title: Pdx1Cre_E13.5_1_28


title: Pdx1Cre_E13.5_1_17

status: Public on Jan 29 2019

type: SRA

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to mouse genome (mm10) using TopHat (v2.1.0) with the parameters “-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq”.
Quantification of reads mapped to each gene was performed with HTSeq (v0.6.0) with the parameters “htseq-count -f bam -r pos -s no -a 30 input_bam gtf”.
The gene expression levels were calculated as transcripts per million (TPM).
mm10
values tab-delimited text files include read count and TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Pancreas

extract_protocol:
The methods of cell lysis and cDNA synthesis (18 cycles for PCR pre-amplification step) followed the Smart-seq2 described by Picelli et al. Then the cDNA was purified with 1X VAHTS DNA Clean Beads (Vazyme. N411-03) twice.
The library was prepared with 2 ng cDNA for 8 cycles PCR amplification using a TruePrep DNA Library Prep Kit (Vazyme, TD502).

tag: cell source

tag: embryonic day


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title: Ngn3Low_E13.5_1_25


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title: Ngn3Low_E13.5_1_05


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title: Ngn3High_E15.5_2_29


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title: Ngn3High_E15.5_2_24


title: Ngn3High_E15.5_2_25


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title: Ngn3High_E13.5_2_05


title: Ngn3High_E13.5_2_04


title: Ngn3High_E13.5_2_18


title: Ngn3High_E13.5_2_01


title: Ngn3High_E13.5_2_02


title: Ngn3High_E13.5_2_19


title: Ngn3High_E13.5_1_37


title: Ngn3High_E13.5_2_17


title: Ngn3High_E13.5_2_16


title: Ngn3High_E14.5_1_03


title: Ngn3High_E13.5_2_10


title: Ngn3High_E13.5_2_14


title: Ngn3High_E13.5_2_09


title: Ngn3High_E13.5_1_35


title: Ngn3High_E13.5_1_34


title: Ngn3High_E13.5_2_08


title: Ngn3High_E13.5_1_31


title: Ngn3High_E13.5_1_30


title: Ngn3High_E13.5_1_29


title: Ngn3High_E13.5_1_27


title: Ngn3High_E13.5_2_06


title: Ngn3High_E13.5_1_25


title: Ngn3High_E13.5_1_38


title: Ngn3High_E13.5_1_23


title: Ngn3High_E13.5_1_36


title: Ngn3High_E13.5_2_12


title: Ngn3High_E13.5_1_21


title: Ngn3High_E13.5_1_33


title: Ngn3High_E13.5_2_07


title: Ngn3High_E13.5_2_03


title: Ngn3High_E13.5_1_32


title: Ngn3High_E13.5_1_17


title: Ngn3High_E13.5_1_15


title: Ngn3High_E13.5_1_39


title: Ngn3High_E13.5_1_11


title: Ngn3High_E13.5_1_13


title: Ngn3High_E13.5_1_18


title: Ngn3High_E13.5_1_24


title: Ngn3High_E13.5_1_12


title: Ngn3High_E13.5_1_08


title: Ngn3High_E13.5_1_19


title: Ngn3High_E13.5_1_09


title: Ngn3High_E13.5_1_20


title: Ngn3High_E13.5_1_07


title: Ngn3High_E13.5_1_22


title: Ngn3High_E13.5_1_28


title: Ngn3High_E13.5_1_14


title: Ngn3High_E13.5_1_26


title: Ngn3High_E13.5_1_16


title: Ngn3High_E13.5_1_01


title: Ngn3High_E13.5_1_05


title: Ngn3High_E13.5_1_10


title: Ngn3Cre_E11.5_2_28


title: Ngn3Cre_E11.5_2_24


title: Ngn3Cre_E11.5_2_27


title: Ngn3Cre_E11.5_2_26


title: Ngn3Cre_E11.5_2_18


title: Ngn3Cre_E11.5_2_20


title: Ngn3Cre_E11.5_2_25


title: Ngn3Cre_E11.5_2_21


title: Ngn3Cre_E11.5_2_23


title: Ngn3Cre_E11.5_2_17


title: Ngn3Cre_E11.5_2_19


title: Ngn3Cre_E11.5_2_13


title: Ngn3Cre_E11.5_2_12


title: Ngn3Cre_E11.5_2_11


title: Ngn3Cre_E11.5_2_16


title: Ngn3Cre_E11.5_2_14


title: Ngn3High_E13.5_1_06


