title: FWY_deletion_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(FWY_deletion)-Mnase (kanMX)


title: E7.5-KO-exe-4

status: Public on Apr 20 2023

type: SRA

city: Shanghai

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

country: China

institute: Chinese Academy of Science

library_source: transcriptomic

data_processing:
The adapter sequences were removed from the 3’ end of the sequenced reads using the fastp program (version 0.20.1) with parameters “-l 15 --length_limit 40”
The remaining reads were mapped to the mouse genome (version GRCm38) using bowtie (version 1.2.1.1) first.
The mapped reads were mapped again to the mature miRNA sequences annotated in miRbase (version 21), allowing -2 or +2 nt to be templated by the corresponding genomic sequence at the 3’ end to determine the expression level of each miRNA.
The differential expression analysis of each miRNA were performed by R package DESeq2 (version 1.30.1).
The miRNAs with foldchange >1.414 and P-value <0.05 were defined as significant different expressed miRNAs.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw miRNA counts for every miRNA and every sample

molecule: total RNA

organism: Mus musculus

source_name: embryo

extract_protocol:
Total RNA was extracted from E6.5 and E7.5 embryos and AG-haESCs by using miRNeasy Micro Kit (QIAGEN, Cat#217084) according to the manufacturer's instructions.
The preparation of CAS-seq cDNA library was mainly followed the published protocol (Yang. Q., et al., 2019, Nature Communications). The extracted RNA (100 pg) underwent the following steps to construct small RNA libraries: adapter ligation, first-strand cDNA synthesis, Cas9/sgRNA treatment, on-bead in vitro transcription, second RT and PCR amplification and gel purification. An Illumina NovaSeq 6000 System was used to sequence the small RNA libraries at the MingmaTechnologies Co., Ltd., China

tag: developmental stage

tag: strain

value: C57BL/6 male X F1 female

tag: tisuue

value: embryo


title: Sample.37

city: Aurora

first: Sana

middle: D

last: Karam

state: CO

address: 1665 Aurora Ct.

department: Radiation Oncology

country: USA

institute: CU Denver Anschutz

data_processing:
Reads were aligned and counts generated using Biospyder TempoSeqr platform. Genes with <1 mean raw counts or <1 mean counts per million (CPM) were removed from the data set. Differential expression was calculated using the limma R package. The resulting fold change was used with the fgsea R package to perform gene set enrichment analysis for Hallmark and C2 Curated gene sets. Heat map displaying Z-score transformed gene expression was generated using the ComplexHeatmap R package (v1.20.0) and hierarchical clustering using Euclidean distance with complete linkage.
Supplementary files format and content: Excel, CPM

organism: Homo sapiens

extract_protocol:
Tumor tissue collected from patients at time of initial biopsy and at time of surgery were used for RNA sequencing. A pathologist reviewed H&E stains of the tumor samples, and areas of tumor cellularity were identified and marked. Only the pathologist-marked areas of tumor cellularity were scraped and processed per BioSpyder kit instructions.
For the human RNA sequencing library preparation, lysates were made from scapes using BioSpyer FFPE lysis protocol, then diluted in 1:5 in 1X TempO-Seq Lysis Buffer, and processed through a TempO-Seq Human Full Transcriptome FFPE Assay 96 sample Kit(BioSpyder, Carlsbad, CA).

tag: tissue

value: Tumor

tag: response

value: Unk

tag: cell type

value: PDAC

tag: timepoint

value: Pre

tag: treatment

value: Neoadjuvant chemo, 30-33.6 Gy SBRT, pancreaticoduodenectomy and adjuvant chemotherapy


title: E7.5-KO-exe-3


title: Macrophage, No treatment, 2

city: Xi'an

first: Jie

last: Qi

state: Shaanxi

address: 256 West youyi Rd.

department: Second Department of Cardiovascular Medicine

institute: Shaanxi Provincial People's Hospital

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
The raw reads were further processed with a bioinformatic pipeline tool, BMKCloud(www.biocloud.net) online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
Assembly: GRCh38_release101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: THP-1 cells was maintained in PRMI-1640 medium supplemented with 10% FBS (Gibco BRL, USA) in a cell culture incubator (5% CO2, 37℃).

extract_protocol:
Total RNA was extracted using the Total RNA Extraction Kit (TAKARA, JPN), 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the NEBNext UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: THP-1 cells were induced into macrophages, and then underwent different treatments for 48 h.

tag: cell line

value: monocyte

tag: pre-treatment

value: induced to macrophages by PMA, LPS plus IFN-gamma

value: No treatment


title: FWY_cluster2_A

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

library_source: genomic

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)
Library strategy: ChEC-seq

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: budding yeast culture at OD=4

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. 2015

tag: genotype

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(FWY_cluster2)-Mnase (kanMX)


title: E7.5-DKO-exe-3


title: Sample.35


title: Macrophage, No treatment, 1


title: FWY_cluster2_B


title: E_nextto_N_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(E_nextto_N)-Mnase (kanMX)


title: E_nextto_N_1


title: COMBO_4

city: London

first: Theodora

middle: Alexandra

last: Constantin

address: Du Cane Rd, ICTEM Building, 1st Floor Office, Imperial College London

department: Surgery & Cancer

country: United Kingdom

institute: Imperial College London

data_processing:
Original image data file was transformed to sequenced reads by CASAVA base recognition.
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website browser directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR v2.5, mismatch = 2) software.
FeatureCounts was used to count the read numbers mapped of each gene.
Assembly: GRCh38.p13

source_name: Xenograft

growth_protocol: Subcutaneous C4-2B xenografts were allowed to grow to a volume of 100 mm^3 before treatment initiation.

extract_protocol:
Following treatment on day 21, xenografts were removed, flash frozen in liquid nitrogen, and RNA was extracted using the Monarch Total RNA Miniprep Kit (NEB, #T2010) following manufacturer's protocols. RNA quality was assessed on the Agilent Bioanalyzer 2100 system.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEB Next® Ultra RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Library quality was assessed on the Agilent Bioanalyzer 2100 system. Library preparations were sequenced on an Illumina NovaSeq 6000 PE150 system and paired-end reads were generated.

treatment_protocol: Mice were gavaged orally once daily with vehicle, CT7001 (50 mg/kg), enzalutamide (25 mg/kg) or combination for 21 consecutive days.

value: Combination

tag: murine host

value: NSG


title: Macrophage, oxLDL induction, 2

value: oxLDL induction


title: Sample.32

value: Post


title: E7.5-KO-exe-1


title: Sample.34

value: R


title: E7.5-Con-exe-4

value: C57BL/6 male X F1 female


title: COMBO_3


title: Macrophage, oxLDL and glucose induction, 1

value: oxLDL and glucose induction


title: E7.5-Con-exe-3

value: embryo


title: COMBO_2


title: E7.5-Con-exe-2


title: Sample.29

value: Tumor


title: E7.5-KO-exe-2


title: E7.5-Con-exe-1


title: Sample.31

value: Unk

value: PDAC


title: Sample.28

value: Neoadjuvant chemo, 30-33.6 Gy SBRT, pancreaticoduodenectomy and adjuvant chemotherapy


title: ED_shift2_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(ED_shift2)-Mnase (kanMX)


title: ED_shift1_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(ED_shift1)-Mnase (kanMX)


title: ED_random3_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(ED_random3)-Mnase (kanMX)


title: Sample.27

value: Pre


title: ED_shift1_A


title: E6.5-TKO-epi-4


title: ENZA_4

value: Enzalutamide


title: ENZA_3


title: E6.5-TKO-epi-3


title: ENZA_2


title: ED_random3_A


title: Sample.23


title: Sample.21


title: ED_shift2_B


title: ENZA_1


title: E6.5-TKO-epi-1


title: ED_random2_A

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(ED_random2)-Mnase (kanMX)


title: COMBO_1

value: Combination

value: NSG


title: CT_4


title: CT_2


title: E6.5-TKO-epi-2


title: E6.5-DKO-epi-3


title: ED_random1_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(ED_random1)-Mnase (kanMX)


title: Sample.8

value: Post


title: Sample.15

value: R


title: E6.5-DKO-epi-4

value: C57BL/6 male X F1 female


title: Sample.25

value: NR


title: ED_random1_A


title: CT_1


title: ED_deletion_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(ED_deletion)-Mnase (kanMX)


title: Sample.7

value: Tumor


title: Sample.6

value: PDAC


title: E6.5-DKO-epi-2

value: embryo


title: ED_deletion_A


title: VEH_4

value: Vehicle


title: VEH_3


title: E6.5-DKO-epi-1


title: E6.5-KO-epi-4


title: Sample.4

value: Neoadjuvant chemo, 30-33.6 Gy SBRT, pancreaticoduodenectomy and adjuvant chemotherapy


title: ED_random2_B


title: VEH_2


title: ED_cluster2_B

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(ED_cluster2)-Mnase (kanMX)


title: Sample.3


title: E6.5-KO-epi-3


title: VEH_1


title: ED_cluster2_A


title: Sample.2


title: HCT116 FOXD2 RNA rep2

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

description: ATCC (CCL-247)

data_processing:
Reads were mapped to the genome (Ensembl GRCh38 release100) using STAR-v2.7.2b with ENCODE option.
RSEM-v1.2.31 was used to calculate read counts and normalization.
Genome_build: hg38
Supplementary_files_format_and_content: tab separated RSEM results

molecule: polyA RNA

source_name: Large intestine; Colon

growth_protocol: DMEM high glucose + 10% FBS + 100 units/ml penicillin + 100 μg/ml  streptomycin  with 5 μg/ml Puromycin selection

extract_protocol:
TRIzol™ Reagent (invitrogen 15596026)
The library was generated using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S) for Illumina with mRNA Magnetic Isolation module (NEB, E7490S)

treatment_protocol: For stable cell lines, we treated pSin empty and pSin. FOXD2 full-length CDS lentivirus onto HCT116 cells. Transduced stable cells were selected by puromycin (5ug/mL) in culture medium.

value: Large intestine; Colon

tag: disease state

value: Carcinoma; Colorectal

value: pSin-FOXD2 epxressing vector


title: E6.5-KO-epi-2


title: D_nextto_N_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(D_nextto_N)-Mnase (kanMX)


title: Sample.1


title: E6.5-KO-epi-1


title: E6.5-Con-epi-4


title: HCT116 Control RNA rep2

description: ATCC (CCL-247)

value: pSin-Pur-MCS-Puro epmty vector


title: D_nextto_N_1


title: DE_to_A_6

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(DE_to_A)-Mnase (kanMX)


title: E6.5-Con-epi-3


title: E6.5-Con-epi-2


title: HCT116 Control RNA rep1

description: ATCC (CCL-247)


title: HCT116 FOXD2 H3K4me3 HiChIP replicate 1 Technical replicate 1

description: ATCC (CCL-247)

data_processing:
Library strategy: HiChIP-seq
BWA was used to align read pairs on Homo sapience genome (UCSC hg38) with "-5SP -T0".
pairtools-0.3.0 was used to remove MAPQ < 40 and duplicated pairs and rescue reads with ligation junction.
FitHiChIP was used to call loops with 'peak to all' background, FDR < 0.01 and multiple bin size (5k, 10k, and 25k). Read pairs with distance > 2M or < 100bp were excluded from loop calling.
Loops with different bin size were merged using HiCExplorer-3.7.2.
The Loops anchoring on two adjacent bins were excluded.
Genome_build: hg38
Supplementary_files_format_and_content: hic files were generated from Juicer Tools pre command; BEDPE files were called loops using FitHiChIP

extract_protocol:
Cultured cells were collected by 0.25% Trypsin-EDTA (Gibco, 25200), then washed with DPBS. Cell pellets were incubated at -80 °C  for a day as manufacturer's instructions.
All HiChIP and sequencing libraries were generated using the Dovetail® HiChIP MNase Kit (Dovetail, #21007) as manufacturer’s instructions using H3K4me3 (Abcam, ab8580) or H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729) antibody.

