title: IMX2210 grown in SMD with vitamins - 2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

data_processing:
RNA-seq reads were aligned to the CEN.PK113-7D reference using STAR version 2.5.4a
resulted sequence alignment map file (SAM) converted in sorted BAM file with samtools
The sorted BAM file was processed with featureCounts for quantification
raw counts TNN normalized with edgeR
For differential analysis  was exactTest applied from edgeR
Genome_build: CEN.PK113-7D ASM257140v2
Supplementary_files_format_and_content: Comma delimited file, TMM normalized transcript counts

organism: Saccharomyces cerevisiae

source_name: steady state chemostat sample (D=0.1 h-1)

growth_protocol: The S. cerevisiae strains used and constructed in this study all derived from the CEN.PK lineage. Yeast cultures were grown in  synthetic medium (SM). The  SM medium were autoclaved at 121°C for 20 min. SM medium was then supplemented with 1 mL L-1 of filter-sterilized vitamin solution (0.05 g L 1 D-(+)-biotin, 1.0 g L-1 D-calcium pantothenate, 1.0 g L-1 nicotinic acid, 25 g L-1 myo-inositol, 1.0 g L 1 thiamine hydrochloride, 1.0 g L-1 pyridoxal hydrochloride, 0.20 g L-1 4-aminobenzoic acid). A concentrated glucose solution was autoclaved separately at 110°C and added to SM at a final concentration of 20 g L-1 yielding SMD, respectively. For medium without vitamins the vitamin solution was not added to obtain SMDΔvitamins.  Yeast strains were inoculated in 100 mL medium in 500-mL-shake flasks or in 20 mL medium in 100-mL-shake flasks and incubated at 30°C, 200 rpm in an Innova Incubator (Brunswick Scientific, Edison, NJ).

extract_protocol:
RNA was extracted with hot-phenol method as described by Schmitt et al. (1990)
cDNA libraries were prepared using the TruSeq stranded mRNA kit (illumina) and sequenced on NovaSeq (illumina) at Macrogen

treatment_protocol: Cultures were sampled into liquid nitrogen and processed as described by Piper et al. (2002)

value: vitamin independent strain

value: MATa can1{delta}::cas9-natNT2 sga1{delta}::ScTEF1p-FMS1-ScADH1t ScTDH3p-INO1-ScTDH1t ScCCW12p-SNZ1-ScENO2t ScTDH3p-ABZ1-ScTDH1t YPRcTau3{delta}::ScPYK1p-CfBIO1-ScBIO1t

tag: cultivation medium

value: SMD

value: class B vitamins

tag: state


title: IMX2210 grown in SMD with vitamins - 1

status: Public on Dec 01 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: genotype

tag: treatment

value: steady state chemostat sample (D=0.1 h-1)


title: IMX2210 grown in SMD without vitamins - 1

value: SMD delta vitamins

value: no vitamins


title: IMX2210 grown in SMD without vitamins - 4


title: IMX2210 grown in SMD with vitamins - 3


title: C6 SNP Bulk RNAseq

city: Wuhan

first: Weize

last: Xu

state: Hubei

address: shizishan street No.1

country: China

institute: Huazhong Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome using hisat2.
SNPs in the exon of expressed gene were called with GATK4.0, allele and reference of each SNP were counted with optional commands mpileup in samtools.
Supplementary_files_format_and_content: RNA-seq count matrix for each samples
Supplementary_files_format_and_content: Haplo-type SNP list for C57

organism: Rattus norvegicus

source_name: brain

extract_protocol:
C6 cell lines or the PVN of C57 was removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. mRNA-seq Lib Prep Kit for Illumina (RK20302) used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: brain

tag: age


title: IMX2210 grown in SMD with vitamins - 4


title: RM9 tumor, RT 3h, mouse 4

city: Dallas

first: Sangeetha

last: Reddy

state: Texas

address: 2280 Inwood Road

country: USA

institute: UT Southwestern Medical Center

data_processing:
Single end demultiplexed fastq files were generated using bcl2fastq2 v 2.17 from NextSeq550 high output v3 bcl files
Fastq files were imported, trimmed for adapter sequences followed by quality trimming using CLC Genomics Workbench v 23.0.3
High-quality reads were mapped against gene regions and transcripts annotated by ENSEMBL v99 GRCm39 using RNA-Seq Analysis tool v2.7 (CLC Genomics Workbench, reverse strand-specific option)
Assembly: ENSEMBL v99 GRCm39
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample

organism: Mus musculus

source_name: RM9 tumor tissue

growth_protocol: RM9 and MC38 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq® Stranded mRNA-Seq Library Prep Kit (Cat. 20020594) following manufacturer's protocols.

treatment_protocol:
1 million RM9 or MC38 cells were injected subcutaneously on the right hind leg of C57BL/6 mice. Allow the tumors to develop and grow to the size of 8mm in diameter. Irradiate the tumors with a single dose of 15 Gy.
Euthanize different groups of mice at 3h, 12h, and 24h after irradiation and collect the tumor tissue for RNA extraction.

tag: cell line

value: RM9 tumor tissue

tag: cell type

value: adenocarcinoma

value: WT

value: Irradiation, 15 Gy

tag: time

value: 3h post RT


title: SNP RNA-seq3

city: Heidelberg

first: Jian

last: Zeng

address: Im Neuenheimer Feld 230

department: Department of Stem Cell Biology

country: Germany

institute: Heidelberg University

data_processing:
Quality control: FastQC
Read alignment: STAR
DEG calling: DESeq2
Assembly: TAIR10
Supplementary files format and content: text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Shoot apices

growth_protocol: 21°C; 65% humidity;  16h light/8h dark

extract_protocol:
RNAeasy plant mini kit according to manufacturer instructions (Qiagen, Hilden, Germany)
The RNA were poly A selected using the NEB Poly (A) Magnetic isolation module (7490), then the NEBnext Ultra Direction RNA Prep Kit (E7420) for Illumina with the NEBnext Multiplex Oligo's for Illumina (E7335). For RNA 1 µg input was used.

treatment_protocol: 0.025% Silwet, with and without 1mM SNP, 24 hours

value: Shoot apices

value: ap1, cal

value: 1mM SNP (sodium nitroprusside)


title: SNP RNA-seq2


title: SNP RNA-seq1


title: Mock RNA-seq3

value: Mock


title: Mock RNA-seq2


title: Mock RNA-seq1


title: Mock EM-seq2

library_source: genomic

data_processing:
Quality control: FastQC
Read alignment and 5mC calling: Bismark
Assembly: TAIR10
Supplementary files format and content: text files include 5mC levels for each Sample

molecule: genomic DNA

extract_protocol:
DNAeasy plant mini kit according to manufacturer instructions (Qiagen)
100 ng of DNA was used to create libraries with the NEBNext Enzymatic Methyl-Seq kit for Illumina. Fragmentation of the material was performed on the Covaris S2 instrument with fragmentation effciency being checked on the Agilent Bioanalyzer using the DNA High Sensitivity kit. Library preparation was perfromed as according to manufacturers recommendations including the use of methylated pUC 19 and unmethylated Lambda DNA as spike in. Library quality was checked on the Bioanalyzer using the DNA 1000 Assay and quantified with the Qubit using the High Sensitivity assay. Libraries were pooled and sequencing performed on the Illumina NextSeq 550 with 150 cycle Mid Output chemistry in 75 paired end modus.
enzymatic methlylation (EM) sequencing


title: SNP EM-seq1


title: SNP EM-seq2


title: Mock EM-seq1


title: e122e22_ethylene_input_rep1

city: Austin

first: Zhengyao

last: Shao

state: TX

address: 2506 Speedway, NMS 5.324

department: MBS

institute: University of Texas at Austin

data_processing:
Paired-end raw reads were first mapped to the Arabidopsis genome (TAIR10) using Bowtie2 software with default parameters. Duplicate reads were removed using SAMtools.
H3K14ac and H3K23ac ChIP-seq data for Col-0 air and ethylene treatment were obtained from previous study (GEO accession code GSE77396). ChIP-seq coverage tracks shown in the genome browser IGV were generated using deeptools3.0.2
bamCoverage function normalized by reads per genomic content (1x normalization, 1X RPGC) and bin size = 1.
Assembly: TAIR10
Supplementary files format and content: bw, bin =1
Supplementary files format and content: bw, bin =1

source_name: etiolated seedlings

growth_protocol: Arabidopsis seeds were first surface-sterilized with solution containing 50% bleach and 0.01% Triton X-100 for 10 minutes, washed with sterile distilled water for four times, sown on Murashige and Skoog (MS) medium plates containing 1% sucrose and 1% phytoblend agar and stratified for three days at 4°C in the dark.

extract_protocol:
Three-day-old etiolated e1-2-2 e2-2 #17 seedlings treated with air or 4h ethylene were harvested and crosslinked in 1% formaldehyde, and the chromatin was isolated and sheared by Bioruptor. Anti-H3K14ac (Millipore; 07-353) and anti-H3K23ac (Millipore; 07-355) antibodies together with Dynabeads were added to the sonicated chromatin followed by incubation overnight to precipitate histone bound DNA fragments.
Chromatin-immunoprecipitated DNA after elution was prepared for library construction by using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads according to standard operating procedures and then sequenced using HiSeq2000 (Illumina).

treatment_protocol: After stratification and light exposure, plated seeds on MS medium were treated with a flow of hydrocarbon free air at 22°C in air-tight containers. After three days in the dark, those etiolated seedlings were subsequently treated with ethylene gas (10 ppm) or hydrocarbon-free air for indicated hours prior to sampling.

value: etiolated seedlings

tag: chip antibody

value: ethylene


title: e122e22_ethylene_H3K23ac_rep2

value: Anti-H3K23ac (Millipore; 07-355)


title: e122e22_ethylene_input_rep2


title: IMX2210 grown in SMD without vitamins - 2

value: vitamin independent strain

value: MATa can1{delta}::cas9-natNT2 sga1{delta}::ScTEF1p-FMS1-ScADH1t ScTDH3p-INO1-ScTDH1t ScCCW12p-SNZ1-ScENO2t ScTDH3p-ABZ1-ScTDH1t YPRcTau3{delta}::ScPYK1p-CfBIO1-ScBIO1t


title: e122e22_ethylene_H3K23ac_rep1


title: e122e22_air_input_rep2

value: air


title: e122e22_air_H3K23ac_rep2


title: e122e22_ethylene_H3K14ac_rep1

value: Anti-H3K14ac (Millipore; 07-353)


title: IMX2210 grown in SMD without vitamins - 3

value: SMD delta vitamins

value: no vitamins

value: steady state chemostat sample (D=0.1 h-1)


title: e122e22_air_input_rep1


title: e122e22_ethylene_H3K14ac_rep2


title: e122e22_air_H3K14ac_rep1


title: e122e22_air_H3K23ac_rep1


title: e22e322_air_rep1

data_processing:
Paired-end raw fastq data were evaluated with FastQC and low-quality reads were removed with Trim Galore (Babraham Institute).
The trimmed and filtered reads were then mapped to the Arabidopsis reference genome (TAIR10) with STAR.
Mapped reads were counted by featureCounts (Subread 2.0.1) and differentially regulated genes were identified using R package DESeq2.
Assembly: TAIR10

source_name: seedling

extract_protocol:
RNA extraction was conducted following the manufacturer’s recommendation using the RNeasy Plant Kit (Qiagen) with DNase I digestion and clean up (Qiagen, RNeasy Mini Kit (250)).
Libraries were generated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770), with 1μg RNA as input, following the manufacturer’s instructions.