title: Ngn3Cre_E11.5_2_10


title: Ngn3Cre_E11.5_2_07


title: Ngn3Cre_E11.5_2_09


title: Ngn3Cre_E11.5_2_08


title: Ngn3High_E13.5_1_04


title: Ngn3Cre_E11.5_2_05


title: Ngn3Cre_E11.5_2_04


title: Ngn3Cre_E11.5_2_06


title: Ngn3High_E13.5_1_03


title: Ngn3Cre_E11.5_2_02


title: Ngn3Cre_E11.5_2_22


title: Ngn3Cre_E11.5_2_03


title: Ngn3Cre_E11.5_2_01


title: Ngn3Cre_E11.5_1_16


title: Ngn3Cre_E11.5_1_15


title: Ngn3High_E13.5_1_02


title: Ngn3Cre_E11.5_1_14


title: Ngn3Cre_E11.5_2_15


title: Ngn3Cre_E11.5_1_11


title: Ngn3Cre_E11.5_1_09


title: Ngn3Cre_E11.5_1_12


title: Ngn3Cre_E11.5_1_06


title: Ngn3Cre_E11.5_1_03


title: Ngn3Cre_E11.5_1_05


title: Ngn3Cre_E11.5_1_02


title: Ngn3Cre_E11.5_1_01


title: Ins1Pos_E15.5_2_27


title: Ins1Pos_E15.5_2_28


title: Ins1Pos_E15.5_2_26


title: Ins1Pos_E15.5_2_29


title: Ins1Pos_E15.5_2_23


title: Ins1Pos_E15.5_2_25


title: Ins1Pos_E15.5_2_24


title: Ngn3Cre_E11.5_1_13


title: Ins1Pos_E15.5_2_20


title: Ins1Pos_E15.5_2_18


title: Ins1Pos_E15.5_2_19


title: 10XGenomics_Pancreas_E14.5_2

data_processing:
Sequencing reads were pre-processed with cellranger count (v2.0.2).
mm10
matrix.mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample File description and contents are described at http://software.10xgenomics.com/single-cell/overview/welcome

extract_protocol:
For the droplet-based method, sc-RNA-seq was performed using the Single Cell 3’ Reagent Kit v2 of 10X Genomics following the user's guide. Briefly, the digested E14.5 pancreatic cells were passed through a 35-µm filter to remove undigested pieces and diluted to a concentration of 700 cells/µl in FACS buffer (HBSS containing 1% FBS, pH 7.4). We loaded approximately 10,000 cells into one channel of the Chromium system. Afterwards, we amplified 11 cycles for cDNA amplification.
We amplified 12 cycles for the cDNA library construction.

tag: tissue

value: Pancreas


title: Ins1Pos_E15.5_2_21


title: Ins1Pos_E15.5_2_22


title: Ins1Pos_E15.5_2_17


title: Ngn3Cre_E11.5_1_10


title: INPUT_shRen_HD3_2

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

library_source: genomic

data_processing:
RNA-seq:
Quality was checked with FastQC
Quality-filtering and -trimming with PRINSEQ-lite
Mapping against the Mus musculus (GRCm38) reference genome with STAR
Mapped reads per gene were counted with featureCounts
Normalization and differential expression analysis was carried out with DESeq2
ChIP-seq:
Quality was checked with FastQC
Quality-filtering and -trimming with PRINSEQ-lite
Mapping against the Mus musculus (GRCm38) reference genome via BWA
Post-processing with SAMtools
RPKM normalization and conversion to BigWig files was carried out with Deeptools
Peak calling for the C/EBPa p30 ChIP-seq dataset was done with MACS2
Peak calling for the MLL ChIP-seq data was done with Sicer
Called peaks were annotated with Homer
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for each sample

molecule: genomic DNA

source_name: myeloid-progenitor-derived cell line

growth_protocol: p30/p30 cells were cultivated in RPMI 640 supplemented with 10% FCS and 2 mM glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. 5 ng/ml mIL-3 was added every 2-3 days.

extract_protocol:
For RNA-seq QIAGEN RNeasy Plus Kit was used, and for ChIP-seq, lysates were sonicated and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols by sequencing facilities.

