title: Huh7 cells, control_rep3

description:
counts.txt.gz
tpms.txt.gz
normal_rep3

source_name: Huh7 cells

tag: passages


title: GMSB_040_PBMC_TDF

status: Public on Jul 07 2020

type: RNA

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

country: USA

institute: University of Washington

hyb_protocol: Standard as recommended by Illumina, except that the temperature was 48C

scan_protocol: Standard Illumina protocol using Illumina iScan system

data_processing:
The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 10 samples were included in the analysis.
Matrix non-normalized table: This table contains raw signal intensity values and detection p-values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC from GMSB_040 treated with TDF

label_protocol: 50 ng of total RNA was labeled using the Ovation PicoSL WTA System V2 kit and the Encore BiotinIL kit (both NuGEN)

extract_protocol: Total RNA was extracted using the Qiagen RNeasy mini kit

tag: tissue

value: PBMC

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

value: injectable

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Positive

tag: rin

tag: valid

value: Included


title: 39_S22_PBMC_macrophages_m2_MCSF_IL4

type: SRA

city: Basel

first: Klas

last: Hatje

state: Basel

address: Grenzacherstrasse 124

country: Switzerland

institute: Roche Pharma Research and Early Development

description:
processed data file: iPSCderived_myeloid_cells_counts.gct
processed data file: iPSCderived_myeloid_cells_rpkms.gct

library_source: transcriptomic

data_processing:
Base calling was performed with BCL to FASTQ file converter bcl2fastq v2.17.1.14 from Illumina (https://support.illumina.com/downloads.html).
In order to estimate gene expression levels, paired-end RNASeq reads were mapped to the human genome (hg38) with STAR aligner version 2.5.2a using default mapping parameters (Dobin et al. 2013).
Aligned reads were quality checked with FastQC and MultiQC version 1.7 (Andrews 2010, Ewels 2016).
Numbers of mapped reads for all RefSeq transcript variants of a gene (counts) were combined into a single value by using SAMTOOLS software (Li et al. 2009) and normalized as RPKMs (number of mapped reads per kilobase transcript per million sequenced reads, Mortazavi et al. 2008).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: iPSCderived_myeloid_cells_counts.gct: Read counts in GCT gene expression matrix format.
Supplementary_files_format_and_content: iPSCderived_myeloid_cells_counts.gct: RPKMs in GCT gene expression matrix format.

molecule: polyA RNA

source_name: PBMC

growth_protocol:
Generation of macrophage progenitors from iPSC: The main elements were previously published by Wilgenburg et al. Briefly, to obtain uniformed EBs, iPSCs were plated into Aggrewell 800 (StemCell Technologies) plates. 2 ml mTesR1, supplemented with 10 μM ROCK inhibitor (Y27632, Callbiochem) and containing a single cell suspension of 4*10e6 single iPSCs, was added to each Aggrewell and centrifuged for 3 minutes at 100 g to assure an even and fast distribution of the iPSCs to the aggrewell microwells. The next day mesoderm induction and subsequent hemogenic endothelium induction was started by exchange of 75% (replacing twice 1 ml of the 2 ml in each well) of the mTeSR1 media with fresh mTeSR1 media supplemented with 50ng/ml hBMP4, 50ng/ml hVEGF and 20ng/ml hSCF, and repeated the following 2 days. At day 4 of differentiation EBs were harvested by gently dislodging the EBs by rinsing the aggrewells with PBS. EBs were collected in a 40µm strainer and transferred to factory media, consisting of XVIVO15 media (Lonza) supplemented with 2mM Glutamax, 1% Penicillin/Streptomycin, 50 ug/ml Mercaptoethanol, M-CSF (100 ng/ml) and IL3 (25 ng/ml). EBs were plated with a density of 1 EBs/cm2 on cell culture vessels (2-1000 cm2/ 6 well to cell disk). In contrast to the description of Wilgenburg et al., the EBs were plated on dishes pre-coated for 1 h at RT with growth factor reduced Matrigel (Corning) diluted in cold DMEM F12 1:1 1x Glutamax (Gibco). In order to allow adherence of EBs, EBs were evenly distributed by slow movements and culture vessels were placed immediately at 37°C with 5% CO2 without any further disturbance for the first week of differentiation. The following two weeks of differentiation 50 % of the starting volume of fresh factory media was added once per week. From the third week of differentiation half-media changes were done, until the production and release of (CD14+) macrophage progenitors (iPSC monocyte) in the supernatant was observed. From this point on, complete media change with fresh factory media was performed twice a week.
Macrophage progenitor harvesting and macrophage differentiation: Macrophage progenitors were collected from the supernatant by centrifugation (4 minutes, 300 g), cells were re-suspended, counted and quality control (CD68, Ki67, CD11b and CD14) of marker expressions by flow cytometry was performed weekly. Macrophage progenitors were transferred into differentiation media and differentiated to macrophages. According to application requirements, macrophages were either directly differentiated in the required plate format or pre-differentiated for 6 days and then re-plated, to the final plate format one day prior to assay start. For differentiation, cells were cultured in XVIVO 15 (supplemented with 2 mM Glutamax, 1 % Penstrep and 100 ng/ml M-CSF) at a density of 150.000 cells per cm2. Media was changed 3 days after plating; cells were differentiated for 7 days. Macrophage progenitors or CD14 positive cells from Lonza were either differentiated into unpolarized (M0) Macrophages using XIVIVO15 media supplemented with 2 mM Glutamax, 1 % Pen/Strep and 100 ng/ml M-CSF or polarized into pro-inflammatory (M1) or regulatory phenotype (M2). M1 polarization was induced by the addition of GM-CSF and 50 ng/ml IFNγ instead of M-CSF. M2 polarization was induced by addition of 100 ng/ml M-CSF and 50 ng/ml IL-4. If not stated otherwise cells were differentiated for 7 days prior to the experiments.

extract_protocol:
After the polarization period, the cells were lyzed and RNA was extracted using RNeasy Mini Kit from Qiagen. RNA content and purity were determined using Nanodrop. RNA integrity was assessed using Agilent Bioanalyzer. RNA sequencing was performed using the HiSeq4000 sequencing system.
mRNA sequencing libraries were prepared using the TruSeq Stranded mRNA library prep kit (Illumina) according to manufacturer's instructions.

tag: cell type

value: PBMC-derived M2 macrophage


title: WNT3A treatment  donor 2

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

data_processing:
Illumina software used for basecalling.
Reads quality was checked, trimmed and filtered by FastQC and FastX-toolkit
Raw data fastq files were generated on NextSeq using bcl2fastq2 V2.19 software
Reads mapping with Homo sapiens UCSC hg38 using TopHat2
FPKM estimation of reference genes and transcripts using Cufflinks 2
Assembly of novel transcriptome with Cufflinks 2 and Cuffmerge
Variant calling (SNVs and small indels) with the Isaac Variant caller
Genes and isoforms differential expression using Cuffdiff2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Stem cells isolated from human exfoliated deciduous teeth

extract_protocol:
After treatment, total RNA was isolated using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment


