title: Splenic B cells, O. tsutsugamushi-infected C57BL/6 mice, Day8, replicate 2, RNAseq

city: Galveston

first: Lynn

last: Soong

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC2. Reads were aligned to the Mus musculus genome build mm10 using STAR3. Individual sample reads were quantified using HTseq4 and normalized via Relative Log Expression (RLE) using DESeq2 R library5. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC6. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library7. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library8, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro9, NCBI10, MSigDB11,12, REACTOME13, WikiPathways14. Enrichment was calculated relative to a set of background genes relevant for the experiment.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include DESeq2-normalized counts

source_name: Spleen

extract_protocol:
Female C57BL/6J mice (8-12 weeks-old, purchased from the Jackson Laboratory #000664) were intravenously inoculated with a lethal dose (8 × 10e4 FFU, 200 µl) of bacteria or PBS (mock). Mice were sacrificed at established timepoints, and spleens were collected in RPMI 1640 medium. Spleen single-cell suspensions were made by passing splenic tissue through a 70-μm cell strainer in RPMI 1640 medium, and these were then treated with Red Blood Cell Lysis Buffer. Untouched B cells were isolated from spleen single-cell suspensions by using the mouse B Cell Isolation Kit (Miltenyi Biotec). B cell samples were then evaluated for purity (~97-98%, based on B220 expression assessed by flow cytometry) and stored in RNALater. Total RNA was extracted by using the RNeasy Mini kit (Qiagen). Total RNA (≥ 1ug) was sent to LC Sciences (Houston, TX) for Poly(A) RNA-Seq Sequencing Service.
The total RNA quantity and purity were analyzed by the Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). High-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. mRNA was purified from total RNA using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat. e6150, USA, under 94℃ 5-7min). Then, the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were then used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat. m0209, USA), RNase H (NEB, cat. m0297, USA) and dUTP Solution (Thermo Fisher, cat. R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat. m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec, and then final extension at 72℃ for 5 min. The average insert sizes for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150 bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC Sciences, Houston, TX, US) following the vendor's recommended protocol.
2×150bp paired-endsequencing (PE150)

value: Spleen

value: B220+ cells

value: 8-12 weeks

value: O. tsutsugamushi lethal dose

tag: time

value: Day 8


title: Splenic B cells, O. tsutsugamushi-infected C57BL/6 mice, Day8, replicate 3, RNAseq

status: Public on Jan 16 2023

type: SRA

state: TX

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: strain

tag: age

tag: treatment


title: CyA_14

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

data_processing:
High throughput sequencing of final pool was performed using NovaSeq6000 S4 system (Illumina) with following instrument settings: paired-end, 150 b, 4500-5000 million reads per lane.
Raw data were automatically processed by Basespace cloud interface (Illumina) in default settings.
The basecalling, adapter clipping, and quality filtering were carried out using bcl2fastq v2.20.0.422 Conversion Software (Illumina).
The quality of raw reads was evaluated using FastQC (v0.11.5) and MultiQC (v1.6).
Clipping adaptor sequences was carried out using cutadapt (v1.18). The trimmed reads were aligned to the human cDNA reference (GeCh38) using bowtie2 (v 2.1.0). The counts of reads mapped to the reference were extracted and used for differential gene expression analysis using SAMtools (v1.2).
DESeq2 R library version 1.2 was applied to normalize read counts and to identify differences in gene expression between sample groups
Assembly: human transcriptome reference (GeCh38)
Supplementary files format and content: Matrix table with raw transcript counts for every transcript and every sample

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Total RNA was isolated from peripheral blood (PAXgene blood RNA kit, Qiagen), concentration was measured by Qubit fluorimetr and RNA integrity number was checked using Agilent Bioanalyzer 2100. Isolated RNA (800ng) was rRNA and globin depleted using NEBNext® Globin & rRNA Depletion Kit (New England, BioLabs, Inc).
Transcriptome libraries for differential gene expression were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads according to the manufacturer’s protocol (New England, BioLabs, Inc). In brief, depleted RNA was randomly sheared by heat digestion in the presence of a divalent metal cation (Mg2+). Sheared RNA was reversibly transcribed making 1st strand of cDNA using random hexamers as primers and reverse transcriptase. The second strand was created using dUTPs and after purification with Sample Purification Beads, NEBNext adapters were ligated. After removal of 2nd strand by uracil-DNA-dependent glycosylase, final amplification of adaptor ligated DNA using NEBNext® Multiplex Oligos for Illumina® was done. Library quality was assessed on a Bioanalyzer 2100 using Agilent DNA 1000 assay.

value: peripheral blood

tag: condition

value: CsA

tag: age at sampling (years)

tag: creatinine at sampling (umol/l)

tag: clinical diagnosis

value: primary glomerulopathies (CKD 1 or 2) treated by Cyclosporine A or Tacrolimus


title: Splenic B cells, O. tsutsugamushi-infected C57BL/6 mice, Day8, replicate 1, RNAseq


title: hASPS_siNC_1

type: RNA

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

description: Gene expression data from human sarcoma cell

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: human ASPS cell line expressing ASPSCR1-TFE3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse and human ASPS cells were grown in IMDM supplemented with 10% fetal bovine serum (FBS) and RPMI-1640 supplemented with 10% FBS, respectively.

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: Mouse ASPS cells were treated with 100 nM JQ1 for 48 hours. Small interfering RNA-mediated gene silencing of human ASPS cells was performed.

value: Alveolar soft part sarcoma


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep10 [KO_SAL+TOL_10]

city: Toronto

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

department: Department of Medicine

country: Canada

institute: University of Toronto

description: Tamoxifen-inducible, kidney-specific, Pkd1 (iKsp-Pkd1del) conditional knock-out kidney

hyb_protocol: Following fragmentation, 5.5 μg of biotin-labelled ss-cDNAs were hybridized to GeneChip mouse Gene 2.0 ST Arrays for 16 hours at 45°C. Hybridized arrays were then stained and washed in the Affymetrix Fluidics Station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The (.DAT) image files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software to generate cell intensity (.CEL) files. The (.CEL) files were uploaded to the Transcriptome Analysis Console (TAC) 4.0 (Thermo Fisher Scientific) for further processing and quality control. The probe set's signal intensities were then extracted and normalized using the robust multi-array average (RMA) algorithm embedded in TAC4.0 software. The differentially expressed genes between different groups were determined by the Limma Bioconductor package implemented in TAC 4.0. Enrichr was used as the primary tool to identify potential gene pathways or key regulatory factors altered by the treatments.

source_name: kidney from Salsalate+Tolvaptan treated Pkd1 KO mouse

label_protocol: Biotin-labelled ss-cDNAs were prepared by using the GeneChip WT PLUS Kit according to the standard Affymetrix protocol for 300 ng of total RNA.

growth_protocol: Pkd1-cKO mice have a homozygously bred kidney-specific, tamoxifen-inducible Cre and two LoxP sites that flank exons 2-11 of the Pkd1 gene. The mice received tamoxifen (150 mg/kg) by oral gavage on days PN18 and PN19 to induce adult onset PKD. At PN30 the Pkd1 mutant mice started on normal chow and randomly allocated to different groups. At PN40, the untreated PKD mice continued on the normal chow and the treated PKD mice were switched to the chow supplemented with 0.25% salsalate, and/or 0.15% tolvaptan-SD. Blood Urea (BU) levels were monitored weekly and the mice with end stage renal disease (ESRD, BU > 20 mmol/L) were sacrificed. The experiment continued until 75% of the untreated mutant mice reached ESRD at 111-120 days of age. For the whole gene expression study, KO and drug-treated KO kidneys were selected around the median of the ratio of two-kidney weight/body weight, and the kidneys from mice not receiving tamoxifen were used as wild type controls.

extract_protocol: The total RNA was extracted using miRNeasy Mini Kit (Qiagen) following the manufacturer’s protocol with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA sample was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the RNA integrity number (RIN) was greater than 9.

treatment_protocol: All kidney samples were snapped frozen in liquid nitrogen, and stored in a -80°C freezer.

tag: Sex

value: Male

value: kidney

tag: genotype

value: Pkd1 KO

value: treated with Salsalate+Tolvaptan


title: CyA_12


title: CyA_11


title: CyA_10


title: CyA_13


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep11 [KO_SAL+TOL_11]


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep8 [KO_SAL+TOL_8]


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep9 [KO_SAL+TOL_9]


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep5 [KO_SAL+TOL_5]


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep12 [KO_SAL+TOL_12]


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep4 [KO_SAL+TOL_4]


title: Splenic B cells, O. tsutsugamushi-infected C57BL/6 mice, Day4, replicate 2, RNAseq

value: Day 4


title: Splenic B cells, O. tsutsugamushi-infected C57BL/6 mice, Day4, replicate 3, RNAseq


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep2 [KO_SAL+TOL_2]


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep7 [KO_SAL+TOL_7]


title: Splenic B cells, O. tsutsugamushi-infected C57BL/6 mice, Day4, replicate 1, RNAseq


title: RHE_S.-epidermidis-ATCC-12228_24hours_rep3

city: Southampton

first: Francesca

last: Ciccarelli

address: Southampton General Hospital

country: United Kingdom

institute: University of Southampton

hyb_protocol: Labelled cRNA samples (2μg) were bought to a volume of 19μl in nuclease free water for incubation with fragmentation buffer, then adding GEx hybridisation buffer HI-RPM to stop the fragmentation process. Hybridisation occurred in an Agilent SureHyb chamber for 17 hours at 65 degrees. A wash step was follwed using Agilent wash buffer 2 followed by acetonitrile for 10 seconds. The slides were allowed to dry and immediately covered with an Agilent Ozone protection cover. The arrays were scanned immediately afterwards.

scan_protocol: The arrays were scanned with the Agilent microarray scanner; the numerical expression data of each array was acquired by the Feature Extraction Software.

data_processing: Further analysis was performed in GeneSpring 14.9 (Agilent) and Ingenuity Pathway Analysis software (QIAGEN) using the RHE_Control_0hours_rep1 samples as a realtive control.

label_protocol: Labelling was performed using the reagents provided with the SurePrint G3 Human Gene Expression v3 8x60K Microarray Kit (Agilent). The dye incorporated cRNA mix was purified using the RNeasy mini kit (QIAGEN) using provided reagents. The cRNA was quantified using a Nanodrop 1000 UV-visible spectrophotometer (Thermo Scientific) measuring at 260nm and 550 nm.

extract_protocol: Following colonisation, models were washed 3 times and separated into separate wells of a 24 well plate. 400μl of RLT lysis buffer (QIAGEN) was added to the surface for a 1hr incubation at room temperature. The RNA was subsequently purified using the RNeasy plus mini kit (QIAGEN) as per the manufacture's instructions.

value: reconsituted human epidermis (RHE)

value: S. epidermidis ATCC 12228


title: HPB-NULL_MI2

city: New Orleans

first: Nakhle

last: Saba

state: LA

address: 1415 Tulane Ave, Room 118

department: Internal Medicine/Hematology

institute: Tulane University

data_processing:
Reads were aligned to hg38 using STAR v2.6.1d (--outReadsUnmapped Fastx --outSAMtype BAM   SortedByCoordinate --outSAMunmapped Within --outWigType bedGraph --outWigStrand Unstranded --outWigNorm None --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 5 --alignSJstitchMismatchNmax 5   -1   5   5 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimOutType Junctions WithinBAM --chimSegmentReadGapMax 3 --chimOutJunctionFormat 1 --twopassMode Basic)
Reads were psuedo-aligned to hg38 transcriptome using kallisto quant v.0.46.0 for abundance measurements
Assembly: hg38
Supplementary files format and content: tab deliminted text file with read counts for genes across all samples

source_name: Acute lymphoblastic leukemia

growth_protocol: cells were cultured in RPMI1640 with 5%FBS and antibiotics (penicillin and streptimycin) at 37C and 5%CO2

