title: scRNA-seq, AT2 cells,  IP-/-(IPKO)  mice

description:
Library name: sample2
10x Genomics

data_processing:
Sequencing data for each sample were aligned to the mouse reference genome GRCm38 (mm10) using CellRanger v4.0.0 (https://www.10xgenomics.com/support/software/cell-ranger) to facilitate cell identifi-cation and expression matrix construction.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
EpCAM+CD31-CD34-CD45-CD24-Sca-1- cells were  sorted by flow cytometry from WT or IP-/-(IPKO) mice. Single-cell suspensions were prepared according to the protocol of Chromium Single Cell 3’Solution (V3 chemistry). All specimens were washed two times with cold 1x phosphate-buffered saline (PBS) .Haemocytometer (Thermo Fisher Scientific) was used to evaluate cell viability rates.Then, we used Countstar to count the concentration of sinale-cell suspension and adiust the concentration to1000 cells/ul. Samples that were lower than the required cell concentration defined in the user guide (i.e., <400 cells/ul) were pelleted and re-suspended in a reduced volume, and then the concentration of the new solution was counted again.
Single-cell RNA sequencing (scRNA-seq) libraries were constructed using the 10x Chromium Single Cell 3’ platform (10X Genomics, Pleasanton, CA, USA) according to the manufacturer’s protocol. Briefly, single-cell suspensions were loaded onto a Chro-mium microfluidic chip to generate single-cell Gel Beads in Emulsion (GEMs). The scRNA-seq libraries were then prepared using the Chromium Single Cell 3’ Reagent Kit v3.1 (10X Genomics, Pleasanton, CA, USA). Library quality was assessed using the Ag-ilent 2100 Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA), and se-quencing was performed on the Illumina NovaSeq 6000 platform (Illumina, San Di-ego, CA, USA) with a sequencing depth of at least 50,000 reads per cell.

value: Lung

value: Alveolar type 2 (AT2) epithelial cells

value: IP-/-(IPKO)  mice


title: mESC_m6A_rep2

status: Public on Jan 14 2026

type: SRA

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St., GCIS E319

country: USA

institute: The University of Chicago

description: Library name: mESC_m6A_rep2

library_source: transcriptomic

data_processing:
The FASTQ file was trimmed using Cutadapt (v4.6) and aligned to ribosomal RNA (rRNA) sequences with Bowtie2 (v2.4.2) to filter out rRNA reads. The remaining non-rRNA reads were aligned to the reference genome using STAR (v2.7.3a), and PCR duplicates were removed with UMI-tools (v1.1.1).
Assembly: GRCh38.p13, GENCODE Release 39; GRCm38.p6, GENCODE Release M25
Supplementary files format and content: bigWig files

molecule: total RNA

organism: Mus musculus

source_name: embryonic stem cell

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and  100 U/mL penicillin-streptomycin (Gibco). Mouse embryonic stem cells were cultured in DMEM (Invitrogen) supplemented with 20% FBS (GeminiBio), 1 mmol/L L-glutamine (Gibco), 1% nonessential amino acid (Gibco), 100 U/mL penicillin-streptomycin (Gibco), 1,000 U/mL leukemia inhibitory factor (LIF, Millipore), 0.1 mmol/L 2-mercaptoethanol (Sigma), 3 μmol/L CHIR99021 (Stemcell), 1 μmol/L PD0325901 (Stemcell), and 1% EmbryoMax nucleosides (100×, Millipore). All cell lines were cultured in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 1.5% paraformaldehyde for 10 minutes, quenched with 125 mM glycine at room temperature for 5 minutes, and permeabilized with 0.5% Triton X-100 on ice for 10 minutes. Samples were then blocked with 1 mg/ml BSA, followed by sequential staining with a primary antibody, a secondary antibody, and protein A/G-reverse transcriptase. In situ reverse transcription was performed at 37°C for 1 h. Subsequently, cells were digested with proteinase K at 37°C for 2 h. Total nucleic acids were extracted using phenol-chloroform and concentrated by ethanol precipitation.
Biotinylated cDNA was enriched using streptavidin beads. A 3' cDNA adapter (5′Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGT-3′SpC3) was ligated using T4 RNA ligase 1 by incubating at 25°C for 16 h. The cDNA was then recovered from the beads. The library was prepared through PCR amplification using NGS sequencing primers, followed by gel purification to isolate fragments between 180 bp and 400 bp.

tag: tissue

value: embryonic stem cell

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment

tag: antibody

value: m6A antibody (CST,Cat #56593)


title: PDAC099

city: Houston

first: Warapen

last: Treekitkarnmongkol

state: TX

address: 2130 W. Holcombe Blvd.,  Unit 2951

department: Translational Molecular Pathology

institute: UT MD Anderson Cancer Center

description: PDAC

library_source: other

data_processing:
Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.
Assembly: The miRNA probe list is based on miRBase version 20.
Supplementary files format and content: Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.

molecule: other

organism: Homo sapiens

source_name: Plasma

extract_protocol:
15 uL of plasma was profiled for miRNAs by the extraction-free method using the HTG edge miRNA whole transcriptome assay kit (HTG Molecular, Tuscon, AZ, Cat# 916-001-024) according to the recommended vendor’s protocol.
Probes hybrized to target miRNAs were retrieved and added sequencing adapters as well as sample barcodes via PCR for preparing library. The libraries were quantified by quantitative PCR (qPCR) using KAPA Library Quantification kit (Roche, Cat# KK4824) and loaded onto the MiSeq (Illumina) together with the MiSeq Reagent Kit v3 (150 cycles) (Illumina, Cat# MS-102-3001).

value: Plasma

tag: cohort

value: Diagnostic cohort

tag: disease

value: PDAC


title: scRNA-seq, AT2 cells, WT  mice

city: Tianjin

first: yujun

last: shen

address: 22 Qixiangtai Road, Heping District

country: China

institute: Tianjin Medical University

description:
Library name: sample1
10x Genomics

library_source: transcriptomic single cell

source_name: Lung

value: WT mice

tag: Sex

value: male


title: PDAC098

description: PDAC


title: MouseEmbryo_E11_50um_pixel_rep1

description: Library name: MouseEmbryo_E11_50um_pixel_rep1

data_processing:
The FASTQ file was initially filtered to remove reads lacking proper adapter ligation, followed by the extraction of unique molecular identifiers (UMIs) and spatial barcodes. Read 1, containing cDNA sequences, was trimmed using Cutadapt (v4.6) and aligned to the ribosome RNA (rRNA) with Bowtie2 (v2.4.2) to isolate non-rRNA reads. These non-rRNA reads were then aligned to the reference genome using STAR (v2.7.3a). PCR duplicates were removed using UMI-tools (v1.1.1), and the data was demultiplexed based on spatial barcodes to generate the gene-by-pixel expression matrix for downstream analysis. Pixel positions lacking tissue coverage were excluded.
Assembly: GRCm38.p6, GENCODE Release M25
Supplementary files format and content: Seurat RDS object
Supplementary files format and content: bigWig files
Library strategy: Spatial Transcriptomics

source_name: Embryo E11

extract_protocol:
The barcoded tissue ROI was enclosed with a clean PDMS reservoir and clamped using acrylic chips. A 2X lysis buffer (20 mM Tris-HCl pH 8.0, 400 mM NaCl, 100 mM EDTA, 4.4% SDS) was prepared. For tissue digestion, 70 μL of lysis mix (30 μL 1X DPBS, 30 μL 2X lysis buffer, 10 μL Proteinase K at 20 μg/μL) was added to the PDMS reservoir, sealed with parafilm, and incubated at 55°C for 2 h. After incubation, the liquid containing cDNA was collected, and 40 μL of fresh lysis mix was added to recover any remaining cDNA. The tissue lysate was incubated overnight at 55°C to reverse crosslinks. Nucleic acids were then extracted by phenol-chloroform (pH 8.0), ethanol-precipitated, and dissolved in 20 μL of water.
Biotinylated cDNA was enriched with streptavidin beads. A 3' cDNA adapter was ligated using T4 RNA ligase 1, with incubation at 25°C for 16 h. The cDNA was subsequently recovered from the beads. Libraries were prepared via PCR amplification using NGS sequencing primers. The amplified libraries were size-selected to a range of 280–500 bp using a 6% Novex TBE gel.

value: Embryo E11

tag: strain

value: C57BL/6 mice

value: m6A-ARTR-DBiT protocol


title: XA0050942-842-1307_TAACGTCG-TCAGCCTT_S72,  ED

city: Chapel Hill

first: Sarah

last: Linnstaedt

state: NC

address: 109 Mason Farm Road

description: Library name: XA0050942-842-1307_TAACGTCG-TCAGCCTT_S72

data_processing:
Sequencing reads aligned using the STAR(v2.7.6a) against the hg38 reference genome, with GENCODEV47 annotation file. Salmon (v1.4.0) was used to quantify aligned transcript-level expression from the aligned reads.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Whole Blood

extract_protocol:
Blood samples were collected at the time of enrollment using PAXgene RNA tubes. Total RNA was isolated using the PAXgene blood miRNA kit (QIAGEN) and RNA was stored at −80˚C until use. RNA concentration and purity were measured using a NanoDrop One (Nanodrop Technologies, Wilmington, DE), and RNA integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Template libraries for total RNA sequencing were produced from 600 ng total RNA using Ovation Human Blood RNA-Seq Library Systems kit (NuGen, San Carlos, CA) according to manufacturer's specifications. Libraries were multiplexed in groups of six and sequenced on a HiSeq 4000 (Illumnia) at the University of North Carolina at Chapel Hill High Throughput Sequencing Facility.

value: whole blood

value: mixed

value: Female

tag: age

value: Midwest

tag: monocytes

value: Black


title: 4T1 pooled tumors, Ctrl, control

city: Rehovot

first: Hila

last: Tishler

address: POB 26

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: shGFP_normal_diet
10x genomics

data_processing:
Reads were processed with Cell Ranger v3.1.0 using the mm10 reference genome. Quality control and clustering were performed in Seurat v3.2.0 (R v4.0.0). Low-quality cells and doublets were removed, leaving 21,873 cells. Data were normalized with SCTransform, clustered using 17 PCs (resolution 1.2), and visualized by UMAP.
Assembly: Mouse mm10
Supplementary files format and content: CellRanger outputs: barcodes, features and matrix for each sample

source_name: 4T1 breast tumor

growth_protocol: Eight-week-old female BALB/c mice were randomly assigned to four experimental groups. Mice were injected orthotopically with 0.3 × 10⁶ 4T1-shGfp or 4T1-shAss1 cells in 50 µL PBS into the lower right mammary fat pad.

extract_protocol:
On day 16 post-inoculation, mice were sacrificed, and tumors were resected and weighed. Excised 4T1 tumors were mechanically and enzymatically dissociated using the gentleMACS system (Miltenyi) in RPMI medium containing collagenase A and DNase I at 37°C. The resulting single-cell suspensions were filtered and subjected to red blood cell lysis. Equal numbers of viable cells from 4–5 tumors per treatment group were pooled, and dead cells were removed using a Dead Cell Removal Kit (Miltenyi).
Single-cell suspensions with viability above 70% were processed on a Chromium Controller (10x Genomics) to generate GEMs. Barcoded cDNA was synthesized, amplified, and used to prepare libraries with the Chromium Single Cell 3′ Library Kit. Libraries were quantified, pooled, and sequenced on an Illumina NovaSeq 6000 (SP 100 cycles), targeting ~50,000 reads per cell.

treatment_protocol: Mice assigned to the AFD groups were switched to the arginine-free diet nine days prior to tumor inoculation.

