title: WT_CTR_exp2_biol_rep_2

first: Ilya

last: Shamovsky

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

data_processing:
The reads were aligned against mouse genome assembly using Hisat2 version 2.1.0. The number of reads in annotated genes was counted using htseq-count version 0.11.0 with option -i set to "gene_id"
Assembly: GRCm38
Supplementary files format and content: .csv,  gene counts  matrix

source_name: liver

growth_protocol: Mice were bred and maintained in the Alexandria Center for the Life Sciences animal facility of the New York University School of Medicine, in specific pathogen-free conditions and were fed LabDiet standard 5053 diet prior to experimentation. C57BL/6 mice (Jax 000664), Gcn2 KO (B6.129S6-Eif2ak4tm1.2Dron/J) and Fgf21 KO (B6.129Sv(Cg)-Fgf21tm1.1Djm/J) mice were purchased from Jackson Laboratories. Cse KO (129/C57BL/6 background) were generated by Rui Wang as previously described and provided  by Christopher Hine13. Mice in all the experiments were at least 9 weeks old at the starting point of various diets unless described specifically. Het and KOs were co-housed except during food intake measurements and calorie restriction experiments.

extract_protocol:
To study transcriptional response in mouse tissues, total RNA was isolated from the homogenates by trizol (1:10 ratio) method. mRNA was purified by NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490S) from Turbo-DNAse treated total RNA.
A NEB Next® Ultra Library Preparation Kit (NEB E7530S) was used to prepare 0.5 µg of total RNA for RNA-seq.

treatment_protocol: All custom diets were procured from TestDiet. All diets were based on the defined amino acid diet 5CC7. For individual or dual amino acid depleted diets, the specific amino acid(s) was completely removed, and all other amino acids were increased in proportion. For pantothenic acid-deficient diet, it was removed from the same 5CC7 defined diet. Unless specified control diet refers to the 5CC7 diet. Where specified the diet was supplemented with L-buthionine sulfoximine (BSO).

value: tissue

value: liver

value: WT

value: control diet


title: Kidney cortex, female, control, vehicle, rep4

status: Public on Mar 10 2025

type: SRA

city: Washington

first: Bryce

last: Jones

state: DC

address: 4000 Reservoir Rd NW

department: Pharmacology and Physiology

country: USA

institute: Georgetown University

library_source: transcriptomic

data_processing:
Sequencing files were aligned and processed with BioJupies, a webserver that automatically analyzes RNA-seq datasets and generates Jupyter Notebooks: https://doi.org/10.1016/j.cels.2018.10.007.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains raw read counts for all 32 samples.
Supplementary files format and content: Tab-delimited text file contains log CPM for all 32 samples.

molecule: polyA RNA

organism: Mus musculus

source_name: Kidney cortex

extract_protocol:
Kidney cortex RNA was isolated with Qiagen RNeasy Mini Kit.
RNA was sent to Genewiz (South Plainfield, NJ, USA) for RNA-sequencing (NEBNext Ultra II RNA Library Prep Kit, poly-A selection method).

tag: tissue

value: Kidney cortex

tag: strain

tag: age

value: 25 weeks

tag: Sex

value: female

tag: genotype

tag: treatment

value: Vehicle


title: WT_CTR_exp2_biol_rep_1

city: New York

state: New York

tag: cell type


title: WT_noTrp_exp2_biol_rep_3

value: no Trp diet


title: HEK293T,EJCEnh,DMSO,1

city: Aurora

first: Divya

last: Kolakada

state: CO

address: 13001 E 17th Place

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz

description:
HEK293T cells with with the EJC-Enhanced NMD reporter library integrated, treated with DMSO. Rep 1
DESeq_RNA_ARTi.csv

data_processing:
Sequencing reads were trimmed to the sequence of interest
Reads 1 and 2 were aligned. Only perfectly aligned reads were accepted
Reads were mapped to a reference file
UMIs were deduplicated and a final bed file was created of reads in the correct orientation
Occurences of each sequence was counted and put through a DESeq2 pipeline, calculating the fold change of DMSO to SMG1i and normalizing to NMD negative sequences
Assembly: N/A, custom reference file consisting of all possible sequences in NNNNNNTRRN used for mapping
Supplementary files format and content: DESeq_RNA_ART.csv: Fold changes for the sequences in the  EJC-Independent population of cells after being put though DESeq2
Supplementary files format and content: DESeq_RNA_ARTi.csv: Fold changes for the sequences in the  EJC-Enhanced population of cells after being put though DESeq2

molecule: total RNA

organism: Homo sapiens

source_name: Kidney

growth_protocol: HEK293T cells were maintained in DMEM and 10% Equalfetal

extract_protocol:
RNA was harvested using TRIzol
RNA was converted into cDNA and libraries were made via a homemade library prep protocol

treatment_protocol: DMSO and SMG1i (0.5 uM) were added 24 hours before harvest

value: Kidney

tag: cell line

value: Human Embryonic Kidney

value: WT integrated with EJC-enhanced reporter library in a single location within the genome

value: DMSO


title: WT_noTrp_exp2_biol_rep_2


title: WT_noTrp_exp2_biol_rep_1


title: Kidney cortex, female, control, vehicle, rep2


title: cse_noTrp_exp2_biol_rep_3

value: cse


title: cse_noTrp_exp2_biol_rep_2


title: cse_noTrp+BSO_exp2__biol_rep_3

value: no Trp diet + BSO


title: HEK293T,EJCInd,SMG1i,2

description:
HEK293T cells with with the EJC-Independent NMD reporter library integrated, treated with SMG1i. Rep 2
DESeq_RNA_ART.csv

value: WT integrated with EJC-independent reporter library in a single location within the genome


title: HEK293T,EJCInd,SMG1i,1

description:
HEK293T cells with with the EJC-Independent NMD reporter library integrated, treated with SMG1i. Rep 1
DESeq_RNA_ART.csv


title: cse_noTrp_exp2_biol_rep_1


title: Kidney cortex, male, Alport, nicotinamide riboside, rep4

value: male

value: Nicotinamide riboside


title: cse_noTrp+BSO_exp2__biol_rep_2

value: tissue

value: liver


title: HEK293T,EJCInd,SMG1i,3

description:
HEK293T cells with with the EJC-Independent NMD reporter library integrated, treated with SMG1i. Rep 3
DESeq_RNA_ART.csv


title: Kidney cortex, female, control, vehicle, rep1


title: HEK293T,EJCEnh,SMG1i,1

description:
HEK293T cells with with the EJC-Enhanced NMD reporter library integrated, treated with SMG1i. Rep 1
DESeq_RNA_ARTi.csv


title: Kidney cortex, male, Alport, nicotinamide riboside, rep3


title: cse_noTrp+BSO_exp2__biol_rep_1


title: HEK293T,EJCInd,DMSO,3

description:
HEK293T cells with with the EJC-Independent NMD reporter library integrated, treated with DMSO. Rep 3
DESeq_RNA_ART.csv


title: cse_noCys_exp2_biol_rep_4

value: no Cys diet


title: Kidney cortex, male, Alport, nicotinamide riboside, rep2

value: Kidney cortex


title: HEK293T,EJCInd,DMSO,2

description:
HEK293T cells with with the EJC-Independent NMD reporter library integrated, treated with DMSO. Rep 2
DESeq_RNA_ART.csv


title: Kidney cortex, male, Alport, nicotinamide riboside, rep1

value: 25 weeks


title: cse_noCys_exp2_biol_rep_3


title: HEK293T,EJCEnh,DMSO,2

description:
HEK293T cells with with the EJC-Enhanced NMD reporter library integrated, treated with DMSO. Rep 2
DESeq_RNA_ARTi.csv


title: Kidney cortex, female, control, vehicle, rep3

value: female


title: HEK293T,EJCInd,DMSO,1

description:
HEK293T cells with with the EJC-Independent NMD reporter library integrated, treated with DMSO. Rep 1
DESeq_RNA_ART.csv


title: cse_noCys_exp2_biol_rep_2


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 15

type: RNA

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 51_ORAL MUCOSA

hyb_protocol: Microarray hybridization and staining was performed by means of GeneChip™ Hybridization, Wash, and Stain Kit (Affymetrix) using the GeneChip System (Affymetrix) following the manufacturer’s recommendations.

scan_protocol: Microarray scanning was performed by means of GeneChip™ Hybridization, Wash, and Stain Kit (Affymetrix) using the GeneChip System (Affymetrix) following the manufacturer’s recommendations.

data_processing: Partek® Genomics Suite® software, version 7.0 (Partek Inc., St. Louis, MO, USA) was used to normalize the probe level data and convert them into expression values by means of robust multiarray average (RMA). An exploratory principal component analysis (PCA) was performed and existing batch effect was removed by means of the specific tool implemented in Partek® GS®.

label: biotin

source_name: ORAL

label_protocol: Biotin-labeled complementary RNA was synthesized starting from 100 ng total RNA by means of GeneChip™ HT 3' IVT PLUS Reagent Kit (Applied Biosystems) according to the standard protocol supplied.

extract_protocol: Total cellular RNA was isolated from feeder layer-depleted holoclone by means of Qiazol Reagent (Qiagen) following manufacturer’s instructions. RNA sample concentration was evaluated using NanoDrop ND-1000 spectrophotometer (ThermoFisher Scientific) and purity was assessed by means of 260/280 nm and 260/230 ratios. Agilent 2100 Bioanalyzer (Agilent Technologies) was used to determine the integrity of total RNA.

tag: donor

value: ORAL

tag: clone id


title: Kidney cortex, male, Alport, vehicle, rep4

value: Vehicle


title: cse_noTrp+BSO_exp2__biol_rep_4


title: Neutrophil, PW_056_IC_rep1

city: Atlanta

first: Min

last: Huang

address: WMB, 101 Woodruff Circle

institute: Emory University

data_processing:
The data pre-processing tool, fastp, was used to perform quality control and adapter trimming. Results were filtered by quality. The software program Hierarchical Indexing for Spliced Alignment of Transcripts 2 (HISAT2) was used to map RNA sequencing reads prior to building the index using the human reference genome grch38. Indices were used to map sequential reads to the human genome. FeatureCounts were applied to generate a matrix of row counts of each of the genes in all the samples.
Assembly: human reference genome grch38
Supplementary files format and content: txt, counts

source_name: blood

growth_protocol: Blood was collected by venipuncture into an ethylenediaminetetraacetic acid (EDTA) vacutainer tube and centrifuged at 400XG to separate cells from platelet-rich plasma. After initial separation, plasma was centrifuged at 3000XG for 10 minutes at 4C to remove any remaining red blood cells or platelets prior to being frozen at -80C. Pelleted blood cells were resuspended in sterile phosphate buffered saline (PBS; Thermo Fisher Scientific, Waltham, MA) with 2.5 mM EDTA up to the original whole blood volume. Neutrophils were purified by negative selection from PBS-EDTA washed whole blood using the EasySep Direct Human Neutrophil Isolation kit (StemCell Technologies, Cambridge, MA) according to the manufacturer’s protocol. There was >99% neutrophil purity based on cytospin staining with Diff-Quik.

extract_protocol:
RNA was isolated from blood neutrophils using the Nucleospin RNA II kit with on-column genomic DNA digestion according to the manufacturer’s protocol (Takara Bio, San Jose, CA). RNA was quantified using a NanoDrop Fluorospectrometer (Thermo Fisher). RNA was quality assessed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA) in the Emory Integrated Genomics Core. cDNA was generated using the SMART-Seq® v4 Ultra® low Input RNA Kit (Takara Bio).
The final RNA-seq library was generated using the Nextera XT kit (Illumina, San Diego, CA).
RNA-seq libraries were sequenced on the Novaseq 6000 with a sequencing depth of 30M paired-end 100 base pair reads per sample.

