title: SG5_WS_mRNA

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

description: mRNA-seq processed data

data_processing:
sRNA-Seq: Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam, Repbase and durum wheat NCBI mRNA entries as references. Unique sRNA sequences were then obtained for each library. Conserved mature miRNAs and 5p- or 3p-derived miRNA variants were identified using BLAST search against the plant miRBase (Release 22.1). MIR (microRNA gene locus) and miRNA sequences from common plant species in the miRBase were used as references. Sequences mapped to the mature miRNA in the hairpin were identified as conserved mature miRNAs. Sequences mapped to the opposite arm of mature miRNA in the hairpin were identified as 5p- or 3p-derived variants. Single mismatch within the sequence and length variation at both 5p and 3p were allowed in the alignment. All the mapped miRNAs were aligned to the durum wheat genome (NCBI UID 3439611, assembly Svevo.v1) to determine their genomic location. The remaining unmatched sRNA sequences were used to identify novel durum miRNAs. Sequences were BLASTed to the durum wheat genome. To identify miRNA precursors, secondary hairpin structures containing matched sequences were predicted using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) from 120nt of flanking genome sequences.
mRNA-Seq: Prior to sequence assembly, low quality reads (those containing primer or adaptor sequence, and those with a sequencing quality score < 20) were removed. Clean reads were aligned to the durum reference genome using the HISAT package (V2.0). Aligned reads of each library were assembled and the transcript abundance were obtained using StringTie (V1.3.0). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
Degradome-Seq: Raw sequencing reads were processed using the ACGT101-DEG program (V4.1, LC Sciences) to remove low-quality reads, reads with adaptor and primer contamination, and reads that can be annotated as non-coding RNA families. The remaining clean reads were used to identify the degraded fragments of mRNAs that are targets of known and novel durum miRNAs with the CleaveLand package V4.0  and the ACGT101-DEG program (LC Sciences, TX, USA). The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Genome_build: Durum wheat genome (NCBI UID 3439611, assembly Svevo.v1)
Supplementary_files_format_and_content: Matrix table with abundance measurements of microRNAs (sRNA-seq), mRNAs (mRNA-seq) and mRNA targets (degradome-seq)

organism: Triticum turgidum subsp. durum

source_name: Developing grain tissue

growth_protocol: Stress-tolerant genotype DBA Aurora and stress-sensitive genotype L6 (University of Adelaide breeding line, UAD1301020-8) were grown in controlled glasshouse conditions as previously described (Liu et al., 2019). Briefly, the standard growing conditions were 22°C/12°C (day/night) with a 12h photoperiod.

extract_protocol:
Total RNA was extracted from a total of 120 samples (2 genotypes × 4 treatments × 5 time-points × 3 biological replicates) using the Tri reagent (Sigma-Aldrich) and treated with TURBO DNase (ThermoFisher Scientific). RNA concentration, quality and integrity was assessed by NanoDrop, gel electrophoresis and Bioanalyzer.
The 118 sRNA libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Kit. Eight transcriptome libraries were constructed using the Illumina mRNA-Seq sample preparation kit. For degradome-seq, mRNA was enriched using oligo-d(T) magnetic beads. The enriched mRNA was mixed with biotinylated random primers and were ligated to 5' adaptors. First-strand cDNA was reverse-transcribed from ligated mRNA products and then amplified with PCR.

treatment_protocol: Four treatment groups were: control group (CG), pre-anthesis water-deficit stress group (WS), post-anthesis heat stress group (HS) and water-deficit plus heat stress group (WH). All plants were well-watered from germination to booting. Water-deficit stress was applied to WS and WH by maintaining the soil water content at 6% (half of the field capacity) from booting until harvest (Liu et al., 2019). Heat stress was applied by placing plants in a growth chamber at 37°C/27°C with a 12h photoperiod. HS and WH plants were treated with heat for 24h at multiple reproductive time-points consecutively [5, 15, 25, 35, and 45 days post anthesis (DPA)] (Liu et al., 2019). After 24h, plants were moved back to the standard conditions and remained there between each treatment time-point. Flag leaf samples were collected at each DPA.

tag: genotype

value: L6 (Stres-sensitive)

tag: treatment group

value: Water-deficit plus heat stress (WH)

tag: time-point (dpa, days post anthesis)


title: Subject 4 technical replicate 5

status: Public on Oct 19 2020

type: SRA

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: Patient 4, Non diabetic Obese, technical replicate 5

library_source: transcriptomic

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for demultiplexing.
The analyses were performed using the Eoulsan pipeline (17), including read filtering, mapping, alignment filtering, read quantification, normalization and differential analysis. Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the human genome from Ensembl version 88 using STAR (version 2.5.2b). Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression, human GTF genome annotation version 88 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3.
Genome_build: Hg19 (Ensembl 88)
Supplementary_files_format_and_content: tab-delimited text files include gene counting for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Subject 4

extract_protocol:
Total RNA was extracted using the RNAeasy Mini Plus Kit (Qiagen)
10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). Afterwards an average of 150 pg of amplified cDNA was used to prepare library following Nextera XT DNA kit (Illumina)

treatment_protocol: For cells sorting experiments, epithelial cells were rinsed in FACS buffer (PBS, 3% FCS, 2 mM EDTA), blocked with Human Fc Receptor Binding Inhibitor Antibody (eBioscience) and stained (30 min, 4°C) with the following antibodies: CD45-BV421 (Bio Legend) and CD24-PeCy7 (Bio Legend). Dead cells were excluded with propidium iodure (eBiosciences). During sorting experiments, cells were placed in FACS buffer with RNAse inhibitor (Life Technologies). CD24 marker was used to select differentiated cells, and CD45 was used to get rid of B lymphocytes that also expressed CD24. Enriched EEC were CD45-negative, CD24-positive sorted by FACS. Cells were isolated on a MoFlo Astrios EQ (Beckam Coulter). Data were analyzed with software FlowJo. V10.0.7 (Tree Star).

tag: individual

value: Patient 4

tag: gender

value: female

tag: phenotype

value: Non diabetic Obese

tag: treatment

value: EEC enrichment

tag: cell type

value: EEC


title: Subject 3 technical replicate 4

description: Patient 3, Non diabetic Obese, technical replicate 4

source_name: Subject 3

value: Patient 3


title: Gestational diabetes Patient 3, delivery (RNA-seq)

city: Los Angeles

first: Giorgia

last: Del Vecchio

address: 610 Charles E Young Dr S, Room 5146

country: USA

institute: University of California Los Angeles

data_processing:
We first used the FastQC (version v0.11.8) program to assess the quality of our sequenced reads. All the samples passed this step of quality control before proceeding further into analysis.
The RNA-seq reads were aligned to the human reference genome (hg19) using the STAR (v 2.5.2b) software with the following configurations:  --quantMode GeneCounts --outFilterMismatchNoverLmax 0.04 --outFilterMultimapNmax 1 --clip5pNbases 5. We used the --quantMode GeneCounts option in STAR that counts the number reads per gene while mapping.
Starting with the RNA-Seq read counts matrix, we then used the DESeq2 (version v1.20.0) package in R to perform data normalization (rlog function) and DEG analysis. We set a cutoff for adjusted P value ≤ 0.05 and a fold change ≥ 1 or ≤  -1.
Genome_build: hg19
Supplementary_files_format_and_content: gene Counts text file

source_name: Plasma

extract_protocol:
Peripheral venous blood was collected into EDTA-coated tubes. Blood was then centrifuged at 2000 X g for 7 minutes at 4°C, in order to collect only the plasma fraction. Plasma was centrifuged at 16000 X g for 10 min at 4°C to remove all the residual cells, aliquoted and stored at −80°C. Cell-free RNA was extracted from 200 μL of plasma using the miRNeasy serum/plasma kit (Qiagen). Total RNA was quantified using the Qubit RNA HS Assay kit  (Thermofisher Scientific). RNA integrity was verified using the Agilent High sensitivity RNA Screen Tape System (Agilent) on a 2200 TapeStation System (Agilent,).
The RNA-sequencing (RNA-seq) library construction was performed using the ultra-low input specific kit, NuGen Ovation SoLo RNA-Seq kit with Human rRNA AnyDeplete kit (NuGen), according to the manufacturer's instructions. Libraries were sequenced using 100 bp single-end reads on the Hiseq4000 System (Illumina)

tag: complication during pregnancy

value: Gestational Diabetes


title: SG5_CG_mRNA

description: mRNA-seq processed data

value: Control group (CG)


title: SG5_HS_mRNA

description: mRNA-seq processed data

value: Heat stress (HS)


title: Gestational diabetes Patient 3, 3rd Trimester (RNA-seq)


title: SG5_WH_mRNA

description: mRNA-seq processed data

value: Water-deficit stress (WS)


title: TG5_HS_mRNA

description: mRNA-seq processed data

value: DBA Aurora (Stress-tolerant)


title: Subject 3 technical replicate 3

description: Patient 3, Non diabetic Obese, technical replicate 3


title: TG5_WS_mRNA

description: mRNA-seq processed data


title: Subject 3 technical replicate 2

description: Patient 3, Non diabetic Obese, technical replicate 2


title: TG5_CG_mRNA

description: mRNA-seq processed data


title: Gestational diabetes Patient 3, 2nd Trimester (RNA-seq)


title: Gestational diabetes Patient 3, 1st Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 6, delivery (RNA-seq)

value: Preeclampsia/gestational hypertension


title: sRNA -SG45_WH - Rep1

description: sRNA-seq processed data.xlsx


title: Subject 3 technical replicate 1

description: Patient 3, Non diabetic Obese, technical replicate 1


title: sRNA -SG45_HS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -SG45_WH - Rep2

description: sRNA-seq processed data.xlsx


title: Gestational diabetes Patient 2, delivery (RNA-seq)


title: sRNA -SG45_WS - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG45_HS - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -SG45_WS - Rep1

description: sRNA-seq processed data.xlsx


title: Subject 2 technical replicate 7

description: Patient 2, Non diabetic Obese, technical replicate 7

source_name: Subject 2

value: Patient 2


title: sRNA -SG45_CG - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -SG45_HS - Rep2

description: sRNA-seq processed data.xlsx


title: TG5_WH_mRNA

description: mRNA-seq processed data


title: Subject 2 technical replicate 6

description: Patient 2, Non diabetic Obese, technical replicate 6


title: sRNA -SG45_CG - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG45_CG - Rep1