value: seedling


title: e22e322_ethylene_rep1


title: e122e22_ethylene_rep1


title: e122e22_ethylene_rep2


title: e22e322_air_rep2


title: e122e22_air_rep2


title: e22e322_ethylene_rep2


title: e122e22_air_rep1


title: e122e22_air_H3K14ac_rep2


title: Lung 3 scRNA seq Multi

city: Glen Cove

first: Stefanos

last: Zafeiropoulos

state: New York

address: 21 Walnut Road

institute: Feinstein Institutes for Medical Research

library_source: transcriptomic single cell

data_processing:
the demultiplexing, barcorded processing, gene counting and aggregation were made using the cell ranger software v2.1.1
Supplementary files format and content: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: lung

extract_protocol:
Freshly collected lungs were extracted. Half of one lobe was dissociated using the Mouse Lung Dissociation kit (Miltenyi Biotec) with the gentleMACS Octo Dissociator following the manufacurer’s recommendation.
Four samples were pooled and labeled using 10X Genomics CellPlex (PN-1000261) before loading onto Chip G and the Chromium Controller. Single Cell Libraries were generated using Next GEM Single Cell 3’ reagents v3.1 with dual indexing (10X Genomics). Library quality was assessed with a High Sensitivity DNA Chip on a BioAnalyzer (Agilent). Sequencing was done on a NovaSeq at MedGenome (Foster City, CA), 500M Paired-End Reads per Library.

value: lung


title: Lung 3 scRNA seq GEXP


title: HCHFD rep1

city: beijing

first: ruijun

last: wang

address: college of life science

institute: Tsinghua university

data_processing:
Demultiplexing and basecalling performed using CASAVA version 1.8.2.
QC was performed on the FASTQ files using FastQC(v0.11.5) software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rat(Rnor_6.0) whole genome using HISAT2(v2.1.0).
Sequence reads aligned to the rat genome were imported into StringTie(v1.3.3b) for sequence read counting.
Sequence reads mapped to different isoforms of individual genes were pooled together, and then were input into the DESeq2(v1.28.0) differential expression analysis program to normalize and determine expression levels and differentially expressed genes.
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each gene per sample

source_name: high cholesterol-high fat diet treated

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions，Illumina TruSeq RNA Sample was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: sample type

value: Model group

value: high cholesterol-high fat diet treated


title: HCHFD+PC rep2

source_name: fed with a HCHFD plus  Pulsatilla Chinensis

value: treatment group


title: HCHFD rep2


title: HCHFD+PC rep1

value: fed with a HCHFD plus  Pulsatilla Chinensis


title: ND rep2

source_name: normal diet treated

value: control group

value: normal diet treated


title: Lung 4 scRNA seq GEXP


title: ND rep3


title: Lung 4 scRNA seq Multi


title: HCHFD rep3


title: HLC - OsmM- day 20 - 3

city: Leuven

first: Jonathan

middle: Sai-Hong

last: Chui

state: Vlaams Brabant

address: Herestraat 49 PB804

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

description:
HC3X_D20_OsmM_N3
iPSC-derived hepatocyte-like cells in hyperosmolar conditions at day 20
TPM_HUH7_HLC.csv

data_processing:
Trimming of adapters, polyA/T tails, and low-quality reads was performed using the Trimgalore package with default parameters. Using the Salmon package with default parameters, the reads were aligned to the transcriptome and quantified using release 32 of the human reference transcriptome sequence and gene annotation. Counts were then imported into R using Tximport.
Assembly: Release 32 (GRCh38.p13)
Supplementary files format and content: tab  seperated file with raw counts per sample
Supplementary files format and content: tabs seperated filew with TPM normalized counts per sample

molecule: polyA RNA

organism: Homo sapiens

source_name: iPSC line (Sigma)

growth_protocol: HUH7.5 and Hep3B lines were plated at a seeding density of 10.4 x 104 cells/cm2 or 50.000 cells/mL in DMEM medium low glucose (Gibco) supplemented with 10% FBS and 1X penicillin-streptomycin. Cell lines were passaged following dissociation using 0.25% Trypsin-EDTA solution (Gibco) upon reaching 70% confluency. The differentiation was started using previously described cytokine regimes and was stopped after 30 days of differentiation30. Briefly, mTeSR medium was replaced by Liver Differentiation Medium (LDM), and 50 ng/mL WNT-3A and 50 ng/mL Activin A was supplemented at day 0, followed by only 50 ng/mL Activin-A at day 2. At day 4, 50 mg/mL BMP4 and 5 µg/mL doxycycline were added. From day 8 until day 12, 20 ng/mL acidic FGF (aFGF) was supplemented to the medium. From day 12 onwards, cells were cultured with 20 ng/mL HGF until the end of the differentiation. All cytokines were purchased from Peprotech. The differentiation medium was supplemented with 0.6% DMSO during the first 12 days of the culture and with 2% DMSO from day 12 onward. Medium was changed every two days of the differentiation.

extract_protocol:
Total RNA was extracted from HUH7.5 cells using the GenElute™ Mammalian Total RNA Miniprep Kit according to the Manufacturer's instructions. Total RNA was extracted from iPSC-HLCs using the Qiagen Rneasy Mini kit according to the Manufacturer's recommendations.
RNA sequencing (RNAseq) libraries were prepared from 4 µg of total RNA using the KAPA stranded mRNA-seq kit (Roche, KK8581) according to manufacturer’s specifications. 100 nM KAPA-single index adapters (Roche, KK8700) were added to A-tailed cDNA, and libraries were amplified for 10 cycles. Finally, 1x library cleanup was performed using Agencourt AMPure XP beads (Beckman Coulter, A63881). Library fragment size was assessed using Agilent Bioanalyzer 2100 with the High Sensitivity DNA analysis kit (Agilent, 5067-4626) and concentration was determined using Qubit™ dsDNA HS Assay kit (Invitrogen, Q32854). Each library was diluted to 4 nM and pooled for sequencing on an Illumina Hiseq4000, aiming at 15-20 million SE50 reads per sample (19 million reads on average).

treatment_protocol: Hepatoma cell lines HUH7.5 and Hep3B under HypOsm conditions were treated with DMEM supplemented with 250 mM of glycine (OsmG) or 250 mM mannitol (OsmM) 16 hours after plated. Hepatocyte-like cell (HLC) differentiation: cells treated with OsmG and OsmM were cultured in LDM supplemented with 250 mM of glycine (OsmG) or 250 mM mannitol (OsmM) on day 12 of the protocol. hiPSC-HLC cells were cultured until day 30 of differentiation. Upon hyperosmolar treatment, 2% DMSO was removed from day 12 onwards.

value: iPSC line (Sigma)

value: iPSC-derived hepatocyte like cells

value: OsmM

tag: timepoint

value: day 20

tag: transcription factor_overexpression

value: HNF1A, FOXA3, PROX1


title: CD14+ monocytes_rep2

type: RNA

city: Nijmegen

first: Jolanda

last: de Vries

address: Geert grooteplein Zuid 28

department: Tumor Immunology Department

institute: Radboud Institute for Molecular Life Sciences, Radboudumc

description: Gene expression data from freshly FACS isolated cells, without culture

hyb_protocol: RNA was processed in collaboration with Eurofins Genomics following standard Affymetrix protocol: Following fragmentation and biotin labelling of amplified ds cDNA, hybridization was performed using the Affymetrix Hyb., wash and stain kit (Ref 900720-C) and in hybridization oven for 16h at 45 °C. Chip type U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: RNA was processed in collaboration with Eurofins Genomics following standard Affymetrix protocol: Arrays were scanned by Eurofins with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocols.

data_processing: RNA was processed in collaboration with Eurofins Genomics following standard Affymetrix protocol: The expression data was analyzed into Robust Multi-Array Average (RMA) normalized data by Eurofins.

label: biotin

source_name: primary CD14+ monocytes donor 2

label_protocol: RNA was processed in collaboration with Eurofins Genomics following standard Affymetrix protocol: Affymetrix IVT Pico Amp Kit, Ref 902762(30rxn)/902786(96rxn) was used to amplify 2ng input RNA. cRNA is then converted to biotinylated double-stranded cDNA (ds-cDNA) hybridization targets, all according to Affymetrix protocol.

growth_protocol: cells were not cultured and kept at 4C untill cell pellets were prepared for RNA extraction

extract_protocol: Total RNA extraction was performed using the Rnease Plus Micro Kit (Qiagen) according to the manufacturer's protocol. All subsequent protocols were performed by Eurofins.

treatment_protocol: PBMCs were isolated using Lymphoprep (Axis-Shield PoC AS). To obtain separate CD1c+CD14- and CD1c+CD14+ populations, and CD14+ monocytes for RNA analysis, PBMCs treated with FcR blocker and depleted for CD3, CD19, and CD56 using MACS microbeads were stained with anti-CD1c-BV421, anti-CD3/CD56/CD20-FITC, and anti-CD14-APC-H7 for 30 min at 4 °C in sterile polypropylene round-bottom tubes (Falcon). Sorting was performed on a BD FACSAria. After sorting, cells were washed twice with PBS and dry cell pellets were stored at -80 until RNA isolation.

tag: individual

value: donor 2

value: blood

value: PBMCs

tag: facs isolated cells

value: CD14+ monocytes

tag: disease status

value: healthy donor


title: CD14+ monocytes_rep3

source_name: primary CD14+ monocytes donor 3

value: donor 3


title: ND rep1

value: Liver


title: HLC - OsmM- day 20 - 2

description:
HC3X_D20_OsmM_N2
iPSC-derived hepatocyte-like cells in hyperosmolar conditions at day 20
TPM_HUH7_HLC.csv


title: CD14- cDC2s_rep3

source_name: primary CD14- CD1c+ cDC2s donor 3

value: CD14- cDC2s


title: CD14- cDC2s_rep4

source_name: primary CD14- CD1c+ cDC2s donor 4

value: donor 4


title: CD14+ monocytes_rep1

source_name: primary CD14+ monocytes donor 1

value: donor 1


title: CD14+ cDC2s_rep2

source_name: primary CD14+ CD1c+ cDC2s donor 2

value: CD14+ cDC2s


title: CD14+ monocytes_rep4

source_name: primary CD14+ monocytes donor 4


title: CD14- cDC2s_rep1

source_name: primary CD14- CD1c+ cDC2s donor 1


title: CD14- cDC2s_rep2

source_name: primary CD14- CD1c+ cDC2s donor 2


title: HLC - OsmM- day 20 - 1

description:
HC3X_D20_OsmM_N1
iPSC-derived hepatocyte-like cells in hyperosmolar conditions at day 20
TPM_HUH7_HLC.csv


title: CD14+ cDC2s_rep4

source_name: primary CD14+ CD1c+ cDC2s donor 4


title: HCHFD+PC rep3

value: treatment group

value: fed with a HCHFD plus  Pulsatilla Chinensis


title: CD14+ cDC2s_rep3

source_name: primary CD14+ CD1c+ cDC2s donor 3


title: CD14+ cDC2s_rep1

source_name: primary CD14+ CD1c+ cDC2s donor 1


title: Fibroblast cell, 3D, rep1

city: Sugito-machi

first: Rii

last: Morimura

state: Saitama

address: 4-2-3 Takanodaiminami

country: Japan

institute: TOPPAN Holdings Inc.

hyb_protocol: 600 ng of cRNA was aliquoted and incubated with the microarray in the DNA Microarray Hybridization Oven for 17 hours (65°C, 10 rpm).

scan_protocol: Microarray scanning was performed using a DNA Microarray Scanner.The scanned image data was quantified and the QC report obtained at the same time was reviewed. The spike-in control added as an external standard was considered acceptable if the slope was 0.85 or greater, the R2 was 0.95 to 1.0, and the median %CV was 20% or less.

data_processing: As an interarray normalization method for the one-color method, the Agilent recommended global normalization was performed under the following conditions.Threshold raw signals: 1.0.Normalization algorithm: Percentile Shift.Percentile target: 75

source_name: Fibroblast cell, 3D, replicate 1

label_protocol: Using 100 ng of total RNA as template, the one-color method protocol recommended by Agilent (file name; One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), ver6.9, December 2015). cDNA synthesis was followed by purification of the amplified and labeled cRNA product obtained from cDNA synthesis, and then absorbance was measured with NanoDrop One to calculate concentrations and other parameters. At that time, samples with an amplification factor of at least 15-fold and an incorporation efficiency of at least 6 pmol/μg of purified labeled cRNA product were considered acceptable.

extract_protocol: A total of 100 µL of cell disruption fluid was added to QIAzol Lysis Reagent to reach 700 µL, and the cells were further disrupted by centrifugation on a QIAshredder column (79656, Qiagen N.V.). Thereafter, 20% (vol) of the filtrate was added to chloroform, mixed thoroughly and centrifuged. After the supernatant was separated, a 1.5-fold volume of 100% ethanol was added to precipitate total RNA and RNA purification was performed using a miRNeasy Micro Kit (217084, Qiagen N.V.). Finally, 20 µL of nuclease-free water was added to elute the total RNA.

