title: NPC_105Q_ATF3WT_2

description:
Library name: NPC_105Q_ATF3WT_2
counts_ATF3KO.csv

value: NPC


title: wk3_KrasWT_Caerulein_B0168

status: Public on Apr 01 2026

type: SRA

city: New York

first: Rohit

last: Chandwani

state: NY

address: 413 East 69th St, BRB 1360G

department: Surgery

country: USA

institute: Weill Cornell Medicine

library_source: transcriptomic

data_processing:
The quality of the sequenced reads was assessed with FastQC v0.11.8 and QoRTs v1.3.6.
Sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR v2.7.9a.
. Gene expression estimates were obtained with featureCounts v2.0.1 using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M25).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

molecule: polyA RNA

organism: Mus musculus

source_name: Adult Pancreas

extract_protocol:
tdTomato+ acinar cells were FACS sorted into 1.5 mL Eppendorf tubes containing Trizol. Total RNA was purified using a standard phenol-chloroform extraction method.
Sequencing libraries were constructed using Illumina TruSeq Library Prep Kit (Non-Stranded and Poly-A selection) and sequenced on either Illumina HiSeq 2500 or NovaSeq 6000 (2x50 cycles paired-end run)

tag: tissue

value: Adult Pancreas

tag: genotype

value: KrasWT

tag: treatment

value: Tamoxifen

value: Caerulein

tag: time


title: NPC_105Q_ATF3WT_1

city: Jerusalem

first: Walaa

middle: Ziad

last: Oweis

state: Israel

country: Israel

institute: Hebrew University of Jerusalem

description:
Library name: NPC_105Q_ATF3WT_1
counts_ATF3KO.csv

data_processing:
Raw fastq files were checked for quality control using fastqc software.
Raw reads were trimmed to remove Illumina adapters using the Trimmomatic software version 0.39
Reads were aligned to the human RefSeq reference genome (GRCh38) using STAR aligner version 2.7.1a with the default parameters.
Raw counts for each gene were generated using - quantMode GeneCounts.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen)
mRNA libraries were prepared using KAPA Stranded mRNA-Seq kit.

tag: cell line

tag: cell type


title: SKMEL2 Control ChIP Rep 3

city: Beijing

first: Zexian

last: Zeng

address: No.5 Yiheyuan Road, Haidian District, Beijing

country: China

institute: Peking University

description: Library name: SKMEL2 Control ChIP Rep 3

library_source: genomic

data_processing:
Raw sequencing reads were assessed using FastQC to evaluate base quality, duplication levels, and adapter content.
Adapters and low-quality bases were removed using Trim Galore (v0.6.10) with paired-end mode and other default parameters.
Trimmed reads were aligned to the hg38 reference genome using Bowtie2 with --very-sensitive preset and maximum insert size of 2000 bp.
Properly paired reads with MAPQ >= 30, excluding secondary, supplementary, and duplicate alignments were retained, mitochondrial reads (chrM) were removed, and duplicate reads were removed using SAMtools (v1.17) pipeline.
Final BAM files were coordinate-sorted and indexed using SAMtools.
bigWig coverage tracks were generated using deepTools bamCoverage (v3.5.3) with 10 bp bin size and RPGC normalization (effective genome size: 2,862,010,428). chrX and chrM were excluded from normalization, and reads were extended to the estimated fragment size..
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Skin

extract_protocol:
A total of 40 million cells for each group were fixed with 1% formaldehyde solution for 8 min. After quencing and cell lysis, chromatin was sonicated using a Qsonica Q800R (50% amplitude, 30 s on / 30 s off, for 20 cycles) to achieve a mean DNA fragment size of 300 bp.
Post-sonication, samples were centrifuged at 12,000×g for 5 min at 4°C, and the supernatant was collected and kept on ice. Samples were diluted 1:10 in dilution buffer  supplemented with 5 M NaCl to reach 150 mM NaCl, and incubated rotating with antibody and Protein A/G magnetic beads, to bind the anti-HA antibody and associated chromatin, for 3 h at 4°C. After washing seven times with high salt buffer and twice with TE buffer, samples were eluted from the beads for 15 min at 65°C in elution buffer. Eluates were treated with RNase A at 37°C for 30 min and reverse cross-linked overnight by heating at 65°C with Proteinase K. Samples were extracted with an equal volume of phenol:chloroform, vortexed, centrifuged at 12,000×g for 10 min. The aqueous phase (~400 μL) was transferred to a new tube and mixed with 1.6 μL GlycoBlue (250×), 40 μL 3 M sodium acetate (pH 5.2), and 800 μL ice-cold ethanol. DNA was precipitated at -20°C overnight. Samples were centrifuged at 12,000×g for 15 min at 4°C, washed twice with 75% ethanol, and resuspended in 20 μL nuclease-free water. The ChIP library for each sample was then prepared using VAHTS Universal Pro DNA Library Prep Kit for lllumina with VAHTS Multiplex Oligos Set 4 for Illumina and VAHTS DNA Clean Beads.

value: Skin

value: Control


title: Homo sapiens Telencephalon CS17 Rep2

city: London

first: Fursham

last: Hamid

address: 1 Newcomen St

country: United Kingdom

institute: KCL

description:
Library name: AZI3602A2
Technical replicate

library_source: transcriptomic single cell

data_processing:
Short reads stored in FASTQ file formats were pre-processed and aligned to custom-built transcriptomes  using the CellRanger software (v3.0.2 or v3.1.0)
Assembly: GRCh38-3.0.0_GFP-tdT or mm10-3.0.0_GFP-tdT
Supplementary files format and content: The gene expression counts from predicted cells were stored in compressed H5 format (libname_filtered_feature_bc_matrix.h5).

source_name: Telencephalon

extract_protocol:
Single cell suspensions from each mouse and human sample were loaded into one and two lanes, respectively, of a Chromium Chip G (10X Genomics, PN-1000120) of 10X Chromium Controller (PN-120270
Sequencing libraries were prepared using  Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (PN-1000121) according to manufacturer’s protocol.

value: Telencephalon

tag: development stage

tag: replicate


title: NPC_105Q_ATF3WT_3

description:
Library name: NPC_105Q_ATF3WT_3
counts_ATF3KO.csv


title: SKMEL2 Control ChIP Rep 1

description: Library name: SKMEL2 Control ChIP Rep 1


title: Homo sapiens Telencephalon CS17 Rep1

description:
Library name: AZI3602A1
Technical replicate


title: SKMEL2 Control ChIP Rep 2

description: Library name: SKMEL2 Control ChIP Rep 2


title: wk3_KrasWT_Caerulein_B0165


title: sample3

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

description: Library name: sample6

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Sequenced reads were mapped to Danio rerio whole genome (Ensembl Zv11) using STAR v. 2.7.0f with default parameters
Raw counts are produced by htseq-count (HTSeq v. 0.9.1) - annotation file: Danio_rerio.GRCz11.105.gtf (Ensembl Zv11)
Normalization and differential expression analysis were performed with edgeR v3.38.4
Assembly: Danio rerio whole genome (Ensembl Zv11)
Supplementary files format and content: normalized counts cpm

organism: Danio rerio

source_name: CHT 36hpf

extract_protocol:
Rneasy Plus Mini Kit (QIAGEN)
SMARTer Ultra Low + Illumina Nextera XT

value: CHT 36hpf

value: Endothelial cells


title: A375 ARNTKO ATAC Rep 3

description: Library name: A375 ARNTKO ATAC Rep 3

extract_protocol:
For each sample, 1 million cells were collected, washed with PBS, resuspended with PBS, and lysed with lysis buffer.
The ATAC library for each sample was then prepared using TruePrep DNA Library Prep Kit V2 for Illumina with TruePrep Index Kit V2 for Illumina.

value: ARNT KO


title: NPC_105Q_ATF3KO_2

description:
Library name: NPC_105Q_ATF3KO_2
counts_ATF3KO.csv


title: wk3_KrasWT_Caerulein_4986


title: sample2

description: Library name: sample5


title: A375 ARNTKO ATAC Rep 2

description: Library name: A375 ARNTKO ATAC Rep 2


title: NPC_105Q_ATF3KO_1

description:
Library name: NPC_105Q_ATF3KO_1
counts_ATF3KO.csv


title: sample1

description: Library name: sample4


title: wk3_KrasWT_Caerulein_4988


title: NPC_105Q_ATF3KO_3

description:
Library name: NPC_105Q_ATF3KO_3
counts_ATF3KO.csv


title: A375 ARNTKO ATAC Rep 1

description: Library name: A375 ARNTKO ATAC Rep 1


title: NPC_180Q(IB+)_3

description:
Library name: NPC_180Q(IB+)_3
counts_NPCs_180Q.csv

value: IB+


title: control3

description: Library name: sample3


title: wk3_KrasG12Vgeo_Saline_B0341

value: Saline


title: A375 AHRKO ATAC Rep 3

description: Library name: A375 AHRKO ATAC Rep 3

value: AHR KO


title: wk3_KrasWT_Caerulein_4946


title: wk3_KrasG12Vgeo_Saline_B0231


title: NPC_180Q(IB+)_1

description:
Library name: NPC_180Q(IB+)_1
counts_NPCs_180Q.csv


title: control2

description: Library name: sample2


title: A375 AHRKO ATAC Rep 2

description: Library name: A375 AHRKO ATAC Rep 2


title: wk3_KrasG12Vgeo_Saline_B0066


title: control1

description: Library name: sample1


title: A375 AHRKO ATAC Rep 1

description: Library name: A375 AHRKO ATAC Rep 1


title: NPC_180Q(IB-)_3

description:
Library name: NPC_180Q(IB-)_3
counts_NPCs_180Q.csv

value: IB-


title: NPC_180Q(IB+)_2

description:
Library name: NPC_180Q(IB+)_2
counts_NPCs_180Q.csv


title: proximal_colon_mucosa,control_diet,pbs_treated,rep6

city: Beltsville

first: Gloria

last: Solano-Aguilar

state: MD

address: 10300 Baltimore Ave

institute: USDA-ARS

description: Library name: 95135

data_processing:
Raw sequencing data was basecalled, de-multiplexed and adapter trimmed with bcl2fastq (v2.20.0.422, Illumina, Inc.). Unaligned FASTQ files were processed with CLC Genomics Workbench version 11.0 (QIAGEN, Bioinformatics, Redwood City CA) for quality trimming. Reads were mapped to a custom, non-redundant (NR) (NR_111819 v2) 8,959 transcript library (Porcine Translational Research Database). Reads were aligned and gene expression profiles were generated for each sample. Gene counts were used for differential gene expression analysis. Gene counts represent “unique gene reads” as defined by the CLC Genomic Workbench.
Assembly: NR_11-13-19
Supplementary files format and content: comma delimited text file containing gene counts for each sample

organism: Sus scrofa

source_name: proximal colon mucosa

growth_protocol: Thirty female, 6 week old pigs (Landrace X Yorkshire) were fed a regular age-matched growth diet ad-libitum for the first week after arrival for acclimatization

extract_protocol:
Whole proximal colon sections (~5 cm) were excised and the mucosa layer was  separated from the submucosal layer, stored in cryotubes, flash frozen in liquid nitrogen, and stored at −80°C until ready for RNA isolation. Total RNA was extracted using the TRI reagent (Zymo Research, Irvine, CA). Residual genomic DNA removed using TURBO DNA-free kit (Invitrogen, Carlsbad, CA) with RNAseOUT (Invitrogen, Carlsbad, CA). RNA quality and concentration was assessed by gel electrophoresis using Experion RNA Standard Sensitivity Analysis Kit (Bio-Rad, Hercules, CA). All samples had an RNA quality indicator (RQI) greater than 8.5
RNA sequencing libraries were prepared with Illumina TruSeq RNA Sample Prep v2 kits (Illumina, San Diego, USA). Libraries were sequenced on an Illumina Next Seq 500 (Illumina, San Diego, CA) and a high output flow-cell to generate 150 base-pair single-end reads.

treatment_protocol: Pigs were fed a daily pre-weighed, fixed amount (750 grs/day) of growth diet supplemented with chicken and fruits & vegetables (FVs) or calorie matching non-FV supplemented growth diet for the two control groups. Group I (n=6) was fed a growth diet with 17% energy (E) from fat, 62% E from carbohydrates and 20% E from protein and designated as the untreated negative control-diet. Group II (n=8) was treated with DSS (DSS-treated control). Group III (n=8) and Group IV (n=8) were fed the same grower diet but supplemented with an equivalent of half or full daily recommendation of FV according to the DGA, respectively. At week 5, 4% DSS was administered to groups II, III, and IV for 10 days while group I was given PBS.

