title: OTHER_U_LI_M_39

source_name: OTHER_U_LI_M_whole intestinal tissue


title: CD_I_LI_M_24

status: Public on Jul 01 2021

type: SRA

city: Oxford

first: Fiona

last: Powrie

address: Roosevelt Drive

department: Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Sequence reads were aligned to the human genome with Hisat2 (version 2.1.0) [1] using a “genome” index built from the GRCh38 release of the human genome and known splice sites extracted from Ensembl version 91 annotations (using the hisat2_extract_splice_sites.py tool). A two-pass mapping strategy was used to discover novel splice sites (with the additional parameters: --dta and --score-min L,0.0,-0.2).
Mapped reads were counted using featureCounts (Subread version 1.6.3; Ensembl version 91 annotations; default parameters).
TPMs were estimated with salmon (version 0.9.1); using a quasi-index (built with Ensembl version 91 annotations and k=31) and gc bias correction (parameter “--gcBias”)
Genome_build: GRCh38
Supplementary_files_format_and_content: (1) "featurecounts_counts.txt" is a tab-delimited text file containing the table of gene-by-sample read counts computed with the featureCounts algorithm. (2) "salmon.genes.tpms.txt" is a tab-delimited text file containing the table of gene-by-sample raw TPMs computed with salmon.

molecule: total RNA

organism: Homo sapiens

source_name: CD_I_LI_M_whole intestinal tissue

extract_protocol:
surgical resection tissue was stored in RNAlater (Qiagen) upon collection until further processing. Tissue was homogenised using the soft tissue homogenizing CK14 kit (Precellys, Stretton Scientific 03961) in 300µl of RLT lysis buffer (Qiagen) and 20µM DTT (Sigma). RNA was isolated using the Qiagen Mini kit with a DNA digestion step (Qiagen).
Sequencing libraries were prepared using either the QuantSeq 3’ mRNA-Seq FWD Library Prep Kit (Lexogen) for whole tissue samples or the Smart-seq2 protocol (Picelli et al., 2013) for bulk and cultured cell populations (with in-house indexing primers)
RNA-sequencing, Libraries were sequenced using an Illumina HiSeq4000 with 75bp paired-end sequencing (Lamble et al., 2013).

tag: disease

value: CD

value: inflamed

tag: gender

value: male

tag: disease_duration (y)

tag: qc

value: include


title: AMP6

city: Helsinki

first: Mridul

last: Johari

state: Uusimaa

address: Haartmaninkatu 8, Biomedicum

country: Finland

institute: Folkhälsan Research Center

data_processing:
Illumina RTA2 for HiSeq 4000
Adapter sequences and low quality bases removed using fastp 0.19.5
STAR 2.7.0d two pass method based on ENCODE guidelines for long RNA
featureCounts v1.6.3,  DESeq2 v1.26.0, Rstudio v1.2.5019 based on R v3.6.1
Genome_build: Gencode.v29 based on ENSEMBL GRCh38.p12
Supplementary_files_format_and_content: raw counts from featureCounts on primary comprehensive gene annotation Gencode.v29
Supplementary_files_format_and_content: normalized abundance measurement using DESeq2

molecule: polyA RNA

source_name: Skeletal muscle (Vastus Lateralis)

extract_protocol:
RNA was extracted from snap formzen skeletal muscle biopsies using Qiagen Rneasy Plus Universal Mini Kit (Cat No./ID: 73404)
tissue homogenization steps were performed using SpeedMill PLUS (Analytik Jena AG, Germany)
Extracted RNA was treated with Invitrogen TURBO Dnase (Catalog number:  AM2238)
PolyA+ RNA selection using NEBNext Ultra II Directional RNA library Prep kit (E7760) for Illumina for the preparation of strand specific RNA-seq libraries

tag: tissue

value: Skeletal muscle (Vastus Lateralis)

tag: group

value: Amputee

tag: age at biopsy (in years)

tag: age of onset (in years)

value: Female


title: AMP8


title: AMP7

value: Male


title: AMP1

source_name: Skeletal muscle (Tibialis Anterior)

value: Skeletal muscle (Tibialis Anterior)


title: AMP2


title: UC_U_LI_M_33

source_name: UC_U_LI_M_whole intestinal tissue

value: UC

value: uninflamed


title: AMP5


title: TMD2

value: Tibial Muscular dystrophy


title: TMD3


title: TMD5

source_name: Skeletal muscle (Gastrocnemius)

value: Skeletal muscle (Gastrocnemius)


title: TMD4

source_name: Skeletal muscle(Extensor Hallucis Longus)


title: TMD9


title: CD_U_SI_M_27

source_name: CD_U_SI_M_whole intestinal tissue

value: EXCLUDE


title: IBM24

extract_protocol:
RNA was extracted from snap frozen skeletal muscle biopsies using Qiagen Rneasy Plus Universal Mini Kit (Cat No./ID: 73404)
tissue homogenization steps were performed using SpeedMill PLUS (Analytik Jena AG, Germany)
Extracted RNA was treated with Invitrogen TURBO Dnase (Catalog number:  AM2238)
PolyA+ RNA selection using NEBNext Ultra II Directional RNA library Prep kit (E7760) for Illumina for the preparation of strand specific RNA-seq libraries

value: Inclusion body myositis


title: AMP4


title: TMD1


title: IBM25


title: IBM23


title: CD_I_SI_F_25

source_name: CD_I_SI_F_whole intestinal tissue

value: female


title: IBM21


title: IBM22


title: CD_M_LI_M_23

source_name: CD_M_whole intestinal tissue


title: IBM17


title: IBM18


title: IBM15


title: IBM16


title: IBM11


title: IBM12


title: IBM8


title: IBM7


title: IBM10


title: IBM9


title: IBM13


title: IBM4


title: IBM20


title: IBM1


title: IBM2


title: hESC_Primed_SOX2_Input

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

country: USA

institute: Columbia University Irving Medical Center

description: ChIP Input in primed hESCs (for KLF4,SOX2)

library_source: genomic

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality
Reads were aligned to the human genome hg38 using the bowtie2 (v2.3.4) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v0.1.19)
ChIP-seq peaks were determined by the MACS program (v.2.0.10), using input as the control data, and all other parameters followed the default settings. Board peaks were called from ChIP of BAF subunits, and narrow peaks were call from transcription factors.
Genome_build: hg38
Supplementary_files_format_and_content: Bed file of MACS called peaks.

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: Conventional (primed) human ESCs were maintained on mitomycin C inactivated mouse embryonic ﬁbroblast (MEF) feeder layers and passaged using Collagenase (1 mg/mL) or manual methods. Primed human ESCs were cultured in human ESC medium (hESM) [DMEM/F12 (Invitrogen) supplemented with 15% fetal bovine serum (Gibco HI FBS, 10082-147), 5% KnockOut Serum Replacement (Invitrogen), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Naive human ESCs were cultured on mitomycin C-inactivated MEF feeder cells, and were passaged by a brief PBS wash followed by single-cell dissociation using 3-5 minute treatment with Accutase (Gibco) and centrifugation in fibroblast medium [DMEM (Invitrogen) supplemented with 10% FBS (Gibco HI FBS, 10082-147), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 1% penicillin-streptomycin (Lonza) and 0.1 mM β-mercaptoethanol (Sigma)]. For conversion of pre-existing primed human ESC lines, we seeded 2 x 105 trypsinized single cells on a MEF feeder layer in hESM supplemented with ROCK inhibitor Y-27632 (Stemgent, 10 μM). 2 days later medium was switched to 5i/L/A or 4i/L/A (no IM12)-containing naive human ESC medium. Following an initial wave of cell death, naive colonies appeared within 10 days and were expanded polyclonally using Accutase (Gibco) on a MEF feeder layer. Naive human pluripotent cells were derived and maintained in serum-free N2B27-based media supplemented with inhibitors and cytokines. 500 mL of medium was generated by including: 240 mL DMEM/F12 (Invitrogen; 11320), 240 mL Neurobasal (Invitrogen; 21103), 5 mL N2 supplement (Invitrogen; 17502048), 10 mL B27 supplement (Invitrogen; 17504044), 10 μg recombinant human LIF (made in-house), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Lonza), 50 µg/ml BSA (Gibco Fraction V, 15260), and the following small molecules and cytokines: PD0325901 (Stemgent, 1 μM), IM-12 (Enzo, 1 μM or 0 µM), SB590885 (R&D systems, 0.5 μM), WH4-023 (A Chemtek or Selleckchem, 1 μM), Y-27632 (Stemgent, 10 μM) and Activin A (Peprotech, 10 ng/mL). All naïve hESC experiments were conducted in 5% O2, 5% CO2.

extract_protocol:
ChIP was performed following the standard protocol of Millipore (#17-371).
For ChIP of KLF4, SOX2, and SNF2L, about 5 million hESCs were used for each ChIP experiment. Sonication was performed on a Bioruptor system, with 30s ON, 30s OFF, 30 cycles, high amplitude. ChIP libraries were prepared using the NEBNext Ultra II DNA library prep kit and index primers sets (NEB, #7645S, #E7335S) followed the standard protocol. Sequencing was performed by Novogene with the Illumina HiSeq 4000 Sequencer. Data with 150 bp paired-end reads were obtained. For BRG1, BRM, and BAF155, about 20 million hESCs were used for each ChIP experiment. Library prep and sequencing was performed on Illumina NextSeq 500 in the Molecular Biology Core Facilities at the Dana-Farber Cancer Institute. Data with 75-bp single-end reads were obtained.

