title: CDX, HuCC-A1 CLDN1 KO, rep4

description: Library name: CDX_A1_KO214


title: CDX, HuCC-A1 CLDN1 KO, rep3

status: Public on Jun 08 2026

type: SRA

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

description: Library name: CDX_A1_KO213

library_source: transcriptomic

data_processing:
Base calling was performed by CASAVA and raw data was stored in FASTQ format.
Raw reads were filtered to remove reads with (I) adapter contamination, (II) more than 10 % uncertain nucleotides (Ns), and (III) with more than 50 % of low quality nucleotides (base quality less than 5).
Reads were mapped using HISAT2 v2.2.1 to the human genome GRCh38.
FeatureCounts v2.0.6 was used to generate gene counts.
Assembly: GRCh38
Supplementary files format and content: Tabulator separated matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Cell line-Derived Xenograft

extract_protocol:
RNA was extracted using Triazol
RNA-Seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA)

treatment_protocol: Mice were engrafted with HuCC-A1 CLDN1 KO cells or CTRL cells

tag: tissue

value: Cell line-Derived Xenograft

tag: cell line

tag: cell type

value: HuCC-A1 CLDN1 KO


title: CDX, HuCC-A1 CLDN1 KO, rep2

description: Library name: CDX_A1_KO212


title: CDX, HuCC-A1 CLDN1 KO, rep1

description: Library name: CDX_A1_KO211


title: CDX, HuCC-A1 control, rep6

description: Library name: CDX_A1_CT208

value: HuCC-A1 CTRL


title: CDX, HuCC-A1 control, rep5

description: Library name: CDX_A1_CT207


title: CDX, HuCC-A1 control, rep3

description: Library name: CDX_A1_CT204


title: E10NNAR

city: Montreal

first: Sahel

last: Jahangiri Esfahani

address: 3775 University Street

country: Canada

institute: McGill

description: Library name: NS.1911.003.NEBNext_dual_i7_238---NEBNext_dual_i5_286.E10NNAR

data_processing:
Neutrophil RNA-seq reads were aligned to the human genome GRCh37/hg19 using STAR. Differential gene expression and interaction-term analyses were performed in R using DESeq2, with age, sex, and BMI included as covariates.
Assembly: GRCh37/hg19
Supplementary files format and content: TPM

molecule: polyA RNA

source_name: Neutrophil from peripheral blood

extract_protocol:
Peripheral blood was collected from participants and neutrophils were isolated directly from whole blood using the MACSxpress Whole Blood Neutrophil Isolation Kit (Miltenyi Biotec) according to the manufacturer's instructions. Isolated neutrophils were counted using a Cellometer Auto T4 (Nexcelom) and resuspended at a concentration of 1 × 10⁶ cells/mL in RPMI-1640 complete medium supplemented with 2 mM L-glutamine, 10% fetal bovine serum (FBS), and 1% penicillin/streptomycin. Cells were plated in 24-well plates (1 mL per well). For inflammatory stimulation, 100 μL of LPS solution (110 ng/mL) was added to designated wells to achieve a final concentration of 10 ng/mL LPS, while control wells received an equal volume of culture medium. Cells were incubated for 1 hour at 37°C and 5% CO₂. Following incubation, neutrophils were collected, centrifuged at 300 × g for 5 minutes at room temperature, and lysed in 650 μL RLT buffer (QIAGEN) supplemented with β-mercaptoethanol (10 μL of 14.5 M β-ME per mL RLT buffer). Lysates were stored at −80°C until RNA extraction.
Total RNA was extracted using the QIAGEN AllPrep DNA/RNA Mini Kit, and libraries were sequenced at the McGill Genome Quebec Centre on an Illumina NovaSeq 6000 platform with a target depth of approximately 30 million reads per sample.

value: Neutrophil from peripheral blood

value: Neutrophil

tag: treatment


title: CDX, HuCC-A1 control, rep4

description: Library name: CDX_A1_CT205


title: CDX, HuCC-A1 control, rep2

description: Library name: CDX_A1_CT202


title: CDX, HuCC-A1 control, rep1

description: Library name: CDX_A1_CT201


title: HuCC-A1, CLDN1-KO, rep2

description: Library name: A1_KO_2

growth_protocol: HuCC-A1 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 1% non-essential amino acids (Gibco) and 0.5% gentamicin (Gibco). Cells were maintained in a humidified incubator at 37 °C and 5% CO2. Cells between passage 3 and 20 were used for all experiments.

extract_protocol:
Cells were harvested for RNA extraction using PicoPure™ RNA Isolation Kit (#KIT0204, Applied Biosystems™) according to the manufacturer’s instructions
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

treatment_protocol: HuCC-A1 were first transduced with cas9 lentivirus and then selected using Blasticidin (8 µg/ml). After selection, a second transduction has been performed using single guide RNA (sg-CTRL) or sgRNA targeting CLDN1 gene expression (sg-CLDN1). Transduced cells were selected under Hygromycin treatment (300 μg/ml). Expression plasmids were provided by Dr. David Root (Broad Institute of Harvard and MIT, Cambridge, USA). Cells were then single-cell sorted, and the resulting clones were named HuCC-A1 sg-CTRL, HuCC-A1 CLDN1 KO

value: Cholangiocarcinoma

tag: genotype

value: CLDN1 knockout


title: HuCC-A1, CLDN1-KO, rep3

description: Library name: A1_KO_3


title: E05NNAR

description: Library name: NS.1911.003.NEBNext_dual_i7_267---NEBNext_dual_i5_219.E05NNAR


title: HuCC-A1, CLDN1-KO, rep1

description: Library name: A1_KO_1


title: E10NAR

description: Library name: NS.1911.003.NEBNext_dual_i7_245---NEBNext_dual_i5_197.E10NAR


title: HuCC-A1, control, rep3

description: Library name: A1_CTRL_3

value: Control


title: HuCC-A1, control, rep2

description: Library name: A1_CTRL_2


title: HuCC-A1, control, rep1

description: Library name: A1_CTRL_1


title: E04NNAR

description: Library name: NS.1911.002.NEBNext_dual_i7_179---NEBNext_dual_i5_179.E04NNAR


title: 013_Week_8

city: Rochester

first: Emma

last: Durrenberger

state: Minnesota

address: 200 First St SW

department: Quantitative Health Sciences

country: USA

institute: Mayo Clinic

description:
Library name: sample_54
ST-01902613_Week_8

data_processing:
Libraries were multiplexed and sequenced in a single lane using the standard protocol for the Illumina NovaSeq 6000 and the NovaSeq XP 4-Lane kit for individual lane loading. The flow cell was sequenced as 100 X 2 paired-end reads using the NovaSeq S4 sequencing kit and NovaSeq Control Software v1.8.0. Base-calling was performed with Illumina’s RTA version 3.4.4.
The raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.5. MAP-RSeq uses STAR to align reads to the reference human genome build hg38. Gene and exon expression quantification were performed using the Subread package to obtain both raw and normalized (FPKM – Fragments Per Kilobase per Million mapped reads) reads. Finally, comprehensive analyses were run on the aligned reads to assess the quality of the sequenced libraries.
Assembly: hg38
Supplementary files format and content: merged_gene_count.tsv tsv file containing merged raw gene counts for all samples
Supplementary files format and content: merged_gene_count_fpkm_by_read.tsv tsv file containing gene count fpkm by read for all samples

source_name: blood

extract_protocol:
Total RNA concentration and quality were determined using Qubit fluorometry (ThermoFisher Scientific, Waltham, MA) and the Agilent Fragment Analyzer (Santa Clara, CA). The total RNA underwent globin depletion using GLOBINclear (ThermoFisher Scientific, Waltham, MA) and a clean-up with DNase I (Zymo Research, Irvine, CA) treatment.
cDNA libraries were prepared using 100 ng of total RNA according to the manufacturer’s instructions for the Illumina Stranded mRNA Prep, Ligation (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries were determined with the Agilent TapeStation and Qubit fluorometry.

value: blood

value: PBMCs

tag: time point


title: p5-Ph-IAA_R1-3369888_SMF107

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

country: China

institute: Soochow University

description: Library name: sample 4

library_source: genomic

data_processing:
Paired-end 50-cycle sequencing was performed on NovaSeq6000 sequencer following the manufacturer’s instructions (Illumina) Raw reads were first trimmed using TrimGalore (v0.6.3). Filtered reads are then aligned the Homo sapiens reference genome GRCh38 using BWA (0.7.17-r1188).
Duplicated reads are then marked using the “bamsormadup” function from the biobambam2 tool (v2.0.87) PCR duplicates and low mapping quality reads (MAPQ < 1) were removed using samtools (version 1.9, parameter ‘-q 1 -F 1024’).
The uniquely mapped reads were then used to estimate the average fragment length in each sample based on the cross-correlation profile calculated from SPP (v1.11) [PMID:19029915]. The smallest fragment size estimated by SPP was used to center and extend reads to generate bigwig files. The bigiwig signal in all samples is scaled to 15 million reads (ie: scaling-factor=15e6/libSize).
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: Blood

growth_protocol: SEM cells were grown in RPMI-1640 with L-Glutamine (Cellgro) containing 10% fetal bovine serum (FBS) (Hyclone) and 1% penicillin/ streptomycin (Thermo Fisher Scientific). The cells maintained at 37 Celsius, 5% CO2.

extract_protocol:
Following HaloTag ChIP and wash steps, DNA was de-crosslinked and eluted from HaloLink resin (Promega) by 1X TE , 1% SDS, proteinase K, and 400 mM NaCl at 65 °C for 4 hours. DNA was purified by phenol:chloroform:isoamyl precipitation.
Libraries were constructed using NEBNext Ultra II NEB Library Prep Kit and NEBNext Multiplex oligos (Illumina).

treatment_protocol: Cells were treated with 1uM 5-Ph-IAA (Abcam) or DMSO for 24 hours.

value: Blood

value: SEM

value: cell line

value: AID-RBM5 fusion protein

value: RBM5 KO


title: SMF101_input-3369882_SMF101

description: Library name: sample 1


title: m5-Ph-IAA_R1-3369883_SMF102

description: Library name: sample 2


title: m5-Ph-IAA_R2-3369884_SMF103

description: Library name: sample 3


title: RNA-seq: GFP control stable transfection Rep 3

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: Library name: RNA_CL0038_GFP_RepC_E005964

data_processing:
RNA-seq reads were mapped to the hg38 genome using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon).
Transcription abundance estimates were generated by Salmon
Assembly: hg38
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10. The reads aligned to the forward strand were processed separately from the reads aligned to the reverse strand. The parameter --scaleFactor -1 was used when generating the reads on the reverse strand.

growth_protocol: Flp-In-293 cells were plated on 6 well plates in DMEM supplemented with 10% FBS, 0.1% Anti-anti, and 0.2% normocin. Two days later, the cells were transfected using Lipofectamine 2000, according to the manufacturer’s protocol, with 0.25 µg of vTR plasmid and 2.25 mg of the pOG44 Flp-Recombinase expression vector. Within three days, the media was changed to media containing hygromycin at 50 mg/mL and the hygromycin was gradually increased to 200 mg/mL to produce a pool of cells stably expressing the vTR. Doxycycline inducible Flp-In T-REx-293 cells were cultured in media also containing 100µg/mL zeocin. These cells were cultured in 1µg/mL doxycycline for overnight prior to collection.

