short-read long sequencing and microfluidic techniques to enable simultaneous transcriptomic profiling of 500-10,000 cells per sample. We combine Gel Beads containing barcode information with a mixture of cells and enzymes, which are then coated with oil surfactant droplets located in a microfluidic "double cross" system to form GEMs (Gel Beads-InEmulsions). GEMs flow into a reservoir and are collected, the gel beads dissolve to release the Barcode sequence, reverse transcrib the cDNA fragment, and label the sample. The gel beads were broken and the oil droplets were broken, and PCR amplification was performed using cDNA as template. The standard sequencing library was constructed by mixing all GEMs products

tag: tissue

value: endometrium

tag: cell line

value: single

tag: cell type

value: endometrium cell


title: RAW264.7 cells,ALBL,2

description: Library name: Sample 5

library_source: transcriptomic

organism: Mus musculus

tag: genotype

value: WT

tag: treatment


title: D#3, 4 hours, mock-infected, untreated

city: Bochum

first: André

last: Gömer

address: University Street 150

department: MMV

country: Germany

institute: Ruhr University Bochum

description: Library name: 68

data_processing:
CLC Genomics Workbench v 24.0.2
Assembly: GenBank accession no. GCA_000003025.6 and GenBank accession no. JQ679013.1
Supplementary files format and content: Mapping statistics exportet from CLC workbench, including count data as RPKM or TPM

source_name: liver

extract_protocol:
Total RNA from primary cells of 4 independent PPH donors was extracted using a NucleoSpin RNA kit (Macherey-Nagel) or a Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer’s instructions.
Poly A enriched libraries were sequenced on a NovaSeq X Plus in PE150 mode.

value: liver

value: primary porcine hepatocytes

tag: donor

value: D#3 (PEI)

tag: time

value: 4 hours

value: mock-infected


title: D#3, 4 hours, HEV-infected, untreated

description: Library name: 66

value: HEV-infected


title: RAW264.7 cells,RANKL,2

description: Library name: Sample 2

value: RANKL intervention


title: RAW264.7 cells,RANKL,3

description: Library name: Sample 3


title: D#3, 72 hours, mock-infected, untreated

description: Library name: 44

value: 72 hours


title: D#3, 72 hours, HEV-infected, untreated

description: Library name: 42


title: RAW264.7 cells,ALBL,1

description: Library name: Sample 4


title: RAW264.7 cells,RANKL,1

description: Library name: Sample 1


title: Aorta, APOE4

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

country: USA

institute: University of Cincinnati

description: Library name: DH-E4-KI_S16

data_processing:
The raw data was de-multiplexed, aligned to the Mus musculus (mm10) reference genome,  quantified and aggregated using the Cell Ranger processing pipelines.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Aorta

growth_protocol: Gene replacement mice, in which the endogenous mouse Apoe gene was replaced with the human APOE2, APOE3, or APOE4 gene at the same locus, were obtained from the Maeda Laboratory at the University of North Carolina and backcrossed to C57BL/6J background. The mice were maintained on a 12-hour light/dark cycle in our institutional pathogen-free animal care facility with free access to normal chow diet (Purina PicoLab Rodent Irradiated Diet 5053; Cincinnati Lab Supply, Cincinnati, OH) and water.

extract_protocol:
Mice were anesthetized and then perfused with phosphate-buffered saline. The whole aorta from the aortic arch to the ileac bifurcation was isolated and trimmed of excess fat tissues surrounding the aorta. The entire aorta was minced into small pieces in phosphate-buffered saline containing 2% BSA, and then incubated for 1 hr at 37 °C in the same buffer containing 450 U/mL collagen-1, 120 U/mL collagen XI, 60 U/mL DNase 1, 60 U/mL hyaluronidase, 1.5 mM CaCl2, and 1.25 mg/mL elastase. The resulting cell suspension was filtered through 70 µm filters, and washed several times to obtain single cell suspension. Quality control was assessed by live/dead cell staining with trypan blue staining. Cell suspensions obtained from 6 APOE2, 5 APOE3, and 7 APOE4 mice were pooled according to APOE genotype for single-cell RNA-seq analysis.
Each pooled single cell suspension was loaded onto a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion and preparation of a bar-coded cDNA library for single cell RNA-sequencing. Quality of the cDNA library was confirmed using an Agilent Bioanalyzer. Full length sequencing was performed on two paired-end 75-bp flow cells using the NovaSeq S4  platform. An overall sequencing depth of approximately 400 million read pairs per sample.

treatment_protocol: Age-matched (12-weeks old) male mice were fed a Western diet containing 42% fat and 0.2% cholesterol (TD88137; Teklad Custom Diets, Madison, WI) for 16 weeks.

value: Aorta


title: D#1, 72 hours, mock-infected, untreated

description: Library name: 72hmock


title: D#1, 4 hours, HEV-infected, untreated

description: Library name: 4hp6


title: Aorta, APOE3

description: Library name: DH-E3-KI_S16


title: Aorta, APOE2

description: Library name: DH-E2-KI_S16


title: Ribo_17hpi_4E-T-overexpressing_rep2

city: Nanjing

first: Pinhua

last: Wang

address: 101 Longmian Avenue, Jiangning District, Nanjing.

institute: Nanjing Medical university

description:
Library name: sample67
FPKM_Ribo_4E-T-overexpressing_ALL.txt.gz

data_processing:
The RNA-seq reads quality was evaluated using  FastQC v0.12.1. The clean reads were mapped to the mm10 genome by STAR v2.7.11b. The gene expression level was determined using RSeQc v5.0.3. Supplementary files format and content: plain txt file, each contains two column. First column means the gene ID, the second column means sample's FPKM.
The Ribo-seq raw reads were trimmed by fastp v0.23.4. The quality of sequencing data, both before and after trimming, was assessed using FastQC v0.12.1. Trimmed reads were filtered by SortMeRNA v4.3.6. The clean reads were mapped to mm10 genome by STAR v2.7.11b, then quantified by Salmon v1.10.3. Gene-level abundance counts were derived from transcript-level estimates using the tximport R package v1.20.1. FPKM values were computed for each gene from their read counts and effective lengths. Read distribution for UTR and CDS were characterized by RseQC v5.0.3. The distribution of RPF 5' ends across the three translation frames was assessed using the quality module of Ribo-TISH v0.2.7. The read length distribution for uniquely mapped reads was obtained from ribotricer v1.3.3.
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: plain txt file, each contains two column. First column means the gene ID, the second column means sample's FPKM.

extract_protocol:
Embryos in this study were derived from  In Vitro fertilization (IVF).Oocytes and embryos were collected at indicated time point.For RNA-seq, the collected samples were immediately transferred in lysis buffer (0.2% Triton X-100 and 2 U/ul RNase inhibitor) and then frozen at -80℃.
For Ribo-seq, the collected samples were were lysed in iced lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml CHX, 1% Triton X-100; 25 U/ml Turbo DNase)  and then frozen at -80℃.
The RNA-seq libraries for the collected samples were generated following the Smart-seq2 methodology.Sequnecing libraries were generated with TruePrep DNA Library Prep Kit (Vazyme, TD502) according to the manufacturer's guidance.
For Ribo-seq, the lysate was then treated with 1 ul RNaseI 100 U/μ and incubated at room temperature for 45 min with gentle mixing. The nuclease digestion was stopped by adding 10μl SUPERase·In. Subsequently, ribosome-protected fragments (RPFs) were separated by the conventional Ribo-seq. RPFs library construction was conducted using Ezra-seq approach as previously described.


title: D#2, 4 hours, HEV-infected, untreated

description: Library name: 62


title: D#2, 4 hours, mock-infected, untreated

description: Library name: 61


title: Ribo_17hpi_control-overexpressing_rep2

description:
Library name: sample65
FPKM_Ribo_4E-T-overexpressing_ALL.txt.gz


title: Ribo_17hpi_control-overexpressing_rep1

description:
Library name: sample64
FPKM_Ribo_4E-T-overexpressing_ALL.txt.gz


title: D#2, 72 hours, HEV-infected, untreated

description: Library name: 91


title: D#2, 72 hours, mock-infected, untreated

description: Library name: 90


title: D#4, 72 hours, HEV-infected, baricitinib

description: Library name: 35

value: 1 µM baricitinib


title: RNA_33hpi_4E-T-overexpressing_rep3

description:
Library name: sample63
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz

molecule: polyA RNA

source_name: 33hpi_mid 2-cells

value: 33hpi_mid 2-cells


title: RNA_33hpi_4E-T-overexpressing_rep1

description:
Library name: sample61
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: RNA_33hpi_control-overexpressing_rep3

description:
Library name: sample60
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: D#4, 72 hours, mock-infected, untreated

description: Library name: 31


title: bves KO-EX knockout exercise group-3

city: Changsha

first: Wanwan

last: Cai

state: Hunan

address: Lushan South Road

institute: Hunan Normal Universit

description:
Library name: sample 3-3
KO_gugeD_3_count

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Assembly: zebrafish genome (taxid:7955)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...

organism: Danio rerio

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions. The RNA-seq transcriptome librariy was prepared following Illumina Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: skeletal muscle


title: RNA_33hpi_control-overexpressing_rep2

description:
Library name: sample59
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: RNA_33hpi_control-overexpressing_rep1

description:
Library name: sample58
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: bves KO-EX knockout exercise group-2

description:
Library name: sample 3-2
KO_gugeD_2_count


title: D#1, 4 hours, mock-infected, untreated

description: Library name: 4hmock


title: bves KO knockout group-3

description:
Library name: sample 2-3
KO_guge_3_count


title: RNA_25hpi_4E-T-overexpressing_rep2

description:
Library name: sample56
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz

source_name: 25hpi_early 2-cells

value: 25hpi_early 2-cells


title: RNA_25hpi_4E-T-overexpressing_rep3

description:
Library name: sample57
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: bves KO knockout group-2

description:
Library name: sample 2-2
KO_guge_2_count


title: WT control group-3

description:
Library name: sample 1-3
WT_guge_3_count


title: RNA_33hpi_4E-T-overexpressing_rep2

description:
Library name: sample62
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: RNA_25hpi_control-overexpressing_rep1

description:
Library name: sample52
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: RNA_17hpi_4E-T-overexpressing_rep3

description:
Library name: sample51
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: WT control group-1

description:
Library name: sample 1-1
WT_guge_1_count


title: PFHxS-high--14L10D-rep-rep4

city: Clemson

first: Subham

last: Dasgupta

state: South Carolina

address: 142 Long Hall

department: Biological Sciences

institute: Clemson University

description: Library name: CLEM_20

data_processing:
Raw data (raw reads) in fastq format was firstly processed throughin-house perl scripts. In this step, clean data (clean reads) was obtainedbyremoving reads containing adapter, reads containing ploy-N and lowqualityreads from raw data. A
Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the referencegenome using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene.
Differential expression analysisof two conditions/groups (4 biological replicates per condition) was performed using the DESeq2R package (1.20.0).
Assembly: GRZ11
Supplementary files format and content: Excel file contains FPKM values for each sample

source_name: whole embryo

growth_protocol: Embryos were spawned and maintained in system water

extract_protocol:
At each time point, embryos were collected in RNA zol, homogenized and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit (Zymo). RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.
For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification(
For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification(

