title: 150720_FR_BB1_liver

extract_protocol:
400 ng of DNase-treated RNA was used to construct poly(A) enriched, strand-specific RNA sequencing libraries using the NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 and NEXTFLEX Poly(A) Beads (2.0) (Perkin Elmer)
Total RNA was extracted from tissue samples (~50 mg) stored in RNAlater using TRIzol Reagent (Invitrogen) following the manufacturer’s guidelines. RNA samples were treated to remove any contaminating DNA using the Turbo DNA-free kit (Invitrogen) according to the protocol.

value: Red


title: 140720_FG_BB1_liver

status: Public on Nov 29 2022

type: SRA

city: Dunedin

first: Donna

last: Bond

address: 270 Great King Street

department: Department of Anatomy

country: New Zealand

institute: University of Otago

library_source: transcriptomic

data_processing:
Raw reads were trimmed using Trim Galore! (v0.6.7) to remove adapters and low-quality base calls (Phred score < 20)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed reads were mapped to the possum reference genome (GCA_011100635.1) using HISAT2 (v2.2.1) with standard parameters
Read count extraction and normalization was performed using SeqMonk v1.48.0 (RNAseq quantitation pipeline)
Assembly: Trichosurus vulpecula (GCA_011100635.1)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Trichosurus vulpecula

source_name: Liver

tag: tissue

value: Liver

tag: developmental stage

value: Adult

tag: Sex

value: Female

tag: coat colour

value: Grey

tag: mother

tag: location

value: Boulder Beach

tag: longtitude

tag: latitude


title: 150720_PY01_liver

value: Pouch young - 99 dpp


title: 140720_PY01_liver

value: Pouch young - 102 dpp

value: Male


title: 030720_FG_SDR1_liver

value: South Dale Rd


title: 250620_PY01_liver

value: Juvenile

value: Woodside Glen


title: 250620_FG_WSG1_liver


title: 150720_MG_BB2_liver


title: HCC tissue with metastasis circRNA 9

type: RNA

city: Shijiazhuang

first: Ping

last: Gao

state: Hebei

address: No. 361 Zhongshan East Road

department: School of Public Health

country: China

institute: Hebei medical university

description: circRNA expression data from Homo sapiens tumor tissue with metastasis

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65℃ in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 6 out of 30 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between  two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

organism: Homo sapiens

source_name: hepatocellular carcinoma (HCC) tissue with metastasis

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: disease state

value: HCC

value: HCC tumor tissue with metastasis

tag: gender

value: male


title: 160620_MG_SDR1_liver


title: HCC tissue with metastasis circRNA 6


title: HCC tissue with metastasis circRNA 8


title: HCC tissue with metastasis circRNA 5


title: HCC tissue with metastasis circRNA 7

value: female


title: 100620_MG_BB1_liver


title: 030720_PY01_liver

value: Pouch young - 84 dpp


title: 280520_PY01_liver

value: Pouch young - 69 dpp


title: 190320_PY01_liver

value: Liver


title: 290520_PY01_liver

value: Pouch young - 45 dpp


title: HCC tissue without metastasis circRNA 10

description: circRNA expression data from Homo sapiens tumor tissue without metastasis

source_name: hepatocellular carcinoma (HCC) tissue without metastasis

value: HCC tumor tissue without metastasis


title: HCC tissue with metastasis circRNA 2


title: HCC tissue with metastasis circRNA 3


title: HCC tissue with metastasis circRNA 1


title: HCC tissue with metastasis circRNA 10


title: HCC tissue without metastasis circRNA 9


title: HCC tissue without metastasis circRNA 6


title: HCC tissue without metastasis circRNA 7


title: 190320_FG_WSG2_liver

value: Adult

value: Female

value: Grey


title: HCC tissue with metastasis circRNA 4


title: HCC tissue without metastasis circRNA 8


title: 030620_PY01_liver

value: Pouch young - 74 dpp


title: HCC tissue without metastasis circRNA 5


title: 030620_FG_WSG1_liver


title: 190320_MR_WSG1_liver

value: Male

value: Red


title: 130320_MB_SDR1_liver

value: Black

value: South Dale Rd


title: 120320_MR_SDR1_liver


title: 120320_MB_SDR2_liver


title: 170320_FR_SDR1_liver


title: Sheila_tongue

source_name: Tongue

value: Tongue

value: Juvenille

value: Puku

value: Sandymount


title: HCC tissue without metastasis circRNA 4

value: HCC

value: male


title: Sheila_liver

value: Liver


title: Puku_liver


title: HCC tissue without metastasis circRNA 1


title: Sandy_spleen

source_name: Spleen

value: Spleen

value: Pouch young - 22 dpp


title: Sandy_lung

source_name: Lung

value: Lung


title: Sandy_stomach

source_name: Stomach

value: Stomach


title: non-tumor tissue circRNA 10

description: circRNA expression data from Homo sapiens liver (hepar)

source_name: liver (hepar) normal tissue

value: normal liver (hepar) tissue from HCC


title: Sandy_eye

source_name: Eye

value: Eye


title: Sandy_large_int

source_name: Large Intestine

value: Large Intestine

value: Male


title: HCC tissue without metastasis circRNA 3

value: HCC tumor tissue without metastasis


title: Sandy_small_int

source_name: Small Intestine

value: Small Intestine


title: Sandy_bladder

source_name: Bladder

value: Bladder


title: Sandy_heart

source_name: Heart

value: Heart


title: Sandy_muscle

source_name: Muscle

value: Muscle

value: Puku


title: Puku_tongue

value: Tongue

value: Adult

value: Female

value: Grey

value: Sandymount


title: Sandy_skin

source_name: Skin

value: Skin

value: Pouch young - 22 dpp


title: Sandy_brain

source_name: Brain

value: Brain


title: non-tumor tissue circRNA 9

value: HCC

value: normal liver (hepar) tissue from HCC

value: male


title: non-tumor tissue circRNA 8

value: female


title: Sandy_liver

value: Liver

value: Male


title: BALB/c_B7KO_3 10X scRNAseq

city: Bethesda

first: Masashi

last: Watanabe

address: 10 Center Dr.

country: USA

institute: NCI

data_processing:
Base calling was performed using RTA 3.9.2
Demultiplexing was performed using cellranger v6.1.1 (Bcl2fastq 2.20.0)
Alignment was performed using cellranger v6.1.1 (STAR 2.7.2a)
Sequenced reads were aligned to the 10x Genomics provided mouse reference sequences (refdata-gex-mm10-2020-A for GEX and refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 for TCR).
For processing the third run, GEX samples were processed using “--r2-length=90” parameter to have the consistent read length for GEX data in all the runs. The rest of metrics are as cellranger default.
Assembly: mm10

organism: Mus musculus

source_name: Thymic iNKT

extract_protocol:
The cellular samples were loaded in the lanes according to the 10X Genomics 5’ v2 Single Cell User Guide with a single capture lane per sample targeting recovery of up to 6,000 cells per lane. Cell partitioning completed successfully with uniform emulsion consistency for all. Reverse transcription PCR was run overnight.
Subsequent library preparation steps performed according to the 10X Gnomics User Guide.

tag: strain

value: BALB/c

tag: genotype

value: B7 KO

value: Thymus

tag: cell type

value: iNKT


title: HCC tissue without metastasis circRNA 2

value: HCC tumor tissue without metastasis


title: non-tumor tissue circRNA 5


title: non-tumor tissue circRNA 4


title: non-tumor tissue circRNA 6


title: Sandy_kidney

source_name: Kidney

value: Kidney

value: Puku


title: BALB/c_B7KO_1 10X scRNAseq


title: BALB/c_WT_3 10X scRNAseq

value: WT


title: BALB/c_WT_2 10X scRNAseq


title: BALB/c_B7KO_2 10X scRNAseq


title: non-tumor tissue circRNA 7


title: wD21P4

city: Aurora

first: Christophe

last: Langouët-Astrié

state: CO

department: Pulmonary Sciences and Critical Care

institute: University of Colorado Denver, Anschutz

description: Gene expression data from bacteria cultured in D21 PR8 BAL for 12 hours

data_processing:
Illumina reads were trimmed for adaptor sequence and for quality in CLC Genomics Workbench (v.21.0.5)
Trimmed sequences were mapped to to the reference genome sequence of Staphylococcus aureus USA300, with the parameters: mismatch cost, 2; insertion and deletion cost, 3; length and similarity fraction, 0.8.
Uniquely mapped transcripts from each sample were exported from CLC Genomics Workbench and used for normalization and differential gene expression analysis with an R package, DESeq2 version 1.32.0
Assembly: USA300_FPR3757
Supplementary files format and content: MRSA_gene_counts_matrix contains uniquely mapped transcripts for each sample with gene name, length, USA300 new locus tag, USA300 old locus tag, and description.
Supplementary files format and content: D3_gene_exp_diff, D7_gene_exp_diff, D10_gene_exp_diff, and D21_gene_exp_diff contains differential gene expression between MRSA conditioned in healthy and PR8 BAL at each mouse timepoint (D3, D7, D10, and D21, respectively) post-IN administration. Files include gene names, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj.
Supplementary files format and content: D7_TCS_gene_exp_diff and D10_TCS_gene_exp_diff,  contains differential gene expression between WT and saePQRS mutant MRSA conditioned in PR8 BAL at each mouse timepoint (D7 and D10 respectively) post-IN administration. Files include gene names, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj.

organism: Staphylococcus aureus

source_name: Bacterial cells

growth_protocol: USA300 (wildtype, WT, and SaePQRS mutant) were cultured in TSB from frozen stock for 18-24 hours. Overnight WT MRSA cultures were diluted 1:1000 in 40% (v/v) cell-free BAL for 12 hours at 37°C, with 1000rpm of horizontal shaking.

extract_protocol:
Frozen bacterial pellets were resuspended in TE buffer, bead beat, and then RNA isolated using Qiagen RNeasy Mini Kit (Cat#74104). Contaminating DNA was removed by treatment with TURBO DNA-free kit (Cat#AM1907).
RNA libraries were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit (Cat#20040529) with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Mice were intranasally (IN) administered with saline or influenza A/PR/8/34 (PR8) and were left to recover for 3, 7, 10, 21 days post-IN (D3, D7, D10, D21). After each timepoint, mice were sacrificed and whole lungs were washed 3 times with 1mL cold PBS. Bronchoalveolar lavage (BAL) fluid was centrifuged and the supernatant, the cell-free portion, was used for bacterial culturing. Overnight WT MRSA cultures were cultured in saline BAL (wD3H, wD7H, wD10H, wD21H) and PR8 BAL (wD3P, wD7P, wD10P, wD21P) for 12 hours at 37°C, with 1000rpm of horizontal shaking. Overnight SaePQRS mutant MRSA cultures were cultured in D7 and D10 IN PR8 BAL (dD7P and dD10P) for 12 hours at 37°C, with 1000rpm of horizontal shaking. All bacterial samples were centrifuged and then the pellet was resuspended in PBS. The opitical density (OD) of WT and SaePQRS mutant  bacterial suspensions were measured and diluted to an OD of 2. DIluted bacteria was centrifuged for pellets were frozen.