value: pSin-FOXD2 expressing vector

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: Moderate-risk Benign [MB3_BC]

city: Honolulu

first: Mayumi

last: Jijiwa

state: HI

address: 651 Ilalo St, BSB222

department: Quantitative Health Sciences

institute: University of Hawaii

description: Circulating small RNA

data_processing:
Illumina’s single-end 76 bp reads were explored using FASTQC and then analyzed with sRNAbench web tool, which is incorporated in the sRNAtoolbox
Within the tool, the raw reads were processed by trimming adapters and UMI, and filtering out those with mean quality Phred score below 20.
The high-quality reads were aligned against GRCh38_p13 human reference genome with MirGeneDB 2.1 as miRNA annotation database using aligner Bowtie with seed length of 20 with no mismatches.
Mature miRNAs read count (mult. map. adj.) for each sample were combined and differential expression analyses were done between different groups (CA vs Be, HB vs Be, MB vs Be, and CA vs HB) using DESeq2 R package [Love MI]. The p-value < 0.05 and log2FC > |0.5| were considered differentially expression.
Supplementary files format and content: csv, xlsx; contains raw read counts, normalized read counts, and DESeq2 results

source_name: Plasma

extract_protocol:
Total RNA including smal non-coding RNAs were extracted using miRNeasy Serum/Plasma Kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using QIASeq miRNA Library kit protocols

value: Plasma

value: cell-free

tag: race

value: White

tag: Sex

value: female

tag: age

tag: bmi

tag: histology

value: Radial scar, sclerosing adenosis, fibrocystic changes, focal duct hyperplasia

value: pre-treatment


title: A_nextto_N_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(A_nextto_N)-Mnase (kanMX)


title: Moderate-risk Benign [MB1_BC]

description: Circulating small RNA

value: Benign breast parenchyma, columnar cell change, usual ductal hyperplasia, intraductal papilloma


title: DE_to_A_2


title: HCT116 Control H3K4me3 HiChIP replicate 1 Technical replicate 1

description: ATCC (CCL-247)


title: Moderate-risk Benign [MB2_BC]

description: Circulating small RNA

value: Fibrocystic changes, usual ductal hyperplasia, small intraductal papilloma


title: High-risk Benign [HB9_BC]

description: Circulating small RNA

value: Focal ALH and focal ductal hyperplasia with microcalcifications


title: E6.5-TKO-exe-3

tag: developmental stage

tag: strain

value: C57BL/6 male X F1 female

tag: tisuue

value: embryo


title: HCT116 FOXD2 RNA rep1

description: ATCC (CCL-247)

tag: tissue

value: Large intestine; Colon

value: Carcinoma; Colorectal

value: pSin-FOXD2 epxressing vector


title: 90p_10n_chargeratio_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(90p_10n_chargeratio)-Mnase (kanMX)


title: E6.5-TKO-exe-4


title: High-risk Benign [HB8_BC]

description: Circulating small RNA

tag: cell type

value: Focal ALH


title: HCT116 FOXD2 H3K27ac HiChIP replicate 1 Technical replicate 1

description: ATCC (CCL-247)

tag: treatment

value: pSin-FOXD2 expressing vector

value: H3K27ac (Abcam, ab4729)


title: 90p_10n_chargeratio_1


title: HCT116 Control H3K27ac HiChIP replicate 1 Technical replicate 1

description: ATCC (CCL-247)

tag: cell line

value: pSin-Pur-MCS-Puro epmty vector


title: E6.5-TKO-exe-2


title: 90p_10n_chargeratio_3


title: E6.5-TKO-exe-1


title: Moderate-risk Benign [MB4_BC]

description: Circulating small RNA

value: Plasma

value: cell-free

value: White

value: female

value: Small intraductal papilloma


title: High-risk Benign [HB7_BC]

description: Circulating small RNA

value: FEA, focal microcalcifications, fibrocystic change, focal usual ductal hyperplasia

value: pre-treatment


title: High-risk Benign [HB6_BC]

description: Circulating small RNA

value: FEA, fibrocystic changes, usual ductal hyperplasia


title: 90_chargedaa_to_random_3_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(90_chargedaa_to_random_3)-Mnase (kanMX)


title: HCT116 Control H3K4me1 HiChIP replicate 1 Technical replicate 1

description: ATCC (CCL-247)

value: Large intestine; Colon

value: H3K4me1 (Abcam, ab8895)


title: 90_chargedaa_to_random_3_1


title: HCT116 FOXD2 H3K4me1 HiChIP replicate 1 Technical replicate 1

description: ATCC (CCL-247)

value: Carcinoma; Colorectal


title: HCT116 FOXD2 MLL4 Input rep1

description: ATCC (CCL-247)

data_processing:
cutadapt-3.4 was used to detect and remove Illumina adapter sequence.
Bowtie2-2.3.4.1 aligned sequences to the Homo sapiens genome (UCSC hg38).
Picard tools removed duplicates with parameters "VALIDATION_STRINGENCY=LENIENT".
MACS2-2.2.7.1 was used for peak calling with parameters "--nomodel --shift -100 --extsize 200" and q-value < 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files were generated using MACS2; bigWig files were generated using genomeCoverageBed and bedGraphToBigWig.

extract_protocol:
Cultured cells were collected by 0.25% Trypsin-EDTA (Gibco, 25200), then washed with DPBS.
Crosslinked 6.0 or 10.0 × 106 HCT116 cells for 7 min at 37 °C with 1% formaldehyde. We perforemd FOXD2-flag or 6xHis ChIP with sonicated chromatin in RIPA buffer (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% NP-40, 0.01% SDS, and 0.5% sodium deoxycholate, 1mM PMSF and 1X protease inhibitor cocktail) with 4μg of antibody; MLL4/KMT2D antibody (Santa crz, sc-293217) or Anti-6X His tag® antibody [HIS.H8] (Abcam, ab18184) or Monoclonal ANTI-FLAG® M2 antibody (Sigma-Aldrich, F1804). For histone ChIP using MNase without crosslinking method, we resuspended 1.0 x 106 HCT116 cells in 50ul of nuclei isolation buffer (Sigma-Aldrich, NUC101) and incubated on ice for 10 min. We then proceeded to MNase digestion with final concentration 2 units/μl (NEB, M0247), pre-clearing and immunoprecipitated chromatin in ChIP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1x Protease inhibitor cocktail, and 1 mM PMSF) with 2μg of antibody; H3K4me3 (Abcam, ab8580) or H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729).

value: pSin-FOXD2 epxressing vector


title: 90_chargedaa_to_random_2_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(90_chargedaa_to_random_2)-Mnase (kanMX)


title: High-risk Benign [HB5_BC]

description: Circulating small RNA

value: ALH and papilloma


title: High-risk Benign [HB4_BC]

description: Circulating small RNA

value: ALH


title: E6.5-Con-epi-1

value: C57BL/6 male X F1 female

value: embryo


title: E6.5-DKO-exe-3


title: E6.5-DKO-exe-2


title: High-risk Benign [HB3_BC]

description: Circulating small RNA

value: Plasma

value: cell-free

value: ADH involving papilloma


title: 90_chargedaa_to_N_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(90_chargedaa_to_N)-Mnase (kanMX)


title: HCT116 FOXD2 MLL4 ChIP rep1

description: ATCC (CCL-247)

value: ML4/KMT2D (Santa crz, sc-293217)


title: 90_chargedaa_to_N_1


title: E6.5-DKO-exe-1


title: HCT116 Control MLL4 ChIP rep1

description: ATCC (CCL-247)

value: pSin-Pur-MCS-Puro epmty vector


title: High-risk Benign [HB2_BC]

description: Circulating small RNA

value: White

value: female

value: ADH

value: pre-treatment


title: HCT116 FOXD2 H3K4me3 ChIP

description: ATCC (CCL-247)

value: Large intestine; Colon

value: Carcinoma; Colorectal

value: H3K4me3 (Abcam, ab8580)


title: High-risk Benign [HB1_BC]

description: Circulating small RNA


title: E6.5-KO-exe-4


title: 90_chargedaa_to_A_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(90_chargedaa_to_A)-Mnase (kanMX)


title: 90_chargedaa_to_F_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(90_chargedaa_to_F)-Mnase (kanMX)


title: High-risk Benign [HB14_BC]

description: Circulating small RNA

value: Right breast ADH, Left breast ALH


title: E6.5-KO-exe-3

value: C57BL/6 male X F1 female

value: embryo


title: E6.5-KO-exe-2


title: E6.5-DKO-exe-4


title: HCT116 Control H3K4me3 ChIP

description: ATCC (CCL-247)


title: E6.5-KO-exe-1


title: 90_E_charged_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(90_E_charged)-Mnase (kanMX)


title: HCT116 Control H3K27ac ChIP rep2

description: ATCC (CCL-247)

value: H3K27ac (Abcam, ab4729)


title: HCT116 Control MLL4 Input rep1

description: ATCC (CCL-247)


title: 90_D_charged_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(90_D_charged)-Mnase (kanMX)


title: HCT116 Control H3K4me1 ChIP rep2

description: ATCC (CCL-247)

value: H3K4me1 (Abcam, ab8895)


title: High-risk Benign [HB12_BC]

description: Circulating small RNA

value: Plasma

value: cell-free


title: High-risk Benign [HB11_BC]

description: Circulating small RNA

value: White

value: female

value: Focal FEA, focal radial scar, usual ductal hyperplasia


title: HCT116 FOXD2 ATAC rep2

description: ATCC (CCL-247)

data_processing:
cutadapt-3.4 was used to detect and remove Illumina adapter sequence.
Bowtie2-2.3.4.1 aligned sequences to the Homo sapiens genome (UCSC hg38).
Picard tools removed duplicates with parameters "VALIDATION_STRINGENCY=LENIENT".
The reads were offset by +4 bases for the + strand and -5 bases for the - strand.
MACS2-2.2.7.1 was used for peak calling with parameters "--nomodel --shift -100 --extsize 200" and q-value < 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files were generated using MACS2; bigWig files were generated using genomeCoverageBed and bedGraphToBigWig.

