title: Sample21: High-fat-male

data_processing:
FastQ files were aligned to the Ensembl release 76 assembly using STAR version 2.0.4b
Gene count analysis in EdgeR; differences in library size accounted for with a TMM normalization, genes with counts of zero filtered out
Weighted likelihoods calculated using the voom function in the R package Limma, based on the mean-variance relationship of each gene and transcript
Generalized linear models were used to test for differential expression
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include gene counts (RPKM values) for each sample

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit
RNA libraries were prepared using standard Illumina protocols

value: Liver


title: daf-16;fer-15 Day5 rep3

status: Public on Nov 26 2018

type: SRA

city: Beijing

first: Wenhui

last: Li

address: 7 Science Park Road ZGC Life Science Park

country: China

institute: National Institute of Biological Sciences

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the C. elegans reference genome (ws235) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated using HTSeq (v0.6.1p1) based on the Ensembl gene annotation v85.
Genome_build: ws235
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were grown on High Growth (HG) plates supplemented with OP50 bacteria at 25 °C and harvested on adult day 1 through day 7.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain/genotype

tag: developmental stage

value: Adult day 5


title: Sample19: High-fat-male

city: Aurora

first: Madeline

last: Keleher

state: CO

department: Pediatrics

country: USA

institute: University of Colorado Anschutz

molecule: total RNA

organism: Mus musculus

source_name: Liver

growth_protocol: Liver tissue was isolated from SM/J mice

tag: strain

value: SM/J

tag: tissue

tag: Sex

value: male


title: Sample20: High-fat-male


title: daf-16;fer-15 Day5 rep2


title: Sample18: High-fat-male


title: daf-16;fer-15 Day5 rep1


title: daf-16;fer-15 Day4 rep3

value: Adult day 4


title: Total RNA in H2B-APEX2 cells

city: Tel Aviv

first: Daniel

last: Benhalevy

address: Tel Aviv University, Green Bldg. Room 205

department: Shmunis School of Biomedicine and Cancer Research

country: Israel

institute: Tel-Aviv University

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat (for RNA seq) or PARalyzer (for RBP footprints)
RNAseq reads and RPKM values per gene were generated by RNAcounter
Genome_build: hg19
Supplementary_files_format_and_content: RNAcounter / PARalyzer output files

organism: Homo sapiens

growth_protocol: Cells were grown and routinely passaged in DMEM supplemented with 10% FCS and 1% pen/strip, and selective agent as required.

extract_protocol:
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion
Cells were extracted in RIPA buffer, RNA was isolated by Phenol-Chloroform extraction

treatment_protocol: 16 hours of 4SU labeling and Dox induction, BP addition for 30 min followed by Proximity biotinylation

tag: cell line

tag: genotype/variation

value: T-Rex stable line inducibly expressing V5-H2B-APEX2


title: daf-16;fer-15 Day4 rep2


title: Sample16: Low-fat-male


title: Sample15: Low-fat-male


title: Low-fat-male [TW886_pool4-LM_MeDIP]

library_source: genomic

data_processing:
Raw reads were aligned to the mm9 genome
methylQA was used to process the BAM file and generate BED files
Genome_build: mm9
Supplementary_files_format_and_content: Bed files include reads for each sample

molecule: genomic DNA

extract_protocol:
Phenol chloroform was used to extract DNA
DNA libraries were prepared as described by: Li D, Zhang B, Xing X, Wang T. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 2015;72:29-40.

value: hepatic

tag: diet

value: Low-fat

tag: age

value: adult


title: daf-16;fer-15 Day4 rep1


title: Sample17: High-fat-male


title: Sample14: Low-fat-male


title: daf-16;fer-15 Day3 rep3

value: Adult day 3


title: Total RNA in APEX2-NES cells

description:
2016_RNAseqTotalAndBound.xlsx
2017_RNAseq_TotalAndBound.xlsx

value: T-Rex stable line inducibly expressing V5-APEX2-NES


title: Young quiescent FAPs_6

type: RNA

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

description: Replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol  Standard Illumina scanning protocol

data_processing: Data were quantile normalised using Illumina Partek GS software

label: biotin

source_name: Fibro/adipogenic progenitors

label_protocol: Illumina TotalPrep RNA Amplification Kit according to protocol

extract_protocol: RNA was extracted from freshly sorted Fibro/adipogenic Progenitors using RNeasy Micro Kit (Qiagen). Quality control was performed with Fragment Analyzer (Advanced Analytical).

treatment_protocol: Tibialis anterior, gastrocnemius and quadriceps muscles were either untreated or intramuscularly injected with 50μl of 50% v/v glycerol

value: 2-4 months old mice

tag: tissue / cells

value: Fibro/adipogenic progenitors

tag: muscles of origin

value: Pool of tibialis anterior, gastrocnemius and quadriceps muscles

tag: injury

value: non-injured

value: wildtype

value: Male


title: Young quiescent FAPs_4

description: Replicate 4


title: daf-16;fer-15 Day3 rep2


title: Young quiescent FAPs_5

description: Replicate 5


title: Young quiescent FAPs_1

description: Replicate 1


title: Sample12: Low-fat-male

data_processing:
FastQ files were aligned to the Ensembl release 76 assembly using STAR version 2.0.4b
Gene count analysis in EdgeR; differences in library size accounted for with a TMM normalization, genes with counts of zero filtered out
Weighted likelihoods calculated using the voom function in the R package Limma, based on the mean-variance relationship of each gene and transcript
Generalized linear models were used to test for differential expression
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include gene counts (RPKM values) for each sample

THE RAW DATA FOR THIS SAMPLE WAS LOST AND IS THEREFORE NOT AVAILABLE FOR SUBMISSION.

value: Liver


title: Sample13: Low-fat-male


title: Young activated FAPs_6

description: Replicate 6

value: 3 days post-glycerol-induced injury


title: Sample11: High-fat-female

value: SM/J

value: female


title: daf-16;fer-15 Day3 rep1


title: Sample10: High-fat-female


title: Young activated FAPs_5

description: Replicate 5


title: daf-16;fer-15 Day2 rep2

value: Adult day 2


title: Sample8: High-fat-female


title: Sample9: High-fat-female


title: daf-16;fer-15 Day1 rep3

value: Adult day 1


title: Sample7: High-fat-female


title: daf-16;fer-15 Day2 rep1


title: Sample6: Low-fat-female


title: daf-16;fer-15 Day1 rep2


title: Young activated FAPs_4

description: Replicate 4


title: Young quiescent FAPs_3

description: Replicate 3


title: Young activated FAPs_2

description: Replicate 2


title: Young quiescent FAPs_2

description: Replicate 2


title: Young activated FAPs_1

description: Replicate 1


title: daf-16;fer-15 Day1 rep1


title: Sample5: Low-fat-female


title: fer-15 Day7 rep3

value: Adult day 7


title: Old quiescent FAPs_4

description: Replicate 4

value: 20-24 months old mice


title: daf-16;fer-15 Day2 rep3


title: Old quiescent FAPs_6

description: Replicate 6


title: fer-15 Day7 rep2


title: Sample4: Low-fat-female


title: fer-15 Day7 rep1


title: fer-15 Day6 rep2

value: Adult day 6


title: Sample2: Low-fat-female


title: Sample1: Low-fat-female


title: Eed_matKO_morula CUT & RUN

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
After quality trimming using Trim Galore version 0.4.5, the H3K27me3 CUT&RUN reads were aligned to a custom mm9 reference genome (B6/129 and PWK SNPs masked as “N”) using Bowtie2 version 2.2.9 with the following parameter: “-t -q -N 1 -L 25 --no-unal -I 150 -X 800 --no-mixed --no-discordant”.
After removing non-uniquely mapped reads and PCR duplicates, MACS2 version 2.2.1 was used to identify H3K27me3 peaks with the following parameters: “-f BAMPE -g mm -q 0.01 --broad --broad-cutoff 0.1 --nolambda --SPMR --nomodel”.
H3K27me3 CUT&RUN bigwig tracks were generated using BamCoverage in deepTools version 3.0.2 and the signal intensities of Eed CTR and matKO samples were normalized as previously described (Inoue et al., 2017 Genes & Development, PMID: 29089420).
For allelic H3K27me3 enrichment analyses, the parental origins of the reads were determined using SNPsplit version 0.3.2.
Genome_build: mm9 with B6/129 and PWK SNPs masked as "N".
Supplementary_files_format_and_content: Bigwig files that can be uploaded on a genome browser to view the relative enrichment of H3K27me3 at different genomic locations.

source_name: morula embryos

extract_protocol:
After removing zona pollucida, the morula embryos were directly used for CUT&RUN .
Eed CTR and matKO morula H3K27me3 CUT&RUN libraries were constructed as previously described (Skene and Henikoff, 2017 eLife. 2017; 6: e21856, PMID: 28079019).
H3K27me3 profiling using CUT&RUN

value: B6/129 x PWK

tag: parental genotypes

value: Gdf9-Cre, Eed-fl/fl x WT

tag: antibody


title: fer-15 Day6 rep1


title: Old quiescent FAPs_1

description: Replicate 1


title: Old quiescent FAPs_2

description: Replicate 2


title: Eed_CTR_morula CUT & RUN

value: Eed-fl/fl x WT


title: fer-15 Day5 rep3

value: Adult day 5


title: Eed_E6.5_ExE_matKO_male5

description: Gene expression of all genes in the ExE.xlsx

data_processing:
To avoid alignment bias when mapping the F1 hybrid (B6/129 x PWK) RNA-seq reads to the mouse reference genome (mm9, B6), a custom reference sequence was constructed with all SNPs between B6/129 and PWK strain masked as “N”.
The RNA-seq reads were aligned to the custom reference genome using Hisat2 version 2.1.0.
For differential gene expression analyses, the transcript abundance of each gene was quantified as reads per kilobase per million (RPKM) using cufflinks version 2.2.1.
For allele-specific gene expression analyses, the parental-origin of each uniquely aligned read was determined using SNPsplit version 0.3.2.
Genome_build: mm9 with B6/129 and PWK SNPs masked as "N".
Supplementary_files_format_and_content: Excel files with the non-SNP and SNP-tracked RPKM values as well as allele-specific read counts.

source_name: E6.5 extra-embryonic ectoderm

extract_protocol:
The morulas and E6.5 ExE samples were lysised and directly used for library preparation.
Reverse transcription and cDNA amplification were performed using whole embryos or ExE lysates with a SMARTer Ultra Low Input RNA cDNA preparation kit (Clontech, 634890). cDNA were then used to construct library using the Nextera XT DNA library Preparation Kit (FC-131-1024).