value: Wildtype

tag: growth medium

value: TSB

tag: growth conditions


title: wD21P5


title: non-tumor tissue circRNA 3


title: non-tumor tissue circRNA 2


title: wD21P3


title: BALB/c_B7KO_1 10X scTCRseq


title: BALB/c_B7KO_2 10X scTCRseq


title: wD21P1


title: BALB/c_B7KO_3 10X scTCRseq


title: BALB/c_WT_2 10X scTCRseq


title: BALB/c_WT_3 10X scTCRseq


title: wD21H2

description: Gene expression data from bacteria cultured in D21 healthy BAL for 12 hours

value: D21 Healthy BAL, 12 h, 37 C


title: wD21H4


title: BALB/c_WT_1 10X scTCRseq


title: wD21H3


title: wD21H1


title: BALB/c_WT_1 10X scRNAseq


title: dD10P6

description: Gene expression data from bacteria cultured in D7 healthy BAL for 12 hours

value: SaePQRS mutant


title: dD10P5

description: Gene expression data from bacteria cultured in D10 PR8 BAL for 12 hours


title: dD10P4


title: non-tumor tissue circRNA 1

value: HCC

value: normal liver (hepar) tissue from HCC


title: dD10P3


title: G4 CTR MQ12

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were processed and normalised using RMA normalisation with Expression Console v1.4.1.46

label: biotin

source_name: G4 CTR

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: tumor


title: G4 CTR MQ06


title: G4 CTR MQ08


title: G4 CTR MQ04


title: G4 CTR MQ02


title: G3 LRGG V MP92

source_name: G3 LRGG V


title: G4 CTR MQ16


title: dD10P1


title: G4 CTR MQ00


title: wD10P6


title: G4 CTR MQ10


title: G3 LRGG V MP96


title: wD10P5


title: G3 LRGG V MP94


title: wD10P4


title: G3 LRGG V MP88


title: G3 LRGG V MP86


title: G3 LRGG V MP80


title: G3 LRGG V MP82


title: G3 LRGG V MP84


title: wD10P3


title: G2 LRGG M MP76

source_name: G2 LRGG M


title: G3 LRGG V MP78


title: G3 LRGG V MP90


title: G2 LRGG M MP72


title: G2 LRGG M MP74


title: wD10P1


title: wD10H5

description: Gene expression data from bacteria cultured in D10 healthy BAL for 12 hours

value: D10 Healthy BAL, 12 h, 37 C


title: G2 LRGG M MP68


title: wD10H4


title: G2 LRGG M MP70


title: wD10H2


title: G2 LRGG M MP66


title: FE_Liver_High_GenX_Rep_4

city: Research Triangle Park

first: Suzanne

middle: E

last: Fenton

state: North Carolina

address: 111 TW ALEXANDER DR

department: Mechanistic Toxicology Branch

institute: Division of the National Toxicology Program, National Institute of Environmental Health Sciences

description: Gene expression data from fetal embryonic liver liver tissue exposed to 10 mg/kg/day GenX

hyb_protocol: Amplified biotin-cDNAs (5 μg/sample) were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit user manual. RNA expression analysis was conducted using Affymetrix Mouse Clariom D Array, previously known as the Mouse Transcriptome Assay 1.0 (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Annotation was derived in R from the Affymetrix annotation file MTA-1_0.na36.mm10.transcript.csv. For each transcript, the raw intensities were background adjusted and RMA normalized.

source_name: Fetal embryonic liver liver tissue exposed to 10 mg/kg/day GenX

label_protocol: Total RNA (25 ng/sample) was first amplified and labeled using the Affymetrix WT Plus Reagent Kit (WT Plus Kit) per manufacturer’s instructions. Amplified biotin-cDNAs (5 μg/sample) were fragmented.

growth_protocol: On gestational day 17.5 pregnant dams were weighed and humanely euthanized by swift decapitation. Trunk blood was collected and serum was used for clinical chemistry. Maternal livers were weighed, and a portion of the left lateral lobe was snap frozen in liquid nitrogen for subsequent RNA extraction. The uterus was removed, and viable embryos were collected in succession within a uterine horn and the livers were removed and immediately snap frozen in liquid nitrogen (n = 2-5 embryos/litter).

extract_protocol: Snap frozen tissues were trimmed on ice and weighed (< 30 mg) and then homogenized using a FastPrep-24™ 5G (MP Biomedicals, Valiant Co., Ltd, China) in Buffer RLT (Qiagen, Hilden, Germany) within 2mL, 2.4mm metal bead homogenization tubes (Thermo Fisher Scientific, Waltham, MA). Homogenized liver samples were then snap frozen and stored at -80°C before use. RNA was extracted from maternal and fetal liver samples using RNeasy kits following manufacturer’s protocols (Qiagen, Hilden, Germany). Resulting purified RNA was subjected to quality control assessments using a NanoDrop™ 2000/2000c Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer High Sensitivity RNA Analysis (Agilent, Santa Clara, CA). All RNA samples used for transcriptomics analysis had a 260/280 ratio > 2.0 and RIN > 5.0. RNA isolates were diluted to a standard concentration of 100 ng RNA/ 1 µL H2O.

treatment_protocol: Matching maternal and female fetal liver samples were used for this study. Fetal livers were selected at random when there was more than one female per litter collected. A total N = 4-6 per treatment group and tissue origin [e.g., maternal or fetal liver] were used in the current study.

value: liver

tag: age

value: gestational day 17.5

tag: treatment

value: GenX

tag: dose

value: 10 mg/kg/day


title: G1 Vanco/Neo MP56

source_name: G1 Vanco/Neo

tag: tissue


title: G1 Vanco/Neo MP50


title: G1 Vanco/Neo MP54


title: G2 LRGG M MP64


title: G2 LRGG M MP62


title: G1 Vanco/Neo MP58


title: wD10H1


title: FE_Liver_Low_GenX_Rep_5

value: 2 mg/kg/day


title: FE_Liver_Low_GenX_Rep_4

description: Gene expression data from fetal embryonic liver liver tissue exposed to 2 mg/kg/day GenX

source_name: Fetal embryonic liver liver tissue exposed to 2 mg/kg/day GenX


title: dD7P5

description: Gene expression data from bacteria cultured in D7 PR8 BAL for 12 hours

value: D7 PR8 BAL, 12 h, 37 C


title: dD7P6


title: G2 LRGG M MP60


title: G1 Vanco/Neo MP48


title: FE_Liver_High_GenX_Rep_1


title: FE_Liver_Low_GenX_Rep_3


title: dD7P3


title: G1 Vanco/Neo MP52


title: FE_Liver_High_GenX_Rep_2


title: T48HKs-2

city: Lanzhou

first: jinqiang

last: huang

address: Yintanlu Stress

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included dirty reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get clean tags, raw reads were further filtered according to the following rules: 1) Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides (N); 2) Removing reads without 3’adapters; 3) Removing reads containing 5’adapters; 4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; 5) Removing reads containing ployA in small RNA fragment; 6) Removing reads shorter than 18nt (not include adapters).
All of the clean tags were aligned with small RNAs in GeneBank database (Release 209.0) and in Rfam database (Release 11.0) to identify and remove ribosomal RNA (rRNA), small conditional RNA (scRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), and transfer RNA (tRNA).
The enriched clean tags were also aligned with reference genome. Those mapped to exons or introns might be fragments from mRNA degradation, so these tags were removed. The tags mapped to repeat sequences were also removed. The remaining tags were searched against miRBase database (Release 22) to identify known miRNAs.
All the unannotated tags were clustered and defined as novel miRNA candidates according to their genome positions and hairpin structures predicted by the software Mireap_v0.2.
Assembly: rainbow trout
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: head kidney tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: head kidney tissues

value: IHNV challenge

tag: phenotype

value: wild-type


title: C48HKs-3

value: control


title: FE_Liver_Low_GenX_Rep_2


title: dD7P2

value: TSB


title: FE_Liver_High_GenX_Rep_3


title: T48HKs-3


title: T48HKs-1


title: dD7P1


title: G1 Vanco/Neo MP42


title: G1s-C2-22_RNA

city: Hirosaki

first: Rika

last: Kanezaki

address: 5 Zaifucho

country: Japan

institute: Hirosaki University Graduate School of Medicine

data_processing:
For ChIP-seq data,sequence reads were aligned to genome by Bowtie2 (ver 2.2.2) with option -N1. For CUT&RUN-seq data, reads were aligned according to the method by Skene and Heinikoff (Nature Protocols 2018 13, 1006-1019). For RNA-seq data, sequence reads were aligned to genome using STAR (ver 2.6.1d). Aligned reads were counted by RSEM (ver 1.3.1). The count data normalized using the DESeq2 package (ver 1.32.0).
Duplicated reads of ChIP-seq and CUT&RUN-seq were removed by Picard (ver. 2.18).
The BAM files of ChIP-seq and CUT&RUN data were converted to bigWig coverage files using bamCoverage command of deepTools (ver 3.1.3). Read coverages were normalized to Read per genomic content (RPGC). For the GATA1 and GATA2 ChIP-seq data, peak call was performed using HOMER (ver 4.11)  with default settings.
Genome_build: hg19 (ChIP-seq, CUT&RUN-seq), hg38 (RNA-seq)
Supplementary_files_format_and_content: bigWig files normalized in reads per genomic content (RPGC) and bed files.

growth_protocol: K562 cells were cultured with RPMI1640 (Sigma-Aldrich) containing 10% heat inactivated fetal bovine serum (FBS) at 37°C in 5% CO2 atmosphere.

extract_protocol:
Chromatin samples were extracted using SimpleChIP Enzymatic Chromatin IP Kit (CST) according to the protocol. For ChIP reactions, Dynabeads anti-rabbit IgG (Thermo Fisher Scientific) was used to reduce noise instead of the Protein G magnetic beads included in the kit. CUT&RUN assay was performed using CUT&RUN Assay Kit (CST), and samples were purified using Monarch PCR & DNA Cleanup Kit (NEB). total RNA was extracted using the RNeasy plus mini kit (Qiagen).
ChIP-seq and CUT&RUN libraries were prepared using KAPA HyperPrep Kit (KAPA Biosystems). Total RNA was purified by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and RNA-seq library was prepared by KAPA RNA Hyper prep kit (KAPA Biosystems).

tag: cell line

value: mutant


title: G1 Vanco/Neo MP46


title: G1 Vanco/Neo MP44


title: FE_Liver_Low_GenX_Rep_1


title: FE_Liver_High_PFOA_Rep_6

value: PFOA

value: 5 mg/kg/day


title: G1s-C2-15_RNA


title: FE_Liver_High_PFOA_Rep_5

description: Gene expression data from fetal embryonic liver liver tissue exposed to 5 mg/kg/day PFOA

source_name: Fetal embryonic liver liver tissue exposed to 5 mg/kg/day PFOA


title: FE_Liver_High_PFOA_Rep_4


title: G1s-C2-4_RNA


title: G1s-C2-1_RNA


title: C48HKs-2


title: C48HKs-1


title: wD7P6

value: Wildtype


title: G1s-C1-26_RNA


title: G1s-C2-14_RNA


title: G1s-C2-16_RNA


title: wD7P3


title: G1s-C1-27_RNA


title: wD7P5


title: G1s-C1-26_Input

library_source: genomic

molecule: genomic DNA

tag: chip antibody


title: wD7H4

value: D7 Healthy BAL, 12 h, 37 C


title: G1s-C1-26_POLR2A

value: Rpb1 CTD (CST, #2629)


title: wD7P2


title: FE_Liver_High_PFOA_Rep_3

value: liver


title: G1s-C1-24


title: FE_Liver_High_PFOA_Rep_1

value: gestational day 17.5


title: WT_3_RNA

source_name: K562, wild type

value: wild


title: FE_Liver_Low_PFOA_Rep_5

description: Gene expression data from fetal embryonic liver liver tissue exposed to 1 mg/kg/day PFOA

source_name: Fetal embryonic liver liver tissue exposed to 1 mg/kg/day PFOA

value: 1 mg/kg/day


title: wD7P1


title: WT_2_RNA


title: WT_1_RNA


title: wD7H1


title: WT_GATA2

value: GATA2 (Santa Cruz, H-116)


title: wD7H3


title: G1s-C1-26_GATA2


title: G1s-C1-26_GATA1

value: GATA1 (Abcam, ab11852)


title: wD7H2


title: WT_Input


title: WT_POLR2A


title: FE_Liver_High_PFOA_Rep_2


title: WT_GATA1


title: wD3P4

description: Gene expression data from bacteria cultured in D3 PR8 BAL for 12 hours

value: D3 PR8 BAL, 12 h, 37 C


title: wD3P5


title: PB50-T48-Rep-2

city: Tampa

first: Caroline

last: Simmons

state: FL

address: 3720 East Spectrum Blvd St. 404

department: Center for Global Health and Infectious Diseases Research

institute: University of South Florida

description: artemisinin-sensitive mutant

data_processing:
RNAseq reads from each sample were aligned to the P. falciparum reference genome using HISAT2.
Mapped reads were used to assemble known transcripts from the reference and their abundances were estimated using SAMtools and the abundances were estimated using Feature Counts.
Assembly: P. falciparum reference genome (PlasmoDB version 47).
Supplementary files format and content: feature_counts_output_KIC5.xlsx is the output of Feature counts and contains ID (GeneID), chromosome (Chr), and the counts (number of reads), for each mapped gene from each RNAseq sample.