value: fibroblast cell


title: Fibroblast cell, 2D, rep1

source_name: Fibroblast cell, 2D, replicate 1


title: HLC - OsmG - day 20 - 2

description:
HC3X_D20_OsmG_N2
iPSC-derived hepatocyte-like cells in hyperosmolar conditions at day 20
TPM_HUH7_HLC.csv

value: iPSC line (Sigma)

value: iPSC-derived hepatocyte like cells

value: OsmG


title: HLC - PlasOsm - day 20 - 2

description:
HC3X_D20_LDM_N2
iPSC-derived hepatocyte-like cells  at day 20
TPM_HUH7_HLC.csv

value: PlasOsm

value: day 20

value: HNF1A, FOXA3, PROX1


title: HLC - OsmG - day 20 - 1

description:
HC3X_D20_OsmG_N1
iPSC-derived hepatocyte-like cells in hyperosmolar conditions at day 20
TPM_HUH7_HLC.csv


title: HLC - OsmM - D12 + 72h - 4

description:
HC3X_D12_+_72h_OsmM_N4
iPSC-derived hepatocyte-like cells in hyperosmolar conditions for 72 hours
TPM_HUH7_HLC.csv

value: OsmM

value: 72 hours


title: HLC - PlasOsm - day 20 - 1

description:
HC3X_D20_LDM_N1
iPSC-derived hepatocyte-like cells  at day 20
TPM_HUH7_HLC.csv


title: HLC - PlasOsm - day 20 - 3

description:
HC3X_D20_LDM_N3
iPSC-derived hepatocyte-like cells  at day 20
TPM_HUH7_HLC.csv


title: HLC - OsmM - D12 + 72h - 2

description:
HC3X_D12_+_72h_OsmM_N2
iPSC-derived hepatocyte-like cells in hyperosmolar conditions for 72 hours
TPM_HUH7_HLC.csv


title: HLC - OsmG - D12 + 72h - 4

description:
HC3X_D12_+_72h_OsmG_N4
iPSC-derived hepatocyte-like cells in hyperosmolar conditions for 72 hours
TPM_HUH7_HLC.csv


title: HLC - OsmM - D12 + 72h - 1

description:
HC3X_D12_+_72h_OsmM_N1
iPSC-derived hepatocyte-like cells in hyperosmolar conditions for 72 hours
TPM_HUH7_HLC.csv


title: HLC - OsmG - D12 + 72h - 1

description:
HC3X_D12_+_72h_OsmG_N1
iPSC-derived hepatocyte-like cells in hyperosmolar conditions for 72 hours
TPM_HUH7_HLC.csv


title: HLC - OsmG - D12 + 72h - 3

description:
HC3X_D12_+_72h_OsmG_N3
iPSC-derived hepatocyte-like cells in hyperosmolar conditions for 72 hours
TPM_HUH7_HLC.csv


title: HLC - OsmG - D12 + 72h - 2

description:
HC3X_D12_+_72h_OsmG_N2
iPSC-derived hepatocyte-like cells in hyperosmolar conditions for 72 hours
TPM_HUH7_HLC.csv


title: HLC - PlasOsm - D12 + 72h - 3

description:
HC3X_D12_+_72h_LDM_N3
iPSC-derived hepatocyte-like cells at 72 hours
TPM_HUH7_HLC.csv


title: HLC - PlasOsm - D12 + 72h - 1

description:
HC3X_D12_+_72h_LDM_N1
iPSC-derived hepatocyte-like cells at 72 hours
TPM_HUH7_HLC.csv


title: HLC - PlasOsm - D12 + 72h - 2

description:
HC3X_D12_+_72h_LDM_N2
iPSC-derived hepatocyte-like cells at 72 hours
TPM_HUH7_HLC.csv


title: HLC - PlasOsm - D12 + 72h - 4

description:
HC3X_D12_+_72h_LDM_N4
iPSC-derived hepatocyte-like cells at 72 hours
TPM_HUH7_HLC.csv


title: HUH7.5 - OsmG + CHIR99021 - 5 days - 1

description:
HUH7.5 cells under hyperosmolar conditions with CHIR99021 treatment at day 5
HUH7_5_b1_5d_GLY_CHIR_1
RNA_seq_HUH7_5_b1_5d_GLY_CHIR_1

source_name: Hepatoma-derived

treatment_protocol: Hepatoma cell lines HUH7.5 and Hep3B under HypOsm conditions were treated with DMEM supplemented with 250 mM of glycine (OsmG) or 250 mM mannitol (OsmM) 16 hours after plated.  Hepatocyte-like cell (HLC) differentiation: cells treated with OsmG and OsmM were cultured in LDM supplemented with 250 mM of glycine (OsmG) or 250 mM mannitol (OsmM) on day 12 of the protocol. hiPSC-HLC cells were cultured until day 30 of differentiation. Upon hyperosmolar treatment, 2% DMSO was removed from day 12 onwards.

value: Hepatoma-derived

value: WT

value: OsmG + CHIR99021

value: 5 days


title: HLC - OsmM - D12 + 72h - 3

description:
HC3X_D12_+_72h_OsmM_N3
iPSC-derived hepatocyte-like cells in hyperosmolar conditions for 72 hours
TPM_HUH7_HLC.csv


title: HUH7.5 - OsmG + CHIR99021 - 5 days - 2

description:
HUH7.5 cells under hyperosmolar conditions with CHIR99021 treatment at day 5
HUH7_5_b1_5d_GLY_CHIR_2
RNA_seq_HUH7_5_b1_5d_GLY_CHIR_2


title: HUH7.5 - Figure 5 - OsmG - 36h - 2

description:
HUH7.5 cells under hyperosmolar conditions after 36 hours
HUH7_5_b2_36h_GLY_3
RNA_seq_HUH7_5_b2_36h_GLY_3

value: 36 hours


title: HUH7.5 - OsmG - 5 days - 3

description:
HUH7.5 cells under hyperosmolar conditions at day 5
HUH7_5_b1_5d_GLY_3
RNA_seq_HUH7_5_b1_5d_GLY_3


title: HUH7.5 - Figure 5 - OsmG + TPCA-1 - 36h - 1

description:
HUH7.5 cells under hyperosmolar conditions with TPCA-1 treatment after 36 hours
HUH7_5_b2_36h_GLY_TPCA_2
RNA_seq_HUH7_5_b2_36h_GLY_TPCA_2

value: OsmG + TPCA-1


title: HUH7.5 - OsmG - 5 days - 2

description:
HUH7.5 cells under hyperosmolar conditions at day 5
HUH7_5_b1_5d_GLY_2
RNA_seq_HUH7_5_b1_5d_GLY_2


title: HUH7.5 - Figure 5 - OsmG - 36h - 1

description:
HUH7.5 cells under hyperosmolar conditions after 36 hours
HUH7_5_b2_36h_GLY_2
RNA_seq_HUH7_5_b2_36h_GLY_2


title: HUH7.5 - OsmG + CHIR99021 - 5 days - 3

description:
HUH7.5 cells under hyperosmolar conditions with CHIR99021 treatment at day 5
HUH7_5_b1_5d_GLY_CHIR_3
RNA_seq_HUH7_5_b1_5d_GLY_CHIR_3


title: HUH7.5 - OsmG - 5 days - 1

description:
HUH7.5 cells under hyperosmolar conditions at day 5
HUH7_5_b1_5d_GLY_1
RNA_seq_HUH7_5_b1_5d_GLY_1


title: HUH7.5 - OsmG + CHIR99021 - 36h - 3

description:
HUH7.5 cells under hyperosmolar conditions with CHIR99021 treatment after 36 hours
HUH7_5_b1_36h_GLY_CHIR_3
RNA_seq_HUH7_5_b1_36h_GLY_CHIR_3


title: HUH7.5 - OsmG + CHIR99021 - 36h - 1

description:
HUH7.5 cells under hyperosmolar conditions with CHIR99021 treatment after 36 hours
HUH7_5_b1_36h_GLY_CHIR_1
RNA_seq_HUH7_5_b1_36h_GLY_CHIR_1


title: HUH7.5 - OsmG + CHIR99021 - 36h - 2

description:
HUH7.5 cells under hyperosmolar conditions with CHIR99021 treatment after 36 hours
HUH7_5_b1_36h_GLY_CHIR_2
RNA_seq_HUH7_5_b1_36h_GLY_CHIR_2


title: HUH7.5 - OsmG - 36h - 2

description:
HUH7.5 cells under hyperosmolar conditions after 36 hours
HUH7_5_b1_36h_GLY_2
RNA_seq_HUH7_5_b1_36h_GLY_2


title: HUH7.5 - OsmG - 36h - 3

description:
HUH7.5 cells under hyperosmolar conditions after 36 hours
HUH7_5_b1_36h_GLY_3
RNA_seq_HUH7_5_b1_36h_GLY_3


title: HUH7.5 - PlasOsm - 36h - 2

description:
HUH7.5 cells after 36 hours
HUH7_5_b1_36h_DM_2
RNA_seq_HUH7_5_b1_36h_DM_2


title: HUH7.5 - OsmG - 36h - 1

description:
HUH7.5 cells under hyperosmolar conditions after 36 hours
HUH7_5_b1_36h_GLY_1
RNA_seq_HUH7_5_b1_36h_GLY_1


title: HUH7.5 - PlasOsm - 36h - 3

description:
HUH7.5 cells after 36 hours
HUH7_5_b1_36h_DM_3
RNA_seq_HUH7_5_b1_36h_DM_3


title: HUH7.5 - PlasOsm - 36h - 1

description:
HUH7.5 cells after 36 hours
HUH7_5_b1_36h_DM_1
RNA_seq_HUH7_5_b1_36h_DM_1


title: HLC - PlasOsm - day 30 - 2

description:
iPSC-derived hepatocyte-like cells  at day 30
HLC_b1_LDM_D30_2
RNA_seq_HLC_b1_LDM_D30_2

value: day 30


title: HUH7.5 - Figure 5 - OsmG + TPCA-1 - 36h - 2

description:
HUH7.5 cells under hyperosmolar conditions with TPCA-1 treatment after 36 hours
HUH7_5_b2_36h_GLY_TPCA_3
RNA_seq_HUH7_5_b2_36h_GLY_TPCA_3


title: HLC - PlasOsm - 72h - 1

description:
iPSC-derived hepatocyte-like cells at 72 hours
HLC_b1_LDM_72H_1
RNA_seq_HLC_b1_LDM_72H_1


title: HLC - OsmG + TPCA-1 - day 30- - 2

description:
iPSC-derived hepatocyte-like cells in hyperosmolar conditions with TPCA-1 treatment at day 30
HLC_b1_GLY_TPCA_D30_2
RNA_seq_HLC_b1_GLY_TPCA_D30_2


title: HLC - OsmG + TPCA-1 - day 30- - 1

description:
iPSC-derived hepatocyte-like cells in hyperosmolar conditions with TPCA-1 treatment at day 30
HLC_b1_GLY_TPCA_D30_1
RNA_seq_HLC_b1_GLY_TPCA_D30_1


title: HLC - OsmG + TPCA-1 - 72h - 1

description:
iPSC-derived hepatocyte-like cells in hyperosmolar conditions with TPCA-1 treatment for 72 hours
HLC_b1_GLY_TPCA_72H_1
RNA_seq_HLC_b1_GLY_TPCA_72H_1


title: HLC - OsmG + TPCA-1 - 72h - 2

description:
iPSC-derived hepatocyte-like cells in hyperosmolar conditions with TPCA-1 treatment for 72 hours
HLC_b1_GLY_TPCA_72H_2
RNA_seq_HLC_b1_GLY_TPCA_72H_2


title: GSC2 non-treated biol rep 2

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

state: NY

address: 1300 Morris Park Avenue

department: Systems and Computational Biology

institute: Albert Einstein College of Medicine

description: RNA with PolyA selection

data_processing:
Sequence reads were aligned to the hg38 assembly of the human genome with hisat2 (Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019).
Sequence-read summarization was done with featureCounts (Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30, 2014) using refSeq exon coordinates extracted from the refGene.txt file (http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz)
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-separated text file with raw counts for refseq protein-coding genes.