description: sRNA-seq processed data.xlsx


title: Gestational diabetes Patient 1, cord blood (RNA-seq)


title: sRNA -SG35_WH - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG35_WH - Rep3

description: sRNA-seq processed data.xlsx


title: Subject 2 technical replicate 4

description: Patient 2, Non diabetic Obese, technical replicate 4


title: Gestational diabetes Patient 2, 1st Trimester (RNA-seq)


title: Gestational diabetes Patient 1, delivery (RNA-seq)


title: Gestational diabetes Patient 2, cord blood (RNA-seq)


title: sRNA -SG35_WH - Rep1

description: sRNA-seq processed data.xlsx


title: Subject 2 technical replicate 5

description: Patient 2, Non diabetic Obese, technical replicate 5


title: sRNA -SG35_HS - Rep2

description: sRNA-seq processed data.xlsx


title: Subject 2 technical replicate 8

description: Patient 2, Non diabetic Obese, technical replicate 8


title: sRNA -SG35_HS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -SG35_HS - Rep1

description: sRNA-seq processed data.xlsx


title: Gestational diabetes Patient 1, 3rd Trimester (RNA-seq)


title: Subject 2 technical replicate 2

description: Patient 2, Non diabetic Obese, technical replicate 2


title: sRNA -SG35_WS - Rep3

description: sRNA-seq processed data.xlsx


title: Gestational diabetes Patient 2, 2nd Trimester (RNA-seq)


title: Gestational diabetes Patient 1, 2nd Trimester (RNA-seq)


title: Subject 2 technical replicate 1

description: Patient 2, Non diabetic Obese, technical replicate 1


title: sRNA -SG35_CG - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -SG35_WS - Rep1

description: sRNA-seq processed data.xlsx


title: Gestational diabetes Patient 1, 1st Trimester (RNA-seq)


title: Subject 1 technical replicate 8

description: Patient 1, Non diabetic Obese, technical replicate 8

source_name: Subject 1

value: Patient 1


title: sRNA -SG35_CG - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -SG35_CG - Rep2

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 9, cord blood (RNA-seq)

value: No Complications


title: Subject 1 technical replicate 7

description: Patient 1, Non diabetic Obese, technical replicate 7


title: sRNA -SG25_WH - Rep1

description: sRNA-seq processed data.xlsx

value: L6 (Stres-sensitive)


title: sRNA -SG25_WH - Rep3

description: sRNA-seq processed data.xlsx

value: Water-deficit plus heat stress (WH)


title: Subject 1 technical replicate 6

description: Patient 1, Non diabetic Obese, technical replicate 6


title: Subject 2 technical replicate 3

description: Patient 2, Non diabetic Obese, technical replicate 3


title: sRNA -SG25_HS - Rep3

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 9, delivery (RNA-seq)


title: Normal Pregnancy Patient 9, 2nd Trimester (RNA-seq)


title: Normal Pregnancy Patient 9, 3rd Trimester (RNA-seq)


title: Normal Pregnancy Patient 9, 1st Trimester (RNA-seq)


title: Subject 1 technical replicate 4

description: Patient 1, Non diabetic Obese, technical replicate 4


title: Subject 1 technical replicate 5

description: Patient 1, Non diabetic Obese, technical replicate 5


title: sRNA -SG25_WH - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG25_WS - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG25_HS - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -SG25_WS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -SG35_WS - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG25_WS - Rep1

description: sRNA-seq processed data.xlsx


title: Subject 1 technical replicate 3

description: Patient 1, Non diabetic Obese, technical replicate 3


title: Normal Pregnancy Patient 8, cord blood (RNA-seq)


title: sRNA -SG25_CG - Rep3

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 8, delivery (RNA-seq)


title: Subject 1 technical replicate 2

description: Patient 1, Non diabetic Obese, technical replicate 2


title: sRNA -SG15_WH - Rep3

description: sRNA-seq processed data.xlsx


title: Subject 1 technical replicate 1

description: Patient 1, Non diabetic Obese, technical replicate 1


title: Normal Pregnancy Patient 8, 3rd Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 6, 2nd Trimester (RNA-seq)


title: sRNA -SG15_WH - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -SG15_WH - Rep2

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=8_h (S95)

city: Boston

first: Luca

last: Gerosa

state: MA

address: 200 Longwood Avenue Warren Alpert Bldg, Apt2

department: Laboratory of Systems Pharmacology

institute: Harvard Medical School

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Bcbio-nextgen software with the following configuration parameters: analysis=RNA-seq genome_build=hg38 algorithm=transcriptome_fasta=./Homo_sapiens_dnarna/Homo_sapiens.GRCh38.allRCNA.fa transcriptome_gtf=./Homo_sapiens_dnarna/Homo_sapiens.GRCh38.93.gtf aligner=hisat2 strandedness=firststrand spikein_fasta=./Homo_sapiens_dnarna/ERCC92/ERCC92.fa
RPM (reads per milion) were calculated and genes with RPM of 0 in all of the samples were discarded.
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing RPM (reads per milion) mean and standard deviation for each gene (rows, N=18261 with ENSG identifiers and gene names) and conditions including the RPM of each individual sample replicate (columns, N=140 made of 22 means, 22 standard deviations for aggregate replicates and 96 individual samples)

growth_protocol: A375 cells were plated in 24-well plates (Corning, #353047) with 475 uL of growth media (DMEM with 4.5 g/l glucose, l‐glutamine, and sodium pyruvate from Corning supplemented with 5% FBS) and allowed to adhere for 24 hours before perturbations.

extract_protocol:
RNA was extracted using Applied Biosystems MagMax 96 total RNA isolation kit (AM1830) with DNAse digestion according to the manufacturer’s protocol.
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kit (RS-122-2103) from 500 ng of purified total RNA according to the manufacturer’s protocol in a reduced reaction volume.

treatment_protocol: 24 hours after seeding cells, DMSO, or  the RAF inhibitor Vemurafenib alone or with Cobimetinib were added to cells that were at  50-60% confluency. After 24 hours in the drug treatment, cells were either lysed in plates or, when define by experimental design, stimulated with EGF (100 ng/mL) for the defined amount of time and then lysed in the plates.  The procedure was repeated on two different days for each of the two experimental designs (Vemurafenib doses or EGF addition time course), giving a total of four replicates per conditions (two day-to-day replicates with two technical replicates each). Technical replicates obtained on the same day have the same Set ID.

tag: cell line

value: A375 melanoma

tag: vemurafenib for 24 hrs (um)

tag: cobimetinib for 24 hrs (um)

tag: egf at 100 ng/ml (h)

tag: set id


title: sRNA -SG15_HS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -SG15_HS - Rep1

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 8, 2nd Trimester (RNA-seq)


title: Normal Pregnancy Patient 7, cord blood (RNA-seq)


title: sRNA -SG15_HS - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG15_WS - Rep2

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=8_h (S96)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=4_h (S93)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=4_h (S94)


title: Normal Pregnancy Patient 8, 1st Trimester (RNA-seq)


title: sRNA -SG15_WS - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -SG25_CG - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG25_CG - Rep1

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 7, 3rd Trimester (RNA-seq)


title: Normal Pregnancy Patient 7, delivery (RNA-seq)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=3_h (S92)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=3_h (S91)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=2_h (S90)


title: sRNA -SG15_CG - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -SG5_WH - Rep3

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 7, 2nd Trimester (RNA-seq)


title: sRNA -SG15_WS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -SG15_CG - Rep1

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=2_h (S89)


title: Normal Pregnancy Patient 6, cord blood (RNA-seq)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=1_h (S88)


title: sRNA -SG5_WS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -SG5_HS - Rep2

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 6, delivery (RNA-seq)


title: Normal Pregnancy Patient 7, 1st Trimester (RNA-seq)


title: sRNA -SG5_WS - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG15_CG - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG5_WS - Rep1

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=1_h (S87)


title: sRNA -SG5_CG - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -SG5_CG - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -SG5_WH - Rep2

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=0.5_h (S85)


title: sRNA -SG5_CG - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -TG45_WH - Rep3

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=0.5_h (S86)


title: sRNA -SG5_WH - Rep1

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=0_h (S84)


title: Normal Pregnancy Patient 6, 1st Trimester (RNA-seq)


title: sRNA -SG5_HS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -TG45_WH - Rep2

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 5, cord blood (RNA-seq)


title: sRNA -SG5_HS - Rep1

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=0_h (S83)


title: sRNA -TG45_WH - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -TG45_HS - Rep3

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 5, delivery (RNA-seq)


title: sRNA -TG45_HS - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -TG45_WS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -TG45_HS - Rep2

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 5, 3rd Trimester (RNA-seq)


title: A375_Drugs=DMSO_EGF_time=0_h (S82)


title: A375_Drugs=DMSO_EGF_time=0_h (S81)


title: Normal Pregnancy Patient 6, 3rd Trimester (RNA-seq)


title: sRNA -TG45_WS - Rep2

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 5, 1st Trimester (RNA-seq)


title: sRNA -TG45_WS - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -TG45_CG - Rep3

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vemurafenib_EGF_time=8_h (S80)


title: A375_Drugs=Vemurafenib_EGF_time=8_h (S79)


title: sRNA -TG35_WH - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -TG45_CG - Rep1

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 6, 2nd Trimester (RNA-seq)


title: sRNA -TG45_CG - Rep2

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 4, cord blood (RNA-seq)


title: sRNA -TG35_WH - Rep2

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 4, delivery (RNA-seq)


title: sRNA -TG35_WH - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -TG35_HS - Rep2

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 4, 3rd Trimester (RNA-seq)


title: A375_Drugs=Vemurafenib_EGF_time=4_h (S77)


title: sRNA -TG35_HS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -TG35_HS - Rep1

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 5, 2nd Trimester (RNA-seq)


title: sRNA -TG35_WS - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -TG35_WS - Rep3

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vemurafenib_EGF_time=3_h (S76)


title: A375_Drugs=Vemurafenib_EGF_time=3_h (S75)


title: Normal Pregnancy Patient 4, 2nd Trimester (RNA-seq)


title: sRNA -TG35_WS - Rep1

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 4, 1st Trimester (RNA-seq)


title: sRNA -TG35_CG - Rep3

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 3, cord blood (RNA-seq)


title: Normal Pregnancy Patient 3, delivery (RNA-seq)


title: A375_Drugs=Vemurafenib_EGF_time=2_h (S74)


title: sRNA -TG35_CG - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -TG25_WH - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -TG35_CG - Rep1