organism: Plasmodium falciparum

source_name: Plasmodium falciparum

growth_protocol: Parasite cultures were maintained according to standard methods with gassing (5% O2 and 5% CO2, nitrogen balanced) and 5% hematocrit (O+ blood; Interstate Blood Bank) in RPMI 1640 medium (Invitrogen) supplemented with 0.5% Albumax II (Invitrogen), 0.25% sodium bicarbonate, and 0.01 mg/ml gentamicin, maintained at 37°C.

extract_protocol:
Parasites were separated from red blood cells via incubation with 0.015% saponin at room temperature for 5 min. Cultures were then pelleted and washed three times in cold PBS. Samples were stored at − 80 °C in 1 mL TRIzol reagent (Fisher Scientific, Hampton, NH) until extraction. At RNA extraction, 200 μl of chloroform was added and samples were vortexed vigorously for 15 seconds, followed by incubation at room temperature for up to 5 minutes. Samples were then spun down at 12000×g (10,800 rpm) at 4 °C for 10 minutes and the supernatant discarded. 1 mL of 75% ethanol was added to the pellet, and samples were spun down at 10000×g (9800 rpm) for 5 minutes. The resulting supernatant was discarded and the pellet briefly allowed to dry. The RNA pellet was then dissolved in 20–50 μl of DEPC-treated water while being incubated at 55 °C for 10–15 min.
0.5 μg–1.0 μg of RNA samples were prepped for sequencing using the Illumina TruSeq Stranded mRNA Kit as per kit protocol. Library quantification was measured by qPCR and TapeStation (Agilent Technologies). Sequencing was performed on an Illumina NextSeq V2.5 mid-output 300-cycle.

treatment_protocol: Cultures of wildtype NF54 and PB50 (KIC5 mutant) were synchronized at ~2% ring stage with 10% sorbitol solution. After 48 hours of growth, cultures were again synchronized with 10% sorbitol. After 8hrs, cultures were synchronized for a third time with 10% sorbitol to yield highly synchronized cultures. 0hpi was determined (half schizonts and half ring cultures) and samples were collected for RNA extraction and sequencing at 6hpi, 12hpi, 24hpi, 36hpi, and 48hpi.

value: PB50 (KIC5 mutant)

value: piggyBac mutant

tag: disrupted gene id

tag: developmental stage

value: late schizont (T48)

value: whole body


title: wD3P1

value: TSB


title: VA-AS-F2

city: Baltimore

first: Joana

middle: C.

last: Silva

state: MD

address: 801 West Baltimore St

institute: Institute for Genome Sciences, University of Maryland School of Medicine

description:
replicate F2
EdgeR_Trinity_mode_transcribed_loci
EdgeR_Trinity_mode_isoforms
EdgeR_gene_map_mode_transcribed_loci
EdgeR_gene_map_mode_isoforms
Cuffdiff_transcribed_loci
Cuffdiff_isoforms
Intersection_all_3_methods_transcribed_loci
Intersection_all_3_methods_isoforms

data_processing:
The IGS GRC QC pipeline screened passed-filter sequence reads against a nucleotide database in order to evaluate data quality, contamination, and proper laboratory sample tracking. The pipeline uses a rapid, high-stringency megablast screen against the NCBI nucleotide and taxonomy databases.
Further sequence quality and trimming was processed with a second in-house pipeline.
Assembly step 1: Trinity de novo
Assembly step 2: TopHat/Cufflinks
Assembly step 3: In-house clustering and redundancy reduction - merged de novo and genome-guided transcriptome
The samples representing biological replicates, VA-AS-M1/VA-AS-M2 were compared with VA-AS-F1/VA-AS-F2 so that DE of females and males could be compared.
EdgeR ("Trinity-mode" and gene-map-mode) was used to identify differentially expressed transcribed loci and isoforms.
Cuffdiff was used to identify differentially expressed transcribed loci and isoforms.
The intersection of the 3 methods were determined for DE transcribed loci and isoforms.
Genome_build: E. affinis genome generated by i5K project: https://www.hgsc.bcm.edu/arthropods/eurytemora-affinis-genome-project
Supplementary_files_format_and_content: Text files representing the output from EdgeR and Cuffdiff for transcribed loci and isoforms and the final working file that is limited to the intersection of the three methods.

molecule: polyA RNA

organism: Eurytemora affinis

source_name: whole animal homogenate

growth_protocol: Standard copepod culture conditions at 13°C, 15 PSU salinity and on a 15L:9D photoperiod, until they reached adulthood.

extract_protocol:
Total RNA was extracted with Trizol reagent and then purified with Qiagen RNeasy Mini Kit.
A modified strand-specific protocol was adapted. Illumina RNA-Seq libraries were prepared with the TruSeq RNA Sample Prep kit, with a variation of the manufacturer's protocol. Eukaryotic mRNA was preferentially targeted with Poly(A) selection. Actinomycin D was added to the first strand synthesis reaction. Between first and second strand cDNA synthesis, the primers and nucleotides were removed from the samples with NucAway spin columns. The second strand was synthesized with a dNTP mix containing dUTP. Adapters containing 6 nucleotide indexes were ligated to the double-stranded cDNA. After adapter ligation, the second strand cDNA was digested with 2 units of Uracil-N-Glycosylase. The DNA was purified between enzymatic reactions and the size selection of the library was performed with AMPure XT beads.

treatment_protocol: Two days prior to RNA extraction males and females were separated. Prior to RNA extraction, copepods were starved and treated with 120 µL/L of 6.0 micron copolymer microsphere beads for the last 24 hours to clear gut contents.

value: female

value: adult

value: whole animal homogenate


title: VA-AS-M1

description:
replicate M1
EdgeR_Trinity_mode_transcribed_loci
EdgeR_Trinity_mode_isoforms
EdgeR_gene_map_mode_transcribed_loci
EdgeR_gene_map_mode_isoforms
Cuffdiff_transcribed_loci
Cuffdiff_isoforms
Intersection_all_3_methods_transcribed_loci
Intersection_all_3_methods_isoforms

value: male


title: VA-AS-M2

description:
replicate M2
EdgeR_Trinity_mode_transcribed_loci
EdgeR_Trinity_mode_isoforms
EdgeR_gene_map_mode_transcribed_loci
EdgeR_gene_map_mode_isoforms
Cuffdiff_transcribed_loci
Cuffdiff_isoforms
Intersection_all_3_methods_transcribed_loci
Intersection_all_3_methods_isoforms


title: wD3P2

value: Wildtype


title: PB50-T36-Rep-1

description: artemisinin-sensitive mutant

value: late trophozoite (T36)


title: FE_Liver_Low_PFOA_Rep_4

value: liver

value: gestational day 17.5

value: PFOA


title: FE_Liver_Low_PFOA_Rep_2

value: 1 mg/kg/day


title: FE_Liver_Low_PFOA_Rep_3


title: VA-AS-F1

description:
replicate F1
EdgeR_Trinity_mode_transcribed_loci
EdgeR_Trinity_mode_isoforms
EdgeR_gene_map_mode_transcribed_loci
EdgeR_gene_map_mode_isoforms
Cuffdiff_transcribed_loci
Cuffdiff_isoforms
Intersection_all_3_methods_transcribed_loci
Intersection_all_3_methods_isoforms


title: PB50-T24-Rep-2

description: artemisinin-sensitive mutant

value: early trophozoite (T24)


title: FE_Liver_Cont_Rep_5

description: Gene expression data from fetal embryonic liver liver tissue exposed to vehicle control

source_name: Fetal embryonic liver liver tissue exposed to vehicle control

value: Vehicle control

value: 0 mg/kg/day


title: PB50-T48-Rep-1

description: artemisinin-sensitive mutant

value: PB50 (KIC5 mutant)

value: piggyBac mutant


title: wD3H5

description: Gene expression data from bacteria cultured in D3 healthy BAL for 12 hours

value: D3 Healthy BAL, 12 h, 37 C


title: FE_Liver_Low_PFOA_Rep_1


title: PB50-T24-Rep-1

description: artemisinin-sensitive mutant

value: whole body


title: FE_Liver_Cont_Rep_3


title: FE_Liver_Cont_Rep_4


title: PB50-T12-Rep-2

description: artemisinin-sensitive mutant

value: ring (T12)


title: wD3H4

value: TSB


title: FE_Liver_Cont_Rep_2


title: PB50-T36-Rep-2

description: artemisinin-sensitive mutant


title: PB50-T12-Rep-1

description: artemisinin-sensitive mutant


title: PB50-T6-Rep-2

description: artemisinin-sensitive mutant

value: early ring (T6)


title: wD3H3


title: PB50-T6-Rep-1

description: artemisinin-sensitive mutant


title: wD3H2


title: NF54-T48-Rep-1

description: control

organism: Plasmodium falciparum NF54

value: wildtype

value: late schizont (T48)


title: NF54-T48-Rep-2

description: control


title: ILC model WEPtn

city: Amsterdam

first: Roebi

middle: de

last: Bruijn

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-3.0.0
Supplementary files format and content: filtered output of cellranger h5 format to load into single cell analysis programs
Supplementary files format and content: h5 format object of scanpy with annotations used for the paper

source_name: mammary gland

extract_protocol:
ILC tumors were harvested from 20 week old WEPtn and WEH1047R mice (n=3 mice per model) Tumors were processed into a single cell suspension as described in the section ‘flow cytometry analysis’. Single cell suspensions were incubated with hashtag antibodies directed against MHC-I and CD45 to label all nucleated cells. Each mouse was labelled with a different hashtag to allow for discrimination between mice from the same model. Samples were FACS-sorted for live single cells (DAPI negative). Sorted cells were spun down and resuspended to 1000 cells/ul in 1xPBS containing 0.04% weight/volume BSA (400 ug/ml). Samples from each model were pooled and Chromium Controller platform of 10X Genomics was used for single cell partitioning and barcoding.
Per sample each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 3’ Gene Expression libraries were prepared according to the manufacturer’s protocol “Chromium Next GEM Single Cell 3’ Reagent Kits v3.1” (CG000204, 10X Genomics). All four Single Cell 3’ Gene Expression libraries were quantified on a 2100 Bioanalyzer Instrument following the manufacturer’s protocol “Agilent DNA 7500 kit” (G2938-90024, Agilent Technologies). These Single Cell 3’ Gene Expression libraries were combined to create one sequence library pool which was quantified by qPCR, according to manufacturer’s protocol “KAPA Library Quantification Kit Illumina® Platforms” (KR0405, KAPA Biosystems). The NextSeq 550 Illumina sequencing system was used for paired end sequencing of the Single Cell 3’ Gene Expression libraries at a sequencing depth of approximately 18.000 reads pairs/cell. NextSeq 550 paired end sequencing was performed using 28 cycles for Read 1, 8 cycles for Read i7 and 56 cycles for Read 2, using NextSeq 500/550 High Output Kit v2.5 (75 Cycles) Reagent Kit (PN 20024906, Illumina).

value: mammary gland

value: live single cells

value: WapCre;Cdh1F/F;PtenF/F (het;hom;hom)


title: NF54-T36-Rep-2

description: control

value: late trophozoite (T36)


title: ILC model H1047R


title: NF54-T36-Rep-1

description: control


title: NF54-T24-Rep-2

description: control


title: NF54-T24-Rep-1

description: control


title: FE_Liver_Cont_Rep_1

value: liver

value: gestational day 17.5


title: dbp1∆::KANMX6 footprint

city: Berkeley

first: Gloria

middle: Ann

last: Brar

state: CA

address: 628 Barker Hall

department: MCB

institute: UC Berkeley

data_processing:
Library strategy: Ribosome profiling
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution.  Alignments of raw reads to SK1 genome. mRNA seq reads were processed similarly except not assigned to one genomic position and counts were rather distribute over the entire read.
Assembly: sk1_revised_100331 (fasta and gtf files published in Brar et. al, Science, 2012  and eisenberg et al., cell systems, 2020)
Supplementary files format and content: mRNA-seq or ribosome profiling footprint RPKM for ever gene with 50 or more raw reads

organism: Saccharomyces cerevisiae

source_name: budding yeast cells

growth_protocol: SK1 budding yeast cells were grown for meiosis experiment as done in Brar et al., 2012. Cells were collected at 4h after transfer into SPO media.