title: GMSB_027_PBMC_Placebo

source_name: PBMC from GMSB_027 treated with Placebo

tag: tissue

tag: ptid

tag: visit

tag: collectiondate

tag: age

tag: arm

value: C

value: Placebo

value: placebo


title: 38_S10_PBMC_macrophages_m1_GMCSF_INFG

value: PBMC-derived M1 macrophage


title: 37_S43_PBMC_macrophages_m0_MCSF

value: PBMC-derived M0 macrophage


title: bFGF treatment donor 3

value: bFGF


title: 36_S21_PBMC_macrophages_m2_MCSF_IL4


title: WNT3A treatment donor 1


title: GMSB_028_PBMC_FTC/TDF

source_name: PBMC from GMSB_028 treated with FTC/TDF

value: B

tag: drug

value: FTC/TDF

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

tag: birthcontrolepi

value: oral

value: NoHC

value: Excluded:undetectable TDF


title: GMSB_031_PBMC_FTC/TDF

source_name: PBMC from GMSB_031 treated with FTC/TDF

value: PBMC

value: prep

value: Yes

value: Nohist

tag: birthcontrollab

tag: mpa

tag: lng

tag: eng

tag: net

tag: nugent

value: Negative

value: unknown


title: bFGF treatment donor 1

tag: treatment


title: Control-donor 3

value: control


title: GMSB_024_PBMC_TDF

source_name: PBMC from GMSB_024 treated with TDF

tag: tissue

tag: ptid

tag: visit

value: A

value: TDF

value: Positive

tag: rin

tag: valid

value: Included


title: 34_S42_PBMC_macrophages_m0_MCSF

tag: cell type

value: PBMC-derived M0 macrophage


title: GMSB_025_PBMC_TDF

source_name: PBMC from GMSB_025 treated with TDF

tag: collectiondate

tag: age

tag: arm

tag: drug

tag: prep

tag: tdfngperml

value: implant


title: GMSB_023_PBMC_FTC/TDF

source_name: PBMC from GMSB_023 treated with FTC/TDF

value: B

value: FTC/TDF

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

value: Excluded:MDS outlier


title: 33_S32_PBMC_macrophages_m2_MCSF_IL4

value: PBMC-derived M2 macrophage


title: GMSB_022_PBMC_TDF

source_name: PBMC from GMSB_022 treated with TDF

tag: tissue

value: PBMC

tag: ptid

value: No

value: precontraceptive

value: injectable

tag: eng

tag: net

tag: nugent

value: Excluded:undetectable TDF


title: bFGF treatment donor 2

tag: treatment

value: bFGF


title: Control-donor 2

value: control


title: GMSB_026_PBMC_Placebo

source_name: PBMC from GMSB_026 treated with Placebo

tag: visit

tag: collectiondate

tag: age

value: C

value: Placebo

value: placebo

value: Nohist

value: NoHC

value: Negative

tag: rin

tag: valid


title: GMSB_017_PBMC_Placebo

source_name: PBMC from GMSB_017 treated with Placebo

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: oral

value: NonDecided

value: Positive


title: 35_S20_PBMC_macrophages_m1_GMCSF_INFG

tag: cell type

value: PBMC-derived M1 macrophage


title: GMSB_016_PBMC_TDF

source_name: PBMC from GMSB_016 treated with TDF

tag: tissue

value: PBMC

value: A

value: TDF

value: prep

value: Yes

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa

tag: lng

value: Included


title: GMSB_021_PBMC_TDF

source_name: PBMC from GMSB_021 treated with TDF

tag: ptid

tag: visit

tag: eng

tag: net

tag: nugent


title: GMSB_020_PBMC_TDF

source_name: PBMC from GMSB_020 treated with TDF

tag: collectiondate

tag: age

tag: arm

tag: rin

tag: valid


title: GMSB_015_PBMC_TDF

source_name: PBMC from GMSB_015 treated with TDF

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: implant


title: 31_S19_PBMC_macrophages_m0_MCSF

tag: cell type

value: PBMC-derived M0 macrophage


title: GMSB_012_PBMC_Placebo

source_name: PBMC from GMSB_012 treated with Placebo

tag: tissue

value: C

value: Placebo

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa


title: GMSB_019_PBMC_TDF

source_name: PBMC from GMSB_019 treated with TDF

tag: ptid

tag: visit

value: precontraceptive

value: injectable

tag: lng

tag: eng

tag: net


title: 32_S31_PBMC_macrophages_m1_GMCSF_INFG

source_name: PBMC


title: GMSB_014_PBMC_FTC/TDF

source_name: PBMC from GMSB_014 treated with FTC/TDF

tag: collectiondate

tag: age

tag: arm

value: B

value: FTC/TDF

value: NoHC

tag: nugent

tag: rin


title: GMSB_013_PBMC_FTC/TDF

source_name: PBMC from GMSB_013 treated with FTC/TDF

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

value: Positive

tag: valid

value: Excluded:undetectable TDF


title: 30_S30_IPS_Microglia_microglia_CD34_GMCSF

source_name: iPSC

tag: cell type

value: iPSC-derived microglia cell


title: GMSB_018_PBMC_Placebo

source_name: PBMC from GMSB_018 treated with Placebo

tag: tissue

value: PBMC

value: placebo

tag: tdfresultdate

tag: birthcontrolepi

tag: birthcontrollab

tag: mpa


title: Control-donor 1

source_name: Stem cells isolated from human exfoliated deciduous teeth

tag: treatment

value: control


title: GMSB_011_PBMC_FTC/TDF

source_name: PBMC from GMSB_011 treated with FTC/TDF

tag: ptid

tag: visit

tag: collectiondate

value: prep

value: Yes

tag: lng

tag: eng

tag: net

value: Indeterminate

value: unknown

value: Included


title: 28_S29_IPS_Microglia_microglia_CD34_GMCSF


title: GMSB_007_PBMC_TDF

source_name: PBMC from GMSB_007 treated with TDF

tag: age

tag: arm

value: A

tag: drug

value: TDF

tag: prep

value: oral

tag: nugent

tag: rin


title: 26_S9_IPS_Microglia_microglia_CD34_GMCSF

tag: cell type


title: 1.5_shC_DamLmnB1

city: Baltimore

first: Karen

last: Reddy

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

institute: Johns Hopkins University

description: LmnC RNAi

library_source: genomic

data_processing:
Library strategy: DamID-Seq
DamID-seq analysis—DamID-seq reads were processed using LADetector (available at https://github.com/thereddylab/LADetector)
Reads were quality trimmed using a sliding window quality score average over 3 bases and a minimum score cutoff of 30.
This was followed by trimming any matching overlap between read-ends and sequencing or DamID adaptor-primer sequence. Reads containing a DamID adaptor-primer sequence were split and adaptor-primer sequence removed.
All resulting reads greater than 20 bp were aligned to mm9 using Bowtie (Langmead et al., 2009) with parameters “—tryhard–best–m 1.” Unaligned reads had 13 bases trimmed from the 5′ end and remapped, and the resultant unmapped reads were trimmed 13 bases from the 3′ end and remapped. Total aligned reads were assigned to DpnI bins, with reads straddling bin boundaries counting toward both. Prior to scoring, a value of 0.5 was added to bins with no reads. Bins falling in unaligned regions were removed prior to analysis. DamID scores were calculated for all non-zero bins as the log2 ratio of Dam-POI over unfused Dam.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files named X.bed (eg shA.bed) include genomic coordinates and scores (log2 ratios) for each sample per Dpn bin.  Tab-delimited text files named X_LADs.bed (eg shA_LADs.bed) include genomic coordinates of LADs
Supplementary_files_format_and_content: Regarding the processed files, each condition has a dam.fastq and a dam_lmn.fastq raw data files.  The dam.fastq files are controls which we use as a normaliser and hence 2 raw files would yield just 1 set (a pair) of processed files (ie shX.bed and shX_LADs.bed)

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEFs were cultured according to their established protocols, in medium containing DMEM High, 10% FBS, Penicillin/Streptomycin and L-glutamine.

extract_protocol:
MEFs were collected by trypsinization and DNA was isolated using QIAamp DNA Mini kit (Qiagen,  51304), followed by ethanol precipitation and resuspension to 1 µg/ul in 10 mM Tris, pH 8.0.  DamID was performed as described previously (L.Guelen et al, Nature 2008)
post-DamID amplified material was randomized  by performing an end repair reaction, followed by ligation and sonication.  Randomized fragments were subjected to sequencing library preparation with NEBNext Ultra DNA library prep kit

treatment_protocol: Cells were treated with lentivirus encoding shRNA against either LmnA or LmnC, selected with puromycin at 2ug/mL and allowed to recover.  Cells were then transduced with lentiviruses harboring an expression cassette for either Dam-only, Dam-Lamin B1and subsequently cultured in DMEM High, 10% FBS, Penicillin/Streptomycin and L-glutamine.

tag: strain

tag: genotype

value: wild type


title: 1.5_shB1_DamLmnA

description: LmnB1 RNAi


title: 1.5_shB1_Dam

description: LmnB1 RNAi


title: 1.5_shC_Dam

description: LmnC RNAi


title: GMSB_009_PBMC_FTC/TDF

source_name: PBMC from GMSB_009 treated with FTC/TDF

tag: tissue

value: B

value: FTC/TDF

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

tag: birthcontrolepi

value: precontraceptive

tag: birthcontrollab

value: NoHC

tag: mpa

tag: valid


title: 27_S28_IPS_Microglia_microglia_CD34_GMCSF

value: iPSC-derived microglia cell


title: 1.5_shA_DamLmnB1

description: LmnA RNAi


title: GMSB_005_PBMC_FTC/TDF

source_name: PBMC from GMSB_005 treated with FTC/TDF

value: PBMC

tag: ptid

tag: visit

tag: collectiondate

tag: age

value: Nohist

value: injectable

tag: lng

tag: eng

tag: net

value: Negative


title: GMSB_010_PBMC_FTC/TDF

source_name: PBMC from GMSB_010 treated with FTC/TDF

tag: arm

tag: drug

tag: prep

value: prep

value: Yes

tag: nugent

value: Positive

tag: rin


title: GMSB_008_PBMC_Placebo

source_name: PBMC from GMSB_008 treated with Placebo

tag: tissue

value: C

value: Placebo

value: placebo

tag: tdfngperml

tag: tdfdetected

tag: tdfresultdate

value: implant

value: Included


title: 25_S8_PBMC_monocytes

tag: cell type

value: PBMC monocyte


title: GMSB_002_PBMC_TDF

source_name: PBMC from GMSB_002 treated with TDF

tag: ptid

value: A

value: TDF

tag: birthcontrolepi

value: oral

tag: birthcontrollab

tag: mpa

tag: valid


title: SG12424241_256902510045_S001_GE1_1105_Oct12_2_3

city: Koshi

first: Manabu

last: Kurita

country: Japan

institute: Kyushu Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute

hyb_protocol: Hybridization and washing were performed according to the manufacturer's instructions.

scan_protocol: Labeled and hybridized slides were scanned using a SureScan Microarray Scanner G4900DA (Agilent Technologies), and the data set was trimmed using Agilent Feature Extraction Software (ver. 11.5.1.1, Agilent Technologies).

data_processing: The data set was trimmed using Agilent Feature Extraction Software (ver. 11.5.1.1, Agilent Technologies).

organism: Cryptomeria japonica

source_name: wild-type 0840

label_protocol: Total RNA from each sample was amplified and labelled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: Cryptomeria japonica was propagated from a single tree by grafting, and grown for several years.

extract_protocol: Three-centimeter twigs of lateral branch apexes were collected from each individual and used for total RNA extraction. Total RNA was extracted using a Plant RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Some branches of GA-treated clones were treated with GA3 in the beginning of July in 2015 to induce production of male strobili.

value: lateral branch apexes

tag: treatment

value: control

tag: sampling point


title: 29_S41_IPS_Microglia_microglia_CD34_GMCSF

value: iPSC-derived microglia cell


title: GMSB_003_PBMC_FTC/TDF

source_name: PBMC from GMSB_003 treated with FTC/TDF

value: PBMC

tag: visit

tag: collectiondate

tag: age

tag: arm

value: B

value: FTC/TDF

tag: lng

tag: eng

tag: net


title: SG12424241_256902510045_S001_GE1_1105_Oct12_2_4

tag: tissue


title: GMSB_006_PBMC_FTC/TDF

source_name: PBMC from GMSB_006 treated with FTC/TDF

tag: drug

tag: prep

value: prep

tag: tdfngperml

tag: tdfdetected

value: Yes

tag: tdfresultdate

value: injectable

tag: nugent

tag: rin

value: Excluded:MDS outlier


title: P2

city: Tianjin

first: zhongcheng

last: zhou

state: Tianjin

address: 94 Weijin Road, Nankai District

department: Cell biology and Genetics

country: China

institute: Nankai Univerisity

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Pold3 inducible-knockout embryonic stem cells

extract_protocol:
Total RNA was purified using a RNA mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: KH2 ESCs

tag: passage


title: GMSB_001_PBMC_TDF

source_name: PBMC from GMSB_001 treated with TDF

tag: ptid

tag: visit

tag: birthcontrolepi

value: Nohist

tag: birthcontrollab

value: NoHC

tag: mpa

value: Positive

tag: valid


title: 24_S7_PBMC_monocytes

source_name: PBMC

tag: cell type

value: PBMC monocyte


title: SG12424241_256902510045_S001_GE1_1105_Oct12_2_1

tag: tissue

tag: treatment

tag: sampling point


title: P1


title: 1.5_shA_Dam

description: LmnA RNAi

tag: strain

tag: genotype

value: wild type


title: SG12424241_256902510045_S001_GE1_1105_Oct12_1_3


title: SG12424241_256902510045_S001_GE1_1105_Oct12_1_4


title: Zebrafish Dnmt1 Mut3 (EpiGnome) reanalysis

city: Freiburg im Breisgau

first: Thomas

last: Boehm

address: Stübeweg 51

department: Immunology

country: Germany

institute: MPI-IE Freiburg

description:
Zebrafish Dnmt1 Mut3 (EpiGnome)
GSM2607717

data_processing:
Basecalling was performed with Illumina HiSeq Control Software/RTA version 1.18.64.
Raw sequencing reads were trimmed with cutadapt version 1.9.1 (Martin, 2011) as follows: first 2 (TruSeq) or 6 (Epignome) 5'-most nucleotides were hard-trimmed and Illumina adapter sequences removed.
Bisulfite-specific operations on reads and reference genome were performed with methylCtools version 0.9.4 (Hovestadt et al., 2014). Bisulfite-converted reads were mapped to bisulfite-converted GRCz10 zebrafish genome with bwa-mem version 0.7.12 separately for the two library types.
Back-converted bam files were sorted with samtools version 1.3.1, PCR duplicates removed and read group information added with Picard tools v1.136. The two resulting bam files per sample were merged with samtools and  methylation bias profiled with MethylDackel v0.1.7. Methylated and unmethylated read counts per CpG position were extracted with methylCtools v0.9.4 with mapping quality threshold of 10, SNP detection, counting only one of two overlapping paired end reads, skipping 5 nucleotides from each read length and zero-padding of uncovered positions.
Data postprocessing was performed in R version 3.2.3. Raw methylation values were set to NA for CpG positions with at least 0.25 SNP allelic frequency as well as for positions with aggregate coverage of less than 10 reads. Single CpG methylation values were aggregated per target genomic interval as mean values.
Genome_build: GRCz10
Supplementary_files_format_and_content: Whole genome single CpG as well as mean methylation values in target genomic intervals are summarized in corresponding tab-separated tables for all samples.

organism: Danio rerio

source_name: dnmt1 mutant rep3

extract_protocol:
Genomic DNA was extracted from 3 dnmt1+/+ and 3 dnmt1-/- zebrafish at 18 dpf using the DNeasy blood and tissue kit (Qiagen).
1mg and 0.5mg of DNA was used for bisulfite reactions and library construction using the TruSeq DNA PCR-free library preparation kit (Illumina) and the EpiGnome Methyl-Seq kit (Epicentre), respectively. The fragments were sequenced in paired-end 100bp mode on 1 lane of Illumina HiSeq 2500 instrument.

