title: YX_1009900102_E17_S113

description:
3.5 weeks old Schistosome cell 141
schisto3.5_tpm_unfiltered.csv.gz


title: H3K9Ac_K2

status: Public on Apr 03 2019

type: SRA

city: Bethesda

first: Suman Kumar

last: Vodnala

state: MD

address: 10 Center Drive

department: Surgery Branch

country: USA

institute: NCI

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2
Peaks were called usingHomer (findPeaks H3k9Ac_Veh_1 -i Input_V -region -size 1000 -minDist 2500), Common peaks between two conditions are merged into a sinle file using bedtools. significantly different peaks between Ctrl / K+ is caluclated using Deseq2 integrated in the homer package.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized bam files were processed to deeptools to generate bigwig files

molecule: genomic DNA

organism: Mus musculus

source_name: Primary T cells cultured for 10 days in Potassium

growth_protocol: CD8+ T cells from pmel mice were stimulated in vitro with 1 μM human gp100 peptide (10 μg/ml) for 5 days and secondary re-stimulation was done for 48hrs with plate-bound anti-CD3 (1 μg/ml; BD Biosciences) and soluble anti-CD28 (1 μg/ml; BD Biosciences) and expanded in culture medium containing 60 IU/mL of IL-2.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: CD8 T cell

tag: strain

tag: chip antibody

value: H3K9Ac_ChIP Grade (ab4441)


title: V1_H3K27me3

source_name: Primary T cells cultured for 10 days in Ctrl

value: H3K27me3_ChIP Grade (ab195477)


title: H3K9Ac_V1


title: H3K9Ac_K1


title: H3K9Ac_V2


title: YX_1009900102_M5_S293

city: Stanford

first: Yuan

last: Xue

state: CA

address: 318 Campus Drive

institute: Stanford University

description:
3.5 weeks old Schistosome cell 140
schisto3.5_tpm_unfiltered.csv.gz

library_source: transcriptomic

data_processing:
Read alignment, STAR, 2.5.0a,  –outSAMstrandField intronMotif --runThreadN {threads} --outFileNamePrefix {wdir} --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS NM MD --outReadsUnmapped Fastx --clip3pAdapterSeq CTGTCTCTTATACACATCT --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1; gene count, htseq-count, 0.10.0, -s no -t exon -r pos -f bam -i Parent -m intersection-strict
Genome_build: schistosoma_mansoni.PRJEA36577.WBPS9.genomic.ercc.fa
Supplementary_files_format_and_content: Comma-separated values of normalized gene count (tpm) matrix where rows are genes and columns are sample names.

molecule: total RNA

organism: Schistosoma mansoni

source_name: Schistosoma mansoni stem cells

extract_protocol:
Triton X-100 was used to lyse individual cells, Smart-seq2 protocol was followed to reverse transcribe and amplify mRNA.
Nextera XT DNA

value: stem cells

tag: mouse strain with s. mansoni

value: Swiss  Webster NR-21963

tag: worm age

value: 3.5 weeks


title: YX_1009900102_N18_S30

description:
3.5 weeks old Schistosome cell 138
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I12_S204

description:
3.5 weeks old Schistosome cell 139
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_N2_S14

description:
3.5 weeks old Schistosome cell 137
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B8_S32

description:
3.5 weeks old Schistosome cell 136
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D21_S93

description:
3.5 weeks old Schistosome cell 135
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C14_S62

description:
3.5 weeks old Schistosome cell 134
schisto3.5_tpm_unfiltered.csv.gz


title: Shenai1

city: Shanghai

first: Chong

last: Wang

address: Gangao Road 271

country: China

institute: Shanghai Liangrun

data_processing:
BWA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then got the clean reads.
Clean reads was classified and annotated to obtain the component and expression information of various sRNA in samples, the miRNA database is from miRBase version 21.
nCRNA sequences other than miRNA sequences in clean data were removed, and the remaining sequences were compared with all mature miRNA sequences of the species in the miRBase database, the number of reads per million (RPM) clean reads that were aligned to a specific miRNA was calculated.
Genome_build: Human NCBI genome Build 36 (hg18)
Supplementary_files_format_and_content: *.miR.expre.txt: Tab-delimited text files include RPM values for each sample.

organism: Homo sapiens

source_name: Urine

extract_protocol:
RNA of cells and exosomes was isolated using Trizol Plus RNA purification kit (Life Technologies, 12183555) according to manufacturer's protocol. The quality of the total RNA was assessed by Agilent 2100 Bioanalyzer using an RNA 6000 Pico Kit (Agilent Technologies). After verifying the quality of RNA, we proceeded to the second part of the protocol of small RNA enrichment from total RNA by increasing ethanol content of the sample and isolation over glass-fiber filter and elution. Later, quality of the small RNA samples was analyzed by Agilent 2100 Bioanalyzer using a Small RNA kit (Agilent Technologies). RNA total concentration was measured by Nanodrop, and miRNA concentration was measured with the Quant-iT RiboGreen Kit (Thermo-Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Urinary exosomes

tag: disease status

value: Clear cell renal cell carcinoma

tag: tumor stage

value: II

tag: age


title: Shenai3

value: III


title: ACHN

source_name: Kidney cancer cells

tag: cell line

value: ACHN

value: Human kidney cancer cells


title: Shenai2

value: I


title: Normal

value: Healthy


title: YX_1009900102_H1_S169

description:
3.5 weeks old Schistosome cell 133
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O4_S40

description:
3.5 weeks old Schistosome cell 132
schisto3.5_tpm_unfiltered.csv.gz


title: Mixture 13: 0% HEK, 100% Jurkat

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

description: RNA-seq of mixture of HEK and Jurkat cells with ERCC spike-ins

data_processing:
quality control: FastqQC
alignment: STAR (v 2.6.1b)
quantification: RSEM (v 1.3.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene level quantification by RSEM

molecule: polyA RNA

source_name: Mixture of HEK and Jurkat cells

growth_protocol: HEK-293T were obtained from ATCC and cultured in DMEM supplemented with 10% FBS, 2 mM l-glutamine and 100 U ml-1 penicillin–streptomycin. Jurkat cells were provided by laboratory of Prof. Robert D. Schreiber and cultured in RPMI supplemented with 10% FBS, 2mM l-glutamine and 100 U ml-1 penicillin–streptomycin. Both cell lines were passaged regularly twice per week. For experiment cells were harvested two days after last passage, pelleted and resuspended in PBS containing 0.2%BSA at concentration 106/mL. Mixtures of given proportions were then prepared by mixing HEK-293T and Jurkat cell suspensions into final volume of 1ml. Cell mixtures were then pelleted and further processed.

extract_protocol:
mRNA was extracted using oligo(dT) beads (Invitrogen)
RNA sequencing libraries were prepared and quantified as described previously in Vincent et al 2015. 1 uL of a 1:25 dilution of ERCC spike-in control (Invitrogen) was added to the mRNA prior to generating barcoded cDNA. At least n=2 technical replicates were performed for each condition.

value: Jurkat

tag: hek percentage

tag: jurkat percentage


title: Mixture 14: 0% HEK, 100% Jurkat


title: YX_1009900102_C12_S60

description:
3.5 weeks old Schistosome cell 130
schisto3.5_tpm_unfiltered.csv.gz


title: Mixture 12: 20% HEK, 80% Jurkat

value: Mixture of HEK and Jurkat cells


title: Mixture 11: 20% HEK, 80% Jurkat


title: YX_1009900102_O23_S59

description:
3.5 weeks old Schistosome cell 129
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O17_S53

description:
3.5 weeks old Schistosome cell 128
schisto3.5_tpm_unfiltered.csv.gz


title: Mixture 10: 40% HEK, 60% Jurkat


title: Mixture 9: 40% HEK, 60% Jurkat


title: YX_1009900102_A13_S13

description:
3.5 weeks old Schistosome cell 126
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J5_S221

description:
3.5 weeks old Schistosome cell 127
schisto3.5_tpm_unfiltered.csv.gz


title: 786-0


title: Mixture 7: 50% HEK, 50% Jurkat


title: YX_1009900102_A20_S20

description:
3.5 weeks old Schistosome cell 124
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D8_S80

description:
3.5 weeks old Schistosome cell 122
schisto3.5_tpm_unfiltered.csv.gz


title: Mixture 6: 60% HEK, 40% Jurkat


title: YX_1009900102_J6_S222

description:
3.5 weeks old Schistosome cell 125
schisto3.5_tpm_unfiltered.csv.gz


title: Mixture 5: 60% HEK, 40% Jurkat


title: YX_1009900102_P4_S64

description:
3.5 weeks old Schistosome cell 123
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K19_S259

description:
3.5 weeks old Schistosome cell 131
schisto3.5_tpm_unfiltered.csv.gz


title: Mixture 4: 80% HEK, 20% Jurkat


title: YX_1009900102_F1_S121

description:
3.5 weeks old Schistosome cell 121
schisto3.5_tpm_unfiltered.csv.gz


title: HK-2

source_name: Human Renal Epithelial Cells

value: Human renal epithelial cells


title: YX_1009900102_K5_S245

description:
3.5 weeks old Schistosome cell 120
schisto3.5_tpm_unfiltered.csv.gz


title: Mixture 2: 100% HEK, 0% Jurkat

value: HEK


title: YX_1009900102_D13_S85

description:
3.5 weeks old Schistosome cell 119
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_O20_S56

description:
3.5 weeks old Schistosome cell 118
schisto3.5_tpm_unfiltered.csv.gz


title: Mixture 1: 100% HEK, 0% Jurkat


title: YX_1009900102_C8_S56

description:
3.5 weeks old Schistosome cell 117
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_D5_S77

description:
3.5 weeks old Schistosome cell 116
schisto3.5_tpm_unfiltered.csv.gz


title: Mixture 8: 50% HEK, 50% Jurkat

description: RNA-seq of mixture of HEK and Jurkat cells with ERCC spike-ins


title: YX_1009900102_P6_S66

description:
3.5 weeks old Schistosome cell 115
schisto3.5_tpm_unfiltered.csv.gz


title: ATACseq_TNF_2

city: Ulsan

first: Sungho

last: Park

address: 50 UNIST-gil, Eonyang-eup

department: Life Science

country: South Korea

institute: Ulsan National Institute of Science and Technology

description: ATAC-seq

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed.
Sequenced reads were mapped to reference human genome (hg19 assembly) using Bowtie2 version 2.2.6 with default parameters.
HOMER version 4.7.2 (Heinz et al., 2010) to identify peaks of ChIP-seq enrichment over background.
Genome_build: hg19

source_name: Primary human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).

extract_protocol:
Nuclei were pelleted by centrifugation for 5 min at 500g, 4°C.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol developed by (Buenrostro et al., 2013); single end protocol.

treatment_protocol: Cells were treated with or without TNF (10ng/ml) for 24 hours.

value: peripheral blood

value: monocytes

tag: treatment

value: TNF (10ng/ml) for 24 hours


title: ATACseq_TNF_1

description: ATAC-seq


title: YX_1009900102_L13_S277

description:
3.5 weeks old Schistosome cell 114
schisto3.5_tpm_unfiltered.csv.gz

value: stem cells

value: Swiss  Webster NR-21963


title: Mixture 3: 80% HEK, 20% Jurkat


title: YX_1009900102_O3_S39

description:
3.5 weeks old Schistosome cell 112
schisto3.5_tpm_unfiltered.csv.gz

value: 3.5 weeks


title: YX_1009900102_G20_S164

description:
3.5 weeks old Schistosome cell 113
schisto3.5_tpm_unfiltered.csv.gz


title: ATACseq_CTL_2

description: ATAC-seq


title: 70VCC_hiseq

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

department: Medicine

institute: Albert Einstein College of Medicine

description:
J909_ACBJLYACXX_lane7_oneSampleInLaneNoDemulti_7OVCC.1
library strategy: OxBS-seq (Oxidative bisulfite sequencing)

data_processing:
adapters were trimmed from fastq files using trim_galore 0.4.0 with default parameters
reads were aligned to the PhiX RTA genome using bowtie2 with parameters: -N 1   Mapped reads were filtered away.
bisulfite mapping was performed with Bismark version 0.14.5 using default parameters.
Duplicate reads were marked with picard-tools 1.92.
number of methylated reads were counted  at each loci with mpileup2methylation.py
Genome_build: hg19
Supplementary_files_format_and_content: The output files are in bedGraph-like format with columns:  Chromosome, Position of C (0-based), Position of C +1, Percentage reads methylated, Count methylated reads, Total read count, Strand

extract_protocol:
Qiagen Gentra Puregene DNA isolation protocol
TrueMethyl® oxBS Module - NuGEN Technologies

treatment_protocol: 786-O ccRCC cells were treated either with control (catalase) or with catalase+ ascorbic acid (AA). Catalase was added 20 min prior to pH neutralized 1mM (millimolar) AA. AA treatment was for 6 hours. The media was then removed and fresh media was added. DNA was extracted 18 hours later. Rationale for adding catalase control was to neutralize the H2O2 produced by high dose AA, when added to culture media.