extract_protocol:
Cells were mixermilled with frozen buffer (20mM Tris pH8, 140mM KCl, 1.5mM MgCl2, 100ug/ml cycloheximide, 1% Trition X-100), buffer was thawed, spun at 3Kg  for 5 minutes, then supernatatant was spun at 20Kg for 10 minutes.
As described in Ingolia et al, Science 2009, except using the linker ligation strategy in place of polyA tailing and rRNA subtraction, both from Ingolia et al, Nature Protocols 2012

treatment_protocol: Cells were pretreated for 1 minute with 100uM cyclohexamide

value: budding yeast cells

value: cells were transferred to sporulation media to induce sporulation then collected 4h post transfer


title: Wild type mRNA

data_processing:
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution.  Alignments of raw reads to SK1 genome. mRNA seq reads were processed similarly except not assigned to one genomic position and counts were rather distribute over the entire read.
Assembly: sk1_revised_100331 (fasta and gtf files published in Brar et. al, Science, 2012  and eisenberg et al., cell systems, 2020)
Supplementary files format and content: mRNA-seq or ribosome profiling footprint RPKM for ever gene with 50 or more raw reads

value: Wild type


title: Wild type footprint


title: Dam_Liver_High_GenX_Rep_5

description: Gene expression data from dam liver tissue exposed to 10 mg/kg/day GenX

source_name: Dam (maternal) liver tissue exposed to 10 mg/kg/day GenX

value: GenX

value: 10 mg/kg/day


title: NF54-T12-Rep-2

description: control

value: whole body


title: NF54-T12-Rep-1

description: control

value: ring (T12)


title: Dam_Liver_High_GenX_Rep_2


title: Dam_Liver_High_GenX_Rep_4


title: lung, WT-2

city: Wuhan

first: Yiqi

last: Wang

state: State...

address: Shizishan Street

institute: Huazhong Agricultural University, China

description:
WT-C-2
PE150

data_processing:
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastq.
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2 (version 2.1.0).
Read count extraction and normalization were performed using DESeq2.
Assembly: mm10
Supplementary files format and content: RBM47count.txt: Tab-delimited text file includes RPKM values for each Sample.

source_name: Lung

growth_protocol: Mice 4 per cage with food and water, housing environment maintained at 22-24°C, 12-hour light/dark schedule (lights on at 6:00, lights off at 18:00).

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

treatment_protocol: No treatment

value: Lung

value: WT

value: 8 weeks


title: lung, WT-3

description:
WT-C-3
PE150


title: dbp1∆::KANMX6 mRNA


title: Dam_Liver_High_GenX_Rep_3


title: NF54-T6-Rep-2

description: control

value: wildtype

value: early ring (T6)


title: lung, WT-1

description:
WT-C-1
PE150


title: Dam_Liver_High_GenX_Rep_1


title: Dam_Liver_Low_GenX_Rep_2

description: Gene expression data from dam liver tissue exposed to 2 mg/kg/day GenX

source_name: Dam (maternal) liver tissue exposed to 2 mg/kg/day GenX

value: 2 mg/kg/day


title: NF54-T6-Rep-1

description: control


title: Dam_Liver_Low_GenX_Rep_5


title: Dam_Liver_Low_GenX_Rep_4


title: AD_13d-2

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

institute: ErasmusMC

description: hMSCs were treated 13 days with Adipogenic medium replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was background subtracted, vst transformation and a quantile normalization was applied. Probes that were detected at least once in the experiments (illumina detection p-value <0.01) were considered to be expressed and further analyzed for differential expression using Limma.

label_protocol: cDNA and Biotinylated cRNA were prepared with the Illumina Totalprep RNA Amplification kit (Ambion)

growth_protocol: aMEM, 20mM HEPES, strep/pen, 1.8 mM CaCl2, 10% HI-FCS. pH7.5 Osteogenic supplement :10 mM beta-glycerophosphate, 100 nM dexamethasone,  Adipogenic supplement :60 uM Indomethasin, 500 uM IBMX, 100 nM dexamethasone

extract_protocol: Total RNA extracted using Trizol (invitrogen)

treatment_protocol: aMEM 10%HI-FCS with Osteogenic differentiation supplement: 10 mM beta-glycerophosphate, 100 nM dexamethasone or Adipogenic differentiation supplement :60 uM Indomethasin, 500 uM IBMX, 100 nM dexamethasone

value: Male

value: Bone Marrow


title: Dam_Liver_Low_GenX_Rep_3

value: liver


title: Dam_Liver_Low_GenX_Rep_1

value: gestational day 17.5


title: AD_13d-1

description: hMSCs were treated 13 days with Adipogenic medium replicate 1


title: AD_13d-3

description: hMSCs were treated 13 days with Adipogenic medium replicate 3


title: lung, R/R-3

description:
HO-C-3
R/R
PE150


title: lung, R/R-1

description:
HO-C-1
R/R
PE150


title: Dam_Liver_High_PFOA_Rep_3

description: Gene expression data from dam liver tissue exposed to 5 mg/kg/day PFOA

source_name: Dam (maternal) liver tissue exposed to 5 mg/kg/day PFOA

value: PFOA

value: 5 mg/kg/day


title: Dam_Liver_High_PFOA_Rep_5


title: Dam_Liver_High_PFOA_Rep_2


title: Dam_Liver_High_PFOA_Rep_4


title: lung, R/R-2

description:
HO-C-2
R/R
PE150


title: Dam_Liver_High_PFOA_Rep_1


title: DR_ P7_Cisplatin_rep3

city: Tianjin

first: Hao

last: Zheng

address: Nankai University

department: college of life science

institute: Nankai University

data_processing:
RNA integrity was assessed using the Agilent Bioanalyzer 2100 system with the RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA).
Library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Assembly: hg38
Supplementary files format and content: comma-delimited text files include FPKM or TPM values for each sample.

source_name: CRC

growth_protocol: CRC organoids were maintained in DMEM F12 supplemented with other chemical reagents and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: CRC organoid were treated with chemotherapy drug (5-FU or Cisplatin) or DMSO as negative control  (Sigma),

value: CRC

value: CRC tumor organoid

value: Cisplatin


title: DR_ P7_5FU_rep3


title: DR_ P7_5FU_rep1


title: Parental_P7_rep2

value: DMSO


title: DR_ P7_Cisplatin_rep1


title: Parental_P7_rep3


title: Parental_P7_rep1


title: DR_ P1_Cisplatin_rep2


title: DR_ P1_Cisplatin_rep3


title: DR_ P1_5FU_rep3


title: DR_ P7_Cisplatin_rep2


title: DR_ P1_5FU_rep1


title: DR_ P7_5FU_rep2


title: H3T11D_H3

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

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 sacCer3 whole genome using bowtie v0.12.2 with parameters -q -p 5 -e 100 -y -a -m 10 --best --strata
Assembly: sacCer3
Supplementary files format and content: bw

source_name: genomic DNA

growth_protocol: Cells were grown in YPD until mid-log phase

extract_protocol:
Lysates were clarified from sonicated yeast cell pellets and histone-DNA complexes were isolated with indicated antibodies.
Libraries were prepared using the HTP KAPA kit

value: genomic DNA

value: H3 (Abcam,ab1791)


title: Dam_Liver_Low_PFOA_Rep_3

description: Gene expression data from dam liver tissue exposed to 1 mg/kg/day PFOA

source_name: Dam (maternal) liver tissue exposed to 1 mg/kg/day PFOA

value: 1 mg/kg/day


title: WT_H3


title: Dam_Liver_Low_PFOA_Rep_2


title: Dam_Liver_Cont_Rep_5

description: Gene expression data from dam liver tissue exposed to vehicle control

source_name: Dam (maternal) liver tissue exposed to vehicle control

value: Vehicle control

value: 0 mg/kg/day


title: Dam_Liver_Cont_Rep_4


title: Dam_Liver_Cont_Rep_3


title: Dam_Liver_Low_PFOA_Rep_5


title: Dam_Liver_Low_PFOA_Rep_4


title: Dam_Liver_Cont_Rep_1


title: DR_ P1_5FU_rep2

value: WT


title: Parental_P1_rep3


title: H3T11D_H3K79me3

value: H3K79me3 (Abclonal,A2369)


title: Parental_P1_rep1


title: Dam_Liver_Low_PFOA_Rep_1


title: Reb1_input

value: FLAG M2 (Sigma-Aldrich,F1804-1MG)


title: Dam_Liver_Cont_Rep_2


title: P39

value: no


title: Ctrol_input


title: Ctrol_IP


title: Progeny 5 of cross 2183, low-bruising group, biol rep 2

city: Lincoln

first: Susan

last: Thomson

address: 74 Gerald Street

department: New Cultivar Innovation

institute: The New Zealand Institute for Plant & Food Research LTD

data_processing:
Read quality assessed with FastQC v0.11.7
rRNA contaminants removed with SortMeRNA with default parameters
Trimming performed with Bbtools v37.93 BBDuk (forcetrimleft = 15, trimpolyg = 30, k = 13, qtrim = r, trimq = 10, minlength = 50)
Alignment to reference genome and counting number of reads aligned to each gene using STAR v2.6.1 (alignMatesGapMax = 20000, outQSconversionAdd = -31, outFilterScoreMinOverLread = 0, outFilterMatchNminOverLread = 0, outFilterMatchNmin = 40, alignSJDBoverhangMin = 10, alignIntronMax = 200000, quantMode = ‘GeneCounts’)
Genes with at least 5 samples with less than 5 reads were filtered out (using the R software)
Assembly: PGSC-DM (genome assembly version v4.03 and gene annotation v4.03)
Supplementary files format and content: Comma-delimited (csv) file contains raw read counts for each sample (rows = genes, columns = samples). First column corresponds to the gene ID

organism: Solanum tuberosum

source_name: tuber

extract_protocol:
RNA was extracted using the PureLink Plant RNA Reagent following manufacturer’s protocols, then incubating at -20degrees Celsuis for 3 hours in a lithium chloride solution
RNA libraries for ssRNA-Seq were prepared using a Lexogen SENSE mRNA polyA library, according to manufacturer’s protocols.

treatment_protocol: Tubers were bruised by letting a lead weight fall from controlled height on the tuber (zone of impact recorded by inking the weight before bruising)

value: tuber

value: mechanical impact (bruising)

tag: time

value: 2h post-bruising


title: Progeny 4 of cross 2183, low-bruising group, biol rep 2


title: Progeny 2 of cross 2183, low-bruising group, biol rep 1


title: Progeny 1 of cross 2183, low-bruising group, biol rep 1


title: P30


title: Progeny 6 of cross 2183, not used in DE analysis, biol rep 2


title: Parental_P1_rep2


title: Reb1_IP


title: H4K16ac_Pyk1ts


title: P24


title: P7


title: H4K16ac_WT

value: H4K16ac (EMD Millipore, 07-329)


title: Progeny 6 of cross 2177, high-bruising group, biol rep 2


title: Dibetic Nephropathy Male 06weeks Glomeruli replicate 2

city: Hamburg

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
Glomeruli were enriched by depleting the PT segment from the kidneys using Percoll density gradient centrifugation [12]. Both kidneys from each mouse were harvested, and the renal papilla of each kidney was removed. The renal tissue was minced into small pieces and transferred to a C tube (130-093-237, Miltenyi Biotec) filled with 5 ml of collagenase solution (1 mg/ml collagenase from Clostridium histolyticum [C9263, Sigma-Aldrich] and 0.25% bovine serum albumin [BSA] in DMEM/F-12 medium [11320074, Gibco]). The renal tissue was incubated at 37 °C for 5 min and homogenized using a gentleMACS™ Dissociator (Miltenyi Biotec) with the program “m. spleen 01_01”; this process was repeated once. Subsequently, the renal tissue was passed through a 250 µm sieve and separated by Percoll density gradient centrifugation using a solution that contained 45% Percoll® (GE17-0891-02, GE Healthcare) and 55% 2× PBS-glucose at 17,500 rpm for 15 min at 4 °C. Red blood cells were removed with a Percoll density gradient. PTs that accumulated in the interphase of the gradient were discarded. The rest of the kidney tissue that accumulated in the upper phase of the gradient was taken, washed twice in ice-cold HBSS and centrifuged at 400 ×g for 4 min at 4 °C. A single-cell suspension was prepared using CAP as described in previous studies [38]. The pellet was suspended in 2 ml of CAP solution (10 mg/ml Bacillus licheniformis protease [P5380, Sigma-Aldrich], 5 mM CaCl 2 , 20 U/ml DNase [4716728001, Roche] in PBS) for 20 min on ice with repeated trituration steps for 20 s every 5 min. The digestion was neutralized by 15 ml PBS supplemented with 10% FBS and passed through a 40 μm Corning® cell strainer. Cells were centrifuged at 400 ×g for 4 min at 4 °C and washed twice in 20 ml PBS supplemented with 0.5% BSA. Dead cells were removed with a dead cell removal kit (130-090-101, Miltenyi Biotec) according to the manufacturer’s protocol. The living cells were passed through a 30 µm cell strainer (04-004-2326, Sysmex), and the cell concentration was determined using a TC20™ automated cell counter (Bio-Rad).
The cells were loaded onto a 10x Genomics Chromium single-cell instrument. All steps were performed according to the standard protocol of the Chromium single-cell 3’ v2/v3 kits to generate high-quality cDNA libraries.

