title: P5E12_Tag06

city: Munich

last: Androvic

state: Bavaria

address: Feodor-Lynen-Strasse 17

country: Germany

institute: LMU Hospital, Institute for Stroke and Dementia Research

data_processing:
Fastq files were quality-controlled with FastQC and reads were then aligned using rnaSTAR to the GRCm38 (mm10) genome with addition of ERCC spike-in sequences. To obtain single cell gene expression matrices reads were counted with rnaSTAR using parameter “quantMode GeneCounts” and unstranded argument.
Assembly: mm10
Supplementary files format and content: Tab-separated counts per cell and cell metadata

extract_protocol:
18 days after LPC injection, mice were deeply anesthetized and perfused with cold HBSS between 9am-11am (to decrease circadian fluctuations). Each brain was removed and under a dissection microscope individually micro-dissected; gray matter was isolated from the frontal cortex and white matter was isolated form optic tract, medial lemniscus and corpus callosum (attached gray matter and choroid plexus were carefully removed). Single cells were isolated using GentleMacs with the Neural Tissue Dissociation Kit (Papain) (Miltenyi Biotec). We added actinomycin D to a final concentration of 45 mM into the dissociation solution and enzyme mix to prevent ex-vivo transcription. The dissociated cell suspension was passed through a 70 mm cell strainer before labeling. Subsequently, cells were blocked with mouse FcR-blocking reagent (CD16/CD32 Monoclonal Antibody) and then stained for with the antibodiy against CD11b (PE/Cy7,M1/70, eBioscience, Cat:48-0451-82,1:200) and afterwards washed with PBS (Sigma, D8537). Cells were then stained with DAPI (4’,6-diamidino-2-phenylindole, 1:10000 dilution; Sigma)  and viable (DAPI-negative) single CD11b-positive cells were sorted by flow cytometry (SH800; Sony) into 96 well plates filled with 4 mL lysis buffer containing 0.05% Triton X-100 (Sigma) and, ERCC spike-in Mix (1:24000000 dilution), 2.5 mM oligo-dT, 2.5 mM dNTP and 2 U/mL of recombinant RNase inhibitor (Clontech).
The 96-well plates containing the sorted single cells were thawed and incubated for 3 min at 72°C and thereafter immediately placed on ice. To perform reverse transcription (RT) we added into each well a master mix of 0.59 μL H2O, 0.5 μL SMARTScribe™ Reverse Transcriptase (Clontech), 2 μL 5x First Strand buffer, 0.25 μL Recombinant RNase Inhibitor (Clontech), 2 μL Betaine (5 M Sigma), 0.5 μL DTT (100 mM) 0.06 μL MgCl2 (1 M Sigma), 0.1 μL Templateswitching oligos (TSO) (100 μM AAGCAGTGGTATCAACGCAGAGTACrGrG+G). Next RT reactions were incubated at 42°C for 90 min followed by 70°C for 5 min and 10 cycles of 50°C 2 min, 42°C 2 min; ending with 70°C for 5 min for enzyme inactivation. Preamplification of cDNA was performed by adding 12.5 μL KAPA HiFi Hotstart 2x (KAPA Biosystems), 2.138 μL H2O, 0.25 μL ISPCR primers (10 μM, 5’ AAGCAGTGGTATCAACGCAGAGT-3), 0.1125 μL Lambda Exonuclease under the following conditions: 37°C for 30 min, 95°C for 3 min, 23 cycles of (98°C for 20 sec, 67°C for 15 sec, 72°C for 4 min), and a final extension at 72°C for 5 min. Libraries were then cleaned using AMPure beads (Beckman-Coulter) cleanup at a 0.7:1 ratio of beads to PCR product. Libraries were assessed by Bio-analyzer (Agilent 2100), using the High Sensitivity DNA analysis kit, and quantified using Qubit’s DNA HS assay kits and a Qubit 4.0 Fluorometer (Invitrogen, LifeTechnologies). Further selection of samples was performed via qPCR assay against ubiquitin transcripts Ubb77 (primer 1 5’-GGAGAGTCCATCGTGGTTATTT-3’ primer 2 5’-ACCTCTAGGGTGATGGTCTT-3’, probe 5’-/5Cy5/TGCAGATCTTCGTGAAGACCTGAC/3IAbRQSp/-3’) measured on a LightCycler 480 Instrument II (Roche). Samples were normalized to 160 pg/μL. Sequencing libraries were constructed by using in-house produced Tn5 transposase. Libraries were barcoded, pooled and purified in 3 rounds of AMPure bead (Beckman-Coulter) cleanup at a 0.8:1 ratio of beads to library. Libraries were then sequenced with 100 bp paired-end sequencing on DNBSeq platform (BGI group).

treatment_protocol: Lysophosphatidylcholine (LPC) injections were administered at the age of 16-18 weeks. A solution of 1% LPC (L4129, Sigma) in PBS was mixed with Monastral blue (274011, SigmaAldrich) at a concentration of 0.03% to aid with visualization of the lesion during tissue processing. Mice were anaesthetized with an intraperitoneal injection of MMF solution (0.5 mg medetomidin/kg (body weight), 5.0 mg midazolam/kg (body weight) and 0.05 mg fentanyl/kg (body weight)). Then, head fur was removed, the eyes were treated with bepanthene cream (1578847, Bayer) and a small incision in the skin was performed to expose the skull. The mouse was positioned into a stereotactic injection apparatus and a small hole was drilled at the following injection coordinates (from bregma): X, ± 1.0 mm; Y, −0.1 mm). A glass capillary containing the LPC–monastral blue solution was then lowered to Z: −1.30 mm from bregma, and 1 µL was injected at a rate of 100 nL/minute. Two minutes after the delivery of LPC, the capillary was slowly retracted. The mouse was then injected with 0.05 mg buprenorphin/kg (body weight), and the skin was sutured. Anesthesia was terminated by a subcutaneous injection of AFN solution, containing 2.5 mg/kg (body weight) atipamezol, 1.2 mg/kg (body weight) naloxon and 0.5 mg/kg (body weight) flumazenil.

value: CD11b+ cells


title: P5H9_Tag06

status: Public on Jun 21 2023

type: SRA

first: Peter

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: tissue

tag: strain

tag: age


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title: P3G8_Tag03


title: P4A12_Tag03


title: P3G6_Tag03


title: P3G1_Tag03


title: P3G5_Tag03


title: P3F9_Tag03


title: P3G10_Tag03


title: P3G12_Tag03


title: P3F6_Tag03


title: P3G2_Tag03


title: P3F8_Tag03


title: P3H2_Tag03


title: P3F4_Tag03


title: P3G11_Tag03


title: P3F7_Tag03


title: P3E5_Tag03


title: P3F2_Tag03


title: P3F11_Tag03


title: P3E6_Tag03


title: P3E12_Tag03


title: P3F3_Tag03


title: P3F12_Tag03


title: P3E4_Tag03


title: P3E3_Tag03


title: P3E8_Tag03


title: P3E10_Tag03


title: P3E11_Tag03


title: P5F6_Tag03


title: P4F2_Tag03


title: P3E1_Tag03


title: P3D9_Tag03


title: P3D7_Tag03


title: P3D6_Tag03


title: P3D3_Tag03


title: P3D4_Tag03


title: P3D5_Tag03


title: P3C7_Tag03


title: P3D11_Tag03


title: P3D1_Tag03


title: P3D12_Tag03


title: P3C8_Tag03


title: P3C6_Tag03


title: P3C10_Tag03


title: P3C1_Tag03


title: P3B9_Tag03


title: P3C3_Tag03


title: P3C4_Tag03


title: P3C5_Tag03


title: P3B8_Tag03


title: P3B4_Tag03


title: P3B3_Tag03


title: P3B7_Tag03


title: P3D8_Tag03


title: P3B2_Tag03


title: P3B12_Tag03


title: P3B11_Tag03


title: P3A7_Tag03


title: P3A5_Tag03


title: P3A4_Tag03


title: P3A2_Tag03


title: P3B6_Tag03


title: P3A1_Tag03


title: P5A2_Tag03


title: P2H1_Tag03


title: P2H3_Tag03


title: P3A12_Tag03


title: P2G3_Tag03


title: P2G4_Tag03


title: P2F5_Tag03


title: P2E3_Tag03


title: P2F1_Tag03


title: P2E4_Tag03


title: P2E2_Tag03


title: P3B10_Tag03


title: P2E1_Tag03


title: P2F2_Tag03


title: P3A8_Tag03


title: P2D5_Tag03


title: P2D4_Tag03


title: P2D2_Tag03


title: P2D1_Tag03


title: P2C5_Tag03


title: P2C3_Tag03


title: P2C4_Tag03


title: P3A6_Tag03


title: P3A10_Tag03


title: P2C2_Tag03


title: P2B4_Tag03


title: P2B3_Tag03


title: P2B2_Tag03


title: P2B1_Tag03


title: P2D3_Tag03


title: P2A5_Tag03


title: P1H9_Tag03


title: P2A3_Tag03


title: P2A1_Tag03


title: P1H6_Tag03


title: P1H7_Tag03


title: P1H5_Tag03


title: P1H3_Tag03


title: P1H4_Tag03


title: P1H12_Tag03


title: P1H11_Tag03


title: P1H2_Tag03


title: P1G7_Tag03


title: P1H10_Tag03


title: P1G11_Tag03


title: P1G1_Tag03


title: P1H1_Tag03


title: P1G9_Tag03


title: P1F9_Tag03


title: P1G5_Tag03


title: P1G4_Tag03


title: P1G2_Tag03


title: P1G3_Tag03


title: P1F7_Tag03


title: P1F5_Tag03


title: P1F6_Tag03


title: P1G10_Tag03


title: P1F2_Tag03


title: P1F3_Tag03


title: P1F12_Tag03


title: P1F10_Tag03


title: P1E9_Tag03


title: P1E8_Tag03


title: P1E7_Tag03


title: P1E6_Tag03


title: P1E2_Tag03


title: P1F1_Tag03


title: P1E4_Tag03


title: P1E12_Tag03


title: P1D9_Tag03


title: P1E1_Tag03


title: P1D5_Tag03


title: P1D8_Tag03


title: P1E5_Tag03


title: P1F11_Tag03


title: P1D12_Tag03


title: P1D2_Tag03


title: P1C6_Tag03


title: P1C12_Tag03


title: P1C4_Tag03


title: P1C7_Tag03


title: P1D11_Tag03


title: P1D3_Tag03


title: anti MacroH2A2 Chromatin Immunoprecipitation, ESCs

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

description:
MacroH2A2_ESCs_IP
single-end

library_source: genomic

data_processing:
The quality of the generated fastq files was examined with the FASTQC software. FASTQ files were aligned against mm10 mouse genome with Bowtie2 aligner. The output file was filtered for low quality reads, duplicates, blacklist regions and mitochondrial genome entries with custom-made pipeline from Bedtools  and Samtools packages. Peak calling was performed with MACS2 with default parameters. Bigwig files were generated with BamCoverage from Deeptools.
Assembly: mm10
Supplementary files format and content: Regarding ChIPseq analysis, the .bw files contain the signal per sample as generated with bamCoverage command. The xlsx files contain the peaks generared with MACS2 compared to the respective Input file