treatment_protocol: Two million neutrophils were resuspended in Roswell Park Memorial Institute (RPMI) medium (Thermo Fisher) without serum and cultured overnight at 37°C and 5% CO2 in a humidified incubator with 740 ng/ml low molecular weight lyoVec poly(I:C) (InvivoGen, San Diego, CA) resuspended in endotoxin-free water. After centrifugation at 400ΧG, neutrophil pellets were saved in RNAlater (Thermo Fisher) and frozen at -80°C.

value: blood

value: primary human cell

value: Neutrophil

tag: individual

value: Not sensitized, male

value: poly(I:C) stimulation


title: WT_noCys_exp2_biol_rep_4

value: WT


title: Kidney cortex, male, Alport, vehicle, rep2


title: Kidney cortex, male, Alport, vehicle, rep1


title: Neutrophil, PW_056_IC_rep2


title: cse_noCys_exp2_biol_rep_1

value: cse


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 14

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 50_ORAL MUCOSA


title: Neutrophil, PW_055_IC_rep1


title: WT_noCys_exp2_biol_rep_2


title: Kidney cortex, male, Alport, vehicle, rep3

value: male


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 12

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 48_ORAL MUCOSA


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 13

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 49_ORAL MUCOSA


title: WT_noCys_exp2_biol_rep_1


title: WT_noCys_exp2_biol_rep_3


title: Kidney cortex, male, control, nicotinamide riboside, rep3

value: Nicotinamide riboside


title: Kidney cortex, male, control, nicotinamide riboside, rep4


title: Neutrophil, PW_052_IC_rep2


title: Neutrophil, PW_052_IC_rep1


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 10

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 46_ORAL MUCOSA


title: Neutrophil, PW_051_IC_rep2

value: Not sensitized, female


title: Kidney cortex, male, control, nicotinamide riboside, rep2


title: Neutrophil, PW_055_IC_rep2


title: cse_adipose_noCys_biol_rep_4

source_name: adipose

treatment_protocol: All custom diets were procured from TestDiet. All diets were based on the defined amino acid diet 5CC7. For individual or dual amino acid depleted diets, the specific amino acid(s) was completely removed, and all other amino acids were increased in proportion. For pantothenic acid-deficient diet, it was removed from the same 5CC7 defined diet. Unless specified control diet refers to the 5CC7 diet.

value: tissue

value: adipose


title: Neutrophil, PW_051_IC_rep1


title: Kidney cortex, male, control, vehicle, rep4

value: Kidney cortex


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 9

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 45_ORAL MUCOSA


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 8

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 44_ORAL MUCOSA


title: Neutrophil, PW_048_IC_rep1


title: WT_adipose_noCys_biol_rep_3

value: no Cys diet


title: cse_adipose_noCys_biol_rep_2


title: Kidney cortex, male, control, nicotinamide riboside, rep1

value: 25 weeks


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 11

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 47_ORAL MUCOSA

value: ORAL


title: HOLOCLONE_CONJUNCTIVA_REPLICATE 9

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 29_CONJ

source_name: CONJUNCTIVA

value: CON 90

value: CONJUNCTIVA


title: Neutrophil, PW_048_IC_rep2

value: blood

value: primary human cell


title: HOLOCLONE_CONJUNCTIVA_REPLICATE 8

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 28_CONJ


title: cse_adipose_noCys_biol_rep_3


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 7

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 43_ORAL MUCOSA


title: Kidney cortex, male, control, vehicle, rep3

value: Vehicle


title: cse_adipose_noCys_biol_rep_1


title: Neutrophil, PW_047_IC_rep1

value: Neutrophil

value: Not sensitized, male

value: poly(I:C) stimulation


title: Kidney cortex, male, control, vehicle, rep2

value: male


title: Neutrophil, PW_047_IC_rep2


title: WT_adipose_noCys_biol_rep_2

value: WT


title: Kidney cortex, male, control, vehicle, rep1


title: Panc_Saline_D7_Acinar_Rep1

city: Baltimore

first: Emily

last: Lo

state: MD

address: 733 N Broadway

institute: Johns Hopkins

description:
Bisulfite-treated DNA
lcm_wbgs_bsseq_smoothed_coverage_filtered_geo.rda

library_source: genomic

data_processing:
Adapter sequences were computationally trimmed with Trim Galore, with 10 additional bp trimmed from the 3’ end of R1 and 10 bp from the 5’ end of R2 to account for the low complexity polynucleotide tail added by the Adaptase enzyme. Bisulfite-aware alignment of the trimmed reads to the mm10 genome was performed using Bismark with default parameters. Samtools was used to merge individual bam files corresponding to fastq file pairs and to name-sort the merged bam file. Bismark was then used to deduplicate merged, name-sorted bam files, then extract CpG methylation information. Bisulfite conversion rate was determined by alignment of trimmed reads to the lambda genome using Bismark with default parameters. Bisulfite conversion rate was at least 99.2% for all samples, with an average of 99.34% among all samples.
Bioconductor package bsseq was used for integrating independent CpG_report files from Bismark’s methylation_extractor. CpG methylation values for each sample were smoothed with the BSmooth function using default parameters. CpGs were coverage-filtered with a cutoff of 2X for each biological replicate. Smoothed, coverage-filtered bsseq object was saved as an .rda (RData) file.
Assembly: mm10
Supplementary files format and content: lcm_wbgs_bsseq_smoothed_coverage_filtered_geo.rda: Rdata file containing smoothed and coverage-filtered bsseq object (with CpG reports from all samples)

molecule: genomic DNA

source_name: Pancreas

extract_protocol:
Following euthanasia, pancreata were immediately harvested. A 2-4 cm incision was made in the abdominal skin along the midline and then into the abdomen. Pancreata were exteriorized and removed using a combination of blunt and sharp dissection. The tail of each pancreas was immediately flash frozen in liquid nitrogen for 5 minutes, then transferred to -80°C for long-term storage. Fresh frozen tissue samples were cryo-sectioned at 10 µm thick onto PEN membrane slides and stored at -20°C. Immediately prior to LCM, slides were fixed briefly in 70% ethanol, then stained with hematoxylin and eosin. LCM for the appropriate targeted cell type was performed using Zeiss PALM Microbeam on 10X or 20X magnification. The number of pooled cuts per cell type needed to reach a desired input of at least 20 ng DNA for WGBS varied for each sample. Genomic DNA was extracted using QIAamp DNA Micro Kit (Qiagen cat. #56304) according to manufacturer’s instructions for the “Isolation of Genomic DNA from Laser-Microdissected Tissues” protocol, with carrier RNA inclusion. To increase final DNA yield, samples were eluted twice, using the eluate from the first elution for the second, and incubating for 5 min each before centrifugation.
Genomic DNA samples were quantified by Qubit dsDNA HS assay (ThermoFisher Scientific, cat. #Q32851). 1% unmethylated Lambda DNA (Promega cat. #D1521) was spiked into genomic DNA to monitor bisulfite conversion efficiency. xGen Methyl-Seq DNA Library Prep Kit (IDT, cat. #10009860) was used for WGBS library preparation. Genomic DNA (19-50 ng) was fragmented to a target peak of 300-400 bp using the Covaris S2 Focused-ultrasonicator in a 50 μl volume according to the manufacturer’s instructions. The fragmented genomic DNA was subjected to bisulfite conversion using the EZ DNA Methylation-Gold Kit (Zymo Research, cat. #D5005) following the manufacturer’s instructions. Methyl-seq libraries were generated according to the manufacturer’s instructions, and the resulting libraries were amplified for 7 PCR cycles using unique dual indexing primers (Swift Bioscience, cat. #X9096-PLATE).  The resulting WGBS libraries were evaluated on a 2100 Bioanalyzer using the Agilent High-Sensitivity DNA Kit (Agilent Technologies, cat. #5067-4626) and quantified via qPCR using the KAPA Library Quantification Kit (KAPA Biosystems, cat. #KK4824). WGBS libraries were sequenced on an Illumina NovaSeq 6000 system at a 2 × 150 bp read length with a 5% spike-in of PhiX control library.

treatment_protocol: All animal procedures were performed in accordance with Johns Hopkins University Animal Care and Use Committee-approved protocols MO18M24 and MO21M20. Ptf1a-rtTA, TRE-KLF4 (AK) mice were generated by crossing strain B6.129S6(SJL)-Ptf1atm3.1(rtTA)Mgn/Mmjax (Jackson Laboratories, cat. #036492-JAX) with strain FVB.Cg-Tg(tetO-KLF4)32831Rup/Mmjax (Jackson Laboratories, cat. #036730-JAX. Mice were genotyped using JAX-supplied primers and protocols. ADM was induced by administering 12.5 mg/kg doxycycline intraperitoneally once every 24 hours for 2 days. For caerulein-induced pancreatitis, C57BL/6J wild-type mice (Jackson Laboratories, cat. #000664) were administered 0.625 mg/kg caerulein (Millipore Sigma, cat. #C9026) intraperitoneally 4x daily for 2 days.  Animals were euthanized according to AVMA guidelines prior to pancreatic extraction.

value: Pancreas

value: acinar

tag: timepoint

value: Day 7

value: Female

value: 7 weeks

value: Saline IP 4x daily at D0 and D1


title: Neutrophil, PW_045_IC_rep2

value: Sensitized, male


title: HOLOCLONE_CONJUNCTIVA_REPLICATE 6

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 26_CONJ

value: CON 89


title: Panc_Saline_D7_Duct_Rep1

value: duct


title: WT_adipose_noCys_biol_rep_1

value: tissue

value: adipose

value: no Cys diet


title: HOLOCLONE_CONJUNCTIVA_REPLICATE 7

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 27_CONJ

value: CON 90

value: CONJUNCTIVA


title: cse_muscle_noTrp_biol_rep_4

source_name: muscle

value: muscle

value: cse

value: no Trp diet


title: Neutrophil, PW_045_IC_rep1

value: blood

value: primary human cell

value: Neutrophil

value: poly(I:C) stimulation


title: cse_muscle_noTrp_biol_rep_3


title: Neutrophil, PW_042_IC_rep2

value: Not sensitized, male


title: cse_muscle_noTrp_biol_rep_2


title: Panc_Saline_D4_Acinar_Rep1

value: Pancreas

value: acinar

value: Day 4

value: Female

value: 6 weeks

value: WT

value: Saline IP 4x daily at D0 and D1


title: HOLOCLONE_CONJUNCTIVA_REPLICATE 3

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 23_CONJ

value: CON 89


title: HOLOCLONE_CONJUNCTIVA_REPLICATE 5

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 25_CONJ

value: CONJUNCTIVA


title: HOLOCLONE_CONJUNCTIVA_REPLICATE 2

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 22_CONJ


title: HOLOCLONE_CONJUNCTIVA_REPLICATE 4

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 24_CONJ


title: Neutrophil, PW_042_IC_rep1


title: cse_muscle_noTrp_biol_rep_1

value: tissue

value: muscle


title: Panc_Saline_D2_Duct_Rep2

value: duct

value: Day 2

value: Male


title: Neutrophil, PW_029_IC_rep2

value: blood

value: primary human cell

value: Neutrophil

value: Sensitized, male


title: HOLOCLONE_CONJUNCTIVA_REPLICATE 1

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 21_CONJ


title: Panc_Saline_D2_Acinar_Rep2

value: Pancreas

value: acinar


title: Neutrophil, PW_029_IC_rep1

value: poly(I:C) stimulation


title: Panc_Saline_D2_Duct_Rep1

value: Female

value: 6 weeks


title: cse_muscle_noTrp_biol_rep_5

value: cse

value: no Trp diet


title: Panc_Saline_D4_Duct_Rep1

value: Day 4

value: WT

value: Saline IP 4x daily at D0 and D1


title: WT_muscle_noTrp_biol_rep_2

value: tissue

value: muscle


title: Neutrophil, PW_027_IC_rep2


title: Panc_Saline_D2_Acinar_Rep1

value: Day 2


title: cse_muscle_noCys_biol_rep_4

value: no Cys diet


title: WT_muscle_noTrp_biol_rep_1


title: HOLOCLONE_LIMBUS_REPLICATE 8

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 20_LIMBUS

source_name: LIMBUS

value: LE 51

value: LIMBUS


title: cse_muscle_noCys_biol_rep_3


title: cse_muscle_noCys_biol_rep_1


title: Neutrophil, PW_027_IC_rep1

value: blood

value: primary human cell

value: Neutrophil

value: Sensitized, male


title: Panc_Caer_D7_Duct_Rep2

value: Pancreas

value: duct

value: Day 7

value: Male

value: 7 weeks

value: 0.625 mg/kg caerulein IP 4x daily at D0 and D1


title: Neutrophil, PW_026_IC_rep2

value: Not sensitized, male

value: poly(I:C) stimulation


title: Panc_Caer_D7_Acinar_Rep2

value: acinar (recovered)