treatment_protocol: Samples DMSO, MI-463 and MI-503 were treated at 0h, 48h and taken at 72h.

tag: strain

tag: genotype

tag: chip antibody


title: Ngn3Cre_E11.5_1_08


title: INPUT_shRen_HD3_1


title: Ins1Pos_E15.5_2_16


title: Ngn3Cre_E11.5_1_07


title: Ngn3Cre_E11.5_1_04


title: C18_shRen_HD3_2

value: C/EBPα C-18 (Santa Cruz, sc-9314)


title: C18_shRen_HD3_1


title: Ins1Pos_E15.5_2_15


title: Ins1Pos_E15.5_2_14


title: 10XGenomics_Pancreas_E14.5_1

data_processing:
Sequencing reads were pre-processed with cellranger count (v2.0.2).
mm10
matrix.mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample
File description and contents are described at http://software.10xgenomics.com/single-cell/overview/welcome
values tab-delimited text files include read count and TPM values for each sample

extract_protocol:
For droplet-based method, sc-RNA-seq was performed using Single Cell 3’ Reagent Kits v2 of 10X Genomics following user guide. Briefly, the digested E14.5 pancreas cells were passed through a 35 µm filter to remove undigested pieces and diluted to a concentration of 700 cells/µl in FACS buffer (HBSS containing 1% FBS, pH 7.4). We loaded about 10,000 cells into one channel of the Chromium system. Afterwards, we amplified 11 cycles for cDNA amplification.
We amplified 12 cycles for the cDNA library construction.


title: Ins1Pos_E15.5_2_13


title: Ins1Pos_E15.5_2_12


title: Ins1Pos_E15.5_2_10


title: Ins1Pos_E15.5_2_09


title: Ins1Pos_E15.5_2_08


title: Ins1Pos_E15.5_2_07


title: Ins1Pos_E15.5_2_06


title: Ins1Pos_E15.5_2_02


title: Ins1Pos_E15.5_2_03


title: Ins1Pos_E15.5_2_01


title: Ins1Pos_E15.5_1_10


title: Ins1Pos_E15.5_1_09


title: Ins1Pos_E15.5_1_08


title: Ins1Pos_E15.5_2_04


title: Ins1Pos_E15.5_1_06


title: Ins1Pos_E15.5_1_02


title: Ins1Pos_E15.5_1_03


title: Ins1Pos_E15.5_1_05


title: Ins1Pos_E15.5_1_07


title: Ins1Pos_E15.5_2_11


title: Ins1Pos_E15.5_1_01


title: Ins1Pos_E15.5_1_04


title: GcgPos_E15.5_2_20

value: Gcg-GFP+


title: GcgPos_E15.5_2_19


title: GcgPos_E15.5_2_18


title: GcgPos_E15.5_2_17


title: Ins1Pos_E15.5_2_05


title: sP14+sCBFA2T_strip2

type: RNA

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

country: Japan

institute: Kwansei Gakuin University

description: Gene expression data of mESCs

hyb_protocol: The labelled single-strand cDNA was hybridized to the GeneChiPTM Mouse Gene 2.1 ST Array Strip (Thermo Fisher Scientific).

scan_protocol: The signal intensities of microarray probes were scanned and quantitated using the GeneAtlas Personal Microarray System (Thermo Fisher Scientific).

data_processing: CEL files of Gene ChiP data were normalized using the Robust Multi-array Average program with the default settings in Affymetrix Expression ConsoleTM.

label: biotin

source_name: Prdm14 KO ESCs co-expressing sea urchin PRDM14 and sea urchin CBFA2T

label_protocol: Total RNA was labelled using the GeneChiPTM WT Terminal Labeling and Control Kit (Thermo Fisher Scientific).

growth_protocol: mESCs are cultured in 2i + LIF medium on STO feeder cells.

extract_protocol: Total RNA was purified using the PureLink RNA Mini Kit (Thermo Fisher Scientific).