value: whole embryo

value: mixed background

tag: surface phenotype


title: SG12424241_256902510045_S001_GE1_1105_Oct12_1_2

value: lateral branch apexes

value: control


title: Zebrafish Dnmt1 Mut3 (TruSeq) reanalysis

description:
Zebrafish Dnmt1 Mut3 (TruSeq)
GSM2607716


title: 22_S18_PBMC_monocytes


title: GMSB_004_PBMC_FTC/TDF

source_name: PBMC from GMSB_004 treated with FTC/TDF

value: PBMC

tag: collectiondate

tag: age

tag: arm

tag: drug

tag: prep

tag: tdfngperml

tag: tdfdetected

value: No

tag: tdfresultdate

value: precontraceptive

tag: lng

tag: eng

tag: net

tag: nugent

value: Excluded:undetectable TDF


title: P0

tag: cell line

tag: passage


title: Zebrafish Dnmt1 Mut2 (EpiGnome) reanalysis

description:
Zebrafish Dnmt1 Mut2 (EpiGnome)
GSM2607715

source_name: dnmt1 mutant rep2

tag: tissue

tag: strain


title: 23_S40_PBMC_monocytes

tag: cell type


title: 21_S17_PBMC_monocytes


title: 20_S27_IPS_monocytes

source_name: iPSC

value: iPSC-derived macrophage progenitors


title: Zebrafish Dnmt1 Mut2 (TruSeq) reanalysis

description:
Zebrafish Dnmt1 Mut2 (TruSeq)
GSM2607714

tag: genotype

tag: surface phenotype


title: 19_S16_IPS_monocytes


title: Gcr1-U-12-ChIP-rep2

city: seoul

first: seungwoo

last: cha

address: 1 Gwanak-ro, Gwanak-gu

department: School of Chemical and Biological Engineering

country: South Korea

institute: Seoul National University

description: ChIP-seq for Gcr1(U) after diauxic shift #2

data_processing:
Image analysis and base calling was performed using HisSeq control software (v1.8.4), and conversion of BCL to fastq format and demultiplexing was processed with bcl2fastq (v1.8.2).
Read quality was assessed using FastQC (v0.10.1), showing about 90% bases above Q30 across all samples.
Reads were aligned to the yeast reference genome (sacCer3 assembly) using BWA (v0.7.15) with the allowance of two mismatches, and redundant reads with identical coordinates were filtered out using Picard (v2.92)
ChIP peaks was called using HOMER ‘findPeaks’ with -style ‘factor’. Called peaks were filtered with the following conditions; (1) peak score ≥ 100, (2) poisson p-value threshold relative to local tag count < 1E-10, (3) fold enrichment over local tag count ≥ 2, and (4) relation to genes.
Peaks overlapped between exponential phase and diauxic shift of Gcr1U and Gcr1S were further selected to compare their binding pattern in the two mutants, and ChIP reads fallen in peaks were then collected using BEDTools ‘intersectbed’.
Genome_build: sacCer3
Supplementary_files_format_and_content: peak files: tab-delimited text files including peak ID, chromosome, start position, end position, strand, normalized tag count, focus ratio, findPeaks score, fold change vs local, p-value vs local, and clonal fold change.

organism: Saccharomyces cerevisiae

growth_protocol: All samples were cultivated in 10mL of YPD medium containing 2% glucose, in a 50 mL erlenmeyer flask. The initial OD600 was 0.5 and incubated at 30℃, with shaking 170 rpm.

extract_protocol:
Cells were lysed with acid-washed glass beads and sonicated, and immunoprecipitated with IgG sepharose beads. RNaseI and proteinase K were treated to eliminate RNA and proteins, and DNA was reverse-crosslinked by high salt and 65℃ overnight incubation. Final DNA was eluted by Phenol/Chloroform method and pelleted.
Libraries were prepared from ChIP DNA fragments (1 to 5 ng) of Gcr1U and Gcr1S with two replicates using ThruPLEX DNA-Seq Kit (TaKaRa) according to the manufacturer’s protocol. In brief, DNA fragments were subjected to steps of end-repair, 3’ A-tailing, and adapter ligation. Then DNA was PCR amplified (15 cycles) and purified. Single-end sequencing with 50 cycles was performed using a HiSeq2500 (Illumina) instrument according to manufacturer’s protocol.

treatment_protocol: Final 1% concentration of formaldehyde were treated in order to crosslink the protein and DNA for 25 min, and 250 mM of glycin was added to quench the reaction.

value: diauxic shift

value: whole cell

tag: chip antibody

value: IgG-sepharose fast flow 6


title: Gcr1-U-12-ChIP-rep1

description: ChIP-seq for Gcr1(U) after diauxic shift #1


title: Zebrafish Dnmt1 Mut1 (TruSeq) reanalysis

description:
Zebrafish Dnmt1 Mut1 (TruSeq)
GSM2607712

source_name: dnmt1 mutant rep1


title: Gcr1-S-12-ChIP-rep1

description: ChIP-seq for Gcr1(S) after diauxic shift #1


title: Gcr1-S-12-ChIP-rep2

description: ChIP-seq for Gcr1(S) after diauxic shift #2


title: Zebrafish WT3 (EpiGnome) reanalysis

description:
Zebrafish WT3 (EpiGnome)
GSM2607711

source_name: control rep3

value: wt


title: Gcr1-S-6-ChIP-rep1

description: ChIP-seq for Gcr1(S) at exponential phase #1

value: exponential phase


title: Gcr1-S-6-ChIP-rep2

description: ChIP-seq for Gcr1(S) at exponential phase #2


title: Zebrafish Dnmt1 Mut1 (EpiGnome) reanalysis

description:
Zebrafish Dnmt1 Mut1 (EpiGnome)
GSM2607713


title: 18_S15_IPS_monocytes


title: Zebrafish WT3 (TruSeq) reanalysis

description:
Zebrafish WT3 (TruSeq)
GSM2607710


title: SG12424241_256902510042_S001_GE1_1105_Oct12_2_4

source_name: wild-type 1725

tag: treatment

tag: sampling point


title: 17_S6_IPS_monocytes


title: 16_S5_IPS_monocytes


title: SG12424241_256902510045_S001_GE1_1105_Oct12_1_1


title: Gcr1-U-6-ChIP-rep2

description: ChIP-seq for Gcr1(U) at exponential phase #2


title: SG12424241_256902510042_S001_GE1_1105_Oct12_2_3


title: Gcr1-U-6-ChIP-rep1

description: ChIP-seq for Gcr1(U) at exponential phase #1


title: SG12424241_256902510045_S001_GE1_1105_Oct12_2_2


title: Zebrafish WT2 (TruSeq) reanalysis

description:
Zebrafish WT2 (TruSeq)
GSM2607708

source_name: control rep2


title: Zebrafish WT2 (EpiGnome) reanalysis

description:
Zebrafish WT2 (EpiGnome)
GSM2607709


title: SG12424241_256902510042_S001_GE1_1105_Oct12_2_2


title: Zebrafish WT1 (EpiGnome) reanalysis

description:
Zebrafish WT1 (EpiGnome)
GSM2607707

source_name: control rep1


title: 14_S38_IPS_macrophages_m1_GMCSF_INFG

value: iPSC-derived M1 macrophage


title: 13_S14_IPS_macrophages_m0_MCSF

value: iPSC-derived M0 macrophage


title: 12_S26_IPS_macrophages_m2_MCSF_IL4

value: iPSC-derived M2 macrophage


title: Zebrafish WT1 (TruSeq) reanalysis

description:
Zebrafish WT1 (TruSeq)
GSM2607706

value: whole embryo


title: SG12424241_256902510042_S001_GE1_1105_Oct12_2_1


title: 15_S39_IPS_macrophages_m2_MCSF_IL4


title: SG12424241_256902510042_S001_GE1_1105_Oct12_1_4


title: SG12424241_256902510042_S001_GE1_1105_Oct12_1_2


title: SG12424241_256902510042_S001_GE1_1105_Oct12_1_1


title: SG12424241_256902510041_S001_GE1_1105_Oct12_2_3

source_name: wild-type 1503


title: SG12424241_256902510041_S001_GE1_1105_Oct12_2_2


title: 11_S25_IPS_macrophages_m1_GMCSF_INFG


title: SG12424241_256902510041_S001_GE1_1105_Oct12_2_4


title: 10_S4_IPS_macrophages_m0_MCSF


title: Zebrafish sperm transmitting G4 rep1 (EpiGnome)

description:
transmitting G4 rep1
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome

data_processing:
Basecalling was performed with Illumina HiSeq Control Software/RTA version 1.18.64.
Raw sequencing reads were trimmed with cutadapt version 1.9.1 as follows: first 2 (TruSeq) or 6 (Epignome) 5'-most nucleotides were hard-trimmed and Illumina adapter sequences removed.
Bisulfite-specific operations on reads and reference genome were performed with methylCtools version 0.9.4 (Hovestadt et al., 2014). Bisulfite-converted reads were mapped to bisulfite-converted GRCz10 zebrafish genome with bwa-mem version 0.7.12 separately for the two library types.
Back-converted bam files were sorted with samtools version 1.3.1, PCR duplicates removed and read group information added with Picard tools v1.136. The two resulting bam files per sample were merged with samtools and  methylation bias profiled with MethylDackel v0.1.7. Methylated and unmethylated read counts per CpG position were extracted with methylCtools v0.9.4 with mapping quality threshold of 10, SNP detection, counting only one of two overlapping paired end reads, skipping 5 nucleotides from each read length and zero-padding of uncovered positions.
Data postprocessing was performed in R version 3.2.3. Raw methylation values were set to NA for CpG positions with at least 0.25 SNP allelic frequency as well as for positions with aggregate coverage of less than 10 reads.
Methylation values for single CpG positions (complete cases) were used as input to metilene v 0.2-6 [doi:10.1101/gr.196394.115]. Wildtype samples were passed in as group A, and mutant as group B. DMRs detected by metilene were re-evaluated for differential methylation in R. At least 20% of detected CpGs per DMR were required and at most 1 sample with an NA value was allowed. Methylation values of detected CpGs were aggregated as mean per interval per replicate sample.  Differential methylation was re-evaluated using limma on logit-transformed interval means.    DMRs were filtered to retain those with  FDR<5%.     Filtered DMRs were further annotated with the distance to the nearest gene using bedtools version 2-2.19.0 and ensembl release 83 gene models for GRCz10.
Bam files obtained through read alignment were re-analyzed with the WGBS workflow in the  snakePipes [https://doi.org/10.1093/bioinformatics/btz436] 1.2.1 version modified to accommodate user-defined formula and contrast [https://github.com/katsikora/snakepipes_fork].  Methylation values were extracted for genomic intervals identifed as hypo- and hyper-methylated DMRs in the comparison of the G1 MT vs WT fish sperm, separately.  Aggregate methylation values per interval were obtained as above for the DMRs. The matrix of logit-transformed methylation values per interval was input to differential analysis with limma version 3.26.9 [https://doi.org/10.1093/nar/gkv007]. The following linear model was fit '~1+batch+condition:batch' where batch differentiated G1 and G4 samples, while condition differentiated treatment (G1 mutant and G4*) from control (G1 wildtype and G4+) samples. Finally, a topTable of differentially methylated intervals was extracted for the contrast 'batchG4_conditionTreatment-batchG1_conditionTreatment'. Results were filtered for an absolute difference of at least 20% and FDR<2% .
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-separated tables with single CpG methylation values per sample source are available, as well as tables with differentially methylated regions in G1 and G4 sperm, and tables with G1 sperm hypo- and hyper-methylated DMRs re-evaluated in G4 sperm samples.
Supplementary_files_format_and_content: Number of intervals filtered with absolute difference of at least 20% and FDR<2% were counted.

source_name: Generation 4 sperm

extract_protocol:
Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen).
1mg and 0.5mg of DNA was used for bisulfite reactions and library construction using the TruSeq DNA PCR-free library preparation kit (Illumina) and the EpiGnome Methyl-Seq kit (Epicentre), respectively. The fragments were sequenced in paired-end 100bp mode on 1 lane of Illumina HiSeq 2500 instrument.

value: mixed background


title: Zebrafish sperm transmitting G4 rep2 (EpiGnome)

description:
transmitting G4 rep2
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome


title: Zebrafish sperm non-transmitting G4 rep3 (EpiGnome)

description:
non-transmitting G4 rep3
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome


title: 09_S3_IPS_macrophages_m2_MCSF_IL4

description:
processed data file: iPSCderived_myeloid_cells_counts.gct
processed data file: iPSCderived_myeloid_cells_rpkms.gct


title: 08_S13_IPS_macrophages_m1_GMCSF_INFG


title: Zebrafish sperm transmitting G4 rep3 (EpiGnome)

description:
transmitting G4 rep3
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome


title: Zebrafish sperm non-transmitting G4 rep2 (EpiGnome)

description:
non-transmitting G4 rep2
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome


title: SG12424241_256902510042_S001_GE1_1105_Oct12_1_3

value: lateral branch apexes


title: 07_S2_IPS_macrophages_m0_MCSF


title: 06_S37_IPS_macrophages_m2_MCSF_IL4


title: Zebrafish sperm non-transmitting G4 rep1 (EpiGnome)

description:
non-transmitting G4  rep1
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome


title: Zebrafish sperm transmitting G4 rep3 (TruSeq)

description:
transmitting G4 rep3
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq


title: MCF-7_Apigenin_rep3

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: Gene expression after 24h of exposure

hyb_protocol: Sample hybridization (Agilent) was performed by the GeT-Biopuces Platform in Toulouse, France.

scan_protocol: Microarray scanning (Agilent) was performed by the GeT-Biopuces Platform in Toulouse, France.