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Coculture with MI-2 at a concentration of during 48hrs

value: Acute lymphoblastic leukemia

tag: cell line

value: HPB-NULL


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep6 [KO_SAL+TOL_6]


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep1 [KO_SAL+TOL_1]


title: RHE_S.-capitis-ATCC-27840_24hours_rep3

value: S. capitis ATCC 27840


title: RHE_S.-aureus-NCTC-8325-4_24hours_rep3

value: S. aureus NCTC-8325-4


title: RHE_Control_24hours_rep3

value: Control


title: Kidney_Pkd1 knockout_Salsalate+Tolvaptan_rep3 [KO_SAL+TOL_3]


title: Kidney_Pkd1 knockout_Tolvaptan_rep12 [KO_TOL_12]

source_name: kidney from Tolvaptan treated Pkd1 KO mouse

value: treated with Tolvaptan


title: CyA_9

value: peripheral blood


title: Splenic B cells, PBS mock-infected C57BL/6 mice, Day0, replicate 2, RNAseq

value: Spleen

value: B220+ cells

value: 8-12 weeks

value: PBS

value: Day 0


title: CyA_7

value: CsA

value: primary glomerulopathies (CKD 1 or 2) treated by Cyclosporine A or Tacrolimus


title: CyA_8


title: Kidney_Pkd1 knockout_Tolvaptan_rep11 [KO_TOL_11]

value: Male

value: kidney

value: Pkd1 KO


title: Splenic B cells, PBS mock-infected C57BL/6 mice, Day0, replicate 1, RNAseq


title: vCAR pIC [9_S3 TCR-seq]

city: Durham

first: Ravi

last: Bellamkonda

state: NC

address: 308 Research Dr.

department: Biomedical Engineering

institute: Duke University

description:
300 bp reads
QIAseqRNA-immune-repertoire-TCR.clonotypes.txt
QIAseqRNA-immune-repertoire-TCR.summary.txt

library_source: other

data_processing:
library strategy: TCR-seq
Quality control was performed using FastQC/MultiQC for all fastq files.
Custom transgenes for GFP, LUC, EGFRVIII, and CAR were added and used
Star Alignment was run using default parameters and soft clipping for the Illumina universal adapter sequence (--clip3pAdapterSeq AGATCGGAAGAG)
FeatureCounts was used for expression quantification of alignment output (featureCounts -p -s 2 -T 8 -t exon -g gene_id -a)
Downstream analysis of the FeatureCounts raw counts output matrix was performed using DESeq2 (version 1.36.0)
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa
Supplementary files format and content: tab-delimited text files include for rnaseq data raw and normalized couts or tcrseq data

molecule: other

extract_protocol:
RNA was harvested using RNeasy Lipid Tissue Mini kit (Qiagen).
The RNA-seq library was prepared with the KAPA Stranded mRNA-Seq kit (Roche). The TCR-seq library was prepared with the mouse T-cell Receptor Panel QIAseq Immune Repetoire RNA Library Kit (Qiagen

value: glioblastoma

value: WT

value: CAR T with poly(I:C)

value: Day 7


title: vIL7 PBS [8_S2 TCR-seq]

value: CAR T with PBS


title: vCAR PBS [6_S1 TCR-seq]


title: CyA_5


title: vCAR pIC [51_S17 TCR-seq]


title: CyA_4


title: RHE_S.-aureus-NCTC-8325-4_24hours_rep2

value: reconsituted human epidermis (RHE)

value: S. aureus NCTC-8325-4


title: vIL7FL PBS [53_S18 TCR-seq]


title: CyA_3

value: peripheral blood


title: CyA_2

value: chronic active antibody-mediated rejection(cg>1)


title: CyA_6


title: RHE_Control_24hours_rep2

value: Control


title: RHE_S.-capitis-ATCC-27840_24hours_rep2

value: S. capitis ATCC 27840


title: vIL7 pIC [50_S16 TCR-seq]


title: CyA_1


title: Kidney_Pkd1 knockout_Tolvaptan_rep7 [KO_TOL_7]

value: treated with Tolvaptan


title: Kidney_Pkd1 knockout_Tolvaptan_rep9 [KO_TOL_9]


title: Kidney_Pkd1 knockout_Tolvaptan_rep8 [KO_TOL_8]


title: RHE_S.-capitis-ATCC-27840_24hours_rep1


title: CR_13

value: CABMR


title: CR_14


title: Kidney_Pkd1 knockout_Tolvaptan_rep6 [KO_TOL_6]


title: Kidney_Pkd1 knockout_Tolvaptan_rep5 [KO_TOL_5]


title: vIL7 PBS [5_S5 TCR-seq]


title: RHE_S.-aureus-NCTC-8325-4_24hours_rep1


title: Kidney_Pkd1 knockout_Tolvaptan_rep10 [KO_TOL_10]


title: Kidney_Pkd1 knockout_Tolvaptan_rep3 [KO_TOL_3]


title: vIL7FL PBS [49_S15 TCR-seq]


title: RHE_Control_3hours_rep4


title: RHE_S.-capitis-ATCC-27840_3hours_rep4


title: RHE_Control_24hours_rep1


title: RHE_S.-epidermidis-ATCC-12228_24hours_rep2

value: S. epidermidis ATCC 12228


title: RHE_S.-epidermidis-ATCC-12228_24hours_rep1


title: vIL7FL pIC [39_S13 TCR-seq]


title: Kidney_Pkd1 knockout_Tolvaptan_rep1 [KO_TOL_1]

value: Male


title: RHE_S.-aureus-NCTC-8325-4_3hours_rep4


title: Kidney_Pkd1 knockout_Salsalate_rep11 [KO_SAL_11]

source_name: kidney from Salsalate treated Pkd1 KO mouse

value: kidney

value: treated with Salsalate


title: RHE_S.-epidermidis-ATCC-12228_3hours_rep3


title: vCAR PBS [44_S14 TCR-seq]

value: glioblastoma


title: vCAR pIC [37_S11 TCR-seq]

value: WT


title: Kidney_Pkd1 knockout_Salsalate_rep9 [KO_SAL_9]

value: Pkd1 KO


title: Kidney_Pkd1 knockout_Tolvaptan_rep4 [KO_TOL_4]


title: CR_10


title: CR_9


title: CR_11


title: CR_12


title: vCAR PBS [38_S12 TCR-seq]

value: Day 7


title: vIL7 pIC [30_S10 TCR-seq]

value: CAR T with poly(I:C)


title: CR_8


title: Kidney_Pkd1 knockout_Salsalate_rep8 [KO_SAL_8]


title: Kidney_Pkd1 knockout_Salsalate_rep10 [KO_SAL_10]


title: CR_6


title: RHE_S.-epidermidis-ATCC-12228_3hours_rep2

value: reconsituted human epidermis (RHE)


title: RHE_S.-capitis-ATCC-27840_3hours_rep3


title: RHE_Control_3hours_rep3


title: CR_7


title: RHE_S.-aureus-ATCC-29213-(NCTC-12973)_3hours_rep4

value: S. aureus ATCC 29213 (NCTC 12973)


title: vIL7FL pIC [28_S9 TCR-seq]


title: CR_5

value: peripheral blood


title: Kidney_Pkd1 knockout_Salsalate_rep7 [KO_SAL_7]


title: RHE_S.-aureus-NCTC-8325-4_3hours_rep3

value: S. aureus NCTC-8325-4


title: RHE_S.-epidermidis-ATCC-12228_3hours_rep1


title: Kidney_Pkd1 knockout_Salsalate_rep6 [KO_SAL_6]


title: RHE_S.-aureus-ATCC-29213-(NCTC-12973)_3hours_rep3


title: Kidney_Pkd1 knockout_Salsalate_rep2 [KO_SAL_2]


title: Kidney_Pkd1 knockout_Salsalate_rep5 [KO_SAL_5]


title: CR_4

value: chronic active antibody-mediated rejection(cg>1)


title: CR_3


title: vIL7 pIC [21_S6 TCR-seq]


title: vIL7 PBS [25_S8 TCR-seq]

value: CAR T with PBS


title: Kidney_Pkd1 knockout_Salsalate_rep3 [KO_SAL_3]


title: vIL7FL pIC [10_S4 TCR-seq]


title: CR_2


title: vCAR pIC [X9_S3_L002]

description:
151 bp reads
Counts_with_gene_names.txt
NormalizedCounts_with_gene_names.txt

data_processing:
Quality control was performed using FastQC/MultiQC for all fastq files.
Custom transgenes for GFP, LUC, EGFRVIII, and CAR were added and used
Star Alignment was run using default parameters and soft clipping for the Illumina universal adapter sequence (--clip3pAdapterSeq AGATCGGAAGAG)
FeatureCounts was used for expression quantification of alignment output (featureCounts -p -s 2 -T 8 -t exon -g gene_id -a)
Downstream analysis of the FeatureCounts raw counts output matrix was performed using DESeq2 (version 1.36.0)
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa
Supplementary files format and content: tab-delimited text files include for rnaseq data raw and normalized couts or tcrseq data


title: vIL7FL PBS [22_S7 TCR-seq]


title: CR_1


title: Kidney_Pkd1 knockout_Tolvaptan_rep2 [KO_TOL_2]

value: treated with Tolvaptan


title: vCAR PBS [X6_S1_L002]


title: Kidney_Pkd1 knockout_Salsalate_rep4 [KO_SAL_4]


title: vIL7FL PBS [X53_S18_L002]


title: RHE_S.-aureus-NCTC-8325-4_3hours_rep2


title: RHE_Control_3hours_rep2

value: Control


title: vCAR pIC [X51_S17_L002]


title: vIL7 PBS [X8_S2_L002]


title: RHE_S.-capitis-ATCC-27840_3hours_rep2

value: S. capitis ATCC 27840


title: Kidney_Pkd1 knockout_rep11 [KO_11]

source_name: kidney from untreated Pkd1 KO mouse

value: Male

value: untreated


title: RHE_Control_3hours_rep1


title: RHE_S.-aureus-ATCC-29213-(NCTC-12973)_3hours_rep2


title: RHE_S.-aureus-ATCC-29213-(NCTC-12973)_3hours_rep1


title: Kidney_Pkd1 knockout_rep10 [KO_10]

value: kidney


title: BNT-BNT-INF-D7

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

country: Germany

institute: BIH at Charité

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files, Comma-separated values file and matrix files
Supplementary files format and content: aggregated processed data in "All"-files

molecule: polyA RNA

source_name: CD4+ Tcells

growth_protocol: PBMC of three BNT-BNT-BNT-vaccinated, three AZ-BNT-BNT vaccinated, and three BNT-BNT-infected donors

extract_protocol:
CD4+ T cells were enriched by MACS (Miltenyi Biotec) and CD40L+4-1BB+ CD4+ T cells FACS sorted using an FACS Melody (BD). The cells were loaded with a maximum concentration of 1000 cells/µl and a maximum cell number of 17.000 cells on a Chromium Chip G (10x Genomics).
Gene expression and TCR libraries were generated according to the manufacturer’s instruction using the Chromium Next GEM single cell 5’Library and Gel bead Kit V1.1 and Chromium Single Cell V(D)J Enrichment Kit for human T cells (10x Genomics).

