title: SV-HUC-1 EVs LN#2

city: Guang zhou

first: YAN

last: LIN

state: China

address: 72 Zhongshan 2nd Road

institute: Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (version:mm10) using HISAT2 (version:2.4).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: popliteal LN

extract_protocol:
The EVs educated popliteal lymph nodes was isolated and subjected into extracting the total RNA by TRIZOL (Invitrogen, Carlsbad, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The EVs was isolated from culture medium of UM-UC-3 or SV-HUC-1 and used to educate the popliteal lymph nodes every other day for 10 days through footpad-injection. The popliteal lymph node was enucleated and conducted with assistance of lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) under manufacturer’s protocols.

value: popliteal LN

value: treating with SV-HUC-1 EVs #2


title: SV-HUC-1 EVs LN#1

status: Public on Oct 10 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment

value: treating with SV-HUC-1 EVs #1


title: Smyd3 ASOs + anti-PD-1, rep3, R (867)

city: ROCKVILLE

first: Vassiliki

last: Saloura

state: MARYLAND

address: 11705 STONEWOOD LN

department: TGMB

country: USA

institute: NCI

data_processing:
Basecalling was performed using RTA version 2.4.11, demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt v1.18 (parameters: --pair-filter=any nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35)
Trimmed reads were mapped to mm10 sequences using STAR 2.7.0f aligner with the following parameters: "--limitSjdbInsertNsj 2500000 --outSAMtype BAM Unsorted --outSAMunmapped Within --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.66 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10 --sjdbScore 1 --quantMode TranscriptomeSAM"
Read count extraction was performed using RSEM v1.3.0
Assembly: mm10/M21
Supplementary files format and content: tab-delimited text file containing raw counts for all samples

molecule: polyA RNA

source_name: oral tongue squamous epithelial carcinoma

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat# 74104) following the manufacturer’s instructions with the addition of 1.5 ml volumes of 100% ethanol to the aqueous phase.
TruSeq Stranded mRNA Prep kit

tag: cell line

tag: cell type

value: oral squamous cell carcinoma

value: Smyd3 ASOs + anti-PD-1

tag: group


title: PBMC, Cycle1, patient 105 TCR

city: Los Angeles

first: Yiqian

last: Gu

state: CA

address: 5000D Terasaki Life Sciences Building

institute: University of California Los Angeles

description: 10x Genomics

data_processing:
Cellranger multi 7.1.0 was used for read alignment to reference genome hg38 and gene quantification.
Assembly: hg38
Supplementary files format and content: Tab separated value files, comma seperated value files, and matrix files
Library strategy: scTCR-seq

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Frozen PBMC thawed and Ficoll purified
10X Single Cell TCR & 5' Gene Expression Sequencing Library Prep

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab

tag: cycle

tag: patient id

value: patient 105


title: shARF, CTR9, rep2

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
Paired end sequenced reads were trimmed for adaptor sequence and filtered for quality with trimgalore (0.6.4).
Reads were aligned to GRCm38 mouse genome assembly using Bowtie2 (2.3.2).
The aligned reads were subsequently filtered for mapping quality (MAPQ 30) and PCR duplicates by SAMtools (1.6) and Picard (2.13.2). Uniquely mappable reads were retained for further analysis.
To generate input normalized ChIP-seq coverage plots in the bigWig file format, reads were normalized to reads per million (rpm) using bamCompare of deeptools (3.5.0).
Assembly: GRCm38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: p53-deleted MEF shARF-neo

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 0.5% formaldehyde at RT for 10 min and then quenched with 150 mM glycine at room temperature for 5 min. Cells were harvested by scraping in cold 1X PBS and pelleted at 1000 x g for 5 min at 4°C. Harvested cells were lysed for 30 min at 4°C in Farnham lysis buffer (5 mM PIPES, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, 1X protease inhibitor cocktail (PIC)). Chromatin was sonicated using a Qsonica sonicator.
For ChIP-seq library preparations, 2 ng of ChIP or input DNA was processed using the KAPA Hyper Prep Kit according to the manufacturer’s protocol. Libraries were amplified using 13 cycles on a thermocycler. Libraries were validated using Agilent D1000 ScreenTape assay.

value: p53-deleted MEF shARF-neo

value: Mouse Embryonic Fibroblasts

tag: knockdown

value: shARF

tag: chip antibody


title: PBMC, Cycle1, patient 103 TCR

description: 10x Genomics

value: patient 103


title: H1522-JIB-04_2

first: Luc

last: Girard

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

description:
Gene_FPKM_uqnorm.txt
H1522-JIB-04_2

data_processing:
Illumina sequencer from UTSW Sequencing Core (single-end) or Novogene (paired-end)
fastq files were aligned to GRCh38 (human) reference genome using STAR v2.7.1a
bam files were processed to remove read duplicates using Picard MarkDuplicates from GATK v4.1.2. Mouse reads were filtered out from CLX samples
FPKM values were obtained using Cufflinks v2.2.1
FPKM values were upper-quartile normalized, then log-transformed
Assembly: GRCh38
Supplementary files format and content: Gene_FPKM_uqnorm.txt

growth_protocol: See publication

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Library preparation was done with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina or according to Novogene specifications (https://en.novogene.com)

treatment_protocol: See publication

value: SCLC

tag: xenograft

value: no

tag: time

value: 24 hours


title: shARF, CTR9, rep1


title: UM-UC-3 EVs LN#3

value: treating with UM-UC-3 EVs #3


title: SHP-77-DMSO_2

description:
Gene_FPKM_uqnorm.txt
SHP-77-DMSO_2

value: DMSO


title: Smyd3 ASOs + anti-PD-1, rep2 (852)

value: oral tongue squamous epithelial carcinoma


title: MlxKO 20 month, omental adipose tissue [Fat-X18F38]

city: pittsburgh

first: Huabo

last: Wang

state: PA

address: 4401 Penn Avenue

institute: Children hospital of pittsburgh

data_processing:
CLC Genomics Workbench v 22.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Mus musculus (GRCm38.p6) using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include CPM(TMM-adjusted) values for each Sample

source_name: omental adipose tissue

growth_protocol: Animal work was conducted in compliance with the Public Health Service Policy on Humane Care and Use of Laboratory Animal Research (ILAR) Guide for Care and Use of Laboratory Animals. All experimental procedures, diets and tests were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Pittsburgh. All mice were housed in a specific pathogen-free facility, maintained under standard conditions at UPMC Children’s Hospital of Pittsburgh.

extract_protocol:
RNAs were isolated from mouse tissues using RNeasy kit,according to the directions of the supplier (Qiagen, Inc. Germantown, MD). Exceptions to this were made in the case of adipose tissue and skeletal muscle for which we utilized an RNeasy Lipid Tissue extraction Kit(Qiagen, Inc., Germantown, MD).
Sequencing libraries were generated using a NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs, Beverly, MA).Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms.

treatment_protocol: CreER activation and Mlx excision were initiated at the time of weaning in mice that had attained a weight of 15 g or greater.  Each mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil.

value: omental adipose tissue

tag: strain

value: B6.129-Gt(ROSA)26Sortm1(cre/ERT2)Tyj/J x Mlx Flox/Flox

tag: age

value: 20 month

tag: genotype

value: MlxKO

value: mouse received 5 daily i.p. injections of freshly-prepared tamoxifen (75 mg/Kg) in corn oil at the time of weaning and mice that had attained a weight of 15 g or greater.


title: PBMC, Cycle1, patient 107 TCR

description: 10x Genomics

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab

value: patient 107


title: H82-JIB-04_1

description:
Gene_FPKM_uqnorm.txt
H82-JIB-04_1


title: Smyd3 ASOs + anti-PD-1, rep1, R (987)

value: oral squamous cell carcinoma

value: Smyd3 ASOs + anti-PD-1


title: PBMC, Cycle17, patient 103 TCR

description: 10x Genomics

value: patient 103


title: H82-DMSO_2

description:
Gene_FPKM_uqnorm.txt
H82-DMSO_2

value: SCLC


title: MlxKO 20 month, omental adipose tissue [Fat-X18F36]


title: H1522-DMSO_1

description:
Gene_FPKM_uqnorm.txt
H1522-DMSO_1

value: no


title: SV-HUC-1 EVs LN#3

value: popliteal LN

value: treating with SV-HUC-1 EVs #2


title: 50% top2 RNAi_3

city: Chengdu

first: Man

last: Zhu

state: Sichuan

address: No. 4, Section 2, Jianshe North Road, Chenghua District, Chengdu City, Sichuan, China

department: School of Medicine

institute: University of Electronic Science and Technology of China

data_processing:
SOAPnuke v1.5.6
Sequence reads for adaptor sequence/low-quality sequence/unknown base ('N' base) using SOAPnuke software. Low-Quality limit (base quality less than or equal to 15):20%, unknown base limit: 5%.
Clean sequence reads analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com)
The clean data were aligned to the reference genome using HISAT2 (v2.1.0) and  aligned to the gene set using Bowtie2.
Expression level of gene was calculated by RSEM (v1.3.1). The differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw FPKM values for each sample

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans

extract_protocol:
RNA was harvested following the Microbial RNA BGI-NGS-TQ-RNA-002 protocol of Beijing Genomics institution
RNA libriaries for RNA-seq were prepared following the BGI-NGS-JK-RNA-001 protocol of Beijing Genomics institution

value: Caenorhabditis elegans

value: WT

value: 50% top2 RNAi_3


title: shARF, PAF1, rep1

value: p53-deleted MEF shARF-neo

value: Mouse Embryonic Fibroblasts

value: shARF

value: PAF1 (Abcam, #ab20662)


title: Control ASOs + anti-PD-1, rep1 (875)

value: oral tongue squamous epithelial carcinoma

value: Control ASOs + anti-PD-1


title: PBMC, Cycle7, patient 103 TCR

description: 10x Genomics

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab


title: PBMC, At progression, patient 102 TCR

description: 10x Genomics

value: At progression

value: patient 102


title: H82-DMSO_1

description:
Gene_FPKM_uqnorm.txt
H82-DMSO_1

value: SCLC

value: DMSO

value: 24 hours


title: UM-UC-3 EVs LN#2

value: popliteal LN

value: treating with UM-UC-3 EVs #2


title: H1522-JIB-04_1

description:
Gene_FPKM_uqnorm.txt
H1522-JIB-04_1

value: no


title: PBMC, Cycle1, patient 102 TCR

description: 10x Genomics


title: 50% top2 RNAi_1

value: Caenorhabditis elegans

value: WT

value: 50% top2 RNAi_1


title: H1522-DMSO_2

description:
Gene_FPKM_uqnorm.txt
H1522-DMSO_2


title: shNT, CTR9, rep1

source_name: p53-deleted MEF shNT-neo

value: p53-deleted MEF shNT-neo

value: Mouse Embryonic Fibroblasts

value: shNT


title: UM-UC-3 EVs LN#1

value: treating with UM-UC-3 EVs #1


title: shNT, CTR9, rep2


title: PBMC, Cycle7, patient 101 TCR

description: 10x Genomics

value: PBMC

value: patient 101


title: PBMC, Cycle1, patient 208

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger multi 7.1.0 was used for read alignment to reference genome hg38 and gene quantification.
Assembly: hg38
Supplementary files format and content: Tab separated value files, comma seperated value files, and matrix files

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab

value: patient 208


title: 50% top2 RNAi_4

value: 50% top2 RNAi_4


title: PBMC, Cycle1, patient 101 TCR

description: 10x Genomics


title: cKO_liver_iNKT1 [KL3]

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

data_processing:
Raw sequence reads were trimmed using Trimmomatic v0.33
Reads were aligned to the mm10 reference genome using Tophat v 2.1.0 or STAR.
Aligned reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78
DESeq2 was used to normalize the gene counts and to calculate differential expression statistics for each gene for each pairwise comparison of sample groups within an nf-Core Differential Abundance workflow
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

extract_protocol:
RNA isolation was performed using  RNeasy mini kits (QIAGEN) following the manufacturer’s protocol.
RNA-seq libraries were constructed using Nugen’s Ovation Ultralow Library systems following the manufacturer's protocol

value: liver

value: primary cells

value: CD1d-Tetramer+ YFP+ iNKT1 cells

value: Tbx21Cre Ets1F/F Rosa26-YFP+


title: WT_H3K9ac

city: Tianjin

first: Jiayuan

last: Chen

state: State...

