title: Patient 4 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 3 unaffected skin scRNA-seq

status: Public on Sep 13 2024

type: SRA

city: Philadelphia

first: Satish

last: Sati

state: Pennsylvania

address: 421 Curie Blvd, BRB 1039

department: Dermatology

country: USA

institute: University of Pennsylvania

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA sequencing data was mapped to the GRCh38 reference genome to generate gene count and cell barcode matrices using the “cellranger count” function from cellranger pipeline (version 5.0.1, 10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Homo sapiens

source_name: Skin

extract_protocol:
The skin punch biopsies were incubated in 200 μl of Dispase solution (2mg/mL) for 30 minutes at  37 C. Following the incubation, the epidermis was peeled from dermis with curved forceps, washed in PBS and successively minced into < 1 mm3 pieces, using scalpel in a serum free RPMI 1640 media with DNase I (0.2 mg/mL), 20 mM HEPES and 0.25 mg/ml Liberase TM, Roche. The suspension was incubated for 90 minutes at 37 C. The digestion was stopped by adding 100 μl FBS and 3 μl of 0.5 M EDTA and filtered through a 70-mm cell strainer. The cells were pelleted and washed twice with PBS containing 1% BSA. Finally the cells were resuspended in PBS containing 0.04% BSA and an aliquot was taken for counting.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue

value: Skin


title: Patient 2 unaffected skin scRNA-seq

description: 10x Genomics


title: 653_PC3_doc_DPT10

city: LOS ANGELES

first: Michaek

middle: James

last: Schmidt

state: CA

address: 1002 Childs Way

department: Cancer Biology and Genomics

institute: University of Southern California

data_processing:
raw fastq files
Assembly: hg19
Supplementary files format and content: RDS file contains gene counts processed with htseq-count and aligned with hisat2
Supplementary files format and content: for RDS file: hisat2 & htseq-count

source_name: prostate

extract_protocol:
smart-seq2
Nextera-XT

treatment_protocol: treat with chemotherapy for 72 hours and then allowed to recover for 1 or 10 days in regular medium.

value: prostate

tag: cell line

tag: cell type

value: epithelial cell line

tag: treatment


title: 654_PC3_doc_DPT10


title: Patient 1 unaffected skin scRNA-seq

description: 10x Genomics


title: Patient 26 affected skin scRNA-seq

description: 10x Genomics


title: 652_PC3_doc_DPT10


title: 650_PC3_doc_DPT10


title: Patient 27 affected skin scRNA-seq

description: 10x Genomics


title: Patient 24 affected skin scRNA-seq

description: 10x Genomics


title: 524_PC3_progeny


title: Patient 25 affected skin scRNA-seq

description: 10x Genomics


title: Patient 23 affected skin scRNA-seq

description: 10x Genomics


title: 646_PC3_doc_DPT10


title: 648_PC3_doc_DPT10


title: 647_PC3_doc_DPT10


title: 645_PC3_doc_DPT10


title: Patient 21 affected skin scRNA-seq

description: 10x Genomics


title: Patient 22 affected skin scRNA-seq

description: 10x Genomics


title: 644_PC3_doc_DPT10


title: Patient 20 affected skin scRNA-seq

description: 10x Genomics


title: 651_PC3_doc_DPT10


title: 643_PC3_doc_DPT10


title: Patient 18 affected skin scRNA-seq

description: 10x Genomics


title: 521_PC3_doc_DPT10


title: Patient 19 affected skin scRNA-seq

description: 10x Genomics


title: Patient 28 affected skin scRNA-seq

description: 10x Genomics


title: Patient 17 affected skin scRNA-seq

description: 10x Genomics


title: 520_PC3_doc_DPT10


title: 519_PC3_doc_DPT10


title: Patient 16 affected skin scRNA-seq

description: 10x Genomics


title: Patient 15 affected skin scRNA-seq

description: 10x Genomics


title: 518_PC3_doc_DPT10


title: 517_PC3_doc_DPT10


title: Patient 14 affected skin scRNA-seq

description: 10x Genomics


title: Patient 13 affected skin scRNA-seq

description: 10x Genomics


title: 516_PC3_doc_DPT10


title: 515_PC3_doc_DPT10


title: Patient 12 affected skin scRNA-seq

description: 10x Genomics


title: 513_PC3_doc_DPT10


title: 514_PC3_doc_DPT10


title: Patient 11 affected skin scRNA-seq

description: 10x Genomics


title: 512_PC3_doc_DPT10


title: Patient 9 affected skin scRNA-seq

description: 10x Genomics


title: Patient 8 affected skin scRNA-seq

description: 10x Genomics


title: 511_PC3_doc_DPT10


title: Patient 7 affected skin scRNA-seq

description: 10x Genomics


title: Patient 6 affected skin scRNA-seq

description: 10x Genomics


title: 510_PC3_doc_DPT10


title: 509_PC3_doc_DPT10


title: Patient 5 affected skin scRNA-seq

description: 10x Genomics


title: Galactose_RNAseq

city: Durham

first: David

last: MacAlpine

state: NC

address: 308 Research Dr, Durham, NC 27710

department: Department of Pharmacology and Cancer Biology

institute: Duke University

library_source: transcriptomic

data_processing:
FASTQ reads were aligned to sacCer3 (Saccharomyces cerevisiae) using bowtie v1.1.1 (Langmead 2010) using the single-end option with the following bowtie flags: -m1 -n 2 -l 20 --best --strata -S - y --phred 33 --nProc 32. Aligned files were processed and converted into BAM format using samtools v1.2 (Heng Li et al. 2009).
Read counts were generated for each gene using featureCounts.
Assembly: sacCer3, R64
Supplementary files format and content: Read counts per gene

molecule: total RNA

organism: Saccharomyces cerevisiae

extract_protocol:
Total RNA was extracted using the hot phenol method.
RNA-seq libraries were prepared using TruSeq Stranded Total RNA-seq Kit (Illumina) and ribosomal RNA was removed with Ribo-Zero Gold Kit (Human-Mouse-Rat, Illumina)

value: yeast

tag: genotype

value: wt

value: Galactose 20 min.


title: 507_PC3_doc_DPT10


title: Patient 4 affected skin scRNA-seq

description: 10x Genomics


title: 506_PC3_doc_DPT10


title: Patient 3 affected skin scRNA-seq

description: 10x Genomics


title: Patient 2 affected skin scRNA-seq

description: 10x Genomics


title: Patient 1 affected skin scRNA-seq

description: 10x Genomics


title: 505_PC3_doc_DPT10


title: 504_PC3_doc_DPT10


title: 502_PC3_doc_DPT10


title: Patient 10 affected skin scRNA-seq

description: 10x Genomics


title: 500_PC3_doc_DPT10


title: 452_PC3_doc_DPT10


title: 415_PC3_doc_DPT10


title: 412_PC3_doc_DPT10


title: 418_PC3_doc_DPT10


title: 508_PC3_doc_DPT10


title: 503_PC3_doc_DPT10


title: 400_PC3_doc_DPT10


title: 499_PC3_doc_DPT10


title: 501_PC3_doc_DPT10


title: 498_PC3_doc_DPT10


title: DA4_J20

type: genomic

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Mus musculus

source_name: DA1-3B clone

label_protocol: probe labeling used Agilent Technologies Genomic DNA Enzymatic Labeling Kit. Labelling was performed following manufacturer's instructions.

extract_protocol: chromosomal DNA were extracted using Qiagen DNA extraction Kit following manufacturer's instructions

tag: disease state

value: myeloid leukemia

source_name: DA1-3B rate control

tag: control

value: DA1-3B rate control


title: 424_PC3_doc_DPT10


title: DA3_J60


title: 396_PC3_doc_DPT10


title: DA6J20


title: DA3_J35


title: 404_PC3_doc_DPT10


title: 309_PC3_doc_DPT10


title: 408_PC3_doc_DPT10


title: DA3_J20


title: 301_PC3_doc_DPT10


title: DA13B_J365


title: 304_PC3_doc_DPT10


title: DA4_J35


title: DA2_J35


title: DA2_J60


title: T3_J60


title: 298_PC3_doc_DPT10


title: 293_PC3_doc_DPT1


title: 295_PC3_doc_DPT10


title: 192_PC3_doc_DPT10


title: T2M0


title: TB5_D365


title: S0_536_T


title: DA5J35


title: 191_PC3_doc_DPT10


title: TB4_J365


title: 190_PC3_doc_DPT10


title: SO_422-4


title: 189_PC3_doc_DPT10


title: SO_422-5


title: SO_422-2


title: 188_PC3_doc_DPT10


title: 649_PC3_doc_DPT10


title: 186_PC3_doc_DPT10


title: MO5365_6


title: SO_422-3


title: 182_PC3_doc_DPT10


title: 181_PC3_doc_DPT10


title: 187_PC3_doc_DPT10


title: 180_PC3_doc_DPT10


title: 179_PC3_doc_DPT10


title: MO560_4


title: TB1_C3H


title: B16F1_D735_n1

source_name: B16 clone

value: melanoma

source_name: C57BL6 rate control

value: C57BL6 rate control


title: 178_PC3_doc_DPT10


title: ArrayB_Proband 3: vehicle EtOH

type: RNA

city: Leipzig

first: Franziska

last: Kuestermann

address: Johannisallee 30

country: Germany

institute: University Hospital of Leipzig

description:
Array B, technical replicate
Probe_34_b

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. data was then processed following a large analysis protocol (main idea: searching for high fold induction by aldosterone, excluding genes strongly down-regulated by cortisol).

label: biotin

source_name: venipuncture, blood sample

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted from PBMC using RNeasy Kit® (Qiagen) according to manufacturer’s instructions.

treatment_protocol: PBMCs of three healthy male probands were incubated at room temperature in homologous plasma with aldosterone, cortisol, the combination of both, or vehicle (as indicated per experiment) for three hours.