molecule: genomic DNA

growth_protocol: MEFs and HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma-Aldrich, Cat. No. D6429) supplemented with 10% heat-inactivated Fetal Bovine Serum (FBS), Penicillin/Streptomycin (100 ug/ml; Thermo Fischer Scientific, Cat. No. 15140122), 2 mM GlutaMAX (Gibco, Cat. No. 35-050-061) and 0.1 mM Non-Essential Amino Acids 100X (Gibco, Cat. No. 11140050), at 37°C and 5% CO2. Bruce4 ESCs were cultured in complete ESC medium [Knock Out DMEM (Gibco, Cat. No. 10829018), 20% ES-tested FBS (Pansera, Cat. No. P30-2602), Penicillin/Streptomycin 1X (Thermo Fischer Scientific, Cat. No. 15140122), GlutaMAX 1X (Gibco, Cat. No. 35-050-061). Non-Essential Amino Acids 1X (Gibco, Cat. No. 11140050) and mLIF 20ng/mL (Santa Cruz Biotechnology, sc-4378)

extract_protocol:
Nuclei extraction protocol as described in Ford et at. 2014 (Ford E, Nikopoulou C, Kokkalis A, Thanos D. A method for generating highly multiplexed ChIP-seq libraries. BMC Res Notes. 2014 May 22;7:312. doi: 10.1186/1756-0500-7-312. PMID: 24885602; PMCID: PMC4048252)
1-15 ng of “ChIPped” DNA was blunt-ended by End Repair Enzyme Mix (T4 DNA Polymerase, Klenow Fragment, T4 DNA Polynucleotide kinase), followed by “A”-tailing of 3΄-ends and ligation with the annealed TruSeq Adapters (Illumina). Conversion of the Y-shaped adapters to dsDNA occurred prior to the library size selection through 2.5% Metaphor/SeaKem LE (3:1 ratio) agarose gel electrophoresis. Each library was purified using miniElute columns (Qiagen) and then subjected to pre-amplification. The final quantification of DNA libraries was carried out according to the Quantification Standards of Illumina on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies).

tag: cell line

value: Embryonic Stem Cells


title: P1D4_Tag03


title: P1C11_Tag03


title: P1C10_Tag03


title: P1B9_Tag03


title: anti MacroH2A2 Chromatin Immunoprecipitation, MEFs

description:
MacroH2A2_MEFs_IP
single-end

source_name: Mouse Embryonic Fibroblasts

value: Mouse Embryonic Fibroblasts

tag: genotype


title: P1B6_Tag03


title: anti MacroH2A1.1 Chromatin Immunoprecipitation, ESCs

description:
MacroH2A1.1_ESCs_IP
single-end


title: P1B12_Tag03


title: anti MacroH2A1.1 Chromatin Immunoprecipitation, MEFs

description:
MacroH2A1.1_MEFs_IP
single-end


title: P1B5_Tag03


title: P1A8_Tag03


title: ESCs, Scramble, (Control), RNAseq, rep3

description:
Counts_all_samples.xlsx
Scramble_ESCs_rep3

library_source: transcriptomic

data_processing:
For RNAseq samples, Quality Control (QC) was performed at the FASTQ raw data file for each sample using the FASTQC software. FASTQ files were aligned to mm10 mouse genome using HISAT2 . Counts were defined using HTSeq htseq-count command with the “intersection non-empty” option. The count files were used as input for DESeq2.
Assembly: mm10
Supplementary files format and content: Regarding RNAseq analysis, the file Counts_all_samples.xlsx contains all the counts per gene for all the samples. The csv files contain the results from  DESeq2 analysis

extract_protocol:
Extraction was performed with NucleoSpin RNA extraction kit-MN (740955.50), according to the manufacturer’s protocols
Libraries for RNAseq were constructed with TruSEQ v2 kit according to manufacturer’s protocols

tag: treatment

value: Transduction with Lentiviral Particles


title: P1B10_Tag03


title: P1A7_Tag03


title: ESCs, MacroH2A2 Knockdown (shRNA), RNAseq, rep3

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A2_KD.csv
MacroH2A2KD_ESCs_rep3


title: ESCs, Scramble, (Control), RNAseq, rep1

description:
Counts_all_samples.xlsx
Scramble_ESCs_rep1


title: ESCs, Scramble, (Control), RNAseq, rep2

description:
Counts_all_samples.xlsx
Scramble_ESCs_rep2


title: P1A6_Tag03


title: ESCs, MacroH2A2 Knockdown (shRNA), RNAseq, rep2

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A2_KD.csv
MacroH2A2KD_ESCs_rep2


title: ESCs, MacroH2A1.1 Knockdown (shRNA), RNAseq, rep2

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.1_KD.csv
MacroH2A1.1KD_ESCs_rep2


title: P1A3_Tag03


title: ESCs, MacroH2A2 Knockdown (shRNA), RNAseq, rep1

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A2_KD.csv
MacroH2A2KD_ESCs_rep1


title: P1A5_Tag03


title: P1A2_Tag03


title: P1A4_Tag03


title: P1A12_Tag03


title: ESCs, MacroH2A1.2 Knockdown (shRNA), RNAseq, rep3

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.2_KD.csv
MacroH2A1.2KD_ESCs_rep3


title: ESCs, MacroH2A1.1 Knockdown (shRNA), RNAseq, rep1

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.1_KD.csv
MacroH2A1.1KD_ESCs_rep1


title: ESCs, MacroH2A1.2 Knockdown (shRNA), RNAseq, rep2

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.2_KD.csv
MacroH2A1.2KD_ESCs_rep2


title: P1B7_Tag03


title: WT.KLF10KD

type: RNA

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each Human HT-12 v4.0 Expression Beadchip for 17h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.

data_processing: The data were normalised using Model-Based Background Correction (PMID: 20502629) in R.

label: biotin

organism: Homo sapiens

label_protocol: Total RNA was amplified and purified using TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (EPICENTRE, Madison, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: RPMI-1640 medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin, 100mg/ml streptomycin and 2mM glutamine at 37°C in a 5% CO2 incubator.

extract_protocol: The total RNA was extracted from Panc-1-pLKO and Panc-1-pLKO-shKLF10 cells by the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA quality and integrity was measured by a 2100 Bioanalyzer (Agilent, Santa Clara, CA).

value: KLF10 knockdown


title: P1A11_Tag03


title: P1A10_Tag03


title: P1A1_Tag03


title: MEFs, Scramble, (Control), RNAseq, rep3

description:
Counts_all_samples.xlsx
Scramble_MEFs_rep3


title: WT.LKO

source_name: Panc-1-pLKO cell line

value: vector control


title: Tag4H9_Tag02


title: MEFs, Scramble, (Control), RNAseq, rep2

description:
Counts_all_samples.xlsx
Scramble_MEFs_rep2


title: Tag4H7_Tag02


title: Tag4H5_Tag02


title: Tag4H2_Tag02


title: MEFs, MacroH2A2 Knockdown (shRNA), RNAseq, rep2

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A2_KD.csv
MacroH2A2KD_MEFs_rep2


title: ESCs, MacroH2A1.1 Knockdown (shRNA), RNAseq, rep3

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.1_KD.csv
MacroH2A1.1KD_ESCs_rep3


title: MEFs, MacroH2A2 Knockdown (shRNA), RNAseq, rep1

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A2_KD.csv
MacroH2A2KD_MEFs_rep1


title: Tag4H11_Tag02


title: Tag4H1_Tag02


title: Tag4G9_Tag02


title: MEFs, MacroH2A1.2 Knockdown (shRNA), RNAseq, rep3

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.2_KD.csv
MacroH2A1.2KD_MEFs_rep3


title: ESCs, MacroH2A1.2 Knockdown (shRNA), RNAseq, rep1

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.2_KD.csv
MacroH2A1.2KD_ESCs_rep1


title: Tag4H12_Tag02


title: Tag4G8_Tag02


title: MEFs, MacroH2A1.2 Knockdown (shRNA), RNAseq, rep2

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.2_KD.csv
MacroH2A1.2KD_MEFs_rep2


title: MEFs, MacroH2A1.1 Knockdown (shRNA), RNAseq, rep3

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.1_KD.csv
MacroH2A1.1KD_MEFs_rep3


title: Tag4G7_Tag02


title: MEFs, MacroH2A1.2 Knockdown (shRNA), RNAseq, rep1

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.2_KD.csv
MacroH2A1.2KD_MEFs_rep1


title: Tag4G2_Tag02


title: MEFs, MacroH2A1.1 Knockdown (shRNA), RNAseq, rep1

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.1_KD.csv
MacroH2A1.1KD_MEFs_rep1


title: MEFs, Scramble, (Control), RNAseq, rep1

description:
Counts_all_samples.xlsx
Scramble_MEFs_rep1


title: MEFs, MacroH2A2 Knockdown (shRNA), RNAseq, rep3

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A2_KD.csv
MacroH2A2KD_MEFs_rep3


title: Genomic DNA from whole blood sample [SUAZ_511_meth_v1]

type: genomic

city: Madrid

first: Juan

middle: Carlos

last: Silla-Castro

address: Melchor Fernandez Almagro 3

department: Bioinformatics

country: Spain

institute: CNIC

hyb_protocol: Converted DNAs were processed to be hybridised in the Infinium MethylationEPIC BeadChip BeadChip following the manufacturer's protocols (Illumina).

scan_protocol: Arrays were scanned using iScan System (Illumina).