address: Heping

institute: Tianjin Medical University

data_processing:
Paired-end reads from ChIP-seq were aligned by the Bowtie2 algorithm against the mouse reference genome mm10.
Homer was used for each sample using fragment sizes obtained from the alignments and a p-value cutoff of 0.05.
Deeptools was used for generating bigWig file.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Kidney

extract_protocol:
Briefly, primary cholangiocytes were divided into 100,000 cells per tube, and the samples were kept on ice or at 4°C. Cells were lysed in 19 μL lysis buffer (0.5% NP-40, 0.5% Tween-20, 0.1% SDS and cOmplete Protease Inhibitor Cocktail), and then incubated with 19 μL MNase buffer (100 mM Tris-HCl pH 8.0 and 2 mM CaCl2) containing 0.02 U MNase (Sigma, N3755) at 37°C for 5 min. Digestion was terminated by adding 5 μL stop buffer (110 mM Tris-HCl pH 8.0 and 55 mM EDTA). Each sample was incubated with 45 μL 2x RIPA buffer (280 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.2% sodium deoxycholate, 5 mM EGTA and cOmplete Protease Inhibitor Cocktail) for 10 min before centrifuged at 14500 rpm for 15 min. The supernatant was transferred to a new tube, and then added with 40 μL RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate and 1 mM EDTA). For IP samples, each sample was incubated overnight with 1 μg antibody of H3K9ac (Abcam, ab4441), H3K9me3 (Abcam, ab8898), H3K4me3 (Millipore, 05-745R), H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729), and followed by immunoprecipitation with Dynabeads Protein G (Thermo Fisher Scientific, 10004D). And then samples were centrifuged and the collected-beads were washed five times with 150 μL RIPA buffer and rinsed once with 150 μL LiCl buffer (10 mM Tris-HCl pH 8.0, 0.5% NP-40, 1 mM EDTA, 0.5% sodium deoxycholate and 250 mM LiCl). Beads were finally resuspended with 30 μL elution buffer containing 1 μL proteinase K (TransGen Biotech, GE201-01), and followed by shaking at 55°C for 90 min. The supernatant was transferred to a new tube, and proteinase K was inactivated by heated at 72°C for 40 min. For Input samples, each sample was treated with 1 μL proteinase K, followed by shaking at 55°C for 90 min, and then DNA was purified using DNA Extraction Reagent (Solarbio, P1012).
Library construction was performed using a VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607). Sequencing was performed on the Illumina platform.

value: Kidney

value: H3K9ac (Abcam, #ab4441)

value: tamoxifen


title: WT_H3K9me3

value: H3K9me3 (Abcam, #ab8898)

value: WT


title: WT_H3K36me3


title: 0% top2 RNAi_4

value: Caenorhabditis elegans

value: 0% top2 RNAi_4


title: PBMC, At progression, patient 207

description: 10x Genomics

value: At progression

value: patient 207


title: WT_H3K4me3

value: H3K4me3 (Millipore, #05-745R)


title: PBMC, At progression, patient 208

description: 10x Genomics

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab


title: 50% top2 RNAi_2

value: 50% top2 RNAi_2


title: PBMC, Cycle7, patient 208

description: 10x Genomics

value: patient 208


title: WT_H3K4me1

value: H3K4me1 (Abcam, #ab8895)


title: shNT, PAF1, rep1

value: p53-deleted MEF shNT-neo

value: Mouse Embryonic Fibroblasts

value: shNT

value: PAF1 (Abcam, #ab20662)


title: WT_H3K27me3

value: Kidney

value: tamoxifen


title: 0% top2 RNAi_3

value: WT

value: 0% top2 RNAi_3


title: PBMC, Cycle17, patient 101 TCR

description: 10x Genomics

value: patient 101


title: shARF, PAF1, rep2

value: p53-deleted MEF shARF-neo

value: shARF


title: WT_H3K27ac

value: H3K27ac (Abcam, #ab4729)


title: PBMC, At progression, patient 206

description: 10x Genomics

value: PBMC

value: At progression

value: patient 206


title: Control_liver_iNKT1 [WL3]

value: liver

value: primary cells

value: CD1d-Tetramer+ YFP+ iNKT1 cells

value: Tbx21Cre Rosa26-YFP+


title: shNT, PAF1, rep2

value: p53-deleted MEF shNT-neo

value: Mouse Embryonic Fibroblasts

value: shNT


title: PBMC, Cycle1, patient 207

description: 10x Genomics

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab

value: patient 207


title: cKO_liver_iNKT1 [KL1]

value: Tbx21Cre Ets1F/F Rosa26-YFP+


title: Control_liver_iNKT1 [WL1]


title: ADPKD_H3K9me3

value: Kidney

value: H3K9me3 (Abcam, #ab8898)

value: ADPKD

value: tamoxifen


title: PBMC, Cycle1, patient 206

description: 10x Genomics

value: PBMC


title: PBMC,  At progression, patient 205

description: 10x Genomics

value: At progression

value: patient 205


title: PBMC, Cycle7, patient 206

description: 10x Genomics

value: patient 206


title: Control_liver_iNKT1 [WL2]

value: liver

value: primary cells


title: ADPKD_H3K4me3

value: H3K4me3 (Millipore, #05-745R)


title: ADPKD_H3K9ac

value: H3K9ac (Abcam, #ab4441)


title: ADPKD_H3K4me1

value: H3K4me1 (Abcam, #ab8895)


title: cKO_liver_iNKT1 [KL2]

value: CD1d-Tetramer+ YFP+ iNKT1 cells


title: ADPKD_H3K4me3_MR


title: cKO_thymic_iNKT1 [KT2]

source_name: thymus

value: thymus


title: PBMC, Cycle7, patient 205

description: 10x Genomics

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab


title: PBMC, Cycle1, patient 205

description: 10x Genomics


title: PBMC,  At progression, patient 204

description: 10x Genomics

value: patient 204


title: Biopsy of tumor Patient3

type: RNA

city: Tokyo

first: Kazushi

last: Fukagawa

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Gastroenterology, Graduate School of Medicine

country: Japan

institute: The University of Tokyo

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Human GA-FG mucosa

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. Purity and concentration of RNA were measured using NanoDrop1000 spectrometer (NanoDrop Technologies, Wilmington, NC, USA) and Agilent 2100 Bioanalyser.

treatment_protocol: One biopsy sample was obtained from each tumor and surrounding normal mucosa.

tag: gender

value: M

value: GA-FG


title: Biopsy of normal mucosa Patient3

source_name: Human gastric normal mucosa

value: normal mucosa


title: Control_thymic_iNKT1 [WT2]

value: Tbx21Cre Rosa26-YFP+


title: cKO_thymic_iNKT1 [KT1]

value: Tbx21Cre Ets1F/F Rosa26-YFP+


title: 0% top2 RNAi_2

value: Caenorhabditis elegans

value: WT

value: 0% top2 RNAi_2


title: Biopsy of normal mucosa Patient2


title: Biopsy of tumor Patient2


title: 0% top2 RNAi_1

value: 0% top2 RNAi_1


title: Biopsy of tumor Patient1

value: F


title: cKO_thymic_iNKT1

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files and matrix fi.es

extract_protocol:
The thymus from 2 Tbx21Cre Rosa26-YFP+ mice and 2 Tbx21Cre Ets1F/F Rosa26-YFP+ mice were isolated in 10X FBS/PBS and YFP+ cells were isolated on an AriaII flow cytometer.
RNA-seq libraries were constructed according the the manufacturers protocol (single cell 3' v2 protocol, 10X Genomics). Briefly, YFP+ cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel based-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primers sequence, Unique Moleular Identifier (UMI) and the 10X Barcode. The pooled barcoded cDNA was then cleaned with the Silane DynaBeads, amplified by PCR and appropriate sized fragments were selected with SPRIselect reagent for subsequent library consturction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: primary cells

value: YFP+


title: donor 4, Periostin

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Raw fastq files were pseudoaligned to human genome assembly GRCh38.p12 using kallisto software version 0.45.0
Assembly: GRCh38.p12
Supplementary files format and content: Tab-separated text file containing length, estimated counts, and transcripts per million (TPM) for each gene isoform

source_name: airway epithelial cells

growth_protocol: DMEM/F12 media with Ultroser G was replaced every two days.

extract_protocol:
RNA was extracted using Qiagen RNeasy Lipid Tissue Mini Kit # 74804.
Total RNA libraries were prepared using Illumina TruSeq stranded mRNA sample preparation kit (Illumina #RS-122-2101).

treatment_protocol: Air-liquid interface cultures of primary airway epithelia from 6 de-identified human donors with no known disease were exposed to basolateral recombinant human periostin or vehicle at a concentration of 200ng/mL for 72 hours.

value: airway epithelial cells

value: periostin


title: donor 5, Periostin


title: donor 3, Periostin


title: PBMC, Cycle7, patient 202

description: 10x Genomics

value: PBMC

value: patient 202


title: PBMC, Cycle1, patient 204

description: 10x Genomics

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab

value: patient 204


title: ADPKD_ATAC_rep1

data_processing:
Paired-end reads from ATAC-seq were aligned by the Bowtie2 algorithm against the mouse reference genome mm10.
Homer was used for each sample using fragment sizes obtained from the alignments and a p-value cutoff of 0.05.
Deeptools was used for generating bigWig file.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
100,000 primary cholangiocytes were lysed in cold ATAC lysis buffer (10 mM Tris–HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) igepal CA-630) for 20 min on ice before centrifuged at 500 g for 10 min. The cell nuclei were collected and incubated with 50 μL transposition reaction buffer (3 μL TruePrep Tagment Enzyme, 10 μL TruePrep Tagment Buffer L from Vazyme TD501) at 37°C for 60 min.
DNA was purified using the QIAquick PCR Purification Kit (QIAGEN, 28106) according to the manufacturer’s instructions. After DNA fragmentation and purification, library construction was performed with TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to the manufacturer’s instructions.

value: Kidney

value: ADPKD

value: tamoxifen


title: Biopsy of normal mucosa Patient1

value: normal mucosa


title: Control_thymic_iNKT1 [WT3]

value: thymus

value: CD1d-Tetramer+ YFP+ iNKT1 cells

value: Tbx21Cre Rosa26-YFP+


title: WT_ATAC_rep2

value: WT


title: PBMC, Cycle7, patient 204

description: 10x Genomics


title: cKO_thymic_iNKT1 [KT3]

value: Tbx21Cre Ets1F/F Rosa26-YFP+


title: ADPKD_H3K27me3


title: mouse αSyn PFF-treated neuron3

city: Kumamoto

first: Yasushi

last: Yabuki

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Genomic neurology

institute: Kumamoto University

data_processing:
Fastq files were processed for quality check and adapter trimming with the Trimgalore! (0.6.6; https://github.com/FelixKrueger/TrimGalore). Trimmed reads were used for mapping the mouse genome (mm10) using STAR (2.7.9a) (Dobin 2013 Bioinformatics). DESeq2 (1.38.3) (Love 2014 Genome Biol) was used.
RNAseqChef (Etoh 2023 JBC) was used for identifying differentially expressed genes between PBS- and αSyn PFF-treated neurons.
Assembly: Mus Musculus
Supplementary files format and content: norm_input_data.csv

source_name: Cortical brain

growth_protocol: Cortical brain tissues of 18-day-old embryonic mice were dissected, trypsin-digested, and mechanically dispersed. Cells were seeded with minimum essential medium (Gibco) supplemented with 10% fetal bovine serum, 0.6% glucose (Fujifilm), and 1 mM pyruvate (Sigma-Aldrich). Cells were cultured in neuron culture medium (Fujifilm), and the medium was changed every 3 days.