value: proximal colon mucosa

tag: Sex

value: female

tag: diet

value: control

value: pbs


title: proximal_colon_mucosa,full_FV_diet,dss_treated,rep8

description: Library name: 95134

value: dss


title: A375 Control ATAC Rep 2

description: Library name: A375 Control ATAC Rep 2

value: Non-targeting control


title: NPC_180Q(IB-)_1

description:
Library name: NPC_180Q(IB-)_1
counts_NPCs_180Q.csv

value: NPC


title: wk3_KrasG12Vgeo_Caerulein_B0538

value: Adult Pancreas

value: Tamoxifen

value: Caerulein


title: A375 Control ATAC Rep 3

description: Library name: A375 Control ATAC Rep 3

value: Skin


title: NPC_180Q(IB-)_2

description:
Library name: NPC_180Q(IB-)_2
counts_NPCs_180Q.csv


title: A375 Control ATAC Rep 1

description: Library name: A375 Control ATAC Rep 1


title: wk3_KrasG12Vgeo_Caerulein_B0493


title: wk3_KrasG12Vgeo_Caerulein_B0232


title: proximal_colon_mucosa,half_FV_diet,dss_treated,rep8

description: Library name: 95133


title: wk3_KrasG12R_Saline_B0503


title: proximal_colon_mucosa,control_diet,pbs_treated,rep5

description: Library name: 95132


title: NPC_105Q(IB+)_3

description:
Library name: NPC_105Q(IB+)_3
counts_NPC_105Q.csv


title: NPC_105Q(IB+)_2

description:
Library name: NPC_105Q(IB+)_2
counts_NPC_105Q.csv


title: wk3_KrasG12R_Saline_B0240


title: proximal_colon_mucosa,full_FV_diet,dss_treated,rep7

description: Library name: 95131


title: CEC4, intestinal organoid, PG008

city: Tokyo

first: Tomohiro

last: Mizutani

address: 1-5-45 Yushima, Bunkyo-ku,

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Institute of Science Tokyo

description:
Library name: Sample 2
10x Genomics

data_processing:
Read alignment, cell-calling, and feature-barcode count matrix generation were performed using the 10x Genomics Cell Ranger v9.0.1 pipeline.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files containing cellular barcodes and genes. Matrix files containing count matrix. Raw data files were pre-processed based on mitochondrial DNA content and raw count and feature distributions.

source_name: Ascending colon derived intestinal organoid

extract_protocol:
Intestinal organoids grown for 8 days were collected, and dissociated into single cells with TrypLE treatment for 15 min. The cells were washed with 1% BSA PBS several times. The cell suspension was passed through 10 μm cell strainer until single cell purity was acceptable. The cells were counted with hemocytometer. Approximately 10000 cells per sample was loaded onto the 10x Chromium X platform.
Library preparation followed the manufacturer's instructions using the GEM X 3' kit v4. The resulting libraries were processed on the Illumina Novaseq 6000 platform resulting in 25000 reads per cell.

value: intestinal epithelia

value: PG008 culture


title: CEC4, intestinal organoid, Wnt3a

description:
Library name: Sample 1
10x Genomics

value: Ascending colon derived intestinal organoid

value: Wnt3a culture


title: NPC_105Q(IB+)_1

description:
Library name: NPC_105Q(IB+)_1
counts_NPC_105Q.csv

value: IB+


title: wk3_KrasG12R_Saline_B0238

value: Saline


title: proximal_colon_mucosa,control_diet,pbs_treated,rep4

description: Library name: 95130

value: proximal colon mucosa


title: NPC_105Q(IB-)_3

description:
Library name: NPC_105Q(IB-)_3
counts_NPC_105Q.csv

value: IB-


title: wk3_KrasG12R_Saline_B0170


title: A431 cells shp53, WWOX Wild-Type, Input DNA

first: Rami

last: Aqeilan

address: Ein Kerem

description: Library name: INPUT

data_processing:
FASTQ files were trimmed using trim_galore utility. During this step, adapters and low quality bases were filtered out. The fastqc utility was applied to examine data quality.
Trimmed FASTQ files were mapped to the genome, assembly hg38, with hisat2 utility.
Coverage bigwig files were created with deepTools utility bamCompare using ration operation relative to input.
Downstream analysis was performed with R custom scripts.
Assembly: Assembly: hg38
Supplementary files format and content: Supplementary files format and content: bigWig

source_name: skin

growth_protocol: A431 cell lines were grown in RPMI (Gibco) supplemented with 10% FBS (Gibco), glutamine, and penicillin/streptomycin (Biological Industries). All cells were grown in 37°C with 5% CO2.  Genetic modification:  Stable clones for WWOX knock-out (KO) were produced using a lentiviral vector containing gRNA for WWOX exon 1 and selected by Blasticidin. Rescue clones were created from the WWOX KO cells using lentivirus containing CMV; WWOX over expression vector and selected by G418 (Gibco 11811031). Clones of shp53 were done on WT/KO/Rescue cells transfected with PLKO.1 p53 shRNA vector and selected using Puromycin.

extract_protocol:
Cells were crosslinked with 1% formaldehyde (methanol free, Thermo Scientific 28906) for 10 min at room temperature and quenched with glycine, 125 mM final concentration.Cells were sonicated using bioruptor sonicator to produce chromatin fragments of ~200–300 bp. The chromatin was immunoprecipitated by incubation with 5 μl of anti- ΔNp63 antibody (Rb polyclonal anti- ΔNp63 antibody (ab203826)). Immune complexes were captured with protein G Dynabeads. DNA was precipitated by phenol/chloroform/isoamylalcohol extraction.
The ChIPed and the Input DNA were used to prepare libraries by Kappa Hyperprep kit

value: skin

value: cSCC

value: shp53, WWOX WT

tag: antibody


title: proximal_colon_mucosa,full_FV_diet,dss_treated,rep6

description: Library name: 95129

value: female

value: dss


title: wk3_KrasG12R_Saline_4948

value: Adult Pancreas


title: NPC_105Q(IB-)_2

description:
Library name: NPC_105Q(IB-)_2
counts_NPC_105Q.csv

value: NPC


title: A431 cells shp53, WWOX rescue

description: Library name: RES

value: shp53, WWOX Res

value: ΔNp63 Rb (Abcam, ab203826)


title: proximal_colon_mucosa,half_FV_diet,dss_treated,rep7

description: Library name: 95128


title: proximal_colon_mucosa,full_FV_diet,dss_treated,rep5

description: Library name: 95127


title: NPC_105Q(IB-)_1

description:
Library name: NPC_105Q(IB-)_1
counts_NPC_105Q.csv


title: wk3_KrasG12R_Caerulein_B0505

value: Tamoxifen

value: Caerulein


title: NPC_105Q_(DELTA)_7F

description: Library name: NPC_105Q_(DELTA)_7F

data_processing:
Raw reads were aligned to the human hg38 reference genome using bowtie2, followed by DNA duplicates removal using rmdup from the samtools.
Peak calling was carried out using MACS2 software with parameters nomodel and extsize=200.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
NPCs were collected and resuspended in 10 ml of 10% FBS in PBS. Then, 277 μl of formaldehyde was added and incubated for 10 min at room temperature (RT) on the rotor, followed by adding 550 μl of 2.5 M glycine for 5 minutes at RT. The treated cells were then centrifuged for 5 minutes, 1600 g at 4°C. Followed by three consecutive washing rounds in 10 ml of ice-cold PBS. A cocktail of protease inhibitors was added to the final washing round. Then, the supernatant was discarded, and the cells were flash-frozen in liquid nitrogen and stored in -80°C. The cell number and sonicator parameters were equilibrated a day before the ChIP procedure. The samples were thawed on ice and resuspended in 500 μl of lysis buffer (1% SDS, 10 mM EDTA pH 8, 50 mM Tris HCl pH 8) for 30 minutes. Samples were sonicated 45 times for 30 s with a 30-s break between each sonication, the sonicate was then centrifuged 15 min, 14000 rpm at 4°C and flash-frozen in liquid nitrogen and stored in -80°C.
ChIP-seq libraries were prepared using a modified protocol by Blecher-Gonen, R. et al


title: wk3_KrasG12R_Caerulein_B0235


title: A431 cells shp53, WWOX Knock-out

description: Library name: KO

value: shp53, WWOX KO


title: A431 cells shp53, WWOX Wild-Type

description: Library name: WT


title: VT10, BQ+

city: Boca Raton

first: Hansraj

last: Jangir

state: Florida

address: 777 glades

institute: Florida Atlantic University

description: Library name: 11425933A3

data_processing:
Raw sequencing reads and manually aligned histology images were analyzed with Space Ranger and the probe set provided by 10x genomics.
Assembly: hg19
Supplementary files format and content: barcodes.tsv.gz
Library strategy: Spatial Transcriptomics

source_name: Oral buccal mucosa

extract_protocol:
FFPE tissues were cut at 4 μm thickness onto 6.5mm x 6.5mm capture areas of the Visium spatial gene expression slides.
RNA ligation to the probe, extension of probe pairs, and library construction were conducted by using the Visium workflow (10x Genomics).

value: Oral buccal mucosa

tag: tumor stage

tag: sample group

value: BQ+

tag: tissue type

value: FFPE


title: wk3_KrasG12R_Caerulein_B0233


title: NPC_105Q_(DELTA)_7E

description: Library name: NPC_105Q_(DELTA)_7E


title: VT9, BQ+

description: Library name: 11843177A3


title: proximal_colon_mucosa,half_FV_diet,dss_treated,rep5

description: Library name: 95125

value: proximal colon mucosa


title: proximal_colon_mucosa,half_FV_diet,dss_treated,rep6

description: Library name: 95126


title: NPC_105Q_(IB+)_6H

description: Library name: NPC_105Q_(IB+)_6H

value: IB+


title: proximal_colon_mucosa,control_diet,pbs_treated,rep3

description: Library name: 95124

value: control

value: pbs


title: wk3_KrasG12R_Caerulein_B0163


title: VT8, BQ+

description: Library name: 11835830


title: NPC_105Q_(IB-)_9A

description: Library name: NPC_105Q_(IB-)_9A

value: IB-


title: wk3_KrasG12R_Caerulein_4954


title: VT7, BQ+

description: Library name: 11820792A3


title: proximal_colon_mucosa,control_diet,pbs_treated,rep2

description: Library name: 95123

value: female


title: wk3_KrasG12D_Saline_B0474

value: Saline


title: VT6, BQ-

description: Library name: 11737011A6

value: BQ-


title: WM115 DMSO RNA Rep 2

description:
Library name: WM115 DMSO RNA Rep 2
D2
WM115_count.csv
WM115_TPM.csv

data_processing:
STAR v2.6.1d, Salmon v0.13.1, tximport v1.22.0, DESeq2 v1.34.0
RNA-seq reads were aligned to hg38 genome v22 using STAR v2.6.1d.
Read alignments were quantified by Salmon v0.13.1 in its alignment-based mode.
Gene-level raw counts as well as transcript per million (TPM) from quantification files were prepared with tximport v1.22.0.
Normalization of raw counts and differential expression analysis were performed by DESeq2 v1.34.0 with default parameters.
Assembly: hg38
Supplementary files format and content: Comma-delimited csv files include TPM values for each sample.
Supplementary files format and content: Comma-delimited csv files include raw counts for each sample.

