title: Ob, 10hrLepLepR1

city: Ann Arbor

first: Martin

middle: G

last: Myers Jr

state: MI

address: 1000 Wall St

institute: University of Michigan

data_processing:
fastq files filtering with fastq_quality_filter 0.0.14 for minimum phred score of 20
read alignment and gene counting with STAR 2.7.6a
Genome_build: Ensembl GRCm38.p6
Supplementary_files_format_and_content: counts of mapped reads

source_name: hypothalamus

growth_protocol: Animals were bred at the University of Michigan and maintained in a 12-h light/12-h dark cycle with ad libitum access to food and water except as noted in experimental protocols.

extract_protocol:
Hypothalami were dissected and mRNA was isolated from eGFP-tagged ribosomes, as well as from the eGFP-depleted supernatant. The GFP antibody is from The Rockefeller University Bi-Institutional Antibody & Bioresource Core Facility, catalog numbers 19C8 and 19F7.
RNA was assessed for quality using the TapeStation (Agilent, Santa Clara, CA). Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepped using the Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS-122-2001, RS-122-2002) (Illumina, San Diego, CA), and 0.1–3 μg of total RNA was converted to mRNA using a polyA purification. The mRNA was fragmented via chemical fragmentation and copied into first strand cDNA using reverse transcriptase and random primers. The 3′ ends of the cDNA were adenylated, and 6-nucleotide-barcoded adapters ligated. The products were purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa's library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems, Wilmington, MA). They were clustered on the cBot (Illumina) and sequenced 4 samples per lane on a 50 cycle single end run on a HiSeq 2000 (Illumina) using version 2 reagents according to manufacturer's protocols.

treatment_protocol: Mixed male and female 10–13 week old LepRbeGFP-L10a and LepRbeGFP-L10a;Lepob/ob mice had food removed at the onset of the light cycle. Animals were immediately treated with metreleptin (5 mg/kg, i.p) (a generous gift from MedImmune, Inc.) or vehicle (0.9% saline) for analysis 3 or 10 h posttreatment.

tag: fraction

value: Bead

value: ob/ob

value: hypothalamus


title: Ob, 10hrLepNon1

status: Public on Dec 03 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: Sup

tag: treatment

tag: genotype

tag: tissue


title: hESC_TCDD_ChIP-seq_INP_rep1

city: Tartu

first: Tõnis

last: Org

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

library_source: genomic

data_processing:
Basecalling was done using Illumina Casava software
Alignment of sequences in fastq files was done using Bowtie 2 version 2.2.3 with following parameters: -k 2 -N 1 --mm -x
Sam files were converted to bam files followed by sorting and indexing using Samtools version: 1.6
deepTools bamcoverage version 2.5.3 was used to create bigwig files using following parameters --normalizeTo1x --ignoreDuplicates --minMappingQuality 40 -bl
Peaks were called using callpeak command of MACS2 version 2.1.0 with the default parameters
Genome_build: hg19
Supplementary_files_format_and_content: read coverage in bigwig format
Supplementary_files_format_and_content: peaks in narrowPeak format

molecule: genomic DNA

organism: Homo sapiens

source_name: hESC H9

growth_protocol: hESCs were cultured on Matrigel-coated (BD Biosciences) 6-well plates (Corning) in mTESRTM1 medium (STEMCELL Technologies), which was changed daily. Cells were maintained at 37oC in 5% CO2 and passaged routinely after 3-4 days. Passaging was carried out manually by detaching the colony pieces and plating onto fresh Matrigel-coated plates. Number of passages were held between 30-55.

extract_protocol:
Prior ChIP cells were treated with DMSO or 100 nM TCDD at 37oC for 1.5 h.1% formaldehyde was used for cross-linking the cells at RT for 10 min. Cross-linking was stopped with glycin at RT for 5 min. Following steps until eluation were performed at 4oC. Cells were washed twice with cold PBS, ~10M cells per sample were harvested by scraping and centrifuged at 1000g for 5 min. For nuclei isolation, pellet was resuspended in 250 µl Nuclei Lysis Buffer 1 (50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 0.5% NP-40, 0.25% Triton X-100, 10 mM KCl) and incubated for 10 min with gentle agitation. Following centrifugation at 1350g for 5 min, pellet was resuspended in 250 µl Nuclei Lysis Buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated for 10 min with gentle agitation. Nuclei were centrifuged at 1350g for 5 min and pellet resuspended in 100 µl SDS Lysis buffer (1% SDS, 20 mM EDTA, 50 mM Tris-HCl pH 8.0, Protease inhibitor cocktail). Lysis was performed on ice for 10 min and chromatin was sheared to appropriate length fragments using BioRuptor Plus sonicator (Diagenode) (10 cycles of 30 sec ON/OFF). Lysates were then diluted with 10X ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, Protease inhibitor cocktail) to total volume 1ml and centrifuged at 10000g for 10 min. Supernatant was collected, 1% was frozen for Input control and 500 µl sample was incubated overnight with 8 ug anti-AHR antibody (SA-210). Lysates were incubated for 2 h with Protein G Dynabeads (Thermo Scientific). Beads were washed for 5 min with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), LiCl buffer (0,25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0) and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Tube switch was performed in between last two washes to enhance specificity [71]. Chromatin-antibody complexes were eluted from Dynabeads twice with 250 µl of elution buffer (50 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% SDS) at 65oC for 15 minutes on a rotator and eluates were combined. NaCl at final concentration of 300 mM was added and tubes were incubated overnight at 65oC. Proteins were digested using 40 µg/ml Proteinase K (Thermo Scientific) at 50oC for 2 h and RNA digested using 20 µg/ml RNase A (Thermo Scientific) at 37oC for 30 min. DNA was purified using FavorPrep™ PCR Clean-UP Kit (Favorgen).
Immunoprecipitated and input DNA was used for library preparation with Ovation Ultralow Library System Kit V2 (NuGen) according to manufacturer’s instructions.

treatment_protocol: hESC H9 cells pre-treated with DMSO (control) or 10 nM TCDD in mTESRTM1 medium for 3 days prior differentiation into endoderm (5 day protocol) or neural progenitors (7 day protocol) using STEMdiff™ Definite Endoderm Kit Medium or STEMdiff™ Neural Induction Medium  (both STEMCELL Technologies)

tag: cell type

value: human embryonic stem cells

tag: cell line

tag: chip antibody

value: TCDD


title: hESC_TCDD_ChIP-seq_AHR_rep1

value: anti-AHR antibody (SA-210)


title: hESC_TCDD_ChIP-seq_AHR_rep2


title: NIM_TCDD_ChIP-seq_INP_rep1

source_name: neural progenitors

value: hESC H9 derived neural progenitors


title: Ob, PbsNon2


title: hESC_DMSO_ChIP-seq_INP_rep2

value: DMSO


title: hESC_DMSO_ChIP-seq_INP_rep1


title: Ob, PbsNon1


title: NIM_DMSO_ChIP-seq_AHR_rep1


title: Ob, PbsLepR1


title: Ob, PbsLepR2


title: hESC_DMSO_ChIP-seq_AHR_rep1


title: WT, 10hrPBSNon1

value: WT


title: EIM_TCDD_ChIP-seq_INP_rep2

source_name: endoderm

value: hESC H9 derived endoderm


title: WT, 10hrPBSLepR1


title: NIM_TCDD_ChIP-seq_INP_rep2


title: NIM_TCDD_ChIP-seq_AHR_rep2


title: hESC_TCDD_ChIP-seq_INP_rep2


title: NIM_DMSO_ChIP-seq_INP_rep2


title: NIM_DMSO_ChIP-seq_INP_rep1


title: WT, 10hrLepNon3


title: EIM_TCDD_ChIP-seq_INP_rep1


title: EIM_TCDD_ChIP-seq_AHR_rep2


title: WT, 10hrLepLepR3


title: WT, 10hrLepNon2


title: WT, 10hrLepLepR2


title: EIM_TCDD_ChIP-seq_AHR_rep1


title: EIM_DMSO_ChIP-seq_INP_rep1


title: hESC_DMSO_ChIP-seq_AHR_rep2


title: EIM_DMSO_ChIP-seq_AHR_rep2


title: WT, 10hrLepLepR1


title: WT, f4LepCon


title: EIM_DMSO_ChIP-seq_AHR_rep1


title: WT, f3PBScon


title: WT, f4LepGFP


title: WT, f3PBSGFP


title: hESC_TCDD_ATAC-seq_rep1

data_processing:
Basecalling was done using Illumina Casava software
Alignment of sequences in fastq files was done using Bowtie 2 version 2.2.3 with following parameters: -k 2 -N 1 --mm -x
Sam files were converted to bam files followed by sorting and indexing using Samtools version: 1.6
deepTools bamcoverage version 2.5.3 was used to create bigwig files using following parameters --normalizeTo1x --ignoreDuplicates --minMappingQuality 40 -bl
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Samples were processsed according to the orginal ATAC-seq protocol (Buenrostro et al., Nature Protocols 2013)
Libraries were constructed according to the orginal ATAC-seq protocol (Buenrostro et al., Nature Protocols 2013) and paired-end 75bp sequencing was performed on the Illumina NextSeq 500 MID platform following the manufacturer's protocols.

treatment_protocol: hESC H9 cells were treated with DMSO (control) or 10 nM TCDD in mTESRTM1 medium for 3 days in three biological replicates


title: hESC_DMSO_ATAC-seq_rep3


title: hESC_DMSO_ATAC-seq_rep2


title: hESC_TCDD_ATAC-seq_rep3


title: WT, f2LepGFP


title: WT, f2LepCon


title: hESC_TCDD_ATAC-seq_rep2


title: hESC_DMSO_ATAC-seq_rep1


title: WT, f1PBSCon


title: EIM_DMSO_ChIP-seq_INP_rep2


title: WT, m3PBScon


title: WT, m3PBSGFP


title: WT, 10hrLepNon1


title: Senescent HUVECs + Metformin replicate 1

city: Ancona

first: Jacopo

last: Sabbatinelli

state: AN

address: Via Tronto 10/A

department: Department of Clinical and Molecular Sciences

country: Italy

institute: Università Politecnica delle Marche

data_processing:
Raw base-call data generated by the Illumina NextSeq 500 system were demultiplexed using Illumina BaseSpace Sequence Hub (https://basespace.illumina.com/home/index) and converted to FASTQ format.
After a quality check with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), sequence reads were quality trimmed using the cutadapt tool.
Sequence reads were aligned to the miRbase version 21.0 database using the STAR algorithm.
For isomiR analysis, the genomic location of each reference mature miRNA was extracted and flanked it by six nucleotides on each side. Only reads that were wholly contained within this wider window were treated as belonging to a miRNA precursor arm.
The isomiR nomenclature used is based upon the one used previously in Loher et al. (doi: 10.18632/oncotarget.2405)
Raw counts from mapped reads were obtained using the htseq-count script from the HTSeq tools (http://www-huber.embl.de/HTSeq/doc/overview.html).
Raw counts were further normalized using DESeq2 bioconductor package (http://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: hg38
Comma-separated value files including miRNA raw counts (HUVEC_metformin_raw.csv) and DESeq2-normalized counts (HUVEC_metformin_normalized.csv), and isomiR raw counts (HUVEC_metformin_isomiR_raw.csv) and DESeq2-normalized counts (HUVEC_metformin_isomiR_normalized.csv) for each sample.

source_name: Senescent HUVECs treated with metformin (SEN+M)

growth_protocol: Cryopreserved human umbilical vein endothelial cells (HUVECs) obtained from pool of donors were purchased from Clonetics (Lonza, Switzerland) and cultured in EGM-2 (CC-3162, Lonza) at 37 °C in a humidified atmosphere containing 5% CO2. Cells were seeded at a density of 5000/cm2 and sub-cultured when they reached 70–80% confluence. All cells tested negative for mycoplasma infection. Before replating, harvested cells were counted using a hemocytometer. Population doublings (PDs) were calculated by the formula: (log10F – log10I)/log102, where F is the number of cells at the end of the passage and I is the number of seeded cells. Cumulative population doubling (cPD) was calculated as the sum of PD changes. Cells were cultured until the arrest of replication and classified based on SA β-galactosidase (β-gal) activity into young (SA β-gal < 5%) and senescent (SEN, SA β-gal > 80%) cells using Senescence Detection Kit (cat. no. K320, BioVision Inc., USA).