data_processing:
Array intensities were extracted from idat files, filtered and normalized using the rnb.run.analysis function from Bioconductor package RnBeads version 2.0.1. Probes with SNPs overlap were removed and the greedy cut algorithm implemented in RnBeads was applied with a detection p-value > 0.05 for probe detection assessment. Normalized by the dasen method  generating M-Values  downstream analysis.
matrix processed value definition: Values after dasen normalization
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: bisulfite converted

source_name: PESA study participant SUAZ_511_meth_v1

label_protocol: DNA was bisulfite converted using EZ DNA Methylation Kits (Zymo Research) following manufacturer's recommendation.

growth_protocol: Blood samples were collected in S-Monovette EDTA K3 tubes (Sarstedt). 600 µl of blood were aliquoted in 0.75 ml 2D Barcoded Storage Tubes (Thermo Scientific) and stored at -80°C until processed.

extract_protocol: Blood samples were thawed quickly in a 37°C water bath for 2 min to avoid degradation. Samples were then processed using the QIAsymphony DNA Mini Kit for the QiAsymphony SP automated station (QiAgen), following the manufacturer´s instructions. Briefly, blood samples were lysed and incubated with magnetic beads for DNA purification. After a wash, DNA was eluted in 200 µl of elution buffer, and DNA concentration and quality were measured by QuBit (Invitrogen) and Nanoquant (Tecan), respectively.

tag: gender

value: Male

tag: pesa score

value: Intermediate


title: Genomic DNA from whole blood sample [SUAZ_516_meth_v1]

source_name: PESA study participant SUAZ_516_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_515_meth_v1]

source_name: PESA study participant SUAZ_515_meth_v1


title: Tag4H3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_514_meth_v1]

source_name: PESA study participant SUAZ_514_meth_v1

value: No


title: Genomic DNA from whole blood sample [SUAZ_510_meth_v1]

source_name: PESA study participant SUAZ_510_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_512_meth_v1]

source_name: PESA study participant SUAZ_512_meth_v1

value: Generalized


title: MEFs, MacroH2A1.1 Knockdown (shRNA), RNAseq, rep2

description:
Counts_all_samples.xlsx
MEFs_scramble_vs_mH2A1.1_KD.csv
MacroH2A1.1KD_MEFs_rep2


title: Genomic DNA from whole blood sample [SUAZ_509_meth_v1]

source_name: PESA study participant SUAZ_509_meth_v1


title: Tag4F7_Tag02


title: Tag4F4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_508_meth_v1]

source_name: PESA study participant SUAZ_508_meth_v1


title: Tag4G4_Tag02


title: Tag4F2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_507_meth_v1]

source_name: PESA study participant SUAZ_507_meth_v1


title: Tag4E5_Tag02


title: Tag4F11_Tag02


title: Tag4E8_Tag02


title: Tag4G1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_505_meth_v1]

source_name: PESA study participant SUAZ_505_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_506_meth_v1]

source_name: PESA study participant SUAZ_506_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_503_meth_v1]

source_name: PESA study participant SUAZ_503_meth_v1

value: Focal


title: Tag4E3_Tag02


title: Tag4E2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_502_meth_v1]

source_name: PESA study participant SUAZ_502_meth_v1


title: Tag4E1_Tag02


title: Tag4F9_Tag02


title: Tag4E12_Tag02


title: Tag4E10_Tag02


title: Genomic DNA from whole blood sample [SUAZ_500_meth_v1]

source_name: PESA study participant SUAZ_500_meth_v1


title: Tag4D9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_499_meth_v1]

source_name: PESA study participant SUAZ_499_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_498_meth_v1]

source_name: PESA study participant SUAZ_498_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_490_meth_v1]

source_name: PESA study participant SUAZ_490_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_504_meth_v1]

source_name: PESA study participant SUAZ_504_meth_v1


title: Tag4D8_Tag02


title: Tag4D11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_491_meth_v1]

source_name: PESA study participant SUAZ_491_meth_v1


title: Tag4D10_Tag02


title: Tag4D5_Tag02


title: Tag4D7_Tag02


title: Tag4D2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_482_meth_v1]

source_name: PESA study participant SUAZ_482_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_489_meth_v1]

source_name: PESA study participant SUAZ_489_meth_v1


title: Tag4D12_Tag02


title: Tag4C6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_479_meth_v1]

source_name: PESA study participant SUAZ_479_meth_v1


title: Tag4C2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_478_meth_v1]

source_name: PESA study participant SUAZ_478_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_483_meth_v1]

source_name: PESA study participant SUAZ_483_meth_v1


title: Tag4C1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_481_meth_v1]

source_name: PESA study participant SUAZ_481_meth_v1


title: Tag4D1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_497_meth_v1]

source_name: PESA study participant SUAZ_497_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_476_meth_v1]

source_name: PESA study participant SUAZ_476_meth_v1


title: Tag4C3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_480_meth_v1]

source_name: PESA study participant SUAZ_480_meth_v1


title: Tag4B7_Tag02


title: Tag4D3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_475_meth_v1]

source_name: PESA study participant SUAZ_475_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_473_meth_v1]

source_name: PESA study participant SUAZ_473_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_492_meth_v1]

source_name: PESA study participant SUAZ_492_meth_v1


title: Tag4B9_Tag02


title: Tag4B6_Tag02


title: Tag4B2_Tag02


title: Tag4A8_Tag02


title: Tag4A5_Tag02


title: Genomic DNA from whole blood sample [SUAZ_472_meth_v1]

source_name: PESA study participant SUAZ_472_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_470_meth_v1]

source_name: PESA study participant SUAZ_470_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_477_meth_v1]

source_name: PESA study participant SUAZ_477_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_464_meth_v1]

source_name: PESA study participant SUAZ_464_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_468_meth_v1]

source_name: PESA study participant SUAZ_468_meth_v1


title: Tag4A2_Tag02


title: Tag4A12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_465_meth_v1]

source_name: PESA study participant SUAZ_465_meth_v1


title: Tag4A10_Tag02


title: Tag4A11_Tag02


title: Tag3H2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_462_meth_v1]

source_name: PESA study participant SUAZ_462_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_459_meth_v1]

source_name: PESA study participant SUAZ_459_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_463_meth_v1]

source_name: PESA study participant SUAZ_463_meth_v1


title: Tag3H8_Tag02


title: Genomic DNA from whole blood sample [SUAZ_471_meth_v1]

source_name: PESA study participant SUAZ_471_meth_v1


title: Tag3H3_Tag02


title: Tag3H11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_460_meth_v1]

source_name: PESA study participant SUAZ_460_meth_v1


title: Tag3H12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_456_meth_v1]

source_name: PESA study participant SUAZ_456_meth_v1


title: Tag3H1_Tag02


title: Tag3G4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_455_meth_v1]

source_name: PESA study participant SUAZ_455_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_453_meth_v1]

source_name: PESA study participant SUAZ_453_meth_v1


title: Tag3G2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_449_meth_v1]

source_name: PESA study participant SUAZ_449_meth_v1


title: Tag3G9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_454_meth_v1]

source_name: PESA study participant SUAZ_454_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_452_meth_v1]

source_name: PESA study participant SUAZ_452_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_448_meth_v1]

source_name: PESA study participant SUAZ_448_meth_v1


title: Tag3G11_Tag02


title: Tag3F6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_451_meth_v1]

source_name: PESA study participant SUAZ_451_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_457_meth_v1]

source_name: PESA study participant SUAZ_457_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_446_meth_v1]

source_name: PESA study participant SUAZ_446_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_450_meth_v1]

source_name: PESA study participant SUAZ_450_meth_v1


title: Tag3G1_Tag02


title: Tag3F8_Tag02


title: Tag3F9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_445_meth_v1]

source_name: PESA study participant SUAZ_445_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_444_meth_v1]

source_name: PESA study participant SUAZ_444_meth_v1


title: Tag3F2_Tag02


title: Tag3F3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_447_meth_v1]

source_name: PESA study participant SUAZ_447_meth_v1


title: Tag3F11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_441_meth_v1]

source_name: PESA study participant SUAZ_441_meth_v1


title: Tag3F4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_443_meth_v1]

source_name: PESA study participant SUAZ_443_meth_v1


title: Tag3F10_Tag02


title: Genomic DNA from whole blood sample [SUAZ_440_meth_v1]

source_name: PESA study participant SUAZ_440_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_439_meth_v1]

source_name: PESA study participant SUAZ_439_meth_v1


title: Tag3E9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_437_meth_v1]

source_name: PESA study participant SUAZ_437_meth_v1


title: Tag3E7_Tag02


title: Tag3E12_Tag02


title: Tag3G3_Tag02


title: Tag3E1_Tag02


title: Tag3E3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_432_meth_v1]

source_name: PESA study participant SUAZ_432_meth_v1


title: Tag3D6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_428_meth_v1]

source_name: PESA study participant SUAZ_428_meth_v1


title: Tag3C8_Tag02


title: Tag3C7_Tag02


title: Tag3F12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_442_meth_v1]

source_name: PESA study participant SUAZ_442_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_436_meth_v1]

source_name: PESA study participant SUAZ_436_meth_v1


title: Tag3C4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_425_meth_v1]

source_name: PESA study participant SUAZ_425_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_433_meth_v1]

source_name: PESA study participant SUAZ_433_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_424_meth_v1]

source_name: PESA study participant SUAZ_424_meth_v1


title: Tag3D9_Tag02


title: Tag3C12_Tag02


title: Tag3C1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_420_meth_v1]

source_name: PESA study participant SUAZ_420_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_431_meth_v1]

source_name: PESA study participant SUAZ_431_meth_v1


title: Tag3B9_Tag02


title: Tag3D2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_430_meth_v1]

source_name: PESA study participant SUAZ_430_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_418_meth_v1]

source_name: PESA study participant SUAZ_418_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_417_meth_v1]

source_name: PESA study participant SUAZ_417_meth_v1


title: Tag3B2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_415_meth_v1]

source_name: PESA study participant SUAZ_415_meth_v1


title: Tag3D12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_429_meth_v1]

source_name: PESA study participant SUAZ_429_meth_v1


title: Tag3C9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_427_meth_v1]

source_name: PESA study participant SUAZ_427_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_426_meth_v1]

source_name: PESA study participant SUAZ_426_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_419_meth_v1]

source_name: PESA study participant SUAZ_419_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_414_meth_v1]

source_name: PESA study participant SUAZ_414_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_412_meth_v1]

source_name: PESA study participant SUAZ_412_meth_v1


title: Tag3A8_Tag02


title: Tag3A3_Tag02


title: Tag3A2_Tag02


title: Tag3C6_Tag02


title: Tag3C3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_423_meth_v1]