source_name: Glioblastoma stem cells 2

growth_protocol: The IRB of Rhode Island Hospital has approved the collection of patient-derived glioblastoma multiforme (GBM) tissue. All collections were performed with patient consent and in completely de-identified manner. Primary hGSC spheres were cultured from human glioma samples as previously described (Galli et al., 2004) All hGCs used in this study were authenticated by ATCC using short tandem repeat (STR) analysis. All human primary cells used were between passages 5 and 30. GSCs were cultured either as spheres or as attached on fibronectin-coated plates (10ug/ml, Millipore Sigma) in a medium of 1X Neurobasal Medium (Fisher Scientific), B27 serum-free supplement, minus Vitamin A (Fisher Scientific), 100X Glutamax (Fisher Scientific), 1mg/ml Heparin (STEMCELL Technologies), 20 ng/ml epidermal growth factor (Peprotech), 20ng/ml basic-fibroblast growth factor (Peprotech), and 1% Antibiotic-Antimycotic (Fisher Scientific).

extract_protocol:
RNA was harvested using the Trizol reagent and the RNeasy mini kit (Qiagen)
Completed with Genewiz (RNA with PolyA selection)

treatment_protocol: GSCs were treated for 2 days with/without CXCL12 2ug/ml.

value: Glioblastoma stem cells 2

value: glioblastoma stem cells

value: Non-treated


title: HLC - OsmG - NT 72h - 2

description:
iPSC-derived hepatocyte-like cells in hyperosmolar conditions for 72 hours
HLC_b1_GLY_72H_2
RNA_seq_HLC_b1_GLY_72H_2

source_name: iPSC line (Sigma)

value: iPSC line (Sigma)

value: iPSC-derived hepatocyte like cells


title: HLC - OsmG - NT 72h - 1

description:
iPSC-derived hepatocyte-like cells in hyperosmolar conditions for 72 hours
HLC_b1_GLY_72H_1
RNA_seq_HLC_b1_GLY_72H_1

value: OsmG


title: GSC2 non-treated biol rep 1

description: RNA with PolyA selection


title: HLC - OsmG - NT day 30 - 2

description:
iPSC-derived hepatocyte-like cells in hyperosmolar conditions at day 30
HLC_b1_GLY_D30_2
RNA_seq_HLC_b1_GLY_D30_2


title: BRD4 short-specific siRNA, replicate 3

city: Singapore

first: Reshma

last: Taneja

address: 10 Medical Dr

country: Singapore

institute: NUS

data_processing:
Raw image data file from sequencing was transformed to Sequenced Reads by CASAVA base recognition (Base Calling).
Bcl2fastq was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR v2.5 with parameters mismatch=2. STAR used the method of Maximal Mappable Prefix (MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis between two condition/groups (three biological replicates per condition) was performed using the DESeq2 R package (v2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg19
Supplementary files format and content: readcount

source_name: RD

growth_protocol: RD cells were cultured in DMEM media supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin

extract_protocol:
Total RNA extraction with Trizol. RNA purity and integrity were assessed with Nanodrop and agarose gel electrophoresis. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA was first fragmented randomly by addition of fragmentation buffer. The first strand of cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-).
RNA libraries were prepared for sequencing using NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: RD cells were transfected with control siRNA (BRD4WT), BRD4 Long siRNA (siBRD4L) or BRD4 Short siRNA (siBRD4S) using Lipofectamine RNAiMAX.

value: RD

value: ERMS

value: FN-RMS

value: BRD4 short-specific siRNA


title: HLC - OsmG - NT day 30 - 1

description:
iPSC-derived hepatocyte-like cells in hyperosmolar conditions at day 30
HLC_b1_GLY_D30_1
RNA_seq_HLC_b1_GLY_D30_1

value: HNF1A, FOXA3, PROX1


title: GSC2 treated with recombinant CXCL12 2ug/ml biol rep 1

description: RNA with PolyA selection

value: CXCL12 2ug/ml 48hrs


title: BRD4 short-specific siRNA, replicate 1


title: BRD4 short-specific siRNA, replicate 2


title: GSC2 treated with recombinant CXCL12 2ug/ml biol rep 2

description: RNA with PolyA selection


title: BRD4 long-specific siRNA, replicate 2

value: BRD4 long-specific siRNA


title: BRD4 long-specific siRNA, replicate 1


title: HLC - PlasOsm - day 30 - 1

description:
iPSC-derived hepatocyte-like cells  at day 30
HLC_b1_LDM_D30_1
RNA_seq_HLC_b1_LDM_D30_1

value: PlasOsm


title: HLC - PlasOsm - 72h - 2

description:
iPSC-derived hepatocyte-like cells at 72 hours
HLC_b1_LDM_72H_2
RNA_seq_HLC_b1_LDM_72H_2

value: 72 hours


title: scrambled siRNA, replicate 1

value: scrambled siRNA


title: HLC - OsmG - day 20 - 3

description:
HC3X_D20_OsmG_N3
iPSC-derived hepatocyte-like cells in hyperosmolar conditions at day 20
TPM_HUH7_HLC.csv

value: day 20


title: scrambled siRNA, replicate 3


title: humanizedNeutrophils_TET2_2A

city: London

first: Dominique

last: Bonnet

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Each sample was sequenced to achieve 30 million Pair-end 100 bp reads/sample.
For the analysis of percentage of fragmented DNA and differentially annotated peaks we use the nf-core pipeline within the nextflow bioinformatics workflow framework (version 19.10.0).
Assembly: FASTQ files were aligned to the GRCh38 human genome
Supplementary files format and content: bigWig, narrowPeak

source_name: Human Neutrophils

extract_protocol:
5x10^4 control and 5x10^4 TET2Mut neutrophils were sorted from the same humanized mouse engrafted with a mix of wild-type and TET2Mut hHSPCs. DNA was isolated using ZYMO DNA Clean kit (cat#D4014)
Library PCR amplification was done with 9 cycles and double-sided size selection was performed using KAPA Pure beads (Roche, 07983280001). Sequencing was then performed in a HiSeq4000 Sequencing System (Illumina) with a loading molarity of 200pM plus 10% Phix (illumine).

value: Human Neutrophils


title: humanizedNeutrophils_TET2_3A


title: humanizedNeutrophils_TET2_1A


title: humanizedNeutrophils_WT_2A

value: WT


title: humanizedNeutrophils_WT_4A


title: humanizedNeutrophils_WT_3A


title: BRD4 long-specific siRNA, replicate 3


title: Adult oligodendrocyte progenitor cell input biol rep 2 (P60)

city: New York

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

description: B-aOPC-Input

data_processing:
The adapter sequences were removed from the FASTQ files using Trim Galore
Trimmed reads were aligned to the Mus musculus reference genome GRCm38 using Bowtie2 (v.2.4.5) program
SAMTools was used to remove PCR duplicates and reads mapped to blacked list regions and alignments with low mapping quality (q < 20).
The deepTools bamCompare function (Ramírez et al., 2016) was used to normalize the ChIP samples to their respective input samples
MACS2 algorithm was used for peak calling
DiffBind was used for differential binding of H4K8ac in aOPCs compared to nOPCs.
Annotation of the H4K8ac peaks was performed with ChIPseeker in R package
Functional enrichment of annotation performed with GREAT tool
Assembly: GRCm38
Supplementary files format and content: bigWig, narrowPeak (except for input samples)

source_name: Forebrain

extract_protocol:
Neonatal and adult OPCs were sorted from PdgfrαH2BEGFP mice at P5 and P60 respectively. Chromatin was crosslinked with 1 % paraformaldehyde and quenched with 125 mM glycine during nuclei purification
Libraries were prepared using 2 ng of ChIP DNA and 10 ng of Input DNA (KAPA Hyper Prep Kit, KK8502)

value: postnatal day 60

value: Forebrain

value: Primary

value: aOPCs


title: Adult oligodendrocyte progenitor cell input biol rep 1 (P60)

description: A-aOPC-Input


title: humanizedNeutrophils_WT_1A


title: Neonatal oligodendrocyte progenitor cell input biol rep 1 (P5)

description: A-nOPC-Input

value: postnatal day 5

value: nOPCs


title: Adult oligodendrocyte progenitor cell biol rep 1 (P60)

value: Active Motif, 61103


title: humanizedNeutrophils_TET2_4A


title: Adult oligodendrocyte progenitor cell biol rep 3 (P60)


title: Neonatal oligodendrocyte progenitor cell input biol rep 2 (P5)

description: B-nOPC-Input


title: Adult oligodendrocyte progenitor cell input biol rep 3 (P60)

description: C-aOPC-Input


title: Neonatal oligodendrocyte progenitor cell biol rep 2 (P5)


title: Adult oligodendrocyte progenitor cell biol rep 2 (P60)


title: liver, Ctrl 8wk, rep2

city: Bethesda

first: Margaret

last: Cam

state: MD

address: 9000 Rockville Pike

institute: NCI

description: 10x Genomics scRNA-Seq 3′ v3.1

data_processing:
10x Genomics cellranger (version 6.0.0) pipeline was used to extract Fastqs for Ctrl, YAP/AKT-5wk, YAP/AKT-8wk samples
For Ctrl-5wk and Ctrl-8wk samples, Base calling was performed using RTA 3.4.4,
demultiplexing was performed using cellranger v6.1.2(Bcl2fastq 2.20.0), and alignment was performed using cellranger v6.1.2(STAR 2.7.2a)
Assembly: refdata-gex-mm10-2020-A

source_name: liver

extract_protocol:
mouse Tumor Dissociation Kit from Miltenyi Biotec (#130-093-237)
10x Genomics scRNA-Seq 3' v3.1: captures and sequencing

value: liver

value: tumor cells

value: harvested 8 weeks after Ctrl injection


title: Neonatal oligodendrocyte progenitor cell input biol rep 3 (P5)

description: C-nOPC-Input


title: liver, Ctrl, rep3

description: 10x Genomics scRNA-Seq 3′ v3.1

value: Control


title: liver, Ctrl, rep1

description: 10x Genomics scRNA-Seq 3′ v3.1


title: liver, Ctrl, rep2

description: 10x Genomics scRNA-Seq 3′ v3.1


title: liver, Ctrl 5wk, rep3

description: 10x Genomics scRNA-Seq 3′ v3.1

value: harvested 5 weeks after Ctrl injection


title: liver, Ctrl 5wk, rep2

description: 10x Genomics scRNA-Seq 3′ v3.1


title: scrambled siRNA, replicate 2

value: RD

value: ERMS

value: FN-RMS


title: Neonatal oligodendrocyte progenitor cell biol rep 3 (P5)


title: liver, Ctrl 8wk, rep3

description: 10x Genomics scRNA-Seq 3′ v3.1


title: Neonatal oligodendrocyte progenitor cell biol rep 1 (P5)


title: liver, Ctrl 8wk, rep1

description: 10x Genomics scRNA-Seq 3′ v3.1


title: liver, YAP/Akt 8wk, rep3

description: 10x Genomics scRNA-Seq 3′ v3.1

value: harvested 8 weeks after YAP/Akt injection


title: liver, YAP/Akt 5wk, rep3

description: 10x Genomics scRNA-Seq 3′ v3.1

value: harvested 5 weeks after YAP/Akt injection


title: liver, YAP/Akt 5wk, rep2

description: 10x Genomics scRNA-Seq 3′ v3.1


title: liver, YAP/Akt 5wk, rep1

description: 10x Genomics scRNA-Seq 3′ v3.1


title: liver, YAP/Akt 8wk, rep2

description: 10x Genomics scRNA-Seq 3′ v3.1


title: liver, Ctrl 5wk, rep1

description: 10x Genomics scRNA-Seq 3′ v3.1


title: epididymal white adipose tissue, Prmt5 knockout 3

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

data_processing:
raw reads from RNA-seq li-braries are filtered to remove reads containing adapters or reads of lowquality.
After filtering, statistics analysis of data production and qualitywas performed to confirm the sequencing quality.
TopHat2 was used for mapping the filtered readsto the reference genome.
HTSeq V0.6.1 was used to analyze the read numbers mapped for eachgene.
Assembly: mm10
Supplementary files format and content: xlsx files include RPKM values for each Sample

source_name: epididymal white adipose tissue

extract_protocol:
RNA was extracted using Trizol reagent, and precipitated for quantification and assessment of quality.
A complementary DNA library was constructed using mRNA enriched by anti-polyA beads, and sequencing was performed according to the Illumina HiSeq standard protocol.