treatment_protocol: Embryos were exposed to 0 or 0.0025 (low) or 25 (high) uM PFHxS in 0.1% DMSO from 0.75 to 120 hpf under dark conditions

value: whole embryo

value: wildtype

value: PFHxS-high


title: PFHxS-high--14L10D-rep-rep3

description: Library name: CLEM_19


title: RNA_17hpi_control-overexpressing_rep3

description:
Library name: sample48
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: PFHxS-high--14L10D-rep-rep2

description: Library name: CLEM_18


title: PFHxS-high--14L10D-rep-rep1

description: Library name: CLEM_17


title: RNA_17hpi_control-overexpressing_rep1

description:
Library name: sample46
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: RNA_17hpi_control-overexpressing_rep2

description:
Library name: sample47
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: PFHxS-low--14L10D-rep-rep4

description: Library name: CLEM_16

value: PFHxS-low


title: RNA_13hpi_4E-T-overexpressing_rep3

description:
Library name: sample45
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: PFHxS-low--14L10D-rep-rep3

description: Library name: CLEM_15


title: RNA_13hpi_4E-T-overexpressing_rep2

description:
Library name: sample44
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: PFHxS-low--14L10D-rep-rep2

description: Library name: CLEM_14


title: RNA_13hpi_4E-T-overexpressing_rep1

description:
Library name: sample43
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: PFHxS-low--14L10D-rep-rep1

description: Library name: CLEM_13


title: RNA_13hpi_control-overexpressing_rep3

description:
Library name: sample42
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: DMSO--14L10D-rep-rep4

description: Library name: CLEM_12

value: DMSO


title: RNA_13hpi_control-overexpressing_rep2

description:
Library name: sample41
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: DMSO--14L10D-rep-rep3

description: Library name: CLEM_11


title: RNA_13hpi_control-overexpressing_rep1

description:
Library name: sample40
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: DMSO--14L10D-rep-rep2

description: Library name: CLEM_10


title: DMSO--14L10D-rep-rep1

description: Library name: CLEM_9


title: bves KO-EX knockout exercise group-1

description:
Library name: sample 3-1
KO_gugeD_1_count


title: RNA_39hpi_MG132-treated_rep2

description:
Library name: sample38
FPKM_RNA_MG132_ALL.txt.gz

source_name: 39hpi_late 2-cells

value: 39hpi_late 2-cells


title: PFHxS-high-24D-rep4

description: Library name: SF19


title: RNA_39hpi_MG132-treated_rep1

description:
Library name: sample37
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_25hpi_4E-T-overexpressing_rep1

description:
Library name: sample55
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: RNA_25hpi_control-overexpressing_rep3

description:
Library name: sample54
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: bves KO knockout group-1

description:
Library name: sample 2-1
KO_guge_1_count


title: RNA_25hpi_control-overexpressing_rep2

description:
Library name: sample53
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: PFHxS-high-24D-rep3

description: Library name: SF18


title: PFHxS-high-24D-rep2

description: Library name: SF17


title: RNA_39hpi_control_rep3

description:
Library name: sample36
FPKM_RNA_MG132_ALL.txt.gz


title: WT control group-2

description:
Library name: sample 1-2
WT_guge_2_count


title: RNA_17hpi_4E-T-overexpressing_rep1

description:
Library name: sample49
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: RNA_17hpi_4E-T-overexpressing_rep2

description:
Library name: sample50
FPKM_RNA_4E-T-overexpressing_ALL.txt.gz


title: RNA_39hpi_control_rep2

description:
Library name: sample35
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_39hpi_control_rep1

description:
Library name: sample34
FPKM_RNA_MG132_ALL.txt.gz


title: PFHxS-high-24D-rep1

description: Library name: SF16


title: PFHxS-low-24D-rep4

description: Library name: SF14


title: RNA_33hpi_MG132-treated_rep3

description:
Library name: sample33
FPKM_RNA_MG132_ALL.txt.gz

source_name: 33hpi_late 2-cells

value: 33hpi_late 2-cells


title: PFHxS-low-24D-rep3

description: Library name: SF13


title: PFHxS-low-24D-rep2

description: Library name: SF12


title: RNA_33hpi_MG132-treated_rep2

description:
Library name: sample32
FPKM_RNA_MG132_ALL.txt.gz


title: PFHxS-low-24D-rep1

description: Library name: SF11


title: RNA_33hpi_MG132-treated_rep1

description:
Library name: sample31
FPKM_RNA_MG132_ALL.txt.gz


title: DMSO-24D-rep4

description: Library name: SF5


title: RNA_33hpi_control_rep3

description:
Library name: sample30
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_33hpi_control_rep1

description:
Library name: sample28
FPKM_RNA_MG132_ALL.txt.gz


title: DMSO-24D-rep1

description: Library name: SF1


title: DMSO-24D-rep2

description: Library name: SF2


title: RNA_33hpi_control_rep2

description:
Library name: sample29
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_31hpi_MG132-treated_rep2

description:
Library name: sample26
FPKM_RNA_MG132_ALL.txt.gz

source_name: 31hpi_mid 2-cells

value: 31hpi_mid 2-cells


title: DMSO-24D-rep3

description: Library name: SF3


title: RNA_31hpi_MG132-treated_rep3

description:
Library name: sample27
FPKM_RNA_MG132_ALL.txt.gz


title: HepG2-CC3_PA

city: Yufu

first: Takuro

last: Uchida

state: Oita

address: 1-1 Idaigaoka, Hasama

country: Japan

institute: Oita University

description: Library name: Sample 16

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

organism: Homo sapiens

extract_protocol:
The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set  according protocols

treatment_protocol: Part of cells were treated with 250uM of palmitic acid for 48H.

value: C/C

value: 250uM of palmitic acid, 55H


title: RNA_31hpi_MG132-treated_rep1

description:
Library name: sample25
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_31hpi_control_rep3

description:
Library name: sample24
FPKM_RNA_MG132_ALL.txt.gz


title: HepG2-CC1_PA

description: Library name: Sample 15

value: 250uM of palmitic acid, 54H


title: RNA_31hpi_control_rep2

description:
Library name: sample23
FPKM_RNA_MG132_ALL.txt.gz


title: HepG2-GC3_PA

description: Library name: Sample 13

value: G/C

value: 250uM of palmitic acid, 52H


title: RNA_31hpi_control_rep1

description:
Library name: sample22
FPKM_RNA_MG132_ALL.txt.gz


title: HepG2-GC4_PA

description: Library name: Sample 14

value: 250uM of palmitic acid, 53H


title: HepG2-GC2_PA

description: Library name: Sample 12

value: 250uM of palmitic acid, 51H


title: RNA_25hpi_MG132-treated_rep2

description:
Library name: sample20
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_25hpi_MG132-treated_rep3

description:
Library name: sample21
FPKM_RNA_MG132_ALL.txt.gz


title: HepG2-GG2_PA

description: Library name: Sample 10

value: G/G

value: 250uM of palmitic acid, 49H


title: HepG2-GG6_PA

description: Library name: Sample 11

value: 250uM of palmitic acid, 50H


title: HepG2-GG1_PA

description: Library name: Sample 9

value: 250uM of palmitic acid, 48H


title: RNA_25hpi_MG132-treated_rep1

description:
Library name: sample19
FPKM_RNA_MG132_ALL.txt.gz

value: 25hpi_early 2-cells


title: RNA_25hpi_control_rep3

description:
Library name: sample18
FPKM_RNA_MG132_ALL.txt.gz


title: HepG2-CC3

description: Library name: Sample 8

value: control


title: HepG2-CC1

description: Library name: Sample 7


title: RNA_25hpi_control_rep1

description:
Library name: sample16
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_25hpi_control_rep2

description:
Library name: sample17
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_17hpi_MG132-treated_rep3

description:
Library name: sample15
FPKM_RNA_MG132_ALL.txt.gz


title: HepG2-GC4

description: Library name: Sample 6


title: RNA_17hpi_MG132-treated_rep1

description:
Library name: sample13
FPKM_RNA_MG132_ALL.txt.gz


title: HepG2-GC3

description: Library name: Sample 5


title: RNA_17hpi_MG132-treated_rep2

description:
Library name: sample14
FPKM_RNA_MG132_ALL.txt.gz


title: HepG2-GC2

description: Library name: Sample 4


title: HepG2-GG6

description: Library name: Sample 3


title: RNA_17hpi_control_rep3

description:
Library name: sample12
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_39hpi_MG132-treated_rep3

description:
Library name: sample39
FPKM_RNA_MG132_ALL.txt.gz


title: HepG2-GG2

description: Library name: Sample 2


title: RNA_17hpi_control_rep2

description:
Library name: sample11
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_17hpi_control_rep1

description:
Library name: sample10
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_13hpi_MG132-treated_rep3

description:
Library name: sample9
FPKM_RNA_MG132_ALL.txt.gz


title: Taf1_humanization_hTAF1~2ndSVAdel

city: New York

first: Weimin

last: Zhang

state: NY

address: 435 E 30th street

department: Institute for Systems Genetics

institute: NYU Langone Health

description:
Library name: BS17204A
Plasmid DNA was prepped from E. coli, but only the plasmid DNA was sequenced.

library_source: other

data_processing:
Sequencing reads were demultiplexed using bcl2fastq v2.20, and subsequently trimmed using Trimmomatic v0.39. Trimmed reads were aligned to references using BWA v0.7.17 for Illumina sequencing and minimap2 for Nanopore sequencing. Duplicates were marked using samblaster v0.1.24.
Coverage depth tracks and quantification was generated using BEDOPS v2.4.35. Sequencing data were visualized using UCSC genome browser, or IGV.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping.
Assembly: mm10, custom TAF1 refernece
Supplementary files format and content: bigwig and bedgraph files mapping to genome references

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
For targeted capture sequencing,1-3 million of mESCs were harvested for genomic DNA extraction by using a QIAamp DNA Mini Kit (QIAGEN, 51306). For plasmid DNA sequencing, plasmids were extracted by using a NucleoBond Xtra BAC kit (Takara, 740436.25).
For targeted capture sequencing and plasmid sequencing, approximately 100 ng DNA was used for the library construction using the NEBNext Ultra II FS DNA library prep kit (E7805). AMPure XP beads (Beckman Coulter, A63881) were used for DNA purification on a magnetic stand.

value: synthetic construct


title: HepG2-GG1

description: Library name: Sample 1


title: Taf1_humanization_hTAF1~mousifiedSVAdel

description:
Library name: BS13639A
Plasmid DNA was prepped from E. coli, but only the plasmid DNA was sequenced.


title: RNA_13hpi_MG132-treated_rep1

description:
Library name: sample7
FPKM_RNA_MG132_ALL.txt.gz


title: Taf1_humanization_hTAF1~mousified

description:
Library name: BS13076A
Plasmid DNA was prepped from E. coli, but only the plasmid DNA was sequenced.