value: 4T1 breast tumor

value: Mammary carcinoma (TNBC)

value: Normal diet


title: PDAC096

description: PDAC


title: MouseBrain_50um_pixel_rep2

description: Library name: MouseBrain_50um_pixel_rep2

source_name: Brain

value: Brain

value: WT

value: m6A antibody (CST,Cat #56593)


title: 4T1 pooled tumors, KD, tumor-intrinsic arginine restriction by Ass1-knockdown

description:
Library name: shASS1_normal_diet
10x genomics

value: Ass1 knockdown


title: PDAC095

description: PDAC

value: Plasma

value: Diagnostic cohort

value: PDAC


title: mESC_m6A_rep1

description: Library name: mESC_m6A_rep1

value: embryonic stem cell


title: 4T1 pooled tumors, AFD, systemic arginine restriction by arginine-free diet

description:
Library name: shGFP_arginine-free
10x genomics

value: Arginine-free diet (AFD)


title: 4T1 pooled tumors, KD-AFD, combined arginine restriction by Ass1-knockdown and arginine-free diet

description:
Library name: shASS1_arginine-free
10x genomics


title: C2C12 w/ Bmal1hep-/- ZT16 serum biological replicate 4

city: Barcelona

first: Jacob

last: Smith

state: Barcelona

address: Av. Diagonal, 643

country: Spain

institute: University of Barcelona

description: Library name: c16

data_processing:
Quantified libraries were pooled and sequenced on the Novoseq 6000 according to the PE150 strategy.
The sequencing depth was ~20 million raw reads/sample.
Quality checking was performed using FastQC v0.11.8 and to mm10 (STAR--outFilter-MultimapNmax 20 --alignSJoverhangMin 8 –alignSJDBoverhangMin1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax0.04 --alignIntronMin 20--alignIntronMax 1000000 --alignMates-GapMax 1000000 --outSAMattributes NH HI NM MD).
RNA-seq quality assessment was performed using RSeQC v3.0.1 tool.
Assembly: GRCm39
Supplementary files format and content: FPKM available at publisher website

source_name: differentiated C2C12 myotubes

extract_protocol:
DirectZol (Zymo) columns
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was completed following end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: differentiated C2C12 myotubes

value: Bmal1hep-/- ZT16 serum for 24 hr


title: mESC_noAb_rep2

description: Library name: mESC_noAb_rep2


title: XA0045353-824-1024_ACAGAACG-CTCCTAAG_S3,  ED

institute: University of North Carolina at Chapel Hill

description: Library name: XA0045353-824-1024_ACAGAACG-CTCCTAAG_S3

value: whole blood

value: mixed

value: Female

value: NorthEast


title: PDAC094

description: PDAC


title: PDAC093

description: PDAC


title: XA0046193-824-1017_ATCGTCTC-AGAAGGAC_S13,  ED

description: Library name: XA0046193-824-1017_ATCGTCTC-AGAAGGAC_S13

value: Other


title: XA0048573-842-1101_TCTAGGAG-TTGCAACG_S26,  ED

description: Library name: XA0048573-842-1101_TCTAGGAG-TTGCAACG_S26

value: Male

value: Midwest

value: Black


title: C2C12 w/ Bmal1hep-/- ZT16 serum biological replicate 3

description: Library name: c15


title: XA0050491-842-1265_AATGACGC-TGGACCAT_S56,  ED

description: Library name: XA0050491-842-1265_AATGACGC-TGGACCAT_S56


title: Pancreatic tumor microenvironment, 9-PAHSA treated, rep5

city: Hangzhou

first: xiaozhen

last: zhang

state: province

address: 79 Qingchun Road

institute: The first affiliated hospital, zhejiang university school of medicine

description: Library name: PA9_10

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Mouse CD8+ T cell

extract_protocol:
A single-cell suspension was prepared from dissociated whole pancreatic tumours harvested from an in situ model following treatment with either a vehicle (control) or 9-PAHSA. In brief, the tumours were minced into small fragments and digested in RPMI 1640 medium supplemented with 1 mg/ml collagenase IV, 0.5 mg/ml dispase II and 40 U/ml DNase I at 37 °C for 20–30 minutes with gentle agitation. The digested tissue was then passed through a 70 µm cell strainer and washed with PBS containing 0.04% BSA. Cell viability and concentration were assessed using trypan blue staining on an automated cell counter.  Finally, the live single-cell suspension was resuspended in PBS containing 0.04% BSA at the optimal concentration for loading onto the 10x Genomics Chromium Controller, in order to generate gel bead-in-emulsions (GEMs) for subsequent library construction.
Single-cell RNA-seq libraries were constructed in accordance with the manufacturer's instructions. In brief, the prepared live single-cell suspension was combined with master mix, partitioning oil and gel beads containing barcoded oligonucleotides. This mixture was then loaded onto a Chromium chip to generate gel bead-in-emulsions (GEMs). Within each GEM, the cells were lysed and the poly-adenylated mRNA was reverse transcribed into barcoded cDNA. This process incorporated a unique molecular identifier (UMI), a cell barcode and an Illumina R1 sequence. Following GEM breakage, the barcoded cDNA from all GEMs was pooled and purified using DynaBeads MyOne SILANE beads. This was then amplified by PCR to generate sufficient material. The amplified cDNA was then fragmented enzymatically, with Illumina adapter sequences and a sample index added during the end repair, A-tailing, adaptor ligation and PCR amplification steps. Final library fragments optimised for sequencing were selected to enrich for constructs of an appropriate length (200–700 bp). The quality of the library was assessed based on fragment size distribution and quantified prior to pooling and sequencing.

value: Mouse CD8+ T cell

value: 9-pahsa treated


title: mESC_noAb_rep1

description: Library name: mESC_noAb_rep1

value: WT


title: C2C12 w/ Bmal1hep-/- ZT16 serum biological replicate 2

description: Library name: c14


title: PDAC091

description: PDAC

value: Plasma

value: Diagnostic cohort


title: XA0046190-824-1011_AAGATGCC-ACTCCAAG_S12,  ED

description: Library name: XA0046190-824-1011_AAGATGCC-ACTCCAAG_S12


title: Pancreatic tumor microenvironment, 9-PAHSA treated, rep3

description: Library name: PA9_8


title: C2C12 w/ Bmal1hep-/- ZT16 serum biological replicate 1

description: Library name: c13


title: PDAC090

description: PDAC

value: PDAC


title: XA0047909-842-1107_GAACCTTC-CAAGGTAC_S20,  ED

description: Library name: XA0047909-842-1107_GAACCTTC-CAAGGTAC_S20


title: XA0047869-842-1104_ACGGACTT-ATCGGAGA_S19,  ED

description: Library name: XA0047869-842-1104_ACGGACTT-ATCGGAGA_S19

value: White


title: Pancreatic tumor microenvironment, 9-PAHSA treated, rep4

description: Library name: PA9_9


title: C2C12 w/ WT ZT16 serum biological replicate 3

description: Library name: c11

value: differentiated C2C12 myotubes

value: WT ZT16 serum for 24 hr


title: XA0047794-842-1095_CGTCTAAC-CAACGAGT_S16,  ED

description: Library name: XA0047794-842-1095_CGTCTAAC-CAACGAGT_S16

value: whole blood


title: Pancreatic tumor microenvironment, 9-PAHSA treated, rep2

description: Library name: PA9_7


title: Pancreatic tumor microenvironment, 9-PAHSA treated, rep1

description: Library name: PA9_6


title: PDAC089

description: PDAC


title: C2C12 w/ WT ZT16 serum biological replicate 4

description: Library name: c12


title: PDAC087

description: PDAC


title: PDAC088

description: PDAC


title: PDAC092

description: PDAC


title: C2C12 w/ WT ZT16 serum biological replicate 2

description: Library name: c10


title: Pancreatic tumor microenvironment, control, rep5

description: Library name: V6


title: C2C12 w/ WT ZT16 serum biological replicate 1

description: Library name: c9


title: XA0046985-847-1004_CTGACACA-TCACCGTA_S18,  ED

description: Library name: XA0046985-847-1004_CTGACACA-TCACCGTA_S18

value: mixed


title: PDAC086

description: PDAC


title: XA0047181-824-1005_ACCGAGAT-CACCACAA_S28,  ED

description: Library name: XA0047181-824-1005_ACCGAGAT-CACCACAA_S28


title: PDAC085

description: PDAC


title: PDAC084

description: PDAC


title: C2C12 w/ Bmal1hep-/- ZT4 serum biological replicate 4

description: Library name: c8

value: Bmal1hep-/- ZT4 serum for 24 hr


title: XA0050607-847-1068_AGGAGTAC-GTCATTGC_S53,  ED

description: Library name: XA0050607-847-1068_AGGAGTAC-GTCATTGC_S53

value: NorthEast


title: XA0048136-847-1034_AACCGGTA-TACTGGAC_S33,  ED

description: Library name: XA0048136-847-1034_AACCGGTA-TACTGGAC_S33

value: Female


title: Pancreatic tumor microenvironment, control, rep3

description: Library name: V3


title: Pancreatic tumor microenvironment, control, rep4

description: Library name: V4


title: Pancreatic tumor microenvironment, control, rep2

description: Library name: V2


title: C2C12 w/ Bmal1hep-/- ZT4 serum biological replicate 3

description: Library name: c7


title: PDAC082

description: PDAC


title: XA0048198-833-1063_CGCTACAT-AACCTACG_S51,  ED

description: Library name: XA0048198-833-1063_CGCTACAT-AACCTACG_S51


title: PDAC080

description: PDAC


title: C2C12 w/ Bmal1hep-/- ZT4 serum biological replicate 1

description: Library name: c5


title: XA0050231-873-1017_CTATGTCG-CGCATATG_S67,  ED

description: Library name: XA0050231-873-1017_CTATGTCG-CGCATATG_S67

value: Male


title: XA0047411-846-1027_GACTACGA-TTACCGAC_S35,  ED

description: Library name: XA0047411-846-1027_GACTACGA-TTACCGAC_S35

value: Other


title: C2C12 w/ WT ZT4 serum biological replicate 4

description: Library name: c4

value: WT ZT4 serum for 24 hr


title: XA0045998-831-1021_GTCGAGAA-CTTACAGC_S7,  ED

description: Library name: XA0045998-831-1021_GTCGAGAA-CTTACAGC_S7

value: SouthEast

value: Black


title: Tumour-infiltrating immune cells, Combination therapy, biol rep4

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

description: Library name: Sample 8

data_processing:
Sequence reads were aligned to the GRCm39 mouse reference genome using STAR software
Transcript expression levels were quantified using RSEM software
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files including transcript per million (TPM) values

source_name: Pancreatic tumor

extract_protocol:
RNA was harvested using RNeasy mini kit with RNase-Free DNase Set (Qiagen).
cDNA was synthesized using the SMART-Seq HT kit for Sequencing (Clontech). cDNA libraries were prepared using the Nextera XT kit (Illumina).