tag: cell line

tag: cell type

value: Embryonic stem cells

tag: culture condition

value: Primed (conventional)

tag: chip antibody


title: IBM5


title: hESC_Naive_SOX2_ChIP

description: SOX2 ChIP in naive hESCs

value: Naive (5i/L/A)

value: SOX2 (R&D Systems, AF2018)


title: IBM19


title: hESC_Primed_SOX2_ChIP

description: SOX2 ChIP in primed hESCs


title: hESC_Naive_SOX2_Input

description: ChIP Input in naive hESCs (for KLF4,SOX2)


title: SUM159-stiff-1

city: Tucson

first: Casey

middle: E

last: Romanoski

state: AZ

address: 1657 E. Helen St.

department: Cellular & Molecular Medicine

institute: University of Arizona

data_processing:
fastq files were mapped using STAR to the human hg38 build
sam files were converted into tag directoires using HOMER (http://homer.ucsd.edu/homer/)
rpkm counts per gene were caldulated using the analyzeRepeats.pl function in HOMER with options: -strand +, -rpkm -condenseGenes -count genes -tbp 1
Genome_build: hg38
Supplementary_files_format_and_content: a spreadheet containing the annotation for each human transcript and the RPKM values for each across the 6 samples

source_name: SUM159 cells

growth_protocol: SUM159 cells were cultured for 2 weeks on collagen I-conjugated hydrogels that reflect native human breast tumor stiffness corresponding to regions of high cellularity/low matrix deposition (0.5 kPa; Petrisoft, Matrigen), versus low cellularity/high matrix deposition (8.0 kPa; Petrisoft, Matrigen). Cells were fed every 2 days and were split or analyzed when ~80% confluent.

extract_protocol:
Lysates were processed for RNA extraction using Isolate II RNA kit (Bioline), and 1µg from each sample was used for polyA selection with [Oligo d(T) Magnetic Beads,New England BioLabs #S1419S]
For RNA-seq, cDNA was synthesized using the SuperScript III system from Invitrogen, followed by second strand synthesis, ds End Repair and UDG treatment to recover strand-specific libraries. Libraries were barcoded with BioO Nextflex adapters and amplified prior to sequencing

treatment_protocol: Continuous mechanical preconditioning

value: SUM159 cells

tag: treatment

value: grown on collagen-coated stiff hydrogel (8.0 kPa)


title: SUM159-soft-1

value: grown on collagen-coated soft hydrogel (0.5 kPa)


title: SUM159-stiff-3


title: SUM159-soft-3


title: SUM159-soft-2


title: 18: GFP-mCherry- D40

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.19 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using STAR v2.5.2b.
Transcript abundances were estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: text file including gene name, Ensembl gene id, RPKM value for each each gene in each sample

source_name: GFP-mCherry- D40

growth_protocol: Differentiation was initiated 72 hours after plating when the culture was approximately 80% confluent. Step 1: Cells were differentiated with 1.5 μM CHIR99021, 20 ng/mL BMP4 and 20 ng/mL Activin A in RPMI supplemented with B27 minus insulin, 2 mM GlutaMAX, 1x NEAA and 1x Pen/Strep for 3 days . Step 2: For cardiomyocyte differentiation, cells were treated for an additional 3 days with 5 µM XAV939 . For hPSC-SAN differentiation, Step 1 was followed by addition of 0.1 μM cucurbitacin, 1 μM retinoic acid, 5 μM SU5402  in RB27-INS from day 3-6. 5 µM XAV939 was added from day 5-6. From day 6 onward, both cardiomyocyte and hPSC-SAN differentiation were carried out in RPMI supplemented with B27, 2 mM GlutaMAX, 1x NEAA and 1x Pen/Strep (RB27+INS). Step 3: hPSC-SAN differentiation included additional treatment with 5 µM Tyrphostin AG 490 (Sigma Aldrich) from day 6-9 in RB27+INS. The HDAC inhibitor, chidamide, was added to the differentiation cocktail from day 7-9 with a final concentration 5 µM.

extract_protocol:
Total RNA was isolated using the Agilent nano kit according to manufacturer instructions.  The quality of RNA samples was examined using an Agilent bioanalyzer
cDNA libraries were generated using TruSeq RNA Sample Preparation (Illumina)

tag: cell line background

value: H9 hESC line

value: Sinoatrial Node (SAN)-like Cells Derived from Human Pluripotent Stem Cells (hPSCs)

tag: genotype/variation

value: GFP-mCherry-

tag: timepoint

value: 40 days after directed differentiation


title: SUM159-stiff-2


title: IBM14

value: Skeletal muscle (Tibialis Anterior)

value: Female


title: Normal Human Dermal Fibroblast cells_Control

city: St. John's

first: Akinola

middle: Adekoya

last: Alafiatayo

state: Newfoundland and Labrador

address: 300 Prince Philip Drive

department: Faculty of Medicine, Division of Biomedical Sciences (Genetics)

country: Canada

institute: Memorial University of Newfoundland

data_processing:
All bioinformatics analysis were carried out using software operating in UNIX command in ubuntu environment. The paired-end raw data from the NGS were subjected to preliminary processing prior to downstream application. Sequenced reads were trimmed with cutadapt software v1.10. With TopHat v2.1.1, Bowtie2 v2.2.6 program, the cleaned raw reads from Illumina sequencer (HiSeq® 4000 125 PE) were mapped against human GRCh38/hg38 reference assembly and cufflinks v2.2.1 was used to assemble the transcripts. Gene model annotation file (GRCh38/hg38 GTF file) was downloaded from UCSC genome browser as reference. For comparing expression analysis between samples cuffdifff v2.2.1 was used with classic method of normalization with FPKM.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: xlsx files include FPKM, log2 FC, test_stat, P_value, q_value and gene symbol

source_name: Primary Fibroblast cells, Untreated

growth_protocol: Normal human adult dermal fibroblast cells (NHDF) were grown in a fibroblast basal medium containing 2% fetal bovine serum, and supplemented with rh FGF β (5 ng/mL), L-glutamine (7.5 nM), hydrocortisone hemisuccinate (1 mg/mL), Rh insulin (5 mg/mL), Ascorbic acid (50 mg/mL) and antibiotics (50 µg/5mL).

extract_protocol:
Total RNA was isolated from both samples with epicentre® MasterPure™ RNA purification kit (cat no. MCR 85102). Illumina TruSeq® RNA preparation v2 guide was used with 1 µg of total RNA for constructing the sequencing libraries.
Standard Illumina protocol for RNA libraries preparation was used to prepare the library for sequencing.

treatment_protocol: The NHDF cells were seeded at 1.0 × 10^4 cells/mL in a 75cm3 culturing flasks which was then incubated at 37oC in 5% CO2 . At 80 - 90% confluence, prior to UV exposure, the cells were washed with Phosphate Buffered Saline (PBS) at pH 7.4 thrice and subsequently replaced the culture medium with 5 mL PBS and the cells were UV irradiated with 20 mJ/cm2. After this, the PBS was discarded and replaced with growth medium and incubated for another 24hrs at 37oC in 5% CO2. Same protocol was carried out for the control sample but it was not exposed to UV radiations.

value: Primary Fibroblast cells

tag: cell source

value: Abdominal Skin

value: Non UV-irradiated


title: 17: GFP-Mcherry+ D40

source_name: GFP-Mcherry+ D40

value: GFP-Mcherry+


title: 11: GFP-Mcherry+ D40


title: 8: GFP-Mcherry+ D25

source_name: GFP-Mcherry+ D25

value: 25 days after directed differentiation


title: 7: GFP+mCherry+- D25

source_name: GFP+mCherry+- D25

value: GFP+mCherry+


title: 9: GFP-mCherry- D25

source_name: GFP-mCherry- D25

value: GFP-mCherry


title: 14: GFP-Mcherry+ D40


title: 15: GFP-mCherry- D40


title: Normal Human Dermal Fibroblast cells_U1

source_name: Primary Fibroblast cells, treated

value: UV-irradiated


title: 1: GFP+mCherry+- D25


title: 4: GFP+mCherry+- D25


title: Recurrent MCF7 H3K9me3, 2

city: Dallas

first: Matt

last: Sieber

state: Texas

address: 5323 Harry Hines blvd, MC 9040 ND12.214

institute: UT Southwestern Medical Center

description: Recurrent MCF7

data_processing:
QC control: FASTQC report with basic sequencing quality statistics
mapping reads:Bowtie
Peak Calling: MACS2/HOMER
HG19
Supplementary_files_format_and_content: bgiwig

source_name: MCF7 cell line

growth_protocol: Cells are grown in DMEM +5% serum.