treatment_protocol: PBMCs were stimulated with 1 µg/ml S-I peptide pool in the presence of purified anti-CD28 (clone CD28.2, BD Biosciences) and anti-CD40 (clone HB14, Miltenyi Biotec).

value: CD4+ Tcells

value: CD40L+4-1BB+ CD4+ T cells

value: 1 ug/ml S-I peptide pool


title: Kidney_Pkd1 knockout_Salsalate_rep1 [KO_SAL_1]

value: Pkd1 KO

value: treated with Salsalate


title: BNT-BNT-BNT-D6

description: 10x Genomics


title: vIL7 pIC [X50_S16_L002]

value: glioblastoma

value: WT

value: CAR T with poly(I:C)

value: Day 7


title: Kidney_Pkd1 knockout_rep8 [KO_8]


title: BNT-BNT-INF-D9

description: 10x Genomics


title: vIL7 PBS [X5_S5_L002]


title: Kidney_Pkd1 knockout_rep12 [KO_12]


title: BNT-BNT-BNT-D5

description: 10x Genomics


title: her3_38aa_72hpf_2

city: Columbus

first: Genevieve

last: Kendall

state: OH

address: 700 Children's Drive, WA5014

institute: Nationwide Children's Hospital / The Ohio State University

data_processing:
# All code is available on github: https://github.com/MVesuviusC/kentRNAseq1  Aligned with HISAT2 v2.2.1 with reads filtered using SAMtools v1.10
Genes counted using featureCounts v2.0.2
Normalization and differential expression performed using EdgeR v3.34.0
Genome_build: danRer11
Supplementary_files_format_and_content: normGeneCounts.txt

organism: Danio rerio

source_name: whole embryo

extract_protocol:
All embryos were dechorionated at 24hpf. Approximately 25 embryos per sample were collected at 24hpf (samples 1-12) or 72hpf (samples 13-18). RNA was extracted with the QIAGEN Rneasy mini kit (Cat #: 74104) with on-column DNase digestion.
Total RNA was spiked with ERCC spike-in (Cat #: 4456740). PolyA RNA was enriched with NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat #: E7490). NEBNext® Ultra™ II Directional RNA Library Prep Kit (Cat #: E7760) was used to prepare the library.

value: whole embryo


title: Kidney_Pkd1 knockout_rep9 [KO_9]


title: vCAR PBS [X44_S14_L002]

value: CAR T with PBS


title: BNT-BNT-BNT-D4

description: 10x Genomics


title: her3_38aa_72hpf_1


title: BNT-BNT-INF-D8

description: 10x Genomics


title: RHE_S.-capitis-ATCC-27840_3hours_rep1

value: reconsituted human epidermis (RHE)


title: Kidney_Pkd1 knockout_rep7 [KO_7]


title: RHE_S.-aureus-NCTC-8325-4_3hours_rep1

value: S. aureus NCTC-8325-4


title: AZT-BNT-BNT-D3

description: 10x Genomics


title: WIK_72hpf_3


title: her3_38aa_72hpf_3


title: Kidney_Pkd1 knockout_rep6 [KO_6]


title: vIL7FL PBS [X49_S15_L002]


title: vIL7FL pIC [X39_S13_L002]


title: Kidney_Pkd1 knockout_rep5 [KO_5]


title: AZT-BNT-BNT-D2

description: 10x Genomics


title: RHE_Control_0hours_rep1

value: Control


title: AZT-BNT-BNT-D1

description: 10x Genomics


title: vCAR pIC [X37_S11_L002]


title: vCAR PBS [X38_S12_L002]


title: WIK_72hpf_1


title: WIK_72hpf_2


title: Kidney_Pkd1 knockout_rep4 [KO_4]

value: Male


title: mm-MO_24hpf_3

value: injected mm-MO at 1-4 cell stage


title: vIL7FL pIC [X28_S9_L002]


title: vIL7 pIC [X30_S10_L002]


title: mm-MO_24hpf_1


title: Kidney_wild type_rep10 [WT_10]

description: Wild type kidney

source_name: kidney from wild type mouse

value: kidney

value: wild type

value: untreated


title: vIL7 PBS [X25_S8_L002]


title: her3-MO_24hpf_3

value: injected her3-MO at 1-4 cell stage


title: Kidney_Pkd1 knockout_rep2 [KO_2]

value: Pkd1 KO


title: vIL7 pIC [X21_S6_L002]


title: her3-MO_24hpf_2


title: her3-MO_24hpf_1


title: vIL7FL pIC [X10_S4_L002]


title: Kidney_Pkd1 knockout_rep1 [KO_1]


title: vCAR pIC [X9_S3_L001]


title: Kidney_wild type_rep7 [WT_7]

description: Wild type kidney


title: her3_38aa_24hpf_3


title: vIL7 PBS [X8_S2_L001]


title: mm-MO_24hpf_2


title: her3_38aa_24hpf_1


title: Kidney_wild type_rep5 [WT_5]

description: Wild type kidney


title: Kidney_wild type_rep8 [WT_8]

description: Wild type kidney


title: vIL7FL PBS [X53_S18_L001]


title: Kidney_wild type_rep9 [WT_9]

description: Wild type kidney


title: WIK_24hpf_3


title: vIL7FL PBS [X22_S7_L002]


title: her3_38aa_24hpf_2


title: Kidney_wild type_rep6 [WT_6]

description: Wild type kidney


title: WIK_24hpf_2


title: vCAR pIC [X51_S17_L001]


title: Kidney_wild type_rep4 [WT_4]

description: Wild type kidney


title: mASPS null K27Ac2

description: Histone H3K27ac (Active Motif, 39133, lot 16119013)

library_source: genomic

data_processing:
Base calls were performed using Bowtie 2.
ChIP-seq reads were aligned to the mm9 or hg19 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
Assembly: mm9 (mouse) and hg19 (human)
Supplementary files format and content: For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max (1, Ci/Ei + 1).

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies
Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Mouse and human ASPS cells were treated with 100 nM JQ1 for 48 hours. Small interfering RNA-mediated gene silencing of human ASPS cells was performed.

value: murine alveolar soft part sarcoma


title: vIL7 pIC [X50_S16_L001]

value: glioblastoma


title: WIK_24hpf_1

value: WT


title: vIL7 PBS [X5_S5_L001]


title: Kidney_wild type_rep2 [WT_2]

description: Wild type kidney


title: mASPS K27Ac2


title: Kidney_wild type_rep3 [WT_3]

description: Wild type kidney


title: mASPS null FLAG

description: FLAG (Sigma, F7425, lot 085M4774V)


title: Kidney_wild type_rep1 [WT_1]

description: Wild type kidney


title: vIL7FL PBS [X49_S15_L001]


title: Compl biological replicate 2

city: London

first: David

last: Heinrichs

state: ON

address: Microbiology and Immunology, 3014 Dental Sciences Building, 1151 Richmond Street

institute: University of Western Ontario

data_processing:
Quality control and adapter trimming was performed with bcl2fastq. Read mapping was performed with RSEM.
Read counts loaded into R  and were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (cpm). Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups.

organism: Chlorocebus sabaeus

source_name: kidney

growth_protocol: Vero E6 cells were grown in DMEM with 10% fetal calf serum at 37˚C, 5% CO2. Staphylcococus aureus was grown in Tryptic Soya Broth at 37˚C with 200 rpm shaking.

extract_protocol:
Pelleted cells were lysed in PBS + 0.1% TritonX-100, and then total RNA was extracted using the Qiagen kit
Libraries were preoered by the Microbial Genome Sequecning center, Pittsburgh USA

treatment_protocol: Vero E6 cells were washed twice with PBS, and serum free DMEM added to the wells. 1x105 CFU of S. aureus or respective mutants were added to the culture medium. 10 hpi, cells were washed twice with PBS, and lysed in RNA cell reagent (Qiagen). S. aureus was ggrown in Tryptic Soya Broth overnight, washed twice with serum free DMEM, and used to inoculate cells.

value: Vero E6

value: Epithelial


title: vCAR PBS [X6_S1_L001]

value: Day 7


title: mASPS FLAG2

description: FLAG (Sigma, F7425, lot 085M4774V)


title: vCAR PBS [X44_S14_L001]

value: CAR T with PBS


title: vIL7FL pIC [X39_S13_L001]

value: CAR T with poly(I:C)


title: IsdA biological replicate 2


title: mASPS_Input

data_processing:
Base calls were performed using Bowtie 2.
ChIP-seq reads were aligned to the mm9 or hg19 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
Genome_build: mm9 (mouse) and hg19 (human)
Supplementary_files_format_and_content: For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max (1, Ci/Ei + 1).

source_name: Alveolar soft part sarcoma

tag: cell type/genotype

value: ASPSCR1-TFE3-expressing murine alveolar soft part sarcoma cells

tag: strain/cell line

value: Balb/c

tag: antibody


title: vCAR PBS [X38_S12_L001]


title: IsdA biological replicate 1


title: vCAR pIC [X37_S11_L001]


title: WT biological replicate 3


title: Kidney_Pkd1 knockout_rep3 [KO_3]

value: Male


title: mASPS-Null_H3K27ac

value: Histone H3K27ac (Active Motif, 39133, lot 16119013)


title: mASPS_JQ1_Brd4

value: Brd4 (Bethyl Laboratories, A301-985A100, lot 7)

value: mASPS cells treated with JQ1


title: mASPS_DMSO_Brd4

value: mASPS cells treated with DMSO control


title: Compl biological replicate 3

value: kidney


title: IsdA biological replicate 3


title: mASPS_H3K27me3

value: Histone H3K27me3 (Abcam, ab6002, lot GR3232152-1)


title: Compl biological replicate 1


title: vIL7FL PBS [X22_S7_L001]


title: WT biological replicate 2


title: vIL7 PBS [X25_S8_L001]


title: mASPS_H3K27ac


title: Mock biological replicate 2


title: vIL7FL pIC [X28_S9_L001]


title: mASPS FLAG3

description: FLAG (Sigma, F7425, lot 085M4774V)

value: murine alveolar soft part sarcoma


title: mASPS_H3K4me3

value: Histon H3K4Me3 (Abcam, ab8580, lot GR3263891-1)


title: vIL7 pIC [X21_S6_L001]

value: glioblastoma

value: WT


title: mASPS_ASPSCR1-TFE3_Flag

value: FLAG (Sigma, F7425, lot 085M4774V)


title: Mock biological replicate 1

value: Vero E6

value: Epithelial


title: vIL7FL pIC [X10_S4_L001]

value: CAR T with poly(I:C)

value: Day 7


title: Mock biological replicate 3


title: SCF4_3

status: Public on Jan 15 2023

city: Jerusalem

first: Avner

last: Ehrlich

address: Silberman 3-512, Edmond J. Safra Campus (Givat Ram)

department: Bioengineering

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Sequencing reads were mapped to the UCSC chicken transcriptome (genome build galGal6) using Bowtie2 (22388286)
expression levels of all genes were quantified using RSEM (21816040).
Differential expression analysis was performed using R package DESeq2 (25516281) using default parameters. Reported are p-values from a negative binomial Wald-test. Overall, 3,641 and 3,739 genes showed significant differential mRNA expression between each primary and immortalized chicken cell line with BH-FDR<0.001, for Israeli Baladi and Broiler Ross breeds, respectively.
Genome_build: UCSC chicken transcriptome (genome build galGal6)
Supplementary_files_format_and_content: RSEM-expression matrix of inferred gene counts. (.txt); Differential expression analysis of primary and immortalized lines (.csv)

organism: Gallus gallus

source_name: Israeli Baladi  Spontaneously Immortalized, anchorage-independent , chicken embryonic fibroblast

growth_protocol: Isolated cells were plated in T75 flasks in DMEM supplemented with 10% FBS, 200 units/mL penicillin and streptomycin, and 2 mM L-alanine-L-Glutamine in a 5% CO2-humidified incubator at 39°C.