extract_protocol:
Total RNA was extracted from αSyn PFF-treated mouse cultured neurons at DIV 18 using an RNeasy Mini Kit.
DNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: For mouse cultured neurons, mouse αSyn PFF(3.45 μM) was added to medium at DIV 10

value: Cortical brain

value: mouse primary cultured cortical neuron

value: PFF


title: WT_ATAC_rep1


title: PBMC, Cycle17, patient 107

description: 10x Genomics

value: patient 107


title: donor 6, Periostin

value: airway epithelial cells

value: periostin


title: ADPKD_ATAC_rep2


title: ADPKD_H3K27ac

value: H3K27ac (Abcam, #ab4729)


title: Control_thymic_iNKT1 [WT1]

value: primary cells


title: ADPKD_H3K36me3

value: Kidney


title: PBMC,  At progression, patient 202

description: 10x Genomics

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab

value: At progression

value: patient 202


title: PBMC, Cycle1, patient 202

description: 10x Genomics


title: mouse αSyn PFF-treated neuron1


title: PBMC, Cycle7, patient 107

description: 10x Genomics


title: Vehicle-treated neuron3

value: PBS


title: RAW264.7 cells, RANKL+ etelcalcetide sample, rep2

city: Taipei

first: Hui-Wen

last: Chiu

address: No.301, Yuantong Rd., Zhonghe Dist., New Taipei City

country: Taiwan

institute: Taipei medical university

data_processing:
The original data obtained by high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format. FastQC and MultiQC were used to check fastq files for quality.
The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1) without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 (v1.22.1) with biological duplicate.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse macrophage

growth_protocol: RAW264.7 cells were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum and 100 nM penicillin/streptomycin.

extract_protocol:
Total RNA was isolated using the EasyPrep Total RNA Kit (Cat:TB-DPT-BD19).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW264.7 cells were seeded 24 hours before treatment on 6-cm dish with 4 ml of medium per dish. Cells were treated at ~80% confluency with the required doses for the required timepoints.

value: RAW264.7 cells

value: immortalized mouse macrophage

value: RAW264.7 cells were incubated with RANKL (50 ng/mL) and etelcalcetide (4 μM) for 6 days.


title: Vehicle-treated neuron1

value: Cortical brain


title: mouse αSyn PFF-treated neuron2

value: mouse primary cultured cortical neuron


title: donor 2, Periostin


title: RAW264.7 cells, RANKL sample, rep2

value: RAW264.7 cells were incubated with RANKL (50 ng/mL) for 6 days.


title: Control_thymic_iNKT1

description: 10X Genomics

value: thymus

value: YFP+

value: Tbx21Cre Rosa26-YFP+


title: RAW264.7 cells, RANKL+ etelcalcetide sample, rep3

value: RAW264.7 cells were incubated with RANKL (50 ng/mL) and etelcalcetide (4 μM) for 7 days.


title: PBMC, Cycle7, patient 105

description: 10x Genomics

value: patient 105


title: PBMC, Cycle1, patient 105

description: 10x Genomics


title: donor 1, Periostin

value: airway epithelial cells

value: periostin


title: donor 2, Control

value: control


title: donor 6, Control


title: PBMC, Cycle1, patient 107

description: 10x Genomics

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab

value: patient 107


title: donor 5, Control


title: RAW264.7 cells, RANKL+ etelcalcetide sample, rep1

value: RAW264.7 cells

value: RAW264.7 cells were incubated with RANKL (50 ng/mL) and etelcalcetide (4 μM) for 5 days.


title: tubular epithelial cell, ADPKD-mmpp, Day115, rep1

first: Zhang

last: Lirong

state: Tianjin

address: No.22 Qixiangtai Road

data_processing:
HISAT2 (version 2.1.0) was used to align paired-end reads to mouse (mm10) genome. Only unique mapped reads were used in further analysis.
FeatureCounts (version 1.6.0) was used to count reads number for each sample.
Assembly: mm10
Supplementary files format and content: FPKM

source_name: kidney

extract_protocol:
DBA positive cells were isolated from mouse kidney. Total RNA was extracted using TRIzol (Invitrogen). Total RNAs from whole kidney were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was finished by Novogene company

value: kidney

tag: agent

value: mmpp

value: kidney tubular epithelial cell


title: PBMC, Cycle1, patient 104

description: 10x Genomics

value: patient 104


title: tubular epithelial cell, ADPKD, Day115, rep2

value: saline


title: PBMC, Cycle17, patient 105

description: 10x Genomics


title: shNT_neo_2_S2_biol rep 2

data_processing:
Reads with phred quality scores lower than 20 or with shorter than 30 bp after trimming were removed from further analysis using trimgalore version 0.4.1.
Trimmed PE reads were aligned to GRCm38 reference genome with HISAT2 2.1.0 reporting up to 5 multimappers in SAM format
Alignments in SAM format were converted to BAM format with Samtools 0.1.19 and the sequences were sorted and duplicate removed by Picard 2.13.2
RNA abundance of transcripts was calculated with Stringtie v1.3.2 and the RNA abundance was converted into a read count table
Differentially-expressed genes were identified with DESeq2 1.34.0
Assembly: GRCm38
Supplementary files format and content: comma-separated text file including readcount values for all samples

source_name: Mouse Embryonic Fibroblasts

growth_protocol: shNT and shARF MEFs 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 is extrated with Zymo Quick-RNA MiniPrep Kit
Using the KAPA Stranded RNA-seq kit with RiboErase (HMR)

treatment_protocol: negative control shRNA or ARF shRNA were delivered by lentivirus infection

value: Mouse Embryonic Fibroblasts

value: p53 deleted mouse embryonic fibroblasts

value: WT

value: negative control shRNA


title: ATAC-seq on HCC1395BL rep2

city: Loma Linda

first: Charles

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

data_processing:
DNA methayltion data were trimmed using trim_galore before mapping. Trimmed fastq were mapped using bismark.
ATAC-seq reads were mapped using bowtie. ATAC peaks were called using MACS2.
Assembly: NCBI_GRCh38
Supplementary files format and content: Processed DNA methayltion files are in BED format, one for each replicate.
Supplementary files format and content: Processed ATAC-seq data is in matrix format where values from 3 replicates are shown in tabular form.

growth_protocol: We obtained the human breast cancer cell line (HCC1395, sample A) and the matched normal B lymphocyte line (HCC1395BL, sample B) from the American Type Culture Collection (ATCC). The two cell lines were derived from the same human patient (43 years old, female). HCC1395 cells were cultured in RPMI 1640 medium supplemented with 10% FBS. HCC1395BL cells were cultured in IMDM supplemented with 20% FBS.

extract_protocol:
DNA extraction Qiagen allprep kit
TruSeq Methyl Capture EPIC Library Prep. Protocol
Bulk label ATAC library prep protocol.

value: normal B lymphocyte


title: ATAC-seq on HCC1395BL rep1


title: tubular epithelial cell, wt, Day115, rep2


title: shARF_neo_2_S2_biol rep 2

value: ARF knockdown

value: p19ARF shRNA


title: RAW264.7 cells, RANKL sample, rep3

value: immortalized mouse macrophage

value: RAW264.7 cells were incubated with RANKL (50 ng/mL) for 7 days.


title: RAW264.7 cells, RANKL sample, rep1

value: RAW264.7 cells were incubated with RANKL (50 ng/mL) for 5 days.


title: tubular epithelial cell, ADPKD-mmpp, Day115, rep2


title: PBMC, Cycle17, patient 104

description: 10x Genomics

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab


title: donor 3, Control

value: airway epithelial cells

value: control


title: Vehicle-treated neuron2

value: Cortical brain

value: mouse primary cultured cortical neuron

value: PBS


title: donor 1, Control


title: shARF_neo_3_S3_biol rep 3

value: Mouse Embryonic Fibroblasts


title: ATAC-seq on HCC1395 rep3

value: breast cancer cell line


title: tubular epithelial cell, wt, Day115, rep1

value: kidney

value: saline

value: kidney tubular epithelial cell

value: WT


title: shARF_neo_1_S1_biol rep 1

value: p53 deleted mouse embryonic fibroblasts

value: ARF knockdown

value: p19ARF shRNA


title: PBMC, Cycle7, patient 104

description: 10x Genomics

value: patient 104


title: donor 4, Control


title: shNT_neo_3_S3_biol rep 3

value: negative control shRNA


title: shNT, Input

value: p53-deleted MEF shNT-neo

value: shNT


title: shNT_neo_1_S1_biol rep 1


title: PBMC, Cycle17, patient 103

description: 10x Genomics

value: PBMC

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab

value: patient 103


title: tubular epithelial cell, ADPKD, Day115, rep1


title: shARF, Input

value: p53-deleted MEF shARF-neo

value: shARF


title: PBMC, Cycle7, patient 103

description: 10x Genomics


title: PBMC, Cycle1, patient 103

description: 10x Genomics


title: ATAC-seq on HCC1395 rep2

value: breast cancer cell line


title: PBMC, Cycle17, patient 101

description: 10x Genomics

value: patient 101


title: shARF, RPB3, rep1

value: Mouse Embryonic Fibroblasts

value: RPB3 (EMD/Millipore, #ABE999)


title: PBMC, Cycle1, patient 102

description: 10x Genomics

value: patient 102


title: shARF, RPB3, rep2


title: TrueSeq_Capture_Epic_methylseq_HCC1395BL_rep1

value: normal B lymphocyte


title: ATAC-seq on HCC1395 rep1


title: LJE1cells,NT,H3K9Ac,rep2

first: Lillian

middle: J

last: Eichner

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: ChIP-seq for H3K9ac in KL LJE1 cells transduced with sgHdac3 #1

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.4.0k) for ChIP-seq.
HOMER (v5.1) (http://homer.ucsd.edu/homer/) was used to process alignment files to generate ChIP-seq bedGraphs. Peaks were called using getDifferentialPeaksReplicates.pl using ChIP-seq data from NT cells as target -t, data from HDAC3 KO as background -b, and input sequencing data as input -i, with -style factor and -F 3
The annotatePeaks.pl command of HOMER was used with -hist 25 to plot average reads across all peaks relative to peak center
Assembly: mm10
Supplementary files format and content: Compressed HOMER Tag Directories
Supplementary files format and content: Bedgraph
Supplementary files format and content: HOMER Peak files

growth_protocol: Cell lines were incubated at 37ºC and maintained in 5% CO2. Cells were grown in DMEM + 10% fetal bovine serum

extract_protocol:
cells were formaldehyde crosslinked. Nuclei were isolated, washed, diluted, and sonicated.  Lysate from 5 million cells per ChIP was incubated with antibody, incubated with Dynabeads, washed, eluted, decrosslinked, and DNA was isolated.
Library preparation and sequencing were performed by Admera Health. Library was constructed on immunoprecipitated DNA according to manufacturer’s recommendations

value: Immortalized cell line derived from Kras-mutant, Lkb1-/- NSCLC lung tumor

value: Kras-mutant, Lkb1-/-


title: LJE1cells,NT,Input

description: Input for ChIP-seq for H3K9ac in KL LJE1 cells transduced with sgHdac3 #1


title: LJE1cells,NT,H3K9Ac,rep1


title: TrueSeq_Capture_Epic_methylseq_HCC1395BL_rep2


title: PBMC, At progression, patient 102

description: 10x Genomics

extract_protocol:
Frozen PBMC thawed and Ficoll purified
10X Single Cell TCR & 5' Gene Expression Sequencing Library Prep

value: At progression


title: shNT, RPB3, rep2

data_processing:
Paired end sequenced reads were trimmed for adaptor sequence and filtered for quality with trimgalore (0.6.4).
Reads were aligned to GRCm38 mouse genome assembly using Bowtie2 (2.3.2).
The aligned reads were subsequently filtered for mapping quality (MAPQ 30) and PCR duplicates by SAMtools (1.6) and Picard (2.13.2). Uniquely mappable reads were retained for further analysis.
To generate input normalized ChIP-seq coverage plots in the bigWig file format, reads were normalized to reads per million (rpm) using bamCompare of deeptools (3.5.0).
Assembly: GRCm38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 0.5% formaldehyde at RT for 10 min and then quenched with 150 mM glycine at room temperature for 5 min. Cells were harvested by scraping in cold 1X PBS and pelleted at 1000 x g for 5 min at 4°C. Harvested cells were lysed for 30 min at 4°C in Farnham lysis buffer (5 mM PIPES, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, 1X protease inhibitor cocktail (PIC)). Chromatin was sonicated using a Qsonica sonicator.
For ChIP-seq library preparations, 2 ng of ChIP or input DNA was processed using the KAPA Hyper Prep Kit according to the manufacturer’s protocol. Libraries were amplified using 13 cycles on a thermocycler. Libraries were validated using Agilent D1000 ScreenTape assay.