value: epididymal white adipose tissue

value: Prmt5 knockout


title: epididymal white adipose tissue, Prmt5 knockout 2


title: epididymal white adipose tissue, wild type 3

value: wild type


title: epididymal white adipose tissue, wild type 2


title: epididymal white adipose tissue, Prmt5 knockout 1


title: epididymal white adipose tissue, wild type 1


title: Sample Chmr21TmPosGCPosYFPPos3

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description:
Chmr21TmPosGCPosYFPPos3
GC+, Tomato+, YFP+ from pooled infected chimeras replicate 3

data_processing:
Reads were trimmed for adapters and low-quality bases using the Cutadapt v1.18.
Reads were aligned to our hybrid genome (mm10_MHV68YFP_Krug.fa) using STAR v2.4.2a in 2-pass mode.
Gene and isoform expression was quantified using RSEM v1.3.3 with our custom GTFs (see below)..
Low count genes were filtered prior to CPM and quantile normalization using Limma voom followed by differential expression of genes analysis, three samples did not pass QC, were excluded from downstream analysis, and are not included in this accession.
To map both host and viral reads, the viral genome was added as an extra chromosome to the mm10 genome, and the viral GTFs appended to the M21 mouse gene annotation (see provided FA and GTF files).
Assembly: The host genome was mm10 using the M21 annotation, while our custom viral genome consisted of MHV68 with our YFP inserted into it. Two GTFs for the viral genome were created, one with full ORF annotaions (Krug_Ov) and one where overlapping sections were removed (Krug_NoOv). The data were analyzed with both GTFs for comparison.
Supplementary files format and content: The FASTA (.fa) file provided contains our hybrid genome consisting of the mm10 mouse genome concatenated to our viral genome represaented as its own chromosome, which is MHV68 with our YFP marker inserted into it.
Supplementary files format and content: The GTF (.gtf) files provided are for our Non-Overlapping (Krug_NoOv) gene annotation (where ORFs are trimmed to remove overlapping regions to make conservative expression estimates) and Overlapping (Krug_Ov) gene annotation, with full-length ORFs.
Supplementary files format and content: The TXT (.txt) files provided are RSEM CPM TMM counts for the expression of our samples aligned against our hybrid genomes (Krug_NoOv and Krug_Ov).

source_name: spleen

growth_protocol: Mixed bone marrow chimeras were allowed to reconstitute immune cells for 6 weeks prior to infection with rMHV68-H2bYFP. Spleens were harvested 16 dpi.

extract_protocol:
Total RNA was extracted using Trizol following manufacturer’s instructions (ThermoFisher Scientific, Waltham, MA, USA).
Prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).
Stranded, Poly A selection.

treatment_protocol: Primary splenic B cells were live sorted based on in vivo and cell surface staining into primary B cell media (RPMI 1640 + 10% FBS + Penn/Strep)

value: spleen

value: primary splenic B cell

value: WT

value: TmPosGCPosYFPPos


title: Sample Chmr21TmNegGCPosYFPPos5

description:
Chmr21TmNegGCPosYFPPos5
GC+, Tomato-, YFP+ from pooled infected chimeras replicate 5

value: STAT3 KO

value: TmNegGCPosYFPPos


title: Sample Chmr21TmPosGCPosYFPPos4

description:
Chmr21TmPosGCPosYFPPos4
GC+, Tomato+, YFP+ from pooled infected chimeras replicate 4


title: Sample Chmr21TmNegGCPosYFPPos6

description:
Chmr21TmNegGCPosYFPPos6
GC+, Tomato-, YFP+ from pooled infected chimeras replicate 6


title: Sample Chmr21TmPosGCPosYFPPos1

description:
Chmr21TmPosGCPosYFPPos1
GC+, Tomato+, YFP+ from pooled infected chimeras replicate 1


title: Sample Chmr21TmPosGCPosYFPPos2

description:
Chmr21TmPosGCPosYFPPos2
GC+, Tomato+, YFP+ from pooled infected chimeras replicate 2


title: Sample Chmr21TmPosGCPosYFPPos5

description:
Chmr21TmPosGCPosYFPPos5
GC+, Tomato+, YFP+ from pooled infected chimeras replicate 5


title: Sample Chmr21TmPosGCPosYFPNeg3

description:
Chmr21TmPosGCPosYFPNeg3
GC+, Tomato+, YFP- from pooled infected chimeras replicate 3

value: TmPosGCPosYFPNeg


title: Sample Chmr21TmPosGCPosYFPNeg2

description:
Chmr21TmPosGCPosYFPNeg2
GC+, Tomato+, YFP- from pooled infected chimeras replicate 2


title: Sample Chmr21TmNegGCPosYFPPos1

description:
Chmr21TmNegGCPosYFPPos1
GC+, Tomato-, YFP+ from pooled infected chimeras replicate 1


title: Sample Chmr21TmNegGCPosYFPPos3

description:
Chmr21TmNegGCPosYFPPos3
GC+, Tomato-, YFP+ from pooled infected chimeras replicate 3


title: liver, YAP/Akt 8wk, rep1

description: 10x Genomics scRNA-Seq 3′ v3.1

value: liver

value: tumor cells


title: Sample Chmr21TmNegGCPosYFPNeg3

description:
Chmr21TmNegGCPosYFPNeg3
GC+, Tomato-, YFP- from pooled infected chimeras replicate 3

value: TmNegGCPosYFPNeg


title: Sample Chmr21TmPosGCPosYFPNeg1

description:
Chmr21TmPosGCPosYFPNeg1
GC+, Tomato+, YFP- from pooled infected chimeras replicate 1


title: Sample Chmr21TmNegGCPosYFPNeg2

description:
Chmr21TmNegGCPosYFPNeg2
GC+, Tomato-, YFP- from pooled infected chimeras replicate 2


title: Sample Chmr21TmPosGCNegYFPNeg3

description:
Chmr21TmPosGCNegYFPNeg3
GC-, Tomato+, YFP- from pooled infected chimeras replicate 3

value: TmPosGCNegYFPNeg


title: Sample Chmr21TmPosGCNegYFPNeg1

description:
Chmr21TmPosGCNegYFPNeg1
GC-, Tomato+, YFP- from pooled infected chimeras replicate 1


title: Sample Chmr21TmNegGCNegYFPNeg3

description:
Chmr21TmNegGCNegYFPNeg3
GC-, Tomato-, YFP- from pooled infected chimeras replicate 3

value: TmNegGCNegYFPNeg


title: Sample Chmr21TmNegGCNegYFPNeg2

description:
Chmr21TmNegGCNegYFPNeg2
GC-, Tomato-, YFP- from pooled infected chimeras replicate 2


title: Sample Chmr21TmNegGCNegYFPNeg1

description:
Chmr21TmNegGCNegYFPNeg1
GC-, Tomato-, YFP- from pooled infected chimeras replicate 1


title: Sample CHRM02StatWTYFPneg

description:
GC sorted, Tomato-, YFP- from pooled infected chimeras replicate 2
CHRM02StatWTYFPneg

data_processing:
Reads were trimmed for adapters and low-quality bases using the Cutadapt v1.18.
Reads were aligned to our hybrid genome (mm10_MHV68YFP_Krug.fa) using STAR v2.4.2a in 2-pass mode.
Gene and isoform expression was quantified using RSEM v1.3.3 with our custom GTFs (see below)..
Low count genes were filtered prior to CPM and quantile normalization using Limma voom followed by differential expression of genes analysis.
To map both host and viral reads, the viral genome was added as an extra chromosome to the mm10 genome, and the viral GTFs appended to the M21 mouse gene annotation (see provided FA and GTF files).
Assembly: The host genome was mm10 using the M21 annotation, while our custom viral genome consisted of MHV68 with our YFP inserted into it. Two GTFs for the viral genome were created, one with full ORF annotaions (Krug_Ov) and one where overlapping sections were removed (Krug_NoOv). The data were analyzed with both GTFs for comparison.
Supplementary files format and content: The FASTA (.fa) file provided contains our hybrid genome consisting of the mm10 mouse genome concatenated to our viral genome represaented as its own chromosome, which is MHV68 with our YFP marker inserted into it.
Supplementary files format and content: The GTF (.gtf) files provided are for our Non-Overlapping (Krug_NoOv) gene annotation (where ORFs are trimmed to remove overlapping regions to make conservative expression estimates) and Overlapping (Krug_Ov) gene annotation, with full-length ORFs.
Supplementary files format and content: The TXT (.txt) files provided are RSEM CPM TMM counts for the expression of our samples aligned against our hybrid genomes (Krug_NoOv and Krug_Ov).

extract_protocol:
Total RNA was extracted using Trizol following manufacturer’s instructions (ThermoFisher Scientific, Waltham, MA, USA).
were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).
Unstranded, Poly A selection.

value: Uninfected


title: Sample CHRM01StatWTYFPpos

description:
GC sorted, Tomato-, YFP+ from pooled infected chimeras replicate 1
CHRM01StatWTYFPpos

value: Infected


title: Sample CHRM02StatWTYFPpos

description:
GC sorted, Tomato-, YFP+ from pooled infected chimeras replicate 2
CHRM02StatWTYFPpos


title: Sample CHRM03StatKOYFPpos

description:
GC sorted, Tomato+, YFP+ from pooled infected chimeras replicate 3
CHRM03StatKOYFPpos


title: Sample CHRM01StatWTYFPneg

description:
GC sorted, Tomato-, YFP- from pooled infected chimeras replicate 1
CHRM01StatWTYFPneg


title: Sample CHRM02StatKOYFPpos

description:
GC sorted, Tomato+, YFP+ from pooled infected chimeras replicate 2
CHRM02StatKOYFPpos


title: Sample Chmr21TmNegGCPosYFPPos4

description:
Chmr21TmNegGCPosYFPPos4
GC+, Tomato-, YFP+ from pooled infected chimeras replicate 4


title: Sample Chmr21TmNegGCPosYFPPos2

description:
Chmr21TmNegGCPosYFPPos2
GC+, Tomato-, YFP+ from pooled infected chimeras replicate 2


title: Sample CHRM03StatKOYFPneg

description:
GC sorted, Tomato+, YFP- from pooled infected chimeras replicate 3
CHRM03StatKOYFPneg


title: frontal cortex,postKD,p7,mouse

city: Los Angeles

first: Gregory

last: Lum

state: California

address: 610 Charles E Young Drive, East

department: Integrative Biology and Physiology

institute: UCLA

data_processing:
FastQC v0.11.5, bbduk v35.92, and RSeQC v2.6.4 were used for quality filtering, trimming, and mapping.
Reads were aligned to UCSC Genome Browser assembly ID: mm10 using STAR v2.5.2a, indexed using samtools v1.3, and aligned using HTSeq-count v0.6.0.
Differential expression analysis was covnducted using DESeq2 1.24.041.
Protein interaction networks were generated using STRING v10.5.
Assembly: mm10
Supplementary files format and content: each .csv file includes total feature count data per sample for each brain region sequenced

source_name: frontal cortex

extract_protocol:
RNA was extracted using the PureLink RNA Mini kit with Turbo DNAse treatment following each kit's protocol
RNA library was prepared using the TruSeq RNA Library Prep kit according to manufacturer's protocol

value: swiss webster

value: wild-type

value: frontal cortex

value: post-KD FMT


title: frontal cortex,postKD,p5,mouse


title: frontal cortex,postKD,p9,mouse


title: Sample CHRM01StatKOYFPneg

description:
GC sorted, Tomato+, YFP- from pooled infected chimeras replicate 1
CHRM01StatKOYFPneg

value: spleen

value: primary splenic B cell


title: frontal cortex,postKD,p8,mouse


title: frontal cortex,postKD,p6,mouse


title: Sample CHRM02StatKOYFPneg

description:
GC sorted, Tomato+, YFP- from pooled infected chimeras replicate 2
CHRM02StatKOYFPneg