data_processing: Data processing (Feature extraction software, Agilent) was performed by the GeT-Biopuces Platform in Toulouse, France.

label_protocol: Sample labeling was performed by the GeT-Biopuces Platform in Toulouse, France.

growth_protocol: MCF-7 cells were maintained in DMEM containing 4.5 g/L glucose supplemented with nonessential amino acids, penicillin/streptomycinand 10 % FBS at 37°C under 5 % CO2

extract_protocol: Total RNA was extracted with an RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Cells were cultured for 30 h in steroid- and serum-deprived DMEM without phenol red and with 1.5 % charcoal/dextran-stripped FBS and then, they were treated with 1 nM E2, 10 nM zearalenone and 10 µM apigenin or solvent as negative control.

value: Apigenin 24h


title: 05_S36_IPS_macrophages_m1_GMCSF_INFG


title: MCF-7_Apigenin_rep2

description: Gene expression after 24h of exposure


title: SG12424241_256902510041_S001_GE1_1105_Oct12_2_1

value: control


title: Zebrafish sperm transmitting G4 rep2 (TruSeq)

description:
transmitting G4 rep2
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq


title: 04_S24_IPS_macrophages_m0_MCSF


title: MCF-7_Estradiol_rep4

description: Gene expression after 24h of exposure


title: MCF-7_Apigenin_rep1

description: Gene expression after 24h of exposure


title: MCF-7_Estradiol_rep2

description: Gene expression after 24h of exposure


title: SG12424241_256902510041_S001_GE1_1105_Oct12_1_4


title: SG12424241_256902510041_S001_GE1_1105_Oct12_1_1


title: Zebrafish sperm transmitting G4 rep1 (TruSeq)

description:
transmitting G4 rep1
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq


title: MCF-7_Apigenin_rep4

description: Gene expression after 24h of exposure


title: SG12424241_256902510041_S001_GE1_1105_Oct12_1_3


title: SG12424241_256902510041_S001_GE1_1105_Oct12_1_2


title: MCF-7_Estradiol_rep3

description: Gene expression after 24h of exposure


title: Zebrafish sperm non-transmitting G4 rep3 (TruSeq)

description:
non-transmitting G4 rep3
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq


title: MCF-7_Estradiol_rep1

description: Gene expression after 24h of exposure


title: SG12424241_256902510038_S001_GE1_1105_Oct12_2_4


title: 03_S1_IPS_macrophages_m2_MCSF_IL4


title: SG12424241_256902510038_S001_GE1_1105_Oct12_2_3


title: MCF-7_Zearalenone_rep4

description: Gene expression after 24h of exposure

value: Zearalenone 24h


title: SG12424241_256902510038_S001_GE1_1105_Oct12_2_2


title: 02_S35_IPS_macrophages_m1_GMCSF_INFG


title: 01_S12_IPS_macrophages_m0_MCSF


title: SG12424241_256902510038_S001_GE1_1105_Oct12_2_1


title: 58-SB431542+VEGFA 48h

first: Jitao David

last: Zhang

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

institute: F. Hoffmann-La Roche

description: hPSC-EC were treated with SB431542+VEGFA 50 ng/mL for 48h

data_processing:
Basecalling and sample de-multiplexing was performed with CASAVA-1.8.4 and default parameters
Reads were quality check with fastqc v0.11.5 default parameters
Reads for each sample/replicate were mapped against the human genome assembly using STAR read aligner v2.5.2a
RefSeq annotated genes were quantified with samtools v1.5 and in-house scripts
Genome_build: hg38
Supplementary_files_format_and_content: Read counts per gene

source_name: SB431542+VEGFA treated hPSC-EC 48h

growth_protocol: Expansion medium consisting of StemPro with 50 ng/mL of VEGFA was used for the first cell division, after which cells were cultured using VascuLife VEGF Endothelial Medium Complete Kit (LifeLine Cell Technology). The final composition of supplements added to the media was as follows: 10% FBS, 4 mM L-glutamine, 0.75 U/mL heparin sulfate, 5 ng/mL FGF-2, 5 ng/mL EGF, 5 ng/mL VEGFA, 15 ng/mL IGF1, 1 µg/mL hydrocortizone hemisuccinate, and 50 µg/mL Ascorbic acid.

extract_protocol:
Cells were lysed in 350 μL RLT lysis buffer (Qiagen) + β-mercaptoethanol (Sigma-Aldrich, 1%) and subsequently vortexed for 1 min at room temperature before being snap frozen. RNA isolation was performed using an automated  automated Maxwell Total RNA purification kit inculding DNaseI digestion (Promega).
Total RNA was subjected to oligo (dT) capture and enrichment, and the resulting mRNA fraction was used to construct cDNA libraries. Sequencing was performed on an Illumina HiSeq 4000 platform using the standard protocol (TruSeq Stranded Total RNA Library, Illumina) that generates approximately 30 million reads of 50 base pairs per sample.

treatment_protocol: hPSC-ECs were treated for 8h or 48 h with DMSO or TGF-beta receptor inhbitors (RepSox or SB431542, both at 10 µM). Cells were stimulated or not with 50 ng/mL VEGFA.

value: Pluripotent stem-cell derived endothelial cells

tag: sample label

tag: replicate


title: Zebrafish sperm non-transmitting G4 rep1 (TruSeq)

description:
non-transmitting G4  rep1
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq


title: Zebrafish sperm dnmt1 mutant rep2 (EpiGnome)

description:
dnmt1 mutant rep2
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome

source_name: Generation 1 sperm


title: Zebrafish sperm dnmt1 mutant rep3 (EpiGnome)

description:
dnmt1 mutant rep3
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome


title: MCF-7_Zearalenone_rep2

description: Gene expression after 24h of exposure


title: MCF-7_Zearalenone_rep3

description: Gene expression after 24h of exposure


title: 55-Repsox+VEGFA 48h

description: hPSC-EC were treated with RepSox+VEGFA 50 ng/mL for 48h

source_name: Repsox+VEGFA treated hPSC-EC 48h

value: RepSox+VEGFA 48h


title: 57-SB431542+VEGFA 48h


title: Zebrafish sperm dnmt1 mutant rep1 (EpiGnome)

description:
dnmt1 mutant rep1
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome


title: MCF-7_Cont_rep4

description: Gene expression after 24h of exposure

value: solvent 24h


title: Zebrafish sperm non-transmitting G4 rep2 (TruSeq)

description:
non-transmitting G4 rep2
G4sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq


title: MCF-7_Zearalenone_rep1

description: Gene expression after 24h of exposure


title: SG12424241_256902510038_S001_GE1_1105_Oct12_1_4


title: Zebrafish sperm control rep3 (EpiGnome)

description:
control rep3
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome


title: NHM-1-3-miRCon1

city: Salt Lake City

first: Robert

middle: L

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah

description: mRNA-Sequencing

data_processing:
fastq files were aligned to GRCh37 using Bowtie.
BAM files resulting from the alignments were summarized to small RNA reference group (miRBase 21) and counted using the feature counts algorithm of DESEq2 in R.
Expression data was normalized using the DESeq2 package's median of ratios method in R.
Differentially expressed genes (£5% false discovery rate) were identified by DESeq2's General Linear Modeling and Bayesian statistics.
Genome_build: human reference genome GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes normalized gene count values from DESeq2 for each sample.

source_name: neonatal foreskin-derived melanocytes

growth_protocol: Melanocytes were plated in 10cm culture-treated dishes and placed in a 5% CO2 37 °C incubator.

extract_protocol:
RNA was isolated using the Trizol Reagent (Ambion/ThermoFisher Scientific) and processed as per manufacturer’s instructions. Resulting RNA was then processed using the RNeasy Power Clean Pro Cleanup kit (Qiagen) and processed as per manufacturer's instructions.
MicroRNA Library Preparation was performed by SeqMatic using the SeqMaticMicroRNA Library Preparation Kit and protocols.

tag: background strain

value: MIRControl


title: NHM-1-3-miRCon2

description: mRNA-Sequencing


title: SG12424241_256902510038_S001_GE1_1105_Oct12_1_1


title: MCF-7_Cont_rep3

description: Gene expression after 24h of exposure


title: 54-Repsox+VEGFA 48h


title: Zebrafish sperm control rep2 (EpiGnome)

description:
control rep2
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome


title: 56-SB431542+VEGFA 48h


title: SG12424241_256902510038_S001_GE1_1105_Oct12_1_2


title: NHM-1-3-ZAP

description: mRNA-Sequencing

value: no treatment control


title: 53-Repsox+VEGFA 48h


title: SG12424241_256902510036_S001_GE1_1105_Oct12_2_4

source_name: wild-type 0840


title: Zebrafish sperm control rep1 (EpiGnome)

description:
control rep1
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
EpiGnome


title: MCF-7_Cont_rep1

description: Gene expression after 24h of exposure


title: SG12424241_256902510036_S001_GE1_1105_Oct12_2_3


title: 52-DMSO+VEGFA 48h

description: hPSC-EC were treated with DMSO+VEGFA 50 ng/mL for 48h

source_name: DMSO+VEGFA treated hPSC-EC 48h

value: DMSO+VEGFA 48h


title: MCF-7_Cont_rep2

description: Gene expression after 24h of exposure


title: NHM-1-1-miR-211-5p

description: mRNA-Sequencing

value: MIR211-5p overexpression


title: 51-DMSO+VEGFA 48h


title: NHM-1-1-miR-21-5p

description: mRNA-Sequencing

value: MIR21-5p overexpression


title: Zebrafish sperm dnmt1 mutant rep3 (TruSeq)

description:
dnmt1 mutant rep3
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq


title: SG12424241_256902510036_S001_GE1_1105_Oct12_2_2


title: Zebrafish sperm dnmt1 mutant rep2 (TruSeq)

description:
dnmt1 mutant rep2
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq


title: SG12424241_256902510036_S001_GE1_1105_Oct12_2_1


title: 50-DMSO+VEGFA 48h


title: NHM-1-1-miRCon2

description: mRNA-Sequencing


title: 49-Repsox+VEGFA 8h

description: hPSC-EC were treated with RepSox 10 µM+VEGFA 50 ng/mL for 8h

source_name: Repsox+VEGFA treated hPSC-EC 8h

value: RepSox+VEGFA 8h


title: NHM-1-1-miR-328-3p

description: mRNA-Sequencing

value: MIR328-3p overexpression


title: SG12424241_256902510036_S001_GE1_1105_Oct12_1_4


title: SG12424241_256902510038_S001_GE1_1105_Oct12_1_3


title: Zebrafish sperm dnmt1 mutant rep1 (TruSeq)

description:
dnmt1 mutant rep1
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq


title: NHM-1-1-miRCon1

description: mRNA-Sequencing


title: Zebrafish sperm control rep3 (TruSeq)

description:
control rep3
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq

value: wt


title: 48-Repsox+VEGFA 8h


title: FS009M-miR-328-3p

description: mRNA-Sequencing


title: Zebrafish sperm control rep2 (TruSeq)

description:
control rep2
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq


title: FS009M-miR-211-5p

description: mRNA-Sequencing


title: 47-Repsox+VEGFA 8h


title: SG12424241_256902510036_S001_GE1_1105_Oct12_1_2


title: 46-SB431542+VEGFA 8h

description: hPSC-EC were treated with SB431542 10 µM+VEGFA 50 ng/mL for 8h

source_name: SB431542+VEGFA treated hPSC-EC 8h

value: SB431542+VEGFA 8h


title: Zebrafish sperm control rep1 (TruSeq)

description:
control rep1
G1sperm_singleCpG_whole_genome_methylation.tsv.gz
TruSeq

value: mixed background


title: FS009M-miR-21-5p

description: mRNA-Sequencing


title: NHM-1-1-ZAP

description: mRNA-Sequencing


title: 45-SB431542+VEGFA 8h


title: Zebrafish whole embryo Dnmt1 Mut3 (TruSeq)

source_name: dnmt1 mutant rep3

value: whole embryo


title: FS009M-miRCon1

description: mRNA-Sequencing


title: FS009M-ZAP

description: mRNA-Sequencing


title: 43-DMSO+VEGFA 8h

description: hPSC-EC were treated with DMSO+VEGFA 50 ng/mL for 8h

source_name: DMSO+VEGFA treated hPSC-EC 8h

value: DMSO+VEGFA 8h


title: SG12424241_256902510036_S001_GE1_1105_Oct12_1_1

value: lateral branch apexes


title: Zebrafish whole embryo Dnmt1 Mut2 (TruSeq)