extract_protocol:
H3K27-ac (Cell signaling #8143-s), H3K27me3 antibody (Millipore, 07- 449),  H3K9me3 antibody (Abcam, ab8898)
DNA was isolated from 400 16hr embryos and subjected to H3K27-me3 immunoprecipatation
Ttakara hruPLEX® DNA-Seq Kit

tag: antibody

value: H3K9-me3 ChIP sample


title: 13: GFP+mCherry+- D40

source_name: GFP+mCherry+- D40


title: IBM3

source_name: Skeletal muscle (Vastus Lateralis)

value: Skeletal muscle (Vastus Lateralis)

value: Inclusion body myositis

tag: gender


title: 10: GFP+mCherry+- D40

value: H9 hESC line


title: MCF7 H3K9me3, 1


title: 12: GFP-mCherry- D40

value: Sinoatrial Node (SAN)-like Cells Derived from Human Pluripotent Stem Cells (hPSCs)


title: 6: GFP-mCherry- D25


title: MCF7 H3k27-ac, 1

value: H3K27-ac ChIP sample


title: Recurrent MCF7 H3K27-me3, 2

description: Recurrent MCF7

value: H3K27-me3 ChIP sample


title: CRC_N_LI_F_81

source_name: CRC_N_LI_F_whole intestinal tissue

tag: disease

value: Control

value: uninflamed

value: female

tag: disease_duration (y)

value: include


title: Recurrent MCF7 H3K9me3, 1

description: Recurrent MCF7


title: 2: GFP-Mcherry+ D25


title: 3: GFP-mCherry- D25


title: 5: GFP-Mcherry+ D25


title: not IRIS, 12875

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

data_processing:
bcl2fastq software (Illumina inc.)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trimmomatic, then mapped to transcriptome GRCh38 version using salmon
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample and Matrix table with raw mRNA counts for every mRNA and every sample

source_name: whole blood

extract_protocol:
RNA was isolated using the miRNeasy Serum/Plasma Advanced Kit (50) (cat# 217204) according to the manufacturers’ recommendation (QIAGEN).
The library preparation was done using the QIAseq RNA Library Kit (QIAGEN). A total of 5ul total RNA was converted into RNA NGS libraries. Adapters containing UMIs were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR, the samples were purified. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent).

tag: disease state

value: not IRIS

tag: iris condition

value: not Mycobacterial

value: Male

tag: bmi

tag: age

tag: tissue

value: whole blood


title: not IRIS, 12876


title: MCF7 H3K9me3, 2

tag: cell line


title: Recurrent MCF7 H3K27-ac, 2

description: Recurrent MCF7


title: MCF7 H3k27-ac, 2


title: Recurrent MCF7 H3K27-ac, 1

description: Recurrent MCF7


title: not IRIS, 12873


title: not IRIS, 12877


title: not IRIS, 12872

value: Female


title: not IRIS, 12869


title: Recurrent MCF7 H3K27-me3, 1

description: Recurrent MCF7


title: IRIS, 12867

value: IRIS


title: not IRIS, 12865


title: IRIS, 12864


title: MCF7 H3k27-me3, 1


title: MCF7 H3k27-me3, 2


title: IRIS, 12879

value: Mycobacterial (CNS)


title: not IRIS, 12863


title: IRIS, 12878

value: Mycobacterial


title: not IRIS, 12860


title: not IRIS, 12874


title: IRIS, 12856


title: IRIS, 12857


title: CD90-CD49f- S3 [NGS-6738]

city: Frankfurt

first: Florian

last: Buettner

state: Germany

address: Theodor-Stern-Kai 7

department: DKTK Frankfurt

country: Germany

institute: DKFZ

data_processing:
Raw sequencing reads were mapped with STAR
Expression counts estimates were generated using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts in txt matrix

extract_protocol:
total RNA using RNeasy Plus Micro Kit (Qiagen) and quality was verified in an Agilent 2100 Bioanalyzer (Agilent).
KAPA Stranded with RiboErase RNA-seq kit (Kapa Biosystems)
RNA-seq 30 million paired-end 100 bp reads/sample

value: post-natal

tag: tissue/cell type

value: cord blood CD34+ cells


title: CD90-CD49f+ S3 [NGS-6739]


title: CD90-CD49f+ S2 [NGS-6735]


title: CD90-CD49f- S2 [NGS-6734]


title: not IRIS, 12871


title: not IRIS, 12870


title: not IRIS, 12868


title: CD90+CD49f+ S2 [NGS-6732]


title: CD90-CD49f+ S1 [NGS-6731]


title: CD90+CD49f+ S3 [NGS-6736]


title: not IRIS, 12862


title: CD90+CD49f- S3 [NGS-6737]


title: not IRIS, 12858


title: CD90-CD49f- S1 [NGS-6730]


title: CD90+CD49f- S2 [NGS-6733]


title: miRNA_AMP8

description: miRNA

data_processing:
Illumina RTA2 for HiSeq 4000
Adapter sequences and low quality bases removed using fastp 0.19.5
STAR 2.7.0d two pass method based on ENCODE guidelines for small RNA
featureCounts v1.6.3,  DESeq2 v1.26.0, Rstudio v1.2.5019 based on R v3.6.1
Genome_build: Gencode.v29 based on ENSEMBL GRCh38.p12
Supplementary_files_format_and_content: raw counts from featureCounts on miRBase release 22.1
Supplementary_files_format_and_content: normalized abundance measurement using DESeq2

extract_protocol:
RNA was extracted from snap formzen skeletal muscle biopsies using Qiagen Rneasy Plus Universal Mini Kit (Cat No./ID: 73404)
tissue homogenization steps were performed using SpeedMill PLUS (Analytik Jena AG, Germany)
Extracted RNA was treated with Invitrogen TURBO Dnase (Catalog number:  AM2238)
Small RNA selection using NEBNext Small RNA Library Prep Set (E7330) for Illumina

value: Skeletal muscle (Vastus Lateralis)

tag: group

value: Amputee

tag: age at biopsy (in years)

tag: age of onset (in years)


title: miRNA_AMP9

description: miRNA

source_name: Skeletal muscle (Tibialis Anterior)

value: Skeletal muscle (Tibialis Anterior)


title: CD90+CD49f+ S1 [NGS-6728]


title: not IRIS, 12859


title: not IRIS, 12861


title: miRNA_AMP10

description: miRNA


title: miRNA_AMP6

description: miRNA


title: miRNA_AMP5

description: miRNA


title: miRNA_AMP7

description: miRNA


title: miRNA_AMP4

description: miRNA


title: miRNA_TMD9

description: miRNA

value: Tibial Muscular dystrophy


title: miRNA_AMP2

description: miRNA


title: not IRIS, 12866


title: miRNA_TMD3

description: miRNA


title: miRNA_AMP1

description: miRNA


title: miRNA_TMD4

description: miRNA

source_name: Skeletal muscle(Extensor Hallucis Longus)


title: CD90+CD49f- S1 [NGS-6729]


title: miRNA_IBM21

description: miRNA

extract_protocol:
RNA was extracted from snap frozen skeletal muscle biopsies using Qiagen Rneasy Plus Universal Mini Kit (Cat No./ID: 73404)
tissue homogenization steps were performed using SpeedMill PLUS (Analytik Jena AG, Germany)
Extracted RNA was treated with Invitrogen TURBO Dnase (Catalog number:  AM2238)
Small RNA selection using NEBNext Small RNA Library Prep Set (E7330) for Illumina

value: Inclusion body myositis


title: miRNA_TMD2

description: miRNA


title: miRNA_IBM19

description: miRNA


title: miRNA_IBM20

description: miRNA


title: miRNA_IBM16

description: miRNA


title: miRNA_IBM14

description: miRNA


title: miRNA_IBM15

description: miRNA


title: miRNA_IBM13

description: miRNA


title: miRNA_IBM11

description: miRNA


title: miRNA_IBM10

description: miRNA


title: miRNA_IBM18

description: miRNA


title: miRNA_IBM7

description: miRNA


title: miRNA_IBM9

description: miRNA


title: miRNA_IBM4

description: miRNA


title: miRNA_IBM3

description: miRNA


title: miRNA_IBM2

description: miRNA


title: ExoT15-miRNA

city: Jinan

first: Xiao

last: Jiang

address: 157 Jingliu Road

country: China

institute: Center for Reproductive Medicine, Shandong University

data_processing:
Unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: mirbase 22
Supplementary_files_format_and_content: miRNA expression profiles

source_name: plasma exosome

growth_protocol: Blood was sampled on day 3 to day 5 of menstruation. Collect whole blood into commercially available EDTA-treated tubes. Centrifugate for 10 minutes at 2500 x g.The resulting supernatant is plasma.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 1 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: Exosome was isolated from plasma using ExoquickTM reagent (EXOQ5A1, System Biosciences) according to the manufacturer’s instructions. Briefly, add 1/4 volume of ExoQuick Solution into plasma to precipitate exosomes. After incubating for at least 30 min at 4°C, the mixture was centrifuged at 1500 × g for 30 min, supernatant was discarded and tubes were centrifuged again (1500 g/5 min). The pellet was re-suspended in 100 µL of sterile PBS, and stored at −80°C.