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vemurafenib_EGF_time=1_h (S72)


title: sRNA -TG25_WH - Rep2

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vemurafenib_EGF_time=4_h (S78)


title: sRNA -TG25_HS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -TG25_WH - Rep3

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vemurafenib_EGF_time=2_h (S73)


title: A375_Drugs=Vemurafenib_EGF_time=1_h (S71)


title: Normal Pregnancy Patient 3, 2nd Trimester (RNA-seq)


title: Normal Pregnancy Patient 3, 3rd Trimester (RNA-seq)


title: sRNA -TG25_WS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -TG25_HS - Rep1

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vemurafenib_EGF_time=0.5_h (S70)


title: sRNA -TG25_HS - Rep2

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 3, 1st Trimester (RNA-seq)


title: A375_Drugs=Vemurafenib_EGF_time=0_h (S68)


title: A375_Drugs=Vemurafenib_EGF_time=0.5_h (S69)


title: sRNA -TG25_WS - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -TG25_CG - Rep3

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 2, cord blood (RNA-seq)


title: Normal Pregnancy Patient 2, delivery (RNA-seq)


title: sRNA -TG25_CG - Rep2

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 2, 3rd Trimester (RNA-seq)


title: A375_Drugs=DMSO_EGF_time=0_h (S66)


title: sRNA -TG15_WH - Rep2

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vemurafenib_EGF_time=0_h (S67)


title: Normal Pregnancy Patient 2, 2nd Trimester (RNA-seq)


title: sRNA -TG15_WH - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -TG15_WH - Rep3

description: sRNA-seq processed data.xlsx


title: A375_Drugs=DMSO_EGF_time=0_h (S65)


title: sRNA -TG25_CG - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -TG15_HS - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -TG15_HS - Rep1

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 1, cord blood (RNA-seq)


title: sRNA -TG15_WS - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -TG15_WS - Rep1

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 1, delivery (RNA-seq)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=8_h (S64)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=8_h (S63)


title: sRNA -TG15_HS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -TG15_CG - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -TG25_WS - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -TG15_WS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -TG15_CG - Rep1

description: sRNA-seq processed data.xlsx


title: Normal Pregnancy Patient 1, 3rd Trimester (RNA-seq)


title: sRNA -TG5_WH - Rep3

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=4_h (S61)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=4_h (S62)


title: Normal Pregnancy Patient 2, 1st Trimester (RNA-seq)


title: Normal Pregnancy Patient 1, 2nd Trimester (RNA-seq)


title: sRNA -TG5_HS - Rep2

description: sRNA-seq processed data.xlsx


title: sRNA -TG5_HS - Rep3

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=3_h (S59)


title: sRNA -TG5_WH - Rep1

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=3_h (S60)


title: Non pregnant Patient 7 (WGBS)

library_source: genomic

data_processing:
We first used the FastQC (version v0.11.8) program to assess the quality of our sequenced reads. All the samples passed this step of quality control before proceeding further into analysis.
Bs-seeker2 (version v2.1.0) was employed to align the reads to the human reference genome (hg19) with the following configurations: -m 5,  --bt2--end-to-end -s 8 -t Y. The PCR duplications were removed using the rmdup function in samtools (v1.9). After the alignment, each read has been assigned to a specific genomic region (we used the methylation signatures from Sun et al. 2015) and translated into binary values (0 or 1) indicating the methylation state of each CpG site: value 0 represents unmethylated CpG while value 1 the methylated CpG. The corresponding txt file was used as input for the new deconvolution method described in the paper and developed in Dr Zhou Lab.
Genome_build: hg19
Supplementary_files_format_and_content: text file in wich the first column represent the corresponding genomic regions (we used the methylation signatures from Sun et al. 2015). In the second column each read was translated into binary values (0 or 1) indicating the methylation state of each CpG site: value 0 represents unmethylated CpG while value 1 the methylated CpG.

molecule: genomic DNA

extract_protocol:
Peripheral venous blood was collected into EDTA-coated tubes. Blood was then centrifuged at 2000 X g for 7 minutes at 4°C, in order to collect only the plasma fraction. Plasma was centrifuged at 16000 X g for 10 min at 4°C to remove all the residual cells, aliquoted and stored at −80°C. Cell-free DNA was extracted from 200 μL of plasma using the QIAmp MiniElute Virus Spin kit (Qiagen). Total DNA was quantified using the Qubit dsDNA HS Assay kit (Thermofisher Scientific).
Whole genome bisulfite libraries were prepared using the pico methyl-Seq library prep kit (Zymo Research) according to manufacturer’s instructions. Libraries were sequenced using 100 bp single-end reads on the Hiseq4000 System (Illumina)

value: Non pregnant


title: sRNA -TG5_HS - Rep1

description: sRNA-seq processed data.xlsx


title: Non pregnant Patient 6 (WGBS)


title: sRNA -TG5_WS - Rep3

description: sRNA-seq processed data.xlsx


title: sRNA -TG5_WS - Rep2

description: sRNA-seq processed data.xlsx


title: Non pregnant Patient 4 (WGBS)


title: Non pregnant Patient 5 (WGBS)


title: sRNA -TG15_CG - Rep2

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=2_h (S58)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=1_h (S56)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=2_h (S57)


title: Non pregnant Patient 3 (WGBS)


title: sRNA -TG5_CG - Rep1

description: sRNA-seq processed data.xlsx


title: sRNA -TG5_CG - Rep3

description: sRNA-seq processed data.xlsx


title: Non pregnant Patient 2 (WGBS)


title: sRNA -TG5_WH - Rep2

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=1_h (S55)


title: Chronic  hypertension Patient 2, cord blood (WGBS)

value: Chronic  hypertension


title: Non pregnant Patient 1 (WGBS)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=0.5_h (S53)


title: sRNA -TG5_CG - Rep2

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vem+Cobimetinib_EGF_time=0_h (S51)


title: A375_Drugs=DMSO_EGF_time=0_h (S50)


title: Chronic  hypertension Patient 2, 3rd Trimester (WGBS)


title: Chronic  hypertension Patient 2, 2nd Trimester (WGBS)


title: Chronic  hypertension Patient 2, 1st Trimester (WGBS)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=0.5_h (S54)


title: A375_Drugs=DMSO_EGF_time=0_h (S49)


title: Chronic  hypertension Patient 2, delivery (WGBS)


title: A375_Drugs=Vem+Cobimetinib_EGF_time=0_h (S52)


title: Chronic  hypertension Patient 1, cord blood (WGBS)


title: A375_Drugs=Vemurafenib_EGF_time=8_h (S47)


title: sRNA -TG5_WS - Rep1

description: sRNA-seq processed data.xlsx


title: A375_Drugs=Vemurafenib_EGF_time=8_h (S48)


title: A375_Drugs=Vemurafenib_EGF_time=4_h (S46)


title: Chronic  hypertension Patient 1, 3rd Trimester (WGBS)


title: sRNA -SG25_HS - Rep2

description: sRNA-seq processed data.xlsx


title: Chronic  hypertension Patient 1, 2nd Trimester (WGBS)


title: A375_Drugs=Vemurafenib_EGF_time=4_h (S45)


title: BJAB-rKSHV I-BET151 #3

type: RNA

city: Hannover

first: Rishikesh

last: Lotke

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Institut für Virologie

country: Germany

institute: Medizinische Hochschule Hannover

description:
M6153
BJAB cells latently infected with recombinant KSHV (rKSHV.219).
Gene expression 48 hours after treatment with 0.5 µM I-BET151 (Inhibitor).

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 1000ng of labeled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing:
Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’.
Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.
Averaged gPS values were normalized by quantile normalization followed by global linear scaling. For the latter approach, all quantile normalized gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array i’ in the formula shown below). Accordingly, finally normalized gPS values for all samples (microarray data sets) were calculated by the following formula:
Finally normalized gPSArray i = quantile normalized gPSArray i x (1500 / 75th PercentileArray i)
Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 finally normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.

label: Alexa Fluor 555

source_name: Human Burkitt lymphoma

label_protocol: 375ng of total RNA were used for synthesis of aminoallyl-UTP-modified (aaUTP) cRNA with the ‘Quick Amp Labeling kit, no dye’ (#5190-0447, Agilent Technologies) according to the manufacturer’s recommendations, except that reaction volumes were quartered and contained NTP-mix was exchanged by NTP Set (ATP, CTP, GTP, UTP) and aminoallyl-UTP (Fermentas, Thermo Scientific; order numbers R1091, R0481, respectively). Final NTP concentrations used for in-vitro transcription were 2.5mM (ATP, CTP, GTP), 1.88mM UTP, and 0.62mM aaUTP. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; Life Technologies) as described in the Amino Allyl MessageAmp™ II Kit Manual (#AM1753; Life Technologies) except that reaction volumes were quartered.

growth_protocol: BJAB-mCherry, BJAB-kLANA and BJAB-rKSHV.219 were cultured in RPMI 1640 (Gibco) with 20% (v/v) Foetal Calf Serum (FCS) (HyClone). All cells were incubated in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total RNA from BJAB-mCherry, BJAB-kLANA and BJAB-rKSHV.219 cells in the absence and presence of 0.5 µM I-BET151 for 48 hours was isolated using the Qiagen RNeasy® Mini kit.

treatment_protocol: BJAB-mCherry, BJAB-kLANA and BJAB-rKSHV.219 cells were plated in T-75 flasks at a cell density of 0.5 x 10^6 cells/ml and in the absence or presence of I-BET151 at a final concentration of 0.5 µM for 48 hours.

tag: modification to cells

value: recombinant KSHV (rKSHV.219)

value: 0.5 uM I-BET151 (Inhibitor)

tag: time point

value: 48 hours


title: Chronic  hypertension Patient 1, delivery (WGBS)


title: BJAB-mCherry DMSO #3

description:
M6148
BJAB cells transduced with lentivirus containing mCherry expression construct.
Gene expression 48 hours after treatment with DMSO (Vehicle).

value: BJAB-mCherry

value: mCherry expression construct

value: DMSO (Vehicle)


title: A375_Drugs=Vemurafenib_EGF_time=3_h (S44)


title: BJAB-kLANA I-BET151 #2

description:
M5987
BJAB cells transduced with lentivirus containing kLANA expression construct.
Gene expression 48 hours after treatment with 0.5 µM I-BET151 (Inhibitor).