source_name: dnmt1 mutant rep2


title: Zebrafish whole embryo Dnmt1 Mut3 (EpiGnome)


title: Zebrafish whole embryo Dnmt1 Mut2 (EpiGnome)


title: SG12424241_256902510035_S001_GE1_1105_Oct12_2_4


title: SG12424241_256902510036_S001_GE1_1105_Oct12_1_3


title: Zebrafish whole embryo Dnmt1 Mut1 (EpiGnome)

source_name: dnmt1 mutant rep1


title: 42-DMSO+VEGFA 8h


title: 41-DMSO+VEGFA 8h


title: SG12424241_256902510035_S001_GE1_1105_Oct12_2_2


title: FS007L-miR-211-5p

description: mRNA-Sequencing


title: SG12424241_256902510035_S001_GE1_1105_Oct12_2_1


title: SG12424241_256902510035_S001_GE1_1105_Oct12_1_4


title: SG12424241_256902510035_S001_GE1_1105_Oct12_1_3


title: SG12424241_256902510035_S001_GE1_1105_Oct12_2_3


title: SG12424241_256902510035_S001_GE1_1105_Oct12_1_2


title: Zebrafish whole embryo Dnmt1 Mut1 (TruSeq)


title: 32-RepSox 48h

description: hPSC-EC were treated with RepSox 10 µM for 48h

source_name: RepSox treated hPSC-EC 48h

value: RepSox 48h


title: Zebrafish whole embryo WT3 (EpiGnome)

source_name: control rep3


title: Cornus_officinalis_Seed

city: Chiba

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

institute: Chiba University

data_processing:
For de novo transcriptome assembly, we pre-processed raw reads, and removed adapter sequences, empty reads, reads with ambiguous ‘N’ bases > 5%, raw reads of low quality (Q<20), and raw reads with an average length less than 30 bases. Filtering of raw reads was performed using Trimmomatic program (Bolger et al., 2014), resulting into paired end raw reads, and unpaired reads which lost its corresponding sequence partner due to quality control.
For generation of the de novo transcriptome assembly, three popular assemblers were used, CLC genomics workbench (https://www.qiagenbioinformatics.com/ ), and Trinity (Grabherr et al., 2011) with their default parameters and SoAPdeNOVO -TRANS (Xi et al., 2014)  with six different k-mer sizes, namely 31, 41, 51, 63, 71, and 91, of which k-mer 41 having best assembly statistics was selected for further use . The SOAPdeNOVO assembly with k-mer size 41 was concatenated with individual assembly obtained from Trinity  and CLC genomics workbench  to obtain the final assembly of C. officinalis. The final assembly obtained was further processed using CD-HIT  (Li and Godzik 2006) to remove any sequence redundancy resulting in our final assembly of 304,371 unigenes with N50 value as 1250bps
We then processed these contigs for read alignment and abundance estimation using Bowtie2.0 (Langmead et al., 2009) and RSEM (Li et al., 2011), respectively. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method.
Supplementary_files_format_and_content: Processed files were generated using RSEM program. Clean reads for each tissues were aligned on Cornus officinalis de novo transcriptome assembly, and abundace were measured using RSEM. Content of each file contains Unigene_id and FPKM values for each tissues. FPKM values for each tissues were used for furthur analysis.
Supplementary_files_format_and_content: tab-delimited text file includes unigene_id, and FPKM values for each tissues. FPKM values were calculated using RSEM program. FPKM values for each tissue was merged against unigene_id

organism: Cornus officinalis

source_name: Plant Material ID MY_Cornus_officinalis#01 in Chiba University, Japan

growth_protocol: All seven tissues, namely young leaf, mature leaf, young stem, mature stem, seed, pericarp and inflorescence were harvested from C. officinalis growing in the natural conditions at Medicinal garden, Graduate School of Pharmaceutical Sciences, Chiba University

extract_protocol:
Frozen samples of C. officinalis were powdered using a Multi Beads Shocker (Yasui Kikai, Japan) for subsequent RNA extraction. Total RNA for each of the seven tissues was extracted using RNeasy Plant Mini Kit (Qiagen, USA), according to the manufacturer’s instruction.
cDNA library was then prepared using SureSelect Strand Specific RNA Library kit (Agilent 150 Technologies, USA) according to the manufacturer’s specifications. mRNA was isolated from total RNA of each tissue using beads containing oligo(dt), which was then added with fragmentation buffer to shear mRNA into short fragments and used as a template for the synthesis of first strand cDNA synthesis using random hexamer primers. The cDNA library for Illumina sequencing was prepared using SureSelect Strand Specific RNA Library kit (Agilent, USA) according to the manufacturer’s instruction.

treatment_protocol: Not applicable

tag: tissues

value: Seed

tag: age


title: SG12424241_256902510035_S001_GE1_1105_Oct12_1_1

source_name: wild-type 1503


title: FS007L-miRCon1

description: mRNA-Sequencing


title: Cornus_officinalis_Pericarp

department: Graduate School of Pharmaceutical Sciences

value: Pericarp


title: Zebrafish whole embryo WT3 (TruSeq)


title: Cornus_officinalis_Inflorescence

value: Inflorescence


title: 30-RepSox 48h

value: Pluripotent stem-cell derived endothelial cells


title: FS007L-ZAP

description: mRNA-Sequencing

value: no treatment control


title: 29-RepSox 48h


title: Zebrafish whole embryo WT2 (EpiGnome)

source_name: control rep2


title: NHM-1-3-miR-328-3p

description: mRNA-Sequencing


title: FS007L-miR-328-3p

description: mRNA-Sequencing


title: Cornus_officinalis_Young_Stem

value: Young Stem


title: Zebrafish whole embryo WT2 (TruSeq)


title: 28-SB431542 48h

description: hPSC-EC were treated with SB431542 10 µM for 48h

source_name: SB431542 treated hPSC-EC 48h


title: FS007L-miR-21-5p

description: mRNA-Sequencing


title: 27-SB431542 48h


title: NHM-1-3-miR-21-5p

description: mRNA-Sequencing


title: Cornus_officinalis_Mature_Leaf

value: Mature Leaf


title: 31-RepSox 48h


title: 26-SB431542 48h


title: 25-SB431542 48h


title: Cornus_officinalis_Mature_Stem

value: Mature Stem


title: H3K27Ac_shEts1_2-1

city: Ann Arbor

first: Mark

middle: Yat-fung

last: Chiang

state: MI

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

institute: University of Michigan

data_processing:
ChIP-Seq: Reads were aligned to the hg19 genome assembly using bwa-aln and bwa-sampe (bwa version 0.7.12)
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq: Data were filtered to remove PCR duplicates and reads mapping to >2 genomic sites. Then bigwig display files were generated with deepTools bamCoverage and UCSC wigToBigWig, and bed peak files were generated with Homer findPeaks (“style -factor” for transcription factors and “style -histone” for H3K27ac).

source_name: THP-6 T-ALL cell line

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone or Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Cells were crosslinked for most samples by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS. For Ets1,  Cells were crosslinked with 2 mM DSG and 1% formaldehyde. For H3K27ac, cells were crosslinked with 1% formaldehyde at room temperature. Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a QSonica Q800 bath sonicator in 0.3% SDS-containing lysis buffer. Samples were diluted 1:3.3 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples, 1:8diluted sonicated chromatin (whole cell extract; wce), was added directly to the reverse crosslinking step without immunoprecipitation.
Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced (38 bp x 2) on illumina NextSeq.

treatment_protocol: THP-6 T-ALL cells were lentivirally transduced with pLKO.1-type shRNA for 2 days  and then selected with puromycin for 2 days prior to harvesting.

value: THP-6 T-ALLs

tag: transduction

value: Ets1-silencing shRNA

tag: disease

value: T lymphoblastic leukemia/lymphoma

value: T lymphocyte

tag: antibody

value: H3K27ac (Active Motif, pAb 39133 )


title: H3K27Ac_shEts1_2-2

tag: cell line


title: 22-DMSO 48h

description: hPSC-EC were treated with DMSO for 48h

source_name: DMSO treated hPSC-EC 48h

tag: tissue

value: DMSO 48h


title: NHM-1-3-miR-211-5p

description: mRNA-Sequencing

source_name: neonatal foreskin-derived melanocytes

value: MIR211-5p overexpression


title: H3K27Ac_shEts1_3-1


title: H3K27Ac_shEts1_3-2


title: P5 [RNA-Seq]

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

institute: Martin Luther University Halle-Wittenberg

description:
DE_Thyroid_totalRNA_all.csv
DE_Thyroid_totalRNA_ATC_others_all.csv

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.4.2) with parameters -q 10 -O 7 -m 20
Trimmed reads were mapped against the human genome (hg19 UCSC) using TopHat2 (v 2.0.12) with parameters  -r 50 -p  6  -g 20 –b2-N 1
Mapped reads were summarized using featureCounts (v 1.4.6) with parameters -p  -M -t exon -g gene_id and Ensembl gene annotations (GRCh 37.75)
Differential gene expression was assessed using R/edgeR (v 3.12.1) using TMM normalization
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text file including FPM, log2 fold change and false discovery rate values for each sample

source_name: primary thyroid tumor

extract_protocol:
RNA extraction was performed using the miRNeasy Isolation Kit (Quiagen) for miRNA and Total RNA isolation, according to the manufacturer's instructions from human tumor and non-transformed tissue.
500 ng of total RNA was depleted of ribosomal RNA using the RiboMinus kit (Life Technologies) according to the instructions of the manufacturer. Depleted RNA was then fragmented by addition of 5  fragmentation buffer (200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and heating at 94 °C for 3 min in a thermocycler followed by ethanol precipitation with ammonium acetate and GlycoBlue (Life Technologies) as carrier. Fragmented RNA was then reversed transcribed using random hexamer and Superscript III (Life Technologies). The second strand was synthesized using the TargetAmp kit (Epicentre) according to the instructions of the manufacturer. The final steps of library preparation, e.g. blunt end repair, adapter ligation, adapter fill-in and amplification were done according to Meyer and Kircher (2010, PMID: 20516186). The barcoded libraries were purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. A pool of up to 10 libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 2x100 bp was performed with an IlluminaHighScan-SQ sequencer at the sequencing core facility of the IZKF Leipzig (Faculty of Medicine, University Leipzig) using version 3 chemistry and flowcell according to the instructions of the manufacturer.

tag: tumor subtype

value: PTC

value: thyroid


title: H3K27Ac_shControl-2

value: non-silencing shRNA

tag: cell type


title: 21-DMSO 48h

description: hPSC-EC were treated with DMSO for 48h


title: p2_uncultured_1

city: Irvine

first: Devon

last: Lawson

state: CA

address: 839 Health Sciences Rd

department: Physiology and Biophysics

institute: University of California, Irvine

data_processing:
Quality check was done using fastqc software, version 0.11.7.
Reads were aligned to GRCh38/hg38 from UCSC using Spliced Transcripts Alignment to a Reference (STAR) software, version 2.5.2a.
Differential expression analysis was performed using DESeq2, version 1.28.1.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: pdx_combined_counts.txt: Matrix with raw counts for every gene and every sample.
Supplementary_files_format_and_content: filtered_data.csv: Filtered data excludes genes with 0 counts.
Supplementary_files_format_and_content: Cultured.DE.Up.In.All.csv: Filtered cultured DE results used for GO term analysis.
Supplementary_files_format_and_content: Uncultured.DE.Up.In.All.csv: Filtered uncultured DE results used for GO term analysis.
Supplementary_files_format_and_content: DE_results.csv: DE results

source_name: HCI002 PDX cells

growth_protocol: HCI010 and HCI002 PDX cells were cultured in Matrigel and EpiCult-B Medium for 2 weeks.