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-Seq Library Prep Kit for Illumina following manufacturer's protocols.

value: Skin

value: WT

value: 0.1% DMSO


title: VT5, BQ-

description: Library name: 11730802A1


title: proximal_colon_mucosa,control_diet,pbs_treated,rep1

description: Library name: 95121


title: NPC_105Q_ATF3_WT_6B

description: Library name: NPC_105Q_ATF3_WT_6B

value: NPC


title: wk3_KrasG12D_Saline_4987

value: Adult Pancreas

value: Tamoxifen


title: wk3_KrasG12D_Saline_4991


title: NPC_105Q_(IB+)_8F

description: Library name: NPC_105Q_(IB+)_8F


title: proximal_colon_mucosa,control_diet,dss_treated,rep8

description: Library name: 95120

value: dss


title: VT4, BQ-

description: Library name: 11713272A3

value: Oral buccal mucosa


title: proximal_colon_mucosa,half_FV_diet,dss_treated,rep4

description: Library name: 95122


title: wk3_KrasG12D_Saline_4913


title: proximal_colon_mucosa,control_diet,dss_treated,rep7

description: Library name: 95119


title: wk3_KrasG12D_Saline_4911


title: VT3, BQ-

description: Library name: 11700080A1

value: FFPE


title: NPC_105Q_ATF3_KO_8D

description: Library name: NPC_105Q_ATF3_KO_8D


title: proximal_colon_mucosa,half_FV_diet,dss_treated,rep3

description: Library name: 95118

value: proximal colon mucosa


title: NPC_105Q_ATF3_WT_8A

description: Library name: NPC_105Q_ATF3_WT_8A


title: NPC_105Q_(IB-)_8G

description: Library name: NPC_105Q_(IB-)_8G


title: VT2, BQ-

description: Library name: 11652922A3


title: VT1, BQ-

description: Library name: 11641859A2


title: wk3_KrasG12D_Caerulein_B0565

value: Caerulein


title: proximal_colon_mucosa,half_FV_diet,dss_treated,rep2

description: Library name: 95117


title: Kras G12V +doxy rep4 R2021-001135

city: Milwaukee

first: Michael

middle: T

last: Zimmermann

state: WI

address: 8701 Watertown Plank Road

department: Mellowes Center

institute: Medical College of Wisconsin

description: Kras G12V +doxy rep4

data_processing:
Reads were aligned to GRCh38.p13 and Gencode v32 (based on Ensembl v98) transcript reference using the STAR aligner and MAPR-Seq3 workflow.
Assembly: GRCh38.p13

source_name: human embryonic kidney cells

growth_protocol: HEK 293 KRAS mutant isogenic cell lines were created by co-transfecting KRAS mutant pcDNA5/FRT/TO plasmid containing KRAS variants with pOG44 plasmid into the human Flp-In™ T-REx™ 293 Cell Line (Invitrogen) and selecting for hygromycin-resistant clones.

extract_protocol:
RNA extraction was done following the miRNeasy Mini Kit protocol (Qiagen), with cells lysed and collected in 700µL QIAzol lysis reagent (Qiagen) per well.
RNA libraries were prepared with the Illumina TruSeq RNA v2 kit

treatment_protocol: Mutant cells were plated at 200,000 cells/well in 6-well plates and induced to express KRAS with 1µg/mL doxycycline the following morning. Twenty-four hours after adding doxycycline, the cells were harvested.

value: Flp-In T-REx HEK 293

tag: kras variant

value: add doxycycline for 24hr

tag: biological replicate


title: proximal_colon_mucosa,full_FV_diet,dss_treated,rep4

description: Library name: 95116


title: wk3_KrasG12D_Caerulein_B0559


title: NPC_105Q_ATF3_KO_8C

description: Library name: NPC_105Q_ATF3_KO_8C


title: Kras G12V -doxy rep4 R2021-001134

description: Kras G12V -doxy rep4

value: control no doxycycline


title: wk3_KrasG12D_Caerulein_B0403


title: proximal_colon_mucosa,control_diet,dss_treated,rep6

description: Library name: 95115

value: female

value: control


title: SCT1, BQ-negative tumor

description: Library name: Sample 1

data_processing:
Barcode processing and sequence alignment against the human hg19 genome were performed by using Cell Ranger Pipeline (10X Genomics) to generate matrices of gene counts by cell barcodes. Gene-cell matrices were analyzed with the Seurat R package.
Assembly: hg19
Supplementary files format and content: Tab-separated  values files and matrix files

extract_protocol:
Fresh primary tumors of buccal mucosa were minced, washed with serum-free DMEM (GIBCO), and dissociated using a Human Tumor Dissociation Kit (Miltenyi Biotec) according to manufacturer guidelines. Cell suspension was filtered using a 70 mm filter (ThermoFisher Scientific), and red blood cells were removed with 1× RBC Lysis Buffer (BD Biosciences).
Cell suspensions were loaded on a Chromium X Instrument (10X Genomics) to generate single-cell gel beads in emulsions (GEMs). scRNA-seq libraries were prepared using Chromium Single cell 3’ GEM, Library, & Gel beads kit (10X Genomics).

value: BQ-negative tumor

tag: cancer stage

value: multiple

tag: batch

value: A


title: Kras S17N +doxy rep3 R2021-001133

description: Kras S17N +doxy rep3


title: wk3_KrasG12D_Caerulein_B0109

tag: tissue

tag: genotype


title: Sample8_TCR

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

description:
Library name: Sample8_TCR
10X genomics

data_processing:
Sequenced data were processed into expression matrices with the Cell Ranger Single Cell Software (v 6.1.2) of 10X Genomics against the GRCh38 human reference genome with default parameters.
Assembly: GRCh38
Supplementary files format and content: 10X Cellranger format

source_name: human atria

extract_protocol:
Samples were washed, chopped into small pieces, and digested in an enzymatic digestion buffer containing 3 mg/ml collagenase type II (#LS004176, Worthington Biochemical Corp, NJ, USA), 0.15 mg/ml collagenase type XI (#H3506, Sigma Aldrich, MO, USA), 0.25 mg/ml soybean trypsin inhibitor (#LS003571, Worthington Biochemical Corp), 0.1875 mg/ml elastase lyophilized (#LS002292, Worthington Biochemical Corp), 0.24 mg/ml hyaluronidase type I (#H3506, Sigma Aldrich), and 2.38 mg/ml 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES, #H4034, Sigma Aldrich) in PBS with Ca2+ and Mg2+, at 37°C for 90 minutes with shaking. The digested samples were filtered through 40 μm cell strainers (#352340, BD Biosciences, NJ, USA), washed, and centrifuged at 3000 × g for 10 minutes.
ScRNA-seq (5’) libraries were prepared using the Single Cell 5’Reagent Kits v3 for scRNA-seq (10x Genomics, CA, USA). TCR Sequencing libraries were generated following the User Guide.

value: human atria

value: immune cells


title: wk3_KrasG12D_Caerulein_B0107

value: Adult Pancreas

tag: treatment

tag: time


title: Kras S17N -doxy rep3 R2021-001132

description: Kras S17N -doxy rep3

tag: cell type


title: SCT2, BQ-positive tumor

description: Library name: Sample 2

value: BQ-positive tumor


title: proximal_colon_mucosa,full_FV_diet,dss_treated,rep2

description: Library name: 95113

value: dss


title: Sample6_TCR

description:
Library name: Sample6_TCR
10X genomics


title: Sample3_TCR

description:
Library name: Sample3_TCR
10X genomics


title: lateProgenitor_PT39B

source_name: developing pancreas

value: developing pancreas

value: KrasWT


title: Kras S17N  -doxy rep2 R2021-001025

description: Kras S17N  -doxy rep2


title: Kras S17N  +doxy rep2 R2021-001023

description: Kras S17N  +doxy rep2


title: lateProgenitor_PT38B


title: proximal_colon_mucosa,full_FV_diet,dss_treated,rep3

description: Library name: 95114

value: proximal colon mucosa


title: proximal_colon_mucosa,control_diet,dss_treated,rep5

description: Library name: 95112


title: proximal_colon_mucosa,control_diet,dss_treated,rep4

description: Library name: 95111


title: Sample2_TCR

description:
Library name: Sample2_TCR
10X genomics


title: Kras Q61P  -doxy rep3 R2021-001021

description: Kras Q61P  -doxy rep3


title: lateProgenitor_PT37B


title: proximal_colon_mucosa,control_diet,dss_treated,rep3

description: Library name: 95110


title: Kras Q61P  +doxy rep3 R2021-001020

description: Kras Q61P  +doxy rep3


title: lateProgenitor_PT29B


title: BEAS-2B cells, αC, biol rep 2

city: Taichung city

first: Yu-Fan

last: Liu

address: No.110. Sec 1, Jianguo N. Rd.

department: Biomedical sciences

country: Taiwan

institute: Chung Shan Medical University

description: Library name: Sample 8

data_processing:
Raw sequencing reads were processed using Trimmomatic (v 0.39) to remove low-quality reads (Phred scores < 30).
High-quality reads were aligned to the human reference genome (GRCh38.p14) using HISAT2 (v 2.2.1).
The aligned reads were compressed and sorted using Samtools (v 1.9) to generate indexed BAM files.
featureCounts (v 1.6.2) was employed to quantify the number of reads mapped to annotated gene features within the reference genome.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes read counts for each sample

source_name: Lung; Bronchus

growth_protocol: Human bronchial epithelial cells (BEAS-2B) were cultured in LHC-9 serum-free medium under standard conditions of 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated from treated cells using the PureLink™ RNA Mini Kit (Thermo Fisher) following the manufacturer's instructions. A total of 2 µg of purified RNA was subsequently used for library preparation for RNA sequencing.
Following mRNA enrichment and fragmentation, first- and second-strand cDNA synthesis was performed using random primers, reverse transcriptase, and DNA polymerase I. Sequencing adaptors were then ligated to both ends of the cDNA fragments. The resulting libraries were PCR-amplified, purified, and quality-checked before sequencing.

treatment_protocol: BEAS-2B cells were treated with fibrinogen (4 ng/µl), Der m 1-derived FCPs (4 ng/µl), or fibrinogen αC-Domain (4 ng/µl) for 4 hours.

value: Lung; Bronchus

tag: cell line

value: Epithelial cell

value: WT

value: Fibrinogen αC domain


title: Kras G13S  -doxy rep2 R2021-001019

description: Kras G13S  -doxy rep2

value: Flp-In T-REx HEK 293

value: control no doxycycline


title: BEAS-2B cells, αC, biol rep 1

description: Library name: Sample 7


title: lateProgenitor_PT25B


title: Kras G13S  +doxy rep2 R2021-001017

description: Kras G13S  +doxy rep2

value: add doxycycline for 24hr


title: proximal_colon_mucosa,full_FV_diet,dss_treated,rep1

description: Library name: 95108

value: female


title: proximal_colon_mucosa,control_diet,dss_treated,rep2

description: Library name: 95109

value: control


title: earlyProgenitor_PT18A-2


title: BEAS-2B cells, FBG, biol rep 2

description: Library name: Sample 4

value: Fibrinogen


title: Kras G13S -doxy rep1 R2021-001018

description: Kras G13S -doxy rep1


title: Kras G13I -doxy rep 3 R2021-001015

description: Kras G13I -doxy rep 3


title: proximal_colon_mucosa,control_diet,dss_treated,rep1

description: Library name: 95106


title: proximal_colon_mucosa,half_FV_diet,dss_treated,rep1

description: Library name: 95107


title: earlyProgenitor_PT17A


title: Kras G13S +doxy rep1 R2021-001016

description: Kras G13S +doxy rep1


title: BEAS-2B cells, M1-FCP, biol rep 1

description: Library name: Sample 5

value: Der m 1-derived FCPs


title: BEAS-2B cells, FBG, biol rep 1

description: Library name: Sample 3


title: earlyProgenitor_PT18A-1


title: BEAS-2B cells, M1-FCP, biol rep 2

description: Library name: Sample 6


title: earlyProgenitor_PT13A


title: BEAS-2B cells, Mock, biol rep 1

description: Library name: Sample 1

value: PBS


title: scRNA seq of Anti-IFN-γ autoantibody-negative NTM infected patient

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

institute: Fudan University

description: Library name: S010_novelbio-A_A292-GEX_AHGCMWDSX3_S2_L002

data_processing:
The original sequencing data were analyzed by using FastQC software. 10X Chromium single cell transcriptome sequencing can be divided into three regions near the polyA and five regions near the transcriptional initiation site. Among them, 5-terminal transcript sequencing is usually performed together with T cell and B cell receptor gene TCR/BCR sequences for sequencing analysis. Different kits (including 3-terminal vs 5-terminal, and different versions) have slightly different library structures: For example, for a sample processed by a 10X single-cell 3-terminal V2 kit, Read 1 consists of a 16bp 10X Cell Barcode and a 10bp UMI sequence; The sample processed by the V3 kit, Read 1, consisted of 16 bp 10X Cell Barcode and 12 bp UMI sequence. In the analysis, 10X Cell Barcode in Read1 was used to separate individual cells, and UMI was used to remove PCR amplification bias and distinguish between transcripts. Read2 is a 151 bp cDNA sequence, and the first 91 bp is generally used for downstream analysis of Cell Ranger.
Assembly: GRCh38
Supplementary files format and content: Matrix table wuth raw gene counts for every gene and every cell

source_name: PBMC

extract_protocol:
For the inspection and counting of single-cell suspension, the survival rate of cells is generally required to be above 85%, and the qualified cells are prepared by washing and re-suspension into a suitable cell concentration of 700~1200 cells/µl
According to the expected number of target cells, Gel Bead in Emulsion was constructed for single cell separation. After the normal formation of GEMs, GEMs were collected for reverse transcription in PCR instrument to realize labeling. For GEMs oil breaking treatment, a strand of cDNA was purified and enriched with magnetic beads, then cDNA amplification and quality inspection were carried out. The qualified cDNA was constructed by the second generation sequencing library, and the quantitative quality of the library was finally tested through the experimental processes of fragmentation, connecting sequencing joints, and sample Index PCR.