value: clear cell Renal Cell Carcinoma cell line

tag: type

value: BS

tag: drug

value: vitamin C


title: 70COC_hiseq

description:
J909_ACBJLYACXX_lane5_oneSampleInLaneNoDemulti_7OCOC.1
library strategy: OxBS-seq (Oxidative bisulfite sequencing)

value: control


title: ATACseq_CTL_1

description: ATAC-seq


title: 70VCO_hiseq

description:
J909_ACBJLYACXX_lane8_oneSampleInLaneNoDemulti_7OVCO.1
library strategy: OxBS-seq (Oxidative bisulfite sequencing)

value: OxBS


title: YX_1009900102_D3_S75

description:
3.5 weeks old Schistosome cell 111
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B3_S27

description:
3.5 weeks old Schistosome cell 109
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P12_S72

description:
3.5 weeks old Schistosome cell 108
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L1_S265

description:
3.5 weeks old Schistosome cell 107
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_I22_S214

description:
3.5 weeks old Schistosome cell 110
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K23_S263

description:
3.5 weeks old Schistosome cell 105
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K3_S243

description:
3.5 weeks old Schistosome cell 103
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_B15_S39

description:
3.5 weeks old Schistosome cell 106
schisto3.5_tpm_unfiltered.csv.gz


title: 43-BM_MSC_PolyIC-1

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the STAR (version 2.5.1) software based on reference genome sequence (Homo sapiens UCSC hg19) and the differential gene expressed values of each sample were calculated by the DESeq2 Bioconductor package.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: Lonza (donor), 0000127756; Walkersville, MD)

growth_protocol: BM-MSC cells were cultured in low-glucose Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS) (Hyclone, Logan, UT) and penicillin (100 U/ml)/streptomycin (100 mg/ml) (Gibco, Carlsbad, CA, USA). The cells were maintained in a humidified incubator with a 95% air/5% CO2 atmosphere at 37°C.The cells were maintained in a humidified incubator with 95% air and a 5% CO2 atmosphere at 37°C. The medium was replaced every 3–4 days. In this study, MSCs were used at passages 5 or 6.

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany). hMSCs or LPS-treated hMSCs were completely lysed with RNAiso Plus, then 200 μl of chloroform was added, and the tubes inverted for 5 min. The mixture was centrifuged at 12,000 x g for 15 min at 4°C, and the upper phase was placed into a new tube and 600 μl of 70% ethanol was added. The mixture was applied to an RNeasy mini column. The column was washed with wash buffer. To elute, RNase-free water (30 μl) was added directly onto the RNase mini column, followed by centrifugation at 12,000 x g for 3 min at 4°C. For ribosomal RNA (rRNA) depletion in total RNA, the RiboMinus Eukaryote kit (Life Technologies, Carlsbad, CA) was employed according to the manufacturer’s instructions. RNA libraries were created using the NEBNext® Ultra™ directional RNA library preparation kit for Illumina® (New England Biolabs, Ipswich, MA). rRNA-depleted total RNA was fragmented into small pieces using divalent cations at elevated temperatures. The first-strand cDNA was synthesized using reverse transcriptase and random primers, and then second-strand cDNA synthesis was performed using DNA polymerase I and RNase H. The cDNA fragments were processed using an end-repair reaction after the addition of a single ‘A’ base, followed by adapter ligation. These products were purified and amplified through PCR to generate the final cDNA library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were incubated with PolyIC (10 ug/ml, Sigma-Aldrich) for the specified time intervals (for 4 hours) under normal culture conditions.

value: Bone marrow Mesenchymal Stem Cells

value: cells were treated with the TLR3 agonist poly(I:C) (10 µg/ml, Sigma-Aldrich, St. Louis, MO) for 4 h

tag: passage

value: passages 5 or 6


title: 70COO_hiseq

description:
J909_ACBJLYACXX_lane6_oneSampleInLaneNoDemulti_7OCOO.1
library strategy: OxBS-seq (Oxidative bisulfite sequencing)


title: 43-BM_MSC_Cont-2


title: 43-BM_MSC_PolyIC-2


title: 43-BM_MSC_Cont-3


title: YX_1009900102_D20_S92

description:
3.5 weeks old Schistosome cell 104
schisto3.5_tpm_unfiltered.csv.gz


title: 23-BM_MSC_PolyIC-3

source_name: Lonza (donor), 7F3674; Walkersville, MD)


title: YX_1009900102_K2_S242

description:
3.5 weeks old Schistosome cell 102
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M22_S10

description:
3.5 weeks old Schistosome cell 101
schisto3.5_tpm_unfiltered.csv.gz


title: 43-BM_MSC_PolyIC-3


title: 43-BM_MSC_Cont-1


title: 23-BM_MSC_PolyIC-2


title: YX_1009900102_D14_S86

description:
3.5 weeks old Schistosome cell 100
schisto3.5_tpm_unfiltered.csv.gz


title: 23-BM_MSC_Cont-2


title: 23-BM_MSC_PolyIC-1


title: YX_1009900102_J22_S238

description:
3.5 weeks old Schistosome cell 99
schisto3.5_tpm_unfiltered.csv.gz


title: 23-BM_MSC_Cont-1


title: YX_1009900102_F17_S137

description:
3.5 weeks old Schistosome cell 97
schisto3.5_tpm_unfiltered.csv.gz


title: HFD_mir181DKO4

city: Philadelphia

first: Jonathan

last: Kotzin

state: PA

address: 421 Curie Boulevard, Biomedical Research Building II/III, Room 312

institute: UPenn

data_processing:
Sequenced reads were quality filtered and trimmed of adapters using Trimmomatic.
Reads were aligned to the GRCm37/mm9 genome using Tophat2.
Gene expression was quantified by counting the number of unique fragments mapped to genes using featureCounts.
Limma was applied to normalize gene expression using Voom and identify differentially expressed genes.
Genome_build: GRCm37/mm9
Supplementary_files_format_and_content: tab-delimited text files of Limma-Voom normalized gene expression

source_name: Epididymal white adipose tissue

extract_protocol:
RNA was extracted from epididymal white adipose tissue (eWAT) from WT and miR-181-double knockout mice following 12 weeks on high fat diet using a combination of TRIzol (Invitrogen) and RNeasy Mini columns (QIAGEN). TRIzol-chloroform extractions were precipitated with ethanol, applied to RNeasy Mini columns, and processed according to the manufacturer’s instructions.
RNA libraries were generated from 1 µg of high-quality RNA from each sample using the TruSeq Stranded mRNA kit (Illumina). Library quality and concentration were assessed by TapeStation and qPCR respectively.
Libraries were 75 base-pair single-end sequenced on the NextSeq550 machine (Illumina).

tag: genotype

value: Mir181 double-knockout

tag: diet

value: High fat diet


title: YX_1009900102_P15_S75

description:
3.5 weeks old Schistosome cell 96
schisto3.5_tpm_unfiltered.csv.gz

tag: cell type


title: YX_1009900102_M15_S3

description:
3.5 weeks old Schistosome cell 94
schisto3.5_tpm_unfiltered.csv.gz


title: HFD_mir181DKO3

tag: strain


title: HFD_mir181DKO2


title: YX_1009900102_M7_S295

description:
3.5 weeks old Schistosome cell 95
schisto3.5_tpm_unfiltered.csv.gz

tag: mouse strain with s. mansoni


title: WT_non_irradiated_75_Ileum

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

description:
75_Ileum_CTTGTA
used for fig2+supp fig 2

data_processing:
Illumina bcl2fastq software used for basecalling.
alignment: hisat 0.1.6  with deafult parameters
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count exons -condenseGenes -strand + -rpkm -raw
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

extract_protocol:
total RNA was extracted from 0.1-1*106 sorted cells with RNeasy Micro Kit (Qiagen).
100 ng of total RNA was processed using the TruSeq Stranded Total RNA HTSample Prep Kit (with Ribo-Zero Gold) of Illumina (RS-122-2303).
Sequencing libraries were constructed with barcodes to allow multiplexing of 24 samples ran on 3 lanes. ~20 million single-end 50-bp reads were sequenced per sample on Illumina HiSeq 2500 high output mode instrument.

value: 8-14 weeks

value: Ileum

tag: selection marker

value: non treated


title: YX_1009900102_H10_S178

description:
3.5 weeks old Schistosome cell 93
schisto3.5_tpm_unfiltered.csv.gz

tag: worm age


title: WT_non_irradiated_73_Ileum

description:
73_Ileum_GCCAAT
used for fig2+supp fig 2

tag: tissue


title: YX_1009900102_K11_S251

description:
3.5 weeks old Schistosome cell 98
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C19_S67

description:
3.5 weeks old Schistosome cell 92
schisto3.5_tpm_unfiltered.csv.gz


title: WT_non_irradiated_75_Colon

description:
75_Colon_CAGATC
used for fig2+supp fig 2

value: colon


title: HFD_mir181DKO1


title: YX_1009900102_F22_S142

description:
3.5 weeks old Schistosome cell 91
schisto3.5_tpm_unfiltered.csv.gz

value: stem cells


title: WT_non_irradiated_72_Ileum

description:
72_Ileum_TGACCA
used for fig2+supp fig 2


title: HFD_WT4

value: wild type


title: WT_non_irradiated_72_Colon

description:
72_Colon_CGATGT
used for fig2+supp fig 2


title: YX_1009900102_A10_S10

description:
3.5 weeks old Schistosome cell 90
schisto3.5_tpm_unfiltered.csv.gz

value: Swiss  Webster NR-21963

value: 3.5 weeks


title: WT_irradiated_61_Ileum

description:
61_Ileum_GATCAG
used for fig2+supp fig 2

value: 8 weeks post chimerism


title: HFD_WT3


title: WT_non_irradiated_73_Colon

description:
73_Colon_ACAGTG
used for fig2+supp fig 2


title: YX_1009900102_H19_S187

description:
3.5 weeks old Schistosome cell 89
schisto3.5_tpm_unfiltered.csv.gz


title: WT_irradiated_61_Colon

description:
61_Colon_ACTTGA
used for fig2+supp fig 2


title: HFD_WT2


title: WT_irradiated_59_Ileum

description:
59_Ileum_TTAGGC
used for fig2+supp fig 2


title: 23-BM_MSC_Cont-3


title: WT_irradiated_59_Colon

description:
59_Colon_ATCACG
used for fig2+supp fig 2


title: KO_late_stage_57_Ileum

description:
57_Ileum_GTGAAA
used for fig2+supp fig 2


title: KO_late_stage_57_Colon

description:
57_Colon_GTCCGC
used for fig2+supp fig 2


title: YX_1009900102_E13_S109

description:
3.5 weeks old Schistosome cell 88
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L21_S285

description:
3.5 weeks old Schistosome cell 87
schisto3.5_tpm_unfiltered.csv.gz


title: KO_late_stage_50_Colon

description:
50_Colon_ATGTCA
used for fig2+supp fig 2


title: YX_1009900102_E18_S114

description:
3.5 weeks old Schistosome cell 86
schisto3.5_tpm_unfiltered.csv.gz


title: KO_late_stage_49_Ileum

description:
49_Ileum_AGTTCC
used for fig2+supp fig 2


title: S2

city: Hefei

first: Jinsen

last: Lu

state: Anhui

address: Lujiang Road No.17

department: orthopaedics

institute: Anhui Provincial Hospital

description:
Cells were treated with 10μM dexamethasone+100μg EPCs-exo and cultivated for 72 hours.
processed data file: gene.count.fpkm.txt
processed data file: transcript.fpkm.txt

data_processing:
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 poly-N and low quality reads from raw data.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group.
Differential expression analysis of two conditions was performed using the DESeq2 R package (1.26.0). P value <0.05 and |FoldChange|≥1.5 were set as the threshold for significantly differential expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: gene.count.fpkm.txt: Tab-delimited text file includes count and FPKM values for each Sample.
Supplementary_files_format_and_content: transcript.fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Osteoblast

growth_protocol: Mice osteoblasts (MC3T3-E1 Subclone 14) were cultured in 1640 medium and maintained at 37 ℃ in a 5% CO2 atmosphere.