extract_protocol:
ATAC lysis buffer (10mM Tris-HCT pH7.4, 10mM NaCl, and 3mM MgCl2 containing 0.1% NP40, 0.1% Tween-20, and 0.01% Triton-X 100)
We lysed 50,000 cells of interest with 50 μl lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% Triton X-100) and incubated them for 10 min on ice. Following centrifugation at 1,000g for 10 min at 4 °C, we resuspended nuclei pellets with 50 μl of transposition mix (25 μl 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2 and 20% dimethyl formamide in sterile water) and 2.5 μl transposase (100 nM final concentration), 16.5 μl PBS, 0.01% Triton X-100, 0.1% Tween-20 and 5 μl H2O) and incubated the mixture with shaking for 1 h at 55 °C in a thermomixer. We purified transposed DNA using DNA Clean and a Concentrator-5 Kit (Zymo Research) then amplified it using the NEBNext High-Fidelity 2× PCR Master Mix for 10 cycles. Subsequently, we then performed ATAC-seq using the Illumina NovaSeq600 dual indexed platform.

value: Large intestine; Colon

value: pSin-FOXD2 epxressing vector


title: E6.5-Con-exe-3


title: High-risk Benign [HB10_BC]

description: Circulating small RNA

value: Focal FEA

value: pre-treatment


title: HCT116 FOXD2 ATAC rep1

description: ATCC (CCL-247)

value: Carcinoma; Colorectal


title: E6.5-Con-exe-2


title: E6.5-Con-exe-1


title: 90_chargedaa_to_A_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(90_chargedaa_to_A)-Mnase (kanMX)


title: 80p_20n_chargeratio_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(80p_20n_chargeratio)-Mnase (kanMX)


title: Early-stage Cancer [CA8_BC]

description: Circulating small RNA

value: ILC

tag: Stage

tag: grade

value: Grade 1

tag: er

value: Pos

tag: pr

value: Neg


title: 70p_30n_chargeratio_2

tag: genotype

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(70p_30n_chargeratio)-Mnase (kanMX)


title: HCT116 Control ATAC rep2

description: ATCC (CCL-247)

tag: disease state

value: pSin-Pur-MCS-Puro epmty vector


title: Early-stage Cancer [CA9_BC]

description: Circulating small RNA

value: Plasma

value: cell-free

tag: race

tag: Sex

value: Ductal carcinoma in situ (DCIS)

value: ypTis(DCIS)


title: 70p_30n_chargeratio_1


title: Early-stage Cancer [CA7_BC]

description: Circulating small RNA

value: White

value: female

tag: age

tag: bmi

value: IDC, NOS

value: Grade 3


title: 60p_40n_chargeratio_3

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(60p_40n_chargeratio)-Mnase (kanMX)


title: High-risk Benign [HB13_BC]

description: Circulating small RNA

tag: histology

value: Multifocal FEA

value: pre-treatment


title: 1-97371-CONTROL

city: Jinan

first: Yanjun

last: Zheng

state: Shandong Province

address: Wenhua West Road

institute: Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University

data_processing:
Agilent Bioanalyzer 2100 was used to evaluate the RNA integrity number (RIN). Qubit®3.0 Fluorometer was used to assess total RNA levels and purity.
We used the TruSeq®Stranded Total Sample Preparation kit (Illumina, USA) to prepare the strand-specific libraries strictly. Purified libraries were quantified using Qubit® 2.0 Fluorometer and confirmed using Agilent 2100 Bioanalyzer to confirm the insert size and calculate the molar concentration.
Cluster was generated by cBot with the library diluted to 10 pM, followed by sequencing on HiSeq X Ten
Genome_build: Human GRCh38
Supplementary_files_format_and_content: To preprocess the sequenced raw reads, we filtered out rRNA reads, sequencing adapters, short-fragment reads, and other low-quality reads. We mapped the cleaned reads to the human GRCh38 reference genome using Tophat v2.0.9, allowing two mismatches. After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models. We used Cuffdiff to identify these differentially expressed genes and set the p-value significance threshold in multiple tests.

source_name: ovarian granulosa cells

growth_protocol: Standard long protocol and/or GnRH antagonist protocol in IVF

extract_protocol:
Total RNA was extracted from GCs using TRIzol Reagent, and we used the TruSeq®Stranded Total Sample Preparation kit (Illumina, USA) to prepare the strand-specific libraries strictly.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GCs were purified by magnetic-activated cell sorting.

tag: body mass index

tag: plasma basic luteinizing hormone


title: HCT116 Control ATAC rep1

description: ATCC (CCL-247)

tag: tissue

value: Large intestine; Colon

value: Carcinoma; Colorectal


title: T8.TN.IgG_2.CutandRun

city: La Jolla

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Trimmed with trimmomatic, aligned with bowtie2, normalized to Ecoli reads, MSPC to combine with ChIP
Assembly: mm10
Supplementary files format and content: Peak set in bed file format
Library strategy: Cut&Run

source_name: spleen

extract_protocol: Cells were sort purified and underwent nuclei extraction. Cut&Run was performed, and DNA was ligated to Illumina adapters, PCR amplified, and sequenced.

value: spleen

tag: cell type

value: OT-I

tag: time

value: Day 0

tag: chip antibody

value: IgG (CST #2729S)


title: Early-stage Cancer [CA6_BC]

description: Circulating small RNA

value: Plasma

tag: Stage

value: Grade 1

value: Pos

value: Neg

tag: treatment


title: T8.TN.IgG_1.CutandRun


title: 60p_40n_chargeratio_2


title: T8.TN.CTCF_2.CutandRun

value: CTCF (Sigma Aldrich #07-729-25UL)


title: E6.5-Con-exe-4

tag: developmental stage

tag: strain

value: C57BL/6 male X F1 female

tag: tisuue

value: embryo


title: 1-97232-CONTROL


title: 60p_40n_chargeratio_1

tag: genotype


title: 1-96725-CONTROL


title: T8.TN.CTCF_1.CutandRun


title: 80p_20n_chargeratio_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(80p_20n_chargeratio)-Mnase (kanMX)


title: Early-stage Cancer [CA4_BC]

description: Circulating small RNA

value: cell-free

tag: race

value: White

value: female

value: IDC with metaplastic features

tag: grade

value: Grade 3

tag: er

tag: pr


title: Early-stage Cancer [CA5_BC]

description: Circulating small RNA

tag: Sex

tag: age

tag: bmi

tag: histology

value: Metaplastic carcinoma, spindle cell type

value: pre-treatment


title: 1-96412-CONTROL

tag: body mass index

tag: plasma basic luteinizing hormone


title: 50p_50n_chargeratio_3

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(50p_50n_chargeratio)-Mnase (kanMX)


title: Early-stage Cancer [CA3_BC]

description: Circulating small RNA

tag: tissue

tag: cell type

value: Invasive papillary carcinoma


title: T8.TE.shCTCF.CTCF_4.CutandRun

value: spleen

value: OT-I

tag: treatment

value: Lm-OVA

tag: time

value: Day 7

tag: chip antibody


title: 1-92393-CONTROL


title: 1-96349-CONTROL


title: Early-stage Cancer [CA2_BC]

description: Circulating small RNA

value: Plasma

value: IDC, NOS

tag: Stage

value: Grade 1

value: Pos

value: Neg


title: 50p_50n_chargeratio_2

tag: genotype


title: 40p_60n_chargeratio_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(40p_60n_chargeratio)-Mnase (kanMX)


title: T8.TE.shCTCF.CTCF_3.CutandRun

value: CTCF (Sigma Aldrich #07-729-25UL)


title: T8.TE.shCD19.CTCF_4.CutandRun


title: Early-stage Cancer [CA1_BC]

description: Circulating small RNA

value: cell-free

tag: race

value: White

value: female


title: 1-97550-PCOS


title: T8.TE.shCD19.CTCF_3.CutandRun


title: No-risk Benign [Be9_BC]

description: Circulating small RNA

value: Microcalcifications, fibrocystic changes, benign ducts and lobules

value: pre-treatment


title: 1-97477-PCOS


title: 30p_70n_chargeratio_3

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(30p_70n_chargeratio)-Mnase (kanMX)


title: T8.TE.IgG_4.CutandRun

value: spleen

value: IgG (CST #2729S)


title: 1-97194-PCOS


title: No-risk Benign [Be8_BC]

description: Circulating small RNA

value: fibrocystic change, microcalcifications


title: 40p_60n_chargeratio_1


title: No-risk Benign [Be7_BC]

description: Circulating small RNA

value: Fibrocystic changes, fibroadenomatiod mastopathy, focal microcalcifications


title: T8.TE.IgG_3.CutandRun

value: OT-I

value: Lm-OVA

value: Day 7


title: 30p_70n_chargeratio_2


title: 30p_70n_chargeratio_1


title: 1-96846-PCOS


title: No-risk Benign [Be6_BC]

description: Circulating small RNA

value: Plasma

value: Fibroadenoma


title: T8.TE.IgG_2.CutandRun


title: 1-95841-PCOS


title: 20p_80n_chargeratio_3

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(20p_80n_chargeratio)-Mnase (kanMX)


title: T8.TE.IgG_1.CutandRun


title: No-risk Benign [Be5_BC]

description: Circulating small RNA


title: 1-95784-PCOS


title: 20p_80n_chargeratio_2


title: T8.TE.CTCF_1.CutandRun

value: CTCF (Sigma Aldrich #07-729-25UL)


title: 20p_80n_chargeratio_1


title: No-risk Benign [Be4_BC]

description: Circulating small RNA

value: cell-free


title: T8.TE.CTCF_2.CutandRun


title: T8.MP.IgG_1.CutandRun


title: 10p_90n_chargeratio_2

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(10p_90n_chargeratio)-Mnase (kanMX)


title: ZF-Ctrl-2

city: Yanghzou

first: Songlei

last: Xue

state: Jiangsu

address: Wenhui Road 48#

institute: Yangzhou University

data_processing:
Quality Control:  In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or  fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by  Trimmomatic (v0.30) to be high quality clean data.
Mapping:  Firstly, reference genome sequences and gene model annotation files of relative species were downloaded  from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index  reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2  (v2.0.1).
Expression analysis:  In the beginning transcripts in fasta format are converted from known gff annotation file and indexed  properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform  expression levels from the pair-end clean data
Differential expression analysis:  Differential expression analysis used the DESeq Bioconductor package, a model based on the negative  binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false  discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones
Genome_build: Zv9
Supplementary_files_format_and_content: RPKM

organism: Danio rerio

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit  (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer  (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose  gel.
1 μg total RNA with RIN value above 7 was used for following library preparation. Next generation  sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext®  Ultra™ RNA Library Prep Kit for Illumina®).

treatment_protocol: Ttdmt1 knockout group in zebrafish named ZF-TKO ,zebrafish control group named ZF-Control.