value: BJAB-kLANA

value: kLANA expression construct


title: BJAB-rKSHV DMSO #1

description:
M5982
BJAB cells latently infected with recombinant KSHV (rKSHV.219).
Gene expression 48 hours after treatment with DMSO (Vehicle).


title: Chronic  hypertension Patient 1, 1st Trimester (WGBS)


title: BJAB-kLANA I-BET151 #3

description:
M6151
BJAB cells transduced with lentivirus containing kLANA expression construct.
Gene expression 48 hours after treatment with 0.5 µM I-BET151 (Inhibitor).


title: A375_Drugs=Vemurafenib_EGF_time=3_h (S43)


title: BJAB-kLANA DMSO #2

description:
M5986
BJAB cells transduced with lentivirus containing kLANA expression construct.
Gene expression 48 hours after treatment with DMSO (Vehicle).


title: BJAB-rKSHV DMSO #2

description:
M5988
BJAB cells latently infected with recombinant KSHV (rKSHV.219).
Gene expression 48 hours after treatment with DMSO (Vehicle).


title: AH-414_K4me1

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

description:
414_K4me1_-_61
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me44

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using bowtie2 with defautl parameters
Genome_build: hg19
Supplementary_files_format_and_content: Peak files from MACS2 and SICER; and TDF files

source_name: liver

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

tag: disease state

value: Alcoholic Hepatitis patient

tag: tissue

value: liver

tag: antibody


title: AH-414_K27me3

description:
414_K27me3_-_64
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me43


title: AH-414_input

description:
414_input_-_65
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me46

value: input


title: BJAB-rKSHV I-BET151 #2

description:
M5989
BJAB cells latently infected with recombinant KSHV (rKSHV.219).
Gene expression 48 hours after treatment with 0.5 µM I-BET151 (Inhibitor).


title: AH-414_K4me3

description:
414_K4me3_-_62
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me45


title: BJAB-rKSHV DMSO #3

description:
M6152
BJAB cells latently infected with recombinant KSHV (rKSHV.219).
Gene expression 48 hours after treatment with DMSO (Vehicle).


title: BJAB-mCherry I-BET151 #1-Rerun

description:
M6147
BJAB cells transduced with lentivirus containing mCherry expression construct.
Gene expression 48 hours after treatment with 0.5 µM I-BET151 (Inhibitor).


title: AH-414_K27ac

description:
414_K27ac_-_63
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me42


title: BJAB-mCherry DMSO #2

description:
M5984
BJAB cells transduced with lentivirus containing mCherry expression construct.
Gene expression 48 hours after treatment with DMSO (Vehicle).


title: BJAB-kLANA DMSO #3

description:
M6150
BJAB cells transduced with lentivirus containing kLANA expression construct.
Gene expression 48 hours after treatment with DMSO (Vehicle).


title: BJAB-rKSHV I-BET151 #1

description:
M5983
BJAB cells latently infected with recombinant KSHV (rKSHV.219).
Gene expression 48 hours after treatment with 0.5 µM I-BET151 (Inhibitor).


title: BJAB-mCherry I-BET151 #3

description:
M6149
BJAB cells transduced with lentivirus containing mCherry expression construct.
Gene expression 48 hours after treatment with 0.5 µM I-BET151 (Inhibitor).


title: Preeclampsia/gestational hypertension Patient 8, cord blood (WGBS)

value: Preeclampsia/gestational hypertension


title: BJAB-mCherry DMSO #1

description:
M5978
BJAB cells transduced with lentivirus containing mCherry expression construct.
Gene expression 48 hours after treatment with DMSO (Vehicle).


title: BJAB-kLANA I-BET151 #1

description:
M5981
BJAB cells transduced with lentivirus containing kLANA expression construct.
Gene expression 48 hours after treatment with 0.5 µM I-BET151 (Inhibitor).


title: AH-413_input

description:
413_input_-_30
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me41


title: AH-413_K4me3

description:
413_K4me3_-_27
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me40


title: A375_Drugs=Vemurafenib_EGF_time=2_h (S42)


title: BJAB-mCherry I-BET151 #1

description:
M5979
BJAB cells transduced with lentivirus containing mCherry expression construct.
Gene expression 48 hours after treatment with 0.5 µM I-BET151 (Inhibitor).


title: Preeclampsia/gestational hypertension Patient 8, delivery (WGBS)


title: A375_Drugs=Vemurafenib_EGF_time=2_h (S41)


title: BJAB-mCherry DMSO #1-Rerun

description:
M6146
BJAB cells transduced with lentivirus containing mCherry expression construct.
Gene expression 48 hours after treatment with DMSO (Vehicle).


title: BJAB-mCherry I-BET151 #2

description:
M5985
BJAB cells transduced with lentivirus containing mCherry expression construct.
Gene expression 48 hours after treatment with 0.5 µM I-BET151 (Inhibitor).


title: BJAB-kLANA DMSO #1

description:
M5980
BJAB cells transduced with lentivirus containing kLANA expression construct.
Gene expression 48 hours after treatment with DMSO (Vehicle).


title: Preeclampsia/gestational hypertension Patient 8, 3rd Trimester (WGBS)


title: AH-413_K27me3

description:
413_K27me3_-_29
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me38


title: A375_Drugs=Vemurafenib_EGF_time=0.5_h (S38)


title: Preeclampsia/gestational hypertension Patient 8, 1st Trimester (WGBS)


title: AH-413_K27ac

description:
413_K27ac_-_28
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me37


title: AH-412_K4me1

description:
412_K4me1_-_21
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me34


title: A375_Drugs=Vemurafenib_EGF_time=1_h (S39)


title: Preeclampsia/gestational hypertension Patient 7, cord blood (WGBS)


title: Preeclampsia/gestational hypertension Patient 8, 2nd Trimester (WGBS)


title: A375_Drugs=Vemurafenib_EGF_time=1_h (S40)


title: AH-412_input

description:
412_input_-_25
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me36


title: AH-412_K4me3

description:
412_K4me3_-_22
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me35


title: AH-410_input

description:
410_input_-_20
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me31


title: AH-410_K4me3

description:
410_K4me3_-_17
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me30


title: Preeclampsia/gestational hypertension Patient 7, delivery (WGBS)


title: Preeclampsia/gestational hypertension Patient 7, 3rd Trimester (WGBS)


title: AH-410_K27me3

description:
410_K27me3_-_19
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me28


title: A375_Drugs=Vemurafenib_EGF_time=0_h (S36)


title: AH-413_K4me1

description:
413_K4me1_-_26
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me39


title: A375_Drugs=Vemurafenib_EGF_time=0.5_h (S37)


title: AH-410_K27ac

description:
410_K27Ac_-_18
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me27


title: A375_Drugs=Vemurafenib_EGF_time=0_h (S35)


title: AH-409_input

description:
409_input_-_40
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me26


title: Preeclampsia/gestational hypertension Patient 7, 2nd Trimester (WGBS)


title: AH-412_K27ac

description:
412_K27Ac_-_23
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me32


title: AH-412_K27me3

description:
412_K27me3_-_24
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me33


title: A375_Drugs=DMSO_EGF_time=0_h (S34)


title: Preeclampsia/gestational hypertension Patient 7, 1st Trimester (WGBS)


title: AH-409_K4me3

description:
409_K4me3_-_37
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me25


title: AH-409_K27me3

description:
409_K27me3_-_39
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me23


title: A375_Drugs=DMSO_EGF_time=0_h (S33)


title: AH-409_K4me1

description:
409_K4me1_-_36
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me24


title: Preeclampsia/gestational hypertension Patient 6, cord blood (WGBS)


title: N400_K27me3

description:
400_K27me3_-_114
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me19

value: Normal human

tag: passages


title: AH-409_K27ac

description:
409_K27ac_-_38
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me22


title: AH-410_K4me1

description:
410_K4me1_-_16
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me29


title: N400_input

description:
400_input_-_115
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me21


title: A375_Time=24_h_DMSO=0_uM (S32)


title: Preeclampsia/gestational hypertension Patient 6, delivery (WGBS)


title: A375_Time=24_h_DMSO=0_uM (S31)


title: N400_K4me1

description:
400_K4me1_-_111
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me20


title: A375_Time=24_h_Vemurafenib=0.001_uM (S30)


title: N399_input

description:
399_input_-_110
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me17


title: A375_Time=24_h_Vemurafenib=0.001_uM (S29)


title: N399_K4me3

description:
399_K4me3_-_107
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me16


title: N400_K27ac

description:
400_K27ac_-_113
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me18


title: N399_K4me1

description:
399_K4me1_-_106
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me15


title: Preeclampsia/gestational hypertension Patient 6, 3rd Trimester (WGBS)


title: Preeclampsia/gestational hypertension Patient 6, 2nd Trimester (WGBS)


title: Preeclampsia/gestational hypertension Patient 6, 1st Trimester (WGBS)


title: A375_Time=24_h_Vemurafenib=0.01_uM (S28)


title: N396_input

description:
396_input_-_5
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me12


title: N399_K27ac

description:
399_K27ac_-_108
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me13


title: Preeclampsia/gestational hypertension Patient 5, cord blood (WGBS)


title: Preeclampsia/gestational hypertension Patient 5, delivery (WGBS)


title: N396_K4me1

description:
396_K4me1_-_1
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me10


title: N396_K4me3

description:
396_K4me3_-_2
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me11


title: N396_K27me3

description:
396_K27me3_-_4
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me9


title: A375_Time=24_h_Vemurafenib=0.0316_uM (S26)


title: N396_K27ac

description:
396_K27Ac_-_3
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me8


title: N389_input

description:
389_input_-_105
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me7


title: Preeclampsia/gestational hypertension Patient 5, 3rd Trimester (WGBS)


title: A375_Time=24_h_Vemurafenib=0.0316_uM (S25)


title: N389_K4me3

description:
389_K4me3_-_102
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me6


title: Preeclampsia/gestational hypertension Patient 5, 2nd Trimester (WGBS)


title: N389_K4me1

description:
389_K4me1_-_101
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me5


title: A375_Time=24_h_Vemurafenib=0.1_uM (S24)


title: N399_K27me3

description:
399_K27me3_-_109
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me14


title: Preeclampsia/gestational hypertension Patient 5, 1st Trimester (WGBS)