value: plasma exosome

value: female

value: PCOS women


title: ExoT14-miRNA


title: miRNA_IBM17

description: miRNA

source_name: Skeletal muscle (Gastrocnemius)

value: Skeletal muscle (Gastrocnemius)


title: ExoT12-miRNA


title: ExoT13-miRNA


title: ExoT11-miRNA


title: ExoT10-miRNA


title: ExoT7-miRNA


title: miRNA_IBM8

description: miRNA


title: ExoT5-miRNA


title: miRNA_IBM5

description: miRNA

value: Male


title: ExoT3-miRNA


title: ExoT1-miRNA


title: ExoT6-miRNA


title: ExoC13-miRNA

value: healthy control women


title: ExoC11-miRNA


title: ExoC9-miRNA


title: ExoC12-miRNA


title: ExoC15-miRNA


title: ExoC14-miRNA


title: ExoC7-miRNA


title: ExoC8-miRNA


title: ExoC4-miRNA


title: ExoT8-miRNA


title: ExoC6-miRNA


title: ExoC10-miRNA


title: ExoT9-miRNA


title: ExoC2-miRNA


title: ExoC5-miRNA


title: ExoT4-miRNA


title: ExoC1-miRNA


title: ExoT2-miRNA


title: Inp TA-2 Input for ACY1035 H3K27ac Sample 2

city: salt lake city

first: Srividya

last: Bhaskara

state: Utah

address: 2000 circle of hope

department: University of Utah

institute: University of Utah

description:
14119X29
Processed data file: Sub_TA_RRPM.bw

data_processing:
Reads were aligned to a reference containing hg19 and dm3 using novoalign (v2.08.01) set to report uniquely aligned reads only.
Normalized coverage tracks (Reference-Adjusted Reads per Million or RRPM) were generated using the deeptools (v2.5.0.1) bamCoverage command using a scaling factor of (1/Nd), where Nd is the number of drosophila alignments in millions.
Coverage Tracks were averaged using Wiggletools (v1.2.1)
Input signal was subtracted from IP using Wiggletools
Heatmaps were generated using the deepTools plotHeatmap command with sorting turned off.  The transcription start and termination sites used in the command were presorted based on RNASeq expression.
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: BigWig files containing normalized coverage (RRPM) across hg19

growth_protocol: Human SupB15 cells were cultured in IMDM media supplemented with 20% heat-inactivated fetal bovine serum, 1% Penicillin-Streptomycin and 1% L-Glutamine. Drosophila S2 cells were cultred in Schneider's media + 20% heat inacivated FBS and 1% penicillin-streptomycin. Control or ACY1035 treated SupB15 cells were mixed with Drosophila S2 cells at 2:1 ratio before crosslinking and nuclei isolation.

extract_protocol:
4.0 × 106 SupB15 cells were combined with 2.0 × 106 Drosophila cells and crosslinked at a final concentration of 1% formaldehyde for 10 minutes. The reaction was quenched with 125mM final concentration of glycine. ChIP with anti-H3K27ac was performed as described in the protocol in the manuscript. DNA was purified using the Qiagen PCR purification kit and elution was done with water.
10ng of CHIP DNA was subjected to library construction using the NEBNext ChIP-seq Library Prep Reagent Set and Index Primer Set1 for Illumina . Adaptor-ligated and index primer-containing amplified DNA corresponding to 300-500bp was gel purified using the Qiagen Minelute Gel Extraction Kit essentially following the manufacturer’s protocol, except incubation to melt the gel was performed at 37°C for 30min. The library was then subjected to 50bp single read sequencing in an Illumina Hiseq2500 sequencer.

treatment_protocol: SupB15 cells were treated with either DMSO or 2uM ACY1035 for 36hr

tag: cell type

value: Ph+ Precursor B-ALL


title: Inp CA-3 Input for DMSO H3K27ac Sample 3

description:
14119X24
Processed data file: Sub_CA_RRPM.bw


title: ExoC3-miRNA


title: Inp CA-1 Input for DMSO H3K27ac Sample 1

description:
14119X22
Processed data file: Sub_CA_RRPM.bw


title: Inp IgG-3 Input for IgG Sample 3

description:
14119X18
Processed data file: Sub_IgG_RRPM.bw


title: Inp CA-2 Input for DMSO H3K27ac Sample 2

description:
14119X23
Processed data file: Sub_CA_RRPM.bw


title: Inp IgG-1 Input for IgG Sample 1

description:
14119X16
Processed data file: Sub_IgG_RRPM.bw


title: Inp TA-1 Input for ACY1035 H3K27ac Sample 1

description:
14119X28
Processed data file: Sub_TA_RRPM.bw


title: IP TA-3 ACY0135-3 IP/H3K27ac

description:
14119X15
Processed data file: Sub_TA_RRPM.bw


title: IP TA-2 ACY0135-2 IP/H3K27ac

description:
14119X14
Processed data file: Sub_TA_RRPM.bw


title: IP CA-3 DMSO-3 IP/H3K27ac

description:
14119X9
Processed data file: Sub_CA_RRPM.bw


title: IP CA-1 DMSO-1 IP/H3K27ac

description:
14119X7
Processed data file: Sub_CA_RRPM.bw


title: IP IgG-2 IP with IgG Sample2

description:
14119X2
Processed data file: Sub_IgG_RRPM.bw


title: IP IgG-3 IP with IgG Sample3

description:
14119X3
Processed data file: Sub_IgG_RRPM.bw


title: 14057F6_1 Sample F

data_processing:
Reads were aligned to a reference containing hg19 and dm3 using novoalign (v2.08.01) set to report uniquely aligned reads only.
Normalized coverage tracks (Reference-Adjusted Reads per Million or RRPM) were generated using the deeptools (v2.5.0.1) bamCoverage command using a scaling factor of (1/Nd), where Nd is the number of drosophila alignments in millions.
Coverage Tracks were averaged using Wiggletools (v1.2.1)
Heatmaps were generated using the deepTools plotHeatmap command with sorting turned off.  The transcription start and termination sites used in the command were presorted based on RNASeq expression.
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: BigWig files containing normalized coverage (RRPM) across hg19

growth_protocol: Human SupB15 cells cells were cultured in IMDM media supplemented with 20% heat-inactivated fetal bovine serum, 1% Penicillin-Streptomycin and 1% L-Glutamine. Drosophila S2 cells ….Control or ACY1035 treated SupB15 cells were mixed with Drosophila S2 cells at 2:1 ratio before crosslinking and nuclei isolation

extract_protocol:
Nuclear pellet from cross-linked cells was digested with micrococcal nuclease and the extent of digestion was checked on a agarose gel that showed ~70% mononucleosomes
10ng of MNase digested DNA was subjected to library construction using the NEBNext ChIP-seq Library Prep Reagent Set and Index Primer Set1 for Illumina and resolved in 1.5% agarose gel. Adaptor-ligated and index primer-containing amplified DNA corresponding to mononuclesomes was gel purified using the Qiagen Minelute Gel Extraction Kit essentially following the manufacturer’s protocol, except incubation to melt the gel was performed at 37°C for 30min. The library was then subjected to 50bp single read sequencing in an Illumina Hiseq2500 sequencer

treatment_protocol: SupB15 cells were treated with either DMSO or 2uM ACY1035 for 62hr

tag: treatment

value: Treated


title: IP IgG-1 IP with IgG Sample1

description:
14119X1
Processed data file: Sub_IgG_RRPM.bw


title: Inp TA-3 Input for ACY1035 H3K27ac Sample 3

description:
14119X30
Processed data file: Sub_TA_RRPM.bw


title: 14057F5_1 Sample E


title: 14057F4_1 Sample D


title: 14057F2_1 Sample B

value: Control


title: 14057F1_1 Sample A


title: Inp IgG-2 Input for IgG Sample 2

description:
14119X17
Processed data file: Sub_IgG_RRPM.bw


title: IP TA-1 ACY0135-1 IP/H3K27ac

description:
14119X13
Processed data file: Sub_TA_RRPM.bw


title: IP CA-2 DMSO-2 IP/H3K27ac

description:
14119X8
Processed data file: Sub_CA_RRPM.bw


title: SupB15_Doxo-3_MNaseSeq

data_processing:
Reads were aligned to hg19 using novoalign (2.08.01), set to report only uniquely aligned reads.
Normalized coverage tracks were generated by extended reads out to 150bp and calculating read depth per million mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized coverage tracks in bigwig format

growth_protocol: Human SupB15 cells were cultured in IMDM media supplemented with 20% fetal bovine serum.

extract_protocol:
Nuclear pellet from cross-linked cells was digested with micrococcal nuclease and the extent of digestion was checked on a agarose gel that showed ~70% mononucleosomes
5ng of MNase digested DNA was subjected to library construction using the NEBNext ChIP-seq Library Prep Reagent Set and Index Primer Set1 for Illumina and resolved in 1.5% agarose gel. Adaptor-ligated and index primer-containing amplified DNA corresponding to mononuclesomes was gel purified using the Qiagen Minelute Gel Extraction Kit essentially following the manufacturer’s protocol, except incubation to melt the gel was performed at 37°C for 30min. The library was then subjected to 50bp single read sequencing in an Illumina Hiseq2500 sequencer

treatment_protocol: SupB15 cells were treated with either DMSO (control) for 46hr or 2 micro molar 1035 for 46hr or 0.1 micro molar doxorubicin for 10hr or 2 micro molar 1035 followed by 0.1 micro molar doxorubicin for 36hr and 10hr, respectively.

value: leukemia

tag: cell population


title: SupB15_1035+Doxo-3_MNaseSeq


title: SupB15_Doxo-1_MNaseSeq


title: SupB15_DMSO-2_MNaseSeq


title: SupB15_1035+Doxo-1_MNaseSeq


title: SupB15_1035+Doxo-2_MNaseSeq


title: SupB15_1035-3_MNaseSeq


title: SupB15_Doxo-2_MNaseSeq


title: SupB15_DMSO-1_MNaseSeq


title: SupB15_1035-1_MNaseSeq


title: SupB15_1035+Doxo-2_RNAseq

data_processing:
A reference sequence was created using hg19 genomic sequence and splice junction sequences.  Ensembl build 74 splice junction sequences were generated with USeq (v8.8.8) MakeTranscriptome using default settings
Reads were aligned to the reference using Novoalign (2.08.01) allowing up to 50 alignments and removing adapter sequences.  The resulting alignments were then run through USeq SamTranscriptomeParser to convert splice alignments back to genomic space and to remove low quality reads.  Reads aligning to multiple locations in the genome were removed.
USeq DefinedRegionDifferentialSeq was used to count the number of aligned reads to each gene.  Only reads aligning to the opposite strand of the annotation were counted.  Genes with fewer than 10 counts across all samples were thrown out.  Differential expression was determined using DESeq2 (v1.4.5) using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing DESeq2 log2FC, DESeq2 adjp, raw counts and FPKM values

growth_protocol: SupB15 cells were cultured in IMDM+20% serum

extract_protocol:
Total RNA was isolated using the Versagene RNA isolation kit according to the manufacturer’s protocol.
Library was prepared using Illumina TruSeq stranded RNA kit with Ribo-Zero Gold and subjected to 50bp single read sequencing in an Illumina HiSeq 2500 sequencer.