value: PBMC


title: d2_KrasWT_Caerulein_B2259

extract_protocol:
tdTomato+ acinar cells were FACS sorted into 1.5 mL Eppendorf tubes containing Trizol. Total RNA was purified using a standard phenol-chloroform extraction method.
Sequencing libraries were constructed using Illumina TruSeq Library Prep Kit (Non-Stranded and Poly-A selection) and sequenced on either Illumina HiSeq 2500 or NovaSeq 6000 (2x50 cycles paired-end run)

value: Adult Pancreas

value: Tamoxifen

value: Caerulein


title: Kras G13C +doxy rep 3 R2021-001012

description: Kras G13C +doxy rep 3


title: d2_KrasG12Vgeo_Caerulein_B2167


title: d2_KrasWT_Caerulein_B2068

value: KrasWT


title: Kras G13I +doxy rep 3 R2021-001014

description: Kras G13I +doxy rep 3


title: U87_shYB-1

city: Shihezi

first: Xiaodong

last: Li

address: No. 31, Beisi East Road, Shihezi City, Xinjiang

institute: Shihezi University

description: Library name: Sample 4

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTiein a reference-based approach.
Assembly: hg38
Supplementary files format and content: The CSV files contain TPM (Transcripts Per Million) values for each sample

source_name: U87 cell line

extract_protocol:
The U87 and U373 glioblastoma cell lines were transduced with either a non-targeting short hairpin RNA (shRNA) (designated as NT) or a YB-1-targeting shRNA (denoted as shYB-1) lentivirus. Upon reaching approximately 90% confluency, the cells were harvested and lysed directly in 10 cm² culture dishes utilizing TRIzol reagent (Beyotime). The resulting cell lysates were promptly frozen at -80℃ and subsequently transported on dry ice to Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China). RNA purification, reverse transcription, library construction and sequencing were performed by Majorbio according to the manufacturer’s instructions (Illumina, San Diego, CA).
The  RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA.  Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150bp read length).

value: U87 cell line

value: Glioblastoma cells

value: YB-1 knockdown (shRNA)


title: Kras WT c1 + doxy rep2 R2021-000646

description: Kras WT c1 + doxy rep2

value: None (wildtype)


title: d2_KrasWT_Caerulein_B2261

data_processing:
The quality of the sequenced reads was assessed with FastQC v0.11.8 and QoRTs v1.3.6.
Sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR v2.7.9a.
. Gene expression estimates were obtained with featureCounts v2.0.1 using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M25).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts


title: Kras G13C -doxy rep 3 R2021-001013

description: Kras G13C -doxy rep 3

value: Flp-In T-REx HEK 293


title: scRNA seq of Anti-IFN-γ autoantibody-positive NTM infected patient

description: Library name: R22007481-A096-jiace-A096_combined


title: Kras WT c1 + doxy rep1 R2021-000645

description: Kras WT c1 + doxy rep1


title: U87_NT-shRNA

description: Library name: Sample 3

value: non-targeting shRNA (control)


title: BEAS-2B cells, Mock, biol rep 2

description: Library name: Sample 2

value: Lung; Bronchus

value: Epithelial cell

value: WT


title: Kras WT c1 -doxy rep2 R2021-000644

description: Kras WT c1 -doxy rep2

value: control no doxycycline


title: Lot_No_44

type: RNA

city: Kurume

first: Hiroki

last: Ohzono

state: Fukuoka

address: Asahimachi 67

department: Orthopedic surgery

institute: Kurume University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: synovium

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: synovium

tag: disease status

value: osteophyte group

tag: age

tag: gender

value: male


title: Mus musculus Telencephalon E12.5 Rep2

description:
Library name: AZI357A8
Biological replicate

extract_protocol:
Single cell suspensions from each mouse and human sample were loaded into one and two lanes, respectively, of a Chromium Chip G (10X Genomics, PN-1000120) of 10X Chromium Controller (PN-120270
Sequencing libraries were prepared using  Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (PN-1000121) according to manufacturer’s protocol.

value: Telencephalon

tag: development stage

tag: replicate


title: d2_KrasWT_Caerulein_B2058

value: Adult Pancreas

value: Tamoxifen


title: Lot_No_1

value: normal group


title: d2_KrasG12Vgeo_Caerulein_B2165

value: Caerulein


title: Lot_No_12


title: Lot_No_34


title: Lot_No_25


title: Lot_No_6


title: Mus musculus Telencephalon E12.5 Rep1

description:
Library name: AZI357A7
Biological replicate


title: U373_NT-shRNA

description: Library name: Sample 1

source_name: U373 cell line

value: U373 cell line

value: Glioblastoma cells


title: FCs+AF 0.5uM 4

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description:
Library name: A14 AU0.5_051917-2
auranofin effect on foam cells (FCs) formation

data_processing:
Reads were mapped using STAR v2.6.1d
Alignments mapping to genes were counted using FeatureCounts from the subread package v1.6.3
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include rawcounts for each Sample

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 250 ng of total RNA was used for the construction of sequencing libraries.
Automated stranded RNA-seq library poly-A preparation.

treatment_protocol: THP-1 cells were grown in RPMI-1640 medium containing 10% fetal bovine serum, 1x penicillin/streptomycin, washed and resuspended in warm media. THP-1-derived macrophage (MP) differentiation was induced with phorbol-12-myristate-13-acetate (50 ng/mL) for 72 hours at 37°C in 5% CO2. MPs were then pre-treated for 24 hours with the following: 1) Dimethyl sulfoxide as vehicle (DMSO,< 0.1% v/v); 2) Auranofin (AF) 0.5 µM. After 24 hours, Cholesteryl Esters-loaded foam cells (FCs) were generated by adding acetylated Low Densitiy Lipoprotein (AcLDL) for 48 hours and drug treatment was maintained until the end of the experiment.

value: FCs+AF 0.5uM


title: d2_KrasG12R_Caerulein_B2260


title: U373_shYB-1

description: Library name: Sample 2

value: YB-1 knockdown (shRNA)


title: Kras R135T c1 + doxy rep1 R2021-000641

description: Kras R135T c1 + doxy rep1

value: Flp-In T-REx HEK 293

value: add doxycycline for 24hr


title: d2_KrasG12Vgeo_Caerulein_B2057


title: Kras WT c1 -doxy rep1 R2021-000643

description: Kras WT c1 -doxy rep1

value: None (wildtype)


title: FCs+AF 0.5uM 3

description:
Library name: A14 AU0.5_051917-1
auranofin effect on foam cells (FCs) formation


title: d2_KrasG12Vgeo_Caerulein_B2059


title: Mus musculus Telencephalon E11.5 Rep2

description:
Library name: AZI357A6
Biological replicate

data_processing:
Short reads stored in FASTQ file formats were pre-processed and aligned to custom-built transcriptomes  using the CellRanger software (v3.0.2 or v3.1.0)
Assembly: GRCh38-3.0.0_GFP-tdT or mm10-3.0.0_GFP-tdT
Supplementary files format and content: The gene expression counts from predicted cells were stored in compressed H5 format (libname_filtered_feature_bc_matrix.h5).


title: Mus musculus Telencephalon E11.5 Rep1

description:
Library name: AZI357A5
Biological replicate


title: Mus musculus Telencephalon E9.5 Rep2

description:
Library name: AZI357A4
Biological replicate


title: Kras R135T c1 -doxy rep2 R2021-000640

description: Kras R135T c1 -doxy rep2


title: Kras R135T c1 + doxy rep2 R2021-000642

description: Kras R135T c1 + doxy rep2


title: Mus musculus Telencephalon E9.5 Rep1

description:
Library name: AZI357A3
Biological replicate


title: d2_KrasG12R_Caerulein_B2257


title: FCs+AF 0.5uM 2

description:
Library name: A13b AU0.5_051917-2
auranofin effect on foam cells (FCs) formation


title: Kras R135T c1 -doxy rep1 R2021-000639

description: Kras R135T c1 -doxy rep1


title: Kras Q61R c2 + doxy rep2 R2021-000638

description: Kras Q61R c2 + doxy rep2


title: d2_KrasG12R_Caerulein_B2066


title: Mus musculus Telencephalon E10.5 Rep2

description:
Library name: AZI357A2
Biological replicate


title: Kras Q61R c2 + doxy rep1 R2021-000637

description: Kras Q61R c2 + doxy rep1


title: FCs+AF 0.5uM 1

description:
Library name: A13 AU0.5_051917-1
auranofin effect on foam cells (FCs) formation


title: Mus musculus Telencephalon E10.5 Rep1

description:
Library name: AZI357A1
Biological replicate


title: d2_KrasG12D_Caerulein_B2243


title: Kras Q61R c2 - doxy rep2 R2021-000636

description: Kras Q61R c2 - doxy rep2


title: RNAseq_Vg6_skin_Saureus_rep3

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

description: Library name: RNAseq_Vg6_skin_Saureus_rep3

data_processing:
RNA-seq samples were mapped to the mm10 mouse genome with STAR. Gene expression was assessed using HOMER’s analyzeRepeats.pl with parameters rna, mm10, -count exons, -condenseGenes. Differential gene expression was calculated using DESeq2. Genes were considered differentially expressed with false discovery rate (FDR) < 0.05 and fold change (FC) > 2.
Assembly: mm10
Supplementary files format and content: tab delimited text

extract_protocol:
Vγ6+ γδ T cells were FACsorted from ear skin of control mice (associated with media TSB) and topical associated mice (topical association with S. aureus (42F02)) 14 days following the first association.
RNA from sorted Vγ6+ γδ T cells was extracted using the RNeasy Plus Micro Kit. mRNA libraries were constructed using SMARTer Ultra Low Input RNA kit with the Nextera XT DNA library prep kit.

value: skin

value: Vg6 gdT cells

value: WT

value: S. aureus association


title: FCs+DMSO 1

description:
Library name: A4 DMSOAcLDL_051917-1
auranofin effect on foam cells (FCs) formation

value: FCs+DMSO


title: d2_KrasG12R_Caerulein_B2067

last: Chandwani


title: FCs+DMSO 3

description:
Library name: A5 DMSOAcLDL_051917-2
auranofin effect on foam cells (FCs) formation


title: RNAseq_Vg6_skin_Saureus_rep4

description: Library name: RNAseq_Vg6_skin_Saureus_rep4


title: FCs+DMSO 4

description:
Library name: A5b DMSOAcLDL_051917-2
auranofin effect on foam cells (FCs) formation


title: FCs+DMSO 2

description:
Library name: A4b DMSOAcLDL_051917-1
auranofin effect on foam cells (FCs) formation


title: d2_KrasG12D_Caerulein_B2242


title: Kras Q61P c2 - doxy rep2 R2021-000634

description: Kras Q61P c2 - doxy rep2

value: control no doxycycline


title: MOLM13_8p_R3

city: Little Rock

first: Samrat

last: Roy Choudhury

state: AR

address: 13 Children's Way, Arkansas Children's Research Institute

institute: University of Arkansas for Medical Sciences

description: Library name: Sample_6

data_processing:
The bioinformatics analysis pipeline began with quality control, where raw fastq reads were processed using in-house Perl scripts to remove adapter-containing, poly-N, and low-quality reads, yielding high-quality clean data with Q20, Q30, and GC content calculated. Clean reads were then mapped to the reference genome using HISAT2 v2.0.5, leveraging splice junctions for improved alignment accuracy. Gene expression levels were quantified with featureCounts v1.5.0-p3, and FPKM was used for normalization. Differential expression analysis was performed using DESeq2 (v1.20.0) for biological replicates, applying a negative binomial model and Benjamini-Hochberg correction (adjusted P ≤ 0.05), while edgeR (v3.22.5) was used for conditions without replicates, normalizing read counts and identifying significant genes with a corrected P ≤ 0.05 and absolute fold change ≥ 2.
Assembly: hg38
Supplementary files format and content: tab limited raw counts of each samples
Supplementary files format and content: FPKM values of gene counts per sample

source_name: Cells

growth_protocol: MOLM-13 cells were grown in RPMI-1640, supplemented with 20% fetal bovine serum, 2mM glutamine, and 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA was extracted from the control and treated MOLM-13 cells using the AllPrep DNA/RNA Kits, Qiagen, following the manufacturer’s instructions. DNA purity and concentration were assessed using a Qubit fluorometer. The integrity of the extracted DNA was evaluated using a bioanalyzer.
mRNA library was prepared by (1) mRNA enrichment by poly (A) capture or rRNA removel, (2) RNA fragmentation, (3) cDNA reverse transcription, and (4) RNA library preparation.