extract_protocol:
Total RNA, including small (< 200 nucleotides) RNAs, was extracted from HUVEC pellets using Norgen’s total RNA Purification Kit (cat. no. 37500, Norgen Biotek Corporation, Canada) according to the manufacturer’s protocol. Purified RNA was stored at −80°C until analysis.
Small RNA sequencing was performed in triplicate on Young and SEN cells, and SEN cells treated with metformin. TruSeq Small RNA Library PrepKit v2 (Illumina; RS-200-0012/24/36/48) was used for library preparation according to the manufacturer’s indications. Briefly, 35 ng purified RNA was linked to RNA 3’ and 5’ adapters, converted to cDNA, and amplified using Illumina primers containing unique indexes for each sample. Each library was quantified using Agilent Bioanalyzer and High Sensitivity DNA Kit (cat. no. 5067-4626, Agilent Technologies, USA) and equal amounts of libraries were pooled together. Size selection allowed keeping 130-160 bp fragments. After ethanol precipitation, the library pool was quantified with Agilent High Sensitivity DNA Kit, diluted to 1.8 pM, and sequenced using NextSeq® 500/550 High Output Kit v2 (75 cycles) (Illumina; FC-404-2005) on the Illumina NextSeq500 platform.

treatment_protocol: When the proportion of SA-β-gal positivity exceeded 10% in replicating cells, 0.2 μM metformin was added at each medium replacement (cat. D150959, Sigma Aldrich, Italy) and cells were cultured until complete growth arrest (SA-β-gal positive cells >80%).

value: Human umbilical vein endothelial cells (HUVECs)

tag: age

value: Beta-Galactosidase activity > 10%

value: Metformin 0.2 μM


title: Senescent HUVECs + Metformin replicate 2


title: Senescent HUVECs + Metformin replicate 3


title: WT, m24LepCon


title: Senescent HUVECs replicate 2

source_name: Senescent HUVECs (SEN)

value: Control


title: WT, m1PBScon


title: WT, m1PBSGFP


title: Senescent HUVECs replicate 3


title: NIH511.3_1

city: Stanford

first: Theo

middle: D

last: Palmer

state: CA

address: 256 Campus Dr., G1141

department: Department of Neurosurgery

institute: Stanford University

data_processing:
To produce kallisto-aligned files, the .fastq files produced by RNA-seq were aligned using kallisto (v0.43.1) to a unique index composed of a  human reference transcriptome (Ensembl GRCh38.93) and plasmid sequences. The mean number of reads  processed per sample was 102,963,875 (range: 65,427,345 – 193,569,749), and these pseudoaligned to a  reference mRNA at a mean rate of 76.34%. By adding plasmid sequences as additional ‘chromosomes’, we were  able to investigate whether sequencing reads aligned to non-genomic as well as genomic DNA.
Estimated counts produced by kallisto for each were imported into RStudio for analysis with R using the tximport function (v.1.8.0) and imported into a DESeq2 object for further analysis.
Genes with one or fewer detected reads across samples were filtered out to expedite computation.
Due to the polycistronic nature of the transcripts produced by plasmids, the same expression value for a given plasmid was considered associated with each of its component reprogramming factor genes.
To produce the STAR-aligned files, a subset of the .fastq files from the previous analysis corresponding to Int- clones were re-aligned using STAR (v2.5.3a, RRID:SCR_015899).
The aligned reads were counted using htseq-count. The mean number of uniquely mapped reads for each sample when imported into R was 83,387,539 reads per sample (range: 54,003,338 - 164,989,807 ). Given that this was a paired-end sequencing experiment, the effective read depth was a mean of 41,693,770 reads per sample.
These raw data were batch corrected using SVA (v3.28.0), and analyzed using DESeq2 for differential expression analysis.DESeq2 uses the given data to model each gene as a negative binomial generalized linear model, and tests for differential expression using the Wald Test and Benjamini-Hochberg adjusted p-values.
For visualization of batch effect corrected data, data were transformed using LIMMA (v3.36.5). Shrunken log2-fold changes are used according to the recommendation in DESeq2 to account for fold change inflation in low expression genes.
Replicates of the same sample from different sequencing batches were collapsed with collapseReplicates() in the DESeq2 package once it was established that these samples clustered together. Clones derived from the same patient were treated as biological replicates due to apparent expression heterogeneity, and patient-of-origin accounted for in part by the surrogate variables produced by SVA.
For ease of interpretation, all sample names have been replaced with the IDs in the metadata column "Roth and Muench et al., hiPSC Clone ID".
Genome_build: For kallisto-aligned files, Ensembl Human Reference Transcriptome (Ensembl GRCh38.93); for STAR-aligned files, Human genome assembly GRCh37 (hg19) from Genome Reference Consortium
Supplementary_files_format_and_content: Comma separated text files (.csv) including normalized, batch corrected expression values for each sample included in analysis and for all genes that passed filtering

molecule: polyA RNA

source_name: iPSC-derived patient neuroepithelium (Day 22 of differentiation)

growth_protocol: The majority of hiPSC available through SFARI were reprogrammed from skin fibroblasts using episomal vectors encoding SOX2, OCT3/4, KLF4, LIN28, L-MYC, and P53-shRNA (75) . These vectors are pCXLE-hOCT3/4-shp53-F (Addgene Plasmid 27077), pCXLE-hSK (Addgene Plasmid 27078), and pCXLE-hUL (Addgene Plasmid 27080). 6 µg of total plasmid DNA (2 µg for each of the three episomal vectors) were electroporated into 5x10^5 fibroblasts with the Amaxa® Human Dermal Fibroblast Nucleofector® Kit (Lonza, VDP-1001). As previously reported, hiPSCs were differentiated in N3 culture medium which consists of DMEM/F12 (1x, Thermo Fisher Scientific, 11320033), Neurobasal (1x, Thermo Fisher Scientific, 21103049), N-2 Supplement (1%, Thermo Fisher Scientific, 17502048), B-27 Supplement (2%, Thermo Fisher Scientific, 17504044), GlutaMax (1%, Thermo Fisher Scientific, 35050061), MEM NEAA (1%, Thermo Fisher Scientific, 11140050), and human recombinant insulin (2.5 µg/mL, Thermo Fisher Scientific, 12585014). From Day 1 to 11, the N3 media was further supplemented with two factors: SB-431542 (5 µM, Tocris, 1614) and LDN-193189 (100 nM, Stemgent, 04007402). At Day 12, the differentiating cells were dissociated with Cell Dissociation Solution (1x, Sigma-Aldrich, C5914), passaged onto Poly-D-Lysine (50 µg/mL, Sigma, P1024) and Laminin (5 µg/mL, Roche, 11243217001) coated plates, and cultured in N3 media without factors until Day 22 when they were passaged again. Between Day 1 and Day 22, media changes were performed daily. However, after Day 22, cells were exposed to media changes every other day with N3 media without factors. Clones were grown in batches ("GrowBatch").

extract_protocol:
Day 22 cortical NPCs were lysed using TRIzol (Thermo Fisher Scientific, 15596026) and stored in -80oC. The samples were then delivered to the Stanford Functional Genomics Facility (SFGF) where they were multiplexed and sequenced using paired end mRNA sequencing on an Illumina NextSeq 500. Raw data were demultiplexed at the sequencing facility.
Libraries were collected using the Kapa mRNA Cat # KK8420 with oligo-dt. Samples were assigned an ID for sequencing ("VialID").

treatment_protocol: No additional treatment was applied to the iPSCs. The analysis focused on their suspected integration status and patient CNV status.

value: iPSC-derived patient neuroepithelium

tag: differentiation day

tag: sequencing batch

tag: alternative id "line"

tag: alternative id "deseqanalysisid"

tag: patient "subjectid"

tag: sequencing batch ("seqbatch")

tag: differentiation batch ("growbatch")

tag: sequencing vial id "vialid"

tag: sequencing lane "lane"

tag: Sex

value: M

tag: integration detected

value: NEG


title: NIH511.3_2

tag: genotype


title: NIH511.1

tag: tissue


title: NIH2788.4

value: F


title: Ctgf floxed control Rep2

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling
Sequenced reads were mapped to mm10 whole genome using STAR_2.6.0a
Unique reads quantified using htseq-count (version 0.6.1), with database generated from Mus_musculus.GRCm38.88, with strand was set to "reverse"
Genome_build: mm10
Supplementary_files_format_and_content: Read counts (calculated using htseq-count).

source_name: Ctgf floxed control

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA  sequencing libraries were constructed with KAPA mRNA HyperPrep Kits (KAPA  Biosystems; Cat # KK8580) followed by manufacturer's protocol

treatment_protocol: Wild type or mutant mice (8-10 week old) were subjected to moderate ethanol feeding using the Lieber-DeCarli liquid diet containing 1% ethanol for 2 days followed by 2% ethanol for 10 days. A single dose of CCl4 (1 μl/g body weight) was administered via intraperitoneal (IP) injection into the ethanol-fed mice at two days before sacrifice.

tag: strain background

value: adult; 8-10 weeks

tag: genotype/variation

value: Ctgf floxed homozygote

value: liver


title: NIH2788.3


title: Ctgf conditional knockout Rep2

source_name: Ctgf conditional knockout

value: Ctgf conditional knockout


title: YapKO (iCre virus infected) ) Rep2

source_name: YapKO (iCre virus infected) )

value: Yap1 hepatocyte specific knockout


title: Ctgf floxed control Rep1


title: DUP_3_3

value: 16p11.2 duplication

value: POS


title: DUP_3_2


title: YapKO (iCre virus infected) Rep1

source_name: YapKO (iCre virus infected)


title: DUP_3_1


title: Control for #9 YapKO (GFP virus infected) Rep1

source_name: Control for YapKO (GFP virus infected)

value: Yap1 floxed homozygote


title: DUP_2_3


title: DUP_2_2


title: WT, m24LepGFP

tag: fraction

value: Bead

tag: treatment

value: WT

value: hypothalamus


title: Senescent HUVECs replicate 1

tag: cell type

value: Human umbilical vein endothelial cells (HUVECs)

tag: age

value: Beta-Galactosidase activity > 10%


title: DUP_2_1

value: iPSC-derived patient neuroepithelium

tag: differentiation day

tag: sequencing batch

tag: alternative id "line"


title: DUP_1_9

tag: alternative id "deseqanalysisid"

tag: patient "subjectid"

tag: sequencing batch ("seqbatch")

value: M


title: evere saline-alkali soil stress treatment (5‰ salt content, pH 8.1) rep2

city: Wuhan

first: Ma

last: Siqi

address: No.1,Shizishan Street

country: China

institute: Huazhong Agricultural Uinveristy

data_processing:
Total RNA was extracted from wild type Sorghum bicolor BTx623 at the four-leaf-stage under normal conditions, moderate saline-alkali soil stress treatment (3‰ salt content, pH 8.1), severe saline-alkali soil stress treatment (5‰ salt content, pH 8.1), with three biological replicates. The RNA samples were sequenced and analyzed by Novogene Bioinformatics Technology (China) with Hiseq-PE150 (Illumina). Raw sequencing reads were filtered by FASTP and mapped to the sorghum genome (v 3.1.1) using HISAT2 (version 2.0.5) with default parameters. Differentially expressed genes, which were defined with an expression change fold ≥ 2 with P < 0.05, were analyzed using DESeq2 (version 1.20.0).
Supplementary_files_format_and_content: count, fpkm

organism: Sorghum bicolor

source_name: sorghum bicolor BTx623

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

value: leaf

tag: protocol

value: evere saline-alkali soil stress treatment (5percent salt content, pH 8.1) rep2


title: evere saline-alkali soil stress treatment (5‰ salt content, pH 8.1) rep1

treatment_protocol: wild type Sorghum bicolor BTx623 at the four-leaf-stage under normal conditions, moderate saline-alkali soil stress treatment (3‰ salt content, pH 8.1), severe saline-alkali soil stress treatment (5‰ salt content, pH 8.1),

value: evere saline-alkali soil stress treatment (5percent salt content, pH 8.1) rep1