extract_protocol:
Uncultured cells were extracted from PDX tumors. Cultured cells were harvested after 2 weeks in culture. Spheres were dissociated to a single cell suspension using dispase and trypsin. Uncultured and cultured cells were stained for FACS using human-specific CD298 and mouse-specific MHCI antibodies.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: HCI002 PDX cells

tag: condition

value: uncultured


title: Cornus_officinalis_Young_Leaf

value: Young Leaf


title: Zebrafish whole embryo WT1 (EpiGnome)

source_name: control rep1

value: whole embryo

tag: genotype

value: wt

tag: strain

value: mixed background

tag: surface phenotype


title: P6 [RNA-Seq]


title: P1 [RNA-Seq]


title: P4 [RNA-Seq]


title: Zebrafish whole embryo WT1 (TruSeq)


title: p2_cultured_3

value: cultured


title: p2_cultured_2


title: 12-RepSox 8h

description: hPSC-EC were treated with RepSox 10 µM for 8h

source_name: RepSox treated hPSC-EC 8h

value: Pluripotent stem-cell derived endothelial cells

tag: treatment

value: RepSox 8h


title: P2 [RNA-Seq]


title: p2_cultured_1


title: P3 [RNA-Seq]


title: p2_uncultured_3


title: p2_uncultured_2


title: 24-DMSO 48h

description: hPSC-EC were treated with DMSO for 48h

tag: sample label


title: N3 [RNA-Seq]

source_name: non-transformed thyroid tissue

value: NT

value: non-transformed thyroid tissue


title: p10_uncultured_3

source_name: HCI010 PDX cells

value: HCI010 PDX cells


title: 23-DMSO 48h

description: hPSC-EC were treated with DMSO for 48h

value: DMSO 48h

tag: replicate


title: 11-RepSox 8h


title: N5 [RNA-Seq]


title: Rbpj_shEts1_2-1

value: THP-6 T-ALLs

value: Ets1-silencing shRNA

value: T lymphoblastic leukemia/lymphoma

value: T lymphocyte

value: Rbpj (Cell Signaling Technology, 5313)


title: 10-RepSox 8h


title: Rbpj_shEts1_3-2


title: 9-RepSox 8h


title: p10_uncultured_2

value: uncultured


title: Rbpj_shEts1_3-1


title: N8 [RNA-Seq]


title: H3K27Ac_shControl-1

value: non-silencing shRNA

value: H3K27ac (Active Motif, pAb 39133 )


title: N7 [RNA-Seq]


title: N2 [RNA-Seq]


title: p10_cultured_3


title: Rbpj_shControl-2


title: 8-SB431542 8h

description: hPSC-EC were treated with SB431542 10 µM for 8h

source_name: SB431542 treated hPSC-EC 8h


title: 7-SB431542 8h


title: p10_cultured_2


title: N4 [RNA-Seq]


title: Rbpj_shControl-1


title: Rbpj_shEts1_2-2


title: p10_cultured_1


title: Input

value: Non-transduced THP-6 T-ALL cells


title: 5-SB431542 8h


title: F4 [RNA-Seq]

value: FTC

value: thyroid


title: 4-DMSO 8h

description: hPSC-EC were treated with DMSO for 8h

source_name: DMSO treated hPSC-EC 8h

value: Pluripotent stem-cell derived endothelial cells

value: DMSO 8h


title: F2 [RNA-Seq]


title: ICN1_shEts1_2-2

value: ICN1 (Cell Signaling Technology, 4147s)


title: Rh30, Ets1-sh2, replicate 3

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

description:
R30Et2_3
R30Et2_3_1.genes.results

data_processing:
raw fastq files were processed with RSEM using bowtie2 and default parameters
 Reads were mapped to the Ensembl v92 transcriptome (hg38)
Differential gene expression was calculated using the voom function in limma after low abundance genes were removed (total count across all samples < 200)
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file containing RSEM count values

growth_protocol: Rh41 and Rh30 cells were grown in RPMI with 10% Fetal bovine serum, 1% Pen/Strep, 10mM Hepes, 1X MEM non-essential amino acids, and 1mM Sodium Pyruvate.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen), and further purified using the Qiagen MinElute column kit.
Illumina directional mRNA prep; per Novogene protocol for PE150 Illumina NGS

treatment_protocol: Cells were transduced with control (Scrambled), KDM3A-targeting or Ets1-targeing shRNA lentivirus and selected with 1 ug/ml Puromycin.

value: Rh30 (SJRH30; ATCC CRL-2061)

value: Rhabdomyosarcoma Cell line

tag: genotype/variation


title: p10_uncultured_1

value: HCI010 PDX cells


title: Rh30, Ets1-sh2, replicate 2

description:
R30Et2_2
R30Et2_2_1.genes.results


title: ICN1_shEts1_2-1

value: THP-6 T-ALLs


title: 3-DMSO 8h

description: hPSC-EC were treated with DMSO for 8h


title: F1 [RNA-Seq]


title: F3 [RNA-Seq]


title: Rh30, Ets1-sh1, replicate 3

description:
R30Et1_3
R30Et1_3_1.genes.results


title: F5 [RNA-Seq]


title: ICN1_shControl-2


title: ICN1_shEts1_3-1

value: Ets1-silencing shRNA


title: Rh30, Ets1-sh1, replicate 2

description:
R30Et1_2
R30Et1_2_1.genes.results


title: 6-SB431542 8h


title: Rh30, Ets1-sh2, replicate 1

description:
R30Et2_1
R30Et2_1_1.genes.results


title: 2-DMSO 8h

description: hPSC-EC were treated with DMSO for 8h


title: Rh30, KDM3A-sh2, replicate 3

description:
R303A2_3
R303A2_3_1.genes.results


title: A7_4_GFP+, SAM24327042 Clone A7_8

description: GFP+ cells represent CLDN5+

source_name: sorted hPSC-EC GFP+ (CLDN5+)

growth_protocol: Expansion medium consisting of StemPro with 50 ng/mL of VEGFA was used for the first cell division, after which cells were cultured using VascuLife VEGF Endothelial Medium Complete Kit (LifeLine Cell Technology). The final composition of supplements added to the media was as follows: 10% FBS, 4 mM L-glutamine, 0.75 U/mL heparin sulfate, 5 ng/mL FGF-2, 5 ng/mL EGF, 5 ng/mL VEGFA, 15 ng/mL IGF1, 1 µg/mL hydrocortizone hemisuccinate, and 50 µg/mL Ascorbic acid. SB431542 (10 µM) was supplemented to the media.

extract_protocol:
After sorting, cells were centrifuged (610 g, 10 min) and lysed in 650 μL RLT lysis buffer (Qiagen) + β-mercaptoethanol (Sigma-Aldrich, 1%) and subsequently vortexed for 1 min at room temperature before being snap frozen. RNA isolation was performed using a RNAeasy micro kit including DNaseI digestion (Qiagen).
Total RNA was subjected to oligo (dT) capture and enrichment, and the resulting mRNA fraction was used to construct cDNA libraries. Sequencing was performed on an Illumina HiSeq 4000 platform using the standard protocol (TruSeq Stranded Total RNA Library, Illumina) that generates approximately 30 million reads of 50 base pairs per sample.

treatment_protocol: hPSC-ECs were dissociated from plates using Accutase (StemCell Technologies) and filtered before sorting with 30 μm filters (Miltenyi Biotec). Dissociated cells were kept in full media during sorting and sorted in cooled collection tubes with complete EC media supplemented with 20% FBS and 25 mM HEPES. Sorting was performed with BD FACSAria III (BD Biosciences) using 4-way purity precision mode. Reporter cells were  sorted by FACS into GFP+ and GFP- populations.

value: GFP+ (CLDN5-) sorted

value: Clone A7_R4_GFP+


title: A7_5_GFP-, SAM24327043 Clone A7_9

description: GFP- cells represent CLDN5-

source_name: sorted hPSC-EC GFP- (CLDN5-)

value: GFP- (CLDN5-) sorted

value: Clone A7_R5_GFP-


title: A7_5_GFP+, SAM24327044 Clone A7_10

description: GFP+ cells represent CLDN5+

value: Clone A7_R5_GFP+


title: A7_6_GFP+, SAM24327046 Clone A7_12

description: GFP+ cells represent CLDN5+

value: Clone A7_R6_GFP+


title: A7_4_GFP-, SAM24327041 Clone A7_7

description: GFP- cells represent CLDN5-

value: Clone A7_R4_GFP-


title: A7_6_GFP-, SAM24327045 Clone A7_11

description: GFP- cells represent CLDN5-

value: Clone A7_R6_GFP-


title: 1-DMSO 8h

description: hPSC-EC were treated with DMSO for 8h


title: A6 [RNA-Seq]

value: ATC

value: thyroid


title: A10 [RNA-Seq]


title: A1 [RNA-Seq]


title: A12 [RNA-Seq]


title: A9 [RNA-Seq]


title: A7 [RNA-Seq]


title: A7_3_GFP+, SAM24327040 Clone A7_6

description: GFP+ cells represent CLDN5+

value: Pluripotent stem-cell derived endothelial cells

value: Clone A7_R3_GFP+


title: F6 [RNA-Seq]

value: FTC


title: ICN1_shEts1_3-2

value: T lymphoblastic leukemia/lymphoma

value: T lymphocyte

value: ICN1 (Cell Signaling Technology, 4147s)


title: Zmiz1_shEts1_2-1

value: THP-6 T-ALLs

value: Ets1-silencing shRNA


title: ICN1_shControl-1

value: non-silencing shRNA


title: Zmiz1_shEts1_3-2


title: Zmiz1_shEts1_3-1


title: Zmiz1_shEts1_2-2


title: Zmiz1_shControl-1


title: Rh30, KDM3A-sh2, replicate 2

description:
R303A2_2
R303A2_2_1.genes.results

value: Rh30 (SJRH30; ATCC CRL-2061)

value: Rhabdomyosarcoma Cell line


title: Rh30, Ets1-sh1, replicate 1

description:
R30Et1_1
R30Et1_1_1.genes.results


title: Rh30, KDM3A-sh2, replicate 1

description:
R303A2_1
R303A2_1_1.genes.results


title: Zmiz1_shControl-2


title: Rh30, KDM3A-sh1, replicate 3

description:
R303A1_3
R303A1_3_1.genes.results


title: Rh30, KDM3A-sh1, replicate 1

description:
R303A1_1
R303A1_1_1.genes.results


title: Rh30, KDM3A-sh1, replicate 2

description:
R303A1_2
R303A1_2_1.genes.results


title: A2 [RNA-Seq]


title: A5 [RNA-Seq]


title: Rh30, control shRNA, replicate 3

description:
R30Sc_3
R30Sc_3_1.genes.results

source_name: Rh30_control shRNA

value: control shRNA


title: Rh30, control shRNA, replicate 1

description:
R30Sc_1
R30Sc_1_1.genes.results


title: A3 [RNA-Seq]


title: Rh30, control shRNA, replicate 2

description:
R30Sc_2
R30Sc_2_1.genes.results


title: A4 [RNA-Seq]


title: Ets1_shControl-1

value: ETS1 (Santa Cruz sc-350)


title: Rh41, Ets1-sh2, replicate 3

description:
R41Et2_3
R41Et2_3_1.genes.results


title: Rh41, Ets1-sh2, replicate 1

description:
R41Et2_1
R41Et2_1_1.genes.results


title: Gcr1-U-12-mRNA-rep1

description: RNA-seq for Gcr1(U) after diauxic shift #1

data_processing:
Image analysis and base calling was performed using HisSeq control software (v1.8.4), and conversion of BCL to fastq format and demultiplexing was processed with bcl2fastq (v1.8.2).
Read quality was assessed using FastQC (v0.10.1), showing about 90% bases above Q30 across all samples.
Clean reads, that quality scores were >Q30, were processed using the Tuxedo protocol with TopHat2 (version 2.1.1) and Cufflinks. Reads for each sample were aligned to the yeast reference genome (sacCer3 assembly) using TopHat2.
Gene expression quantification was performed using Cufflinks, and fragments per kilobase of transcript per million reads mapped (FPKM) was calculated as the expression value.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample; U-6 (rep1, rep2), U-12 (rep1, rep2), S-6 (rep1, rep2), S-12 (rep1, rep2).

extract_protocol:
Total RNA was extracted from yeast cells using hot phenol method.
RNA-Seq libraries were prepared using a TruSeq Stranded mRNA Sample Prep Kit (Illumina) according the manufacturer’s protocol. Paired-end sequencing with 100 cycles was performed using a HiSeq2500 (Illumina) instrument according to manufacturer’s protocol.