extract_protocol:
Total RNA was isolated using the mirVana RNA extraction kit
rRNA depleted, stranded libraries were generated by the sequencing center. Samples were sequenced at either Novogene or the Cincinnati Children’s Hospital Medical Center Genomics Sequencing Facility (CCHMC)

tag: transfection type

value: Stable cell line

tag: transfection plasmid

value: GFP control

tag: sequencing center

value: CCHMC


title: 023_Week_4

description:
Library name: sample_50
023_Week_4


title: RNA-seq: GFP control stable transfection Rep 2

description: Library name: RNA_CL0038_GFP_RepB_E005963


title: p5-Ph-IAA_R2-3369887_SMF106

description: Library name: sample 5


title: RNA-seq: GFP control transient transfection (Novogene) Rep 1

description: Library name: RNA_GFP_only_Novogene_RepA_E04808

value: Transient transfection

value: Novogene


title: RNA-seq: GFP control transient transfection (Novogene) Rep 2

description: Library name: RNA_GFP_only_Novogene_RepB_E04809


title: RNA-seq: GFP control transient transfection (Novogene) Rep 3

description: Library name: RNA_GFP_only_Novogene_RepC_E04810


title: RNA-seq: GFP control stable transfection Rep 1

description: Library name: RNA_CL0038_GFP_RepA_E005962


title: RNA-seq: Puromycin control transient transfection (Novogene) Rep 3

description: Library name: RNA_puro_only_Novogene_RepC_E05668

value: puromycin control


title: RNA-seq: Puromycin control transient transfection (Novogene) Rep 2

description: Library name: RNA_puro_only_Novogene_RepB_E05667


title: RNA-seq: Puromycin control transient transfection (Novogene) Rep 1

description: Library name: RNA_puro_only_Novogene_RepA_E05666


title: RNA-seq: cGFP tagged RTA stable transfection Rep 3

description: Library name: RNA_CL0062_RTA_RepC_E005941

value: cGFP tagged RTA


title: RNA-seq: nGFP tagged EBNA3C stable transfection Rep 2

description: Library name: RNA_CL0057_EBNA3C_RepB_E005960

value: nGFP tagged EBNA3C


title: RNA-seq: nGFP tagged EBNA3C stable transfection Rep 3

description: Library name: RNA_CL0057_EBNA3C_RepC_E005961


title: RNA-seq: cGFP tagged RTA stable transfection Rep 2

description: Library name: RNA_CL0062_RTA_RepB_E005940


title: RNA-seq: cGFP tagged RTA stable transfection Rep 1

description: Library name: RNA_CL0062_RTA_RepA_E005939


title: RNA-seq: nGFP tagged EBNA3C stable transfection Rep 1

description: Library name: RNA_CL0057_EBNA3C_RepA_E005959


title: RNA-seq: nGFP tagged EBNA3B stable transfection Rep 3

description: Library name: RNA_CL0055_EBNA3B_RepC_E005958

value: nGFP tagged EBNA3B


title: RNA-seq: nGFP tagged EBNA3B stable transfection Rep 2

description: Library name: RNA_CL0055_EBNA3B_RepB_E005957


title: RNA-seq: nGFP tagged EBNA3A stable transfection Rep 3

description: Library name: RNA_CL0053_EBNA3A_RepC_E005955

value: nGFP tagged EBNA3A


title: RNA-seq: nGFP tagged EBNA3B stable transfection Rep 1

description: Library name: RNA_CL0055_EBNA3B_RepA_E005956


title: RNA-seq: nGFP tagged EBNA3A stable transfection Rep 2

description: Library name: RNA_CL0053_EBNA3A_RepB_E005954


title: RNA-seq: nGFP tagged EBNA2 stable transfection Rep 3

description: Library name: RNA_CL0041_EBNA2_RepC_E005952

value: nGFP tagged EBNA2


title: RNA-seq: nGFP tagged EBNA2 stable transfection Rep 1

description: Library name: RNA_CL0041_EBNA2_RepA_E005950


title: RNA-seq: nGFP tagged EBNA3A stable transfection Rep 1

description: Library name: RNA_CL0053_EBNA3A_RepA_E005953


title: RNA-seq: nGFP tagged EBNA2 stable transfection Rep 2

description: Library name: RNA_CL0041_EBNA2_RepB_E005951


title: RNA-seq: untagged BVLF1 transient transfection Rep 3

description: Library name: RNA_BVLF1_only_RepC_E006245

value: untagged BVLF1


title: RNA-seq: untagged BVLF1 transient transfection Rep 2

description: Library name: RNA_BVLF1_only_RepB_E006246


title: 019_Week_12

description:
Library name: sample_38
019_Week_12

value: blood

value: PBMCs


title: 017_Week_12

description:
Library name: sample_35
017_Week_12


title: RNA-seq: untagged BVLF1 transient transfection Rep 1

description: Library name: RNA_BVLF1_only_RepA_E006247


title: RNA-seq: untagged BGLF3 transient transfection Rep 3

description: Library name: RNA_BGLF3_only_RepC_E006248

value: untagged BGLF3


title: RNA-seq: untagged BFRF2 transient transfection Rep 3

description: Library name: RNA_BFRF2_only_RepC_E006251

value: untagged BFRF2


title: RNA-seq: untagged BFRF2 transient transfection Rep 2

description: Library name: RNA_BFRF2_only_RepB_E006252


title: RNA-seq: untagged BGLF3 transient transfection Rep 2

description: Library name: RNA_BGLF3_only_RepB_E006249


title: RNA-seq: untagged BGLF3 transient transfection Rep 1

description: Library name: RNA_BGLF3_only_RepA_E006250


title: RNA-seq: untagged BFRF2 transient transfection Rep 1

description: Library name: RNA_BFRF2_only_RepA_E006253


title: RNA-seq: untagged BDLF4 transient transfection Rep 2

description: Library name: RNA_BDLF4_only_RepB_E006255

value: untagged BDLF4


title: RNA-seq: untagged BDLF4 transient transfection Rep 1

description: Library name: RNA_BDLF4_only_RepA_E006256


title: RNA-seq: untagged BDLF3 transient transfection Rep 1

description: Library name: RNA_BDLF3_only_RepA_E006259

value: untagged BDLF3


title: RNA-seq: untagged BCRF1 transient transfection Rep 3

description: Library name: RNA_BCRF1_only_RepC_E006260

value: untagged BCRF1


title: RNA-seq: untagged BALF2 transient transfection Rep 1

description: Library name: RNA_BALF2_only_RepA_E006265

value: untagged BALF2

value: CCHMC


title: RNA-seq: untagged ZTA transient transfection Rep 3

description: Library name: RNA_ZTA_only_RepC_E004953

value: Transient transfection

value: untagged ZTA

value: Novogene


title: RNA-seq: untagged BCRF1 transient transfection Rep 2

description: Library name: RNA_BCRF1_only_RepB_E006261


title: RNA-seq: untagged ZTA transient transfection Rep 2

description: Library name: RNA_ZTA_only_RepB_E004952


title: RNA-seq: untagged ZTA transient transfection Rep 1

description: Library name: RNA_ZTA_only_RepA_E004951


title: RNA-seq: nGFP tagged ZTA transient transfection Rep 3

description: Library name: RNA_ZTA_nGFP_RepC_E004956

value: nGFP tagged ZTA


title: RNA-seq: nGFP tagged ZTA transient transfection Rep 1

description: Library name: RNA_ZTA_nGFP_RepA_E004954


title: RNA-seq: untagged RTA transient transfection Rep 3

description: Library name: RNA_RTA_only_RepC_E004962

value: untagged RTA


title: RNA-seq: cGFP tagged ZTA transient transfection Rep 2

description: Library name: RNA_ZTA_cGFP_RepB_E004958

value: cGFP tagged ZTA


title: RNA-seq: cGFP tagged ZTA transient transfection Rep 1

description: Library name: RNA_ZTA_cGFP_RepA_E004957


title: RNA-seq: untagged RTA transient transfection Rep 2

description: Library name: RNA_RTA_only_RepB_E004961


title: RNA-seq: untagged RTA transient transfection Rep 1

description: Library name: RNA_RTA_only_RepA_E004960


title: RNA-seq: nGFP tagged RTA transient transfection Rep 2

description: Library name: RNA_RTA_nGFP_RepB_E004964

value: nGFP tagged RTA


title: RNA-seq: nGFP tagged RTA transient transfection Rep 1

description: Library name: RNA_RTA_nGFP_RepA_E004963


title: RNA-seq: cGFP tagged RTA transient transfection Rep 3

description: Library name: RNA_RTA_cGFP_RepC_E004965

value: cGFP tagged RTA


title: RNA-seq: cGFP tagged RTA transient transfection Rep 2

description: Library name: RNA_RTA_cGFP_RepB_E004967


title: RNA-seq: cGFP tagged RTA transient transfection Rep 1

description: Library name: RNA_RTA_cGFP_RepA_E004966


title: RNA-seq: untagged EBNALP transient transfection Rep 2

description: Library name: RNA_EBNALP_only_RepB_E006025

value: untagged EBNALP


title: RNA-seq: untagged EBNALP transient transfection Rep 1

description: Library name: RNA_EBNALP_only_RepA_E006024


title: RNA-seq: untagged EBNALP transient transfection Rep 3

description: Library name: RNA_EBNALP_only_RepC_E006026


title: RNA-seq: nGFP tagged EBNALP transient transfection Rep 2

description: Library name: RNA_EBNALP_nGFP_RepB_E006028

value: nGFP tagged EBNALP


title: RNA-seq: nGFP tagged EBNALP transient transfection Rep 1

description: Library name: RNA_EBNALP_nGFP_RepA_E006027


title: RNA-seq: untagged EBNA3C transient transfection Rep 2

description: Library name: RNA_EBNA3C_only_RepB_E05664

value: untagged EBNA3C


title: RNA-seq: untagged EBNA3C transient transfection Rep 3

description: Library name: RNA_EBNA3C_only_RepC_E05665


title: RNA-seq: nGFP tagged EBNA3C transient transfection Rep 2

description: Library name: RNA_EBNA3C_nGFP_RepB_E05658

value: nGFP tagged EBNA3C


title: RNA-seq: cGFP tagged EBNA3C transient transfection Rep 3

description: Library name: RNA_EBNA3C_cGFP_RepC_E05662

value: cGFP tagged EBNA3C


title: RNA-seq: cGFP tagged EBNA3C transient transfection Rep 2

description: Library name: RNA_EBNA3C_cGFP_RepB_E05661


title: RNA-seq: untagged EBNA3B transient transfection Rep 2

description: Library name: RNA_EBNA3B_only_RepB_E04943

value: untagged EBNA3B


title: RNA-seq: untagged EBNA3B transient transfection Rep 3

description: Library name: RNA_EBNA3B_only_RepC_E04944


title: RNA-seq: untagged EBNA3B transient transfection Rep 1

description: Library name: RNA_EBNA3B_only_RepA_E04942


title: RNA-seq: nGFP tagged EBNA3B transient transfection Rep 2

description: Library name: RNA_EBNA3B_nGFP_RepB_E04946

value: nGFP tagged EBNA3B


title: RNA-seq: nGFP tagged EBNA3B transient transfection Rep 3

description: Library name: RNA_EBNA3B_nGFP_RepC_E04947


title: RNA-seq: nGFP tagged EBNA3B transient transfection Rep 1

description: Library name: RNA_EBNA3B_nGFP_RepA_E04945


title: RNA-seq: cGFP tagged EBNA3B transient transfection Rep 1

description: Library name: RNA_EBNA3B_cGFP_RepA_E04948

value: cGFP tagged EBNA3B


title: RNA-seq: untagged EBNA3A transient transfection Rep 3

description: Library name: RNA_EBNA3A_only_RepC_E05656

value: untagged EBNA3A


title: RNA-seq: untagged EBNA3A transient transfection Rep 2

description: Library name: RNA_EBNA3A_only_RepB_E05655

value: Transient transfection


title: RNA-seq: nGFP tagged EBNA3A transient transfection Rep 3

description: Library name: RNA_EBNA3A_nGFP_RepC_E05653

value: nGFP tagged EBNA3A


title: RNA-seq: untagged EBNA3A transient transfection Rep 1

description: Library name: RNA_EBNA3A_only_RepA_E05654

value: Novogene


title: RNA-seq: nGFP tagged EBNA3A transient transfection Rep 2

description: Library name: RNA_EBNA3A_nGFP_RepB_E05652


title: RNA-seq: nGFP tagged EBNA3A transient transfection Rep 1

description: Library name: RNA_EBNA3A_nGFP_RepA_E05651


title: paya_mng_288

type: genomic

city: Heidelberg

first: Philipp

last: Sievers

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description: PAYA MNG

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
Average Beta
Unmethylated and methylated signal intensities