title: AH5

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (hg19) using Tophat (v2.0.6) with default parameters
Raw count and RPKM were calcualted using RSeQC (v2.3.6) on hg19.refseq.bed12
Genome_build: hg19
Supplementary_files_format_and_content: tsv file for raw count

extract_protocol:
RNA was extracted using the Qiagen All Prep DNA/RNA/Protein kit as per manufacturer's recommendations
TruSeq Stranded Total RNA RiboZero Gold kit from Illumina was used for library construction

value: alcoholic hepatitis


title: N389_K27me3

description:
389_K27me3_-_104
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me4


title: AH3


title: AH4


title: N389_K27ac

description:
389_K27ac_-_103
Rabbit monoclonal antibodies for anti-H3K27ac and anti-H3K27me3;  and in-house generated antibodies for anti-H3K4me1, anti-H3K4me3


title: A375_Time=24_h_Vemurafenib=0.316_uM (S22)

value: A375 melanoma


title: A375_Time=24_h_Vemurafenib=0.316_uM (S21)


title: AH1


title: Preeclampsia/gestational hypertension Patient 4, cord blood (WGBS)


title: A375_Time=24_h_Vemurafenib=0.01_uM (S27)


title: AH2


title: A375_Time=24_h_Vemurafenib=1_uM (S20)


title: Preeclampsia/gestational hypertension Patient 4, 3rd Trimester (WGBS)


title: Preeclampsia/gestational hypertension Patient 4, 2nd Trimester (WGBS)


title: A375_Time=24_h_Vemurafenib=1_uM (S19)


title: Preeclampsia/gestational hypertension Patient 4, delivery (WGBS)


title: Control3

value: control


title: Control1


title: wt-proB-Rep2 (RNA-seq)

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Gene expression in wt proB cells

data_processing:
The base calling was performed by using BCL2Fastq pipeline (version: 0.3.1) and bcl2fastq (version 2.20.0.422).
RNA-seq: The paired-end RNA-seq datasets were mapped to the mouse reference genome (mm9) using STAR aligner (2.5.3a).
RNA-seq: The mapped reads were further assembled by using Cufflinks (v2.2.1) and the expression level of the annotated genes (UCSC, mm9) was calculated by Cuffquant. The differential gene expression between the conditions was calculated by using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: The normalized gene expression values (FPKM) calculated by Cuffnorm (v2.2.1) are provided in TXT format.

organism: Mus musculus

source_name: wt proB cells, Replicate2

growth_protocol: dHet leukemic cells were derived from the lymph node of Ebf1+/-Pax5+/- leukemic mice. dHet proB cells were derived by culturing the single-cell suspensions of freshly isolated c-Kit positive fetal liver cells were plated on OP9 feeder cells in OptiMEM medium, supplemented with 4% FCS, 1% PSG, 50 μM β-mercaptoethanol, 5 ng/ml interleukin 7 (IL-7), 10 ng/ml Flt3 ligand (Flt3L) and 10 ng/ml stem cell factor (SCF). wt proB (FrBC) cells were sorted from the control mice.

extract_protocol:
RNA-seq: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
The RNA-seq libraries were prepared by using the NEB E6420 RNA library preparation kit according to the manufacturer's instructions.

tag: strain

value: wt proB (Fraction BC) bone marrow

value: wt proB cells

tag: genotype


title: Preeclampsia/gestational hypertension Patient 4, 1st Trimester (WGBS)


title: wt-proB-Rep1 (RNA-seq)

description: Gene expression in wt proB cells

source_name: wt proB cells, Replicate1


title: Control4


title: A375_Time=24_h_Vemurafenib=0.1_uM (S23)


title: A375_Time=24_h_Vemurafenib=10_uM (S18)


title: dHet-proB-Rep3 (RNA-seq)

description: Gene expression in dHet proB cells

source_name: Ebf1+/- Pax5+/- dHet fetal liver proB cells,Replicate2

value: Ebf1+/- Pax5+/- Rag2-/- proB fetal liver

value: dHet proB cells


title: Preeclampsia/gestational hypertension Patient 3, delivery (WGBS)


title: Preeclampsia/gestational hypertension Patient 3, 3rd Trimester (WGBS)


title: Preeclampsia/gestational hypertension Patient 3, 2nd Trimester (WGBS)


title: Control2


title: Preeclampsia/gestational hypertension Patient 3, 1st Trimester (WGBS)


title: A375_Time=24_h_Vemurafenib=0.001_uM (S14)


title: A375_Time=24_h_Vemurafenib=10_uM (S17)


title: A375_Time=24_h_DMSO=0_uM (S16)


title: A375_Time=24_h_Vemurafenib=0.001_uM (S13)


title: Preeclampsia/gestational hypertension Patient 3, cord blood (WGBS)


title: Preeclampsia/gestational hypertension Patient 2, delivery (WGBS)


title: Preeclampsia/gestational hypertension Patient 2, cord blood (WGBS)


title: Preeclampsia/gestational hypertension Patient 2, 3rd Trimester (WGBS)


title: A375_Time=24_h_Vemurafenib=0.01_uM (S11)


title: A375_Time=24_h_Vemurafenib=0.01_uM (S12)


title: A375_Time=24_h_Vemurafenib=0.0316_uM (S10)


title: dHet-B-ALL-760-Rep2 (RNA-seq)

description: Gene expression in dHet B-ALL (760) cells

source_name: Ebf1+/- Pax5+/- dHet leukemic cells derived from lymph node (mouse 760),Replicate2

value: Ebf1+/- Pax5+/- lymph node

value: dHet B-ALL (760) cells


title: dHet-B-ALL-686-Rep2 (RNA-seq)

description: Gene expression in dHet B-ALL (686) cells

source_name: Ebf1+/- Pax5+/- dHet leukemic cells derived from lymph node (mouse 686),Replicate2

value: dHet B-ALL (686) cells


title: dHet-B-ALL-713-Rep1 (RNA-seq)

description: Gene expression in dHet B-ALL (713) cells

source_name: Ebf1+/- Pax5+/- dHet leukemic cells derived from lymph node (mouse 713),Replicate1

value: dHet B-ALL (713) cells


title: dHet-B-ALL-760-Rep1 (RNA-seq)

source_name: Ebf1+/- Pax5+/- dHet leukemic cells derived from lymph node (mouse 760),Replicate1


title: A375_Time=24_h_DMSO=0_uM (S15)


title: dHet-proB-Rep2 (RNA-seq)

description: Gene expression in dHet proB cells


title: dHet-B-ALL-713-Rep2 (RNA-seq)

source_name: Ebf1+/- Pax5+/- dHet leukemic cells derived from lymph node (mouse 713),Replicate2


title: INDY_KO_replicate_5

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's Sentrix Mouse Ref-8 v2 Expression Bead Chips (Illumina, San Diego, CA).  The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.54 um using the Illumina iScan Bead Station.

data_processing: Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.

source_name: Adrenals_INDY KO78

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

growth_protocol: Mice were generated as previously described (Birkenfeld et al., Cell Metab. 2011; 14(2):184-195): Pups carrying the SLC13A5tm1.1Helf allele were genotyped at the expected frequency of about 25%. Mice carrying SLC13A5tm1.2Helf allele (ƒ¢1-6) were obtained by mating SLC13A5tm1.1Helf/+ mice with animals carrying Hprt1-Cre transgene (129S1-Hprttm1(Cre)Mnn, Jackson Lab). The offspring was then backcrossed more than 10 times to the C57B/6J background and studies were performed with age matched littermate control WT mice. Homozygous mINDY KO mice were obtained from mating heterozygous mINDY KO mice. Littermate animals were used in all experiments. All breeding and procedures were carried out at the animal facilities of the Charite Berlin and Technical University Dresden according to institutional regulations and the local guide for the use and care of laboratory animals. Experiments based on BP measurements by telemetry were performed on . The animals had free access to standard chow (0.25% sodium,SNIFF GmbH, Soest, Germany) and drinking water ad libitum. Animals were cared for within the Institutional Animal Care Committee guidelines, and all animal procedures were approved by local government authorities (Landesamt fur Gesundheit und Soziales, Berlin, Germany and Landesdirektion Sachsen, Dresden, Germany).

extract_protocol: Total RNA was extracted from 12-16 week old male mouse adrenals using the Trizol reagent (Invitrogen, Carlsbad CA) according to standard protocols. RNA quality and quantity was assessed using the RNA 6000 Nano Chip on an Agilent Bioanalyzer (Agilent, Wilmington, DE).

tag: condition

value: C57B/6J backcross

tag: age

value: 12-16 week old

tag: Sex

value: Male

value: adrenals


title: dHet-proB-Rep1 (RNA-seq)

description: Gene expression in dHet proB cells

source_name: Ebf1+/- Pax5+/- dHet fetal liver proB cells,Replicate1

tag: cell type


title: dHet-B-ALL-686-Rep1 (RNA-seq)

source_name: Ebf1+/- Pax5+/- dHet leukemic cells derived from lymph node (mouse 686),Replicate1


title: A375_Time=24_h_Vemurafenib=0.1_uM (S8)

tag: cell line


title: Preeclampsia/gestational hypertension Patient 2, 1st Trimester (WGBS)

tag: complication during pregnancy

value: Preeclampsia/gestational hypertension


title: A375_Time=24_h_Vemurafenib=0.1_uM (S7)

tag: vemurafenib for 24 hrs (um)

tag: cobimetinib for 24 hrs (um)


title: INDY_KO_replicate_4

source_name: Adrenals_INDY KO58


title: Preeclampsia/gestational hypertension Patient 1, cord blood (WGBS)

source_name: Plasma


title: INDY_KO_replicate_1

source_name: Adrenals_INDY KO28


title: Preeclampsia/gestational hypertension Patient 2, 2nd Trimester (WGBS)


title: WT_CTR_replicate_4


title: WT_CTR_replicate_2


title: WT_CTR_replicate_5


title: WT_CTR_replicate_3


title: INDY_KO_replicate_2

source_name: Adrenals_INDY KO47


title: INDY_KO_replicate_3

source_name: Adrenals_INDY KO57


title: A375_Time=24_h_Vemurafenib=0.316_uM (S5)

tag: egf at 100 ng/ml (h)

tag: set id


title: WT_CTR_replicate 1_TR


title: WT_CTR_replicate_1


title: A375_Time=24_h_Vemurafenib=0.0316_uM (S9)


title: A375_Time=24_h_Vemurafenib=1_uM (S4)


title: Preeclampsia/gestational hypertension Patient 1, delivery (WGBS)


title: A375_Time=24_h_Vemurafenib=1_uM (S3)


title: A375_Time=24_h_Vemurafenib=0.316_uM (S6)


title: Preeclampsia/gestational hypertension Patient 1, 3rd Trimester (WGBS)


title: Gestational diabetes Patient 7, 3rd Trimester (WGBS)

value: Gestational Diabetes


title: Gestational diabetes Patient 7, delivery (WGBS)


title: Preeclampsia/gestational hypertension Patient 1, 2nd Trimester (WGBS)


title: Gestational diabetes Patient 7, cord blood (WGBS)


title: A375_Time=24_h_Vemurafenib=10_uM (S1)


title: A375_Time=24_h_Vemurafenib=10_uM (S2)


title: K14_hyal1_colon

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
Raw data was analyzed using Partek Flow and Partek Genomics Suite software to determine transcript abundance and differentially expressed genes between samples
Genome_build: mm10
Supplementary_files_format_and_content: transcript abundance and differentially expressed genes between samples

extract_protocol:
Total cellular RNA was extracted using the PureLink RNA Mini Kit (Life Technologies Corporation, Grand Island, NY)
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kits (Illumina) and run on a HiSeq 2500 instrument (Illumina).