value: Ph+Pre-B-ALL


title: SupB15_1035+Doxo-1_RNAseq


title: SupB15_Doxo-2_RNAseq


title: SupB15_Doxo-1_RNAseq


title: 14057F3_1 Sample C


title: SupB15_1035-1_RNAseq


title: SupB15_1035-2_RNAseq


title: SupB15_DMSO-2_RNAseq


title: Plate5_E05

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d7_5E05

data_processing:
Data from cell lysate generated by BioSpyder Inc (Carlsbad, CA)
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R. The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample. Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
Genome_build: BioSpyder Rat whole transcriptome array panel
Supplementary_files_format_and_content: Tab delimited text file of gene counts

organism: Rattus norvegicus

source_name: Primary hepatocytes (Lonza, RTP)

growth_protocol: Primary hepatocytes and non-parenchymal cells were obtained from Lonza (Research Triangle Park, NC). The hepatocytes were spun at 50 x g for 10 minutes at 4°C.  The supernatant was removed, and the hepatocytes were resuspended in Williams E media with no phenol red (Gibco, Gaithersburg, MD) with 10% FBS and hepatocyte culture supplements (Thermo Fisher, Waltham, MA). The NPCs were spun at 50 x g for 10 minutes to remove any remaining hepatocytes. The supernatant was spun at 800 x g for 10 minutes at 4°C to pellet NPCs.  The pellet was resuspended in 1 ml red blood cell lysis buffer (Sigma-Aldrich, St. Louis, MO) on ice with agitation for 3-5 minutes.   The solution was then diluted with 4 ml of Gey’s balanced salt solution (GBSS) (Sigma-Aldrich, St. Louis, MO) and spun at 800 x g for 10 min at 4°C.  The NPCs were re-suspended in GBSS and fractionated over an Optiprep density gradient (Sigma-Aldrich). The purified NPCs were recovered from the interface, re-centrifuged, and resuspended in culture media.

extract_protocol:
The cells were treated 24 hours prior to sample collection at 3 timepoints (days 1, 3, and 7 post plating).  After 24 hours, the cells were lysed in TempO-Seq buffer and libraries were prepared for sequencing per manufacturer’s protocols (n=4 biological replicates).
TempO-Seq ligation assays, sequencing and generation of count tables performed by BioSpyder Inc. (Carlsbad, CA)

treatment_protocol: Hepatocytes and NPCs were seeded on collagen coated PerkinElmer Viewplate 96 well black-walled plates (PerkinElmer, Akron, OH) (catalog # 6005182) and exposed to the following four compounds: Ketoconazole (Sigma Aldrich, St. Louis, MO, catalog # K1003) CAS # 65277-42-1; GW7647 (Sigma Aldrich, St. Louis, MO, catalog # G6793) CAS # 265129-71-3; Gemfibrozil (Sigma Aldrich, St. Louis, MO, catalog # G9518) CAS # 25812-30-0 and Phenobarbital (Sigma Aldrich, St. Louis, MO, catalog # P1636) CAS # 50-06-6.