value: WT


title: Panc_Caer_D7_Duct_Rep1

value: Female


title: Neutrophil, PW_025_IC_rep2

value: Not sensitized, female


title: WT_muscle_noCys_biol_rep_4

value: tissue

value: muscle

value: no Cys diet


title: HOLOCLONE_LIMBUS_REPLICATE 7

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 19_LIMBUS

value: LE 51

value: LIMBUS


title: Panc_Caer_D7_Acinar_Rep1

value: Pancreas


title: WT_muscle_noCys_biol_rep_2


title: HOLOCLONE_LIMBUS_REPLICATE 2

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 8_LIMBUS


title: HOLOCLONE_LIMBUS_REPLICATE 4

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 10_LIMBUS


title: HOLOCLONE_LIMBUS_REPLICATE 6

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 12_LIMBUS


title: WT_muscle_noCys_biol_rep_1


title: HOLOCLONE_LIMBUS_REPLICATE 5

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 11_LIMBUS


title: Neutrophil, PW_025_IC_rep1

value: blood

value: primary human cell

value: Neutrophil


title: HOLOCLONE_LIMBUS_REPLICATE 3

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 9_LIMBUS


title: Neutrophil, PW_023_IC_rep1

value: Sensitized, male


title: HOLOCLONE_LIMBUS_REPLICATE 1

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 7_LIMBUS


title: Panc_Caer_D4_Duct_Rep1

value: duct

value: Day 4

value: 6 weeks

value: 0.625 mg/kg caerulein IP 4x daily at D0 and D1


title: cse_muscle_CTR_biol_rep_3

value: cse

value: control diet


title: Neutrophil, PW_026_IC_rep1

value: Not sensitized, male

value: poly(I:C) stimulation


title: Panc_Caer_D4_Duct_Rep2

value: Male

value: WT


title: Neutrophil, PW_023_IC_rep2


title: Panc_Caer_D4_ADM_Rep2

value: ADM


title: cse_muscle_CTR_biol_rep_4

value: tissue

value: muscle


title: Neutrophil, PW_021_IC_rep2

value: blood

value: Not sensitized, female


title: Panc_Caer_D4_ADM_Rep1

value: Pancreas

value: Female


title: Neutrophil, PW_021_IC_rep1

value: primary human cell

value: Neutrophil


title: cse_muscle_CTR_biol_rep_1


title: Neutrophil, PW_013_IC_rep1


title: Panc_Caer_D2_ADM_Rep2

value: Day 2

value: 6 weeks


title: WT_muscle_CTR_biol_rep_3


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 3

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 3_ORAL

value: ORAL


title: Panc_Caer_D2_Duct_Rep1

description:
Bisulfite-treated DNA
lcm_wbgs_bsseq_smoothed_coverage_filtered_geo.rda

value: duct

value: 0.625 mg/kg caerulein IP 4x daily at D0 and D1


title: WT_muscle_CTR_biol_rep_2

value: control diet


title: Neutrophil, PW_012_IC_rep2

value: poly(I:C) stimulation


title: ChIPbis_AtT_ERPax7_Tam96h

city: Montréal

first: Juliette

middle: Emilie

last: Harris

state: Québec

address: 110 avenue des Pins O

country: Canada

institute: IRCM

data_processing:
Paired-end reads were first trimmed for adapter content and aligned to the mouse mm10 reference genome using Bowtie2/2.4 (--no-unal --no-mixed --no-discordant).
Bam files were created and duplicated reads removed using view (-b) and markdup (-r) from SAMtools/1.12.
Coverage tracks were created using bamCoverage (-bs 10 -e 150 --normalizeUsing BPM) from deepTools 3.5
Peaks were called using callpeak (-f BAMPE -p 1e-3/1e-5 -g mm -- min-length 100 --max-gap 50) from MACS/2.2.7.1.
Assembly: mm10
Supplementary files format and content: Bigwig, unit: counts per million

growth_protocol: AtT-20 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS) and antibiotics (penicillin, streptomycin).

extract_protocol:
Nuclei lysates were sonicated and protein-DNA complexes were isolated with specific antibodies. Fragments of 200-500 bp were kept and six to twelve independent ChIPs were pooled. Bisulfite conversion was done with EZ DNA Methylation-Lightning (Zymo Research).
Libraries and flow cells were prepared by the IRCM Molecular Biology Core Facility according to Illumina’s recommendation

value: Corticotrope

value: Tam 96h


title: ChIPbis_AtT_ERPax7_Tam48h_rep2

value: Tam 48h


title: Neutrophil, PW_012_IC_rep1


title: Panc_Caer_D2_ADM_Rep1

value: ADM

value: WT


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 4

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 4_ORAL


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 5

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 5_ORAL


title: Pank_AK_Ctrl_D7_Duct_Rep1

value: Day 7

value: 8 weeks

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: WT_muscle_CTR_biol_rep_1

value: tissue

value: muscle


title: Panc_Caer_D2_Duct_Rep2

value: Pancreas

value: Day 2

value: Male


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 2

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 2_ORAL

value: ORAL


title: LPN2

city: Chicago

first: Ronen

last: Sumagin

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data was demultiplexed using Cell Ranger from 10x Genomics (version 7.0.1), converting the base call format (.bcl) into the FASTQ format. The FASTQ files were then aligned to the mouse reference genome mm10. The generated filtered feature-barcode matrix was loaded into R 4.2.3 and analyzed with the R package Seurat (v4.3.0).
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz (barcodes), features.tsv.gz (gene IDs), matrix.mtx.gz (gene expression count matrix)

source_name: Colon

extract_protocol:
Excised colons were opened longitudinally, briefly washed, and were placed in a tube containing 10mL Hanks’ Balanced Salt Solution without calcium, magnesium, and phenol red (HBSS-) supplemented with 1 mM N-Acetyl-L-cysteine (NAC). The tissue was vortexed for 15 seconds, followed by a 15-second rest on ice. This was repeated for a total of 2 minutes. To collect the epithelial fraction, the rinsed colon was incubated in 10mL HBSS-, 1mM NAC, and 10mM EDTA for 2 rounds of 15 minutes each at 37C with shaking motion, followed by brief vortexing and passing through a 100um strainer. Filtered epithelial fraction was pelleted while the remaining lamina propria tissue was minced. Both fractions were further digested into single cells in HBSS- supplemented with1.5mg/mL of collagenase type VIII, 5% FBS and 25ug/mL DNase I for 25 minutes at 37C with shaking motions. The single cell suspension was achieved by filtering through a 40um strainer.
Sixteen thousand cells, with a viability of over 70%, were loaded into the Chromium Controller (10X Genomics, PN-120223) on a Chromium Next GEM Chip G (10X Genomics, PN-1000120), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000286) and Dual Index Kit TT Set A (10X Genomics, PN-1000215) according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. The multiplexed libraries were pooled and sequenced on Illumina HiSeq 4000 sequencer with 2 × 50 paired-end kits using the following read length: 28 bp Read1 for cell barcode and UMI, and 90 bp Read2 for transcript.

treatment_protocol: Mice were provided with regular food and drinking water containing 3% (wt/vol) DSS  for 5 days.

value: Colon

value: Neutrophils

value: 3% DSS, 5 days


title: Neutrophil, PW_011_IC_rep2

value: blood

value: primary human cell

value: Neutrophil

value: Not sensitized, male

value: poly(I:C) stimulation


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 1

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 1_ORAL


title: HOLOCLONE_ORAL MUCOSA_REPLICATE 6

description:
Gene expression of holoclones from limbual, conjunctival and oral mucosa holoclones.
HOLO 6_ORAL


title: cse_muscle_CTR_biol_rep_2

value: cse

value: control diet


title: Pank_AK_Ctrl_D7_Acinar_Rep1

value: acinar

value: Day 7

value: Female

value: 8 weeks

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: IEN2

description: 10X Genomics


title: cse_noTrp_biol_rep_3

value: liver

value: no Trp diet


title: Neutrophil, PW_011_IC_rep1


title: Neutrophil, PW_013_IC_rep2


title: cse_noTrp_biol_rep_2


title: Pank_AK_Ctrl_D4_Acinar_Rep1

value: Pancreas

value: Day 4


title: Pank_AK_Ctrl_D4_Duct_Rep1

value: duct


title: LPN1

description: 10X Genomics

value: Colon

value: Neutrophils

value: 3% DSS, 5 days


title: Pank_AK_Ctrl_D2_Duct_Rep2

value: Day 2

value: Male

value: 10 weeks

value: WT


title: WT_noTrp_biol_rep_2


title: cse_noTrp_biol_rep_4

value: cse


title: Neutrophil, PW_009_IC_rep2

value: blood

value: primary human cell

value: Neutrophil

value: Sensitized, female

value: poly(I:C) stimulation


title: IEN1

description: 10X Genomics


title: Neutrophil, PW_008_IC_rep1

value: Sensitized, male


title: Neutrophil, PW_009_IC_rep1


title: Pank_AK_Ctrl_D2_Duct_Rep1

value: Pancreas

value: Female

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: cse_noTrp_biol_rep_1

value: liver

value: no Trp diet


title: Pank_AK_Ctrl_D2_Acinar_Rep1

value: acinar


title: MBNL1 MBNL2 DKO IFNg treated replicate 1

city: Seattle

first: Edie

middle: I

last: Crosse

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

data_processing:
RNA-seq reads were mapped to an annotated transcriptome that was created using Ensembl 71, UCSC knownGene and Misov2.0 annotations using RSEM version 1.2.4 (modified to call Bowtie with option ‘-v 2’).
Unaligned reads were mapped to the corresponding genome (hg19/GRCh37 assembly, mm10/GRCmc38 assembly) as well as a database containing all possible pairings of 5’ and 3′ splice sites per gene contained in out merged transcriptome annotation using TopHat version 20.8b.
Assembly: mm10/GRCmc38
Supplementary files format and content: CSV file containing TPM counts for each sample

extract_protocol:
Cells were first pelleted and then RNA was isolated using the Qiagen ReasyA kit (Qiagen 74104)
Poly(A)-selected, unstranded Illumina libraries were prepared according to the TruSeq protocol per manufacturer’s instructions.