value: Pancreatic tumor

value: CD45+ cells

value: PD-1, CLTA-4, and agonistic CD40 antibodies


title: Pancreatic tumor microenvironment, control, rep1

description: Library name: V1

value: Mouse CD8+ T cell


title: Tumour-infiltrating immune cells, Combination therapy, biol rep3

description: Library name: Sample 7


title: Tumour-infiltrating immune cells, Combination therapy, biol rep2

description: Library name: Sample 6


title: C2C12 w/ WT ZT4 serum biological replicate 3

description: Library name: c3


title: XA0046284-830-1053_ACGGACTT-ATCGGAGA_S17,  ED

description: Library name: XA0046284-830-1053_ACGGACTT-ATCGGAGA_S17

value: White


title: Tumour-infiltrating immune cells, control, biol rep4

description: Library name: Sample 4

value: Control antibodies


title: Tumour-infiltrating immune cells, Combination therapy, biol rep1

description: Library name: Sample 5


title: PDAC078

description: PDAC

value: Plasma

value: Diagnostic cohort

value: PDAC


title: PDAC079

description: PDAC


title: XA0045995-831-1009_CGAAGCAA-CCACAATC_S20,  ED

description: Library name: XA0045995-831-1009_CGAAGCAA-CCACAATC_S20

value: whole blood

value: mixed


title: PDAC081

description: PDAC


title: C2C12 w/ WT ZT4 serum biological replicate 1

description: Library name: c1

value: differentiated C2C12 myotubes


title: PDAC083

description: PDAC


title: XA0047004-830-1037_ACTCGACA-GCACAAGA_S23,  ED

description: Library name: XA0047004-830-1037_ACTCGACA-GCACAAGA_S23

value: Female


title: Bmal1hep-/- ZT20 biological replicate 2

description: Library name: B35

data_processing:
Quantified libraries were pooled and sequenced on the Novoseq 6000 according to the PE150 strategy.
The sequencing depth was ~20 million raw reads/sample.
Quality checking was performed using FastQC v0.11.8 and to mm10 (STAR--outFilter-MultimapNmax 20 --alignSJoverhangMin 8 –alignSJDBoverhangMin1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax0.04 --alignIntronMin 20--alignIntronMax 1000000 --alignMates-GapMax 1000000 --outSAMattributes NH HI NM MD).
RNA-seq quality assessment was performed using RSeQC v3.0.1 tool.
Assembly: GRCm39
Supplementary files format and content: supplementary file FPKM

source_name: gastrocnemius muscle

value: gastrocnemius muscle

tag: time point

value: zeitgeber time 20


title: Bmal1hep-/- ZT20 biological replicate 1

description: Library name: B34


title: XA0044925-830-1000_ACGCACAA-CACTGCAA_S1,  ED

description: Library name: XA0044925-830-1000_ACGCACAA-CACTGCAA_S1

value: SouthEast


title: C2C12 w/ Bmal1hep-/- ZT4 serum biological replicate 2

description: Library name: c6

value: Bmal1hep-/- ZT4 serum for 24 hr


title: PDAC077

description: PDAC


title: Tumour-infiltrating immune cells, control, biol rep3

description: Library name: Sample 3

value: Pancreatic tumor


title: Tumour-infiltrating immune cells, control, biol rep2

description: Library name: Sample 2

value: CD45+ cells


title: XA0048436-829-1032_GACATGAG-CAGAGAGT_S53,  ED

description: Library name: XA0048436-829-1032_GACATGAG-CAGAGAGT_S53

value: Midwest


title: C2C12 w/ WT ZT4 serum biological replicate 2

description: Library name: c2

value: WT ZT4 serum for 24 hr


title: XA0048241-828-1078_ACAACAGC-ACCGACAA_S38,  ED

description: Library name: XA0048241-828-1078_ACAACAGC-ACCGACAA_S38

value: NorthEast

value: White


title: PDAC076

description: PDAC

value: Plasma


title: Bmal1hep-/- ZT20 biological replicate 3

description: Library name: B36


title: PDAC073

description: PDAC

value: Diagnostic cohort


title: Tumour-infiltrating immune cells, control, biol rep1

description: Library name: Sample 1

value: Control antibodies


title: PDAC074

description: PDAC

value: PDAC


title: Bmal1hep-/- ZT16 biological replicate 1

description: Library name: B31

value: zeitgeber time 16


title: PDAC071

description: PDAC


title: mm_atac_spreb_jk1-del57.2

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Library name: mm_atac_spreb_jk1-del57.2

library_source: genomic

data_processing:
Raw data were aligned to reference genome mm9 using BWA MEM. Read alignments were adjusted to account for TAC transposon binding: +4bp for + strand alignments, -5bp for - strand alignments. Peaks were called using Macs2 with --nomodel set and no background provided, and peaks with score >5 were retained. Nucleosome positioning signal was computed by first binning properly paired read pairs into nucleosome-free or nucleosome-containing bins, based on their fragment size. Fragments <=100bp were considered nucleosome free (background) and converted to a single read covering the length of the fragment. Fragments 180-247bp were considered single-nucleosome-containing and converted to a single read the length of the fragment; similarly, fragments 315-473bp or 558-615bp were considered two- or three-nucleosome containing, and split into 2 or 3 reads covering half or 1/3 of the total fragment length. Single-, two-, and three- nucleosome reads were combined into the nucleosome signal read set. Nucleosome positioning analysis was run using danpos (Chen et al., 2013) with command dpos and parameters -m 1 -a 10 -jd 20 --clonalcut 0, and contrasting nucleosome signal to nucleosome background for each sample. Wig tracks from danpos were re-normalized to counts per billion bases using the sum of alignment lengths over 1 billion from the original BAM file, and converted to bigWig using UCSC tool wigToBigWig (Kent et al., 2010).
Assembly: mm9
Supplementary files format and content: *.bw: bigWig
Supplementary files format and content: bed (tab-delimited text)

molecule: genomic DNA

source_name: Small pre-B cells

extract_protocol:
Cells were washed with PBS, then lysed with ATAC lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Resulting nuclei were then incubated with tagmentation enzyme (Illumina).
Libraries from purified samples were made with the Nextera Indexing kit (Illumina).

treatment_protocol: Small pre-B cells were flow sorted as B220+CD19+CD43-IgM-FSClo.

value: Small pre-B cells

value: Cells were isolated from bone marrow


title: mm_atac_spreb_jk1-GAGA-del.1

description: Library name: mm_atac_spreb_jk1-GAGA-del.1


title: PDAC075

description: PDAC


title: XA0047776-828-1095_AACACTGG-ACAGGCAT_S30,  ED

description: Library name: XA0047776-828-1095_AACACTGG-ACAGGCAT_S30

value: whole blood

value: mixed

value: Male

value: Black


title: XA0054957-826-1096_ACAGATCC-AGCGTACA_S125,  ED

description: Library name: XA0054957-826-1096_ACAGATCC-AGCGTACA_S125


title: Bmal1hep-/- ZT12 biological replicate 3

description: Library name: B30

value: gastrocnemius muscle

value: zeitgeber time 12


title: mm_atac_spreb_jk1-GAGA-del.2

description: Library name: mm_atac_spreb_jk1-GAGA-del.2


title: XA0053514-842-1241_ACAGCAAG-GTCTGCAA_S82,  ED

description: Library name: XA0053514-842-1241_ACAGCAAG-GTCTGCAA_S82

value: Female

value: Midwest


title: Bmal1hep-/- ZT16 biological replicate 3

description: Library name: B33


title: XA0045055-828-1057_ACGATCAG-ATCGCAAC_S4,  ED

description: Library name: XA0045055-828-1057_ACGATCAG-ATCGCAAC_S4

value: NorthEast


title: mm_atac_spreb_jk1-del40.1

description: Library name: mm_atac_spreb_jk1-del40.1


title: Bmal1hep-/- ZT12 biological replicate 2

description: Library name: B29


title: PDAC072

description: PDAC


title: Bmal1hep-/- ZT12 biological replicate 1

description: Library name: B28


title: Bmal1hep-/- ZT16 biological replicate 2

description: Library name: B32


title: [HEK293] [Cycloheximide]

city: Nijmegen

first: Wim

last: Velema

address: Heyendaalseweg 135

country: Netherlands

institute: Radboud University

description:
Library name: Cyc
Column Name: Cyclohexamide in All_Mutations.csv

data_processing:
RNA Framework by Danny Incarnato (https://github.com/dincarnato/RNAFramework)
Mapping was carried by rf-map (which uses bowtie2 and cutadapt): -mp enables soft-clipping during alignment. Commands -ctn and -ctm remove reads with or trims ambiguously called bases. -cq5 trims all bases with phred quality lower than 20 on the 5’ end.
Mutations were counted with: “rf-count -m -es -ni -nd -na”. This counts the mutations, whilst ignoring all insertions, deletions and ambiguously mapped segments and ensuring that nucleotides neighboring the mutation are above 20 in quality.
Mutation rates were calculated using rf-norm, ignoring G and T bases and setting minimum coverage to 400: “rf-norm -nm 1 -n 400 -rb AC -ni -sm 4“. Mutation rate was calculated as #mutations/#coverage and normalized with 2-8% normalization.
Assembly: hg38
Supplementary files format and content: Comma delimited CSV files contain the normalized mutational rates.

growth_protocol: HEK293T/17 cells were seeded at a concentration of 1x105 cells/mL in a 6-well plate, in Dulbecco's modified Eagle's medium (DMEM, ThermoFisher) supplemented with 4.5 g/L D-Glucose, L-glutamine, Sodium Pyruvate, 10% (v/v) fetal bovine serum (FBS, ThermoFisher) and antibiotic solution (50 U/mL Penicillin and 50 U/mL Streptomycin), two days before treatment.

extract_protocol:
Cells were extracted with TRIzol™ (as per manufacter's instructions) and further cleaned with Zymo® Research Clean & Concentrator-5 kit, as per manufacturer’s instructions.
The probed RNA (0,5-1 µg) was reverse transcribed using TGIRT-III™ Reverse transcriptase. Briefly, to 5 μL of probed RNA, 1 μL of 5X Reverse Transcription buffer (250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2), 0.5 μL of random hexamers (10 μM) and 0.5 μL of dNTPs (10 mM) was added. The mixture was incubated for 8 min at 98 °C, to simultaneously fragment and denature the RNA, and immediately transferred to ice. Sample was supplemented with 0.25 μL of SUPERaseIn (20 U/μL), 0.25 μL DTT (0.1 M) and 0.25 μL TGIRT-III™ Reverse transcriptase (200 U/L). Reverse transcription was carried out at typical conditions (25 °C 10 min, 57 °C 2 hours, hold 4 °C). Then, 1 μL of ice-cold proteinase K (1 μg/μL) was added to each sample, to degrade the reverse-transcriptase. Reaction was carried out at 37 °C for 20 minutes. Proteinase K was deactivated by adding 1 μL proteinase inhibitor cocktail (Sigma Aldrich, cat. P186; 1:2 dilution in water). Library was then prepared using the of NEBNext® Ultra II™ workflow.

treatment_protocol: At the moment of treatment, the culture medium was replaced with warm complete DMEM supplemented with 10 μM probe, 10 μM CHX or an equivalent volume of DMSO. Cells were harvested after 30 minute incubation.


title: Bmal1hep-/- ZT8 biological replicate 2

description: Library name: B26

value: zeitgeber time 8


title: PDAC069

description: PDAC

value: Plasma


title: XA0050299-827-1019_CAACACAG-AGAAGCCT_S87,  ED

description: Library name: XA0050299-827-1019_CAACACAG-AGAAGCCT_S87

value: White


title: PDAC066

description: PDAC

value: Diagnostic cohort


title: XA0047517-826-1032_ACGGACTT-ATCGGAGA_S44,  ED

description: Library name: XA0047517-826-1032_ACGGACTT-ATCGGAGA_S44


title: mm_atac_spreb_jk1-del40.2

description: Library name: mm_atac_spreb_jk1-del40.2


title: [HEK293] [DMSO]

description:
Library name: DMSO
Column Name: DMSO in All_Mutations.csv


title: mm_atac_spreb_jk1-del57.1

description: Library name: mm_atac_spreb_jk1-del57.1


title: PDAC070

description: PDAC

value: PDAC


title: Bmal1hep-/- ZT8 biological replicate 1

description: Library name: B25


title: PDAC067

description: PDAC


title: Ileum organoids derived from human samples under 2 days under normoxic conditions-4

city: Gainesville

first: Steeve

last: Boulant

state: FL

address: 1200 Newell Drive

department: MGM

institute: University of Florida

description: Library name: normoxia_2days_replicate4

data_processing:
Fastq files were aligned to the GRCh38 human reference genome (Homo_sapiens.GRCh38.dna.primary_assembly) and reads mapped and counted using the R library Rsubread. We use for transcriptome annotation the following version Homo_sapiens.GRCh38.102
No adapter or base trimming applied (nTrim5 = 0, nTrim3 = 0)
Gene expression quantified using exon-level annotation setting GTF.featureType = "exon"
Fragments filtered to retain insert sizes between 50 and 600 bp.
Assembly: GRCh38
Supplementary files format and content: csv; filtered gene counts

source_name: Intestine

growth_protocol: Human ileum-derived organoids were cultured as 3D-spheroids in matrigel in 5% CO2 and 20% O2 at 37°C in high Wnt media (1x B-27 supplement (Thermo Fisher Scientific #17504001), 1 mM N-Acetyl-L-Cystein (Merck #A9165), 500 nM A8301 (Merck #SML0788), 50 ng/ml recombinant human FGF-basic (Preprotech #10018B), 25 ng/ml mouse Noggin recombinant protein (Thermo Fisher Scientific #25038), 100 ng/ml recombinant human IGF-1 (Fisher Scientific #590908), 10 nM [Leu15]-Gastrin I human (Merck #G9145), and 50 ng/ml recombinant mouse EGF (Thermo Fisher Scientific #PMG8041) in L-WRN  (Wnt-3A, R-spondin, Noggin) cell conditioned advanced DMEM/F12 medium). Media was exchanged every two days and organoids were split weekly in a 1:2 – 1:4 ratio.