tag: tisssue

value: PBMC

tag: gender

value: male


title: 176_PC3_doc_DPT10


title: ArrayB_Proband 2: 1 ng/ml Aldosterone+1000 ng/ml Cortisol

description:
Array B, technical replicate
Probe_23_b


title: B16F1_D733_n1


title: B16F1_Dn2


title: ArrayB_Proband 3: 1000 ng/ml Cortisol

description:
Array B, technical replicate
Probe_32_b


title: 307_PC3_doc_DPT10


title: 175_PC3_doc_DPT10


title: B16F1_Mn1


title: 173_PC3_doc_DPT10


title: B16F1_D739_n1


title: ArrayB_Proband 2: 1 ng/ml Aldosterone

description:
Array B, technical replicate
Probe_21_b


title: 174_PC3_doc_DPT10


title: 166_PC3_doc_DPT10


title: 164_PC3_doc_DPT10


title: 165_PC3_doc_DPT10


title: 177_PC3_doc_DPT10


title: ArrayB_Proband 2: vehicle EtOH

description:
Array B, technical replicate
Probe_24_b


title: ArrayB_Proband 3: 1 ng/ml Aldosterone+1000 ng/ml Cortisol

description:
Array B, technical replicate
Probe_33_b


title: ArrayB_Proband 2: 1000 ng/ml Cortisol

description:
Array B, technical replicate
Probe_22_b


title: ArrayB_Proband 3: 1 ng/ml Aldosterone

description:
Array B, technical replicate
Probe_31_b


title: ArrayA_Proband 3: vehicle EtOH

description:
Array A
Probe_34_a


title: ArrayB_Proband 1: 1 ng/ml Aldosterone

description:
Array B, technical replicate
Probe_11_b


title: ArrayB_Proband 1: vehicle EtOH

description:
Array B, technical replicate
Probe_14_b


title: 162_PC3_doc_DPT10


title: ArrayB_Proband 1: 1000 ng/ml Cortisol

description:
Array B, technical replicate
Probe_12_b


title: 163_PC3_doc_DPT10


title: 161_PC3_doc_DPT10


title: ArrayA_Proband 3: 1000 ng/ml Cortisol

description:
Array A
Probe_32_a


title: 121_PC3_doc_DPT10


title: 108_PC3_doc_DPT10


title: 73_PC3_doc_DPT10


title: 95_PC3_doc_DPT10


title: ArrayB_Proband 1: 1 ng/ml Aldosterone+1000 ng/ml Cortisol

description:
Array B, technical replicate
Probe_13_b


title: 71_PC3_doc_DPT10


title: 160_PC3_doc_DPT10


title: 50_PC3_doc_DPT10


title: ArrayA_Proband 2: 1 ng/ml Aldosterone

description:
Array A
Probe_21_a


title: ArrayA_Proband 2: 1000 ng/ml Cortisol

description:
Array A
Probe_22_a


title: ArrayA_Proband 2: 1 ng/ml Aldosterone+1000 ng/ml Cortisol

description:
Array A
Probe_23_a


title: 27_PC3_doc_DPT10


title: ArrayA_Proband 3: 1 ng/ml Aldosterone

description:
Array A
Probe_31_a


title: Liver_fetal_PFO4DA_62.5 mg/kg/d_4

city: Research Triangle Park

first: Thomas

last: Jackson

address: 109 TW Alexander Dr

department: CPHEA

institute: United States Environmental Protection Agency

data_processing:
Raw FASTQ files provided by BioSpyder were uploaded into Partek Flow and reads ends were quality trimmed (bases with Phred score ≤ 20 were removed) and filtered based on length (n <=25 were removed). Filtered reads were aligned to Ensembl Rattus norvegicus mRatBN7.2 using STAR v.2.7.8a (default settings) and quantified to Ensembl transcript release 106 by Partek Expectation Maximization.
A total of 20,311 genes were identified, with 14,928 genes having at least 1 read in 10% of samples. One unexposed fetal liver sample had extremely low reads, and with our thresholds of >500,000 total read alignments and > 100 transcripts per gene, that sample was removed. The remaining samples had an average of 10.2 million reads with a standard deviation of 1.6 million reads and had an average of 683 ± 105 counts per gene.
Differential gene expression was assessed in DESeq2 package in R (v1.34.0).
Assembly: mRatBN7.2
Supplementary files format and content: Raw count matrices

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Time-mated Sprague-Dawley rats (Crl:CD(SD)), ~11-12 weeks old, were purchased from Charles River Laboratories (Raleigh, NC, USA) and shipped to USEPA (Research Triangle Park, NC, USA) on gestational day (GD) 6 (GD0 = bred date; GD1 = plug positive date).  Dams were housed individually in clear polycarbonate cages (20 x 25 x 47 cm) with heat-treated, laboratory-grade pine shavings (Northeast Products, Warrensburg, NY) and fed NIH07 Rat Chow and municipal tap water (Durham, NC; treated with particle filtration (50µm), granular activated charcoal filtration, and re-chlorinated) ad libitum.  Animals were housed in a facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care and maintained at 20-22°C, 45-55% humidity, and a 12:12 h photoperiod (06:00 – 18:00 EST).  Dams were weight-ranked, stratified into weight blocks based on the number of dose groups, and dams from each weight block were randomly assigned to treatment groups using a random sequence generator (www.random.org) to produce similar mean weights and variances.  This study was conducted in accordance with a protocol approved by the USEPA Center for Public Health and Environmental Assessment Institutional Animal Care and Use Committee.

extract_protocol:
Subsamples of maternal and fetal liver (~30-50 mg) were collected into polypropylene microcentrifuge tubes containing 500 µL TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) on ice, then individually homogenized using a Bullet Blender (Next Advance, Troy, NY, USA) with 1mm zirconium oxide beads and stored at -80°C prior to RNA extraction.  RNA extraction was conducted according to TRIzol Reagent manufacturer specifications using chloroform and isopropanol.  Following extraction, RNA was purified using GeneJet RNA clean up and concentration kit (Cat no. K08401; Thermo Fisher Scientific, Waltham, MA, USA).  RNA concentration and purity (260:280 ratio ≥1.8) were determined with a NanoDrop 2000 spectrophotometer (Thermo Scientific).
Transcriptome sequencing was conducted for maternal and fetal liver samples using the Rat Whole Transcriptome Assay on the Templated Oligo Detection Assay platform (TempO-Seq, BioSpyder Technologies, Carlsbad, CA, USA), which used 22,253 detector oligo probes targeting 20,924 protein coding genes. Sequencing was performed on an Illumina HiSeq 2500 with alignment and data analysis conducted in Partek Flow build 10.0.22.1115 (Partek Incorporated, St. Louis, MO, USA).
TempO-sequencing

treatment_protocol: Rat dams were exposed to each chemical from GD18-22.  PFO5DoA exposure levels included 0 (n=6), 0.1 (n=2), 0.3 (n=3), 1 (n=3), 3 (n=4), 10 (n=4), 30 (n=4), or 62.5 (n=4) mg/kg/d.  PFO4DA exposure levels included 0 (n=6), 0.3 (n=4), 1 (n=4), 3 (n=4), 10 (n=4), 30 (n=4), or 62.5 (n=4) mg/kg/d. PFO5DoA exposure at 62.5 mg/kg/d resulted in acute toxicity with ~11% reduction in mean bodyweight compared to controls after only two days of exposure and dams were euthanized on GD20 and not included in the present analyses.  Dams exposed to 30 mg/kg/d PFO5DoA initially gained weight but by GD22 had bodyweights ~17% less than controls with apparent fetotoxicity in one dam.  Groups with a sample size less than n=3 (i.e., only n=2 at 0.1 mg/kg/d PFO5DoA) were also excluded from differential expression analysis. Dams and fetuses were euthanized by decapitation 2-4 hours after the final oral dose (~08:30-10:30 EST).  Euthanasia order was stratified such that the timing of necropsy was equally distributed across dose groups.  Trunk blood was collected from dams and serum was isolated.  Subsamples of maternal and fetal liver were collected for mRNA extraction.

value: Liver

tag: strain

value: Sprague-Dawley

tag: lifestage

value: fetal

tag: dose (mg/kg/d)