title: shNT, RPB3, rep1


title: Mid-secretory phase of the menstrual cycle, subject 6

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

data_processing:
Filter reads of Qual score <20
Remove reads carrying adaptor sequences using cutadapt (v1.12).
Agilgn reads to hg38 genome using DESeq2 aligner
Assembly: hg38
Supplementary files format and content: Count reads mapped to each gene using DESeq2

source_name: Myometrium

growth_protocol: Not applicable

extract_protocol:
RNA was extracted using TRIzol, followed by the Qiagen RNAeasy MiniPrep kit according to manufacturer's instructions.
RNA libraries were constructed by the Illumina Tru-Seq RNA kit.

treatment_protocol: All specimens were flash frozen with warm ischemia times < 30 minutes and stored at <-80C until laboratory use. Phase of menstrual cycle was dated as per clinical history and was confirmed histologically using standard criteria to evaluate companion H&E-stained cross-sections of the endometrium. Evaluation was confirmed by at least two board-certified anatomic pathologists. Menopausal status was assess using standard clinical criteria (absence of menses >12 months and/or prior bilateral surgical oophorectomy)  A subset of subjects received provera at dose of 5-10 mg daily for at least one month prior to surgery in an attempt to control symptoms of abnormal uterine bleeding.

tag: status

value: Nonpregnant


title: TBP ARPE ADAR1 shRNA + ADARp150 -FCS replicate 3

city: Amsterdam

first: Frank

middle: van

last: Gemert

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Seqpurge adaper trimming
Alignment: Hisat2(2.1.0) --min-intronlen 20 --max-intronlen 500000 --rna-strandness FR -k 5 --minins 0 --maxins 500 –fr
Samtools(1.11) fixmate -m, coordinate sorting and file conversion
Duplicate marking: (https://github.com/NKI-GCF/rumidup) rumidup -p 2500
Gene counts (https://github.com/NKI-GCF/gensum) gensum --mapq 5 --strandness F --method union –gtf Homo_sapiens.GRCh38.102.gtf
Assembly: GRCh38 hisat2 build, GRCh38.102 for annotation
Supplementary files format and content: Tab delimited text including annotated raw counts per sample
Supplementary files format and content: Raw readcounts were used in combination with the standard protocol of the DESeq2 package in R to perform differenetial expression analysis.

source_name: Retinal Pigment Epithelial

growth_protocol: DMEM + 10% FCS

extract_protocol:
Cells were harvested and resuspended in RLT buffer
Library preparation was performed with the TruSeq polyA stranded RNA prep kit (Illumina) according to the manufacturer protocol

treatment_protocol: Serum starvation

tag: tissue

value: Retinal Pigment Epithelial

value: RB1, RBL1, RBL2, p53 knockout, Bcl2 overexpressing (TBP) ARPE

value: Cell line

value: Male

value: Serum starved


title: TrueSeq_Capture_Epic_methylseq_HCC1395_rep3


title: LJE1cells,H3KO,H3K9Ac,rep1

value: Kras-mutant, Lkb1-/-, HDAC3-/-


title: LJE1cells,H3KO,Input


title: Mid-secretory phase of the menstrual cycle, subject 5


title: LJE1cells,H3KO,H3K9Ac,rep2


title: PBMC, Cycle1, patient 101

description: 10x Genomics

source_name: PBMC

value: PBMC

tag: treatment

value: platinum-based chemotherapy in combination with PD-1 antagonist pembrolizumab


title: TBP ARPE ADAR1 shRNA + ADARp150 -FCS replicate 2

tag: cell line


title: TrueSeq_Capture_Epic_methylseq_HCC1395BL_rep3

tag: cell type


title: PBMC, Cycle7, patient 101

description: 10x Genomics

value: patient 101


title: TBP ARPE ADAR1 shRNA + ADARp150 -FCS replicate 1


title: Gad2-cre, GFP, RNA, Group B, sample2

city: Shang Hai

first: Yan

last: Tao

address: Dong An Road

institute: Fudan University

data_processing:
Sequencing was performed on the sequencing platform (Illumina NovaSeq X Plus). The sequencing depth for RNA-seq was based on the recommendations outlined in Illumina's article regarding the number of reads per sample. The RNA-seq analysis started with quality control of the raw sequencing reads using Fastp, which included adapter trimming, low-quality base filtering, and QC report generation. Clean reads were then aligned to the reference genome (ensembl 92, mm10) using HISAT2, a spliced aligner tailored for RNA-seq data. Gene-level quantification of the aligned reads was performed with FeatureCounts, resulting in a count matrix for each sample. This count data was subsequently analyzed using DESeq2 for differential expression analysis. DESeq2 normalized the data to account for variations in sequencing depth and sample size.
Assembly: GRCm38 (mm10), ensemble 92
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: Brain, piriform cortex

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, China), which were next used to synthesise U-labeled second-stranded DNAs with VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, China). The average insert size for the final cDNA library was 300±50 bp.

treatment_protocol: The treatment was achieved bystereotactically injecting AAV-DIO-Caspase3 or AAV-DIO-GFP into the unilateral PC of Gad2-Cre mice

value: Brain, piriform cortex

value: Gad2-cre mice

value: AAV-DIO-GFP


title: TrueSeq_Capture_Epic_methylseq_HCC1395_rep1

value: breast cancer cell line


title: Mid-secretory phase of the menstrual cycle, subject 3


title: Gad2-cre, GFP, RNA, Group B, sample1


title: HCT116, TTC7BKO-2-IP

city: Beijing

first: ren

middle: qian

last: wen

state: Beijing

address: Fu-Cheng-Lu #52, Haidian District

department: Division of Etiology

institute: Peking University Cancer Hospital & Institute

data_processing:
Raw reads (Raw Data) are generated after sequencing on a sequencer, image analysis, base identification and QC. Q30 was first used for quality control. Then, cutadapt software (v1.9.3) was used to remove splice information and remove low quality reads to obtain high quality clean reads. The clean reads were matched to the reference genome using Hisat2 (v2.0.4). Methylated genes in each sample were then identified using MACS (1.4.2). Differential methylation gene identification was performed using diffReps (1.55.6). The peaks located mRNA were screened using our own programs and annotated accordingly. GO and Pathway analyses were performed for differentially methylated gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include intersection_mRNA values for each sample
Library strategy: MeRIP-Seq

source_name: Colon

growth_protocol: HCT116 cells were cultured in RPMI1640 medium with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin, maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
The m6A MeRIP-Seq service was provided by CloudSeq Inc. (Shanghai, China). Total RNA was subjected to immunoprecipitation with the GenSeq® m6A MeRIP Kit (GenSeq Inc.) by following the manufacturer’s instructions.
Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer (Agilent) and then sequenced.

treatment_protocol: We used the CRISPR/Cas9 editing system to generate TTC7B knockout cells.

value: Colon

value: Colorectal adenocarcinoma epithelial cells

value: TTC7B knockout

value: untreated


title: HCT116, TTC7BKO-2-Input

data_processing:
Raw reads (Raw Data) are generated after sequencing on a sequencer, image analysis, base identification and QC. Q30 was first used for quality control. Then, cutadapt software (v1.9.3) was used to remove splice information and remove low quality reads to obtain high quality clean reads. The clean reads were matched to the reference genome using Hisat2 (v2.0.4). Methylated genes in each sample were then identified using MACS (1.4.2). Differential methylation gene identification was performed using diffReps (1.55.6). The peaks located mRNA were screened using our own programs and annotated accordingly. GO and Pathway analyses were performed for differentially methylated gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include intersection_mRNA values for each sample


title: ATAC-seq on HCC1395BL rep3

value: normal B lymphocyte


title: TBP ARPE ADAR1 shRNA + vector only -FCS replicate 2

value: Retinal Pigment Epithelial

value: RB1, RBL1, RBL2, p53 knockout, Bcl2 overexpressing (TBP) ARPE


title: Gad2-cre, Caspase, RNA, Group A, sample3


title: HCT116, TTC7BKO-1-IP


title: Mid-secretory phase of the menstrual cycle, subject 1

value: Nonpregnant


title: TrueSeq_Capture_Epic_methylseq_HCC1395_rep2


title: Gad2-cre, Caspase, RNA, Group A, sample2


title: Gad2-cre, GFP, RNA, Group B, sample3


title: TBP ARPE ADAR1 shRNA + vector only -FCS replicate 1

value: Cell line

value: Male

value: Serum starved


title: Provera treated, subject 10


title: TBP ARPE Non-targeting shRNA -FCS replicate 3


title: HCT116, WT-2-IP

value: WT


title: Provera treated, subject 9


title: HCT116, TTC7BKO-1-Input


title: HCT116, WT-2-Input


title: Gad2-cre, Caspase, RNA, Group A, sample1


title: TBP ARPE Non-targeting shRNA -FCS replicate 2


title: FbDTA_2

city: Pittsburgh

first: guang

last: li

address: 530 45th St. 8116 Rangos Research Center

institute: university of pittsburgh

description: FbDTA_2_metadata; Integrate_metadata; multiSeqBarcodes_to_samples.xlsx

data_processing:
Reads were processed using the Cell Ranger (version 7.1.0) count pipeline.
Sample demultiplexing was performed using the R package deMULTIplex (version 1.0.2) [https://github.com/chris-mcginnis-ucsf/MULTI-seq].
Assembly: GRCm38
Supplementary files format and content: rds, xlsx, and csv files.

source_name: heart

extract_protocol:
Cardiac cells from emryonic hearts were dissociated through sequencial incubation in 0.25% Trypsin/EDTA and a collagenase HBSS+/+ mixture before filtered through a 40 μm filter. The cells from each sample were stained with with a unique MULTI-seq barcode separately and pooled before library preparation.
The pooled cells were captured in 10X Chromium Xi by following the single cell 3’ reagent kits v3.1 user guide. Briefly, cells were loaded into each chip well to be partitioned into gel beads in emulsion (GEMs) in the Chromium controller. We targeted for 25,000 cells in each experiment. The cells were then lysed and barcoded reverse transcribed in the GEMs. After breaking the GEMs and further cleanup and amplification, the cDNA was enzymatically fragmented and 3′ end fragments were selected for library preparation. After further processing including end repair, A-tailing, adaptor ligation, and PCR amplification, a string of sequences including sample index, UMI sequences, barcode sequences, and sequencing primer P5 and P7 were added to cDNA on both ends. The libraries were sequenced on Illumina Nova-seq X plus platform.

value: heart

value: heart cells

value: Control or ablated embryonic hearts from Pdgfra-CreER; Rosa-DTA mouse strain


title: TBP ARPE Non-targeting shRNA -FCS replicate 1


title: TBP ARPE ADAR1 shRNA + vector only -FCS replicate 3


title: Provera treated, subject 8


title: HCT116, WT-1-IP


title: TBP ARPE ADAR1 shRNA + ADARp150 +FCS replicate 3


title: Mid-secretory phase of the menstrual cycle, subject 4


title: HCT116, WT-1-Input


title: Provera treated, subject 7


title: RNAseq_ZT20_Q5A_Cohort2_Rep2

city: New York

first: Benjamin

middle: H

last: Weekley

state: NY

address: 1470 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Samples were demultiplexed using bcl2fastq2 (Illumina, v2.20).
Samples were aligned to the GRCm38 mouse genome using STAR (2.7.11b) alignReads in mode BAM SortedByCoordinate.
Gene counts were generated using htseq-count (HTSeq 2.0.5)  with the following parameters: --format=bam --minaqual=10 --type=exon --idattr=gene_name --stranded=yes --mode=union
Gene counts were normalized using DEseq2 (1.44.0) prior to analysis using JTKcycle (3.1)
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Htseq-counts

source_name: Brain-TMN

extract_protocol:
Tissue was resuspended in 800 uL of Trizol and homogenized using a small dounce homogenizer (30 strokes loose, 30 strokes tight) at room temperature. Chloroform was added and aqueos phase isolated. 70 % ethanol was added 1:1, and then passed over an RNAeasy mini-elute column. The Qiagen RNAeasy MicroKit protocol was followed, including all optional steps/DNAse treatment. RNA was eluted in 15 uL and quantitated using a nanodrop spectrophotometer. RNA quality was assessed using a tapestation RNA screentape. 100 ug of total RNA was used as input for library prep.
Illunia Stranded mRNA Prep, Ligation

treatment_protocol: Mice brains were collected every 4 hours across the zeitgeber time following IACUC protocols. They were flash-frozen using methylbutane and stored at -80 degrees celsius. Brains were sliced and TMN punched (1 mm punches) according to previously published coordinates. TMN were frozen at -80 degrees celsius until CUT&RUN was performed.