extract_protocol:
RNA was extracted from primary and anchorage-independent cell lines using RNeasy Micro kit (Qiagen, USA) according to the manufacturer’s directions.
Library preparation and RNA sequencing were performed by Syntezza Bioscience (Israel). Library construction was conducted using NuGEN TrioRNA-Seq kit (Tecan, USA) and sequenced on Illumina HiSeqX with paired-end, 150 bp reads using the High Output V2 Kit.

treatment_protocol: Primary fibroblasts were passaged regularly, recording changes in doubling time and morphology as cells underwent senescence (crisis) and breakthrough (immortalization). Cells were considered to be immortalized once the culture showed stable morphology and doubling time following at least 120 population doublings from isolation. Immortalized lines were expanded and cryopreserved in four immortalized-cell banks labeled HUN-CF-1 to 4.     Suspension culture of immortalized chicken fibroblasts  Fibroblasts spheroids were created using Aggrewell 400 according to the manufacturer’s directions. Briefly, 1.2x106 spontaneously immortalized fibroblasts were seeded in DMEM with 10% FBS at a density of 3,867 cells per microwell for 48 hrs. Spheroids were then gently detached and transferred to a low-attachment 10 cm petri dish, in culture media supplemented with 0.1% Pluronic F-68. Spheroids were mechanically disturbed daily for 4 consecutive days by vigorous pipetting. Spheroids were transferred to baffled shaker flasks on day 7 and cultured in a humified shaker incubator at 39°C, 5% CO2 and 80 RPM in DMEM10 culture media supplemented with 0.1% Pluronic F-68. Large cellular aggregates were broken down by TrypLE™ digestion each week, and cells reseeded at a density of 200,000 cells/mL. Suspension cultures were counted and diluted back to initial density 2-3 times a week. Following 30 days of culture, the shaker speed was increased to 100 RPM leading to aggregate breakdown and single-cell suspensions developing for 60 days. Cells were considered anchorage-independent once culture showed stable doubling time and viability above 94%. Anchorage-independent cell lines were expanded and cryopreserved in two master-cell banks labeled FMT-SCF-2 and FMT-SCF-4 showing a doubling time of 192 and 202 hrs, respectively.

tag: breed

value: Broiler Ross 308

value: Spontaneously Immortalized chicken embryonic fibroblast

value: anchorage-independent


title: SCF4_1


title: SCF2_3

source_name: Broiler Ross 308 Spontaneously Immortalized, anchorage-independent , chicken embryonic fibroblast

value: Israeli Baladi


title: SCF4_2


title: m.pectoralis sample, trained [RNA_S3848Nr8]

city: Balice

first: Monika

last: Stefaniuk-Szmukier

address: ul.Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institution of Animal Production

data_processing:
Illumina bcl2fastq (2.20)
Quality Control FastQC v0.11.5
Adapters were trimmed, reads of low quality (<20) and under the length of 36 bp were removed with the use of  Flexbar software
The reads were mapped with STAR software to Colliv 2.1 genome and counted with the use of htseq-count software to the respective gtf file.
Deseq2 was used to find differentially expressed genes.
Assembly: 2.1_Colliv
Supplementary files format and content: counts

organism: Columba livia

source_name: skeletal muscle

extract_protocol:
The total RNA was isolated using by TriReagent (Ambion, Life Technologies) and according to the method described by Chomczyński (Chomczynski 1993).
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.

value: skeletal muscle

value: case-trained


title: m.pectoralis sample, trained [RNA_S3848Nr9]


title: SCF2_2


title: HNC-OECM1 cell line Parent cell rep 1

city: Taoyuan

first: Ann-Joy

last: Cheng

address: No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City

country: Taiwan

institute: CGU

description: Gene expression data from parental cells

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The data were analyzed with RMA normalization by using Partek Genomics Suite software version 7

source_name: HNC-OECM1 cell line

label_protocol: Affymetrix

extract_protocol: Trizol extraction of total RNA was performed to according manufacture's instructions

treatment_protocol: After matrigel invasion method to generate highly invasive cells and samples were collected for futher RNA extraction

tag: group

value: Parent cell

value: HNC-OECM1 cell line


title: HNC-Fadu cell line Parent cell rep 2

source_name: HNC-Fadu cell line

value: HNC-Fadu cell line


title: m.pectoralis sample, trained [RNA_S3848Nr7]

tag: tissue


title: HNC-OECM1 cell line Invasion subline rep 2

description: Gene expression data from invasion subline cells

value: Invasion subline


title: HNC-Detroit cell line Invasion subline rep 2

source_name: HNC-Detroit cell line

value: HNC-Detroit cell line


title: Cocaine_M

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

data_processing:
Cell demultiplexing and genome alignment in Cell Ranger using Emsemble pre-mRNA reference assembly GTF file. Raw count data obtained in Cell Ranger.
Assembly: rn7
Supplementary files format and content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

organism: Rattus norvegicus

source_name: Nucleus accumbens

growth_protocol: Sprague-Dawley 90-120-day-old male or female rats were purchased from Charles River Laboratories. Male or female adult rats were co-housed in pairs in plastic filtered cages with nesting enrichment in an AAALAC-approved animal care facility maintained between 23-24°C on a 12-hour light/dark cycle with ad libitum food (Lab Diet Irradiated rat chow) and water. Bedding and enrichment were changed weekly by animal resources program staff. Animals were randomly assigned to experimental groups.

extract_protocol:
1mm brain sections were taken at the level of the nucleus accumbens, and nucleus accumbens tissue was dissected using a 2mm punch tool centered on the nucleus accumbens core subregion. Frozen tissue punches were thawed slowly on ice prior to being chopped by scalpel 100 times in 2 orthogonal directions. Tissue from 4 animals in the same treatment condition was then combined and transferred to 5mL of chilled (4°C) Lysis Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2 (Thermo Fisher, BP214-500), 0.1% Igepal in Nuclease-Free Water (Sigma, 18896-50ML)) for 15 min, mixing the tissue by inversion every 2 min. Lysis was quenched immediately at 15 min with 5mL of complete Hibernate-A (Thermo Fisher, A1247501) supplemented with B27 and Glutamax (Life Technologies, 35050-061)). Tissue was then triturated by fire-polished Pasteur pipette (2 pipettes of decreasing diameter; 8-10 passes per pipette) for 35 min and passed through a 40µm pre-wet filter. The samples were then pelleted at 500rcf for 10 min at 4°C followed by a wash in 10mL of Nuclei Wash & Resuspension Buffer (1X PBS, 1% BSA, 0.2U/ul NxGen RNase inhibitor (Lucigen, 30281-2)). Supernatant was then removed and the pellet was gently resuspended in a total volume of 800µl prior to 7-AAD (Thermo Fisher, 00-6993-50) staining and FACS to further purify the nuclei for sequencing. Immediately after FACS, nuclei were washed a final time at 200rcf in 10mL supplemented Hibernate-A containing 1% BSA for 10 minutes at 4°C to remove any remaining fine debris and nascent RNA. Nuclei were brought to a concentration of 1,500 nuclei/µl and an average total of 12,500 nuclei pooled from 4 rats were loaded per sex and treatment group.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplification, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries were quantified and underwent sequencing (~550M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: Rats were injected with either cocaine (20mg/kg, dissolved in physiological saline) intraperitoneally or equal volumes of physiological saline and placed in an open field for behavioral tracking. Injections occured daily across 7 consecutive days. Tissue was harvested 1hr after the final (7th) injection, when rats were sacrificed, the brain was blocked into 1mm sections, abd the NAc was harvested and flash frozen. A total of 16 rats (8 male, 8 female, 4 per GEMwell) were used for this experiment.

value: Sprague-Dawley

value: Cocaine

value: Male


title: Saline_M

value: Saline


title: HNC-OECM1 cell line Invasion subline rep 1


title: HNC-Detroit cell line Parent cell rep 1


title: HNC-Detroit cell line Invasion subline rep 1


title: gacA_fed_6h_Biol_rep2

city: Worcester

first: Zeynep

last: Mirza

state: MA

address: 373 Plantation Street

department: Molecular Medicine

institute: University of Massachusetts Chan Medical School

data_processing:
Cutadapt/1.4.1 was used to trim adaptor sequences and filter out the reads shorter than 15 nt
The reads were mapped to the C. elegans genome (Wbcel235) by Star/ 2.5.3 aligner
Samtools/ 1.9 was used for sorting data, and gene counts were obtained with Featurecounts
Differential gene expression analysis was performed with DEBrowser. The data was normalized by median ratio normalization (MRN) and batch effects were corrected with the ComBat method
Assembly: C. elegans genome (Wbcel235)
Supplementary files format and content: Excel files contain all detected genes names, Debrowser normalized counts, fold changes and p values.

organism: Caenorhabditis elegans

source_name: L1 larvae exposed to CF18 gacA for 6 hours-biological replicate 2

growth_protocol: Animals were maintained on nematode growth media (NGM) and fed with E. coli HB101 at 20°C.Bleached eggs were obtained by bleaching adult hermaphrodites and synchronized L1s were obtained by incubating bleached eggs in M9 buffer overnight.

extract_protocol:
TRIZOL
The libraries were prepared with the NebNext Ultra II non directional kit (NEB, Cat: E7775, E7335, E7500), according to the manufacturer’s instructions.

treatment_protocol: P. aeruginosa CF18 and P. aeruginosa CF18 gacA mutant were seeded on slow-killing plates. The plates were incubated for 24 h at 37ºC and then for 24 h at 25ºC. Synchronized L1 animals were transferred onto the plates. Plates were incubated at 25°C and L1s were collected after 4 hours and 6 hours of exposures. (Three biological replicates per bacterial diet per time point).