tag: dam identifier

tag: vehicle

tag: dose interval


title: Liver_maternal_PFO4DA_62.5 mg/kg/d_4

value: maternal


title: 48_PC3_doc_DPT10


title: 25_PC3_doc_DPT10


title: Liver_maternal_PFO4DA_62.5 mg/kg/d_3


title: ArrayA_Proband 2: vehicle EtOH

description:
Array A
Probe_24_a


title: Liver_fetal_PFO4DA_62.5 mg/kg/d_3


title: 6_PC3_doc_DPT10


title: Liver_maternal_PFO4DA_62.5 mg/kg/d_2


title: ArrayA_Proband 1: 1 ng/ml Aldosterone+1000 ng/ml Cortisol

description:
Array A
Probe_13_a


title: ArrayA_Proband 1: 1000 ng/ml Cortisol

description:
Array A
Probe_12_a


title: Liver_fetal_PFO4DA_62.5 mg/kg/d_2


title: ArrayA_Proband 3: 1 ng/ml Aldosterone+1000 ng/ml Cortisol

description:
Array A
Probe_33_a


title: ArrayA_Proband 1: vehicle EtOH

description:
Array A
Probe_14_a


title: 4_PC3_doc_DPT10


title: ArrayA_Proband 1: 1 ng/ml Aldosterone

description:
Array A
Probe_11_a


title: Liver_maternal_PFO4DA_62.5 mg/kg/d_1


title: Liver_maternal_PFO4DA_30 mg/kg/d_4


title: Liver_fetal_PFO4DA_62.5 mg/kg/d_1


title: 148_PC3_doc_DPT1


title: 149_PC3_doc_DPT1


title: 147_PC3_doc_DPT1


title: 146_PC3_doc_DPT1


title: Liver_fetal_PFO4DA_30 mg/kg/d_4


title: Liver_maternal_PFO4DA_30 mg/kg/d_3


title: Liver_fetal_PFO4DA_30 mg/kg/d_3


title: 141_PC3_doc_DPT1


title: Liver_fetal_PFO4DA_10 mg/kg/d_4


title: Liver_maternal_PFO4DA_3 mg/kg/d_4


title: 143_PC3_doc_DPT1


title: 150_PC3_doc_DPT1


title: Liver_fetal_PFO4DA_3 mg/kg/d_4


title: Liver_maternal_PFO4DA_1 mg/kg/d_4


title: 139_PC3_doc_DPT1


title: 140_PC3_doc_DPT1


title: Liver_maternal_PFO4DA_10 mg/kg/d_4


title: 137_PC3_doc_DPT1


title: Liver_fetal_PFO4DA_1 mg/kg/d_4


title: 136_PC3_doc_DPT1


title: Liver_maternal_PFO4DA_0.3 mg/kg/d_4


title: 134_PC3_doc_DPT1


title: 130_PC3_doc_DPT1


title: Liver_maternal_PFO4DA_1 mg/kg/d_3


title: Liver_fetal_PFO4DA_0.3 mg/kg/d_4


title: 129_PC3_doc_DPT1


title: Liver_maternal_PFO4DA_0 mg/kg/d_6


title: 138_PC3_doc_DPT1


title: 131_PC3_doc_DPT1


title: Liver_fetal_PFO4DA_0 mg/kg/d_6


title: 128_PC3_doc_DPT1


title: 142_PC3_doc_DPT1


title: MO_1


title: Liver_fetal_PFO4DA_0.3 mg/kg/d_3


title: Liver_maternal_PFO4DA_0 mg/kg/d_5


title: Liver_fetal_PFO4DA_1 mg/kg/d_3


title: 125_PC3_doc_DPT1


title: Liver_fetal_PFO4DA_0 mg/kg/d_5


title: 126_PC3_doc_DPT1


title: 127_PC3_doc_DPT1


title: Liver_maternal_PFO4DA_0.3 mg/kg/d_3


title: 135_PC3_doc_DPT1


title: 124_PC3_doc_DPT1


title: Liver_maternal_PFO4DA_30 mg/kg/d_2


title: Liver_fetal_PFO4DA_0 mg/kg/d_4


title: 44_PC3_doc_DPT1


title: Liver_fetal_PFO4DA_10 mg/kg/d_3


title: 46_PC3_doc_DPT1


title: Liver_maternal_PFO4DA_0 mg/kg/d_4


title: Liver_maternal_PFO4DA_10 mg/kg/d_3


title: Liver_maternal_PFO4DA_30 mg/kg/d_1


title: Liver_maternal_PFO4DA_10 mg/kg/d_2


title: 42_PC3_doc_DPT1


title: 54_PC3_doc_DPT1


title: 52_PC3_doc_DPT1


title: 60_PC3_doc_DPT1


title: 56_PC3_doc_DPT1


title: 123_PC3_doc_DPT1


title: 58_PC3_doc_DPT1


title: Liver_fetal_PFO4DA_30 mg/kg/d_2


title: Liver_fetal_PFO4DA_30 mg/kg/d_1


title: Liver_maternal_PFO4DA_10 mg/kg/d_1


title: Liver_fetal_PFO4DA_10 mg/kg/d_2


title: Liver_fetal_PFO4DA_10 mg/kg/d_1


title: 38_PC3_doc_DPT1


title: 35_PC3_doc_DPT1


title: Liver_maternal_PFO4DA_3 mg/kg/d_3


title: 40_PC3_doc_DPT1


title: 33_PC3_doc_DPT1


title: Liver_maternal_PFO4DA_3 mg/kg/d_2


title: Liver_fetal_PFO4DA_3 mg/kg/d_3


title: 36_PC3_doc_DPT1


title: 31_PC3_doc_DPT1


title: 29_PC3_doc_DPT1


title: 22_PC3_doc_DPT1


title: Liver_fetal_PFO4DA_3 mg/kg/d_1


title: Liver_maternal_PFO4DA_1 mg/kg/d_2


title: 17_PC3_doc_DPT1


title: Liver_maternal_PFO4DA_1 mg/kg/d_1


title: Liver_fetal_PFO4DA_1 mg/kg/d_1


title: 497_PC3_ctrl

value: DMSO


title: 10_PC3_doc_DPT1


title: 15_PC3_doc_DPT1


title: Liver_fetal_PFO4DA_0.3 mg/kg/d_2


title: 496_PC3_ctrl


title: 19_PC3_doc_DPT1


title: 494_PC3_ctrl


title: 492_PC3_ctrl


title: 493_PC3_ctrl


title: 491_PC3_ctrl


title: 495_PC3_ctrl


title: Liver_maternal_PFO4DA_0.3 mg/kg/d_1


title: Liver_maternal_PFO4DA_0 mg/kg/d_3


title: Liver_fetal_PFO4DA_0.3 mg/kg/d_1


title: Liver_maternal_PFO4DA_0.3 mg/kg/d_2


title: Liver_fetal_PFO4DA_0 mg/kg/d_3


title: Liver_fetal_PFO4DA_0 mg/kg/d_2


title: Liver_maternal_PFO4DA_0 mg/kg/d_2


title: 490_PC3_ctrl


title: Liver_maternal_PFO4DA_3 mg/kg/d_1


title: Liver_fetal_PFO4DA_1 mg/kg/d_2


title: 13_PC3_doc_DPT1


title: 489_PC3_ctrl


title: Liver_fetal_PFO4DA_0 mg/kg/d_1


title: 488_PC3_ctrl


title: 487_PC3_ctrl


title: Liver_fetal_PFO5DoA_30 mg/kg/d_3


title: Liver_maternal_PFO5DoA_30 mg/kg/d_4


title: Liver_maternal_PFO5DoA_30 mg/kg/d_3


title: 486_PC3_ctrl


title: 485_PC3_ctrl


title: Liver_fetal_PFO5DoA_30 mg/kg/d_2


title: 484_PC3_ctrl


title: Liver_maternal_PFO5DoA_30 mg/kg/d_1


title: Liver_maternal_PFO5DoA_10 mg/kg/d_4


title: 480_PC3_ctrl


title: 479_PC3_ctrl


title: 483_PC3_ctrl


title: Liver_fetal_PFO5DoA_10 mg/kg/d_3


title: 482_PC3_ctrl


title: 478_PC3_ctrl


title: Liver_fetal_PFO4DA_3 mg/kg/d_2


title: 477_PC3_ctrl


title: 481_PC3_ctrl


title: Liver_fetal_PFO5DoA_10 mg/kg/d_4


title: Liver_maternal_PFO4DA_0 mg/kg/d_1


title: Liver_maternal_PFO5DoA_3 mg/kg/d_4


title: 476_PC3_ctrl


title: Liver_fetal_PFO5DoA_3 mg/kg/d_4


title: Liver_maternal_PFO5DoA_3 mg/kg/d_3


title: 447_PC3_ctrl


title: Liver_fetal_PFO5DoA_0 mg/kg/d_6


title: Liver_maternal_PFO5DoA_0 mg/kg/d_6


title: 445_PC3_ctrl


title: 442_PC3_ctrl


title: Liver_fetal_PFO5DoA_3 mg/kg/d_3


title: Liver_maternal_PFO5DoA_30 mg/kg/d_2


title: Liver_maternal_PFO5DoA_10 mg/kg/d_3


title: Liver_fetal_PFO5DoA_30 mg/kg/d_1


title: 436_PC3_ctrl


title: 430_PC3_ctrl


title: Liver_fetal_PFO5DoA_0 mg/kg/d_5


title: Liver_maternal_PFO5DoA_10 mg/kg/d_2


title: 427_PC3_ctrl


title: Liver_fetal_PFO5DoA_0 mg/kg/d_4


title: Liver_fetal_PFO5DoA_10 mg/kg/d_2


title: 420_PC3_ctrl


title: Liver_fetal_PFO5DoA_10 mg/kg/d_1


title: 433_PC3_ctrl


title: 372_PC3_ctrl


title: Liver_maternal_PFO5DoA_0 mg/kg/d_4


title: 451_PC3_ctrl


title: Liver_maternal_PFO5DoA_10 mg/kg/d_1


title: 375_PC3_ctrl


title: 381_PC3_ctrl


title: 369_PC3_ctrl


title: 366_PC3_ctrl


title: Liver_maternal_PFO5DoA_3 mg/kg/d_2


title: Liver_fetal_PFO5DoA_3 mg/kg/d_2


title: Liver_maternal_PFO5DoA_0 mg/kg/d_5


title: 439_PC3_ctrl


title: Liver_maternal_PFO5DoA_1 mg/kg/d_3


title: 357_PC3_ctrl


title: Liver_maternal_PFO5DoA_1 mg/kg/d_2


title: Liver_maternal_PFO5DoA_3 mg/kg/d_1


title: Liver_fetal_PFO5DoA_3 mg/kg/d_1


title: 354_PC3_ctrl


title: Liver_fetal_PFO5DoA_1 mg/kg/d_3


title: 348_PC3_ctrl


title: Liver_fetal_PFO5DoA_1 mg/kg/d_2


title: 343_PC3_ctrl


title: 351_PC3_ctrl


title: Liver_maternal_PFO5DoA_0.3 mg/kg/d_3


title: 363_PC3_ctrl


title: Liver_maternal_PFO5DoA_0.3 mg/kg/d_2


title: 340_PC3_ctrl


title: 338_PC3_ctrl


title: Liver_fetal_PFO5DoA_0.3 mg/kg/d_2


title: Liver_maternal_PFO5DoA_1 mg/kg/d_1


title: Liver_fetal_PFO5DoA_1 mg/kg/d_1


title: Liver_maternal_PFO5DoA_0.3 mg/kg/d_1


title: 360_PC3_ctrl


title: 335_PC3_ctrl


title: 333_PC3_ctrl


title: Liver_maternal_PFO5DoA_0.1 mg/kg/d_2


title: Liver_fetal_PFO5DoA_0.3 mg/kg/d_1


title: Liver_fetal_PFO5DoA_0.3 mg/kg/d_3


title: Liver_fetal_PFO5DoA_0.1 mg/kg/d_2


title: 332_PC3_ctrl


title: 330_PC3_ctrl


title: 329_PC3_ctrl


title: 345_PC3_ctrl


title: 327_PC3_ctrl


title: Liver_fetal_PFO5DoA_0.1 mg/kg/d_1


title: 326_PC3_ctrl


title: Liver_fetal_PFO5DoA_0 mg/kg/d_3


title: 339_PC3_ctrl


title: Liver_maternal_PFO5DoA_0 mg/kg/d_3


title: 323_PC3_ctrl


title: Liver_maternal_PFO5DoA_0 mg/kg/d_2


title: 324_PC3_ctrl


title: Liver_maternal_PFO5DoA_0 mg/kg/d_1


title: 321_PC3_ctrl


title: 336_PC3_ctrl


title: 320_PC3_ctrl


title: Liver_fetal_PFO5DoA_0 mg/kg/d_1


title: 287_PC3_ctrl


title: 315_PC3_ctrl


title: CJ067-2

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

data_processing:
Illumina HiSeq-2500 for sequencing
BWA (0.7.12-r1039) was used for indexing the reference genome and aligning the reads (q >= 20)
SAMTOOLS (0.1.19-96b5f2294a) (option -q0) was used to map the reads
BEDTOOLS(2.25.0) (option -S) was used to calculate the read counts per gene in a strand specific manner
Normalisation and differential gene expression analysis was done using edgeR (genes with atleast 10 reads were selected for each comparative analysis). DGE analysis was done in RStudio (1.1.447) (citation below) with R version 3.4.4.
Assembly: Reference genome used : Mycobacterium tuberculosis H37Rv, accession number : NC_000962.3
Supplementary files format and content: .txt files containing raw reads count, comparison of genes’ expression for sample pair, processed annotation  file, in-house scripts for analysis
Supplementary files format and content: raw_read_coverage.txt: The file contains raw read coverage obtained after mapping of the reads in a strand specific manner
Supplementary files format and content: groupTreated-groupUntreated.txt: The file contains DGE analysis output. It contains genes with their log fold change and FDR values.
Supplementary files format and content: annotation.txt: This is a processed annotation file used to map the reads
Supplementary files format and content: raw_read-to-Coverage.txt: This file contains customised python script to obtain raw read coverage files from raw reads
Supplementary files format and content: coverage-to-DEGs.txt: This file contains customised R script to obtain DGE output

organism: Mycobacterium tuberculosis H37Rv

source_name: bacteria grown in 7H9 media

growth_protocol: Mycobacterium tuberculosis H37Rv strains were grown in 7H9-ADS till log phase ~0.4 OD600 at 37 degrees Celcius at 180 rpm.

extract_protocol:
Total RNA was extracted from bacteria and subjected to purification and removal of genomic DNA contamination. Ribosomal RNA was depleted to obtain enriched mRNA for library preparation.
Fragmentation and random priming of samples was done for 15 nanograms of mRNA for each sample. First and second strand cDNA synthesis was carried out using NEBNextUltra Dirctional RNA library prep kit for Illumina according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a highthroughput run on the Illumina HiSeq 2500 sequencer using 1X50 bp single-end reads and a 1% PhiX spike-in control.

treatment_protocol: 0.4 OD600 Mycobacterium tuberculosis H37Rv cultures were treated with and without 2X MIC of CJ067 for 2 hours (sublethal dose) in biological triplicates

value: Wild type Mtb treated with 2X MIC CJ067

value: bacteria


title: Untreated-3

value: Wild type Mtb


title: CJ067-3


title: Liver_maternal_PFO5DoA_0.1 mg/kg/d_1


title: 254_PC3_ctrl

value: prostate

value: epithelial cell line


title: Untreated-2


title: 241_PC3_ctrl


title: 240_PC3_ctrl


title: Untreated-1


title: Liver_fetal_PFO5DoA_0 mg/kg/d_2


title: 317_PC3_ctrl


title: 237_PC3_ctrl


title: 236_PC3_ctrl


title: 238_PC3_ctrl


title: 235_PC3_ctrl


title: W303 coq10-R147*, replicate 3, nanopore

city: Los Angeles

first: Guillaume

last: Chanfreau

state: California

address: 607 Charles E Young Dr E

institute: University of California, Los Angeles

description: Nanopore PCR-cDNA (SQK-PCB114.24)

data_processing:
Basecalling was performed using the built in Dorado basecaller in Minknow (Dorado version: 7.4.12).
Reads were then mapped to S288C reference genome  using Minimap 2 (Version 2.17-r941).
Read counts were generated by featureCounts and normalized using DESeq2
Assembly: R64-1-1
Supplementary files format and content: comma-separated text file includes the raw counts for each sample

extract_protocol:
Total RNAs were extracted from frozen cell pellets using hot phenol-chloroform extraction followed by ethanol precipitation.
RNA libraries were prepared from 500 ng of total RNAs using the PCR-cDNA barcoding kit from Oxford Nanopore (ONT, catalog #: SQK-PCB114.24) as per the manufacturer's instructions.