tag: strain

value: Sprague Dawley

tag: Sex

value: male

tag: culture model

value: mono-culture

tag: chemical

value: Untreated vehicle control

tag: dose

value: 0 microM

tag: sampling time

value: day 7


title: Plate7_C03

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d3_7C03

value: day 3


title: SupB15_DMSO-1_RNAseq


title: SupB15_1035-2_MNaseSeq


title: Plate7_E05

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d7_7E05


title: Plate3_D08

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d7_3D08


title: Plate1_E05

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d7_1E05


title: Plate5_C03

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d3_5C03


title: Plate7_A01

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d1_7A01

value: day 1


title: Plate1_C03

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d3_1C03


title: Plate3_C03

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d3_3C03


title: Plate5_A01

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d1_5A01


title: Plate1_A01

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d1_1A01


title: Plate3_E02

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d7_3E02

value: Ketoconazole

value: 10 microM


title: Plate7_E11

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d7_7E11


title: Plate5_C09

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d3_5C09


title: Plate1_E11

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d7_1E11


title: Plate3_A01

description:
exposure in collagen coated 96 well plate
2D_Heps_UT_d1_3A01


title: Plate1_C09

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d3_1C09


title: Plate3_A07

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d1_3A07


title: Plate5_A07

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d1_5A07


title: Plate1_A07

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d1_1A07


title: Plate7_E09

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d7_7E09

value: 1 microM


title: Plate3_D12

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d7_3D12


title: Plate5_C07

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d3_5C07


title: Plate5_E09

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d7_5E09


title: Plate7_C07

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d3_7C07


title: Plate5_E11

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d7_5E11


title: Plate1_C07

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d3_1C07


title: Plate7_C09

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d3_7C09


title: Plate3_A05

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d1_3A05


title: Plate1_A05

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d1_1A05


title: Plate3_D10

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d7_3D10

value: 0.1 microM


title: Plate5_A05

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d1_5A05


title: Plate5_E07

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d7_5E07


title: Plate7_A07

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_10_d1_7A07


title: Plate1_E07

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d7_1E07


title: Plate7_E07

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d7_7E07


title: Plate7_C05

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d3_7C05


title: Plate7_A03

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d1_7A03


title: Plate5_A03

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d1_5A03


title: Plate7_A05

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d1_7A05


title: Plate1_C05

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d3_1C05


title: Plate3_A03

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d1_3A03


title: Plate7_F05

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d7_7F05

value: 30 microM


title: Plate1_E09

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_1_d7_1E09


title: Plate1_A03

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d1_1A03


title: Plate3_E08

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d7_3E08


title: Plate5_F05

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d7_5F05


title: Plate7_D03

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d3_7D03


title: Plate3_C09

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d3_3C09


title: Plate1_D03

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d3_1D03


title: Plate1_F05

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d7_1F05


title: Plate5_D03

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d3_5D03


title: Plate7_B01

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d1_7B01


title: Plate1_B01

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d1_1B01


title: Plate5_F03

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d7_5F03


title: Plate3_B01

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d1_3B01


title: Plate5_B01

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_30_d1_5B01


title: Plate5_C05

description:
exposure in collagen coated 96 well plate
2D_Heps_PB_0dot1_d3_5C05


title: Plate7_F03

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d7_7F03


title: Plate1_F03

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d7_1F03


title: Plate7_D01

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d3_7D01


title: Plate1_D01

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d3_1D01


title: Plate3_C07

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d3_3C07


title: Plate5_D01

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d3_5D01


title: Plate5_F01

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d7_5F01


title: Plate7_A11

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d1_7A11


title: Plate1_F01

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d7_1F01


title: Plate3_E04

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d7_3E04


title: Plate5_A11

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d1_5A11


title: Plate7_F01

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d7_7F01


title: Plate1_A11

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d1_1A11


title: Plate3_A11

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d1_3A11


title: Plate1_C11

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d3_1C11


title: Plate5_A09

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d1_5A09


title: Plate5_C11

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d3_5C11


title: Plate7_C11

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d3_7C11


title: Plate7_A09

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d1_7A09


title: Plate5_F11

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d7_5F11


title: Plate3_E06

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_10_d7_3E06


title: Plate1_F11

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d7_1F11


title: Plate7_F11

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d7_7F11


title: Plate9_A08

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d3_9A08


title: Plate7_D09

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d3_7D09


title: Plate5_B07

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d1_5B07


title: Plate1_D09

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d3_1D09


title: Plate1_B07

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d1_1B07


title: Plate5_D09

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d3_5D09


title: Plate7_D07

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d3_7D07


title: Plate3_E12

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d7_3E12


title: Plate3_B07

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d1_3B07


title: Plate1_A09

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d1_1A09


title: Plate7_B07

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d1_7B07


title: Plate3_C05

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d3_3C05


title: Plate7_B05

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d1_7B05


title: Plate3_B05

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d1_3B05


title: Plate7_F09

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d7_7F09


title: Plate7_F07

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d7_7F07

value: 0.01 microM


title: Plate1_F09

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d7_1F09


title: Plate5_F09

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d7_5F09


title: Plate5_D07

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d3_5D07


title: Plate3_A09

description:
exposure in collagen coated 96 well plate
2D_Heps_Keto_1_d1_3A09


title: Plate1_D05

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d3_1D05


title: Plate5_B03

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d1_5B03


title: Plate3_D01

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d3_3D01


title: Plate5_G05

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d7_5G05

value: Gemfibrozil

value: 1000 microM


title: Plate1_B03

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d1_1B03


title: Plate5_B05

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d1_5B05


title: Plate3_F02

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_1_d7_3F02


title: Plate7_D05

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d3_7D05


title: Plate7_C01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d1_7C01


title: Plate5_F07

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d7_5F07


title: Plate3_E10

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d7_3E10


title: Plate5_D05

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d3_5D05


title: Plate3_C11

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d3_3C11


title: Plate7_G03

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d7_7G03

value: 100 microM


title: Plate3_F06

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d7_3F06

value: Sprague Dawley


title: Plate1_D07

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d3_1D07

value: male


title: Plate7_G05

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d7_7G05

value: mono-culture


title: Plate3_B03

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d1_3B03


title: Plate1_B05

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot1_d1_1B05


title: Plate3_F08

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d7_3F08


title: Plate1_G05

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d7_1G05


title: Plate9_A05

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d3_9A05


title: Plate7_E03

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d3_7E03


title: Plate5_E03

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d3_5E03


title: Plate7_B11

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d1_7B11


title: Plate1_E03

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d3_1E03


title: Plate1_F07

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d7_1F07


title: Plate1_E01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d3_1E01


title: Plate7_B03

description:
exposure in collagen coated 96 well plate
2D_Heps_GW_0dot01_d1_7B03


title: Plate5_C01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d1_5C01


title: Plate5_G01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d7_5G01


title: Plate7_G01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d7_7G01


title: Plate5_G03

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d7_5G03


title: Plate3_F04

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d7_3F04


title: Plate1_C01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d1_1C01


title: Plate3_C01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d1_3C01


title: Plate1_G03

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d7_1G03


title: Plate9_A03

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d3_9A03


title: Plate7_E01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d3_7E01


title: Plate5_E01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d3_5E01


title: Plate3_D07

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_1000_d3_3D07


title: Plate7_D11

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d3_7D11


title: Plate9_A01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d3_9A01


title: Plate3_D03

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d3_3D03


title: Plate3_D05

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d3_3D05


title: Plate1_D11

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d3_1D11


title: Plate3_B09

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d1_3B09


title: Plate5_E06

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d7_5E06

source_name: Primary hepatocytes and non-parenchymal cells (Lonza, RTP)

value: co-culture

value: Untreated vehicle control


title: Plate7_B09

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d1_7B09


title: Plate5_B11

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d1_5B11


title: Plate5_B09

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d1_5B09


title: Plate7_E06

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d7_7E06

value: 0 microM

value: day 7


title: Plate3_D09

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d7_3D09


title: Plate3_B11

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d1_3B11

value: day 1


title: Plate1_E06

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d7_1E06


title: Plate5_A02

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d1_5A02


title: Plate1_B11

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_100_d1_1B11


title: Plate1_C04

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d3_1C04

value: day 3


title: Plate1_A02

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d1_1A02


title: Plate1_G01

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d7_1G01

value: 10 microM


title: Plate1_B09

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d1_1B09


title: Plate3_E03

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d7_3E03

value: Phenobarbital


title: Plate7_C04

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d3_7C04


title: Plate5_D11

description:
exposure in collagen coated 96 well plate
2D_Heps_Gem_10_d3_5D11


title: Plate5_C04

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d3_5C04


title: Plate3_C04

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d3_3C04


title: Plate7_A02

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d1_7A02


title: Plate7_A08

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d1_7A08


title: Plate3_E01

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d7_3E01

value: 1 microM


title: Plate7_E12

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d7_7E12


title: Plate3_A02

description:
exposure in collagen coated 96 well plate
2D_Cocult_UT_d1_3A02


title: Plate7_C08

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d3_7C08


title: Plate5_C08

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d3_5C08


title: Plate5_A06

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d1_5A06


title: Plate5_E12

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d7_5E12


title: Plate1_E12

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d7_1E12


title: Plate1_A06

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d1_1A06


title: Plate7_C10

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d3_7C10


title: Plate5_C10

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d3_5C10


title: Plate1_C10

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d3_1C10


title: Plate3_D11

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d7_3D11

value: 0.1 microM


title: Plate3_A08

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d1_3A08


title: Plate5_A08

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d1_5A08


title: Plate5_C06

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d3_5C06


title: Plate1_A08

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_10_d1_1A08


title: Plate7_A04

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d1_7A04


title: Plate7_E10

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d7_7E10


title: Plate5_E10

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d7_5E10


title: Plate7_F06

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d7_7F06

value: Ketoconazole

value: 30 microM


title: Plate5_F06

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d7_5F06


title: Plate1_E10

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d7_1E10


title: Plate7_A06

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d1_7A06


title: Plate1_C08

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d3_1C08


title: Plate7_D04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d3_7D04


title: Plate1_F06

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d7_1F06


title: Plate5_D04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d3_5D04


title: Plate7_C06

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d3_7C06


title: Plate5_E08

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d7_5E08


title: Plate1_E08

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d7_1E08


title: Plate3_C10

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d3_3C10


title: Plate1_C06

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d3_1C06


title: Plate7_E08

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d7_7E08


title: Plate3_A06

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_1_d1_3A06


title: Plate1_B02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d1_1B02


title: Plate1_A04

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d1_1A04


title: Plate5_A04

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d1_5A04


title: Plate5_B02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d1_5B02


title: Plate1_D04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d3_1D04


title: Plate7_B02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d1_7B02


title: Plate3_A04

description:
exposure in collagen coated 96 well plate
2D_Cocult_PB_0dot1_d1_3A04


title: Plate5_A12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d1_5A12


title: Plate3_E09

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d7_3E09


title: Plate7_F04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d7_7F04


title: Plate3_E07

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d7_3E07


title: Plate1_A12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d1_1A12


title: Plate5_F04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d7_5F04


title: Plate3_B02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_30_d1_3B02


title: Plate7_D02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d3_7D02


title: Plate1_F04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d7_1F04


title: Plate5_D02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d3_5D02


title: Plate3_C08

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d3_3C08


title: Plate1_D02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d3_1D02


title: Plate5_A10

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d1_5A10


title: Plate7_A12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d1_7A12


title: Plate7_F02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d7_7F02


title: Plate5_F02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d7_5F02


title: Plate3_A12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_10_d1_3A12


title: Plate3_F03

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d7_3F03


title: Plate3_E05

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d7_3E05


title: Plate7_C12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d3_7C12


title: Plate1_C12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d3_1C12


title: Plate1_F02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d7_1F02


title: Plate3_C06

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d3_3C06


title: Plate5_C12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d3_5C12


title: Plate7_D10

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d3_7D10


title: Plate7_D08

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d3_7D08


title: Plate5_D08

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d3_5D08


title: Plate3_D02

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d3_3D02


title: Plate7_A10

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d1_7A10


title: Plate7_B08

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d1_7B08


title: Plate5_F12

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d7_5F12


title: Plate1_A10

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d1_1A10


title: Plate3_A10

description:
exposure in collagen coated 96 well plate
2D_Cocult_Keto_1_d1_3A10


title: Plate7_F12

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d7_7F12


title: Plate5_F10

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d7_5F10


title: Plate1_F12

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d7_1F12


title: Plate9_A09

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d3_9A09


title: Plate9_A07

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d3_9A07


title: Plate5_D10

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d3_5D10


title: Plate1_D10

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d3_1D10


title: Plate1_B08

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d1_1B08


title: Plate1_D08

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d3_1D08


title: Plate3_B06

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d1_3B06


title: Plate5_F08

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d7_5F08

value: 0.01 microM


title: Plate1_F08

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d7_1F08


title: Plate3_B08

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d1_3B08


title: Plate7_F10

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d7_7F10


title: Plate1_F10

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d7_1F10


title: Plate1_D06

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d3_1D06


title: Plate7_B06

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d1_7B06


title: Plate1_B04

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d1_1B04


title: Plate3_B04

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d1_3B04


title: Plate7_B04

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d1_7B04


title: Plate7_G06

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d7_7G06

value: Gemfibrozil

value: 1000 microM


title: Plate3_F01

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d7_3F01

value: Sprague Dawley

value: male


title: Plate1_B06

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d1_1B06

value: co-culture


title: Plate3_E11

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d7_3E11


title: Plate7_E04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d3_7E04


title: Plate9_A06

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d3_9A06


title: Plate7_D06

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d3_7D06


title: Plate5_B08

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_1_d1_5B08


title: Plate5_B06

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot1_d1_5B06


title: Plate5_D06

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d3_5D06


title: Plate3_F09

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d7_3F09


title: Plate3_C12

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d3_3C12


title: Plate7_G04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d7_7G04

value: 100 microM


title: Plate3_C02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d1_3C02


title: Plate5_B04

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d1_5B04


title: Plate5_G06

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d7_5G06


title: Plate7_C02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d1_7C02


title: Plate1_C02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d1_1C02


title: Plate7_F08

description:
exposure in collagen coated 96 well plate
2D_Cocult_GW_0dot01_d7_7F08


title: Plate5_C02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d1_5C02


title: Plate5_E04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d3_5E04


title: Plate7_B12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d1_7B12


title: Plate5_G04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d7_5G04


title: Plate3_F07

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d7_3F07


title: Plate1_G04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d7_1G04


title: Plate3_F05

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d7_3F05


title: Plate7_E02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d3_7E02


title: Plate9_A04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d3_9A04


title: Plate5_E02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d3_5E02


title: Plate1_E02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d3_1E02


title: Plate5_B10

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d1_5B10


title: Plate3_B12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d1_3B12


title: Plate1_B12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d1_1B12


title: Plate7_G02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d7_7G02


title: Plate1_E04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_1000_d3_1E04


title: Plate5_B12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d1_5B12


title: Plate1_G02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d7_1G02


title: Plate9_A02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d3_9A02


title: Plate7_D12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d3_7D12


title: Plate5_D12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d3_5D12


title: Col-0-99A-1

city: Shanghai

first: hui

last: lin

address: Shanghai fenfglinroad 300

institute: National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences,

data_processing:
illumina Hiseq 2000/2500 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using hisat2 v2.0.4 with default parameters.
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.
Genome_build: TAIR10
Supplementary_files_format_and_content: raw counts and FPKM