title: RNA_13hpi_control_rep3

description:
Library name: sample6
FPKM_RNA_MG132_ALL.txt.gz


title: RNA-seq of ZZ1-144h treatment repeat3

city: Nanning

first: Yixue

last: Bao

address: No. 100 Daxue East Road, Xixiangtang District

institute: Guangxi university

description: Library name: S144h-3

data_processing:
Raw reads in fastq format were first processed through fastp (version 0.20.0) to remove adapter sequences and trim low-quality reads (reads with more than 50% of bases having Q-score ≤ 20).
Clean reads were mapped to the sugarcane reference genome (ZZ1) using HISAT2 (version 2.1.0) with default parameters.
The mapped reads of each sample were assembled and quantified using FeatureCounts (subread v1.6.2) to calculate the number of reads mapped to each gene.Gene expression levels were normalized as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Differential expression analysis between the control (0h) and each infection time point was performed using the DESeq2 R package (version 1.22.1).
Assembly: https://ngdc.cncb.ac.cn/gwh/Assembly/83532/show
Supplementary files format and content: csv files include Counts values for each Sample

source_name: leaf

growth_protocol: Sugarcane hybrid ZZ1 (Saccharum officinarum x Saccharum spontaneum) plants were grown in a greenhouse under controlled conditions (28±2°C, 60-70% relative humidity, 14h light/10h dark cycle). Healthy and uniform plants at the 4-5 leaf stage were selected for the experiment.

extract_protocol:
Total RNA was extracted from sugarcane leaf samples using the RNAprep Pure Plant Kit (Tiangen, China) according to the manufacturer’s instructions. RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoDrop spectrophotometer, and RNA concentration was measured using the Qubit RNA Assay Kit in Qubit 2.0 Flurometer.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. The library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The leaves of ZZ1 were inoculated with a spore suspension of Fusarium sacchari (adjusted to 1×106spores/mL). Control samples (0h) and treated samples were collected at 12h, 24h, 48h, 72h, 120h, and 144h post-inoculation. For each time point, leaf tissues were harvested from three biological replicates, immediately frozen in liquid nitrogen, and stored at -80°C.

value: leaf

value: Fusarium sacchari inoculation 144h


title: Taf1_humanization_hTAF1~WT

description:
Library name: BS11309A
Plasmid DNA was prepped from E. coli, but only the plasmid DNA was sequenced.


title: RNA_13hpi_control_rep2

description:
Library name: sample5
FPKM_RNA_MG132_ALL.txt.gz


title: RNA-seq of ZZ1-144h treatment repeat2

description: Library name: S144h-2

organism: Saccharum officinarum x Saccharum spontaneum


title: RNA_13hpi_control_rep1

description:
Library name: sample4
FPKM_RNA_MG132_ALL.txt.gz


title: RNA-seq of ZZ1-144h treatment repeat1

description: Library name: S144h-1


title: RNA-seq of ZZ1-120h treatment repeat3

description: Library name: S120h-3

value: Fusarium sacchari inoculation 120h


title: RNA_MII_control_rep3

description:
Library name: sample3
FPKM_RNA_MG132_ALL.txt.gz

source_name: MII oocytes

value: MII oocytes


title: RNA_MII_control_rep2

description:
Library name: sample2
FPKM_RNA_MG132_ALL.txt.gz


title: RNA_MII_control_rep1

description:
Library name: sample1
FPKM_RNA_MG132_ALL.txt.gz


title: RNA-seq of ZZ1-120h treatment repeat2

description: Library name: S120h-2


title: RNA-seq of ZZ1-120h treatment repeat1

description: Library name: S120h-1


title: Ox44_TCR

city: Tuscaloosa

first: Sergei

last: Bombin

state: AL

address: 739 University Blvd

institute: The University of Alabama

description:
Library name: Sample2_TCR
10X Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger v8.0.1, which aligned reads to the mouse reference transcriptome (refdata-gex-mm10-2020-A) and the V(D)J reference (refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0) to generate filtered feature-barcode matrices and contig annotation files. Downstream analyses were performed in R using the Seurat v5.0.1 package. Low-quality cells were excluded based on the following criteria: fewer than 500 unique molecular identifiers (UMIs), fewer than 200 detected genes (features), counts exceeding the median plus 3 times the median absolute deviation (MAD) for either UMIs or features, or >15% mitochondrial UMI content. Putative doublets were identified and removed using DoubletFinder v2.0.3.
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5 and filtered_contig_annotations.csv

source_name: Brain

extract_protocol:
To perform the scRNA-seq experiment, CD45+ immune cells were isolated from 005 GSC tumor-bearing hemisphere of female C57BL/6 mice 5 days post-oHSV treatment (10X Genomics Inc. Pleasanton, CA). Cells were resuspended in PBS (without Ca or Mg) with 0.04% BSA and freshly processed. Cell viability was assessed with Cellometer Auto 2000 (Nexcelom) using an AOPI staining. Samples with viability ≥80% were loaded in the Chromium X instrument (10X Genomics) to capture ~10 × 103 targeted cells using Chromium Next GEM Single Cell 5' HT Reagent Kits v2 (Dual Index) paired with TCR immune seq from 10X Genomics.
scRNA-seq libraries were generated according to the manufacturer’s instructions. QC (quality control) analysis was performed prior to sequencing with 2100 Bioanalyzer and 2200 TapeStation (Agilent, Santa Clara, CA, USA). Library concentration was assessed prior to sequencing using a Qubit Fluorometer (Thermo Fisher). Sequencing was performed with Novaseq6000 System Illumina (Illumina Inc. San Diego, CA) platform following 10X Genomics guideline; read lengths U26|I10|I10|Y90and sequencing depth of 40,000 paired-end reads per cell for the gene expression libraries and 5,000 paired-end reads per cell for the TCR libraries. Samples were processed at the Integrated Genomics Core Shared Resource (RRID: SCR_026483) at Georgia Cancer Center at Augusta University.

treatment_protocol: To perform the scRNA-seq experiment, CD45+ immune cells were isolated from 005 GSC tumor-bearing hemisphere of female C57BL/6 mice 5 days post-oHSV treatment.

value: Brain

value: murine glioma cells

value: oncolytic HSV1 encoding extracellular domain of CD44 (Ox44)

tag: library type

value: TCR


title: Ox44_GEX

description:
Library name: Sample2_GEX
10X Genomics

value: mRNA


title: RNA-seq of ZZ1-72h treatment repeat3

description: Library name: S72h-3

value: Fusarium sacchari inoculation 72h


title: RNA_13hpi_MG132-treated_rep2

description:
Library name: sample8
FPKM_RNA_MG132_ALL.txt.gz


title: RNA-seq of ZZ1-72h treatment repeat2

description: Library name: S72h-2


title: Ctl_TCR

description:
Library name: Sample1_TCR
10X Genomics

value: oncolytic HSV1


title: RNA-seq of ZZ1-72h treatment repeat1

description: Library name: S72h-1


title: Ctl_GEX

description:
Library name: Sample1_GEX
10X Genomics


title: RNA-seq of ZZ1-48h treatment repeat3

description: Library name: S48h-3

value: Fusarium sacchari inoculation 48h


title: RNA-seq of ZZ1-48h treatment repeat2

description: Library name: S48h-2


title: bulk RNA-seq Yap OE 5

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: Sample15
bulk RNA-seq Yap OE 5

data_processing:
Quality control was first performed on the raw sequencing data by tool FastQC. Based on this, low-quality reads and adapter sequences were filtered out by tool Trimmomatic
After pre-processing, surviving reads were aligned to mouse reference genome mm10 by aligner STAR. The gene counts per sample were quantified by STAR --quantMode GeneCounts function.
Assembly: mm10
Supplementary files format and content: TAB for gene count

extract_protocol:
Liver tissues from NASH-treated three WT and three Cyr61DHep mice were measured by bulk transcriptome sequencing. RNA was isolated using Total RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. RNA-seq libraries were validated by MedGenome (San Francisco, CA) prior to being sequenced on a Nova-Seq 6000 (Illumina).

value: liver

value: bulk RNA-seq Yap OE 5


title: RNA-seq of ZZ1-48h treatment repeat1

description: Library name: S48h-1


title: bulk RNA-seq Yap OE 4

description:
Library name: Sample14
bulk RNA-seq Yap OE 4

value: bulk RNA-seq Yap OE 4


title: bulk RNA-seq Yap OE 3

description:
Library name: Sample13
bulk RNA-seq Yap OE 3

value: bulk RNA-seq Yap OE 3


title: bulk RNA-seq Yap OE 2

description:
Library name: Sample12
bulk RNA-seq Yap OE 2

value: bulk RNA-seq Yap OE 2


title: RNA-seq of ZZ1-24h treatment repeat2

description: Library name: S24h-2

value: leaf

value: Fusarium sacchari inoculation 24h


title: bulk RNA-seq Yap OE 1

description:
Library name: Sample11
bulk RNA-seq Yap OE 1

value: bulk RNA-seq Yap OE 1


title: RNA-seq of ZZ1-24h treatment repeat3

description: Library name: S24h-3


title: RNA-seq of ZZ1-24h treatment repeat1

description: Library name: S24h-1


title: bulk RNA-seq LATS KO 6

description:
Library name: Sample10
bulk RNA-seq LATS KO 6

value: bulk RNA-seq LATS KO 6


title: RNA-seq of ZZ1-12h treatment repeat3

description: Library name: S12h-3

value: Fusarium sacchari inoculation 12h


title: D#1, 72 hours, HEV-infected, untreated

description: Library name: 72hp6

value: primary porcine hepatocytes

value: 72 hours

value: HEV-infected


title: RNA-seq of ZZ1-12h treatment repeat2

description: Library name: S12h-2


title: bulk RNA-seq LATS KO 5

description:
Library name: Sample9
bulk RNA-seq LATS KO 5

value: bulk RNA-seq LATS KO 5


title: bulk RNA-seq LATS KO 4

description:
Library name: Sample8
bulk RNA-seq LATS KO 4

value: bulk RNA-seq LATS KO 4


title: RNA-seq of ZZ1-12h treatment repeat1

description: Library name: S12h-1


title: bulk RNA-seq LATS KO 3

description:
Library name: Sample7
bulk RNA-seq LATS KO 3

value: bulk RNA-seq LATS KO 3


title: Ribo_17hpi_4E-T-overexpressing_rep1

description:
Library name: sample66
FPKM_Ribo_4E-T-overexpressing_ALL.txt.gz


title: RNA-seq of ZZ1-CK treatment repeat3

description: Library name: S0h-3

value: Fusarium sacchari inoculation 0h


title: bulk RNA-seq LATS KO 2

description:
Library name: Sample6
bulk RNA-seq LATS KO 2

value: liver

value: bulk RNA-seq LATS KO 2


title: RNA-seq of ZZ1-CK treatment repeat2

description: Library name: S0h-2


title: bulk RNA-seq TdTomato 4

description:
Library name: Sample4
bulk RNA-seq TdTomato 4

value: bulk RNA-seq TdTomato 4


title: RNA-seq of ZZ1-CK treatment repeat1

description: Library name: S0h-1


title: bulk RNA-seq LATS KO 1

description:
Library name: Sample5
bulk RNA-seq LATS KO 1

value: bulk RNA-seq LATS KO 1


title: P. putida KT2440 grown in 2 uM La2Ox3 rep 2

city: Berkeley

first: Nathan

last: Good

state: CA

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: UC-Berkeley

description:
Library name: putida_oxide2_expression
oxide growth rep2

data_processing:
HISAT2 - v2.1.0 to align reads
StringTie v2.1.5 to assemble and quantify transcripts
DeSeq v1.20.0 for differential expression analysis
Assembly: GCA_045571375.1
Supplementary files format and content: spreadsheet with gene counts for every gene and every sample

organism: Pseudomonas putida KT2440

source_name: bacterial cells

growth_protocol: Pseudomonas putida KT2440 grown in MP minimal media with 2 uM La2O3 or 2 uM LaCl3, 35 mM EtOH, 5 uM FeSO4, no citrate.