title: RNA_MTX2_03-06_2

city: Paris

first: Chloé

last: Talarmin-Gas

state: Ile de France

address: 2, rue ambroise Paré

department: Biochemistry

institute: APHP

data_processing:
Fastq files were aligned using STAR algorithm (version 2.7.6a), on the Ensembl release 104, Caenorhabditis elegans WBcel23581.
Reads were counted with RSEM (v1.3.182) and statistical analyses were performed with R Core Team83 (2015, version 3.6.3), platform: x86_64-pc-linux-gnu (64-bit) and DESeq284 (DESeq2_1.26.0) to determine the proportion of differentially expressed genes (DEGs) between two conditions.
The standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function) was used, with a pre-filter of reads and genes (reads uniquely mapped on the genome, or up to 10 different loci with a count adjustment, and genes with at least 10 reads in at least 3 different samples85).
The Wald test with the contrast function and Benjamini-Hochberg FDR control procedure was used to identify DEGs (adjusted p-value < 0.05). The R scripts and parameters used in this study are freely available on GitHub (https://github.com/BSGenomique/genomic-rnaseq-pipeline/releases/tag/v1.0420).
The standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function) was used.
Assembly: Ensembl release 104, Caenorhabditis elegans Wbcel 235
Supplementary files format and content: tab-delimited text file includes raw counts (RSEMresults) and names for all the samples
Supplementary files format and content: tab-delimited text file includes Raw data (fastq.gz)  for each sample

organism: Caenorhabditis elegans

source_name: mutant strain

growth_protocol: All strains were cultured at 20°C on nematode growth medium (NGM) agar plates seeded with E.coli OP50 in lysogeny broth (LB) (referred to as NGM agar/OP50). Unless specifically stated, prior to each experiment, worms were synchronized with a bleaching solution [0,5N NaOH and 3% solution of sodium hypochlorite in M9 buffer77 (22 mM KH2PO4, 42 mM Na2HPO4, 86 mM NaCl, 1 mM MgSO4) and the larval stage was visually assessed under a S9E binocular stereo microscope (Leica, Wetzlar, Germany).

extract_protocol:
Total RNA was extracted from approximately 300 L4 stage worms using TRIzol® (Thermo Fisher Scientific, Waltham, MA) according to the manufacturer’s protocol. RNA quantification and purity assessment were performed using a NanoDrop™ 2000 (Thermo Fisher Scientific) and the RNA quality assessment using a 2100 Bioanalyzer (Agilent Technologies).
library(biomaRt) library(tximport) library(readr) library(DESeq2) library(reshape) library(ggplot2) library(RColorBrewer) library(pheatmap) library(ggrepel) library(factoextra)

value: mutant strain

value: strain

value: L4 stage mtx-2 (gk444)


title: RNA_MTX2_03-06_3


title: RNA_N2_03-06_3

source_name: strain

value: L4 stage, WT (N2 Bristol)


title: 203_PC3_ctrl


title: RNA_MTX2_04-06_2


title: RNA_N2_04-06_2


title: CJ067-1


title: 211_PC3_ctrl


title: RNA_N2_03-06_3bis


title: W303 coq10-R147*, replicate 2, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)


title: W303 coq10-R147*, replicate 1, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)


title: 202_PC3_ctrl


title: 201_PC3_ctrl


title: W303a coq10- L96S, replicate 3, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)


title: 200_PC3_ctrl


title: W303a coq10- L96S, replicate 2, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)


title: 199_PC3_ctrl


title: W303a coq10- L96S, replicate 1, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)


title: 198_PC3_ctrl


title: 239_PC3_ctrl


title: W303a coq10Δ , replicate 3, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)

source_name: W303a coq10{delta}

value: W303a coq10{delta}


title: 195_PC3_ctrl


title: 224_PC3_ctrl


title: W303a coq10Δ, replicate 2, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)


title: 193_PC3_ctrl


title: W303, replicate 3, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)


title: 185_PC3_ctrl


title: W303a coq10Δ, replicate 1, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)


title: 194_PC3_ctrl


title: 159_PC3_ctrl


title: 168_PC3_ctrl


title: 158_PC3_ctrl


title: 172_PC3_ctrl


title: 157_PC3_ctrl


title: W303, replicate 2, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)


title: 155_PC3_ctrl


title: 154_PC3_ctrl


title: 153_PC3_ctrl


title: 152_PC3_ctrl


title: 151_PC3_ctrl


title: 145_PC3_ctrl


title: 133_PC3_ctrl


title: genomic DNA from isolated B cells from non-responder 29

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

description:
U03375928
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged on Illumina iScan scanner using iScan Control Software (ICS) with standard recommended Illumina scanner settings

data_processing:
R v3.6.3
Average Beta (non normalized) values filtered with a set of 21948 unique Illumina Infinium MethylationEPIC BeadChip probes which are included in five DNAm-based surrogates analyzed in the respective publication : DNAmAge [1], DNAmTL [2], DunedinPoAm [3], AltumAge [4] and CRP_CpG_risk_score [5].
[1] Genome Biol. 2013, 14, R115; Erratum in Genome Biol. 2015, 16, 96. https://doi.org/10.1186/gb-2013-14-10-r115.
[2] Aging 2019, 11, 5895–5923, https://doi.org/10.18632/aging.102173.
[3] eLife [Internet]. 2020 May 5;9. Available Online: https://elifesciences.org/articles/54870 (accessed on 14 December 2022Date Month Year).
[4] npj Aging 2022, 8, 1–15, https://doi.org/10.1038/s41514-022-00085-y.
[5] ]Nat. Commun. 2022, 13, 1–14, https://doi.org/10.1038/s41467-022-29792-6.

label: Cy3 and Cy5

source_name: genomic DNA from isolated B cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from isolated B cells using QIAamp DNA Blood Mini kit (Qiagen) according to manufacturer’s instructions.

value: genomic DNA from isolated B cells

tag: Sex

tag: phenotype

value: non-responder


title: genomic DNA from isolated B cells from responder 40

description:
U03376694
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine

tag: tissue

value: female

value: responder


title: genomic DNA from isolated B cells from responder 41

description:
U03379840
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine

value: male


title: genomic DNA from isolated B cells from non-responder 30

description:
U03378095
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 118_PC3_ctrl

tag: cell line


title: genomic DNA from isolated B cells from responder 37

description:
U03376800
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 39

description:
U03380779
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: W303, replicate 1, nanopore

description: Nanopore PCR-cDNA (SQK-PCB114.24)


title: genomic DNA from isolated B cells from non-responder 26

description:
U03373408
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 120_PC3_ctrl

tag: cell type


title: genomic DNA from isolated B cells from non-responder 28

description:
U03378797
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 122_PC3_ctrl

tag: treatment


title: genomic DNA from isolated B cells from responder 35

description:
U03380652
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 115_PC3_ctrl


title: 114_PC3_ctrl


title: genomic DNA from isolated B cells from responder 36

description:
U03375063
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 25

description:
U03380806
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 113_PC3_ctrl


title: 112_PC3_ctrl


title: 116_PC3_ctrl


title: 117_PC3_ctrl


title: genomic DNA from isolated B cells from non-responder 22

description:
U03373409
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 34

description:
U03380653
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 107_PC3_ctrl


title: genomic DNA from isolated B cells from responder 33

description:
U03378590
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 24

description:
U03376799
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 27

description:
U03379302
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 38

description:
U03378976
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 21

description:
U03377549
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 72_PC3_ctrl


title: 26_PC3_ctrl


title: 49_PC3_ctrl


title: 94_PC3_ctrl


title: 5_PC3_ctrl


title: genomic DNA from isolated B cells from non-responder 23

description:
U03380005
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 421_PC3_cis_DPT10


title: 392_PC3_cis_DPT10


title: 390_PC3_cis_DPT10


title: genomic DNA from isolated B cells from non-responder 20

description:
U03375252
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 30

description:
U03378097
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 29

description:
U03376830
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 31

description:
U03378242
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 28

description:
U03378241
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 32

description:
U03373634
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 27

description:
U03375833
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 382_PC3_cis_DPT10


title: genomic DNA from isolated B cells from non-responder 19

description:
U03376115
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 26

description:
U03375251
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 25

description:
U03375679
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 1_PC3_ctrl


title: 376_PC3_cis_DPT10


title: genomic DNA from isolated B cells from non-responder 18

description:
U03377550
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 373_PC3_cis_DPT10


title: 379_PC3_cis_DPT10


title: 349_PC3_cis_DPT10


title: 367_PC3_cis_DPT10


title: 318_PC3_cis_DPT10


title: 291_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 24

description:
U03377493
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 22

description:
U03375680
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 288_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 21

description:
U03380780
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 282_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 23

description:
U03379839
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 285_PC3_cis_DPT10


title: genomic DNA from isolated B cells from non-responder 15

description:
U03376646
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 279_PC3_cis_DPT10


title: 276_PC3_cis_DPT10


title: genomic DNA from isolated B cells from non-responder 16

description:
U03377494
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 17

description:
U03377492
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 273_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 20

description:
U03378243
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 14

description:
U03379025
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 13

description:
U03375250
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 12

description:
U03378588
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 270_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 19

description:
U03379914
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 267_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 17

description:
U03378240
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 11

description:
U03375499
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 255_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 18

description:
U03380326
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 231_PC3_cis_DPT10


title: 232_PC3_cis_DPT10


title: 230_PC3_cis_DPT10


title: 229_PC3_cis_DPT10


title: 227_PC3_cis_DPT10


title: 228_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 16

description:
U03376797
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 10

description:
U03381867
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 15

description:
U03378098
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 225_PC3_cis_DPT10


title: 221_PC3_cis_DPT10


title: 219_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 13

description:
U03378589
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 12

description:
U03376114
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 8

description:
U03377272
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 11

description:
U03380436
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 9

description:
U03377287
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 6

description:
U03375062
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 10

description:
U03379096
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 218_PC3_cis_DPT10


title: 217_PC3_cis_DPT10


title: 220_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 14

description:
U03380851
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 216_PC3_cis_DPT10


title: 214_PC3_cis_DPT10


title: 213_PC3_cis_DPT10


title: 215_PC3_cis_DPT10


title: genomic DNA from isolated B cells from non-responder 7

description:
U03375064
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 212_PC3_cis_DPT10


title: 208_PC3_cis_DPT10


title: 207_PC3_cis_DPT10


title: 206_PC3_cis_DPT10


title: genomic DNA from isolated B cells from non-responder 4

description:
U03380001
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 204_PC3_cis_DPT10


title: 205_PC3_cis_DPT10


title: 169_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 6

description:
U03376354
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 8

description:
U03375364
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 91_PC3_cis_DPT10


title: genomic DNA from isolated B cells from non-responder 1

description:
U03375397
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: 89_PC3_cis_DPT10


title: Inositol_240701,PE150_rep1

city: hangzhou

first: bo

last: zhong

state: zhejiang

address: No. 928, 2nd Street, Xiasha Higher Education Park, Qiantang District, Hangzhou City, Zhejiang Province

country: China

institute: Zhejiang Sci-Tech University

description: Ulp1 Knockout,add inositol to a final concentration of 75 μM.