value: wildtype


title: ZF-Ctrl-3


title: ZF-Ctrl-1


title: No-risk Benign [Be2_BC]

description: Circulating small RNA

value: White

value: female

value: Benign breast tissue, focal fibrocystic changes


title: ZF-TKO-3

value: Trdmt1 knockout


title: T8.MP.CTCF_2.CutandRun

value: spleen


title: miRNA-seq_Plasma exosome methamphetamine4

city: Ningbo

first: Wenjin

last: Xu

state: Zhejiang Province

address: 42 Xibei Street

institute: School of Medicine, Ningbo University,

data_processing:
Sequencing library was determined by Agilent 2100 Bioanalyzer using the Agilent DNA 1000 chip kit (Agilent, part # 5067-1504)
Q30 was calculated for the raw sequencing data of each sample after sequencing.
Trimmed sequence reads were mapped to GrCM38/mm10 using bowtie.
Read count extraction and normalization were performed using mirdeep2.
Supplementary files format and content: mm10

extract_protocol:
Total RNA was extracted from  exosomes using the  Trizol reagent (Thermo Fisher Scientific, Massachusetts, USA), according to the manufacturer’s protocol. Subsequently, RNA concentration and purity were detected using nanodrop 2000 apparatus (Thermo Fisher Scientific, Massachusetts, USA).
RNA libraries for RNA-seq were prepared using RiboZero Magnetic Gold Kit following manufacturer's protocols.

value: Peripheral Blood plasma exosome

tag: gender


title: No-risk Benign [Be3_BC]

description: Circulating small RNA

value: pre-treatment


title: No-risk Benign [Be1_BC]

description: Circulating small RNA

value: Benign breast tissue, stromal fibrosis, small fibroadenomas


title: T8.MP.IgG_2.CutandRun

value: OT-I

value: Lm-OVA

value: IgG (CST #2729S)


title: EF19-5-9

city: New Haven

first: Erol

last: Fikrig

address: 300 Cedar Street

institute: Yale University School of Medicine

description:
bite
4 days post tick bite

data_processing:
reads were trimmed for quality and filtered for length using trimmomatic.  Only those bases with quality values of Q30+ and read lengths of 45+ were used for further analysis.  The trimmed reads were aligned to guinea pig genome (Cavea porcellus, Cavpor 3.0 from Ensembl)
The alignment files were processed with stringTie, and ballgown to generate per gene counts.  These count matrices were processed further with R and DESeq to obtain significantly differentially expressed genes
Genome_build: Cavpor 3.0 from Ensembl
Supplementary_files_format_and_content: TSV files with TPM values in each cell.  All genes on rows, all samples in columns.

organism: Cavia porcellus

source_name: skin

extract_protocol:
RNA isolation (Qiagen Rneasy)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

tag: immunization

value: ticks 2 bites


title: EF19-5-11

description:
no bite
4 days post tick bite

value: naïve


title: ZF-TKO-1


title: miRNA-seq_Plasma exosome methamphetamine3


title: EF19-5-7

description:
bite
4 days post tick bite


title: ZF-TKO-2


title: T8.TE.Spl2.shCTCF.ATAC

description: TE.shCTCF.ATAC.optimalpeak.bed

data_processing:
ENCODE ATACSeq Pipeline
Assembly: mm10
Supplementary files format and content: Peak set in bed file format

extract_protocol: Omni-ATAC was performed on sort purified cells and DNA was PCR amplified for sequencing.

value: Day 7


title: 10p_90n_chargeratio_1

value: MATa his3[delta]0 leu2[delta]0 met15[delta]0 ura3[delta]0 Msn2 ::Msn2(10p_90n_chargeratio)-Mnase (kanMX)


title: T8.TE.Spl1.shCTCF.ATAC

description: TE.shCTCF.ATAC.optimalpeak.bed


title: miRNA-seq_Plasma exosome methamphetamine1

value: male


title: EF19-5-1

description:
bite
4 days post tick bite

value: ticks 3 bites


title: T8.TE.Spl2.shCD19.ATAC

description: TE.shCtrl.ATAC.optimalpeak.bed


title: miRNA-seq_Plasma exosome Control4

value: female


title: T8.TE.Spl1.shCD19.ATAC

description: TE.shCtrl.ATAC.optimalpeak.bed


title: CK1-N

description:
No bite
4 days post tick bite

value: Naïve


title: miRNA-seq_Plasma exosome Control2


title: miRNA-seq_Plasma exosome Control3


title: CK1-NN

description:
No bite
4 days post tick bite


title: metformin 3

city: JINAN

first: Yongzhi

last: Cao

address: NO. 44 Wenhuaxi Road

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: oocyte

growth_protocol: To retrieve fully grown GV oocytes, mice were injected intraperitoneally with 10 IU Pregnant Mares Serum Gonadotropin (PMSG) (Ningbo Hormone Product Company, China). After 46–48 h, cumulus-oocyte complexes were collected by manual rupturing of antral ovarian follicles, cumulus cells were removed by repeatedly pipetting.

extract_protocol: The sample library was built with the smart-seq ® HT Kit(Takara，USA )，the standard operating procedure manual provided by the Kit manufacturer was strictly followed during the experiment

treatment_protocol: For IVM, denuded GV oocytes cultured were cultured in the small drops in M16 medium supplemented with or without different concentrations of metformin (10 μM, 20 μM, or 50 μM), subsequently covered with mineral oil were incubated under 6% CO2, 5% O2, and 90% N2 at 37 °C for 16h to M2 stage oocytes.

value: oocyte

value: metformin


title: T8.MP.CTCF_1.CutandRun

value: spleen

value: CTCF (Sigma Aldrich #07-729-25UL)


title: metformin 2


title: metformin 1


title: Case4-ZY

city: Nanjing

first: Dijun

last: Chen

address: Xianlin

institute: Nanjing University

data_processing:
Sample demultiplexing, barcode processing, and single cell 3’ gene counting were performed by the Cell Ranger pipelines (v3.1.0,10X Genomics).
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively.
Supplementary_files_format_and_content: matrix.mtx: Filtered gene-barcode matrix file (demultiplexed)

source_name: hepatic metastases

growth_protocol: Normal pancreatic tissue, primary pancreatic tumors and paired hepatic metastases

extract_protocol:
Human pancreatic or liver were excised and mechanically dissociated into single cells using pancreatic digestive enzymes
Single cells were captured in the 10×Genomics Chromium Single Cell 3' Solution, and RNA-seq libraries were prepared following the manufacturer’s protocol (10×Genomics). The libraries were subjected to high-throughput sequencing on an illumina NextSeq500 platform, and 150-bp paired-end reads were generated.

treatment_protocol: All samples came from the affiliated hospital of Nanjing University Medical School of, Nanjing China and this work obtained patients informed consent approved by the Institutional Review Board of Nanjing University Medical School.

value: liver


title: CK1-B

description:
bite
4 days post tick bite

value: saliva immune


title: miRNA-seq_Plasma exosome Control1

value: Peripheral Blood plasma exosome


title: control 3

value: control


title: EF19-5-5

description:
bite
4 days post tick bite

value: skin


title: miRNA-seq_Plasma exosome methamphetamine2


title: CK1-A

description:
bite
4 days post tick bite


title: Case3-ZY


title: CK1-3

description:
bite
4 days post tick bite

value: 1st exposure


title: control 2


title: Case3-YF

source_name: primary pancreatic tumors

value: pancreas


title: control 1


title: CK1-C

description:
bite
4 days post tick bite


title: EF19-6-17

description:
no bite
4 days post tick bite

data_processing:
Raq-paired-end sequencing data were processed and normalized using Partek v 8.0.19
Sequences were mapped to NIH-GRCm38.p6 - NIH-R106 using STAR
Samples were normalize and CPM (counts per million) were calculated
Genome_build: NIH-GRCm38.p6 - NIH-R106 using STAR
Supplementary_files_format_and_content: CSV files with Counts per million number for each gene on a row for each sample in the column

value: naïve

value: Skin


title: Case2-YF


title: Case2-ZY


title: CK1-1

description:
bite
4 days post tick bite


title: Case2-ZC

source_name: normal pancreatic tissue


title: Case1-ZY


title: EF19-6-11

description:
bite
4 days post tick bite

value: ticks 3x


title: Case1-YF


title: EF19-6-9

description:
bite
4 days post tick bite


title: iPS-cell

type: RNA

city: Kyoto

first: Yoshiki

last: Nakashima

state: Kyoto

address: Kyoto Research Park KISTIC Building Room 501, 5th floor, KISTIC building,  134 Chudoji Minami-cho, Shimogyo-ku

department: Research and Development Center

country: Japan

institute: Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation)

description: public database as controls (GSE43328)

hyb_protocol: Hybridise Cy3-labelled cDNA to Agilent Technologies microarrays for gene expression.

scan_protocol: Acquire images with the SureScan microarray scanner (G2600D).

data_processing: QC Report and quantified data are calculated using dedicated analysis software Feature Extraction (Agilent Technologies).

source_name: public database as controls (GSE43328)

label_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Ovation FFPE WTA System

extract_protocol: Total RNA was extracted from cells using NucleoSpin RNANucleo Spin RNA (U0955B, Takara).

treatment_protocol: 201B7 cells were cultured on iMatrix-511 for 4 days after cell seeding in Stem Fit AK03 medium or CTS Essential 8 medium (2 samples each), and separately, different 201B7 cells (2 samples each) were cultured in Stem Fit AK03 medium or gelatin solution (10%) + MFGE 8 (2 µg/mL) in CTS Essential 8 medium for 4 days from cell seeding. A hierarchical cluster analysis of the 10 cell types is shown (Figure 2A). The 5,919 probes with variable expression are shown in a heatmap. Comparisons between samples based on 'human ES cell' were made using a hierarchical cluster analysis, and 4,825 probes with variable expression in each of the four comparisons are shown in the heatmap (Figure 2B). Comparisons between samples based on 'human iPSC N116213' were performed using a hierarchical cluster analysis, and 4,886 probes with variable expression in each of the four comparisons are also shown in a heatmap (Figure 2C).

value: iPS cell


title: E8-iMatrix511-1

description: 201B7 cells were cultured on iMatrix-511 for 4 days after cell seeding in CTS Essential 8 medium

value: female


title: E8-MFGE8-1

description: 201B7 cells were cultured in gelatin solution (10%) + MFGE 8 (2 µg/mL) for 4 days after cell seeding in CTS Essential 8 medium


title: E8-iMatrix511-2

source_name: 201B7 cells were cultured on iMatrix-511 for 4 days after cell seeding in CTS Essential 8 medium


title: E8-MFGE8-2

source_name: 201B7 cells were cultured in gelatin solution (10%) + MFGE 8 (2 µg/mL) for 4 days after cell seeding in CTS Essential 8 medium


title: CK1-2

description:
bite
4 days post tick bite


title: AK03-iMatrix511-1

description: 201B7 cells were cultured on iMatrix-511 for 4 days after cell seeding in Stem Fit AK03 medium


title: EF19-6-7

description:
bite
4 days post tick bite


title: EF19-6-15

description:
no bite
4 days post tick bite


title: Ent. faecalis 14 delta pnpA rep. 3 [P3-6h]

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

description: Gene expression after 6h of culture

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-086007 EfaecalisDD14_V2 microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides 8x15K were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting

data_processing: The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Enterococcus faecalis

source_name: Ent. faecalis 14 delta pnpA-6h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cultures of E. faecalis strains were performed in M17 medium supplemented with glucose at 0.5% (w/v) to obtain the GM17, or in brain heart infusion (BHI), under semi-aerobic condition at 37°C. When necessary, media were supplemented with erythromycin (Em) (150 µg/mL) or chloramphenicol (Cm) (15 µg/mL). Growth of E. faecalis cultures was followed by measuring the optical density at a wavelength of 600 nm (OD600) with a spectrophotometer (Aquoalabo, France), and by determining cfu counts on agar plates. E. coli strains were cultivated at 37°C in Luria-Bertani (LB) broth with shaking (160 rpm) or on LB agar medium. When appropriate, erythromycin (150 µg/mL) or chloramphenicol (10 µg/mL) or ampicillin (100µ/mL) was added to the medium. Bacterial stocks were stored at - 80°C in GM17, BHI or LB broth supplemented with 50% (v/v) glycerol.