extract_protocol:
RNA was extracted using the Rneasy RNA extraction kit from Qiagen according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed on the Illumina NovaSeq X Plus platform using a 300 cycle flow cell kit to produce 2x150bp paired reads.

value: bacterial cells

value: WT

value: ethanol + lanthanum growth_2 uM La2Ox3


title: D#4, 72 hours, mock-infected, baricitinib

description: Library name: 33

value: mock-infected

value: 1 µM baricitinib


title: bulk RNA-seq TdTomato 3

description:
Library name: Sample3
bulk RNA-seq TdTomato 3

value: bulk RNA-seq TdTomato 3


title: P. putida KT2440 grown in 2 uM La2Ox3 rep 1

description:
Library name: putida_oxide1_expression
oxide growth rep1


title: bulk RNA-seq TdTomato 2

description:
Library name: Sample2
bulk RNA-seq TdTomato 2

value: bulk RNA-seq TdTomato 2


title: D#4, 72 hours, HEV-infected, untreated

description: Library name: 32

value: primary porcine hepatocytes

value: 72 hours


title: P. putida KT2440 grown in 2 uM LaCl3 rep 2

description:
Library name: putida_chloride2_expression
chloride growth rep2

value: ethanol + lanthanum growth_2 uM LaCl3


title: bulk RNA-seq TdTomato 1

description:
Library name: Sample1
bulk RNA-seq TdTomato 1

value: bulk RNA-seq TdTomato 1


title: P. putida KT2440 grown in 2 uM LaCl3 rep 1

description:
Library name: putida_chloride1_expression
chloride growth rep1


title: normal urothelial tissue, rep11

city: Chongqing

first: Hongwen

last: Liang

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

description: Library name: N6

data_processing:
Raw FASTQ reads were processed using fastp software for quality control, generating clean reads for downstream analysis.
Paired clean reads are to be aligned to the hg38 reference genome using HISAT2 v2.0.5.
Gene expression levels were quantified using RSEM. Read counts mapped to each gene were estimated, and FPKM values were calculated based on gene length and sequencing depth.
Assembly: hg38
Supplementary files format and content: Gene-level raw read count matrix generated by RSEM based on hg38 reference genome, including gene symbol and gene name columns for annotation purposes.

source_name: normal urothelial tissue

growth_protocol: Tumor and normal urothelial tissues were collected during surgical resection, immediately immersed in an RNA stabilisation solution, snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

extract_protocol:
Total RNA was extracted from tumor and normal urothelial tissues using TRIzol (Invitrogen, CA, USA) according to the manufacturer's instructions.
RNA sequencing libraries were prepared from >500 ng of total RNA using the NEBNext® UltraTM RNA Library Prep Kit (NEB, USA) according to the manufacturer’s instructions. Briefly, poly(A)+ mRNA was enriched using Oligo(dT)25 magnetic beads and fragmented in fragmentation buffer. First-strand cDNA was synthesized using ProtoScript® II Reverse Transcriptase with random primers, followed by second-strand cDNA synthesis using DNA polymerase I. The double-stranded cDNA was then end-repaired, a-tailed, and ligated with sequencing adapters. Fragments of approximately 250 bp were selected using magnetic beads, followed by PCR amplification and purification to generate the final sequencing libraries.

treatment_protocol: No experimental treatment was applied prior to RNA extraction.

value: normal urothelial tissue


title: sample  5 - TECs from Partial Response  tumours

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

description: Library name: STOP_s5

data_processing:
Gene expression reads were aligned using cellranger count (v6.0.1). Expression matrices were analyzed using the Seurat package (v4.0.3).
Assembly: Mm10
Supplementary files format and content: seurat object containing feature counts and meta data

source_name: Breast tumour

extract_protocol:
Tumours were removed and cut to small pieces with a scissor. Then they were digested using 0.1% collagenase type I diluted in DMEM (Gibco), supplemented with 10% of EGM2 media (Promocell), 1% of BSA (Sigma), DNAse I, 100 mM HEPES and 2 mM EDTA. First the mix of tumour pieces was mixed with the digestion media, and tumours were processed in gentleMACS™ Dissociator (Miltenyi), then incubated at 37 degrees for 30 min, and then processed again in the Dissociator. Homogenized tumours were filtered with a 70-um filter and then the cell pellet was subjected to different procedures. Endothelial cells were isolated using cell death removal and EC isolation bead kits from Miltenyi. To obtain a pure population of ECs, we selected DAPI-, CD45-, EPCAM-, CD31+ cells by FACs. Cells were immediately processed for scRNAseq.
Single-cell suspensions were prepared and Live CD45- CD31+ populations were sorted. After this, cells were loaded and processed on the 10X Chromium Controller using the CG000331 Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) User guide enabled us to process the gene expression and immune profiling of the samples. Each library can be recognized by its unique sample index. Sample sequencing was performed at Novogene using a Novaseq 6000 platform and PE150 sequencing strategy.

treatment_protocol: Doxorubicin 4mg/kg per week

value: Breast tumour

value: primary cells

value: Endothelial

value: Doxorubicin


title: sample  14 - TECs from Partial Response  tumours

description: Library name: STOP_s14


title: sample 4 - TECs from Partial Response  tumours

description: Library name: STOP_s4


title: normal urothelial tissue, rep10

description: Library name: N8


title: normal urothelial tissue, rep9

description: Library name: N5


title: sample 4  - TECs from Responder  tumours

description: Library name: SEN_s4


title: sample 13 - TECs from Responder  tumours

description: Library name: SEN_s13


title: sample 3 - TECs from Responder  tumours

description: Library name: SEN_s3


title: sample 3 - TECs from Acute Doxorubicin treated tumours

description: Library name: DOX_s3


title: normal urothelial tissue, rep5

description: Library name: N9


title: normal urothelial tissue, rep6

description: Library name: N4


title: normal urothelial tissue, rep7

description: Library name: N3


title: sample 12 - TECs from Acute Doxorubicin treated tumours

description: Library name: DOX_s12


title: normal urothelial tissue, rep3

description: Library name: N7


title: normal urothelial tissue, rep2

description: Library name: N1


title: sample 11 -  TECs from Acute Placebo treated tumours

description: Library name: PLA_s11


title: normal urothelial tissue, rep4

description: Library name: N2


title: sample 2 - TECs from Acute Placebo treated tumours

description: Library name: PLA_s2


title: normal urothelial tissue, rep1

description: Library name: N10


title: bladder tumor, rep10

description: Library name: T15

source_name: bladder tumor tissue

value: bladder tumor tissue


title: sample 1 - TECs from Acute Placebo treated tumours

description: Library name: PLA_s1


title: Pancreatic islet cells, ATF6a cKO, High-fat diet-fed

city: Kyoto

first: Takaaki

last: Murakami

state: 選択してください

address: 25 Shogoin-Kawahara-cho, Sakyo-ku

department: Department of Diabetes, Endocrinology and Nutrition

institute: Kyoto University Graduate School of Medicine

description:
Library name: Sample 5
10x Genomics

data_processing:
Data processing was made using Cell Ranger software v7.1.0 (10x Genomics) for alignment, barcode assignment, and UMI quantification.
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated filtered count matrices containing gene-by-cell expression values, as well as annotation tables mapping cell barcodes to clusters, cell types, sample identifiers, and UMAP coordinates.

source_name: Pancreas

growth_protocol: RIP-Cre;Atf6afl/fl (ATF6αβKO) and Atf6afl/fl mice were maintained in a specific-pathogen-free, temperature-controlled environment under a 14:10-h light/dark cycle with free access to food and water.

extract_protocol:
Islets were isolated by collagenase digestion through the bile duct using collagenase P with incubation at 37°C for 30 min, followed by density gradient centrifugation with Histopaque solutions. Isolated islets from two mice were hand-picked and pooled for each sample, filtered through a cell strainer, dissociated into single cells with accutase, and adjusted to ~1,000 cells/µL in PBS.
Library construction was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 5’ Reagent Kit v2 and Chromium Controller, 10x Genomics). Briefly, single-cell resuspensions were loaded onto the Chromium Controller for Gel Bead-in-Emulsion (GEM) generation. Within each GEM, reverse transcription attached a cell-specific barcode and Unique Molecular Identifier (UMI) to cDNA generated from poly-A RNA. After GEM breakage, barcoded cDNA was recovered, cleaned using Silane DynaBeads, and amplified. The amplified cDNA was then fragmented, end-repaired, A-tailed, ligated with sequencing adaptors, and indexed by PCR to generate libraries. Libraries were sequenced on an Illumina NovaSeq 6000 using 150-bp paired-end reads.

treatment_protocol: Mice were fed either a normal diet (10 kcal% fat) or a high-fat diet (60 kcal% fat) starting at 6 weeks old (up to 22 weeks old).

value: Pancreas

value: Islet cells

value: ATF6a cKO

value: High-fat diet

tag: batch


title: Pancreatic islet cells, ATF6a cKO, Normal diet-fed, Batch 1

description:
Library name: Sample 3
10x Genomics

value: Normal diet


title: Pancreatic islet cells, ATF6a Control, High-fat diet-fed

description:
Library name: Sample 2
10x Genomics

value: ATF6a Control


title: bladder tumor, rep8

description: Library name: T3


title: bladder tumor, rep7

description: Library name: T18


title: bladder tumor, rep6

description: Library name: T11


title: APP_cortex, TRAZ, 2weeks, rep4

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

description: Library name: CAT6

data_processing:
Low-quality reads were removed, and adaptor trimming was performed using fastp. The processed FASTQ files were aligned to the GRCm38 (mm10) genome assembly using the STAR aligner. The resulting BAM files were quantified using Stringtie2. Differential gene expression analysis was conducted using the DESeq2 package. Differentially expressed genes (DEGs) were defined as genes with an adjusted P < 0.05 and log2(fold-change) >0.4 or <−0.4. The biological functions of DEGs were annotated according to GO analysis
Assembly: mm10
Supplementary files format and content: CSV with TPM and FPKM

extract_protocol:
The mice were then perfused with cold filtered Dulbecco’s phosphate-buffered saline (DPBS), and the forebrains were isolated. The right hemispheres were surgically dissected to isolate the cortices. The cortices were homogenized in 1100 µL TRIzol. Chloroform were added to homogenate, vortexed, and centrifuged. Aqueous phase were isolated and total RNA were extracted with NucleoSpin RNA Extraction Kit (Macherey-Nagel).
We performed paired-end sequencing using a NextSeq 500 or NovaSeq 6000 instrument (Novogene) according to the manufacturer’s instructions.