extract_protocol:
RNA was extracted using the RNAeasy RNA extraction kit (Qiagen #74136) according to the manufacturer’s instructions.
Libraries were prepared using poly(a) selection and random hexamer priming, followed by second-strand cDNA synthesis using dTTP.

treatment_protocol: To evaluate the gene expression profiles of human ileum-derived organoids incubated under normoxic  (20% O2) vs. hypoxic (1% O2) conditions for 6 h, 12 h, 24 h or 48 h in low Wnt media (1x B-27 supplement (Thermo Fisher Scientific #17504001), 500 nM A8301 (Merck #SML0788), 50 ng/ml recombinant human FGF-basic (Preprotech #10018B), 50 ng/ml mouse Noggin recombinant protein (Thermo Fisher Scientific #25038), 100 ng/ml recombinant human IGF-1 (Fisher Scientific #590908), 10 nM [Leu15]-Gastrin I human (Merck #G9145), and 50 ng/ml recombinant mouse EGF (Thermo Fisher Scientific #PMG8041) in HEK-R-spondin cell conditioned advanced DMEM/F12 medium) followed by RNA extraction and bulk RNA sequencing.

value: Intestine

value: Ileum

value: WT

value: normoxia

tag: time

value: 2 days


title: XA0050254-873-1003_ACGAACGA-CCACATAC_S44,  ED

description: Library name: XA0050254-873-1003_ACGAACGA-CCACATAC_S44

value: whole blood

value: mixed

value: Male


title: XA0050029-873-1020_CACAACGT-GATCGTAC_S38,  ED

description: Library name: XA0050029-873-1020_CACAACGT-GATCGTAC_S38

value: Black


title: Ileum organoids derived from human samples under 2 days under normoxic conditions-3

description: Library name: normoxia_2days_replicate3


title: XA0050478-842-1184_TAGGAGCT-CTAGCAGT_S54,  ED

description: Library name: XA0050478-842-1184_TAGGAGCT-CTAGCAGT_S54

value: Female


title: Bmal1hep-/- ZT8 biological replicate 3

description: Library name: B27

value: gastrocnemius muscle


title: Bmal1hep-/- ZT4 biological replicate 1

description: Library name: B22

value: zeitgeber time 4


title: PDAC068

description: PDAC


title: PDAC065

description: PDAC


title: XA0048603-826-1030_CTCGAACA-CCAACGAA_S58,  ED

description: Library name: XA0048603-826-1030_CTCGAACA-CCAACGAA_S58

value: Midwest


title: PDAC062

description: PDAC

value: Plasma


title: Bmal1hep-/- ZT0 biological replicate 3

description: Library name: B21

value: zeitgeber time 0


title: Ileum organoids derived from human samples under 2 days under normoxic conditions-1

description: Library name: normoxia_2days_replicate1


title: [HEK293] [RiboBright]

description:
Library name: Ribo
Column Name: RiboBright in All_Mutations.csv


title: Bmal1hep-/- ZT4 biological replicate 3

description: Library name: B24


title: XA0049789-842-1144_CGAACAAC-TCGATGAC_S36,  ED

description: Library name: XA0049789-842-1144_CGAACAAC-TCGATGAC_S36


title: PDAC064

description: PDAC

value: Diagnostic cohort


title: Bmal1hep-/- ZT4 biological replicate 2

description: Library name: B23


title: Bmal1hep-/- ZT0 biological replicate 2

description: Library name: B20


title: PDAC063

description: PDAC

value: PDAC


title: XA0050470-842-1169_CAGGTTCA-AACGTAGC_S53,  ED

description: Library name: XA0050470-842-1169_CAGGTTCA-AACGTAGC_S53

value: White


title: Ileum organoids derived from human samples under 2 days under hypoxic conditions-2

description: Library name: hypoxia_2days_replicate2

value: Intestine

value: Ileum

value: hypoxia


title: WT ZT20 biological replicate 3

description: Library name: B18

value: zeitgeber time 20

value: wildtype


title: XA0050482-842-1175_AGGCAATG-ACCTAGAC_S55,  ED

description: Library name: XA0050482-842-1175_AGGCAATG-ACCTAGAC_S55

value: whole blood

value: mixed


title: PDAC061

description: PDAC


title: XA0044796-826-1008_GTACACCT-GAGACCAA_S3,  ED

description: Library name: XA0044796-826-1008_GTACACCT-GAGACCAA_S3

value: Male

value: Black


title: Ileum organoids derived from human samples under 2 days under hypoxic conditions-4

description: Library name: hypoxia_2days_replicate4

value: WT

value: 2 days


title: XA0054452-873-1033_CGCACATA-ACCACTGA_S107,  ED

description: Library name: XA0054452-873-1033_CGCACATA-ACCACTGA_S107

value: NorthEast


title: Bmal1hep-/- ZT0 biological replicate 1

description: Library name: B19

value: gastrocnemius muscle


title: Ileum organoids derived from human samples under 1 day under normoxic conditions-3

description: Library name: normoxia_1day_replicate3

value: normoxia

value: 1 day


title: PDAC060

description: PDAC

value: Plasma

value: Diagnostic cohort

value: PDAC


title: PDAC056

description: PDAC


title: Ileum organoids derived from human samples under 2 days under hypoxic conditions-3

description: Library name: hypoxia_2days_replicate3

value: Intestine

value: Ileum


title: PDAC059

description: PDAC


title: PDAC055

description: PDAC


title: XA0055257-825-1110_ATCGACGT-CAGATACG_S130,  ED

description: Library name: XA0055257-825-1110_ATCGACGT-CAGATACG_S130

value: Female

value: Midwest


title: Ileum organoids derived from human samples under 2 days under normoxic conditions-2

description: Library name: normoxia_2days_replicate2


title: WT ZT20 biological replicate 2

description: Library name: B17

value: zeitgeber time 20

value: wildtype


title: WT ZT16 biological replicate 3

description: Library name: B15

value: zeitgeber time 16


title: PDAC058

description: PDAC


title: XA0048374-842-1080_CGTCCATT-TTCCTCCT_S23,  ED

description: Library name: XA0048374-842-1080_CGTCCATT-TTCCTCCT_S23

value: whole blood

value: mixed

value: Male

value: Black


title: Ileum organoids derived from human samples under 1 day under normoxic conditions-1

description: Library name: normoxia_1day_replicate1

value: WT


title: PDAC054

description: PDAC


title: XA0048568-842-1088_CAGTGCTT-ACACCTCA_S25,  ED

description: Library name: XA0048568-842-1088_CAGTGCTT-ACACCTCA_S25


title: Ileum organoids derived from human samples under 2 days under hypoxic conditions-1

description: Library name: hypoxia_2days_replicate1

value: hypoxia

value: 2 days


title: Ileum organoids derived from human samples under 1 day under normoxic conditions-4

description: Library name: normoxia_1day_replicate4

value: normoxia

value: 1 day


title: PDAC057

description: PDAC

value: Plasma

value: Diagnostic cohort

value: PDAC


title: XA0045032-825-1009_GTCGAGAA-CTTACAGC_S5,  ED

description: Library name: XA0045032-825-1009_GTCGAGAA-CTTACAGC_S5

value: Female

value: White


title: PDAC053

description: PDAC


title: WT ZT12 biological replicate 3

description: Library name: B12

value: gastrocnemius muscle

value: zeitgeber time 12


title: WT ZT20 biological replicate 1

description: Library name: B16

value: zeitgeber time 20

value: wildtype


title: PDAC052

description: PDAC


title: XA0050687-842-1321_CTACATCC-TCACCTAG_S60,  ED

description: Library name: XA0050687-842-1321_CTACATCC-TCACCTAG_S60

value: whole blood

value: mixed

value: Midwest


title: Ileum organoids derived from human samples under 1 day under hypoxic conditions-4

description: Library name: hypoxia_1day_replicate4

value: Intestine

value: Ileum

value: WT


title: WT ZT12 biological replicate 2

description: Library name: B11


title: XA0053393-825-1074_GAATGGCA-GATCCACT_S107,  ED

description: Library name: XA0053393-825-1074_GAATGGCA-GATCCACT_S107

value: Male

value: Black


title: Ileum organoids derived from human samples under 1 day under hypoxic conditions-2

description: Library name: hypoxia_1day_replicate2

value: hypoxia

value: 1 day


title: Ileum organoids derived from human samples under 1 day under normoxic conditions-2

description: Library name: normoxia_1day_replicate2

value: normoxia


title: XA0047313-842-1017_GTCGAGAA-CTTACAGC_S11,  ED

description: Library name: XA0047313-842-1017_GTCGAGAA-CTTACAGC_S11


title: WT ZT16 biological replicate 2

description: Library name: B14

value: zeitgeber time 16


title: HFF cells, HSV1 infection, 16hpi, biol rep3

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

country: Germany

institute: Institute of Virology, University Medical Center Freiburg

description:
Library name: HFF_16hpi3
Column Name counts_HFF.tsv: 16hpi3

data_processing:
mRNASeq pipeline from snakePipes 3.1.0 was used; TrimGalore was used for adapter and base quality trimming, STAR was used for the alignment.
Assembly: Hybrid genomes of host and virus: HFF: hg38 (GRCh38.p14, Release 47) & GCA_027937515.1; Ederm: TB-T2T genome (GCF_041296265.1) & GCA_000844025.1; MDBK: ARS-UCD2.0 (GCF_002263795.3) & GCA_008777455.1
Supplementary files format and content: counts files generated by featurecounts

molecule: polyA RNA

source_name: cell line

extract_protocol:
Prior to RNA isolation and purification samples were thawed (frozen at -80°C) and incubated at room temperature for at least 5 min. RNA was isolated and purified following manufacturers’ instructions  (RNA clean and concentrator kit Zymo Research).
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) with 9 cycles PCR amplification

value: cell line

value: Human Foreskin Fibroblasts

tag: batch


title: WT ZT16 biological replicate 1

description: Library name: B13

value: gastrocnemius muscle


title: Ileum organoids derived from human samples under 1 day under hypoxic conditions-3

description: Library name: hypoxia_1day_replicate3


title: HFF cells, HSV1 infection, 16hpi, biol rep1

description:
Library name: HFF_16hpi1
Column Name counts_HFF.tsv: 16hpi1


title: PDAC048

description: PDAC

value: Plasma

value: Diagnostic cohort

value: PDAC


title: Ileum organoids derived from human samples under 1 day under hypoxic conditions-1

description: Library name: hypoxia_1day_replicate1


title: XA0054062-842-1291_ACTCTGAG-AGTTGTGC_S99,  ED

description: Library name: XA0054062-842-1291_ACTCTGAG-AGTTGTGC_S99

value: whole blood

value: mixed

value: Female


title: WT ZT4 biological replicate 3

description: Library name: B6

value: zeitgeber time 4

value: wildtype


title: PDAC050

description: PDAC


title: Ileum organoids derived from human samples under 12 hours under normoxic conditions-1

description: Library name: normoxia_12hours_replicate1

value: Intestine

value: Ileum

value: WT

value: 12 hours


title: HFF cells, HSV1 infection, 16hpi, biol rep2

description:
Library name: HFF_16hpi2
Column Name counts_HFF.tsv: 16hpi2


title: PDAC049

description: PDAC


title: WT ZT8 biological replicate 1

description: Library name: B7

value: zeitgeber time 8


title: WT ZT8 biological replicate 3

description: Library name: B9


title: WT ZT8 biological replicate 2

description: Library name: B8


title: PDAC046

description: PDAC


title: WT ZT12 biological replicate 1

description: Library name: B10

value: zeitgeber time 12


title: PDAC051

description: PDAC


title: Ileum organoids derived from human samples under 12 hours under normoxic conditions-3