title: Young activated FAPs_3

description: Replicate 3

value: 2-4 months old mice

value: Fibro/adipogenic progenitors

value: Pool of tibialis anterior, gastrocnemius and quadriceps muscles


title: fer-15 Day5 rep2


title: Eed_E6.5_ExE_matKO_male4


title: fer-15 Day5 rep1


title: Old quiescent FAPs_5

description: Replicate 5

value: non-injured

value: wildtype

value: Male


title: Old quiescent FAPs_3

description: Replicate 3


title: fer-15 Day6 rep3


title: PrimPol input DNA

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description:
processed data file:
DT40_primpol_broad_peaks.tsv
SLX-15836_S5

data_processing:
library strategy: DNA-RNA immunoprecipitation (DRIP)-seq
Reads were quality trimmed and filtered for adaptor sequences using trim galore v0.4.4
Reads were aligned to Ggal 5.0 and Dmel r6.18 using bowtie2 v2.2.6
Uniquely mapping reads were separated into those aligning to the sample and the spike-in
Peaks were called using MACS2 v2.1.1.20160309 with options -g 1.87e9 –broad
Genome_build: Ggal 5.0 and Dmel r6.18
Supplementary_files_format_and_content: Tab-delimited files produced by MACS2 containing processing metadata and per peak information

organism:
Drosophila melanogaster
Gallus gallus

source_name: DT40 cell line, S2 cell line

growth_protocol: DT40 cells were grown at 37 degrees Centrigrade and 5% CO2 atmosphere, in RPMI 1640 with Glutamax (Gibco) supplemented with 7% FBS (Gibco), 3% chicken serum (Sigma) and penicillin-streptomycin. Drosophila S2 cells were grown in Insect-XPRESS Protein-Free Insect Cell medium with L-glutamine (Lonza), supplemented with 1% penicillin-streptomycin. S2 cells were grown in suspension, at 27 ºC, ambient CO2 and 105 rpm agitation.

extract_protocol:
Upon mixing the DT40 cells with the S2 cells (3.75:1 ratio) , the nuclear fraction was extracted (then treated with rnaseH for the control),  genomic DNA containing containing DNA:RNA hybrid purified and fragmented with restriction enzyme digest. Soluble contaminating RNA was digested with Rnase A treatments and DNA:RNA hybrids immunoprecipitated with S9.6 antibody. Following low, high, LiCl and TE buffer washes of Protein-G captured immunocomplexes, DNA was eluted, phenol:chloroform purified and fragmented to 300 bp average size with Covaris M220
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) as per provided instruction for low input DNA samples, from approximately 30 ng of immunoprecipateted DNA. Size selection was ommited and total of 7 PCR amplification cycles.

tag: cell type

value: chicken B-cell line

value: PrimPol deficient

tag: spiked with

value: Drosophila S2 cells


title: Old activated FAPs_3

description: Replicate 3

value: 3 days post-glycerol-induced injury


title: Old activated FAPs_5

description: Replicate 5


title: Old activated FAPs_6

description: Replicate 6


title: fer-15 Day4 rep3

value: Adult day 4


title: fer-15 Day4 rep2


title: PrimPol rep 2

description:
processed data file:
DT40_primpol_broad_peaks.tsv
SLX-15836_S6

value: monoclonal hybridoma purified S9.6 antibody


title: Eed_E6.5_ExE_matKO_male3


title: Eed_E6.5_ExE_matKO_male2


title: Eed_E6.5_ExE_matKO_male1


title: PrimPol rep 1

description:
processed data file:
DT40_primpol_broad_peaks.tsv
SLX-15836_S4


title: fer-15 Day4 rep1


title: Old activated FAPs_2

description: Replicate 2

value: 20-24 months old mice


title: WT input DNA

description:
processed data file:
DT40_WT_broad_peaks.tsv
SLX-15836_S2

value: wild type


title: Eed_E6.5_ExE_matKO_female4

value: B6/129 x PWK

value: Gdf9-Cre, Eed-fl/fl x WT


title: fer-15 Day3 rep3

value: Adult day 3


title: Eed_E6.5_ExE_matKO_female3


title: fer-15 Day3 rep2


title: Old activated FAPs_1

description: Replicate 1


title: WT rep 2

description:
processed data file:
DT40_WT_broad_peaks.tsv
SLX-15836_S3


title: WT rep 1

description:
processed data file:
DT40_WT_broad_peaks.tsv
SLX-15836_S1


title: fer-15 Day3 rep1


title: Eed_E6.5_ExE_matKO_female2


title: WT+rnaseH BOBSC (negative control)

data_processing:
Reads were quality trimmed and filtered for adaptor sequences using trim galore v0.4.4
Reads were aligned to Ggal 5.0 and GRCh38 using bowtie2 v2.2.6
Uniquely mapping reads were separated into those aligning to the sample and the spike-in
Peaks were called using MACS2 v2.1.1.20160309 with options -g 1.87e9 –broad
Genome_build: Ggal 5.0 and GRCh38
Supplementary_files_format_and_content: Tab-delimited files produced by MACS2 containing processing metadata and per peak information

organism:
Gallus gallus
Homo sapiens

source_name: human iPS cell line, spiked in with DT40 cell line

extract_protocol:
Upon mixing the 50-60 million BOBSC iPS cells with the DT40 cells (10:1 ratio) , the nuclear fraction was extracted  (then treated with rnaseH for the control),  genomic DNA containing containing DNA:RNA hybrid purified, soluble contaminating RNA was digested with RNase I, sonicated to average size of 300 bp with Bioruptor Diagenodtreatments and immunoprecipitated DNA:RNA hybrids with S9.6 antibody. Following low, high, LiCl and TE buffer washes of Protein-G captured immunocomplexes, DNA:RNA hybrids were eluted, phenol:chloroform purified, denatured for 5 minutes at 95 C, DNA moity digested with DNaseI, and RNA moiety of the DNA:RNA hybrid purified with Trizol.
Directional RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7645) per instructions provided. Steps from random priming to End Prep of cDNA was followed as instructed in for rRNA depleted FFPR RNA samples, and further steps where followed as instructed for purified mRNA or rRNA depleted RNA.

value: BOBSC iPS cell line

value: chicken DT40 cell line

tag: molecule subtype

value: nuclear RNA


title: Eed_E6.5_ExE_matKO_female1


title: fer-15 Day2 rep3

tag: strain/genotype

value: Adult day 2


title: Eed_E6.5_ExE_CTR_male2

value: Eed-fl/fl x WT


title: PRIMPOL BOBSC

value: PRIMPOL -/-


title: Eed_E6.5_ExE_CTR_male1


title: fer-15 Day2 rep2

tag: developmental stage


title: fer-15 Day2 rep1


title: Eed_E6.5_ExE_CTR_female2

tag: strain


title: Sample3: Low-fat-female

value: SM/J

tag: tissue

value: Liver

value: female


title: N7-5F

city: Bandar Baru Bangi

first: Siew-Eng

last: Ooi

state: Selangor

address: 6 Persiaran Institusi

department: Advanced Biotechnology and Breeding Centre

country: Malaysia

institute: Malaysian Palm Oil Board

description: clonal plant

data_processing:
Basecalls performed using CASAVA ver.1.8.2
Quality trimming was done with TrimGalore! at a Phred score of Q20
Cutadapt to trim reads containing more than 35 consecutive A or T bases from read 1 and read 2 respectively. Trimming of first five to six bases done from reads 1 and 2 respectively, according to recommendations by Clontech Laboratories Inc. Reads shorter than 20 bases were removed with cutadapt.
Trimmed and filtered reads corresponding to same sample was concatenated prior to read mapping of paired reads to Pisifera P5 reference genome with Tophat2 v.2.0.13 with parameters  --min-intron-length 30 --max-intron-length 50000 --library-type fr-secondstrand
Read counts tabulated with HTSeq-Count ver 0.6.1p1 (Anders et al., 2015) with options -s yes -t CDS.
Genome_build: E. guineensis P5-build of an AVROS pisifera palm (Singh et al., 2015)
Supplementary_files_format_and_content: text files of raw counts for cds feature in P5 gene models (Chan et al., 2017, Biology Direct; http://palmxplore.mpob.gov.my)

organism: Elaeis guineensis

source_name: carpel

extract_protocol:
Total RNA was extracted from the laser-capture microdissected cryopreserved inflorescences using Arcturus® PicoPure® RNA Isolation Kit and DNase-treated, followed by rRNA removal.
Stranded RNA-seq libraries prepared with SMARTer® Stranded RNA-Seq Kit. RNA-seq to generate 150bp paired-end reads (PE150) or 100bp reads (PE100) on Illumina HiSeq or MiSeq platforms. Adapter primers are identical to the Illumina TruSeq® Universal Adapter& Illumina TruSeq DNA LT Sample Prep Kit (adapters AD001–AD012).

value: carpel

tag: gender

value: stage 3

tag: phenotype

value: normal

tag: palm tree id


title: Eed_E6.5_ExE_CTR_female1


title: N12F2

description: clonal plant


title: fer-15 Day1 rep2

value: Adult day 1


title: fer-15 Day1 rep1


title: fer-15 Day1 rep3


title: N12F1

description: clonal plant


title: M15F

description: clonal plant

value: mantled


title: M15-2F

description: clonal plant


title: Eed_matKO_morula_rep1

description: Gene expression of all genes at the morula stage.xlsx

value: B6/129 x PWK


title: DRY_BAW2_rep2

city: Nijmegen

first: Duy

last: Nguyen

address: Heyendaalseweg 135

department: Molecular Plant Physiology

country: Netherlands

institute: Radboud University

hyb_protocol: 600 ng of the cRNA were hybridised using the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) following the manufacturer's protocol at 65°C for 17 h.

scan_protocol: Fluorescence signals were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron per pixel.

data_processing: Raw data were spatial- and background-corrected using normexp method. Probe averaging was performed for targets with multiple probes and intensity data were normalised between microarrays using the quantile method.

organism: Solanum dulcamara

source_name: leaf, drought, 48h BAW damage, replicate 2

label_protocol: Fluorescent cyanine 3-CTP-labelled cRNA was generated using the Low Input QuickAmp Labeling Kit (Agilent Technologies) using oligo-dT primer following the manufacturer's protocol.

growth_protocol: Solanum dulcamara plants were grown from seeds in a greenhouse a 16-h photoperiod, with minimum temperatures set to 20°C/17°C (day/night). Greenhouse light was supplemented with sodium lamps when natural light fell below 250 µmol m-2 s-1.

extract_protocol: For each microarray sample, leaf material from 3 independent biological replicates was pooled. Leaf material was ground under liquid nitrogen. Total RNA was extracted with the RNeasy Plant Mini Kit (Bio-Rad) and treated with DNase I (Thermo Fisher Scientific) according to the manufacturers' instructions.

treatment_protocol: 30-days-old plants were kept in control watering regime or subjected to mild drought treatment for 5 days before herbivory treatments. The youngest fully expanded leaf of each plant was enclosed in a meshbag containing 1-2 insect larvae for herbivory treatments or without insects for undamaged controls.

tag: water

value: drought

tag: insect damage

value: 48h BAW


title: Old activated FAPs_4

description: Replicate 4

tag: age

value: 20-24 months old mice

tag: tissue / cells

value: Fibro/adipogenic progenitors

value: Pool of tibialis anterior, gastrocnemius and quadriceps muscles

value: 3 days post-glycerol-induced injury

tag: genotype/variation

value: wildtype

tag: Sex

value: Male


title: DRY_CPB2_rep2

source_name: leaf, drought, 48h CPB damage, replicate 2

value: 48h CPB


title: DRY_BAW2_rep1

source_name: leaf, drought, 48h BAW damage, replicate 1


title: DRY_BAW2_rep3

source_name: leaf, drought, 48h BAW damage, replicate 3


title: Eed_matKO_morula_rep2

tag: parental genotypes

value: Gdf9-Cre, Eed-fl/fl x WT


title: Eed_CTR_morula_rep1

value: Eed-fl/fl x WT


title: Eed_CTR_morula_rep2


title: M14F

description: clonal plant

value: carpel

value: female


title: N12M2

description: clonal plant

source_name: staminodia

value: staminodia

value: male

value: stage 3

value: normal


title: DRY_CPB2_rep1

source_name: leaf, drought, 48h CPB damage, replicate 1

value: drought


title: N12M1

description: clonal plant


title: patient_3_blood (RRBS)