value: whole animal

tag: time

value: P. aeruginosa CF18 gacA


title: Saline_F

tag: strain

value: Female


title: Cocaine_F

tag: age


title: HNC-Fadu cell line Parent cell rep 1


title: HNC-OECM1 cell line Parent cell rep 2


title: HNC-Fadu cell line Invasion subline rep 1


title: HNC-Fadu cell line Invasion subline rep 2


title: HNC-Detroit cell line Parent cell rep 2


title: gacA_fed_6h_Biol_rep3

source_name: L1 larvae exposed to CF18 gacA for 6 hours-biological replicate 3

tag: treatment


title: SCF2_1

tag: cell type

value: Spontaneously Immortalized chicken embryonic fibroblast


title: m.pectoralis sample, trained [RNA_S3848Nr6]


title: gacA_fed_6h_Biol_rep1

source_name: L1 larvae exposed to CF18 gacA for 6 hours-biological replicate 1


title: CF18_fed_6h_Biol_rep3

source_name: L1 larvae exposed to CF18 for 6 hours-biological replicate 3

value: P. aeruginosa CF18


title: CEF2_3

source_name: Broiler Ross 308 Primary chicken embryonic fibroblast

value: Broiler Ross 308

value: Primary chicken embryonic fibroblast


title: m.pectoralis sample, trained [RNA_S3848Nr13]

value: skeletal muscle

value: case-trained


title: CF18_fed_6h_Biol_rep2

source_name: L1 larvae exposed to CF18 for 6 hours-biological replicate 2


title: m.pectoralis sample, trained [RNA_S3848Nr11]


title: m.pectoralis sample, trained [RNA_S3848Nr10]


title: CEF2_2


title: m.pectoralis sample, untrained [RNA_S3848Nr5]

value: control-untrained


title: CF18_fed_6h_Biol_rep1

source_name: L1 larvae exposed to CF18 for 6 hours-biological replicate 1


title: CEF4_3

source_name: Israeli Baladi Primary chicken embryonic fibroblast

value: Israeli Baladi


title: m.pectoralis sample, untrained [RNA_S3848Nr4]


title: CEF2_1


title: gacA_fed_4h_Biol_rep3

source_name: L1 larvae exposed to CF18 gacA for 4 hours-biological replicate 3


title: gacA_fed_4h_Biol_rep1

source_name: L1 larvae exposed to CF18 gacA for 4 hours-biological replicate 1


title: m.pectoralis sample, untrained [RNA_S3848Nr2]


title: CF18_fed_4h_Biol_rep3

source_name: L1 larvae exposed to CF18 for 4 hours-biological replicate 3


title: m.pectoralis sample, untrained [RNA_S3848Nr12]


title: gacA_fed_4h_Biol_rep2

source_name: L1 larvae exposed to CF18 gacA for 4 hours-biological replicate 2


title: CEF4_2


title: m.pectoralis sample, untrained [RNA_S3848Nr3]

source_name: skeletal muscle


title: CEF4_1


title: gacA_Biol_rep2

description: processed data column name:gac3bac

data_processing:
Cutadapt/1.4.1 was used to trim adaptor sequences and filter out the reads shorter than 15 nt
The reads were mapped to the CF18 genome by Star/ 2.5.3 aligner
Samtools/ 1.9 was used for sorting data, and gene counts were obtained with Featurecounts
Differential gene expression analysis was performed with DEBrowser.
Assembly: RefSeq assembly accession: GCF_000481925.1
Supplementary files format and content: gac1-2 vs cf1-2-3 all detected genes.csv file contains all detected genes names, Debrowser normalized counts, fold changes and p values.

organism: Pseudomonas aeruginosa CF18

source_name: Bacterium

growth_protocol: P. aeruginosa CF18 and P. aeruginosa CF18 gacA were grown in Luria Bertani broth overnight at 37oC while shaking.

extract_protocol:
NEB Monarch Total RNA Miniprep Kit and NEBNext rRNA Depletion Kit (Bacteria)
The libraries were prepared with the NebNext Ultra II non directional kit (NEB, Cat: E7775, E7335, E7500), according to the manufacturer’s instructions.

treatment_protocol: P. aeruginosa CF18 and P. aeruginosa CF18 gacA mutant were seeded on slow-killing plates. The plates were incubated for 24 h at 37ºC and then for 24 h at 25ºC. °C. Then, bacteria were collected from the plates and total RNAs were extracted. (Three biological replicates for WT CF18 and 2 biological replicates for gacA mutant) mutants)

value: Bacterium

value: gacA mutant

value: grown on slow-killing plates


title: CF18_fed_4h_Biol_rep2

source_name: L1 larvae exposed to CF18 for 4 hours-biological replicate 2


title: CF18_Biol_rep3

description: processed data column name:CF183bac

value: WT


title: CF18_Biol_rep2

description: processed data column name:CF182bac


title: CF18_Biol_rep1

description: processed data column name: CF181bac


title: leaf tissue, ERDL4-overexpressor 1, 4-week-old, biol rep 2

city: Kaiserslautern

first: Benjamin

last: Pommerrenig

address: Paul-Ehrlich-Str. 22

department: Biology

institute: University of Kaiserslautern

data_processing:
The data processing steps are according to Novogene methods: Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Alignment: Algorithm for mapping sequences: HISAT2 is selected to map the filtered sequenced reads to the reference genome. In general, HISAT2 supports genomes of any size, including those larger than 4 billion bases and most of the parameters are set to default. Spliced reads of RNA Seq data can be effictively aligned using HISAT2. HISAT2 v2.0.5 was run using the --dta --phred33 parameters.
Novel gene prediction was performed with StringTie v.1.3.3 and GffCompare v0.10.6 using default parameters
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: tab-delimited xls files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: plants were grown for 4-5 weeks under short days (10h light/14h dark) at 130 mE, 65% relative humidity, 21°C in standard soil substrate

extract_protocol:
RNA was extracted from leaves or leaf discs using the NucleoSpin® RNA Plant Kit (Macherey-Nagel) according to the manufacturer's instructions. 50 mg of fresh plant material was used for this purpose. The RNA was eluted from the column with 40 μl of RNase-free ddH2O
Directional library construction was perfomed by Novogene Sequencing Service. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: leaf discs of mature rosette leaves from 4-week-old plants were exised and incubated over night in half-strength MS medium supplemented with 1% mannitol (osmotic control), 1% glucose, or 1% fructose

value: leaf tissue

tag: ecotype

tag: condition

value: ERDL4-overexpressor 1


title: leaf tissue, wild type, 4-week-old, biol rep 1

value: wild type


title: leaf tissue, wild type, 4-week-old, biol rep 2


title: leaf disc, 1% fructose, biol rep 2

source_name: leaf disc

value: leaf disc

value: 1% fructose over night


title: leaf tissue, ERDL4-overexpressor 1, 4-week-old, biol rep 1


title: leaf tissue, ERDL4-overexpressor 2, 4-week-old, biol rep 1

value: ERDL4-overexpressor 2


title: leaf tissue, ERDL4-overexpressor 1, 4-week-old, biol rep 3


title: leaf tissue, ERDL4-overexpressor 2, 4-week-old, biol rep 2


title: leaf tissue, ERDL4-overexpressor 2, 4-week-old, biol rep 3


title: leaf disc, 1% fructose, biol rep 1


title: leaf tissue, wild type, 4-week-old, biol rep 3


title: gacA_Biol_rep1

description: processed data column name:gac2bac


title: leaf disc, 1% glucose, biol rep 3

value: 1% glucose over night


title: leaf disc, 1% glucose, biol rep 2


title: leaf disc, 1% fructose, biol rep 3


title: CF18_fed_4h_Biol_rep1

source_name: L1 larvae exposed to CF18 for 4 hours-biological replicate 1

value: whole animal

value: P. aeruginosa CF18


title: SDF1_1

description: expr.chicken.new.txt

data_processing:
Sequencing reads were mapped to the UCSC chicken transcriptome (genome build galGal6) using Bowtie2 (22388286)
expression levels of all genes were quantified using RSEM (21816040).
Differential expression analysis was performed using R package DESeq2 (25516281) using default parameters. Reported are p-values from a negative binomial Wald-test. Overall, 3,641 and 3,739 genes showed significant differential mRNA expression between each primary and immortalized chicken cell line with BH-FDR<0.001, for Israeli Baladi and Broiler Ross breeds, respectively.
Genome_build: UCSC chicken transcriptome (genome build galGal6)
Supplementary_files_format_and_content: RSEM-expression matrix of inferred gene counts. (.txt); Differential expression analysis of primary and immortalized lines (.csv)
Assembly: galGal6

source_name: Anchorage-independent Fibroblasts

growth_protocol: Primary fibroblasts were passaged regularly, recording changes in doubling time and morphology as cells underwent senescence (crisis) and breakthrough (immortalization). Cells were considered to be immortalized once the culture showed stable morphology and doubling time following at least 120 population doublings from isolation. Immortalized lines were expanded and cryopreserved in four immortalized-cell banks labeled HUN-CF-1 to 4. Suspension culture of immortalized chicken fibroblasts Fibroblasts spheroids were created using Aggrewell 400 according to the manufacturer’s directions. Briefly, 1.2x106 spontaneously immortalized fibroblasts were seeded in DMEM with 10% FBS at a density of 3,867 cells per microwell for 48 hrs. Spheroids were then gently detached and transferred to a low-attachment 10 cm petri dish, in culture media supplemented with 0.1% Pluronic F-68. Spheroids were mechanically disturbed daily for 4 consecutive days by vigorous pipetting. Spheroids were transferred to baffled shaker flasks on day 7 and cultured in a humified shaker incubator at 39°C, 5% CO2 and 80 RPM in DMEM10 culture media supplemented with 0.1% Pluronic F-68. Large cellular aggregates were broken down by TrypLE™ digestion each week, and cells reseeded at a density of 200,000 cells/mL. Suspension cultures were counted and diluted back to initial density 2-3 times a week. Following 30 days of culture, the shaker speed was increased to 100 RPM leading to aggregate breakdown and single-cell suspensions developing for 60 days. Cells were considered anchorage-independent once culture showed stable doubling time and viability above 94%. Anchorage-independent cell lines were expanded and cryopreserved in two master-cell banks labeled FMT-SCF-2 and FMT-SCF-4 showing a doubling time of 192 and 202 hrs, respectively.

treatment_protocol: Immortalized chicken fibroblasts were seeded at a density of 4103 cells/cm2 or 0.3106 cells/mL for adherent and suspension cells, respectively. Transdifferentiation medium was composed of DMEM10 containing 200 µM oleic acid supplemented with 12 µg/mL L--Phosphatidylcholine (soy lecithin). Transdifferentiation medium was replaced every 2 d for 7 d. Cells were split on day 2 and reseeded back at starting cell density.

value: Fibroblasts

value: Anchorage-independent Fibroblasts

value: East Lansing Line 0


title: SDF1_2

description: expr.chicken.new.txt


title: FAT_3

description: expr.chicken.new.txt

source_name: Fat

value: Fat

value: Israeli Baladi


title: DF1_3

description: expr.chicken.new.txt

source_name: Immortalized Fibroblasts

value: Immortalized Fibroblasts


title: DF1_1

description: expr.chicken.new.txt


title: SDF1_3

description: expr.chicken.new.txt


title: WTN240,NPCs,WT,2months

city: San Diego

first: Hong

last: Gao

state: California

address: 9500 Gilman Drive

department: Medicine

institute: University of California, San Diego

data_processing:
FastQC v0.11.9
Raw sequence reads were mapped to GrCM39 using  STAR 2.7.10a and Samtools 1.9
Read count extraction were performed using featureCounts v2.0.3
Assembly: GrCM39
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Liver

growth_protocol: The Shp2ΔK (Shp2f/f:Clec4f-Cre+/-) mouse line in C57BL/6 background was generated by breeding Shp2f/f mouse with Clec4f-Cre+/- transgenic mice.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit following manufacturer's protocols.

treatment_protocol: No

value: Liver

value: NPC

value: No


title: WTN231,NPCs,WT,2months

value: WT


title: KN230,NPCs,Shp2 KO mice,2months

value: Shp2 Knock out


title: KN248,NPCs,Shp2 KO mice,2months

value: Shp3 Knock out


title: DF1_2

description: expr.chicken.new.txt


title: KN228,NPCs,Shp2 KO mice,2months

value: Shp1 Knock out


title: leaf disc, 1% glucose, biol rep 1

value: leaf disc


title: TCR-CD8_EomesTG_Liv

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description:
cr-mm-MLE4-TCR-CD8_EomesTG_Liv-E1
10x Genomics

data_processing:
Cell Ranger (10x Genomics) functions mkfastq and count were used to align to the mm10 genome and demultiplex the sequencing data and generate gene-barcode matrices.
Assembly: mm10
Supplementary files format and content: Cell ranger output files

extract_protocol:
Single-cell suspension from splenocytes and liver T cells from three C57BL/6 mice and three EomesTg/Tg mice were obtained as described. Cells from each strain were pooled and CD8+ T cells from spleens and livers were sorted. Microscope assessment after Trypan blue staining allowed to count viable cells following FACS sorting. Cell preparations were centrifuged at 500 RCF for 7 min and pellets were resuspended in 10%FCS/RPMI medium. Cells were loaded on the Chromium Controller (10x Genomics)
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5′ v1 Reagent Kit (10x Genomics) according to manufacturer’s protocol.