value: Glomeruli cells

value: kidney

value: BTBR ob/ob

value: 6 weeks


title: Dibetic Nephropathy Male 12weeks Glomeruli replicate 2

description: 10x Genomics

value: 12 weeks


title: P9

value: CRC

value: CRC tumor organoid


title: Dibetic Nephropathy Male 06weeks Glomeruli replicate 1

description: 10x Genomics


title: P5


title: P4


title: Progeny 3 of cross 2177, low-bruising group, biol rep 2


title: Input_Pyk1ts

value: genomic DNA


title: Input_WT BY4741


title: Dibetic Nephropathy Male 12weeks Glomeruli replicate 1

description: 10x Genomics


title: Progeny 2 of cross 2177, high-bruising group, biol rep 2


title: P1


title: Dibetic Nephropathy Female 06weeks Glomeruli replicate 2

description: 10x Genomics


title: shDAZL_6_rep1

city: BEIJING

first: XIAOYU

last: FENG

state: BEIJING

address: QINGHUAYUAN street，HAIDIAN distribute

institute: Tsinghua University

data_processing:
For RNA-seq data,  sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Trim galore (v0.6.4) with parameters  -q 25 --phred33 --stringency 3 --length 120. For miRNA-seq  sequenced reads were treated by Cutadapt (v1.18) with parameters -j 16  -a AAAAAAAAAA -u 3 --discard-untrimmed -m 15.
For RNA-seq data,reads were mapped to hg38 whole genome using Hisat2 (v2.1.0) with default parameters. For miRNA-seq, reads were mapped to  mirBase using bowtie  (1.0.0) with default parameters.
For RNA-seq, gene count and TPM value were calculated by Stringtie (2.1.4).
Assembly: hg38
Supplementary files format and content: For RNA-seq, tab-delimited text files include TPM values for each Sample .
Supplementary files format and content: For miRNA-seq, tab-delimited text files include counts for each Sample .

extract_protocol:
Total RNA was extracted using the TRIzol® Reagent (Life Technologies).
For RNA-seq, libraries were constructed by berrygenomic. For miRNA-seq, libraries were constructed  using SMARTer® smRNA-Seq Kit for Illumina (635030, TAKARA).

value: hPGCLCs derived from hESCs

value: DAZL KD

value: H1-shDAZL-GFP infection during differentiation


title: shDAZL_4_rep2


title: NHDF hnRNPC iCLIP (repl.3)

city: Brno

first: Vaclav

last: Hejret

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

data_processing:
bcl2fastq v. 2.20.0.422 software used for basecalling
Demultiplexing by inline 4-nt barcodes was perfromered using Cutadapt v1.15, 5-nt long UMIs were extracted using and afterwards deduplicated by UMI-tools v. 0.5.5
The adapters and quality trimming of raw fastq reads was performed using Trimmomatic v. 0.36
Trimmed iCLIP-Seq reads were mapped against the human genome (hg38) and Ensembl GRCh38 v.91 annotation using STAR v. 2.5.3a with default parameters default parameters except -outFilterMismatchNoverLmax 0.1 and -twopassMode Basic
PCR duplicates and multimapped reads were removed from the alignment and such filtered alignments were converted into bedgraphs genomic coverage tracks using deeptools bamCoverage v. 3.3.0 with settings -of bedgraph --binSize 1 --normalizeUsing None. Bedgraphs were further normalized on number of mapped reads per million (CPM).
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph files were generated using deeptools bamCoverage; Scores represent CPM normalized coverage of uniquelly mapped and deduplicated reads.

source_name: normal human dermal fibroblasts

growth_protocol: Normal Human Dermal Fibroblasts (NHDF) were grown in DMEM supplemented with FBS to 85-90% confluency. Three 150mm tissue culture dishes were used for each replicate of iCLIP.

extract_protocol:
hnRNPC-RNAs complex was resolved on a gradient NuPAGE gel and blotted onto nitrocellulose membrane. Post-autoradiography the membrane was cut between 48-100kDa size and Proteinase K treatment was performed to isolate RNA.  The reactions were stopped with 1V of Urea buffer and incubated for additional 20 min. RNA was purified by adding equal volumes of Phenol chloroform isoamylalcohol and precipitated with 3V of 100 % ethanol overnight at -20°C.
RNA pellets were washed 2x with ice cold 80% ethanol and resuspended in 8μl of RT annealing mixture. The samples were denatured three min at 70°C and cooled to 25°C for 10 min. 12 μl RT reaction mix was added and reverse transcription reaction was carried out. The samples were snap-chilled on ice and passed through the QIAquick columns (QIAGEN) following the manufacturer’s protocol. DNA was eluted in 20μl ddH2O. DNA circularization was carried in a final reaction volume of 40 μl of the circligaseII reaction mix at 60°C for 1hour. The circularised samples were supplemented with oligo annealing mix and incubated 4 min at 95°C. Post hybridization the reaction mix was supplemented with 3μl of BamHI and incubated for 1hour at 37°C. Linearized cDNA was further purified using the QIAquick columns. cDNA PCR amplification was carried out and the PCR products were resolved by a gel electrophoresis. The fragments of 180-300 bp were excised and purified. The purified library was analyzed by 75bp single end high-throughput sequencing at Illumina HiSeq2500

treatment_protocol: NHDFs were grown to 85-90% confluency and exposed to 150 mJ/cm2 at 254 nm in a Stratalinker 2400 on ice. Cell pellets were resuspended in 1ml of ice-cold lysis buffer (Supplementary Methods). The insoluble fraction was removed by centrifugation at 20.000g for 20 min at 4°C and the supernatant was used for the iCLIP experiment. Dynabeads Protein G (Invitrogen) (100 µl/sample) were incubated with 15 µg of anti hnRNPC1/C2 antibody (Santa Cruz) in a total volume of 100 µl of lysis buffer for 1 h at RT. Antibody coupled beads were mixed with 1ml of soluble cell lysate and incubated for 1hour on a rotator at 4°C. RNase I treatment and dephosphorylation  was carried out on the protein-RNA complex. Protein-RNA complex labeling was done using γ-ATP and 3’ end adapter ligation was performed.

value: normal human dermal fibroblasts


title: Progeny 8 of cross 2175, low-bruising group, biol rep 1


title: Progeny 1 of cross 2177, low-bruising group, biol rep 1


title: Progeny 7 of cross 2177, not used in DE analysis, biol rep 1


title: Dibetic Nephropathy Female 06weeks Glomeruli replicate 1

description: 10x Genomics


title: shDAZL_4_rep1


title: Progeny 7 of cross 2175, high-bruising group, biol rep 1


title: NHDF hnRNPC iCLIP (repl.1)


title: shLacz_rep2

value: wt

value: H1-shLACZ-GFP infection during differentiation


title: Control Male 12weeks Glomeruli replicate 2

description: 10x Genomics

value: BTBR +/+


title: Progeny 5 of cross 2177, not used in DE analysis, biol rep 1

value: tuber

value: mechanical impact (bruising)

value: 2h post-bruising


title: shDAZL_6_rep2


title: Control Male 12weeks Glomeruli replicate 1

description: 10x Genomics

value: Glomeruli cells

value: kidney


title: Progeny 5 of cross 2175, high-bruising group, biol rep 1


title: Dibetic Nephropathy Female 12weeks Glomeruli replicate 2

description: 10x Genomics

value: BTBR ob/ob


title: shLacz_rep1


title: Progeny 4 of cross 2175, low-bruising group, biol rep 1


title: HCT116 ATF4

city: Beijing

first: Zhimin

last: Jiang

address: Yuanmingyuang west road 2

institute: Chinese Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: HCT116 ATF4.bw (bigWig data)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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.

value: Human colorectal cancer


title: Control Male 06weeks Glomeruli replicate 1

description: 10x Genomics

value: 6 weeks


title: Progeny 3 of cross 2175, not used in DE analysis, biol rep 2


title: NHDF hnRNPC iCLIP (repl.2)


title: Control Female 12weeks Glomeruli replicate 2

description: 10x Genomics

value: 12 weeks


title: Progeny 2 of cross 2175, high-bruising group, biol rep 2


title: Progeny 1 of cross 2175, low-bruising group, biol rep 1


title: Control Female 06weeks Glomeruli replicate 2

description: 10x Genomics


title: Control Female 12weeks Glomeruli replicate 1

description: 10x Genomics


title: Progeny 7 of cross 2172, low-bruising group, biol rep 1


title: Progeny 6 of cross 2175, not used in DE analysis, biol rep 2


title: Progeny 6 of cross 2172, high-bruising group, biol rep 2


title: DR_ P1_Cisplatin_rep1

value: CRC

value: CRC tumor organoid

value: WT

value: Cisplatin


title: Control Male 06weeks Glomeruli replicate 2

description: 10x Genomics


title: Progeny 5 of cross 2172, not used in DE analysis, biol rep 1


title: Progeny 4 of cross 2172, low-bruising group, biol rep 2


title: Progeny 3 of cross 2172, high-bruising group, biol rep 1


title: WT_H3K79me3

value: genomic DNA

value: H3K79me3 (Abclonal,A2369)


title: OIA 5 TUM

data_processing:
Reads were mapped to the genome with Hisat version: 2.2.1
index was created with grcm38_snp_tran
Gene counts were created with gensum https://github.com/NKI-GCF/gensum using ensembl
Assembly: Mus_musculus.GRCm38_100
Supplementary files format and content: ensembl gene id vs 10 samples plus gene annotation columns

extract_protocol:
Based on the amount of cells homogenized in the RLT buffer (79216, Qiagen), the total RNA was isolated using the RNeasy Mini Kit (74106, Qiagen) and RNeasy Micro Kit (74004, Qiagen), including an on column DNase digestion (79254, Qiagen), according to the manufacturer’s instructions. Quality and quantity of the total RNA was assessed on the 2100 Bioanalyzer instrument following manufacturer’s instructions “Agilent RNA 6000 Nano” (G2938-90034, Agilent Technologies) and “Agilent RNA 6000 Pico” (G2938-90046, Agilent Technologies). Total RNA samples having RIN>7 were subjected to TruSeq stranded mRNA library preparation, according to the manufacturer's instructions (Document # 1000000040498 v00 , Illumina). The stranded mRNA libraries were analyzed on a 2100 Bioanalyzer instrument following the manufacturer’s protocol “Agilent DNA 7500 kit” (G2938-90024, Agilent Technologies), diluted to 10nM and pooled equimolar into multiplex sequencing pools for sequencing on the HiSeq 2500 and NovaSeq 6000 Illumina sequencing platforms. NovaSeq 6000 paired-end sequencing was performed using 54 cycles for Read 1, 19 cycles for Read i7, 10 cycles for Read i5 and 54 cycles for Read 2, using the NovaSeq6000 SP Reagent Kit v1.5 (100 cycles) (20028401, Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mammary gland

value: ILC tumor cells (10-SJK-221)

value: co-culture 5:fibroblasts + tumor cells (10-SJK-221)


title: Gastrocnemius EXO, biological rep3

city: Barcelona

first: Carlos

last: Castaño

address: Rossello 153

country: Spain

institute: CIBER

description: Gene expression data from Gastrocnemius of EXO mice.