tag: cell type

value: mESCs


title: GcgPos_E15.5_2_16


title: sea urchin_strip2

description: Gene expression data of mESCs

source_name: Prdm14 KO ESCs expressing sea urchin PRDM14


title: amphioxus_strip1

description: Gene expression data of mESCs

source_name: Prdm14 KO ESCs expressing amphioxus PRDM14


title: mouse_strip2

description: Gene expression data of mESCs

source_name: Prdm14 KO ESCs expressing mouse PRDM14


title: GcgPos_E15.5_2_14


title: empty_strip1

description: Gene expression data of mESCs

source_name: Prdm14 KO ESCs expressing empty vector


title: sea urchin_strip1

description: Gene expression data of mESCs


title: GcgPos_E15.5_2_09


title: GcgPos_E15.5_2_13


title: mouse_strip1

description: Gene expression data of mESCs


title: empty_strip2

description: Gene expression data of mESCs


title: HC_S1_PBMC

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

country: USA

institute: NINDS/NIH

description: HC

data_processing:
RTA 1.13.48 and CASAVA 1.8.2. software used for basecalling and deplexing.
Post deplexing, the .fastq files produced per sample were processed via MiGEC software (https://github.com/mikessh/migec); resulting in a tab deliminated text file of counts per sample describing the expansion of every TCR-β clone detected when the ImmunoGenetics database (IMGT) is used as the reference (http://www.imgt.org/). These counts were then import into the "tcR" and "vdjtools" packages supported in R (https://www.r-project.org/) for repertoire-level analysis.
Genome_build: IMGT
Supplementary_files_format_and_content: Tab-delimited text files containing counts for TCR-β clones detected in each sample sequenced.

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Peripheral mononuclear cells were obtained by Ficoll-Hypaque density gradient centrifugation method (blood collected from 2008 to 2014) and crypreserved in liquid nitrogen until date of use. A total of 2 million PBMCs from each subject were taken to generate a TCR-β library. Total RNA from PBMCs samples was extracted using the RNeasy plus kit (Qiagen, USA) in the presence of carrier poly-RNA, and DNA was digested on-column using DNase I according to the manufacturer’s instruction. cDNA synthesis was performed using the anchored switch 5’rapid amplification of cDNA ends (5’RACE) PCR-based primer combined with a Unique Molecular Identifier (UMI) that consists of 10 random nucleotides sequence (AAGCAGTGGTATCAACGCAGAGTACNNNNNNNNNNUCTTrGrGrGrG). The human TCR V-D-J β-chain region was amplified using a pair of primers (12μM) specific for the TCR constant region (TGCTTCTGATGGCTCAAACACAGCGACCT) and 5’RACE region.
Libraries per sample were prepared using the KAPA Real-time Library Amplification kit (KAPA Biosystems, USA) following 4 PCR steps: 1 cycle at 95° for 5min; 5 cycles at 98° for 15s, 72° for 1min; 5 cycles at 98° for 15s, 70° for 10s, 72° for 1min; 20 cycles at 98° for 15s, 68° for 10s, 72° for 1min. The 1st PCR reaction was stopped when the amplified product ranged between standard 2 and standard 3. Then, the DNA library double-stranded was purified using XS beads clean up assay (Beckman Coulter, USA) and a TCR product of ≈650 bp was obtained using a 2% E-gel SizeSelection electrophoresis system (Invitrogen, USA). During this PCR reaction, a unique index barcode was introduced in the reverse complementary sequence for each subject’s TCR library and also paired-end adaptors ligation for HTS system. In order to increase the concentration of DNA, a 2nd PCR was done using also Kapa real-time library amplification kit, followed by 4 PCR steps: 1 cycle at 95° for 5min; 9 cycles at 98° for 20s, 54° for 30s, 68° for 1min; 7 cycles at 98° for 20s, 68° for 1min, 1 cycle at 72° for 1min. After another clean up step, the size of TCR library was analyzed using Bioanalyzer system (Agilent Technology, USA) and concentration was measured on Qubit Fluorometric Quantitation System (Invitrogen, USA). TCR-β library from each subject was re-quantified using Kapa Library Quantification kit according to the manufacturer’s instruction (Kapa Biosystems, USA) and a final pooled cDNA concentration of 30pmol was obtained for seqeuncing on the Illumina HiSeq 2500 system.