value: CD8 T cell

value: Eomes TG

tag: strain background

tag: library type

value: TCR


title: WTN229,NPCs,WT,2months

tag: genotype


title: WTN204,NPCs,WT,2months

tag: cell line


title: leaf disc, 1% mannitol, biol rep 2

value: 1% mannitol over night


title: leaf disc, 1% mannitol, biol rep 1


title: FAT_2

description: expr.chicken.new.txt


title: GEX-CD8_EomesTG_Liv

description:
cr-mm-MLE4-GEX-CD8_EomesTG_Liv-E2
10x Genomics

value: GEX


title: TCR-CD8_WT_Liv

description:
cr-mm-MLE3-TCR-CD8_WT_Liv-D1
10x Genomics


title: CF_4_1

description: expr.chicken.new.txt

value: Fibroblasts


title: CF_4_3

description: expr.chicken.new.txt


title: CF_4_2

description: expr.chicken.new.txt


title: FAT_1

description: expr.chicken.new.txt

value: Fat


title: Wildtype intestinal stem cells Tamoxifen 14 days rep5

city: San Francisco

first: Tomas

last: Wald

address: 513 Parnassus Ave

institute: UCSF

description: Wildtype intestinal stem cells

data_processing:
basecalling with bcl2fastq v2.20.0.422
Alignment and read count per gene estimation with STAR v2.4.2a
Assembly: Alignment to Ensembl Mouse build GRCm38.87
Supplementary files format and content: Format: Text file; Content: gene by read counts matrix

source_name: Intestinal epithelium

growth_protocol: mice 8-16 weeks old

extract_protocol:
In total, 5,000 – 10,000 ISCs were FACS sorted into 500 μl sterile PBS, pelleted and mRNA was isolated using the polyA Dynabeads mRNA direct Kit (Invitrogen, 61012) according to the manufacture’s protocol.
cDNA and libraries were made by the UCSF Genomic Core Laboratories using the SmartSeq/NexteraXT DNA library preparation Kits (Takarabio, 634471; Illumina, FC-131-1024).

treatment_protocol: tamoxifen injection 48 hours or 14 days prior tissue dissection

value: Intestinal epithelial cell

value: wildtype

value: Tamoxifen 14 days


title: Wildtype intestinal stem cells Tamoxifen 14 days rep3

description: Wildtype intestinal stem cells


title: CF_2_1

description: expr.chicken.new.txt

value: Immortalized Fibroblasts

value: Broiler Ross 308


title: TCR-CD8_EomesTG_Sp

description:
cr-mm-MLE2-TCR-CD8_EomesTG_Sp-C1
10x Genomics

source_name: Spleen

value: Spleen


title: Wildtype intestinal stem cells Tamoxifen 14 days rep4

description: Wildtype intestinal stem cells


title: GEX-CD8_EomesTG_Sp

description:
cr-mm-MLE2-GEX-CD8_EomesTG_Sp-C2
10x Genomics


title: CF_2_3

description: expr.chicken.new.txt


title: CF_2_2

description: expr.chicken.new.txt


title: WT biological replicate 1

source_name: kidney

value: kidney

value: Vero E6

value: Epithelial


title: Wildtype intestinal stem cells Tamoxifen 14 days rep2

description: Wildtype intestinal stem cells


title: GEX-CD8_WT_Sp

description:
cr-mm-MLE1-GEX-CD8_WT_Sp-B2
10x Genomics

value: WT


title: leaf disc, 1% mannitol, biol rep 3

value: leaf disc


title: CD8_EomesTG_Liver_PD1_High_2

data_processing:
Adapters were removed with TrimmomaticPE with the following parameters : LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to hg38 by Bowtie2 with the following parameters: –X 2000 –fr –very-sensitive –no-discordant –no-mixed –non-deterministic
Reads from the alignment were sorted and indexed according to chromosomes
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Reads mapping within the blacklist of the ENCODE project were removed with a custom script and samtools view
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Assembly: mm10
Supplementary files format and content: bigwig files for read signal

source_name: CD8 T cell

extract_protocol:
20 000 to 50 000 sorted CD14+ monocytes were collected in 1mL of RPMI media supplemented with 10% FCS at 4°C.Cells were centrifuged, then cell pellets were resuspended in 50 μL of lysis buffer (Tris HCl 10 mM, NaCl 10 mM, MgCl2 3 mM, Igepal 0,1%) and centrifuged (500 g) for 10 minutes at 4°C. Supernatant was discarded and nuclei were resuspended in 50 μL of reaction buffer (Tn5 transposase 2,5 μL, TD buffer 22,5 μL and 25 μL H2O – Nextera DNA sample preparation kit, Illumina). Tagmentation was performed for 30 minutes at 37°C. DNA was purified using the MinElute purification kit (QIAGEN).
Purified DNA was amplified and indexed by PCR using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs) with 10-12 cycles. Llibraries were purified using MinElute PCR Purification Kit (Qiagen) and quality controlled using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).

value: CD8 T cell

value: Eomes TG


title: Dlg1 knock out intestinal stem cells Tamoxifen 14 days rep4

description: Dlg1 knock out intestinal stem cells

value: Dlg1 conditional knock out


title: GEX-CD8_WT_Liv

description:
cr-mm-MLE3-GEX-CD8_WT_Liv-D2
10x Genomics

value: Liver

value: GEX


title: Wildtype intestinal stem cells Tamoxifen 14 days rep1

description: Wildtype intestinal stem cells


title: Dlg1 knock out intestinal stem cells Tamoxifen 14 days rep5

description: Dlg1 knock out intestinal stem cells


title: TCR-CD8_WT_Sp

description:
cr-mm-MLE1-TCR-CD8_WT_Sp-B1
10x Genomics

value: TCR


title: Chicken HD3 Hi-C rep2

city: Saint-Petersburg

first: Antonina

last: Maslova

address: 7-9 Universitetskaya Embankment

country: Russia

institute: Saint-Petersburg State University

description:
HD3_HiC.hic
HD3_TADs_50000.txt
HD3_PC1_50000.bedGraph

data_processing:
Reads generated from two replicates were filtered, mapped to the reference genome and assembled in Hi-C heatmap form using Juicer tools (v.1.6) by Durand et al. Cell Syst. 2016 (PMID: 27467249). Due to high correlation of contacts between the replicates (Pearson=0.993) valid genomic contacts from both replicates were combined to generate HD3_HiC.hic file. The first principal component (compartments) was calculated using Juicer tools at 50 Kb resolution. Topologically-associating domains (TADs) were called by Armatus algorithm at 50Kb resolution using parameter γ=0.2.
Assembly: Gallus_gallus-5.0
Supplementary files format and content: Hi-C heatmap for HD3 cells in .hic format for visualization via Juicebox tools.
Supplementary files format and content: Compartment coordinates in HD3 cells in *.bedGraph format.
Supplementary files format and content: TAD coordinates in HD3 cells in *.txt format.

growth_protocol: DMEM, 8% fetal bovine serum, 2% chicken serum, 50 µg/ml gentamicin. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
1x10*6 cells/ml of cells were fixed in 1% PFA in serum-free DMEM for 10 minutes with constant mixing. PFA was quenched by 125 mM glycine, cells were pelleted and washed by DPBS at 4°C . Cell pellets were snap-frozen in liquid nitrogen for further processing.
Hi-C libraries were prepared from 5 millions of crosslinked cells according to Hi-C 2.0 protocol as described  in Belaghzal et al, Methods. 2017 (PMID: 28435001) with minor modifications using two replicates of cross-linked HD3 cells. Cells were lysed on ice and the cell pellets were washed twice in NEB3.1 buffer, containing 0,1% SDS. Chromatin was digested with DpnII and 5'-overhangs were filled with biotinylated dCTP. After chromatin ligation crosslinks were reversed  at 65°С overnight in the presence of proteinase К. After DNA extraction, biotin-dCTP was removed from unligated (dangling) ends by incubation with Т4 DNA polymerase. DNA was sonicated, size-selected twice with magnetic beads and biotin pulldown was performed using Streptavidin-coated beads. Libraries were assembled using KAPA Hyper Prep Kit and KAPA Single-Indexed Adapter Kit Set A in 9 PCR cycles.

value: Chicken erythroblast


title: CD8_EomesTG_Liver_PD1_High_1


title: Chicken HD3 Hi-C rep1


title: Dlg1 knock out intestinal stem cells Tamoxifen 14 days rep3

description: Dlg1 knock out intestinal stem cells

value: Intestinal epithelial cell


title: Senescent wild-type IMR90 cells rep2

city: Seoul

first: Kyeonghwan

last: Roh

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
The sequence reads were trimmed with Trimmomatic version 0.36 and mapped against the human reference genome (hg38) using Hisat2 version 2.1.0.
Read counts per gene were calculated by using featureCounts version 1.6.3.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: IMR90 cells

growth_protocol: IMR90 cells expressing hTERT were maintained in 3% O2 and cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (FBS), penicillin/streptomycin, and 0.1 mM nonessential amino acids.

extract_protocol:
Total RNAs were isolated using the acidic phenol extraction method.
One microgram of high-quality RNA samples (RIN > 7.0) was used to construct RNA-seq libraries using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). Total RNA integrity was checked using an Agilent 2200 TapeStation. RNA-seq was performed on an Illumina NovaSeq 6000 sequencer at Macrogen.

treatment_protocol: IMR90 cells expressing hTERT were treated with bleomycin (10 ug/ml for 24 h) to induce senescence.