data_processing:
Raw data (raw reads) in FASTQ format were first processed using fastp software. During this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data. Additionally, Q20, Q30, and GC content of the clean data were calculated.
All downstream analyses were based on the high-quality clean data. The reference genome and gene model annotation files were downloaded directly from the genome website. The index of the reference genome was built using Hisat2, and paired-end clean reads were aligned to the reference genome using Hisat2(Kim et al., 2019). Gene read counts were calculated using HTSeq, and differentially expressed genes were identified using DESeq2.
Assembly: GCA_000027005.1_ASM2700v1_genomic
Supplementary files format and content: bigwig,Comparison of processed reads with genomes

organism: Komagataella pastoris

extract_protocol:
Total RNA was used as the input material for RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3’ ends of DNA fragments, adaptors with hairpin loop structures were ligated to prepare for hybridization.

treatment_protocol: Plasmids pPICZ-FLP-DouH5, pPICZ-FLP-DouH3, pPICZ-FLP-DouH3a, pUFRT-GFP-Avi, and pUFRT-GFP-Avi-INO1 were constructed according to the manual of the Seamless Cloning Kit (Beyotime, D7010M). Newly prepared yeast competent cells were made using 1 mol/L sorbitol. Plasmids were linearized with appropriate primer pairs and transformed into yeast competent cells using the BIO-RAD MicroPulser, Fungi2-Pic at 2 kV. The cells were then cultured at 28°C for 2-3 days. Clones were picked and validated by PCR.For the FLP inducible cutting steps(Andrews et al., 1985), cells were cultured in Glycerol medium (BMGY) for 24 hours, then transferred to 1% Methanol medium (BMMY) and induced for 48-72 hours, with extra methanol added to the culture every 24 hours.

tag: genotype

value: Ulp1 Knockout


title: 87_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 3

description:
U03376256
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: Inositol_240701,PE150_rep2

growth_protocol: cells were cultured in Glycerol medium (BMGY) for 24 hours, then transferred to 1% Methanol medium (BMMY) and induced for 48-72 hours, with extra methanol added to the culture every 24 hours.


title: INO1_240701,PE150_rep2

description: Ulp1 Knockout,Overexpression of INO1

value: Ulp1 Knockout,Overexpression of INO1


title: genomic DNA from isolated B cells from responder 4

description:
U03378975
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 2

description:
U03377286
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 3

description:
U03375500
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from non-responder 5

description:
U03381793
bisulfite converted DNA from B cells isolated from HCW non-responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 1

description:
U03377271
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: genomic DNA from isolated B cells from responder 2

description:
U03376798
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 86_PC3_cis_DPT10


title: genomic DNA from isolated B cells from responder 5

description:
U03379915
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: X33_240701,PE150_rep2

value: WT


title: X33_240701,PE150_rep1


title: 82_PC3_cis_DPT10


title: INO1_240701,PE150_rep1

description: Ulp1 Knockout,Overexpression of INO1


title: 80_PC3_cis_DPT10


title: Ulp1 KO_231122,PE150_rep2

description: Ulp1 Knockout


title: X33_231122,PE150_rep2


title: Ulp1 KO_231122,PE150_rep1

description: Ulp1 Knockout


title: X33_231122,PE150_rep1


title: 76_PC3_cis_DPT10


title: 2_PC3_cis_DPT10


title: 462_PC3_cis_DPT1


title: 84_PC3_cis_DPT10


title: 74_PC3_cis_DPT10


title: 448_PC3_cis_DPT1


title: B6C3TAG_275

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

hyb_protocol: Labeled cDNA was hybridized to the plate using GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Affymetrix)

scan_protocol: arrays were scanned using GeneTitan

data_processing: Quality control and differential gene expression was conducted using TAC4 software (Affymetrix)

label: Biotin

source_name: tumor

label_protocol: The GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) was used to prepare the samples

growth_protocol: cell lines were cultured in RPMI with 10% FBS and 2mM glutamine, then orthotopically transplanted into C57BL6/J mice. Tumors were removed and RNA extracted for analysis

extract_protocol: RNA extracted with trizol reagent then isolated with EZNA HP Total RNA kit (omega bio-tek)

treatment_protocol: no treatments were applied

tag: sample type


title: 453_PC3_cis_DPT1


title: B6C3TAG_273


title: B6C3TAG_277


title: B6C3TAG_271


title: 459_PC3_cis_DPT1


title: genomic DNA from isolated B cells from responder 9

description:
U03378096
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: B6C3TAG_274


title: B6C3TAG_272


title: 446_PC3_cis_DPT1


title: B6C3TAG_270


title: genomic DNA from isolated B cells from responder 7

description:
U03375135
bisulfite converted DNA from B cells isolated from HCW responding to anti-HBV vaccine


title: 443_PC3_cis_DPT1


title: 78_PC3_cis_DPT10


title: B6C3TAG_269


title: B6C3TAG_268


title: 440_PC3_cis_DPT1


title: 437_PC3_cis_DPT1


title: B6C3TAG_278


title: B6C3TAG_265


title: B6C3TAG_267


title: 434_PC3_cis_DPT1


title: 431_PC3_cis_DPT1


title: B6C3TAG_232


title: B6C3TAG_229


title: 428_PC3_cis_DPT1


title: 416_PC3_cis_DPT1


title: B6C3TAG_227


title: B6C3TAG_226


title: B6C3TAG_224


title: 425_PC3_cis_DPT1


title: 409_PC3_cis_DPT1


title: B6C3TAG_222


title: B6C3TAG_221


title: B6C3TAG_219


title: 226_PC3_cis_DPT10


title: B6C3TAG_218


title: 386_PC3_cis_DPT10


title: 387_PC3_cis_DPT1


title: 383_PC3_cis_DPT1


title: B6C3TAG_217


title: 2.51_3

source_name: cell line

growth_protocol: cell lines were cultured in RPMI with 10% FBS and 2mM glutamine

extract_protocol: RNA was isolated with EZNA HP Total RNA kit (omega bio-tek)


title: 305_PC3_cis_DPT1


title: 310_PC3_cis_DPT1


title: 2.51_2


title: B6C3TAG_225


title: 422_PC3_cis_DPT1


title: 302_PC3_cis_DPT1


title: B6C3TAG_223


title: 299_PC3_cis_DPT1


title: 2.10_2


title: 405_PC3_cis_DPT1


title: 2.10_1


title: 289_PC3_cis_DPT1


title: 283_PC3_cis_DPT1


title: 2.10_3


title: 296_PC3_cis_DPT1


title: 2.03_2


title: 280_PC3_cis_DPT1


title: 277_PC3_cis_DPT1


title: 313_PC3_cis_DPT1


title: 2.03_1


title: 274_PC3_cis_DPT1


title: 271_PC3_cis_DPT1


title: 2.51_1


title: 2.03_3


title: 397_PC3_cis_DPT1


title: 401_PC3_cis_DPT1


title: 1.02_1


title: 265_PC3_cis_DPT1


title: 465_PC3_cis_DPT1


title: 1.02_3


title: 259_PC3_cis_DPT1


title: 250_PC3_cis_DPT1


title: 262_PC3_cis_DPT1


title: 256_PC3_cis_DPT1


title: ICI-related pneumonitis patient 3, scRNA-seq

city: beijing

first: lei

last: zhang

address: xueyuan road 38th

department: heath science center

institute: peking university

description: 10x genomics

data_processing:
Raw sequencing data were aligned and quantified with the Cell Ranger Software v6.0 (10×Genomics) using the human reference genome GRCh38 v5.0.0.
Assembly: GRCh38
Supplementary files format and content: H5ad files for scanpy analysis

source_name: bronchoalveolar lavage fluid

extract_protocol:
A total of 30ml of lavage fluid was retrieved from each patient, with 5-10ml reserved for routine clinical tests and the remainder used for scRNA-seq. The collected BALF samples were encapsulated using 20ml centrifuge tubes and immediately placed on ice. The cooled BALF samples were mixed with RPMI 1640 complete medium and filtered through a 100mm nylon cell strainer to obtain single-cell suspensions. To minimize the potential for blood cell contamination, red blood cells were removed using Red Blood Cell Lysis Buffer. After two washes with 1x PBS (Invitrogen), the cell pellets were resuspended in sorting buffer (PBS supplemented with 1% FBS). Based on fluorescence-activated cell sorter (FACS) analysis, single CD45+cells from each patient’s samples were sorted using anti-human CD45 antibodies (Biolegend) into 1.5 ml low binding tubes (Eppendorf) with 50 ml of sorting buffer for scRNA-seq.
Cell suspensions were barcoded through the 10x Chromium Single Cell platform using Chromium Next GEM Single Cell 5’ Kit v2. Single cells were washed once with PBS containing 0.04% bovine serum albumin (BSA) and resuspended in PBS containing 0.04% BSA to a final concentration of 500-1200 cells/ml as determined by Rigel S2 cell counter (Countstar). The loaded cell numbers ranged from 300-500000 aiming for 300-14000 single cells per reaction. 5000 cells were captured in droplets to generate nanoliter-scale Gel bead in EMulsion (GEMs). GEMs were then reverse transcribed in a C1000 Touch Thermal Cycler (BioRad) programmed at 53℃ for 45 min, 85℃ for 5 min, and held at 4℃. After reverse transcription and cell barcoding, emulsions were broken and cDNA was isolated and purified with Cleanup Mix containing DynaBeads and SPRIselect reagent (ThermoFisher Scientific), followed by PCR amplification. Amplified cDNA was then used for 5’ gene expression library construction. For RNA-seq library construction, amplified cDNA was fragmented and end-repaired, double-sided size-selected, PCR-amplified with sample indexing primers, and repeated double-sided size-selection. For T-cell receptor (TCR) library construction, TCR transcripts were enriched from amplified cDNA by PCR. Subsequently, enriched PCR product was fragmented and end-repaired, size-selected, PCR-amplified with sample-indexing primers, and size-selected. Libraries prepared according to the manufacturer’s instructions were then purified and profiled for quality assessment. Single-cell RNA and TCR V(D)J libraries were sequenced by an Illumina NovaSeq 6000 sequencer with 150 bp paired-end reads.

value: bronchoalveolar lavage fluid

value: Immune cell

value: immune checkpoint inhibitor


title: ICI-related pneumonitis patient 5, TCR-seq

description: 10x genomics


title: ICI-related pneumonitis patient 4, TCR-seq

description: 10x genomics


title: ICI-related pneumonitis patient 4, scRNA-seq

description: 10x genomics


title: ICI-related pneumonitis patient 5, scRNA-seq

description: 10x genomics


title: ICI-related pneumonitis patient 2, scRNA-seq

description: 10x genomics


title: 245_PC3_cis_DPT1

value: prostate

value: epithelial cell line


title: ICI-related pneumonitis patient 2, TCR-seq

description: 10x genomics


title: 233_PC3_cis_DPT1


title: ICI-related pneumonitis patient 1, scRNA-seq

description: 10x genomics


title: 222_PC3_cis_DPT1


title: ICI-related pneumonitis patient 1, TCR-seq

description: 10x genomics


title: 242_PC3_cis_DPT1


title: 268_PC3_cis_DPT1


title: HeLa cells, EAPP knockout, rep2

city: Shanghai

first: Haiping

last: Zhao

address: 131 DongAn Road

institute: Fudan University

data_processing:
The integrity of RNA was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent, USA).
Paired-end clean reads were aligned to the hg38 reference genome using HISAT2 (v2.0.5).
Differential expression analysis of the two conditions was performed using the edgeR R package (3.22.5).
rMATS (4.1.0) software was used to analyze the alternative splicing events.
Assembly: hg38
Supplementary files format and content: Excel  file includes raw counts for each Sample
Supplementary files format and content: Excel  file includes differentially expressed gene
Supplementary files format and content: Excel  file includes alternative splicing events