tag: diagnosis

value: HC

tag: technical replicate

value: No

tag: biological replicate

tag: longitudinal replicate

tag: gender

value: M

tag: race

value: African-American

tag: age

value: PBMC


title: Input seq

city: Singapore

first: Reshma

last: Taneja

state: Singapore

address: 2 Medical Drive, MD9, National University of Singapore

department: Department of Physiology

country: Singapore

institute: National University of Singapore

data_processing:
Sequencing reads were mapped to the human reference genome (hg19) using BWA. High quality mapped reads (MAPQ>=10) were retained and potential duplicates were removed using SAMtools. Binding sites were predicted from the libraries using MACS2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Refer to the following website for the file format: https://github.com/taoliu/MACS

source_name: ARMS Lung metastasis 7-year-old female

growth_protocol: Cells were culture in RPMI1640 (Gibco) supplemented with 10% FBS

extract_protocol:
Cells were lysed with Farnham lysis buffer followed by RIPA buffer, Chromatin sheared and DNA was extracted as per manufacturer’s protocol ChIP kit (#17-295, Mercmillipore, Bedford, MA, USA).
30ng ChIPed DNA and corresponding input were used for ChIP-seq library construction (New England Biolabs). Library fragment size was determined using the DNA 1000 Kit on the Agilent Bioanalyzer (Agilent Technologies).
Libraries were pooled in equimolar and cluster generation was performed on the Illumina cBOT system. Sequencing (150bp pair-end) was performed on the Illumina MiSeq according to manufacturer's protocol at the Duke-NUS Genome Biology Facility, Singapore. Sequencing reads were mapped against hg19 and G9a bound regions were identified by MACS2.

treatment_protocol: Cells were treated with protein crosslinker DSG (Di-Succinimidyl Glutarate) followed by chromatin crosslinking with 1% formaldehyde

value: Alveolar rhabdomyosarcoma metastatic cell line

tag: passages

tag: cell line

value: input


title: GcgPos_E15.5_2_12


title: GcgPos_E15.5_2_11


title: GcgPos_E15.5_2_10


title: GcgPos_E15.5_2_15


title: EHMT2_ChIPSeq


title: GcgPos_E15.5_2_08


title: GcgPos_E15.5_2_03


title: GcgPos_E15.5_2_07


title: GcgPos_E15.5_2_04


title: GcgPos_E15.5_2_06


title: GcgPos_E15.5_2_05


title: GcgPos_E15.5_2_02


title: ADR_12

city: Boston

first: Derek

last: Drake

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were aligned to GRCh38 with Ensembl GRCh38.92 gene models using STAR version 2.5.4a with options --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMultimapNmax 20 --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 5000000 --alignMatesGapMax 5000000. Expression levels of genes were quantified as gene counts using STAR version 2.5.4a with option --twopassMode Basic.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file indicates gene counts for each sample

source_name: Parental APOE E4E4 line

growth_protocol: Cerebral organoids were differentiated using an approach adapted from a previously described protocol (Lancaster et al. 2013). 900,000 iPSCs were seeded into a 96-well ultra-low attachment plate (Thermo Fisher) with 15ml of mTeSR (Stemcell Technologies) and 50µM ROCK inhibitor (Santa Cruz), to obtain embryoid bodies (EBs). The EBs were transferred to 500l of neural induction media individually into each well of 24-well ultra-low attachment plates (Thermo Fisher) on Day 6, and another 500µl of neural induction media was added to each well 2 days later. On Day 10, each organoid was placed on parafilm substrate, and 40l of Matrigel (Corning 354234) was used for each organoid. Subsequently, we used 1ml of differentiation media with 10% pencillin streptomycin per well every 2-4 days to passage the organoids, and the 24-well plates with the organoids were placed on an orbital shaker at 90rpm in the incubator.

extract_protocol:
For each biological replicate, 15 organoids were pooled and pelleted at 1000g for 1 minute. The supernatant was removed and the organoids were washed twice in D-PBS without calcium and magnesium, before homogenization in lysis buffer and RNA extraction using the PureLink RNA Mini Kit (Thermo Fisher). Purified RNA was treated with DNase I (Thermo Fisher)
Purified RNA was sent on dry ice to Macrogen for rRNA-depletion using TruSeq Stranded RNA with Ribo-Zero (Human)