hyb_protocol: Following fragmentation and terminal labeling,  ss-cDNA was hybridized for 17hr at 45ºC on Clariom™ S  HT, mouse array plate, using the automated GeneTitan System (Affymetrix), which includes the hybridization oven, Fluidic Station and Scanner.

scan_protocol: Chips were scanned using the Scanner of the GeneTitan System.

data_processing: Transcriptome Analysis Console 4.0 Software. Summarization Method: Gene Level-SST-RMA. Gene-Level Fold Change < -1,5 or > 1,5. Gene-Level P-Value < 0,05. Anova Method: ebayes

label_protocol: 150 ng of good quality RNA samples (RIN >8) with a Ratio 260/280 = 1.8-2 were used.  Fragmentation and Biotin labelling of ss-cDNA was prepared according to Affymetrix WT PLUS Reagent Kit user guide, using an automated system (Biomek FX System, Beckman Coulter).

growth_protocol: 15 weeks old male mice were fed chow diet or a high-fat diet (45% lipids) for 10 weeks and then treated for the next 4 weeks as described below.

extract_protocol: Total RNA was extracted from frozen liver, sWAT and gastrocnemius muscle with miRNeasy Mini Kit and treated with DNAse, following standard procedures.

treatment_protocol: CT mice were fed chow diet throughout the procedure. HFD mice were fed high-fat diet and remained untreated throughout the procedure. HIIT mice were fed high-fat diet and subjected to a HIIT protocol for the last 4 weeks. EXO mice were fed high-fat diet and injected through the tail vein with exosomes isolated from plasma of control mice and transfected with miR-122 and miR-192 antimiRs and miR-133b mimic, for the last 4 weeks for a total of 8 injections.

value: Gastrocnemius

value: high-fat diet + exosomes

tag: background strain

tag: Sex

value: male


title: Gastrocnemius EXO, biological rep4


title: Progeny 1 of cross 2172, not used in DE analysis, biol rep 1

value: tuber

value: mechanical impact (bruising)

value: 2h post-bruising


title: Progeny 8 of cross 2170, low-bruising group, biol rep 2


title: CD26+ NFs + CM 13/138, sample 18

description: sample 18

data_processing:
Reads were mapped to the genome with Hisat version: 2.1.0
Read counts were determined with Icount, which is based on HTSeq-count, using mode union
Assembly: Mus_musculus.GRCm38_87
Supplementary files format and content: ensembl gene id vs 18 samples plus gene annotation columns

extract_protocol:
Based on the amount of cells homogenized in the RLT buffer (79216, Qiagen), the total RNA was isolated using the RNeasy Mini Kit (74106, Qiagen) and RNeasy Micro Kit (74004, Qiagen), including an on column DNase digestion (79254, Qiagen), according to the manufacturer’s instructions. Quality and quantity of the total RNA was assessed on the 2100 Bioanalyzer instrument following manufacturer’s instructions “Agilent RNA 6000 Nano” (G2938-90034, Agilent Technologies) and “Agilent RNA 6000 Pico” (G2938-90046, Agilent Technologies). Total RNA samples having RIN>7 were subjected to TruSeq stranded mRNA library preparation, according to the manufacturer's instructions (Document # 1000000040498 v00 , Illumina). The stranded mRNA libraries were analyzed on a 2100 Bioanalyzer instrument following the manufacturer’s protocol “Agilent DNA 7500 kit” (G2938-90024, Agilent Technologies), diluted to 10nM and pooled equimolar into multiplex sequencing pools for sequencing on the HiSeq 2500 and NovaSeq 6000 Illumina sequencing platforms. HiSeq 2500 single-end sequencing was performed using 65 cycles for Read 1, 10 cycles for Read i7, using HiSeq SR Cluster Kit v4 cBot (GD-401-4001, Illumina) and HiSeq SBS Kit V4 50 cycle kit (FC-401-4002, Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD26+ fibroblasts

value: FVB/n

value: conditioned medium from WEPtn 13-MCB-138


title: CD26+ NFs + CM 13/90, sample 17

description: sample 17

value: conditioned medium from WEPtn 13-MCB-90


title: Gastrocnemius EXO, biological rep1


title: Gastrocnemius HIIT, biological rep4

description: Gene expression data from Gastrocnemius of HIIT mice.

value: high-fat diet + exercise


title: Gastrocnemius EXO, biological rep2


title: Gastrocnemius HFD, biological rep4

description: Gene expression data from Gastrocnemius of HFD mice.

value: high-fat diet


title: Gastrocnemius HIIT, biological rep2


title: Progeny 7 of cross 2170, low-bruising group, biol rep 2


title: Gastrocnemius HIIT, biological rep3


title: OIA 5 Tom+

value: CD26- fibroblasts

value: mTmG


title: OIA 5 GFP+

value: mammary gland


title: Gastrocnemius HIIT, biological rep1


title: OIA 4 TUM

value: ILC tumor cells (13-MCB-17)

value: co-culture 4:fibroblasts + tumor cells (13-MCB-17)


title: Progeny 2 of cross 2172, not used in DE analysis, biol rep 2


title: Control Female 06weeks Glomeruli replicate 1

description: 10x Genomics

value: Glomeruli cells

value: kidney

tag: strain

value: BTBR +/+

value: 6 weeks


title: CD26+ NFs + CM 18/12, sample 15

description: sample 15

tag: genotype

value: conditioned medium from WEPtn 18-MCB-12


title: Progeny 6 of cross 2170, not used in DE analysis, biol rep 2

value: tuber

value: mechanical impact (bruising)

value: 2h post-bruising


title: Gastrocnemius HFD, biological rep1

value: Gastrocnemius

value: male


title: OIA 4 GFP+

tag: cell type

value: CD26+ fibroblasts


title: CD26+ NFs + CM 10/221, sample 14

description: sample 14

value: FVB/n

value: conditioned medium from WEPtn 10-SJK-221


title: Gastrocnemius HFD, biological rep2

value: high-fat diet


title: Progeny 5 of cross 2170, low-bruising group, biol rep 1


title: CD26+ NFs + CM 13/44, sample 16

description: sample 16

value: mammary gland

value: conditioned medium from WEPtn 13-MCB-44


title: Gastrocnemius CT, biological rep4

description: Gene expression data from Gastrocnemius of CT mice.

value: chow diet


title: CD26+ NFs + CM 13/17, sample 13

description: sample 13

value: conditioned medium from WEPtn 13-MCB-17


title: OIA 4 Tom+

value: CD26- fibroblasts

value: mTmG

value: co-culture 4:fibroblasts + tumor cells (13-MCB-17)


title: Gastrocnemius HFD, biological rep3


title: Progeny 4 of cross 2170, low-bruising group, biol rep 1


title: Progeny 3 of cross 2170, low-bruising group, biol rep 1


title: OIA 3 TUM

value: ILC tumor cells (10-SJK-221)

value: co-culture 3:tumor cells alone


title: OIA 2 TUM

value: ILC tumor cells (13-MCB-17)

value: co-culture 2:tumor cells alone


title: Progeny 1 of cross 2170, low-bruising group, biol rep 1

value: tuber

value: mechanical impact (bruising)

value: 2h post-bruising


title: CD26- NFs + CM 13/138, sample 9

description: sample 9

value: FVB/n

value: conditioned medium from WEPtn 13-MCB-138


title: CD26+ NFs control, sample 11

description: sample 11

value: CD26+ fibroblasts

value: control conditioned medium


title: Gastrocnemius CT, biological rep2

value: Gastrocnemius

value: male


title: Gastrocnemius CT, biological rep3

value: chow diet


title: CD26+ NFs control, sample 10

description: sample 10

value: mammary gland


title: Progeny 8 of cross 2168, high-bruising group, biol rep 1


title: Progeny 6 of cross 2168, high-bruising group, biol rep 2


title: OIA 1 Tom+

value: CD26- fibroblasts

value: mTmG

value: co-culture 1:fibroblasts alone


title: CD26+ NFs control, sample 12

description: sample 12


title: Gastrocnemius CT, biological rep1


title: CD26- NFs + CM 13/90, sample 8

description: sample 8

value: conditioned medium from WEPtn 13-MCB-90


title: Progeny 2 of cross 2170, low-bruising group, biol rep 1


title: Progeny 4 of cross 2168, not used in DE analysis, biol rep 2


title: Progeny 5 of cross 2168, low-bruising group, biol rep 2


title: Myc #69 (8x8) CD26+ fibroblasts

data_processing:
Reads were mapped to the genome with Hisat version: 2.2.1
index was created with grcm38_snp_tran
Gene counts were created with gensum https://github.com/NKI-GCF/gensum using ensembl
Assembly: Mus_musculus.GRCm38_100
Supplementary files format and content: ensembl gene id vs 43 samples plus gene annotation columns

value: fibroblasts

value: WB1P-Myc transplanted


title: Myc #69 (8x8) -/- fibroblasts


title: CD26- NFs + CM 13/44, sample 7

description: sample 7

value: conditioned medium from WEPtn 13-MCB-44


title: Myc #69 (8x8) EN1+ fibroblasts


title: Myc #69 (8x8) +/+ fibroblasts


title: sWAT EXO, biological rep3

description: Gene expression data from sWAT of EXO mice.

value: sWAT

value: high-fat diet + exosomes


title: CD26- NFs + CM 18/12, sample 6

description: sample 6

value: FVB/n

value: conditioned medium from WEPtn 18-MCB-12


title: sWAT EXO, biological rep4


title: Progeny 3 of cross 2168, high-bruising group, biol rep 1

value: tuber

value: mechanical impact (bruising)

value: 2h post-bruising


title: Myc #23 (8x8) -/- fibroblasts


title: sWAT EXO, biological rep1

value: male


title: CD26- NFs + CM 13/17, sample 4

description: sample 4

value: conditioned medium from WEPtn 13-MCB-17


title: OIA 1 GFP+

value: mammary gland

value: CD26+ fibroblasts


title: sWAT EXO, biological rep2


title: sWAT HIIT, biological rep3

description: Gene expression data from sWAT of HIIT mice.

value: high-fat diet + exercise


title: sWAT HIIT, biological rep4


title: CD26- NFs control, sample 3

description: sample 3

value: CD26- fibroblasts

value: control conditioned medium


title: Myc #23 (8x8) +/+ fibroblasts

value: fibroblasts


title: CD26- NFs + CM 10/221, sample 5

description: sample 5

value: conditioned medium from WEPtn 10-SJK-221


title: Myc #23 (8x8) CD26+ fibroblasts

value: WB1P-Myc transplanted


title: CD26- NFs control, sample 2

description: sample 2


title: Progeny 1 of cross 2168, low-bruising group, biol rep 1


title: Progeny 10 of cross 2165, high-bruising group, biol rep 1


title: Myc #23 (8x8) EN1+ fibroblasts


title: CD26- NFs control, sample 1

description: sample 1


title: Progeny 9 of cross 2165, high-bruising group, biol rep 1


title: sWAT HIIT, biological rep2

value: sWAT


title: sWAT HIIT, biological rep1


title: sWAT HFD, biological rep4

description: Gene expression data from sWAT of HFD mice.