title: evere saline-alkali soil stress treatment (5‰ salt content, pH 8.1) rep3

value: evere saline-alkali soil stress treatment (5percent salt content, pH 8.1) rep3


title: moderate saline-alkali soil stress treatment (3‰ salt content, pH 8.1) rep3

value: moderate saline-alkali soil stress treatment (3percent salt content, pH 8.1) rep3


title: DUP_1_8

tag: differentiation batch ("growbatch")

tag: sequencing vial id "vialid"

tag: sequencing lane "lane"

tag: Sex

value: NEG


title: Ctgf conditional knockout Rep1

tag: strain background

value: adult; 8-10 weeks

value: Ctgf conditional knockout

tag: tissue

value: liver


title: moderate saline-alkali soil stress treatment (3‰ salt content, pH 8.1) rep1

value: moderate saline-alkali soil stress treatment (3percent salt content, pH 8.1) rep1


title: DEL_9_987

tag: genotype

value: 16p11.2 deletion

tag: integration detected


title: DUP_1_7

value: 16p11.2 duplication

value: POS


title: WT rep3

value: normal


title: DEL_9_984


title: WT rep2


title: control for #12 YapKO (GFP virus infected) Rep2

source_name: control for YapKO (GFP virus infected)

tag: genotype/variation

value: Yap1 floxed homozygote


title: DEL_8_4

value: iPSC-derived patient neuroepithelium


title: DEL_9_986

value: M


title: 3985_D: Mouse 3 WI pool

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

data_processing:
Per-gene expression levels were determined by applying Salmon v0.8.2 to unaligned read sequences using transcript sequences from Gencode Mouse Release M12
Genome_build: GRCm38
Supplementary_files_format_and_content: Salmon gene quantification output as tab-separated text file. Columns: gene_id,  gene_length,  EffectiveLength, TPM,  NumReads

source_name: colorectal epithelium

growth_protocol: WI organoids derived from pks+ E.coli infected cells were grown in medium lacking Wnt and CHIR99021, uninfected control organoids were grown in complete medium including Wnt Nad CHIR99021. See accompanying publication for details.

extract_protocol:
Mechanically disrupt organoids and Matrigel with cold 1X PBS and transfer into a 15ml falcon  tube containing 10ml cold 1X PBS. Centrifuge at 300g for 5 minutes at 4°C. Remove supernatant  and add 1ml of Trizol to the pellet and transfer to a 1.5ml tube and keep overnight or longer at -80°C. Defreeze the samples at RT and add 200µl of chloroform. Mix the tubes for 15 seconds (do no vortex) and incubate at RT for 5 min. Centrifuge at 13000g for 15 minutes at 4°C. Transfer the top aqueous phase to a new 1.5ml tube (do not transfer anything from the interphase). Add 500µl of isopropanol, 120µl of 5M ammonium acetate, and 10µl of glycogen (5mg/ml). Vortex briefly and store for a minimum of 15 minutes at -20°C. Centrifuge at 13000g for 15 minutes at 4°C and discard the supernatant. Wash the pellet with 1ml 75% cold ethanol and vortex until you see the pellet floating. Centrifuge again at 13000g for 10 minutes at 4°C. Carefully discard the supernatant and air dry the pellet. Dissolve the pellet in 50µl of nuclease free H2O. Measure the concentration at the NanoDrop and store at -80°C.
cDNA was generated from polyA enriched RNA.

treatment_protocol: Prior to selection of WI organoids, primary mouse colon epithelial cells were infected with pks+ E.coli at MOI 5

value: colorectal epithelium

tag: condition

value: Wnt-independent pool

tag: mouse


title: DEL_8_2

tag: differentiation day

tag: sequencing batch


title: 3985_C: Mouse 3 NI pool

value: Uninfected control pool


title: DEL_7_3

tag: alternative id "line"

tag: alternative id "deseqanalysisid"


title: 3985_B: Mouse 2 WI pool


title: DEL_7_2

tag: patient "subjectid"

tag: sequencing batch ("seqbatch")


title: 3985_A: Mouse 2 NI pool


title: 2534_F: Mouse 1 NI clone 2

value: Uninfected control clone


title: moderate saline-alkali soil stress treatment (3‰ salt content, pH 8.1) rep2

value: leaf

tag: protocol

value: moderate saline-alkali soil stress treatment (3percent salt content, pH 8.1) rep2


title: DEL_7_1

tag: differentiation batch ("growbatch")

tag: sequencing vial id "vialid"

value: NEG


title: 2534_E: Mouse 1 NI clone 1


title: 2534_D: Mouse 1 WI pool


title: DEL_5_983

tag: sequencing lane "lane"

tag: Sex

value: F


title: DEL_6_7

tag: tissue


title: 2534_C: Mouse 1 WI clone 3

value: Wnt-independent clone


title: 2534_B: Mouse 1 WI clone 2


title: 2534_A: Mouse 1 WI clone 1


title: DEL_5_979

tag: genotype


title: WT, f1PBSGFP

tag: fraction

value: Bead

tag: treatment

value: WT

value: hypothalamus


title: WT rep1


title: DEL_4_3

value: 16p11.2 deletion

tag: integration detected

value: POS


title: DEL_5_9


title: DEL_5_8


title: DEL_8_3


title: DEL_4_2


title: DEL_3_1


title: DEL_4_1


title: DEL_5_7


title: H3K9ac Uveal melanoma cell-MUM2B-3

city: Shanghai

first: AI

last: ZHUANG

address: 639 Zhizaoju Road

department: Ophthalmology

institute: Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine

description: Uveal melanoma cell-MUM2B-3

data_processing:
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
We calculate the fragment sizes for read pairs given a BAM file from paired-end sequencing. Several regions are sampled depending on the size of the genome and number of processors to estimate the summary statistics on the fragment lengths. Properly paired reads are used for computation.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.
GO Analysis: Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of unique genes in the significant or representative profiles of the gene in the experiment [Ashburner M, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25-9.]. We downloaded the GO annotations from NCBI (http://www.ncbi.nlm.nih.gov/), UniProt (http://www.uniprot.org/) and the Gene Ontology (http://www.geneontology.org/). Fisher’s exact test was applied to identify the significant GO categories and FDR was used to correct the p-values.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using MACS

source_name: Uveal melanoma patient

growth_protocol: The Mum2B cells were cultured in DMEM supplemented with 10% FBS. The PIG1 cells were cultured in f-12k with 10%FBS.

extract_protocol:
For library construction, 21μl DNA was mixed with 2μl of a universal i5 and a uniquely barcoded i7 primer, and then 25μl NEB Next HiFi 2× PCR Master mix was added and mixed. A total volume of 50μl sample was placed in a PCR thermal cycler with a heated lid via the following program: 72°C for 5min; 98°C for 30s; 16 cycles of 98°C for 10s and 63°C for 30s; final extension at 72°C for 1 min and hold at 4°C. To purify PCR products, 1.5 × volumes of AMPure XP beads (Beckman Coulter) were added and incubated for 15 min at RT. Next, the libraries were washed twice gently in 80% ethanol, and eluted in 30μl 10mM Tris pH 8.0. The size distribution of libraries was determined by Agilent 2100 TapeStation analysis
CUT&Tag

treatment_protocol: The cells were digested by trypsin and resuspended with culture medium.

value: Uveal melanoma


title: H3K9ac Uveal melanoma cell-MUM2B-2

description: Uveal melanoma cell-MUM2B-2


title: DEL_2_3

value: iPSC-derived patient neuroepithelium


title: IgG Uveal melanoma cell-MUM2B-2

description: Uveal melanoma cell-MUM2B-2


title: IgG Uveal melanoma cell-MUM2B-3

description: Uveal melanoma cell-MUM2B-3


title: H3K9ac Normal melanocyte-PIG1-2

description: Normal melanocyte-PIG1-2

source_name: Nevus

value: Nevus


title: DEL_10_993

value: M


title: DEL_5_980


title: IgG Uveal melanoma cell-MUM2B-1

description: Uveal melanoma cell-MUM2B-1


title: DEL_2_4


title: DEL_10_991


title: H3K9ac Normal melanocyte-PIG1-1

description: Normal melanocyte-PIG1-1


title: DEL_3_3


title: H3K9ac Uveal melanoma cell-MUM2B-1

description: Uveal melanoma cell-MUM2B-1


title: IgG Normal melanocyte-PIG1-2

description: Normal melanocyte-PIG1-2


title: DEL_6_8


title: IgG Normal melanocyte-PIG1-3

description: Normal melanocyte-PIG1-3


title: IgG Normal melanocyte-PIG1-1

description: Normal melanocyte-PIG1-1


title: DHA3

first: Rui

last: Li

address: Huangpu area

department: Rheumatology

institute: Shanghai Jiao Tong university, School of Medicine, affiliated Renji hospital

data_processing:
The Skewer software was used to dynamically remove the adapter sequence fragments and low-quality fragments from the 3'end of the sequencing data, and the FastQC software was used to perform quality control analysis on the preprocessed data and count the base ratios of Q20 and Q30.
For each sample, STAR software was used to compare the preprocessed sequence with the reference genome sequence. Among them, the matching parameter requirements are set to --twopassMode Basic|--outSAMstrandField intronMotif|--alignSJstitchMismatchNmax 5 -1 5 5, and the rest are default, and RSEQC is used to compare the statistics.
For each sample, the result of the comparison from Reads to the reference genome uses StringTie software based on the known transcript position information file on the genome as a guide to assemble the transcripts in the sample, and filter the transcripts whose expression level is equal to 0. Reassemble the assembled transcripts of StringTie from all samples.
For all samples, StringTie software is used to count the original sequence counts of known genes, and the expression of known genes is calculated using FPKM to calculate metrics
Genome_build: Genome Reference Consortium Human Build 38(GRCh38)
Supplementary_files_format_and_content: read count values for each sample

source_name: Primary skin fibroblast

extract_protocol:
Total RNA was extracted from fibroblast cultures with a  SimpleP RNA kit(BioFlux, China).
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell cultures were treated by 25μM DHA or DMSO for 24 hours.

tag: sample origin

value: Healthy people

value: 25μM DHA


title: H3K9ac Normal melanocyte-PIG1-3

description: Normal melanocyte-PIG1-3


title: DEL_1_4

tag: differentiation day


title: DHA2


title: DHA1


title: DEL_1_3

tag: sequencing batch


title: DEL_1_2

tag: alternative id "line"


title: DEL_10_989

tag: alternative id "deseqanalysisid"


title: DMSO2

value: DMSO


title: 8343.5_2

value: Control

tag: patient "subjectid"


title: DMSO1


title: RNA-Seq F103-C35-T1

city: Palo Alto

first: Akshay

last: Sanghi

state: California

address: 3165 Porter Drive

data_processing:
Illumina software used for basecalling.
Sequenced reads were mapped to hg38 genome using STAR two-pass alignment and gencode v32
Gene counts were done with ht-seq using parameters -s reverse -r pos -t exon -i gene_name -f bam
hg38
rmatrix of raw gene counts per sample
table of all non-promoter peaks with their gene links

source_name: Thyroid tumor

extract_protocol:
Fresh primary tissue were flash frozen on dry ice, and RNA was harvested using AllPrep. Illumina TruSeq RNA Sample Prep Kit (Cat#20020598) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient id

tag: disease state

value: Tumor


title: RNA-Seq F106-C27-M2

source_name: Cervical LymphNode Metastases

value: Metastatic


title: 2242.3

tag: sequencing batch ("seqbatch")

tag: differentiation batch ("growbatch")


title: 8343.4_2

tag: sequencing vial id "vialid"

tag: sequencing lane "lane"