source_name: PESA study participant SUAZ_423_meth_v1


title: Tag3C2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_407_meth_v1]

source_name: PESA study participant SUAZ_407_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_413_meth_v1]

source_name: PESA study participant SUAZ_413_meth_v1


title: Tag2H8_Tag02


title: Genomic DNA from whole blood sample [SUAZ_422_meth_v1]

source_name: PESA study participant SUAZ_422_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_421_meth_v1]

source_name: PESA study participant SUAZ_421_meth_v1


title: Tag3B8_Tag02


title: Tag2H7_Tag02


title: Tag3B4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_401_meth_v1]

source_name: PESA study participant SUAZ_401_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_416_meth_v1]

source_name: PESA study participant SUAZ_416_meth_v1


title: Tag2H3_Tag02


title: Tag3B11_Tag02


title: Tag3A9_Tag02


title: Tag3B12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_411_meth_v1]

source_name: PESA study participant SUAZ_411_meth_v1


title: Tag2G9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_410_meth_v1]

source_name: PESA study participant SUAZ_410_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_395_meth_v1]

source_name: PESA study participant SUAZ_395_meth_v1


title: Tag3A12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_409_meth_v1]

source_name: PESA study participant SUAZ_409_meth_v1


title: Tag3A10_Tag02


title: Genomic DNA from whole blood sample [SUAZ_394_meth_v1]

source_name: PESA study participant SUAZ_394_meth_v1


title: Tag2G7_Tag02


title: Tag2G5_Tag02


title: Genomic DNA from whole blood sample [SUAZ_392_meth_v1]

source_name: PESA study participant SUAZ_392_meth_v1


title: Tag3A1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_406_meth_v1]

source_name: PESA study participant SUAZ_406_meth_v1


title: Tag2G4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_404_meth_v1]

source_name: PESA study participant SUAZ_404_meth_v1


title: Tag2H6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_390_meth_v1]

source_name: PESA study participant SUAZ_390_meth_v1


title: Tag2G2_Tag02


title: Tag2G12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_403_meth_v1]

source_name: PESA study participant SUAZ_403_meth_v1

value: Female


title: Genomic DNA from whole blood sample [SUAZ_387_meth_v1]

source_name: PESA study participant SUAZ_387_meth_v1


title: Tag2H5_Tag02


title: Tag2H4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_385_meth_v1]

source_name: PESA study participant SUAZ_385_meth_v1


title: Tag2G10_Tag02


title: Genomic DNA from whole blood sample [SUAZ_384_meth_v1]

source_name: PESA study participant SUAZ_384_meth_v1


title: Tag2H2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_405_meth_v1]

source_name: PESA study participant SUAZ_405_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_438_meth_v1]

source_name: PESA study participant SUAZ_438_meth_v1


title: Tag2F9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_399_meth_v1]

source_name: PESA study participant SUAZ_399_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_380_meth_v1]

source_name: PESA study participant SUAZ_380_meth_v1


title: Tag2H1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_379_meth_v1]

source_name: PESA study participant SUAZ_379_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_398_meth_v1]

source_name: PESA study participant SUAZ_398_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_396_meth_v1]

source_name: PESA study participant SUAZ_396_meth_v1


title: Tag2F6_Tag02


title: Tag2G8_Tag02


title: Genomic DNA from whole blood sample [SUAZ_402_meth_v1]

source_name: PESA study participant SUAZ_402_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_400_meth_v1]

source_name: PESA study participant SUAZ_400_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_376_meth_v1]

source_name: PESA study participant SUAZ_376_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_374_meth_v1]

source_name: PESA study participant SUAZ_374_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_393_meth_v1]

source_name: PESA study participant SUAZ_393_meth_v1


title: Tag2G6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_391_meth_v1]

source_name: PESA study participant SUAZ_391_meth_v1


title: Tag2G3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_388_meth_v1]

source_name: PESA study participant SUAZ_388_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_372_meth_v1]

source_name: PESA study participant SUAZ_372_meth_v1


title: Tag2G11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_383_meth_v1]

source_name: PESA study participant SUAZ_383_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_371_meth_v1]

source_name: PESA study participant SUAZ_371_meth_v1


title: Tag2F1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_382_meth_v1]

source_name: PESA study participant SUAZ_382_meth_v1


title: Tag2E9_Tag02


title: Tag2F5_Tag02


title: Tag2F8_Tag02


title: Tag2E8_Tag02


title: Tag2E7_Tag02


title: Tag2F7_Tag02


title: Genomic DNA from whole blood sample [SUAZ_377_meth_v1]

source_name: PESA study participant SUAZ_377_meth_v1


title: Tag2F4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_375_meth_v1]

source_name: PESA study participant SUAZ_375_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_366_meth_v1]

source_name: PESA study participant SUAZ_366_meth_v1


title: Tag2E5_Tag02


title: Genomic DNA from whole blood sample [SUAZ_365_meth_v1]

source_name: PESA study participant SUAZ_365_meth_v1


title: Tag2F3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_370_meth_v1]

source_name: PESA study participant SUAZ_370_meth_v1


title: Tag2G1_Tag02


title: Tag2E3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_364_meth_v1]

source_name: PESA study participant SUAZ_364_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_363_meth_v1]

source_name: PESA study participant SUAZ_363_meth_v1


title: Tag2E4_Tag02


title: Tag2E11_Tag02


title: Tag2D9_Tag02


title: Tag2F12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_369_meth_v1]

source_name: PESA study participant SUAZ_369_meth_v1


title: Tag2F10_Tag02


title: Genomic DNA from whole blood sample [SUAZ_359_meth_v1]

source_name: PESA study participant SUAZ_359_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_358_meth_v1]

source_name: PESA study participant SUAZ_358_meth_v1


title: Tag2D8_Tag02


title: Tag2D7_Tag02


title: Genomic DNA from whole blood sample [SUAZ_368_meth_v1]

source_name: PESA study participant SUAZ_368_meth_v1


title: Tag2D6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_367_meth_v1]

source_name: PESA study participant SUAZ_367_meth_v1


title: Tag2D5_Tag02


title: Genomic DNA from whole blood sample [SUAZ_356_meth_v1]

source_name: PESA study participant SUAZ_356_meth_v1


title: Tag2D4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_354_meth_v1]

source_name: PESA study participant SUAZ_354_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_353_meth_v1]

source_name: PESA study participant SUAZ_353_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_351_meth_v1]

source_name: PESA study participant SUAZ_351_meth_v1


title: Tag2D1_Tag02


title: Tag2E6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_362_meth_v1]

source_name: PESA study participant SUAZ_362_meth_v1


title: Tag2E2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_347_meth_v1]

source_name: PESA study participant SUAZ_347_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_361_meth_v1]

source_name: PESA study participant SUAZ_361_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_349_meth_v1]

source_name: PESA study participant SUAZ_349_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_360_meth_v1]

source_name: PESA study participant SUAZ_360_meth_v1


title: Tag2C6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_345_meth_v1]

source_name: PESA study participant SUAZ_345_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_346_meth_v1]

source_name: PESA study participant SUAZ_346_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_344_meth_v1]

source_name: PESA study participant SUAZ_344_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_357_meth_v1]

source_name: PESA study participant SUAZ_357_meth_v1


title: 26-29 hours after egg lay, posterior part of the germband, rep3

city: Graz

first: Leila

last: Taher

address: Stremayrgasse 16/I

country: Austria

institute: Graz University of Technology

data_processing:
adapter trimming, cutadapt, parameters “-u 15 -U 15 -q 30 -m 35 --max-n 0 -e 0.10 -a CTGTCTCTTATA -A CTGTCTCTTATA”
mapping, BWA-MEM, version 0.7.12-r1039
marking duplicates, Picard MarkDuplicates, version 2.15.0
filtering of low quality reads and duplicates, samtools view, version 1.10, parameters "-F 1804 -f 2 -q 30"
filtering of blacklisted regions, samtools view, version 1.7, parameters "-L" and "-U"
generation of BigWig files, BAMscale, version 1.0, parameters "scale --frag --binsize 20 --smoothen 2"
Assembly: Tcas5.2, GCA_000002335.3
Supplementary files format and content: bw

organism: Tribolium castaneum

source_name: germband stage embryo

growth_protocol: Adults were allowed to lay eggs for three hours on flour supplemented with 5 % dried yeast at 24 °C. Embryos were collected and incubated for additional 23 (for 23-26 hours after egg lay) or 26 hours (for 26-29 hours after egg lay) at 24 °C.

extract_protocol:
Embryos were dechorionated by immersion in 1 % bleach for 30 s twice. Selected embryos were dissected into three parts (anterior, middle, and posterior). Embryo parts were homogenized using a plastic pestle in ice-cold lysis buffer. The nuclear pellet was collected by centrifugation.
For tagmentation, 0.5 µl of Tn5 transposase from the Nextera DNA Library Prep Kit (Illumina) was used in a reaction volume of 15 µl. The reaction mix was incubated for 8 min at 37 °C.  Sample purification was performed using the MinElute PCR Purification Kit (QIAGEN).