treatment_protocol: MOLM-13 cells were treated with 8p at a concentration of 3.5 nM, which is half of the IC50 value of 7 nM. Both treated and control cells were incubated for 48 hours.

value: Cells

value: Acute Myeloid Leukemia Cells

value: 8p (RET/CDK8i)


title: d2_KrasG12D_Caerulein_B2106

first: Rohit

address: 413 East 69th St, BRB 1360G

institute: Weill Cornell Medicine

source_name: Adult Pancreas

value: Adult Pancreas

value: Tamoxifen

value: Caerulein


title: Kras Q61R c2 - doxy rep1 R2021-000635

description: Kras Q61R c2 - doxy rep1


title: Kras Q61P c2 + doxy rep2 R2021-000633

description: Kras Q61P c2 + doxy rep2


title: Kras Q61P c2 + doxy rep1 R2021-000632

description: Kras Q61P c2 + doxy rep1


title: MOLM13_8p_R2

description: Library name: Sample_5


title: Kras Q61P c2 - doxy rep1 R2021-000631

description: Kras Q61P c2 - doxy rep1


title: RNAseq_Vg6_skin_naive_rep2

description: Library name: RNAseq_Vg6_skin_naive_rep2

value: TSB association (control)


title: d2_KrasG12D_Caerulein_B2104


title: 10d_KrasWT_2499

value: KrasWT


title: RNAseq_Vg6_skin_Saureus_rep1

description: Library name: RNAseq_Vg6_skin_Saureus_rep1


title: 10d_KrasWT_2568


title: RNAseq_Vg6_skin_Saureus_rep2

description: Library name: RNAseq_Vg6_skin_Saureus_rep2


title: ductal4

data_processing:
Reads were processed with the ENCODE ATAC-seq pipeline v2.2.2 (https://github.com/ENCODE-DCC/atac-seq-pipeline/) and were aligned to the human genome build mm10
Briefly, adapters were trimmed with cutadapt v2.5 and aligned to Encode mm10 with Bowtie2 v2.3.4.3.
Duplicate reads and reads mapping to the mitochondrial chromosome were removed.
Signal files and peak calls were generated using MACS2 v2.2.4.
Peaks overlapping ENCODE blacklisted regions (ENCFF547MET.bed) were excluded.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
tdTomato+ acinar cells, tdTomato+ progenitor cells or CD133+ CD49f+ ductal cells were FACS sorted as applicable. Standard ATAC-seq protocol was followed (Buenrostro et al. 2013).
Illumina Nextera kit


title: MOLM13_8p_R1

description: Library name: Sample_4


title: Kras Q61L c1 + doxy rep1 R2021-000629

description: Kras Q61L c1 + doxy rep1

value: Flp-In T-REx HEK 293


title: 10d_KrasWT_2567


title: MOLM13_C_R2

description: Library name: Sample_2

value: Control


title: RNAseq_Vg6_skin_naive_rep3

description: Library name: RNAseq_Vg6_skin_naive_rep3


title: MOLM13_C_R3

description: Library name: Sample_3


title: RNAseq_Vg6_skin_naive_rep1

description: Library name: RNAseq_Vg6_skin_naive_rep1


title: 10d_KrasG12Vgeo_2559


title: Kras Q61L c1 + doxy rep2 R2021-000630

description: Kras Q61L c1 + doxy rep2

value: add doxycycline for 24hr


title: ductal3


title: 10d_KrasG12Vgeo_2562


title: Kras Q61L c1 - doxy rep2 R2021-000628

description: Kras Q61L c1 - doxy rep2


title: Kras Q61L c1 - doxy rep1 R2021-000627

description: Kras Q61L c1 - doxy rep1


title: 10d_KrasG12R_2503


title: MOLM13_C_R1

description: Library name: Sample_1


title: Kras Q61K c1 + doxy rep2 R2021-000626

description: Kras Q61K c1 + doxy rep2


title: Dep01pre

city: Chiba-shi

first: Makoto

last: Fujiya

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

institute: Chiba university

description: Library name: Dep01pre

data_processing:
Raw reads in FASTQ format were trimmed using cutadapt (v. 2.5) with parameters “-q 20 --max-n 3 --cores=0 --minimum-length 75 -a "A{75}" -a "G{75}" -a "C{75}" -a "T{75}" -a Ill_Univ_Adapt”. The trimmed reads were aligned to the human reference genome assembly GRCh38 (UCSC version hg38) using STAR (v. 2.7.3a). Reads aligned to each gene annotated in GENCODE (v45) were quantified using featureCounts (v. 1.6.3).
Assembly: hg38
Supplementary files format and content: The .gct file format (tab-delimited text) contains transcript abundance data in HCC tumor tissues from 9 patients.

source_name: Liver

extract_protocol:
Total RNA was isolated from frozen tissue samples using the AllPrep DNA/RNA Mini Kit (Qiagen)
RNA-seq libraries were prepared using the SMART-Seq Stranded Kit (Takara Bio Inc.).

value: Liver

tag: patient diagnosis

value: Hepatocellular carcinoma (HCC)

value: carbon-ion radiotherapy and durvalumab monotherapy


title: E13.5 ovary cells p27null rep4

city: Edinburgh

first: Güneş

last: Taylor

address: 4-5 Little France Drive

department: Centre of Reproductive Health

institute: University of Edinburgh

description: Sample 29 (FRO238A32)

data_processing:
Sequencing was performed on an machine. The "Trim Galore!" utility version 0.4.2 was used to remove sequencing adaptors and to quality trim individual reads with the q-parameter set to 20. Then sequencing reads were aligned to the mouse genome and transcriptome (Ensembl release-95) using RSEM version 1.3.0  in conjunction with the STAR aligner version 2.5.2. Sequencing quality of individual samples was assessed using FASTQC version 0.11.5
Assembly: Ensembl release-95
Supplementary files format and content: rll352.count.data.txt

source_name: Ovary

extract_protocol: RNA was extracted from the dissociated cells using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s protocol. RNA quality was assessed the TapeStation (Agilent) to confirm quantity and purity.

value: Ovary

tag: developmental stage

value: Cdkn1b -/-


title: 10d_KrasG12R_2502

city: New York


title: Dep08pre

description: Library name: Dep08pre

value: carbon-ion radiotherapy and durvalumab plus tremelimumab


title: E13.5 ovary cells p27null rep1

description: Sample 27 (FRO238A29)


title: 10d_KrasG12R_2500


title: Kras Q61K c1 + doxy rep1 R2021-000625

description: Kras Q61K c1 + doxy rep1

tag: kras variant


title: 10d_KrasG12D_2651


title: E13.5 ovary cells WT rep3

description: Sample 25 (FRO238A27)

value: Cdkn1b +/+


title: E13.5 ovary cells WT rep2

description: Sample 24 (FRO238A26)


title: Dep11pre

description: Library name: Dep11pre


title: Kras Q61H c2 + doxy rep2 R2021-000622

description: Kras Q61H c2 + doxy rep2

tag: biological replicate


title: 10d_KrasG12D_1890


title: E13.5 ovary cells p27null rep3

description: Sample 28 (FRO238A31)


title: 10d_KrasG12Vgeo_2120


title: Dep15pre

description: Library name: Dep15pre


title: E13.5 ovary cells WT rep4

description: Sample 26 (FRO238A28)


title: Dep10pre

description: Library name: Dep10pre


title: E13.5 ovary cells WT rep1

description: Sample 23 (FRO238A25)


title: Dep02post

description: Library name: Dep02post


title: Kras Q61K c1 - doxy rep1 R2021-000623

description: Kras Q61K c1 - doxy rep1

value: control no doxycycline


title: 10d_KrasG12D_1761


title: Kras Q61K c1 - doxy rep2 R2021-000624

description: Kras Q61K c1 - doxy rep2


title: Dep09post

description: Library name: Dep09post


title: E18.5 ovary cells p27null rep3

description: Sample 21 (FRO238A23)


title: Dep07pre

description: Library name: Dep07pre


title: E18.5 ovary cells p27null rep2

description: Sample 20 (FRO238A22)


title: retina with uveitis dataset sc-mRNA

city: SAN FRANCISCO

first: Mianmian

last: Yin

state: CA

address: 513 Parnassus Avenue

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

data_processing:
Fastq files from 10x gene expression library were processed with Cell Ranger, using default parameters.
Assembly: mouse mm10
Supplementary files format and content: For each sample, gene expression (mRNA) file contains a named filtered_feature_bc_matrix.tar file.

source_name: Retina

extract_protocol:
P2+ cells were sorted from lymph nodes and retina of AireGW/+ Lyn-/- and AireGW/+ Lyn-/-IRBP-/-mice, and then send to genomic core of UCSF to generate the library by using the kits.
libraries were prepared using the 10x Genomics Chromium Single Cell 5′ Reagent (GEX + VDJ) Kit version 1.1 according to manufacturer’s protocol
10x Genomics Chromium Single Cell 5′

value: Retina

value: CD4 single positive T cells

value: AireGW/+ Lyn-/-


title: Dep05pre

description: Library name: Dep05pre


title: Kras Q61H c2 - doxy rep2 R2021-000620

description: Kras Q61H c2 - doxy rep2


title: E18.5 ovary cells p27null rep4

description: Sample 22 (FRO238A24)


title: Dep10post

description: Library name: Dep10post


title: Kras Q61H c2 + doxy rep1 R2021-000621

description: Kras Q61H c2 + doxy rep1


title: E18.5 ovary cells p27null rep1

description: Sample 19 (FRO238A21)


title: uveitis dataset2 sc-mRNA

source_name: Lymph nodes

value: Lymph nodes


title: IRBP immunization dataset sc-mRNA

value: AireGW/+ Lyn-/-IRBP-/-


title: Kras Q61E c1 + doxy rep2 R2021-000618

description: Kras Q61E c1 + doxy rep2


title: Kras Q61E c1 + doxy rep1 R2021-000617

description: Kras Q61E c1 + doxy rep1


title: E18.5 ovary cells WT rep4

description: Sample 18 (FRO238A20)


title: uveitis dataset1 sc-mRNA


title: Dep02pre

description: Library name: Dep02pre


title: Dep09pre

description: Library name: Dep09pre


title: wild-type B6 cells from naive mice, mRNA-derived cDNA

city: Berkeley

first: Dmitri

middle: I

last: Kotov

address: 415 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: polyA RNA

data_processing:
Raw sequencing reads for the mRNA libraries were processed into raw count matrices with CellRanger version 6.0.0 (10X Genomics).
The raw counts for mRNA were analyzed using Seurat v4.3.0 using default settings for normalizing the data, finding variable features, and scaling the data. Data was filtered to only include single cells with between 200 and 2500 genes and less than 5% mitochondrial reads. The data was then scaled and analyzed by PCA with 30 principal components followed by UMAP analysis with 30 dimensions. Clustering was performed by using 30 dimensions with the FindNeighbors function and a resolution of 1.5 for the FindClusters function.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Lung

extract_protocol:
FACS isolated cells were loaded into 4 different lanes on a Chromium Next GEM Chip. Lane 1 was loaded with IL-1R KO cells from Mtb-infected lungs. Lane 2 was loaded with IL-1R KO cells from naive lungs. Lane 3 was loaded with wild-type B6 cells from Mtb-infected lungs. Lane 4 was loaded with wild-type B6 cells from naive lungs. All 4 lanes of the Chromium Next GEM Chip were loaded with 12500 cells with a target of 7000 single cells per lane.
The scRNA-sequencing libraries were generated using the v3.1 chemistry Chromium Single Cell 3’ Reagent Kit (10X Genomics) following this kits protocol. Following cDNA purification, samples were decontaminated by 2 rounds of centrifugation through 0.2 µM filter microcentrifuge tubes and then removed from the BSL3. Library preparations were completed outside of the BSL3 following the 10X Genomics protocol for the cDNA. Quality control of the libraries was performed with a Fragment Analyzer (Agilent). Libraries were sequenced on a NovaSeq 6000 (Illumina) using one lane of a S1 flow cell and the following cycles read 1 (28 cycles), i7 index (10 cycles), i5 index (10 cycles), read 2 (90 cycles).