value: Brain

value: Trazodone


title: Pancreatic islet cells, ATF6a Control, Normal diet-fed

description:
Library name: Sample 1
10x Genomics


title: APP_cortex, TRAZ, 2weeks, rep3

institute: Hong Kong University of Science and Technology

description: Library name: CAT5


title: APP_cortex, TRAZ, 2weeks, rep2

description: Library name: CAT4


title: bladder tumor, rep3

description: Library name: T6


title: bladder tumor, rep4

description: Library name: T1


title: bladder tumor, rep5

description: Library name: T14


title: APP_cortex, TRAZ, 2weeks, rep1

description: Library name: CAT3


title: bladder tumor, rep2

description: Library name: T7


title: APP_cortex, CTRL, 2weeks, rep3

description: Library name: CAC6

value: Distilled water


title: bladder tumor, rep1

description: Library name: T13


title: APP_cortex, CTRL, 2weeks, rep2

description: Library name: CAC5


title: APP_cortex, CTRL, 2weeks, rep1

description: Library name: CAC3


title: scRNA-seq for mitochondrial DNA-depleted derivatives of the four mixed cell lines (HEK293, A549, 143B, WAL2A)

city: Philadelphia

first: Ting

last: Peng

address: CTRB 6200

department: Pathology and Laboratory Medicine

institute: Children's hospital of Philadelphia

description:
Library name: Rho0
10X Genomics

data_processing:
scRNA-seq was analyzed by using scMOCHA; PacBio long-read DNA-seq data analysis: Reads were aligned with pbmm2 to the GRCh38 reference genome, in which the mitochondrial contig (chrM) was duplicated head-to-tail (33,138 bp) to accommodate mitochondrial genome circularity; mitochondrial positions were folded to canonical 16,569 bp rCRS coordinates. Reads with mapping quality (MAPQ)≥40 and PacBio predicted read quality (rq)≥0.998 were retained. Reads in the following categories were excluded: putative NUMT-derived reads identified from supplementary alignments (≥500 bp, MAPQ≥20), reads outside the expected long-range PCR amplicon boundaries (±100 bp from primer positions), and reads<10 kb. Variant AF was calculated as the number of reads carrying the variant allele divided by the total number of reads spanning that position. Homopolymer-associated indels were excluded based on the systematic error pattern characterized in a 2.5 kb mtDNA plasmid control, with position-level assessment against the control applied within the region it covered. Variants with AF≥5% were reported.
Assembly: GRCh38, rCRS
Supplementary files format and content: RDS, sc_azimuth.rds

source_name: mixture of 4 cell lines(HEK293, A549, 143B, WAL2A)

extract_protocol:
All cell lines were maintained at 37°C in a humidified incubator with 5% CO2. The human osteosarcoma thymidine kinase-deficient cell line 143B(TK−) (ATCC CRL-8303) and human embryonic kidney HEK293 cells were maintained in Dulbecco’s Modified Eagle Medium GlutaMAX (DMEM; Thermo Fisher Scientific, 10569044) containing high glucose (4.5 g/L) and sodium pyruvate (110 mg/L), supplemented with 1% non-essential amino acids (NEAA) and 10% fetal bovine serum (FBS). The human lung adenocarcinoma cell line A549 and the WAl2A WAL2A lymphoblastoid49 cell line were cultured in RPMI 1640 medium with ATCC modifications (Thermo Fisher Scientific, A1049101), supplemented with 1% NEAA and 10% FBS. Corresponding mitochondrial DNA-depleted (ρ⁰ or Rho0) derivatives were maintained in the same medium supplemented with 50 μg/mL uridine (Sigma-Aldrich, U3750-100G). Adherent cell lines were passaged at 70-95% confluence by washing with PBS (Thermo Fisher Scientific, 14190250) and dissociating with 0.25% trypsin-EDTA (Thermo Fisher Scientific, 25200114). Cells used for comparative experiments were harvested at the same passage number.
Single-cell RNA-seq Library Preparation
For the WT and Rho0 samples, an equal mixture of four cell lines (143B, WAL2A, HEK293, A549) was processed using the Chromium Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Cell barcoding, reverse transcription, cDNA amplification, and 3′ gene expression library preparation were performed according to the manufacturer's protocol.
PacBio Library Preparation
Genomic DNA was extracted from cell pellets and quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q33231). Full-length mitochondrial genomes were amplified by long-range PCR using using PrimeSTAR GXL DNA Premix (Takara, R051B) with custom primers and reaction conditions as previously described50. PCR products were purified with SMRTbell Cleanup Beads (PacBio, 102-158-300), and assessed for fragment size distribution using the Femto Pulse system (Agilent, FP-1002-0275). PacBio libraries were prepared using the SMRTbell Prep Kit 3.0 (PacBio, 102-182-700) according to their standard protocol. Following adapter ligation and nuclease treatment, libraries were size-selected using AMPure PB beads (PacBio, 100-265-900). Libraries were annealed to sequencing primers using the Sequel II Binding Kit 3.2 (PacBio, 102-333-300), bound to Sequel II Polymerase 2.2, loaded onto SMRT Cell 8M (PacBio, 102-281-700).

value: osteosarcoma cell line, lung adenocarcinoma cell line,  embryonic kidney cell line, lymphoblastoid cell line


title: WT_cortex, CTRL, 2weeks, rep6

description: Library name: CWC6

value: WT


title: myocarditis 5

city: Harbin

first: Mingming

last: Wu

state: Heilongjiang

address: 23 Youzheng St

department: Departments of Cardiology

institute: The First Affiliated Hospital of Harbin Medical University

description: Library name: Sample 12

data_processing:
Raw data were processed using Cell Ranger software v5.0.0 (10x Genomics) for alignment to the human reference genome (GRCh38/hg38) and transcript quantification.
Assembly: Homo sapiens (GRCh38/hg38)
Supplementary files format and content: Filtered gene-barcode expression matrices in HDF5 (.h5) formats.

source_name: PBMC

extract_protocol:
Venous blood (2 mL) was collected in EDTA anticoagulant tubes and processed within 4 h. Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation using Ficoll-Paque medium. Cell viability exceeded 85%, determined by trypan blue staining. Approximately 15,000 cells per sample were prepared for downstream capture.
Libraries were constructed using the Chromium Single Cell V(D)J 5' Reagent V2 Kit (10x Genomics). For each sample, 15,000 cells were loaded for gel bead-in-emulsion (GEM) generation. Released RNA was barcoded through reverse transcription. cDNA was amplified and library quality was assessed via Agilent 2100 Bioanalyzer. Paired-end sequencing (2 × 150 bp) was performed on an Illumina NovaSeq platform (Novogene).

treatment_protocol: The cohort comprised patients with anti-PD-1 antibody therapy-associated cardiac injury (diagnosed as “possible myocarditis”; n = 7), and control patients without signs of cardiac injury after anti-PD-1 antibody therapies (n = 7).

value: PBMC

tag: sample group

value: myocarditis

tag: antibody

value: anti-PD-1 antibody


title: myocarditis 7

description: Library name: Sample 14


title: WT_cortex, CTRL, 2weeks, rep4

description: Library name: CWC4


title: WT_cortex, CTRL, 2weeks, rep5

description: Library name: CWC5


title: myocarditis 6

description: Library name: Sample 13


title: Control 7

description: Library name: Sample 11

value: control


title: WT_cortex, CTRL, 2weeks, rep3

description: Library name: CWC3


title: Control 6

description: Library name: Sample 10


title: WT_cortex, CTRL, 2weeks, rep2

description: Library name: CWC2


title: WT_cortex, CTRL, 2weeks, rep1

description: Library name: CWC1


title: Atrx-_2

city: HOUSTON

first: Ajay

middle: Kumar

last: Saw

state: TX

address: 7900 Cambdrige St

department: Department of Genomic Medicine

institute: University Of Texas MD Anderson Cancer Center, Houston, Texas, USA.

description: Library name: Atrx-_2

library_source: genomic

data_processing:
Hi-C data processing was performed using the Hicexplorer package.
The Hi-C contact matrix and other signal tracks were visualized using "pyGenomeTracks" and the Integrative Genomics Viewer (IGV).
Assembly: mm9
Supplementary files format and content: h5 format contact matrix

molecule: genomic DNA

source_name: Primary cell line

growth_protocol: Neuroprogenitor Cells were grown in NeuroCult Basal Medium containing NeuroCult Proliferation Supplement, 20 ng/ml EGF, 10 ng/ml basic FGF, 2 μg/ml heparin (Stemcell Technologies), 50 units/ml penicillin, and 50 μg/ml streptomycin (Thermo Fisher Scientific) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Hi-C on mNPCs was performed using the Genome-Wide Hi-C Kit (Arima Genomics) following manufacturer instructions. Briefly, 10 million cells were cross-linked using 1% formaldehyde for 10 mins and quenched with 0.125M glycine for 10 mins at room temperature. Fixed cells were permeabilized using lysis buffer and then digested with restriction enzyme cocktail. The resulting overhangs were biotinylated, followed by ligation and DNA purification. Proximity ligated DNA was sheared using Diagenode Bioruptor Plus and fragments were size selected from 200-600 bps using DNA purification beads (Ampure XP Beads).
Libraries were made using Swift Bioscience Accel-NGS Plus DNA library Kit (Cat #21024) and sequenced using 2x150 base pair-end format on an Illumina NovaSeq6000 following the manufacturer protocol.

value: brain

value: Neuroepithelial progenitor cell

value: Control


title: Control 5

description: Library name: Sample 9


title: Multiome, central amygdala, RT0480N, CON, human, GEX

city: New Haven

first: Matthew

last: Girgenti

state: CT

address: 34 Park St

department: Psychiatry

institute: Yale University

description: Library name: RT0480N_GEX

data_processing:
Multiome files were demultiplexed using Cellranger-arc mkfastq
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5,  atac_fragments.tsv.gz

source_name: Central Amygdala

extract_protocol:
Nuclei were isolated from fresh-frozen human central amygdala tissue and purified to generate single-nucleus suspensions for simultaneous chromatin accessibility and gene-expression profiling.
Single-nucleus multiome libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow, which constructs matched ATAC-seq (genomic DNA accessibility) and gene-expression (polyA nuclear RNA) libraries from the same nucleus.

value: Central Amygdala


title: Multiome, central amygdala, RT0480N, CON, human, ATAC

description: Library name: RT0480N_ATAC

library_source: genomic single cell


title: Atrx-_1

description: Library name: Atrx-_1


title: Atrx+_2

description: Library name: Atrx+_2


title: Atrx+_1

description: Library name: Atrx+_1


title: Control 4

description: Library name: Sample 8


title: Multiome, central amygdala, RT0479N, CON, human, ATAC

description: Library name: RT0479N_ATAC


title: Multiome, central amygdala, RT0479N, CON, human, GEX

description: Library name: RT0479N_GEX


title: Control-3

city: 蚌埠市

first: aonan

last: yu

state: 安徽省

address: 龙子湖区

institute: 蚌埠医科大学

description:
Library name: Sample3
Control-3_FPKM

data_processing:
Raw FASTQ reads were trimmed using Cutadapt and quality checked with FastQC. Clean reads were aligned to the reference genome using HISAT2. Gene counts were obtained with HTSeq, and differential expression analysis was performed using DESeq2 (|log2FC| ≥ 1, FDR < 0.05).
Assembly: GRCm39.107
Supplementary files format and content: Processed data files include a gene-by-sample count matrix generated by HTSeq (v0.6.1), containing raw read counts for each gene in each sample. Differential expression analysis results generated by DESeq2 (v1.34.0) include log2 fold changes, p-values, and adjusted p-values (FDR).