value: F

value: NEG


title: RNA-Seq F105-C36-T1

tag: tissue


title: RNA-Seq F099-C32-T2


title: 2242.5

tag: genotype

tag: Sex


title: 8343.2


title: 8343.4_1


title: 2242.1


title: RNA-Seq F097-C31-M3


title: 8343.5_1


title: RNA-Seq F098-C32-T1


title: RNA-Seq F093-C31-N1

source_name: Normal thyroid

value: Normal


title: RNA-Seq F100-C33-T1


title: RNA-Seq F104-C35-N1


title: RNA-Seq F096-C31-M2


title: RNA-Seq F095-C31-M1


title: RNA-Seq F089-C30-N1


title: RNA-Seq F090-C30-M1


title: RNA-Seq F088-C30-T1


title: RNA-Seq F086-C29-M1


title: DMSO3

tag: treatment


title: RNA-Seq F087-C29-M2


title: RNA-Seq F084-C28-M1


title: RNA-Seq F080-C27-N1


title: RNA-Seq F081-C27-M1


title: RNA-Seq F083-C28-N1


title: RNA-Seq F072-C25-M1


title: RNA-Seq F070-C25-T1


title: RNA-Seq F074-C26-T1


title: RNA-Seq F073-C25-M2


title: RNA-Seq F079-C27-T1


title: RNA-Seq F064-C23-T1


title: RNA-Seq F067-C23-M2


title: RNA-Seq F078-C26-M3


title: RNA-Seq F071-C25-N1


title: RNA-Seq F062-C22-T1


title: RNA-Seq F063-C22-N1


title: RNA-Seq F069-C24-N1


title: RNA-Seq F075-C26-N1


title: RNA-Seq F068-C24-T1


title: RNA-Seq F066-C23-M1


title: RNA-Seq F058-C20-N1


title: RNA-Seq F059-C21-T1


title: RNA-Seq F060-C21-N1


title: RNA-Seq F061-C21-M1


title: RNA-Seq F057-C20-T1


title: RNA-Seq F085-C28-M2


title: RNA-Seq F055-C19-T1


title: RNA-Seq F056-C19-N1


title: RNA-Seq F053-C18-M2


title: RNA-Seq F076-C26-M1


title: RNA-Seq F065-C23-N1


title: RNA-Seq F051-C18-N1


title: RNA-Seq F049-C17-N1


title: RNA-Seq F050-C18-T1


title: RNA-Seq F047-C16-N1


title: RNA-Seq F048-C17-T1


title: RNA-Seq F045-C15-N1


title: RNA-Seq F044-C15-T1


title: RNA-Seq F043-C14-N1


title: RNA-Seq F041-C13-T1


title: RNA-Seq F039-C12-M2


title: RNA-Seq F040-C12-M3


title: RNA-Seq F037-C12-N1


title: RNA-Seq F042-C13-N1


title: RNA-Seq F054-C18-M3


title: RNA-Seq F030-C10-M2


title: RNA-Seq F024-C9-T1


title: RNA-Seq F028-C10-N1


title: RNA-Seq F029-C10-M1


title: RNA-Seq F033-C11-N1


title: RNA-Seq F025-C9-M1


title: RNA-Seq F035-C11-M2


title: RNA-Seq F036-C12-T1


title: RNA-Seq F026-C10-T1


title: RNA-Seq F032-C11-T1


title: RNA-Seq F023-C8-M2


title: RNA-Seq F022-C8-M1


title: RNA-Seq F020-C8-T1


title: RNA-Seq F019-C7-M1


title: RNA-Seq F018-C7-N1


title: RNA-Seq F017-C7-T1


title: RNA-Seq F014-C5-N1


title: RNA-Seq F034-C11-M1


title: RNA-Seq F007-C3-T1


title: RNA-Seq F004-C2-T1


title: RNA-Seq F005-C2-N1


title: RNA-Seq F002-C1-N1


title: RNA-Seq F046-C16-T1


title: ATAC-Seq F104-C35-N1

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt 1.9.1, and, then mapped to hg38 whole genome using Bowtie2 version 2.2.6
ENCODE pipeline standard parametsrs were used
hg38
matrix with each sample replicate's tag-align counts in the thyroid-data peak set
table of all non-promoter peaks with their gene links
table of all promoter peak regions

extract_protocol:
Fresh primary tissue were flash frozen on dry ice, and intact nuclei were harvested. Omni-ATAC protocal was used  to extract 50,000 nuclei per sequencing library.
ATAC libraries were prepared for sequencing using standard Illumina protocols


title: RNA-Seq F001-C1-T1


title: ATAC-Seq F106-C27-M2


title: RNA-Seq F003-C1-M1


title: RNA-Seq F010-C4-N1


title: ATAC-Seq F103-C35-T1


title: RNA-Seq F009-C4-T1


title: ATAC-Seq F101-C34-T1


title: ATAC-Seq F097-C31-M3


title: ATAC-Seq F100-C33-T1


title: ATAC-Seq F099-C32-T2


title: ATAC-Seq F102-C34-N1


title: ATAC-Seq F095-C31-M1


title: ATAC-Seq F096-C31-M2


title: ATAC-Seq F091-C30-M2


title: ATAC-Seq F093-C31-N1


title: ATAC-Seq F089-C30-N1


title: ATAC-Seq F088-C30-T1


title: ATAC-Seq F092-C30-M3


title: LPO 3

city: Edinburgh

first: Amanda

middle: J.

last: Drake

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

data_processing:
Reads trimmed using Trimmomatic
QC performed with Fastqc
Reads aligned using STAR version 2.7.1a
tab delimited text files were generated using featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files were generated using featureCounts and contain FPKM and TPM values for each sample

source_name: Hepatocyte-like cells_LPO treated

growth_protocol: Human ES cells were differentiated to hepatocyte-like cells, over the course of 17 days, as per the protocol from Wang, et al (2017), Defined and Scalable Generation of Hepatocyte-like Cells from Human Pluripotent Stem Cells

extract_protocol:
mRNA was harvested from adherent cells using the standard TRIzol protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At day 17 of differentiation, when cells had differentiated to mature hepatocyte-like cells, they were treated with a cocktail of lactate (10 mM), pyruvate (1 mM), and octanoate (2 mM) to stimulate intracellular lipid accumulation

tag: cell type

value: ES-derived hepatocyte-like cells

value: lactate (10 mM), pyruvate (1 mM) and octanoate (2 mM)


title: LPO 2


title: ATAC-Seq F087-C29-M2


title: LPO 1


title: ATAC-Seq F086-C29-M1


title: Control 3

source_name: Hepatocyte-like cells_control

value: none (control)


title: ATAC-Seq F083-C28-N1


title: ATAC-Seq F082-C28-T1


title: ATAC-Seq F080-C27-N1


title: ATAC-Seq F081-C27-M1


title: Control 1


title: Control 2


title: ATAC-Seq F090-C30-M1


title: ATAC-Seq F079-C27-T1


title: ATAC-Seq F077-C26-M2


title: ATAC-Seq F076-C26-M1


title: ATAC-Seq F075-C26-N1


title: E18 wild-type rep 2

city: Tampa

first: Derek

middle: E

last: Wildman

state: Florida

address: 3720 Spectrum Blvd

department: College of Public Health

institute: University of South Florida

data_processing:
Adaptor sequences were trimmed from the 3’-end of the reads using Trimmomatic v0.36
Transcriptomes were aligned against Mus musculus reference genome GRCm38 using STAR v2.4.2a
Numbers of reads assigned to features were counted using featureCounts on Subread v1.5.0
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include feature counts for each sample
Supplementary_files_format_and_content: Matrix table with feature counts for every transcript and every sample

source_name: fetal membrane

extract_protocol:
Fetal membranes were dissected in 0.1mol/L phosphate buffered saline, pH 7.4, snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction was performed. Fetal membranes were ground using a micropestle while maintaining the sample in liquid nitrogen. RNA was extracted using the RNeasy Midi Kit (Qiagen, Valencia, CA) following manufacturer’s instructions. Samples were treated with RNase-Free DNase (Qiagen, Valencia, CA) to remove any contaminating DNA.
Illumina's TruSeq Stranded mRNAseq Sample Prep kit (Illumina, San Diego, CA) was used to prepare RNA-Seq libraries using 2µg of total RNA and following manufacturer’s instructions.

tag: strain

value: fetal membrane

tag: age

value: Wild-type


title: E18 wild-type rep 1


title: E18 wild-type rep 3


title: ATAC-Seq F072-C25-M1


title: ATAC-Seq F074-C26-T1


title: ATAC-Seq F073-C25-M2


title: ATAC-Seq F078-C26-M3


title: ATAC-Seq F071-C25-N1


title: E18 double knockout rep 2

value: C3H and C57BL/6

value: Double knockout of biglycan and decorin


title: ATAC-Seq F070-C25-T1


title: E18 double knockout rep 3


title: ATAC-Seq F068-C24-T1


title: ATAC-Seq F069-C24-N1


title: ATAC-Seq F085-C28-M2


title: E18 double knockout rep 1


title: ATAC-Seq F084-C28-M1


title: ATAC-Seq F066-C23-M1


title: ATAC-Seq F065-C23-N1


title: E12 wild-type rep 2


title: ATAC-Seq F067-C23-M2


title: E12 wild-type rep 1


title: ATAC-Seq F064-C23-T1


title: PO70M6_1

city: Utrecht

first: Jorke

last: Kamstra

state: Non United States Or Canada

address: PO Box 80177

department: Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

data_processing:
Adaptor trimming using trim_galore (v0.4.5, Babraham Institute, UK) under standard parameters
Alignment was performed with STAR aligner (v2.5.4b) to align and map sequences to the zebrafish genome (GRCz11, https://www.ensembl.org) with a recent release of the zebrafish transcriptome GTF (v92, www.ensembl.org)
Generated BAM files were loaded to SeqMonk sequence analysis tool (v1.41, Babraham institute, UK) and mRNAs were quantified using the built-in mRNA seq pipeline. Library quality was evaluated with the RNA-seq QC plot and cumulative distribution plots using SeqMonk. Filter was applied to analyze mRNAs that had at least a log2 = 0 expression in either of the samples, to assure that for statistical analysis only mRNAs with enough reads were included. Deseq2 filter using R (v3.5.0) within SeqMonk was used on raw read counts to calculate differential expression. After Deseq2 analysis, data were normalized by reads per million (RPM)
Genome_build: GRCz11
Supplementary_files_format_and_content: The processed data files is an excel file containing log2 normalized data

organism: Danio rerio

source_name: Adult brain tissue

extract_protocol:
RNA from samples for RNA-seq analysis were purified using NucleoSpin® RNA extraction kit (Macherey-Nagel, Germany). RA1 lysismix (Macherey-Nagel, Germany) was added to each sample and homogenized with a bead homogenizer. Total RNA was extracted from samples following manufacturer’s instructions. Each sample was eluted in 50 μL RNase-free water and stored at -80 °C until further analysis
A total of 2 μg was used for library preparation. A quality check (QC) of total RNA was performed with a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), Agilent 2100 (Agilent Technologies, CA, USA) and agarose gel electrophoresis prior to library construction. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, mRNA was purified from total RNA using poly-T oligo attached magnetic beads. Fragments were randomly created in fragmentation buffer. First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina, CA, USA) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection, and PCR enrichment. PCR products were purified (AMPure XP system, Beckman, US) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Libraries were analyzed with a Hiseq 4000 (Illumina, Ca, USA), using 150bp paired-end reads, with a depth of 20 million reads per sample.