value: IMR90 cells

value: Lung fibroblast

value: wild-type

value: 10 days after exposure to bleomycin (10 ug/ml for 24 h)


title: Senescent ABCA1 knockout IMR90 cells rep1

value: ABCA1 knockout


title: Senescent wild-type IMR90 cells rep1


title: Dlg1 knock out intestinal stem cells Tamoxifen 14 days rep2

description: Dlg1 knock out intestinal stem cells

value: Tamoxifen 14 days


title: CD8_EomesTG_Liver_PD1_Low_1


title: Dlg1 knock out intestinal stem cells Tamoxifen 14 days rep1

description: Dlg1 knock out intestinal stem cells


title: Dlg1 knock out intestinal stem cells Tamoxifen 48 hours rep4

description: Dlg1 knock out intestinal stem cells

value: Tamoxifen 48 hours


title: CD8_WT_Liver_PD1_Low_2

value: WT


title: Senescent ABCA1 knockout IMR90 cells rep2


title: vIL7 pIC [X30_S10_L001]

data_processing:
Quality control was performed using FastQC/MultiQC for all fastq files.
Custom transgenes for GFP, LUC, EGFRVIII, and CAR were added and used
Star Alignment was run using default parameters and soft clipping for the Illumina universal adapter sequence (--clip3pAdapterSeq AGATCGGAAGAG)
FeatureCounts was used for expression quantification of alignment output (featureCounts -p -s 2 -T 8 -t exon -g gene_id -a)
Downstream analysis of the FeatureCounts raw counts output matrix was performed using DESeq2 (version 1.36.0)
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa
Supplementary files format and content: tab-delimited text files include for rnaseq data raw and normalized couts or tcrseq data

extract_protocol:
RNA was harvested using RNeasy Lipid Tissue Mini kit (Qiagen).
The RNA-seq library was prepared with the KAPA Stranded mRNA-Seq kit (Roche). The TCR-seq library was prepared with the mouse T-cell Receptor Panel QIAseq Immune Repetoire RNA Library Kit (Qiagen

value: glioblastoma

value: CAR T with poly(I:C)

value: Day 7


title: Proliferating ABCA1 knockout IMR90 cells rep1

value: untreated


title: CD8_WT_Liver_PD1_Low_1

value: CD8 T cell


title: Dlg1 knock out intestinal stem cells Tamoxifen 48 hours rep3

description: Dlg1 knock out intestinal stem cells

value: Dlg1 conditional knock out


title: Dlg1 knock out intestinal stem cells Tamoxifen 48 hours rep2

description: Dlg1 knock out intestinal stem cells


title: Proliferating wild-type IMR90 cells rep1


title: Dlg1 knock out intestinal stem cells Tamoxifen 48 hours rep1

description: Dlg1 knock out intestinal stem cells


title: Proliferating wild-type IMR90 cells rep2


title: Wildtype intestinal stem cells Tamoxifen 48 hours rep4

description: Wildtype intestinal stem cells

value: wildtype


title: WT, MICE BRAIN, INFECTION,  DAY 7

city: Rochester

first: Yanyan

last: Zheng

state: Minnesota

address: 839 16th ST SW, Apt421

institute: Mayo Clinic

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: BRAIN TISSUE

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a  sample index, and R2 (read 2 primer sequence) were added during library construction via End  Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers  used in Illumina bridge amplification.

value: BRAIN TISSUE

tag: agent

tag: time point

value: DAY 7

value: 6-8 weeks old


title: WT, MICE BRAIN, INFECTION,  DAY 3

description: 10x Genomics

value: DAY 3


title: KO, MICE BRAIN, INFECTION,  DAY 3

description: 10x Genomics


title: Wildtype intestinal stem cells Tamoxifen 48 hours rep3

description: Wildtype intestinal stem cells

value: Intestinal epithelial cell


title: MDA-MB-231, control, rep3

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
Processing raw data for both format conversion and de-multiplexing were performed by Bcl2Fastq version 2.20 of the Illumina pipeline.
Sequence reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute Cambridge, UK) tool then adapter sequences were masked with Cutadapt version 1.11 from raw fastq data using the following parameters: --anywhere --overlap 5 --times 2 --minimum-length 35 --mask-adapter.
Then reads were mapped to the mouse Ensembl GRCh38 build reference genome using HISAT2 version 2.2.0 using Gene annotations according to the Ensembl database. Gene-level quantification was performed using salmon version 1.8.0 (12).
To identify differentially expressed genes (DEGs) data was filtered to remove from the analysis the genes having < 10 counts per million across all replicates for each comparison.
The data normalization and differential analysis for gene expression were performed using Bioconductor R package DESeq2 version 1.34 accounting for the presence of batch effects.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized values (by DESeq2) for each Sample

source_name: breast

extract_protocol:
Total RNA was extracted from purified from cell pellets of control and KDM5B-NTT-overexpressing cultures using Qiagen RNeasy kits
RNA-Seq libraries from total RNA (1 g) from each sample were prepared using the Illumina TruSeq Stranded mRNA Kit (Illumina, San Diego, CA) according to manufacturer’s instructions.

value: breast


title: Wildtype intestinal stem cells Tamoxifen 48 hours rep1

description: Wildtype intestinal stem cells


title: MDA-MB-231, KDM5B-NTT overexpression, rep2


title: Wildtype intestinal stem cells Tamoxifen 48 hours rep2

description: Wildtype intestinal stem cells


title: MDA-MB-231, control, rep4


title: db/m 12w

city: Guangzhou

first: Yandi

last: Wu

address: Zhongshan Road

country: China

institute: Sun Yat-sen University

data_processing:
We used Seqtk(https://github.com/lh3/seqtk) to filter reads, followed as:  1) removal of splice sequences contained in the reads; 2) removal of bases with a quality Q of less than 20 at the 3' end, where Q = -10logerror_ratio; 3) removal of reads less than 25 in length; 4) Removal of ribosome RNA reads of Mus musculus.
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2（version:2.0.4).
We first applied Stringtie (version:1.3.0) to count the number of Fragments for each gene after Hisat2 matching, then normalized them using the TMM (trimmed mean of M values) method, and finally calculated the FPKM value for each gene using a perl script.
Assembly: mm10
Supplementary files format and content: FPKM and count

source_name: heart

extract_protocol:
heart tissues were removed, flash frozen on dry ice, and RNA was harvested using TruSeq™RNA Sample Preparation Kits v2.
1)rRNA depleted and RNA fragmentation-Optional;2)Purify the mRNA and Fragmentation-Optional;3)Synthesize First Strand cDNA;4)Synthesize Second Strand cDNA;5)Adenylate 3' Ends;6)Ligate Adapter;7)Amplification;8)QC the Library.

treatment_protocol: no treatment

value: heart

value: 12 weeks old

value: db/+


title: MDA-MB-231, KDM5B-NTT overexpression, rep4


title: db/m 24w

value: 24 weeks old


title: CD8_EomesTG_Liver_PD1_Low_2

value: Eomes TG


title: MDA-MB-231, KDM5B-NTT overexpression, rep3


title: DM12d

city: Chicago

first: Md Zahid

last: Akhter

state: IL

address: 835 S Wolcott Ave

department: Pharmacology

institute: University of Illinois at Chicago

description:
Flow sorted GFP+CD31+CD45- (S1PR1+ Endothelial cell)
gene_counts.txt

data_processing:
Raw reads were aligned to reference genome mm10 using STAR (Dobin et al., 2013). Ensembl gene expression was quantified using featureCounts (Liao et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text of read counts per gene

source_name: S1PR1-GFP reporter mice lung

growth_protocol: S1PR1-GFP reporter mice were maintained following Institute Animal Care and Use guidelines.

extract_protocol:
Lungs harvested from LPS challenged mice were subjected to single cell suspension and stained with anti-CD31 and CD45 antibodies. S1PR1+ EC (GFP+CD31+CD45-) were flow sorted and RNA isolation was performed using Trizol. RNA was subjected to quality check by Bioanalyzer. RNA-seq was performed on samples with RIN 7-10.
Oligo-dT library

treatment_protocol: The mice were challenged with Lipopolysaccharide (10 mg/Kg, i.p) at 0h, 8h, 16h, 20h and 24h.


title: KO, MICE BRAIN, INFECTION,  DAY 7

description: 10x Genomics


title: DM11d


title: db/m 4w

value: 4 weeks old


title: db/db 32w

value: 32 weeks old

value: db/db


title: MDA-MB-231, KDM5B-NTT overexpression, rep1


title: db/m 32w


title: db/db 12w


title: DM9d

value: No LPS


title: MDA-MB-231, control, rep1


title: DM10d


title: MCF7, KDM5B-NTT overexpression, rep4


title: db/db 4w


title: MCF7, control, rep4


title: MCF7, KDM5B-NTT overexpression, rep3


title: 3585_15: Patient 2 3h LPA 1-9.2

city: Amsterdam

first: Wouter

last: Moolenaar

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Basecalling and demultiplexing was performed using the standard Illumina pipeline
The reads were mapped to the human reference genome (GRCh38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Genecounts were generated using a custom script, based on HTSeq-count, that generates counts per gene.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample.

source_name: human lymphocytes

growth_protocol: Melanoma-derived TILs were isolated and expanded ex vivo.

extract_protocol:
RNA from melanoma TILs before and after LPA treatment was extracted and subjected to RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina polyA+ selection.

treatment_protocol: TILs were treated with LPA (5 uM) for 2 or 3 hrs.

value: melanoma-derived tumor-infiltrating lymphocytes (TILs)

value: LPA-stimulated (3hrs)


title: MCF7, control, rep3


title: 3585_16: Patient 2 3h LPA 2-10.2


title: 3585_14: Patient 2 Not st 2-8.2

value: Non-stimulated


title: RAW264.7, Control_sample_1

city: Kolkata

first: Abhishake

last: Lahiri

address: 4, Raja S. C. Mullick Road

country: India

institute: CSIR-Indian Institute of Chemical Biology

data_processing:
ChIP-seq reads were aligned to the mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
MACS2 2.2.6 was used for peak calling. For both the treatments, peak calling was performed against the control bams and p-value set at 0.001.
Assembly: mm39
Supplementary files format and content: narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and cross-linking was done using glycine for 10 minutes. For nucleic preparation and chromatin digestion, two separate buffers were used containing DTT and micrococcal nuclease was used, followed by sonication.
ChIP-seq libraries were performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, Cat# E7645L).

value: Control

tag: chip antibody


title: RAW264.7, LPS Treated_sample_1

value: LPS


title: RAW264.7, Control_sample_2


title: Wild type replicate 8

city: Bethesda

first: Karen

last: Laky

state: MD

address: 9000 Rockville Pike

department: NIAID

institute: NIH

data_processing:
Raw fastq files were trimmed for quality and adapter contamination using Cutadapt v2.10
Trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3
Gene-level expression quantification was performed using RSEM v1.3.0
Differential expression analysis was performed using the R package limma with voom normalization
Genome_build: mm10
Supplementary_files_format_and_content: raw counts and fpkm

source_name: Esophagus

extract_protocol:
Esophagi were snap frozen with liquid nitrogen and stored at ‐80°C until RNA isolation. Total RNA was isolated from the inner esophagi of WT or R1 mice (Direct‐zol RNA miniprep Plus; Zymo Research Corp., Irvine CA). PolyA selected mRNA libraries were generated using the Illumina TruSeq Stranded Library protocol, and mRNA samples were pooled and sequenced on a HiSeq2500.
PolyA selected mRNA libraries were generated using the Illumina TruSeq Stranded Library protocol, and mRNA samples were pooled and sequenced on a HiSeq2500.

value: Esophagus

value: wild type


title: RAW264.7, LPS+NaBu Treated_sample_2

value: LPS+NaBu


title: db/db 24w

value: heart


title: Proliferating ABCA1 knockout IMR90 cells rep2

value: IMR90 cells

value: Lung fibroblast

value: ABCA1 knockout

value: untreated


title: 3585_13: Patient 2 Not st 1-7.2


title: MCF7, KDM5B-NTT overexpression, rep2

value: breast


title: RAW264.7, LPS+NaBu Treated_sample_1


title: Wild type replicate 6


title: MCF7, control, rep2


title: 3585_4: Patient 1 3h LPA 2


title: RAW264.7, Control, rep3

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 mm39 whole genome using STAR v2.7.7a with parameters --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM
FPKM values were calculated using DeSeq2 package.
Assembly: mm39
Supplementary files format and content: Tab-delimited file containing the FPKM values of the gene counts

extract_protocol:
Total RNA was extracted from the RAW264.7 cells using TRIzol and purified according to manufacter's instructions.
A modified NEBNext RNA Ultra II directional protocol was used to prepare the libraries for total RNA.