description: Library name: normoxia_12hours_replicate3

value: normoxia


title: Ileum organoids derived from human samples under 12 hours under normoxic conditions-2

description: Library name: normoxia_12hours_replicate2


title: HFF cells, HSV1 infection, 9hpi, PAA treated, biol rep2

description:
Library name: HFF_9hpi_PAA2
Column Name counts_HFF.tsv: 9hpi_PAA2

value: cell line

value: Human Foreskin Fibroblasts

value: HSV1 + PAA


title: HFF cells, HSV1 infection, 9hpi, PAA treated, biol rep3

description:
Library name: HFF_9hpi_PAA3
Column Name counts_HFF.tsv: 9hpi_PAA3


title: Ileum organoids derived from human samples under 12 hours under hypoxic conditions-2

description: Library name: hypoxia_12hours_replicate2

value: hypoxia


title: HFF cells, HSV1 infection, 9hpi, biol rep2

description:
Library name: HFF_9hpi2
Column Name counts_HFF.tsv: 9hpi2


title: WT ZT4 biological replicate 2

description: Library name: B5

value: gastrocnemius muscle


title: WT ZT0 biological replicate 3

description: Library name: B3

value: zeitgeber time 0


title: HFF cells, HSV1 infection, 9hpi, PAA treated, biol rep1

description:
Library name: HFF_9hpi_PAA1
Column Name counts_HFF.tsv: 9hpi_PAA1


title: Ileum organoids derived from human samples under 6 hours under normoxic conditions-3

description: Library name: normoxia_6hours_replicate3

value: 6 hours


title: PDAC043

description: PDAC

value: Plasma

value: Diagnostic cohort

value: PDAC


title: Ileum organoids derived from human samples under 12 hours under hypoxic conditions-1

description: Library name: hypoxia_12hours_replicate1

value: Intestine


title: HFF cells, HSV1 infection, 9hpi, biol rep1

description:
Library name: HFF_9hpi1
Column Name counts_HFF.tsv: 9hpi1


title: PDAC042

description: PDAC


title: WT ZT0 biological replicate 2

description: Library name: B2

value: wildtype


title: PDAC047

description: PDAC


title: PDAC045

description: PDAC


title: WT ZT4 biological replicate 1

description: Library name: B4

value: zeitgeber time 4


title: Ileum organoids derived from human samples under 6 hours under normoxic conditions-4

description: Library name: normoxia_6hours_replicate4

value: Ileum

value: WT


title: WT ZT0 biological replicate 1

description: Library name: B1


title: HFF cells, HSV1 infection, 6hpi, PAA treated, biol rep3

description:
Library name: HFF_6hpi_PAA3
Column Name counts_HFF.tsv: 6hpi_PAA3


title: HFF cells, HSV1 infection, 9hpi, biol rep3

description:
Library name: HFF_9hpi3
Column Name counts_HFF.tsv: 9hpi3


title: C

city: Zunyi

first: lin

last: Wang

state: 贵州省遵义市新蒲新区

address: 贵州省遵义市新蒲新区学府西路6号

institute: Zunyi Medical University

description:
Library name: Sample6
T3

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Mus_musculus.GRCm38.89
Supplementary files format and content: tab-delimited text files include FPKM values for each samples.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: hepatic macrophages

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: hepatic macrophages

value: primary macrophages


title: Ileum organoids derived from human samples under 6 hours under normoxic conditions-2

description: Library name: normoxia_6hours_replicate2

value: normoxia


title: PDAC041

description: PDAC


title: Ileum organoids derived from human samples under 6 hours under hypoxic conditions-4

description: Library name: hypoxia_6hours_replicate4


title: PDAC044

description: PDAC


title: Ileum organoids derived from human samples under 6 hours under normoxic conditions-1

description: Library name: normoxia_6hours_replicate1


title: PDAC040

description: PDAC


title: HFF cells, HSV1 infection, 6hpi, PAA treated, biol rep2

description:
Library name: HFF_6hpi_PAA2
Column Name counts_HFF.tsv: 6hpi_PAA2

value: cell line

value: Human Foreskin Fibroblasts


title: Ileum organoids derived from human samples under 6 hours under hypoxic conditions-2

description: Library name: hypoxia_6hours_replicate2

value: hypoxia


title: HFF cells, HSV1 infection, 6hpi, PAA treated, biol rep1

description:
Library name: HFF_6hpi_PAA1
Column Name counts_HFF.tsv: 6hpi_PAA1

value: HSV1 + PAA


title: PDAC039

description: PDAC


title: HFF cells, HSV1 infection, 6hpi, biol rep2

description:
Library name: HFF_6hpi2
Column Name counts_HFF.tsv: 6hpi2


title: B

address: 贵州省遵义市新蒲新区学府西路6号

description:
Library name: Sample5
T2


title: 2

address: 贵州省遵义市新蒲新区学府西路6号

description:
Library name: Sample2
C2

value: PBS


title: PDAC035

description: PDAC


title: Ileum organoids derived from human samples under 6 hours under hypoxic conditions-1

description: Library name: hypoxia_6hours_replicate1

value: 6 hours


title: HFF cells, HSV1 infection, 6hpi, biol rep3

description:
Library name: HFF_6hpi3
Column Name counts_HFF.tsv: 6hpi3


title: HFF cells, HSV1 infection, 6hpi, biol rep1

description:
Library name: HFF_6hpi1
Column Name counts_HFF.tsv: 6hpi1


title: Ileum organoids derived from human samples under 6 hours under hypoxic conditions-3

description: Library name: hypoxia_6hours_replicate3


title: 3

address: 贵州省遵义市新蒲新区学府西路6号

description:
Library name: Sample3
C3


title: Ileum organoids derived from human samples under 2 days under normoxic conditions - sample S9

city: Heidelberg

first: CARL

last: HERRMANN

state: Baden-Wurtemberg

address: INF 364

department: Institut für Pharmazie und Molekulare Biotechnologie

institute: CRomLab

description: Library name: D2N3_S9

data_processing:
Fastq files were processed using the kallisto kb-python implementation version 0.46.2 setting -x 10xv3. The human genome was constructed by running `kb ref -d human --workflow standard`
We pre-processed all the samples independently. We calculated log-Rank inflection points using the barcodeRanks from DropletUtils and kept droplets above this threshold, additionally we filter-in cells with a number of features > 500. We removed genes expressed in less than 0.01 % of cells.
Then we kept cells with less than 20 % mitochondrial reads and classified as doublets using DoubletFinder()
Assembly: GRCh38
Supplementary files format and content: hypoxia_seurat.rds. Contains a R Seurat object with the filtered processed samples.

growth_protocol: Human ileum-derived organoids were cultured as 3D-spheroids in matrigel in 5% CO2 and 20% O2 at 37°C in high Wnt media (1x B-27 supplement (Thermo Fisher Scientific #17504001), 1 mM N-Acetyl-L-Cystein (Merck #A9165), 500 nM A8301 (Merck #SML0788), 50 ng/ml recombinant human FGF-basic (Preprotech #10018B), 25 ng/ml mouse Noggin recombinant protein (Thermo Fisher Scientific #25038), 100 ng/ml recombinant human IGF-1 (Fisher Scientific #590908), 10 nM [Leu15]-Gastrin I human (Merck #G9145), and 50 ng/ml recombinant mouse EGF (Thermo Fisher Scientific #PMG8041) in L-WRN (Wnt-3A, R-spondin, Noggin) cell conditioned advanced DMEM/F12 medium). Media was exchanged every two days and organoids were split weekly in a 1:2 – 1:4 ratio.

extract_protocol:
To harvest organoids for single-cell RNA sequencing, organoids were incubated in TrypLE Express (Thermo Fisher Scientific #12604013) for 25 minutes at 37°C. When organoids were dissociated and formed single cells, cells were resuspended in DMEM/F12 (10% FBS), subsequently washed in 0.04% BSA in PBS and passed through a 40 μm-cell strainer. Single‐cell suspensions were loaded onto the 10x Chromium controller using the 10x Genomics Single Cell Single Cell 5’ Library Kit NextGem V1.1 (10x Genomics) according to the manufacturer’s instructions.
Libraries were prepared using the 10x Genomics Single Cell Single Cell 5’ Library Kit NextGem V1.1 (10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: Human ileum organoids generated from three different donors were incubated for 24 h or 48 h normoxia (20% O2) vs. hypoxia (1% O2) in low Wnt media (1x B-27 supplement (Thermo Fisher Scientific #17504001), 500 nM A8301 (Merck #SML0788), 50 ng/ml recombinant human FGF-basic (Preprotech #10018B), 50 ng/ml mouse Noggin recombinant protein (Thermo Fisher Scientific #25038), 100 ng/ml recombinant human IGF-1 (Fisher Scientific #590908), 10 nM [Leu15]-Gastrin I human (Merck #G9145), and 50 ng/ml recombinant mouse EGF (Thermo Fisher Scientific #PMG8041) in HEK-R-spondin cell conditioned advanced DMEM/F12 medium).

value: 2 Days


title: HFF cells, HSV1 infection, 2hpi, biol rep3

description:
Library name: HFF_2hpi3
Column Name counts_HFF.tsv: 2hpi3


title: PDAC037

description: PDAC

value: Plasma

value: Diagnostic cohort


title: PDAC038

description: PDAC

value: PDAC


title: PDAC036

description: PDAC


title: A

address: 贵州省遵义市新蒲新区学府西路6号

description:
Library name: Sample4
T1


title: Ileum organoids derived from human samples under 2 days under hypoxic conditions - sample S12

description: Library name: D2H3_S12

value: Intestine


title: ms10-Par_aCSF1R

city: Marseille

first: Rejane

last: Rua

address: 163 Avenue de Luminy

country: France

institute: Centre d'Immunologie de Marseille Luminy

description: Library name: Sample 8

data_processing:
Alignments of fastq files obtained after sequencing were generated with STAR 2.7.10b software using the GRCm38 reference genome. The number of reads mapped to each gene was determined with featureCounts v1.6.3 using Mus_musculus.GRCm39.gtf annotation file.
Assembly: mouse reference genome (GRCm39)
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Parietal bone

extract_protocol:
Parietal skull bone was homogenized in TRIzol and RNA was isolated using the RNeasy Mini Kit (Qiagen, Cat# 74104) following the manufacturer’s instructions.
RNA quality and integrity were assessed using 2200 TapeStation with RNA Screen Tape (Agilent Technologies). Library preparation and sequencing were performed by Macrogen using their standard bulk RNA-seq service. Briefly, 1 µg RNA was used as an input for the TruSeq Stranded mRNA Library Prep Kit (Illumina). Sequencing was carried out on an Illumina NovaSeq 6000 platform using paired-end 101 bp reads, with a throughput of 6 Gb per sample.

treatment_protocol: B6 mice were treated at PND2, 4 and 6 with isotype or αCSF1R to deplete myeloid cells, then euthanized and perfused at PND9.