label: cy3, cy5

source_name: PAYA MNG

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE

tag: Sex

value: Male

tag: age group

tag: methylation class

value: int

tag: localisation


title: RNA-seq: cGFP tagged EBNA3A transient transfection Rep 3

description: Library name: RNA_EBNA3A_cGFP_RepC_E05650

value: cGFP tagged EBNA3A


title: paya_mng_286

description: PAYA MNG

value: Female

value: ben

value: supratentoriell


title: paya_mng_285

description: PAYA MNG

value: skull base


title: RNA-seq: untagged EBNA1 transient transfection Rep 3

description: Library name: RNA_EBNA1_only_RepC_E006020

value: untagged EBNA1

value: CCHMC


title: paya_mng_284

description: PAYA MNG


title: RNA-seq: cGFP tagged EBNA3A transient transfection Rep 1

description: Library name: RNA_EBNA3A_cGFP_RepA_E05648


title: RNA-seq: untagged EBNA1 transient transfection Rep 2

description: Library name: RNA_EBNA1_only_RepB_E006019


title: paya_mng_283

description: PAYA MNG

value: posterior fossa


title: paya_mng_277

description: PAYA MNG


title: RNA-seq: nGFP tagged EBNA1 transient transfection Rep 3

description: Library name: RNA_EBNA1_nGFP_RepC_E006023

value: nGFP tagged EBNA1


title: paya_mng_274

description: PAYA MNG


title: paya_mng_270

description: PAYA MNG


title: RNA-seq: nGFP tagged EBNA1 transient transfection Rep 1

description: Library name: RNA_EBNA1_nGFP_RepA_E006021


title: RNA-seq: cGFP tagged EBNA1 transient transfection Rep 3

description: Library name: RNA_EBNA1_cGFP_RepC_E006136

value: cGFP tagged EBNA1


title: paya_mng_267

description: PAYA MNG


title: RNA-seq: cGFP tagged EBNA1 transient transfection Rep 2

description: Library name: RNA_EBNA1_cGFP_RepB_E006135


title: paya_mng_266

description: PAYA MNG


title: RNA-seq: cGFP tagged EBNA1 transient transfection Rep 1

description: Library name: RNA_EBNA1_cGFP_RepA_E006134


title: paya_mng_265

description: PAYA MNG


title: ChIP-seq: anti-GFP in GFP control stable transfection Rep 3

description: Library name: ChIP_CL0038_GFP_RepC_E006150

data_processing:
ChIP-seq alignment, quality control, and peak calling was performed using a version of the ChIP-Seq Transcription Factor Pipeline v2.2.0 from the ENCODE Project slightly modified to run within a Nextflow environment.
ChIP-seq reads were aligned to the human genome (hg38) using Bowtie2. Aligned reads were then sorted using samtools and duplicate reads were removed using Picard.
Peaks were called using the default parameters of MACS2.
Conservative overlap peaks, generated from the ENCODE pipeline, were obtained for each transfection plasmid and used for downstream analyses.
Assembly: hg38
Supplementary files format and content: Conservative overlap peaks in narrowPeak format.
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10

extract_protocol:
Cells were crosslinked and nuclei were sonicated as described previously (Lu et al. 2015).
Libraries were prepared via ChIPmentation (Schmidl et al. 2015).

value: GFP control

tag: chip target

value: GFP

tag: antibody

value: Abcam ab290

tag: antibody lot_number


title: ChIP-seq: anti-GFP in GFP control stable transfection Rep 2

description: Library name: ChIP_CL0038_GFP_RepB_E006149


title: paya_mng_258

description: PAYA MNG


title: paya_mng_264

description: PAYA MNG


title: RNA-seq: untagged BDLF3 transient transfection Rep 2

description: Library name: RNA_BDLF3_only_RepB_E006258

value: Transient transfection

value: untagged BDLF3


title: RNA-seq: untagged BCRF1 transient transfection Rep 1

description: Library name: RNA_BCRF1_only_RepA_E006262

value: untagged BCRF1


title: RNA-seq: untagged BALF2 transient transfection Rep 2

description: Library name: RNA_BALF2_only_RepC_E006263

value: untagged BALF2


title: RNA-seq: nGFP tagged ZTA transient transfection Rep 2

description: Library name: RNA_ZTA_nGFP_RepB_E004955

value: nGFP tagged ZTA

value: Novogene


title: paya_mng_254

description: PAYA MNG

value: FFPE

value: Female

value: ben


title: RNA-seq: nGFP tagged RTA transient transfection Rep 3

description: Library name: RNA_RTA_nGFP_RepC_E004968

value: nGFP tagged RTA


title: ChIP-seq: anti-GFP in cGFP tagged RTA stable transfection Rep 3

description: Library name: ChIP_CL0062_RTA_RepF_E006273

value: cGFP tagged RTA


title: ChIP-seq: anti-GFP in GFP control stable transfection Rep 1

description: Library name: ChIP_CL0038_GFP_RepA_E006148


title: ChIP-seq: anti-GFP in cGFP tagged RTA stable transfection Rep 2

description: Library name: ChIP_CL0062_RTA_RepE_E006272


title: paya_mng_255

description: PAYA MNG

value: mal

value: supratentoriell


title: paya_mng_253

description: PAYA MNG

value: int

value: skull base


title: RNA-seq: untagged EBNA3C transient transfection Rep 1

description: Library name: RNA_EBNA3C_only_RepA_E05663

value: untagged EBNA3C


title: RNA-seq: nGFP tagged EBNA3C transient transfection Rep 3

description: Library name: RNA_EBNA3C_nGFP_RepC_E05659

value: nGFP tagged EBNA3C


title: ChIP-seq: anti-GFP in cGFP tagged RTA stable transfection Rep 1

description: Library name: ChIP_CL0062_RTA_RepD_E006271

value: GFP

value: Abcam ab290


title: RNA-seq: nGFP tagged EBNALP transient transfection Rep 3

description: Library name: RNA_EBNALP_nGFP_RepC_E006029

value: Transient transfection

value: nGFP tagged EBNALP

value: CCHMC


title: ChIP-seq: anti-GFP in nGFP tagged EBNA3B stable transfection Rep 2

description: Library name: ChIP_CL0055_EBNA3B_RepF_E006106

value: nGFP tagged EBNA3B


title: paya_mng_243

description: PAYA MNG

value: FFPE

value: posterior fossa


title: RNA-seq: nGFP tagged EBNA3C transient transfection Rep 1

description: Library name: RNA_EBNA3C_nGFP_RepA_E05657

value: Novogene


title: paya_mng_244

description: PAYA MNG

value: Male

value: ben


title: ChIP-seq: anti-GFP in nGFP tagged EBNA3B stable transfection Rep 1

description: Library name: ChIP_CL0055_EBNA3B_RepD_E006104


title: paya_mng_239

description: PAYA MNG

value: Female


title: paya_mng_238

description: PAYA MNG

value: supratentoriell


title: ChIP-seq: anti-GFP in nGFP tagged EBNA3A stable transfection Rep 3

description: Library name: ChIP_CL0053_EBNA3A_RepF_E006103

value: nGFP tagged EBNA3A


title: paya_mng_232

description: PAYA MNG

value: int

value: ventricel


title: RNA-seq: cGFP tagged EBNA3C transient transfection Rep 1

description: Library name: RNA_EBNA3C_cGFP_RepA_E05660

value: cGFP tagged EBNA3C


title: ChIP-seq: anti-GFP in nGFP tagged EBNA3A stable transfection Rep 1

description: Library name: ChIP_CL0053_EBNA3A_RepD_E006101

value: GFP


title: paya_mng_229

description: PAYA MNG


title: CDX, HuCC-A1, H3L3 48h, batch2, rep3

description: Library name: H3L348h_2_3

data_processing:
Base calling was performed by CASAVA and raw data was stored in FASTQ format.
Raw reads were filtered to remove reads with (I) adapter contamination, (II) more than 10 % uncertain nucleotides (Ns), and (III) with more than 50 % of low quality nucleotides (base quality less than 5).
Reads were mapped using HISAT2 v2.0.5 to the human genome GRCh38.
FeatureCounts v1.5.0-p3 was used to generate gene counts.
Assembly: GRCh38
Supplementary files format and content: Tabulator separated matrix table with raw gene counts for every gene and every sample

treatment_protocol: Mice were treated with CLDN1 mAb (25 mg/kg i.p.,), or with vehicle control (PBS i.p. ) for 48h

tag: tissue

value: Cell line-Derived Xenograft

value: H3L3 anti-Cldn1 mAb 48h

tag: batch


title: ChIP-seq: anti-GFP in nGFP tagged EBNA3A stable transfection Rep 2

description: Library name: ChIP_CL0053_EBNA3A_RepE_E006102

tag: cell line

value: Abcam ab290


title: paya_mng_227

description: PAYA MNG

value: mal


title: RNA-seq: cGFP tagged EBNA3B transient transfection Rep 3

description: Library name: RNA_EBNA3B_cGFP_RepC_E04950

value: Transient transfection

value: cGFP tagged EBNA3B


title: CDX, HuCC-A1, H3L3 48h, batch2, rep2

description: Library name: H3L348h_2_2

tag: treatment


title: paya_mng_218

description: PAYA MNG

value: FFPE

value: skull base


title: RNA-seq: cGFP tagged EBNA3B transient transfection Rep 2

description: Library name: RNA_EBNA3B_cGFP_RepB_E04949

value: Novogene


title: CDX, HuCC-A1, H3L3 48h, batch2, rep1

description: Library name: H3L348h_2_1


title: CDX, HuCC-A1, H3L3 48h, batch1, rep3

description: Library name: H3L348h_1_3


title: paya_mng_214

description: PAYA MNG

value: ben


title: paya_mng_212

description: PAYA MNG

value: Female

value: spinal


title: CDX, HuCC-A1, H3L3 48h, batch1, rep2

description: Library name: H3L348h_1_2


title: paya_mng_210

description: PAYA MNG

value: Male

value: supratentoriell


title: paya_mng_209

description: PAYA MNG


title: CDX, HuCC-A1, Isotype 48h, batch2, rep1

description: Library name: Ctrl48h_2_1

value: Vehicle control 48h


title: paya_mng_205

description: PAYA MNG

value: posterior fossa


title: paya_mng_204

description: PAYA MNG


title: paya_mng_202

description: PAYA MNG


title: CDX, HuCC-A1, Isotype 48h, batch1, rep3

description: Library name: Ctrl48h_1_3


title: CDX, HuCC-A1, Isotype 48h, batch1, rep2

description: Library name: Ctrl48h_1_2


title: paya_mng_197

description: PAYA MNG


title: CDX, HuCC-T1, rep5

description: Library name: T1_PBS259_5

treatment_protocol: Mice wereinjected with vehicle control (PBS i.p. once per week,n= 5 mice) for 6 weeks (HuCC-A1 CDX) or 4 weeks (EGI-1 CDX)

value: PBS


title: CDX, HuCC-A1, Isotype 48h, batch1, rep1

description: Library name: Ctrl48h_1_1

value: Cell line-Derived Xenograft


title: CDX, HuCC-T1, rep4

description: Library name: T1_PBS258_4


title: CDX, HuCC-T1, rep3

description: Library name: T1_PBS256_3


title: paya_mng_182

description: PAYA MNG


title: CDX, HuCC-T1, rep2

description: Library name: T1_PBS251_2


title: paya_mng_183

description: PAYA MNG


title: CDX, HuCC-T1, rep1

description: Library name: T1_PBS250_1


title: paya_mng_165

description: PAYA MNG

value: int


title: CDX, EGI-1, rep4

description: Library name: EGICDX_PBS4


title: paya_mng_163

description: PAYA MNG


title: CDX, EGI-1, rep3

description: Library name: EGICDX_PBS3


title: paya_mng_141

description: PAYA MNG


title: CDX, EGI-1, rep2

description: Library name: EGICDX_PBS2


title: paya_mng_124

description: PAYA MNG


title: CDX, EGI-1, rep1

description: Library name: EGICDX_PBS1


title: CDX, HuCC-A1, rep5

description: Library name: A1_PBS67_5


title: paya_mng_106

description: PAYA MNG


title: CDX, HuCC-A1, rep4

description: Library name: A1_PBS52_4


title: paya_mng_105

description: PAYA MNG


title: CDX, HuCC-A1, rep3

description: Library name: A1_PBS64_3


title: paya_mng_097

description: PAYA MNG

value: tentorial


title: CDX, HuCC-A1, rep2

description: Library name: A1_PBS632_2


title: paya_mng_096

description: PAYA MNG


title: CDX, HuCC-A1, rep1

description: Library name: A1_PBS631_1


title: paya_mng_095

description: PAYA MNG


title: HM038_TCR

city: Melbourne

first: Andrea

last: Di Pietro

state: VIC

address: 305 Grattan Street

department: Cancer Immunology program

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: Sample 12

data_processing:
Demultiplexing, sequence assembly and clonotype calling was completed using the Cellranger VDJ software version 3.0.2.
Assembly: Human GRCh38
Supplementary files format and content: Cellranger outputs; comma-separated clonotype summaries and filtered contig annotations.
Library strategy: TCR-Seq