title: RAW264.7, Control, rep2


title: Wild type replicate 5


title: 3585_3: Patient 1 3h LPA 1


title: RAW264.7, Control, rep1


title: RAW264.7, LPS Treated_sample_2


title: Wild type replicate 9


title: Wild type replicate 7


title: 3585_2: Patient 1 Not st 2


title: Wild type replicate 4


title: Wild type replicate 3


title: 3585_1: Patient 1 Not st 1


title: RAW264.7, LPS, rep3


title: A549, NK resistant

city: Ann Arbor

first: Sunitha

last: Nagrath

state: Michigan

address: 2800 Plymouth Road

institute: University of Michigan

data_processing:
Snakemake was used to manage the bioinformatics workflow in a reproducible manner.
The reads were trimmed using Cutadapt and were evaluated with FastQC to determine quality of the data
Reads were mapped to the reference genome GRCh38 (ENSEMBL) using STAR, and assigned count estimates to genes with RSEM v1.3.3. Alignment options followed ENCODE standards for RNA-seq.
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files that include RSEM values for each samples

growth_protocol:
Cells were maintained in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS) (Sigma) and 1% Antibiotic-antimycotic (Gibco).
Cells were maintained at 37°C and 5% CO2. They were grown to 70 - 80% confluence before subculturing using 0.05% Trypsin-EDTA (Gibco).

extract_protocol:
Cells were seeded with 1.5 ×10^5 cells per well in 12-well plates. After 72 hrs, the cells were lysed using 700 µL TRIzolTM Reagent (Life Technologies) and incubated for 5 min at room temperature on a plate rocker. RNA was then isolated and purified using the Total RNA Purification kit (Norgen) under the manufacturer’s instructions.
The purified RNA samples were then submitted to the Advanced Genomics Core at the University of Michigan for library prep and next-generation sequencing. Input RNA is normalized to 200ng per sample. The RNA library was prepared with Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs), and NEBNext Multiplex Oligos for Illumina Unique dual (New England BioLabs).

value: Lung cancer cell line


title: RAW264.7, LPS, rep2


title: 3813_10: Patient 2 2h LPA Stimulated 2

value: LPA-stimulated (2hrs)


title: Wild type replicate 1


title: 3813_9: Patient 2 2h LPA Stimulated 1


title: H1650, NK resistant


title: RAW264.7, LPS, rep1


title: H3255, NK resisitant


title: RAW264.7, LPS+NaBu, rep3


title: TGFBR1 mutant replicate 8


title: H1975, NK resistant


title: 3813_8: Patient 2 Not Stimulated 2


title: RAW264.7, LPS+NaBu, rep2


title: MCF7, KDM5B-NTT overexpression, rep1


title: H441, NK sensitive


title: TGFBR1 mutant replicate 7


title: 3813_7: Patient 2 Not Stimulated 1


title: CTC-Lu1, NK sensitive

value: In-house derived CTC line


title: 3813_4: Patient 1 2h LPA Stimulated 2

value: melanoma-derived tumor-infiltrating lymphocytes (TILs)


title: RAW264.7, LPS+NaBu, rep1


title: Wild type replicate 2


title: TGFBR1 mutant replicate 6


title: MCF7, control, rep1


title: 3813_3: Patient 1 2h LPA Stimulated 1


title: TGFBR1 mutant replicate 9


title: TGFBR1 mutant replicate 4


title: 3813_2: Patient 1 Not Stimulated 2


title: TGFBR1 mutant replicate 3


title: 3813_1: Patient 1 Not Stimulated 1


title: TGFBR1 mutant replicate 2


title: Castration-sensitive prostate cancer [CSPC #1]

city: Shanghai

first: Zehua

last: Ma

address: Pujian road 160

institute: Shanghai Jiaotong university

data_processing:
Raw sequencing data were converted to FASTQ files with Illumina bcl2fastq, version 2.19.1, and data were aligned to the human genome reference se_x0002_quence (GRCH38)
The CellRanger (10X Genomics, 2.1.1 version) analysis pipeline was used for sample demultiplexing, barcode processing and single-cell 3′ gene counting to generate a digital gene-cell matrix from these data.
Cell Ranger filters any barcode that contains less than 10% of the 99th percentile of total UMI counts per barcode, as these are considered to be associated with low quality cell barcodes
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: primary prostate cancer

extract_protocol:
Tumor tissues were ressected by biopsy surgery and transported in DMEM/F12 medium on ice to the laboratory within an hour. For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.
The cell suspension of each sample was run in the Chromium Controller with appropriate reagents to generate single cell gel bead-in-emulsions (GEMs) for sample and cell barcoding. The libraries were then pooled and sequenced on a NovaSeq 6000 (Illumina) at a depth of ~400 M reads per sample.

treatment_protocol: CSPC recevied no treatment, CRPC received ADT and androgen receptor antagonist

value: primary prostate cancer

tag: Sex

value: Male


title: CTC-Lu2, NK sensitive


title: TGFBR1 mutant replicate 5


title: TGFBR1 mutant replicate 1


title: DNAm peripheral blood sample_408

status: Public on Jan 14 2023

type: genomic

city: Munich

first: Natan

last: Yusupov

address: Kraepelinstr. 2-10

department: Dept. Genes and Environment

institute: Max Planck Institute of Psychiatry

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi pipline with stratified quantile normalization and subsequently beta-mixture quantile normalization. Batch effects corrected with ComBat

label: cy3, cy5

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral whole blood samples according to standard procedures

tag: study

value: Never Smoker

tag: bmi

value: Non-Exposed


title: DNAm peripheral blood sample_406

value: Female


title: DNAm peripheral blood sample_407

value: Former Smoker

value: Exposed


title: DNAm peripheral blood sample_413


title: DNAm peripheral blood sample_411


title: DNAm peripheral blood sample_412

value: Current Smoker


title: DNAm peripheral blood sample_409


title: DNAm peripheral blood sample_410


title: DNAm peripheral blood sample_400


title: DNAm peripheral blood sample_399


title: DNAm peripheral blood sample_398


title: MNRR1 KO, rep 1

city: Detroit

first: Gil

middle: G.

last: Mor

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

institute: Wayne State University School of Medicine

data_processing:
Base calling was conducted using HiSeq Control Software, converted to fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR aligner v.2.5.2b
Read count extraction was performed using Subread package v.1.5.2
Read count normalization was performed using DESeq2 package
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count values for each sample

source_name: Ovary

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit (Qiagen) according to manufacturer's instructions. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

tag: tissue

value: Ovary

value: TKO

value: MNRR1 KO

tag: disease state

value: Ovarian cancer


title: DNAm peripheral blood sample_401

tag: age


title: DNAm peripheral blood sample_403


title: DNAm peripheral blood sample_404


title: WT, rep 1

value: Wild Type


title: DNAm peripheral blood sample_414


title: WT, rep 2


title: MNRR1 KO, rep 3


title: MNRR1 KO, rep 2


title: WT, rep 3


title: DNAm peripheral blood sample_416


title: DNAm peripheral blood sample_415


title: DNAm peripheral blood sample_418


title: DNAm peripheral blood sample_405


title: DNAm peripheral blood sample_417


title: DNAm peripheral blood sample_402


title: DNAm peripheral blood sample_419


title: DNAm peripheral blood sample_420


title: DNAm peripheral blood sample_396


title: DNAm peripheral blood sample_397


title: DNAm peripheral blood sample_393


title: DNAm peripheral blood sample_395


title: DNAm peripheral blood sample_394


title: DNAm peripheral blood sample_390


title: DNAm peripheral blood sample_389


title: DNAm peripheral blood sample_391


title: DNAm peripheral blood sample_392


title: DNAm peripheral blood sample_374


title: DNAm peripheral blood sample_388


title: DNAm peripheral blood sample_387


title: DNAm peripheral blood sample_383


title: DNAm peripheral blood sample_386


title: DNAm peripheral blood sample_382


title: DNAm peripheral blood sample_385


title: DNAm peripheral blood sample_380


title: DNAm peripheral blood sample_378


title: DNAm peripheral blood sample_377


title: DNAm peripheral blood sample_379


title: DNAm peripheral blood sample_376


title: DNAm peripheral blood sample_375


title: DNAm peripheral blood sample_381


title: DNAm peripheral blood sample_371


title: DNAm peripheral blood sample_369


title: DNAm peripheral blood sample_370


title: DNAm peripheral blood sample_372


title: DNAm peripheral blood sample_384


title: DNAm peripheral blood sample_368


title: DNAm peripheral blood sample_367


title: DNAm peripheral blood sample_366


title: DNAm peripheral blood sample_364


title: DNAm peripheral blood sample_363


title: DNAm peripheral blood sample_365


title: DNAm peripheral blood sample_362


title: DNAm peripheral blood sample_361


title: DNAm peripheral blood sample_355


title: DNAm peripheral blood sample_358


title: DNAm peripheral blood sample_359


title: DNAm peripheral blood sample_349


title: DNAm peripheral blood sample_357


title: DNAm peripheral blood sample_354


title: DNAm peripheral blood sample_348


title: DNAm peripheral blood sample_351


title: DNAm peripheral blood sample_345


title: DNAm peripheral blood sample_344


title: DNAm peripheral blood sample_347


title: DNAm peripheral blood sample_346


title: DNAm peripheral blood sample_352


title: DNAm peripheral blood sample_360


title: DNAm peripheral blood sample_343


title: DNAm peripheral blood sample_341


title: DNAm peripheral blood sample_356


title: DNAm peripheral blood sample_350


title: DNAm peripheral blood sample_353


title: DNAm peripheral blood sample_339


title: DNAm peripheral blood sample_342


title: DNAm peripheral blood sample_338


title: DNAm peripheral blood sample_340


title: DNAm peripheral blood sample_337


title: DNAm peripheral blood sample_334


title: DNAm peripheral blood sample_336


title: DNAm peripheral blood sample_330


title: DNAm peripheral blood sample_331


title: DNAm peripheral blood sample_335


title: DNAm peripheral blood sample_329


title: DNAm peripheral blood sample_318


title: DNAm peripheral blood sample_320


title: DNAm peripheral blood sample_327


title: DNAm peripheral blood sample_333


title: DNAm peripheral blood sample_326


title: DNAm peripheral blood sample_319


title: DNAm peripheral blood sample_325


title: DNAm peripheral blood sample_323


title: DNAm peripheral blood sample_328


title: DNAm peripheral blood sample_332


title: DNAm peripheral blood sample_316


title: DNAm peripheral blood sample_312


title: DNAm peripheral blood sample_314


title: DNAm peripheral blood sample_317


title: DNAm peripheral blood sample_315


title: DNAm peripheral blood sample_313


title: DNAm peripheral blood sample_322


title: DNAm peripheral blood sample_321


title: DNAm peripheral blood sample_324


title: DNAm peripheral blood sample_311


title: DNAm peripheral blood sample_310


title: DNAm peripheral blood sample_307


title: DNAm peripheral blood sample_308


title: DNAm peripheral blood sample_306


title: DNAm peripheral blood sample_305


title: DNAm peripheral blood sample_309


title: DNAm peripheral blood sample_302


title: DNAm peripheral blood sample_304


title: DNAm peripheral blood sample_284


title: DNAm peripheral blood sample_300


title: DNAm peripheral blood sample_301


title: DNAm peripheral blood sample_299


title: DNAm peripheral blood sample_303


title: DNAm peripheral blood sample_283


title: DNAm peripheral blood sample_287


title: DNAm peripheral blood sample_298


title: DNAm peripheral blood sample_297


title: DNAm peripheral blood sample_295


title: DNAm peripheral blood sample_294


title: DNAm peripheral blood sample_289


title: DNAm peripheral blood sample_293


title: DNAm peripheral blood sample_292


title: DNAm peripheral blood sample_282


title: DNAm peripheral blood sample_290