value: germband stage embryo

tag: tissue part

value: posterior part of the germband

tag: time point

value: 26-29 hours after egg lay

value: Tribolium line expresses nuclear-localized GFP under the control of a ubiquitous promoter


title: Genomic DNA from whole blood sample [SUAZ_355_meth_v1]

source_name: PESA study participant SUAZ_355_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_340_meth_v1]

source_name: PESA study participant SUAZ_340_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_352_meth_v1]

source_name: PESA study participant SUAZ_352_meth_v1


title: Tag2D12_Tag02


title: Tag2D2_Tag02


title: Tag2D11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_338_meth_v1]

source_name: PESA study participant SUAZ_338_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_339_meth_v1]

source_name: PESA study participant SUAZ_339_meth_v1


title: 26-29 hours after egg lay, posterior part of the germband, rep1


title: Tag2C9_Tag02


title: Tag2C12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_332_meth_v1]

source_name: PESA study participant SUAZ_332_meth_v1


title: Tag2C8_Tag02


title: 26-29 hours after egg lay, middle part of the germband, rep3

value: middle part of the germband


title: Genomic DNA from whole blood sample [SUAZ_343_meth_v1]

source_name: PESA study participant SUAZ_343_meth_v1


title: Tag2C7_Tag02

value: CD11b+ cells


title: Tag2C11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_330_meth_v1]

source_name: PESA study participant SUAZ_330_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_342_meth_v1]

source_name: PESA study participant SUAZ_342_meth_v1


title: Tag2C1_Tag02


title: 26-29 hours after egg lay, anterior part of the germband, rep2

value: anterior part of the germband


title: Genomic DNA from whole blood sample [SUAZ_327_meth_v1]

source_name: PESA study participant SUAZ_327_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_326_meth_v1]

source_name: PESA study participant SUAZ_326_meth_v1


title: Tag2B9_Tag02


title: 26-29 hours after egg lay, posterior part of the germband, rep2


title: Genomic DNA from whole blood sample [SUAZ_337_meth_v1]

source_name: PESA study participant SUAZ_337_meth_v1


title: Tag2C2_Tag02


title: Tag2C3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_324_meth_v1]

source_name: PESA study participant SUAZ_324_meth_v1


title: Tag2B8_Tag02


title: Genomic DNA from whole blood sample [SUAZ_335_meth_v1]

source_name: PESA study participant SUAZ_335_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_320_meth_v1]

source_name: PESA study participant SUAZ_320_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_322_meth_v1]

source_name: PESA study participant SUAZ_322_meth_v1


title: Tag2B7_Tag02


title: Tag2C5_Tag02


title: Genomic DNA from whole blood sample [SUAZ_333_meth_v1]

source_name: PESA study participant SUAZ_333_meth_v1


title: 26-29 hours after egg lay, middle part of the germband, rep2

source_name: germband stage embryo


title: Genomic DNA from whole blood sample [SUAZ_331_meth_v1]

source_name: PESA study participant SUAZ_331_meth_v1


title: Tag2C4_Tag02


title: Tag2B6_Tag02


title: 26-29 hours after egg lay, anterior part of the germband, rep1


title: Genomic DNA from whole blood sample [SUAZ_329_meth_v1]

source_name: PESA study participant SUAZ_329_meth_v1


title: 26-29 hours after egg lay, anterior part of the germband, rep3


title: Genomic DNA from whole blood sample [SUAZ_328_meth_v1]

source_name: PESA study participant SUAZ_328_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_325_meth_v1]

source_name: PESA study participant SUAZ_325_meth_v1


title: Tag2B4_Tag02


title: Tag2C10_Tag02


title: Genomic DNA from whole blood sample [SUAZ_323_meth_v1]

source_name: PESA study participant SUAZ_323_meth_v1


title: 26-29 hours after egg lay, middle part of the germband, rep1


title: 23-26 hours after egg lay, posterior part of the germband, rep3

value: 23-26 hours after egg lay


title: Genomic DNA from whole blood sample [SUAZ_312_meth_v1]

source_name: PESA study participant SUAZ_312_meth_v1


title: 23-26 hours after egg lay, anterior part of the germband, rep3


title: Genomic DNA from whole blood sample [SUAZ_318_meth_v1]

source_name: PESA study participant SUAZ_318_meth_v1


title: 23-26 hours after egg lay, posterior part of the germband, rep2


title: Tag2B12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_317_meth_v1]

source_name: PESA study participant SUAZ_317_meth_v1


title: Tag2B5_Tag02


title: Genomic DNA from whole blood sample [SUAZ_315_meth_v1]

source_name: PESA study participant SUAZ_315_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_314_meth_v1]

source_name: PESA study participant SUAZ_314_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_316_meth_v1]

source_name: PESA study participant SUAZ_316_meth_v1


title: 23-26 hours after egg lay, middle part of the germband, rep2


title: Genomic DNA from whole blood sample [SUAZ_309_meth_v1]

source_name: PESA study participant SUAZ_309_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_313_meth_v1]

source_name: PESA study participant SUAZ_313_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_311_meth_v1]

source_name: PESA study participant SUAZ_311_meth_v1


title: Tag2B3_Tag02


title: 23-26 hours after egg lay, middle part of the germband, rep1


title: 23-26 hours after egg lay, anterior part of the germband, rep1


title: Brucella melitensis M5-90 irr mutant biol rep3

city: Shihezi

first: Huan

last: Zhang

address: North 4th Road, Nos 221 street.

country: China

institute: Shihezi University

data_processing:
RNA was sequenced on an Illumina Hiseq 2500 sequencer and paired-end reads were generated
Clean data (clean reads) were obtained by removing reads containing adaptor and poly-N, and low-quality reads from the raw data.
Reference genome and gene model annotation files were downloaded from the genome website. Then, the clean reads were aligned to the reference genome using Bowtie2-2.2.3
HTSeq v0.6.1 was used to count the number of reads mapped to each gene and the expected number of Fragments Per Kilobase of transcript sequence per Million base pairs sequenced method was used to evaluate the expression level of each gene
Differential expression analysis of two groups was performed using the DESeq R package
Assembly: Chromosome I: AE008917.1; Chromosome II: NC_003318.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Brucella melitensis M5-90

source_name: Brucella melitensis M5-90 irr mutant

growth_protocol: B. melitensis M5-90 (M5-90) and B. melitensis M5-90 irr mutant (M5-90 irr mutant) were respectively grown in normal, iron-sufficient or iron-deficient tryptic soy broth (TSB) (Difco, BD, USA) at 37°C and 150 rpm.

extract_protocol:
Total RNA was extracted from M5-90 or M5-90 irr mutant cells with TRIzol (CWBIO, Beijing, China).
The extracted RNA was reverse-transcribed to cDNA using a HiFiScript cDNA Kit (CWBIO, Beijing, China) according to the manufacturer’s protocol.

treatment_protocol: TSB with 0.45 mM of the iron chelator 2,2ʹ-dipyridyl (DIP, Sigma-Aldrich) or 50 µM FeCl3 (MACKLIN, Shanghai, China) was used as an iron-deficient or iron-sufficient medium, respectively.

value: bacterial cells

value: irr knockdown

value: iron chelator 2,2ʹ-dipyridyl treatment

tag: time


title: Genomic DNA from whole blood sample [SUAZ_319_meth_v1]

source_name: PESA study participant SUAZ_319_meth_v1

value: Male


title: Tag2B10_Tag02


title: Genomic DNA from whole blood sample [SUAZ_310_meth_v1]

source_name: PESA study participant SUAZ_310_meth_v1


title: Tag2B2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_303_meth_v1]

source_name: PESA study participant SUAZ_303_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_308_meth_v1]

source_name: PESA study participant SUAZ_308_meth_v1

value: Intermediate


title: 23-26 hours after egg lay, posterior part of the germband, rep1

source_name: germband stage embryo


title: 23-26 hours after egg lay, middle part of the germband, rep3


title: Genomic DNA from whole blood sample [SUAZ_299_meth_v1]

source_name: PESA study participant SUAZ_299_meth_v1

value: No


title: Genomic DNA from whole blood sample [SUAZ_307_meth_v1]

source_name: PESA study participant SUAZ_307_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_296_meth_v1]

source_name: PESA study participant SUAZ_296_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_306_meth_v1]

source_name: PESA study participant SUAZ_306_meth_v1


title: Tag2B11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_305_meth_v1]

source_name: PESA study participant SUAZ_305_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_291_meth_v1]

source_name: PESA study participant SUAZ_291_meth_v1

value: Generalized


title: Tag2A4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_304_meth_v1]

source_name: PESA study participant SUAZ_304_meth_v1

value: Focal


title: Genomic DNA from whole blood sample [SUAZ_301_meth_v1]

source_name: PESA study participant SUAZ_301_meth_v1


title: Tag2B1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_302_meth_v1]

source_name: PESA study participant SUAZ_302_meth_v1


title: VC

city: Austin

first: Bryan

last: Davies

address: 2500 Speedway

country: USA

institute: University of Texas at Austin

description: PE300 V3

library_source: other

data_processing:
Sequence data was assesed for quality of reads
Sequences were counted using Tally
Tallied sequences were filtered for correct and unique VHH translated sequences and the CDR sequences were extracted as well
Translated sequences with more than 1 read were kept for further analysis
A. baumannii binding dataset was filtered by each of the three CDRs (peptide1,2,3) to identify VHHs completely unique to the A. baumannii dataset compared to the control GFP and V. cholerae datasets.  See "Filtered A.baumannii Binding VHH.csv" linked to the Series record.
Assembly: NA
Supplementary files format and content: csv of the tallied read counts per VHH identified and the corresponding amino acid sequences for each dataset
Library strategy: Phage Display

molecule: other

organism: Escherichia coli

extract_protocol:
Phagemids were prepared from infected E. coli using the Zymo mini prep kit for each dataset. Then using PCR phagemid VHH inserts were amplified using primers that added Illumina adapters and barcodes to th PCR product to be sequenced.
Using PCR phagemid VHH inserts were amplified using primers that added Illumina adapters and barcodes to th PCR product to be sequenced.

tag: phage

value: M13 Bacteriophage

tag: phagemid

tag: phage display vector

value: pMopac24 M13 bacteriophage display vector

value: V. cholerae bound phage


title: 23-26 hours after egg lay, anterior part of the germband, rep2

value: germband stage embryo


title: Brucella melitensis M5-90 irr mutant biol rep2


title: Genomic DNA from whole blood sample [SUAZ_289_meth_v1]

source_name: PESA study participant SUAZ_289_meth_v1


title: Tag2A9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_300_meth_v1]

source_name: PESA study participant SUAZ_300_meth_v1


title: Tag2A8_Tag02


title: Genomic DNA from whole blood sample [SUAZ_295_meth_v1]

source_name: PESA study participant SUAZ_295_meth_v1


title: Tag2A7_Tag02


title: Genomic DNA from whole blood sample [SUAZ_288_meth_v1]

source_name: PESA study participant SUAZ_288_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_293_meth_v1]

source_name: PESA study participant SUAZ_293_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_287_meth_v1]

source_name: PESA study participant SUAZ_287_meth_v1


title: Brucella melitensis M5-90 irr mutant biol rep1

source_name: Brucella melitensis M5-90 irr mutant


title: Tag2A3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_290_meth_v1]

source_name: PESA study participant SUAZ_290_meth_v1


title: Brucella melitensis M5-90  biol rep1

source_name: Brucella melitensis M5-90

value: WT


title: Genomic DNA from whole blood sample [SUAZ_286_meth_v1]

source_name: PESA study participant SUAZ_286_meth_v1


title: Brucella melitensis M5-90  biol rep2


title: Genomic DNA from whole blood sample [SUAZ_298_meth_v1]