value: Lung

value: stromal cells

value: naïve

tag: library type

value: mRNA


title: Kras Q61E c1 - doxy rep2 R2021-000616

description: Kras Q61E c1 - doxy rep2

data_processing:
Reads were aligned to GRCh38.p13 and Gencode v32 (based on Ensembl v98) transcript reference using the STAR aligner and MAPR-Seq3 workflow.
Assembly: GRCh38.p13

extract_protocol:
RNA extraction was done following the miRNeasy Mini Kit protocol (Qiagen), with cells lysed and collected in 700µL QIAzol lysis reagent (Qiagen) per well.
RNA libraries were prepared with the Illumina TruSeq RNA v2 kit

value: Flp-In T-REx HEK 293


title: E18.5 ovary cells WT rep3

description: Sample 17 (FRO238A19)


title: 194 ileum Cad.LPS 4H,rep3

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

description: Library name: 66-194_I_64H

data_processing:
FastQC (version 0.11.9) and MultiQC (version 1.12) were used for quality control of raw paired-end fastq files.
Illumina's adaptors as well as low quality reads were trimmed out using TrimGalore (version 0.6.7)
Transcript quantification was performed using Salmon (version 1.10.0) on trimmed fastqs against GENCODE V44 transcript reference database (assembly GRCh38)
Quantified transcripts were imported in R (version 4.3.9) using the package tximport (version 1.30.0)
Count data handling and differential analysis were performed using the package EBSeq (version 2.0.0)
Genes were pre-filtered out if they expressed (count > 0) in less than 60% of samples of 1 group.
Assembly: GENCODE 44/GRCh38
Supplementary files format and content: tab delimited transcript quantification (Salmon output)

source_name: ileum

extract_protocol:
RNA was extracted using Qiagen RNeasay kit following manufacturer instruction
mRNA library preparation were realized following manufacturer’s recommendations (Stranded Total RNA Prep Ligation with Ribo-Zero Plus from ILLUMINA). Final samples pooled library prep were sequenced on Novaseq 6000 ILLUMINA with S1-200 cycles cartridge (2x1600Millions of 100 bases reads) corresponding to 2x33Millions of reads per sample after demultiplexing.

treatment_protocol: F. prausnitzii EXL01 strain was grown at 37°C in a Exeliom Bisociences’ proprietary medium according to an in-house production process based on the know-how of Exeliom Biosciences. The test material was prepared to be ready-to-use in PBS/glycerol, characterized by enumerating the number of morphologically intact bacteria i.e. the Total Cell Count (TCC). Total CD14+ isolated cells (1. 105) were treated with control medium, LPS (100 ng/ml) or EXL01 strain at 2 doses (MOI 10 and 100) for 6 or 16 h

value: ileum

value: CD14+ monocytes


title: no uveitis dataset sc-mRNA


title: Kras Q61E c1 - doxy rep1 R2021-000615

description: Kras Q61E c1 - doxy rep1


title: Kras I36M c1 + doxy rep2 R2021-000614

description: Kras I36M c1 + doxy rep2

value: add doxycycline for 24hr


title: Kras I36M c1 + doxy rep1 R2021-000613

description: Kras I36M c1 + doxy rep1


title: Kras Q61H c2 - doxy rep1 R2021-000619

description: Kras Q61H c2 - doxy rep1


title: 182 ileum Cad.LPS 4H,rep2

description: Library name: 42-182_I_64H


title: E18.5 ovary cells WT rep2

description: Sample 16 (FRO238A18)

value: Ovary


title: 188 ileum Cad.LPS 4H,rep1

description: Library name: 12-188_I_64h


title: E18.5 ovary cells WT rep1

description: Sample 15 (FRO238A17)


title: wild-type B6 cells from Mtb-infected mice, mRNA-derived cDNA

description: polyA RNA

value: Mtb infected


title: IL-1R-deficient cells from Mtb-infected mice, mRNA-derived cDNA

description: polyA RNA

value: IL-1R KO


title: PND8 ovary cells p27null rep4

description: Sample 14 (FRO238A16)

value: Cdkn1b -/-


title: 188 ileum Cad.LPS 2H,rep3

description: Library name: 6-188_I_6


title: IL-1R-deficient cells from naive mice, mRNA-derived cDNA

description: polyA RNA


title: Kras I36M c1 -doxy rep2 R2021-000612

description: Kras I36M c1 -doxy rep2

value: control no doxycycline


title: PND8 ovary cells p27null rep3

description: Sample 13 (FRO238A15)


title: Innate lymphoid cells from Mtb-infected mixed bone marrow chimera mice, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Raw sequencing reads for the mRNA libraries were processed into raw count matrices with CellRanger version 6.0.0 (10X Genomics). The ADT and HTO libraries were processed into raw count matrices with CITE-Seq-Count version 1.4.3.
The raw counts for mRNA, ADT, and HTO were analyzed using Seurat v4.3.0 using default settings for normalizing the data, finding variable features, and scaling the data. The T cell dataset and innate lymphoid cell dataset were analyzed separately. HTO demultiplexing was performed with the HTODemux function. Data was filtered to only include single cells with between 200 and 2500 genes and less than 5% mitochondrial reads. The data was then scaled and analyzed by PCA with 30 principal components followed by UMAP analysis with 30 dimensions. Weighted nearest neighbor analysis was used to cluster cells based on protein and mRNA expression at a resolution of 1.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

extract_protocol:
FACS isolated cells were pooled and loaded into 2 different lanes on a Chromium Next GEM Chip. Lane 1 was loaded with T cells. Lane 2 was loaded with innate lymphoid cells. Both lanes of the Chromium Next GEM Chip were super-loaded with 25000 cells with a target of 13200 single cells per lane.
The scRNA-sequencing libraries were generated using the v3.1 chemistry Chromium Single Cell 3’ Reagent Kit (10X Genomics) largely following this kits protocol and the CITE-seq protocol. 0.5 U/µL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen) was added to single cell RT master mix during the loading step and 1 µL of ADT and HTO additive primers (0.2 µM stock) were added during the cDNA amplification. Following cDNA, ADT, and HTO purification, samples were decontaminated by 2 rounds of centrifugation through 0.2 µM filter microcentrifuge tubes and then removed from the BSL3. Library preparations were completed outside of the BSL3 following the 10X Genomics protocol for the cDNA and the CITE-seq and Cell Hashing Protocol for the ADT and HTO libraries. Quality control of the libraries was performed with a Fragment Analyzer (Agilent). The mRNA, ADT, and HTO libraries were pooled at the following proportions: 50% T cell mRNA, 33% ILC mRNA, 6% T cell ADT, 4% ILC ADT, 4% T cell HTO, and 3% ILC HTO. Libraries were sequenced on a NovaSeq 6000 (Illumina) using one lane of a S1 flow cell and the following cycles read 1 (28 cycles), i7 index (10 cycles), i5 index (10 cycles), read 2 (90 cycles).

value: lymphocytes

value: wild-type and IL-1R KO mixed bone marrow chimera

value: HTO

tag: antibodies

value: Anti CD45 + Anti MHC classI :Mouse 1--/TotalSeq-A0301 ;Mouse 2--/TotalSeq-A0302 ; Mouse 3--/TotalSeq-A0303


title: 194 ileum Cad.LPS 2H,rep2

description: Library name: 54-194_I_6

tag: tissue


title: 182 ileum Cad.LPS 2H,rep1

description: Library name: 30-182_I_6


title: Kras I142T c1 + doxy rep2 R2021-000610

description: Kras I142T c1 + doxy rep2


title: Kras I36M c1 -doxy rep1 R2021-000611

description: Kras I36M c1 -doxy rep1


title: PND8 ovary cells p27null rep1

description: Sample 12 (FRO238A13)

tag: genotype


title: 194 ileum Cad 4H,rep3

description: Library name: 65-194_I_54H

tag: treatment

value: Cad


title: PND8 ovary cells WT rep4

description: Sample 11 (FRO238A12)

value: Cdkn1b +/+


title: T cells from Mtb-infected mixed bone marrow chimera mice, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

value: Lung

value: Anti CD45 + Anti MHC classI :Mouse 1--/TotalSeq-A0304; Mouse 2--/TotalSeq-A0305; Mouse 3--/TotalSeq-A0306


title: Kras I142T c1 + doxy rep1 R2021-000609

description: Kras I142T c1 + doxy rep1

value: Flp-In T-REx HEK 293


title: Kras I142T c1 -doxy rep2 R2021-000608

description: Kras I142T c1 -doxy rep2


title: PND8 ovary cells WT rep3

description: Sample 10 (FRO238A11)


title: PND8 ovary cells WT rep2

description: Sample 9 (FRO238A10)


title: 182 ileum Cad 4H,rep2

description: Library name: 41-182_I_54H

value: ileum

tag: time


title: T cells from Mtb-infected mixed bone marrow chimera mice, mRNA-derived cDNA

description: polyA RNA

tag: cell type

value: mRNA


title: Kras I142T c1 -doxy rep1 R2021-000607

description: Kras I142T c1 -doxy rep1


title: Innate lymphoid cells from Mtb-infected mixed bone marrow chimera mice, ADT-derived cDNA

description: Antibody-derived oligonucleotide (ADT)

value: ADT

value: anti-Ly-6C (TotalSeq-A0013); CD44 (TotalSeq-A0073); PD-L1 (TotalSeq-A0190); CX3CR1 (TotalSeq-A0563); CD62L (TotalSeq-A0112); TCRb (TotalSeq-A0120); CD49a (TotalSeq-A0850); NKp46 (TotalSeq-A0184); CD4 (TotalSeq-A0001); ST2 (TotalSeq-A0837); CD25 (TotalSeq-A0097); CD45.1 (TotalSeq-A0178) ; CD45.2 (TotalSeq-A0157) ; CD8a (TotalSeq-A0002) ; CXCR5 (TotalSeq-A0846); CCR6 (TotalSeq-A0225)


title: T cells from Mtb-infected mixed bone marrow chimera mice, ADT-derived cDNA

description: Antibody-derived oligonucleotide (ADT)

value: Mtb infected


title: 188 ileum Cad 4H,rep1

description: Library name: 11-188_I_54h

value: CD14+ monocytes


title: Kras G13V c1 + doxy rep2 R2021-000606

description: Kras G13V c1 + doxy rep2

value: add doxycycline for 24hr


title: Innate lymphoid cells from Mtb-infected mixed bone marrow chimera mice, mRNA-derived cDNA

description: polyA RNA


title: 194 ileum Cad 2H,rep3

description: Library name: 53-194_I_5


title: PND8 ovary cells WT rep1

description: Sample 8 (FRO238A9)

value: Ovary


title: 188 ileum Cad 2H,rep2

description: Library name: 5-188_I_5


title: 12wk ovary cells p27null rep4

description: Sample 7 (FRO238A8)

value: Cdkn1b -/-


title: Kras G13V c1 + doxy rep1 R2021-000605

description: Kras G13V c1 + doxy rep1


title: Irg1- and iNOS-deficient bystander cells, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
RVDK005I