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Mice osteoblasts were cultivated and divided into 3 experimental groups (n=2) respectively receiving treatment of 10μM dexamethasone (D1 and D2), 10μM dexamethasone+100μg EPCs-exo (S1 and S2) and 100μL PBS (M1 and M2) for 72 hours (5*10e6/sample and 6 samples in total).

value: Osteoblast

value: Dexamethasone + EPCs-exo


title: S1


title: YX_1009900102_M3_S291

description:
3.5 weeks old Schistosome cell 85
schisto3.5_tpm_unfiltered.csv.gz


title: KO_early_stage_120_Colon

description:
120_Colon_GTGGCC
used for fig2+supp fig 2

value: 2 weeks post chimerism


title: D2

description:
Cells were treated with 10μM dexamethasone and cultivated for 72 hours.
processed data file: gene.count.fpkm.txt
processed data file: transcript.fpkm.txt

value: Dexamethasone


title: KO_early_stage_120_Ileum

description:
120_Ileum_GTTTCG
used for fig2+supp fig 2


title: YX_1009900102_A16_S16

description:
3.5 weeks old Schistosome cell 84
schisto3.5_tpm_unfiltered.csv.gz


title: HFD_WT1


title: KO_late_stage_49_Colon

description:
49_Colon_AGTCAA
used for fig2+supp fig 2


title: mouse brain Lrrc33+/+ biological replcate 1 [exon-level]

type: RNA

city: Boston

first: Timothy

last: Springer

state: MA

address: 3 Blackfan Circle, Room 3103

institute: Harvard University

hyb_protocol: Samples were hybridized with Affymetrix Mouse Exon 1.0 ST arrays

scan_protocol: not provided

data_processing: Arrays were processed using the BioConductor oligo package and normalized using RMA to provide expression summaries at the exon level. Significantly different genes were identified using limma.

label: biotin

label_protocol: not applicable

extract_protocol: Microglia were isolated by FACS-sorting (CD45low CD11b+ CD39+ Ter119-)  from brain cell suspensions prepared from 3-week old mice. Total RNA was isolated using Trizol (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: not applicable

value: microglia


title: D1


title: mouse brain Lrrc33+/+ biological replcate 3 [exon-level]

growth_protocol: mouse brain Lrrc33+/+ biological replcate 1


title: M2

description:
Cells were treated with 100μL PBS and cultivated for 72 hours.
processed data file: gene.count.fpkm.txt
processed data file: transcript.fpkm.txt

value: PBS


title: mouse brain Lrrc33-/- biological replcate 1 [exon-level]


title: KO_early_stage_117_Colon

description:
117_Colon_TAGCTT
used for fig2+supp fig 2


title: KO_early_stage_100_Ileum

description:
100_Ileum_GAGTGG
used for fig2+supp fig 2


title: M1


title: KO_early_stage_118_Ileum

description:
118_Ileum_ATTCCT
used for fig2+supp fig 2


title: YX_1009900102_K18_S258

description:
3.5 weeks old Schistosome cell 83
schisto3.5_tpm_unfiltered.csv.gz


title: KO_early_stage_117_Ileum

description:
117_Ileum_GGCTAC
used for fig2+supp fig 2


title: YX_1009900102_F7_S127

description:
3.5 weeks old Schistosome cell 81
schisto3.5_tpm_unfiltered.csv.gz


title: KO_early_stage_100_Colon

description:
100_Colon_CGTACG
used for fig2+supp fig 2


title: KO_early_stage_118_Colon

description:
118_Colon_ACTGAT
used for fig2+supp fig 2


title: YX_1009900102_A2_S2

description:
3.5 weeks old Schistosome cell 80
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_L14_S278

description:
3.5 weeks old Schistosome cell 79
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H14_S182

description:
3.5 weeks old Schistosome cell 77
schisto3.5_tpm_unfiltered.csv.gz


title: mouse brain Lrrc33+/+ biological replcate 2 [exon-level]


title: YX_1009900102_J13_S229

description:
3.5 weeks old Schistosome cell 78
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C6_S54

description:
3.5 weeks old Schistosome cell 82
schisto3.5_tpm_unfiltered.csv.gz


title: mouse brain Lrrc33-/- biological replcate 3 [exon-level]


title: YX_1009900102_N3_S15

description:
3.5 weeks old Schistosome cell 73
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K20_S260

description:
3.5 weeks old Schistosome cell 76
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J21_S237

description:
3.5 weeks old Schistosome cell 72
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_K1_S241

description:
3.5 weeks old Schistosome cell 75
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_J11_S227

description:
3.5 weeks old Schistosome cell 70
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M10_S298

description:
3.5 weeks old Schistosome cell 71
schisto3.5_tpm_unfiltered.csv.gz


title: RNAseq_3_TNF_Fatostatin_1

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed(http://www.bioinformatics.babraham.ac.uk/project/trim_galore).
Sequenced reads were mapped to reference human genome (hg19 assembly) using STAR aligner (2.5.2b, Dobin et al., 2013 Bioinformatics) with default parameters.
EdgeR(Robinson et al., 2010) or Cuffdiff2 (Trapnell et al., 2012) was used to estimate the abundance of transcripts.
Genome_build: hg19

extract_protocol:
RNA extraction kit from QIAGEN, according to company's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with or without TNF (10ng/ml) for 16 hours in the presence of various inhibitors (Fatostatin, Atrovastatin, Cholesterol and DMSO)

value: peripheral blood

value: monocytes

value: TNF (10ng/ml) for 16 hours

tag: inhibitors

value: Fatostatin


title: YX_1009900102_J4_S220

description:
3.5 weeks old Schistosome cell 69
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_P13_S73

description:
3.5 weeks old Schistosome cell 68
schisto3.5_tpm_unfiltered.csv.gz


title: mouse brain Lrrc33-/- biological replcate 2 [exon-level]


title: YX_1009900102_B7_S31

description:
3.5 weeks old Schistosome cell 67
schisto3.5_tpm_unfiltered.csv.gz


title: RNAseq_3_TNF_DMSO_2

value: DMSO


title: YX_1009900102_A14_S14

description:
3.5 weeks old Schistosome cell 74
schisto3.5_tpm_unfiltered.csv.gz


title: RNAseq_3_TNF_Cholesterol_1

value: Cholesterol


title: YX_1009900102_J20_S236

description:
3.5 weeks old Schistosome cell 66
schisto3.5_tpm_unfiltered.csv.gz

value: stem cells


title: YX_1009900102_J18_S234

description:
3.5 weeks old Schistosome cell 65
schisto3.5_tpm_unfiltered.csv.gz


title: RNAseq_3_TNF_Atrovastatin_1

value: Atrovastatin


title: kd-1

hyb_protocol: Following fragmentation, ~5 microg of cRNA were hybridized for 16 hr at 45C on HuGene-1 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station

scan_protocol: Standard Affymetrix Scanner protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings; CEL files were generated. CEL files processed/normalized using DNA-Chip Analyzer (dChip) to generate probeset-level signal intensity data.

source_name: CAF cells with CXCR4 siRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: CAFs were generated from mesenchymal stem cells (MSCs) after chronic explosure to conditioned media from pancreatic cancer cells

extract_protocol: RNA extraction was done with Qiagen's RNA-Easy Micro protocol and used for cDNA prepration used in microarray studies

treatment_protocol: CAFs were treated with CXCR4 and control siRNAs

value: Cancer associated fibroblasts

tag: transfection

value: CXCR4 siRNA


title: kd-2


title: sorted cDC populations_Wnt2

city: Vari

first: Maria

last: Tsoumakidou

state: Attica

address: 34 Fleming Street

country: Greece

institute: B.S.R.C. "Alexander Fleming"

data_processing:
The RNA-Seq FASTQ files obtained after Ion Proton sequencing were mapped using TopHat2 [Kim2013], with default settings and using additional transcript annotation data for the mm10 genome from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). According to the Ion Proton manufacturers recommendation, the reads which remained unmapped were submitted to a second round of mapping using Bowtie2 [Langmead2012] against the mm10 genome with the --very-sensitive switch turned on and merged with the initial mappings.
The raw bam files were summarized to read counts table using the Bioconductor package GenomicRanges.
The gene counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples.
The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq.
All the above were performed through the Bioconductor package metaseqr.
Genome_build: mm10
Supplementary_files_format_and_content: txt (tab separated) files containing all the results from metaseqr analysis including expression per replicate, fold change compared to control and p-values.

source_name: classical dendritic cells

extract_protocol:
Intratumoral cDCs were isolated from lung tumors by CD45 enrichment, followed by FACS sorting  and total RNA was extracted using RNAeasy Mini kit (QIAGEN), according to the manufacturer's instructions.
The quantity and quality of RNA samples from sorted cells were analyzed using the bioanalyzer form Agilent in combination with the Agilent RNA 6000 Nano. RNA samples with RNA Integrity Number (RIN) > 7 were further used for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. The quantity and quality of libraries were assessed using the DNA High Sensitivity Kit in the bioanalyzer, according to the manufacturer’s instructions (Agilent Technologies). Libraries were subsequently pooled and templated using the Ion PI IC200 Chef Kit (ThermoFisher Scientific) on an Ion Proton Chef instrument or Ion OneTouch System. Sequencing was performed using the Ion PI™ Sequencing 200 V3 Kit and Ion Proton PI™ V2 chips (ThermoFisher Scientific) on an Ion Proton™ System, according to the manufacturer's instructions.
3’ RNA-Seq (QuantSeq)

value: wt

value: lung tumor

tag: expressing

value: WNT1 overexpressing

value: classical dendritic cells (cDCs)

tag: cell isolation

value: Fresh isolation


title: ctrl-2

source_name: CAF cells with ctrl siRNA

value: ctrl siRNA


title: sorted cDC populations_Wnt3


title: ctrl-1


title: RNAseq_3_TNF_1


title: MEF expression analysis Pten Null rep4

city: New York

first: Ramon

last: Parsons

address: 1425 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Samples were analyzed by Applied Biosystems

data_processing: Results were imported into R for quality control (including consistency of probe hybridization and signal intensity) and normalization was performed using the Affymetrix package

source_name: cell culture

label_protocol: indirect labeling using the Ambion® Whole Transcript (WT) Expression Array (Life Technologies)

growth_protocol: grown in DMEM supplemented with 10% FBS, penicillin and streptomycin, and 2mM L-glutamine

extract_protocol: RNA was extracted from MEFs 4 passages after infection with Adeno-CMV-Cre or Adeno-CMV-Null virus using the Qiagen RNeasy Kit.

treatment_protocol: For deletion of Pten, primary MEFs, that have loxP sites flanking exon 5 inserted into the endogenous locus of Pten, were infected with adenovirus Adeno-CMV-Cre-recombinase (Vector Biolabs) or Adeno-CMV-Null (Vector Biolabs) as a control.