value: cell line

value: double knock out of MBNL1 and MBNL2 (DKO)

value: IFNg stimulated


title: Neutrophil, PW_008_IC_rep2


title: cse_noCys_biol_rep_4

value: no Cys diet


title: Neutrophil, PW_007_IC_rep2


title: MBNL1 MBNL2 DKO IFNg treated replicate 3

value: double knock out  of MBNL1 and MBNL2 (DKO)


title: Pank_AK_Ctrl_D2_Acinar_Rep2

value: Day 2

value: Male

value: 10 weeks

value: WT


title: Neutrophil, PW_006_IC_rep2

value: blood

value: primary human cell

value: Neutrophil

value: Not sensitized, male

value: poly(I:C) stimulation


title: MBNL1 MBNL2 DKO untreated replicate 3

value: Unstimulated


title: MBNL1 MBNL2 DKO IFNg treated replicate 2


title: Neutrophil, PW_007_IC_rep1

value: Sensitized, female


title: cse_noCys_biol_rep_3

value: liver

value: cse


title: MBNL1 MBNL2 DKO untreated replicate 2

value: cell line

value: double knock out of MBNL1 and MBNL2 (DKO)


title: Panc_AK_D7_Duct_Rep2

value: Pancreas

value: duct

value: Day 7

value: 8 weeks

value: Ptf1a-rtTA; TRE-KLF4

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: WT_noTrp_biol_rep_1

value: WT

value: no Trp diet


title: MBNL1 MBNL2 DKO untreated replicate 1


title: Panc_AK_D7_Acinar_Rep2

value: acinar (recovered)

value: Male


title: No template control IFNg treated replicate 3

value: No template control

value: IFNg stimulated


title: cse_noCys_biol_rep_1

value: no Cys diet


title: cse_noTrp_biol_rep_5

value: liver


title: Panc_AK_D7_Acinar_Rep1

value: Female

value: 18 weeks


title: Panc_AK_D7_Duct_Rep1


title: Panc_AK_D4_Duct_Rep2

value: Day 4


title: No template control IFNg treated replicate 2

value: cell line


title: WT_noCys_biol_rep_4


title: No template control IFNg treated replicate 1


title: Neutrophil, PW_005_IC_rep1

value: blood

value: primary human cell

value: Neutrophil

value: Sensitized, male

value: poly(I:C) stimulation


title: WT_noCys_biol_rep_3

value: WT


title: WT_noCys_biol_rep_2


title: No template control untreated replicate 3

value: Unstimulated


title: Panc_AK_D4_Duct_Rep1

value: Pancreas

value: duct

value: 24 weeks

value: Ptf1a-rtTA; TRE-KLF4

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: Neutrophil, PW_060_rep1

value: Sensitized, female

value: Baseline


title: WT_noCys_biol_rep_1

value: liver

value: no Cys diet


title: No template control untreated replicate 2

value: cell line

value: No template control


title: Neutrophil, PW_006_IC_rep1

value: blood

value: primary human cell

value: Not sensitized, male


title: Neutrophil, PW_059_rep2

value: Neutrophil

value: Sensitized, male


title: Panc_AK_D4_ADM_Rep1

value: ADM

value: Day 4

value: Male


title: Neutrophil, PW_059_rep1


title: cse_CTR_biol_rep_3

value: cse

value: control diet


title: cse_CTR_biol_rep_4


title: Panc_AK_D2_Duct_Rep2

value: Pancreas

value: duct

value: Day 2

value: 20 weeks

value: Ptf1a-rtTA; TRE-KLF4

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: Neutrophil, PW_005_IC_rep2

value: poly(I:C) stimulation


title: Neutrophil, PW_058_rep2

value: blood

value: Baseline


title: cse_CTR_biol_rep_2

value: liver


title: Panc_AK_D2_ADM_Rep2


title: Brain, PWS-IC deleted 3

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

country: Belgium

institute: Genomics Core Leuven

data_processing:
Adapter removal Ea-utils fastq-mcf  v1.05
Read aligment HISAT2
Count Files HTSeq-count
Assembly: mm10
Supplementary files format and content: Count files in text format

source_name: Brain, PWS-IC deleted 3

growth_protocol: Mouse model

extract_protocol:
Total RNA extraction
Lexogen Quantseq
Poly A capture 3’ sequencing

treatment_protocol: WT vs Prepl knockout

value: Brain

value: PWS-IC deleted


title: Neutrophil, PW_058_rep1

value: primary human cell

value: Neutrophil

value: Not sensitized, male


title: cse_CTR_biol_rep_1

value: cse


title: Panc_AK_D2_Duct_Rep1

value: Male

value: 28 weeks


title: Neutrophil, PW_057_rep2


title: WT_CTR_biol_rep_3

value: WT

value: control diet


title: Brain, PWS-IC deleted 2

source_name: Brain, PWS-IC deleted 2


title: Panc_AK_D2_ADM_Rep1

value: Pancreas

value: ADM

value: Day 2


title: Brain, PWS-IC deleted 1

source_name: Brain, PWS-IC deleted 1


title: Neutrophil, PW_060_rep2

value: Sensitized, female


title: Panc_AK_D4_ADM_Rep2

value: Day 4

value: Female

value: 18 weeks

value: Ptf1a-rtTA; TRE-KLF4

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: Neutrophil, PW_057_rep1

value: blood

value: primary human cell

value: Baseline


title: Neutrophil, PW_056_rep2

value: Neutrophil

value: Not sensitized, male


title: Brain, WT 4 (control for PWS-IC deleted)

source_name: Brain, WT 4

value: Brain


title: WT_CTR_biol_rep_2

value: liver

value: WT


title: WT_CTR_biol_rep_1

value: control diet


title: No template control untreated replicate 1

value: cell line

value: No template control

value: Unstimulated


title: Panc_Saline_Ctrl_D7_Rep1

description: Visium FFPE whole-transcriptome probes

data_processing:
Visium data was preprocessed using spaceranger (v 1.3.0) against 10X Genomics-provided mm10 reference transcriptome build refdata-gex-mm10-2020-A to generate gene-by-spot expression matrices. If necessary, manual image alignment was performed using the 10X Loupe Browser (v 5.1.0).
R package Seurat was used to log-normalize, integrate, and perform Leiden clustering on spot expression profiles.
Assembly: mm10
Supplementary files format and content: Tab-separated values barcode and feature files, matrix expression files, H&E png images, csv tissue position files, json scale factor files
Library strategy: Spatial Transcriptomics

extract_protocol:
Following euthanasia, pancreata were immediately harvested. A 2-4 cm incision was made in the abdominal skin along the midline and then into the abdomen. Pancreata were exteriorized and removed using a combination of blunt and sharp dissection. The head of each pancreas was placed in 10% neutral-buffered formalin for fixation for 24 hrs, then transferred to 70% ethanol. Tissue was then dehydrated in a graded ethanol and xylene series, then embedded in paraffin. Paraffin tissue blocks were stored long-term at 4°C. Prior to library preparation, the DV200 quality metric of RNA from FFPE pancreas tissue was first verified using RNA 6000 Nano Kit (Agilent #5067-1511) according to manufacturer’s instructions. All pancreas sections used as input for Visium ST had a DV200 of ≥ 57%, with most samples ≥70%.
Whole-transcriptome ST was performed using Visium Spatial Gene Expression Reagent Kits for FFPE (10X Genomics #1000185, #1000362, and #1000366). Mouse probe set Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A was used. Library preparation was performed according to manufacturer’s instructions (CG000407, Rev. A), with the following custom parameters: 1) each H&E-stained section was imaged in 12 parts on a Nikon Eclipse Ti Research Photomicroscope at 4X magnification, then images were stitched post-capture using ImageJ; 2) 0.5 µL RNase Block (Agilent #300151) was added per sample (e.g. 2.2 uL for 4X + 10%) at pre-hybridization (Step 1.1.a) and probe hybridization (Step 1.1.g); and 3) PCR cycle number (Step 4.2.d) ranged from 14-17 depending on the Cq value from Step 4.1.e. Sample Index PCR (Step 4.2.a) for each sample was performed with a unique index well from Dual Index Plate TS Set A (10X Genomics #3000511). The 20 FFPE Visium libraries were sequenced on one lane of an S4 flowcell on an Illumina NovaSeq 6000 system at a 2 x 150 bp read length. Libraries were loaded onto the flowcell at a ratio to achieve at least 25,000 reads per spatial spot covered by tissue.

value: Pancreas

value: Day 7

value: 7 weeks

value: Saline IP 4x daily at D0 and D1

tag: slide serial_number


title: Panc_Saline_Ctrl_D4_Rep1

description: Visium FFPE whole-transcriptome probes

value: Day 4

value: Female

value: 6 weeks


title: Brain, PWS-IC deleted 4

source_name: Brain, PWS-IC deleted 4

value: PWS-IC deleted


title: Brain, WT 3 (control for PWS-IC deleted)

source_name: Brain, WT 3


title: Brain, WT 2 (control for PWS-IC deleted)

source_name: Brain, WT 2


title: Neutrophil, PW_055_rep2

value: blood

value: primary human cell

value: Neutrophil

value: Baseline


title: Neutrophil, PW_056_rep1

value: Not sensitized, male


title: Panc_Saline_Ctrl_D2_Rep2

description: Visium FFPE whole-transcriptome probes

value: Day 2

value: Male

value: WT


title: Neutrophil, PW_055_rep1


title: Panc_Saline_Ctrl_D2_Rep1

description: Visium FFPE whole-transcriptome probes


title: Pat3-IVS_19

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

description: Library name: Sample 19

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 101) with STAR 2.7.11b (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Contrasts were created with DESeq2 based on the raw count matrix.
Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585.
The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts of genes.

source_name: myocardial interventricular septum biopsy

extract_protocol:
For RNA-seq, RNA was isolated by RNeasy PowerLyzer Tissue & Cells Kit (Qiagen) according to the manufacturer's instructions. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 500ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian (Takara Bio). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

value: Healthy Control


title: Pat5-IVS_20

description: Library name: Sample 20

value: myocardial interventricular septum biopsy


title: Brain, WT 1 (control for PWS-IC deleted)

source_name: Brain, WT 1

value: Brain


title: Panc_Caer_ADM_D7_Rep2

description: Visium FFPE whole-transcriptome probes

value: Pancreas

value: Day 7

value: 7 weeks

value: 0.625 mg/kg caerulein IP 4x daily at D0 and D1


title: Pat22-IVS_18

description: Library name: Sample 18


title: Neutrophil, PW_053_rep2

value: Not sensitized, female


title: Pat21-IVS_17

description: Library name: Sample 17


title: Brain, Prepl knockout 3

source_name: Brain, Prepl knockout 3

value: Prepl knockout


title: Panc_Caer_ADM_D7_Rep1

description: Visium FFPE whole-transcriptome probes

value: Female


title: Neutrophil, PW_053_rep1

source_name: blood

value: blood

value: primary human cell


title: Panc_Caer_ADM_D4_Rep2

description: Visium FFPE whole-transcriptome probes

value: Day 4

value: 6 weeks


title: Pat20-IVS_16

description: Library name: Sample 16


title: Brain, Prepl knockout 2

source_name: Brain, Prepl knockout 2


title: Neutrophil, PW_052_rep2

value: Neutrophil

value: Not sensitized, male

value: Baseline


title: Pat18-IVS_15

description: Library name: Sample 15

value: Healthy Control


title: Brain, Prepl knockout 1

source_name: Brain, Prepl knockout 1


title: Pat16-IVS_14

description: Library name: Sample 14

value: myocardial interventricular septum biopsy

value: Male


title: Panc_Caer_ADM_D4_Rep1

description: Visium FFPE whole-transcriptome probes

source_name: Pancreas

value: Pancreas

value: WT


title: Panc_Caer_ADM_D2_Rep2

description: Visium FFPE whole-transcriptome probes

value: Day 2


title: Brain, WT 4 (control for Prepl knockout)