value: Parietal bone


title: PDAC033

description: PDAC


title: 1

address: 贵州省遵义市新蒲新区学府西路6号

description:
Library name: Sample1
C1


title: HFF cells, HSV1 infection, 2hpi, biol rep1

description:
Library name: HFF_2hpi1
Column Name counts_HFF.tsv: 2hpi1


title: PDAC034

description: PDAC


title: ms8-Par_aCSF1R

description: Library name: Sample 6


title: Ileum organoids derived from human samples under 2 days under normoxic conditions - sample S7

description: Library name: D2N1_S7

value: Ileum


title: HFF cells, HSV1 infection, 2hpi, biol rep2

description:
Library name: HFF_2hpi2
Column Name counts_HFF.tsv: 2hpi2

value: WT


title: ms9-Par_aCSF1R

description: Library name: Sample 7


title: PDAC032

description: PDAC


title: ms7-Par_aCSF1R

description: Library name: Sample 5


title: HFF cells, Mock, biol rep2

description:
Library name: HFF_Mock2
Column Name counts_HFF.tsv: Mock2

value: Mock


title: Ileum organoids derived from human samples under 2 days under normoxic conditions - sample S8

description: Library name: D2N2_S8


title: Ileum organoids derived from human samples under 2 days under hypoxic conditions - sample S11

description: Library name: D2H2_S11


title: PDAC031

description: PDAC


title: ms5-Par_ISO

description: Library name: Sample 4

value: Isotype


title: PDAC030

description: PDAC


title: Ileum organoids derived from human samples under 2 days under hypoxic conditions - sample S10

description: Library name: D2H1_S10


title: Ileum organoids derived from human samples under 1 day under normoxic conditions - sample S3

description: Library name: D1N3_S3

value: normoxia

value: 1 Day


title: ms4-Par_ISO

description: Library name: Sample 3


title: HFF cells, Mock, biol rep3

description:
Library name: HFF_Mock3
Column Name counts_HFF.tsv: Mock3

value: cell line

value: Human Foreskin Fibroblasts


title: MULTIseq barcode lane 3

city: San Francisco

first: Kiet

middle: Tuan

last: Phong

state: California

address: 600 16th Street

department: Department of Pharmaceutical Chemistry

institute: University of California, San Francisco

description:
Library name: KP_BC_3
MULTIseq barcode library

data_processing:
10X Genomics Cellranger v5.0.0 was used for sequence alignment, data filtering, and generating the count matrix. Manual filtering for droplets with > 630 RNA UMIs and < 10% of reads being mitochondrial genes to exclude empty droplets and low-quality cells.
SCTransform was used to normalize the raw counts across the 10X lanes.
For sample demultiplexing, deMULTIplex2 (Zhu et al. 2024) was used to process the MULTIseq barcode libraries and classify each cell barcode to a single donor. Additionally, cellsnp-lite (Huang et al. 2021) and Vireo (Huang et al. 2019) pipelines were used to classify cells to different donors based on single nucleotide polymorphisms (SNPs).
Cell type assignment was done using the Seurat package (v5.1.0) in Rstudio (build 561).
Assembly: GRCh38-3.0.0
Supplementary files format and content: Gzipped RDS files containing: 1) matrix tables with raw gene counts for each cell, 2) a processed Seurat object for all cells  3) sample metadata table including demographics information for each cell, 4-6) matrix tables with raw MULTIseq barcode counts for each cell
Supplementary files format and content: raw_counts.rds.gz (RDS - gene counts matrix table)
Supplementary files format and content: cell_metadata.rds.gz (RDS - metadata table)
Supplementary files format and content: breast_data.rds.gz (RDS - processed Seurat object)
Supplementary files format and content: barcode.counts.lane1.rds.gz (RDS - barcode counts matrix table)
Supplementary files format and content: barcode.counts.lane2.rds.gz (RDS - barcode counts matrix table)
Supplementary files format and content: barcode.counts.lane3.rds.gz (RDS - barcode counts matrix table)

source_name: breast

extract_protocol:
Breast tissues were chopped into a slurry, then digested overnight in collagenase type III and hyaluronidase in a spinner flask at 37°C. Filtration through 100 µm cell strainer was used to collect epithelium-enriched tissue microfragments, which were then cryopreserved. For sequencing experiment, the tissue microfragments were thawed and digested to single cells by trypsin treatment, followed by DNAseI and dispase. Samples were then labeled by MULTIseq LMO barcodes, and then pooled and sorted for live single cells as DAPI-negative cells.
The single live cells were encapsulated into droplets on the 10X Chromium Controller, and library prep for sequencing was performed according to the 10X Chromium Single Cell 3' v3.1 User Guide Rev D and MULTI-seq library preparation protocol (McGinnis et al. 2019).

value: breast

value: primary breast cells

value: untreated


title: Ileum organoids derived from human samples under 1 day under normoxic conditions - sample S2

description: Library name: D1N2_S2


title: PDAC028

description: PDAC


title: PDAC029

description: PDAC


title: HFF cells, Mock, biol rep1

description:
Library name: HFF_Mock1
Column Name counts_HFF.tsv: Mock1


title: ms2-Par_ISO

description: Library name: Sample 1


title: PDAC027

description: PDAC


title: PDAC026

description: PDAC


title: Ileum organoids derived from human samples under 1 day under normoxic conditions - sample S1

description: Library name: D1N1_S1


title: MULTIseq barcode lane 2

description:
Library name: KP_BC_2
MULTIseq barcode library


title: Ileum organoids derived from human samples under 1 day under hypoxic conditions - sample S6

description: Library name: D1H3_S6

value: hypoxia


title: 10X lane 3

description:
Library name: KP_cDNA_3
transcriptomic library


title: Ileum organoids derived from human samples under 1 day under hypoxic conditions - sample S5

description: Library name: D1H2_S5


title: D2

city: Harbin

first: Qingbo

last: Cui

state: Heilongjiang, China

address: No.998 Aiying Street

institute: The Sixth Affiliated Hospital of Harbin Medical University

description: Library name: Sample11

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample.

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

value: Mouse hepatocytes

value: Treated with TCA (1000 μM) for 24 h


title: PDAC025

description: PDAC

data_processing:
Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.
Assembly: The miRNA probe list is based on miRBase version 20.
Supplementary files format and content: Raw FASTQ file of each sample was parsed, normalized into count per million and transformed to log2CPM using HTG EdgeSeq Parser and HTG EdgeSeq Reveal software.

value: Plasma

value: Diagnostic cohort

value: PDAC


title: Ileum organoids derived from human samples under 1 day under hypoxic conditions - sample S4

description: Library name: D1H1_S4

value: Intestine

value: Ileum


title: 10X lane 2

description:
Library name: KP_cDNA_2
transcriptomic library


title: PDAC024

description: PDAC


title: 10X lane 1

description:
Library name: KP_cDNA_1
transcriptomic library


title: C3

description: Library name: Sample9

value: WT

value: Treated with CuCl₂ (300 μM)/ES (40 nM)/TCA (1000 μM) for 24 h


title: HM-3

city: Chongqing

first: boxuan

last: wang

address: 重庆市渝中区医学院路1号

institute: 重庆医科大学

description: Library name: Sample 6

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz.
Assembly: GRCm38
Supplementary files format and content: File include Count and  FPKM values for each sample

source_name: liver

growth_protocol: For the liver-specific metastasis mouse model, 100 μl of PBS containing 1×10⁶ 4T1 (BALB/c mice) cells was injected in situ into mammary fat pad of mice. Cells from primary tumors and liver metastases were separately isolated and cultured (cells isolated from mouse primary tumors were named 4T1-Pri, the metastatic tumor cells isolated from liver organs were named HM). After stable clones were established, liver organ metastatic cells were reinoculated into new mice to generate metastatic tumors. After at least three rounds of screening, highly liver organotropic metastasis cells were successfully established, designated as 4T1/HM3 (liver-preferential metastases). The firefly luciferase reporter gene (for bioluminescence tracking) retrovirus was infected with 4T1-derived cells and puromycin (1 μg/mL, Sigma Aldrich, USA) was selected for 14 days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: liver

value: Primary cell

value: Cells from liver metastases


title: MULTIseq barcode lane 1

description:
Library name: KP_BC_1
MULTIseq barcode library


title: D1

description: Library name: Sample10


title: ms3-Par_ISO

description: Library name: Sample 2

value: Parietal bone

value: Isotype


title: C2

description: Library name: Sample8


title: JG056_LU28_ND_D21_S5

city: Lund

first: Petter

last: Storm

state: Select...

address: Sölvegatan 19, BMC A11

country: Sweden

institute: Lund University

description: Library name: JG056_LU28_ND_D21_S5

data_processing:
Raw base calls were demultiplexed and converted into sample specific fastq files using default parameters of the bcl2fastq program (v 2.20, Illumina). Transcript expression was quantified from RNA-seq data using Salmon (v.1.2.1) against an index built from the Ensembl GRCh38 v.99 transcriptome model with default parameters implemented in a Snakemake workflow.
Assembly: GRCh38 v.99
Supplementary files format and content: Count values from Salmon

growth_protocol: hESC-derived GPCs were thawed and seeded onto poly-L-ornithine (100 μg/mL) and laminin (5 μg/mL) coated tissue culture plates (6 well plate, Corning) in glial medium (GM) containing DMEM/F12 basal medium, B27 supplement, N1 supplement, MEM NEAA, Antibiotic-Antimycotic, T3 (60 ng/mL), db-cAMP (1 μM), Biotin (100 ng/mL), recombinant human PDGF-AA protein (10 ng/mL), recombinant human IGF-I (10 ng/mL) and recombinant human NT-3 protein (10 ng/mL).

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen)
cDNA libraries were prepared using the Illumina TruSeq library preparation kit and sequenced with 2 x 150 bp paired end reads on an Illumina NextSeq 2000 using the P3 flow cell (~37M reads per sample).

treatment_protocol: 100,000 single hGPCs were mixed with the lentiviral reprogramming cocktail (multiplicity of infection of 1–2 per vector) in 50 μL of GM and plated in 96-well round-bottom plates (Corning, Cat# CLS7007). On the day after seeding, Tet-controlled transgene expression was induced into the self-aggregated spheroids by exchanging 50 μL of fresh GM containing doxycycline (5 μg/mL). At D2 post transgene activation, GM was replaced with 150 μlL of neural differentiation (ND) medium (NDiff227) containing doxycycline (5 μg/mL), small molecules (CHIR99021, 2 μM; SB-431542, 10 μM; noggin, 0.5 μg/mL; LDN-193189, 0.5 μM; VPA, 1 mM) and growth factors (LM-22A4, 2 μM; GDNF, 2 ng/mL; NT3, 10 ng/mL; db-cAMP, 0.5 mM). Subsequently, ND was exchanged every 2 to 3 days. At D9 post transduction, the small molecules were withdrawn from the ND medium and doxycycline administration was stopped at D21. The reprogrammed spheroids were further cultured using ND medium supplemented with growth factors.

value: cell line

value: hESC derived glia

value: ND


title: PDAC023

city: Houston

first: Warapen

last: Treekitkarnmongkol

institute: UT MD Anderson Cancer Center

description: PDAC

source_name: Plasma

extract_protocol:
15 uL of plasma was profiled for miRNAs by the extraction-free method using the HTG edge miRNA whole transcriptome assay kit (HTG Molecular, Tuscon, AZ, Cat# 916-001-024) according to the recommended vendor’s protocol.
Probes hybrized to target miRNAs were retrieved and added sequencing adapters as well as sample barcodes via PCR for preparing library. The libraries were quantified by quantitative PCR (qPCR) using KAPA Library Quantification kit (Roche, Cat# KK4824) and loaded onto the MiSeq (Illumina) together with the MiSeq Reagent Kit v3 (150 cycles) (Illumina, Cat# MS-102-3001).


title: D3

description: Library name: Sample12

value: Mouse hepatocytes


title: C1

description: Library name: Sample7


title: JG056_LU28_ALNR_D21_S7

description: Library name: JG056_LU28_ALNR_D21_S7

value: ALNR


title: PDAC022

description: PDAC

value: Plasma


title: JG056_LU28_ALNR_D50_S8

description: Library name: JG056_LU28_ALNR_D50_S8


title: B3

description: Library name: Sample6

value: Treated with CuCl₂ (300 μM)/ES (40 nM) for 24 h


title: PDAC021

description: PDAC

value: Diagnostic cohort

value: PDAC


title: PDAC020

description: PDAC


title: HM-1

address: 重庆市渝中区医学院路1号

description: Library name: Sample 4


title: B2

description: Library name: Sample5


title: PDAC018

description: PDAC


title: B1

description: Library name: Sample4


title: JG056_LU28_GM_D0_S3

description: Library name: JG056_LU28_GM_D0_S3

value: GM


title: JG056_LU28_ALNR_D14_S6

description: Library name: JG056_LU28_ALNR_D14_S6


title: Pri-1

address: 重庆市渝中区医学院路1号

description: Library name: Sample 1

source_name: Breast

value: Breast

value: Cells from primary tumors


title: A3

description: Library name: Sample3

value: WT

value: Cultured in standard growth medium for 24 h


title: JG056_LU28_GM_D21_S4

description: Library name: JG056_LU28_GM_D21_S4


title: JG056_J4_ND_D21_S11

description: Library name: JG056_J4_ND_D21_S11


title: House Dust Mite (HDM) 100 - 12 weeks - 5

city: Bialystok

first: Andrzej

last: Eljaszewicz

state: Podlaskie

address: Jana Kilinskiego 1

department: Centre for Regenerative Medicine

country: Poland

institute: Medical University of Bialystok

description: Library name: MICE25

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence (bbduk; minlength=30, qtrim=rl, trimq=15). Reads were then mapped to the reference genome of Mus musculus (GRCm38) using STAR aligner version 2.5.3a with parameters --quantMode GeneCounts --runThreadN 4
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
Lung lobes were stored in RNA later solution (Invitrogen) to prevent cellular RNA degradation during tissue thawing and to protect its integrity. Samples were disrupted using TissueRuptor II (Qiagen) in RNA Lysis Buffer (RLT, Qiagen) supplemented with 10% b-mercaptoethanol. Total lung RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. Only the RNA with high integrity (RIN>8) was subjected to cDNA library preparation according to TruSeq Stranded Total RNA protocol (Illumina), followed by the quality confirmation (Agilent Technologies 2100 Bioanalyzer).
cDNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were intranasally administered with 10 and 100 μg of HDM extract in short (2 week) and 100 μg in long (12 week) models. Control mice were administered saline.