extract_protocol: For microarray analysis, three distinct cultures of Ent. faecalis 14 ∆pnpA were used (P1, P2 and P3) in order to carry comparisons with Ent. faecalis 14 (WT1, WT2 and WT3), after 3h and after 6h of growth in GM17 medium respectively. Analyses were performed with total RNA isolated using NucleoSpinTM RNA Plus columns (Macherey-Nagel, Hoerdt, France). RNA quality was observed with Nanodrop and absorbance ratios A260/280 and A260/230 were found between 2.0 and 2.2. RNA quality was also examined with Bioanalyzer 2100 (Agilent, Les Ulis, France) and a minimal RNA integrity number (RIN) of 0.8 was required for all samples.

treatment_protocol: The ∆pnpA mutant strain was constructed by allelic exchange using a method based on the conditional replication of the pLT06 vector.

tag: strain background

value: delta pnpA

value: 6 hours


title: D816+NAG-1

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

institute: INSERM

data_processing:
Short reads were quality-filtered according to the Illumina pipeline. Sequencing adaptors were removed, and trimmed reads were aligned to the human genome (hg19) using tophat2 (Version 2.0.11) and then filtered according to mapping quality value (mapq value, option –q 10).
Then, peaks detection was made independently on each of these filtered bam files by macs2 (v 2.1.1) with no control and default options
Then all peaks from D816+NAG and D816-NAG samples were pooled and merged together with bedtools (v 2.26.0).
Genome_build: hg19

source_name: Mast cells

growth_protocol: The human mast cell lines ROSA KIT WT and ROSA KIT D816V were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% heat inactivated fetal calf serum FCS, 100 μg/mL streptomycin, 100 IU/mL penicillin, 2 mM L-glutamine and 1mM sodium pyruvate (complete medium) (Saleh et al., 2014) with additional 80ng/mL murine stem cell factor.

extract_protocol:
100K cells were harvested and resuspended in 500 μl of growth media plus 5% DMSO, transferred to a 1.7 mL microfuge tube on ice and frozen at a slow cooling rate. ATAC-seq was performed at Active Motif (Carlsbab, CA) following a previously published protocol (Buenrostro et al., 2015).
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ROSAKIT WT and ROSAKIT D816V cells were cultured overnight in low glucose (1g/L) medium and incubated with GlcNAc 20 mM for 24 hours.

value: ROSA Kit D816V mast cell line

tag: passage

value: 20 mM NAG (or GlcNAc) for 24h


title: AK03-MFGE8-2

description: 201B7 cells were cultured in gelatin solution (10%) + MFGE 8 (2 µg/mL) for 4 days after cell seeding in Stem Fit AK03 medium


title: AK03-MFGE8-1

source_name: 201B7 cells were cultured in gelatin solution (10%) + MFGE 8 (2 µg/mL) for 4 days after cell seeding in Stem Fit AK03 medium


title: Ent. faecalis 14 wild type rep.3 [WT3-6h]

description: Gene expression after 6h of culture

source_name: Ent. faecalis 14 wild type-6h

value: wild type

tag: age


title: Es-cell

description: public database as controls (GSE43328)


title: AK03-iMatrix511-2

source_name: 201B7 cells were cultured on iMatrix-511 for 4 days after cell seeding in Stem Fit AK03 medium


title: D816+NAG-2


title: Ent. faecalis 14 wild type rep.1 [WT1-6h]

description: Gene expression after 6h of culture


title: Ent. faecalis 14 delta pnpA rep.1 [P1-6h]

description: Gene expression after 6h of culture


title: EF19-6-3

description:
bite
4 days post tick bite

value: ticks 2x


title: WT+NAG-2

value: ROSA Kit WT mast cell line


title: EF19-6-1

description:
bite
4 days post tick bite


title: EF19-6-5

description:
bite
4 days post tick bite


title: Ent. faecalis 14 wild type rep.2 [WT2-6h]

description: Gene expression after 6h of culture


title: EF19-4-7

description:
bite
4 days post tick bite

value: saliva immune


title: Ent. faecalis 14 delta pnpA rep. 2 [P2-6h]

description: Gene expression after 6h of culture


title: Ent. faecalis 14 delta pnpA rep.2 [P2-3h]

description: Gene expression after 3h of culture

source_name: Ent. faecalis 14 delta pnpA-3h

value: 3 hours


title: Ent. faecalis 14 delta pnpA rep.3 [P3-3h]

description: Gene expression after 3h of culture


title: WT2


title: WT+NAG-1


title: D816-2


title: EF19-4-5

description:
bite
4 days post tick bite


title: D816-1


title: EF19-4-1

description:
bite
4 days post tick bite


title: WT1


title: Ent. faecalis 14 wild type rep.3 [WT3-3h]

description: Gene expression after 3h of culture

source_name: Ent. faecalis 14 wild type-3h


title: Ent. faecalis 14 delta pnpA rep.1 [P1-3h]

description: Gene expression after 3h of culture


title: follicular granulosa cell layers-F1 RNA-seq replicate_3

status: Public on Apr 19 2023

city: ChengDu

first: Diyan

last: Li

state: SiChuan

address: 2025 Shiling Street, Chengluo Avenue, Chengdu City, Sichuan Province, China

institute: Chengdu University

data_processing:
sequence reads are aligned to chicken reference genome (GRCg6a) by HISAT2 2.1.0.
the processed reads were mapped to the chicken reference genome (GRCg6a) using HISAT2 2.1.0
mapped reads were assembled and then quantified for gene expression based on the FPKM values of each mRNA using StringTie v1.3.3
cutoff. MaSigPro (v 3.12)72 was used to identify the genes with dynamic temporal expression profiles
Assembly: GRCg6a
Supplementary files format and content: mRNA expression level (FPKM), xlsx file

organism: Gallus gallus

source_name: follicular granulosa cell layers

extract_protocol:
total RNA was extracted from each sample using RNAiso Plus reagent (TaKaRa, Otsu, Shiga, Japan) following the manufacturer’s instructions.
Strand-specific libraries (total of 10 stages with three biological replicates in each stage) were generated after depleting rRNA by the Ribo-Zero™ Gold Kit (Illumina, San Diego, CA, USA). cDNA libraries were  sequenced on HiSeq X Ten (Illumina) platform to produce  150-bp paired-end raw reads.

tag: breed

value: Luhua hens

tag: developmental stage

value: preovulatory follicles

value: 31 weeks


title: follicular granulosa cell layers-POF RNA-seq replicate_1

value: postovulatory follicles


title: follicular granulosa cell layers-F1 RNA-seq replicate_2


title: follicular granulosa cell layers-POF RNA-seq replicate_2


title: follicular granulosa cell layers-POF RNA-seq replicate_3


title: EF19-4-3

description:
bite
4 days post tick bite

value: 1st exposure

value: Skin


title: follicular granulosa cell layers-F2 RNA-seq replicate_2


title: follicular granulosa cell layers-F3 RNA-seq replicate_3


title: follicular granulosa cell layers-F2 RNA-seq replicate_3


title: follicular granulosa cell layers-F2 RNA-seq replicate_1


title: Ent. faecalis 14 wild type rep.1 [WT1-3h]

description: Gene expression after 3h of culture


title: Ent. faecalis 14 wild type rep.2 [WT2-3h]

description: Gene expression after 3h of culture


title: follicular granulosa cell layers-F3 RNA-seq replicate_2


title: follicular granulosa cell layers-F4 RNA-seq replicate_3


title: follicular granulosa cell layers-F1 RNA-seq replicate_1


title: follicular granulosa cell layers-F4 RNA-seq replicate_2


title: follicular granulosa cell layers-F4 RNA-seq replicate_1


title: follicular granulosa cell layers-F5 RNA-seq replicate_2


title: follicular granulosa cell layers-F5 RNA-seq replicate_3


title: follicular granulosa cell layers-F5 RNA-seq replicate_1


title: follicular granulosa cell layers-LYF RNA-seq replicate_1

value: prehierarchical follicles


title: follicular granulosa cell layers-F3 RNA-seq replicate_1


title: follicular granulosa cell layers-LYF RNA-seq replicate_2


title: follicular granulosa cell layers-SYF RNA-seq replicate_1


title: follicular granulosa cell layers-SYF RNA-seq replicate_2


title: follicular granulosa cell layers-LWF RNA-seq replicate_3


title: follicular granulosa cell layers-LWF RNA-seq replicate_2


title: follicular granulosa cell layers-LWF RNA-seq replicate_1


title: follicular granulosa cell layers-SWF RNA-seq replicate_2


title: follicular granulosa cell layers-SWF RNA-seq replicate_3


title: follicular granulosa cell layers-SWF RNA-seq replicate_1


title: follicular granulosa cell layers-SYF RNA-seq replicate_3


title: oocyte_PL_rep5

city: Raleigh

first: Nathan

last: Harry

state: North Carolina

address: 112 Derieux Place

institute: North Carolina State University

description: 2 tech replicates

data_processing:
Base trimming with TrimGalore (catadapt) and FastP
rRNA read removal with SortMErna
Alignment to reference genome with HISAT2, stranded, splice-site aware, default params
Gene expression counting with HTSeq-count
Assembly: NCBI: PRJNA721660
Supplementary files format and content: count matrix for each sample produced by HTSeq-count

organism: Streblospio benedicti

growth_protocol: Females reared in isolation to avoid fertilization

extract_protocol:
Arcturus PicoPure
NEB UltraII Stranded RNA library prep kit for Illumina

value: oocyte

value: PL

tag: morphotype

value: F1-cross offspring

tag: population

value: Lab cross


title: oocyte_LL_rep6

description: 2 tech replicates

tag: tissue

value: LL

value: Lecithotrophic

value: Long Beach, CA


title: oocyte_PL_rep3

description: 2 tech replicates


title: oocyte_PL_rep4

description: 2 tech replicates


title: oocyte_PL_rep2

description: 2 tech replicates


title: oocyte_PL_rep1

description: 2 tech replicates


title: follicular granulosa cell layers-LYF RNA-seq replicate_3


title: oocyte_LP_rep5

description: 2 tech replicates

value: LP


title: oocyte_LP_rep4

description: 2 tech replicates


title: oocyte_LP_rep1

description: 2 tech replicates


title: oocyte_LP_rep2

description: 2 tech replicates


title: oocyte_PP_rep7

description: 2 tech replicates

value: PP

value: Planktotrophic

value: Bayonne, NJ


title: oocyte_LL_rep5


title: oocyte_LL_rep4


title: oocyte_LL_rep2


title: oocyte_PP_rep5


title: oocyte_PP_rep4


title: oocyte_LL_rep3


title: oocyte_PP_rep3


title: oocyte_PP_rep2


title: oocyte_LP_rep3

description: 2 tech replicates


title: oocyte_PP_rep6


title: oocyte_PP_rep1


title: oocyte_LL_rep1


title: oocyte_LL_rep7

description: 2 tech replicates


title: R2: 100nM Rapa

type: genomic

city: Rio de Janeiro

first: Mariana

last: Boroni

state: RJ

address: Rua André Cavalcanti 37

country: Brazil

institute: Instituto Nacional de Câncer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC chip using standard Illumina protocol