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: The seeds were plated on 1/2 Murashige and Skoog (MS) agar medium and stratified at 4 °C in darkness for 4 day, and then moved to a greenhouse and germinated at 22 °C for 1 week. The seedlings were transplanted to the soil in plastic pots and grown at 22 °C under short-day conditions (8-h light/16-h dark) and 50–70% relative humidity as previously described.

extract_protocol:
arabidopsis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. HiScript Q RT SuperMix  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2×108 cfu/ml PXO99A grown on PSA medium (10 g/L tryptone, 10 g/L sucrose,1g/L glutamate, 15 mg/L cephalexin, pH 7.0, 28℃) were used for syringe-infiltration.

tag: inoculation stage

tag: ecotype

tag: genotype

value: wildtype

value: 4 weeks

value: Xanthomonas oryzae pv. oryzae PXO99A


title: Col-0-99A-2

tag: age


title: Plate3_D04

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d3_3D04

value: day 3


title: ntx1-99A-1


title: Plate1_D12

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d3_1D12

value: 10 microM


title: Plate7_B10

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d1_7B10

value: day 1


title: Plate3_D06

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_100_d3_3D06


title: Col-0-2

value: water


title: ntx1-1


title: ntx1-99A-2


title: Plate1_B10

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d1_1B10


title: ntx1-99A-3


title: Plate5_G02

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d7_5G02

value: day 7


title: Plate3_B10

description:
exposure in collagen coated 96 well plate
2D_Cocult_Gem_10_d1_3B10


title: Col-0-1


title: Col-0-99A-3


title: ntx1-2


title: Col-0-3


title: ntx1-3


title: Biotin-rep2

city: Nanjing

first: Pengyue

last: Zhang

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argriculture University

data_processing:
Raw G4-ChIP-seq data were cleaned through trimming adapter contamination and removing low-quality reads using Trim Galore! (version 0.4.4). All cleaned reads were aligned to the MSU v7.0 reference genome using BWA (Burrows-Wheeler Aligner) (mem algorithm, version 0.7.17) with default parameters. Any PCR duplicates were removed using Picard. Reads with mapping quality below ten were excluded using SAMtools (version 1.5, option -q). Only reads with alignment length greater than 50 were used for G4 peak calling and further analyses.
G4 Peak calling was performed using MACS (version 2.1.1) with the following command and parameters: macs2 callpeak -g 3.8e+8 -f BAM --extsize 200 -p 1e-5 –nomodel, and the input library was used as control.
The PQS loci file were generate using fastaRegexFinder.py through the rice7 MSU genome
Genome_build: Rice MSU v7.0
Supplementary_files_format_and_content: Supplementary_files_format_and_content: wig files were generated using bamCoverage and bigWigToWig, bed files were generated using macs2

organism: Oryza sativa

source_name: Seedling

growth_protocol: Rice (Oryza. sativa L. spp. japonica) seeds were immerged in tap water at RT in the lab for three days. Uniformly germinated seeds were sowed in the nutrient soil and grown in a greenhouse at a temperature at 28-30 ℃ and a 14 h/10 h light-dark cycle. Two-week-old rice seedlings were collected and cross-linked using 1% of formaldehyde for 10 min under vacuum. The cross-linked seedlings were ground into a fine powder in liquid nitrogen, and stored in -80 ℃ or immediately used for preparation of genomic DNA.

extract_protocol: The fragmented chromatin was diluted in G4DP buffer (10mM Tris-HCl, 5mM EDTA, 150mM KCl, 0.5mM DTT and 0.5% NP-40, pH=7.4) until the final concentration of SDS was below 0.1%. 1/10 volume of supernatant was kept as input. 30 μl of 1 mM BioTASQ was added into diluted chromatin and incubated overnight at 4 °C, then 30 μl of washed M280 Streptavidin Dynalbeads (11206D, Invitrogen) was added and incubated for another 4 h at 4°C. The washed BioTASQ-bound DNA was eluted with 200 μl elution buffer at 65°C for two times with 15 min each, followed by de-crosslinking at 65°C overnight. De-crosslinked G4DPed DNA was extracted using phenol/chloroform followed by cold ethanol precipitation. 30 nm biotin (Sigma, cat, no. 2031) was used as control. Two biological replicates were conducted for BioTASQ and biotin only. All G4DPed DNA was used for the library preparation, which was constructed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S). All libraries were sequenced using paired-end mode on Illumina NovaSeq platform

tag: cultivar

value: Nipponbare

tag: tissue

value: Seedling

value: two weeks


title: Biotin-rep1


title: AML#55 MSCs

type: RNA

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from MSCs isolated from BM at diagnosis of leukemia

hyb_protocol: 15 ug were fragmented; following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

label: biotin

source_name: Mesenchymal stromal cells isolated from BM of pediatric patients at diagnosis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting  from 100ng of Total RNA using the Affymetrix 3' IVT Plus Kit

growth_protocol: MSCs were cultured in StemMACS™ MSC Expansion Media Kit XF

extract_protocol: RNA was extracted using Trizol

treatment_protocol: No treatment

value: Mesenchymal stromal cells (MSCs)

tag: disease state

value: acute myeloid leukemia (AML)


title: AML#48 MSCs


title: BioTASQ-ChIP-rep1


title: AML#46 MSCs


title: AML#6 MSCs


title: AML#35 MSCs


title: AML#7 MSCs


title: AML#49 MSCs


title: AML#44 MSCs


title: AML#11 MSCs


title: AML#45 MSCs


title: AML#34 MSCs


title: AML#30 MSCs


title: AML#38 MSCs


title: AML#22 MSCs


title: AML#71 MSCs


title: AML#1 MSCs


title: AML#29 MSCs


title: AML#57 MSCs


title: AML#3 MSCs


title: AML#60 MSCs


title: AML#4 MSCs


title: V63, 30-35h

city: Barcelona

first: Anastasia

last: Pickford

state: Barcelona

address: Carrer Rosselló 153

country: Spain

institute: ISGlobal

hyb_protocol: Hybridization performed as previously described (Painter, H. et al., 2013. PMID: 22990780).

scan_protocol: Microarrays images were obtained using the Agilent G2505C Microarray Scanner.

data_processing: Initial data processing of microarray data, including normalization, was performed using the GE2_1105_Oct12_ACC_2 extraction protocol in Agilent Feature Extraction 11.5.1.1 software. The next steps of the analysis were performed using Bioconductor in an R environment (R version 3.5.3). For each individual microarray, we calculated Cy3 and Cy5 background signal as the median of the 100 lowest signal probes for each channel. Probes with both Cy3 and Cy5 signals below three times the array background were excluded (set to NA). Gene level log2(Cy5/Cy3) values and statistical estimation of parasite age were computed as described (Rovira-Graells et al., 2012. PMID: 22415456). Genes with missing values or genes that in all samples had expression values within the lowest 20th percentile of intensity (Cy5 channel) were excluded from downstream analysis, including identification of differentially expressed genes, because differences in genes expressed at near-background levels are of low confidence. To account for the progression delay induced by HS exposure, which can be a major confounder in the downstream analysis, we estimated the age (hours post-invasion, hpi) of each microarray sample by calculating the most likely time post-invasion along the asexual cycle compared to the HB3 transcriptome as reference, using a statistical likelihood method as previously described [Lemieux et al., 2009, PMID: 19376968].

organism: Plasmodium falciparum NF54

label_protocol: Test sample, Cy5; reference pool, Cy3. As previously described (Painter, H. et al., 2013. PMID: 22990780)

growth_protocol: Parasites were cultured in B+ erythrocytes at a 3 % haematocrit under standard culture conditions in RPMI-based supplemented with 10% human serum, in a 5% CO2, 3% O2, balance N2 atmosphere at 35ºC. Tight synchronization (5 h age window) was achieved by Percoll purification followed by sorbitol treatment 5 h later.

extract_protocol: RNA was purified using the TRIzol method following the manufacturer instructions.

treatment_protocol: No treatment performed on samples, just samples of different origin. The NF54 parental line was an in vitro adapted strain always cultured in standard conditions and the volunteer samples came from a previous controlled human malaria infection (CHMI) study in which volunteers were injected with NF54 sporozoites and blood samples were collected 11-14 days later (Gomez-Perez, G. P. et al., 2013. PMID: 26245196). We cultured the volunteer parasites in the same conditions as the NF54 parental line but for the minimum time possible so that their transcriptome wouldn’t be altered by in vitro growth conditions.

tag: type

value: mosquito and human passaged parasites

tag: time point

tag: estimated age

source_name: NF54 mixed stage Reference Pool

value: 3 samples of synchronized cultures covering the whole asexual cycle


title: V63, 40-45h


title: V63, 10-15h


title: V48, 40-45h


title: BioTASQ-ChIP-rep2


title: V35, 20-25h


title: V35, 40-45h


title: V63, 20-25h


title: V18, 30-35h


title: NF54, 30-35h, replicate II

value: premosquito in vitro culture


title: V18, 20-25h


title: V48, 30-35h


title: V18, 10-15h


title: NF54, 10-15h, replicate II


title: Developing mouse embryo sections H09E08_S93

city: Seattle

first: Sanjay

middle: R

last: Srivatsan

state: WA

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

institute: University of Washington

description:
Developing mouse embryo sections
sci-Space Slides 7-14
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)

organism: Mus musculus

source_name: E14 saggital sections 8-10um thick

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.