title: frontal cortex,preKD,p10,mouse

value: pre-KD FMT


title: frontal cortex,postKD,p3,mouse


title: frontal cortex,postKD,p4,mouse


title: frontal cortex,postKD,p10,mouse


title: frontal cortex,preKD,p8,mouse


title: frontal cortex,preKD,p7,mouse


title: Sample CHRM03StatWTYFPpos

description:
GC sorted, Tomato-, YFP+ from pooled infected chimeras replicate 3
CHRM03StatWTYFPpos

value: WT


title: frontal cortex,postKD,p2,mouse


title: Sample CHRM03StatWTYFPneg

description:
GC sorted, Tomato-, YFP- from pooled infected chimeras replicate 3
CHRM03StatWTYFPneg


title: frontal cortex,preKD,p6,mouse


title: frontal cortex,preKD,p5,mouse


title: frontal cortex,preKD,p4,mouse


title: frontal cortex,preKD,p3,mouse


title: hippocampus,postKD,p10,mouse

source_name: hippocampus

value: hippocampus


title: hippocampus,postKD,p9,mouse


title: hippocampus,postKD,p8,mouse


title: Sample CHRM01StatKOYFPpos

description:
GC sorted, Tomato+, YFP+ from pooled infected chimeras replicate 1
CHRM01StatKOYFPpos

value: STAT3 KO


title: hippocampus,postKD,p7,mouse


title: frontal cortex,postKD,p1,mouse


title: hippocampus,postKD,p3,mouse


title: hippocampus,postKD,p5,mouse


title: frontal cortex,preKD,p9,mouse


title: hippocampus,postKD,p1,mouse


title: hippocampus,postKD,p2,mouse


title: hippocampus,postKD,p6,mouse


title: hippocampus,preKD,p8,mouse


title: hippocampus,postKD,p4,mouse


title: hippocampus,preKD,p6,mouse


title: hippocampus,preKD,p7,mouse


title: hippocampus,preKD,p5,mouse


title: hippocampus,preKD,p3,mouse


title: hippocampus,preKD,p1,mouse


title: hippocampus,preKD,p10,mouse


title: CON_ONE_QUAD

city: Fayetteville

first: Kevin

last: Murach

state: AR

address: 155 Stadium Dr.

department: Health, Human Performance, and Recreation

institute: University of Arkansas

data_processing:
Sequenced reads were mapped to mm10 mouse genome assembly using STAR 2.7.8a with default parameters.
Aligned reads were quantified for gene counts, filtered to exclude genes  with high noise or a maximum count of less than or equal to 50.
The filtered counts were median ratio normalized and tested for statistical significance using DESeq2.
All steps were performed using the Partek® Flow® Software.
Assembly: mm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Quad

extract_protocol:
Soleus muscles were flash frozen in liquid nitrogen and RNA was isolated using TRIzol and the Zymo MicroPrep Kit and prepared for RNA-sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adult mice (>2 months) were administered doxycycline to overexpress myc overnight and were harvested 12 hours after doxycycline was removed. Age-matched mice served as controls.

value: Skeletal Muscle

tag: conditions

value: Control


title: CON_TWO_QUAD


title: hippocampus,preKD,p4,mouse


title: frontal cortex,preKD,p2,mouse


title: MYC_FOUR_SOL

source_name: Soleus

value: Myc overexpression


title: hippocampus,preKD,p2,mouse


title: MYC_THREE_SOL


title: MYC_ONE_QUAD


title: MYC_ONE_SOL


title: MYC_TWO_QUAD


title: frontal cortex,preKD,p1,mouse


title: CON_THREE_SOL


title: CON_TWO_SOL


title: hippocampus,preKD,p9,mouse


title: MYC_TWO_SOL


title: CON_ONE_SOL


title: GOF E15.5 WT_4

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed with cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.91 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Assembly: GRCm38.91
Supplementary files format and content: Ensembl gene and transcript IDs, and RSEM-estimated raw counts for 53,465 annotated genes, in each sample.

source_name: Heart ventricles

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Total RNA (100 ng) was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification. The size of the libraries was checked using the Agilent 2100 Bioanalyzer and the concentration was determined using the Qubit® fluorometer (ThermoFisher)
Libraries were sequenced on a HiSeq4000 (Illumina) to generate 60 bases single reads.FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina)

value: Heart ventricles


title: GOF E15.5 R26_4


title: GOF E15.5 WT_1


title: GOF E15.5 WT_2


title: GOF E15.5 R26_2


title: GOF E15.5 R26_1


title: Heart_Wild-type_IP

city: Qingdao

first: Kun

last: Wang

state: Shandong

address: 308 Ningxia Road

institute: Qingdao University

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC MM10)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Genome_build: UCSC MM10
Supplementary_files_format_and_content: The fold enrichment within the peak in the IP sample compared with the input sample

source_name: Wild type mice heart

extract_protocol:
Total RNAs were extracted from ABRO1 Knockout or Wild type (WT) mice  hearts using Trizol reagent (Invitrogen). RNA were quantified using a NanoDrop ND-1000 instrument.
m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library  Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.

tag: strain background

value: heart

value: wild type

tag: antibody

value: anti-N6-methyadenosine (m6A) antibody


title: Heart_Wild-type_input

tag: genotype


title: ND-75 strong knockdown heads 4

first: Debbra

middle: Y.

last: Knorr

address: 125 Coldharbour Lane

institute: King's College London

description:
CTRLVSNDstrong_DEG.xls
NDstrongVSNDweak_DEG

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. Paired-end clean reads were mapped to the Drosophila_melanogaster ensemble 102 genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene, then RPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between conditions was performed using DESeq2 R package. P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. GO enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes.
Assembly: Drosophila_melanogaster ensemble 102 genome
Supplementary files format and content: Excel files include RPKM values for each sample

organism: Drosophila melanogaster

source_name: Adult head, 2 days old

extract_protocol:
20 snap frozen fly heads (10 male and 10 female, 2 days old) were used for each replicate and placed into 100 µL of lysis buffer + β-mercaptoethanol from the Absolutely RNA Microprep kit (Agilent Technologies). Each genotype was prepared in quadruplicate. RNA was extracted from using the Absolutely RNA Microprep kit according to the manufacturer’s protocol.
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: Adult head, 2 days old

value: nSybGal4/ND-75 strong RNAi


title: Heart_ABRO1_Knockout_IP

source_name: ABRO1 Knockout mice heart

value: ABRO1 Knockout


title: Heart_ABRO1_Knockout_input


title: ND-75 weak knockdown heads 4

description:
CTRLVSNDweak_DEG.xls
NDstrongVSNDweak_DEG

value: nSybGal4/ND-75 weak RNAi


title: ND-75 weak knockdown heads 3


title: ND-75 strong knockdown heads 3


title: ND-75 strong knockdown heads 1


title: Control heads replicate 1

description:
CTRLVSNDweak_DEG.xls
CTRLVSNDstrong_DEG.xls


title: Control heads replicate 3


title: Control heads replicate 2


title: ND-75 weak knockdown heads 1


title: ken3

city: Toulouse

first: Helene

last: Chanut

address: 118 route de Narbonne

department: CBI

country: France

institute: CNRS

data_processing:
NEBNext® Ultra™ II mRNA-Seq
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR (version 2.6.1d) aligner with default parameters
Read count extraction was done using STAR quantMode and normalization was performed using DESeq2 (v1.32.0)
Assembly: Dm6/dmel-all-r6.31
Supplementary files format and content: tab-delimited text files include raw and normalized count values for each sample and gene

source_name: ken mutant embryos

extract_protocol:
RNA was harvested from embryos with Trizol (Ambion). 100 ng of total RNA was used for the construction of polyA sequencing libraries. The quality of RNA was evaluated on Fragment Analyser.
mRNA libraries (polyA) for RNA-seq were prepared using NEBNext® Ultra™ II mRNA-Seq (strand specific) following manufacturer's protocols.

value: embryo

value: ken


title: Control heads replicate 4


title: ken2


title: pri3

source_name: pri mutant embryos

value: pri


title: ken1


title: pri2


title: pri1


title: GOF E15.5 R26_3


title: w3

source_name: control embryos

value: WT


title: w2


title: w1


title: GOF E15.5 WT_3


title: ND-75 strong knockdown heads 2


title: Third instar CNS, rWT3

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

institute: igred

description:
fpkm_wt_tet.txt
Sample 9
Brain_WT3

data_processing:
Illumina Hiseq2500 reads were trimmed using Trimmomatic and checked  with FASTQC
Illumina reads were aligned to the Drosophila reference genome (dm6 Ensembl release 70) with Hisat2
Read counts were generated for each annotated gene using HTSeq-Count. RPKM (Reads Per Kilobase of exon per Megabase of library size) values were calculated using Cufflinks. Reads normalization, variance estimation and pair-wise differential expression analysis with multiple testing correction were conducted using the R Bioconductor DESeq2 package
SMRT-seq reads were aligned using pbmm2 tool (https://github.com/PacificBiosciences/pbmm2) on Drosophila genome (dm6 Ensembl realease 70)
6mA detection was performed on every samples and on merged ones with IpdSummary tool from KineticTools (http://github.com/PacificBiosciences/kineticsTools) applying following parameters: --identify m6A --numWorkers 16 --pvalue 0.01 --identifyMinCov 5 –methylFraction
Assembly: Drosophila genome (dm6 Ensembl release 70)
Supplementary files format and content: text file with RNA-seq expression
Supplementary files format and content: Excel file with 6mA detected localization and scores

source_name: central nervous system

extract_protocol:
Third instar CNS were dissected in ice cold PBS. Samples 1-6: Tissues were crushed in lysis buffer (100 mM Tris-HCl pH9, 1 mM EDTA, 1% SDS), digested with RNAse A for 15 min at room temperature and 30 min at 65°C, before being incubated with 4 volumes of 3.2 M LiCl, 0.9 M KAc for 30 min at 4°C. After centrifugation at 12000 g for 20 min at 4°C, the supernatant was extracted  with phenol-chloroform-isoamyl alcohol and DNA was precipitated with isopropanol. Samples 7-11:RNAs were extracted with Qiagen RNeasy Plus Micro kit and samples were converted to cDNA using Nugen’s Ovation RNA-Seq System.
Samples 1-6: libraries were prepared using a SMRTbell Express 2 Template prep kit. Samples 7-11: library preparation was performed using Kapa Biosystems library preparation kit.
Samples 1-6: SMRT-seq. Samples 7-11: RNA-seq

value: central nervous system

tag: developmental stage

value: third instar larvae


title: Third instar CNS, rTET2

description:
fpkm_wt_tet.txt
Sample 11
Brain_RS2

tag: tissue

value: tet null


title: ND-75 weak knockdown heads 2


title: Third instar CNS, rWT1

description:
fpkm_wt_tet.txt
Sample 7
Brain_WT1


title: SW1353-shfirefly-1

city: Seoul

first: Hyeonkyeong

last: Kim

state: Seoul

address: Molecular regenerative medicine lab, 301ho, Building 502, Gwanak_1 Gwanak-ro, Gwanak-gu,

country: South Korea

institute: Seoul National University

data_processing:
The sequence reads were trimmed with Trimmomatic and mapped against the human reference genome (GRCh38) using the STAR aligner.
Read counts per gene were calculated using STAR quantMode GeneCount option.
For differential expression analysis, DESeq2 R package was used.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file inludes raw counts for each Sample, fold change and p value

growth_protocol: SW1353 cells were maintained at 37 °C in 3% O2 for 48 h after seeding.

extract_protocol:
Total RNA was isolated using TRI reagent (TR 118; Molecular Research Center, Inc.).
Library for RNA sequencing (RNA-seq) was generated by Macrogen with TruSeq Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: SW1353 cells were transduced with the firefly or EPAS1 shRNA.