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

data_processing: Raw methylation files (idat) were converted to beta values using the minfi package version 1.32.0 66 after the quality control and quantile normalization using the function betaqn from the wateRmelon package version 1.30.0 67.

label: Cy3, Cy5

source_name: Ex vivo skins - Rapa treatment

label_protocol: Standard Illumina Protocol

extract_protocol: Total DNA samples were obtained from human skin biopsy samples (female, caucasian, 79 yr) using the QIAamp DNA Mini Kit (Qiagen) and applied to the human Illumina Infinium EPIC 850K chip, as described previously Boroni et al (2022).

treatment_protocol: DNA samples included control, 5 days treatment with 12.5 μM Pep 14, and 5 days treatment with 100 nM Rapamycin, 3 independent replicates each.

tag: Sex

value: Female

value: Ex vivo skin

value: Rapa treatment


title: R1: 100nM Rapa

tag: treatment


title: P1: 12.5uM Pep14

source_name: Ex vivo skins - Pep treatment

value: Pep treatment


title: FU05-OC

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: Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software

label: biotin

source_name: Ovarian Cancer (OC)

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

extract_protocol: RNA was extracted with miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

tag: disease state

value: Ovarian Cancer (OC)

value: Angiogenic

value: Chemo+BEVA

tag: egfr status

value: M

tag: cell type

value: tumor cells


title: FP44-OC

value: nonAngiogenic

value: MM


title: FT38-OC


title: FT39-OC


title: R4: 100nM Rapa


title: FT37-OC


title: FT36-OC


title: P2: 12.5uM Pep14


title: C4: Ctrl

source_name: Ex vivo skins - no treatment

value: no treatment


title: FP42-OC


title: R3: 100nM Rapa


title: P3: 12.5uM Pep14


title: FP43-OC


title: FT30-OC


title: FT29-OC


title: FP40-OC


title: FU04-OC


title: FU02-OC


title: FP41-OC


title: FT27-OC


title: FT28-OC


title: FT33-OC


title: FT26-OC


title: C1: Ctrl


title: P5: 12.5uM Pep14


title: C3: Ctrl


title: C2: Ctrl


title: FT25-OC


title: FT34-OC


title: FT22-OC


title: FP38-OC


title: FT19-OC


title: FT23-OC


title: FT20-OC


title: FT21-OC


title: FT99-OC


title: FT14-OC


title: FP34-OC


title: FT16-OC


title: FT17-OC


title: FT13-OC


title: FT12-OC


title: FT09-OC


title: FT11-OC


title: FT04-OC


title: FP32-OC


title: FT02-OC


title: FT96-OC


title: FT03-OC


title: FT95-OC


title: FT98-OC


title: FT10-OC


title: FT06-OC


title: FS99-OC


title: FP33-OC


title: FT18-OC


title: FT97-OC


title: FS95-OC


title: FT08-OC


title: FT00-OC


title: FS96-OC


title: FS98-OC


title: FP31-OC


title: FS91-OC


title: FS90-OC


title: FP29-OC


title: FT24-OC


title: FP28-OC


title: FT93-OC


title: FS93-OC


title: FS85-OC


title: FS86-OC


title: FP30-OC


title: FP27-OC


title: FP25-OC


title: FT90-OC


title: GD28-OC


title: FS84-OC


title: FT92-OC


title: FS79-OC


title: FS82-OC


title: FS78-OC


title: FS76-OC


title: FP22-OC


title: FS88-OC


title: FP24-OC


title: FS87-OC


title: FT88-OC


title: FP26-OC


title: FS74-OC


title: FS72-OC


title: FT85-OC


title: FS68-OC


title: FS70-OC


title: FT87-OC


title: FS69-OC


title: FP23-OC


title: FT86-OC


title: FS75-OC


title: FP19-OC


title: FS73-OC


title: FP20-OC


title: FU01-OC


title: FS65-OC


title: FS62-OC


title: FS63-OC


title: FS64-OC


title: FT84-OC


title: FS66-OC


title: FT83-OC


title: FP18-OC


title: FT82-OC


title: FP17-OC


title: FS60-OC


title: FP15-OC


title: FP12-OC


title: FS58-OC


title: FS55-OC


title: FS53-OC


title: FP08-OC


title: FS54-OC


title: FP14-OC


title: FP11-OC


title: FT79-OC


title: FP07-OC


title: FT81-OC


title: FS51-OC


title: FP06-OC


title: FS46-OC


title: FP04-OC


title: FS48-OC


title: FP10-OC


title: FT76-OC


title: FP05-OC


title: FS49-OC


title: FT78-OC


title: FS56-OC


title: FS52-OC


title: FS45-OC


title: FS40-OC


title: FS42-OC


title: FS39-OC


title: FS36-OC


title: FT73-OC


title: FS31-OC


title: FP00-OC


title: FQ96-OC


title: FS28-OC


title: FS34-OC


title: FS24-OC


title: FQ98-OC


title: FQ93-OC


title: FT71-OC


title: FS23-OC


title: FS33-OC


title: FT72-OC


title: FS29-OC


title: FS27-OC


title: FS26-OC


title: FQ95-OC


title: FS22-OC


title: FS25-OC


title: FP02-OC


title: GC64-OC


title: GD20-OC


title: FS21-OC


title: FQ89-OC


title: FQ92-OC


title: FS17-OC


title: FQ87-OC


title: FS18-OC


title: FQ90-OC


title: FS20-OC


title: FS15-OC


title: FQ91-OC


title: FQ84-OC


title: FS19-OC


title: GC53-OC


title: FQ82-OC


title: FT65-OC


title: FS14-OC


title: FT64-OC


title: FS11-OC


title: FS13-OC


title: FQ81-OC


title: FS43-OC


title: FT69-OC


title: FS05-OC


title: FS35-OC


title: FS09-OC


title: Raji WGS

city: Guangzhou

first: yuyan

last: wang

address: Zhongshan 2nd Road, Yuexiu

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
RNA-seq: The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
ChIP-seq: Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports
Library strategy: WGS

source_name: Raji

extract_protocol:
Genome DNA were extracted using DNeasy Blood & Tissue Kit (69,506, Qiagen, Germany). The PCR reaction was conducted using Q5 Hot Start High-Fidelity 2X Master Mix (M0494S, NEW ENGLAND BioLabs, USA).
For short reads sequencing, PE100 bp read length sequencing was performed on the BGISEQ-500 sequencer after size selection by gel electrophoresis and 10 to 12 cycles of PCR. For long reads sequencing, size-select long DNA fragments used the BluePippin system and then libraries were constructed and sequenced following Nanopore standard protocol.

tag: cell line

value: Raji


title: S12 WGS


title: C33A WGS


title: FS04-OC


title: FS03-OC


title: FQ69-OC


title: FR98-OC


title: FQ67-OC


title: FQ78-OC


title: FT68-OC


title: Th17 cells from 2# WT mouse, 72h

city: Beijing

first: ziheng

last: zhao

address: 38 Xueyuan Road, Haidian District

institute: Peking university

description: Naïve CD4+ T cells were entiched from 2#WT mouse and were polarized into Th17 cells for 72h in vitro. All the cells on day3 were collected and used for sequence.

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2), removing the sequencing adapter and low-quality reads, which was defined as low-quality (≤5) base ratio is more than 20% or the unknown base ratio is more than 5%), afterwards clean reads were obtained and stored in FASTQ format.
Thefiltered reads were mapped to mus musculus genome(GRCm38.p6) using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5)  was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Assembly: GRCm38.p6
Supplementary files format and content: The "gene_expression"  file includes FPKM, TPM and read count values for all the samples, which is tab-delimited

source_name: Th17 cells

extract_protocol: Total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions. Further processing was completed by using a BGISEQ platform (Shenzhen Huada Gene Science and Technology Service Co., Ltd., Shenzhen, China).

value: Th17 cells

tag: genotype

value: Wild type

value: Th17 differentiation

tag: time


title: Th17 cells from 1# WT mouse, 72h

description: Naïve CD4+ T cells were entiched from 1#WT mouse and were polarized into Th17 cells for 72h in vitro. All the cells on day3 were collected and used for sequence.


title: Th17 cells from 2# PRAK KO mouse, 72h

description: Naïve CD4+ T cells were entiched from 2#PRAK KO mouse and were polarized into Th17 cells for 72h in vitro. All the cells on day3 were collected and used for sequence.

value: PRAK KO


title: FS06-OC

tag: gender

value: Female


title: Th17 cells from 1# PRAK KO mouse, 72h

description: Naïve CD4+ T cells were entiched from 1#PRAK KO mouse and were polarized into Th17 cells for 72h in vitro. All the cells on day3 were collected and used for sequence.


title: FQ77-OC


title: FQ83-OC


title: FR97-OC


title: FQ79-OC


title: CaSki WGS

source_name: CaSki

value: CaSki


title: FS00-OC


title: CL56+EPS

city: Blommenholm

first: Kari Bente

middle: Foss

last: Haug

address: Skogstien 28

department: Medical Biochemistry

country: Norway

institute: Oslo University Hospital

description: total RNA, short <200 bp

hyb_protocol: Labeled RNA was hybridized to the Affymetrix GeneChip Multispecies miRNA-4_0 Array (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix)

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization.

source_name: Mature myotubes from m.obliquus internus abdominis with EPS for 24 h, collected after 24 h serum free cultivation

label_protocol: 2.5 ng of total RNA was subjected to the Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit, following the manufacturer’s protocol (Affymetrix).

growth_protocol: Cultures of multinucleated human myotubes were established by activation and proliferation of satellite cells isolated from muscle biopsy samples from m. obliquus internus abdominis.The biopsies were taken from 6 donors during gastric bypass surgery.All donors were female, average age 49 (± 12) years, BMI 45 (± 5) kg/m2, and all were diagnosed with T2D and treated with peroral antidiabetics or insulin. Average HbA1c was 6.7 (± 1.2) %, and fasting plasma glucose was 6.8 (± 0.9) mmol/L in blood samples collected the day before surgery.Satellite cells were isolated from biopsy samples by enzymatic digestion [35]. Briefly, the muscle biopsies were cut into small pieces, rinsed for adipose tissue, and trypsinized 3 times. The supernatants were collected, and the cells seeded in SkGMTM-2 (Skeletal Muscle Cell Growth Medium-2 BulletKit, (Lonza, Basel, Switzerland). For proliferation of myoblasts, DMEM-GlutamaxTM (5.5 mM glucose) medium supplemented with FBS (2 %) and Ultroser G (2 %) was used. At approximately 80 % confluence, the culture medium was changed to DMEM-GlutamaxTM (5.5 mM glucose) supplemented with FBS (2 %) and insulin (25 pM) to initiate differentiation into multinucleated myotubes. Both cell media contained gentamicin and amphotericin B. The cells were grown in 6-well plates pre-coated with extracellular matrix gel (ECM). The cells were allowed to differentiate for seven days. During the culturing process muscle cells were incubated in a humidified CO2 (5 %) atmosphere at 37°C, and medium was changed every 2nd to 3rd day.