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

institute: University of Edinburgh

data_processing:
Raw Illumina sequencing output from the NextSeq were converted to paired FASTQ files without demultiplexing using ‘bcl2fastq’ and default settings (v2.17.1.14). These FASTQ files were then demultiplexed using custom python scripts considering indexes with perfect matches to the sample indexes. The different lanes for each sample were then combined.
Sequencing quality was assessed with FASTQC (v0.11.4). Low quality reads and remaining adaptors were removed using TrimGalore (v0.4.1, Settings: --adapter AGATCGGAAGAGC --adapter2 AAATCAAAAAAAC). NuGen adaptors contain extra diversity bases to facilitate sequencing. These were removed using the ‘trimRRBSdiversityAdaptCustomers.py’ Python script provided by NuGen (v1.11). The paired end reads were then aligned to the hg19 genome using Bismark (v 0.16.3 with Bowtie2 v2.2.6 with settings: -N 0 -L 20) before PCR duplicates were identified and removed using the 6bp UMIs present in the index reads and the ‘nudup.py’ Python script supplied by NuGen (v2.3). Aligned BAM files were processed to report coverage and number of methylated reads for each CpG observed. Forward and reverse strands were combined using Bismark’s methylation extractor and bismark2bedgraph modules with custom Python and AWK scripts.
Processed RRBS files were assessed for conversion efficiency based on the proportion of methylated reads mapping to the λ genome spike-in (>99.5% in all cases).
BigWigs were generated from RRBS data using CpGs with coverage ≥5
Genome_build: hg19
Supplementary_files_format_and_content: Processed coverage values for each CpG observed in sample. CpG position and total coverage (T) and methylated coverage (M) combining both strands. Columns = chr, start, end, T, M. Positions are 0-based, ie BED format.
Supplementary_files_format_and_content: bigWig files for each sample also supplied. Only contain CpGs with coverage >= 5 in that sample.
Raw sequencing reads are available through EGA (protected patient data): EGAS00001003232

source_name: peripheral blood leukocytes

extract_protocol:
Genomic DNA isolated with DNeasy Blood & Tissue Kit (QIAGEN) or Nucleon BACC2 Genomic DNA Extraction Kit (illustra) and quantified by Qubit (Invitrogen). DNA from mouse cortex samples were concentrated using Agencourt AMPure XP technology.
200ng of purified DNA samples were processed using the Ovation RRBS Methyl-Seq system kit according to instructions with the following modifications (NuGen Technologies). Briefly, unmethylated phage λ DNA 0.5ng (NEB) was spiked into each sample to allow assessment of bisulfite conversion efficiency. The methylation-insensitive restriction enzyme MspI was then used to digest the gDNA, and digested fragments were ligated to adapters. Adapter ligated fragments were then repaired before bisulfite conversion with the Qiagen Epitect fast bisulfite conversion kit. Bisulfite-treated adapter-ligated fragments were amplified by 9 cycles of PCR and purified using Agencourt RNAClean XP beads. Libraries were quantified using the Qubit dsDNA HS assay and assessed for size and quality using the Agilent Bioanalyzer DNA HS kit. Sequencing was performed using the NextSeq 500/550 high-output version 2 kit (75bp paired end reads) on the Illumina NextSeq 550 platform. As instructed for the NuGen RRBS kit, 12bp index reads were generated to sequence the Unique Molecular Identifiers (UMI) in addition to the index present in the adaptors. Libraries were combined into equimolar pools and run on a single flow cell. 10% PhiX control library was spiked in to facilitate sequencing by generating additional sequence diversity. Library preparation and sequencing performed by WTCRF, Edinburgh.

tag: disease state

value: microcephalic dwarfism

tag: cell type

value: peripheral blood leukocytes

tag: genotype

value: DNMT3A D333N heterozygous


title: N7-5M

description: clonal plant


title: DRY_NO_rep1

source_name: leaf, drought, no damage, replicate 1

value: no damage


title: DRY_CPB2_rep3

source_name: leaf, drought, 48h CPB damage, replicate 3


title: control_3_blood (RRBS)

value: healthy control

value: control


title: WT BOBSC

tag: cell line

value: BOBSC iPS cell line

value: wild type

tag: antibody

tag: spiked with

value: chicken DT40 cell line

tag: molecule subtype

value: nuclear RNA


title: DRY_NO_rep2

source_name: leaf, drought, no damage, replicate 2


title: pcnt_mutant_1_fibroblast

type: genomic

hyb_protocol: Infinium® MethylationEPIC BeadChip performed according to manufacturer instructions by Edinburgh WTCRF

data_processing: Raw idat files were processed to beta and detection p-values using the Bioconducter package minfi (v1.22.1) using single-sample normal exponential out of band (ss noob) background correction and dye bias normalization together with Bioconductor EPIC array annotations (IlluminaHumanMethylationEPICmanifest v0.3.0 and IlluminaHumanMethylationEPICanno.ilm10b2.hg19 v0.6.0). Probes overlapping known SNPs (MAF>1% and within 5 bp of the probe’s CpG target, based on Zhou et al PMID: 27924034), located on sex chromosomes, or with detection p-value > 0.01 were excluded. These exclusion steps have not been applied to the processed data included in GEO submission, ie it contains all probes on the arrays.

label: Cy5 and Cy3

source_name: primary fibroblast cell line

growth_protocol: Fibroblast cell lines were maintained at 3% O2 in Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies) supplemented with 10% FBS and 5% penicillin-streptomycin antibiotics or in AmnioMAX-C100 (Life Technologies).

extract_protocol: Fibroblast and blood genomic DNA extracted using the DNeasy Blood & Tissue Kit (QIAGEN).

value: primary fibroblast cell line

value: PCNT null


title: Control 2 ChIPseq K4me3 Input

data_processing:
ChIP-seq read quality was analyzed using FASTQC (v0.11.4), with low quality reads and adaptors removed using trim-galore with default settings (v0.4.1). Reads were aligned to the hg19 genome using bowtie 2 (v2.3.1, with settings: -N 1 -L 20 -- no-unal). Multi-mapping reads excluded using SAMtools (v1.6, with settings: -bq 10). PCR duplicates excluded using SAMBAMBA (v0.5.9). For ChIP Rx-seq, reads were aligned to combined hg19 and dm6 genomes using the same settings.
Tracks for data visualization generated using Homer (v4.8)73. Aligned BAMs were converted to tag directories setting the fragment length to 180bp and converted to bigWig files using Homer’s makeUCSCfile function after filtering with the removeOutOfBounds.pl function.
ChIP-seq peaks were called from tag directories using Homer’s findPeaks function (settings: -style histone) and the corresponding input chromatin control sample.
Genome_build: hg19, dm6
Supplementary_files_format_and_content: bigWig files derived as described above.
Supplementary_files_format_and_content: BED file of Homer peaks for ChIP samples.
Raw sequencing reads are available through EGA (protected patient data): EGAS00001003232

extract_protocol:
Cross-linked chromatin immunoprecipitation was adapted from a previous publication (Illingworth et al, PMID: 27723457) with the following modifications. 2x106 cells were harvested, washed and crosslinked with 1% methanol-free formaldehyde in PBS. Crosslinked cells were lysed directly for 15 min on ice in cold lysis buffer (10 mM EDTA, 50 mM Tris-HCl (pH8), 1% SDS). All buffers used during chromatin capture were freshly supplemented with protease inhibitors (Roche) and 1 mM DTT. For ChIP-Rx crosslinked Drosophila chromatin (S2 cells) was spiked into samples before sonication (ratio of 20:1 human to Drosophila cells). Lysates were sonicated with two 30 sec pulses using a soniprep 150 plus (MSE) followed by 10 cycles (30 s on / 30 s off on ‘high’ setting at 4°C) on a Bioruptor Plus (Diagenode). Following centrifugation for 10 min at 20,000xg, 4°C, supernatant was supplemented with Triton X-100 (final concentration 1%) and 50 μg/ml BSA and then added to Protein A dynabeads (Invitrogen) pre-coupled with the respective antibody (H3K27me3 antibody (Cell Signaling; C36B11; Cat.no. 9733S); H3K4me3 (Millipore; 07-473); H3K36me3 (Active Motif; #61101)). 10% of input material was retained for use as a reference. The bead-chromatin mixture was incubated under rotation at 4°C overnight. Beads were then washed twice for 10 min at 4°C with each of the following buffers: IP dilution buffer (2 mM EDTA, 150 mM NaCl, 20 mM Tris HCl pH8, 1% Triton X-100), buffer A’ (20 mM Tris pH8, 500 mM NaCl, 1 mM EDTA pH8, 1% TritonX-100, 0.1% Na-deoxycholate, 0.1% SDS), buffer B’ (20 mM Tris pH8, 1 mM EDTA pH8, 250 mM LiCl, 1% NP-40, 0.1% Na-deoxycholate). Finally, beads were washed three times with 1xTE buffer (1 mM EDTA pH8, 10 mM Tris pH8). Captured chromatin was eluted, followed by reverse crosslinking through addition of Tris HCl pH6.8 (100 mM), NaCl (300 mM) and 20 μg RNAse A at 65°C overnight. Input material was similarly de-crosslinked. Degradation of proteins with 20 μg Proteinase K and incubation at 37°C for 2 hrs. Samples purified with the MinElute PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645) according to the manufacturer instructions using barcoded adapters (NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1 or 2), E7335; E7500S). For input reference libraries 50 ng material were used. Adapter197 ligated DNA was size selected for an insert size of 150 or 200 bp using AMPure XP beads. Libraries were amplified for 7 cycles in the final PCR amplification step. Amplified libraries were purified using AMPure XP beads and eluted in EB. Libraries were pooled in an equimolar ratios. For H3K27me3 single-end 50bp reads were generated on an Illumina HiSeq machine (GATC Biotech Konstanz, Germany). For H3K4me3, H3K36me3 ChIP-Rx and H3K27me3 ChIP-Rx single-end 75bp reads were generated on an Illumina NextSeq 550 machine.