value: primary mouse embryonic fibroblasts (passage 6-8)

tag: genotype/variation

value: Pten was deleted using  Adeno-CMV-Cre virus


title: MEF expression analysis Pten Null rep2

scan_protocol: Samples were analyzed by Applied Biosystems


title: MEF expression analysis Pten WT rep3

value: infected with Adeno-CMV-Null virus


title: MEF expression analysis Pten WT rep4


title: MEF expression analysis Pten WT rep2


title: MEF expression analysis Pten WT rep1


title: MEF expression analysis Pten Null rep3


title: sorted cDC populations_Empty3

value: control


title: RNAseq_3_Fatostatin_1

value: peripheral blood

value: monocytes

value: Fatostatin


title: RNAseq_3_TNF_DMSO_1

tag: treatment

value: TNF (10ng/ml) for 16 hours

value: DMSO


title: sorted cDC populations_Empty2


title: MEF expression analysis Pten Null rep1


title: YX_1009900102_L3_S267

description:
3.5 weeks old Schistosome cell 62
schisto3.5_tpm_unfiltered.csv.gz

value: stem cells

value: Swiss  Webster NR-21963

value: 3.5 weeks


title: sorted cDC populations_Wnt4

value: wt

value: lung tumor


title: bin4-2_1

city: Marseille

first: Christophe

last: Laloi

state: France

address: 163 avenue de Luminy

department: Biology

country: France

institute: Aix-Marseille Université

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA processed with background adjustment and quantile normalization

organism: Arabidopsis thaliana

source_name: Seedlings

label_protocol: standard Affymetrix protocol

extract_protocol: total RNA


title: RNAseq_3_DMSO_2


title: YX_1009900102_A5_S5

description:
3.5 weeks old Schistosome cell 61
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A7_S7

description:
3.5 weeks old Schistosome cell 64
schisto3.5_tpm_unfiltered.csv.gz


title: bin4-2


title: RNAseq_3_DMSO_1


title: YX_1009900102_P18_S78

description:
3.5 weeks old Schistosome cell 63
schisto3.5_tpm_unfiltered.csv.gz


title: Alfacalcidol rep2

city: Durham

first: Yanchao

last: Han

state: NC

address: 307 Research Dr

department: Cell Biology

institute: Duke University Medical Center

data_processing:
Base calling with Casava
Alignment with TopHat2
Count with featureCounts
Analyzed using edgeR
Genome_build: GRCz10
Supplementary_files_format_and_content: "VitaminD_counts.txt" is a tab delimited text file containing summarized counts, "vitaminD_edgeR.txt' is edgeR output file of differentially expressed genes.

organism: Danio rerio

source_name: zebrafish heart

growth_protocol: zebrafish were grown at 28 ºC.

extract_protocol:
Total RNA were harvested using TRIzol reagent, digested with DNaseI, and purified with Zymo Quick-RNA MiniPrep kit.
Libraries were prepared and sequenced using an Illumina HiSeq2000 at the Duke Center for Genomic and Computational Biology.

treatment_protocol: Zebrafish were injected with vehicle or alfacalcidol.

value: Ekkwill

tag: developmental stage

value: adult

value: heart

value: Alfacalcidol


title: RNAseq_3_CTL_1

value: untreated


title: Alfacalcidol rep1


title: bin4-1_1


title: YX_1009900102_B23_S47

description:
3.5 weeks old Schistosome cell 59
schisto3.5_tpm_unfiltered.csv.gz


title: RNAseq_3_Cholesterol_1


title: Vehicle rep2

value: vehicle


title: bin4-1


title: YX_1009900102_F14_S134

description:
3.5 weeks old Schistosome cell 58
schisto3.5_tpm_unfiltered.csv.gz


title: RNAseq_3_Atrovastatin_1


title: RNAseq_2_untransduced_2

tag: overexpression

value: untransduced


title: YX_1009900102_C16_S64

description:
3.5 weeks old Schistosome cell 56
schisto3.5_tpm_unfiltered.csv.gz


title: 70VCO_miseq

description:
70VCO_S9_L001_R1_001
library strategy: OxBS-seq (Oxidative bisulfite sequencing)

tag: cell line

value: clear cell Renal Cell Carcinoma cell line

tag: type

value: OxBS

tag: drug

value: vitamin C


title: Vehicle rep1


title: 70VCC_miseq

description:
70VCC_S8_L001_R1_001
library strategy: OxBS-seq (Oxidative bisulfite sequencing)

value: BS


title: YX_1009900102_K7_S247

description:
3.5 weeks old Schistosome cell 57
schisto3.5_tpm_unfiltered.csv.gz

tag: cell type


title: WT_1

tag: genotype

value: WT


title: YX_1009900102_F23_S143

description:
3.5 weeks old Schistosome cell 55
schisto3.5_tpm_unfiltered.csv.gz

value: stem cells

tag: mouse strain with s. mansoni


title: RNAseq_2_untransduced_1

value: peripheral blood

value: monocytes


title: 70COO_miseq

description:
70COO_S7_L001_R1_001
library strategy: OxBS-seq (Oxidative bisulfite sequencing)

value: control


title: RNAseq_2_TNF_SREBP_2

value: TNF (10ng/ml) for 16 hours

value: SREBP


title: YX_1009900102_A3_S3

description:
3.5 weeks old Schistosome cell 60
schisto3.5_tpm_unfiltered.csv.gz

value: Swiss  Webster NR-21963

value: 3.5 weeks


title: RNAseq_2_TNF_SREBP_1


title: YX_1009900102_P14_S74

description:
3.5 weeks old Schistosome cell 53
schisto3.5_tpm_unfiltered.csv.gz


title: 70COC_miseq

description:
70COC_S6_L001_R1_001
library strategy: OxBS-seq (Oxidative bisulfite sequencing)


title: RNAseq_2_TNF_GFP_2

value: GFP


title: KO_late_stage_50_Ileum

description:
50_Ileum_CCGTCC
used for fig2+supp fig 2

tag: strain

tag: age

value: 8-14 weeks

value: Ileum

tag: selection marker

value: 8 weeks post chimerism


title: RNAseq_2_TNF_GFP_1

tag: tissue


title: YX_1009900102_J12_S228

description:
3.5 weeks old Schistosome cell 51
schisto3.5_tpm_unfiltered.csv.gz

tag: worm age


title: RNAseq_2_SREBP_2


title: WT


title: mouse brain Lrrc33-/- biological replicate 2

data_processing:
Background correction and normalization:
Affymetrix provides additional annotation files that define meta-probesets (MPSs), used to summarize the data to the gene level. These MPSs are classified in three groups – ‘core’, ‘extended’ and ‘full’ – depending on the level of confidence of the sources used to generate such annotations. We used the ‘core’ annotations to summarize expression at the gene level. RMA was applied to this summarized matrix for background correction and normalization.
Filtering and annotation:
We used the NetAffx gene annotations provided by Affymetrix to further filter our normalized expression matrix, We kept only those genes that comprised the main category, filtering out probes designed to detect background noise.

label_protocol: not provided

value: microglia


title: mouse brain Lrrc33-/- biological replicate 1


title: mouse brain Lrrc33-/- biological replicate 3


title: YX_1009900102_B14_S38

description:
3.5 weeks old Schistosome cell 50
schisto3.5_tpm_unfiltered.csv.gz

data_processing:
Read alignment, STAR, 2.5.0a,  –outSAMstrandField intronMotif --runThreadN {threads} --outFileNamePrefix {wdir} --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS NM MD --outReadsUnmapped Fastx --clip3pAdapterSeq CTGTCTCTTATACACATCT --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1; gene count, htseq-count, 0.10.0, -s no -t exon -r pos -f bam -i Parent -m intersection-strict
Genome_build: schistosoma_mansoni.PRJEA36577.WBPS9.genomic.ercc.fa
Supplementary_files_format_and_content: Comma-separated values of normalized gene count (tpm) matrix where rows are genes and columns are sample names.


title: mouse brain Lrrc33+/+ biological replicate 2


title: mouse brain Lrrc33+/+ biological replicate 3


title: YX_1009900102_C18_S66

description:
3.5 weeks old Schistosome cell 54
schisto3.5_tpm_unfiltered.csv.gz


title: RNAseq_2_SREBP_1


title: mouse brain Lrrc33+/+ biological replicate 1


title: 2_2_DAI

city: Mérida

first: Víctor M.

last: Loyola-Vargas

state: Yucatán

department: Unidad de Bioquímica y Biología Molecular de Plantas

country: Mexico

institute: Centro de Investigación Científica de Yucatán

data_processing:
The reads quality was corroborated using FastQC (v.0.11.5) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The sequences were pre-processed to remove Illumina adapters using Cutadapt (v. 1.14).
After removing adapters, the sequences were pre-processed to remove low quality reads (Q<20) using FASTQ Quality Trimmer (Part of FASTX Toolkit 0.0.14) (http://hannonlab.cshl.edu/fastx_toolkit/).
Filtered sequences were mapped to the reference genome of C. canephora (v1.0).
Htseq-count (v. 0.10.0) was used with options by default to quantify the gene expression.
Genome_build: C. canephora v1.0 (http://coffee-genome.org/)
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files include counts.

organism: Coffea canephora

source_name: Foliar tissue

extract_protocol:
Isolate II RNA Plant Kit (Bioline).
Applied Biological Materials Inc. services were used for RNA-seq library preparation and sequencing (https://www.abmgood.com).

value: Leaves

value: Embryogenic condition

tag: growth medium

value: Yasuda salts with benzyladenine (BA)

tag: time point

value: 2 days DAI


title: 21_2_DAI

value: 21 days DAI


title: 21_1_DAI


title: RNAseq_2_GFP_2

value: peripheral blood


title: YX_1009900102_D22_S94

description:
3.5 weeks old Schistosome cell 49
schisto3.5_tpm_unfiltered.csv.gz

source_name: Schistosoma mansoni stem cells

extract_protocol:
Triton X-100 was used to lyse individual cells, Smart-seq2 protocol was followed to reverse transcribe and amplify mRNA.
Nextera XT DNA

value: stem cells


title: YX_1009900102_K10_S250

description:
3.5 weeks old Schistosome cell 48
schisto3.5_tpm_unfiltered.csv.gz


title: 1_1_DAI

value: 1 day DAI


title: YX_1009900102_N17_S29

description:
3.5 weeks old Schistosome cell 47
schisto3.5_tpm_unfiltered.csv.gz


title: RNAseq_2_GFP_1

value: monocytes


title: 0_2_DBI

value: Pre-embryogenic condition

value: MS salts with naphthaleneacetic acid (ANA) and kinetin (KIN)

value: 0 days DBI


title: YX_1009900102_F3_S123

description:
3.5 weeks old Schistosome cell 52
schisto3.5_tpm_unfiltered.csv.gz

value: Swiss  Webster NR-21963

value: 3.5 weeks


title: 0_1_DBI


title: RNAseq_1_TNF_3

value: TNF (10ng/ml) for 16 hours


title: YX_1009900102_J14_S230

description:
3.5 weeks old Schistosome cell 46
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M13_S1

description:
3.5 weeks old Schistosome cell 45
schisto3.5_tpm_unfiltered.csv.gz


title: RNAseq_1_TNF_2


title: RNAseq_1_TNF_1


title: YX_1009900102_N21_S33

description:
3.5 weeks old Schistosome cell 44
schisto3.5_tpm_unfiltered.csv.gz


title: 9_2_DBI

value: 9 days DBI


title: RNAseq_1_CTL_1

value: untreated


title: 1_2_DAI

value: Leaves


title: FC023: 1h_MitoCDNB_6

city: Cambridge

first: Filip

last: Cvetko

state: Cambridgeshire

address: Cambridge Biomedical Campus Hill Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

data_processing:
Illumina Casava 1.8.4 software usedto demultiplex BCL files to FASTQ files.
Sequenced reads were processed to remove low quality reads and adapter sequences using TrimGalore!
Reads were aligned to the mm10 genome using hisat2.
A count table was produced using Feature counts from Rsubread.
Normalisation and differential expression analysis was carried out using DESEQ2 within the R statistical environment.
Genome_build: mm10
Supplementary_files_format_and_content: Counts table in a .csv format

source_name: Liver tissue

extract_protocol:
RNA was extracted from liver tisue using the PureLink RNA Mini Kit (Invitrogen)
NEBNext Ultra RNA library Prep kit for Illumina (New England Biolabs)

treatment_protocol: Mice were injected with either Vehicle (0.1% ethanol) or  5mg/kg of MitoCDNB and liver samples were taken at 1or 4 hours (n=6)

value: medial liver lobe


title: YX_1009900102_C1_S49

description:
3.5 weeks old Schistosome cell 43
schisto3.5_tpm_unfiltered.csv.gz


title: FC024: 1h_Vehicle_6


title: 9_1_DBI


title: 14_1_DBI

description: Control

value: MS salts without growth regulators

value: 14 days DBI


title: RNAseq_1_CTL_3


title: ChIPseq_SREBP_2

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed.
Sequenced reads were mapped to reference human genome (hg19 assembly) using Bowtie2 version 2.2.6 with default parameters.
HOMER version 4.7.2 (Heinz et al., 2010) to identify peaks of ChIP-seq enrichment over background.
Genome_build: hg19