treatment_protocol: No treatment applied to the cultures

value: diauxic shift

value: whole cell


title: Gcr1-U-12-mRNA-rep2

description: RNA-seq for Gcr1(U) after diauxic shift #2


title: Rh41, Ets1-sh1, replicate 3

description:
R41Et1_3
R41Et1_3_1.genes.results


title: Gcr1-S-12-mRNA-rep1

description: RNA-seq for Gcr1(S) after diauxic shift #1


title: Gcr1-S-12-mRNA-rep2

description: RNA-seq for Gcr1(S) after diauxic shift #2


title: Rh41, Ets1-sh2, replicate 2

description:
R41Et2_2
R41Et2_2_1.genes.results


title: A7_3_GFP-, SAM24327039 Clone A7_5

description: GFP- cells represent CLDN5-

value: GFP- (CLDN5-) sorted

value: Clone A7_R3_GFP-


title: A7_2_GFP+, SAM24327038 Clone A7_4

description: GFP+ cells represent CLDN5+

value: Pluripotent stem-cell derived endothelial cells

value: GFP+ (CLDN5-) sorted

value: Clone A7_R2_GFP+


title: 44-SB431542+VEGFA 8h

source_name: SB431542+VEGFA treated hPSC-EC 8h

value: SB431542+VEGFA 8h


title: Rh41, Ets1-sh1, replicate 2

description:
R41Et1_2
R41Et1_2_1.genes.results


title: Gcr1-S-6-mRNA-rep1

description: RNA-seq for Gcr1(S) at exponential phase #1

value: exponential phase


title: Rh41, KDM3A-sh2, replicate 3

description:
R413A2_3
R413A2_3_1.genes.results


title: Gcr1-U-6-mRNA-rep2

description: RNA-seq for Gcr1(U) at exponential phase #2


title: Rh41, KDM3A-sh2, replicate 2

description:
R413A2_2
R413A2_2_1.genes.results


title: Gcr1-U-6-mRNA-rep1

description: RNA-seq for Gcr1(U) at exponential phase #1


title: Rh41, KDM3A-sh1, replicate 3

description:
R413A1_3
R413A1_3_1.genes.results


title: Rh41, KDM3A-sh2, replicate 1

description:
R413A2_1
R413A2_1_1.genes.results


title: Gcr1-S-6-mRNA-rep2

description: RNA-seq for Gcr1(S) at exponential phase #2


title: Rh41, Ets1-sh1, replicate 1

description:
R41Et1_1
R41Et1_1_1.genes.results


title: Rh41, KDM3A-sh1, replicate 2

description:
R413A1_2
R413A1_2_1.genes.results


title: Rh41, KDM3A-sh1, replicate 1

description:
R413A1_1
R413A1_1_1.genes.results


title: R3

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

data_processing:
Bases were called using the Real Time Analysis 2 software of the NextSeq500.
Reads were trimmed with Trim Galore version 0.4.0 using default settings
Trimmed reads were mapped with Bismark version 0.18.1_dev using the following parameters: --bowtie2; -q; -un; --score_min L,0,-0.3; -p 4.
The resulting SAM files were converted to BAM format and sorted. Files of multiplexed files were merged using samtools (version 1.3). Duplicate reads were removed using Picard (version 1.119).
Methylated and unmethylated read counts were extracted per cytosine using the Bismark methylation extractor for every cytosine context. The resulting SAM files were converted to BAM format and sorted. Files of multiplexed files were merged using samtools (version 1.3)
Genome_build: Oryza sativa subsp. Japonica build MSU7.0
Supplementary_files_format_and_content: Bismark Coverage report in a GZIP compressed format

organism: Oryza sativa

source_name: Roots

growth_protocol: Oryza sativa L. cv ‘Nipponbare’ (GSOR-100, USDA) seeds were germinated for 5 days in darkness at 30 °C, after which they were transferred to synthetic absorbent polymer (SAP) substrate in polyvinylchloride (PVC) tubes (58) and grown at 28 °C (16 h light/8 h darkness).

extract_protocol:
DNA was extracted using the DNeasy plant mini kit  (Qiagen) according to manufacturer’s instructions and dissolved in DNase free water. DNA concentration was quantified using Quant-it PicoGreen dsDNA Assay kit (Thermo Fisher  Scientific) and 100 ng of DNA per sample was sheared to 400 bp fragments using Covaris S2  Focused-ultrasonicator Sonicator settings were as following: duty cycles of 10 %, intensity of  4, cycles/burst of 200 for 65 seconds. Fragmented DNA was cleaned and concentrated using the DNA clean and concentrator kit (Zymo Research). Bisulfite conversion was performed by using the EZ DNA methylation Gold kit (Zymo Research). Evaluation of bisulfite conversion efficiency was done by shearing the unmethylated Lambda DNA (48502 bp) as above. Size distribution was verified using the high sensitivity DNA chip of Bioanalyzer 2100 (Agilent technologies).
The preparation of sequencing libraries from bisulfite-converted DNA was performed using Accel-NGS Methyl-Seq DNA library kit according to manufacturer’s instructions (Swift Biosciences). The quality of DNA was again checked by using the high sensitivity DNA chip of Bioanalyzer 2100 (Agilent technologies). After gel purification, qPCR was performed to determine the concentration of each sample. Finally, a 2.1 pM library was loaded on a single read flow cell, and sequenced using an Illumina Nextseq500 (single end, 76 cycles).

treatment_protocol: Two-week-old plants were inoculated by 250 J2 nematodes per plant or mock-inoculated with water as a control. After 36 hours, they were transferred to 50 % Hoagland solution in glass tubes to synchronize the infection process. Three days later, galls of infected plants and roots tips of control plants were harvested and snap frozen in liquid nitrogen.

tag: cultivar

value: Nipponbare

value: Roots

tag: infected with

value: not infected


title: R1


title: G3

source_name: Galls

value: Galls

value: Meloidogyne graminicola


title: R2


title: Rh41, control shRNA, replicate 3

description:
R41Sc_3
R41Sc_3_1.genes.results

source_name: Rh41_control shRNA

value: Rhabdomyosarcoma Cell line


title: G2


title: B5_2_GFP-, SAM24327025 Clone B5_3

description: GFP- cells represent CLDN5-

value: Clone B5_R2_GFP-


title: A7_1_GFP+, SAM24327036 Clone A7_2

description: GFP+ cells represent CLDN5+

value: Clone A7_R1_GFP+


title: A7_2_GFP-, SAM24327037 Clone A7_3

description: GFP- cells represent CLDN5-

value: Clone A7_R2_GFP-


title: B5_1_GFP+, SAM24327024 Clone B5_2

description: GFP+ cells represent CLDN5+

value: Clone B5_R1_GFP+


title: B5_3_GFP+, SAM24327028 Clone B5_6

description: GFP+ cells represent CLDN5+

value: Clone B5_R3_GFP+


title: B5_4_GFP+, SAM24327030 Clone B5_8

description: GFP+ cells represent CLDN5+

value: Clone B5_R4_GFP+


title: B5_5_GFP+, SAM24327032 Clone B5_10

description: GFP+ cells represent CLDN5+

value: Pluripotent stem-cell derived endothelial cells

value: Clone B5_R5_GFP+


title: B5_5_GFP-, SAM24327031 Clone B5_9

description: GFP- cells represent CLDN5-

value: GFP- (CLDN5-) sorted

value: Clone B5_R5_GFP-


title: A7_1_GFP-, SAM24327035 Clone A7_1

description: GFP- cells represent CLDN5-

value: Clone A7_R1_GFP-


title: B5_4_GFP-, SAM24327029 Clone B5_7

description: GFP- cells represent CLDN5-

value: Clone B5_R4_GFP-


title: B5_3_GFP-, SAM24327027 Clone B5_5

description: GFP- cells represent CLDN5-

value: Clone B5_R3_GFP-


title: B5_6_GFP+, SAM24327034 Clone B5_12

description: GFP+ cells represent CLDN5+

value: GFP+ (CLDN5-) sorted

value: Clone B5_R6_GFP+


title: B5_6_GFP-, SAM24327033 Clone B5_11

description: GFP- cells represent CLDN5-

value: Clone B5_R6_GFP-


title: Rh41, control shRNA, replicate 2

description:
R41Sc_2
R41Sc_2_1.genes.results

value: Rhabdomyosarcoma Cell line

value: control shRNA


title: shEts1_3-4

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems
The Tuxedo Suite was used to align reads to the reference transcriptome (hg19 and FANTOM_CAT.lv3_robust.all_lncRNA) (http://genome.ucsc.edu/) using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
HTSeq and DESeq2 were used for expression quantitation and differential expression analysis.
we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ 1.5.
Genome_build: hg19 and FANTOM_CAT.lv3_robust.all_lncRNA
Supplementary_files_format_and_content: raw counts

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Whole RNA was extracted from 5 million cells using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.
Sequencing libraries were prepped using the Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS-122-2001, RS-122-2002)
Illumina TruSeq mRNA, ribodepletion, single End 50 Cycle, strand specific

treatment_protocol: THP-6  cells were lentivirally transduced with shControl, shEts1_3, or shEts1_2. Two days later the cells were selected in 10 ug/ml puromycin. The next day, the cells were harvested.

tag: group

value: Transduced THP-6 cells

value: T lymphoblastic leukemia/lymphoma


title: B5_1_GFP-, SAM24327023 Clone B5_1

description: GFP- cells represent CLDN5-

value: Clone B5_R1_GFP-


title: EDmix_PFHxS_19

description: Retroperitoneal fat pad, rat exposed to PFHxS and a background mixture of 12 endocrine disrupting chemicals (EDmix)

hyb_protocol: RNAs were hybridized to the Rat Clariom S Array (ThermoFischer Scientific).

scan_protocol: Arrays were immediately scanned, and images were analyzed and rigorously quality controlled for hybridization artifacts.

data_processing: The resulting CEL files were processed using the oligo package available performed in R/Bioconductor (Gentleman et al., 2004). Data were then normalized and background corrected using the RMA method with the Brainarray custom CDF file for directly mapping Affymetrix probe to Entrez gene identifiers (Dai et al., 2005).

label: biotin

organism: Rattus norvegicus

source_name: Retroperitoneal fat pad

label_protocol: Total RNA was amplified and labelled using the Gene Chip WT PLUS Reagent Kit according to the manufacturer’s instructions (ThermoFischer Scientific).

growth_protocol: The animals were housed in a room with controlled environmental conditions with reversed light/dark cycles of 12 hours with light intensity 500 lux starting at 9 PM, humidity 55% 6 5, temperature at 21 +/- 1C and ventilation changing air 10 times per hour. All animals had ad libitum access to standard diet with ALTROMIN 1314 (soy- and alfalfa-free, ALTROMIN GmbH, Lage, Germany) and acidified tap water (to prevent microbial growth) in PSU bottles (84-ACBTO702SU Tecniplast)

extract_protocol: Total RNA was extracted from the left retroperitoneal fat pad using the RNeasy Lipid Tissue Mini kit (Qiagen) including on-column DNase I treatment according to manufacturer’s instructions

treatment_protocol: Retroperitoneal fat pad was placed in RNAlater and stored at -80 °C until preparation for transcriptional analysis

value: Wistar

value: Exposed to EDmix and PFHxS

tag: age

value: Adult (13 months old)

value: Retroperitoneal fat pad

tag: Sex

value: Female


title: EDmix_89

description: Retroperitoneal fat pad, rat exposed to a background mixture of 12 endocrine disrupting chemicals (EDmix)

value: Exposed to EDmix


title: EDmix_PFHxS_43


title: EDmix_PFHxS_44


title: EDmix_117


title: Rh41, control shRNA, replicate 1

description:
R41Sc_1
R41Sc_1_1.genes.results

tag: cell line


title: EDmix_90

tag: tissue


title: PFHxS_85

description: Retroperitoneal fat pad, rat exposed to PFHxS

value: Exposed to PFHxS


title: PFHxS_48


title: G1

value: Nipponbare

value: Galls

value: Meloidogyne graminicola


title: shControl-4

value: shControl

tag: disease


title: Invivo-FM17

city: Pittsburgh

first: Samira

last: Kiani

state: Pennsylvania

address: A809-B Scaife Hall 3550 Terrace Street Pittsburgh

department: Division of Experimental Pathology

institute: University of Pittsburgh

description:
fpkm_invivo.txt
Invivo-FM17

data_processing:
Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
To allow for log adjustment, genes with 0 FPKM are assigned a value of 0.001. Correlation were determined using the cor.test function in R with options set alternative =”greater” and method = “Spearman”.
To identify the correlation between difference, we clustered different samples using expression level FPKM to see the correlation using hierarchical clustering distance method with the function of heatmap, SOM(Self-organization mapping) and kmeans using silhouette coefficient to adapt the optimal classification with default parameter in R.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecularlevel information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: GRCm38
Supplementary_files_format_and_content: A text file with fpkm genename

source_name: Bone Marrow

growth_protocol: For the invitro data, Neuro-2a cell lines (purchased from ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM - Life Technologies) with 10% fetal bovine serum (FBS - Life Technologies), 2mM glutamine, 1.0 mM sodium pyruvate (Life Technologies) and 1% streptomycin– penicillin mix (Gibco) in incubators at 37 °C and 5% CO2.