extract_protocol: Myotubes were disrupted by adding 150 µL RLT Plus Lysis buffer (Qiagen) to each well of the 6-well culturing plate. Cell lysates were incubated at 4 oC for 15 min and shaken, before further storage at -20 oC. Total RNA was isolated by combining two procedures; long RNA (>200 bp) was extracted using RNeasy Plus Mini-kit (Qiagen), whereas short RNA (<200 bp) was isolated from the flow-through of the first procedure by the RNeasy MinElute Cleanup kit (Qiagen), essentially following the manufacturer´s protocols.   Lysates were gently thawed, thoroughly vortexed, and transferred to a gDNA Eliminator spin column for centrifugation at 8000 g for 15 s in RT. Flow-through was added 1 volume of 70 % ethanol, mixed by pipetting, and immediately loaded on a RNeasy Mini spin column for centrifugation at 8000 g for 15 s.  Whereas the spin column was stored at 4 oC until isolation of large RNA, the flow-through was transferred to a new tube, added 0.65 volume 100 % ethanol, and mixed by vortexing. The samples were immediately transferred to a RNeasy MinElute spin column and centrifuged at 8000 g for 15 s. The columns were washed twice by RPE buffer, added 80 % ethanol, and centrifugation was repeated. The columns were placed in a new tube, centrifuged at 8000 g for 1 min with open lid and transferred to new 1.5 mL tubes. Finally, small RNA was eluted from the column by 14 µL RNase-free water and centrifuged for 1 min at 8000 g.

treatment_protocol: Electrical pulse stimulation of mature myotubes for 24 hours.  Human myotubes grown in 6-well EMC coated Costar plates (Corning®) were stimulated via carbon electrodes (C-dish, Ionoptics, Ireland) by applying continuous, low-frequency electrical pulse stimulation (EPS) (single, bipolar pulses of 2 ms, 30 V, 1 Hz) for 24 h from day 6 to 7 of the differentiation period, as described previously [34]. Electrical pulses were generated by a self-designed pulse generator (the Electronics Lab, Institute of Chemistry, University of Oslo, Norway), and the effect was investigated by measuring IL-6 concentration in the supernatants before and after EPS.

value: female

tag: age years

value: type 2 diabetes, morbidly obese

value: Metformin

tag: cells

value: skeletal muscle, mature myotubes, in vitro model


title: CL56-EPS

description: total RNA, short <200 bp

source_name: Mature myotubes from m.obliquus internus abdominis without EPS for 24 h, collected after 24 h serum free cultivation


title: CL47-EPS

description: total RNA, short <200 bp


title: CL14+EPS

description: total RNA, short <200 bp

value: Metformin + glimeperide


title: EXO56-EPS

source_name: Extracellular vesicles, exosomes from mature myotubes without EPS for 24 h, collected after 24 h serum free cultivation

label_protocol: 2.5  ng of total RNA was subjected to the Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit, following the manufacturer’s protocol (Affymetrix).

growth_protocol: Cultures of multinucleated human myotubes were established by activation and proliferation of satellite cells isolated from muscle biopsy samples from m. obliquus internus abdominis. The biopsies were taken from 6 donors during gastric bypass surgery. All donors were female, average age 49 (± 12) years, BMI 45 (± 5) kg/m2, and all were diagnosed with T2D and treated with peroral antidiabetics or insulin. Average HbA1c was 6.7 (± 1.2) %, and fasting plasma glucose was 6.8 (± 0.9) mmol/L in blood samples collected the day before surgery.  Satellite cells were isolated from biopsy samples by enzymatic digestion [35]. Briefly, the muscle biopsies were cut into small pieces, rinsed for adipose tissue, and trypsinized 3 times. The supernatants were collected, and the cells seeded in SkGMTM-2 (Skeletal Muscle Cell Growth Medium-2 BulletKit, (Lonza, Basel, Switzerland). The cells were split twice before storage in liquid nitrogen. For proliferation of myoblasts, DMEM-GlutamaxTM (5.5 mM glucose) medium supplemented with FBS (2 %) and Ultroser G (2 %) was used. At approximately 80 % confluence, the culture medium was changed to DMEM-GlutamaxTM (5.5 mM glucose) supplemented with FBS (2 %) and insulin (25 pM) to initiate differentiation into multinucleated myotubes. Both cell media contained gentamicin and amphotericin B. The cells were grown in 6-well plates pre-coated with extracellular matrix gel (ECM). The cells were allowed to differentiate for seven days. During the culturing process muscle cells were incubated in a humidified CO2 (5 %) atmosphere at 37°C, and medium was changed every 2nd to 3rd day. Exosome and microvesicle isolation  After 24 h of EPS, cell medium was changed to serum free DMEM-GlutamaxTM (5.5 mM glucose) with 25 pM insulin, gentamicin, and amphotericin B, 1 ml/well for collecting EVs. The cells were incubated for another 24 h for synthesis and secretion of EVs and then harvested. EV-containing media were collected, and both exosomes and microvesicles (MV) were isolated. Briefly, media from parallel 6-well plates were combined, remnant cells and cell debris were removed by centrifugation at 4500 g for 5 min, and the final cell free supernatants were stored at -80°C.   Supernatants were thawed at 37°C, and MV were isolated by centrifugation at 17000 g for 30 min using a fixed-angle Sorvall SS-34 rotor (Kendro Laboratory Products, Newtown, CT, USA). The remaining supernatant was transferred to a new vial for exosome isolation.  MV pellets were thoroughly dissolved in the residual supernatant (2 ml) and concentrated using Amicon Ultra-4 100 kDa Centrifugal Filter Devices (Merck Millipore, Cork, Ireland). To exclude particles greater than 220 nm in the exosome preparation, the 17000 g supernatant was gently filtered through a 0.22 um filter (Merk Millipore) before exosomes were isolated by Centricon-70 Plus 100 kDa Centrifugal Filter Columns (Merk Millipore). Column units were centrifuged at 3500 g for 15 min, filters washed with PBS and further centrifuged at 3500 g for 10 min. Finally, the filters were turned upside down, centrifuged at 1000 g for 2 min, and the exosome concentrates were collected. All centrifugations were performed at room temperature (RT), and all samples were stored in aliquots at -80°C.

extract_protocol: Total RNA from the exosomes and MV suspensions were isolated using miRNeasy Micro kit (Qiagen, Hilden, Germany) following the manufacturer´s protocol. In short, up to 150 µL EV-solution was transferred to an Eppendorf tube containing 700 µL Qiazol, incubated in RT, added chloroform, and shaken vigorously, before the tube was incubated for 3 min at RT and centrifuged at 12000 g for 15 min at 4 oC. The upper phase was transferred to a new tube, mixed thoroughly with 1.5 volume 100% ethanol, and filled into a RNeasy Min Elute column before a short centrifugation step at 8000 g. Flow-through was discarded, the column washed with buffers RWT and RPE, centrifuged at 8000 g before   80 % ethanol was added, and the column centrifuged dry with open lid. Finally, RNA was eluted in 14 µl nuclease free water and stored at -80 oC until analyzed.

treatment_protocol: Electrical pulse stimulation of myotubes for 24 h and secretion of exosomes after 24 h in serum free medium  Human myotubes grown in 6-well EMC coated Costar plates (Corning®) were stimulated via carbon electrodes (C-dish, Ionoptics, Ireland) by applying continuous, low-frequency electrical pulse stimulation (EPS) (single, bipolar pulses of 2 ms, 30 V, 1 Hz) for 24 h from day 6 to 7 of the differentiation period, as described previously [34]. Electrical pulses were generated by a self-designed pulse generator (the Electronics Lab, Institute of Chemistry, University of Oslo, Norway), and the effect was investigated by measuring IL-6 concentration in the supernatants before and after EPS.

tag: age

value: type 2 diabetes, mobidly obese

value: metformin

value: exosomes, secreted from mature myotubes, in vitro model from skeletal muscle


title: CL14-EPS

description: total RNA, short <200 bp


title: EXO46+EPS

source_name: Extracellular vesicles, exosomes from mature myotubes with EPS for 24 h, collected after 24 h serum free cultivation

value: insulin


title: CL46-EPS

description: total RNA, short <200 bp


title: EXO46-EPS


title: CL46+EPS

description: total RNA, short <200 bp


title: 3_TNF-α-induced chondrocytes_NFL

city: Hangzhou

first: Yanzhi

last: Ge

address: 548 Binwen Road, Binjiang District

institute: Zhejiang Chinese Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2).
Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%
Removing reads whose unkown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained  and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: tab-delimited text files include FPKM, TPM values and read count for each Sample

organism: Rattus norvegicus

source_name: Primary chondrocytes

extract_protocol:
Total RNA was extracted from the chondrocytes using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo (dT)-attached magnetic beads were used to purified mRNA. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq 500 platform (BGI-Shenzhen, China).

tag: strain

value: Sprague-Dawley

value: Primary chondrocytes

value: WT

value: TNF-α+NFL


title: 2_TNF-α-induced chondrocytes_NFL


title: 1_TNF-α-induced chondrocytes_NFL


title: 3_TNF-α-induced chondrocytes_Ctrl

value: TNF-α


title: MV56+EPS

source_name: Extracellular vesicles, microvesicles secreted from EPS treated mature myotubes after 24 h

growth_protocol: Cultures of multinucleated human myotubes were established by activation and proliferation of satellite cells isolated from muscle biopsy samples from m. obliquus internus abdominis. The biopsies were taken from 6 donors during gastric bypass surgery. All donors were female, average age 49 (± 12) years, BMI 45 (± 5) kg/m2, and all were diagnosed with T2D and treated with peroral antidiabetics or insulin. Average HbA1c was 6.7 (± 1.2) %, and fasting plasma glucose was 6.8 (± 0.9) mmol/L in blood samples collected the day before surgery.  Satellite cells were isolated from biopsy samples by enzymatic digestion [35]. Briefly, the muscle biopsies were cut into small pieces, rinsed for adipose tissue, and trypsinized 3 times. The supernatants were collected, and the cells seeded in SkGMTM-2 (Skeletal Muscle Cell Growth Medium-2 BulletKit, (Lonza, Basel, Switzerland). The cells were split twice before storage in liquid nitrogen. For proliferation of myoblasts, DMEM-GlutamaxTM (5.5 mM glucose) medium supplemented with FBS (2 %) and Ultroser G (2 %) was used. At approximately 80 % confluence, the culture medium was changed to DMEM-GlutamaxTM (5.5 mM glucose) supplemented with FBS (2 %) and insulin (25 pM) to initiate differentiation into multinucleated myotubes. Both cell media contained gentamicin and amphotericin B. The cells were grown in 6-well plates pre-coated with extracellular matrix gel (ECM). The cells were allowed to differentiate for seven days. During the culturing process muscle cells were incubated in a humidified CO2 (5 %) atmosphere at 37°C, and medium was changed every 2nd to 3rd day. Exosome and microvesicle isolation  After 24 h of EPS, cell medium was changed to serum free DMEM-GlutamaxTM (5.5 mM glucose) with 25 pM insulin, gentamicin, and amphotericin B, 1 ml/well for collecting EVs. The cells were incubated for another 24 h for synthesis and secretion of EVs and then harvested. EV-containing media were collected, and both exosomes and microvesicles (MV) were isolated. Briefly, media from parallel 6-well plates were combined, remnant cells and cell debris were removed by centrifugation at 4500 g for 5 min, and the final cell free supernatants were stored at 80 C.   Supernatants were thawed at 37 C, and MV were isolated by centrifugation at 17000 g for 30 min using a fixed-angle Sorvall SS-34 rotor (Kendro Laboratory Products, Newtown, CT, USA). The remaining supernatant was transferred to a new vial for exosome isolation.  MV pellets were thoroughly dissolved in the residual supernatant (2 ml) and concentrated using Amicon Ultra-4 100 kDa Centrifugal Filter Devices (Merck Millipore, Cork, Ireland). To exclude particles greater than 220 nm in the exosome preparation, the 17000 g supernatant was gently filtered through a 0.22 m filter (Merk Millipore) before exosomes were isolated by Centricon-70 Plus 100 kDa Centrifugal Filter Columns (Merk Millipore). Column units were centrifuged at 3500 g for 15 min, filters washed with PBS and further centrifuged at 3500 g for 10 min. Finally, the filters were turned upside down, centrifuged at 1000 g for 2 min, and the exosome concentrates were collected. All centrifugations were performed at room temperature (RT), and all samples were stored in aliquots at 80 C.