value: cerebral organoids

tag: apoe genotype

tag: coriell #


title: ADR_13

source_name: Parental APOE E4E4 line edited to E3E3


title: ADR_14


title: ADR_5


title: ADR_6


title: GcgPos_E15.5_1_15

tag: cell source

tag: embryonic day


title: ADR_11

tag: tissue


title: MS_S34_PBMC

description: MS

value: MS

value: F

value: Caucasian


title: GcgPos_E15.5_2_01


title: MS_S33_PBMC

description: MS


title: MS_S31_PBMC

description: MS


title: MS_S32_PBMC

description: MS


title: MS_S30_CD8

description: MS

value: CD8 T cell


title: GcgPos_E15.5_1_13


title: GcgPos_E15.5_1_16


title: MS_S30_CD4

description: MS

value: CD4 T cell


title: MS_S29_PBMC

description: MS


title: Non-act Jurkat BC2, techn. Rep3

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

country: United Kingdom

institute: King's College London

description: replicate 3

hyb_protocol: Illumina HT12.v4 arrays were hybridized using standard Illumina protocols at 48 C

scan_protocol: Standard Illumina scanning

data_processing: data was quantile normalized within Illumina Genome Studio

source_name: Non-act Jurkat BC2, techn. Rep3

label_protocol: cDNA was labelled  usin NuGen Encore Biotin IL kits

extract_protocol: Genomic DNA and RNA was isolated using Qiagen Allprep. 5pg total RNA was amplified using  NuGen Ovation Pico WTA System V2

treatment_protocol: Cells were unactivated

value: Jurkat cytoplasmic tail 2


title: SAMPLE 3

city: Wuhan

first: Lei

last: Zhang

address: 1095 Jiefang Avenue

institute: Tongji Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using Cubic Spline normalisation

source_name: primary cultured hepatocytes isolated from the livers of aflatoxin B1-treated mice (100mg/kg)

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Ambion Illumina TotalPrep RNA Amplification kit in accordance with the prescribed protocol. Quality control was performed with Polyacrylamide gel electrophoresis.

tag: strain background

value: BALB/c

value: 10 months

tag: Sex

value: male

tag: mouse group

value: aflatoxin B1-treated

value: hepatocytes


title: GcgPos_E15.5_1_14

value: Gcg-GFP+


title: MS_S30_PBMC

description: MS

tag: diagnosis

value: No

tag: cell type


title: SAMPLE 4

source_name: primary cultured oval cells isolated from the livers of aflatoxin B1-treated mice (100mg/kg)

value: hepatic progenitor cells (oval cells)


title: Non-act Jurkat BC2, techn. Rep1

description: replicate 1

source_name: Non-act Jurkat BC2, techn. Rep1


title: SAMPLE 2

source_name: primary cultured oval cells isolated from the livers of healthy mice

value: healthy


title: Non-act Jurkat BC2, techn. Rep2

description: replicate 2

source_name: Non-act Jurkat BC2, techn. Rep2


title: Non-act Jurkat BC1, techn. Rep3

description: replicate 3

source_name: Non-act Jurkat BC1, techn. Rep3

value: Jurkat cytoplasmic tail 1


title: Non-act Jurkat BC1, techn. Rep2

description: replicate 2

source_name: Non-act Jurkat BC1, techn. Rep2


title: Non-act Jurkat BC1, techn. Rep1

description: replicate 1

source_name: Non-act Jurkat BC1, techn. Rep1


title: MS_S28_PBMC

description: MS

tag: technical replicate

tag: biological replicate

value: M

value: PBMC


title: GcgPos_E15.5_1_09

source_name: Pancreas


title: GcgPos_E15.5_1_12


title: control.CM128 W00

city: Minnespolis

first: Irina

last: Vlasova-St. Louis

state: MN

address: 2001 6th St SE

department: Medicine

institute: University of Minnesota

description: control.CM128-C 00_low;yes

hyb_protocol: Standard Illumina hybridization protocol Seven hundred nanograms of labelled cRNA were hybridized overnight to Illumina human-HT-12v4 BeadChip arrays (Illumina Inc. USA), which contained 47,400 hybridization probes

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: peripheral blood

label_protocol: 1ug of total RNA was used to prepare amplified and biotinylated antisense complementary cRNA targets using the Illumina TotalPrep RNA amplification kit (Thermo Fisher Scientific, USA).