tag: chip antibody


title: Control 2 ChIPseq K4me3 ChIP

value: H3K4me3 (Millipore; 07-473)


title: control_5_fibroblast

scan_protocol: Infinium® MethylationEPIC BeadChip performed according to manufacturer instructions by Edinburgh WTCRF


title: CON_BAW2_rep3

source_name: leaf, control water, 48h BAW damage, replicate 3

value: 48h BAW


title: DRY_NO_rep3

source_name: leaf, drought, no damage, replicate 3


title: pcnt_mutant_2_fibroblast

label_protocol: Infinium® MethylationEPIC BeadChip performed according to manufacturer instructions by Edinburgh WTCRF


title: M15-2M

description: clonal plant

tag: tissue

value: staminodia

tag: gender

value: male

tag: developmental stage

value: stage 3

tag: phenotype

value: mantled


title: Control 2 ChIPseq K36me3Rx Input


title: M15M

description: clonal plant

tag: palm tree id


title: Control 1 ChIPseq K36me3Rx Input


title: Control 2 ChIPseq K36me3Rx ChIP

tag: spike-in

value: crosslinked Drosophila chromatin (S2 cells)

value: H3K36me3 (Active Motif; #61101)


title: patient_1_fibroblast_replicate_2

value: microcephalic dwarfism

value: DNMT3A W330R heterozygous


title: control_2_fibroblast

value: healthy control

value: control


title: Control 1 ChIPseq K4me3 Input


title: Patient 1 ChIPseq K4me3 ChIP


title: M14M

description: clonal plant


title: control_1_fibroblast


title: Control 1 ChIPseq K4me3 ChIP


title: patient_2_blood

value: peripheral blood leukocytes


title: Patient 1 ChIPseq K36me3Rx Input


title: control_4_blood


title: Patient 1 ChIPseq K36me3Rx ChIP


title: Control 1 ChIPseq K36me3Rx ChIP


title: patient_1_fibroblast_replicate_1


title: Patient 1 ChIPseq K4me3 Input


title: control_3_blood


title: Patient 2 ChIPseq K36me3Rx Input


title: PrimPol + rnaseH (negative control)

value: chicken B-cell line

tag: genotype/variation

value: PrimPol deficient

value: monoclonal hybridoma purified S9.6 antibody

value: Drosophila S2 cells


title: CON_CPB1_rep3

source_name: leaf, control water, 24h CPB damage, replicate 3

tag: water

tag: insect damage

value: 24h CPB


title: CON_BAW1_rep3

source_name: leaf, control water, 24h BAW damage, replicate 3

value: 24h BAW


title: CON_CPB2_rep3

source_name: leaf, control water, 48h CPB damage, replicate 3

value: 48h CPB


title: CON_BAW2_rep2

source_name: leaf, control water, 48h BAW damage, replicate 2

value: 48h BAW


title: Patient 2 ChIPseq K4me3 Input

tag: disease state

value: primary fibroblast cell line


title: CON_BAW2_rep1

source_name: leaf, control water, 48h BAW damage, replicate 1


title: CON_BAW1_rep1

source_name: leaf, control water, 24h BAW damage, replicate 1


title: CON_BAW1_rep2

source_name: leaf, control water, 24h BAW damage, replicate 2


title: CON_CPB2_rep2

source_name: leaf, control water, 48h CPB damage, replicate 2


title: WT + rnaseH (negative control)

source_name: DT40 cell line, S2 cell line

tag: cell type

value: wild type


title: ERC45KI4742 genomic DNA from whole blood

status: Public on Nov 25 2018

city: London

first: Juan

last: Castillo-Fernandez

address: St Thomas Hospital

department: Department of Twin Research

institute: King's College London

description: whole blood

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BMIQ normalization

label: Cy5, Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from whole blood

tag: age

tag: Sex

value: F

tag: ChIP

tag: position


title: ERC45KI4731 genomic DNA from whole blood

description: whole blood


title: CON_CPB2_rep1

source_name: leaf, control water, 48h CPB damage, replicate 1


title: ERC45KI4711 genomic DNA from whole blood

description: whole blood


title: dnmt3a_overgrowth_1_blood

source_name: peripheral blood leukocytes

value: Tatton-Brown Rahman syndrome

tag: genotype

value: DNMT3A G464R heterozygous


title: CON_CPB1_rep1

source_name: leaf, control water, 24h CPB damage, replicate 1


title: CON_CPB1_rep2

source_name: leaf, control water, 24h CPB damage, replicate 2


title: ERC45KI4732 genomic DNA from whole blood

description: whole blood


title: Patient 2 ChIPseq K4me3 ChIP

source_name: primary fibroblast cell line

value: microcephalic dwarfism

tag: cell line

value: DNMT3A W330R heterozygous

tag: chip antibody

value: H3K4me3 (Millipore; 07-473)


title: ERC45KI4721 genomic DNA from whole blood

description: whole blood


title: ERC45KI4702 genomic DNA from whole blood

description: whole blood


title: ERC45KI4672 genomic DNA from whole blood

description: whole blood


title: ERC45KI4741 genomic DNA from whole blood

description: whole blood


title: ERC45KI4671 genomic DNA from whole blood

description: whole blood


title: ERC45KI4701 genomic DNA from whole blood

description: whole blood


title: ERC45KI4652 genomic DNA from whole blood

description: whole blood


title: ERC45KI4661 genomic DNA from whole blood

description: whole blood


title: dnmt3a_overgrowth_2_blood

value: peripheral blood leukocytes

value: DNMT3A Q696R FsTer9 heterozygous


title: ERC45KI4712 genomic DNA from whole blood

description: whole blood


title: patient_2_fibroblast


title: ERC45KI4681 genomic DNA from whole blood

description: whole blood


title: ERC45KI4651 genomic DNA from whole blood

description: whole blood


title: CON_NO_rep1

source_name: leaf, control water, no damage, replicate 1

value: control

value: no damage


title: ERC45KI4642 genomic DNA from whole blood

description: whole blood


title: ERC45KI4641 genomic DNA from whole blood

description: whole blood


title: CON_NO_rep3

source_name: leaf, control water, no damage, replicate 3


title: ERC45KI4632 genomic DNA from whole blood

description: whole blood


title: ERC45KI4662 genomic DNA from whole blood

description: whole blood


title: Patinet 2 ChIPseq K36me3Rx ChIP

value: crosslinked Drosophila chromatin (S2 cells)

value: H3K36me3 (Active Motif; #61101)