tag: strain background

tag: genotype/variation

tag: tissue/cell type

value: colon lamina propria


title: Gestational diabetes Patient 7, 1st Trimester (WGBS)


title: Gestational diabetes Patient 6, cord blood (WGBS)


title: sCJD114

type: genomic

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

description: Anonymized patient/sample code

hyb_protocol: According to Illumina's Instructions

scan_protocol: According to Illumina's Instructions

data_processing: Analyses were performed in RStudio version 1.0.136 using R v3.4.1. IDAT files were loaded into ChAMP version 2.10.2 and normalized using the BMIQ method. Positional batch effects were removed by using ComBat to correct for Sentrix_ID and Sentrix_Position. Leukocyte population heterogeneity was estimated and corrected for using the RefBase function.

label: Cy3, Cy5

source_name: DNA from EDTA-stored blood

label_protocol: According to Illumina's Instructions

extract_protocol: Zymo gDNA Extraction kit

treatment_protocol: Blood taken by venupuncture and stored in an EDTA tube

value: sCJD

tag: codon129 genotype

tag: mrc scale

tag: tissue

value: blood


title: Control1_colon

source_name: Control

value: Control


title: Preeclampsia/gestational hypertension Patient 1, 1st Trimester (WGBS)


title: sCJD113

description: Anonymized patient/sample code


title: Gestational diabetes Patient 7, 2nd Trimester (WGBS)


title: Leuk_spleen_EP1016_p2_3_6

description: Library of 96 cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right read (R2) of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read (R1) contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for quantification.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: B lymphoid cells from spleen

growth_protocol: Hematopoietic stroma cells and hematopoietic progenitors were isolated from Ebf1+/+ Prx1-Cre and Ebf1 fl/fl Prx1-Cre

extract_protocol:
Intact bones (femora and tibia) were chopped into small fragments and crushed in FACS buffer (PBS-2% FCS) using pestle and mortar. Bone marrow cells were collected and RBC lysis was performed. Next, the cells were washed with FACS buffer and stained for analysis. For sorting of HSPCs the cells were enriched by magnetic depletion. Briefly, the BM cells were labeled with a cocktail of biotinylated antibodies (CD3, CD19, B220, CD11b, Gr1 and Ter119) and then with streptavidin-conjugated magnetic nanobeads (BioLegend). The Lineage- cells obtained were stained with following antibodies: anti-lineage (CD3, CD19, B220, CD11b, Gr1 and Ter119), anti-Sca1, anti-c-kit, anti-CD135, anti-CD48, anti-150, and then further purified by FACS sorting. The immunophenotypes of assayed hematopoietic cells were as follow: LSKs (Lin-Sca1+c-kit+), HSCs (CD135-CD48-CD150+LSK), MMP3 (CD135-CD48+CD150-LSK), MPP4 (CD135+ CD150-LSK), CLPs (Lin-Sca1loc-kitloIL-7Rα+CD135+), pro-B cells (B220+CD43+), pre-B cells (B220loCD43-), rec-B cells (B220hiCD43-), B cells (B220+CD19+), T cells (CD3+), myeloid cells (Mac1+Gr1+) and erythroid cells (Ter119+). For non-hematopoietic BM cell isolation, the bone chips were digested with 0.3% collagenase type II and 0.02% DNase I at 37°C for 45 min with gentle shaking. After enzymatic digestion, the cells were filtered, washed with FACS buffer, and stained accordingly. CAR cells were identified as CD45-CD31-Lin-PDGFRα+Sca1-, PαS cells were identified as CD45-CD31-Lin-PDGFRα+ Sca1+.
The aRNA was reversely transcribed in order to generate libraries for sequencing, as previously described18. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)

treatment_protocol: no treatment

tag: strain

value: spleen

tag: sequencing runs

tag: illumina barcode

tag: barcode sequence

value: GCCAAT

tag: genotype

tag: celltype

value: B cells


title: Leuk_spleen_EP1016_p2_4_7

description: Library of 96 cells

value: CAGATC


title: Leuk_spleen_EP1016_p2_2_5

description: Library of 96 cells

value: ACAGTG


title: Gestational diabetes Patient 6, 3rd Trimester (WGBS)

tag: complication during pregnancy


title: sCJD110

description: Anonymized patient/sample code

tag: age

tag: Sex

value: VV


title: sCJD99

description: Anonymized patient/sample code

value: Female

value: MM


title: sCJD107

description: Anonymized patient/sample code


title: sCJD101

description: Anonymized patient/sample code


title: sCJD109

description: Anonymized patient/sample code


title: Gestational diabetes Patient 6, delivery (WGBS)


title: sCJD96

description: Anonymized patient/sample code


title: sCJD106

description: Anonymized patient/sample code


title: sCJD108

description: Anonymized patient/sample code


title: sCJD104

description: Anonymized patient/sample code


title: sCJD105

description: Anonymized patient/sample code


title: Gestational diabetes Patient 6, 2nd Trimester (WGBS)


title: sCJD112

description: Anonymized patient/sample code


title: sCJD98

description: Anonymized patient/sample code

value: MV


title: sCJD103

description: Anonymized patient/sample code


title: sCJD100

description: Anonymized patient/sample code

value: Male


title: sCJD93

description: Anonymized patient/sample code


title: Gestational diabetes Patient 6, 1st Trimester (WGBS)


title: sCJD94

description: Anonymized patient/sample code


title: Leuk_spleen_EP1016_p1_3

description: Library of 96 cells


title: sCJD91

description: Anonymized patient/sample code


title: Gestational diabetes Patient 5, cord blood (WGBS)


title: sCJD111

description: Anonymized patient/sample code


title: sCJD92

description: Anonymized patient/sample code


title: Leuk_spleen_EP1016_p1_1

description: Library of 96 cells


title: Leuk_spleen_EP1016_p1_2

description: Library of 96 cells


title: Gestational diabetes Patient 5, 3rd Trimester (WGBS)


title: Leuk_BM_EP1016_p2_4

description: Library of 96 cells

source_name: bone marrow cells

value: bone marrow

value: CTTGTA


title: Gestational diabetes Patient 5, 2nd Trimester (WGBS)

value: Gestational Diabetes


title: sCJD90

description: Anonymized patient/sample code


title: Gestational diabetes Patient 5, delivery (WGBS)


title: Leuk_spleen_EP1016_p1_4

description: Library of 96 cells

value: ACTTGA


title: Leuk_BM_EP1016_p2_2

description: Library of 96 cells

value: TAGCTT


title: Leuk_BM_EP1016_p2_1

description: Library of 96 cells

value: GATCAG


title: sCJD97

description: Anonymized patient/sample code

value: sCJD

value: blood


title: Gestational diabetes Patient 4, delivery (WGBS)


title: Leuk_BM_EP1016_p2_3

description: Library of 96 cells

value: GGCTAC


title: Gestational diabetes Patient 5, 1st Trimester (WGBS)


title: sCJD102

description: Anonymized patient/sample code


title: sCJD89

description: Anonymized patient/sample code


title: Leuk_BM_EP1016_4

description: Library of 96 cells

value: TGACCA

value: B cells


title: sCJD95

description: Anonymized patient/sample code


title: Leuk_spleen_EP1016_p2_1_4

description: Library of 96 cells

value: spleen


title: sCJD87

description: Anonymized patient/sample code


title: sCJD86

description: Anonymized patient/sample code


title: Gestational diabetes Patient 4, 2nd Trimester (WGBS)


title: Gestational diabetes Patient 4, 1st Trimester (WGBS)


title: Gestational diabetes Patient 4, 3rd Trimester (WGBS)


title: Gestational diabetes Patient 3, cord blood (WGBS)


title: sCJD88

description: Anonymized patient/sample code


title: Leuk_BM_EP1016_3

description: Library of 96 cells

value: TTAGGC


title: sCJD85

description: Anonymized patient/sample code

value: Female

value: VV


title: Leuk_blood_EP1016_1

description: Library of 96 cells

source_name: B lymphoid cells from blood

value: ATCACG


title: Gestational diabetes Patient 3, delivery (WGBS)


title: sCJD84

description: Anonymized patient/sample code


title: sCJD83

description: Anonymized patient/sample code

value: Male

value: MV


title: sCJD82

description: Anonymized patient/sample code

value: MM


title: A703_CLP_WT_4

description: Library of 96 cells

value: bone marrow

value: wild type

value: common lymphoid progenitors


title: sCJD76

description: Anonymized patient/sample code


title: sCJD81

description: Anonymized patient/sample code


title: Gestational diabetes Patient 3, 3rd Trimester (WGBS)

value: Gestational Diabetes


title: sCJD78

description: Anonymized patient/sample code

value: sCJD


title: Leuk_blood_EP1016_2

description: Library of 96 cells

value: blood

value: CGATGT


title: A703_CLP_WT_3

description: Library of 96 cells

value: CAGATC


title: sCJD75

description: Anonymized patient/sample code


title: Gestational diabetes Patient 3, 2nd Trimester (WGBS)