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
Raw sequencing reads for the mRNA libraries were processed into raw count matrices with CellRanger version 6.0.0 (10X Genomics). The ADT and HTO libraries were processed into raw count matrices with CITE-Seq-Count version 1.4.3.
The raw counts for mRNA, ADT, and HTO were analyzed using Seurat v4.3.0 using default settings for normalizing the data, finding variable features, and scaling the data. HTO demultiplexing was performed with the HTODemux function. Data was filtered to only include single cells with between 200 and 4500 genes and less than 5% mitochondrial reads. The resulting datasets were integrated together alongside our previously published datasets of myeloid cells in Mtb-infected B6 and Sp140-deficient mouse lungs using 30 dimensions for the FindIntegrationAnchors function and 30 dimensions for the IntegrateData function. The data was then scaled and analyzed by PCA with 30 principal components followed by UMAP analysis with 30 dimensions. Clustering was performed by using 30 dimensions with the FindNeighbors function and a resolution of 1.5 for the FindClusters function.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
FACS isolated cells were pooled and loaded into 3 different lanes on a Chromium Next GEM Chip. Lane 1 was loaded with naive cells from 3 Irg1- and 3 iNOS-deficient lungs. Lane 2 was loaded with Mtb-infected myeloid cells from  3 Irg1- and 3 iNOS-deficient lungs. Lane 3 was loaded with Mtb-infected cells  from 3 Irg1- and 3 iNOS-deficient lungs. All 3 lanes of the Chromium Next GEM Chip were super-loaded with 34243 cells with a target of 17000 single cells per lane.
The scRNA-sequencing libraries were generated using the v3.1 chemistry Chromium Single Cell 3’ Reagent Kit (10X Genomics) largely following this kits protocol and the CITE-seq protocol. 0.5 U/µL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen) was added to single cell RT master mix during the loading step and 1 µL of ADT and HTO additive primers (0.2 µM stock) were added during the cDNA amplification. Following cDNA, ADT, and HTO purification, samples were decontaminated by 2 rounds of centrifugation through 0.2 µM filter microcentrifuge tubes and then removed from the BSL3. Library preparations were completed outside of the BSL3 following the 10X Genomics protocol for the cDNA and the CITE-seq and Cell Hashing Protocol for the ADT and HTO libraries. Quality control of the libraries was performed with a Fragment Analyzer (Agilent). The mRNA, ADT, and HTO libraries were pooled at the following proportions: 85% mRNA, 9% ADT, and 6% HTO. Libraries were sequenced on a NovaSeq 6000 (Illumina) using two lanes of a S1 flow cell and the following cycles read 1 (28 cycles), i7 index (10 cycles), i5 index (10 cycles), read 2 (90 cycles).

value: myeloid cells

value: Irg1- and iNOS-deficient

value: Anti CD45 + Anti MHC classI :Irg1--/TotalSeq-A0301 ; Irg1--/TotalSeq-A0302 ; Irg1--/TotalSeq-A0303 ; iNOS--/TotalSeq-A0304; iNOS--/TotalSeq-A0305; iNOS--/TotalSeq-A0306


title: Irg1- and iNOS-deficient Mtb-infected cells, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
RVDK005H

value: HTO


title: 182 ileum Cad 2H,rep1

description: Library name: 29-182_I_5

value: Cad


title: Irg1- and iNOS-deficient Mtb-infected cells, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
RVDK005E

value: Lung

value: anti-Ly-6C (TotalSeq-A0013); CD44 (TotalSeq-A0073); Siglec F (TotalSeq-A0431); PD-L1 (TotalSeq-A0190); CSF-1R (TotalSeq-A0105); Ly-6G (TotalSeq-A0015); CD11b (TotalSeq-A0014); CD86 (TotalSeq-A0200); I-A/I-E (TotalSeq-A0117); CX3CR1 (TotalSeq-A0563); CD11c (TotalSeq-A0106); CCR2 (TotalSeq-A0426); CD62L (TotalSeq-A0112); CD45.2 (TotalSeq-A0157)


title: Kras G13V c1 -doxy rep1 R2021-000603

description: Kras G13V c1 -doxy rep1

value: Flp-In T-REx HEK 293

value: control no doxycycline


title: 182 ileum LPS 4H,rep1

description: Library name: 38-182_I_24H

value: ileum

value: LPS


title: 12wk ovary cells p27null rep1

description: Sample 5 (FRO238A5)


title: 12wk ovary cells p27null rep3

description: Sample 6 (FRO238A7)


title: 12wk ovary cells WT rep4

description: Sample 4 (FRO238A4)

value: Cdkn1b +/+


title: Irg1- and iNOS-deficient naive cells, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
RVDK005G

value: naïve


title: Irg1- and iNOS-deficient bystander cells, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
RVDK005F

value: Mtb infected

value: ADT


title: 12wk ovary cells WT rep3

description: Sample 3 (FRO238A3)

value: Ovary


title: Kras G13R c1 + doxy rep1 R2021-000601

description: Kras G13R c1 + doxy rep1

value: add doxycycline for 24hr


title: Irg1- and iNOS-deficient naive cells, ADT-derived cDNA

description:
Antibody-derived oligonucleotide (ADT)
RVDK005D

value: myeloid cells


title: 194 ileum LPS 4H,rep2

description: Library name: 62-194_I_24H

value: CD14+ monocytes


title: Kras G13R c1 + doxy rep2 R2021-000602

description: Kras G13R c1 + doxy rep2


title: Kras G13R c1 -doxy rep2 R2021-000600

description: Kras G13R c1 -doxy rep2


title: 12wk ovary cells WT rep1

description: Sample 1 (FRO238A1)


title: Irg1- and iNOS-deficient bystander cells, mRNA-derived cDNA

description:
polyA RNA
RVDK005C

value: Irg1- and iNOS-deficient

value: mRNA


title: 12wk ovary cells WT rep2

description: Sample 2 (FRO238A2)


title: 194 ileum LPS 2H,rep3

description: Library name: 50-194_I_2


title: 188 ileum LPS 4H,rep3

description: Library name: 8-188_I_24h


title: Kras G13R c1 -doxy rep1 R2021-000599

description: Kras G13R c1 -doxy rep1


title: 182 ileum LPS 2H,rep2

description: Library name: 26-182_I_2


title: Irg1- and iNOS-deficient Mtb-infected cells, mRNA-derived cDNA

description:
polyA RNA
RVDK005B


title: Tpa-3

city: Indianapolis

first: Reuben

last: Kapur

state: IN

address: 1044 W Walnut St

institute: Indiana University

data_processing:
Data is mapping to genome UCSC mm10 using STAR software
counts data are extract using featureCounts
Assembly: UCSC mm10
Supplementary files format and content: Gene counts in txt file

source_name: Sorted LSK cells

growth_protocol: Whole bonemarrow cells wildytype, p85a knockout, Tet2 knockout, Tet2'P85a double knockout mice were subjected to lineage depletiona and LSKs (Lineage-Sca1+Kit+) sorted.

extract_protocol:
Total RNA was extrated and purified with Quiagen Rneasy Plus Micro Kit Cat # 74034
Clontech SMART-Seqv4 Ultra Low Input RNA Kit (Cat#634889), 24rxns; Illumina Nextera XT DNA Lib Kit. Dual Index

treatment_protocol: Mice bearing wildytype, p85a knockout, Tet2 knockout, Tet2'P85a double knockout were aged 10 months and sorted LSK cells were used for experiment

tag: cell line

value: Sorted LSK cells

value: Tet2;P85alpa double knockout


title: 188 ileum LPS 2H,rep1

description: Library name: 2-188_I_2


title: 194 ileum FP100 4H,rep3

description: Library name: 64-194_I_44H


title: Tpa-2


title: Irg1- and iNOS-deficient naive cells, mRNA-derived cDNA

description:
polyA RNA
RVDK005A

value: Lung


title: Kras G13I c1 -doxy rep2 R2021-000596

description: Kras G13I c1 -doxy rep2

source_name: human embryonic kidney cells

value: Flp-In T-REx HEK 293


title: Kras G13I c1 + doxy rep2 R2021-000598

description: Kras G13I c1 + doxy rep2


title: 182 ileum FP100 4H,rep2

description: Library name: 40-182_I_44H


title: Tpa-1


title: Tet2-3

value: Tet2 knockout


title: Kras G13D c1 + doxy rep2 R2021-000594

description: Kras G13D c1 + doxy rep2


title: Kras G13D c1 + doxy rep1 R2021-000593

description: Kras G13D c1 + doxy rep1


title: 188 ileum FP100 4H,rep1

description: Library name: 10-188_I_44h

value: ileum


title: S-2MeGlu_rep3

city: Stanford

first: Eloise

last: Berson

address: 291 Campus Drive

institute: Stanford University

description: 10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation was performed using Cell Ranger (7.0.1)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cerebral cortex

extract_protocol:
Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396
Libray was constructed by Stanford Functional Genomics Facility (SFGF), according to 10X Genomics instructions ( Single Cell 3' v3)

treatment_protocol: intraperitoneal injection (i.p.)

value: cerebral cortex

tag: strain


title: R-4APA_rep2

description: 10X Genomics


title: Kras G13D c1 -doxy rep2 R2021-000592

last: Zimmermann

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: Kras G13D c1 -doxy rep2

value: control no doxycycline


title: R-4APA_rep3

description: 10X Genomics


title: Tet2-2


title: S-2MeGlu_rep2

description: 10X Genomics


title: Tet2-1


title: 182 ileum FP100 2H,rep1

description: Library name: 28-182_I_4


title: 194 ileum FP100 2H,rep2

description: Library name: 52-194_I_4


title: P85a-3

value: P85alpha knockout


title: mTSC_siMETTL3 MeRIP-seq rep 3

first: Junpeng

last: Dong

address: 145 Guangyuan Rd, Xuhui District

department: School of Medicine, Shanghai Jiao Tong University

institute: The International Peace Maternity and Child Health Hospital

data_processing:
Raw reads obtained from RNA sequences were subjected to statistical analysis and quality control. Adaptor or low-quality bases as well as poly-N sequences were trimmed using fastp to obtain clean data.
SortMeRNA software was used for removing rRNA reads. The remaining clean reads were mapped to the mm10  by using Hisat2with default parameters, and unique reads with high mapping quality were retained.
The Guitar R package and deepTools software were used for evaluating the quality of the MeRIP-Seq data.
m6A-enriched peaks in each m6A IP sample were identified using MeTDiff peak calling software where the corresponding siNC sample served as a control.
Sequence motifs were identified using MEME and DREME and annotated using Tomtom software.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: mTSC

growth_protocol: Mouse trophoblast stem cells (mTSCs)  were cultured in stem cell medium (SCM): 30% standard medium (Roswell Park Memorial Institute (RPMI) 1640 supplemented with 20% fetal bovine serum, 100 mM 2-mercaptoethanol, 2 mM L-glutamine, 2 mM sodium pyruvate), 25 ng/ml FGF4, 1 mg/ml heparin, and 70% mouse embryonic fibroblast‑feeder condition medium (FCM). Differentiation medium (DM) consisted of unconditioned SCM without FGF4 and heparin.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen)  following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit. RNA libraries were prepared for sequencing using standard Illumina protocols. RNA fragmentation Reagents (Ambion) was used to randomly fragment RNA. m6A-specific antibody (Synaptic Systems) was applied for m6A pull down. Then, final library preparation was constructed.Finally, we performed the paired-end  sequencing on an Illumina NovaSeq 6000 platform following the vendor's recommended protocol.
MeRIP-seq

treatment_protocol: mTSCs transfected with control (i.e., siNC) or Mettl3 siRNA (i.e., siMETTL3) under stem conditions were harvested at 48 h post transfection. The transfection reagent was combined with OptiMEM media. Transfection was performed using Lipofectamine RNAiMAX Transfection Reagent for siRNAs in  stem cell medium. The knockdown efficiency was confirmed by qRT-PCR and western blot. mTSCs transfected with control (i.e., siNC) or Mettl3 siRNA (i.e., siMETTL3) were selected for genome-genome-wide m6A-sequencing (m6A-Seq) assays, in triplicate.