value: AB

tag: developmental stage

value: 219 dpf

tag: agent

tag: genotype/variation

value: wild type


title: PO70M6_2


title: PO70M5_2

value: 226 dpf


title: ATAC-Seq F063-C22-N1


title: ATAC-Seq F061-C21-M1


title: PO70M4_1

value: 233 dpf


title: ATAC-Seq F062-C22-T1

value: Tumor


title: ATAC-Seq F060-C21-N1


title: PO70M4_2


title: ATAC-Seq F059-C21-T1


title: ATAC-Seq F056-C19-N1


title: E12 double knockout rep 2


title: E12 wild-type rep 3


title: ATAC-Seq F055-C19-T1


title: E12 double knockout rep 1


title: E12 double knockout rep 3


title: PO70M5_1


title: PO70F6_2


title: ATAC-Seq F054-C18-M3

value: Metastatic


title: PO70M3_2

value: 240 dpf


title: PO70M3_1


title: PO70F5_1


title: PO70F5_2


title: Cardiac_RNA-seq_ID8

city: London

first: YuJin

last: Chung

address: Westminster Bridge Rd

institute: Kings College London

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to mm10 whole genome using the aligner software Spliced Transcripts Alignment to a Reference (STAR). PCR duplicates were removed using SAM tools and table of sequenced genes generated using FeatureCounts tool.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix Table with raw gene counts for every gene and every sample

source_name: Cardiac tissue

extract_protocol:
Hearts were removed, washed in 1x PBS, snap frozen in liquid nitrogen, pulverized and RNA extracted from 30mg tissue using RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fed a control or iron-deficient diet (>2 ppm) for 6 weeks starting at age 3 weeks

value: male

value: heart

value: 9 weeks

value: iron-deficient diet (<2 ppm)


title: Cardiac_RNA-seq_ID4


title: Cardiac_RNA-seq_ID6


title: Cardiac_RNA-seq_ID9


title: Cardiac_RNA-seq_ID10


title: Cardiac_RNA-seq_ID7


title: ATAC-Seq F049-C17-N1

value: Normal


title: PO70F4_1


title: ATAC-Seq F048-C17-T1


title: PO70F3_2


title: ATAC-Seq F050-C18-T1


title: PO70F3_1


title: Cardiac_RNA-seq_ID1


title: Cardiac_RNA-seq_ID2


title: Cardiac_RNA-seq_ID3


title: ATAC-Seq F047-C16-N1


title: Cardiac_RNA-seq_CD10

value: control diet


title: PO70F6_1


title: PO10M6_2


title: ATAC-Seq F052-C18-M1


title: Cardiac_RNA-seq_ID5


title: ATAC-Seq F046-C16-T1


title: ATAC-Seq F045-C15-N1


title: Cardiac_RNA-seq_CD8


title: Cardiac_RNA-seq_CD9


title: PO10M6_1


title: ATAC-Seq F051-C18-N1


title: PO70F4_2


title: PO10M5_2


title: PO10M5_1


title: PO10M4_2


title: Cardiac_RNA-seq_CD6


title: ATAC-Seq F043-C14-N1


title: ATAC-Seq F044-C15-T1


title: ATAC-Seq F042-C13-N1


title: Cardiac_RNA-seq_CD5


title: ATAC-Seq F039-C12-M2


title: PO10M3_1


title: PO10F6_2


title: ATAC-Seq F040-C12-M3


title: Cardiac_RNA-seq_CD3


title: Cardiac_RNA-seq_CD4


title: ATAC-Seq F038-C12-M1


title: PO10F6_1


title: ATAC-Seq F037-C12-N1


title: Cardiac_RNA-seq_CD2


title: ATAC-Seq F036-C12-T1


title: PO10F5_2


title: PO10F5_1


title: Cardiac_RNA-seq_CD7


title: Cardiac_RNA-seq_CD1


title: ATAC-Seq F035-C11-M2


title: cells h3k27me3

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

country: France

institute: Institut Jean-Pierre Bourgin - INRAE

data_processing:
Single-end 36 nucleotide reads were mapped to TAIR10 genome with bowtie2, using the --very-sensitive preset option.
Genome alignments were intersected with genomic features using Bedtools.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files with number of reads mapped to TAIR10 features

organism: Arabidopsis thaliana

source_name: cell cultures

growth_protocol: Arabidopsis cell line (ecotype Col-0) was maintained in Gamborg’s B5 basal medium with minor organics (Sigma G5893) supplemented with 1.1 mg/l 2,4-D, 3 mM MES, and 3% sucrose. The cells were grown on a shaker at 160 rpm under consistent light condition at 23ºC and were subcultured every 7 d with a 1:10 (inoculum:fresh medium) dilution ratio. Leaf samples were prepared from wild-type Col-0 plants grown on MS agar plates under standard conditions (day/light).

extract_protocol: ChIP DNA was prepared for Illumina sequencing using NEBNext ChIP Seq Library Prep mix (NEB).

treatment_protocol: An approximate volume of 5 mL of sedimented cells from cell suspension culture were cross-linked by treating with 1% paraformaldehyde for 15 min. After adding 2 M glycine (100 mM final concentration) and incubating for 5 min to stop the cross-linking, the cells were washed three times with PBS by centrifuging at 1,500 rpm for 5 min. The fixed cells were snap-frozen in liquid nitrogen and stored at 80ºC. Chromatin isolation and immunoprecipitation with antibodies against specific histone modifications (anti-H3, anti- H3K9me2, anti-H3K4me3 and anti-H3K27me3) were done according to (Tanurdžić et al., 2008 PLoS Biology) with minor modifications (an extra wash at each washing step).

tag: ecotype

tag: sample type

value: cell cultures

tag: chip antibody

value: anti-H3K27me3 cat# 04-449 [lot 1999691], Upstate/Millipore


title: cells h3k9me2

value: anti-H3K9me2 cat# 07–212 [lot# 27563], Upstate/Millipore


title: PO10F4_2

value: AB


title: cells h3k4me3

value: anti-H3K4me3 cat# 07-473 [lot# 2289139], Upstate/Millipore


title: cells h3

value: anti-H3, cat# 07-690 [lot 2019743], Upstate/Millipore


title: ATAC-Seq F034-C11-M1

tag: patient id

tag: disease state


title: PO10F4_1

value: wild type


title: leaf h3k9me2

source_name: leaf

value: leaf


title: ATAC-Seq F041-C13-T1

value: Tumor


title: PO10F3_2


title: PO10M3_2


title: PO10M4_1

value: 233 dpf


title: PF70M6_2

value: 219 dpf


title: ATAC-Seq F032-C11-T1


title: leaf h3


title: ATAC-Seq F029-C10-M1

value: Metastatic


title: leaf h3k27me3


title: leaf h3k4me3


title: PF70M6_1


title: ATAC-Seq F028-C10-N1


title: ATAC-Seq F026-C10-T1


title: PF70M5_2

value: 226 dpf


title: PF70M5_1


title: PF70M4_2


title: T47D shRON

city: Cincinnati

first: Susan

last: Waltz

state: Ohio

address: 3125 Eden Ave

department: Cancer Biology

institute: University of Cincinnati

description: RON knockdown

data_processing:
Following removal of primers and barcodes, raw reads were aligned to the hg19 genome using UCSC annotations in GeneSpring NGS software (Agilent)
Data were quantified, log2 transformed, and normalized using the DESeq algorithm.
Data were baselined to the median of all samples.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab delimited with Gene ID, Gene Symbol, and RPKM

growth_protocol: Maintained in regular DMEM high glucose with 10% serum

extract_protocol:
Total RNA was extracted using the TRIZOL method
Libraries prepared using the Illumina TruSeq RNA preparation kit

treatment_protocol: Cells were transduced, selected with 5 ug/mL Puromycin, and maintained in 1 ug/mL Puromycin

tag: cell line

value: Hairpin targeting RON

value: Luminal A breast cancer cells


title: ATAC-Seq F025-C9-M1


title: ATAC-Seq F033-C11-N1

value: Normal


title: ATAC-Seq F024-C9-T1


title: T47D shNT

description: RON proficient

value: Non-targeting hairpin


title: ATAC-Seq F023-C8-M2


title: PF70M4_1


title: PF70M3_2

value: 240 dpf


title: PF70M3_1


title: ATAC-Seq F022-C8-M1


title: ATAC-Seq F021-C8-N1


title: ATAC-Seq F030-C10-M2


title: PO10F3_1


title: PF70F6_2


title: ATAC-Seq F020-C8-T1


title: ATAC-Seq F019-C7-M1


title: ATAC-Seq F018-C7-N1


title: PF70F5_2


title: 06_HCC_Metformin_Sorafenib_Sequential_rep3

type: RNA

city: Paris

first: Christèle

last: Desbois-Mouthon

address: 15 rue de l'école de médecine

institute: INSERM

description: Transcriptomic analysis

hyb_protocol: Each RNA sample was hybridized to Human ClariomTM S GeneChip (ThermoFischer Scientific).

scan_protocol: Arrays were scanned (one-color) and images were analyzed and controlled for hybridization artefacts.

data_processing:
The microarray data were normalized using Signal Space Transformation-RMA (SST-RMA) which is optimized for under-estimation of true fold changes. Following normalization, differential expression was carried out using eBayes function and One-Way Anova statistical analysis. The analysis was carried out using Transcriptome Analysis Console software (ThermoFischer Scientific, version 4.0.2) with p < 0.05 considered as statistically significant. The differentially expressed genes were then subjected to absolute GSEA searching through more than 10,000 different cellular pathways. C2 is an MSigDB (The Molecular Signature Database) collection consisting of sets curated from biomedical literature and online pathway databases such as the Kyoto Encyclopedia of Genes and Genome (KEGG) or Reactome. The gene ontology set C5 contains curated sets derived from Gene Ontology.
Data are log2 normalised and compared against untreated

label: Biotin

source_name: RNA from tumors collected from mice xenografed with PLC/PRF5 cells and treated with metformin (50 mg/kg/day) followed 6 hours later by sorafenib (15 mg/kg/day) (sequential schedule)

label_protocol: Total RNA was amplified and labelled using the GeneChipTM WT PLUS Reagent Kit (ThermoFischer Scientific)

growth_protocol: Six week-old female athymic mice (Rj:NMRI-Foxn1nu/Foxn1nu, Janvier Labs, Le Genest-Saint-Isle, France) were inoculated s.c. in the right flank with 2 x 106 PLC/PRF5 cells suspended in 50% Matrigel (BD Biosciences, San Jose, CA). Mice were treated by gavage with vehicles (control), sorafenib alone (15 mg/kg/day), metformin alone (50 mg/kg/day), metformin combined to sorafenib (concomitant schedule) and metformin followed 6 h later by sorafenib (sequential schedule).

extract_protocol: Total RNA was extracted using Trizol (ThermoFischer Scientific). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Xenografed mice were treated with vehicle (control, n=3), metformin (50 mg/kg/day) combined to sorafenib (15 mg/kg/day) (concomitant schedule, n=3) or metformin (50 mg/kg/day) followed 6 hours later by sorafenib (15 mg/kg/day) (sequential schedule, n=3).

value: HCC tumors collected from mice xenografted with PLC/PRF5 cells


title: ATAC-Seq F017-C7-T1


title: 08_HCC_Metformin_Sorafenib_Concomitant_rep2

description: Transcriptomic analysis

source_name: RNA from tumors collected from mice xenografed with PLC/PRF5 cells and treated with metformin (50 mg/kg/day) combined to sorafenib (15 mg/kg/day) (concomitant schedule)


title: PF70F4_2


title: ATAC-Seq F014-C5-N1


title: ATAC-Seq F010-C4-N1


title: Cells T87

data_processing:
Pre-processed high quality reads were mapped to the TAIR10 genome using bismark (Krueger and Andrews 2011, Bioinformatics) with default settings for paired-end libraries, and all downstream analysis were performed using custom R scripts
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files with cytosine methylation values (CG,CHG,CHH)

source_name: cell culture

growth_protocol: T87 derived cell suspension culture has been maintained in Jouanneau and Péaud-Lenoël (JPL) medium under continuous light at 22˚C and subcultured at two-week intervals (Axelos et al. 1992, Plant Physiol Biochem).

extract_protocol:
Genomic DNA was extracted from unsynchronized cells after 4 days in culture using the Edwards method (Edwards et al. 1991, NAR).
Whole genome bisulfite sequencing was performed by BGI Genomics (Hong Kong). Briefly, genomic DNA was fragmented to 100-300 bp by sonication, end-repaired, and ligated to methylated adaptors. Bisulfite treatment was then performed using the EZ DNA Methylation-Gold kit (Zymo), and the bisulfite-treated fragments were PCR amplified and sequenced as paired-end 150 bp reads (PE150) with Illumina technology.