value: chondrosarcoma

tag: treatment

value: lentiviral infection - shfirefly


title: SW1353-shfirefly-2

tag: cell line


title: SW1353-shSIRT1-3

tag: cell type

value: lentiviral infection - shSIRT1


title: SW1353-shSIRT1-1


title: SW1353-shSIRT1-2


title: HT-29 SGG replicate c

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.
Only sequences at least 25 nt in length were considered for further analysis.
STAR version 2.5.0a with default parameters was used for the alignment on the reference genome ().
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t exon -g gene_id -s 1).
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0.
Assembly: Human genome hg38 from Ensembl
Supplementary files format and content: Count data from featureCounts

source_name: colon

growth_protocol: The human normal colon epithelial cell lines, FHC (ATCC: CRL-183132) and CCD 841 CoN (ATCC CRL-1790) were cultured in DMEM/F12 medium (Gibco, France) supplemented with 10% heat-inactivated calf serum and additional factors (25 mM HEPES; 10 ng/mL cholera toxin; 0.005 mg/mL insulin; 0.005 mg/mL transferrin; 100 ng/mL hydrocortisone; EFG 20 ng/mL; 10% SVF) to sustain their growth and could be passed 5-10 times only. The human cancerous cell lines HT-29 (ATCC: HTB-38 33) were cultivated in DMEM with 10% heat-inactivated calf serum and supplemented with 25 mM HEPES. The cells were cultured in ventilated T75 flasks at 37 °C and 5 % CO2.

extract_protocol:
Total RNA was extracted from cell monolayers with the RNeasy Plus Mini kit (Qiagen, USA), according to the manufacturer's instructions.
Illumina TruSeq Stranded mRNA Sample preparation kit
Directional libraries were prepared using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer’s instructions (Illumina). Libraries were checked for quality on DNA 1000 chips (Bioanalyzer, Agilent)

treatment_protocol: Stationary phase bacteria were scratched from fresh THY plates (o.n. culture) and washed with sterile phosphate buffered saline, pH 7.4 (PBS). The bacteria are diluted in DMEM (Gibco, Ref. 12320032, low glucose, pyruvate, HEPES) to obtain the desired concentration of: (i) SGM of 6,5x10’5 CFU/ml and (ii) SGG UCN34 of 6,5x10’4 CFU/ml. Cells are washed once with DMEM and then infected with the medium containing the bacteria by adding 2 ml of bacterial suspension per well of 6-well plate. For NT conditions only 2 ml of fresh media was added.

value: colon

value: adenocarcinoma

value: SGG


title: HT-29 SGM replicate b

value: SGM


title: HT-29 SGM replicate c


title: HT-29 SGG replicate b


title: HT-29 SGG replicate a


title: HT-29 Non-treated (NT) replicate a

value: Non-treated (NT)


title: HT-29 SGM replicate a


title: Third instar CNS, rTET1

description:
fpkm_wt_tet.txt
Sample 10
Brain_RS1


title: HT-29 Non-treated (NT) replicate b


title: FHC SGG replicate c

value: FHC

value: normal


title: FHC SGM replicate c


title: FHC SGG replicate b


title: FHC SGM replicate a


title: FHC SGM replicate b


title: FHC SGG replicate a


title: FHC Non-treated (NT) replicate a


title: FHC Non-treated (NT) replicate b


title: SW1353-shfirefly-3


title: ribosome-OE1

city: Nanjing

first: Shukui

address: No.68, Changle Road, Nanjing

institute: Nanjing First Hospital

data_processing:
Use fastp to control the quality of raw reads, filter low quality data, and get clean reads.
Use the short reads comparison tool bowtie2 to compare clean reads to the ribosome database of the species, and retain unmapped reads. Carry out comparative analysis based on reference genome using HISAT2 software.
Calculate the distribution of reads in the reference genome according to the comparison results of all the reads (Total_Mapped reads) that can be located on the genome.
According to the comparison results of HISAT2, the transcripts were reconstructed using Stringtie, and the expression amount of all genes in each sample was calculated using RSEM
Assembly: hg18
Supplementary files format and content: tab-delimited text files include count values for each sample
Library strategy: Ribo-seq

source_name: 5-FU-resistant HCT8

extract_protocol:
The ribosome new peptide chain complex was treated with low concentration RNase to degrade the RNA fragments without ribosome coverage, and then the ribosome was removed
Then the enriched ribosome footprints were reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: 5-FU-resistant HCT8

value: CRC cell

value: OE

value: transfected with METTL14 overexpression plasmids


title: ribosome-NC2

value: NC

value: transfected with negative control plasmids


title: ribosome-OE2


title: Third instar CNS, rWT2

description:
fpkm_wt_tet.txt
Sample 8
Brain_WT2

value: central nervous system

value: third instar larvae


title: ribosome-NC1


title: HT-29 Non-treated (NT) replicate c


title: mRNA-NC1

data_processing:
Use fastp to control the quality of raw reads, filter low quality data, and get clean reads.
Use the short reads comparison tool bowtie2 to compare clean reads to the ribosome database of the species, and retain unmapped reads. Carry out comparative analysis based on reference genome using HISAT2 software.
Calculate the distribution of reads in the reference genome according to the comparison results of all the reads (Total_Mapped reads) that can be located on the genome.
According to the comparison results of HISAT2, the transcripts were reconstructed using Stringtie, and the expression amount of all genes in each sample was calculated using RSEM
Assembly: hg18
Supplementary files format and content: tab-delimited text files include count values for each sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).


title: mRNA-OE1


title: RCCD1_replication_3

city: Beijing

first: Yani

last: Peng

state: State...

address: Xueyuan load number 38

institute: Peking University

data_processing:
Raw sequencing data were preprocessed through fastp version 0.23.0 for adapter and low-quality reads removal
The clean reads were aligned to the GRCh38/hg38 reference genome by using Spliced Transcripts Alignment to a Reference (STAR) version2.7.10A
Sequencing was performed with biologically triplicate of each group of MCF-7 cells.
Read count extraction and normalization were performed using CLC genomic benchwork
Expression abundance estimation was performed through HTSeq version 1.99.2and differential expression gene identification were done using DESeq2 R package, with |log2FC| > 0.5 and p value < 0.05 deemed significant differential expression between the two groups.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: MCF-7 cells

growth_protocol: Mammary adenocarcinoma MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from MCF-7 cells using the TRIzol reagent (Invitrogen)
The sequencing libraries were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01/02)

treatment_protocol: The mammary adenocarcinoma MCF-7 cells were infected with lentivirus carrying FLAG-RCCD1 construction or control vector.

value: MCF-7 cells

value: mammary adenocarcinoma cells


title: mRNA-OE2


title: mRNA-NC2


title: RCCD1_replication_1


title: Vector_replication_3

value: WT+Vector


title: Vector_replication_2


title: 3-SM-vumc-omo_S3

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: VUMC-DIPG-10 cells containing doxycycline-inducible Omomyc expression vector left untreated for 72 hours

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
adaptor was trimmed from raw sequencing files, RRNA was removed from sequencing data using bowtie. Files were then aligned to hg38 using STAR2 and counts  per gene were generated using HTSeq.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw values for each Sample.

source_name: OMO

extract_protocol:
RNA was extracted from cell cultures after 72 hours of treatment with or without 0.5ug/ml Doxycycline. RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific) as well as TapeStation Analysis (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: untreated


title: 2-SM-vumc-GFP-dox_S2

description: VUMC-DIPG-10 cells containing doxycycline-inducible GFP control vector treated with 0.5ug/ml Doxycycline for 72 hours

source_name: GFP

value: +Dox


title: 15755X8 iPSC-CMsQX3

city: salt lake city

first: Sihem

last: Boudina

state: Utah

department: Nutrition and Integrative Physiology

institute: University of Utah

data_processing:
Human GRCh38 genome and gene feature files were downloaded from Ensembl release 94
Reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads
Reads were trimmed of adapters using cutadapt 1.16 and aligned to the reference database using STAR in two pass mode
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.20.0
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: iPSC-CMs

growth_protocol: iPSC-CMs

extract_protocol: Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold (human, mouse, rat, etc.)

treatment_protocol: untreated

value: iPSC-CMS

tag: status

value: Patient with PRDM16Q187X

tag: Sex

value: Male


title: 1-SM-vumc-GFP_S1

description: VUMC-DIPG-10 cells containing doxycycline-inducible GFP control vector left untreated for 72 hours


title: 15755X1 iPSC-CMsWT1

value: Control patient


title: FHC Non-treated (NT) replicate c

value: colon

value: FHC

value: normal

value: Non-treated (NT)


title: 15755X2 iPSC-CMsWT2


title: 4-SM-vumc-omo-dox_S4

description: VUMC-DIPG-10 cells containing doxycycline-inducible Omomyc expression vector treated with 0.5ug/ml Doxycycline for 72 hours


title: 15755X7 iPSC-CMsQX2


title: 15755X3 iPSC-CMsWT3


title: CEN.PK113-7D  grown in SMD- 1

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

institute: Delft University of Technology

data_processing:
RNA-seq reads were aligned to the CEN.PK113-7D reference using STAR version 2.5.4a
resulted sequence alignment map file (SAM) converted in sorted BAM file with samtools
The sorted BAM file was processed with featureCounts for quantification
raw counts TNN normalized with edgeR
For differential analysis  was exactTest applied from edgeR
Genome_build: CEN.PK113-7D ASM257140v2
Supplementary_files_format_and_content: Comma delimited file, TMM normalized transcript counts

source_name: steady state chemostat sample (D=0.1 h-1)

extract_protocol:
RNA was extracted with hot-phenol method as described by Schmitt et al. (1990)
cDNA libraries were prepared using the TruSeq stranded mRNA kit (illumina) and sequenced on NovaSeq (illumina) at Macrogen

tag: strain

value: reference strain

tag: cultivation medium

value: SMD

value: class B vitamins

tag: state


title: DAP_HSF24_Met_SE150_SE50

city: East Lasing

first: Erich

last: Grotewold

state: MI

address: 603 Wilson Rd.

department: Biochemistry and Molecular Biology

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.
Sample quality control was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, V0.11.5). Adapters and low quality reads were trimmed with Trimmomatic (Bolger et al., 2014) using the following parameters: ILLUMINACLIP:Adapter.fastq:2:40:15 SLIDINGWINDOW:4:20 MINLEN:30
ChIP- and DAP-seq: Cleaned reads were mapped to the reference genome (AGPv4) using bowtie2 v2.3.4.1.
RNA-seq: Cleaned reads were mapped to the reference genome (AGPv4) using HISAT2 (2.0.4)
RNA-seq: Reads aligned to genes were counted with the R package Rsubread v1.32.2
Assembly: AGPv4
Supplementary files format and content: txt with raw counts
Supplementary files format and content: bed
Library strategy: DAP-Seq

organism: Zea mays

source_name: Leave

growth_protocol: DAP-seq: Plant materials were grown in the growth chamber for two weeks at 22 C and under 16:8 hrs light/dark cycles. A pool of eight seedlings were used for collection of leaf tissues from B73xMo17 F1 hybrids. RNA-seq:  For silk and pericarp, three biological replicates of tissues obtained from silks at silking stage (exposed silks are about 2-5 cm long), pericarp at 14 days after pollination (DAP)  were collected from P1-rr and P1-ww, B73, A632 and A632 x Mo17 F1 hybrid in the MSU fields in the summer of 2019. ChIP-seq For protoplast experiment, seeds were soaked in water overnight before sawing in soil. Plants were growing in dark at 26C for 12 days. The 2nd leaves were collected for 12 seedlines and pooled as one replicates. Transforamtion were done using electroporation.