value: Lung

value: wild type

value: 100 μg HDM treated lungs for 12 weeks

value: 12 weeks


title: PDAC019

address: 2130 W. Holcombe Blvd.,  Unit 2951

description: PDAC


title: PDAC016

description: PDAC


title: Pri-2

address: 重庆市渝中区医学院路1号

description: Library name: Sample 2

value: Primary cell


title: House Dust Mite (HDM) 100 - 12 weeks - 4

description: Library name: MICE24


title: A1

description: Library name: Sample1


title: JG056_J4_GM_D21_S10

description: Library name: JG056_J4_GM_D21_S10

value: cell line

value: hESC derived glia


title: A2

description: Library name: Sample2

value: Mouse hepatocytes


title: JG056_J4_GM_D0_S9

description: Library name: JG056_J4_GM_D0_S9


title: PDAC017

description: PDAC

value: Plasma


title: CUT&Tag for Smarcb1 in murine NPCs, Mecp2 overexpression, biol rep 1

city: Milan

first: Michal

last: Kubacki

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

description:
Library name: NPC_Smarcb1_Mecp2_rep1
CUT&Tag using anti-Smarcb1 antibody in Mecp2-overexpressing NPCs to map endogenous Smarcb1 binding.

data_processing:
Raw sequencing reads from all experiments underwent quality control using FastQC. Adapters and low-quality bases were removed using Trim Galore or Trimmomatic.
Reads were aligned to mm10 using Bowtie2. Post-alignment filtering removed PCR duplicates and low-quality mapped reads.
Normalized signal tracks (bigWig format) were generated using deepTools bamCoverage.
Peaks were called using MACS2 and SEACR, and differential binding analysis was performed using DiffBind. Statistical significance was determined using FDR < 0.05.
Peaks were annotated to genomic features using the ChIPseeker R package. Gene Ontology (GO) functional enrichment analysis was performed on gene lists derived from all experiments using clusterProfiler.
Assembly: mm10
Supplementary files format and content: Peak coordinates in BED format. Normalized signal tracks in bigWig format. Tables of differentially bound regions with associated statistics (fold change, p-value, FDR).
Library strategy: CUT&Tag

source_name: telencephalon

growth_protocol: Murine Neural Progenitor Cells (NPCs): Derived from the telencephalic cortex of E13.5 mouse embryos, NPCs were cultured in adhesion on flasks coated with 1:100 Matrigel. The culture medium was Neural Inducing Medium (NIM) composed of DMEM/F12, Hormon Mix, penicillin/streptomycin, glutamine, glucose, Heparin, 10 ng/ml bFGF, and 10 ng/ml EGF. Murine Primary Neurons (Ns): Prepared from E18.5 wild-type mouse embryos, neurons were maintained in Neurobasal medium supplemented with glucose, penicillin/streptomycin, L-glutamine, and 1% B27.Human iPSC-derived Neurons (hNs): Wild-type human NPCs were differentiated into cortical neurons. Differentiation was induced in DMEM/F1 with N2 and B27 supplements, SU5402, PD0325901, and DAPT. Following dissociation, cells were plated on Poly-L-Lysine/Laminin/Fibronectin coated plates in neuronal maturation medium (Neurobasal A with B-27, Glutamine, BDNF, Ascorbic acid, Laminin, DAPT, and dbcAMP) for at least 3 weeks before experiments.

extract_protocol:
Nuclei from 100,000 cells were isolated and immobilized on Concanavalin A-coated beads. They were then incubated overnight at 4°C with primary antibodies (anti-MeCP2, anti-V5, or anti-Smarcb1). Following incubation with a secondary antibody, pA-Tn5 transposase was applied to fragment and tag antibody-bound DNA sites.
Following tagmentation, amplicon libraries were generated using the Nextera® DNA Library Prep Kit (Illumina). Barcoded libraries were pooled and sequenced on the NovaSeq 6000 platform.

treatment_protocol: Lentiviral particles (LV) were produced in 293T cells and concentrated by ultracentrifugation. Murine NPCs and Ns: Cells were transduced one day after seeding. NPCs were transduced with LV-Mecp2 or LV-EGFP at a Multiplicity of Infection (MOI) of 10. Ns were transduced at an MOI of 5. Cells were harvested for analysis 5 days post-transduction. Human iPSC-derived Neurons: Neurons cultured for 4 weeks were transduced with LV-MECP2 or LV-EGFP at an MOI of 10. Cells were harvested 5 days after infection.

value: telencephalon

value: primary neuronal progenitor cells

value: wild-type

value: lentiviral transduction with Mecp2


title: JG056_J4_ALNR_D50_S14

description: Library name: JG056_J4_ALNR_D50_S14

value: ALNR


title: PDAC015

description: PDAC

value: Diagnostic cohort

value: PDAC


title: House Dust Mite (HDM) 100 - 12 weeks - 2

description: Library name: MICE22


title: HM-2

address: 重庆市渝中区医学院路1号

description: Library name: Sample 5

value: liver

value: Cells from liver metastases


title: PDAC014

description: PDAC


title: PDAC013

description: PDAC


title: House Dust Mite (HDM) 100 - 12 weeks - 3

description: Library name: MICE23

value: Lung

value: wild type


title: JG056_J4_ALNR_D14_S12

description: Library name: JG056_J4_ALNR_D14_S12


title: CUT&Tag for Smarcb1 in murine NPCs, EGFP control, biol rep 3

description:
Library name: NPC_Smarcb1_EGFP_rep3
CUT&Tag using anti-Smarcb1 antibody in EGFP-transduced NPCs to map endogenous Smarcb1 binding.

value: lentiviral transduction with EGFP


title: CUT&Tag for Smarcb1 in murine NPCs, EGFP control, biol rep 2

description:
Library name: NPC_Smarcb1_EGFP_rep2
CUT&Tag using anti-Smarcb1 antibody in EGFP-transduced NPCs to map endogenous Smarcb1 binding.


title: Pri-3

address: 重庆市渝中区医学院路1号

description: Library name: Sample 3

value: Breast

value: Primary cell

value: Cells from primary tumors


title: NaCl - 12 weeks - 5

description: Library name: MICE20

value: untreated lungs

value: 12 weeks


title: House Dust Mite (HDM) 100 - 12 weeks - 1

description: Library name: MICE21

value: 100 μg HDM treated lungs for 12 weeks


title: JG056_J4_ALNR_D21_S13

description: Library name: JG056_J4_ALNR_D21_S13

value: cell line

value: hESC derived glia


title: PDAC011

description: PDAC

value: Plasma


title: NaCl - 12 weeks - 4

description: Library name: MICE19


title: NaCl - 12 weeks - 3

description: Library name: MICE18


title: PDAC009

description: PDAC


title: PDAC010

description: PDAC


title: JG056_J1_ALNR_D50_S2

description: Library name: JG056_J1_ALNR_D50_S2

value: ALNR


title: PDAC008

description: PDAC

value: Diagnostic cohort


title: JG056_J1_ALNR_D14_S18

description: Library name: JG056_J1_ALNR_D14_S18


title: JG056_J1_GM_D21_S16

description: Library name: JG056_J1_GM_D21_S16

value: GM


title: JG056_J1_ND_D21_S17

description: Library name: JG056_J1_ND_D21_S17

value: ND


title: NaCl - 12 weeks - 2

description: Library name: MICE17


title: House Dust Mite (HDM) 100 - 2 weeks - 5

description: Library name: MICE15

value: 100 μg HDM treated lungs for 2 weeks

value: 2 weeks


title: CUT&Tag for exogenous (V5-tagged) Mecp2 in murine neurons, biol rep 2

description:
Library name: NeuV_exo_rep2
CUT&Tag using anti-V5 antibody in Mecp2-overexpressing neurons derived from E18.5 embryos.

source_name: embryonic brain

value: embryonic brain

value: primary neurons

value: wild-type

value: lentiviral transduction with Mecp2


title: CUT&Tag for endogenous MeCP2 in murine neurons, EGFP control, biol rep 3

description:
Library name: NeuM_endo_rep3
CUT&Tag using anti-Mecp2 antibody in EGFP-transduced neurons derived from E18.5 embryos.

value: lentiviral transduction with EGFP


title: PDAC012

description: PDAC

value: PDAC


title: CUT&Tag for Smarcb1 in murine NPCs, EGFP control, biol rep 1

description:
Library name: NPC_Smarcb1_EGFP_rep1
CUT&Tag using anti-Smarcb1 antibody in EGFP-transduced NPCs to map endogenous Smarcb1 binding.

value: telencephalon

value: primary neuronal progenitor cells


title: CUT&Tag for endogenous MeCP2 in murine neurons, EGFP control, biol rep 2

description:
Library name: NeuM_endo_rep2
CUT&Tag using anti-Mecp2 antibody in EGFP-transduced neurons derived from E18.5 embryos.


title: PDAC007

description: PDAC


title: JG056_J1_ALNR_D21_S1

description: Library name: JG056_J1_ALNR_D21_S1

value: cell line


title: CUT&Tag for exogenous (V5-tagged) Mecp2 in murine neurons, biol rep 1

description:
Library name: NeuV_exo_rep1
CUT&Tag using anti-V5 antibody in Mecp2-overexpressing neurons derived from E18.5 embryos.


title: House Dust Mite (HDM) 100 - 2 weeks - 3

description: Library name: MICE13

value: Lung

value: wild type


title: CUT&Tag for IgG control in murine NPCs/Ns

description:
Library name: IgG_control
IgG antibody control for CUT&Tag experiment.

value: primary neuronal progenitor cells and primary neurons


title: Input, Igg, ChIPseq

city: Austin

first: Bum-Kyu

last: Lee

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

description:
Library name: Input
Input

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to human hg38 genome using Bowtie 2.4.5
Peaks were called using MACS3 peak caller with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

source_name: Placenta

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in human TSCs and EVTs. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for the generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E7370L ) following by manufacturer’s instructions.

value: Placenta

value: Human trophoblast stem cells


title: CUT&Tag for exogenous (V5-tagged) Mecp2 in murine neurons, biol rep 3

description:
Library name: NeuV_exo_rep3
CUT&Tag using anti-V5 antibody in Mecp2-overexpressing neurons derived from E18.5 embryos.


title: JG056_J1_GM_D0_S15

description: Library name: JG056_J1_GM_D0_S15

value: hESC derived glia

value: GM


title: EVT, TCF7L2, ChIPseq

description:
Library name: TCF7L2_EVT
Chromatin IP against TCF7L2


title: PDAC006

description: PDAC

value: Plasma

value: Diagnostic cohort


title: PDAC005

description: PDAC


title: House Dust Mite (HDM) 100 - 2 weeks - 2

description: Library name: MICE12

value: 100 μg HDM treated lungs for 2 weeks

value: 2 weeks


title: CUT&Tag for exogenous (V5-tagged) Mecp2 in murine NPCs, biol rep 2

description:
Library name: NSCv_exo_rep2
CUT&Tag using anti-V5 antibody in Mecp2-overexpressing NPCs derived from E13.5 embryos.