extract_protocol: RNA was extracted from whole blood using PAXgene Blood RNA kits (QIAGEN Inc, USA) according to the manufacturer’s protocol. The total RNA yield was determined in a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, USA) and submitted to University of Minnesota Biomedical Genomics facility for quality controls and testing. Total RNA integrity was assessed by Agilent 2100Bioanalyzer (Agilent Technologies, USA). All RNA samples had integrity numbers >6.0 and were determined to be acceptable for analysis.

tag: group

value: control

tag: group description

value: peripheral blood


title: GcgPos_E15.5_1_10


title: MS_S27_PBMC_L3

description: MS

value: MS

tag: longitudinal replicate

value: Yes

tag: gender

value: F

tag: race

value: Caucasian

tag: age


title: GcgPos_E15.5_1_11


title: Non-act Jurkat, techn. rep1

description: replicate 1

source_name: Non-act Jurkat, techn. rep1

tag: cell line

value: Jurkat


title: MS_S27_PBMC_L2

description: MS


title: MS_S27_PBMC_L1

description: MS


title: GcgPos_E15.5_1_06

tag: cell source


title: MS_S26_PBMC

description: MS

value: African-American


title: control.CM128 W12

description: control.CM128-C 12_


title: SAMPLE 1

source_name: primary cultured hepatocytes isolated from the livers of healthy mice

value: BALB/c

value: 10 months

value: male


title: Non-act Jurkat, techn. rep2

description: replicate 2

source_name: Non-act Jurkat, techn. rep2


title: Non-act Jurkat, techn. rep3

description: replicate 3

source_name: Non-act Jurkat, techn. rep3


title: MS_S25_PBMC

description: MS

source_name: PBMC

value: No


title: control.CM115 W12

description: control.CM115-C 12_


title: control.CM123 W12

description: control.CM123-C 12_


title: control.CM115 W00

description: control.CM115-C 00_low;yes


title: control.CM123 W04

description: control.CM123-C 04_


title: MS_S24_PBMC

description: MS


title: control.CM111 W12

description: control.CM111-C 12_


title: control.CM128 W04

description: control.CM128-C 04_


title: control.CM111 W04

description: control.CM111-C 04_


title: GcgPos_E15.5_1_08

value: Gcg-GFP+

tag: embryonic day


title: control.CM115 W04

description: control.CM115-C 04_

tag: tissue


title: GcgPos_E15.5_1_04


title: control.CM123 W00

description: control.CM123-C 00_low;no


title: control.CM111 W00

description: control.CM111-C 00_low;yes


title: control.CM106 W04

description: control.CM106-C 04_


title: GcgPos_E15.5_1_03


title: control.CM100 W12

description: control.CM100-C 12_


title: control.CM106 W00

description: control.CM106-C 00_low;no


title: GcgPos_E15.5_1_05


title: GcgPos_E15.5_1_02


title: MS_S22_PBMC

description: MS


title: MS_S23_PBMC

description: MS


title: GcgPos_E15.5_1_01


title: control.CM106 W12

description: control.CM106-C 12_


title: control.CM100 W04

description: control.CM100-C 04_


title: MS_S20_PBMC

description: MS


title: neonatal-7

first: Edroaldo

last: Lummertz da Rocha

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: sorted neonatal LICs

data_processing:
RNA-seq reads were trimmed for adaptor sequence using Trimmomatic and aligned to mouse genome mm10 using Bowtie/Tophat
Counts were generated using featureCounts
Normalization was performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing gene expression counts

source_name: hematopoietic stem and progenitor cells (HSPCs)

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) per the manufacturer’s protocol.  Purified RNA was subjected to polyA selection using the NEBNext Polyadenylated mRNA Magnetic Isolation Module and subsequently used for library preparation with the NEBNext Ultra RNA Library Prep Kit (both from New England Biolabs). Libraries were analyzed on a Tapestation (Agilent) for quality control, quantified using the Qubit dsDNA HS Assay (Invitrogen) and equimolar pools were sequenced on HiSeq 2500 using 75-bp single-end protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: sorted LICs