value: E14 Mouse Embryo

tag: sample type

value: Sagigital section


title: NF54, 40-45h, replicate I

tag: strain


title: V48, 20-25h


title: NF54, 20-25h, replicate I


title: NF54, 40-45h, replicate II


title: NF54, 20-25h, replicate II


title: V35, 10-15h


title: Developing mouse embryo sections H07E09_S187


title: V35, 30-35h


title: V18, 40-45h


title: V48, 10-15h


title: Developing mouse embryo sections H04E09_S184


title: Developing mouse embryo sections H05E08_S89


title: NF54, 30-35h, replicate I


title: Developing mouse embryo sections H12E09_S192


title: Developing mouse embryo sections H03E08_S87


title: Developing mouse embryo sections H03E09_S183


title: Developing mouse embryo sections H02E09_S182


title: Developing mouse embryo sections H12E08_S96


title: Developing mouse embryo sections H10E09_S190


title: Developing mouse embryo sections H11E09_S191


title: Developing mouse embryo sections H11E08_S95


title: Developing mouse embryo sections H10E08_S94


title: Developing mouse embryo sections G12E08_S84


title: Developing mouse embryo sections G11E08_S83


title: Developing mouse embryo sections H01E08_S85


title: Developing mouse embryo sections G10E09_S178


title: Developing mouse embryo sections G10E08_S82


title: Developing mouse embryo sections H08E09_S188


title: Developing mouse embryo sections G09E08_S81


title: NF54, 10-15h, replicate I


title: Developing mouse embryo sections H09E09_S189


title: Developing mouse embryo sections H07E08_S91


title: Developing mouse embryo sections H05E09_S185


title: Developing mouse embryo sections G07E08_S79


title: Developing mouse embryo sections G06E09_S174


title: Developing mouse embryo sections H08E08_S92


title: Developing mouse embryo sections G06E08_S78


title: Developing mouse embryo sections H06E09_S186


title: Developing mouse embryo sections H06E08_S90


title: Developing mouse embryo sections G05E09_S173


title: Developing mouse embryo sections H02E08_S86


title: Developing mouse embryo sections H04E08_S88


title: Developing mouse embryo sections G05E08_S77


title: Developing mouse embryo sections G04E08_S76


title: Developing mouse embryo sections G08E08_S80


title: Developing mouse embryo sections G08E09_S176


title: Developing mouse embryo sections G12E09_S180


title: Developing mouse embryo sections G02E09_S170


title: Developing mouse embryo sections H01E09_S181


title: Developing mouse embryo sections G07E09_S175


title: Developing mouse embryo sections F12E09_S168


title: Developing mouse embryo sections G11E09_S179


title: Developing mouse embryo sections G01E09_S169


title: RPMI + galactose_50345

city: Sydney

first: Antibiotic Resistant Sepsis Pathogens Framework Initiative

last: Bioplatforms Australia

state: NSW

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

country: Australia

institute: Bioplatforms Australia

description: Additional information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900618555.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations

organism: Streptococcus pneumoniae

source_name: Bacteria in growth media

growth_protocol: Complete information about the bacterial cultures is available from the Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Initiative website. https://data.bioplatforms.com/organization/about/bpa-sepsis

extract_protocol: Bacterial rRNA depletion with Illumina Ribo-Zero rRNA Removal Kit (Bacteria) followed by strand RNAseq sample preparation with Illumina TruSeq Stranded mRNA Library Prep Kit

tag: growth media

value: RPMI + galactose

tag: growth time

tag: growth phase

value: Mid log phase

tag: od600 reading

tag: temperature

tag: bpa identifier

tag: serovar


title: Developing mouse embryo sections G09E09_S177

tag: genotype


title: RPMI + glucose_50344

value: RPMI + glucose


title: Developing mouse embryo sections F11E09_S167


title: RPMI + galactose_50330


title: Developing mouse embryo sections G04E09_S172


title: Developing mouse embryo sections F10E08_S70


title: Pooled sera_50328

value: Pooled sera

value: 2 hrs exposure to sera


title: Developing mouse embryo sections G02E08_S74


title: RPMI + glucose_50314


title: Pooled sera_50313


title: Developing mouse embryo sections F08E08_S68


title: Developing mouse embryo sections F11E08_S71


title: Developing mouse embryo sections G03E08_S75


title: RPMI + glucose_50299


title: Developing mouse embryo sections F06E09_S162


title: RPMI + galactose_50315


title: RPMI + glucose_50329


title: RPMI + glucose_50284


title: Developing mouse embryo sections F04E09_S160


title: Developing mouse embryo sections F10E09_S166


title: Developing mouse embryo sections F05E09_S161


title: RPMI + galactose_50270


title: RPMI + glucose_50269


title: Developing mouse embryo sections G03E09_S171


title: Developing mouse embryo sections F09E09_S165


title: Developing mouse embryo sections F02E09_S158


title: Pooled sera_50343


title: Developing mouse embryo sections F08E09_S164


title: Developing mouse embryo sections G01E08_S73


title: Developing mouse embryo sections F07E09_S163


title: Pooled sera_50298


title: Developing mouse embryo sections F01E09_S157


title: RPMI + galactose_50300


title: Pooled sera_50334

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900618585.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2


title: RPMI + galactose_50285


title: Developing mouse embryo sections F02E08_S62


title: Pooled sera_50283


title: Developing mouse embryo sections F12E08_S72


title: RPMI + galactose_50351


title: Developing mouse embryo sections F03E09_S159


title: Developing mouse embryo sections F05E08_S65


title: Pooled sera_50319


title: Developing mouse embryo sections F06E08_S66


title: Developing mouse embryo sections F04E08_S64


title: RPMI + galactose_50321


title: Developing mouse embryo sections F07E08_S67


title: Developing mouse embryo sections F03E08_S63


title: Developing mouse embryo sections F09E08_S69


title: RPMI + glucose_50305


title: RPMI + glucose_50335


title: Developing mouse embryo sections E12E09_S156


title: Developing mouse embryo sections E09E09_S153


title: RPMI + glucose_50290


title: Developing mouse embryo sections F01E08_S61


title: RPMI + glucose_50350


title: RPMI + galactose_50276


title: RPMI + glucose_50275


title: RPMI + galactose_50336


title: Pooled sera_50274


title: RPMI + glucose_50320


title: Pooled sera_50268


title: Pooled sera_50349


title: Developing mouse embryo sections E11E09_S155


title: Developing mouse embryo sections E11E08_S59


title: Developing mouse embryo sections E12E08_S60


title: Developing mouse embryo sections E05E08_S53


title: Developing mouse embryo sections E10E08_S58


title: RPMI + glucose_50317

data_processing:
Software used to transform the raw fastq files into abundance measures are listed along with their command line arguments. Values wrapped with ${} indicate variables. ${sample} can be replaced by individual file names. Others indicate command line parameters and genome reference or annotation files.
Note that not all genes were annotated. Genes that were annotated are assigned a name in the genenames column, and those without have their gene ids replicated in the genenames column.
Paired end reads were aligned to the genome with bwa 0.7.12. bwa mem -t ${cpu} ${ref} ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz > ${sample}.sam
Alignments were sorted with samtools 1.9. samtools sort -@ ${cpu} -o ${sample}_SORTED.bam ${sample}.bam
Alignments were then quantified with featureCounts within subread 1.5.1. featureCounts -p -Q 10 -t ${CDS} -g ${gene_id} -a ${gtf} -o ${gene_counts_GENEID.txt} -T ${cpu} ${input_bams}
Genome_build: GCF_900618575.1
Supplementary_files_format_and_content: tab delimited text files with unannotated and annotated abundance measurements
Supplementary_files_format_and_content: gene counts
Supplementary_files_format_and_content: cpm log2
Supplementary_files_format_and_content: genome annotations


title: Developing mouse embryo sections E07E09_S151


title: Developing mouse embryo sections E08E09_S152


title: Developing mouse embryo sections E03E08_S51


title: RPMI + galactose_50291


title: Pooled sera_50316


title: RPMI + galactose_50306


title: Developing mouse embryo sections E09E08_S57


title: Developing mouse embryo sections E07E08_S55


title: Developing mouse embryo sections E10E09_S154


title: Developing mouse embryo sections E05E09_S149


title: Pooled sera_50289


title: RPMI + galactose_50348


title: RPMI + galactose_50333


title: Developing mouse embryo sections E06E08_S54


title: Pooled sera_50304


title: Developing mouse embryo sections E06E09_S150


title: RPMI + glucose_50347


title: Developing mouse embryo sections E03E09_S147


title: Developing mouse embryo sections E02E08_S50


title: RPMI + galactose_50318


title: RPMI + glucose_50332


title: Developing mouse embryo sections E01E08_S49


title: Developing mouse embryo sections E04E09_S148


title: Pooled sera_50301


title: Pooled sera_50331


title: RPMI + glucose_50287


title: Developing mouse embryo sections D12E08_S48


title: Developing mouse embryo sections D12E09_S144


title: Developing mouse embryo sections E04E08_S52


title: Developing mouse embryo sections E02E09_S146


title: Pooled sera_50346


title: Pooled sera_50271


title: Developing mouse embryo sections D10E08_S46


title: Developing mouse embryo sections D09E09_S141


title: RPMI + galactose_50303


title: Developing mouse embryo sections D11E08_S47


title: Developing mouse embryo sections D11E09_S143


title: Developing mouse embryo sections E08E08_S56


title: Developing mouse embryo sections D08E09_S140


title: Developing mouse embryo sections E01E09_S145


title: RPMI + glucose_50272


title: RPMI + galactose_50288