source_name: PESA study participant SUAZ_298_meth_v1


title: Brucella melitensis M5-90  biol rep3


title: GFP

description: PE300 V3

value: GFP bound phage


title: Tag2A2_Tag02

value: CD11b+ cells


title: Tag2A11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_285_meth_v1]

source_name: PESA study participant SUAZ_285_meth_v1


title: Tag1H8_Tag02


title: AB

description: PE300 V3

value: A.baumannii bound phage


title: Tag1H9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_279_meth_v1]

source_name: PESA study participant SUAZ_279_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_278_meth_v1]

source_name: PESA study participant SUAZ_278_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_281_meth_v1]

source_name: PESA study participant SUAZ_281_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_284_meth_v1]

source_name: PESA study participant SUAZ_284_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_276_meth_v1]

source_name: PESA study participant SUAZ_276_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_282_meth_v1]

source_name: PESA study participant SUAZ_282_meth_v1


title: Tag1H5_Tag02


title: Tag1H7_Tag02


title: Genomic DNA from whole blood sample [SUAZ_292_meth_v1]

source_name: PESA study participant SUAZ_292_meth_v1


title: Tag1H4_Tag02


title: Tag1H3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_275_meth_v1]

source_name: PESA study participant SUAZ_275_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_274_meth_v1]

source_name: PESA study participant SUAZ_274_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_273_meth_v1]

source_name: PESA study participant SUAZ_273_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_272_meth_v1]

source_name: PESA study participant SUAZ_272_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_271_meth_v1]

source_name: PESA study participant SUAZ_271_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_270_meth_v1]

source_name: PESA study participant SUAZ_270_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_283_meth_v1]

source_name: PESA study participant SUAZ_283_meth_v1


title: Tag1H12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_268_meth_v1]

source_name: PESA study participant SUAZ_268_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_269_meth_v1]

source_name: PESA study participant SUAZ_269_meth_v1


title: Tag1H2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_267_meth_v1]

source_name: PESA study participant SUAZ_267_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_277_meth_v1]

source_name: PESA study participant SUAZ_277_meth_v1


title: Tag1H1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_262_meth_v1]

source_name: PESA study participant SUAZ_262_meth_v1


title: Tag1G9_Tag02


title: Tag1G8_Tag02


title: Genomic DNA from whole blood sample [SUAZ_259_meth_v1]

source_name: PESA study participant SUAZ_259_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_255_meth_v1]

source_name: PESA study participant SUAZ_255_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_257_meth_v1]

source_name: PESA study participant SUAZ_257_meth_v1


title: Tag1G6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_254_meth_v1]

source_name: PESA study participant SUAZ_254_meth_v1


title: Tag1G7_Tag02


title: Genomic DNA from whole blood sample [SUAZ_253_meth_v1]

source_name: PESA study participant SUAZ_253_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_252_meth_v1]

source_name: PESA study participant SUAZ_252_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_251_meth_v1]

source_name: PESA study participant SUAZ_251_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_249_meth_v1]

source_name: PESA study participant SUAZ_249_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_250_meth_v1]

source_name: PESA study participant SUAZ_250_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_266_meth_v1]

source_name: PESA study participant SUAZ_266_meth_v1

value: Female


title: Genomic DNA from whole blood sample [SUAZ_263_meth_v1]

source_name: PESA study participant SUAZ_263_meth_v1


title: Tag1G5_Tag02


title: Genomic DNA from whole blood sample [SUAZ_248_meth_v1]

source_name: PESA study participant SUAZ_248_meth_v1


title: Tag1G4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_247_meth_v1]

source_name: PESA study participant SUAZ_247_meth_v1


title: Tag1G3_Tag02


title: Tag1G2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_245_meth_v1]

source_name: PESA study participant SUAZ_245_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_243_meth_v1]

source_name: PESA study participant SUAZ_243_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_240_meth_v1]

source_name: PESA study participant SUAZ_240_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_241_meth_v1]

source_name: PESA study participant SUAZ_241_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_239_meth_v1]

source_name: PESA study participant SUAZ_239_meth_v1


title: Tag1G10_Tag02


title: Genomic DNA from whole blood sample [SUAZ_238_meth_v1]

source_name: PESA study participant SUAZ_238_meth_v1


title: Rec-WT  HIC 24h rep1

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

country: France

institute: IGMM

data_processing:
All sequencing reads were aligned to the hg19 genome using Bowtie2 or TopHat2 (allowing 2 mismatches, keeping uniquely aligned reads only).
For RNA-seq experiments, reads that aligned to + or – strand were seperated and processed seperately to produce wig files with strand specific enrichment scores.
For ChIP-seq experiments, replicates were merged and all wig files were rescaled to normalize the enrichment scores to reads per million.
Peak-callings were performed using parameters from the Thresholding function of IGB (thresh: background level, min run: minimum bin to be considered as enriched, min gap: minimum gap between two peaks to be considered as distincts) fed to an in-house script.
For HiC data, raw sequencing reads were cleaned using by default parameters of HiCUP pipeline and HOMER pipeline was then used to generate contact maps and PCA.
Assembly: hg19
Supplementary files format and content: wig

source_name: Raji B cells

growth_protocol: Human Raji B cells were cultured under standard growth conditions and transfected with full-length recombinant Rpb1 expression plasmids (rWT, YFFF, and Δ5).

extract_protocol:
Cells were harvested after 24 or 48 hours of α-amanitin treatment to perform western-blot analysis. Since Δ5 is unstable after 48 hours of α-amanitin treatment, cells were harvest after 24 hours to perform ChIP using specific antibodies (HA, H3K4me1, H3K4me3 and CTCF) or extraction of Total RNA, PolyA-RNA and chromatin-associated RNA (ChrRNA) using corresponding protocols as described in manuscript.
ChIP-seq libraries were prepared with Illumina's ChIP Sample Prep Kit according to standard protocol. RNA-seq libraries were prepared with Illumina's Small RNA Library Prep Kit by using a modified protocol described in manuscript. HiC libraries were prepared by proceeding to end-repair, A-tailing followed by the ligation of Illumina adaptaters and amplification.

treatment_protocol: Polyclonal cell lines were established after G418 (1 mg/mL) selection for 2-3 weeks. Expression of mutant Rpb1 was induced by culturing the cells in Tetracycline free medium. 24 hours after inductioncells were cultured in the presence of 2 µg/ml of α-amanitin to inhibit endogenous Pol II.

value: B lymphocyte

value: Burkitt's lymphoma

value: Raji

value: Rec-WT


title: Tag1G1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_237_meth_v1]

source_name: PESA study participant SUAZ_237_meth_v1

value: Male


title: Genomic DNA from whole blood sample [SUAZ_236_meth_v1]

source_name: PESA study participant SUAZ_236_meth_v1

value: Intermediate


title: Tag1F9_Tag02


title: Tag1F8_Tag02


title: Genomic DNA from whole blood sample [SUAZ_234_meth_v1]

source_name: PESA study participant SUAZ_234_meth_v1

value: No


title: Rec-WT PolyA 24h rep2

description:
Rec-WT_PolyA_24h_Merge_rep1_2_neg.wig
Rec-WT_PolyA_24h_Merge_rep1_2_pos.wig

molecule: polyA RNA


title: Genomic DNA from whole blood sample [SUAZ_233_meth_v1]

source_name: PESA study participant SUAZ_233_meth_v1

value: Generalized


title: DELTA-5 HIC 24h rep1


title: Genomic DNA from whole blood sample [SUAZ_230_meth_v1]

source_name: PESA study participant SUAZ_230_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_246_meth_v1]

source_name: PESA study participant SUAZ_246_meth_v1

value: Focal


title: Genomic DNA from whole blood sample [SUAZ_228_meth_v1]

source_name: PESA study participant SUAZ_228_meth_v1


title: Tag1F7_Tag02


title: Genomic DNA from whole blood sample [SUAZ_229_meth_v1]

source_name: PESA study participant SUAZ_229_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_226_meth_v1]

source_name: PESA study participant SUAZ_226_meth_v1


title: Rec-WT PolyA 24h rep1


title: Genomic DNA from whole blood sample [SUAZ_227_meth_v1]

source_name: PESA study participant SUAZ_227_meth_v1


title: Tag1F6_Tag02


title: Tag1F5_Tag02


title: DELTA-5 PolyA 24h rep3

description:
DELTA-5_PolyA_24h_Merge_rep1_2_3_neg.wig
DELTA-5_PolyA_24h_Merge_rep1_2_3_pos.wig


title: Genomic DNA from whole blood sample [SUAZ_223_meth_v1]

source_name: PESA study participant SUAZ_223_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_222_meth_v1]

source_name: PESA study participant SUAZ_222_meth_v1


title: DELTA-5 PolyA 24h rep2


title: Genomic DNA from whole blood sample [SUAZ_218_meth_v1]

source_name: PESA study participant SUAZ_218_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_221_meth_v1]

source_name: PESA study participant SUAZ_221_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_217_meth_v1]

source_name: PESA study participant SUAZ_217_meth_v1


title: DELTA-5 PolyA 24h rep1


title: Tag1F4_Tag02


title: Genomic DNA from whole blood sample [SUAZ_216_meth_v1]

source_name: PESA study participant SUAZ_216_meth_v1


title: Rec-WT H3K4me3 24h rep2

source_name: Raji B cells

tag: antibody

value: H3K4me3 (Abcam Reference:ab8580 and lot:GR273043-3)


title: Tag1F3_Tag02


title: Tag1F2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_215_meth_v1]

source_name: PESA study participant SUAZ_215_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_213_meth_v1]

source_name: PESA study participant SUAZ_213_meth_v1


title: Tag1F11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_211_meth_v1]

source_name: PESA study participant SUAZ_211_meth_v1


title: Rec-WT H3K4me3 24h rep1


title: Tag1F1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_209_meth_v1]

source_name: PESA study participant SUAZ_209_meth_v1


title: DELTA-5 H3K4me3 24h rep2


title: Genomic DNA from whole blood sample [SUAZ_208_meth_v1]

source_name: PESA study participant SUAZ_208_meth_v1


title: DELTA-5 H3K4me3 24h rep1


title: Genomic DNA from whole blood sample [SUAZ_212_meth_v1]

source_name: PESA study participant SUAZ_212_meth_v1


title: Tag1E8_Tag02


title: Tag1E9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_204_meth_v1]

source_name: PESA study participant SUAZ_204_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_205_meth_v1]