value: Brain


title: Neutrophil, PW_052_rep1


title: Neutrophil, PW_051_rep1

value: Not sensitized, female


title: Neutrophil, PW_051_rep2


title: Pat12-IVS_12

description: Library name: Sample 12


title: Brain, WT 2 (control for Prepl knockout)


title: Panc_AK_Ctrl_D7_Rep1

description: Visium FFPE whole-transcriptome probes

value: Day 7

value: 8 weeks

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: Neutrophil, PW_050_rep2

value: blood

value: primary human cell


title: Brain, Prepl knockout 4

source_name: Brain, Prepl knockout 4

value: Prepl knockout


title: Pat11-IVS_1

description: Library name: Sample 11


title: Neutrophil, PW_050_rep1

value: Neutrophil


title: Pat5-RV_10

description: Library name: Sample 10

source_name: Right ventricular myocardial free wall biopsy


title: Neutrophil, PW_049_rep2


title: Panc_AK_Ctrl_D2_Rep2

description: Visium FFPE whole-transcriptome probes

value: 10 weeks


title: Pat3-RV_9

description: Library name: Sample 9

value: Right ventricular myocardial free wall biopsy

value: Female


title: Panc_AK_Ctrl_D2_Rep1

description: Visium FFPE whole-transcriptome probes


title: Neutrophil, PW_049_rep1

value: Baseline


title: Neutrophil, PW_048_rep2


title: Pat13-IVS_13

description: Library name: Sample 13

value: myocardial interventricular septum biopsy

value: Healthy Control


title: P14-3

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

institute: UT Dallas

data_processing:
The fastq data from RNA-seq were processed by kallisto for quantification with default parameter setting.
Mouse genome GRCm38 together with the gene annotation in Gencode vM15 were used.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: choroid plexus P14

growth_protocol: Choroid plexus tissues were dissected out from mice at different developmental stages, and were immediately put into trizol for RNA preparation.

extract_protocol:
Total RNA from each samples was collected using Trizol, following manufacturer's protcol.
Libraries were prepared according to manufactuer's instructions accompanying the  Kapa mRNA HyperPrep Kit (KAPA Biosysterms cat# KK8580).

value: choroid plexus


title: Pat22-RV_8

description: Library name: Sample 8

value: Male


title: P14-1


title: Panc_Caer_ADM_D2_Rep1

description: Visium FFPE whole-transcriptome probes

value: Pancreas

value: Day 2

value: 6 weeks

value: WT

value: 0.625 mg/kg caerulein IP 4x daily at D0 and D1


title: Pat21-RV_7

description: Library name: Sample 7


title: Panc_AK_ADM_D7_Rep2

description: Visium FFPE whole-transcriptome probes

value: Day 7

value: 8 weeks

value: Ptf1a-rtTA; TRE-KLF4

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: P0-3

source_name: choroid plexus P0


title: Pat20-RV_6

description: Library name: Sample 6


title: Neutrophil, PW_048_rep1

value: blood

value: primary human cell

value: Neutrophil

value: Not sensitized, female


title: Panc_AK_Ctrl_D4_Rep1

description: Visium FFPE whole-transcriptome probes

value: Day 4

value: Female


title: Panc_AK_ADM_D4_Rep1

description: Visium FFPE whole-transcriptome probes

value: 18 weeks


title: Pat18-RV_5

description: Library name: Sample 5

value: Right ventricular myocardial free wall biopsy

value: Healthy Control


title: P0-1

value: choroid plexus


title: Pat16-RV_4

description: Library name: Sample 4

value: Male


title: Panc_AK_ADM_D4_Rep2

description: Visium FFPE whole-transcriptome probes

value: Pancreas

value: 24 weeks


title: Brain, WT 1 (control for Prepl knockout)

value: Brain

value: WT


title: Neutrophil, PW_047_rep2

value: Not sensitized, male

value: Baseline


title: E12.5-3

source_name: choroid plexus E12.5


title: Pat13-RV_3

description: Library name: Sample 3


title: P14-2


title: Neutrophil, PW_046_rep2

value: blood


title: Neutrophil, PW_047_rep1

value: primary human cell


title: Panc_AK_ADM_D2_Rep1

description: Visium FFPE whole-transcriptome probes

value: Day 2

value: 28 weeks

value: Ptf1a-rtTA; TRE-KLF4

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: E12.5-2


title: Pat12-RV_2

description: Library name: Sample 2


title: 19_146_4

city: Bethesda

first: Heather

middle: D

last: Hickman

address: Building 10 Rm 11N244A

department: LCIM

institute: NIAID

description: mRNA extracted from T cells from a mucosal biopsy

data_processing:
data mapped using STAR
gene & isoform expression extracted using RSEM
Assembly: GRCm38

source_name: Oral Mucosa

growth_protocol: Mice were grown following standard lab protocols & infected prior to biopsy.

extract_protocol:
performed standard RNA-sequencing extraction
Illumina TruSeq Stranded mRNA Library prep

treatment_protocol: performed biopsy from labial mucosa from mice of different mutations

value: oral mucosa biopsy

value: T cells


title: Neutrophil, PW_044_rep2

value: Neutrophil


title: E12.5-1

value: choroid plexus


title: Neutrophil, PW_046_rep1

value: Not sensitized, female


title: Panc_AK_ADM_D7_Rep1

description: Visium FFPE whole-transcriptome probes

value: Pancreas

value: Day 7

value: Female

value: 18 weeks


title: A6m-3

source_name: choroid plexus adult

value: Adult 6 month


title: P0-2


title: Pat11-RV_1

description: Library name: Sample 1

value: Right ventricular myocardial free wall biopsy

value: Healthy Control

value: Male


title: Neutrophil, PW_044_rep1

value: blood

value: primary human cell

value: Not sensitized, male

value: Baseline


title: Brain, WT 3 (control for Prepl knockout)

value: Brain

value: WT


title: 9_146_3

value: oral mucosa biopsy

value: T cells


title: 3_B6_3

description: mRNA extracted from ILC1 cells from a mucosal biopsy

value: ILC1 cells


title: A6m-2

value: choroid plexus


title: Neutrophil, PW_043_rep2

value: Neutrophil

value: Sensitized, male


title: Neutrophil, PW_043_rep1


title: Panc_AK_ADM_D2_Rep2

description: Visium FFPE whole-transcriptome probes

value: Pancreas

value: Day 2

value: 20 weeks

value: Ptf1a-rtTA; TRE-KLF4

value: 12.5 mg/kg doxycycline IP at D0 and D1


title: 2_B6_2


title: A6m-1

value: Adult 6 month


title: proximal jejunum, replicate 2, scRNAseq

city: New Haven

first: Kaelyn

last: Sumigray

state: CT

address: 333 Cedar St, SHM I 336A; Yale School of Medicine

department: Genetics

institute: Yale School of Medicine

description: 10X genomics, 3' Next Gem 3.1

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 6.0.1, default parameters).
FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("count pipeline", version 6.0.1, default parameters).
Assembly: rn6
Supplementary files format and content: tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: Proximal jejunum

extract_protocol:
Rats were fasted overnight prior to euthanasia. The proximal jejunum of adult male Sprague Dawley rats was isolated and rinsed in ice-cold PBS. The tissue was segmented into ~2 cm fragments and opened longitudinally to expose the epithelium. The tissue was incubated in 30 mM EDTA in HBSS at 37˚C for 20 min. The tissue was vigorously shaken to release epithelium. The epithelium was collected into a 15 mL conical tube, incubated on ice, and allowed to settle via gravity. The epithelium was washed twice in HBSS, then incubated in 1 mg/ml dispase II in HBSS for 10-12 minutes at 37˚C with frequent shaking. A total of 1 mL FBS and 2 µL DNase I was added to the cell suspension, and the cells were passed through 70 µm strainers. Cells were collected by centrifugation at 300 G for 5 min at 4˚C. Cell pellets were washed with HBSS + 10% FBS and centrifuged again at 300 G for 5 min at 4˚C. Cells were resuspended in HBSS + 10% FBS
Single-cell libraries were generated following the manual instructions of 10x Genomic (Chromium™ Single Cell 3’ v3). Libraries were sequenced with a minimum of 200 million paired end reads and parameters as described in the manual.

value: Proximal jejunum

value: epithelium

value: Sprague Dawley

value: male

value: 6-8 weeks

tag: weight


title: Neutrophil, PW_042_rep2

value: blood

value: primary human cell

value: Not sensitized, male

value: Baseline


title: proximal jejunum, replicate 1, scRNAseq

description: 10X genomics, 3' Next Gem 3.1


title: 15_111_3

value: oral mucosa biopsy

value: T cells


title: 1_B6_1

value: ILC1 cells


title: mtC_S12

city: Nanjing

first: cheng

last: gao

state: Jiangsu

address: Nanjing Agricultural University

country: China

institute: Nanjing Agricultural University

description:
Library name: Sample-24
Column name in Raw_Gene_counts_matrix.txt:  mtC_S12

data_processing:
Reads with an average mass fraction lower than Q20 were removed, and the filtered Reads were compared to the reference genome TAIR10.fas using the upgraded HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml ) software of TopHat2.
Assembly: TAIR10.fas
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Shoots

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer's protocols

value: Shoots

value: stm1 cad1-3

value: Cd

tag: batch

value: the same batch


title: 14_111_2


title: 13_111_1


title: mtC_S11

description:
Library name: Sample-23
Column name in Raw_Gene_counts_matrix.txt: mtC_S11


title: mtC_S10

description:
Library name: Sample-22
Column name in Raw_Gene_counts_matrix.txt: mtC_S10


title: 8_146_2


title: WTC_S9

description:
Library name: Sample-21
Column name in Raw_Gene_counts_matrix.txt: WTC_S9


title: EgtU-Y390A-treated BB10, 24 h, Biol. Rep. 3

city: West Haven

first: Anna

middle: B

last: Seminara

state: Connecticut

address: 840 West Campus Drive

department: MCDB

institute: Yale University

data_processing:
Reads were mapped to H. pylori PMSS1 strain reference genome (GCF_001991095.1) using Bowtie2 v.2.5.1.
Differentially expressed genes were identified using DESeq2 (v 1.22.1) within PartekFlow v.11.0.24.0414.
Assembly: GCF_001991095.1
Supplementary files format and content: Tab-delimited file containing raw transcript counts for each sample
Supplementary files format and content: Tab-delimited file containing raw gene counts for each sample

organism: Helicobacter pylori PMSS1

source_name: WT PMSS1

extract_protocol:
Total RNA wasisolated using a ZymoDirect-zol™ RNA MiniPrep Plus w/ TRI Reagent®kit.
Using the NEBNext rRNA Depletion Kit (Bacteria) (E7850X), bacterial rRNA is depleted starting from 10-1000ng of total RNA by hybridization of rRNA to complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed to DNA. Next library prep is completed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L). Samples are first fragmented at high heat in the presence of divalent cations prior to 1st strand synthesis using random priming. 2nd strand synthesis incorporates dUTPs into the 2nd strand cDNA. End repair creates blunt phosphorylated ends and an adenine overhang is added to the 3 prime end for efficient adapter ligation. The addition of USER enzyme removes the uracil containing strand. The remaining strand is then amplified in a PCR reaction. Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/µl are used for sequencing.