source_name: lymph node

extract_protocol:
Fresh tissue samples were digested in collagenase IV/Dnase solution to obain a single cell solution. Dead cells were removed by using the Dead Removal kit (Miltenyi) to achieve at least 70% of viable cells. Cells were resuspended in 0.04% BSA-PBS and  handed to the genomic core for the RNA extraction and library preparation.
The 10X Chromium 5' Gene Expression Reagent Kit (CG000331) and Chip K were used. Gene expression libraries were generated according to the Next GEM Single Cell 5' Reagent Kits v2. The cells were resuspended in PBS with 0.04% BSA and 0.2–1 U/µL Protector RNase Inhibitor (Roche), mixed with the reverse transcription master mix, and then loaded with gel beads and partitioning oil in Chromium X. Gel beads-in-emulsion (GEMs) were cleaned with Silane Dynabeads, and PCR amplification was performed to generate cDNA. Gene expression libraries were then generated following several steps of fragmentation, ligation, and indexing. T-cell receptor (TCR) libraries were generated after amplification and enrichment steps, followed by fragmentation, ligation, and indexing. All libraries were sequenced on the NovaSeq 6000 (paired-end 150 bp reads, targeting 40,000 reads per cell for gene expression and 5,000 reads per cell for TCR libraries.

value: lymph node

value: ICI-responder


title: paya_mng_078

description: PAYA MNG


title: HM035_TCR

description: Library name: Sample 11


title: paya_mng_067

description: PAYA MNG


title: paya_mng_062

description: PAYA MNG

value: ventricel


title: HM019_TCR

description: Library name: Sample 8

value: ICI-resistant


title: paya_mng_061

description: PAYA MNG

value: FFPE


title: HM014_TCR

description: Library name: Sample 7

value: Untreated


title: paya_mng_060

description: PAYA MNG

value: ben


title: HM012_TCR

description: Library name: Sample 6


title: paya_mng_059

description: PAYA MNG

value: Female


title: HM009_TCR

description: Library name: Sample 5


title: paya_mng_041

description: PAYA MNG

value: spinal


title: paya_mng_068

description: PAYA MNG


title: HM006_TCR

description: Library name: Sample 4


title: HM028_TCR

description: Library name: Sample 10


title: HM026_TCR

description: Library name: Sample 9


title: paya_mng_039

description: PAYA MNG

value: skull base


title: HM005_TCR

description: Library name: Sample 3


title: paya_mng_038

description: PAYA MNG

value: Male

value: supratentoriell


title: HM004_TCR

description: Library name: Sample 2


title: paya_mng_032

description: PAYA MNG


title: HM002_TCR

description: Library name: Sample 1


title: paya_mng_030

description: PAYA MNG


title: paya_mng_029

description: PAYA MNG


title: HM038_GEX

description: Library name: Sample 12

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and filtering were performed using Cell Ranger software version 6.0.2.
Assembly: GRCh38-3.0.0
Supplementary files format and content: Cellranger filtered output files: matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz


title: HM035_GEX

description: Library name: Sample 11


title: paya_mng_024

description: PAYA MNG


title: HM028_GEX

description: Library name: Sample 10


title: HM026_GEX

description: Library name: Sample 9


title: paya_mng_012

description: PAYA MNG


title: paya_mng_011

description: PAYA MNG

value: posterior fossa


title: HM019_GEX

description: Library name: Sample 8


title: paya_mng_215

description: PAYA MNG


title: paya_mng_010

description: PAYA MNG


title: CDX, HuCC-A1, H3L3 48h, batch1, rep1

description: Library name: H3L348h_1_1

value: H3L3 anti-Cldn1 mAb 48h


title: CDX, HuCC-A1, Isotype 48h, batch2, rep2

description: Library name: Ctrl48h_2_2

value: Cell line-Derived Xenograft

value: Vehicle control 48h


title: CDX, HuCC-A1, Isotype 48h, batch2, rep3

description: Library name: Ctrl48h_2_3


title: HM014_GEX

description: Library name: Sample 7


title: HM012_GEX

description: Library name: Sample 6


title: paya_mng_009

description: PAYA MNG


title: HM009_GEX

description: Library name: Sample 5


title: Spatial sample

city: Chongqing

first: Jian

last: Wang

address: No. 725, Jiangzhou Avenue, Dingshan Subdistrict, Jiangjin District

department: Department of Oncology

institute: Chongqing University Affiliated Jiangjin Hospital

description:
Library name: Spatial sample
Spatial sample, Spatial transcriptomics sequence

data_processing:
Raw sequencing data were demultiplexed and aligned to the reference genome. Spots with low UMI counts or mitochondrial contamination were filtered. Spatial barcode mapping enabled reconstruction of gene expression matrices aligned with tissue coordinates.
Dimensionality reduction using PCA was followed by graph-based clustering to identify spatially distinct regions. Differential gene expression between clusters revealed spot-specific signatures. Visualization using t-SNE or UMAP facilitated interpretation of spatial heterogeneity.
Spot clusters were annotated by matching marker genes with known cell types. Spatial mapping visualized the distribution of immune and tumor cells. Ligand-receptor interaction analysis inferred cell–cell communication networks within the tissue architecture.
Assembly: GRCm39
Supplementary files format and content: tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Colon tumor tissue

extract_protocol:
Fresh colon tumor tissues were embedded in optimal cutting temperature (OCT) compound and cryosectioned onto gene expression slides. Tissue sections were fixed, stained, and imaged for morphological annotation. Permeabilization was performed to release mRNA, which was captured by spatially barcoded probes. cDNA was synthesized, amplified, and sequenced to generate spatial gene expression profiles.
After mRNA capture on spatially barcoded slides, reverse transcription was performed to generate cDNA with positional barcodes. Second-strand synthesis was followed by denaturation and cDNA amplification. Amplified cDNA was enzymatically fragmented, end-repaired, and poly(A)-tailed. Adaptors were ligated, and the library was indexed by PCR. Final libraries were quantified and sequenced on an Illumina platform to obtain spatial gene expression data.

value: Colon tumor tissue


title: WT

description: Library name: WT

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCm39  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm39
Supplementary files format and content: tab-separated values files and matrix files

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

tag: genotype


title: paya_mng_195

description: PAYA MNG


title: paya_mng_196

description: PAYA MNG


title: HM005_GEX

description: Library name: Sample 3

value: lymph node


title: KO

description: Library name: KO

source_name: ECM1Flox/Flox, Villin-Cre

value: ECM1Flox/Flox, Villin-Cre


title: HM006_GEX

description: Library name: Sample 4


title: RNA_CTRL_rep2_P14

city: Shanghai

first: Jiang

last: Yamei

address: Songhu Road

institute: Fudan University

description: Library name: RNA_CTRL_rep2

data_processing:
We performed RNA-seq analysis as described previously (Pertea et al., 2016). Briefly, after removing adapters using Cutadapt (v2.5) (Kechin et al., 2017), paired-end reads were aligned to the annotated mouse transcripts (mm10 Gencode vM23 release) using Hisat2 (v2.2.1) (Kim et al., 2015; Kim et al., 2019). Gene expression levels were calculated using StringTie (v2.2.1) (Pertea et al., 2015). Read counts were calculated using a Python script (prepDE.py3) provided by the StringTie development team. Differentially expressed genes were identified using the R package DESeq2 (v1.38.3) (Love et al., 2014). Genes with read counts > 50 in at least one sample were kept for further analysis. A given gene was considered to significantly changed if the adjusted P value (padj) was < 0.05, the P value was < 0.01, and the fold-change was≥ 2. Gene Set Enrichment Analysis (GSEA) was carried out using GSEA software (Subramanian et al., 2005). GO analysis was performed using clusterProfiler (v4.6.2) (Wu et al., 2021).
Assembly: mm10
Supplementary files format and content: all sample raw count matrix and differentially expressed genes file

source_name: testis

extract_protocol: Total RNA from fresh testes was isolated and mRNA was purified with magnetic beads (Vazyme, N401-01). Then, mRNA was fragmented and processed to generate RNA-seq libraries (Vazyme, NR605-01). Over 40 million reads were obtained per sample using the Illumina NovaSeq platform for 2 independent biological replicates.

value: testis

tag: cell type

value: testis cells

value: CTRL


title: HM004_GEX

description: Library name: Sample 2

value: ICI-resistant


title: RNA_CTRL_rep1_P14

description: Library name: RNA_CTRL_rep1


title: RNA_KO_rep2_P14

description: Library name: RNA_KO_rep2


title: HM002_GEX

description: Library name: Sample 1

value: Untreated


title: paya_mng_181

description: PAYA MNG

value: FFPE

value: ben


title: Mel-TIL-030_RNA-seq

description:
Library name: Sample 29
RNA-Seq on lymph node

data_processing:
Adapter sequence removal was performed with cutadapt version 2.1. Alignment was performed with hisat2 version 2.0.4. samtools version 1.8 and picard version 2.17.3 were used for further processing. Counts were produced using subread version 2.0.4 featurecount.
Assembly: GRCh37
Supplementary files format and content: featurecount files output from subread.

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Plus Mini Kit according to the manufacturer’s instructions.
Library preparation was performed using stranded ribosomal RNA (rRNA) depletion to selectively enrich for non-ribosomal RNA, using the Illumina TruSeq Stranded Total RNA Library Prep Kit.


title: CDX, EGI-1, rep5

description: Library name: EGICDX_PBS5

value: PBS


title: Mel-TIL-026_RNA-seq

description:
Library name: Sample 28
RNA-Seq on lymph node


title: RNA_KO_rep1_P14

description: Library name: RNA_KO_rep1


title: ATAC_CTRL_rep2_P35

description: Library name: ATAC_CTRL_rep2

data_processing:
ATAC-seq data were analyzed using a standardized ENCODE ATAC-seq pipeline (v2.2.2, https://github.com/ENCODE-DCC/atac-seq-pipeline). The mouse reference genome (mm10) was used in the pipeline. Trimming, mapping, and duplicate-removing were performed as the ENCODE pipeline suggested using Cutadapt (v2.5) (Kechin et al., 2017), Bowtie2 (v2.3.4.3) (Langmead et al., 2009), and Picard (v2.20.7) (https://broadinstitute.github.io/picard/) respectively. MACS2 (v2.2.4) (Zhang et al., 2008) was used for peak calling.
Assembly: mm10
Supplementary files format and content: bigwig files and peak files

extract_protocol: For ATAC-seq, pachytene nuclei were isolated and fragmented with Tn5 transposase. DNA was isolated using the DNA Clean and Concentrator kit (Zymo, D4013) and subjected to library construction using Q5 high-fidelity DNA polymerase (New England Biolabs, M0544S). For high-throughput sequencing, over 30 million reads were obtained per sample using the Illumina NovaSeq platform for 2 independent biological replicates.