extract_protocol:
Total RNA was extracted using MagZol Reagent (Magen) following the manufacturer’s protocol. RNA was purified, dissolved in RNase-free water, and treated with DNase I to remove genomic DNA contamination.
Total RNA (1 μg) was used for library preparation. mRNA was enriched using Oligo(dT) beads or rRNA depletion and fragmented. cDNA was synthesized, end-repaired, A-tailed, and ligated to adapters. Libraries were PCR-amplified, size-selected, and sequenced on an Illumina HiSeq/Novaseq/MGI2000 platform (2 × 150 bp paired-end).

tag: group

value: non tumor


title: Multiome, AP-1 mutant SeV infected lung epithelial cells, ATAC

city: Cincinnati

first: Jichao

last: Chen

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: 14dpi_SeV_mut_ATAC
all samples were aggregated to one processed data file

data_processing:
Cellranger-arc (version 2.0.0) was used to run “cellranger-arc count” on all samples to align fastq files to a custom mm10 reference genome containing the Sun1GFP and Fos-GFP transcripts. Wildtype control, wildtype Sendai infected, mutant control, and mutant Sendai infected samples were then aggregated together using “cellranger-arc aggr”.
Assembly: custom reference of mm10 with the addition of Sun1GFP and FosGFP sequences
Supplementary files format and content: cellranger-outputs: totalaggr_filtered_feature_bc_matrix.h5, totalaggr_atac_fragments.tsv.gz, totalaggr_atac_fragments.tsv.gz.tbi, totalaggr_atac_peak_annotation.tsv, totalaggr_atac_peaks.bed, totalaggr_cloupe.cloupe

source_name: lung

extract_protocol:
Epithelial cells from 8 week old SftpcCreER/+;RosaSun1GFP/+ and SftpcCreER/+;RosaSun1GFP/+;FosF/F;FosbF/F;JunbF/F mice were sorted from Sendai infected or PBS mock infected lungs 14 days post infection and cell extraction was performed with 10X genomics manufacturer instructions
libraries were generatd using the 10X Genomics Single Cell Multiome ATAC + Gene Expression kit with 10,000 nuclei loaded per lane

value: lung

value: Sendai virus infected

value: ATAC


title: Multiome, central amygdala, RT00500N, CON, human, ATAC

description: Library name: RT00500N_ATAC


title: Multiome, AP-1 mutant SeV infected lung epithelial cells, GEX

description:
Library name: 14dpi_SeV_mut_RNA
all samples were aggregated to one processed data file

value: mRNA


title: Multiome, AP-1 mut PBS control lung epithelial cells, ATAC

description:
Library name: 14dpi_PBScotrol_mut_ATAC
all samples were aggregated to one processed data file

value: PBS mock infected


title: Multiome, central amygdala, RT00499N, AUD, human, ATAC

description: Library name: RT00499N_ATAC

value: alcohol use disorder


title: Multiome, AP-1 mut PBS control lung epithelial cells, GEX

description:
Library name: 14dpi_PBScontrol_mut_RNA
all samples were aggregated to one processed data file


title: normal urothelial tissue, rep8

description: Library name: N11

value: normal urothelial tissue


title: Multiome, central amygdala, RT00500N, CON, human, GEX

description: Library name: RT00500N_GEX


title: Multiome, central amygdala, RT00498N, AUD, human, ATAC

description: Library name: RT00498N_ATAC


title: Multiome, wildtype SeV infected lung epithelial cells, ATAC

description:
Library name: 14dpi_SeV_wt_ATAC
all samples were aggregated to one processed data file


title: Multiome, wildtype SeV infected lung epithelial cells, GEX

description:
Library name: 14dpi_SeV_wt_RNA
all samples were aggregated to one processed data file


title: Multiome, wildtype PBS control lung epithelial cells, ATAC

description:
Library name: 14dpi_PBScontrol_wt_ATAC
all samples were aggregated to one processed data file


title: Multiome, central amygdala, RT00499N, AUD, human, GEX

description: Library name: RT00499N_GEX


title: Multiome, central amygdala, RT00498N, AUD, human, GEX

description: Library name: RT00498N_GEX


title: Multiome, central amygdala, RT00497N, CON, human, ATAC

description: Library name: RT00497N_ATAC


title: sample 2 - TECs from Acute Doxorubicin treated tumours

description: Library name: DOX_s2

value: Breast tumour

value: primary cells

value: Endothelial

value: Doxorubicin


title: Multiome, wildtype PBS control lung epithelial cells, GEX

description:
Library name: 14dpi_PBScontrol_wt_RNA
all samples were aggregated to one processed data file


title: Multiome, central amygdala, RT00497N, CON, human, GEX

description: Library name: RT00497N_GEX

value: control


title: bladder tumor, rep11

description: Library name: T17

value: bladder tumor tissue


title: Atrx+_Trim28kd_2

description: Library name: Atrx+_Trim28kd_2

data_processing:
The raw fastq files were subjected to FASTQC analysis for quality control analysis, followed by alignment to mouse mm9 genome using RNASTAR (version 2.7.8a)
Raw transcript counts were generated using HTseq-count tool (version 0.9.1), followed by Principal Component Analysis (PCA).
Differentially expressed genes (DEGs) were calculated using DESeq2 (version 2.11.40.7) and were later subjected to Gene Set Enrichment Analysis (GSEA) analysis using a desktop version of the analysis tool
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

extract_protocol:
Total RNA extraction using Qiagen RNeasy Plus kit
RNA libraries for RNA-seq were prepared using Truseq library preparation kits (Illumina)  following manufacturer's protocols.

value: brain

value: Primary cell line

value: Neuroepithelial progenitor cell

value: Trim28 knockdown


title: Multiome, central amygdala, RT00496N, CON, human, ATAC

description: Library name: RT00496N_ATAC

value: Central Amygdala


title: Atrx+_Trim28kd_3

description: Library name: Atrx+_Trim28kd_3


title: bladder tumor, rep9

description: Library name: T10


title: Atrx+_Trim28kd_1

description: Library name: Atrx+_Trim28kd_1


title: Pancreatic islet cells, ATF6a cKO, Normal diet-fed, Batch 2

description:
Library name: Sample 4
10x Genomics

value: Pancreas

value: Islet cells

value: ATF6a cKO

value: Normal diet


title: Atrx+_Control_3

description: Library name: Atrx+_Control_3

value: Control


title: Multiome, central amygdala, RT00496N, CON, human, GEX

description: Library name: RT00496N_GEX


title: Multiome, central amygdala, RT00495N, AUD, human, ATAC

description: Library name: RT00495N_ATAC

value: alcohol use disorder


title: Multiome, central amygdala, RT00495N, AUD, human, GEX

description: Library name: RT00495N_GEX


title: Multiome, central amygdala, RT00494N, CON, human, ATAC

description: Library name: RT00494N_ATAC


title: Atrx+_Control_2

description: Library name: Atrx+_Control_2


title: Atrx+_Control_1

description: Library name: Atrx+_Control_1


title: Multiome, central amygdala, RT00494N, CON, human, GEX

description: Library name: RT00494N_GEX


title: ST1_S29_L001

city: Huntington

first: Mohit

last: Verma

state: WV

address: 1676 3rd Ave, 4th Floor, Suite #4109

department: Department of Biomedical Sciences

institute: Marshall University

description:
Library name: ST1_S29_L001_001_val_1.fq.gz
Column name in Gene_FPKM_1.txt  ST1_S29_R1

data_processing:
Illumina NovaSeq 6000
Sdequence reads were trimmed for adapter/ low quality reads using multiQC
Trimmed sequence reads were mapped on GRCm39 using HISAT2 tool
Reat count extraction and normalization were performed
cudiff was using to perform differential expression analysis
Assembly: GCRm39
Supplementary files format and content: Text files includes raw reads counts for each samples
Supplementary files format and content: Tab delimeted text file includes FPKM counts for each samples

source_name: Skin

growth_protocol: BALB/cJ mice (8-12 weeks old) were obtained from Jackson Laboratory and maintained under standard housing conditions in accordance with protocols approved by the Institutional Animal Care and Use Committee.

extract_protocol:
Tissues stored in RNA later were homogenized using a handheld microtissue homogenizer. Total RNA was extracted using the RNeasy Mini Kit (Qiagen) per manufacturer’s instructions. RNA quality and quantity were assessed using a Nanodrop One spectrophotometer and Agilent Bioanalyzer.
Batches of RNA were shipped to Genomics Technology core at university of missouri for poly(A) RNA sequencing. cDNA library was prepared followed by Illumina TrueSeq-standard sample preparation protocol.

treatment_protocol: BTK inhibitor acalabrutinib was provided by AstraZeneca.The mice groups were subsequently treated orally using oral gavage with acalabrutinib 25 mg/kg or placebo from week 3 to week 8.

value: Skin

tag: strain

value: BALB/cJ

value: WT

value: Acalabrutinib


title: Multiome, central amygdala, RT00493N, CON, human, ATAC

description: Library name: RT00493N_ATAC

value: control


title: ST2_S30_L001

description:
Library name: ST2_S30_L001_001_val_1.fq.gz
Column name in Gene_FPKM_1.txt  ST2_S30_R1


title: Multiome, central amygdala, RT00493N, CON, human, GEX

description: Library name: RT00493N_GEX


title: SC2_S28_L001

description:
Library name: SC2_S28_L001_001_val_1.fq.gz
Column name in Gene_FPKM_1.txt  SC2_S28_R1

value: vehicle


title: Multiome, central amygdala, RT00492N, AUD, human, GEX

description: Library name: RT00492N_GEX


title: SC1_S27_L001

description:
Library name: SC1_S27_L001_001_val_1.fq.gz
Column name in Gene_FPKM_1.txt  SC1_S27_R1


title: AT3_S36_L001

description:
Library name: AT3_S36_L001_001_val_1.fq.gz
Column name in Gene_FPKM_1.txt  AT3_S36_R1


title: Multiome, central amygdala, RT00492N, AUD, human, ATAC

description: Library name: RT00492N_ATAC


title: Multiome, central amygdala, RT00491N, CON, human, ATAC

description: Library name: RT00491N_ATAC


title: AT2_S35_L001

description:
Library name: AT2_S35_L001_001_val_1.fq.gz
Column name in Gene_FPKM_1.txt  AT2_S35_R1


title: Multiome, central amygdala, RT00490N, CON, human, ATAC

description: Library name: RT00490N_ATAC


title: AT1_S34_L001

description:
Library name: AT1_S34_L001_001_val_1.fq.gz
Column name in Gene_FPKM_1.txt  AT1_S34_R1