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit.

treatment_protocol: Cells were treated with or without TNF (10ng/ml) for 16 hours.

tag: antibody

value: anti-SREBP2 (Abcam, ab30682)


title: ChIPseq_TNF_SREBP_2

value: peripheral blood

tag: treatment


title: YX_1009900102_H12_S180

description:
3.5 weeks old Schistosome cell 40
schisto3.5_tpm_unfiltered.csv.gz

value: stem cells


title: YX_1009900102_A11_S11

description:
3.5 weeks old Schistosome cell 39
schisto3.5_tpm_unfiltered.csv.gz


title: RNAseq_1_CTL_2


title: 2_1_DAI

value: Embryogenic condition

value: Yasuda salts with benzyladenine (BA)

value: 2 days DAI


title: YX_1009900102_I16_S208

description:
3.5 weeks old Schistosome cell 42
schisto3.5_tpm_unfiltered.csv.gz


title: FC022: 1h_MitoCDNB_5


title: PP7_invitro.PP7_21_GTTTCG_L001

city: Haifa

first: Oz

last: Solomon

address: Technion

institute: Technion

data_processing:
Alignment - paired-end reads were aligned to the reference sequence using Bowtie2 (--local)
RT Drop-off calling - RT drop-off positions were called using in house Perl script
Samples normalization - samples were normalized to the sum of read-ends in the maximal sample, so after normalization the sum of the read-ends in all the samples under comparison was equal.
Reactivity calculation - the drop-off values were used for reactivity calculation, inspired by Talkish et al. (2014, pmid: 24664469)
Genome_build: Composite reference sequence that is constructed from : 5s Rrna of E.coli, PP7-wt mCherry sequence or PP7-Uss mCherry sequence
Supplementary_files_format_and_content: Katz_et_al_2019_Cell_Systems_count_read_ends.xlsx (excel file with SHAPE-seq drop-off counts per position in all samples)

organism:
Escherichia coli
Pseudomonas phage PP7

source_name: PP7-wt construct

growth_protocol: LB medium supplemented with appropriate concentrations of Amp and Kan was inoculated with glycerol stocks of bacterial strains harboring both the binding-site plasmid and the RBP-fusion plasmid and grown at 37°C for 16 hours while shaking at 250 rpm. Overnight cultures were diluted 1:100 into SPM. Each bacterial sample was divided into a non-induced sample and an induced sample in which RBP protein expression was induced with 250 nM N-butanoyl-L-homoserine lactone (C4-HSL), as described above. Bacterial cells were grown until OD600=0.3, 2 ml of cells were centrifuged and gently resuspended in 0.5 ml SPM.

extract_protocol:
RNA isolation of 5S rRNA was performed using TRIzol-based standard protocols. Briefly, cells were lysed using Max Bacterial Enhancement Reagent followed by TRIzol treatment (both from Life Technologies). Phase separation was performed using chloroform. RNA was precipitated from the aqueous phase using isopropanol and ethanol washes, and then resuspended in RNase-free water. For the strains harboring PP7-wt δ=-29 and PP7-USs δ=-29, column-based RNA isolation (RNeasy mini kit, QIAGEN) was performed.
To produce the dsDNA for sequencing 10ul of purified cDNA from the SHAPE procedure (see above) were PCR amplified using 3 primers: 4nM mCherry selection (#4) or 5S rRNA selection primer (#5), 0.5µM TruSeq Universal Adapter (#6) and 0.5µM TrueSeq Illumina indexes (one of #7-26) (Table S3) with PCR reaction mix (1x Q5 HotStart reaction buffer, 0.1 mM dNTPs, 1 U Q5 HotStart Polymerase [NEB]). A 15-cycle PCR program was used: initial denaturation at 98°C for 30 s followed by a denaturation step at 98°C for 15 s, primer annealing at 65°C for 30 s and extension at 72°C for 30 s, followed by a final extension 72°C for 5 min. Samples were chilled at 4°C for 5 min. After cool-down, 5 U of Exonuclease I (ExoI, NEB) were added, incubated at 37°C for 30 min followed by mixing 1.8x volume of Agencourt AMPure XP beads to the PCR/ExoI mix and purified according to manufacturer’s protocol. Samples were eluted in 20 µl ultra-pure water. After library preparation, samples were analyzed using the TapeStation 2200 DNA ScreenTape assay (Agilent) and the molarity of each library was determined by the average size of the peak maxima and the concentrations obtained from the Qubit fluorimeter (Thermo Fisher Scientific). Libraries were multiplexed by mixing the same molar concentration (2-5 nM) of each sample library, and library and sequenced using the Illumina HiSeq 2500 sequencing system using either 2X51 paired end reads for the 5S-rRNA control and in vitro experiments or 2x101 bp paired-end reads for all other samples.
SHAPE-seq

treatment_protocol: For in vivo SHAPE modification, cells were supplemented with a final concentration of 30 mM 2-methylnicotinic acid imidazole (NAI) suspended in anhydrous dimethyl sulfoxide (DMSO, Sigma Aldrich) (Spitale et al., 2013), or 5% (v/v) DMSO. Cells were incubated for 5 min at 37°C while shaking and subsequently centrifuged at 6000 g for 5 min. In vitro modification was carried out on DMSO-treated samples (3 and 4) and has been described elsewhere (Flynn et al., 2016)

tag: pp7-wt or pp7-uss

tag: in-vivo or in-vitro

value: In-vitro

tag: induced or non-induced

value: Non-induced

tag: modified by nai

value: Non-modified

tag: replicate


title: ChIPseq_TNF_SREBP_1

tag: cell type

value: monocytes


title: YX_1009900102_B11_S35

city: Stanford

first: Yuan

last: Xue

institute: Stanford University

description:
3.5 weeks old Schistosome cell 38
schisto3.5_tpm_unfiltered.csv.gz

value: Swiss  Webster NR-21963

value: 3.5 weeks


title: PP7_invitro.PP7_20_GTGGCC_L002

value: modified by NAI


title: PP7_invitro.PP7_21_GTTTCG_L002


title: YX_1009900102_N14_S26

description:
3.5 weeks old Schistosome cell 41
schisto3.5_tpm_unfiltered.csv.gz


title: ChIPseq_SREBP_1


title: YX_1009900102_F8_S128

description:
3.5 weeks old Schistosome cell 37
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_C22_S70

description:
3.5 weeks old Schistosome cell 36
schisto3.5_tpm_unfiltered.csv.gz


title: PP7_invitro.PP7_19_GTGAAA_L002

value: induced


title: PP7_invitro.PP7_18_GTCCGC_L001


title: ChIPseq_Input_1


title: FC019: 1h_MitoCDNB_4

value: medial liver lobe


title: FC021: 1h_Vehicle_5


title: ChIPseq_eGFP_2

value: eGFP


title: FC018: 1h_Vehicle_3


title: ChIPseq_eGFP_1


title: YX_1009900102_L16_S280

description:
3.5 weeks old Schistosome cell 33
schisto3.5_tpm_unfiltered.csv.gz


title: FC020: 1h_Vehicle_4


title: YX_1009900102_E4_S100

description:
3.5 weeks old Schistosome cell 34
schisto3.5_tpm_unfiltered.csv.gz


title: PP7_invitro.PP7_18_GTCCGC_L002


title: PP7_invitro.PP7_16_CCGTCC_L002

source_name: PP7-Uss construct


title: PP7_invitro.PP7_16_CCGTCC_L001


title: FC017: 1h_MitoCDNB_3


title: YX_1009900102_E5_S101

description:
3.5 weeks old Schistosome cell 35
schisto3.5_tpm_unfiltered.csv.gz


title: FC015: 1h_Vehicle_2


title: YX_1009900102_K8_S248

description:
3.5 weeks old Schistosome cell 31
schisto3.5_tpm_unfiltered.csv.gz


title: PP7_invitro.PP7_19_GTGAAA_L001


title: YX_1009900102_G15_S159

description:
3.5 weeks old Schistosome cell 32
schisto3.5_tpm_unfiltered.csv.gz


title: FC016: 1h_MitoCDNB_2


title: PP7_invitro.PP7_15_ATGTCA_L001


title: FC014: 1h_Vehicle_1


title: ChIPseq_Input_2


title: CHM1 RNA biological replicate A

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

description:
RNA unmodified
CHM1_RNASeq_replicate_A.xlsx

data_processing:
Adaptors trimmed with Cutadapt (1.0)
Alignment with STAR 2.5.0a (--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000)
RPKMs generated with edgeR_3.12.1
Genome_build: hg38
Supplementary_files_format_and_content: xlsx - RPKMs

source_name: hydatidiform mole

growth_protocol: CHM1 cells were grown in 450ml AmnioMax C-100 basal medium (Thermo Fisher Scientific, Cat. No. 17001074) supplemented with 75ml AmnioMax C-100 Supplement (Thermo Fisher Scientific, Cat. No. 12556023) and antibiotics.

extract_protocol:
published in Koziol et al, 2016, 10.21769/BioProtoc.1990
Illumina TruSeq

tag: cell line

value: hydatidiform mole

value: Biological replicate A


title: CHM1 RNA biological replicate C

description:
RNA unmodified
CHM1_RNASeq_replicate_C.xlsx

value: Biological replicate C


title: PP7_invitro.PP7_15_ATGTCA_L002


title: FC013: 1h_MitoCDNB_1


title: YX_1009900102_I20_S212

address: 318 Campus Drive

description:
3.5 weeks old Schistosome cell 29
schisto3.5_tpm_unfiltered.csv.gz

value: stem cells

tag: mouse strain with s. mansoni


title: CHM1 genomic DNA m6dA immunopreciptiation biological replicate C

description:
dA6m antibody DNA immunoprecipitation
CHM1_m6dA_peaks_replicate_C.xlsx

data_processing:
Library strategy: DIP-seq
Adaptors trimmed with Cutadapt (1.0)
Alignment with bwa mem (0.7.12-r1039)
Duplicates Marked with picard (2.9.0-1-gf5b9f50-SNAPSHOT)
Peaks Called with MACS2 (-B --nomodel --shift 0 --extsize 500 -p 1e-3 -g hs)
Genome_build: hg38
Supplementary_files_format_and_content: xlsx - Peaks


title: PP7_invitro.PP7_14_AGTTCC_L001


title: CHM1 genomic DNA input control  biological replicate B

description:
input control for DNA immunoprecipitation
CHM1_m6dA_peaks_replicate_B.xlsx

value: Biological replicate B


title: FC012: 4h_Vehicle_6

tag: strain


title: CHM1 RNA biological replicate B

description:
RNA unmodified
CHM1_RNASeq_replicate_B.xlsx


title: YX_1009900102_F15_S135

description:
3.5 weeks old Schistosome cell 28
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_H23_S191

description:
3.5 weeks old Schistosome cell 27
schisto3.5_tpm_unfiltered.csv.gz


title: FC011: 4h_MitoCDNB_6


title: YX_1009900102_D6_S78

description:
3.5 weeks old Schistosome cell 26
schisto3.5_tpm_unfiltered.csv.gz


title: FC010: 4h_MitoCDNB_5


title: CHM1 genomic DNA input control  biological replicate C

description:
input control for DNA immunoprecipitation
CHM1_m6dA_peaks_replicate_C.xlsx


title: CHM1 genomic DNA m6dA immunopreciptiation biological replicate B

description:
dA6m antibody DNA immunoprecipitation
CHM1_m6dA_peaks_replicate_B.xlsx


title: CHM1 genomic DNA input control  biological replicate A

description:
input control for DNA immunoprecipitation
CHM1_m6dA_peaks_replicate_A.xlsx


title: PP7_invitro.PP7_13_AGTCAA_L002


title: PP7_invitro.PP7_13_AGTCAA_L001


title: CHM1 genomic DNA m6dA immunopreciptiation biological replicate A

description:
dA6m antibody DNA immunoprecipitation
CHM1_m6dA_peaks_replicate_A.xlsx