value: pachytene spermatocytes


title: Mel-TIL-022_RNA-seq

description:
Library name: Sample 27
RNA-Seq on lymph node


title: paya_mng_164

description: PAYA MNG

value: Female

value: spinal


title: ATAC_CTRL_rep1_P35

description: Library name: ATAC_CTRL_rep1


title: Mel-TIL-019_RNA-seq

description:
Library name: Sample 26
RNA-Seq on lymph node


title: ATAC_KO_rep2_P35

description: Library name: ATAC_KO_rep2


title: Mel-TIL-011_RNA-seq

description:
Library name: Sample 25
RNA-Seq on lymph node


title: ATAC_KO_rep1_P35

description: Library name: ATAC_KO_rep1


title: Vehicle_rep4

city: Glasgow

first: Heather

last: Mathie

state: --None--

address: Sir Graeme Davies Building, 126 University Place

country: United Kingdom

institute: University of Glasgow

description: Library name: Sample8

data_processing:
Raw reads of fastq format were processed through in-house scripts, removing adapter, poly-N and low-quality reads from raw data. Index of the reference genome was built and paired-end clean 1 reads were aligned using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads for each gene. Differential expression analysis of two conditions/groups was performed using the DESeq2Rpackage (1.20.0). The resulting p-values were adjusted suing the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed
Assembly: mm10
Supplementary files format and content: csv file containing the read counts from this experiment

source_name: inguinal fat pads

extract_protocol:
Excised inguinal fat pads were digested for 1 hour using Liberase (0.44 Wunch units/sample).  Macrophages were magnetically isolated from digested tissue using Anti-F480 MicroBeads Ultrapure (Miltenyi Biotech). Purity of the samples were tested using flow cytometry and RNA extraction was performed on samples with >90% F480+CD64+ cells. After F480-magnetic positive selection, the eluted cell suspensions from 6 inguinal fat pads were pooled together to obtain enough ATMs (around 30,000 cells) for low-input RNA sequencing. Cells were spun down at 1000g for 10 minutes, lysed, and spun again to remove bound magnetic beads before proceeding with RNA extraction. RNA was extracted using the RNeasy Microkit with on-column DNAse I digestion (Qiagen), following manufacturer’s instructions, obtaining samples of around 100-150ng of total RNA in water.  RNA samples were then sent to a commercial sequencing provider (Novogene), for RNA QC, mRNA library preparation (poly-A enrichment) and Illumina Sequencing
Total RNA was amplified using  SMARTer Ultra Low Input RNA Kit for Sequencing (Takara Bio) and reverse transcribed into the first-strand cDNA. The double-strand cDNA was synthesized by LD-PCR amplification, followed by the purification with AMPure XP beads and quantification with Qubit. The cDNA samples were then fragmented, end-repaired, A-tailed, and ligated with adaptors. After size selection and PCR enrichment, the RNA library was ready for sequencing.

treatment_protocol: WT female mice were given a ~62.5 mg dose of Aldara™ (Meda AB) cream containing 5% Imiquimod or an equivalent volume of control cream (Boots Aqueous Cream/10% Vaseline Lanette Cream) by application to shaved dorsal skin near the base of the tail. Cream was applied for 3 consecutive days (day 1, day 2 and day 3) and the mice culled 24h after the final application.

value: inguinal fat pads

value: female

value: WT


title: Mel-TIL-002_RNA-seq

description:
Library name: Sample 24
RNA-Seq on lymph node


title: HM038_RNA-seq

description:
Library name: Sample 22
RNA-Seq on lymph node


title: HM041_RNA-seq

description:
Library name: Sample 23
RNA-Seq on lymph node


title: Vehicle_rep3

description: Library name: Sample7

value: Boots Aqueous Cream/10% Vaseline Lanette Cream


title: HM036_RNA-seq

description:
Library name: Sample 21
RNA-Seq on lymph node

value: lymph node


title: Vehicle_rep2

description: Library name: Sample6


title: paya_mng_122

description: PAYA MNG

value: orbital


title: Vehicle_rep1

description: Library name: Sample5


title: HM035_RNA-seq

description:
Library name: Sample 20
RNA-Seq on lymph node


title: HM032_RNA-seq

description:
Library name: Sample 19
RNA-Seq on lymph node


title: Aldara_rep4

description: Library name: Sample4

value: Aldara


title: HM030_RNA-seq

description:
Library name: Sample 18
RNA-Seq on lymph node


title: Aldara_rep3

description: Library name: Sample3


title: Aldara_rep2

description: Library name: Sample2


title: HM028_RNA-seq

description:
Library name: Sample 17
RNA-Seq on lymph node


title: Aldara_rep1

description: Library name: Sample1


title: HM025_RNA-seq

description:
Library name: Sample 15
RNA-Seq on lymph node


title: 4_Fast_72hpi

city: HOUSTON

first: Ajay

middle: Kumar

last: Saw

state: TX

address: 7900 Cambdrige St

department: Department of Genomic Medicine

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

description: Library name: 4_Fast_72hpi

library_source: genomic single cell

data_processing:
Single cell multiome fastq files were aligned to the mouse (mm10) genome and preprocessed using the cellranger-arc count command using default parameters.
We used the ArchR pipeline for most of our single-cell ATAC-seq datasets analysis.
Assembly: mm10
Supplementary files format and content: "atac_fragments.tsv.gz" for each sample

source_name: small intesitnal crypt

growth_protocol: mice were grown in normal contion before total abdominal irradiation

extract_protocol:
small intestinal crypt were isolated by shacking in HBSS+edta, followed by trypsin treatment to make single cells
Library was constructed using 10x genomics Multiome Library Prep Kit.

treatment_protocol: Mice were treated with or without IR and smaple collected at 0h, 24h, 48h, 72h

value: small intesitnal crypt

value: small intestinal epithelial cells

tag: strain

tag: age

value: 9-10 weeks, male

value: IR 72h


title: HM026_RNA-seq

description:
Library name: Sample 16
RNA-Seq on lymph node


title: 3_Fast_72hpi

description: Library name: 3_Fast_72hpi


title: HM020_RNA-seq

description:
Library name: Sample 14
RNA-Seq on lymph node

value: Untreated


title: 2_Fast_72hpi

description: Library name: 2_Fast_72hpi


title: HM019_RNA-seq

description:
Library name: Sample 13
RNA-Seq on lymph node


title: HM017_RNA-seq

description:
Library name: Sample 12
RNA-Seq on lymph node


title: 1_Fast_72hpi

description: Library name: 1_Fast_72hpi


title: 3_Fast_48hpi

description: Library name: 3_Fast_48hpi

value: IR 48h


title: HM015_RNA-seq

description:
Library name: Sample 11
RNA-Seq on lymph node


title: HM014_RNA-seq

description:
Library name: Sample 10
RNA-Seq on lymph node


title: 2_Fast_48hpi

description: Library name: 2_Fast_48hpi


title: HM009_RNA-seq

description:
Library name: Sample 8
RNA-Seq on lymph node


title: 4_Fast_24hpi

description: Library name: 4_Fast_24hpi

value: IR 24h


title: HM012_RNA-seq

description:
Library name: Sample 9
RNA-Seq on lymph node


title: 1_Fast_48hpi

description: Library name: 1_Fast_48hpi


title: HM007_RNA-seq

description:
Library name: Sample 7
RNA-Seq on lymph node


title: 3_Fast_24hpi

description: Library name: 3_Fast_24hpi


title: HM006_RNA-seq

description:
Library name: Sample 6
RNA-Seq on lymph node


title: HM005_RNA-seq

description:
Library name: Sample 5
RNA-Seq on lymph node


title: 2_Fast_24hpi

description: Library name: 2_Fast_24hpi


title: 1_Fast_24hpi

description: Library name: 1_Fast_24hpi


title: HM004_RNA-seq

description:
Library name: Sample 4
RNA-Seq on lymph node


title: 4_Fast_0h

description: Library name: 4_Fast_0h

value: No IR


title: paya_mng_287

description: PAYA MNG

value: FFPE

value: Female

value: ben

value: skull base


title: HM003-Small_RNA-seq

description:
Library name: Sample 3
RNA-Seq on lymph node


title: 3_Fast_0h

description: Library name: 3_Fast_0h


title: HM003-Large_RNA-seq

description:
Library name: Sample 2
RNA-Seq on lymph node


title: HM002_RNA-seq

description:
Library name: Sample 1
RNA-Seq on lymph node


title: 1_Fast_0h

description: Library name: 1_Fast_0h


title: Ishikawa cells, XPO1 R749Q#3

city: 上海

first: zeheng

last: Lv

address: 2699 Pudong New Area High Tech West Road

institute: Tongji university

description:
Library name: Knockin749-3
Knockin749.3_counts

data_processing:
Raw paired-end fastq reads were filtered by TrimGaloreto discard the adapters and low quality bases via calling the Cutadapt tool. The clean reads obtained were then aligned to the hg19 human genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie. Differentially expressed genes (DEGs) were identified by DEseq2 with a cut-off value of log2|fold-change|>1 and p-adjust <0.05. The clusterProfiler was used to perform functional enrichment analysis for the annotated significant DEGs, the potential genes in identified modules based on gene ontology (GO) and KEGG pathway categories. Terms with pvalue<0.05 were considered significant. Gene set enrichment analysis (GSEA) was performed by the function in package clusterProfiler with a gene list sorted by log2 fold-change.
Assembly: hg19
Supplementary files format and content: counts, tpm

source_name: Ishikawa cells

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry. High-quality RNA  with a 260/280 absorbance ratio of 1.8-2.2 was used for library construction and sequencing.
Illumina library construction was performed according to the manufacturer's instructions (Illumina,USA). Oligo-dT primers are used to transverse mRNA to obtain cDNA(APExBIO, Cat. No. K1159). Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA). After library construction, library fragments were enriched by PCR amplification and selected according to a fragment size of 350-550 bp. The library was quality-assessed using an Agilent 2100 Bioanalyzer (Agilent, USA).The library was sequenced using the Illumina NovaSeq 6000 sequencing platform (Paired end150) to generate raw reads.

value: Ishikawa cells

value: XPO1 R749Q


title: Ishikawa cells, XPO1 R749Q#2

description:
Library name: Knockin749-2
Knockin749.2_counts


title: 4_Fed_72hpi

description: Library name: 4_Fed_72hpi


title: 3_Fed_72hpi

description: Library name: 3_Fed_72hpi


title: Ishikawa cells, XPO1 R749Q#1

description:
Library name: Knockin749-1
Knockin749.1_counts


title: 2_Fast_0h

description: Library name: 2_Fast_0h


title: 2_Fed_72hpi

description: Library name: 2_Fed_72hpi


title: Ishikawa cells, Parental#3

description:
Library name: Control3
Control3_counts

value: WT


title: 1_Fed_72hpi

description: Library name: 1_Fed_72hpi


title: Ishikawa cells, Parental#2

description:
Library name: Control2
Control2_counts


title: 4_Fed_48hpi

description: Library name: 4_Fed_48hpi


title: Ishikawa cells, Parental#1

description:
Library name: Control1
Control1_counts


title: 3_Fed_48hpi

description: Library name: 3_Fed_48hpi


title: 2_Fed_48hpi

description: Library name: 2_Fed_48hpi


title: SW480 cells, AFB1, rep3

city: Fuzhou

first: Peichun

last: Ye

address: No.1 Xuefu North Road, Fuzhou, Fujian, China

institute: Fujian Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DESeq2.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: mm10
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels.

source_name: Rectum

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched.