title: ERC45KI4631 genomic DNA from whole blood

description: whole blood


title: ERC45KI4622 genomic DNA from whole blood

description: whole blood


title: CON_NO_rep2

source_name: leaf, control water, no damage, replicate 2


title: ERC45KI4551 genomic DNA from whole blood

description: whole blood


title: ERC45KI4531 genomic DNA from whole blood

description: whole blood


title: ERC45KI4561 genomic DNA from whole blood

description: whole blood


title: ERC45KI4562 genomic DNA from whole blood

description: whole blood


title: ERC45KI4581 genomic DNA from whole blood

description: whole blood


title: ERC45KI4621 genomic DNA from whole blood

description: whole blood


title: ERC45KI4601 genomic DNA from whole blood

description: whole blood


title: ERC45KI4541 genomic DNA from whole blood

description: whole blood


title: ERC45KI4521 genomic DNA from whole blood

description: whole blood


title: ERC45KI4492 genomic DNA from whole blood

description: whole blood


title: ERC45KI4511 genomic DNA from whole blood

description: whole blood


title: ERC45KI4431 genomic DNA from whole blood

description: whole blood


title: ERC45KI4412 genomic DNA from whole blood

description: whole blood


title: ERC45KI4461 genomic DNA from whole blood

description: whole blood


title: ERC45KI4471 genomic DNA from whole blood

description: whole blood


title: ERC45KI4411 genomic DNA from whole blood

description: whole blood


title: ERC45KI4382 genomic DNA from whole blood

description: whole blood


title: ERC45KI4602 genomic DNA from whole blood

description: whole blood


title: ERC45KI4592 genomic DNA from whole blood

description: whole blood


title: ERC45KI4462 genomic DNA from whole blood

description: whole blood


title: ERC45KI4381 genomic DNA from whole blood

description: whole blood


title: ERC45KI4361 genomic DNA from whole blood

description: whole blood


title: ERC45KI4352 genomic DNA from whole blood

description: whole blood


title: ERC45KI4372 genomic DNA from whole blood

description: whole blood


title: ERC45KI4341 genomic DNA from whole blood

description: whole blood


title: ERC45KI4331 genomic DNA from whole blood

description: whole blood


title: ERC45KI4491 genomic DNA from whole blood

description: whole blood


title: ERC45KI4311 genomic DNA from whole blood

description: whole blood


title: ERC45KI4272 genomic DNA from whole blood

description: whole blood


title: ERC45KI4252 genomic DNA from whole blood

description: whole blood


title: ERC45KI4251 genomic DNA from whole blood

description: whole blood


title: ERC45KI4241 genomic DNA from whole blood

description: whole blood


title: ERC45KI4232 genomic DNA from whole blood

description: whole blood


title: ERC45KI4342 genomic DNA from whole blood

description: whole blood


title: ERC45KI4371 genomic DNA from whole blood

description: whole blood


title: ERC45KI4221 genomic DNA from whole blood

description: whole blood


title: ERC45KI4202 genomic DNA from whole blood

description: whole blood


title: ERC45KI4201 genomic DNA from whole blood

description: whole blood


title: ERC45KI4222 genomic DNA from whole blood

description: whole blood


title: ERC45KI4152 genomic DNA from whole blood

description: whole blood


title: ERC45KI4191 genomic DNA from whole blood

description: whole blood


title: ERC45KI4171 genomic DNA from whole blood

description: whole blood


title: ERC45KI4182 genomic DNA from whole blood

description: whole blood


title: ERC45KI4231 genomic DNA from whole blood

description: whole blood


title: ERC45KI4192 genomic DNA from whole blood

description: whole blood


title: ERC45KI4151 genomic DNA from whole blood

description: whole blood


title: ERC45KI4322 genomic DNA from whole blood

description: whole blood


title: ERC45KI4351 genomic DNA from whole blood

description: whole blood


title: ERC45KI4122 genomic DNA from whole blood

description: whole blood


title: ERC45KI4091 genomic DNA from whole blood

description: whole blood


title: ERC45KI4142 genomic DNA from whole blood

description: whole blood


title: ERC45KI4102 genomic DNA from whole blood

description: whole blood


title: ERC45KI4072 genomic DNA from whole blood

description: whole blood


title: ERC45KI4271 genomic DNA from whole blood

description: whole blood


title: ERC45KI4141 genomic DNA from whole blood

description: whole blood


title: ERC45KI4112 genomic DNA from whole blood

description: whole blood


title: ERC45KI4132 genomic DNA from whole blood

description: whole blood


title: ERC45KI4261 genomic DNA from whole blood

description: whole blood


title: ERC45KI4121 genomic DNA from whole blood

description: whole blood


title: ERC45KI4111 genomic DNA from whole blood

description: whole blood


title: ERC45KI4092 genomic DNA from whole blood

description: whole blood


title: ERC45KI4071 genomic DNA from whole blood

description: whole blood


title: ERC45KI4131 genomic DNA from whole blood

description: whole blood


title: ERC45KI4062 genomic DNA from whole blood

description: whole blood


title: ERC45KI4001 genomic DNA from whole blood

description: whole blood


title: ERC45KI4041 genomic DNA from whole blood

description: whole blood


title: ERC45KI3971 genomic DNA from whole blood

description: whole blood


title: ERC45KI4061 genomic DNA from whole blood

description: whole blood


title: ERC45KI4042 genomic DNA from whole blood

description: whole blood


title: ERC45KI3942 genomic DNA from whole blood

description: whole blood


title: ERC45KI3962 genomic DNA from whole blood

description: whole blood


title: ERC45KI3941 genomic DNA from whole blood

description: whole blood


title: ERC45KI3991 genomic DNA from whole blood

description: whole blood


title: ERC45KI3952 genomic DNA from whole blood

description: whole blood


title: ERC45KI3931 genomic DNA from whole blood

description: whole blood


title: ERC45KI3901 genomic DNA from whole blood

description: whole blood


title: ERC45KI3902 genomic DNA from whole blood

description: whole blood


title: ERC45KI3912 genomic DNA from whole blood

description: whole blood


title: ERC45KI3871 genomic DNA from whole blood

description: whole blood


title: ERC45KI3872 genomic DNA from whole blood

description: whole blood


title: ERC45KI3891 genomic DNA from whole blood

description: whole blood


title: ERC45KI3892 genomic DNA from whole blood

description: whole blood


title: ERC45KI3861 genomic DNA from whole blood

description: whole blood


title: ERC45KI3911 genomic DNA from whole blood

description: whole blood


title: ERC45KI3851 genomic DNA from whole blood

description: whole blood


title: ERC45KI3852 genomic DNA from whole blood

description: whole blood


title: ERC45KI3841 genomic DNA from whole blood

description: whole blood


title: ERC45KI3961 genomic DNA from whole blood

description: whole blood


title: ERC45KI3832 genomic DNA from whole blood

description: whole blood


title: ERC45KI3812 genomic DNA from whole blood

description: whole blood


title: ERC45KI3802 genomic DNA from whole blood

description: whole blood


title: ERC45KI3972 genomic DNA from whole blood

description: whole blood


title: ERC45KI3951 genomic DNA from whole blood

description: whole blood


title: ERC45KI3801 genomic DNA from whole blood

description: whole blood


title: ERC45KI3791 genomic DNA from whole blood

description: whole blood


title: ERC45KI3751 genomic DNA from whole blood

description: whole blood


title: ERC45KI3771 genomic DNA from whole blood

description: whole blood


title: ERC45KI3752 genomic DNA from whole blood

description: whole blood


title: ERC45KI3781 genomic DNA from whole blood

description: whole blood


title: ERC45KI3762 genomic DNA from whole blood

description: whole blood


title: ERC45KI3772 genomic DNA from whole blood

description: whole blood


title: ERC45KI3722 genomic DNA from whole blood

description: whole blood


title: ERC45KI3712 genomic DNA from whole blood

description: whole blood


title: ERC45KI3711 genomic DNA from whole blood

description: whole blood


title: ERC45KI3701 genomic DNA from whole blood

description: whole blood


title: ERC45KI3702 genomic DNA from whole blood

description: whole blood


title: ERC45KI3682 genomic DNA from whole blood

description: whole blood


title: ERC45KI3681 genomic DNA from whole blood

description: whole blood


title: ERC45KI3691 genomic DNA from whole blood

description: whole blood


title: ERC45KI3782 genomic DNA from whole blood

description: whole blood


title: ERC45KI3792 genomic DNA from whole blood

description: whole blood


title: ERC45KI3672 genomic DNA from whole blood

description: whole blood


title: ERC45KI3671 genomic DNA from whole blood

description: whole blood


title: ERC45KI4682 genomic DNA from whole blood

description: whole blood


title: ERC45KI3662 genomic DNA from whole blood

description: whole blood


title: ERC45KI3661 genomic DNA from whole blood

description: whole blood


title: ERC45KI3641 genomic DNA from whole blood

description: whole blood


title: ERC45KI3622 genomic DNA from whole blood

description: whole blood


title: ERC45KI3621 genomic DNA from whole blood

description: whole blood


title: ERC45KI3611 genomic DNA from whole blood

description: whole blood


title: ERC45KI3602 genomic DNA from whole blood

description: whole blood


title: ERC45KI3601 genomic DNA from whole blood

description: whole blood


title: ERC45KI3592 genomic DNA from whole blood

description: whole blood


title: ERC45KI3591 genomic DNA from whole blood

description: whole blood


title: ERC45KI3581 genomic DNA from whole blood

description: whole blood


title: ERC45KI3651 genomic DNA from whole blood

description: whole blood


title: ERC45KI3571 genomic DNA from whole blood

description: whole blood


title: ERC45KI3652 genomic DNA from whole blood

description: whole blood


title: ERC45KI3582 genomic DNA from whole blood

description: whole blood


title: ERC45KI3542 genomic DNA from whole blood

description: whole blood


title: ERC45KI3551 genomic DNA from whole blood

description: whole blood


title: ERC45KI3541 genomic DNA from whole blood

description: whole blood


title: ERC45KI3552 genomic DNA from whole blood

description: whole blood


title: ERC45KI3522 genomic DNA from whole blood

description: whole blood


title: ERC45KI3532 genomic DNA from whole blood

description: whole blood


title: ERC45KI3521 genomic DNA from whole blood

description: whole blood


title: ERC45KI3512 genomic DNA from whole blood

description: whole blood


title: ERC45KI3491 genomic DNA from whole blood

description: whole blood


title: ERC45KI3501 genomic DNA from whole blood

description: whole blood


title: ERC45KI3492 genomic DNA from whole blood

description: whole blood


title: ERC45KI3511 genomic DNA from whole blood

description: whole blood


title: ERC45KI3442 genomic DNA from whole blood

description: whole blood


title: ERC45KI3481 genomic DNA from whole blood

description: whole blood


title: ERC45KI3441 genomic DNA from whole blood

description: whole blood


title: ERC45KI3452 genomic DNA from whole blood

description: whole blood


title: ERC45KI3451 genomic DNA from whole blood

description: whole blood


title: ERC45KI3482 genomic DNA from whole blood

description: whole blood


title: ERC45KI3462 genomic DNA from whole blood

description: whole blood


title: ERC45KI3431 genomic DNA from whole blood

description: whole blood


title: ERC45KI3432 genomic DNA from whole blood

description: whole blood


title: ERC45KI3422 genomic DNA from whole blood

description: whole blood


title: ERC45KI3572 genomic DNA from whole blood

description: whole blood


title: ERC45KI3412 genomic DNA from whole blood

description: whole blood


title: ERC45KI3531 genomic DNA from whole blood

description: whole blood


title: ERC45KI3361 genomic DNA from whole blood

description: whole blood


title: ERC45KI3352 genomic DNA from whole blood

description: whole blood


title: ERC45KI3362 genomic DNA from whole blood

description: whole blood


title: ERC45KI3382 genomic DNA from whole blood

description: whole blood


title: ERC45KI3401 genomic DNA from whole blood

description: whole blood


title: ERC45KI3392 genomic DNA from whole blood

description: whole blood


title: ERC45KI3342 genomic DNA from whole blood

description: whole blood


title: ERC45KI3331 genomic DNA from whole blood

description: whole blood


title: ERC45KI3322 genomic DNA from whole blood

description: whole blood


title: ERC45KI3302 genomic DNA from whole blood

description: whole blood


title: ERC45KI3292 genomic DNA from whole blood

description: whole blood


title: ERC45KI3281 genomic DNA from whole blood

description: whole blood


title: ERC45KI3291 genomic DNA from whole blood

description: whole blood


title: ERC45KI3301 genomic DNA from whole blood

description: whole blood


title: ERC45KI3311 genomic DNA from whole blood

description: whole blood


title: ERC45KI3321 genomic DNA from whole blood

description: whole blood


title: ERC45KI3282 genomic DNA from whole blood

description: whole blood


title: ERC45KI3252 genomic DNA from whole blood

description: whole blood


title: ERC45KI3312 genomic DNA from whole blood

description: whole blood


title: ERC45KI3242 genomic DNA from whole blood

description: whole blood


title: ERC45KI3251 genomic DNA from whole blood

description: whole blood


title: ERC45KI3272 genomic DNA from whole blood