extract_protocol:
For the invitro data, Cells were lysed, and RNA was extracted using RNeasy Plus mini kit (Qiagen) 72 hrs post transfection and sent to UCLA TCGB core on dry ice. For the invivo data, RNA was extracted from mice bone marrow samples using RNeasy Plus Mini Kit (Qiagen) followed by globin mRNA depletion using GLOBINclear™ Kit, mouse/rat kit (Thermofisher).
For the invitro data,, Ribosomal RNA depletion and paired end read library preparation were performed at UCLA core followed by RNA sequencing using NextSeq500.  Coverage was 20 million reads per sample.  FASTQ files with pair-ended 75bp reads were then aligned to the mouse GRCm38 reference genome sequence (Ensembl release 90) with STAR, and uniquely-mapped read counts (an average of 14.8  million reads per sample) were obtained with Cufflink.  The read counts for each sample were then normalized for the library size to CPM (counts per million reads) with edgeR .  Custom R scripts were then used to generate plots. For the invivo data, None-directional library preparation was performed at Novogene Corporation Inc. followed by RNA sequencing using Illumina Nova Platform with paired-end 150 run (2×150 bases). Coverage was minimum 25 million reads per sample. FASTQ files were then aligned to mouse genome sequence using STAR software and uniquely mapped read counts were visualized with Integrative Genomics Viewer (IGV). Gene expression level was calculated by the number of mapped reads. According to all gene expression level (RPKM or FPKM) of each sample, correlation coefficient of sample between groups was calculated. Read counts obtained from Gene Expression Analysis were used for differential expression analysis and differential expression analysis of different groups was performed using the DESeq2 R package51. Hierarchical clustering analysis was carried out of log10 (FPKM+1) of union differential expression genes, within all comparison groups. ClusterProfiler52 software was used for enrichment analysis, including GO Enrichment, DO Enrichment, KEGG Enrichment and Reactome Enrichment.

treatment_protocol: For the invitro data, Neuro-2a cells were co-transfected with 10ng gRNA targeting Myd88 loci, respectively. 200ng dCas9 constructs, 100ng MS2-HP1aKRAB, 50ng puromycin resistant gene, and 25ng transfection control. Cells were treated with 0.5ug/ml puromycin (Gibco-life tech) at 24 hours post-transfection.

value: Rosa26-Cas9 knockin mice (JAX Stock number 026179)

value: Bone Marrow

value: Cas9 nuclease transgenic mice received AAV1-Myd88-Ms2-HP1aKRAB


title: GSI-2

value: GSI

value: Transduced THP-6 cells


title: Invivo-FM22

description:
fpkm_invivo.txt
Invivo-FM22

value: Cas9 nuclease transgenic mice received AAV1-Myd88-Ms2-KRAB


title: Invivo-FM21

description:
fpkm_invivo.txt
Invivo-FM21


title: GSI-3

value: T lymphoblastic leukemia/lymphoma


title: B5_2_GFP+, SAM24327026 Clone B5_4

description: GFP+ cells represent CLDN5+

value: Pluripotent stem-cell derived endothelial cells

value: GFP+ (CLDN5-) sorted

value: Clone B5_R2_GFP+


title: Invivo-FM18

description:
fpkm_invivo.txt
Invivo-FM18


title: GSI-1


title: DMSO-3

value: DMSO


title: EDmix_PFHxS_11

value: Wistar

value: Exposed to EDmix and PFHxS

value: Adult (13 months old)

value: Retroperitoneal fat pad

value: Female


title: EDmix_60

value: Exposed to EDmix


title: Corpus_2

city: Houston

last: Garcia

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Fastq files were trimmed with Trim Galore!
Trimmed files were aligned to GRCm38 using HISAT2.
Aligned features were quantified using featureCounts.

source_name: Corpus

extract_protocol:
RNA was extracted using Trizol/chloroform followed by purification using a Rneasy Mini kit from Qiagen with an on-column Dnase treatment.
Libraries were constructed using a KAPA standed mRNA-seq kit.

value: Corpus


title: Corpus_3


title: Corpus_1


title: Sample10_glucose5%_BHB25mM

city: Honolulu

first: Michael

last: Weichhaus

state: Hawaii

address: 3140 Waialae Avenue

department: Natural Sciences and Mathematics

institute: Chaminade University of Honolulu

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Illumina fastq files were pseudoaligned using "kallisto" (v0.46.1) using their prebuilt indices constructed from Ensembl Homo_sapiens.GRCh38 databases  creating abundance files (attached as processed data files)
Samples were loaded into "R" (version 4.0) using tximport and analyzed using the DESeq2 (version 1.28.1) pipeline.
Differential gene expression was established after shrinking DESeq2 outputs according to the the protocol established by Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: Matrix with FPKM of all sample, treatment conditions and genes

source_name: metastatic breast cancer

growth_protocol: Cells were routinely maintained in DMEM with 10% FBS, 2 mM glutamine and 50 ng/ml gentamycin

extract_protocol:
Total RNA was extracted using Qiagen’s RNeasy Mini Kit
TruSeq Stranded mRNA LT Sample Prep Kit/TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: Cells were treated as indicated with reduced glucose and/or beta-hydroxybutyrate

value: glucose concentration [g/l]:0.225

tag: treatment 2

value: beta hydroxybutyrate [mm]:25


title: Sample15_glucose5%_BHB0mM

value: beta hydroxybutyrate [mm]:0


title: Sample17_glucose5%_BHB25mM


title: Sample21_glucose100%_BHB0mM

value: glucose concentration [g/l]:4.5


title: Sample14_glucose100%_BHB0mM


title: Sample16_glucose5%_BHB10mM

value: beta hydroxybutyrate [mm]:10


title: Cauda_3

source_name: Cauda

value: Cauda


title: Sample8_glucose5%_BHB0mM


title: Seabass_PostStress_T4_C3

city: MONTPELLIER

first: Bruno

last: GUINAND

address: Place E. Bataillon - Campus Triolet

institute: Université de Montpellier

data_processing:
Raw sequencing data were trimmed of low quality reads and adapter residues using Trim Galore!. The trimmed reads were then demultiplexed with STACKS.The option disable_rad_check was applied to avoid reads with bisulfite-modified restriction sites to be discarded. The demultiplexed reads were trimmed a second time on both 5’ and 3’ ends with the options --clip_R1 --clip_R2 and --three_prime_clip_R1 --three_prime_clip_R2 to remove introduced methylated cytosines during adapter ligation.
Using the bismark_genome_preparation function of the program bismark (Krieger and Andrews 2011, Bioinformatics, doi: 10.1093/bioinformatics/btr167), a bisulfite converted version of the European sea bass genome was prepared against which the demultiplexed and trimmed reads were mapped
The R package MethylKit was used to determine differential methylation between pre- and post-stress fish. Coverage was normalized across samples. Using Methylkit, differentially methylated CpG sites were determined between pre- and post-stress individuals using logistic regression (30X read depth; nominal q-value: 0.001; 15% methylation threshold)
Genome_build: GCA_000689215.1
Supplementary_files_format_and_content: Txt files providing chromosomes, posotions, strand, percentages cytosine and thymine for each methylated sites

organism: Dicentrarchus labrax

growth_protocol: 20 sea bass families were reared separately in open circulation tanks at Nireus S.A. research facilities (Greece). Fish were tagged at ~280 days post-hatch and distributed in 20 tanks; each tank receiving 1 fish from each family (i.e., 20 fish per tank). Throughout the experimental period, the photoperiod was set at 12L:12D, the water temperature and the salinity held constant (18.1 ± 0.2°C and 28 ppt, respectively). Fish were submitted to one acute challenge test per month for three consecutive months, from July to October 2018.

extract_protocol:
Blood from the caudal vessel was collected. Plasma and red blood celles were separated by centrifugation at 2,000g for 10 min. Careful separation of the plasma and RBCs was performed using 200 µl pipettes. RBC extracts were heparinized (heparin sodium; Sigma-Aldrich), transferred in microtubes and conserved at -20°C in 1 ml of RNA later. Genomic DNA was extracted using the Macherey Nagel Nucleo Spin Tissue DNA kit and quantified using a Qubit fluorometer (Qubit dsDNA BR Assay Kit, Q32853, Invitrogen).
EpiGBS approach adapted from van Gurp et al. (2016, Nature Methods doi: 10.1038/nmeth.3763), with main addition of a second restriction enzyme in the protocol. The couple of enzymes retained: MspI/ SfbI. A single libray was prepared: 200 ng of DNA of each sample were digested in a 40 µl reaction, using 0.25 µl MspI (NEB, 20,000 U/ml R0106S), 0.25 µl SbfI-HiFi (NEB 20,000 U/ml R3642L) and 4 µl of 10X cutsmart buffer. The reaction was run overnight at 37°C. Unique forward and reverse adapter combinations allow multiplexing samples in the library. We added forward and reverse adapters in unique combinations (1 µl of adapter, 2.5 µM), 0.5 µl T4 Ligase (NEB, 400,000 U/ml m0202L), 6 µl of 10X T4 ligase buffer and 11.5µl water were added directly to the digested DNA. Adapters were ligated for 3 h at 23°C followed by 10 min of enzyme inactivation at 65°C. After ligation, all samples were pooled and one third of the total volume was used in the following step. The mixture volume was reduced using a Qiaquick PCR purification kit (28104 Qiagen). The resulting product was cleaned a second time to ensure the removal of small fragments and adapter remnants using CleanPCR paramagnetic beads (Proteigene, CPCR-0050) with a ratio of 0.8X [sample : beads]. a nick translation was performed to repair the nick of the DNA at the restriction site and to fully methylate the hemi-methylated adapters. To do so, 19.25 µl of the concentrated and purified ligation pool were used in a 25 µl reaction, including 0.75 µl DNA Polymerase I (E. coli, 10,000 U/ml M0209S), 2.5 µl of 10 mM 5-Methylcytosine dNTP mix (Zymo Research, D1030), and incubated at 15 °C for one hour. The library was then treated with sodium bisulfite using the EZ DNA Methylation Gold Kit (D5005, Zymo Research) following manufacturer instructions to convert unmethylated cytosines to uracil, paying attention to the optimal DNA amount per reaction. After bisulfite conversion, 14 cycles of PCR (95°C for 1 min, 91°C for 10s, 65°C for 15s, 72°C for 10s and a final elongation step at 72°C for 5 min) were performed, followed by a paramagnetic bead clean up with a 0.8X ratio. The library quality was verified on an Agilent 5300 Fragment Analyzer (Santa Clara, USA). It was sequenced (paired-end, 150 bp) on one lane of a SP flow cell on an ILLUMINA NovaSeq 6000.

treatment_protocol: Fish were exposed to high density stress by lowering water levels in the tank to 1/3 of the original volume, followed by chasing of the fish with a net for five minutes and a 30 min waiting period before sampling. This protocol took place in each tank then for each fish individual entering the experiment. It was repeated for 3 consecutive times at 20-21 day intervals (period long enough for fish to recover). An initial blood sampling occurred two weeks prior to the implementation of the stress challenge (T0 label, July 19th, 2018, pre-stress/control group) then at the end of the challenge test (T4 label, October 5th, 2018).

tag: developmental stage

value: juvenile

value: 9 months

value: post-stress

tag: family

value: C

tag: cell type

value: blood red cells


title: Seabass_PostStress_T4_M17

value: M


title: Seabass_PostStress_T4_S19

value: S