value: Rectum

value: Cancer cell

value: Wild type

value: treat with AFB1


title: SW480 cells, AFB1, rep2


title: 1_Fed_48hpi

description: Library name: 1_Fed_48hpi

value: small intesitnal crypt

value: small intestinal epithelial cells

value: 9-10 weeks, male


title: SW480 cells, AFB1, rep1


title: 4_Fed_24hpi

description: Library name: 4_Fed_24hpi


title: SW480 cells, Control, rep2

value: Control


title: 2_Fed_24hpi

description: Library name: 2_Fed_24hpi

value: IR 24h


title: 3_Fed_24hpi

description: Library name: 3_Fed_24hpi


title: SW480 cells, Control, rep1


title: 1_Fed_24hpi

description: Library name: 1_Fed_24hpi


title: SW480 cells, Control, rep3


title: 521

data_processing:
Base calling was performed using Real-Time Analysis Software.
Base calls were converted into lane-specific unaligned BAM files using IlluminaBasecallsToMultiplexSam and demultiplexed using IlluminaSamDemux.
Raw reads were mapped to using STAR v2.7.5a utilising the Ensembl transcript annotation from version e100 (April 2020) as reference transcriptome.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HuCC-A1 CDX tumors

extract_protocol:
Tumors were dissociated using the gentleMACS dissociator, and RNA was extracted using Triazol.
RNA-Seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA)

treatment_protocol: Mice were treated with CLDN1 mAb (25mg/kg i.p. once per week, n=5 mice), or with vehicle control (PBS i.p. once per week,n= 5 mice) for 6 weeks

value: HuCC-A1 CDX tumors

value: CLDN1 mAb


title: 4_Fed_0h

description: Library name: 4_Fed_0h

value: No IR


title: 515


title: 3_Fed_0h

description: Library name: 3_Fed_0h


title: 2_Fed_0h

description: Library name: 2_Fed_0h


title: 1_Fed_0h

description: Library name: 1_Fed_0h


title: 512


title: 514


title: 508


title: 2_Fast

description: Library name: 2_Chow_Fast2

data_processing:
Sequences from the Fed and Fasted samples were processed using Cellranger.
Doublets were removed using scDblFinder with default parameters.
Data were normalized, scaled, and variance stabilized using Seurat package.
Assembly: mm10
Supplementary files format and content: "filtered feature bc matrix.h5"  for each Sample

extract_protocol:
small intestinal crypt were isolated by shacking in HBSS+edta, followed by trypsin treatment to make single cells
Library was constructed using 10x genomics 5' scRNA Library Prep Kit.

treatment_protocol: Mice were fed or fasted for 24hours

value: 11 weeks, male

value: FAST


title: 1_Fast

description: Library name: 1_Chow_Fast2

value: 10 weeks, male


title: 517

value: Vehicle control


title: 516


title: 2_Fed

description: Library name: 2_Chow_Fed2

value: 9 weeks, male

value: FED


title: 510


title: 1_Fed

description: Library name: 1_Chow_Fed2


title: 509


title: Myeloid-derived suppressor cells, Cancer cell-derived CM 3

city: Cleveland

first: Lizhi

last: Pang

state: OH

address: 9500 Euclid Avenue

department: Department of Cancer Biology

institute: Cleveland Clinic

description: Library name: PC-LP-09

data_processing:
Galaxy server
Trimmomatic was performed to read and trim paired-end reads.
HISAT2 program was used to align the data where mm10 was selected as the reference genome.
Samtools merge was performed on BAM files to merge data from different flowcells.
Gene expression was then determined by FeatureCounts.
Limma was used to calculate differential expression genes and generate DE table.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: BM-MDSC

growth_protocol: MDSCs were maintained in RPMI with 10% FBS, supplemented with 40 ng/mL GM-CSF and 80 ng/mL IL-13 in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared at The University of Chicago Functional Genomics (RRID:SCR_019196).

treatment_protocol: Cells were treated with cancer cell-derived CM or GAL recombinant protein

value: BM-MDSC

value: Myeloid-derived suppressor cells

value: WT

value: Cancer cell-derived CM


title: Myeloid-derived suppressor cells, Cancer cell-derived CM 2

description: Library name: PC-LP-08


title: 506


title: Fast (+Tetra)

description: Library name: Tetra-FAST

data_processing:
Trimmed sequenced read were mapped mouse genome (mm10) transcriptomes using the Salmon tool
Read count and normalization were performed using  tximeta R-package
DESeq2 package has been used for differential expression analysis
Assembly: mm10
Supplementary files format and content: csv text file includes Differential expression of SPF and Tetra Sample

growth_protocol: mice were grown in normal contion before the tetracycline treatment

extract_protocol:
small intestinal crypt were isolated by shacking in HBSS+edta, followed by trypsin treatment to make single cells
Library was constructed using NEBNext Ultra II Non-Directional RNA Library Prep Kit from Illumina.

treatment_protocol: Mice were treated with tetracycline for 21 days, fed or fasted for 24hrs.

value: small intesitnal crypt

value: small intestinal epithelial cells

value: 9 weeks

value: male

value: (+Tetra)


title: Myeloid-derived suppressor cells, Cancer cell-derived CM 1

description: Library name: PC-LP-07


title: 4_Fast_48hpi

description: Library name: 4_Fast_48hpi

value: 9-10 weeks, male

value: IR 48h


title: Myeloid-derived suppressor cells, GAL 3

description: Library name: PC-LP-06

value: GAL


title: Fed (+Tetra)

description: Library name: Tetra-FED


title: Myeloid-derived suppressor cells, GAL 1

description: Library name: PC-LP-04


title: Myeloid-derived suppressor cells, GAL 2

description: Library name: PC-LP-05


title: PDM17_H3L33

growth_protocol: Organoids were re-suspended in 50 µl Cultrex Basement Membrane Extract (BME) Type 2 (#3532-005-02, R&D), seeded as domes onto 24 well plates and covered with organoid medium.

extract_protocol:
Organoids were harvested for RNA extraction using PicoPure™ RNA Isolation Kit (#KIT0204, Applied Biosystems™) according to the manufacturer’s instructions
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

treatment_protocol: Pre-washed organoid cell  pellet was pre-incubated with 10 µg/ml CLDN1 mAb or isotype control mAb for 1h at room temperature. Cell pellet was then washed once with PBS and resuspended in Matrigel and  seeded as 50µl  domes onto 24 well plates. Following solidification of Matrigel for 15 minutes at 37°C, 500 µl prewarmed organoid medium supplemented by 10 µg/ml CLDN1 mAb or isotype control antibody was added to each well, with media and treatment being renewed 3 days after treatment initiation. At day 7, organoids were harvested for RNA extraction.

value: CLDN1 mAb


title: Fast (-Tetra)

description: Library name: SPF-FAST

value: (-Tetra)


title: Myeloid-derived suppressor cells, Control 3

description: Library name: PC-LP-03


title: PDM17_H3L32


title: Myeloid-derived suppressor cells, Control 2

description: Library name: PC-LP-02


title: Fed (-Tetra)

description: Library name: SPF-FED


title: Cardiomyocyte Cells, 4 days, 12h WNT inhibitor

city: Aberdeen

first: Ellen

middle: Elizabeth

last: Smith

address: University of Aberdeen

department: School of Biological Sciences

institute: University of Aberdeen

description:
Library name: D412i
10x Genomics

data_processing:
Reads were demultiplexed, barcoded, aligned, counted  and matrices constructed using 10x CellRanger v3.0.2
Assembly: GRCh28
Supplementary files format and content: Human reference genome
Supplementary files format and content: Matrix and count files

source_name: embryonic stem cell-derived cardiomyocytes

growth_protocol: H7 hESCs (WA07; 46,XX; WiCell) were maintained feeder-free on growth factor–reduced Matrigel (Corning) and passaged every 3–4 days at 1:6 as aggregates using Versene (Thermo Fisher Scientific). Once confluent, cells were dissociated with TrypLE Express, resuspended in mTeSR1 containing Y-27632 (Tocris), counted (NC200, Chemometec), and seeded at 0.65×10^5 cells/cm² and grown for 3 days, then cardiomyocyte differentiation was performed (see below).

extract_protocol:
Cells weredissociated with TrypLE, filtered through a 35 μm strainer (Thermo Fisher), resuspended in RPMI + B27 (noinsulin) with L-ascorbic acid and 10% DMSO,and frozen at −80 °C in a CoolCell LX container
After thawing,cells were resuspended in fresh RPMI + B27 (no insulin) with L-ascorbic acid, kept on ice, stained with DAPI,and live singlets (DAPI−) were sorted on a CytoFLEX SRT into RPMI 1640 + B27 (noinsulin). Cell counts andviability were assessed by trypan blue on a Countess II. Approximately 6,000 cells per sample were loaded ontoa 10x Genomics Chromium Controller; libraries were prepared with the Chromium Single Cell 3′ v3 kit, pooled,and sequenced on a NextSeq 500

treatment_protocol: RPMI 1640 media was added (ThermoFisher) supplemented with B27 minus insulin (ThermoFisher), Activin A (5 ng/ml, R&D), CHIR999021 (2 μM, Sellek Chemikals), BMP4 (5-6 ng/ml, R&D) and FGF2 (5 ng/ml, R&D) for 24 hours and replaced with RPMI 1640 media supplemented with B27 minus insulin for one additional day. On Day 2, media was replaced with RPMI 1640 media supplemented with B27 minus insulin, L-ascorbic acid (65 μg/ml, Sigma), and depending on the experimental design, with or without the Wnt inhibitor IWP2 (5 μM, Sigma) for 48 hours.

value: H7 hESC (WA07)

value: Human ES

value: CHIR99021 2 μM for 24 h followed by IWP2 5 μM for final 12 h before Day 4 collection


title: PDM17_H3L31

data_processing:
Base calling was performed by CASAVA and raw data was stored in FASTQ format.
Raw reads were filtered to remove reads with (I) adapter contamination, (II) more than 10 % uncertain nucleotides (Ns), and (III) with more than 50 % of low quality nucleotides (base quality less than 5).
Reads were mapped using HISAT2 v2.0.5 to the human genome GRCh38.
FeatureCounts v1.5.0-p3 was used to generate gene counts.
Assembly: GRCh38
Supplementary files format and content: Tabulator separated matrix table with raw gene counts for every gene and every sample


title: PDM17_ctl3

value: Isotype control (Motavizumab)


title: Het_Neg514

city: Birmingham

first: Andrew

last: Arrant

state: AL

address: 1825 University Blvd SHEL 1106

institute: University of Alabama at Birmingham

description: Library name: 514

data_processing:
Reads were aligned to a custom genome composed from Gencode vM32 genome with vH43 TARDBP using STAR with the following settings: (--twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --outSAMtype BAM Unsorted SortedByCoordinate --quantMode TranscriptomeSAM).
Bam files were indexed with samtools.
Aligned transcripts were quantified using Salmon.
Salmon quantification files were imported into R using tximport.
Non-protein coding genes and genes where there were fewer than three samples with normalized counts less than or equal to five were filtered out.
Normalization and differential expression analysis were performed using the R package DESeq2.
After initial principal component analysis, one mouse (WT_Pos470) was excluded as an outlier from all further analysis.
Assembly: Gencode vM32 with vH43 TARDBP
Supplementary files format and content: .sf files with TPM for each sample

source_name: Frontal Cortex

growth_protocol: Grn+/- mice and hTDP transgenic mice were crossed to generate littermates of four genotypes: Grn+/+:hTDP-, Grn+/+:hTDP+, Grn+/-:hTDP-, and Grn+/-:hTDP+. Mice were housed in standard conditions to an average age of around 10 months. Brains were collected by anesthetizing mice with pentobarbital, transcardially perfusing with 0.9% saline, removing brains, and flash freezing. Brains were later thawed for dissection of frontal cortex.