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM medium supplemented with 10% fetal bovine serum and 100 U/mL of penicillin and 100 μg/mL of streptomycin, and the cells were cultured in a humidified incubator at 37°C in the presence of 5% CO2

extract_protocol:
TRIzol reagent (Invitrogen) was used for total RNA extraction according to the manufacturer’s instructions
RNA-seq library was loaded on an Illumina NovaSeq 6000 instrument for sequencing using a 2×150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: RNA was harvested using TRIzol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries

value: HeLa

value: cervical cancer cell

value: EAPP knockout

value: puromycine selection


title: 132_PC3_cis_DPT1


title: HeLa cells, EAPP knockout, rep3


title: 110_PC3_cis_DPT1


title: HeLa cells, Wildtype, rep3


title: ICI-related pneumonitis patient 3, TCR-seq

description: 10x genomics


title: 105_PC3_cis_DPT1


title: 248_PC3_cis_DPT1


title: 209_PC3_cis_DPT1


title: HeLa cells, Wildtype, rep2


title: 103_PC3_cis_DPT1


title: HeLa cells, EAPP knockout, rep1


title: 104_PC3_cis_DPT1


title: 101_PC3_cis_DPT1


title: 98_PC3_cis_DPT1


title: HeLa cells, Wildtype, rep1


title: 99_PC3_cis_DPT1


title: 97_PC3_cis_DPT1


title: 92_PC3_cis_DPT1


title: 8505C cells,siNUF2-3,24h

city: Hangzhou

first: Lisha

last: Bao

address: Shangtang

institute: Zhejiang provincial people's hospital

data_processing:
Sequence quality control was performed using fastp software(adaptor contamination, low quality bases and undetermined bases with default parameter)
Reads were mapped to the reference genome of Homo sapiens GRCh38 using HISAT2 and then assembled and calculated using StringTie
StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
The differentially expressed genes were screened with fold change > 2 or < 0.5 and with parametric F-test comparing nested linear models (P < 0.05).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: thyroid cancer

growth_protocol: 8505C cells were cultivated in RPMI-1640 supplied with 10% fetal bovine serum (FBS) in 37 °C humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen) following the manufacturer's procedure.  1μg of total RNA was used for the construcion of sequencing library.
Poly (A) RNA was purified and fragmented into small pieces which be synthesized into cDNA using Invitrogen SuperScript™ II Reverse Transcriptase (Thermo Fisher). Then, the ligated products were amplified with PCR. Finally, the 2×150 bp paired-end sequencing was carried out on illumina Novaseq™ 6000 (LC-Bio Technology).

value: thyroid cancer

value: anaplastic thyroid cancer cells

value: NUF2 knockdown


title: 96_PC3_cis_DPT1

source_name: prostate


title: 8505C cells,siNUF2-1,24h


title: 90_PC3_cis_DPT1


title: 109_PC3_cis_DPT1


title: 8505C cells,siCtrl1,24h


title: 8505C cells,siCtrl3,24h


title: 88_PC3_cis_DPT1


title: 85_PC3_cis_DPT1


title: 8505C cells,siNUF2-2,24h


title: 8505C cells,siCtrl2,24h


title: 81_PC3_cis_DPT1


title: 102_PC3_cis_DPT1


title: 77_PC3_cis_DPT1


title: OT6, peripheral blood, scTCR-seq

city: BALTIMORE

first: Daniel

middle: H

last: Shu

state: Maryland

address: CRB1, RM 416, 1550 ORLEANS ST.

department: Oncology

institute: Johns Hopkins Sidney Kimmel Cancer Center

description:
PBMC_OT6_TCR
10x Genomics

data_processing:
Cell Ranger v6.1.2 was used to demultiplex FASTQ reads, perform sequence alignment to the GRCh38 transcriptome, and extract unique molecular identifier (UMI) barcodes.
Assembly: GRCh38
Supplementary files format and content: Gene expression data are in tab-separated values files and matrix files. T and B cell receptor repertoire data are in comma-separated values files.

source_name: peripheral blood

extract_protocol:
Single cell sequencing was obtained for peripheral blood and tumor T and B cells isolated by Fluorescence-Activated Cell Sorting (FACS). For 6 of 7 patients, peripheral blood samples collected after completion of neoadjuvant ICB and prior to surgical resection were used; for 1 patient, the peripheral blood sample used was obtained 4 weeks after resection. For this patient, single cell sequencing was also performed on tumor infiltrating T and B cells sorted from resected tumor. In all cases, cryopreserved PBMC or tumor suspension were thawed and washed with pre-warmed RPMI with 10% FBS. Cells were resuspended in 0.04% BSA in PBS and stained with a viability marker (Zombie NIR, BioLegend) and Fc block (Biolegend, Cat. no. 422302) for 10 minutes at room temperature in the dark. Cells were then stained with antibodies against CD3 (FITC, clone HIT3a) and CD19 (PE/dazzle, clone SJ25C1). After staining, viable CD3+ and CD19+ cells were sorted into 0.04% BSA in PBS using a BD FACS Aria II Cell Sorter at a 4:1 ratio.
scRNA/TCR/BCR-seq; The single-cell library preparations for gene expression and V(D)J were performed with the Chromium Next GEM Single Cell 5’ GEM Kit v2 (10x Genomics) and Chromium Single Cell V(D)J Amplification Kit (human TCR) (10x Genomics), respectively. The cells were partitioned into nanoliter-scale Gel Beads in-emulsion (GEMs) and cells were barcoded. The cDNA synthesis and amplification was performed prior to sample split for the gene expression and for V(D)J libraries. Single cell libraries were sequenced on an Illumina NovaSeq instrument using 2 × 150- bp paired end sequencing. 5′ VDJ libraries were sequenced to a depth of 5,000 reads per cell. 5′ DGE libraries were sequenced to a depth of 50,000 reads per cell.

value: peripheral blood

value: T cell

value: neoadjuvant ICB


title: OT6, TIL, scBCR-seq

description:
TIL_OT6_BCR
10x Genomics

value: tumor

value: B cell


title: OT6, peripheral blood, scBCR-seq

description:
PBMC_OT6_BCR
10x Genomics


title: 79_PC3_cis_DPT1


title: OT6, TIL, scTCR-seq

description:
TIL_OT6_TCR
10x Genomics


title: RPTEC, TET2 knockdown, RNAseq

first: Xiujie

last: Liang

address: 12-188 Smilow Translational Research Center, 3400 Civic Center Blvd

department: Department of Medicine

data_processing:
For RNAseq: RNA-seq reads were aligned to the human genome (hg19) using STAR based on GENCODE annotations. RSEM was used to quantify gene-level read counts and transcripts per million.
For snRNAseq: The quality control (QC) included removing ambient mRNA contamination, eliminating low-quality cells and genes, and excluding doublet-like cells. We used “SoupX” to remove ambient mRNA. We defined low-quality cells as those with the following criteria: unique molecular identifiers (UMI) ≤ 500 or ≥ 10,000, the number of detected genes ≤300 or ≥ 3000, the percentage of mitochondrially encoded genes reads > 1%, complex ≥ 0.25.  We further removed genes that were expressed in ＜ 10 cells. “DoubletFinder” was used to exclude doublet-like cells. To process the data, we used Seurat 4.0.4.
Assembly: hg19 for RNAseq, mm10 for snRNAseq
Supplementary files format and content: RNAseq: txt file includes TPM values for each sample, snRNAseq: matrix

source_name: kidney

extract_protocol:
For RNA seq: RNA was extracted using Rneasy mini kit (Qiagen); for snRNAseq, Nuclei were extracted from flash-frozen kidney tissue. Briefly, 10-30 mg frozen kidney tissue were minced on ice into pieces in lysis buffer (Tris-HC, NaCl, MgCl2, NP40, and RNAse inhibitor), transferred into a gentleMACS C tube and homogenized using gentleMACS homogenizer. Next, the homogenized tissue was filtered through a 40 μm strainer (Fisher Scientific, #08-771-1) and then centrifuged at 500 × g for 5 mins at 4°C. The pellet was resuspended in wash buffer (BSA, RNAse inhibitor, 1× PBS) and then filtered through a 40 μm Flowmi cell strainer (Sigma Aldrich, #BAH136800040-50EA).
RNA-Seq libraries were generated using the NEB's non-directional RNA seq kit; For snRNAseq libraries, the cDNA libraries were constructed using the 10X Chromium library construction kit (PN-1000190).

value: kidney

value: RPTEC

value: proximal tubule cell

value: TET2 knockdown


title: 83_PC3_cis_DPT1

extract_protocol:
smart-seq2
Nextera-XT

value: prostate

value: epithelial cell line


title: OT1, peripheral blood, scTCR-seq

description:
PBMC_OT1_TCR
10x Genomics


title: RPTEC, non-targeting control, RNAseq

value: WT


title: 69_PC3_cis_DPT1


title: 642_MDAMB231_ctrl

source_name: breast

value: breast

value: DMSO


title: OT1, peripheral blood, scBCR-seq

description:
PBMC_OT1_BCR
10x Genomics


title: 641_MDAMB231_ctrl


title: P12, peripheral blood, scBCR-seq

description:
PBMC_P12_BCR
10x Genomics


title: P12, peripheral blood, scTCR-seq

description:
PBMC_P12_TCR
10x Genomics


title: 640_MDAMB231_ctrl


title: P08, peripheral blood, scTCR-seq

description:
PBMC_P08_TCR
10x Genomics


title: 639_MDAMB231_ctrl


title: 638_MDAMB231_ctrl


title: P07, peripheral blood, scTCR-seq

description:
PBMC_P07_TCR
10x Genomics


title: P07, peripheral blood, scBCR-seq

description:
PBMC_P07_BCR
10x Genomics


title: 75_PC3_cis_DPT1


title: 637_MDAMB231_ctrl


title: P08, peripheral blood, scBCR-seq

description:
PBMC_P08_BCR
10x Genomics


title: 636_MDAMB231_ctrl


title: 635_MDAMB231_ctrl


title: P03, peripheral blood, scTCR-seq

description:
PBMC_P03_TCR
10x Genomics


title: 631_MDAMB231_ctrl


title: All samples, peripheral blood (n=7) and tumor (n=1), aggregated scRNA-seq

description:
all_samples_GEX
10x Genomics

source_name: peripheral blood and tumor

value: peripheral blood and tumor

value: T and B cell


title: 633_MDAMB231_doc_DPT10


title: 634_MDAMB231_ctrl


title: OT6, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
OT6_tumor_bulkRNAseq
Personalis

data_processing:
Reads were aligned to the hs37d5 reference genome build. Sequence aligment was performed as described in Abbott et al. Clin Cancer Res. 2021.
Assembly: hs37d5
Supplementary files format and content: Gene expression and reconstructed T and B cell repertoire data are in tab-separated values files.