treatment_protocol: Electrical pulse stimulation of myotubes for 24 h and collecting microvesicles after 24 h in serum free medium  Human myotubes grown in 6-well EMC coated Costar plates (Corning®) were stimulated via carbon electrodes (C-dish, Ionoptics, Ireland) by applying continuous, low-frequency electrical pulse stimulation (EPS) (single, bipolar pulses of 2 ms, 30 V, 1 Hz) for 24 h from day 6 to 7 of the differentiation period, as described previously [34]. Electrical pulses were generated by a self-designed pulse generator (the Electronics Lab, Institute of Chemistry, University of Oslo, Norway), and the effect was investigated by measuring IL-6 concentration in the supernatants before and after EPS

value: microvesicles, secreted from mature myotubes, in vitro model from skeletal muscle


title: 2_TNF-α-induced chondrocytes_Ctrl


title: CL47+EPS

description: total RNA, short <200 bp


title: 1_TNF-α-induced chondrocytes_Ctrl


title: Heart  Dp16 + baricitinib; sample 4

city: Aurora

first: Matthew

last: Galbraith

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQ files from multiple sequencing lanes were merged to obtain sufficient raw reads.
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCm38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCm38 index with a Gencode M24 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode M24 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing per-gene strand-specific fragment counts.
Supplementary files format and content: Tab-delimited text files containing per gene normalized fragments-per-kilobase-per-million-mapped (FPKM).

source_name: heart

extract_protocol:
Total RNA was isolated using the AllPrep Kit (QIAGEN) per manufacturer instructions.
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA)

treatment_protocol: Mice 7-11 weeks old were treated with 10 mg/kg of baricitinib (or an equivalent volume of 0.5% methylcellulose vehicle) once a day via oral gavage for 17 days. Sham indicates a daily saline injection for comparison to animals treated with polyI:C (see PMID 33207208). Mice were euthanized by CO2 asphyxiation and cervical dislocation then immediately perfused with 1x PBS using a Perfusion Two Automated Perfusion Instrument (Leica).

value: heart

value: Female

tag: age in_days_post_birth

value: Sham+baricitinib (10mg/kg)


title: Heart  Dp16 + baricitinib; sample 3

value: Male


title: EXO56+EPS

value: female


title: MV14+EPS

value: type 2 diabetes, morbidly obese

value: metformin + glimepiride


title: MV47-EPS

source_name: Extracellular vesicles, microvesicles secreted from unstimulated mature myotubes after 24 h


title: MV14-EPS


title: MV47+EPS


title: EXO14+EPS

value: type 2 diabetes, mobidly obese


title: EXO14-EPS


title: Heart  Dp16 + baricitinib; sample 1


title: Heart  Dp16 + baricitinib; sample 2


title: FQ71-OC

value: Ovarian Cancer (OC)

value: nonAngiogenic

value: Chemo+BEVA

value: tumor cells


title: Heart  Dp16 + vehicle; sample 4

value: Sham+Vehicle


title: Heart Wild-type + vehicle; sample 2

value: wild-type


title: Heart  Dp16 + vehicle; sample 1


title: Heart Wild-type + vehicle; sample 1


title: Heart  Dp16 + vehicle; sample 2


title: Heart  Dp16 + vehicle; sample 3


title: Heart Wild-type + baricitinib; sample 2


title: MV56-EPS

value: metformin


title: Whole brain Dp16 + baricitinib; sample 4

source_name: whole brain

value: whole brain


title: Whole brain Dp16 + baricitinib; sample 2


title: Whole brain Dp16 + baricitinib; sample 3


title: Whole brain Dp16 + vehicle; sample 1


title: Whole brain Wild-type + baricitinib; sample 2


title: Whole brain Dp16 + vehicle; sample 2


title: Whole brain Dp16 + baricitinib; sample 1


title: Whole brain Dp16 + vehicle; sample 3


title: Whole brain Dp16 + vehicle; sample 4


title: Whole brain Wild-type + vehicle; sample 2


title: Whole brain Wild-type + baricitinib; sample 1


title: Dp16 + vehicle; sample 4

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCm38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCm38 index with a Gencode M24 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode M24 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing per-gene strand-specific fragment counts.
Supplementary files format and content: Tab-delimited text files containing per gene normalized fragments-per-kilobase-per-million-mapped (FPKM).

source_name: liver

value: liver


title: Dp16 + baricitinib; sample 4


title: Dp16 + baricitinib; sample 3


title: Dp16 + baricitinib; sample 1


title: Dp16 + baricitinib; sample 2


title: Dp16 + vehicle; sample 3


title: Dp16 + vehicle; sample 2


title: Dp16 + vehicle; sample 1


title: Wild-type + baricitinib; sample 2

value: wild-type C57BL/6


title: Wild-type + vehicle; sample 2


title: Heart Wild-type + baricitinib; sample 1

value: heart

value: Female


title: Wild-type + baricitinib; sample 1

value: Sham+baricitinib (10mg/kg)


title: 32406, Cerebral cortex, Dp(16)1/Df(16)8

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using bcl2fastq2 version 2.20
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v25) using STAR (v2.7.9a)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Assembly: GRCm38.p6 GENCODE r25
Supplementary files format and content: RawCounts.csv

source_name: Cerebral cortex

extract_protocol:
RNA was extracted by using an miRNeasy mini kit.
RNA-Seq libraries were prepared from 500 ng total RNA by using an RNA HyperPrep Kit along with RiboErase (HMR) kit.

value: Cerebral cortex


title: 32403, Cerebral cortex, Dp(16)1/Df(16)8

value: Male


title: 32346, Cerebral cortex, Dp(16)1/Df(16)8


title: 32130, Cerebral cortex, Dp(16)1/Df(16)8


title: 32334, Cerebral cortex, Dp(16)1/Df(16)8


title: 32401, Cerebral cortex, Dp(16)1/Df(16)8


title: 32341, Cerebral cortex, Dp(16)1/Df(16)8


title: 32251, Cerebral cortex, Dp(16)1/Df(16)8


title: 32370, Cerebral cortex, Ts65Dn;Df(17)2


title: 32368, Cerebral cortex, Ts65Dn;Df(17)2


title: 32141, Cerebral cortex, Dp(16)1/Df(16)8


title: 32359, Cerebral cortex, Ts65Dn;Df(17)2


title: 32358, Cerebral cortex, Ts65Dn;Df(17)2


title: 32142, Cerebral cortex, Dp(16)1/Df(16)8


title: Whole brain Wild-type + vehicle; sample 1


title: 27950, Cerebral cortex, Ts65Dn;Df(17)2


title: 32352, Cerebral cortex, Ts65Dn;Df(17)2


title: 32405, Cerebral cortex, +/+


title: FS01-OC

value: M


title: 32252, Cerebral cortex, +/+


title: 32395, Cerebral cortex, +/+


title: Wild-type + vehicle; sample 1


title: 32371, Cerebral cortex, +/+


title: 32342, Cerebral cortex, +/+


title: 32143, Cerebral cortex, +/+


title: 32356, Cerebral cortex, +/+


title: 32144, Cerebral cortex, +/+


title: 32350, Cerebral cortex, +/+


title: 32351, Cerebral cortex, +/+


title: 32369, Cerebral cortex, Ts65Dn;Df(17)2


title: 32373, Cerebral cortex, Ts65Dn;Df(17)2


title: 27951, Cerebral cortex, Ts65Dn;Df(17)2


title: 32372, Cerebral cortex, Ts65Dn;Df(17)2


title: 32333, Cerebral cortex, +/+


title: WT-Untreated-biol rep 4

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

data_processing:
Bulk RNAseq analysis: On average we received 30 million paired ends for each of the replicates. RNAseq libraries were checked for their quality using the fastqc program http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. The results from fastqc were aggregated using multiqc software1. Reads were mapped with the “splice aware” aligner ‘STAR’,2 to the transcriptome and genome of mm10 genome build. The HTseq3 software will be used to count aligned reads that map onto each gene. The count table was imported to R to perform differential gene expression analysis using the DESeq2 package4. Low expressed genes (genes expressed only in a few replicates and had low counts) was excluded from the analysis before identifying differentially expressed genes. Data normalization, dispersion estimates, and model fitting (negative binomial) was carried out with the DESeq function. The log-transformed, normalized gene expression of 500 most variable genes will be used to perform an unsupervised principal component analysis. The differentially expressed genes was ranked based on the log2fold change and FDR corrected p-values. The ranked file was used to perform pathway analysis using GSEA software5.  The enriched pathways were selected based on enrichment scores as well as normalized enrichment scores. The Enrichment Analysis for Gene Ontology was performed by topGO. The heatmaps were generated using pheatmap function in R.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: BMDMs

extract_protocol:
Cell pellets (10^6 cells) were sent to Genewiz, Azenta Life Sciences for extraction and sequencing
Library was constructed at Genewiz, Azenta Life Sciences

value: BMDMs

value: Macrophage

value: WT

value: Untreated


title: KO-Zymosan-3hr-biol rep 3

value: Mcu-/-

value: Zymosan 3hrs


title: WT-Untreated-biol rep 2


title: WT-Zymosan-3hr-biol rep 5


title: WT-Zymosan-3hr-biol rep 4


title: WT-Untreated-biol rep 1


title: WT-Zymosan-BAPTA-3hr-biol rep 3

value: Zymosan 3hrs + BAPTA


title: WT-Untreated-biol rep 3


title: WT-Zymosan-BAPTA-3hr-biol rep 4


title: WT-Zymosan-BAPTA-3hr-biol rep 2