extract_protocol:
RNA was isolated from frontal cortex using the Qiagen RNeasy mini kit. Samples were further processed with the Zymo Research RNA clean and concentrate kit.
After poly-A selection, RNA was fragmented and subjected to first strand cDNA synthesis using random hexamers. Second strand DNA was synthesized using dUTPs for the directional library and dTTPs for the non-directional library. The directional library was then prepared by end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The non-directional library was prepared by end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Frontal Cortex

tag: grn genotype

tag: htdp genotype

value: Female

tag: age (months)


title: Het_Neg511

description: Library name: 511

tag: Sex

value: Male


title: Cardiomyocyte Cells, 4 days, 48h WNT inhibitor

description:
Library name: D448i
10x Genomics

value: embryonic stem cell-derived cardiomyocytes

value: CHIR99021 2 μM for 24 h followed by IWP2 5 μM for 48 h; collected at Day 4


title: Cardiomyocyte Cells, 4 days, 0 WNT inhibitor

description:
Library name: D40i
10x Genomics

value: CHIR99021 2 μM for 24 h followed by no WNT inhibitor; collected at Day 4


title: Myeloid-derived suppressor cells, Control 1

description: Library name: PC-LP-01

value: BM-MDSC

value: Myeloid-derived suppressor cells

value: WT


title: PDM17_ctl2


title: Cardiomyocyte Cells, 2 days

description:
Library name: D2
10x Genomics

value: CHIR99021 2 μM for 24 h; collected at Day 2


title: Het_Neg503

description: Library name: 503


title: Primed_H3K27me3_Rep2

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

description: Library name: library2

data_processing:
Reads were trimmed with trim_galore v0.6.10 using default parameters.
Trimmed reads were aligned to GRCh38 using bowtie2 v2.4.1 using default parameters
Reads were sorted and indexed with samtools
BigWig files were created with deeptools bamCoverage using options --normalizeUsing CPM  --binSize 10
Assembly: GRCh38
Supplementary files format and content: BigWig quantitated with CPM
Library strategy: CUT&Run

growth_protocol: Primed hPSCs were routinely cultured on irradiated mouse embryonic fibroblasts (MEFs) in KOSR/FGF medium comprised of Advanced DMEM (ThermoFisher, 12491023) with 20% Knockout Serum Replacement (ThermoFisher, 10828028), 2 mM L-glutamine (ThermoFisher, A2916801), 50 U/mL Pen-strep (ThermoFisher, 15140122), 0.1 mM 2-mercaptoethanol (ThermoFisher, 31350010) and 4 ng/mL FGF2 (Cambridge Stem Cell Institute).

extract_protocol:
Concanavalin A conjugated paramagnetic beads (EpiCypher, 21-1401) were resuspended and washed twice on a magnetic rack in bead activation buffer composed of 20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2 and 1 mM MnCl2. Cells were dissociated and counted. Cell pellets were washed twice with a wash buffer composed of 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine and supplemented with EDTA-free protease inhibitor. 50,000 cells were added in wash buffer to Concanavalin A beads and incubated for 10 min at room temperature with rotation to immobilise cells. Concanavalin A beads were collected with a magnetic rack, the supernatant discarded, and beads were resuspended in antibody buffer, composed of wash buffer supplemented with 0.08% Digitonin (Millipore) and 2 mM EDTA. H3K27me3 (Cell Signalling, C36B11) antibody (1 μg) was added to the beads, which were incubated overnight at 4 °C with rotation. The following day, beads were washed twice with digitonin buffer, composed of wash buffer supplemented with 0.08% Digitonin. To 50 μl digitonin buffer, 2.5 μl CUTANA pA/G MNase (EpiCypher, 15-1016) was added and incubated for 10 min at room temperature. Beads were again washed twice with digitonin buffer and MNase was activated with 2 mM CaCl2 and incubated for 2 h at close to 0 °C. MNase activity was terminated by adding 100 μl stop buffer, composed of 340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/ml RNase A and 50 μg/ml Glycogen. Cleaved DNA fragments were released from nuclei by incubation for 10 min at 37 °C, centrifugation for 5 min at 16,000 x g at 4 °C, collecting the supernatant from the beads on a magnetic rack. DNA was purified by incubation with 1 μl SDS (20 %) and 1.5 μl Proteinase K (20 mg/ml) at 70 °C for 10 min, followed by a 1.8x AMPure XP bead (Beckman Coulter) clean-up into DNA lo-bind tubes (Eppendorf) and eluted in 50 μl 0.1x TE.
Libraries were prepared using the NEBNext Ultra II DNA library preparation kit for Illumina (NEB) using the manufacturer’s protocol. Following library preparation, library fragment size and concentration were determined using the Qubit fluorometer double stranded DNA high sensitivity assay kit, using an Agilent Bioanalyzer 2100 and by KAPA Library Quantification Kit (KAPA Biosystems).

treatment_protocol: No treament applied

value: Human pluripotent stem cell

value: Wild-type


title: Primed_H3K27me3_Rep1

description: Library name: library1


title: PDM17_ctl1

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110


title: WT_Primed_P300

description: Library name: library3

data_processing:
Reads were trimmed with trim_galore v0.6.10 using default parameters.
Trimmed reads were aligned to GRCh38 using bowtie2 v2.4.1 using default parameters
Reads were sorted and indexed with samtools
BigWig files were created with deeptools bamCoverage using options --normalizeUsing CPM  --binSize 10
Assembly: GRCh38
Supplementary files format and content: BigWig quantitated with CPM

growth_protocol: Naive hPSCs were cultured in in t2i/L+PKCi conditions in a 1:1 mixture of DMEM/F12 and Neurobasal, 0.5x N-2 supplement, 0.5x B-27 supplement, 2 mM L-Glutamine, 50 U/ml Penicillin-Streptomycin, 0.1 mM beta-mercaptoethanol (all from ThermoFisher Scientific), 1 µM PD0325901, 1 µM CHIR99021, 20 ng/ml human LIF (all from Cambridge Stem Cell Institute) and 2 µM Gö6983 (PKCi; Tocris) on a layer of irradiated mouse embryonic fibroblasts (MEF) seeded at a density of 2 million cells per 6-well plate. Primed hPSCs were cultured in 80 % Advanced DMEM, 20 % Knockout Serum Replacement, 2 mM L-glutamine, 50 U/ml penicillin-streptomycin, 0.1 mM beta-mercaptoethanol (all from ThermoFisher Scientific) and 4 ng/ml basic fibroblast growth factor (bFGF; Cambridge Stem Cell Institute) on MEF seeded at a density of 1 million cells per 6-well plate. Cells were passaged by 5 min incubation with 200 U/ml Collagenase type IV at 37 °C (ThermoFisher Scientific).

extract_protocol:
Twenty million cells were used for each ChIP-sequencing sample. Cells were cross-linked in solution with 2 mM di(N-succinimidyl) glutarate (Sigma-Aldrich) in PBS for 45 min at RT on a rocker, then cells were collected by centrifugation at 500 x g for 5 min. Cells were then cross-linked in solution with 1 % methanol-free paraformaldehyde (Agar Scientific) in PBS for 12.5 min at RT on a rocker. Fixation was quenched with 0.125 M glycine for 5 min at RT on a rocker and cells were collected by centrifugation at 500 x g for 5 min. All buffers were kept at 4 °C and contained an cOmpleteTM EDTA-free protease inhibitor (Roche) unless stated otherwise. Fixed cells were resuspended in 10 mL nuclei extraction buffer (10 mM HEPES pH 7.5, 10 mM EDTA, 0.5 mM EGTA and 0.75 % Triton X-100) and incubated for 10 min at 4°C with rotation. Cells were collected by centrifugation at 4,000 rpm for 5 min and nuclei were resuspended in 10 mL nuclei wash buffer (10 mM HEPES pH 7.5, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) and incubated for 10 min at 4 °C with rotation. Nuclei were resuspended up to 600 μL in lysis and sonication buffer (25 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.1 % Triton X-100, 1 % SDS and 0.5 % Sodium Deoxycholate), transferred to protein lobind tubes and incubated for 30 min at 4°C for complete nuclear lysis. Fragmented chromatin was centrifuged at 20,000 x g for 15 min at 4°C to remove debris and the supernatant was collected and diluted 1:10 with ChIP dilution buffer (150 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1 % Triton X-100, 0.1 % SDS and 0.5 % Sodium Deoxycholate). Five percent of the diluted chromatin volume was kept as an input for each condition, and the remaining chromatin was split across six protein lobind tubes and incubated with a total of 10 μg of anti-KAT3B/P300 antibody (Abcam, ab14984) overnight at 4°C with rotation. Alongside this, Protein G Dynabeads (Thermo Fisher Scientific), 60 μL per immunoprecipitation, were washed three times with wash buffer A (50 M Tris pH 8, 150 mM NaCl, 0.1 % SDS, 1 % NP-40, 1 mM EDTA and 0.5 % Sodium Deoxycholate) and were blocked for 1 h in wash buffer A containing 100 μg/mL BSA (NEB) and 40 μg/mL yeast tRNA (Thermo Fisher Scientific) at 4°C with rotation. Beads were washed a further three times with wash buffer A and resuspended in 200 μL per original 60 μL of beads and stored overnight at 4°C with rotation. The following day, 33.3 μL of washed Protein G Dynabeads were added to each of the six antibody-chromatin complexed tubes to capture the antibody bound sequences and incubated at 4°C with rotation. After a minimum of 7 h, the beads were collected on a magnetic rack, the liquid was discarded and the beads were sequentially washed with buffers of increasing stringency, with each wash involving complete resuspension of beads off the magnet and incubation for 10 min at 4°C with rotation. First, the beads were washed twice with wash buffer A, allowing the chromatin-antibody complexed beads to be collected into a single tube per immunoprecipitation. Beads were subsequently washed once with wash buffer B (50 mM Tris pH 8, 500 mM NaCl, 0.1 % SDS, 1 % NP-40, 1 mM EDTA and 0.5 % Sodium Deoxycholate), once with wash buffer C (50 mM Tris pH 8, 250 mM LiCl, 1 % NP-40, 1 mM EDTA and 0.5 % Sodium Deoxycholate) and rinsed once with 1x TE buffer (10 mM Tris pH 8, 1 mM EDTA). Chromatin was eluted from the beads, as well as the inputs, using elution buffer lacking protease inhibitors (1 % SDS and 0.1 M NaHCO3) at RT containing 500 μg/mL Proteinase K (Roche) and 100 μg/mL RNase A (Promega). The samples were incubated in a thermomixer at 37 °C for 2 h, followed by incubation at 65 °C overnight with shaking to reverse cross-links. DNA was collected into DNA lobind tubes and purified using 1.5x AMPure XP beads (Beckman Coulter).
Libraries were generated using NEBNext Ultra II DNA library preparation kit for Illumina (NEB) using the manufacturer’s protocol, with libraries indexed using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2) (NEB). Following library preparation, library fragment size and concentration were determined using a Qubit fluorometer double-stranded DNA high-sensitivity assay kit (Thermo Fisher Scientific), Agilent Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems).

treatment_protocol: No treatments were applied.

value: primed


title: Het_Pos500

description: Library name: 500


title: WT_Naive_P300_1

description: Library name: library1

value: naïve


title: CGA009, PM LD, r2

city: Saint Paul

first: Nathan

last: Lewis

email: nalewis159@gmail.com, lewi1449@umn.edu

state: MN

address: 1445 Gortner Ave

department: Plant & Microbial Biology

institute: University of Minnesota

description:
Library name: sample 4
Column name in hisat2_counts.csv: LD_r2

data_processing:
Sequencing was done on an Illumina NovaSeq X plus producing 150 bp paired reads
Quality control and adapter trimming was performed with bcl-convert version 4.2.4
read mapping was performed with HISAT2 version 2.2.0
Assembly: NZ_CP116810.1
Supplementary files format and content: hisat2_counts.tsv is a tab separated variable file containing normalized counts data for each gene in R. palustris CGA009 grown in medium with acetate and medium with decayed wood extract under photoheterotrophic conditions

organism: Rhodopseudomonas palustris

growth_protocol: Cultures of R. palustris CGA009 were grown In 10 mL of phosphate buffered mineral medium with 20 mM acetate as a sole carbon source or with decayed wood extract as a carbon source. Decayed wood extract was made by adding 10 mL of phosphate buffered medium per gram of crushed, decayed wood and allowing infusion to continue overnight at 4 C. The decayed wood extract was centrifuged and filtered (0.22 um filter) to sterilize and remove larger wood fragments. Liquid cultures with decayed wood extract contained 2 mL of decayed wood extract in 8 mL of medium (10 mL final volume). Cultures were inoculated into medium with acetate or decayed wood extract in biological triplicate at a starting optical density (660 nm) of 0.025 and grown to early stationary phase (OD660 = 0.9) when they were harvested by centrifugation. Cell pellets were flash frozen in liquid nitrogen and stored at -80 C until RNA could be extracted.