value: Brain-TMN

tag: timepoint

tag: virus

tag: cohort

tag: replicate


title: TBP ARPE ADAR1 shRNA + ADARp150 +FCS replicate 2


title: Provera treated, subject 6


title: RNAseq_ZT20_Q5A_Cohort2_Rep1


title: RNAseq_ZT20_Q5A_Cohort1_Rep4


title: TBP ARPE ADAR1 shRNA + ADARp150 +FCS replicate 1


title: Provera treated, subject 5


title: hrpA_smrB_rep2

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
The linker was trimmed using cutadapt. Reads were aligned using Bowtie allowing two mistmatches. Reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome version 2. Separately, the reads were mapped to the IRAGP_reporter plasmid sequence. In the WIG files, rpm values include the fraction of reporter reads in all the uniquely mapped reads, both the chromosome and the plasmid.
Assembly: NC_000913.2 and the IRAGP_reporter plasmid (separately)
Supplementary files format and content: WIG files for the genome and the plasmid giving the ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.
Library strategy: Ribo-seq

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacterial cells

growth_protocol: Cultures with the IRAGP_reporter plasmid grown at 37 C in MOPS complete media were harvested at OD600 = 0.3.

extract_protocol:
50 mL of culture was sprayed into liquid nitrogen; frozen pellets were pulverized in a Spex 6870 cryo-mill with 10 cycles of 1 min grinding and 1 min cooling at 8 Hz. Lysates were pelleted over a sucrose cushion, then ribosome pellets were resuspended and footprints generated by MNase digestion.
Ribosome footprints and total RNA fragments 15-45 nt in length were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.

value: hrpA / smrB double knockout


title: TBP ARPE ADAR1 shRNA + vector only +FCS replicate 3


title: TBP ARPE ADAR1 shRNA + vector only +FCS replicate 2


title: Provera treated, subject 4


title: FbDTA_1

description: FbDTA_1_metadata;Integrate_metadata; multiSeqBarcodes_to_samples.xlsx


title: RNAseq_ZT20_Q5A_Cohort1_Rep1


title: TBP ARPE ADAR1 shRNA + vector only +FCS replicate 1


title: RNAseq_ZT20_Q5A_Cohort1_Rep2


title: Provera treated, subject 3


title: hrpA_rep2

value: hrpA knockout


title: Provera treated, subject 1


title: hrpA_rep1


title: WT_rep2

value: wild-type


title: RNAseq_ZT20_H3.3_Cohort2_Rep2


title: TBP ARPE Non-targeting shRNA +FCS replicate 3


title: TBP ARPE Non-targeting shRNA +FCS replicate 2


title: RNAseq_ZT20_H3.3_Cohort2_Rep1


title: Proliferative phase of the menstrual cycle, subject 12


title: RNAseq_ZT20_H3.3_Cohort1_Rep4


title: TBP ARPE Non-targeting shRNA +FCS replicate 1


title: Root, co-cultivated (R+Af), 15DAT, replicate 3

city: Milano

first: Chiara

last: Paleni

address: Via Celoria, 26

country: Italy

institute: Università degli Studi di Milano

data_processing:
Filtering and trimming with Fastq-mcf with parameters -l 50 -q 30
Mapping and transcript quantification with Rsem v1.3.3 on Os-Nipponbare-Reference-IRGSP-1.0 with annotation version 2022-03-11
Read count extraction and per-gene read counts with Tximport v1.16.1
Differential gene expression analysis with DESeq2 v1.28.1
Assembly: IRGSP-1.0
Supplementary files format and content: xlsx file includes raw gene counts for each sample

organism: Oryza sativa

source_name: Root

growth_protocol: The seeds were sowed in Petri dishes containing half-strength MS nutrients (½MS) for 2 days in the dark at 30°C for germination, and successively in small Magenta boxes for 10 days for seedlings growth. Four 13-day-old seedlings per replicate were then transplanted into specifically designed plex hydroponic boxes (230x230x150 mm) harbouring 4 pivots sticking out of the base and containing ca. 5 L of Yoshida’s nutritive solution. Each pivot could hold a hydroponics net pot that, once filled with expanded clay taken in place by a piece of non-woven tissue, supported rice growth for the entire duration of the experiment. Boxes containing sole rice plants (control, R) or rice co-cultivated with A. filiculoides (co-cultivated, R+Af) were kept in a growth chamber under a 14 h light photoperiod at an irradiance of 220 μmol m−2 s−1 (PAR) and a light/dark temperature of 25/19°C. The growth solution was completely replaced every 2 weeks and refilled when necessary. No water-aeration system was applied. The walls of all the boxes were wrapped with aluminium foil to prevent the development of algae. Unless differently specified, at least three boxes per treatment with four rice plants each were employed as replicates for each experiment and the entire experimental set up was run three times.

extract_protocol:
Rice plants were rinsed with distilled water and the distal portions, up to 1 cm from the apices, of rice roots were cut with a sterile blade and immediately frozen in liquid nitrogen. RNA from the roots of three biological replicates per treatment at 15 DAT was isolated with Qiagen RNeasy Plant Mini Kit and treated with Qiagen Rnase-Free Dnase Set.
Stranded mRNA libraries were prepared by Novogene with poly-T oligo-attached magnetic beads, followed by random hexamer priming and second strand cDNA synthesis with dUTP.

treatment_protocol: The co-cultivated samples (R+Af) were grown in the presence of actively growing Azolla filiculoides. When necessary, dying A. filiculoides substituted with fresh one to ensure the same level of Azolla coverage. The surface of the boxes without Azolla (control, R) were covered to avoid growth of algae.

value: Root

value: 15 DAT

tag: cultivar

value: Kitaake

value: co-cultivation with A. filiculoides (R+Af)


title: RNAseq_ZT20_Q5A_Cohort1_Rep3


title: Proliferative phase of the menstrual cycle, subject 11


title: Root, co-cultivated (R+Af), 15DAT, replicate 2


title: RNAseq_ZT20_H3.3_Cohort1_Rep3


title: control volunteer 006

city: Nanjing

first: Qiong

last: Li

state: Jiangsu

address: Dingjiaqiao Road 87#

institute: Southeast University

description: YCL

data_processing:
Use the analysis process of Stringtie to quantify the expression of known genes and transcripts. Use Deseq2 software to analyze the differentially expressed genes between the case group and the control group in pairwise groups. Type is the screening result, and if pvalues<0.05 and | log2 (fold change) |>1 is the differential gene,
Assembly: hg38

source_name: blood

extract_protocol:
Whole blood (2.5 ml) samples from all participants were collected using The PAXgene® Blood RNA Tube (BD, cat. USA), immediately mixed vigorously for 10s and frozen at -80°C until use. The PAXgene Blood RNA Kit (PreAnalytiX) was used to isolate total RNA from whole blood according to the kit instructions. Total RNA quality was assessed using agarose gel electrophoresis and quantified using a NanoDrop2000 spectrophotometer (Thermo Fisher Scientific, USA). The Agilent Bioanalyzer 2100 (Agilent Technologies, USA) was used to verify RNA integrity.
The fragmented RNA was used as a template for first strand cDNA synthesis, using random primers (Random Hexamers).The second strand of cDNA was synthesized using DNA polymerase and the double stranded cDNA was purified with magnetic beads (AMPure XP; Beckman Coulter,USA).Then addition of adenlylate 3′ ends, connection sequencing adapters, selection library size, PCR amplification and checking library quality were performed in turn.
The whole transcriptome sequencing project requires the construction of two sequencing libraries simultaneously, including a strand-specific library for rRNA removal and a small RNA library. The constructed library was sequenced using Illumina high-throughput sequencing platform according to standard protocol (Genesky Biotechnologies Inc., Shanghai, China). Detailed experimental procedures are provided in the Supplementary Material. This study obtained the expression landscape of mRNAs, miRNAs, circRNAs, and lncRNAs from the same samples in the discovery set and conducted subsequent bioinformatics analysis.The cDNA library was sequenced on an Illumina NovaSeq 6000 sequencing platform to generate read pairs of 150 bp length.

value: blood

tag: disease state

value: control


title: hrpA_smrB_rep1


title: Provera treated, subject 2

value: Nonpregnant


title: Root, co-cultivated (R+Af), 15DAT, replicate 1

tag: time


title: RNAseq_ZT20_H3.3_Cohort1_Rep2


title: control volunteer 005

description: XR


title: Proliferative phase of the menstrual cycle, subject 10


title: control volunteer 004

description: LQ


title: WT_rep1

tag: strain


title: Root, control (R), 15DAT, replicate 3

value: control (R)


title: Proliferative phase of the menstrual cycle, subject 13


title: Proliferative phase of the menstrual cycle, subject 8


title: control volunteer 003

description: JF


title: Proliferative phase of the menstrual cycle, subject 9


title: RNAseq_ZT20_GFP_Cohort1_Rep5

value: GFP


title: RNAseq_ZT20_H3.3_Cohort1_Rep1


title: Root, control (R), 15DAT, replicate 2


title: control volunteer 002

description: DY


title: Proliferative phase of the menstrual cycle, subject 7


title: RNAseq_ZT20_GFP_Cohort1_Rep4


title: Proliferative phase of the menstrual cycle, subject 6


title: Proliferative phase of the menstrual cycle, subject 5


title: RNAseq_ZT20_GFP_Cohort1_Rep2


title: HAPE patient 006

description: ZYY

value: HAPE


title: Proliferative phase of the menstrual cycle, subject 4


title: Liver, CDAA-HFD Lanifibranor, Rep 8

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

description:
18801
CDAA_intervention_counts.txt

data_processing:
Reads were aligned to the GRCm38 Ensembl Mus musculus genome and counted using STAR v.2.7.0f with default settings.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file contaning raw counts from each sample

source_name: Liver

extract_protocol:
Liver tissue were collected and snap-frozen in liquid nitrogen. RNA was isolated using the NucleoSpin® kit (MACHEREY-NAGEL).
RNA sequence libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on NextSeq 550 (Illumina) with NextSeq 500/550 High Output Kit V2 (#75 CYS, Illumina)