title: Multiome, central amygdala, RT00491N, CON, human, GEX

description: Library name: RT00491N_GEX


title: Multiome, central amygdala, RT00490N, CON, human, GEX

description: Library name: RT00490N_GEX


title: AL2_S32_L001

description:
Library name: AL2_S32_L001_001_val_1.fq.gz
Column name in Gene_FPKM_1.txt  AL2_S32_R1


title: AL3_S33_L001

description:
Library name: AL3_S33_L001_001_val_1.fq.gz
Column name in Gene_FPKM_1.txt  AL3_S33_R1


title: AL1_S31_L001

description:
Library name: AL1_S31_L001_001_val_1.fq.gz
Column name in Gene_FPKM_1.txt  AL1_S31_R1


title: Multiome, central amygdala, RT00489N, AUD, human, ATAC

description: Library name: RT00489N_ATAC


title: Multiome, central amygdala, RT00489N, AUD, human, GEX

description: Library name: RT00489N_GEX


title: AC5_S45_L003

description:
Library name: AC5_S45_L003_001_val_1.fq.gz
Column name in Gene_FPKM_2.txt  AC5_S45_R1


title: Multiome, central amygdala, RT00488N, CON, human, GEX

description: Library name: RT00488N_GEX


title: Multiome, central amygdala, RT00487N, AUD, human, ATAC

description: Library name: RT00487N_ATAC


title: AC1_S42_L003

description:
Library name: AC1_S42_L003_001_val_1.fq.gz
Column name in Gene_FPKM_2.txt  AC1_S42_R1


title: Multiome, central amygdala, RT00484, AUD, human, ATAC

description: Library name: RT00484_ATAC


title: Multiome, central amygdala, RT00487N, AUD, human, GEX

description: Library name: RT00487N_GEX


title: AC2_S41_L003

description:
Library name: AC2_S41_L003_001_val_1.fq.gz
Column name in Gene_FPKM_2.txt  AC2_S41_R1


title: Multiome, central amygdala, RT00485, CON, human, ATAC

description: Library name: RT00485_ATAC


title: KRAS induced, AT2 cells, replicate 02, ATAC

description: Library name: KRAS_induced_02, ATAC

data_processing:
Fastq files were generated through demultiplexing using BCL2Fastq and quality checked using FastQC
Poor quality bases were removed using Trimmomatic and filtered reads were aligned to the UCSC mm10 reference genome with Bowtie2
Aligned reads were converted from sam files to bam files using Samtools and filtered for poor alignment and unmapped reads using Picard, MarkDuplicates, and Samtools with the following parameters: –f 3 –F 4 –F 256 –F 1024 –F 2048 –q 30
Peak calling was conducted using MACS2 with the following parameters: -q 0.05 –nomodel –shift -100 –extsize 200 –broad and filtered for a−log10 q value greater than 5 and removal of mm10 blacklist sites
Assembly: mm10
Supplementary files format and content: MACS2 output peak files as .broadpeak
Supplementary files format and content: MACS2 output peak files as .gappedpeak
Supplementary files format and content: MACS2 output peak files as .txt

extract_protocol:
Mouse lungs were harvested, dissociated and sorted for 100,000 tdT+ AT2 cells. Cells were centrifuged in 4°C at 1098 rcf  for 5 minutes in a fixed angle centrifuge. The supernatant was discarded, and the pellets were resuspended in 50 µL of cold ATAC-RSB lysis buffer (0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, 10 mM Tris-HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2). The resuspension was incubated on ice for 3 minutes followed by the addition of 1mL of cold ATAC-RSB+Tween (10 mM Tris-HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and inverted 3 times to mix. Nuclei were pelleted through centrifugation in 4°C at 1098 rcffor 10 minutes in a fixed angle centrifuge. The supernatant was discarded, and the pellet was resuspended in 50 µL of transposition buffer that included the following: 22.5 µL of Tn5 Reaction Mix (PBS, 2.2% Digitonin, 2.2% Tween-20), 25 µL of Tn5 Buffer (10 mM MgCl2, 20 mM Tris-HCl, 20% Dimethyl Formamide), and 2.5 µL of Tn5 Enzyme (NX#-TDE1, Tagment DNA Enzyme, 15027865, Illumina). The reaction was incubated in a thermocycler at 37°C for 30 minutes. DNA was purified using the Qiagen MinElute PCR Purification Kit (29004) following the manufacturer instructions with one modification of eluting with 10 µL of distilled water.
Sample barcoding and PCR amplification was performed using the Greenleaf ATAC primers (Buenrostro et al., 2013) following the OMNI-ATAC protocol PCR parameters.  To assess amplification efficiency, 5 µL of each sample was saved and set aside while the remainder of each sample continued to size selection purification using SPRIselect beads (Beckman Coulter, B23318). Following the manufacturer instructions for double size selection, the sample was incubated for upper size selection with 0.5X the volume and for lower size selection at 1.8X the volume. Size selection was verified using agarose gel electrophoresis with 1 µL of final sample as well as the previously saved pre size selection sample. Final DNA quantification was measured using the Qubit HS dsDNA assay (Thermo Fisher Scientific, Q32851).

value: lung

value: KRAS induction


title: KRAS induced, AT2 cells, replicate 03, ATAC

description: Library name: KRAS_induced_03, ATAC


title: Multiome, central amygdala, RT00483, AUD, human, GEX

description: Library name: RT00483_GEX


title: KRAS negative control, AT2 cells, replicate 02, ATAC

description: Library name: KRAS_control_02, ATAC

value: SftpcCreER/+;RosatdT/+


title: Multiome, central amygdala, RT00483, AUD, human, ATAC

description: Library name: RT00483_ATAC


title: KRAS negative control, AT2 cells, replicate 01, ATAC

description: Library name: KRAS_control_01, ATAC


title: Multiome, central amygdala, RT00295N, AUD, human, ATAC

description: Library name: RT00295N_ATAC


title: 49 day SeV infected, AT2 cells, replicate 02, ATAC

description: Library name: 49dpi_SeV_02, ATAC

value: Sendai virus infected


title: Multiome, central amygdala, RT00295N, AUD, human, GEX

description: Library name: RT00295N_GEX

value: Central Amygdala


title: 49 day mock PBS, AT2 cells, repliate 02, ATAC

description: Library name: 49dpi_PBScontrol_02, ATAC


title: Multiome, central amygdala, RT00294N, AUD, human, GEX

description: Library name: RT00294N_GEX


title: 49 day SeV infected, AT2 cells, replicate 01, ATAC

description: Library name: 49dpi_SeV_01, ATAC


title: Multiome, central amygdala, RT00293NRP, AUD, human, GEX

description: Library name: RT00293NRP_GEX


title: Multiome, central amygdala, RT00294N, AUD, human, ATAC

description: Library name: RT00294N_ATAC


title: 14 day SeV infected, AT2 cells, replicate 02, ATAC

description: Library name: 14dpi_SeV_02, ATAC


title: scRNA-seq, WT BM Lin- KIThi-int cells, HTO

status: Public on Jul 02 2026

city: St. Louis

first: Feiya

last: Ou

state: MO

address: 4939 Children's Place

department: Pathology & Immunology

institute: Washington University in St. Louis

description: Library name: wt_hto

data_processing:
Raw sequencing data were processed using Cell Ranger (v8.0.0) for alignment to the mm10 reference genome, barcode processing, UMI counting, and generation of the gene expression matrix.
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: bone marrow

extract_protocol:
BM cells were harvested from three mice per genotype. Lineage-positive cells were depleted using antibodies against CD3e, CD8b, CD11b, CD19, B220, Ly-6G, and TER-119. The remaining cells were stained with fluorochrome-conjugated antibodies, labeled with unique Antibody Capture TotalSeq B antibodies (BioLegend), and sorted for lin- KIThi-int cells. Three samples from each genotype were pooled and resuspended in PBS containing 0.04% BSA at a final concentration of ~1,000 cells/uL. Single-cell suspensions were loaded onto a 10x Genomics Chromium Single Cell Controller at GTAC@MGI.
Library preparation, sequencing, and Cell Ranger processing were performed by GTAC@MGI. Libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3 and sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads, targeting depths of 1 billion reads for the gene expression library and 100 million reads for the feature barcode library.

value: bone marrow

value: Lin- KIThi-int cells

value: HTO

tag: hto

value: TotalSeq™-B0301 anti-mouse Hashtag 1, TotalSeq™-B0302 anti-mouse Hashtag 2, TotalSeq™-B0303 anti-mouse Hashtag 3


title: Multiome, central amygdala, RT00292N, CON, human, GEX

description: Library name: RT00292N_GEX


title: 14 day mock PBS, AT2 cells, repliate 02, ATAC

description: Library name: 14dpi_PBScontrol_02, ATAC

value: PBS mock infected


title: 14 day mock PBS, AT2 cells, repliate 01, ATAC

description: Library name: 14dpi_PBScontrol_01, ATAC


title: 14 day SeV infected, AT2 cells, replicate 01, ATAC

description: Library name: 14dpi_SeV_01, ATAC


title: Multiome, central amygdala, RT00292N, CON, human, ATAC

description: Library name: RT00292N_ATAC


title: Multiome, central amygdala, RT00291N, CON, human, GEX

description: Library name: RT00291N_GEX


title: Multiome, central amygdala, RT00291N, CON, human, ATAC

description: Library name: RT00291N_ATAC


title: Multiome, central amygdala, RT00288N, CON, human, ATAC

description: Library name: RT00288N_ATAC


title: T cells, PRMT7 KO, replicate 3

city: Montréal

first: Stéphane

last: Richard

state: Québec

address: 3755 Côte Ste-Catherine Road

department: Departments of Oncology and Medicine

country: Canada

institute: Lady Davis Institute - JGH, McGill University

description: Library name: PRMT7KO3

data_processing:
Sequenced reads were first trimmed with Trimmomatic-0.39 to remove the adapter sequence and then mapped to the mouse genome (mm10) through STAR v2.7.11b
Read counts were quantified and normalized through Cufflinks v2.2.1
Assembly: mm10
Supplementary files format and content: xlsx: normalized gene read counts for each sample

source_name: Splenocytes from mice

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini kit (Ref:74104) according to the manufacturer’s instructions.
Library preparation: polyA- enriched RNA (stranded). Sequencing Type: Illumina NovaSeq PE100 25M. Sequencing fraction: 2 per sample. Primary analysis: Dragen RNA.