extract_protocol:
RNA was extracted from flash-frozen cell pellets using the miRNeasy mini kit (Qiagen) following the manufacturer's guidelines. Contaminating DNA was removed from the RNA using TURBO DNase (Invitrogen) and the DNA-depleted RNA was re-purified using the RNeasy MinElute cleanup kit (Qiagen). 1 ug of each sample was sent to SeqCenter for library synthesis
Illumina Stranted Total RNA prep ligation with Ribo-Zero rRNA depletion kit and 10 bp unique dual indicies

value: planktonic bacterial cells in early stationary phase

value: Wild type

value: phototrophic mineral medium with decayed wood extract as a carbon source


title: WT_Pos498

description: Library name: 498

value: Frontal Cortex


title: WT_Naive_P300_2

description: Library name: library2


title: CGA009, PM LD, r1

description:
Library name: sample 3
Column name in hisat2_counts.csv: LD_r1


title: Tumor6_TC

city: Boston

first: Yuemeng

last: Jia

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description: Library name: HCC6_TC

data_processing:
The identities of the DARLIN arrays were determined using a custom MATLAB script described in the manuscript.
Assembly: mm10
Supplementary files format and content: txt.gz

source_name: Liver

extract_protocol:
Frozen tissues were embedded in OCT and sectioned at 10 μm.
DARLIN arrays were amplified by nested PCR according to the SPACE-seq protocol described in the manuscript.

value: Liver


title: Tumor2_TC

description: Library name: HCC2_TC


title: Brain_spikeIn_5_CC_Miseq

description: Library name: Brain_spikeIn_5_CC_Miseq

data_processing:
The identities of the DARLIN arrays were determined using a custom MATLAB script described in the manuscript.
Assembly: mm10
Supplementary files format and content: tsv.gz
Supplementary files format and content: mtx.gz

source_name: Brain

value: Brain


title: Het_Neg497

description: Library name: 497

value: Male


title: WT_Neg496

description: Library name: 496


title: Tumor1_TC

description: Library name: HCC1_TC


title: Brain_spikeIn_1_CC_Miseq

description: Library name: Brain_spikeIn_1_CC_Miseq


title: CGA009, PMac_r1

description:
Library name: sample 1
Column name in hisat2_counts.csv: CGA009_r1

value: phototrophic mineral medium with acetate as a carbon source


title: Brain_spikeIn_0_CC_Miseq

description: Library name: Brain_spikeIn_0_CC_Miseq


title: WT_Neg493

description: Library name: 493

value: Female


title: Brain_spikeIn_5_RC_Miseq

description: Library name: Brain_spikeIn_5_RC_Miseq


title: CGA009, PMac, r3

description:
Library name: sample 2
Column name in hisat2_counts.csv: CGA009_r3


title: Brain_spikeIn_1_RC_Miseq

description: Library name: Brain_spikeIn_1_RC_Miseq


title: Brain_spikeIn_0_RC_Miseq

description: Library name: Brain_spikeIn_0_RC_Miseq


title: Het_Pos490

description: Library name: 490


title: Brain_spikeIn_5_TC_Miseq

description: Library name: Brain_spikeIn_5_TC_Miseq


title: WT_Pos487

description: Library name: 487


title: Mel-TIL-026

type: RNA

hyb_protocol: Total RNA was hybridised to a custom nCounter CodeSet that includes the commercial PanCancer Immune Profiling Panel plus a Panel Plus (PLS) extension targeting TRM-related genes. Hybridisations were performed per manufacturer instructions using the NanoString nCounter system. RNA Hybridization was performed following the manufacturer's protocol (Nanostring).

scan_protocol: nCounter

data_processing:
NanoString Gene Expression Data Analysis Guidelines
Data were normalised and quality-controlled using NanoString nSolver and further analysed to identify differentially expressed genes and pathway enrichment associated with treatment response.

label: not provided

label_protocol: 150 ng of purified RNA were hybridized with the gene probes

growth_protocol: RNA extracted from FFPE blocks

extract_protocol: The RNA was extracted from 10 µm scrolls. Deparaffinisation was condicted by dissolving the scrolls into xylene solution. The RNA was purified using the AllPrep DNA/RNA FFPE Kit (QIAGEN) and quantified at the RNA-TapeStation (Agilent).

treatment_protocol: FFPE blocks from patients that were treatment-naïve (n=13), ICI-resistant (n=5), or ICI-responsive (n=6).


title: Mel-TIL-030


title: Brain_spikeIn_0_TC_Miseq

description: Library name: Brain_spikeIn_0_TC_Miseq


title: Brain_spikeIn_1_TC_Miseq

description: Library name: Brain_spikeIn_1_TC_Miseq


title: Mel-TIL-022

value: Untreated


title: WT_Neg481

description: Library name: 481


title: CCA_Treated_Tum2_plate165

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cel barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg38 with BWA (Anders and Huber, 2010).
Data was demultiplexed as described in Grün et al. 2014.
Mapping and generation of count tables was automated using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell of every sample

source_name: Cholangiocarcinoma

extract_protocol:
Tumors were dissociated using gentleMACS Dissociator and Tumor dissocation kit (Miltenyi Biotech). Cells were stained using Zombie green viability kit (BioLegend). Viable single cells from the PDX tumors treated with the CLDN1 mAb or control were FACS sorted into 384-well plates (cell capture plates) that were ordered from Single-Cell Discoveries B.V.
scRNA-Seq was performed by Single-Cell Discoveries B.V. using SORT-seq protocol
SORT-seq (partially robotized version of the CEL-seq2 protocol)

treatment_protocol: Mice were treated with CLDN1 mAb (25mg/kg i.p. once per week, n=11 treated mice), or with vehicle control (PBS i.p. once per week, n= 10 ctrl mice) for 6 weeks

value: Cholangiocarcinoma

value: anti-CLDN1 mAb


title: CCA_Treated_Tum2_plate164


title: Cd19_KO_rep1

status: Public on Jun 09 2026

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

description: Library name: Cd19_KO_rep1

data_processing:
Quality control of raw reads was performed with FastQC (v0.11.9), and sequences were aligned to the Mus musculus reference genome (mm10) using STAR (v2.7.10a). Read quantification was carried out using the featureCounts function of the Rsubread package (v2.12.3) at gene-level using GENCODE annotation retaining only uniquely mapping reads.
Assembly: mm10
Supplementary files format and content: comma separated text file (.csv) of raw counts with all samples.

source_name: lung

extract_protocol:
Total RNA was isolated from FACS-sorted spleen and lung cells of WT and Dpp3−/− mice using QIAzol Lysis Reagent (QIAGEN) according to the manufacturer’s instructions. RNA concentration and purity were assessed prior to downstream applications.
total RNA was subjected to poly(A) mRNA sequencing using SMARTer-Stranded Total RNA Kit (Clontech), according to the manufacturer’s instructions.

value: lung

value: KO


title: WT_Pos478

description: Library name: 478


title: Mel-TIL-019


title: CCA_Treated_Tum2_plate163


title: CCA_Treated_Tum2_plate162


title: WT_Neg476

description: Library name: 476


title: CCA_CTRL_Tum1_plate154

value: vehicle control


title: Mel-TIL-011


title: CCA_CTRL_Tum1_plate153


title: Het_Pos474

description: Library name: 474


title: CCA_CTRL_Tum1_plate152


title: Mel-TIL-002


title: WT_Pos471

description: Library name: 471


title: HM038


title: CCA_CTRL_Tum1_plate151


title: mdx:Utrn+/- treated with high dose PB1046-3

city: Kansas city

last: Huang

state: KS

address: 3901 Rainbow Boulevard

department: Cardiovascular Medicine

institute: KUMC

description: Library name: Sample_N2692

data_processing:
NextSeq System Suite v2.2.0
The gene differential expressions were analyized using EdgeR
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Heart

extract_protocol:
Frozen cell pellets (isolated cardiomyocytes) were thawed at room temperature, and total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (74704, QIAGEN) according to the manufacturer's instructions.
Samples were run on the Agilent Tapestation 4200 to determine level of degradation thus ensuring only high quality was used (RIN Score>=8). The Qubit fluorimeter was used to determine the concentration prior to starting library prep. 1.0 μg of total RNA (DNAse treated) was then prepared with the TruSeq Stranded mRNA Library Prep Kit from Illumina. Poly-A RNA was purified and fragmented before strand specific cDNA synthesis. cDNA were then a-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again.

treatment_protocol: Animals received PB1046 (0.75 or 1.5 mg/kg) or saline every other day from 4 to 12 weeks of age. Cardiac function was assessed weekly by echocardiography, and hearts were collected at 14 weeks of age for histological and molecular analyses.

value: Heart

value: Cardiomyocytes

value: High dose PB1046

value: mdx:Utrn+/- treated


title: mdx:Utrn+/- treated with high dose PB1046-2

description: Library name: Sample_N2683


title: mdx:Utrn+/- treated with saline2

description: Library name: Sample_N2658

value: Saline (control)

value: mdx:Utrn+/- control


title: HM027

source_name: lymph node


title: Het_Pos467

description: Library name: 467

value: Frontal Cortex


title: mdx:Utrn+/- treated with saline1

description: Library name: Sample_N2611


title: HM026


title: mdx mice treated with high dose PB1046-2

description: Library name: Sample_N2706

value: mdx

value: mdx treated


title: WT_Neg463

description: Library name: 463

value: Male


title: mdx mice treated with high dose PB1046-3

description: Library name: Sample_N2708


title: mdx mice treated with high dose PB1046-1

description: Library name: Sample_N2609


title: HM019


title: mdx mice treated with saline3

description: Library name: Sample_N2702

value: mdx control


title: Het_Pos461

description: Library name: 461


title: HM017

value: Untreated


title: WT_Pos460

description: Library name: 460


title: WT MA10-infected mouse 4; Day 6

city: Charlottesville

first: G. Brett

last: Moreau

state: Virginia

address: 345 Crispell Drive

institute: University of Virginia

description:
Library name: MA10-4
Column name in MJU4200_genecounts.csv: MJU4200.9

data_processing:
RNA-Seq reads were first processed using Cutadapt to trim the adapter sequences and then the quality of the reads was assessed by FastQC  and MultiQC. After these processes, the reads were aligned to the mouse mm10 using STAR v2.5.3a  in a 2-passing mode to generate a gene matrix for differential gene expression.
Assembly: mm10
Supplementary files format and content: CSV file including DESeq2-normalized counts for genes identified in this study.

source_name: Lung

extract_protocol:
A snip from the lower inferior lobe was taken and RNA was extracted from murine lung tissue preserved in trizol by bead beating (TissueLyserII, Qiagen), followed by a phenol-chloroform extraction and RNA Isolation Kit (Qiagen). RNA quality was assessed using Agilent Tape Station RNA kit.
cDNA libraries were prepared using the NEB ultra-directional library preparation kit 2.0 following manufacturer's protocol

treatment_protocol: Wildtype mice were either mock infected (saline) or infected with the mouse adapted SARS-CoV-2 strain MA10. After six days mice were euthanized and lung tissue was collected for RNA isolation.

value: Lung

value: WT

value: MA-10 infection

tag: time

value: Day 6


title: WT MA10-infected mouse 5; Day 6

description:
Library name: MA10-5
Column name in MJU4200_genecounts.csv: MJU4200.10


title: WT_Neg455

description: Library name: 455


title: HM015

city: Melbourne

last: Di Pietro

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre


title: mdx:Utrn+/- treated with high dose PB1046-1

description: Library name: Sample_N2610


title: WT MA10-infected mouse 2; Day 6

description:
Library name: MA10-2
Column name in MJU4200_genecounts.csv: MJU4200.7


title: WT MA10-infected mouse 1; Day 6

description:
Library name: MA10-1
Column name in MJU4200_genecounts.csv: MJU4200.6


title: WT Control mouse 5; Day 6

description:
Library name: Control-5
Column name in MJU4200_genecounts.csv: MJU4200.5

value: No infection


title: Het_Neg448

description: Library name: 448

value: Female


title: WT Control mouse 4; Day 6

description:
Library name: Control-4
Column name in MJU4200_genecounts.csv: MJU4200.4


title: HM012


title: Het_Neg441

description: Library name: 441