description: whole blood


title: ERC45KI3402 genomic DNA from whole blood

description: whole blood


title: ERC45KI3261 genomic DNA from whole blood

description: whole blood


title: ERC45KI3391 genomic DNA from whole blood

description: whole blood


title: ERC45KI3372 genomic DNA from whole blood

description: whole blood


title: ERC45KI3381 genomic DNA from whole blood

description: whole blood


title: ERC45KI3241 genomic DNA from whole blood

description: whole blood


title: ERC45KI3351 genomic DNA from whole blood

description: whole blood


title: ERC45KI3191 genomic DNA from whole blood

description: whole blood


title: ERC45KI3162 genomic DNA from whole blood

description: whole blood


title: ERC45KI3161 genomic DNA from whole blood

description: whole blood


title: ERC45KI3151 genomic DNA from whole blood

description: whole blood


title: ERC45KI3132 genomic DNA from whole blood

description: whole blood


title: ERC45KI3141 genomic DNA from whole blood

description: whole blood


title: ERC45KI3112 genomic DNA from whole blood

description: whole blood


title: ERC45KI3131 genomic DNA from whole blood

description: whole blood


title: ERC45KI3111 genomic DNA from whole blood

description: whole blood


title: ERC45KI3101 genomic DNA from whole blood

description: whole blood


title: ERC45KI3091 genomic DNA from whole blood

description: whole blood


title: ERC45KI3102 genomic DNA from whole blood

description: whole blood


title: ERC45KI3092 genomic DNA from whole blood

description: whole blood


title: ERC45KI2961 genomic DNA from whole blood

description: whole blood


title: ERC45KI2912 genomic DNA from whole blood

description: whole blood


title: ERC45KI3061 genomic DNA from whole blood

description: whole blood


title: ERC45KI2972 genomic DNA from whole blood

description: whole blood


title: ERC45KI2861 genomic DNA from whole blood

description: whole blood


title: ERC45KI2962 genomic DNA from whole blood

description: whole blood


title: ERC45KI3042 genomic DNA from whole blood

description: whole blood


title: ERC45KI3001 genomic DNA from whole blood

description: whole blood


title: ERC45KI2991 genomic DNA from whole blood

description: whole blood


title: ERC45KI2911 genomic DNA from whole blood

description: whole blood


title: ERC45KI3062 genomic DNA from whole blood

description: whole blood


title: ERC45KI3021 genomic DNA from whole blood

description: whole blood


title: ERC45KI2922 genomic DNA from whole blood

description: whole blood


title: ERC45KI2891 genomic DNA from whole blood

description: whole blood


title: ERC45KI2802 genomic DNA from whole blood

description: whole blood


title: ERC45KI2811 genomic DNA from whole blood

description: whole blood


title: ERC45KI2851 genomic DNA from whole blood

description: whole blood


title: ERC45KI2771 genomic DNA from whole blood

description: whole blood


title: ERC45KI3152 genomic DNA from whole blood

description: whole blood


title: ERC45KI2772 genomic DNA from whole blood

description: whole blood


title: ERC45KI2842 genomic DNA from whole blood

description: whole blood


title: ERC45KI2752 genomic DNA from whole blood

description: whole blood


title: ERC45KI2742 genomic DNA from whole blood

description: whole blood


title: ERC45KI2741 genomic DNA from whole blood

description: whole blood


title: ERC45KI2732 genomic DNA from whole blood

description: whole blood


title: ERC45KI2712 genomic DNA from whole blood

description: whole blood


title: ERC45KI2721 genomic DNA from whole blood

description: whole blood


title: ERC45KI2812 genomic DNA from whole blood

description: whole blood


title: ERC45KI2852 genomic DNA from whole blood

description: whole blood


title: ERC45KI2761 genomic DNA from whole blood

description: whole blood


title: ERC45KI2522 genomic DNA from whole blood

description: whole blood


title: ERC45KI2521 genomic DNA from whole blood

description: whole blood


title: ERC45KI2542 genomic DNA from whole blood

description: whole blood


title: ERC45KI2541 genomic DNA from whole blood

description: whole blood


title: ERC45KI2472 genomic DNA from whole blood

description: whole blood


title: ERC45KI2462 genomic DNA from whole blood

description: whole blood


title: ERC45KI2511 genomic DNA from whole blood

description: whole blood


title: ERC45KI2491 genomic DNA from whole blood

description: whole blood


title: ERC45KI2471 genomic DNA from whole blood

description: whole blood


title: ERC45KI2461 genomic DNA from whole blood

description: whole blood


title: ERC45KI2432 genomic DNA from whole blood

description: whole blood


title: ERC45KI2442 genomic DNA from whole blood

description: whole blood


title: ERC45KI2431 genomic DNA from whole blood

description: whole blood


title: ERC45KI2632 genomic DNA from whole blood

description: whole blood


title: ERC45KI2641 genomic DNA from whole blood

description: whole blood


title: ERC45KI2582 genomic DNA from whole blood

description: whole blood


title: ERC45KI2701 genomic DNA from whole blood

description: whole blood


title: ERC45KI2702 genomic DNA from whole blood

description: whole blood


title: ERC45KI2592 genomic DNA from whole blood

description: whole blood


title: ERC45KI2661 genomic DNA from whole blood

description: whole blood


title: ERC45KI2601 genomic DNA from whole blood

description: whole blood


title: ERC45KI2552 genomic DNA from whole blood

description: whole blood


title: ERC45KI2421 genomic DNA from whole blood

description: whole blood


title: ERC45KI2662 genomic DNA from whole blood

description: whole blood


title: ERC45KI2591 genomic DNA from whole blood

description: whole blood


title: ERC45KI2691 genomic DNA from whole blood

description: whole blood


title: ERC45KI2562 genomic DNA from whole blood

description: whole blood


title: ERC45KI2642 genomic DNA from whole blood

description: whole blood


title: ERC45KI2692 genomic DNA from whole blood

description: whole blood


title: ERC45KI2371 genomic DNA from whole blood

description: whole blood


title: ERC45KI2332 genomic DNA from whole blood

description: whole blood


title: ERC45KI2321 genomic DNA from whole blood

description: whole blood


title: ERC45KI2331 genomic DNA from whole blood

description: whole blood


title: ERC45KI2361 genomic DNA from whole blood

description: whole blood


title: ERC45KI2302 genomic DNA from whole blood

description: whole blood


title: ERC45KI2301 genomic DNA from whole blood

description: whole blood


title: ERC45KI2291 genomic DNA from whole blood

description: whole blood


title: ERC45KI2272 genomic DNA from whole blood

description: whole blood


title: ERC45KI2281 genomic DNA from whole blood

description: whole blood


title: ERC45KI2232 genomic DNA from whole blood

description: whole blood


title: ERC45KI2231 genomic DNA from whole blood

description: whole blood


title: ERC45KI2242 genomic DNA from whole blood

description: whole blood


title: ERC45KI2181 genomic DNA from whole blood

description: whole blood


title: ERC45KI2031 genomic DNA from whole blood

description: whole blood


title: ERC45KI2132 genomic DNA from whole blood

description: whole blood


title: ERC45KI2222 genomic DNA from whole blood

description: whole blood


title: ERC45KI2022 genomic DNA from whole blood

description: whole blood


title: ERC45KI2042 genomic DNA from whole blood

description: whole blood


title: ERC45KI2221 genomic DNA from whole blood

description: whole blood


title: ERC45KI2021 genomic DNA from whole blood

description: whole blood


title: ERC45KI2041 genomic DNA from whole blood

description: whole blood


title: ERC45KI1952 genomic DNA from whole blood

description: whole blood


title: ERC45KI1961 genomic DNA from whole blood

description: whole blood


title: ERC45KI1951 genomic DNA from whole blood

description: whole blood


title: ERC45KI1922 genomic DNA from whole blood

description: whole blood


title: ERC45KI2012 genomic DNA from whole blood

description: whole blood


title: ERC45KI1902 genomic DNA from whole blood

description: whole blood


title: ERC45KI1871 genomic DNA from whole blood

description: whole blood


title: ERC45KI1852 genomic DNA from whole blood

description: whole blood


title: ERC45KI1851 genomic DNA from whole blood

description: whole blood


title: ERC45KI1822 genomic DNA from whole blood

description: whole blood


title: ERC45KI1842 genomic DNA from whole blood

description: whole blood


title: ERC45KI1812 genomic DNA from whole blood

description: whole blood


title: ERC45KI1791 genomic DNA from whole blood

description: whole blood


title: ERC45KI1831 genomic DNA from whole blood

description: whole blood


title: ERC45KI1781 genomic DNA from whole blood

description: whole blood


title: ERC45KI1772 genomic DNA from whole blood

description: whole blood


title: ERC45KI1742 genomic DNA from whole blood

description: whole blood


title: ERC45KI2111 genomic DNA from whole blood

description: whole blood


title: ERC45KI1721 genomic DNA from whole blood

description: whole blood


title: ERC45KI1732 genomic DNA from whole blood

description: whole blood


title: ERC45KI1741 genomic DNA from whole blood

description: whole blood


title: ERC45KI1661 genomic DNA from whole blood

description: whole blood


title: ERC45KI1682 genomic DNA from whole blood

description: whole blood


title: ERC45KI1722 genomic DNA from whole blood

description: whole blood


title: ERC45KI1631 genomic DNA from whole blood

description: whole blood


title: ERC45KI1641 genomic DNA from whole blood

description: whole blood


title: ERC45KI1592 genomic DNA from whole blood

description: whole blood


title: ERC45KI1681 genomic DNA from whole blood

description: whole blood


title: ERC45KI1702 genomic DNA from whole blood

description: whole blood


title: ERC45KI1602 genomic DNA from whole blood

description: whole blood


title: ERC45KI1841 genomic DNA from whole blood

description: whole blood


title: ERC45KI1782 genomic DNA from whole blood

description: whole blood


title: ERC45KI1582 genomic DNA from whole blood

description: whole blood


title: ERC45KI1591 genomic DNA from whole blood

description: whole blood


title: ERC45KI1581 genomic DNA from whole blood

description: whole blood


title: ERC45KI1562 genomic DNA from whole blood

description: whole blood


title: ERC45KI1771 genomic DNA from whole blood

description: whole blood


title: ERC45KI1502 genomic DNA from whole blood

description: whole blood


title: ERC45KI1492 genomic DNA from whole blood

description: whole blood


title: ERC45KI1482 genomic DNA from whole blood

description: whole blood


title: ERC45KI1501 genomic DNA from whole blood

description: whole blood


title: ERC45KI1521 genomic DNA from whole blood

description: whole blood


title: ERC45KI1551 genomic DNA from whole blood

description: whole blood


title: ERC45KI1491 genomic DNA from whole blood

description: whole blood


title: ERC45KI1462 genomic DNA from whole blood

description: whole blood


title: ERC45KI1642 genomic DNA from whole blood

description: whole blood


title: ERC45KI1422 genomic DNA from whole blood

description: whole blood


title: ERC45KI1452 genomic DNA from whole blood

description: whole blood


title: ERC45KI1382 genomic DNA from whole blood

description: whole blood


title: ERC45KI1352 genomic DNA from whole blood

description: whole blood


title: ERC45KI1392 genomic DNA from whole blood

description: whole blood


title: ERC45KI1351 genomic DNA from whole blood

description: whole blood


title: ERC45KI1342 genomic DNA from whole blood

description: whole blood


title: ERC45KI1332 genomic DNA from whole blood

description: whole blood


title: ERC45KI1321 genomic DNA from whole blood

description: whole blood


title: ERC45KI1311 genomic DNA from whole blood

description: whole blood


title: ERC45KI1312 genomic DNA from whole blood

description: whole blood


title: ERC45KI1302 genomic DNA from whole blood

description: whole blood


title: ERC45KI1481 genomic DNA from whole blood

description: whole blood


title: ERC45KI1292 genomic DNA from whole blood

description: whole blood


title: ERC45KI1211 genomic DNA from whole blood

description: whole blood


title: ERC45KI1232 genomic DNA from whole blood

description: whole blood


title: ERC45KI1291 genomic DNA from whole blood

description: whole blood


title: ERC45KI1472 genomic DNA from whole blood

description: whole blood


title: ERC45KI1222 genomic DNA from whole blood

description: whole blood


title: ERC45KI1191 genomic DNA from whole blood

description: whole blood


title: ERC45KI1182 genomic DNA from whole blood

description: whole blood


title: ERC45KI1202 genomic DNA from whole blood

description: whole blood


title: ERC45KI1241 genomic DNA from whole blood

description: whole blood


title: ERC45KI1231 genomic DNA from whole blood

description: whole blood


title: ERC45KI1172 genomic DNA from whole blood

description: whole blood


title: ERC45KI1181 genomic DNA from whole blood

description: whole blood


title: ERC45KI1451 genomic DNA from whole blood

description: whole blood


title: ERC45KI1402 genomic DNA from whole blood

description: whole blood


title: ERC45KI1171 genomic DNA from whole blood

description: whole blood


title: ERC45KI1162 genomic DNA from whole blood

description: whole blood


title: ERC45KI1142 genomic DNA from whole blood