value: Liver

value: CDAA-HFD Lanifibranor


title: HAPE patient 005

description: WKN


title: Liver, CDAA-HFD Lanifibranor, Rep 9

description:
18804
CDAA_intervention_counts.txt


title: RNAseq_ZT20_GFP_Cohort1_Rep1


title: HAPE patient 004

description: TWZ


title: Proliferative phase of the menstrual cycle, subject 3


title: HAPE patient 003

description: HJC


title: HAPE patient 002

description: CYB


title: Liver, CDAA-HFD Lanifibranor, Rep 6

description:
18795
CDAA_intervention_counts.txt


title: Proliferative phase of the menstrual cycle, subject 2


title: RNAseq_ZT16_Q5A_Cohort2_Rep1


title: RNAseq_ZT16_Q5A_Cohort2_Rep2


title: Liver, CDAA-HFD Lanifibranor, Rep 5

description:
18792
CDAA_intervention_counts.txt


title: Root, control (R), 15DAT, replicate 1


title: Liver, CDAA-HFD Lanifibranor, Rep 7

description:
18798
CDAA_intervention_counts.txt


title: control volunteer 001

description: CXW


title: Post menopausal, subject 14


title: Liver, CDAA-HFD Lanifibranor, Rep 4

description:
18789
CDAA_intervention_counts.txt


title: RNAseq_ZT16_Q5A_Cohort3_Rep1


title: Proliferative phase of the menstrual cycle, subject 1


title: RNAseq_ZT16_Q5A_Cohort1_Rep4


title: Liver, CDAA-HFD Lanifibranor, Rep 3

description:
18786
CDAA_intervention_counts.txt


title: Liver, CDAA-HFD Lanifibranor, Rep 10

description:
18807
CDAA_intervention_counts.txt


title: HAPE patient 001

description: CNS


title: RNAseq_ZT20_GFP_Cohort1_Rep3


title: multiplexed samples

city: Oss

first: Monica

last: Raimo

state: Noord-Brabant

address: Kloosterstraat 9

department: Research

institute: Glycostem

data_processing:
Fastq files were processed using the BD Rhapsody WTA Analysis Pipeline 2.0 in SevenBridges
The DBEC files with molecules per cell were imported in the R package Seurat version 4.3.0 for further downstream analysis
Assembly: human GRCh38
Supplementary files format and content: CSV files containing Abseq, RNA and metadata information in separate matrix tables

source_name: NK cell derived from UCB CD34+ cells

growth_protocol: CD34+ cells from 10 UCB donors were seeded in 6-wells tissue culture treated plates (Corning Incorporated) for expansion culture in Glycostem Basal Growth Medium (GBGM®; Fertipro) supplemented with human serum (Sanquin), thrombopoietin (TPO), interleukin (IL)-7, FMS-like tyrosine kinase 3 ligand (Flt-3L), granulocyte-macrophage colony-stimulating factor (GM-CSF), IL-6, stem cell factor (SCF) (all from Cellgenix) and Neupogen (G-CSF; Amgen) as previously described. After 9 days, TPO was replaced by IL-15 (Cellgenix) and after 14 days of NK progenitor expansion, Flt-3L was replaced by Proleukin (IL-2; Novartis) for the NK cell differentiation phase. Cells were cultured until day 28 and cryopreserved. Upon thawing, cells were directly used for assays, or cultured for an additional 7 days in differentiation medium before use. 8 donors were selected to sequence at day28 directly after thawing.

extract_protocol:
Cells were resuspended in stain buffer, and each donor was labelled with a Sample Tag from the Human Single-Cell Multiplexing Kit. After washing, donors were pooled and stained with the BD AbSeq Immune Discovery Panel (BD Biosciences). Next, cells were loaded into a BD Rhapsody cartridge and checked for viability by Calcein AM (ThermoFisher) and DRAQ7 (BD Biosciences) in the BD Rhapsody™ Scanner. Cells were captured in the microwells of the cartridge and cDNA and exonuclease treatment was performed using the Rhapsody™ cDNA kit according to manufacturer’s instruction
Libraries were prepared using the BD Rhapsody™ WTA Amplification kit according to manufacturer’s instruction

value: NK cell derived from UCB CD34+ cells

tag: day of_culture


title: RNAseq_ZT16_Q5A_Cohort1_Rep3

value: Brain-TMN

tag: genotype


title: Liver, CDAA-HFD Lanifibranor, Rep 2

description:
18783
CDAA_intervention_counts.txt


title: Post menopausal, subject 12


title: HCT116, TTC7B-2

data_processing:
Illumina Casava2.19 software used for basecalling.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: We used the CRISPR/Cas9 editing system to generate TTC7B knockout cells, and transfected TTC7B plasmid generate to TTC7B overexpression.

value: Colon

value: Colorectal adenocarcinoma epithelial cells

value: TTC7B overexpression

value: untreated


title: RNAseq_ZT16_Q5A_Cohort1_Rep2


title: Post menopausal, subject 13


title: Mid-secretory phase of the menstrual cycle, subject 2


title: Liver, CDAA-HFD Lanifibranor, Rep 1

description:
18780
CDAA_intervention_counts.txt


title: HCT116, TTC7B-1


title: Post menopausal, subject 11


title: Liver, CDAA-HFD Semaglutide, Rep 9

description:
18817
CDAA_intervention_counts.txt

value: CDAA-HFD Semaglutide


title: HCT116, Vector-2

value: Vector overexpression


title: RNAseq_ZT16_Q5A_Cohort1_Rep1


title: Post menopausal, subject 10


title: RNAseq_ZT16_H3.3_Cohort3_Rep2


title: Liver, CDAA-HFD Semaglutide, Rep 8

description:
18816
CDAA_intervention_counts.txt


title: RNAseq_ZT16_H3.3_Cohort2_Rep2


title: Post menopausal, subject 8


title: Liver, CDAA-HFD Semaglutide, Rep 7

description:
18815
CDAA_intervention_counts.txt


title: RNAseq_ZT16_H3.3_Cohort3_Rep1


title: Post menopausal, subject 9


title: HCT116, TTC7BKO-2

value: TTC7B knockout


title: Liver, CDAA-HFD Semaglutide, Rep 6

description:
18814
CDAA_intervention_counts.txt


title: RNAseq_ZT16_H3.3_Cohort2_Rep1


title: HCT116, Vector-1


title: HCT116, Ctrl-2

value: WT


title: Liver, CDAA-HFD Semaglutide, Rep 5

description:
18813
CDAA_intervention_counts.txt


title: Post menopausal, subject 6


title: Post menopausal, subject 7


title: RNAseq_ZT16_H3.3_Cohort1_Rep4


title: Liver, CDAA-HFD  Semaglutide, Rep 4

description:
18812
CDAA_intervention_counts.txt


title: HCT116, Ctrl-1


title: Post menopausal, subject 5


title: RNAseq_ZT16_H3.3_Cohort1_Rep3


title: Liver, CDAA-HFD  Semaglutide, Rep 3

description:
18811
CDAA_intervention_counts.txt


title: Post menopausal, subject 4


title: Liver, CDAA-HFD Semaglutide, Rep 2

description:
18810
CDAA_intervention_counts.txt


title: RNAseq_ZT16_H3.3_Cohort1_Rep1


title: control EVs #2

city: Guang zhou

first: YAN

last: LIN

state: China

address: 72 Zhongshan 2nd Road

institute: Sun Yat-sen University

data_processing:
fastpe (v0.23.2)
We used fastpe (v0.23.2) to filter the raw reads, the filtering rules were as follows: 1) Removed reads containing adapters, 2) Removed reads with N ratio greater than 5%, 3) Removed low-quality reads (the number of bases with quality value Q<=15 accounts for more than 20% of the entire read).
We used CIRCexplorer2(v2.3.8) and find_circ(v1.2) to predict circRNA, and integrate the results of the two software according to the start and end positions of circRNA. CircRNAs that satisfied both starting and ending positions within 10 bases before and after were merged into one class. The known circRNAs were identified according to the circBase database, and the source genes of the circRNAs were determined according to the location information of the reference genome and functional annotations were performed on the source genes (3 error bases were allowed for both the start and end positions).
We calculated the expression of circRNA according to the number of back-spliced reads aligned to both ends of the circRNA. Since two software CIRI and find_circ were used for prediction, the final number of back-spliced reads was the average of the prediction results of the two softwares.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: isolated EVs

extract_protocol:
Total RNA was extracted from the isolated ITGA6+EVs and control EVs using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). Then, 3μg of total RNA was treated with DNase I which degraded double-stranded and single-stranded DNA presenting in RNA samples. And the ribosomal RNA was removed using the Ribo-off rRNA Depletion Kit (Vazyme, Inc.). Linear RNA was removed using RNase R (Epicentre, lnc). Purification was performed using Agencourt RNAClean XP magnetic beads. All other steps were performed according to the manufacturer's protocols. The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using BMG (OMEGA).
RNA libraries were prepared for sequencing using standard DNBSEQ protocols

treatment_protocol: We isolated ITGA6+EVs from total UM-UC-3-EVs by affinity capture using anti-ITGA6 magnetic beads. The isolated EVs was conducted with assistance of lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) under manufacturer’s protocols.

value: isolated EVs

value: control


title: control EVs #3


title: Post menopausal, subject 3

value: Nonpregnant


title: Liver, CDAA-HFD Semaglutide, Rep 1

description:
18809
CDAA_intervention_counts.txt


title: HCT116, TTC7BKO-1


title: RNAseq_ZT16_GFP_Cohort2_Rep2

value: GFP


title: control EVs #1


title: Post menopausal, subject 2


title: Liver, CDAA-HFD Chow reversal, Rep 8

description:
18805
CDAA_intervention_counts.txt

value: CDAA-HFD Chow reversal


title: RNAseq_ZT16_GFP_Cohort2_Rep1


title: Liver, CDAA-HFD Chow reversal, Rep 9

description:
18808
CDAA_intervention_counts.txt

value: Liver


title: ITGA6+ EVs #3


title: ITGA6+ EVs #2


title: Post menopausal, subject 1


title: RNAseq_ZT16_GFP_Cohort1_Rep5


title: ITGA6+ EVs #1


title: Liver, CDAA-HFD Chow reversal, Rep 7

description:
18802
CDAA_intervention_counts.txt


title: Myometrial transcriptome of subject 2, term not in labor

data_processing:
Filter reads of Qual score <20
Remove reads carrying adaptor sequences using cutadapt (v1.12).
Agilgn reads to hg38 genome using STAR aligner (V2.5.2b)
Count reads mapped to each gene using featureCounts ( v1.5.0-p1) function in Subread program
Assembly: hg38
Supplementary files format and content: FPKM was calculated for each gene in each sample by using Cufflinks version 2.0.2.

treatment_protocol: Not applicable

tag: Stage

value: Term not in labor (TNL)


title: Liver, CDAA-HFD Chow reversal, Rep 6

description:
18796
CDAA_intervention_counts.txt


title: RNAseq_ZT16_GFP_Cohort1_Rep4


title: Myometrial transcriptome of subject 3, term not in labor


title: gRNA

description: gRNA expression profiles

data_processing:
Raw reads were processed by Cell Ranger with default setting.
Assembly: hg38
Supplementary files format and content: The filtered feature count matrix was generated from Cell Ranger.

source_name: hTERT-HM Cells

growth_protocol: Growth media: 900ml of DMEM/F12 (Gibco 11330) + 100ml fetal bovine serum (Gibco 16000) + 10ml Antibiotic Antimycotic (Gibco 15240062).

extract_protocol:
RNA and gRNA capture processes were conducted per the intruction of 10X Genomics Chromium Single Cell 3' Reagent kits v3.
Gene expression and gRNA libraries were constructed using the 10X Genomics Chromium Single Cell 3' Reagent kits v3 per the user's manual.
Perturb-seq

treatment_protocol: In immortalized human myometrial cell line hTERT-HM: Lentiviral transduction conferring expression of Guide RNA (gRNA) targeted to putative enhancers of interest and GFP selection marker at Multiplicity of Infection (MOI) 0.4, Cell enrichment via neomycin resistance, Lentiviral transduction conferring dCas9-VPR expression and mCherry selection marker at MOI 4.0, Sell selection via Flow Cytometry for GFP and mCherry double positive cells, Sorted cells sent directly to Perturb-Seq library construction.

value: hTERT-HM


title: RNAseq_ZT16_GFP_Cohort1_Rep3

value: Brain-TMN


title: Myometrial transcriptome of subject 1, term not in labor


title: RNAseq_ZT16_H3.3_Cohort1_Rep2


title: Liver, CDAA-HFD Chow reversal, Rep 5

description:
18793
CDAA_intervention_counts.txt


title: scRNA-seq

description: mRNA expression profiles


title: Pool of genomic DNA from all three myometrial specimens

data_processing:
The raw reads were initially processed by applying a filter with an average quality score of 20.
Adaptors were removed using "cutadapt" program (v 1.12)
Reads were aligned against hg38 genome using "bowtie" (v1.2), using parameters:  -q --phred33-quals -m 1 -v 2 -S
The duplicate reads were removed using the MarkDuplicates tool in picard-tools-1.96.
The retained read alignments were sorted by coordinates, extended to 300 bases
Assembly: hg38
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig from UCSC.