title: 20_GTTTCG_L001

value: In-vivo


title: YX_1009900102_J2_S218

description:
3.5 weeks old Schistosome cell 25
schisto3.5_tpm_unfiltered.csv.gz


title: FC009: 4h_Vehicle_5


title: YX_1009900102_G14_S158

description:
3.5 weeks old Schistosome cell 24
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_M12_S300

description:
3.5 weeks old Schistosome cell 30
schisto3.5_tpm_unfiltered.csv.gz


title: 19_GTGGCC_L001


title: caa39 BS-seq_2

data_processing:
Checking sequence quality with FASTQC (0.11.5)
Adaptator trimming with trimmomatic (0.36)
sequences were aligned with bowtie 2 (2.2.9) againt TAIR10.31 and filtered with bamtools filter (2.4.0) to remove sequence with a MapQuality below 20. Finally MarkDuplicate (2.8.1) was used to remove PCR duplicate
Peak calling with diffReps-nb (1.55.2)
BamCoverage (2.4.1) was used to create bigwig files for visualization
Genome_build: TAIR10-31
Supplementary_files_format_and_content: bigwig files

source_name: 6 day-old aerial parts

extract_protocol:
Genomic DNA samples were obtained from 400 mg of fresh aerial parts of 6 day-old plants crushed in liquid nitrogen. Genomic DNA was prepared using the NucleoSpin® Plant II Midi kit (Macherey-Nagel), with the addition of Poly(vinylpyrrolidone) to the powdered sample.
According to BGI

tag: genotype


title: PP7_invitro.PP7_14_AGTTCC_L002


title: FC007: 4h_Vehicle_4


title: 18_GTGAAA_L001


title: caa39 BS-seq_1


title: YX_1009900102_M21_S9

description:
3.5 weeks old Schistosome cell 22
schisto3.5_tpm_unfiltered.csv.gz


title: FC006: 4h_MitoCDNB_3


title: WT Col0 BS-seq_2

value: WT


title: WT Col0 BS-seq_1


title: FC005: 4h_Vehicle_3


title: YX_1009900102_L20_S284

description:
3.5 weeks old Schistosome cell 20
schisto3.5_tpm_unfiltered.csv.gz


title: FC004: 4h_Vehicle_2


title: FC003: 4h_MitoCDNB_2


title: 7_CAGATC_L001


title: FC008: 4h_MitoCDNB_4


title: YX_1009900102_G11_S155

description:
3.5 weeks old Schistosome cell 19
schisto3.5_tpm_unfiltered.csv.gz


title: 6_GCCAAT_L001


title: FC002: 4h_Vehicle_1


title: YX_1009900102_C4_S52

description:
3.5 weeks old Schistosome cell 18
schisto3.5_tpm_unfiltered.csv.gz


title: 5_ACAGTG_L001


title: FC001: 4h_MitoCDNB_1


title: YX_1009900102_K17_S257

description:
3.5 weeks old Schistosome cell 23
schisto3.5_tpm_unfiltered.csv.gz


title: YX_1009900102_A19_S19

description:
3.5 weeks old Schistosome cell 17
schisto3.5_tpm_unfiltered.csv.gz


title: PP7_invivo.16_CCGTCC_L001


title: YX_1009900102_C23_S71

description:
3.5 weeks old Schistosome cell 16
schisto3.5_tpm_unfiltered.csv.gz


title: 8_ACTTGA_L001


title: YX_1009900102_P7_S67

description:
3.5 weeks old Schistosome cell 21
schisto3.5_tpm_unfiltered.csv.gz


title: 5srRNA.12_CTTGTA_L001

organism: Escherichia coli

source_name: E.coli 5srRNA


title: YX_1009900102_L11_S275

description:
3.5 weeks old Schistosome cell 15
schisto3.5_tpm_unfiltered.csv.gz


title: 5srRNA.12_CTTGTA_L002


title: YX_1009900102_P9_S69

description:
3.5 weeks old Schistosome cell 14
schisto3.5_tpm_unfiltered.csv.gz


title: 5srRNA.11_GGCTAC_L001


title: YX_1009900102_K15_S255

description:
3.5 weeks old Schistosome cell 13
schisto3.5_tpm_unfiltered.csv.gz


title: 5srRNA.11_GGCTAC_L002


title: WM793TR LacZ suspension, Rep3

first: Andrew

middle: E

last: Aplin

address: 233 South 10th St.

institute: Thomas Jefferson University

hyb_protocol: Affymetrix gene chips, Human Clariom D array (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (5 μg) in 200 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization with rotation 60 rpm for 16 hour at 45°C.

scan_protocol: Chips (Human Clariom D array) were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Microarray data were processed in Matlab® using the RMA background adjustment and quantile normalization methods and a custom chip file (brainarray ClariomDHuman_Hs_ENTREZG_21).

source_name: Melanoma

label_protocol: Amplified cDNA was synthesized from 100 ng of total RNA using NuGen Ovation Pico WTA systems V2 (NuGen Technologies, Inc.). 5 μg cDNA was fragmented and chemically labeled with biotin to generate biotinylated cDNA using Encore biotin module (NuGen Technologies, Inc.).

growth_protocol: 1.0x10^6 WM793TR LacZ and CADM1 cells were seeded on 10cm plates win WM media with or without bacto-agar coating.

extract_protocol: RNA was harvested via RNeasy Plant Mini Kit (Qiagen #74904) according to manufacture's protocol.

treatment_protocol: Transgene (CADM1 or LacZ as a control) was induced via addition of 100ng/mL of doxycycline.

value: Melanoma

tag: genotype/variation

value: LacZ

tag: growth

value: Suspension


title: WM793TR CADM1 suspension, Rep3

tag: tissue


title: WM793TR CADM1 adherent, Rep3

value: Plated


title: PP7_invivo.13_AGTCAA_L001


title: PP7_invivo.4_TGACCA_L001

value: Non-induced

value: Non-modified


title: 5srRNA.6_GCCAAT_L001

value: In-vitro


title: YX_1009900102_F2_S122

description:
3.5 weeks old Schistosome cell 12
schisto3.5_tpm_unfiltered.csv.gz

value: Swiss  Webster NR-21963

tag: worm age

value: 3.5 weeks


title: 17_GTCCGC_L001

value: induced

value: modified by NAI


title: WM793TR CADM1 adherent, Rep2


title: WM793TR LacZ adherent, Rep2


title: YX_1009900102_M23_S11

description:
3.5 weeks old Schistosome cell 11
schisto3.5_tpm_unfiltered.csv.gz


title: WM793TR CADM1 suspension, Rep2


title: WM793TR LacZ adherent, Rep3


title: WM793TR LacZ suspension, Rep2


title: PP7_invivo.14_AGTTCC_L001


title: PP7_invivo.2_CGATGT_L001


title: YX_1009900102_D2_S74

description:
3.5 weeks old Schistosome cell 10
schisto3.5_tpm_unfiltered.csv.gz


title: 5srRNA.5_ACAGTG_L002


title: YX_1009900102_M8_S296

description:
3.5 weeks old Schistosome cell 9
schisto3.5_tpm_unfiltered.csv.gz


title: PP7_invivo.1_ATCACG_L001


title: WM793TR CADM1 suspension, Rep1


title: PP7_invivo.3_TTAGGC_L001


title: YX_1009900102_A17_S17

description:
3.5 weeks old Schistosome cell 8
schisto3.5_tpm_unfiltered.csv.gz


title: TORoe-3rd

city: Seoul

first: Dong-Gi

last: Lee

address: 50 Yonsei-ro, Seodaemun-gu

institute: Yonsei University

description: Sequencing platform: Illumina HiSeq 2500

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic v0.32 with adapter seq of TruSeq3-PE.fa and MINLEN:36.
Expected count and deg analysis were conducted using RSEM (v1.2.24) with bowtie2 v2.2.3 and EdgeR v3.8.6 respectively.
Genome_build: BROAD institute : Cryptococcus neoformans H99
Supplementary_files_format_and_content: Tab-delimited text files include FPKM and expected counts for each Sample

organism: Cryptococcus neoformans H99

source_name: Cryptococcus neoformans H99 TOR1oe R3

growth_protocol: Each strains were incubated in YPD liquid medium overnight at 30°C, subcultured in fresh YPD liquid medium, and then further incubated at 30°C until OD600 was approximately 0.6–0.8. The WT cells were divided in half. One-half was used as a WT control while the other half was treated with rapamycin (3 ng/ml) and further incubated for 3 h at 30°C.

extract_protocol:
1. Freeze cells in Liquid Nitrogen for 30min. 2. Lyophilize samples overnight. 3. Add 3ml of 3mm glass beads and vortex vigorously until fine powder is created. 4. Add 4ml of Easyblue (dissolve powder completely) and let them sit 5 minutes. 5. Add 800 ul of chloroform (invert 10 times). 6. Let them sit 3 minutes and transfer to 14 ml round bottle tubes. 7. Spin at 10,000 rpm for 15 minutes. 8. Transfer supernatant to new round-bottom tubes. 9. Add 2 ml of isopropanol and capping and gently invert. 10. Store for 5-10 minutes at room temperaturea. 11. Spin for 10 minutes at 10,000 rpm. 12. Pour off supernatant. 13. Add 4 ml of 75% EtOH (made with DEPC dH2O) and invert 4-5 times. 14. Spin for 5 minutes at 8,000 rpm. 15. Pour off EtOH (Let tubes air-dry upside down). 16. Resuspend in appropriate volume of DEPC dH2O. 17. Heat at 55℃ for 10 minutes. 18. Transfer RNA to microtube and mesuring the concentration. 19. For purification of the extracted total RNA, we used Rneasy spin column (Qiagen) following the manufacturer’s protocol.
The library was prepared using the Illumina TruSeq RNA Sample Prep Kit v2.

value: TOR1oe mutant


title: TORoe-2nd

source_name: Cryptococcus neoformans H99 TOR1oe R2

treatment_protocol: The WT cells were divided in half. One-half was used as a WT control while the other half was treated with rapamycin (3 ng/ml) and further incubated for 3 h at 30°C.


title: PP7_invivo.15_ATGTCA_L001


title: Control 4

city: Beijing

first: shi

last: yuanyuan

state: Bejing

address: No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

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

treatment_protocol: Cartilage tissues were collected from medial and lateral femoral condyles of anterior cruciate ligament transection-operated rat knee joints treated with normal saline (vehicle) twice a week for 4 w.

value: Cartilage tissue of rat knee joints


title: YX_1009900102_M17_S5

description:
3.5 weeks old Schistosome cell 7
schisto3.5_tpm_unfiltered.csv.gz

value: stem cells


title: TORoe-1st

source_name: Cryptococcus neoformans H99 TOR1oe R1


title: Control 3

source_name: rat knee joints treated with normal saline (vehicle) twice a week for 4 w


title: WM793TR shTWIST1, Rep3

hyb_protocol: Affymetrix gene chips, Human gene 1.0 ST array (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (2.5 μg) in 110 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h.

scan_protocol: Chips (Human  array HA 1.0) were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Microarray data were processed in Matlab® using the RMA background adjustment and quantile normalization methods and a custom chip file (brainarray hugene10st_Hs_ENTREZG_21).

label_protocol: Amplified cDNA was synthesized from 50 ng of total RNA using NuGen Ovation Pico WTA systems V2 (NuGen Technologies, Inc.). 2.5 μg cDNA was fragmented and chemically labeled with biotin to generate biotinylated cDNA using Encore biotin module (NuGen Technologies, Inc.).

growth_protocol: Human melanoma cell lines WM793TR control shRNA, TWIST1 shRNA, or TWIST1 shRNA + TWIST1 cDNA for overexpression were induced with 100ng/mL doxycycline for 96 hours.

treatment_protocol: Transgene or shRNA was induced via addition of 100ng/mL of doxycycline.