description: whole blood


title: ERC45KI1152 genomic DNA from whole blood

description: whole blood


title: ERC45KI1141 genomic DNA from whole blood

description: whole blood


title: ERC45KI1161 genomic DNA from whole blood

description: whole blood


title: ERC45KI1132 genomic DNA from whole blood

description: whole blood


title: ERC45KI1102 genomic DNA from whole blood

description: whole blood


title: ERC45KI1101 genomic DNA from whole blood

description: whole blood


title: ERC45KI1221 genomic DNA from whole blood

description: whole blood


title: ERC45KI1091 genomic DNA from whole blood

description: whole blood


title: ERC45KI1092 genomic DNA from whole blood

description: whole blood


title: ERC45KI1112 genomic DNA from whole blood

description: whole blood


title: ERC45KI1111 genomic DNA from whole blood

description: whole blood


title: ERC45KI1192 genomic DNA from whole blood

description: whole blood


title: ERC45KI1021 genomic DNA from whole blood

description: whole blood


title: ERC45KI1072 genomic DNA from whole blood

description: whole blood


title: ERC45KI1031 genomic DNA from whole blood

description: whole blood


title: ERC45KI922 genomic DNA from whole blood

description: whole blood


title: ERC45KI1011 genomic DNA from whole blood

description: whole blood


title: ERC45KI912 genomic DNA from whole blood

description: whole blood


title: ERC45KI1052 genomic DNA from whole blood

description: whole blood


title: ERC45KI1012 genomic DNA from whole blood

description: whole blood


title: ERC45KI911 genomic DNA from whole blood

description: whole blood


title: ERC45KI902 genomic DNA from whole blood

description: whole blood


title: ERC45KI1151 genomic DNA from whole blood

description: whole blood


title: ERC45KI901 genomic DNA from whole blood

description: whole blood


title: ERC45KI871 genomic DNA from whole blood

description: whole blood


title: ERC45KI872 genomic DNA from whole blood

description: whole blood


title: ERC45KI861 genomic DNA from whole blood

description: whole blood


title: ERC45KI862 genomic DNA from whole blood

description: whole blood


title: ERC45KI851 genomic DNA from whole blood

description: whole blood


title: ERC45KI842 genomic DNA from whole blood

description: whole blood


title: ERC45KI841 genomic DNA from whole blood

description: whole blood


title: ERC45KI812 genomic DNA from whole blood

description: whole blood


title: ERC45KI802 genomic DNA from whole blood

description: whole blood


title: ERC45KI762 genomic DNA from whole blood

description: whole blood


title: ERC45KI781 genomic DNA from whole blood

description: whole blood


title: ERC45KI801 genomic DNA from whole blood

description: whole blood


title: ERC45KI782 genomic DNA from whole blood

description: whole blood


title: ERC45KI792 genomic DNA from whole blood

description: whole blood


title: ERC45KI742 genomic DNA from whole blood

description: whole blood


title: ERC45KI752 genomic DNA from whole blood

description: whole blood


title: ERC45KI761 genomic DNA from whole blood

description: whole blood


title: ERC45KI712 genomic DNA from whole blood

description: whole blood


title: ERC45KI751 genomic DNA from whole blood

description: whole blood


title: ERC45KI711 genomic DNA from whole blood

description: whole blood


title: ERC45KI721 genomic DNA from whole blood

description: whole blood


title: ERC45KI701 genomic DNA from whole blood

description: whole blood


title: ERC45KI702 genomic DNA from whole blood

description: whole blood


title: ERC45KI921 genomic DNA from whole blood

description: whole blood


title: ERC45KI692 genomic DNA from whole blood

description: whole blood


title: ERC45KI672 genomic DNA from whole blood

description: whole blood


title: ERC45KI691 genomic DNA from whole blood

description: whole blood


title: ERC45KI681 genomic DNA from whole blood

description: whole blood


title: ERC45KI831 genomic DNA from whole blood

description: whole blood


title: ERC45KI852 genomic DNA from whole blood

description: whole blood


title: ERC45KI661 genomic DNA from whole blood

description: whole blood


title: ERC45KI662 genomic DNA from whole blood

description: whole blood


title: ERC45KI642 genomic DNA from whole blood

description: whole blood


title: ERC45KI641 genomic DNA from whole blood

description: whole blood


title: ERC45KI651 genomic DNA from whole blood

description: whole blood


title: ERC45KI621 genomic DNA from whole blood

description: whole blood


title: ERC45KI622 genomic DNA from whole blood

description: whole blood


title: ERC45KI731 genomic DNA from whole blood

description: whole blood


title: ERC45KI581 genomic DNA from whole blood

description: whole blood


title: ERC45KI582 genomic DNA from whole blood

description: whole blood


title: ERC45KI561 genomic DNA from whole blood

description: whole blood


title: ERC45KI512 genomic DNA from whole blood

description: whole blood


title: ERC45KI532 genomic DNA from whole blood

description: whole blood


title: ERC45KI531 genomic DNA from whole blood

description: whole blood


title: ERC45KI511 genomic DNA from whole blood

description: whole blood


title: ERC45KI492 genomic DNA from whole blood

description: whole blood


title: ERC45KI462 genomic DNA from whole blood

description: whole blood


title: ERC45KI491 genomic DNA from whole blood

description: whole blood


title: ERC45KI461 genomic DNA from whole blood

description: whole blood


title: ERC45KI412 genomic DNA from whole blood

description: whole blood


title: ERC45KI402 genomic DNA from whole blood

description: whole blood


title: ERC45KI371 genomic DNA from whole blood

description: whole blood


title: ERC45KI372 genomic DNA from whole blood

description: whole blood


title: ERC45KI442 genomic DNA from whole blood

description: whole blood


title: ERC45KI382 genomic DNA from whole blood

description: whole blood


title: ERC45KI401 genomic DNA from whole blood

description: whole blood


title: ERC45KI652 genomic DNA from whole blood

description: whole blood


title: ERC45KI352 genomic DNA from whole blood

description: whole blood


title: ERC45KI351 genomic DNA from whole blood

description: whole blood


title: ERC45KI312 genomic DNA from whole blood

description: whole blood


title: ERC45KI321 genomic DNA from whole blood

description: whole blood


title: ERC45KI311 genomic DNA from whole blood

description: whole blood


title: ERC45KI261 genomic DNA from whole blood

description: whole blood


title: ERC45KI262 genomic DNA from whole blood

description: whole blood


title: ERC45KI222 genomic DNA from whole blood

description: whole blood


title: ERC45KI221 genomic DNA from whole blood

description: whole blood


title: ERC45KI211 genomic DNA from whole blood

description: whole blood


title: Z1500

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

country: Germany

institute: Uniklinikum Erlangen

data_processing:
Illumina RTA 1.18.66.3 used for basecalling
Illumina bcl2fastq v2.17.1.14 used for demultiplexing
cutadapt 1.9.1 used for quality triming
bwa mem 0.7.14-r1136 used for filter mapping
STAR 2.5.4a used for mapping
subread v1.5.2 featureCounts to get raw read counts
Genome_build: Ensembl GRCm38.85
Supplementary_files_format_and_content: tab-delimited text file containing rlog normalized reads from DESeq2

source_name: LPMCs

extract_protocol:
RNA was isolated from cells with the MicroSpin Total RNA kit (Peqlab) according to the manufacturer’s instructions. RNA was transcribed to cDNA with the AffinityScript kit (Agilent).
RNA libraries were prepared for sequencing using Illumina stranded mRNA protocols

value: mild signs of colitis

tag: treatment

value: transfer of Hobit x Blimp DKO CD4 cells


title: ERC45KI212 genomic DNA from whole blood

description: whole blood


title: ERC45KI202 genomic DNA from whole blood

description: whole blood


title: Z1490


title: Z1486

value: pronounced signs of colitis

value: transfer of wt CD4 cells


title: ERC45KI141 genomic DNA from whole blood

description: whole blood


title: ERC45KI142 genomic DNA from whole blood

description: whole blood


title: ERC45KI132 genomic DNA from whole blood

description: whole blood


title: Z1489


title: ERC45KI111 genomic DNA from whole blood

description: whole blood


title: Female_3

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

data_processing:
Reads were mapped on mm10 mouse reference genome and quantified using CLC Genomics Workbench version 10.1.1 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 10.1.1.
Filtering characteristics of fold-change -2 to 2 (false discovery rate (FDR) at P < 0.05) were used to identify the DEGs.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts and RPKM normalized values for all genes from each sample.

extract_protocol:
Mouse embryonic fibroblasts (MEFs) from E14 male and female mice (C57BL/6) were generated using standard methods and then were grown in Dulbecco's modified Eagle medium (DMEM, Nacalai Tesque). Media were supplemented with 10% (v/v) fetal bovine serum (FBS) (Gibco), 1% of penicillin-streptomycin (Sigma) at 37°C with 5% CO2. In this study, we used MEFs within 3 passages to avoid replicative senescence. Total RNA was extracted from MEFs using ISOGEN II reagent (Nippon Gene). 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: embryonic day (e)

value: female

value: Mouse embryonic fibroblast (MEFs)

tag: passage (p)


title: Female_1


title: Male_5

value: male


title: Male_4


title: Female_5


title: Male_3


title: Male_2


title: sir2 sample 2

city: New York

first: Scott

last: Keeney

state: NY

address: 1275 York Ave

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

description: Spo11-associated DNA oligonucleotides

data_processing:
Demultiplexing and base calls perfomed using CASAVA v. 1.8.1 (with options--use-bases-mask Y50n,I6n --force) and HiSeq Control Software v.1.4.8 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 24 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 10001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled in R (RStudio version  0.99.893, R version 3.2.4)
Genome_build: Reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: wig files include total unique read count (number of 5' ends of Spo11 oligos that mapped uniquely at a given position) at each non-zero base position in the nuclear genome

organism: Saccharomyces cerevisiae

source_name: meiotic culture

growth_protocol: Synchronized meiotic cultures were prepared in 1% potassium acetate at 30°C by the YPA pre-growth method as described in Lam et al. Methods Mol Bio 1471: 51-98 (2017). Cells were collected at 4 hr after transfer to sporulation medium.

extract_protocol:
As described in Zhu and Keeney, Genetics 201: 525-542 (2015)
As described in Zhu and Keeney, Genetics 201: 525-542 (2015) and Lam et al. Methods Mol Bio 1471: 51-98 (2017).

value: sir2, SPO11-flag


title: ERC45KI101 genomic DNA from whole blood

description: whole blood

value: F


title: sir2 sample 1

description: Spo11-associated DNA oligonucleotides


title: ERC45KI92 genomic DNA from whole blood

description: whole blood


title: Male_1


title: Female_4


title: ERC45KI91 genomic DNA from whole blood

description: whole blood


title: ERC45KI161 genomic DNA from whole blood

description: whole blood


title: Female_2


title: pch2 sample 1

description: Spo11-associated DNA oligonucleotides

value: pch2, SPO11-flag


title: ERC45KI82 genomic DNA from whole blood

description: whole blood


title: ERC45KI81 genomic DNA from whole blood

description: whole blood


title: ERC45KI62 genomic DNA from whole blood

description: whole blood


title: ERC45KI21 genomic DNA from whole blood

description: whole blood


title: pch2 sample 2

description: Spo11-associated DNA oligonucleotides


title: 12GF Ins

city: Valhalla

first: Bistra

last: Nankova

address: 95 Grassland Rd

institute: New York Medical College

description: gene expression data from insulin treated GF animal

hyb_protocol: Following fragmentation in the presence of heat and Mg2+ the biotynilated cRNA was hybridized to Clariom_S_Mouse array. The array was washed and stained with streptavidin phycoerythtin (SAPE) using fluidics.

scan_protocol: The arrays were scanned using GeneChip Scanner 3000

data_processing: The data were normalized by RMA and quantile normalization using Partecl Genomics Suite 6.6. Quality control was performed by PCA. Differentially expressed genes were selected with adjusted p value (Benjamini-Hochberg Procedure) ≤ 0.05 and fold change ≥ 1.5. DEGs between selected pairs was tested using Limma R package.

source_name: insulin 90 min

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was isolated from dissected aadrenal medullae using RNeasy kit according to the manufacturer’s procedure (Qiagen,Hilden, Germany) with DNAse on column treatment. RNA quality and quantity was assessed using a NanoDrop® Spectrophotometer ND-2000c (ThermoFisher, Waltham, MA). Genome-wide transcriptome profiling (3 individual samples per experimental group) was performed at Yale Center for Genome Analysis, New Haven, CT.

treatment_protocol: All treatments (intraperitoneal injection of regular human insulin Humulin at a dose of 2IU/kg or same volume of saline were performed after 3 hrs fasting period (water ad libitum). The animals were sacrificed 90 min after injection. The adrenal medullae were dissected and immediately frozen until further analyses.