extract_protocol:
RNA was dual-isolated with DNA from FFPE samples utilizing the AllPrep DNA/RNA FFPE Tissue kit (Qiagen).
Exome capture was performed using Agilent SureSelect Clinical Research Exome v2 (SSCRv2) according to manufacturers’ recommendations. Additional supplementation with Personalis ACE proprietary target probes was performed to enhance coverage in difficult to sequence regions within sets of biomedically and medically relevant genes. Details regarding Personalis ACE assay design are described further in Patwardhan et al. 2015. In brief, manufacturer protocols were modified to adjust the average library insert length to approximately 250bp and included the use of the KAPA Stranded RNA Sequencing kit (Kapa Biosystems). Paired-end sequencing was performed using the Illumina NovaSeq 6000 sequencer.


title: 630_MDAMB231_ctrl

data_processing:
raw fastq files
Assembly: hg19
Supplementary files format and content: RDS file contains gene counts processed with htseq-count and aligned with hisat2
Supplementary files format and content: for RDS file: hisat2 & htseq-count


title: P02, peripheral blood, scBCR-seq

description:
PBMC_P02_BCR
10x Genomics


title: 629_MDAMB231_ctrl


title: 632_MDAMB231_ctrl


title: OT5, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
OT5_tumor_bulkRNAseq
Personalis


title: 628_MDAMB231_ctrl


title: OT2, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
OT2_tumor_bulkRNAseq
Personalis


title: 625_MDAMB231_cis_DPT10


title: P14, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
P14_tumor_bulkRNAseq
Personalis


title: OT4, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
OT4_tumor_bulkRNAseq
Personalis


title: 624_MDAMB231_cis_DPT10


title: 626_MDAMB231_ctrl


title: OT1, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
OT1_tumor_bulkRNAseq
Personalis


title: P13, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
P13_tumor_bulkRNAseq
Personalis


title: P03, peripheral blood, scBCR-seq

description:
PBMC_P03_BCR
10x Genomics


title: P12, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
P12_tumor_bulkRNAseq
Personalis


title: 623_MDAMB231_cis_DPT10


title: P02, peripheral blood, scTCR-seq

description:
PBMC_P02_TCR
10x Genomics


title: P11, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
P11_tumor_bulkRNAseq
Personalis


title: 622_MDAMB231_doc_DPT10


title: P08, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
P08_tumor_bulkRNAseq
Personalis


title: 620_MDAMB231_cis_DPT10


title: P07, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
P07_tumor_bulkRNAseq
Personalis


title: 619_MDAMB231_cis_DPT10


title: P02, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
P02_tumor_bulkRNAseq
Personalis


title: 618_MDAMB231_cis_DPT10


title: P01, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
P01_tumor_bulkRNAseq
Personalis


title: 617_MDAMB231_cis_DPT10


title: 627_MDAMB231_ctrl


title: 616_MDAMB231_cis_DPT10


title: 615_MDAMB231_cis_DPT10


title: P03, tumor, bulkRNAseq and reconstructed TCR/BCR repertoires

description:
P03_tumor_bulkRNAseq
Personalis


title: 3D Replicate 2

city: Milwaukee

first: Roshan

last: Kumar

state: Wisconsin

address: 8701 W Watertown Plank Rd

department: Obstetrics & Gynecology

institute: Medical College of Wisconsin

data_processing:
Reads were aligned to the custom, hybrid human-virus reference genome using the STAR v2.7.10b aligner (Dobin et al., 2013).
Transcript/gene-level expression abundance was quantified from aligned reads using RSEM v1.3.3 (Li and Dewey, 2011).
Assembly: hg38
Supplementary files format and content: csv

source_name: Uterine Tissue

growth_protocol: The SiHa cervical cancer cell line was obtained from the American Type Culture Collection (ATCC; HTB35™) and maintained in Dulbecco's Minimum Essential Medium (DMEM, ThermoFisher) with 10% Fetal Bovine Serum (FBS, Omega Scientific)

extract_protocol:
Total RNA was extracted using the PureLink™ RNA Mini Kit (ThermoFisher) as per manufacturer’s protocol, including on-column DNase treatment.
library preparation was done by Novogene

treatment_protocol: For 3D cultures, 5000 cells were seeded in each well of a 96-well Nunclon Sphera, U-bottom plate (ThermoFisher), then centrifuged at 70 × g for 5 min before placing in the incubator. Media replacement was performed every 2-3 days, and spheroid formation was monitored for 7-9 days

value: Uterine Tissue

value: SiHa

value: squamous cell carcinoma cell


title: 3D Replicate 3


title: 3D Replicate 1


title: 613_MDAMB231_cis_DPT10

first: Michaek

last: Schmidt

address: 1002 Childs Way


title: 2D Replicate 5


title: 2D Replicate 4


title: 612_MDAMB231_cis_DPT10


title: 2D Replicate 3


title: 610_MDAMB231_cis_DPT10


title: 621_MDAMB231_cis_DPT10


title: 2D Replicate 2


title: 608_MDAMB231_cis_DPT10


title: M_wt_1

city: Yuxi

first: Zuohui

state: --- Select One ---

address: No. 21 Nieer Rd, Yuxi, Yunan

institute: The People’s Hospital of Yuxi City

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Homo sapiens hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: skin

growth_protocol: A375 were cultured in DMEM medium with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A375 were treated with DITC for 105 days.

value: skin

value: melanoma

tag: group


title: 607_MDAMB231_cis_DPT10

city: LOS ANGELES

institute: University of Southern California


title: M_BR_5_1

value: DR


title: 606_MDAMB231_cis_DPT10


title: Exposed to 0.5µg/L of Fluoxetine, 36 hours Replicate 2

city: Kingston-Upon-Hull

first: Quentin

last: Rodriguez-Barucg

address: University of Hull, Cottingham Road

department: HYMS Centre for Biomedicine

country: United Kingdom

institute: University of Hull

data_processing:
Illumina Sequencing PE150
Assembly: hg38
Supplementary files format and content: txt file the significance analysis result of each gene in all compare groups (all_compare.txt)
Supplementary files format and content: txt files showing the differential significance analysis for each compared group

source_name: HaCat

extract_protocol:
RNA was isolated using the PureLink™ RNA Mini Kit (#12183020, Thermo Fisher Scientific) following the manufacturer's instructions
mRNA library preparation (poly A enrichment)

value: HaCat

value: spontaneously immortalised human keratinocytes

value: 0.5ug/L of Fluoxetine

tag: time

value: 36 hours


title: 604_MDAMB231_cis_DPT10


title: Exposed to 0.5µg/L of Fluoxetine, 36 hours Replicate 4


title: 609_MDAMB231_cis_DPT10


title: 605_MDAMB231_cis_DPT10


title: 603_MDAMB231_cis_DPT10


title: Exposed to 0.5µg/L of Fluoxetine, 36 hours Replicate 1


title: 602_MDAMB231_cis_DPT10


title: 614_MDAMB231_cis_DPT10


title: Control cells, 36 hours Replicate 4

value: Control


title: 601_MDAMB231_cis_DPT10

value: epithelial cell line


title: Control cells, 36 hours Replicate 3


title: 2D Replicate 1


title: Exposed to 0.5µg/L of Fluoxetine, 36 hours Replicate 3


title: Control cells, 36 hours Replicate 2


title: 599_MDAMB231_cis_DPT10


title: Exposed to 0.5µg/L of Fluoxetine, 6 hours Replicate 4

value: 6 hours


title: 598_MDAMB231_cis_DPT10

value: breast


title: Exposed to 0.5µg/L of Fluoxetine, 6 hours Replicate 3


title: 611_MDAMB231_doc_DPT10


title: Exposed to 0.5µg/L of Fluoxetine, 6 hours Replicate 2


title: Control cells, 36 hours Replicate 1


title: Control cells, 6 hours Replicate 4


title: 600_MDAMB231_cis_DPT10


title: 593_MDAMB231_cis_DPT10


title: Control cells, 6 hours Replicate 3


title: 596_MDAMB231_cis_DPT10


title: 597_MDAMB231_cis_DPT10


title: 595_MDAMB231_cis_DPT10


title: Control cells, 6 hours Replicate 1


title: 590_MDAMB231_cis_DPT10


title: 588_MDAMB231_cis_DPT10


title: 587_MDAMB231_cis_DPT10


title: Exposed to 0.5µg/L of Fluoxetine, 6 hours Replicate 1


title: 594_MDAMB231_cis_DPT10


title: 592_MDAMB231_cis_DPT10


title: 589_MDAMB231_cis_DPT10


title: 591_MDAMB231_cis_DPT10


title: 1.02_2


title: 585_MDAMB231_cis_DPT10


title: 586_MDAMB231_cis_DPT10


title: 582_MDAMB231_doc_DPT10


title: 583_MDAMB231_doc_DPT10


title: 579_MDAMB231_doc_DPT10


title: 580_MDAMB231_doc_DPT10


title: 578_MDAMB231_doc_DPT10


title: OA_PA B50

city: Antwerpen

first: Cédric

last: Peleman

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

data_processing:
Adapter sequences and low-quality parts of the raw reads were trimmed with SeqPurge.
BAM files were sorted and indexed using SAMtools, followed by quantification of the number of reads per gene per sample with featureCounts.
Assembly: Mapping to the indexed human reference genome GRCh38 (hg38) was performed using STAR to produce a BAM file.
Supplementary files format and content: Tab-delimited text file with raw counts per gene for each Sample.

growth_protocol: HepG2 hepatoblastoma cells were maintained in EMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Library preparation started with isolation of intact poly(A) RNA by means of NEBNext poly(A) mRNA magnetic isolation
Directional RNA libraries were set up by means of NEBNext Ultra II directional RNA library prep kit (E7760) in combination with NEBNext multiplex oligos for Illumina.

treatment_protocol: The OA/PA condition was exposed for 48 hours to oleic acid (100microM) and palmitic acid (50microM), as well as hyperglycemia (4.5 mg/mL), hyperinsulinemia (100 nM), tumor necrosis factor alpha (50 ng/mL), interleukin 1-beta (25 ng/mL) and transforming growth factor-beta (8ng/mL). Control samples were exposed to solvents needed to dissolve oleic acid and palmitic acid in medium.

value: hepatoblastoma

value: wild-type

value: OA/PA


title: Control cells, 6 hours Replicate 2


title: 577_MDAMB231_doc_DPT10


title: OA_PA B49


title: 576_MDAMB231_doc_DPT10


title: 575_MDAMB231_doc_DPT10


title: Control B47


title: Control B46


title: 574_MDAMB231_doc_DPT10


title: OA_PA B28


title: OA_PA B29


title: 573_MDAMB231_doc_DPT10


title: 571_MDAMB231_doc_DPT10


title: 568_MDAMB231_doc_DPT10


title: Control B5


title: OA_PA B8


title: 570_MDAMB231_doc_DPT10


title: 581_MDAMB231_doc_DPT10


title: Control B25


title: 567_MDAMB231_doc_DPT10


title: Control B26


title: 572_MDAMB231_doc_DPT10


title: OA_PA B7


title: 569_MDAMB231_doc_DPT10


title: Control B4


title: 564_MDAMB231_doc_DPT10


title: 566_MDAMB231_doc_DPT10


title: MV411_invivo_MS41_rep3

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Read counts were generated by HTSeq (v0.11.3).
Assembly: hg38
Supplementary files format and content: txt file, read counts from HTseq.

extract_protocol:
Total RNA were extracted by RNeasy Plus Mini Kit (QIAGEN, Cat. 74136).
Libraries were constructed using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Cat. 634888).