growth_protocol: Not Applicable

extract_protocol:
The uterus were frozen and sent to Active motif for ChIP-Seq analysis
Libraries were prepared by Active Motif Services - FactorPath assays for CTCF (Active Motif cat# 25006) and HistonePath assays for H3K27ac and H3K4me1 (Active Motif cat# 25015).

treatment_protocol: All specimens were flash frozen with warm ischemia times < 30 minutes and stored at <-80C until laboratory use.

tag: chip target

value: Not applicable

tag: pregnancy day

value: Term not in labor

tag: antibody


title: Hi-C of subject 3, term not in labor

description: The Hi-C library was prepared by the Active Motif using the Arima-HiC Kit of the Arima Genomics.

data_processing:
Reads were mapped to the human genome (hg38) using HiCUP (v0.7.1)
Assembly: hg38
Supplementary files format and content: Chromatin loops were identified with Juicer tool

extract_protocol: by Arima Genomics and Active Motif

tag: tissue

value: Myometrium


title: H3K4me1 histone mark of subject 3, term not in labor

value: Active Motif, cat # 39297


title: Liver, CDAA-HFD Chow reversal, Rep 3

description:
18787
CDAA_intervention_counts.txt

tag: treatment


title: RNAseq_ZT12_Q5A_Cohort3_Rep1


title: RNAseq_ZT16_GFP_Cohort1_Rep1


title: Hi-C of subject 1, term not in labor

description: The Hi-C library was prepared by the Arima HiC service of the Arima Genomics.


title: Liver, CDAA-HFD Chow reversal, Rep 2

description:
18784
CDAA_intervention_counts.txt


title: H510-CLX-SD-70_3

city: Dallas

first: Luc

last: Girard

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description:
Gene_FPKM_uqnorm.txt
H510-CLX-SD-70_3

data_processing:
Illumina sequencer from UTSW Sequencing Core (single-end) or Novogene (paired-end)
fastq files were aligned to GRCh38 (human) reference genome using STAR v2.7.1a
bam files were processed to remove read duplicates using Picard MarkDuplicates from GATK v4.1.2. Mouse reads were filtered out from CLX samples
FPKM values were obtained using Cufflinks v2.2.1
FPKM values were upper-quartile normalized, then log-transformed
Assembly: GRCh38
Supplementary files format and content: Gene_FPKM_uqnorm.txt

source_name: SCLC cell line xenografts (CLX)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Library preparation was done with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina or according to Novogene specifications (https://en.novogene.com)

treatment_protocol: See publication

tag: cell line

tag: cell type

value: SCLC

tag: xenograft

value: yes

value: 5x a week


title: RNAseq_ZT12_Q5A_Cohort1_Rep5

tag: timepoint

tag: virus

tag: cohort


title: H510-CLX-SD-70_2

description:
Gene_FPKM_uqnorm.txt
H510-CLX-SD-70_2


title: H3K27ac histone mark of subject 3, term not in labor

value: Active Motif, cat # 39133


title: H3K4me1 histone mark of subject 2, term not in labor


title: Liver, CDAA-HFD Chow reversal, Rep 1

description:
18781
CDAA_intervention_counts.txt


title: RNAseq_ZT12_Q5A_Cohort1_Rep4

tag: replicate


title: Liver, CDAA-HFD vehicle, Rep 10

description:
18806
CDAA_intervention_counts.txt

value: CDAA-HFD vehicle


title: Liver, CDAA-HFD vehicle, Rep 9

description:
18803
CDAA_intervention_counts.txt


title: CTCF genome occupancy of subject 2, term not in labor

value: CTCF

value: Active Motif, cat # 61311


title: H510-CLX-DMSO_3

description:
Gene_FPKM_uqnorm.txt
H510-CLX-DMSO_3

value: DMSO

tag: time


title: H510-CLX-SD-70_1

description:
Gene_FPKM_uqnorm.txt
H510-CLX-SD-70_1


title: RNAseq_ZT12_Q5A_Cohort1_Rep2


title: Liver, CDAA-HFD Chow reversal, Rep 4

description:
18790
CDAA_intervention_counts.txt

value: CDAA-HFD Chow reversal


title: H510-CLX-DMSO_2

description:
Gene_FPKM_uqnorm.txt
H510-CLX-DMSO_2


title: H3K27ac histone mark of subject 2, term not in labor


title: Liver, CDAA-HFD vehicle, Rep 8

description:
18800
CDAA_intervention_counts.txt

value: Liver


title: H3K4me1 histone mark of subject 1, term not in labor


title: Liver, CDAA-HFD vehicle, Rep 7

description:
18797
CDAA_intervention_counts.txt


title: RNAseq_ZT12_Q5A_Cohort2_Rep1


title: RNAseq_ZT12_H3.3_Cohort3_Rep1


title: CTCF genome occupancy of subject 3, term not in labor


title: Liver, CDAA-HFD vehicle, Rep 6

description:
18794
CDAA_intervention_counts.txt


title: H446-CLX-SD-70_3

description:
Gene_FPKM_uqnorm.txt
H446-CLX-SD-70_3


title: CTCF genome occupancy of subject 1, term not in labor


title: H3K27ac histone mark of subject 1, term not in labor


title: Liver, CDAA-HFD vehicle, Rep 4

description:
18788
CDAA_intervention_counts.txt


title: H446-CLX-SD-70_2

description:
Gene_FPKM_uqnorm.txt
H446-CLX-SD-70_2


title: H446-CLX-SD-70_1

description:
Gene_FPKM_uqnorm.txt
H446-CLX-SD-70_1


title: RNAseq_ZT12_H3.3_Cohort2_Rep1


title: 12h_Alpha_3

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

institute: University of Padua

data_processing:
Alignment was performed with STAR (v. 2.7.6a); STAR parameters were set following Lexogen guidelines for data analysis.
Quantification was performed with Subread package featureCounts (v. 2.0.1); featureCounts was used with default parameters.
Assembly: Homo sapiens: GRCh38.p13 Ensembl release 100; SARS-CoV-2: NC_045512.2
Supplementary files format and content: raw_counts_table.txt is a TSV containing official gene symbols, EnsemblID, reference genome and raw counts for each condition

growth_protocol: Calu-3 cells (ATCC®, HB-55) were maintained in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F-12, Thermo Fisher Scientific). Media were supplemented with 10% (v/v) fetal bovine serum (FBS, Thermo Fisher Scientific) and penicillin/streptavidin (Thermo Fisher Scientific). Cell cultures were maintained at 37°C and 5% CO2 in humidified atmosphere and routinely tested for mycoplasma contamination (Euroclone, Cat: EMK090020). For seeding and subcultivation, cells were first washed with phosphate buffered saline (PBS) and then incubated in the presence of trypsin/EDTA solution (Gibco, Thermo Fisher Scientific) until cells detached. Upon seeding of Calu-3 cells, 10 μM ROCK inhibitor Y27632 (Axon Medchem, Cat #1683) was added for 24 h to the culture medium.

extract_protocol:
Total RNA purified with Total RNA Purification Kit (NorgenBiotek, Canada, Cat #48400), following manufacturer’s protocol.
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) was used for library construction.

treatment_protocol: Calu-3 cells were seeded (1.2x105/well) in 12 well plate, and after 24 h the cell culture supernatant was removed and replaced with virus inoculum (MOI of 1 PFU/cell). Following 1 h adsorption at 37 °C, the virus inoculum was removed, the cell monolayer was washed in PBS prior to medium replacement (10% FBS DMEM/F-12). Cells were harvested at 6, 9, 12 and 24 hours post infection.