value: WT PMSS1

value: EgtU-Y390A-treated BB10, 24 h


title: WTC_S8

description:
Library name: Sample-20
Column name in Raw_Gene_counts_matrix.txt: WTC_S8


title: Neutrophil, PW_041_rep1

value: Neutrophil


title: Neutrophil, PW_039_rep1


title: EgtU-Y390A-treated BB10, 24 h, Biol. Rep. 2


title: Neutrophil, PW_039_rep2


title: Neutrophil, PW_037_rep2

value: Not sensitized, female


title: Neutrophil, PW_037_rep1


title: EgtU-Y390A-treated BB10, 21 h, Biol. Rep. 3

value: EgtU-Y390A-treated BB10, 21 h


title: EgtU-Y390A-treated BB10, 24 h, Biol. Rep. 1


title: mt_S6

description:
Library name: Sample-18
Column name in Raw_Gene_counts_matrix.txt: mt_S6

value: Control


title: EgtU-Y390A-treated BB10, 21 h, Biol. Rep. 2


title: Neutrophil, PW_042_rep1

value: blood


title: Neutrophil, PW_035_rep1

value: primary human cell


title: Neutrophil, PW_035_rep2

value: Not sensitized, male


title: mt_S5

description:
Library name: Sample-17
Column name in Raw_Gene_counts_matrix.txt: mt_S5


title: Glucose-Pyruvate cells, ATAC

first: Yi

last: Fu

address: 430 E 67th Street – RRL 1141

institute: MSKCC

description:
ATAC: read1 and read2 are for transcript; read3 is for cell barcode; I1 is index reads.
46 ARPE-19 clones with 0 - 100% heteroplasmy of ScaI mtDNA deletion were pooled and cultured in Glucose-Pyruvate media (DMEM, dialyzed FBS, 25mM glucose, uridine, NEAA, and Pen/Strep) for 3 days.

data_processing:
DOGMA-seq fastq files were processed using CellRanger ARC v2.0.2.  However, we made the following changes to run Cellranger ARC: - Used a custom CellRanger ARC reference genome. We blacklisted nuclear regions that were homologous to the mitochondrial genome in our reference genome. We followed the steps here (https://github.com/caleblareau/mitoblacklist). This prevents mito reads from being multimapped and thrown out and increased the coverage of our mitochondrial reads. - Move `chrM` from `non_nuclear_contigs` to `primary_contigs` in the CellRanger ARC configuration file. This ensures the mitochondrial reads are not discarded during processing.  After processing, CellRanger ARC provides us with filtered_featuer_bc_matrx.h5 (GEX) and atac_fragments.tsv.gz (ATAC) as output. We also provide the processed HTO output for our 8HetClonesHashtagMix experiment.
Assembly: hg38
Supplementary files format and content: CellRanger output files: 8HetClonesHashtagMix_filtered_feature_bc_matrix.h5, 8HetClonesHashtagMix_atac_fragments.tsv.gz, 8HetClonesHashtagMix_atac_fragments.tsv.gz.tbi. Processed Hashtag maps: 8HetClonesHashtagMix_hashtags.csv
Supplementary files format and content: CellRanger output files: Galactose_filtered_feature_bc_matrix.h5, Galactose_atac_fragments.tsv.gz, Galactose_atac_fragments.tsv.gz.tbi
Supplementary files format and content: CellRanger output files: Glucose+Pyruvate_filtered_feature_bc_matrix.h5, Glucose+Pyruvate_atac_fragments.tsv.gz, Glucose+Pyruvate_atac_fragments.tsv.gz.tbi
Supplementary files format and content: CellRanger output files: Glucose-Pyruvate_filtered_feature_bc_matrix.h5, Glucose-Pyruvate_atac_fragments.tsv.gz, Glucose-Pyruvate_atac_fragments.tsv.gz.tbi
Library strategy: DOGMA-seq

source_name: eye

extract_protocol:
Single Cell Multiome ATAC + Gene Expression was performed with 10X genomics system using Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog no. 1000282) and ATAC Kit A (catalog no. 1000280). We followed Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide with the difference that single cell suspension was prepared almost as described in Mimitou et al., 28 (DOGMAseq LLL protocol with NP- 40 buffer). However, to further increase mitochondria DNA coverage, we optimized the lysis step by increasing NP-40 concentration to 0.3% and the time of lysis to 3’.
Final libraries were sequenced on Illumina NovaSeq X+ platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

value: eye

value: retinal pigmental epithelial cells

value: Glucose-Pyruvate

tag: library type

value: scATAC-seq


title: EgtU-Y390A-treated BB10, 21 h, Biol. Rep. 1


title: Neutrophil, PW_032_rep2

value: Baseline


title: Neutrophil, PW_041_rep2


title: Glucose-Pyruvate cells, mRNA

description:
GEX (3' mRNA) library: read1 files contains cell barcode and UMI; read2 file contains transcript; I1 and I2 are index reads.
46 ARPE-19 clones with 0 - 100% heteroplasmy of ScaI mtDNA deletion were pooled and cultured in Glucose-Pyruvate media (DMEM, dialyzed FBS, 25mM glucose, uridine, NEAA, and Pen/Strep) for 3 days.

value: scRNA-seq


title: EgtU-Y390A-treated BB10, 8 h, Biol. Rep. 3

value: EgtU-Y390A-treated BB10, 8 h


title: WT_S3

description:
Library name: Sample-15
Column name in Raw_Gene_counts_matrix.txt: WT_S3

value: Shoots

value: the same batch


title: Neutrophil, PW_031_rep2


title: WT_S2

description:
Library name: Sample-14
Column name in Raw_Gene_counts_matrix.txt: WT_S2


title: Glucose+Pyruvate cells, GEX

description:
GEX (3' mRNA) library: read1 files contains cell barcode and UMI; read2 file contains transcript; I1 and I2 are index reads.
46 ARPE-19 clones with 0 - 100% heteroplasmy of ScaI mtDNA deletion were pooled and cultured in Glucose+Pyruvate media (DMEM, dialyzed FBS, 25mM glucose, uridine, NEAA, pyruvate, and Pen/Strep) for 3 days.

value: Glucose+Pyruvate


title: EgtU-Y390A-treated BB10, 8 h, Biol. Rep. 2

value: WT PMSS1


title: EgtU-Y390A-treated BB10, 8 h, Biol. Rep. 1


title: WTC_S7

description:
Library name: Sample-19
Column name in Raw_Gene_counts_matrix.txt: WTC_S7

value: Cd


title: Glucose+Pyruvate cells, ATAC

description:
ATAC: read1 and read2 are for transcript; read3 is for cell barcode; I1 is index reads.
46 ARPE-19 clones with 0 - 100% heteroplasmy of ScaI mtDNA deletion were pooled and cultured in Glucose+Pyruvate media (DMEM, dialyzed FBS, 25mM glucose, uridine, NEAA, pyruvate, and Pen/Strep) for 3 days.


title: WT_S1

description:
Library name: Sample-13
Column name in Raw_Gene_counts_matrix.txt: WT_S1


title: mtC_R12

description:
Library name: Sample-12
Column name in Raw_Gene_counts_matrix.txt: mtC_R12

source_name: Roots

value: Roots

value: stm1 cad1-3


title: EgtU-WT-treated BB10, 24 h, Biol. Rep. 3

value: EgtU-WT-treated BB10, 24 h


title: Neutrophil, PW_031_rep1

value: blood

value: primary human cell

value: Neutrophil


title: EgtU-WT-treated BB10, 24 h, Biol. Rep. 2


title: mt_S4

description:
Library name: Sample-16
Column name in Raw_Gene_counts_matrix.txt: mt_S4

value: Control


title: Neutrophil, PW_029_rep2

value: Sensitized, male


title: Galactose cells, ATAC

description:
ATAC: read1 and read2 are for transcript; read3 is for cell barcode; I1 is index reads.
46 ARPE-19 clones with 0 - 100% heteroplasmy of ScaI mtDNA deletion were pooled and cultured in Galactose media (DMEM, dialyzed FBS, 10mM galactose, uridine, NEAA, pyruvate, and Pen/Strep) for 3 days.

value: eye

value: retinal pigmental epithelial cells

value: Galactose

value: scATAC-seq


title: Neutrophil, PW_030_rep1

value: Not sensitized, female

value: Baseline


title: 8ClonesHashtagMix cells, ATAC

description:
ATAC: read1 and read2 are for transcript; read3 is for cell barcode; I1 is index reads.
8 ARPE-19 clones with 0, 25, 40, 41, 58, 60, 75, and 100% heteroplasmy of ScaI mtDNA deletion (estimated by bulk qPCR) were hashtagged and multiplexed on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO).


title: mtC_R11

description:
Library name: Sample-11
Column name in Raw_Gene_counts_matrix.txt: mtC_R11

value: the same batch


title: EgtU-WT-treated BB10, 21 h, Biol. Rep. 3

value: WT PMSS1

value: EgtU-WT-treated BB10, 21 h


title: EgtU-WT-treated BB10, 24 h, Biol. Rep. 1


title: 8ClonesHashtagMix cells, HTO

description:
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads; I1 and I2 are index reads.,
8 ARPE-19 clones with 0, 25, 40, 41, 58, 60, 75, and 100% heteroplasmy of ScaI mtDNA deletion (estimated by bulk qPCR) were hashtagged and multiplexed on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO).

library_source: other

molecule: protein

value: HTO

tag: hto

value: TotalSeq-A0251:0% heteroplasmy; TotalSeq-A0252:25% heteroplasmy; TotalSeq-A0253:40% heteroplasmy; TotalSeq-A0254:40% heteroplasmy; TotalSeq-A0255:58% heteroplasmy; TotalSeq-A0256 60% heteroplasmy; TotalSeq-A0257 75% heteroplasmy; TotalSeq-A0258 100% heteroplasmy.


title: Neutrophil, PW_029_rep1

tag: tissue


title: Neutrophil, PW_030_rep2


title: WTC_R9

description:
Library name: Sample-9
Column name in Raw_Gene_counts_matrix.txt: WTC_R9

value: Roots

value: Cd


title: EgtU-WT-treated BB10, 21 h, Biol. Rep. 2


title: 8ClonesHashtagMix cells, GEX

description:
GEX (3' mRNA) library: read1 files contains cell barcode and UMI; read2 file contains transcript; I1 and I2 are index reads.
8 ARPE-19 clones with 0, 25, 40, 41, 58, 60, 75, and 100% heteroplasmy of ScaI mtDNA deletion (estimated by bulk qPCR) were hashtagged and multiplexed on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO).

value: scRNA-seq


title: Neutrophil, PW_032_rep1

value: blood

value: primary human cell

value: Neutrophil

value: Not sensitized, male


title: WTC_R8

description:
Library name: Sample-8
Column name in Raw_Gene_counts_matrix.txt: WTC_R8


title: mtC_R10

description:
Library name: Sample-10
Column name in Raw_Gene_counts_matrix.txt: mtC_R10

value: stm1 cad1-3


title: Neutrophil, PW_028_rep2


title: Neutrophil, PW_028_rep1


title: EgtU-WT-treated BB10, 8 h, Biol. Rep. 3

value: EgtU-WT-treated BB10, 8 h


title: WTC_R7

description:
Library name: Sample-7
Column name in Raw_Gene_counts_matrix.txt: WTC_R7


title: Enfortumab vedotin_2

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

description:
Library name: Sample 4
treat group of Enfortumab vedotin (1 nM, 48h)
Drug intervention

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library quality assessment
Illumina sequencing
Assembly: hg38
Supplementary files format and content: Comma-separated text file includes read count values for each Sample.

growth_protocol: HT1376 cells were cultured in MEM medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Treat with WFI or Enfortumab vedotin (1nM) for 48 hours.

value: bladder cancer cells

value: Enfortumab vedotin


title: EgtU-WT-treated BB10, 21 h, Biol. Rep. 1


title: Galactose cells, GEX

description:
GEX (3' mRNA) library: read1 files contains cell barcode and UMI; read2 file contains transcript; I1 and I2 are index reads.
46 ARPE-19 clones with 0 - 100% heteroplasmy of ScaI mtDNA deletion were pooled and cultured in Galactose media (DMEM, dialyzed FBS, 10mM galactose, uridine, NEAA, pyruvate, and Pen/Strep) for 3 days.