title: A703_CLP_WT_2

description: Library of 96 cells

value: GCCAAT


title: sCJD80

description: Anonymized patient/sample code


title: sCJD74

description: Anonymized patient/sample code


title: Gestational diabetes Patient 2, cord blood (WGBS)


title: sCJD72

description: Anonymized patient/sample code


title: Gestational diabetes Patient 2, delivery (WGBS)


title: sCJD73

description: Anonymized patient/sample code


title: sCJD68

description: Anonymized patient/sample code


title: sCJD69

description: Anonymized patient/sample code


title: sCJD66

description: Anonymized patient/sample code


title: sCJD71

description: Anonymized patient/sample code


title: sCJD77

description: Anonymized patient/sample code


title: A703_CLP_dHet_4

description: Library of 96 cells

value: TGACCA


title: A703_CLP_dHet_2

description: Library of 96 cells


title: A703_CLP_dHet_3

description: Library of 96 cells

value: TTAGGC


title: sCJD67

description: Anonymized patient/sample code

value: Female


title: sCJD79

description: Anonymized patient/sample code


title: sCJD63

description: Anonymized patient/sample code

value: VV


title: sCJD70

description: Anonymized patient/sample code


title: sCJD65

description: Anonymized patient/sample code


title: A703_CLP_dHet_1

description: Library of 96 cells

value: ATCACG


title: sCJD64

description: Anonymized patient/sample code

value: Male


title: A703_CLP_WT_1

description: Library of 96 cells

value: ACAGTG


title: A701_dHet_FrC_3

description: Library of 96 cells

value: GGCTAC

value: B cells


title: A701_dHet_FrC_4

description: Library of 96 cells

value: bone marrow

value: CTTGTA


title: Gestational diabetes Patient 2, 1st Trimester (WGBS)

value: Gestational Diabetes


title: Gestational diabetes Patient 1, cord blood (WGBS)


title: Gestational diabetes Patient 2, 2nd Trimester (WGBS)


title: Gestational diabetes Patient 1, delivery (WGBS)


title: sCJD62

description: Anonymized patient/sample code

value: sCJD


title: sCJD61

description: Anonymized patient/sample code

value: MM

value: blood


title: Gestational diabetes Patient 1, 3rd Trimester (WGBS)


title: A701_dHet_FrC_2

description: Library of 96 cells

value: TAGCTT


title: Gestational diabetes Patient 1, 2nd Trimester (WGBS)


title: sCJD60

description: Anonymized patient/sample code

value: MV


title: Gestational diabetes Patient 3, 1st Trimester (WGBS)


title: Gestational diabetes Patient 1, 1st Trimester (WGBS)


title: A701_dHet_FrB_4

description: Library of 96 cells

value: ACTTGA


title: Normal Pregnancy Patient 9, cord blood (WGBS)

value: No Complications


title: A701_dHet_FrC_1

description: Library of 96 cells

value: GATCAG


title: Normal Pregnancy Patient 9, delivery (WGBS)


title: A701_dHet_FrB_3

description: Library of 96 cells

value: CAGATC


title: sCJD59

description: Anonymized patient/sample code

value: Female


title: Normal Pregnancy Patient 9, 3rd Trimester (WGBS)


title: A701_dHet_FrB_2

description: Library of 96 cells

value: GCCAAT


title: sCJD58

description: Anonymized patient/sample code

value: Male


title: sCJD57

description: Anonymized patient/sample code


title: A701_dHet_FrB_1

description: Library of 96 cells

value: ACAGTG


title: Normal Pregnancy Patient 9, 2nd Trimester (WGBS)


title: Normal Pregnancy Patient 9, 1st Trimester (WGBS)


title: sCJD55

description: Anonymized patient/sample code


title: sCJD54

description: Anonymized patient/sample code

value: VV


title: sCJD53

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 8, cord blood (WGBS)


title: sCJD52

description: Anonymized patient/sample code


title: sCJD49

description: Anonymized patient/sample code


title: sCJD50

description: Anonymized patient/sample code


title: sCJD48

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 8, delivery (WGBS)


title: sCJD51

description: Anonymized patient/sample code


title: sCJD46

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 8, 3rd Trimester (WGBS)


title: sCJD31

description: Anonymized patient/sample code


title: sCJD47

description: Anonymized patient/sample code


title: sCJD44

description: Anonymized patient/sample code


title: sCJD45

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 8, 2nd Trimester (WGBS)


title: sCJD56

description: Anonymized patient/sample code


title: sCJD32

description: Anonymized patient/sample code


title: sCJD42

description: Anonymized patient/sample code


title: sCJD39

description: Anonymized patient/sample code


title: sCJD43

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 8, 1st Trimester (WGBS)


title: sCJD30

description: Anonymized patient/sample code


title: sCJD41

description: Anonymized patient/sample code


title: A700_WT_FrC_3

description: Library of 96 cells

value: bone marrow

value: GGCTAC

value: wild type

value: B cells


title: A701_dHet_FrA_4

description: Library of 96 cells

value: TGACCA


title: A700_WT_FrC_2

description: Library of 96 cells


title: A700_WT_FrC_4

description: Library of 96 cells

value: CTTGTA


title: A701_dHet_FrA_3

description: Library of 96 cells

value: TTAGGC


title: sCJD29

description: Anonymized patient/sample code

value: sCJD

value: MM

value: blood


title: A701_dHet_FrA_2

description: Library of 96 cells

value: CGATGT


title: A701_dHet_FrA_1

description: Library of 96 cells

value: ATCACG


title: sCJD38

description: Anonymized patient/sample code


title: A700_WT_FrC_1

description: Library of 96 cells

value: GATCAG


title: sCJD24

description: Anonymized patient/sample code

value: Female


title: sCJD36

description: Anonymized patient/sample code

value: Male


title: sCJD40

description: Anonymized patient/sample code


title: sCJD28

description: Anonymized patient/sample code


title: sCJD37

description: Anonymized patient/sample code

value: MV


title: sCJD27

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 7, delivery (WGBS)

value: No Complications


title: A700_WT_FrB_3-4

description: Library of 192 cells

value: bone marrow

value: CAGATC


title: Normal Pregnancy Patient 7, 3rd Trimester (WGBS)


title: sCJD33

description: Anonymized patient/sample code


title: A700_WT_FrB_2

description: Library of 96 cells

value: GCCAAT

value: wild type


title: sCJD22

description: Anonymized patient/sample code


title: sCJD25

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 7, 2nd Trimester (WGBS)


title: sCJD34

description: Anonymized patient/sample code


title: A700_WT_FrB_1

description: Library of 96 cells

value: ACAGTG

value: B cells


title: Normal Pregnancy Patient 7, 1st Trimester (WGBS)


title: sCJD26

description: Anonymized patient/sample code


title: A700_WT_FrA_4

description: Library of 96 cells

value: TGACCA


title: sCJD23

description: Anonymized patient/sample code

value: sCJD

value: VV


title: sCJD35

description: Anonymized patient/sample code

value: blood


title: sCJD21

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 6, cord blood (WGBS)


title: A700_WT_FrA_3

description: Library of 96 cells

value: TTAGGC


title: sCJD20

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 7, cord blood (WGBS)


title: Normal Pregnancy Patient 6, delivery (WGBS)


title: sCJD17

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 6, 3rd Trimester (WGBS)


title: A700_WT_FrA_1

description: Library of 96 cells

value: ATCACG


title: sCJD19

description: Anonymized patient/sample code

value: MM


title: A700_WT_FrA_2

description: Library of 96 cells

value: CGATGT


title: sCJD18

description: Anonymized patient/sample code

value: Female


title: Normal Pregnancy Patient 6, 2nd Trimester (WGBS)


title: A551_WT_FrC5_7

description: Library of 96 cells


title: Normal Pregnancy Patient 6, 1st Trimester (WGBS)


title: Normal Pregnancy Patient 5, cord blood (WGBS)


title: Normal Pregnancy Patient 5, delivery (WGBS)


title: sCJD11

description: Anonymized patient/sample code

value: Male


title: sCJD10

description: Anonymized patient/sample code


title: sCJD16

description: Anonymized patient/sample code


title: sCJD13

description: Anonymized patient/sample code


title: A551_WT_FrC3_3

description: Library of 96 cells


title: A551_WT_FrC4_6

description: Library of 96 cells


title: A551_WT_FrC2_2

description: Library of 96 cells


title: sCJD14

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 5, 3rd Trimester (WGBS)

value: No Complications


title: sCJD9

description: Anonymized patient/sample code


title: sCJD5

description: Anonymized patient/sample code


title: sCJD7

description: Anonymized patient/sample code


title: sCJD4

description: Anonymized patient/sample code


title: sCJD15

description: Anonymized patient/sample code


title: A499_WT_FrB_8

description: Library of 96 cells

value: bone marrow

value: ACTTGA


title: A499_WT_FrB_7

description: Library of 96 cells

value: CAGATC


title: Normal Pregnancy Patient 4, cord blood (WGBS)


title: A551_WT_FrC1_1

description: Library of 96 cells

value: wild type


title: sCJD8

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 5, 1st Trimester (WGBS)


title: sCJD3

description: Anonymized patient/sample code


title: A499_WT_FrB_6

description: Library of 96 cells

value: GCCAAT


title: sCJD6

description: Anonymized patient/sample code


title: A499_WT_FrB_5

description: Library of 96 cells

value: ACAGTG

value: B cells


title: sCJD12

description: Anonymized patient/sample code

value: sCJD


title: ATACSeq in wt-proB-Rep2

data_processing:
Basecalling and fastq files generation was performed by using Illumina bcl2fastq 2.17.1.14 (pipeline version 0.2.1)
ChIPSeq: The reads were aligned to the mm9 genome assembly using bowtie2 with default configurations
ChIPSeq: Duplicated reads were filtered and blacklisted regions were removed using samtools and Picard.
ChIPSeq: Peaks were identified using MACS2 (v2.1.0.20150731) with q-value cutoff 0.01 and filtered for p-value cut-off 10e-10 (EBF1) or 10e-7 (Pax5). The peaks were further filtered with the fold change cut-off 4.
ATACSeq: The paried-end sequencing reads were trimmed using trim galore (0.4.0), which is a wrapper for the Cutadapt (1.8.1) tools. The trimmed reads were mapped to the mouse genome (mm9) using bowtie2 (2.2.8) with the default settings.
ATACSeq: The duplicated reads were removed using Picard tools (1.136). The reads mapping to blacklisted regions, mitochondrial genome and the reads with mapping quality below 30 were removed. The properly mapped reads were used for identifying peaks by MACS2 (2.1.1) with the BAMPE mode and q-value cut off 0.01. The differentially induced peaks were identified by comapring between the samples and further filtered for a p-value cutoff 10-10 and fold change 4.
The reads were normalized to 10 million mapped reads using Homer tools (v 4.1) in bedGraph format for visualization.
Genome_build: mm9
Supplementary_files_format_and_content: The reads normalized to 10 million in the bedGraph format were generated using Homer tools

source_name: wt proB cells, Replicate2

growth_protocol: The normal pro-B cell lines were established by culturing c-Kit+ fetal liver cells of Ebf1+/+ or Ebf1+/-Pax5+/- cells with OP9 feeder cells in OptiMEM medium supplemented with 4%FCS, 50μM 2-ME, 1% Penicillin-Streptmycin-Glutamine, 10ng/ml Stem cell factor (SCF), 10ng/ml Flt3-L, and 5ng/ml IL-7. Leukemic Ebf1+/-Pax5+/- cell lines were established similarly using bone marrow CD19+AA4.1hi cells.