value: cell culture


title: ATAC-Seq F009-C4-T1


title: 05_HCC_Metformin_Sorafenib_Sequential_rep2

description: Transcriptomic analysis


title: PF70F3_2

value: AB


title: 03_HCC_untreated_rep3

description: Transcriptomic analysis

source_name: RNA from tumors collected from mice xenografed with PLC/PRF5 cells and treated with vehicle


title: 09_HCC_Metformin_Sorafenib_Concomitant_rep3

description: Transcriptomic analysis


title: 07_HCC_Metformin_Sorafenib_Concomitant_rep1

description: Transcriptomic analysis


title: 02_HCC_untreated_rep2

description: Transcriptomic analysis


title: PF10M6_2


title: ATAC-Seq F007-C3-T1


title: Lung, Amiodarone and Dabigatran

city: Kyoto

first: Kazuki

last: Nagayasu

address: 46-29 Yoshidashimoadachicho, Sakyo

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Kyoto University

data_processing:
The reads were cleaned using SOAPnuke v1.5.2
The clean reads were mapped to the genome and gene sequences using HISAT and Bowtie2, respectively.
Gene expression was calculated using RSEM.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: gene_expression.txt

source_name: Lung

extract_protocol:
After chronic treatment, lung was dissected and snap frozen in liquid N2. Total RNA was isolated using ISOGEN reagent.
RNA libraries were prepared for sequencing using standard DNBSeq protocols

value: lung

value: amiodarone and dabigatran for 28 days


title: Lung, Amiodarone

value: amiodarone for 28 days


title: PF70F6_1

value: wild type


title: 04_HCC_Metformin_Sorafenib_Sequential_rep1

description: Transcriptomic analysis


title: Lung, Dabigatran

value: dabigatran for 28 days


title: Lung, Vehicle

value: vehicle for 28 days


title: 01_HCC_untreated_rep1

description: Transcriptomic analysis


title: PF70F5_1


title: PF70F3_1


title: PF70F4_1

value: 233 dpf


title: ATAC-Seq F004-C2-T1

value: Tumor


title: ATAC-Seq F002-C1-N1


title: PF10M5_2

value: 226 dpf


title: ATAC-Seq F001-C1-T1

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt 1.9.1, and, then mapped to hg38 whole genome using Bowtie2 version 2.2.6
ENCODE pipeline standard parametsrs were used
hg38
matrix with each sample replicate's tag-align counts in the thyroid-data peak set
table of all non-promoter peaks with their gene links
table of all promoter peak regions


title: PF10M4_2


title: PF10M4_1


title: Day1.HER2ISAC.5

city: Redwood City

first: Lisa

middle: K

last: Blum

email: lblum@boltbio.com, info@boltbio.com

address: 640 Galveston Dr

institute: Bolt Biotherapeutics

hyb_protocol: Hydridized according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

scan_protocol: Scanned according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

data_processing: nSolver software, background and internal control standardization. Normalization was performed in nsolver with house keeping genes as internal controls

label: nanostring oligonucleotide probe

source_name: MMC syngeneic tumor

label_protocol: Labeled according to the manufacturer's protocol. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

growth_protocol: MMC cells were obtained from Dr. Disis (University of Washington) and were cultured in RPMI 1640 supplemented with 20% FBS, 1% penicillin-streptomycin, and L-glutamine at 37C and 5% CO2 until 80-90% confluent. Cells were harvested by detaching with Accutase (Stemcell) and washing with PBS. Harvested cells were resuspended at 20x 10^6cells/mL in PBS and kept at 4C until use. 100 μL of suspended cells were implanted subcutaneously into 6-8-week-old FVB/N-TgN(MMTV-Erbb2)NK1Mul/J mice (MMC model, The Jackson Laboratory). Once tumors reached 200-500 mm^3, usually within one week from tumor implantation, mice were randomized into groups by tumor size and treatments were initiated.

extract_protocol: Tumor samples were stored in RNAlater prior to extraction with the RNEasy kit (Qiagen).

treatment_protocol: Antibody and ISAC treatments were prepared in PBS at 1 mg/mL and administered at 5 mg/kg intraperitoneally

value: MMC syngeneic tumor

tag: timepoint

value: Day 1 post-treatment

tag: replicate number

value: anti-rHER2 T785-ISAC


title: PF10M3_2


title: Day1.HER2ISAC.3

tag: tissue


title: Day1.HER2ISAC.2


title: ATAC-Seq F005-C2-N1

value: Normal


title: PF10M3_1

value: 240 dpf


title: PF10M6_1

value: 219 dpf


title: Day1.HER2ISAC.1


title: PF10F6_2


title: Day1.HER2.5


title: PF10F6_1


title: K562 (K01) treated with ascorbate rep1

city: Cleveland

first: Babal

last: Jha

address: 9500 Euclid Ave, NE6-253

department: Translational Hematology and Oncology

institute: Cleveland Clinic

data_processing:
Raw reads were mapped to human genome, hg19, using RNA STAR. Computational analysis was performed using Galaxy server (https.usegalaxy.org).
Differential expression and gene set enrichment analysis was assessed using edgeR 3.24.3 and limma 3.38.3 with R 3.5.
Genome_build: hg19
Supplementary_files_format_and_content: gene_counts_matrix: raw counts

source_name: K562 Cell line

growth_protocol: SIGM5 cell lines were cultured in IMDM with 10% FBS and 100 U/ml pen-strep. K562 cell lines were cultured in RPMI with 10% FBS and 100 U/ml pen-strep.

extract_protocol:
RNA was purified by using NucleoSpin RNA kit ((Takara Bio USA, Inc Cat #740955) according to the manufacturer’s instruction. RNA quality was validated by RNA integrity number (RIN >9) calculated by Agilent 2100 Bioanalyzer. mRNA was enriched using oligo(dT) beads.
RNA was fragmented randomly by adding fragmentation buffer. The cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina, dNTPs, RNase H and DNA polymerase I) was added to initiate the second-strand synthesis. After a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Cells at density of 0.3 M/ml were treated with 12.5 or 25 µM TETi76 or DMSO for 24 hours in the presence or absence of 100 µM ascorbate.

value: 100 microM Ascorbate


title: K562 (K01) treated with ascorbate rep2


title: K562 (K01) treated with TETi76 and ascorbate rep2

value: 12.5 microM TETi76 + 100 microM Ascorbate


title: K562 (K01) treated with TETi76 rep2

value: 12.5 microM TETi76


title: PF10F5_2

value: AB


title: K562 (K01) treated with TETi76 and ascorbate rep1


title: Day1.HER2.4


title: Day1.HER2.3


title: PF10M5_1


title: ATAC-Seq F003-C1-M1

value: Metastatic


title: K562 (K01) treated with TETi76 rep1


title: Day1.HER2.2


title: Day1.HER2ISAC.4


title: Day1.HER2.1


title: K562 TET2-/- (K18) treated with DMSO rep2

value: DMSO


title: PF10F4_2

value: wild type


title: K562 TET2-/- (K18) treated with DMSO rep1


title: Day1.IsotypeISAC.5

value: Isotype T785-ISAC


title: K562 (K01) treated with DMSO rep2


title: PF10F3_2


title: PF10F3_1


title: K562 (K01) treated with DMSO rep1


title: PF10F4_1

value: 233 dpf


title: Day1.IsotypeISAC.4


title: Day1.IsotypeISAC.3


title: CM6_1

value: Control


title: Day1.IsotypeISAC.1


title: Day1.IsotypeISAC.2


title: Day1.Isotype.5

value: Isotype Control


title: SIGM5 treated with DMSO rep1

description: SIGa

source_name: SIGM5 Cell line


title: SIGM5 treated with TETi76 rep1


title: SIGM5 treated with TETi76 rep2


title: SIGM5 treated with DMSO rep2

description: SIGb


title: Day1.Isotype.4

value: MMC syngeneic tumor


title: CM5_1

value: 226 dpf


title: PF10F5_1


title: CM4_2


title: 2 CD SP140 SNP+/+ LPS + ETO

city: Boston

first: Kate

middle: L

last: Jeffrey

state: Massachusetts

address: 50 Blossom St, Thier 340

department: Medicine

institute: Massachusetts General Hospital, Harvard Medical School

data_processing:
Illumina software used for basecalling.
Reads were mapped using the STAR aligner (Dobin, Davis et al. 2013) and the hg19 assembly of the human genome. Due to large differences in the number of reads per sample, aligned reads were down-sampled, resulting in 14 - 52 million mapped reads per sample.
Read counts for individual transcripts were obtained using HTSeq (Anders, Pyl et al. 2014) and the Ensembl gene annotation (GRCh37 release 75)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: Peripheral blood mononuclear cells were isolated from the 12 -15mL blood of Crohn's disease patients using a Ficoll-based density gradient. Cells were washed with 1x PBS 3 times before being plated for treatments.

extract_protocol:
Cells were lysed in 350µL buffer RLT and RNA was isolated using the Qiagen RNeasy Mini Kit with on-column DNase digest (all according to manufacturer's instruction).
100ng of total RNA from each sample was used for library preparation. First, poly(A)-tailed RNA was enriched for using the NEBnext Poly(A) mRNA magnetic isolation module (E7490; according to manufacturer's instructions). This poly(A)-enriched RNA was then used to construct libraries using the NEBnext Ultra II RNA Library Prep Kit for Illumina (E7770; according to manufacturer's instructions). To allow for multiplexed reads, libraries were dual indexed using indices from NEBnext Multiplex Oligos for Illumina (E6440). Sequencing was done on a NovaSeq S2 flow cell.

treatment_protocol: Cells were pre-treated with DMSO, topotecan (100nM), or etoposide (25mM) 1 hour prior to LPS (100ng/mL) treatment for 4 hours.

value: Blood

tag: diagnosis

value: Crohn's disease

tag: genotype

value: CD SP140 SNP +/+

value: PBMC

value: LPS (100 ng/mL, 4h) + Etoposide (25 mM)


title: 2 CD SP140 SNP+/+ LPS + TPT

tag: cell type

tag: treatment

value: LPS (100 ng/mL, 4h) + Topotecan (100nM)


title: Day1.Isotype.3

tag: strain

value: Day 1 post-treatment


title: CM5_2

value: AB

tag: developmental stage


title: CM4_1

tag: agent


title: Day1.Isotype.1


title: Day1.Isotype.2


title: CM6_2

value: 219 dpf

tag: genotype/variation


title: 2 CD SP140 SNP+/+ LPS + DMSO

tag: age

value: LPS (100 ng/mL, 4h) + DMSO


title: 2 CD SP140 SNP+/+ Con + ETO

value: Unstimulated control + Etoposide (25 mM)


title: CM3_1

value: 240 dpf

value: wild type


title: 2 CD SP140 SNP+/+ Con + TPT

value: Unstimulated control + Topotecan (100nM)


title: 2 CD SP140 SNP+/+ Con + DMSO

value: Unstimulated control + DMSO


title: CF6_1

value: Control


title: CF6_2


title: 1 CD SP140 SNP+/+ LPS + ETO


title: CF5_2

value: 226 dpf


title: CF5_1


title: 1 CD SP140 SNP+/+ LPS + TPT

value: Blood


title: 1 CD SP140 SNP+/+ LPS + DMSO

value: Crohn's disease


title: CF4_1

value: 233 dpf


title: CF4_2


title: 1 CD SP140 SNP+/+ Con + ETO

value: CD SP140 SNP +/+

value: PBMC


title: Day1.Trastuzumab-T785-ISAC.4

source_name: HCC1954 tumor xenograft

growth_protocol: The HCC1954 tumor cell line was purchased from ATCC and grown according to manufacturer’s guidelines. Cells were harvested when they reached 80-90% confluency by detaching with Accutase (Stemcell), washed with PBS, resuspended at 40 x 10^6cells/mL in PBS and placed on ice for no longer than two hours. Immediately prior to implantation, suspended cells were mixed with an equal volume of Cultrex PathClear BME, Type 3 (R&D Systems), and 100 μL of the mixture (2 x 10^6cells) were implanted subcutaneously into the right flank of 6-8-week-old female SCID/beige mice. Tumor size was recorded twice a week and was estimated using the following formula: (length x width2)/2. Once tumors reached 50-100 mm^3, usually within one week from tumor implantation, treatments were initiated. Mice were randomized by tumor size into treatment groups prior to initial treatment.

extract_protocol: Tumor samples were stored in RNAlater prior to extraction.

value: SCID/beige

value: Trastuzumab T785-ISAC


title: Day1.Trastuzumab-T785-ISAC.3

value: Day 1 post-treatment


title: Day1.Trastuzumab-T785-ISAC.2


title: Day1.Trastuzumab.4

value: Trastuzumab


title: Day1.Trastuzumab-T785-ISAC.5


title: CF3_2

value: AB


title: 1 CD SP140 SNP+/+ Con + TPT


title: CM3_2


title: CF3_1


title: 3 CD SP140 SNP-/- LPS + ETO

value: CD SP140 SNP -/-

value: LPS (100 ng/mL, 4h) + Etoposide (25 mM)


title: Day1.Trastuzumab.5


title: Day1.Trastuzumab-T785-ISAC.1


title: 1 CD SP140 SNP+/+ Con + DMSO


title: Day1.Trastuzumab.3


title: WT leaf

data_processing:
Single-end 50-nt reads were pre-processed by filtering collapsed reads according to length and quality.
Filtered reads were mapped to the Arabidopsis TAIR10 genome annotation with Bowtie, reporting all multi-mappers.
Only perfect-match reads were used for all downstream analysis.
Reads were normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30 nt) and perfectly mapped reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files showing the number of reads per million (RPM) of 18-30nt reads mapped to TAIR10 features, and summarized based on read length (size).