source_name: PESA study participant SUAZ_205_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_202_meth_v1]

source_name: PESA study participant SUAZ_202_meth_v1


title: DELTA-5 CTCF 24h rep1

value: CTCF (Diagenode Reference:C15410210-50 and lot:2896463)


title: Genomic DNA from whole blood sample [SUAZ_200_meth_v1]

source_name: PESA study participant SUAZ_200_meth_v1


title: Tag1E6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_199_meth_v1]

source_name: PESA study participant SUAZ_199_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_197_meth_v1]

source_name: PESA study participant SUAZ_197_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_196_meth_v1]

source_name: PESA study participant SUAZ_196_meth_v1


title: Tag1E5_Tag02


title: Genomic DNA from whole blood sample [SUAZ_195_meth_v1]

source_name: PESA study participant SUAZ_195_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_192_meth_v1]

source_name: PESA study participant SUAZ_192_meth_v1


title: Tag1E4_Tag02


title: Rec-WT H3K4me1 24h rep1

value: H3K4me1 (Abcam Reference:ab8895 and lot:GR276935-1)


title: Genomic DNA from whole blood sample [SUAZ_190_meth_v1]

source_name: PESA study participant SUAZ_190_meth_v1


title: Tag1E3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_191_meth_v1]

source_name: PESA study participant SUAZ_191_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_189_meth_v1]

source_name: PESA study participant SUAZ_189_meth_v1


title: DELTA-5 H3K4me1 24h rep1

source_name: Raji B cells


title: Rec-WT CTCF 24h rep1


title: Tag1E12_Tag02


title: Tag1E2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_203_meth_v1]

source_name: PESA study participant SUAZ_203_meth_v1


title: Tag1E7_Tag02


title: M_HSB_XDL_2

city: Nanjing

first: Jun

last: Kang

address: Xiaoling Wei Street

institute: Nanjing Agricultural Unversity

data_processing:
For data analysis, all related information was transformed into raw data after online sequencing, removing the low quality, linker contamination and reads with unknown base N content to obtain clean reads. Clean reads were mapped to the V. vinifera reference genome (ftp://ftp.ensemblgenomes.org/pub/release-23/plants/gtf/vitis_vinifera/) by using HISAT2 (Gong et al. 2022)
The mapped fragments for each gene were counted by featureCounts and transcripts per million (TPM) were calculated. Genes with averaged TPM (replicates = 3) were considered expressed.
Supplementary files format and content: Tab-delimited text file including TPM values for each sample

organism: Vitis vinifera

source_name: M-HSB

extract_protocol:
Total RNA was extracted separately with the Trizol   (Invitrogen) method following the steps as described   in instructions. Te genomic DNA was digested using   DNase (TAKARA, Dalian, China).
MRNA libraries were constructed for each sample and sequenced using the Illumina HiSeq-2000 platform.

value: fruit

tag: developmental stage

value: maturity

tag: ecological zone

value: HSB


title: M_HSB_XDL_3

tag: tissue


title: Genomic DNA from whole blood sample [SUAZ_185_meth_v1]

source_name: PESA study participant SUAZ_185_meth_v1


title: Tag1E11_Tag02

tag: cell type

value: CD11b+ cells

tag: strain


title: M_HSB_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_184_meth_v1]

source_name: PESA study participant SUAZ_184_meth_v1

tag: age


title: Rec-WT H3K4me1 24h rep2

tag: cell line

tag: genotype


title: Genomic DNA from whole blood sample [SUAZ_186_meth_v1]

source_name: PESA study participant SUAZ_186_meth_v1

tag: gender


title: Genomic DNA from whole blood sample [SUAZ_188_meth_v1]

source_name: PESA study participant SUAZ_188_meth_v1

tag: pesa score


title: Genomic DNA from whole blood sample [SUAZ_183_meth_v1]

source_name: PESA study participant SUAZ_183_meth_v1


title: Tag1E10_Tag02


title: Genomic DNA from whole blood sample [SUAZ_180_meth_v1]

source_name: PESA study participant SUAZ_180_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_181_meth_v1]

source_name: PESA study participant SUAZ_181_meth_v1


title: DELTA-5 H3K4me1 24h rep2


title: Genomic DNA from whole blood sample [SUAZ_179_meth_v1]

source_name: PESA study participant SUAZ_179_meth_v1


title: V_HSB_XDL_2

source_name: V-HSB

value: veraison


title: Tag1E1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_177_meth_v1]

source_name: PESA study participant SUAZ_177_meth_v1


title: V_HSB_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_176_meth_v1]

source_name: PESA study participant SUAZ_176_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_175_meth_v1]

source_name: PESA study participant SUAZ_175_meth_v1


title: Tag1D9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_187_meth_v1]

source_name: PESA study participant SUAZ_187_meth_v1


title: Tag1D8_Tag02


title: Genomic DNA from whole blood sample [SUAZ_171_meth_v1]

source_name: PESA study participant SUAZ_171_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_173_meth_v1]

source_name: PESA study participant SUAZ_173_meth_v1


title: V_HSB_XDL_3


title: Genomic DNA from whole blood sample [SUAZ_170_meth_v1]

source_name: PESA study participant SUAZ_170_meth_v1


title: E_HSB_XDL_2

source_name: E-HSB

value: enlargement


title: Tag1D6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_172_meth_v1]

source_name: PESA study participant SUAZ_172_meth_v1


title: Tag1D7_Tag02


title: Genomic DNA from whole blood sample [SUAZ_169_meth_v1]

source_name: PESA study participant SUAZ_169_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_167_meth_v1]

source_name: PESA study participant SUAZ_167_meth_v1


title: Tag1D5_Tag02


title: E_HSB_XDL_3


title: Genomic DNA from whole blood sample [SUAZ_163_meth_v1]

source_name: PESA study participant SUAZ_163_meth_v1


title: M_X_XDL_3

source_name: M-X

value: XLS


title: Genomic DNA from whole blood sample [SUAZ_164_meth_v1]

source_name: PESA study participant SUAZ_164_meth_v1


title: Tag1D4_Tag02


title: E_HSB_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_161_meth_v1]

source_name: PESA study participant SUAZ_161_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_160_meth_v1]

source_name: PESA study participant SUAZ_160_meth_v1


title: Tag1D3_Tag02


title: M_X_XDL_2


title: Genomic DNA from whole blood sample [SUAZ_159_meth_v1]

source_name: PESA study participant SUAZ_159_meth_v1


title: M_X_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_155_meth_v1]

source_name: PESA study participant SUAZ_155_meth_v1

value: Female


title: Tag1D2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_156_meth_v1]

source_name: PESA study participant SUAZ_156_meth_v1


title: V_X_XDL_3

source_name: V-X


title: Tag1D12_Tag02


title: Tag1D11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_153_meth_v1]

source_name: PESA study participant SUAZ_153_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_154_meth_v1]

source_name: PESA study participant SUAZ_154_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_152_meth_v1]

source_name: PESA study participant SUAZ_152_meth_v1


title: V_X_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_149_meth_v1]

source_name: PESA study participant SUAZ_149_meth_v1


title: V_X_XDL_2


title: Tag1D10_Tag02


title: Tag1D1_Tag02


title: E_X_XDL_3

source_name: E-X


title: Genomic DNA from whole blood sample [SUAZ_150_meth_v1]

source_name: PESA study participant SUAZ_150_meth_v1


title: E_X_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_145_meth_v1]

source_name: PESA study participant SUAZ_145_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_148_meth_v1]

source_name: PESA study participant SUAZ_148_meth_v1


title: Tag1C8_Tag02


title: Tag1C9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_146_meth_v1]

source_name: PESA study participant SUAZ_146_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_144_meth_v1]

source_name: PESA study participant SUAZ_144_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_157_meth_v1]

source_name: PESA study participant SUAZ_157_meth_v1


title: E_X_XDL_2


title: M_XG_XDL_3

source_name: M-XG

value: XG


title: Genomic DNA from whole blood sample [SUAZ_143_meth_v1]

source_name: PESA study participant SUAZ_143_meth_v1

value: Male


title: Genomic DNA from whole blood sample [SUAZ_142_meth_v1]

source_name: PESA study participant SUAZ_142_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_141_meth_v1]

source_name: PESA study participant SUAZ_141_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_151_meth_v1]

source_name: PESA study participant SUAZ_151_meth_v1


title: Tag1C6_Tag02


title: Genomic DNA from whole blood sample [SUAZ_140_meth_v1]

source_name: PESA study participant SUAZ_140_meth_v1


title: Tag1C7_Tag02


title: M_XG_XDL_2


title: Genomic DNA from whole blood sample [SUAZ_139_meth_v1]

source_name: PESA study participant SUAZ_139_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_147_meth_v1]

source_name: PESA study participant SUAZ_147_meth_v1


title: M_XG_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_138_meth_v1]

source_name: PESA study participant SUAZ_138_meth_v1


title: Tag1C5_Tag02


title: Tag1C4_Tag02


title: V_XG_XDL_2

source_name: V-XG


title: V_XG_XDL_3


title: Genomic DNA from whole blood sample [SUAZ_127_meth_v1]

source_name: PESA study participant SUAZ_127_meth_v1

value: Intermediate


title: Tag1C3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_135_meth_v1]

source_name: PESA study participant SUAZ_135_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_130_meth_v1]

source_name: PESA study participant SUAZ_130_meth_v1


title: Tag1C2_Tag02


title: Genomic DNA from whole blood sample [SUAZ_126_meth_v1]

source_name: PESA study participant SUAZ_126_meth_v1


title: V_XG_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_123_meth_v1]

source_name: PESA study participant SUAZ_123_meth_v1


title: E_XG_XDL_3

source_name: E-XG


title: Genomic DNA from whole blood sample [SUAZ_124_meth_v1]

source_name: PESA study participant SUAZ_124_meth_v1

value: No


title: Genomic DNA from whole blood sample [SUAZ_122_meth_v1]

source_name: PESA study participant SUAZ_122_meth_v1

value: Generalized


title: Tag1C12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_116_meth_v1]

source_name: PESA study participant SUAZ_116_meth_v1


title: E_XG_XDL_2


title: Tag1C11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_114_meth_v1]

source_name: PESA study participant SUAZ_114_meth_v1


title: E_XG_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_112_meth_v1]

source_name: PESA study participant SUAZ_112_meth_v1


title: Tag1C10_Tag02


title: Genomic DNA from whole blood sample [SUAZ_111_meth_v1]