value: TWIST1 knockdown


title: YX_1009900102_N13_S25

description:
3.5 weeks old Schistosome cell 6
schisto3.5_tpm_unfiltered.csv.gz


title: Control 2


title: Rapa-3rd

source_name: Cryptococcus neoformans H99 Rapamycin-treated WT R3

value: Rapa


title: WM793TR CADM1 adherent, Rep1


title: YX_1009900102_G4_S148

description:
3.5 weeks old Schistosome cell 5
schisto3.5_tpm_unfiltered.csv.gz


title: WM793TR TWIST1 overexpression, Rep3

value: TWIST1 overexpression


title: WM793TR LacZ adherent, Rep1

value: Melanoma


title: Rapa-2nd

source_name: Cryptococcus neoformans H99 Rapamycin-treated WT R2


title: WM793TR at basal expression, Rep3

value: TWIST1 basal


title: PP7_invitro.PP7_20_GTGGCC_L001


title: 14_2_DBI

description: Control

value: Leaves

value: Pre-embryogenic condition

tag: growth medium

value: MS salts without growth regulators

tag: time point

value: 14 days DBI


title: WM793TR TWIST1 overexpression, Rep2


title: Case 3

treatment_protocol: Cartilage tissues were collected from medial and lateral femoral condyles of anterior cruciate ligament transection-operated rat knee joints treated with BNTA (1.5 mg kg-1) twice a week for 4 w.


title: YX_1009900102_E6_S102

description:
3.5 weeks old Schistosome cell 4
schisto3.5_tpm_unfiltered.csv.gz


title: Rapa-1st

source_name: Cryptococcus neoformans H99 Rapamycin-treated WT R1

tag: treatment


title: Case 2

source_name: rat knee joints treated with BNTA (1.5 mg kg-1) twice a week for 4 w


title: YX_1009900102_E20_S116

description:
3.5 weeks old Schistosome cell 3
schisto3.5_tpm_unfiltered.csv.gz


title: Case 1


title: WM793TR shTWIST1, Rep2


title: WT-2nd

source_name: Cryptococcus neoformans H99 WT R2


title: YX_1009900102_L7_S271

description:
3.5 weeks old Schistosome cell 2
schisto3.5_tpm_unfiltered.csv.gz

source_name: Schistosoma mansoni stem cells


title: WM793TR basal expression, Rep2


title: CK

city: hangzhou

first: bohui

last: wu

address: No. 666 Wusu Street, Lin‘an City

institute: Zhejiang A&F University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Cunninghamia lanceolata

source_name: Root

growth_protocol: 1/8 Hoagland nutrient solution was applied for cultivating strong plantlets for one month.

extract_protocol:
Total roots RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Chinese fir were treated by low nitrogen (LN, the nitrogen present in distilled water, which was determined to be less than 0.01mM) and nitrogen sufficient (CK, nitrogen concentration of 5.03 mM) for four months.

value: Root

tag: nitrogen concentration

tag: treatment time

value: four months


title: YX_1009900102_D19_S91

description:
3.5 weeks old Schistosome cell 1
schisto3.5_tpm_unfiltered.csv.gz

value: Swiss  Webster NR-21963

value: 3.5 weeks


title: WM793TR TWIST1 overexpression, Rep1


title: LN


title: WT-1st

source_name: Cryptococcus neoformans H99 WT R1


title: WM793TR shTWIST1, Rep1


title: WM793TR at basal expression, Rep1


title: WT-3rd

source_name: Cryptococcus neoformans H99 WT R3


title: IPF26 TGF-b1

status: Public on Apr 02 2019

city: BATH

first: Marina

last: Hadjicharalambous

address: PHARMACY AND PHARMACOLOGY (5 WEST), CLAVERTON DOWN

institute: University of Bath

description: RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes. • Transfer 200μl of hyb solution to each array • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Raw data  (CEL files)  were processed by the Affymetrix Expression Console™ using Robust Multi-chip Analysis (RMA) to generate CHP files (Probe-level summarisation) following the manufacturers manual. CHP files generated by the Expression Console Software were used in the Transcriptome Analysis Console (TAC) Software to perform statistical analysis and obtain a list of differentially expressed genes between the study groups

source_name: Primary cell culture

label_protocol: Samples were enzymatically fragmented and biotinylated using the GeneChip WT PLUS Reagent Kit (Affymetrix)

growth_protocol: Lung fibroblasts were cultured in DMEM growth media (10% FBS, 1% Pen/strep, 0.1% Fungizone)

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen) including an on-column DNase treatment (Qiagen) according to the manufacturer's instructions.

treatment_protocol: TGF-b1 (3ng/ml) for 24 hours

value: IPF lung fibroblasts

tag: stimulation

value: TGF-b1-stimulated 24 hours


title: IPF8 TGF-b1


title: AG02603 TGF-b1

value: Control lung fibroblasts


title: NL-59 NS

value: non-stimulated 24 hours


title: IPF38 NS


title: IPF8 NS


title: donor 3 TGF-b1


title: IPF38 TGF-b1


title: AG02262 NS


title: AG02258 TGF-b1


title: donor 3 NS


title: IPF32 NS


title: AG02603 NS


title: IPF36 NS


title: AG02258 NS


title: IPF32 TGF-b1


title: IPF36 TGF-b1


title: IPF26 NS


title: NL59 TGF-b1


title: bladder tumour 2452

city: Leeds

first: Margaret

middle: A

last: Knowles

state: West Yorkshire

address: Becket Street

department: LICAP

institute: University of Leeds

description: primary bladder tumour

hyb_protocol: Microarrays were washed and stained using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit according to manufacturer's instructions using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip 7G microarray scanner.

data_processing:
Data QC was analysed using Affymetrix Expression Console Software and samples were normalised using RMA.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

source_name: fresh frozen bladder tumour tissue

label_protocol: Total RNA was amplified using the Affymetrix GeneChip WT PLUS Reagent Kit according to manufacturer's instructions. The resulting cDNA was quantified using OD (NanoDrop). The cDNA was normalised and hybridised onto Affymetrix Human Transcriptome 2.0 microarrays for 16 hours at 45 degrees C.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from fresh frozen tissue samples comprising at least 70% tumour using an RNeasy  Plus Micro Kit (Qiagen). The protocol for fibrous tissue was followed with the inclusion of an on-column DNase digestion step

tag: tumour stage

value: Ta


title: AG02262 TGF-b1


title: bladder tumour 2498

description: primary bladder tumour


title: bladder tumour 2334

description: primary bladder tumour


title: bladder tumour 2161

description: primary bladder tumour


title: bladder tumour 2425

description: primary bladder tumour


title: bladder tumour 2338

description: primary bladder tumour


title: bladder tumour 2118

description: primary bladder tumour


title: bladder tumour 2220

description: primary bladder tumour


title: bladder tumour 2055

description: primary bladder tumour


title: bladder tumour 2065

description: primary bladder tumour


title: bladder tumour 2032

description: primary bladder tumour


title: bladder tumour 2074

description: primary bladder tumour


title: bladder tumour 2063

description: primary bladder tumour


title: bladder tumour 1992

description: primary bladder tumour


title: bladder tumour 1719

description: primary bladder tumour


title: 5srRNA.5_ACAGTG_L001

source_name: E.coli 5srRNA

tag: pp7-wt or pp7-uss

tag: in-vivo or in-vitro

value: In-vitro

tag: induced or non-induced

value: Non-induced

tag: modified by nai

value: modified by NAI

tag: replicate


title: bladder tumour 2047

description: primary bladder tumour


title: bladder tumour 1858

description: primary bladder tumour


title: bladder tumour 1931

description: primary bladder tumour


title: bladder tumour 2082

description: primary bladder tumour


title: bladder tumour 2100

description: primary bladder tumour


title: bladder tumour 2013

description: primary bladder tumour


title: bladder tumour 2104

description: primary bladder tumour


title: bladder tumour 1930

description: primary bladder tumour


title: bladder tumour 1932

description: primary bladder tumour


title: bladder tumour 1566

description: primary bladder tumour


title: bladder tumour 1971

description: primary bladder tumour


title: bladder tumour 2086

description: primary bladder tumour


title: bladder tumour 1390

description: primary bladder tumour


title: bladder tumour 1514

description: primary bladder tumour


title: bladder tumour 1289

description: primary bladder tumour


title: bladder tumour 1798

description: primary bladder tumour


title: bladder tumour 1732

description: primary bladder tumour


title: bladder tumour 1567

description: primary bladder tumour


title: bladder tumour 1103

description: primary bladder tumour


title: 14-day OVCAR-8 2D replicate 3

city: Bethesda

first: Michael

middle: M.

last: Gottesman

address: 37 Convent Dr. Bldg. 37 RM 2112

department: National Cancer Institute

institute: National Institutes of Health

description:
processed data file:
14-day_OVCAR-8_RawCount_genes_unfiltered.txt

data_processing:
Sequencing reads were trimmed for adapters and low quality bases using Trimmomatic software and overall quality was verified with FastQC.
Reads were then aligned with reference human genome hg19 using two-pass STAR alignment, quantified with featureCounts, and normalized with TMM.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read count values for each sample.

source_name: 14-day OVCAR-8 2D

growth_protocol: For both cell lines: 2D cultures were grown in T-75 polystyrene culture flasks, allowing cells to reach approximately 80% confluency. Dulbecco’s Modified Eagle Medium (DMEM) 1X was supplemented with 10% fetal bovine serum (FBS) (Atlanta Biologicals, Lawrenceville, GA), penicillin (100 units/mL), streptomycin (100 μg/mL), and L-glutamine (2 mM), which were purchased from Life Technologies (Carlsbad, CA) and used as received. 3D cultures were plated in Matrigel (Corning Life Sciences, Bedford, MA) 3 mg/mL at a density of 6x10^4 per well. The same 10% FBS media was used. 3D cultures were exposed to one of three oxygen conditions: 3% oxygen, 21% oxygen, or gradient oxygen.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 2D cultures were grown in 21% oxygen. 3D cultures were exposed to one of three oxygen conditions: 3% oxygen, 21% oxygen, or gradient oxygen (bioreactor condition).

tag: cell line

tag: tissue source

value: High grade ovarian serous adenocarcinoma

tag: culture dimension

value: 2D (polystyrene)

tag: culture condition

value: 21% Oxygen

tag: library prep kit

value: Illumina NeoPrepTM Library Prep System (Ref:20003841)


title: 14-day OVCAR-8 3D 21% oxygen replicate 4

source_name: 14-day OVCAR-8 3D 21% oxygen

value: 3D (Matrigel)


title: 14-day OVCAR-8 3D gradient oxygen replicate 3

source_name: 14-day OVCAR-8 3D gradient oxygen

value: Gradient Oxygen


title: 14-day OVCAR-8 3D gradient oxygen replicate 1


title: 14-day OVCAR-8 3D 3% oxygen replicate 2

source_name: 14-day OVCAR-8 3D 3% oxygen

value: 3% Oxygen


title: 14-day OVCAR-8 2D replicate 4


title: 14-day OVCAR-8 3D gradient oxygen replicate 2


title: 14-day OVCAR-8 3D 21% oxygen replicate 1


title: 14-day OVCAR-8 3D 21% oxygen replicate 2


title: bladder tumour 787

description: primary bladder tumour


title: 14-day OVCAR-8 3D 3% oxygen replicate 4


title: 14-day OVCAR-8 3D gradient oxygen replicate 4


title: bladder tumour 437

description: primary bladder tumour


title: bladder tumour 390

description: primary bladder tumour


title: bladder tumour 1181

description: primary bladder tumour


title: bladder tumour 66

description: primary bladder tumour


title: WM793TR LacZ suspension, Rep1

city: Philadelphia

source_name: Melanoma

tag: tissue

value: Melanoma

tag: genotype/variation

value: LacZ

tag: growth

value: Suspension


title: bladder tumour 1067

description: primary bladder tumour


title: 7-day OVCAR-8 3D gradient oxygen replicate 4

description:
processed data file:
7-day_OVCAR-8_RawCount_genes_unfiltered.txt

source_name: 7-day OVCAR-8 3D gradient oxygen

value: TruSeq Stranded mRNA Library Prep Kit (RS-122-2101)