source_name: Leaf

growth_protocol: The cells were cultured in 1x B5 medium with minimal organics supplemented with 3% sucrose and 1.1 mg/l 2,4-D with a 1:1 and 1:9 final dilution. Cells were grown in 50 mL medium and propagated every 7 days by transferring a 6 mL aliquot to a fresh 50 mL fresh and pre-warmed medium.

extract_protocol:
Total RNA was extracted from cycling cells (7 days in culture + 16h after addition of fresh medium), arrested cells (8 days in culture without addition of fresh medium) and wild-type leaf tissue using the Direct-zol kit (Zymo Research)
Library construction and sequencing was performed at BGI genomics (Hong Kong)

tag: ecotype

value: wild-type leaf


title: 3 CD SP140 SNP-/- LPS + TPT

value: LPS (100 ng/mL, 4h) + Topotecan (100nM)


title: Day1.Trastuzumab.1


title: Cells 8d

value: arrested cells


title: 3 CD SP140 SNP-/- Con + ETO

value: Unstimulated control + Etoposide (25 mM)


title: 3 CD SP140 SNP-/- Con + TPT

value: Unstimulated control + Topotecan (100nM)


title: Cells 7d Split + 16h

value: cycling cells


title: Day1.Trastuzumab.2


title: 3 CD SP140 SNP-/- Con + DMSO

value: Blood

value: Crohn's disease

value: Unstimulated control + DMSO


title: 2 CD SP140 SNP-/- LPS + ETO

value: PBMC


title: 3 CD SP140 SNP-/- LPS + DMSO

value: LPS (100 ng/mL, 4h) + DMSO


title: cuff_rep2

city: Chuo-ku

first: Takashi

last: Hozumi

state: Chiba

address: 1-8-1, Inohana

institute: Chiba University

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of FASTQ format were processed by Trimmomatic (v0.30) to be high quality clean data.
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website (UCSC, NCBI, ENSEMBL).  Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence (mm10).  Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis: In the beginning transcripts in FASTA format are converted from known gff annotation file and indexed properly.  Then, with the file as a reference gene file, FeatureCounts estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Spinal cord

extract_protocol:
Total RNAs were extracted from the spinal cord at L4-6 level of the mice.
Strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina after poly(A) selection by the NEBNext poly(A) mRNA Isolation Module (New England Biolabs Inc.).  Samples were barcoded using the recommended NEBNext Multiplex Oligos.  Size range and quality of libraries were verified on the Agilent 2100 Bioanalyzer (Agilent Technologies).  RNA-seq libraries were quantified by quantitative polymerase chain reaction using the KAPA library quantification kit (KAPA Biosystems).  Each library was normalized to 2 nM and pooled in equimolar concentrations.  Paired-end 150 sequencing was performed on an Illumina HiSeq4000 (Illumina, San Diego, CA).  Libraries were pooled and sequenced using two lanes of one HiSeq4000 flow cell to an average depth of 33.6 million reads per sample.  Strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina after poly(A) selection by the NEBNext poly(A) mRNA Isolation Module (New England Biolabs Inc.).  Samples were barcoded using the recommended NEBNext Multiplex Oligos.  Size range and quality of libraries were verified on the Agilent 2100 Bioanalyzer (Agilent Technologies).  RNA-seq libraries were quantified by quantitative polymerase chain reaction using the KAPA library quantification kit (KAPA Biosystems).  Each library was normalized to 2 nM and pooled in equimolar concentrations.  Paired-end 150 sequencing was performed on an Illumina HiSeq4000 (Illumina, San Diego, CA).  Libraries were pooled and sequenced using two lanes of one HiSeq4000 flow cell to an average depth of 33.6 million reads per sample.  Strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina after poly(A) selection by the NEBNext poly(A) mRNA Isolation Module (New England Biolabs Inc.).  Samples were barcoded using the recommended NEBNext Multiplex Oligos.  Size range and quality of libraries were verified on the Agilent 2100 Bioanalyzer (Agilent Technologies).  RNA-seq libraries were quantified by quantitative polymerase chain reaction using the KAPA library quantification kit (KAPA Biosystems).  Each library was normalized to 2 nM and pooled in equimolar concentrations.  Paired-end 150 sequencing was performed on an Illumina HiSeq4000 (Illumina, San Diego, CA).  Libraries were pooled and sequenced using two lanes of one HiSeq4000 flow cell to an average depth of 33.6 million reads per sample.

value: Spinal cord

tag: gende

value: Male


title: cuff_rep1


title: Day1.Rituximab-T785-ISAC.2

value: SCID/beige

value: Day 1 post-treatment

value: Rituximab T785-ISAC


title: Day1.Rituximab-T785-ISAC.4


title: Day1.Rituximab-T785-ISAC.1


title: 2 CD SP140 SNP-/- LPS + TPT

value: CD SP140 SNP -/-


title: Day1.Rituximab-T785-ISAC.3


title: sham_rep1


title: Day1.Rituximab-T785-ISAC.5


title: Day1.Rituximab.5

value: Rituximab


title: 2 CD SP140 SNP-/- LPS + DMSO


title: 2 CD SP140 SNP-/- Con + ETO


title: Day1.Rituximab.4


title: 2 CD SP140 SNP-/- Con + TPT


title: HFD_8

city: Chicago

first: Raghavendra

last: Mirmira

state: IL

address: 900 E. 57th Street

institute: University of Chicago

data_processing:
CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat 3.1.0 was used for data normalization, data scaling, graph-based clustering, cluster marker genes idenfification, and integrative analysis of multiple samples.
muscat was used for differential gene expression analysis between conditions within a cell cluster of the intergrative analysis
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 file of filtered gene-barcode matrices

source_name: Cells from pancreatic islets

extract_protocol:
Single cell 3’ RNA-seq experiment was conducted using the Chromium single cell system (10x Genomics, Inc). Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics). Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v3 single cell reagent kit (10X Genomics). Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing library was then prepared with the amplified cDNA.
10X genomics 3' RNA-seq V3 single cell reagent kit

tag: Sex

tag: diet

value: HFD

value: 8 weeks old


title: Day1.Rituximab.2


title: HFD_2


title: ZSF1 obese rat dosed with Cmpd1 #5

city: Cambridge

first: Ju

last: Wang

state: MA

address: 610 Main Street

department: Inflammation & Immunology

institute: Pfizer Inc

data_processing:
40 M or more 2x100 paired end reads were generated from an Illumina HiSeq 4000 Platform
Following raw reads were filtered: reads containing adaptors, reads containinng N>10% (N represents the base connot be determined); reads containing low quality (Qscore<=5) bases which is over 50% of the total reads.
QuickRNASeq pipeline was used in reads mapping and counting: STAR 2.5.2.a was used for mapping; featureCounts subread-1.5.1 was used for counting; RSeQC was used for read QC; VarScan.v2.4.0 was used for SNP calling.
Genome_build: Genome fasta file is GRCh38.primary.genome.fa. Gene annotation file is GRCh38.gencode v25 annotation file. Gtf file is GRCh38.gencode.v25.gtf;  Bed file is GRCh38.gencode.v25.bed
Supplementary_files_format_and_content: Processed data is a tab delimited text file contains gene name as row, and the fpkm for that gene from each sample is the column.

organism: Rattus norvegicus

source_name: inguinal white adipose tissue

extract_protocol:
Tissues were homogenized with Tissulyzer (Qiagen) and RNA extraction was performed with RNeasy Plus Universal Kits (Qiagen 73404).
1 ug of RNA was used for cDNA library construction at BGI using a Truseq stranded mRNA kit (cat# 20020594, Illumina, Inc., San Diego, CA, USA) according to the manufacture's protocol.
RNA-Seq (HiSeq Strand-Specific Transcriptome)

value: inguinal white adipose tissue

value: Purina 5008 mixed with Cmpd1

tag: phenotype

value: obese


title: sham_rep2


title: HFD_1


title: 2 CD SP140 SNP-/- Con + DMSO

value: Blood


title: ZSF1 obese rat dosed with Cmpd1 #4


title: Day1.Rituximab.3

tag: timepoint


title: 1 CD SP140 SNP-/- LPS + ETO

value: Crohn's disease

value: LPS (100 ng/mL, 4h) + Etoposide (25 mM)


title: ZSF1 obese rat dosed with Cmpd1 #2


title: ZSF1 obese rat dosed with Cmpd1 #1


title: 1 CD SP140 SNP-/- LPS + TPT

value: PBMC

value: LPS (100 ng/mL, 4h) + Topotecan (100nM)


title: LFD_1

value: LFD


title: LFD_2

value: Male


title: 1 CD SP140 SNP-/- LPS + DMSO

value: LPS (100 ng/mL, 4h) + DMSO


title: LFD_3


title: ZSF1 obese rat with calorie restriction #5

value: Purina 5008

value: calorie restriction

value: lean


title: ZSF1 obese rat with calorie restriction #4


title: 1 CD SP140 SNP-/- Con + ETO

value: CD SP140 SNP -/-

value: Unstimulated control + Etoposide (25 mM)


title: 1 CD SP140 SNP-/- Con + TPT

value: Unstimulated control + Topotecan (100nM)


title: 1 CD SP140 SNP-/- Con + DMSO

value: Unstimulated control + DMSO


title: Day1.Rituximab.1

value: SCID/beige

value: Day 1 post-treatment

tag: replicate number

value: Rituximab


title: ZSF1 obese rat with calorie restriction #2

tag: tissue

value: inguinal white adipose tissue


title: ZSF1 obese rat with calorie restriction #1


title: ZSF1 obese rat dosed with Cmpd1 #3

value: Purina 5008 mixed with Cmpd1

value: obese


title: ZSF1 obese rat #5


title: ZSF1 obese rat with calorie restriction #3


title: ZSF1 obese rat #3


title: ZSF1 obese rat #2


title: ZSF1 obese rat #1


title: ZSF1 lean rat #4


title: ZSF1 lean rat #5


title: ZSF1 lean rat #2


title: ZSF1 obese rat #4


title: ZSF1 lean rat #1


title: ZSF1 lean rat #3


title: HFD_6

value: HFD

value: 8 weeks old


title: PBMCs-cDC2-R848-3

status: Public on Dec 02 2020

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

institute: Biozentrum

description: reporter code sets (Nanostring Technologies, nCounter_Hs_Myeloid_Innate_Immunity_V2 Panel)

hyb_protocol: Hybridization was performed as described in the manufacturers instruction. Briefly, samples were hybridized with reporter code sets (target-specific Reporter and Capture Probes) for 24h in a thermal cycler at 65°C

scan_protocol: nCounter Prep Station v4.1.0.1 was used. Scanning and image aquisition using the Nanostring Digital Analyzer.

data_processing: nanostring data were analyzed and exported using nSolver software (version 4.0). RUVg method was applied to remove the batch effect and data were normalized using NanoStringNorm according to 14 control genes and 40 housekeeping spikes genes. Differential gene expression analysis were conducted using edgeR

source_name: cDC2s isolated from PBMCs of a healthy individual, 3h R848-treated

label_protocol: Labeling was performed as described in the manufacturers instruction (Nanostring Technologies). Briefly, samples were labeled with reporter code sets (nCounter_Hs_Myeloid_Innate_Immunity_V2 Panel) consisting of many RNA capture probes targeting specific mRNAs. Each probe is labeled with a unique combination of fluorochromes (molecular barcode).