value: high-fat diet


title: Myc #95 +/+ fibroblasts


title: Progeny 7 of cross 2165, high-bruising group, biol rep 1


title: Myc #95 -/- fibroblasts


title: Progeny 2 of cross 2168, high-bruising group, biol rep 2


title: WB1P-Myc sample 3 hiseq

description:
counts_4880_4954_houthuijzen.txt
adata_4880_4954_houthuijzen.h5

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using dropseq_tools versions 1.12
Assembly: mm10
Supplementary files format and content: counts of gene symbol vs. cell per sample
Supplementary files format and content: matrix of counts of gene symbol vs. cell
Supplementary files format and content: h5 format object with annotations for paper made with scanpy

extract_protocol:
Single cell suspensions of the tumors were sorted by FACS to isolate live single cells (FSC-A x FSC-H to define singlets, dapi-negative cells to define live cells). After sorting the cells were subjected to Dropseq RNA sequencing according to the protocol of Macosko et al.[61] using WB1P cells (275 cells/ul) and WB1P-Myc cells (270 cells/ul) both in 1xPBS+0.01%BSA. Dropseq beads ’MACOSKO-2011-10’ were purchased from ChemGenes. Ready-made Drop-Seq microfluidic devices were purchased from Nanoshift. During droplet generation, of both samples multiple 5 minute fractions of droplets were collected and based on droplet quality assessment for each sample 4 fractions were selected for further processing according to “Drop-seq laboratory protocol v3.1”. After breakage, reverse transcription and Exocuclease I treatment, of each fraction the cDNA was amplified in triplicate PCR reactions.
After PCR the amplified cDNA products were pooled, cleaned by a 0.6X AMPure XP bead cleanup and quantified on a 2100 Bioanalyzer Instrument following the manufacturer’s protocol “Agilent High Sensitivity DNA Kit” (G2938-90321, Agilent Technologies). This procedure was done twice for every fraction selected. The amplified cDNA product was concentrated by speedvac and all was used as input for the final Nextera XT library preparations. All Libraries were quantified on a 2100 Bioanalyzer Instrument following the manufacturer’s protocol “Agilent High Sensitivity DNA Kit” and diluted to 10 nM before paired-end sequencing on the MiSeq and HiSeq2500 Illumina sequencing platforms. Sequencing was performed using 25 cycles for Read 1, 8 cycles for Read i7 and 117 cycles for Read 2, using MiSeq Reagent Kit v3 (150-cycle) (MS-102-3001, Illumina), HiSeq PE Rapid Cluster Kit v2 (PE-402-4002, Ilumina) and HiSeq Rapid SBS Kit v2 (200 cycles) (FC-402-4021, Illumina). Sequencing was performed on the MiSeq and HiSeq2500 Illumina sequencing platforms.

value: tumor WB1P-Myc


title: Progeny 6 of cross 2165, low-bruising group, biol rep 1


title: Myc #67 -/- fibroblasts


title: WB1P-Myc sample 4 hiseq


title: Myc #67 +/+ fibroblasts


title: WB1P-Myc sample 2 hiseq


title: Progeny 5 of cross 2165, high-bruising group, biol rep 1


title: WB1P-Myc sample 1 hiseq


title: sWAT HFD, biological rep3


title: sWAT HFD, biological rep2


title: Progeny 4 of cross 2165, high-bruising group, biol rep 1


title: WB1P sample 4 hiseq

value: tumor WB1P


title: Myc #67 EN1+ fibroblasts


title: Myc #21 -/- fibroblasts


title: Progeny 3 of cross 2165, high-bruising group, biol rep 1

value: tuber


title: sWAT CT, biological rep4

description: Gene expression data from sWAT of CT mice.

value: chow diet


title: sWAT CT, biological rep3


title: Myc #21 +/+ fibroblasts


title: Progeny 2 of cross 2165, high-bruising group, biol rep 2

value: mechanical impact (bruising)

value: 2h post-bruising


title: WB1P sample 2 hiseq


title: sWAT HFD, biological rep1

value: male


title: sWAT CT, biological rep2


title: Myc #21 CD26+ fibroblasts

value: mammary gland


title: Progeny 1 of cross 2165, low-bruising group, biol rep 1


title: sWAT CT, biological rep1


title: WB1P sample 1 hiseq


title: WB1P #35 -/- fibroblasts

value: WB1P transplanted


title: Progeny 16 of cross 2159, not used in DE analysis, biol rep 1


title: WB1P #35 +/+ fibroblasts


title: Progeny 14 of cross 2159, high-bruising group, biol rep 1


title: Liver EXO, biological rep4

description: Gene expression data from liver of EXO mice.

value: Liver

value: high-fat diet + exosomes


title: Dibetic Nephropathy Female 12weeks Glomeruli replicate 1

description: 10x Genomics

value: Glomeruli cells

value: kidney

value: BTBR ob/ob

value: 12 weeks


title: WB1P #35 CD26+ fibroblasts

value: fibroblasts


title: Progeny 15 of cross 2159, not used in DE analysis, biol rep 2


title: WB1P sample 3 hiseq


title: WB1P #35 EN1+ fibroblasts


title: Progeny 12 of cross 2159, high-bruising group, biol rep 1


title: Progeny 13 of cross 2159, low-bruising group, biol rep 1


title: Progeny 11 of cross 2159, low-bruising group, biol rep 2


title: WB1P #14 -/- fibroblasts


title: Liver EXO, biological rep3


title: Liver EXO, biological rep1


title: Liver EXO, biological rep2


title: Liver HIIT, biological rep4

description: Gene expression data from liver of HIIT mice.

value: high-fat diet + exercise


title: Liver HIIT, biological rep3


title: Progeny 10 of cross 2159, not used in DE analysis, biol rep 1


title: WB1P #14 CD26+ fibroblasts


title: Progeny 9 of cross 2159, high-bruising group, biol rep 1


title: Progeny 8 of cross 2159, low-bruising group, biol rep 2


title: WB1P #14 EN1+ fibroblasts


title: WB1P #12 R4 -/- fibroblasts


title: Liver HIIT, biological rep2


title: Progeny 7 of cross 2159, low-bruising group, biol rep 1


title: WB1P #12 R4 EN1+ fibroblasts


title: Progeny 6 of cross 2159, high-bruising group, biol rep 2


title: WB1P #12 R4 +/+ fibroblasts


title: Progeny 5 of cross 2159, not used in DE analysis, biol rep 2


title: Liver HIIT, biological rep1


title: Liver HFD, biological rep2

description: Gene expression data from liver of HFD mice.

value: high-fat diet


title: Liver HFD, biological rep1


title: Liver CT, biological rep4

description: Gene expression data from liver of CT mice.


title: WB1P #14 +/+ fibroblasts


title: Progeny 4 of cross 2159, high-bruising group, biol rep 1


title: WB1P #93 -/- fibroblasts


title: WB1P #93 +/+ fibroblasts


title: Progeny 2 of cross 2159, low-bruising group, biol rep 1


title: Progeny 3 of cross 2159, low-bruising group, biol rep 1


title: Progeny 1 of cross 2159, low-bruising group, biol rep 2


title: Liver CT, biological rep3


title: Liver HFD, biological rep3

description:
Gene expression data from liver of HFD mice.
This sample failed quality control and was not included in the analysis.


title: WB1P #93 CD26+ fibroblasts


title: WB1P #93 EN1+ fibroblasts


title: wildtype 44/46 -/- fibroblasts

value: control transplanted


title: Liver CT, biological rep2


title: WB1P #10 EN1+ fibroblasts


title: Progeny 15 of cross 2158, low-bruising group, biol rep 1

value: tuber


title: wildtype 44/46 +/+ fibroblasts


title: 69 DAA biol rep 1

city: Haikou

first: Junjie

last: Peng

address: renmmin 58 street

institute: Hainan university

data_processing: After the library was constructed, real-time PCR, a Qubit 2.0 fluorometer, and an Agilent 2100 bioanalyzer were used for quality inspection.Transcriptome sequencing was performed on the Illumina HiSeq platform after the library was qualified. Then, the raw reads were filtered to remove low-quality reads with adapters to obtain clean reads.  Trinity software was used to splice clean reads, and Corset (https://code.google.com/p/corset-project/) was used to perform hierarchical clustering on the number of reads and expression patterns of the aligned transcripts. The obtained data were stored in FASTA format, and the longest transcript obtained after hierarchical clustering was used as a unigene.  Unigenes were compared to the KEGG, NR, Swiss-Prot, GO, COG/KOG, and TrEMB databases using BLAST software, and the predicted amino acid sequences of unigenes were compared to the Pfam database using HMMER software to obtain annotation information. RSEM software was used for mapping, and fragments per kilobase of transcript per million fragments mapped (FPKM) was used to calculate the expression of unigenes.

organism: Litchi chinensis

source_name: fruit pulp

growth_protocol: Under natural growing conditions

extract_protocol:
RNA was harvested using RNAprep Pure Plant Plus Kit (Tiangen Biochemical Technology Co., Ltd.)
RNA libraries were constructed by Wuhan Metwell Biotechnology Co. Ltd

treatment_protocol: non-treatment

value: fruit pulp

value: Flesh cell

value: WT

tag: timepoint

value: 69 DAA


title: 69 DAA biol rep 2


title: 63 DAA biol rep 3

value: 63 DAA


title: 69 DAA biol rep 3


title: Progeny 13 of cross 2158, not used in DE analysis, biol rep 2

value: mechanical impact (bruising)

value: 2h post-bruising


title: 63 DAA biol rep 1


title: Liver CT, biological rep1

value: Liver

value: chow diet

value: male


title: Progeny 14 of cross 2158, not used in DE analysis, biol rep 2


title: Progeny 11 of cross 2158, low-bruising group, biol rep 1


title: Liver HFD, biological rep4


title: wildtype 44/46 CD26+ fibroblasts

value: mammary gland


title: 35 DAA biol rep 3

value: 35 DAA


title: wildtype 44/46 EN1+ fibroblasts

value: fibroblasts


title: Progeny 10 of cross 2158, not used in DE analysis, biol rep 2


title: 35 DAA biol rep 2


title: Progeny 8 of cross 2158, low-bruising group, biol rep 1


title: 35 DAA biol rep 1


title: wildtype 49/52 CD26+ fibroblasts


title: wildtype 49/52 +/+ fibroblasts


title: Progeny 7 of cross 2158, high-bruising group, biol rep 1


title: 300719_PY04_Somatic

city: Dunedin

first: Donna

last: Bond

address: 270 Great King Street

institute: University of Otago

data_processing:
Raw reads were trimmed using Trim Galore! (v0.4.2) by removing 10 bp from the 5’ end of all reads and removing low-quality base calls (Phred score < 20). Bismark (v0.19.0), with the -pbat option, was used to map the trimmed reads to the possum genome reference (GCA_011100635). The Bismark output report was used to determine the global methylation in the CG dinucleotide context (calculated as the proportion of total methylated cytosines over total cytosines). The bisulfite non-conversion rate was estimated by calculating the proportion of non-CG methylation.
Assembly: Trichosurus vulpecula (GCA_011100635.1)
Supplementary files format and content: tab-delimited text file that includes Bismark mapping report for each sample

source_name: Somatic

extract_protocol:
Gonads were collected from male pouch young aged between 7 and 106 days postpartum (n=17). Germ cells were isolated from gonads using the isolation protocol outlined in Suzuki et al (2013; PMID: 23732002). The resulting pellet was resuspended in Zombie Near-Infra Red Viability Dye (BioLegend) and incubated at room temperature for 20 min. The lysate was washed in 5 % FBS (in PBS), then resuspended in SSEA1 monoclonal antibody (Invitrogen, MC-480) conjugated to DyLight 488 (1:300 in PBS/5% FBS; Invitrogen, MA1-022-D488) on ice for 30 min. The lysate was then washed, resuspended in sort buffer (5% FBS, 0.5 mM EDTA in PBS) and kept on ice prior to cell sorting. Germ cells were isolated from the cell lysate using a BD FACSAria Fusion which detects GFP using a 488 argon laser (BD Biosciences). A gonadal cell profile was produced using forward scatter (FSC) and side scatter (SSC) and was gated to exclude doublets and dead cells. GFP-negative cells (somatic cells) were sorted as negative controls into 0.2 % Triton-X and stored at -80 °C.
Bisulfite conversion and library preparation from low cell input followed the single cell bisulfite sequencing protocol by Clark et al., 2017 (PMID: 28182018)

value: Male

value: Somatic

value: 106 days postpartum

value: GFP (SSEA1) negative

tag: number of_cells


title: wildtype 49/52 EN1+ fibroblasts

value: control transplanted


title: NL3

city: Birmingham

first: Ravi

last: Bhatia

state: Alabama

address: 1824 6th Avenue South

department: Hematology/Oncology

institute: University of Alabama at Birmingham

description: Normal c-KitLow LT-HSC_3

data_processing:
DRAGEN Host Software Version 01.011.222.02.04.04.36875 was used for basecalling
STAR version 2.5.3a aligned the sequences using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated with HTSeq-count version 0.9.1 using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Normalization and differential expression of transcript abundances were calculated using DESeq2 version 1.22.2 using their default parameters in their vignette
Genome_build: Gencode mouse GRCm38 p4 Release M11
Supplementary_files_format_and_content: tab-delimited Excel file containing Ensembl IDs and raw transcript abundances for each gene in each sample

source_name: Normal c-KitLow LT-HSC_3

extract_protocol:
c-KitLow and c-KitHigh LT-HSCs from the BM of normal B6 and leukemic Scl-tTA-BCR-ABL mice were sorted, RNA extracted using RNeasy Plus Micro kit (Cat#74004, Qiagen, Valencia, CA), with four biological replicates from each group.
Sequencing libraries were prepared with the SMARTer Ultra Low Input RNA Kit for Sequencing (v4, TaKaRa Clontech, catalog no. 634891) and Nextera XT DNA Library Preparation Kit (96 samples, Illumina, cat no. FC-131-1096).
Sequencing was performed using the HiSeq 2500 platform with the HiSeq SBS Kit V4 (Illumina). STAR (version 2.5.3a) was used to align raw RNA-Seq FASTQ reads to the mouse reference genome (Gencode Release M11), and number of reads mapping to each gene enumerated using HTSeq-count50.