extract_protocol:
DAP-seq: All the DNA protein interaction process was done as published (Bartlett, 2017).  RNA-seq: RNA extraction was conducted using Trizol (Invitrogen) following the company’s recommended procedure. The RNA integrity and concentration were checked on 1.5 % agarose gel and Qubit RNA HS assay, respectively.
DAP-seq: All the DNA protein interaction process was done as published (Bartlett, 2017) except for the following: Approximate 200 ng of DAP-seq gDNA library was added as an input for incubation with each pIX-HALO-TF protein extract. To perform double-size selection of 200-300 bp fragments for each sample, 0.8 volume of Agencout AMPure XP beads (40ul) to 1 volume of sample (50ul) were mixed for 5 minutes and the bead were discarded to remove fragments with size larger than 300 bp. Next, the supernatant (90 ul) contain < 300bp fragments were added to 0.2 volume of Agencout AMPure XP beads (10 ul) and mixed for 15 minutes. Bound DNA was eluted by adding 18 ul UltraPure™ DNase/RNase-Free Distilled Water (Invitrogen). The DNA concentration of DAP-seq libraries was evaluated using Qubit HS dsDNA assay kit, and approximate 5-20 ng/μl final concentration were obtained. Fragment sizes were further examined by agarose gel electrophoresis after six cycles of PCR using 2ul of DAP-seq library in 20 ul total volume with library specific primer pairs. RNA-seq: Samples with sharp rRNA bands were used for RNA-seq library preparation using TruSeq RNA library pre kit v2 (Illumina) following the manufacturer instructions. The RNA libraries (in pools of 9 samples each using Illumina barcodes) were sent to the Genomic Core Facility at Michigan State University for 50 bp single-end sequencing on the Illumina Hiseq 4000. ChIP-seq: All ChIP-seq librares were made using NEBNext Ultra II DNA library Prep kit for Illumina (NEB#7645 S/L, $E7103 S/L). Hiseq4000 were used for all SE50 sequencing.

tag: cultivar

value: 2 week old seedling

value: Methylated


title: CEN.PK113-7D  grown in SMD- 3

value: steady state chemostat sample (D=0.1 h-1)


title: CEN.PK113-7D  grown in SMD- 2


title: DAP_F1_Halo_deM_SE150

value: deMethylated


title: BV2 murine microglial cells, Inoculum, Biol rep. 4

city: Geneva

first: Thierry

last: Soldati

address: 30 quai Ernest Ansermet, Sciences II

country: Switzerland

institute: University of Geneva

data_processing:
Quality control, alignment with Bowtie2, filtering out of non-transposon reads, PCR amplicon deduplication
Evaluation of TA sites & TA sites within annotated genes with TRANSIT HMM (default parameters); Hierarchical clustering of gene profiles (Manhattan distance, ward.D linkage)
Comparison of insertion frequency per gene to the reference condition using the TRANSIT resampling methods
Overrepresentation analysis with the GO and KEGG database with R
Assembly: NC_010612.1, NC_010604.1
Supplementary files format and content: FileS1.pdf, contains key parameters of all analyzed genes such as insertion sites, number, essentiality call, profile across experimental conditions
Supplementary files format and content: Table_S1_transposons_counts_per_Tasite.xlsb, contains information about insertion sites
Supplementary files format and content: Table_S2_Counts_per_gene.xlsx, contains information about insertion sites per gene
Supplementary files format and content: Table_S3_Conditional_essentiality.xlsx, contains information from the TRANSIT resampling method, comparisons of experimental conditions to the reference condition
Supplementary files format and content: Table_S4_Enrichment_analyses.xlsx, contains information about GO and KEGG enrichment analyses
Library strategy: Tn-Seq

organism: Mycobacterium marinum

source_name: Mycobacterium marinum M strain

extract_protocol:
M. marinum gDNA was extracted following an adapted protocol from Belisle et Sonnenberg (Belisle & Sonnenberg, 1998). Briefly, M. marinum mutant pools were centrifuged and resuspended in breaking buffer (50 mM Tris, 10 mM EDTA, 100 mM NaCl, pH8). Mechanical lysis was performed with the Fastprep homogenizer during 30 s, this step was repeated three times. The upper phase was chemically lysed with RNase (200 µg/mL) and Lysozyme (100 µg/mL) 1h at 37°C. Then, 0.1 volume of SDS 10% and 0.01 volume of Proteinase K (100 µg/mL) were added for 1 h at 55°C.  Extraction steps were realized with equal volume of phenol:chlorophorm:isopropanol 25:24:1 for 30 min followed by chlorophorm:isopropanol during 5 min.  Precipitation was performed with 3 M sodium acetate pH 5.2 and 1 volume of isopropanol 100 %, gDNA was pelleted and washed with ethanol 70%. The extracted gDNA was quantified using Qubit (Invitrogen) and its quality was checked with the TapeStation system (Agilent).
A 2 µg aliquot of gDNA in Tris Buffer (10 mM Tris, 0.1 mM EDTA, pH8) was sheared in a Covaris S2 machine following these parameters: Intensity 4, Duty cycle 10%, cycles 200 and time 65 s. After purification with AMPure XP purification kit (Agencourt), 1000 ng of sheared DNA fragment ends were repaired, blunt ended and a d-A Tail added following NEBNextEnd/d A-Tailing module protocol. Specific adapters 1 and 2 described in Table B were self-hybridized and then ligated to the ‘A’ tail ends by T4 ligase (Promega). After purification with AMPure XP purification kit (Agencourt), 40 ng of libraries were amplified by PCR using KAPA polymerase with the following parameters: 95°C 3 min; 98°C 20 s, 60°C 15 s, 72°C 15 s (repeated for 25 cycles); 72°C 1 min for elongation. Transposon junctions were amplified with the IS6 primer: 5’ CAAGCAGAAGACGGCATACGA 3’ and specific primers MarA to MarP described in Table B. PCR products were purified with AMPure XP purification kit and Sixteen-plexed samples were pooled in approximately equimolar amounts of 5 nM and run in a single and double index reads on a Hiseq 4000 (Illumina).

value: Mycobacterium marinum M strain

tag: biological replicate

tag: sample condition

value: Inoculum

tag: passaged in

value: BV2 murine microglial cells


title: DAP_GBP20_Met_SE150


title: BV2 murine microglial cells, 48hpi, Biol rep. 3


title: 15755X6 iPSC-CMsQX1

value: iPSC-CMS

value: Patient with PRDM16Q187X


title: BV2 murine microglial cells, 48hpi, Biol rep. 2


title: BV2 murine microglial cells, Inoculum, Biol rep. 3


title: BV2 murine microglial cells, Inoculum, Biol rep. 2


title: BV2 murine microglial cells, 48hpi, Biol rep. 1


title: BV2 murine microglial cells, Inoculum, Biol rep. 1


title: Dictyostelium discoideum, 96hpi, Biol rep. 6

value: Dictyostelium discoideum


title: Dictyostelium discoideum, 96hpi, Biol rep. 5


title: Vector_replication_1

value: MCF-7 cells

value: mammary adenocarcinoma cells

value: WT+Vector


title: Dictyostelium discoideum, 96hpi, Biol rep. 4


title: Dictyostelium discoideum, Inoculum_bis, Biol rep. 5


title: Dictyostelium discoideum, Inoculum_bis, Biol rep. 6


title: Dictyostelium discoideum, Inoculum_bis, Biol rep. 4


title: Dictyostelium discoideum, 96hpi, Biol rep. 3


title: Dictyostelium discoideum, 96hpi, Biol rep. 2


title: Dictyostelium discoideum, Inoculum_bis, Biol rep. 3


title: Dictyostelium discoideum, 96hpi, Biol rep. 1


title: Dictyostelium discoideum, Inoculum_bis, Biol rep. 1


title: Dictyostelium discoideum, Inoculum_bis, Biol rep. 2


title: RCCD1_replication_2


title: Dictyostelium discoideum, 48hpi, Biol rep. 7


title: Dictyostelium discoideum, Inoculum, Biol rep. 7


title: Dictyostelium discoideum, 24hpi, Biol rep. 5


title: Dictyostelium discoideum, 48hpi, Biol rep. 6


title: Dictyostelium discoideum, 24hpi, Biol rep. 4


title: Dictyostelium discoideum, 24hpi, Biol rep. 3


title: Dictyostelium discoideum, Inoculum, Biol rep. 6


title: Dictyostelium discoideum, 48hpi, Biol rep. 4


title: Dictyostelium discoideum, Inoculum, Biol rep. 5


title: Dictyostelium discoideum, 48hpi, Biol rep. 3


title: Dictyostelium discoideum, 48hpi, Biol rep. 2


title: Dictyostelium discoideum, 24hpi, Biol rep. 2


title: Dictyostelium discoideum, Inoculum, Biol rep. 3


title: Dictyostelium discoideum, 48hpi, Biol rep. 1


title: Dictyostelium discoideum, 24hpi, Biol rep. 1


title: Dictyostelium discoideum, 48hpi, Biol rep. 8


title: Dictyostelium discoideum, 24hpi, Biol rep. 6


title: B.thetaiotaomicron, inulin, R2

city: JOUY EN JOSAS

first: paul

last: Biscarrat

state: ile de france

address: 4 AVENUE JEAN JAURES-DOMAINE VILVERT

institute: INRAE

description:
BT_I_R2
counts_BT.csv
BT_inuline_vs_controle1_DESeq_results.csv

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 3.2 (adapter trimming)
FastQC v0.11.5 (quality control)
Assembly: B.xylanisolvens:NZ_JH724294,NZ_JH724295,NZ_JH724296,NZ_JH724297,NZ_JH724298,NZ_JH724299,NZ_JH724300,NZ_JH724301,NZ_JH724302,NZ_JH724303,NZ_JH724304,NZ_JH724305,NZ_JH724306/B;thetaiotaomicron:NC_004663.1/R.intestinalis:NZ_LR027880.1/S.variabile:NZ_GG704769,NZ_GG704770,NZ_GG704771,NZ_GG704772,NZ_GG704773,NZ_GG704774,NZ_GG704775,NZ_GG704776,NZ_GG704777,NZ_GG704778,NZ_GG704779
Supplementary files format and content: Table xxxx_DESeq_results.csv contains the raw, unfiltered results. There is one gene per row and in columns the metrics calculated by DEseq2 during the analysis: ID: gene name//baseMean: average of normalized counts for all samples/replicates involved in the comparison/log2FoldChange: log2 of the ratio of counts between the 2 conditions/lfcSE: standard error of this fold change/stat: the value of the statistical (Wald) test, used to calculate the pvalue. It is the ratio between log2FoldChange and lfcSE./pvalue: This value determines the significance of the statistical value or test. It indicates the probability that an observed fold change could be due to chance. The closer the p-value is to 0, the more significant the test, and the more real the differential in expression observed between the 2 conditions./- padj: adjusted (or corrected) pvalue, which takes into account multiple tests. As the statistical test is performed on each gene and each test is associated with a possible error, accumulating tests increases this error. We need to take this into account and make a correction for the number of tests performed. DEseq2 uses the Benjamini-Hochberg method./- then normalized counts for the samples involved in the comparison

organism: Bacteroides thetaiotaomicron

source_name: Bacteria

growth_protocol: Bacteria were cultured in Hungate tubes with a containing 90 % N2, 5 % CO2, 5 % H2 atmosphere. Cultures were performed in a minimum medium adapted from YCFA medium supplemented with 0.5 % or 0.1% carbohydrate. Cultures were stopped 12 h after inoculation.

extract_protocol:
RNA was harvested using RNeasy kit (Qiagen)
Directional RNA-Seq Libraries were constructed using the TruSeq Stranded Total RNA library prep kit, with bacteria Ribo-Zero reagents (Illumina), following the manufacturer’s instructions. After the Ribo-Zero step, the samples were checked on the Agilent Bioanalyzer for proper rRNA depletion. Final libraries quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.
Libraries were pooled in equimolar proportions and sequenced on a single read 75pb run, on an Illumina NextSeq500 instrument.

value: Bacteria

value: Inulin


title: B.thetaiotaomicron, inulin, R3

description:
BT_I_R3
counts_BT.csv
BT_inuline_vs_controle1_DESeq_results.csv


title: B.thetaiotaomicron, inulin, R1

description:
BT_I_R1
counts_BT.csv
BT_inuline_vs_controle1_DESeq_results.csv


title: B.thetaiotaomicron, corn fiber, R3

description:
BT_M_R3
counts_BT.csv
BT_fibre_mais_vs_controle1_DESeq_results.csv

value: Corn Fiber


title: B.thetaiotaomicron, glucose, R2

description:
BT_G_R2
counts_BT.csv

value: Glucose


title: B.thetaiotaomicron, corn fiber, R1

description:
BT_M_R1
counts_BT.csv
BT_fibre_mais_vs_controle1_DESeq_results.csv


title: B.thetaiotaomicron, glucose, R1

description:
BT_G_R1
counts_BT.csv


title: B.thetaiotaomicron, glucose, R3

description:
BT_G_R3
counts_BT.csv


title: Dictyostelium discoideum, 48hpi, Biol rep. 5