value: human leukeima cell

value: WT


title: MV411_invivo_MS41_rep1


title: 565_MDAMB231_doc_DPT10


title: 563_MDAMB231_doc_DPT10


title: MV411_invivo_Veh_rep1

value: vehicle


title: 560_MDAMB231_doc_DPT10


title: 561_MDAMB231_doc_DPT10


title: MV411_invivo_Veh_rep2


title: 562_MDAMB231_doc_DPT10


title: MV411_MS41_6h_H3K4me3_rep2

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to hg38 by HISAT2 (v2.1.0).
Bigwig is generated with Deeptools (v3.5.2).
Assembly: hg38
Supplementary files format and content: bigwig file, ChIP density profiles for genome browser.

growth_protocol: Human leukaemia cell lines MV4;11, was maintained in RPMI (Corning, 10-040-CV) 10% Fetal Bovine Serum (Sigma, F4135) supplemented with 2 mM l-glutamine and 100 U ml−1 penicillin/streptomycin (Corning, 30-009-CI).

extract_protocol:
Eluted DNA were decrosslinked and extracted by QIAquick PCR Purification Kit (QIAGEN, Cat. 28106).
Libraries were constructed using Illumina standard protocols.

treatment_protocol: Human leukaemia cell lines are treated with DMSO, 100 nM MS41for 6h or 24h. Then cells are collected for Chip assay.

value: human leukemia cell

tag: chip antibody


title: MV411_MS41_6h_H3K4me3_rep3


title: MV411_MS41_6h_H3K4me3_rep1


title: 555_MDAMB231_doc_DPT10


title: 557_MDAMB231_doc_DPT10


title: MV411_invivo_Veh_rep3


title: MV411_MS41_6h_H3K27ac_rep3


title: MV411_DMSO_6h_H3K4me3_rep3

value: DMSO


title: 556_MDAMB231_doc_DPT10


title: MV411_DMSO_6h_H3K4me3_rep2


title: 553_MDAMB231_doc_DPT10


title: 551_MDAMB231_doc_DPT10


title: 550_MDAMB231_doc_DPT10


title: MV411_DMSO_6h_H3K27ac_rep2


title: MV411_DMSO_6h_H3K27ac_rep3


title: 552_MDAMB231_doc_DPT10


title: 558_MDAMB231_doc_DPT10


title: MV411_DMSO_6h_H3K4me3_rep1


title: 554_MDAMB231_doc_DPT10


title: 549_MDAMB231_doc_DPT10


title: MV411_MS41_6h_H3K27ac_rep2


title: MV411_DMSO_6h_H3K27ac_rep1


title: 559_MDAMB231_doc_DPT10


title: MV411_invivo_MS41_rep2


title: 360.SNP.24h

city: Toulouse

first: Jean-Charles

last: Guery

address: CHU Purpan – BP 3028

institute: INSERM

description:
SNP.24h.360
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS

data_processing:
Raw sequencing FASTQ files were processed using nf-core/rnaseq pipeline (v3.8.1) on genotoul SLURM cluster using -profile genotoul, --fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa, --gtf Homo_sapiens.GRCh38.104.gtf ,-- aligner star_salmon options.
Raw sequencing FASTQ files were quality controlled using FASTQC (v0.11.9)
Adapter and quality trimming was performed using Trim Galore! (v3.4)
Trimmed reads were aligned to reference genome using STAR (v2.7.10a), BAM files were sorted and indexed using samtools (v1.15.1), duplicates were marked using picard MarkDuplicates (v 2.26.10)
Pseudo-alignment and quantification were performed using salmon (v 1.5.2)
Salmon transcripts quantification files (quant.sf) were imported into R/Rstudio using R ‘tximport’ package and a file linking Transcript ID to Gene ID (‘tx2gene’ file) generated by the nf-core/rnaseq pipeline to produce the raw counts matrix. TPMs values were retrieved from the abundance slot of tximport generated list.
For differential gene expression analyses, the raw count matrix was converted to a DESeq2 object using ‘DESeq2::DESeqDataSetFromTximport’  function with design : ~ group, where the group represent the combination of Genotype (i.e. WT for rs736631C/CD226-307Gly protective allele or SNP for rs736631T/CD226-307Ser risk allele) and treatment time (i.e. WT.0h, SNP.0h, WT.4h, SNP.4H, WT.12h, SNP.12h, WT.24h, SNP.24h).
Raw count matrix was further processed to remove genes that have low / inconsistent gene expression level in samples from the same ‘Group’ (i.e. WT.0h, WT.4h, WT.12h, WT.24h,  SNP.0h, SNP.4h, SNP.12h, SNP.24h). Raw counts were normalized using DESeq2::counts function and genes having less than 10 normalized counts in all groups in 2 of the 10 samples from the same group were filtered out yielding a normalized count matrix with 14965 genes.
Pairwise differential gene expression analyses were performed to compare SNP.0h vs WT.0h; SNP.4h vs WT.4h; SNP.12h vs WT.12h; SNP.24h vs WT.24h; SNP.4h vs SNP.0h; SNP.12h vs SNP.0h; SNP.24h vs SNP.0h; WT.4h vs WT.0h; WT.12h vs WT.0h and WT.24h vs WT.0h groups using DESeq2::results function with options lfcThreshold set to 0 and alpha set to 0.05.
For each pairwise comparison, DESeq2 results were exported as a tab-delimited file with raw counts, normalized counts and TPMs for all samples being compared.
Assembly: ENSEMBL GRCh38 (hg38) v104
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes DESeq2 normalized counts for each sample
Supplementary files format and content: Tab-delimited text file includes Transcript-per-Million (TPMs) counts for each sample
Supplementary files format and content: RDS file holding sample information
Supplementary files format and content: RDS file holding Transcript ID to GeneID mapping info (i.e. tx2gene file used to import salmon quantification file in R using Tximport)
Supplementary files format and content: RDS file for raw count matrix
Supplementary files format and content: RDS file for DESeq2 filtered normalized counts matrix
Supplementary files format and content: RDS file holding Ensembl gene mapping information for annotation of genes in count matrices

source_name: CD3+CD8+ CD8 T cells

growth_protocol: Peripheral blood mononuclear leukocytes (PBMCs) were purified from buffy coat preparations obtained from consenting healthy blood donors. PBMCs were prepared by gradient centrifugation of buffy coats and kept in frozen in liquid nitrogen. Genotyping of the CD226 SNP rs763361 was performed using TaqMan SNP Genotyping assay. rs763361T expressing CD226-307Ser represented the risk allele, whereas rs763361C expressing CD226-307Gly represented the protective allele. Experiments were performed on cells form male donors homozygous for either allele.Frozen PBMCs were thawed, monocytes removed by plastic adherence and CD8 T cells were purified by negative selection. The percentage of residual CD4 T cells after depletion was always  less than 0.5% and the remaining populations consisted of 95-98% CD8 T cells.

extract_protocol:
RNA was extracted using RNAeasy Micro Kit (Qiagen) following manufacturer’s instructions.
Libraries were prepared using the Illumina Stranded Total RNA Prep kit starting from 7.5 ng of total RNA and using 14 PCR cycles for library amplification. The kit for the index sequences used was IDT Illumina RNA UDI A Lig 96 Indexes 96 Spl. RNA sequencing was  performed on one S4 lane on an Illumina NovaSeq 6000 sequencer, using NovaSeq 6000 S4 v1.5 Reagent Kit (300 cycles), and a paired-end 2 x 150 pb strategy. Between 20 and 44 million paired-end raw reads were produced per library.

treatment_protocol: FACS-sorted CD3+CD8+ T cells from healthy donors homozygous for either the protective (CD226-307Gly, N = 10) or risk allele (CD226-307Ser, N = 10) cultured in complete medium RPMI and stimulated with anti-CD3 and anti-CD28 monoclonal antibodies for 0h, 4h and 24h were subjected to RNA extraction using RNeasy Micro Kit. Paired-end (2x150pb) sequencing libraries were prepared using  Illumina’s Stranded Total RNA prep kit starting from 7,5ng of total RNA using 14 PCR cycles for library amplification. Sequencing libraries were indexed using IDT Illumina UDI A Lig 96 indexes 96 Sp1. RNA sequencing was performed on one S4 lane on an Illumina Novaseq 6000 sequencer using Novaseq 6000 S4 1v5 Reagent Kit (300 cycles) yielding between 20 and 40 millions raw paired-end reads per library.

value: CD3+CD8+ CD8 T cells

tag: cd226 allele

value: anti-CD3/anti-CD28 mAbs


title: 359.SNP.24h

description:
SNP.24h.359
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 475_MDAMB231_cis_DPT10


title: 350.SNP.24h

description:
SNP.24h.350
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: MV411_MS41_6h_H3K27ac_rep1


title: 474_MDAMB231_cis_DPT10


title: 332.SNP.24h

description:
SNP.24h.332
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 473_MDAMB231_cis_DPT10


title: 315.SNP.24h

description:
SNP.24h.315
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 471_MDAMB231_ctrl


title: 469_MDAMB231_ctrl


title: 246.SNP.24h

description:
SNP.24h.246
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 295.SNP.24h

description:
SNP.24h.295
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 466_MDAMB231_ctrl


title: 463_MDAMB231_ctrl


title: 181.SNP.24h

description:
SNP.24h.181
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 110.SNP.24h

description:
SNP.24h.110
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 322.WT.24h

description:
WT.24h.322
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 101.SNP.24h

description:
SNP.24h.101
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
SNP.24h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 320.WT.24h

description:
WT.24h.320
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 457_MDAMB231_ctrl


title: 547_MDAMB231_doc_DPT10


title: 232.WT.24h

description:
WT.24h.232
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 454_MDAMB231_ctrl


title: 444_MDAMB231_doc_DPT10


title: 548_MDAMB231_doc_DPT10


title: 441_MDAMB231_doc_DPT10


title: 460_MDAMB231_ctrl


title: 450_MDAMB231_cis_DPT1


title: 230.WT.24h

description:
WT.24h.230
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 316.WT.24h

description:
WT.24h.316
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 435_MDAMB231_doc_DPT10


title: 438_MDAMB231_doc_DPT10


title: 223.WT.24h

description:
WT.24h.223
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 167.WT.24h

description:
WT.24h.167
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 161.WT.24h

description:
WT.24h.161
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 432_MDAMB231_doc_DPT10


title: 429_MDAMB231_doc_DPT10


title: 426_MDAMB231_doc_DPT10


title: 360.SNP.12h

description:
SNP.12h.360
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
SNP.12h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 417_MDAMB231_doc_DPT10


title: 91.WT.24h

description:
WT.24h.91
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.24h.vs.WT.24h.tsv
WT.24h.vs.WT.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 359.SNP.12h

description:
SNP.12h.359
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
SNP.12h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 423_MDAMB231_doc_DPT10


title: 295.SNP.12h

description:
SNP.12h.295
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
SNP.12h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 246.SNP.12h

description:
SNP.12h.246
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
SNP.12h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 350.SNP.12h

description:
SNP.12h.350
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
SNP.12h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 110.SNP.12h

description:
SNP.12h.110
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
SNP.12h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 414_MDAMB231_doc_DPT10


title: 332.SNP.12h

description:
SNP.12h.332
raw_counts.tsv
DESeq2_normalized_counts.tsv
TPMs.tsv
SNP.12h.vs.WT.12h.tsv
SNP.12h.vs.SNP.0h.tsv
samples.RDS
salmon_tx2gene.RDS
hsapiens_gene_ensembl_v104.RDS
deseq2_unfiltered_60664_genes.RDS
deseq2_filtered_14965_genes.RDS


title: 385_MDAMB231_doc_DPT10