value: Hematopeitic stem cell


title: 63 DAA biol rep 2

value: fruit pulp

value: Flesh cell

value: WT


title: 300719_PY04_PGC

source_name: PGC

extract_protocol:
Gonads were collected from male pouch young aged between 7 and 106 days postpartum (n=17). Germ cells were isolated from gonads using the isolation protocol outlined in Suzuki et al (2013; PMID: 23732002). The resulting pellet was resuspended in Zombie Near-Infra Red Viability Dye (BioLegend) and incubated at room temperature for 20 min. The lysate was washed in 5 % FBS (in PBS), then resuspended in SSEA1 monoclonal antibody (Invitrogen, MC-480) conjugated to DyLight 488 (1:300 in PBS/5% FBS; Invitrogen, MA1-022-D488) on ice for 30 min. The lysate was then washed, resuspended in sort buffer (5% FBS, 0.5 mM EDTA in PBS) and kept on ice prior to cell sorting. Germ cells were isolated from the cell lysate using a BD FACSAria Fusion which detects GFP using a 488 argon laser (BD Biosciences). A gonadal cell profile was produced using forward scatter (FSC) and side scatter (SSC) and was gated to exclude doublets and dead cells. Germ cells were identified as a small subpopulation that were very bright (GFP >10^4) with higher SSC (approx. 0.1 % of total cells). This population was gated conservatively, sorted into 0.2 % Triton-X and stored at -80 °C.
Bisulfite conversion and library preparation from low cell input followed the single cell bisulfite sequencing protocol by Clark et al., 2017 (PMID: 28182018)

value: PGC

value: GFP (SSEA1) sorted


title: wildtype 82/83 -/- fibroblasts

source_name: mammary gland


title: NL2

description: Normal c-KitLow LT-HSC_2

source_name: Normal c-KitLow LT-HSC_2


title: 140720_PY01_Somatic

value: 102 days postpartum


title: Progeny 4 of cross 2158, not used in DE analysis, biol rep 2

value: tuber

value: mechanical impact (bruising)

value: 2h post-bruising


title: NL1

description: Normal c-KitLow LT-HSC_1

source_name: Normal c-KitLow LT-HSC_1


title: Progeny 5 of cross 2158, low-bruising group, biol rep 1


title: Progeny 2 of cross 2158, low-bruising group, biol rep 1


title: NH3

description: Normal c-KitHigh LT-HSC_3

source_name: Normal c-KitHigh LT-HSC_3


title: wildtype 49/52 -/- fibroblasts

value: mammary gland


title: Progeny 3 of cross 2158, high-bruising group, biol rep 1


title: wildtype 82/83 +/+ fibroblasts

value: fibroblasts


title: wildtype 82/83 CD26+ fibroblasts


title: Progeny 1 of cross 2158, low-bruising group, biol rep 2


title: 300719_PY02_Somatic

value: Male

value: 91 days postpartum


title: NH2

description: Normal c-KitHigh LT-HSC_2

source_name: Normal c-KitHigh LT-HSC_2


title: 300719_PY02_PGC


title: wildtype 82/83 EN1+ fibroblasts


title: PR8 + MRSA #10 (P+M10)

city: Aurora

first: Christophe

last: Langouët-Astrié

institute: University of Colorado Denver, Anschutz

description: Gene expression data from total lungs treated with IN PR8 on D0 and IT MRSA on D10

data_processing:
Illumina reads were trimmed for adaptor sequence and for quality in CLC Genomics Workbench (v.21.0.5)
Trimmed sequences were mapped to to the reference genome sequence of Mus musculus assembly mm10, with the parameters: mismatch cost, 2; insertion and deletion cost, 3; length and similarity fraction, 0.8.
Uniquely mapped transcripts from each sample were exported from CLC Genomics Workbench and used for normalization and differential gene expression analysis with an R package, DESeq2 version 1.32.0
Assembly: mm10
Supplementary files format and content: MRSA_gene_exp_diff contains differential gene expression between MRSA vs Control treatment. PR8_gene_exp_diff contains differential gene expression between PR8 vs Control treatment. PR8MRSA_gene_exp_diff contains differential gene expression between PR8+MRSA vs Control treatment. All files includes mouse gene names, baseMean, log2FoldChange, IfcSE, stat, pvalue, padj. Raw_gene_counts_matrix contains uniquely mapped transcripts for each sample with gene name and ENSEMBL ID.

source_name: Lung

growth_protocol: USA300 was cultured in TSB from frozen stock for 18-24 hours. Overnight culture was diluted 1:50 and was incubated for 2.5 hours. Samples were centrifuged for 15 min at 4°C, then the pellet was resuspended in PBS,  centrifuged for 3 min at room temperature, and resuspended in saline. The opitical density of the bacterial suspension was measured and diluted three times to ensure bacterial samples were at desired optical density and bacterial concentration (1*10^8 CFU/30uL). Serial dilutions of the bacterial suspension was plated on TSB plates in triplicate and incubated for 24 hours at 37°C to confirm bacterial concentration.

extract_protocol:
Lungs were removed, snap frozen, homogenized, and RNA isolated using Qiagen RNeasy Midi Kit (Cat#75144).
RNA libraries were prepared using Zymo-Seq RiboFree Total RNA Library Kit (Cat#R3000) with 1 ug of total RNA for the construction of sequencing libraries. Invitrogen ERCC spike in controls (Cat#4456740) were added to all samples

treatment_protocol: Mice were intranasally (IN) administered with saline or PR8 (30k FFU). 10 days (D10) post-IN administration, mice were intratracheally (IT) administered saline or MRSA (1*10^8 CFU/30uL) and were left to recover for 24 hours.

value: Lung

tag: gender


title: NH1

description: Normal c-KitHigh LT-HSC_1

source_name: Normal c-KitHigh LT-HSC_1


title: Progeny 6 of cross 2158, not used in DE analysis, biol rep 1

tag: treatment


title: Progeny 13 of cross 2155, not used in DE analysis, biol rep 1


title: PR8 + MRSA #8 (P+M8)


title: PR8 + MRSA #7 (P+M7)


title: 040822_PY02_PGC

value: 76 days postpartum


title: Progeny 12 of cross 2155, not used in DE analysis, biol rep 2


title: 140720_PY01_PGC


title: 280520_PY01_Somatic

value: Somatic

value: 69 days postpartum

value: GFP (SSEA1) negative


title: PR8 + MRSA #5 (P+M5)


title: 280520_PY01_PGC


title: CL2

description: CML c-KitLow LSC_2

source_name: CML c-KitLow LSC_2

value: Leukemic stem cells


title: CL1

description: CML c-KitLow LSC_1

source_name: CML c-KitLow LSC_1


title: Progeny 11 of cross 2155, high-bruising group, biol rep 1


title: Progeny 10 of cross 2155, low-bruising group, biol rep 2


title: CH2

description: CML c-KitHigh LSC_2

source_name: CML c-KitHigh LSC_2


title: CH3

description: CML c-KitHigh LSC_3

source_name: CML c-KitHigh LSC_3


title: CL3

description: CML c-KitLow LSC_3

source_name: CML c-KitLow LSC_3


title: 270520_PY01_Somatic

value: 63 days postpartum


title: 270520_PY01_PGC

value: PGC


title: CH1

description: CML c-KitHigh LSC_1

source_name: CML c-KitHigh LSC_1


title: Progeny 9 of cross 2155, low-bruising group, biol rep 2

source_name: tuber


title: 040822_PY02_Somatic

source_name: Somatic


title: 210619_PY02_Somatic

value: 60 days postpartum


title: PR8 infected #8 (P8)

description: Gene expression data from total lungs treated with IN PR8 on D0 and IT saline on D10


title: WB1P-Myc sample 4 miseq

value: tumor WB1P-Myc


title: PR8 infected #9 (P9)


title: Progeny 8 of cross 2155, low-bruising group, biol rep 1

value: tuber


title: Progeny 7 of cross 2155, low-bruising group, biol rep 1

value: mechanical impact (bruising)


title: PR8 infected #7 (P7)


title: Progeny 6 of cross 2155, high-bruising group, biol rep 1

value: 2h post-bruising


title: 210619_PY02_PGC

value: GFP (SSEA1) sorted


title: 140722_PY03_Somatic

value: 50 days postpartum


title: Healthy + MRSA #8 (H+M8)

description: Gene expression data from total lungs treated with IN saline on D0 and IT MRSA on D10

value: Male


title: PR8 infected #12 (P12)


title: Progeny 11 of cross 2121, not used in DE analysis, biol rep 1


title: Progeny 5 of cross 2155, not used in DE analysis, biol rep 1


title: 290520_PY01_PGC

value: 45 days postpartum


title: WB1P-Myc sample 2 miseq

value: mammary gland


title: Healthy + MRSA #7 (H+M7)

value: Lung


title: 140722_PY03_PGC


title: WB1P sample 3 miseq

value: tumor WB1P


title: Progeny 2 of cross 2155, low-bruising group, biol rep 1


title: WB1P-Myc sample 1 miseq


title: Progeny 9 of cross 2121, high-bruising group, biol rep 1


title: WB1P-Myc sample 3 miseq


title: WB1P sample 4 miseq


title: Healthy #8 (H8)

description: Gene expression data from total lungs treated with IN saline on D0 and IT Saline on D10


title: WB1P sample 1 miseq


title: Survivin ChIPseq sample 4, activated CD4 cells

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

description: mapped to HG38

data_processing:
bcl conversion and demultiplexing (bcl2fastq), to fastq files
fastq mapping to hg38 reference (STAR, default parameters apart alignIntronMax flag set to 1 for end-to-end mapping)
quality control (MultiQC v.0.9dev0, default parameters)
peak calling (MACS2, narrow peaks, default parameters)
peak filtering and merging (MACS2, peaks with enrichment versus surrounding region and input (adjusted p<10-5) selected, >=1bp overlapping peaks in four samples merged to single annotation and further used as “survivin-ChIP peaks” (“cmd=annotatePeaks.pl peaks/peaksMrg.txt hg38 -pc 1 -noadj -d”  for all four samples))
Genome_build: HG38
Supplementary_files_format_and_content: matrix with peak location (chromosome, strand, start, stop), peak score and sample redundancy in S1-S4

source_name: Primary activated CD4 cells from PBMC

growth_protocol: Lymphoprep separation of PBMC, Magnetic separation of CD4 cells, culture activated with ConA+LPS for 72h

extract_protocol:
EpiTect ChIP OneDay kit (Qiagen), quality control TapeStation (Agilent, Santa Clara, CA, USA)
ThruPLEX (Rubicon)
Hiseq2000,Illumina, single end, default parameters (100bp reads)

treatment_protocol: ChIP with anti-Survivin (2 microg/ml, 10811, SantaCruz Biotechnology)

tag: agent

value: ConA+LPS

tag: antibody

value: Survivin


title: 290520_PY01_Somatic

value: Somatic

value: GFP (SSEA1) negative


title: WB1P sample 2 miseq

city: Amsterdam

last: Bruijn

institute: Netherlands Cancer Institute

tag: tissue


title: 040822_PY01_PGC

source_name: PGC

value: PGC

value: 34 days postpartum


title: 140421_PY03_Somatic

value: 38 days postpartum


title: Healthy + MRSA #6 (H+M6)


title: Healthy + MRSA #9 (H+M9)


title: Progeny 10 of cross 2121, high-bruising group, biol rep 1

value: tuber


title: Healthy #9 (H9)


title: 140421_PY03_PGC


title: Healthy #11 (H11)