value: eye

value: retinal pigmental epithelial cells

value: Galactose


title: Enfortumab vedotin_1

description:
Library name: Sample 3
treat group of Enfortumab vedotin (1 nM, 48h)
Drug intervention


title: mt_R5

description:
Library name: Sample-5
Column name in Raw_Gene_counts_matrix.txt: mt_R5

value: Control

value: the same batch


title: mt_R6

description:
Library name: Sample-6
Column name in Raw_Gene_counts_matrix.txt: mt_R6


title: WFI_2

description:
Library name: Sample 2
control group of Enfortumab vedotin treatment
Drug intervention

value: WFI


title: WFI_1

description:
Library name: Sample 1
control group of Enfortumab vedotin treatment
Drug intervention


title: Neutrophil, PW_027_rep1

value: Sensitized, male

value: Baseline


title: Neutrophil, PW_027_rep2


title: EgtU-WT-treated BB10, 8 h, Biol. Rep. 1

value: WT PMSS1


title: Neutrophil, PW_026_rep2

value: blood


title: mt_R4

description:
Library name: Sample-4
Column name in Raw_Gene_counts_matrix.txt: mt_R4

value: Roots


title: siYTHDC1_3

description:
Library name: Sample 6
treat group of siYTHDC1 by plasmid

data_processing:
Total RNA qualification
mRNA enrichment
Double-strand cDNA synthesis
End repair, ploy-A & adaptor addition
Fragment selection and PCR
Library quality assessment
Illumina sequencing
Assembly: hg38
Supplementary files format and content: Excel file includes read count values for each Sample.

growth_protocol: 5637 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and incubated at 37 °C in 5% CO2.

value: transfection infection


title: Neutrophil, PW_026_rep1

value: primary human cell

value: Neutrophil

value: Not sensitized, male


title: siYTHDC1_2

description:
Library name: Sample 5
treat group of siYTHDC1 by plasmid

value: bladder cancer cells


title: HCC_SnRNAseq2

first: XINGYU

last: CHEN

address: 3501 St Paul St, Baltimore, MD 21218

department: Department of Urology

institute: Cedars-Sinai Medical Center

description:
Library name: LibGEM79259258T
Murine hepatocellular carcinoma single-nucleus RNA-seq study

data_processing:
Raw FASTQ files were generated from the Illumina NovaSeq X Plus sequencing platform.
Reads were aligned to the mouse reference genome (mm10) using Cell Ranger v8.0.1 (10X Genomics).
Gene expression matrices were generated using Cell Ranger count.
Filtered and raw feature-barcode matrices were produced.
Data quality control and downstream analysis were performed using Seurat and Scanpy.
Assembly: Mouse reference genome (mm10, 2020-A version).
Supplementary files format and content: Filtered feature-barcode matrices in HDF5 (.h5) format containing gene expression counts per nucleus.
Supplementary files format and content: Raw sequencing files in FASTQ format, aligned and preprocessed count matrices.

source_name: Liver

growth_protocol: Mice (MUP-uPA+) were fed a Western Diet (Teklad, TD.88137) for 8 months starting at 8 weeks of age. HCC development was analyzed at 10 months.

extract_protocol:
Livers were isolated, and tumor tissues were dissected. For single-nucleus isolation, 50 mg tumor tissue pieces were frozen in dry ice and stored in liquid nitrogen until nuclei extraction.
Single-nucleus suspensions were prepared and processed using the Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (Dual Index) (10X Genomics, 1000268) to generate single-nucleus RNA-seq libraries. cDNA amplification and library preparation followed manufacturer protocols.

treatment_protocol: Mice were maintained on a Western Diet throughout the study.

value: Liver

value: Single Nuclei

value: MUP-uPA+

value: Western Diet

value: Batch 2


title: WT_R2

description:
Library name: Sample-2
Column name in Raw_Gene_counts_matrix.txt: WT_R2

value: Control

value: the same batch


title: HCC_SnRNAseq3

description:
Library name: LibGEM7926T
Murine hepatocellular carcinoma single-nucleus RNA-seq study

value: Batch 3


title: Neutrophil, PW_024_rep2

data_processing:
The data pre-processing tool, fastp, was used to perform quality control and adapter trimming. Results were filtered by quality. The software program Hierarchical Indexing for Spliced Alignment of Transcripts 2 (HISAT2) was used to map RNA sequencing reads prior to building the index using the human reference genome grch38. Indices were used to map sequential reads to the human genome. FeatureCounts were applied to generate a matrix of row counts of each of the genes in all the samples.
Assembly: human reference genome grch38
Supplementary files format and content: txt, counts

source_name: blood

value: Sensitized, male

value: Baseline


title: siYTHDC1_1

description:
Library name: Sample 4
treat group of siYTHDC1 by plasmid


title: Neutrophil, PW_024_rep1

value: blood


title: WT_R1

description:
Library name: Sample-1
Column name in Raw_Gene_counts_matrix.txt: WT_R1

value: Roots


title: HCC_SnRNAseq1

description:
Library name: LibGEM7564T
Murine hepatocellular carcinoma single-nucleus RNA-seq study

value: Batch 1


title: siNC_2

description:
Library name: Sample 2
control group of siYTHDC1 by plasmid

value: siNC

value: transfection infection


title: Neutrophil, PW_021_rep2

value: primary human cell

value: Neutrophil

value: Not sensitized, female


title: siNC_3

description:
Library name: Sample 3
control group of siYTHDC1 by plasmid

value: bladder cancer cells


title: EgtU-WT-treated BB10, 8 h, Biol. Rep. 2

value: WT PMSS1

value: EgtU-WT-treated BB10, 8 h


title: HCC_ScRNAseq2

description:
Library name: LibGEX2824T
Murine hepatocellular carcinoma single-cell RNA-seq study

data_processing:
FASTQ files were generated from the Illumina NovaSeq X Plus sequencing run.
Reads were aligned to the mouse reference genome (mm10) using Cell Ranger v8.0.1 (10X Genomics).
Gene expression matrices were generated using Cell Ranger count.
Filtered and raw feature-barcode matrices were produced.
Data quality control and preprocessing were conducted using Seurat and Scanpy.
Assembly: Mouse reference genome (mm10) - 2020-A version.
Supplementary files format and content: Filtered feature-barcode matrices in HDF5 (.h5) format, containing gene expression counts per cell.
Supplementary files format and content: Raw sequencing files in FASTQ format, aligned and preprocessed count matrices.

extract_protocol:
Livers were isolated, tumor tissues were dissected, and prepared for single-cell isolation. Single-cell suspensions were prepared using collagenase I and DNase I digestion, followed by immune cell enrichment via density-gradient centrifugation.
Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (10X Genomics) was used to generate single-cell cDNA libraries. Amplification and sequencing library preparation followed manufacturer instructions.

value: Liver

value: Single Cell

value: MUP-uPA+

value: Western Diet


title: IgG

city: Chengdu

first: Hongyu

last: Gao

state: Sichuan

address: hengdu City, Sichuan Province, Wuhou District people's South Road, three 14

institute: Sichuan University

description: Library name: IgG

data_processing:
Paired-end reads were harvested and were quality controlled by Q30, FastQC, and FastQ Screen. After 3’adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Binding sites on RNAs (peaks) were identified by MACS software. Differentially binding sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.GO and Pathway enrichment analysis were performed by the differentially binding mRNA coding genes.
Assembly: hg38
Supplementary files format and content: This table contains information on the RNA modification sites identified for each sample.

source_name: human adipose-derived mesenchymal stem cell

growth_protocol: Human adipose-derived mesenchymal stem cells were cultured in basal medium at 5% CO2 and 37°C. When the cell density reached 70-80%, the cells were induced to osteogenic differentiation for 10 days.

extract_protocol:
Cell lysate was immuno-precipitated by using antibody to protein of hnRNPA2B1 or IgG along with protein A/G magnetic beads. After proteinase K digestion, the RNA co-immunoprecipitated with proteins was purified by phenol/chloroform extraction and precipitated in ethanol. Then, RNA was re-suspended in RNase-free water and subjected to GenSeq rRNA Removal Kit (GenSeq, Inc.) to remove rRNA.
RNA libraries were constructed by using rRNA-depleted RNAs with GenSeq Low Input RNA Library Prep Kit (GenSeq, Inc.), according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc.). Library sequencing was sequenced with 150bp paired end reads.


title: Neutrophil, PW_021_rep1

extract_protocol:
RNA was isolated from blood neutrophils using the Nucleospin RNA II kit with on-column genomic DNA digestion according to the manufacturer’s protocol (Takara Bio, San Jose, CA). RNA was quantified using a NanoDrop Fluorospectrometer (Thermo Fisher). RNA was quality assessed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA) in the Emory Integrated Genomics Core. cDNA was generated using the SMART-Seq® v4 Ultra® low Input RNA Kit (Takara Bio).
The final RNA-seq library was generated using the Nextera XT kit (Illumina, San Diego, CA).
RNA-seq libraries were sequenced on the Novaseq 6000 with a sequencing depth of 30M paired-end 100 base pair reads per sample.


title: IP

description: Library name: IP

value: human adipose-derived mesenchymal stem cell


title: HCC_ScRNAseq3

description:
Library name: LibGEX2826T
Murine hepatocellular carcinoma single-cell RNA-seq study


title: Neutrophil, PW_020_rep2

value: Baseline


title: HCC_ScRNAseq1

description:
Library name: LibGEX2823T
Murine hepatocellular carcinoma single-cell RNA-seq study


title: SCLC tumor, PE300, 18 weeks, Sample_ID LA77_11

city: Stanford

first: Haiqing

last: Xu

state: CA

address: 327 Campus Drive

department: Biology

institute: Stanford University

description: Library name: SCLC_tumor_PE300_18_weeks_Sample_ID_LA77_11

data_processing:
Paired-end reads were processed with regular expressions to identify the crRNA arrays and clonal barcodes. When identifying guide sequences, we strictly required a perfect match with the designed sequences.
For the same crRNA array, when we encountered low-frequency clonal barcodes within a 1-hamming distance of high-frequency clonal barcodes, we attributed them to sequencing or PCR errors. These low-frequency barcodes were merged with barcodes of higher frequencies
After extracting barcode and crRNA information, we converted the read counts associated with clonal tumors into absolute neoplastic cell numbers. This conversion was accomplished by normalizing the reads of the clonal tumor to the number of reads of the "spike-in" benchmark cell lines added to each sample prior to lung lysis and DNA extraction
Assembly: GRCm39
Supplementary files format and content: PDAC_Batch1.txt: This file contains processed Tuba-seq data for PDAC tumors, sequenced using NovaSeq 6000 PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: OncogeneNegative_Batch1.txt: This file contains processed Tuba-seq data for oncogene-negative tumors, sequenced using NovaSeq 6000 PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: SCLC_Batch1.txt: This file contains processed Tuba-seq data for SCLC tumors, sequenced using NovaSeq 6000 PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: PDAC_Batch2.txt: This file contains processed Tuba-seq data for PDAC tumors, sequenced using MiSeq PE300. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: OncogeneNegative_Batch2.txt: This file contains processed Tuba-seq data for oncogene-negative tumors, sequenced using MiSeq PE300. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: SCLC_Batch2.txt: This file contains processed Tuba-seq data for SCLC tumors, sequenced using MiSeq PE300. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: Efficiency.txt: This file contains processed Tuba-seq data for tumors from the Cas12a efficiency experiment, sequenced using NovaSeq X Plus PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: Triple_TSG_KO.txt: This file contains processed Tuba-seq data for tumors from the triple TSG knockout experiment, sequenced using NovaSeq X Plus PE150. It includes information on mouse genotype, sex, ID, sample weight, tumor growth duration, tumor crRNA array, tumor clonal barcodes, and tumor size.
Supplementary files format and content: off_target_summary.csv: This file contains the indel sequencing results for three samples of oncogene-negative tumors. It includes the designed guide sequence, the chromosome, position, and sequence of predicted off-target sites (with lowercase letters indicating mismatches with the designed guide sequence), as well as the indel percentage.