growth_protocol: cDC1 and cDC2 were sorted from PBMCs of healthy blood donors after enrichment with the EasySep Human Pan-DC Pre-Enrichment Kit (Stemcell Technologies) using a BD FACSAria II SOP. 1.5*10^5 isolated DCs were cultured for 3h at 37°C in optimized DC medium

extract_protocol: Cell pellets were lysed using 1/3 RLT buffer and sample mRNAs were stored at -80°C

treatment_protocol: Cells were stimulated with 5µg/ml R848 (TLR7-ligand) or control treated for 3h

tag: tag

value: PBMCs of a healthy blood donor


title: PBMCs-cDC2-Control-3

source_name: cDC2s isolated from PBMCs of a healthy individual, 3h control-treated


title: PBMCs-cDC2-R848-2


title: PBMCs-cDC2-R848-1


title: PBMCs-cDC1-R848-3

source_name: cDC1s isolated from PBMCs of a healthy individual, 3h R848-treated


title: PBMCs-cDC1-R848-2


title: PBMCs-cDC1-R848-1


title: PBMCs-cDC1-Control-3

source_name: cDC1s isolated from PBMCs of a healthy individual, 3h control-treated


title: OA 4

type: genomic

city: Xi'an

first: Yue

last: Fan

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

description: cartilage methylation

hyb_protocol: Amplified, hybridized to HumanMethylation450 array, stained and washed following standard protocol.

scan_protocol: iScan SQ scanner

data_processing: data was normalized and analyzed using minfi R packages.

label: Cy5 and Cy3

source_name: Knee cartilage

label_protocol: Standard Illumina protocol for Human Methylation 450 BeadChip

extract_protocol: QIAamp DNA Blood Mini Kit

tag: disease

value: OA

value: Male


title: OA 1

description: cartilage methylation


title: PBMCs-cDC1-Control-2

tag: cell type


title: PBMCs-cDC1-Control-1


title: PBMCs-cDC2-Control-1


title: PBMCs-cDC2-Control-2


title: OA 5

description: cartilage methylation

value: Female

tag: Age 65


title: Control 4

description: cartilage methylation

value: healthy control


title: OA 3

description: cartilage methylation


title: R_3: ∆orrA_3

city: Shanghai

first: Yinhua

last: Lu

address: 100 Guilin Road

department: College of Life Sciences

institute: Shanghai Normal University

description: Gene expression after growth on MS agar plate for 48h

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.
The gene expression ratio (n-fold change:  ∆ohkA/M145 or ∆orrA/M145) was calculated from the noramlized signal intensities.

organism: Streptomyces coelicolor

source_name: the ∆orrA mutant

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Cultures of Streptomyces coelicolor wild-type strain M145, the ∆ohkA and ∆orrA mutants grown on MS solid medium with plastic cellophane were collected at 48h.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The collected samples were frozen immediately in liquid nitrogen and then ground into powder.

tag: strain

tag: genotype

value: orrA mutant


title: KBD 5

description: cartilage methylation

value: KBD


title: R_2: ∆orrA_2


title: H_1: ∆ohkA _1

source_name: the ∆ohkA mutant

value: ohkA mutant


title: Control 3

description: cartilage methylation


title: R_1: ∆orrA_1


title: KBD 2

description: cartilage methylation

tag: Age 59


title: WT M145_2

source_name: the wild-type strain M145

value: wild-type


title: KBD 4

description: cartilage methylation


title: KBD 3

description: cartilage methylation

tag: Age 69


title: WT M145_1


title: Control 5

description: cartilage methylation

tag: age


title: H_3: ∆ohkA _3


title: H_2: ∆ohkA _2


title: Control 1

description: cartilage methylation

tag: Age 55


title: Control 2

description: cartilage methylation

tag: Age 46


title: OA 2

description: cartilage methylation

tag: Sex


title: BM mononuclear cells of MM22

city: Beijing

first: yuan

middle: jiu

last: yun

address: Beijing xizhimen station

institute: Company

hyb_protocol: Following labeling, cDNA was hybridized on a Clariom  D Assay(human, Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip Scanner 3000 7G

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

label: biotin

source_name: BM mononuclear cells from MM patient

label_protocol: Biotinylated cDNA was prepared from 250 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

extract_protocol: 0.5mL mononuclear cells of blood marrow samples were placed into 1.5ml EP tubes containing Trizol lysate and total RNA was extracted using the RNeasy Mini Kit according to the manufacturer's instruction.

treatment_protocol: BM mononuclear cells of multiple myeloma patients and normal donors were immediately stored in liquid nitrogen or stored in the -80 ℃ refrigerator after 2 hours

tag: subject status

value: multiple myeloma patient

tag: tissue/cell type

value: BM mononuclear cells


title: KBD 1

description: cartilage methylation


title: BM mononuclear cells of MM13


title: BM mononuclear cells of MM21


title: BM mononuclear cells of C11

source_name: BM mononuclear cells from normal donor

value: normal donor


title: BM mononuclear cells of MM2


title: Spo_L_M_negative_rep2

city: Vilnius

first: Elena

last: Serviene

address: Akademijos 2

country: Lithuania

institute: Nature Research Centre

data_processing:
Obtained reads were processed using CLC Genomics Workbench v. 12.0 (CLC Inc., Aarhus, Denmark) (http://www.clcbio.com). Raw reads were trimmed for sequencing adapters, ambiguous nucleotides (ambiguities 1), low quality sequences (limit = 0.01) and sequences less than 50 nt in length. Filtered reads were mapped to the S. paradoxus CBS432 reference genome (NCBI reference sequence: https://yjx1217.github.io/Yeast_PacBio_2016/data/, 5531 genes in total) using the following alignment scores: mismatch cost 2; minimum length fraction 0.9; minimum identity within the mapped sequence 0.99; maximum number of best-scoring hits for a read 30.
The expression values for each transcript were calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using CLC Genomic workbench v 12.0
Supplementary_files_format_and_content: Fold change

organism: Saccharomyces paradoxus

source_name: yeast cells

extract_protocol:
The total RNA was isolated using GeneJET RNA Purification Kit (Thermo Fisher), according to the Yeast Total RNA Purification Protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation


title: Spo_L_M_negative_rep3


title: BM mononuclear cells of C13


title: BM mononuclear cells of MM17


title: Spo_L_positive_M_negative_rep2


title: BM mononuclear cells of MM23


title: BM mononuclear cells of C18


title: BM mononuclear cells of MM15


title: BM mononuclear cells of MM16


title: BM mononuclear cells of MM7


title: BM mononuclear cells of C17


title: WT_40gen_vs_240gen_R3

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

hyb_protocol: Labeled probes were hybridized to microarrays in 8x15k format, made by Agilent (Design ID: 016322) using Gene Expression Hybridization Kit, Hybridization Chamber and Hybridization oven (all from Agilent) for 17 hours at 65°C.

scan_protocol: After washing using Gene Expression Wash Buffer Set (Agilent) the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5μm and 100% laser power. PMT gain was set to around 600 and 750 for 532 nm and 635 nm excitation respectively with minor adjustments to normalize images. Feature extraction was done using GenePix Pro 6.1 (Molecular Devices, USA).

data_processing: GPR files were analyzed further with Acuity 4.0 software starting with lowess normalization. Normalized Log2 Ratio data from technical replicates (dye swap) were averaged.

organism: Saccharomyces cerevisiae W303

source_name: cells from continuous culture

label_protocol: Samples of total RNA (5μg) were labeled with QuickAmp Labeling Kit, Two-Color (Agilent) with Cy3- and Cy5-UTP according to the manufacturer’s protocol.

growth_protocol: Continuous cultures of W303 Saccharomyces cerevisiae strain were conducted in chemostat at a dilution rate of 0.17–0.18 volumes per hour, and the culture was continued for 240 generations at a constant temperature of 30 °C. Cell samples were collected after 40 genrations and after 240 generations. Cells were sedimented by centrifugation, flash-frozen in LN2 and kept at –80oC.

extract_protocol: Total RNA was prepared from deeply frozen yeast cell pellet samples using the hot acidic phenol procedure.

tag: growth period

value: 40 generations

value: 240 generations


title: Spo_L_positive_M_negative_rep3


title: WT_40gen_vs_240gen_R1


title: BM mononuclear cells of C9


title: BM mononuclear cells of MM18


title: Wt2_L_M_positive_rep3


title: BM mononuclear cells of C1


title: BM mononuclear cells of C8


title: Wt2_L_M_positive_rep1


title: Pet_L_M_negative_rep3


title: BM mononuclear cells of C6


title: Spo_L_positive_M_negative_rep1


title: Pet_L_positive_M_negative_rep3


title: Wt1_L_M_positive_rep3


title: Pet_L_M_negative_rep2


title: Pet_L_M_negative_rep1


title: Wt2_L_M_positive_rep2


title: Pet_L_positive_M_negative_rep2


title: Wt1_L_M_positive_rep1


title: Pet_L_positive_M_negative_rep1


title: Wt1_L_M_positive_rep2


title: BM mononuclear cells of C3


title: H3K9me2_ChIP-Seq_O.sativa_60d

first: Lei

last: Li

state: Beijing

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

description: H3K9me2 ChIP-Seq O.sativa 60d

data_processing:
Typically 16-25 million read pairs for each library were obtained after removal of adaptor and low quality reads by flexbar2.5.
Clean reads were then mapped to genomes by Bowtie with default parameters (-v 0 –m 1). For repressive marks (H3K9me2 and H3K27me), we simply let Bowtie to randomly choose multi-hit positions when reads align to repeat-rich regions (-v 0 –M1 --best).
Since a single nucleosome often occupies about 147bp DNA, we linked mapped read pairs into single end reads for all ChIP libraries.
The resulting bed file was then used to call signal enrichment peaks by MACS2 and at the same time a genome wide signal density file was generated by genomeCoverageBed. The final peaks and density results were used for downstream qualitative and quantitative analysis.
We developed a pipeline to simultaneously visualize the comparative genomic features and the chromatin state.
Genome_build: We downloaded and used the rice genome version 6.1 from the MSU official ftp.  Four IOMAP (International Oryza Map Alignment Project) genomes, Oryza glaberrima, Oryza punctata, Oryza brachyantha RS2, Leersia perrieri and the sorgJGI2.0 were applied for bowtie mapping.

organism: Oryza sativa Japonica Group

source_name: tillering stage plant

growth_protocol: green-house plant

extract_protocol:
Sixty-day fresh above-ground tissues were collected at the tillering stage for O. sativa vg. japonica, O. glaberrima, O. punctata, O. brachyantha, L. perrieri, and S. bicolor. Two-week fresh above-ground tissues at the seedling stage were also collected for O. sativa and O. brachyantha. ChIP experiments were performed as described in Gendrel et al. 2005 with minor modification. Briefly, 4g (for seedling stage) or 8g (for tillering stage) tissue were fine grounded in liquid nitrogen, followed by 3% formaldehyde fixation step. Nucleus were extracted and chromatin was sonicated into 300-500bp fragments in Bioruptor (Diagenode). Since each antibody has its own concentration and binding efficiency, we tested the optimal antibody volume for each antibodies. Typically we use 20ul antibody (1ug/ul) in a 350ul-400ul hybrid solution.
The final DNA precipitation was used for library construction with the NEB Next N6240 kit (New England BioLabs) and decoded by Hiseq 2000 (Ilumina) with pair end 90bp strategy.

tag: tissue

value: aerial tissue

tag: developmental stage

value: tillering stage 60d after germination

tag: antibody

value: H3K9me2 (ab1220 Abcam)


title: H3K4me3_ChIP-Seq_O.sativa_60d

description: H3K4me3 ChIP-Seq O.sativa 60d

value: H3K4me3 (07-473 Millipore )


title: input_H3K9me2_H3K4me3_ChIP-Seq_O.sativa_60d

description: input H3K9me2 H3K4me3 ChIP-Seq O.sativa 60d

value: no antibody


title: input_H3K56Ac_ChIP-Seq_O.sativa_2weeks

description: input H3K56Ac ChIP-Seq O.sativa 2weeks

source_name: seedling stage plant

value: seedling shoot

value: seedling stage 2 weeks after germination


title: H3K27me_ChIP-Seq_O.sativa_2weeks

description: H3K27me ChIP-Seq O.sativa 2weeks

value: H3K27me (07448 Millipore)


title: H3K56Ac_ChIP-Seq_O.sativa_2weeks

description: H3K56Ac ChIP-Seq O.sativa 2weeks

value: H3K56Ac (39281 Active Motif)