tag: disease

value: lung adenocarcinoma

value: infected with Alpha SARS_CoV2 variant


title: RNAseq_ZT12_Q5A_Cohort1_Rep3

value: Brain-TMN


title: 12h_Alpha_4


title: RNAseq_ZT12_H3.3_Cohort1_Rep4


title: H446-CLX-DMSO_6

description:
Gene_FPKM_uqnorm.txt
H446-CLX-DMSO_6

growth_protocol: See publication


title: RNAseq_ZT12_H3.3_Cohort1_Rep3


title: RNAseq_ZT12_Q5A_Cohort1_Rep1


title: 12h_Alpha_2


title: 12h_Alpha_1


title: H446-CLX-DMSO_5

description:
Gene_FPKM_uqnorm.txt
H446-CLX-DMSO_5


title: RNAseq_ZT12_H3.3_Cohort1_Rep2


title: H510-CLX-DMSO_1

description:
Gene_FPKM_uqnorm.txt
H510-CLX-DMSO_1


title: Liver, CDAA-HFD vehicle, Rep 1

description:
18779
CDAA_intervention_counts.txt


title: Liver, CDAA-HFD 20 weeks, Rep 8

description:
7696
CDAA_progression_counts.txt

value: CDAA-HFD 20 weeks


title: 12h_D614G_3

value: infected with D614G SARS_CoV2 variant


title: H446-CLX-DMSO_4

description:
Gene_FPKM_uqnorm.txt
H446-CLX-DMSO_4


title: RNAseq_ZT12_H3.3_Cohort2_Rep2


title: 12h_D614G_4


title: RNAseq_ZT12_H3.3_Cohort1_Rep1


title: Liver, CDAA-HFD vehicle, Rep 5

description:
18791
CDAA_intervention_counts.txt


title: H446-CLX-JIB-04_3

description:
Gene_FPKM_uqnorm.txt
H446-CLX-JIB-04_3

value: 3x a week


title: Liver, CDAA-HFD 20 weeks, Rep 7

description:
7691
CDAA_progression_counts.txt


title: Liver, CDAA-HFD vehicle, Rep 3

description:
18785
CDAA_intervention_counts.txt


title: Liver, CDAA-HFD 20 weeks, Rep 6

description:
7686
CDAA_progression_counts.txt


title: H446-CLX-JIB-04_2

description:
Gene_FPKM_uqnorm.txt
H446-CLX-JIB-04_2


title: 12h_D614G_2


title: H446-CLX-JIB-04_1

description:
Gene_FPKM_uqnorm.txt
H446-CLX-JIB-04_1


title: RNAseq_ZT12_GFP_Cohort1_Rep4

value: GFP


title: 12h_D614G_1


title: RNAseq_ZT12_GFP_Cohort1_Rep5


title: RNAseq_ZT12_GFP_Cohort2_Rep1


title: H446-CLX-DMSO_3

description:
Gene_FPKM_uqnorm.txt
H446-CLX-DMSO_3

value: SCLC


title: Liver, CDAA-HFD 20 weeks, Rep 5

description:
7681
CDAA_progression_counts.txt


title: Liver, CDAA-HFD vehicle, Rep 2

description:
18782
CDAA_intervention_counts.txt


title: 12h_Wuhan_4

value: infected with Wuhan SARS-CoV2 variant


title: RNAseq_ZT12_GFP_Cohort1_Rep3


title: RNAseq_ZT12_GFP_Cohort1_Rep2


title: H446-CLX-DMSO_2

description:
Gene_FPKM_uqnorm.txt
H446-CLX-DMSO_2

value: yes


title: Liver, CDAA-HFD 20 weeks, Rep 4

description:
7676
CDAA_progression_counts.txt


title: Liver, CDAA-HFD 20 weeks, Rep 3

description:
7671
CDAA_progression_counts.txt


title: 12h_Wuhan_3


title: H446-CLX-DMSO_1

description:
Gene_FPKM_uqnorm.txt
H446-CLX-DMSO_1


title: 12h_Wuhan_2


title: Liver, CDAA-HFD 20 weeks, Rep 2

description:
7666
CDAA_progression_counts.txt


title: H446-JIB-04_3 48 hours

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04-48h_3

value: no

value: 48 hours


title: 12h_Wuhan_1


title: H446-JIB-04_2 48 hours

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04-48h_2


title: RNAseq_ZT12_GFP_Cohort1_Rep1


title: Liver, CDAA-HFD 20 weeks, Rep 1

description:
7661
CDAA_progression_counts.txt


title: 12h_Mock_4

value: uninfected control


title: Liver, CDAA-HFD 12 weeks, Rep 8

description:
7695
CDAA_progression_counts.txt

value: CDAA-HFD 12 weeks


title: RNAseq_ZT8_Q5A_Cohort2_Rep1


title: 12h_Mock_2


title: RNAseq_ZT8_Q5A_Cohort1_Rep4


title: H446-JIB-04_1 48 hours

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04-48h_1


title: 12h_Mock_3


title: Liver, CDAA-HFD 12 weeks, Rep 6

description:
7685
CDAA_progression_counts.txt


title: H446-DMSO_3 48 hours

description:
Gene_FPKM_uqnorm.txt
H446-DMSO-48h_3

value: DMSO


title: Liver, CDAA-HFD 12 weeks, Rep 7

description:
7690
CDAA_progression_counts.txt


title: H446-DMSO_2 48 hours

description:
Gene_FPKM_uqnorm.txt
H446-DMSO-48h_2


title: Liver, CDAA-HFD 12 weeks, Rep 5

description:
7680
CDAA_progression_counts.txt


title: H446-DMSO_1 48 hours

description:
Gene_FPKM_uqnorm.txt
H446-DMSO-48h_1


title: 12h_Mock_1


title: RNAseq_ZT8_Q5A_Cohort1_Rep2


title: 9h_Alpha_4

value: 9 h.p.i


title: RNAseq_ZT8_Q5A_Cohort1_Rep1


title: Liver, CDAA-HFD 12 weeks, Rep 4

description:
7675
CDAA_progression_counts.txt

value: Liver


title: H510-SD-70_3

description:
Gene_FPKM_uqnorm.txt
H510-SD-70_3

value: 24 hours


title: 9h_Alpha_3

value: lung adenocarcinoma

value: infected with Alpha SARS_CoV2 variant


title: RNAseq_ZT8_H3.3_Cohort3_Rep1

value: Brain-TMN


title: Liver, CDAA-HFD 12 weeks, Rep 3

description:
7670
CDAA_progression_counts.txt


title: H510-SD-70_2

description:
Gene_FPKM_uqnorm.txt
H510-SD-70_2


title: 9h_Alpha_2


title: RNAseq_ZT8_Q5A_Cohort1_Rep5


title: Liver, CDAA-HFD 12 weeks, Rep 2

description:
7665
CDAA_progression_counts.txt


title: RNAseq_ZT8_H3.3_Cohort2_Rep2


title: 9h_Alpha_1


title: H510-SD-70_1

description:
Gene_FPKM_uqnorm.txt
H510-SD-70_1


title: RNAseq_ZT8_H3.3_Cohort2_Rep1


title: Liver, CDAA-HFD 12 weeks, Rep 1

description:
7660
CDAA_progression_counts.txt


title: RNAseq_ZT8_Q5A_Cohort1_Rep3


title: RNAseq_ZT8_H3.3_Cohort1_Rep4


title: H510-JIB-04_9

description:
Gene_FPKM_uqnorm.txt
H510-JIB-04_9


title: H510-JIB-04_8

description:
Gene_FPKM_uqnorm.txt
H510-JIB-04_8


title: Liver, CDAA-HFD 6 weeks, Rep 10

description:
19743
CDAA_progression_counts.txt

value: CDAA-HFD 6 weeks


title: H510-JIB-04_7

description:
Gene_FPKM_uqnorm.txt
H510-JIB-04_7


title: RNAseq_ZT8_H3.3_Cohort1_Rep3


title: Liver, CDAA-HFD 6 weeks, Rep 9

description:
19521
CDAA_progression_counts.txt


title: RNAseq_ZT8_H3.3_Cohort1_Rep2


title: 9h_D614G_1

value: infected with D614G SARS_CoV2 variant


title: H510-DMSO_9

description:
Gene_FPKM_uqnorm.txt
H510-DMSO_9


title: Liver, CDAA-HFD 6 weeks, Rep 7

description:
19517
CDAA_progression_counts.txt


title: RNAseq_ZT8_H3.3_Cohort1_Rep1


title: 9h_Wuhan_4


title: H510-DMSO_8

description:
Gene_FPKM_uqnorm.txt
H510-DMSO_8


title: RNAseq_ZT8_GFP_Cohort2_Rep1

value: GFP


title: Liver, CDAA-HFD 6 weeks, Rep 6

description:
19515
CDAA_progression_counts.txt


title: H510-DMSO_7

description:
Gene_FPKM_uqnorm.txt
H510-DMSO_7

value: SCLC


title: 9h_Wuhan_3

value: infected with Wuhan SARS-CoV2 variant


title: RNAseq_ZT8_GFP_Cohort1_Rep5


title: Liver, CDAA-HFD 6 weeks, Rep 5

description:
19513
CDAA_progression_counts.txt


title: H446-SD-70_3 5x IC50 4 hours

description:
Gene_FPKM_uqnorm.txt
H446-SD-70_3

value: 4 hours


title: Liver, CDAA-HFD 6 weeks, Rep 4

description:
19511
CDAA_progression_counts.txt


title: 9h_Wuhan_2


title: 9h_D614G_4


title: H446-SD-70_2 5x IC50 4 hours

description:
Gene_FPKM_uqnorm.txt
H446-SD-70_2

value: no


title: 9h_D614G_3


title: RNAseq_ZT8_GFP_Cohort1_Rep4


title: 9h_D614G_2


title: 9h_Wuhan_1


title: 9h_Mock_4


title: Liver, CDAA-HFD 6 weeks, Rep 2

description:
19505
CDAA_progression_counts.txt


title: RNAseq_ZT8_GFP_Cohort1_Rep3


title: H446-JIB-04_3 5x IC50 4 hours

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04_9


title: H446-SD-70_1 5x IC50 4 hours

description:
Gene_FPKM_uqnorm.txt
H446-SD-70_1


title: H446-JIB-04_2 5x IC50 4 hours

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04_8


title: RNAseq_ZT8_GFP_Cohort1_Rep1


title: 9h_Mock_2


title: Liver, CDAA-HFD 6 weeks, Rep 1

description:
19503
CDAA_progression_counts.txt


title: Liver, CDAA-HFD 6 weeks, Rep 8

description:
19519
CDAA_progression_counts.txt


title: RNAseq_ZT4_Q5A_Cohort3_Rep1


title: Liver, CDAA-HFD 3 weeks, Rep 9

description:
19520
CDAA_progression_counts.txt

value: CDAA-HFD 3 weeks


title: H446-JIB-04_1 5x IC50 4 hours

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04_7


title: 9h_Mock_1

value: uninfected control


title: 9h_Mock_3


title: RNAseq_ZT4_Q5A_Cohort2_Rep3


title: 6h_Alpha_4

value: 6 h.p.i


title: H446-DMSO_9

description:
Gene_FPKM_uqnorm.txt
H446-DMSO_9

value: DMSO


title: RNAseq_ZT4_Q5A_Cohort2_Rep2


title: Liver, CDAA-HFD 3 weeks, Rep 8

description:
19518
CDAA_progression_counts.txt


title: H446-DMSO_8

description:
Gene_FPKM_uqnorm.txt
H446-DMSO_8


title: H446-DMSO_7

description:
Gene_FPKM_uqnorm.txt
H446-DMSO_7


title: RNAseq_ZT4_Q5A_Cohort2_Rep1


title: RNAseq_ZT8_GFP_Cohort1_Rep2


title: Liver, CDAA-HFD 3 weeks, Rep 7

description:
19516
CDAA_progression_counts.txt


title: Liver, CDAA-HFD 6 weeks, Rep 3

description:
19509
CDAA_progression_counts.txt


title: Liver, CDAA-HFD 3 weeks, Rep 6

description:
19514
CDAA_progression_counts.txt


title: 6h_Alpha_2


title: 6h_Alpha_3


title: RNAseq_ZT4_Q5A_Cohort1_Rep4


title: RNAseq_ZT4_Q5A_Cohort1_Rep3


title: Liver, CDAA-HFD 3 weeks, Rep 5

description:
19512
CDAA_progression_counts.txt


title: Liver, CDAA-HFD 3 weeks, Rep 4

description:
19510
CDAA_progression_counts.txt


title: H446-JIB-04_6

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04_6


title: H446-JIB-04_5

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04_5


title: RNAseq_ZT4_Q5A_Cohort1_Rep2


title: 6h_D614G_4


title: H446-JIB-04_4

description:
Gene_FPKM_uqnorm.txt
H446-JIB-04_4


title: 6h_D614G_3


title: Liver, CDAA-HFD 3 weeks, Rep 3

description:
19508
CDAA_progression_counts.txt


title: Liver, CDAA-HFD 3 weeks, Rep 2

description:
19504
CDAA_progression_counts.txt


title: 6h_D614G_2


title: 6h_D614G_1


title: Liver, CDAA-HFD 3 weeks, Rep 1

description:
19502
CDAA_progression_counts.txt


title: H446-DMSO_5

description:
Gene_FPKM_uqnorm.txt
H446-DMSO_5


title: Liver, Chow, Rep 8

description:
8056
CDAA_progression_counts.txt
CDAA_intervention_counts.txt

value: Chow


title: 6h_Alpha_1


title: RNAseq_ZT4_H3.3_Cohort1_Rep4


title: 6h_Wuhan_4


title: H446-Cas9_3

description:
Gene_FPKM_uqnorm.txt
H446-Cas9_3


title: Liver, Chow, Rep 7

description:
7692
CDAA_progression_counts.txt
CDAA_intervention_counts.txt

value: Liver


title: 6h_Wuhan_3


title: RNAseq_ZT4_H3.3_Cohort1_Rep3


title: RNAseq_ZT4_Q5A_Cohort1_Rep1


title: H446-Cas9_1

description:
Gene_FPKM_uqnorm.txt
H446-Cas9_1


title: Liver, Chow, Rep 6

description:
7687
CDAA_progression_counts.txt
CDAA_intervention_counts.txt


title: Liver, Chow, Rep 4

description:
7677
CDAA_progression_counts.txt
CDAA_intervention_counts.txt


title: 6h_Wuhan_1


title: H446-Cas9_KDM4A_3

description:
Gene_FPKM_uqnorm.txt
H446-Cas9_KDM4A_3


title: 6h_Wuhan_2


title: RNAseq_ZT4_H3.3_Cohort1_Rep2


title: RNAseq_ZT4_H3.3_Cohort1_Rep1


title: Liver, Chow, Rep 5

description:
7682
CDAA_progression_counts.txt
CDAA_intervention_counts.txt


title: H446-DMSO_6

description:
Gene_FPKM_uqnorm.txt
H446-DMSO_6

value: 24 hours


title: RNAseq_ZT4_GFP_Cohort1_Rep5


title: H446-Cas9_KDM4A_2

description:
Gene_FPKM_uqnorm.txt
H446-Cas9_KDM4A_2


title: 6h_Mock_3

value: lung adenocarcinoma


title: H446-Cas9_2

description:
Gene_FPKM_uqnorm.txt
H446-Cas9_2


title: Liver, Chow, Rep 3

description:
7672
CDAA_progression_counts.txt
CDAA_intervention_counts.txt


title: RNAseq_ZT4_H3.3_Cohort2_Rep1


title: H446-DMSO_4

description:
Gene_FPKM_uqnorm.txt
H446-DMSO_4


title: RNAseq_ZT4_H3.3_Cohort3_Rep1


title: RNAseq_ZT4_GFP_Cohort1_Rep3


title: H446-Cas9_KDM4A_1

description:
Gene_FPKM_uqnorm.txt
H446-Cas9_KDM4A_1


title: Liver, Chow, Rep 2

description:
7667
CDAA_progression_counts.txt
CDAA_intervention_counts.txt


title: RNAseq_ZT4_GFP_Cohort1_Rep4


title: 6h_Mock_2


title: RNAseq_ZT4_GFP_Cohort1_Rep2


title: 6h_Mock_1


title: H524-JIB-04_3

description:
Gene_FPKM_uqnorm.txt
H524-JIB-04_3


title: Liver, Chow, Rep 1

description:
7662
CDAA_progression_counts.txt
CDAA_intervention_counts.txt