extract_protocol:
Cells were crosslinked  with formaldehyde, lysed and DNA was fragmented into pieces of average 300bp by sonication. Chromatin was precipitated with a specific antibody and protein A-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified via QIAquick PCR Purification Kit according to the manufacturer's manual.
Library preparation for ChIP analysis was performed with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (Catalog #E7370) according to the manufacturer’s protocol. No size selection was used and amplification was performed using 10 PCR cycles. The ATAC-seq libraries were prepared using the NEB Nextera DNA sample preparation kit according to the manufacturer's instructions.

tag: cell type

value: wt proB fetal liver cells


title: A499_WT_FrA_3

description: Library of 96 cells


title: A499_WT_FrA_4

description: Library of 96 cells

value: TGACCA


title: Normal Pregnancy Patient 4, 3rd Trimester (WGBS)


title: Control105

description: Anonymized patient/sample code

value: CTRL

value: blood


title: Control100

description: Anonymized patient/sample code


title: Control101

description: Anonymized patient/sample code


title: sCJD2

description: Anonymized patient/sample code


title: sCJD1

description: Anonymized patient/sample code


title: Control104

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 4, 1st Trimester (WGBS)


title: Control106

description: Anonymized patient/sample code


title: ATACSeq in wt-proB-Rep1

source_name: wt proB cells, Replicate1


title: Normal Pregnancy Patient 5, 2nd Trimester (WGBS)


title: Control99

description: Anonymized patient/sample code


title: Control97

description: Anonymized patient/sample code

value: VV


title: Control98

description: Anonymized patient/sample code


title: Control103

description: Anonymized patient/sample code

value: MM


title: Normal Pregnancy Patient 3, delivery (WGBS)


title: ATACSeq in dHet-B-ALL-3313

source_name: Ebf1+/- Pax5+/- dHet leukemic cells derived from lymph node (mouse 3313)

value: Ebf1+/- Pax5+/- B-ALL cells


title: A499_WT_FrA_1

description: Library of 96 cells

value: ATCACG


title: Normal Pregnancy Patient 4, 2nd Trimester (WGBS)

value: No Complications


title: Normal Pregnancy Patient 3, 3rd Trimester (WGBS)


title: A499_dHet_FrB_8

description: Library of 96 cells

value: bone marrow


title: ATACSeq in dHet-proB-Rep1

source_name: Ebf1+/- Pax5+/- Rag2-/- dHet fetal liver proB cells,Replicate1

value: Ebf1+/- Pax5+/-  proB fetal liver cells


title: Normal Pregnancy Patient 3, cord blood (WGBS)


title: Control102

description: Anonymized patient/sample code

value: Female


title: Control90

description: Anonymized patient/sample code


title: Control96

description: Anonymized patient/sample code

value: MV


title: Control94

description: Anonymized patient/sample code

value: Male


title: A499_dHet_FrB_7

description: Library of 96 cells

value: CAGATC


title: ATACSeq in dHet-proB-Rep2

source_name: Ebf1+/- Pax5+/- Rag2-/- dHet fetal liver proB cells,Replicate2


title: Control95

description: Anonymized patient/sample code


title: ATACSeq in dHet-B-ALL-713

source_name: Ebf1+/- Pax5+/- dHet leukemic cells derived from lymph node (mouse 713)


title: Normal Pregnancy Patient 3, 2nd Trimester (WGBS)


title: Normal Pregnancy Patient 4, delivery (WGBS)


title: Control91

description: Anonymized patient/sample code


title: SG5_WHdgd

description: degradome-seq processed data

data_processing:
Library strategy: degradome-seq
sRNA-Seq: Small RNA sequencing analysis was performed using the ACGT101-miR program (LC Sciences, TX, USA). Raw reads were first processed by removing low-quality reads and adapter sequences to obtain clean sequences. Reads with a nucleotide (nt) length <18 nt or >25 nt were removed. Non-coding (nc) RNA families (rRNA, tRNA, snRNA and snoRNA), repeats and mRNA sequences were discarded using RFam, Repbase and durum wheat NCBI mRNA entries as references. Unique sRNA sequences were then obtained for each library. Conserved mature miRNAs and 5p- or 3p-derived miRNA variants were identified using BLAST search against the plant miRBase (Release 22.1). MIR (microRNA gene locus) and miRNA sequences from common plant species in the miRBase were used as references. Sequences mapped to the mature miRNA in the hairpin were identified as conserved mature miRNAs. Sequences mapped to the opposite arm of mature miRNA in the hairpin were identified as 5p- or 3p-derived variants. Single mismatch within the sequence and length variation at both 5p and 3p were allowed in the alignment. All the mapped miRNAs were aligned to the durum wheat genome (NCBI UID 3439611, assembly Svevo.v1) to determine their genomic location. The remaining unmatched sRNA sequences were used to identify novel durum miRNAs. Sequences were BLASTed to the durum wheat genome. To identify miRNA precursors, secondary hairpin structures containing matched sequences were predicted using RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi) from 120nt of flanking genome sequences.
mRNA-Seq: Prior to sequence assembly, low quality reads (those containing primer or adaptor sequence, and those with a sequencing quality score < 20) were removed. Clean reads were aligned to the durum reference genome using the HISAT package (V2.0). Aligned reads of each library were assembled and the transcript abundance were obtained using StringTie (V1.3.0). Normalised relative abundance was expressed in FPKM (Fragments Per Kilobase Million).
Degradome-Seq: Raw sequencing reads were processed using the ACGT101-DEG program (V4.1, LC Sciences) to remove low-quality reads, reads with adaptor and primer contamination, and reads that can be annotated as non-coding RNA families. The remaining clean reads were used to identify the degraded fragments of mRNAs that are targets of known and novel durum miRNAs with the CleaveLand package V4.0  and the ACGT101-DEG program (LC Sciences, TX, USA). The mRNA cleavage sites at the 10th position of miRNA alignment with P value < 0.05 were considered as significant.
Genome_build: Durum wheat genome (NCBI UID 3439611, assembly Svevo.v1)
Supplementary_files_format_and_content: Matrix table with abundance measurements of microRNAs (sRNA-seq), mRNAs (mRNA-seq) and mRNA targets (degradome-seq)

source_name: Developing grain tissue

value: L6 (Stres-sensitive)

tag: treatment group

value: Water-deficit stress (WS)

tag: time-point (dpa, days post anthesis)


title: A499_dHet_FrB_6

description: Library of 96 cells

value: GCCAAT

value: B cells


title: A499_dHet_FrB_5

description: Library of 96 cells

value: ACAGTG


title: SG5_WSdgd

description: degradome-seq processed data

value: Water-deficit plus heat stress (WH)


title: A499_dHet_FrA_4

description: Library of 96 cells

value: TGACCA


title: Control89

description: Anonymized patient/sample code

value: CTRL

value: MM

value: blood


title: Normal Pregnancy Patient 2, cord blood (WGBS)

value: No Complications


title: SG5_HSdgd

description: degradome-seq processed data

value: Heat stress (HS)


title: A499_dHet_FrA_3

description: Library of 96 cells

value: bone marrow

value: TTAGGC


title: Normal Pregnancy Patient 2, delivery (WGBS)


title: Normal Pregnancy Patient 3, 1st Trimester (WGBS)


title: Control93

description: Anonymized patient/sample code

value: Female

value: MV


title: SG5_CGdgd

description: degradome-seq processed data

value: Control group (CG)


title: Control88

description: Anonymized patient/sample code


title: A499_dHet_FrA_2

description: Library of 96 cells

value: CGATGT


title: Normal Pregnancy Patient 2, 2nd Trimester (WGBS)


title: A499_dHet_FrA_1

description: Library of 96 cells

value: ATCACG


title: TG5_WHdgd

description: degradome-seq processed data

value: DBA Aurora (Stress-tolerant)

value: Water-deficit stress (WS)


title: Normal Pregnancy Patient 2, 3rd Trimester (WGBS)


title: Control87

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 2, 1st Trimester (WGBS)


title: Control86

description: Anonymized patient/sample code


title: Normal Pregnancy Patient 1, cord blood (WGBS)


title: TG5_HSdgd

description: degradome-seq processed data


title: TG5_CGdgd

description: degradome-seq processed data


title: TG5_WSdgd

description: degradome-seq processed data


title: Input for Pax5-ChIP in dHet-B-ALL-713

source_name: Ebf1+/- Pax5+/- dHet leukemic cells (mouse 713)

value: Ebf1+/- Pax5+/- lymph node

tag: chip antibody


title: Normal Pregnancy Patient 1, delivery (WGBS)

source_name: Plasma


title: Control85

description: Anonymized patient/sample code


title: Input for Pax5-ChIP in dHet-proB

source_name: Ebf1+/- Pax5+/- dHet fetal liver proB cells

value: Ebf1+/- Pax5+/- proB fetal liver cells


title: Normal Pregnancy Patient 1, 3rd Trimester (WGBS)


title: Pax5-ChIP_proB

value: Ebf1-deficient B cell progenitors

tag: stage post dox treatment


title: Pax5-ChIP in dHet-proB


title: Normal Pregnancy Patient 1, 2nd Trimester (WGBS)


title: Pax5-ChIP in dHet-B-ALL-713