tag: tissue

value: adrenal medulla

tag: gut microbiota status

value: germ free


title: NM3

status: Public on Nov 24 2018

city: Yangling

first: HUI

last: TIAN

institute: Northwest A&F University

data_processing:
Sequences obtained for each of the six libraries were imported and individually processed using RSEM version 1.3.0
For quality filtering, a trimming step was performed on raw reads with the following conditions: (1) removing reads containing adapters; (2) removing reads containing more than 10% of unknown nucleotides; and (3) removing low-quality reads containing more than 50% of low-quality (Q-value ≤ 20) bases. Sequencing coverage was estimated according to the RSEM algorithm by dividing the total number of acquired sequence bases per condition by the number of reference bases. High-quality reads were then mapped against the wheat reference transcriptome “Ensembl release 30 IWGSC1.0” (http://archive.plants.ensembl.org/Triticum_aestivum/Info/Index) using the following mapping parameters: maximum read mismatch, 2; distance between mate-pair reads, 50 bp; and error of distance between mate-pair reads, ±80 bp. To check if there are RNA sequences belonging to R. irregularis, reads were also mapped against the genome of R. irregularis ((http://genome.jgi.doe.gov/Gloin1/Gloin1.home.html) (Tisserant et al. 2013). The reconstruction of transcripts was carried out with software Cufflinks, which, together with TopHat2, allows biologists to identify new genes. All of the reconstructed transcripts were aligned to the reference genome and divided into twelve categories by using Cuffcompare. Genes with class code “u” (the transcripts were unknown or in the intergenic spacer region) were defined as novel genes. The parameters used to identify reliable novel genes were as follows: length of the transcript longer than 200 bp and exon number greater than 2
Genome_build: Ensembl release 30 IWGSC1.0 (http://archive.plants.ensembl.org/Triticum_aestivum/Info/Index)
Supplementary_files_format_and_content: txt file. Gene expression level of each genes

organism: Triticum aestivum

source_name: no molecular signal added_roots

growth_protocol: The experiment was conducted in Northwest A&F University, Yangling, Shaanxi province, China (34.26°N, 108.06°E) from 23th March-13th April, 2017. Wheat seeds (T. aestivum L., Cultivar: Chinese spring) were surface-sterilized by submerging with 1% NaClO for 10 min, rinsed with deionized water, and then pre-germinated on moist ﬁlter paper in the dark at 25 °C for 24 h. The pre-germinated wheat seeds were planted into pots filled with approximately 2.5 L of steam-sterilized soil-quartz sand mixture (1:3) (v/v). The soil was clay loam and was classiﬁed as a Eum-Orthic Anthrosol (FAO Soil Classiﬁcation, Gong et al. 2003). Its basic fertility characteristics were: nitrate 10.2 mg kg-1, ammonium 1.95 mg kg-1, available phosphorus (P) (Olsen-P) 7.35 mg kg-1, available potassium (K) 143.0 mg kg-1 and organic matter 8.55 g kg-1.Twenty-five pre-germinated wheat seeds were planted into each pot, and plants were thinned to 15 plants for each pot 5 days after seeding. Wheat plants were cultured outdoors and watered when necessary.

extract_protocol:
Total RNA was extracted from approximately 100 mg of wheat root of three biological replicates of the two treatments using the RNeasy Plant Mini Kit (Qiagen, USA). according to the manufacturer’s instructions.The concentration and quality of the total RNA were estimated using a NanoDrop Spectrometer (Thermo; USA) and verified using agarose gel electrophoresis and an Agilent 2100 bioanalyzer (Agilent, USA).
mRNA of each sample was respectively enriched by Oligo(dT) beads, then the enriched mRNA was fragmented into short fragments (~300bp) using fragmentation buffer, followed by reverse transcription into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis. Six independent complementary DNA (cDNA) libraries corresponding to the three biological replicates for each treatment were constructed. cDNA library quality and fragment length were verified using an Agilent 2100 bioanalyzer and real-time PCR. Fragment length distributions were within the expected ranges according to the CLC Sequence Viewer software, and the average read length was 150 bp.

treatment_protocol: Two treatments were established: (1) non-mycorrhizal treatment (NM), in which there was no AM inoculum in pots; and (2) molecular signals communication treatment (MSC), in which each pot contained 15 bags filled with 25 g of the inoculum of Rhizophagus irregularis (BGC-HEB07D). The bags were 10 cm × 10 cm and were made of a 0.25 µm filter membrane. This membrane can physically separate wheat roots, AM spores and AM hyphae but allows the communication of the molecular signals secreted by the host plants or the AM fungus. To eliminate the influence of the buried bags on the growth of wheat, 15 bags of the same size were filled with 20 g of steam-sterilized inoculum of R. irregularis (to maintain a similar microbial community with the bags used in the MSC treatment, the filtrate from the unsterilized AM inoculum was added to the bags) were also buried in the pots of the NM treatments.

tag: cultivar

value: Chinese Spring

value: non-mycorrhizal treatment (NM)

value: roots


title: NM1


title: NM2


title: 5C Ins

description: gene expression data from insulin treated control animal

value: normally colonized


title: MSC3

source_name: molecular signal added_roots

value: molecular signals communication treatment (MSC)


title: MSC2


title: 11GF Ins


title: 8GF Sal

description: gene expression data from saline treated GF animal

source_name: saline 90 min


title: 7GF Sal


title: 3C Sal

description: gene expression data from saline treated control animal


title: MSC1


title: D27 LSK mouse BM cells YFP+ rep3

city: Paris

first: Thierry

last: JAFFREDO

address: 9, Quai St Bernard

department: Developmental Biology

country: France

institute: CNRS

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MouseGene 2.0 ST (Affymetrix) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls.

data_processing: The data were analyzed with Partek Genomic Suite version 7.18.0518 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: D27 LSK mouse BM cells YFP+

label_protocol: After validation of the RNA quality with Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), 500 pg of total RNA is reverse transcribed following the Ovation Pico V2 system (Nugen). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3.6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

extract_protocol: Lysis with 350µL RLT+ buffer (RNeasy Plus Micro kit, Qiagen) and conserved at -80°C. All RNA isolations were performed at the same time, according to the manufacturer’s guidelines.

treatment_protocol: Femurs and tibias were flushed with DMEM (Gibco) supplemented with 10% FCS (Eurobio). Cells were dissociated with Collagenase type 1 (C0130, Sigma) 1.25mg/ml in PBS+10% FCS for 30 min at 37°C, and washed twice with DMEM+10% FCS. 1 to 5.106 cells were stained with fluorescent antibodies in PBS+0.5% BSA for at least 30 min at 4°C. Cells were washed, and suspended in PBS+0.5% BSA supplemented with 1.25 µg/ml DAPI (D9542, Sigma) for cell viability and analysed on a MACSQuant VYB (Miltenyi Biotec) or a LSR II (Becton-Dickinson) flow cytometer. Data were reanalysed with FlowJo X software.

tag: strain background

tag: genotype/variation

value: tamoxifen inducible Tg(Cdh5-Cre/ERT2) mice crossed to Rosa 26 YFP mice

value: Post natal Day 27

value: bone marrow LSK cells

tag: cell population

value: YFP positive cells


title: 6C Ins


title: D27 LSK mouse BM cells YFP+ rep2

tag: age

tag: cell type


title: 10GF Ins

tag: Sex


title: 9GF Sal


title: D27 LSK mouse BM cells YFP- rep2

source_name: D27 LSK mouse BM cells YFP-

value: YFP negative cells


title: EyeBank_cultured_choroid_stroma_fibroblast_cells_001_rep1

city: Québec

first: Stéphanie

last: Proulx

state: Qc

address: 1050 Chemin Ste-Foy

country: Canada

institute: Université Laval

description: Gene expression of passage 2 cells cultivated 6 days

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary choroidal fibroblast cell population

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: Fibroblats and RPE cells were expanded in the same culture medium : Dulbecco-Vogt Modified Eagle Medium supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol:
isolation protocol: RPE sheets were dislodged from the choroid after an ezymatic digestion (0.02% EDTA or 2U/ml dispase), rinsed and seeded for cell expansion. Choroidal fibroblats were obtained after treatment with 0.125 U/ml collagenase H.
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

value: eye

value: choroidal stromal fibroblasts

value: Male


title: EyeBank_cultured_choroid_stroma_fibroblast_cells_001_rep2

description: Gene expression of passage 4 cells cultivated 6 days

value: female


title: D27 LSK mouse BM cells YFP- rep3


title: EyeBank_cultured_retinal_pigment_epithelial_cells_001_rep1

description: Gene expression of passage 5 cells cultivated 3 days

source_name: primary retinal pigment epithelium population

value: retinal pigment epithelium


title: D27 LSK mouse BM cells YFP+ rep1


title: D27 LSK mouse BM cells YFP- rep1


title: EyeBank_cultured_choroid_stroma_fibroblast_cells_001_rep3

description: Gene expression of passage 3 cells cultivated 6 days


title: 4C Ins

value: adrenal medulla

value: male


title: 1C Sal


title: XPCCPDrep1

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

description: Replicate 1

data_processing:
Library strategy: XR-seq
Adaptor trimming
Filtering reads based on length
Random sampling
Alignment
Read filtering based on nucleotide composition
Strand separation
Gene coverage count
Remove mismatches and gaps and duplicates
Genome_build: rDNA and DHFR
Supplementary_files_format_and_content: wig files

source_name: xeroderma pigmentosum complementation group C cells

growth_protocol: NHF1, CSB, XPC, GM12878 and wild-type mouse skin fibroblast cells were grown in DMEM (Life Technologies, Gaithersburg, MD) supplemented with 10% fetal bovine serum (Gemini, Woodland, CA). Cells were maintained in an incubator at 37°C under 5% CO2.

extract_protocol:
Cells were lysed gently and small molecular weight DNA, consisting mostly of excised 26-27 mers, was separated from chromosomal high molecular weight DNA by centrifugation.
Briefly, the excised oligomers are immunoprecipitated with anti-TFIIH (anti-XPB and anti-p62) antibodies because the excision product is released in a relatively stable complex with TFIIH, which also protects the excision product from degradation by non-specific nucleases. This is followed by extraction of the excised oligomers and ligation to adaptors and a second immunoprecipitation with anti-CPD antibodies. Then photolyase repairs the CPD damage. This is followed by PCR amplification with index primers and NGS sequencing on HiSeq platform.

treatment_protocol: Cells were grown to about 80% confluence in 150mm dishes. Media was removed, cells were washed with PBS, irradiated with 20 J/m2 of UV, and then warm, fresh media was added and cells were incubated for 3hr at 37°C (MSF), 1hr at 37°C (NHF1, XPC, CSB). GM12878 were treated with cisplatin 2hr at 37°C. Cells were then harvested and processed using the XR-seq procedure.

value: skin fibroblasts

value: XP-C mutant

value: UV


title: XPCCPDrep2

description: Replicate 2


title: CSBCPDrep2

description: Replicate 2

source_name: Cockayne syndrome cells

value: CS-B mutant


title: NHF1CPDrep22

description: Replicate 2

source_name: normal human fibroblast cells

value: foreskin fibroblasts

value: wild type


title: CSBCPDrep1

description: Replicate 1


title: NHF1CPDrep21

description: Replicate 1