source_name: Lung

extract_protocol:
Bulk tumor-bearing tissues were homogenized in 6 mL of cell lysis buffer (Puregene, 158063, Qiagen) using a FastPrep-24 5G tissue homogenizer (116005500, MP Biomedicals) and digested overnight with proteinase K (AM2544, Life Technologies). Benchmark control cell lines containing unique barcodes (50,000 or 100,000 cells each) were added to each lung sample prior to lysis to enable the calculation of the absolute number of neoplastic cells in each tumor.
Q5 High-Fidelity 2x Master Mix (M0494X, New England Biolabs) was used to amplify the U6-BC-crRNA region from 32 μg of genomic DNA in a total reaction volume of 800 μL per sample using unique dual-indexed primers.

value: Lung


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_01

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_01


title: piggybac-SD-2

city: Xiamen

first: Mengjun

last: Zhang

address: State Key Laboratory of Cellular Stress Biology

department: Department of biochemistry

institute: Xiamen university

description: Library name: sample 8

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.
Assembly: /
Supplementary files format and content: Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were applied to determine the statistical significance. Gene ontology (GO) analysis for differentially expressed genes were implemented by KOBAS software (version: 2.1.1). Alternative splicing events were detected by using rMATS (version 3.2.5) with an FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.

source_name: Embryonic kidney

growth_protocol: HEK293T (CRL-1573) cell line acquired from the American Type Culture Collection (ATCC) was maintained in DMEM (L120KJ) supplemented with 10% fetal bovine serum (Moybio; S450), penicillin/streptomycin (BasalMedia; S110JV), and GlutaMAX (BasalMedia; S210JV) at 37°C (5% CO2). The cell line was routinely tested negative for mycoplasma contamination.

extract_protocol:
RNA was extracted using standard Trizol RNA extraction kit. RNA quality was determined by examining A260/A280 with NanodropTM NanoDrop (Thermo Fisher Scientific Inc). RNA integrity was confirmed by agarose gel electrophoresis. Qualified RNAs were then quantified by Qubit3.0 with QubitTM RNA Broad Range Assay Kit (Life Technologies，Q10210).
2 μg total RNA was used for library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina (Wuhan Seqhealth, DR08402) following the manufacturer’s instruction. PCR products at 200-500 bps were enriched, quantified and sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China).

treatment_protocol: After SRRM2 gene was knocked out in 293T cells,we use we use Piggybac transposon vector and Piggybac transposase to create stable cell line of SRRM2-IDR WT,SRRM2-IDRSA,SRRM2-IDRSD.The splicing differences of piggybac-WT, piggybac-SA and piggybac-SD cell lines were compared.

value: Embryonic kidney cell


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_15

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_15

value: KT


title: siNC_1

description:
Library name: Sample 1
control group of siYTHDC1 by plasmid

value: siNC


title: piggybac-SD-3

description: Library name: sample 9


title: SCLC tumor, PE300, 18 weeks, Sample_ID LA77_09

description: Library name: SCLC_tumor_PE300_18_weeks_Sample_ID_LA77_09


title: piggybac-SD-1

description: Library name: sample 7


title: Neutrophil, PW_018_rep1

first: Min

last: Huang

address: WMB, 101 Woodruff Circle

institute: Emory University

value: blood

value: Not sensitized, male


title: Neutrophil, PW_018_rep2

value: primary human cell

value: Neutrophil


title: SCLC tumor, PE300, 18 weeks, Sample_ID LA77_07

description: Library name: SCLC_tumor_PE300_18_weeks_Sample_ID_LA77_07


title: piggybac-SA-3

description: Library name: sample 6


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_02

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_02


title: SCLC tumor, PE300, 18 weeks, Sample_ID LA77_05

description: Library name: SCLC_tumor_PE300_18_weeks_Sample_ID_LA77_05


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_11

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_11


title: piggybac-SA-2

description: Library name: sample 5


title: Neutrophil, PW_017_rep2

value: Sensitized, male


title: SCLC tumor, PE300, 18 weeks, Sample_ID LA77_03

description: Library name: SCLC_tumor_PE300_18_weeks_Sample_ID_LA77_03


title: SCLC tumor, PE300, 18 weeks, Sample_ID LA77_01

description: Library name: SCLC_tumor_PE300_18_weeks_Sample_ID_LA77_01


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_08

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_08


title: Neutrophil, PW_017_rep1


title: piggybac-SA-1

description: Library name: sample 4


title: piggybac-WT-3

description: Library name: sample 3


title: Neutrophil, PW_016_rep2


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_05

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_05


title: WT_R3

description:
Library name: Sample-3
Column name in Raw_Gene_counts_matrix.txt: WT_R3

value: Roots

value: Control

value: the same batch


title: Neutrophil, PW_020_rep1

value: Not sensitized, female


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_12

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_12


title: oncogene negative tumor, PE300, 9 weeks, Sample_ID LA75_65

description: Library name: oncogene_negative_tumor_PE300_9_weeks_Sample_ID_LA75_65


title: Neutrophil, PW_016_rep1


title: oncogene negative tumor, PE300, 9 weeks, Sample_ID LA75_66

description: Library name: oncogene_negative_tumor_PE300_9_weeks_Sample_ID_LA75_66


title: piggybac-WT-1

description: Library name: sample 1


title: piggybac-WT-2

description: Library name: sample 2


title: Neutrophil, PW_013_rep2


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_10

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_10


title: ProB_6

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

description: Library name: ProB_6

data_processing:
4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length. 4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length
Aligned to hg38 using BWA with default parameters
Duplicates removed using PICARD. All ENCODE hg38 blacklist regions removed, as well as reads from outside autosomes/sex chromosomes.
MACS2 used to call peaks
Bedtools used to compute maximum fold change over background from MACS2 data over catalogue of all called peaks.
Assembly: hg38
Supplementary files format and content: bed files of called narrowPeaks, and gzipped bedgraphs of fold enrichment over background computed with MACS2

source_name: primary

growth_protocol: Cells were freshly sorted from Cord Blood samples and resuspended in lysis buffer.

extract_protocol:
DNA purification following Buenrostro et al. 2013 protocol
Nextera DNA Sample Preparation kit (Illumina) following Buenrostro et al. 2013 protocol. 4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length. 4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length

value: primary

value: Pro-B


title: ProB_5

description: Library name: ProB_5


title: oncogene negative tumor, PE300, 9 weeks, Sample_ID LA75_62

description: Library name: oncogene_negative_tumor_PE300_9_weeks_Sample_ID_LA75_62


title: Neutrophil, PW_012_rep2

city: Atlanta


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_16

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_16


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_17

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_17


title: ProB_4

description: Library name: ProB_4


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_03

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_03


title: Neutrophil, PW_012_rep1


title: oncogene negative tumor, PE300, 9 weeks, Sample_ID LA75_68

description: Library name: oncogene_negative_tumor_PE300_9_weeks_Sample_ID_LA75_68


title: Neutrophil, PW_010_rep2


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_06

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_06


title: ProB_3

description: Library name: ProB_3


title: oncogene negative tumor, PE300, 9 weeks, Sample_ID LA75_64

description: Library name: oncogene_negative_tumor_PE300_9_weeks_Sample_ID_LA75_64


title: ProB_2

description: Library name: ProB_2


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_09

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_09


title: oncogene negative tumor, PE300, 9 weeks, Sample_ID LA75_60

description: Library name: oncogene_negative_tumor_PE300_9_weeks_Sample_ID_LA75_60


title: ProB_1

description: Library name: ProB_1


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_04

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_04


title: oncogene negative tumor, PE300, 9 weeks, Sample_ID LA75_61

description: Library name: oncogene_negative_tumor_PE300_9_weeks_Sample_ID_LA75_61


title: Neutrophil, PW_009_rep2

value: Sensitized, female


title: Neutrophil, PW_009_rep1

value: Baseline


title: PreProB_4

description: Library name: PreProB_4

value: Pre-Pro-B


title: oncogene negative tumor, PE300, 9 weeks, Sample_ID LA75_69

description: Library name: oncogene_negative_tumor_PE300_9_weeks_Sample_ID_LA75_69

value: Lung


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_07

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_07


title: Neutrophil, PW_013_rep1


title: oncogene negative tumor, PE300, 9 weeks, Sample_ID LA75_67

description: Library name: oncogene_negative_tumor_PE300_9_weeks_Sample_ID_LA75_67

value: KT


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_19

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_19


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_14

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_14


title: PreProB_3

description: Library name: PreProB_3


title: PDAC tumor, PE300, 10 weeks, Sample_ID LA75_78

description: Library name: PDAC_tumor_PE300_10_weeks_Sample_ID_LA75_78

source_name: Pancreas

value: Pancreas


title: PreProB_2

description: Library name: PreProB_2


title: Neutrophil, PW_008_rep2

value: blood


title: Neutrophil, PW_008_rep1


title: triple TSG KO tumor, PE150, 7.0 weeks, Sample_ID LA87_18

description: Library name: triple_TSG_KO_tumor_PE150_7.0_weeks_Sample_ID_LA87_18


title: PDAC tumor, PE300, 10 weeks, Sample_ID LA75_77

description: Library name: PDAC_tumor_PE300_10_weeks_Sample_ID_LA75_77


title: Neutrophil, PW_007_rep2


title: PreProB_1

description: Library name: PreProB_1


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_08

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_08


title: PDAC tumor, PE300, 10 weeks, Sample_ID LA75_79

description: Library name: PDAC_tumor_PE300_10_weeks_Sample_ID_LA75_79


title: PreB_3

description: Library name: PreB_3

value: Pre-B


title: Neutrophil, PW_010_rep1

value: primary human cell

value: Not sensitized, male


title: Neutrophil, PW_007_rep1

value: Neutrophil


title: PDAC tumor, PE300, 10 weeks, Sample_ID LA75_81

description: Library name: PDAC_tumor_PE300_10_weeks_Sample_ID_LA75_81


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_02

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_02


title: oncogene negative tumor, PE300, 9 weeks, Sample_ID LA75_63

description: Library name: oncogene_negative_tumor_PE300_9_weeks_Sample_ID_LA75_63


title: PreB_2

description: Library name: PreB_2


title: Neutrophil, PW_006_rep2


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_03

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_03


title: PDAC tumor, PE300, 10 weeks, Sample_ID LA75_73

description: Library name: PDAC_tumor_PE300_10_weeks_Sample_ID_LA75_73


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_17

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_17


title: Neutrophil, PW_006_rep1


title: Neutrophil, PW_005_rep2

value: Sensitized, male


title: MLP_3

description: Library name: MLP_3

value: MLP


title: PDAC tumor, PE300, 10 weeks, Sample_ID LA75_80

description: Library name: PDAC_tumor_PE300_10_weeks_Sample_ID_LA75_80


title: efficiency tumor, PE150, 10.0 weeks, Sample_ID LA85_10

description: Library name: efficiency_tumor_PE150_10.0_weeks_Sample_ID_LA85_10


title: PDAC tumor, PE300, 10 weeks, Sample_ID LA75_70

description: Library name: PDAC_tumor_PE300_10_weeks_Sample_ID_LA75_70