title: 7-day OVCAR-8 3D gradient oxygen replicate 3


title: bladder tumour 705

description: primary bladder tumour


title: 14-day OVCAR-8 3D 21% oxygen replicate 3


title: 14-day OVCAR-8 2D replicate 1


title: bladder tumour 419

description: primary bladder tumour


title: 14-day OVCAR-8 3D 3% oxygen replicate 3


title: 7-day OVCAR-8 3D gradient oxygen replicate 2


title: 14-day OVCAR-8 2D replicate 2


title: bladder tumour 1083

description: primary bladder tumour


title: bladder tumour 103

description: primary bladder tumour


title: 7-day OVCAR-8 3D 21% oxygen replicate 3

source_name: 7-day OVCAR-8 3D 21% oxygen


title: 7-day OVCAR-8 3D gradient oxygen replicate 1


title: 7-day OVCAR-8 3D 21% oxygen replicate 2


title: 7-day OVCAR-8 2D replicate 4

source_name: 7-day OVCAR-8 2D


title: 7-day OVCAR-8 2D replicate 1


title: 7-day OVCAR-8 2D replicate 2


title: 7-day OVCAR-8 3D 3% oxygen replicate 1

source_name: 7-day OVCAR-8 3D 3% oxygen


title: 7-day OVCAR-8 3D 21% oxygen replicate 4


title: 14-day MCF-7 3D 21% oxygen replicate 2

description:
processed data file:
14-day_MCF-7_RawCount_genes_unfiltered.txt

source_name: 14-day MCF-7 3D 21% oxygen

value: Invasive ductal carcinoma


title: 14-day MCF-7 3D gradient oxygen replicate 4

source_name: 14-day MCF-7 3D gradient oxygen


title: 14-day MCF-7 3D 21% oxygen replicate 1


title: 7-day OVCAR-8 2D replicate 3


title: 14-day MCF-7 3D gradient oxygen replicate 2


title: 7-day OVCAR-8 3D 21% oxygen replicate 1


title: 14-day MCF-7 3D 3% oxygen replicate 3

source_name: 14-day MCF-7 3D 3% oxygen


title: 14-day MCF-7 2D replicate 2

source_name: 14-day MCF-7 2D


title: 14-day MCF-7 3D 21% oxygen replicate 3


title: 14-day MCF-7 2D replicate 4


title: 14-day MCF-7 2D replicate 1


title: 5srRNA.6_GCCAAT_L002

value: Non-modified


title: 7-day OVCAR-8 3D 3% oxygen replicate 2


title: 7-day MCF-7 3D gradient oxygen replicate 4

description:
processed data file:
7-day_MCF-7_RawCount_genes_unfiltered.txt

source_name: 7-day MCF-7 3D gradient oxygen


title: 7-day MCF-7 3D gradient oxygen replicate 3


title: 7-day OVCAR-8 3D 3% oxygen replicate 3


title: 7-day OVCAR-8 3D 3% oxygen replicate 4


title: 14-day MCF-7 3D 21% oxygen replicate 4


title: 14-day MCF-7 3D 3% oxygen replicate 2


title: 7-day MCF-7 3D gradient oxygen replicate 2


title: 7-day MCF-7 3D gradient oxygen replicate 1


title: 14-day MCF-7 2D replicate 3


title: 7-day MCF-7 3D 21% oxygen replicate 4

source_name: 7-day MCF-7 3D 21% oxygen


title: 7-day MCF-7 3D 21% oxygen replicate 3


title: 7-day MCF-7 2D replicate 2

source_name: 7-day MCF-7 2D


title: 7-day MCF-7 3D 3% oxygen replicate 4

source_name: 7-day MCF-7 3D 3% oxygen


title: 7-day MCF-7 3D 3% oxygen replicate 3


title: 7-day MCF-7 2D replicate 4


title: 7-day MCF-7 2D replicate 3


title: Day0_DroNc_BioRep2

city: Chicago

first: Alan

last: Selewa

state: IL

address: 5454 S Shore Dr, Apt 503

institute: University of Chicago

data_processing:
Alignment to hg38 using STAR in single-pass mode
Trim reads with cutadapt
Assign reads to gene features using featureCounts
Construct expression matrix using umi_tools count
Merged expression matrices into a single matrix for Drop-seq and DroNc-seq data
Genome_build: hg38
Supplementary_files_format_and_content: TSV; read counts at per gene/cell

source_name: Nuclei_ hiPSC-CM_Day0

growth_protocol: At each time-point, cells were harvested from 100 mm plates by treating with Accutase (BD 385  Biosciences, #561527) to generate a single cell suspension; from Day 7 onward, a cell scraper was 386  also employed to release adherent cells from plates. Post-mortem human heart tissue was provided by the National Disease Research Interchange (NDRI). The sample (m, 68 yrs) had been stored at -80oC for 11 years before it was processed for DroNc-seq.

extract_protocol:
For Drop-seq, 2 mL of cells at 200,000 cells/mL in PBS-BSA was loaded in a 3 mL syringe (BD #309657). A custom-built 90 μm Drop-seq microfluidic device (CAD file supplied separately) was used for droplet generation, creating droplets smaller than the standard Drop-seq protocol. For DroNc-seq, a 75 μm microfluidic device9 was used. 2 mL of nuclei at 300,000 nuclei/mL were loaded into a 3 mL syringe and flowed at 1.5 mL/hr (similar parameters were used for nuclei from primary heart tissue).
Drop-seq and DroNc-seq samples for each differentiation time-point were sequenced in a single run, with 150-200 million reads allocated per sample. Sample libraries were loaded at ~1.5 pM concentration and sequenced on an Illumina NextSeq 500 using the NextSeq 75 cycle v3 kits for paired-end sequencing.

tag: sample type

value: Nuclei

tag: cell type

value: human induced Pluripotent Stem Cells differentiating into Cardiomyocytes

tag: time point

value: day 0


title: Male_Heart_DroNc

source_name: Primary Heart Tissue

value: post-mortem frozen primary heart tissue


title: Day1_Drop_BioRep2

source_name: Cells_ hiPSC-CM_Day1

value: Cells

value: day 1


title: 7-day MCF-7 3D 3% oxygen replicate 2


title: 7-day MCF-7 2D replicate 1

value: 2D (polystyrene)

value: 21% Oxygen


title: 7-day MCF-7 3D 3% oxygen replicate 1

value: 3D (Matrigel)

value: Illumina NeoPrepTM Library Prep System (Ref:20003841)


title: Day1_DroNc_BioRep2

source_name: Nuclei_ hiPSC-CM_Day1


title: Day7_Drop_BioRep2

source_name: Cells_ hiPSC-CM_Day7

value: day 7


title: Day3_Drop_BioRep2

source_name: Cells_ hiPSC-CM_Day3

value: day 3


title: Day0_Drop_BioRep2

source_name: Cells_ hiPSC-CM_Day0


title: Day3_DroNc_BioRep2

source_name: Nuclei_ hiPSC-CM_Day3


title: Day7_DroNc_BioRep2

source_name: Nuclei_ hiPSC-CM_Day7


title: Day3_DroNc_BioRep1_TechRep2


title: Day1_Drop_BioRep1_TechRep2


title: Day7_DroNc_BioRep1_TechRep1


title: Day7_DroNc_BioRep1_TechRep2


title: Day15_DroNc_BioRep2

source_name: Nuclei_ hiPSC-CM_Day15

value: day 15


title: Day15_Drop_BioRep2

source_name: Cells_ hiPSC-CM_Day15


title: Day3_DroNc_BioRep1_TechRep1


title: 7-day MCF-7 3D 21% oxygen replicate 1


title: Day3_Drop_BioRep1_TechRep1


title: Day1_Drop_BioRep1_TechRep1


title: Day3_Drop_BioRep1_TechRep2


title: Day7_Drop_BioRep1_TechRep1

source_name: Cells_ hiPSC-CM_Day3+ciPSC

value: day 7+ chimp induced Pluripotent Stem Cells


title: Day7_Drop_BioRep1_TechRep2


title: Day0_DroNc_BioRep1_TechRep2


title: Day0_DroNc_BioRep1_TechRep1


title: Day0_Drop_BioRep1_TechRep2


title: Day0_Drop_BioRep1_TechRep1


title: not differentiated PA, rep1

city: Solna

first: Adil

last: Mardinoglu

address: Tomtebodavägen 23B

department: Systems biology

country: Sweden

institute: SciLifeLab, KTH

description:
Hs_Diff_PA_not_differentiated_rep1
Raw data not provided due to patient privacy concerns and European Union law.

data_processing:
Quantification of the data was done using BCBIO version 1.0.1.
Hisat2 version 2.0.5 was used within BCBIO to align the data against the human hg38 assembly.
Sailfish 0.10.1 was used within BCBIO to quantify gene and exon counts.
Genome_build: hg38 (GRCh38) assembly
Supplementary_files_format_and_content: *txt: Tab-delimited text files include raw count values for each sample, along with Ensembl IDs and gene symbols.

source_name: Adipose tissue

extract_protocol:
The adipose tissue was removed of fibrous material, finely minced, and digested in collagenase buffer containing HBSS +CaCl2+MgCl2 (Gibco 14065-49), 2% BSA, and 800U/g of tissue (~3mg/g of tissue) of type 2 collagenase (Worthington-LS004177) for approximately 40 min at 37°C. Digested material was passed through a 250 um strainer and washed 3 times with a total of 1L of KRHB buffer (1x KRH, 25mM HEPES, 2mM glucose, 2%BSA) using a separation funnel (VWR 527-0007) to separate the infranatant which contains the preadipocytes from the floating mature adipocytes.
RNA quality and quantity were assessed using a Fragment Analyzer standard sensitivity RNA kit (AATI # DNF-471) according to manufacturer’s instructions. Libraries were prepared using Illumina’s stranded total RNA library prep kit with “ribo-gold” rRNA depletion (catalog# RS-122-2303). The quality of the libraries were assessed using a Fragment Analyzer standard-sensitivity NGS kit (AATI # DNF-473). Samples were pooled so that they were present at an equal molarity. Pooled samples were sequenced 2x with NextSeq high output 150 cycle kits (Illumina # FC-404-2002), paired-end reads.

value: Adipose

value: Not differentiated PA


title: not differentiated PA, rep2

description:
Hs_Diff_PA_not_differentiated_rep2
Raw data not provided due to patient privacy concerns and European Union law.


title: not differentiated PA, rep3

description:
Hs_Diff_PA_not_differentiated_rep3
Raw data not provided due to patient privacy concerns and European Union law.


title: Differentiated PA, 1week, rep2

description:
Hs_Diff_PA_1_wk_rep2
Raw data not provided due to patient privacy concerns and European Union law.

value: Differentiated PA, 1 week


title: Differentiated PA, 2week, rep4

description:
Hs_Diff_PA_2_wk_rep4
Raw data not provided due to patient privacy concerns and European Union law.

value: Differentiated PA, 2 week


title: Differentiated PA, 2week, rep6

description:
Hs_Diff_PA_2_wk_rep6
Raw data not provided due to patient privacy concerns and European Union law.


title: Differentiated PA, 2week, rep1

description:
Hs_Diff_PA_2_wk_rep1
Raw data not provided due to patient privacy concerns and European Union law.


title: Differentiated PA, 2week, rep5

description:
Hs_Diff_PA_2_wk_rep5
Raw data not provided due to patient privacy concerns and European Union law.


title: Differentiated PA, 2week, rep7

description:
Hs_Diff_PA_2_wk_rep7
Raw data not provided due to patient privacy concerns and European Union law.


title: Differentiated PA, 1week, rep4

description:
Hs_Diff_PA_1_wk_rep4
Raw data not provided due to patient privacy concerns and European Union law.


title: Differentiated PA, 2week, rep8

description:
Hs_Diff_PA_2_wk_rep8
Raw data not provided due to patient privacy concerns and European Union law.


title: Differentiated PA, 2week, rep3

description:
Hs_Diff_PA_2_wk_rep3
Raw data not provided due to patient privacy concerns and European Union law.


title: MAAC, 2week, rep4

description:
Hs_TW_2_wk_rep4
Raw data not provided due to patient privacy concerns and European Union law.

value: MAAC, 2 week


title: not differentiated PA, rep5

description:
Hs_Diff_PA_not_differentiated_rep5
Raw data not provided due to patient privacy concerns and European Union law.


title: not differentiated PA, rep4

description:
Hs_Diff_PA_not_differentiated_rep4
Raw data not provided due to patient privacy concerns and European Union law.