source_name: PESA study participant SUAZ_111_meth_v1


title: M_CC_XDL_3

source_name: M-CC

value: CC


title: Genomic DNA from whole blood sample [SUAZ_129_meth_v1]

source_name: PESA study participant SUAZ_129_meth_v1


title: Tag1C1_Tag02


title: M_CC_XDL_2


title: Genomic DNA from whole blood sample [SUAZ_110_meth_v1]

source_name: PESA study participant SUAZ_110_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_106_meth_v1]

source_name: PESA study participant SUAZ_106_meth_v1


title: M_CC_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_104_meth_v1]

source_name: PESA study participant SUAZ_104_meth_v1


title: Tag1B9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_098_meth_v1]

source_name: PESA study participant SUAZ_098_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_097_meth_v1]

source_name: PESA study participant SUAZ_097_meth_v1


title: Tag1B7_Tag02


title: Tag1B8_Tag02


title: V_CC_XDL_2

source_name: V-CC


title: Genomic DNA from whole blood sample [SUAZ_115_meth_v1]

source_name: PESA study participant SUAZ_115_meth_v1

value: Focal


title: V_CC_XDL_1


title: Tag1B6_Tag02


title: E_CC_XDL_3

source_name: E-CC


title: Tag1B3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_092_meth_v1]

source_name: PESA study participant SUAZ_092_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_090_meth_v1]

source_name: PESA study participant SUAZ_090_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_108_meth_v1]

source_name: PESA study participant SUAZ_108_meth_v1


title: Tag1B5_Tag02


title: Genomic DNA from whole blood sample [SUAZ_103_meth_v1]

source_name: PESA study participant SUAZ_103_meth_v1


title: V_CC_XDL_3


title: Tag1B2_Tag02


title: E_CC_XDL_1


title: E_CC_XDL_2


title: Genomic DNA from whole blood sample [SUAZ_088_meth_v1]

source_name: PESA study participant SUAZ_088_meth_v1


title: M_ZH_XDL_3

source_name: M-ZH

value: ZHYS


title: Genomic DNA from whole blood sample [SUAZ_086_meth_v1]

source_name: PESA study participant SUAZ_086_meth_v1


title: Tag1B12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_096_meth_v1]

source_name: PESA study participant SUAZ_096_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_095_meth_v1]

source_name: PESA study participant SUAZ_095_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_081_meth_v1]

source_name: PESA study participant SUAZ_081_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_079_meth_v1]

source_name: PESA study participant SUAZ_079_meth_v1


title: Tag1B11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_080_meth_v1]

source_name: PESA study participant SUAZ_080_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_093_meth_v1]

source_name: PESA study participant SUAZ_093_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_094_meth_v1]

source_name: PESA study participant SUAZ_094_meth_v1


title: M_ZH_XDL_2


title: Genomic DNA from whole blood sample [SUAZ_084_meth_v1]

source_name: PESA study participant SUAZ_084_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_078_meth_v1]

source_name: PESA study participant SUAZ_078_meth_v1


title: M_ZH_XDL_1


title: Tag1B1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_075_meth_v1]

source_name: PESA study participant SUAZ_075_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_089_meth_v1]

source_name: PESA study participant SUAZ_089_meth_v1


title: V_ZH_XDL_3

source_name: V-ZH


title: Tag1A9_Tag02


title: Genomic DNA from whole blood sample [SUAZ_085_meth_v1]

source_name: PESA study participant SUAZ_085_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_074_meth_v1]

source_name: PESA study participant SUAZ_074_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_072_meth_v1]

source_name: PESA study participant SUAZ_072_meth_v1


title: V_ZH_XDL_1


title: V_ZH_XDL_2


title: Tag1A8_Tag02


title: Genomic DNA from whole blood sample [SUAZ_067_meth_v1]

source_name: PESA study participant SUAZ_067_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_063_meth_v1]

source_name: PESA study participant SUAZ_063_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_062_meth_v1]

source_name: PESA study participant SUAZ_062_meth_v1


title: E_ZH_XDL_3

source_name: E-ZH


title: Tag1A6_Tag02


title: E_ZH_XDL_2


title: Genomic DNA from whole blood sample [SUAZ_058_meth_v1]

source_name: PESA study participant SUAZ_058_meth_v1


title: Tag1A5_Tag02


title: E_ZH_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_056_meth_v1]

source_name: PESA study participant SUAZ_056_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_053_meth_v1]

source_name: PESA study participant SUAZ_053_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_057_meth_v1]

source_name: PESA study participant SUAZ_057_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_054_meth_v1]

source_name: PESA study participant SUAZ_054_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_077_meth_v1]

source_name: PESA study participant SUAZ_077_meth_v1


title: Tag1A4_Tag02


title: M_HJZ_XDL_2

source_name: M-HJZ

value: HJZ


title: Tag1A3_Tag02


title: Genomic DNA from whole blood sample [SUAZ_049_meth_v1]

source_name: PESA study participant SUAZ_049_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_071_meth_v1]

source_name: PESA study participant SUAZ_071_meth_v1


title: Tag1A2_Tag02


title: M_HJZ_XDL_1

value: fruit


title: V_HJZ_XDL_3

source_name: V-HJZ


title: Tag1B10_Tag02


title: Tag1A7_Tag02


title: Genomic DNA from whole blood sample [SUAZ_047_meth_v1]

source_name: PESA study participant SUAZ_047_meth_v1


title: Tag1A12_Tag02


title: Genomic DNA from whole blood sample [SUAZ_046_meth_v1]

source_name: PESA study participant SUAZ_046_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_044_meth_v1]

source_name: PESA study participant SUAZ_044_meth_v1


title: Tag1A11_Tag02


title: Genomic DNA from whole blood sample [SUAZ_059_meth_v1]

source_name: PESA study participant SUAZ_059_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_038_meth_v1]

source_name: PESA study participant SUAZ_038_meth_v1


title: Tag1A1_Tag02


title: Genomic DNA from whole blood sample [SUAZ_039_meth_v1]

source_name: PESA study participant SUAZ_039_meth_v1


title: V_HJZ_XDL_2


title: Genomic DNA from whole blood sample [SUAZ_034_meth_v1]

source_name: PESA study participant SUAZ_034_meth_v1


title: V_HJZ_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_048_meth_v1]

source_name: PESA study participant SUAZ_048_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_031_meth_v1]

source_name: PESA study participant SUAZ_031_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_033_meth_v1]

source_name: PESA study participant SUAZ_033_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_029_meth_v1]

source_name: PESA study participant SUAZ_029_meth_v1


title: E_HJZ_XDL_2

source_name: E-HJZ


title: Tag8H4_Tag01


title: E_HJZ_XDL_3


title: Tag8H7_Tag01


title: Genomic DNA from whole blood sample [SUAZ_027_meth_v1]

source_name: PESA study participant SUAZ_027_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_024_meth_v1]

source_name: PESA study participant SUAZ_024_meth_v1


title: Tag8H3_Tag01


title: Genomic DNA from whole blood sample [SUAZ_025_meth_v1]

source_name: PESA study participant SUAZ_025_meth_v1


title: Genomic DNA from whole blood sample [SUAZ_023_meth_v1]

source_name: PESA study participant SUAZ_023_meth_v1


title: E_HJZ_XDL_1


title: Genomic DNA from whole blood sample [SUAZ_022_meth_v1]

source_name: PESA study participant SUAZ_022_meth_v1


title: input

city: Nantes

first: Benjamin

last: Ory

address: 1 rue Gaston Veil

description: 4_064F_00U8Nantes_CD14_pat1_Input_hs_i88

data_processing:
RNA-Seq: FASTP was used for adpater trimming and to remove low-quality reads (Q>30). Reads were mapped to human genome (hg19) using HISAT2 (v. 2.1.0) and read quantification was performed using stringtie (v. 2.1.1).
ChIP-Seq: reads were aligned to human genome (hg19) using bwa mem (v. 0.7.17). Low quality reads (-q 20), PCR duplicates and non-uniquely aligned reads using samtools (v. 1.9). Inorder to remove repliacte specific signals (alignement files of replicates from the same donor were merged into one alignement file using samtools merge. Peak calling was then performed on the merged alignement files using recommendations from github page of MACS2 (https://github.com/taoliu/MACS/wiki/Advanced\%3A-Call-peaks-using-MACS2-subcommands). Using the recommandations, ChIP and input tracks were built separately and then broad peak calling was perfomed using q-value threshold of 1e-5. ROSE2 was used to identify super-enhancers among peaks outside of promoters (TSS +/-2500 b.p.).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files per sample include coverage, TPM, FPKM values for each gene.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: comma-delimited text files per sample include all enhancers and super-enhancers identified, as output from ROSE2

source_name: PBMC

extract_protocol:
RNA-Seq: Cells were harvested, frozen and sent to Active Motif Inc. platform for library preparation and sequencing. Illumina TruSeq Stranded mRNA Sample Preparation Kit was used for library preparation.
ChIP-Seq: Cells were harvested, frozen and sent to Broad Institute’s Genomics Services platform for the ChIP data and to Active Motif Inc. platform for the input data. H3K27ac antibodies (Acetyl-Histone H3 K27 (D5E4) XR Rabbit mAB, Cell Signaling Technologies were used for precipitation. Library preparation and Sequencing for the ChIP-data were performed in a multiplexed system on a 96-well plate.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: healthy donor

value: PBMC

value: CD14+ pre-monocytes

tag: chip antibody

value: none (input)


title: Genomic DNA from whole blood sample [SUAZ_021_meth_v1]

source_name: PESA study participant SUAZ_021_meth_v1


title: Day 10 - Diff. Medium rep3

description:
d10.-.diff_rep3
36_3931Nantes_s21_CD14-J10minus_C_RNASeq_hs_i7

source_name: Day 10 - Diff. Medium_PBMC

tag: treatment

value: Day 10 - Diff. Medium


title: Tag8H12_Tag01

value: CD11b+ cells


title: Tag8H10_Tag01


title: Tag8H1_Tag01


title: Day 10 - Diff. Medium rep2

description:
d10.-.diff_rep2
35_3931Nantes_s20_CD14-J10minus_B_RNASeq_hs_i6


title: Tag8G9_Tag01


title: Day 10 - Diff. Medium rep1

description:
d10.-.diff_rep1
34_3931Nantes_s19_CD14-J10minus_A_RNASeq_hs_i5