value: Splenocytes from mice

value: PRMT7 KO


title: Multiome, central amygdala, RT00288N, CON, human, GEX

description: Library name: RT00288N_GEX


title: T cells, PRMT7 KO, replicate 1

description: Library name: PRMT7KO1


title: T cells, PRMT7 control, replicate 3

description: Library name: PRMT7CTL3

value: PRMT7 CTL


title: Multiome, central amygdala, RT00287N, CON, human, ATAC

description: Library name: RT00287N_ATAC


title: Multiome, central amygdala, RT00286N, CON, human, ATAC

description: Library name: RT00286N_ATAC


title: T cells, PRMT7 control, replicate 2

description: Library name: PRMT7CTL2


title: T cells, PRMT7 control, replicate 1

description: Library name: PRMT7CTL1


title: Multiome, central amygdala, RT00286N, CON, human, GEX

description: Library name: RT00286N_GEX


title: T cells, WT PROTAC, replicate 3

description: Library name: WTPROTAC3

value: WT PROTAC


title: Multiome, central amygdala, RT00285N, CON, human, ATAC

description: Library name: RT00285N_ATAC


title: Multiome, central amygdala, RT00285N, CON, human, GEX

description: Library name: RT00285N_GEX


title: Multiome, central amygdala, RT00284N, AUD, human, ATAC

description: Library name: RT00284N_ATAC

value: alcohol use disorder


title: T cells, WT PROTAC, replicate 1

description: Library name: WTPROTAC1


title: T cells, WT DMSO, replicate 3

description: Library name: WTDMSO3

value: WT DMSO


title: Multiome, central amygdala, RT00284N, AUD, human, GEX

description: Library name: RT00284N_GEX


title: T cells, WT DMSO, replicate 2

description: Library name: WTDMSO2


title: Multiome, central amygdala, RT00283N, AUD, human, ATAC

description: Library name: RT00283N_ATAC


title: T cells, WT DMSO, replicate 1

description: Library name: WTDMSO1


title: Multiome, central amygdala, RT00283N, AUD, human, GEX

description: Library name: RT00283N_GEX


title: 6419c5-Tn mPDAC cells

first: Avery

middle: D

last: Posey

address: 3400 Civic Center Blvd SPE 8-106

institute: University of Pennsylvania

description: Library name: 6419c5-Tn

data_processing:
Read processing was carried out using UseGalaxy.org. Reads were cleaned by removal of low-quality bases from 5’ and 3’ ends, trimming Illumina adaptors and ambiguous nucleotides, and enforcing a minimum length of 30 bases using Cutadapt 5.1. Cleaned reads were mapped to the mouse reference genome (mm39) using STAR v2.7.11b, and gene-level counts were generated with featureCounts 2.1.1. Transcript counts were normalized using DESeq2 v2.11.40.8.
Assembly: mm39
Supplementary files format and content: csv file includes TPM values for each sample

source_name: 6419c5 mPDAC

growth_protocol: mPDAC cell lines were maintained in high-glucose Dulbecco’s Modified Essential Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 ug/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
Total RNA was extracted from fresh frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). ERCC RNA Spike-In Mix kit (cat. 4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on one flowcell lane. After clustering, the flowcell was loaded on the Illumina instrument (NovaSeq 6000; S4 flow cell) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software. Raw sequence data (.bcl files) generated from the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

value: 6419c5 mPDAC

value: pancreatic ductal adenocarcinoma


title: 6419c5 mPDAC cells

description: Library name: 6419c5

value: WT


title: Multiome, central amygdala, RT00281N, AUD, human, ATAC

description: Library name: RT00281N_ATAC


title: 6499c4 mPDAC cells

description: Library name: 6499c4

source_name: 6499c4 mPDAC

value: 6499c4 mPDAC


title: 6499c4-Tn mPDAC cells

description: Library name: 6499c4-Tn


title: 2838c3-Tn mPDAC cells

description: Library name: 2838c3-Tn

source_name: 2838c3 mPDAC

value: 2838c3 mPDAC


title: Multiome, central amygdala, RT00280N, CON, human, ATAC

description: Library name: RT00280N_ATAC

value: Central Amygdala

value: control


title: 2838c3 mPDAC cells

description: Library name: 2838c3


title: Multiome, central amygdala, RT00280N, CON, human, GEX

description: Library name: RT00280N_GEX


title: 6694c2-Tn mPDAC cells

description: Library name: 6694c2-Tn

source_name: 6694c2 mPDAC

value: 6694c2 mPDAC


title: Multiome, central amygdala, RT00279NRP, CON, human, ATAC

description: Library name: RT00279NRP_ATAC


title: Multiome, central amygdala, RT00279NRP, CON, human, GEX

description: Library name: RT00279NRP_GEX


title: L9 B

city: Boston

first: Ke

last: Zhang

state: MA

address: 360 Huntington Ave

institute: Northeastern University

description:
Library name: Sample 24
Column name in raw_counts_all_samples.csv: Free_2

data_processing:
Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome (GRCm39/mm39) with Hisat2 v2.0.5. using standard workflows (Novogene)
Additional analysis was conducted in Rstudio using the DEseq2, clusterProfiler, fgsea, and gsva packages
Assembly: mm39
Supplementary files format and content: csv file of raw counts for each sample titled raw_counts_all_samples.csv

source_name: quadricep

extract_protocol:
Individual muscle sections were homogenized in a lysis buffer containing 10% BME on a Beadblaster 24R Microtube Homogenizer (Benchmark scientific, NJ, USA.). Total cellular RNA was extracted using the RNeasy® Fibrous Tissue Mini Kit (Qiagen), and RNA quality and quantity were assessed on a NanoDrop® ND-1000 UV-Vis Spectrophotometer.
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNAsynthesis After polyA enrichment and quality control, libraries were sequenced on an Illumina NovaSeq6000 PE150 system to obtain paired-end reads of 150 bp.

treatment_protocol: 8 week old HSA-LR20b or FVB/N wildtype mice were injected by tail vein with drug or control. Mice were humanely sacrificed by carbon dioxide two weeks after the final injection and muscle sections were immediately harvested and flash frozen in liquid nitrogen.

value: quadricep

value: FVB/N

value: 5.3 mg/kg L9


title: L9 A

description:
Library name: Sample 23
Column name in raw_counts_all_samples.csv: Free_1


title: Multiome, central amygdala, RT00278N, CON, human, GEX

description: Library name: RT00278N_GEX


title: pacDNA-Scr B

description:
Library name: Sample 22
Column name in raw_counts_all_samples.csv: Scr_Pac_1

value: 5.3 mg/kg pacDNA-Scr


title: Multiome, central amygdala, RT00277N, CON, human, ATAC

description: Library name: RT00277N_ATAC


title: Multiome, central amygdala, RT00281N, AUD, human, GEX

description: Library name: RT00281N_GEX


title: pacDNA-Scr A

description:
Library name: Sample 21
Column name in raw_counts_all_samples.csv: L9S_A_DM1_71


title: Multiome, central amygdala, RT00277N, CON, human, GEX

description: Library name: RT00277N_GEX


title: Brush B

description:
Library name: Sample 20
Column name in raw_counts_all_samples.csv: Brush_2

value: 40 nanomoles brush polymer


title: Multiome, central amygdala, RT00276N, CON, human, ATAC

description: Library name: RT00276N_ATAC


title: Brush A

description:
Library name: Sample 19
Column name in raw_counts_all_samples.csv: Brush_A_70


title: Multiome, central amygdala, RT00276N, CON, human, GEX

description: Library name: RT00276N_GEX


title: 6694c2 mPDAC cells

description: Library name: 6694c2


title: pacDNA-L9 8C

description:
Library name: Sample 18
Column name in raw_counts_all_samples.csv: L9_Pac_H3

value: 42.4 mg/kg pacDNA-L9


title: Multiome, central amygdala, RT00275N, AUD, human, ATAC

description: Library name: RT00275N_ATAC


title: AC6_S46_L003

description:
Library name: AC6_S46_L003_001_val_1.fq.gz
Column name in Gene_FPKM_2.txt  AC6_S46_R1

value: Skin

value: BALB/cJ

value: Acalabrutinib


title: Multiome, central amygdala, RT00488N, CON, human, ATAC

description: Library name: RT00488N_ATAC


title: AC4_S44_L003

description:
Library name: AC4_S44_L003_001_val_1.fq.gz
Column name in Gene_FPKM_2.txt  AC4_S44_R1

value: vehicle


title: pacDNA-L9 8B

description:
Library name: Sample 17
Column name in raw_counts_all_samples.csv: L9_Pac_H2


title: pacDNA-L9 8A

description:
Library name: Sample 16
Column name in raw_counts_all_samples.csv: L9_Pac_H1


title: Multiome, central amygdala, RT00275N, AUD, human, GEX

description: Library name: RT00275N_GEX

value: alcohol use disorder


title: Multiome, central amygdala, RT00278N, CON, human, ATAC

description: Library name: RT00278N_ATAC


title: Multiome, central amygdala, RT00485, CON, human, GEX

description: Library name: RT00485_GEX


title: Multiome, central amygdala, RT00484, AUD, human, GEX

description: Library name: RT00484_GEX


title: KRAS induced, AT2 cells, replicate 01, ATAC

description: Library name: KRAS_induced_01, ATAC

value: lung

value: KRAS induction


title: Multiome, central amygdala, RT00274N, AUD, human, ATAC

description: Library name: RT00274N_ATAC


title: AC3_S43_L003

description:
Library name: AC3_S43_L003_001_val_1.fq.gz
Column name in Gene_FPKM_2.txt  AC3_S43_R1

value: WT


title: Multiome, central amygdala, RT00274N, AUD, human, GEX

description: Library name: RT00274N_GEX

value: Central Amygdala


title: pacDNA-L9 4B

description:
Library name: Sample 15
Column name in raw_counts_all_samples.csv: L9P_F_DM1_68

value: 21.2 mg/kg pacDNA-L9


title: pacDNA-L9 4A

description:
Library name: Sample 14
Column name in raw_counts_all_samples.csv: L9P_E_DM1_67


title: pacDNA-L9 1B

description:
Library name: Sample 13
Column name in raw_counts_all_samples.csv: L9P_DM1_25

value: 5.3 mg/kg pacDNA-L9


title: Multiome, central amygdala, RT00273N, AUD, human, ATAC

description: Library name: RT00273N_ATAC


title: Multiome, central amygdala, RT00273N, AUD, human, GEX

description: Library name: RT00273N_GEX


title: pacDNA-L9 1A

description:
Library name: Sample 12
Column name in raw_counts_all_samples.csv: L9P_DM1_61

value: quadricep


title: Multiome, central amygdala, RT00271N, CON, human, GEX

description: Library name: RT00271N_GEX

value: control


title: Multiome, central amygdala, RT00271N, CON, human, ATAC

description: Library name: RT00271N_ATAC


title: NT5

description:
Library name: Sample 10
Column name in raw_counts_all_samples.csv: NT_H_3

value: FVB/N

value: no treatment


title: Multiome, central amygdala, RT00270N, AUD, human, ATAC

description: Library name: RT00270N_ATAC


title: High Phosphate Exercised Sample 2

city: Columbus

first: Kedryn

last: Baskin

state: OH

address: 460 W 12th Ave

department: Physiology and Cell Biology

institute: The Ohio State University

description:
Library name: XJD947_6_HP18_17_HPE
HPE_2

data_processing:
Fastq files were trimmed using TrimGalore, and aligned using the STAR aligner. Count matrices were analyzed in pairwise comparisons using DESeq2.
Assembly: GRCm39
Supplementary files format and content: excel file containing CPM values and pairwise comparison output from DESeq2

source_name: GP

extract_protocol:
RNA was extracted using the TRI-zol kit and manufacterer instructions. At minumum, 500ng of RNA, quality determined by RIN, was used to generate libraries for each sample.
Libraries were generated by Plasmidsaurus sequencing service. Poly-A mRNA capture, second strand synthesis and tagmentation, and Illumina library amplification.

value: GP

value: High Phosphate Exercised


title: NT6

description:
Library name: Sample 11
Column name in raw_counts_all_samples.csv: NT_2