value: mTSC

value: trophoblast stem cells

value: METTL3 knockdown


title: S-2MeGlu_rep1

description: 10X Genomics


title: 188 ileum FP10 4H,rep3

description: Library name: 9-188_I_34h


title: Kras G13A c2 + doxy rep2 R2021-000586

first: Michael

description: Kras G13A c2 + doxy rep2

value: add doxycycline for 24hr


title: Kras G13C c1 + doxy rep2 R2021-000590

description: Kras G13C c1 + doxy rep2


title: Kras G13C c1 -doxy rep2 R2021-000588

description: Kras G13C c1 -doxy rep2


title: 194 ileum FP10 4H,rep2

description: Library name: 63-194_I_34H


title: P85a-2


title: Kras G13D c1 -doxy rep1 R2021-000591

description: Kras G13D c1 -doxy rep1


title: P85a-1


title: WT-3

value: WT-group

value: widltype


title: Veh_rep1

description: 10X Genomics

value: Vehicle


title: WT-2


title: R-4APA_rep1

description: 10X Genomics


title: Kras G13A c2 -doxy rep2 R2021-000584

description: Kras G13A c2 -doxy rep2


title: Veh_rep2

description: 10X Genomics


title: Kras G13A c2 + doxy rep1 R2021-000585

description: Kras G13A c2 + doxy rep1


title: 182 ileum FP10 4H,rep1

description: Library name: 39-182_I_34H

value: CD14+ monocytes


title: 194 ileum FP10 2H,rep3

description: Library name: 51-194_I_3


title: mTSC_siMETTL3 MeRIP-seq rep 2


title: WT-1

value: Sorted LSK cells


title: 182 ileum FP10 2H,rep2

description: Library name: 3-188_I_3


title: Kras G13V c1 -doxy rep2 R2021-000604

description: Kras G13V c1 -doxy rep2


title: 182 ileum FP10 2H,rep1

description: Library name: 27-182_I_3


title: Kras G13A c2 -doxy rep1 R2021-000583

description: Kras G13A c2 -doxy rep1


title: mTSC_siMETTL3 MeRIP-seq rep 1


title: scRNAseq Control

city: Rochester

first: Vijay

middle: H

last: Shah

state: MN

address: 200 First Street SW, Guggenheim Building 10th Floor

institute: Mayo Clinic

data_processing:
scRNAseq fastq files were processed via CellRanger 3.0.2 and mapped to mm10 genome. scRNA data processed using Seurat versions 3_ and R version 4.0.3
Assembly: mm10
Supplementary files format and content: .h5 filtered feature matrix
Supplementary files format and content: .h5 filtered peak matrix

source_name: Mixed liver single cell suspension

growth_protocol: Starting at 8 weeks of age, C57B6 mice were acclimated to liquid Leiber-DeCarli diet over 2 weeks with an increasing ethanol dose from 1-5%. Mice received 5% ethanol for the next 6 weeks. Controls were pair-fed. Mice were harvested at 16 weeks of age.

extract_protocol:
Mice non-parenchymal cells were isolated using previously published protocols. Primary mice hepatocytes were isolated using a modification of the two-step collagenase perfusion method. Cell viability was >95% as measured by Trypan Blue staining.
For scRNAseq:Samples were then prepared as outlined by the 10x Genomics Single Cell 3v2 Reagent Kit user guide. Briefly, the samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. Following counting, the appropriate volume for each sample was calculated for a target capture of 12000 cells. Samples were loaded onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen): cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).
The molarity of each library was calculated based on library size as measured using a bioanalyzer (Agilent Technologies) and qPCR amplification data (Kappa/Roche). Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.1 N NaOH at equal volumes for 5 min at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 14 pM. 150 μl from the 14 pM pool was loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles.

value: Liver

value: Control


title: mTSC_siNC MeRIP-seq rep 3

value: WT


title: scRNAseq Alcohol

value: Alcohol


title: 182 ileum CTR 4H,rep1

description: Library name: 37-182_I_14H

value: ileum

value: CTR


title: 194 ileum CTR 2H,rep3

description: Library name: 49-194_I_1


title: 194 ileum CTR 4H,rep2

description: Library name: 61-194_I_14H


title: mTSC_siNC MeRIP-seq rep 1


title: 182 ileum CTR 2H,rep2

description: Library name: 25-182_I_1


title: Kras G12V c1 + doxy rep2 R2021-000582

city: Milwaukee

description: Kras G12V c1 + doxy rep2

value: Flp-In T-REx HEK 293


title: hiPSC-CMs, OGPs, hypoxia, biological replicate3

city: Cincinnati

first: JIALIANG

last: LIANG

address: 231 Albert Sabin Way

department: Department of Pathology and Laboratory Medicine

institute: University of Cincinnati

description: Library name: C3

data_processing:
Raw reads were quality-filtered and aligned to the human reference genome using Salmon. Differential gene expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: .tsv format files (DESeq2 normalized counts)

source_name: ipsc

growth_protocol: Human induced pluripotent stem cell (hiPSC) lines (ATCC#CYS0105) were maintained under standard pluripotent culture conditions in mTeSR Plus basal medium (Stemcell Technologies) and passaged at ~70% confluency. Six-well plates were coated with extracellular matrix by diluting 50 µL of ATCC basement membrane gel (ACS-3035) in 5 mL cold serum-free DMEM/F-12 and incubating at 37°C for 1 h. For CM differentiation, hiPSCs were dissociated into a single-cell suspension using 0.5 mM EDTA and replated onto matrix-coated plates (either Matrigel or ATCC basement membrane gel) at ~70% confluency. Mesoderm induction was initiated by treating cells with 10 µM CHIR99021 in RPMI 1640 supplemented with B-27 minus insulin for 24 h, followed by 2 µM CHIR99021 for an additional 24 h. At ~48 h, due to observed cell loss, Wnt inhibition was performed using 4 µM ZAV939 in RPMI/B-27 minus insulin for 24-48 h. Subsequently, cultures were maintained in RPMI 1640 supplemented with B-27 with insulin, with medium changes every 24-48 h. Spontaneous beating was observed between days 7--10, consistent with cardiomyocyte differentiation. Thereafter, cells were maintained with medium changes every 1-2 days. Metabolic selection of hiPSC-CMs was performed using RPMI 1640 without glucose, supplemented with B-27 with insulin and 4 µM L-lactate. Cells were used for experiments once stable contractility and CM-like morphology were established.

extract_protocol:
PureLink RNA Mini Kit, according to
Approximately 200ng of total RNA for each sample was prepared for conventional sequencing libraries using the TruSeq RNA Library Prep Kit (Illumina) as per the manufacturer’s instructions, with mRNA enriched via poly-A-selection using oligoDT beads. RNA was then thermally fragmented with random priming, converted to cDNA, and PCR amplified.

treatment_protocol: Oxygen-generating PLGA microparticles were fabricated using a modified oil-in-water (O/W) emulsion-solvent evaporation method. PLGA was dissolved in dichloromethane (DCM) at a concentration of 100mg/mL, after which sodium percarbonate (20% w/w relative to PLGA) and β-carotene (1-2% w/w relative to PLGA) were added and dispersed using probe sonication (30-second pulse in an ice bath) to ensure homogeneous suspension of oxygen-generating components. The organic phase was then emulsified into a 1% (w/v) polyvinyl alcohol (PVA) aqueous solution using high-speed homogenization at 12,000 rpm for 2 minutes to produce an O/W emulsion targeting a final microparticle size of 5-20µm. After emulsification, the mixture was stirred magnetically at room temperature for 4 hours to allow solvent diffusion and evaporation, leading to particle solidification. Microparticles were collected by centrifugation at 5,000 × g for 5 minutes, washed 3 times with sterile deionized water to remove residual PVA, and frozen at -80°C overnight, then lyophilized for 48 hours. The dry OGPs were stored at -80°C until use. Hypoxic chamber (INVIVO2-500) condition: 1% O2, 5% CO2, 94% N2.

value: ipsc

value: CMs

value: differentiatiated, hypoxia, OGP


title: Kras G12R c2 -doxy rep2 R2021-000576

description: Kras G12R c2 -doxy rep2

value: control no doxycycline


title: Kras G12V c1 -doxy rep2 R2021-000580

description: Kras G12V c1 -doxy rep2


title: scATAC Control hepatocytes

data_processing:
Single cell Assay for Transposase Accessible Chromatin (scATAC-seq) peak matrices, metadata, and fragment files were generated via CellRanger-atac v1.2.0. Fragments were aligned to the mm10 genome and genes annotated via EnsDb.Mmusculus.v79.  Subsequent analyses were performed - via Signac version 1.2.0 and Seurat version 4.0  in R version 4.0.3.
Assembly: mm10
Supplementary files format and content: .h5 filtered feature matrix
Supplementary files format and content: .h5 filtered peak matrix

source_name: Hepatocyte

extract_protocol:
For snATACseq: Hepatocytes were isolated by 2-step collagenase perfusion method from pair-fed and alcohol-fed mice and counted after trypan blue staining. About 200 - 250K hepatocytes were washed with 1 ml PBS (0.04% BSA) and were lysed for 15 min on ice using 1X lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween 20, 0.1% NP40, 0.01% Digitonin). Nuclei were washed with 1 ml of wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween 20) and resuspended in 10 - 30 ml of wash buffer. A fraction of nuclei was stained with DAPI and the number of nuclei was counted from the merged images of bright field and DAPI-positive.
. Transposition reaction targeting approximately 3,000 - 8,000 nuclei per sample was performed by mixing 10 μL of 1X Tn5 Transposition enzyme (10X Genomics) with 5uL of the diluted nuclei suspension and incubating the reaction at 50°C for 1h. The tagmented nuclei were partitioned into Gel Bead-In Emulsions (GEMs) and barcoded by unique molecular identifiers (UMIs) using the Chromium Next GEM Single Cell ATAC library & Gel Bead kit and the C1 Chromium Instrument following the manufacturer’s instructions (10X Genomics).  scATAC-seq libraries were amplified by PCR and indexed using the Chromium i7 Sample Index kit (10X Genomics). The size of purified library DNA was determined by Fragment Analyzer (Advanced Analytical Technologies) and the enrichment of accessible region was determined by the fold difference between positive and negative genomic loci using real-time PCR. The following primers were used: AT-MDusp6, forward: GGCTTATCCGGAGCGGAAAT; AT-MDusp6, reverse: GGCTGGAACAGGTTGTGTTG; AT-MVmn2r17, forward: TCCCCTTTACTGTTTTCCTCTAC; AT-MVmn2r17, reverse: GGATTGATGAGGAAACAGCCTC. Two libraries per lane on an Illumina Hiseq4000 instrument were sequenced to 51 base pairs from both ends in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.


title: mTSC_siNC MeRIP-seq rep 2

value: mTSC

value: trophoblast stem cells


title: scATAC Alcohol hepatocytes


title: Kras G12R c2 + doxy rep1 R2021-000577

description: Kras G12R c2 + doxy rep1

value: add doxycycline for 24hr


title: 188 ileum CTR 4H,rep3

description: Library name: 7-188_I_14h


title: S8_3

city: Yangzhou

first: Guoqing

last: Wang

state: Jiangsu province

address: 48 East Wenhui Road

institute: yangzhou university

description: Library name: Exprimental group 6

data_processing:
After sequencing, the raw reads that were generated by sequencers were saved in the fastq format. Then, clean reads were obtained by removing reads containing rRNA sequences, poly-N, adapter sequences, and low-quality reads from the dirty raw reads. All high-quality clean reads were used for downstream analyses.
Clean reads were aligned to the mouse mm10 reference genome using HISAT2 v2.2.0.
Aligned clean reads were assembled into transcripts using StringTie v2.1.5.
Gene expression levels were quantified using FPKM values, which were calculated through StringTie v2.1.5 to normalize transcriptional abundance. Differential expression analysis for lncRNAs and mRNAs between the infected and the mock groups was performed using the edgeR package. The p value and false discovery rate (FDR) for each gene were determined based on the negative binomial distribution model.
Assembly: mouse mm10 reference genome
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: lung

growth_protocol: Mice were housed in negative-pressure isolators with HEPA filters in bio-safety level 3 (BSL3) animal facilities

extract_protocol:
Total RNAs from mouse lung samples were extracted using TRIzolTM reagent (Invitrogen, USA) according to the manufacturer’s instructions. The concentration and RNA integrity number (RIN) of the purified RNAs were assessed using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit), and the purity of total RNAs was detected by NanoDropTM.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six-week-old female BALB/c mice (n = 3 per group) were intranasally inoculated with S8 or SDL124 virus, respectively. Mice inoculated with PBS were served as the mock group.Mice lung samples were collected at 2 days post infection (dpi) and frozen immediately in liquid nitrogen.

value: lung