value: wild-type

value: lentiviral transduction with Mecp2


title: PDAC003

description: PDAC

value: PDAC


title: NaCl - 12 weeks - 1

description: Library name: MICE16

value: untreated lungs

value: 12 weeks


title: CUT&Tag for endogenous MeCP2 in murine NPCs, EGFP control, biol rep 3

description:
Library name: NSCM_endo_rep3
CUT&Tag using anti-Mecp2 antibody in EGFP-transduced NPCs derived from E13.5 embryos.

value: telencephalon

value: primary neuronal progenitor cells

value: lentiviral transduction with EGFP


title: House Dust Mite (HDM) 10 - 2 weeks - 5

description: Library name: MICE10

value: Lung

value: wild type

value: 10 μg HDM treated lungs for 2 weeks


title: TSC differentiation into EVT, Control, KD, rep3

description: Library name: EVT_Cont_KD_rep3

data_processing:
Paired-end reads were aligned to human transcript (hg38) using Salmon mapper  (v1.10.2)
Expression levels of each gene were calculated using R library tximport as transcripts per million (TPM). The read counts were quantified and normalized by median of ratio method and differentially expressed genes (DEGs) were obtained with the selection criteria of P-adjusted value < 0.01 and fold change > 2 using the R package DESeq2 (v1.30.1).
Assembly: hg38
Supplementary files format and content: xlsx, TPM

extract_protocol:
Total RNAs were extracted using the RNeasy plus mini kit following the manufacturer’s instructions. RNA-seq libraries were generated with 500 ng of total RNA using NEB Next Ultra II RNA Library prep kit (NEB, E7770) following the manufacturer’s protocol.
mRNAs were enriched from total RNAs with Magnetic mRNA Isolation Kit (oligo(dT) beads) (NEB, E7490), and then cDNAs were synthesized using random primers. cDNAs were purified by NEBNext Sample Purification Beads (NEB, E7767). End prep reactions were performed followed by ligation with a sample-specific adaptor and index.

value: Placenta

value: TSC-derived EVT

value: TSC differentiation into EVT


title: PDAC001

description: PDAC

value: Plasma

value: Diagnostic cohort


title: House Dust Mite (HDM) 100 - 2 weeks - 1

description: Library name: MICE11

value: 100 μg HDM treated lungs for 2 weeks

value: 2 weeks


title: TSC, TCF7L2, ChIPseq

description:
Library name: TCF7L2_TSC
Chromatin IP against TCF7L2

value: Human trophoblast stem cells


title: House Dust Mite (HDM) 100 - 2 weeks - 4

description: Library name: MICE14


title: House Dust Mite (HDM) 10 - 2 weeks - 4

description: Library name: MICE9


title: CUT&Tag for exogenous (V5-tagged) Mecp2 in murine NPCs, biol rep 3

description:
Library name: NSCv_exo_rep3
CUT&Tag using anti-V5 antibody in Mecp2-overexpressing NPCs derived from E13.5 embryos.

value: wild-type

value: lentiviral transduction with Mecp2


title: House Dust Mite (HDM) 10 - 2 weeks - 3

description: Library name: MICE8


title: TSC differentiation into EVT, Control, KD, rep1

description: Library name: EVT_Cont_KD_rep1


title: PDAC004

description: PDAC

value: PDAC


title: CUT&Tag for endogenous MeCP2 in murine NPCs, EGFP control, biol rep 2

description:
Library name: NSCM_endo_rep2
CUT&Tag using anti-Mecp2 antibody in EGFP-transduced NPCs derived from E13.5 embryos.

value: telencephalon


title: PDAC002

description: PDAC


title: CUT&Tag for endogenous MeCP2 in murine NPCs, EGFP control, biol rep 1

description:
Library name: NSCM_endo_rep1
CUT&Tag using anti-Mecp2 antibody in EGFP-transduced NPCs derived from E13.5 embryos.

value: primary neuronal progenitor cells


title: CTRL081

description: Control

value: Control


title: House Dust Mite (HDM) 10 - 2 weeks - 2

description: Library name: MICE7

value: Lung


title: TSC differentiation into EVT, Control, KD, rep2

description: Library name: EVT_Cont_KD_rep2


title: TSC differentiation into EVT, TCF7L2, KD, rep2

description: Library name: EVT_TCF7L2_KD_rep2


title: CTRL082

description: Control


title: CUT&Tag for exogenous (V5-tagged) Mecp2 in murine NPCs, biol rep 1

description:
Library name: NSCv_exo_rep1
CUT&Tag using anti-V5 antibody in Mecp2-overexpressing NPCs derived from E13.5 embryos.


title: Cortex, Aldh1l1-Cre RVAff RVBff Pos, rep4

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

description: Library name: 54_aldh1l1_rvab

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.7.9a
Gene counts quantitated with Subread:featureCount 2.0.3 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: cortex

extract_protocol:
Purified RNA extracted from homogenized coritcal tissue using PureLink RNA extraction kit. 5-10 ug of total RNA was used for construction of sequencing libraries
RNA libraries were created using Poly-A selection

value: cortex

value: Aldh1l1-Cre.pos; Reverb.Alpha.fl/fl ; Reverb.Beta.fl/fl

value: Tamoxifen 4mg/day x 5 days at 2 months old via gavage


title: Cortex, Aldh1l1-Cre RVAff RVBff Neg control, rep4

description: Library name: 53_aldh1l1_rvab

value: Aldh1l1-Cre.neg; Reverb.Alpha.fl/fl ; Reverb.Beta.fl/fl


title: CTRL080

description: Control


title: TSC differentiation into EVT, TCF7L2, KD, rep3

description: Library name: EVT_TCF7L2_KD_rep3

value: Placenta

value: TSC-derived EVT

value: TSC differentiation into EVT


title: TSC differentiation into EVT, TCF7L2, KD, rep1

description: Library name: EVT_TCF7L2_KD_rep1


title: House Dust Mite (HDM) 10 - 2 weeks - 1

description: Library name: MICE6

value: wild type

value: 10 μg HDM treated lungs for 2 weeks


title: CTRL079

description: Control

value: Plasma

value: Diagnostic cohort


title: Cortex, Aldh1l1-Cre RVAff RVBff Neg control, rep3

description: Library name: 51_aldh1l1_rvab


title: CTRL077

description: Control


title: Cortex, Aldh1l1-Cre RVAff RVBff Pos, rep2

description: Library name: 50_aldh1l1_rvab


title: NaCl - 2 weeks - 1

description: Library name: MICE1

value: untreated lungs

value: 2 weeks


title: CTRL078

description: Control


title: CTRL076

description: Control


title: NaCl - 2 weeks - 2

description: Library name: MICE2


title: Cortex, Aldh1l1-Cre RVAff RVBff Pos, rep3

description: Library name: 52_aldh1l1_rvab


title: HeLa_Miliporem6A_rep1

city: Chicago

first: Chuan

last: He

address: 929 E 57th St., GCIS E319

institute: The University of Chicago

description: Library name: HeLa_Miliporem6A_rep1

data_processing:
The FASTQ file was trimmed using Cutadapt (v4.6) and aligned to ribosomal RNA (rRNA) sequences with Bowtie2 (v2.4.2) to filter out rRNA reads. The remaining non-rRNA reads were aligned to the reference genome using STAR (v2.7.3a), and PCR duplicates were removed with UMI-tools (v1.1.1).
Assembly: GRCh38.p13, GENCODE Release 39; GRCm38.p6, GENCODE Release M25
Supplementary files format and content: bigWig files

source_name: Cervical cancer

extract_protocol:
Cells were fixed with 1.5% paraformaldehyde for 10 minutes, quenched with 125 mM glycine at room temperature for 5 minutes, and permeabilized with 0.5% Triton X-100 on ice for 10 minutes. Samples were then blocked with 1 mg/ml BSA, followed by sequential staining with a primary antibody, a secondary antibody, and protein A/G-reverse transcriptase. In situ reverse transcription was performed at 37°C for 1 h. Subsequently, cells were digested with proteinase K at 37°C for 2 h. Total nucleic acids were extracted using phenol-chloroform and concentrated by ethanol precipitation.
Biotinylated cDNA was enriched using streptavidin beads. A 3' cDNA adapter (5′Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGT-3′SpC3) was ligated using T4 RNA ligase 1 by incubating at 25°C for 16 h. The cDNA was then recovered from the beads. The library was prepared through PCR amplification using NGS sequencing primers, followed by gel purification to isolate fragments between 180 bp and 400 bp.

value: Cervical cancer

value: HeLa

value: Cervical cancer cells

value: WT

value: m6A antibody (Millipore, Cat #ABE572-I-25ug)


title: HeLa_Miliporem6A_strongWash_rep2

description: Library name: HeLa_Miliporem6A_strongWash_rep2

value: strong washing strength


title: HeLa_Miliporem6A_mediumWash_rep1

description: Library name: HeLa_Miliporem6A_mediumWash_rep1

value: medium washing strength


title: Cortex, Aldh1l1-Cre RVAff RVBff Pos, rep1

description: Library name: 47_aldh1l1_rvab

value: cortex

value: Aldh1l1-Cre.pos; Reverb.Alpha.fl/fl ; Reverb.Beta.fl/fl

value: Tamoxifen 4mg/day x 5 days at 2 months old via gavage


title: HeLa_sysym6A_rep2

description: Library name: HeLa_sysym6A_rep2

value: m6A antibody (Synaptic Systems, Cat #202003)


title: CTRL074

description: Control

value: Control


title: CTRL075

description: Control


title: NaCl - 2 weeks - 5

description: Library name: MICE5

value: Lung

value: wild type


title: Raw264.7, wt-2

city: Xi'an

first: Jing

last: Geng

address: No.30 Huangcheng West Road, Xiwu Av (Administration, Teaching, Residential area

department: The Second Affiliated Hospital

institute: Xi’an Jiaotong University

description:
WT-2
wild type

data_processing:
The libraries were sequenced on an DNBSEQ-T7 platform and 150 bp paired-end reads were generated. About 49M raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
Then about 48M clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the reference genome using HISAT22. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: grcm38
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

growth_protocol: RAW264.7 cell lines were obtained from the National Collection of Authenticated Cell Cultures (Shanghai, China), tested for mycoplasma contamination and were found to be negative, then were cultured in DMEM supplemented with 10% FBS and 1× penicillin-streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: macrophage


title: NaCl - 2 weeks - 4

description: Library name: MICE4

value: untreated lungs


title: Cortex, Aldh1l1-Cre RVAff RVBff Neg control, rep1

description: Library name: 45_aldh1l1_rvab

value: Aldh1l1-Cre.neg; Reverb.Alpha.fl/fl ; Reverb.Beta.fl/fl


title: HeLa_sysym6A_rep1

description: Library name: HeLa_sysym6A_rep1

value: Cervical cancer


title: Raw264.7, wt-1

description:
WT-1
wild type


title: CTRL073

description: Control

value: Plasma

value: Diagnostic cohort


title: NaCl - 2 weeks - 3

description: Library name: MICE3

value: 2 weeks


title: CTRL072

description: Control


title: HeLa_CSTm6A_rep2

description: Library name: HeLa_CSTm6A_rep2

value: HeLa

value: Cervical cancer cells

value: WT

value: m6A antibody (CST,Cat #56593)


title: Raw264.7, OE-Calhm6iso-2

description:
C6iso3-2
overexpression of Calhm6 isoform


title: HeLa_Miliporem6A_rep2

description: Library name: HeLa_Miliporem6A_rep2

value: m6A antibody (Millipore, Cat #ABE572-I-25ug)


title: Cortex, CAG-Cre Neg RVAff, rep3

description: Library name: 837

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

value: cortex

value: CAG-Cre.neg; Reverb.Alpha.fl/fl

value: Tamoxifen 4mg/day x 5 days at 2 months


title: Cortex, CAG-Cre Neg RVAff, rep5

description: Library name: 844


title: HeLa_IgG_rep1

description: Library name: HeLa_IgG_rep1

value: IgG


title: CTRL070

description: Control

value: Control