value: neonatal


title: neonatal-8

description: sorted neonatal LICs


title: MS_S19_PBMC

description: MS


title: control.CM100 W00

description: control.CM100-C 00_High;yes


title: neonatal-4

description: sorted neonatal LICs


title: adult-4

description: sorted adult LICs

value: adult


title: control.CM098 W04

description: control.CM098-C 04_


title: MS_S21_PBMC

description: MS

value: PBMC


title: MS_S17_PBMC

description: MS


title: MS_S17_CD8

description: MS

value: CD8 T cell


title: control.CM098 W00

description: control.CM098-C 00_low;yes

value: control

value: peripheral blood


title: control.CM098 W12

description: control.CM098-C 12_


title: adult-2

description: sorted adult LICs


title: adult-1

description: sorted adult LICs


title: control.CM097 W00

description: control.CM097-C 00_low;no


title: MS_S17_CD4

description: MS

value: MS

value: CD4 T cell


title: control.CM092 W00

description: control.CM092-C 00_low;yes


title: MS_S16_PBMC

description: MS

value: M

value: Caucasian


title: control.CM092 W04

description: control.CM092-C 04_


title: control.CM092 W12

description: control.CM092-C 12_


title: control.CM089 W12

description: control.CM089-C 12_


title: control.CM089 W04

description: control.CM089-C 04_


title: control.CM087 W04

description: control.CM087-C 04_


title: control.CM084 W12

description: control.CM084-C 12_


title: control.CM089 W00

description: control.CM089-C 00_High;yes


title: control.CM087 W12

description: control.CM087-C 12_


title: control.CM087 W00

description: control.CM087-C 00_High;yes


title: control.CM084 W00

description: control.CM084-C 00_low;yes


title: MS_S15_PBMC

description: MS

value: F


title: control.CM078 W12

description: control.CM078-C 12_


title: control.CM084 W04

description: control.CM084-C 04_


title: MS_S14_PBMC

description: MS


title: control.CM078 W00

description: control.CM078-C 00_low;yes


title: control.CM074 W12

description: control.CM074-C 12_


title: MS_S13_PBMC

description: MS


title: MS_S12_PBMC

description: MS


title: MS_S11_PBMC

description: MS

value: African-American


title: MS_S10_PBMC

description: MS


title: MS_S8_PBMC

description: MS


title: control.CM074 W00

description: control.CM074-C 00_low;no


title: MS_S9_PBMC

description: MS


title: control.CM051 W12

description: control.CM051-C 12_


title: control.CM062 W00

description: control.CM062-C 00_low;yes


title: control.CM059 W00

description: control.CM059-C 00_low;yes


title: MS_S5_PBMC

description: MS


title: control.CM057 W04

description: control.CM057-C 04_


title: control.CM057 W00

description: control.CM057-C 00_low;yes


title: control.CM078 W04

description: control.CM078-C 04_


title: control.CM057 W12

description: control.CM057-C 12_


title: control.CM051 W04

description: control.CM051-C 04_


title: MS_S7_PBMC

description: MS


title: control.CM051 W00

description: control.CM051-C 00_low;no


title: control.CM044 W12

description: control.CM044-C 12_


title: control.CM049 W04

description: control.CM049-C 04_


title: control.CM042 W12

description: control.CM042-C 12_


title: control.CM044 W04

description: control.CM044-C 04_


title: control.CM049 W00

description: control.CM049-C 00_low;no


title: control.CM042 W04

description: control.CM042-C 04_


title: MS_S4_PBMC

description: MS


title: MS_S3_PBMC

description: MS


title: control.CM039 W12

description: control.CM039-C 12_


title: control.CM039 _06

description: control.CM039-C 04_


title: control.CM039 W00

description: control.CM039-C 00_low;yes


title: MS_S1_PBMC

description: MS


title: control.CM044 W00

description: control.CM044-C 00_low;yes


title: control.CM074 W04

description: control.CM074-C 04_


title: control.CM042 W00

description: control.CM042-C 00_low;no


title: HAM_TSP_S14_PBMC

description: HAM/TSP

value: HAM/TSP


title: control.CM059 W04

description: control.CM059-C 04_


title: control.CM059 W12

description: control.CM059-C 12_


title: control.CM049 W12

description: control.CM049-C 12_


title: GcgPos_E15.5_1_07


title: control.CM026 _08

description: control.CM026-C 04_


title: control.CM023 W12

description: control.CM023-C 12_


title: control.CM026 W00

description: control.CM026-C 00_low;yes


title: HAM_TSP_S14_CD8

description: HAM/TSP


title: HAM_TSP_S14_CD4

description: HAM/TSP


title: MS_S2_PBMC

description: MS


title: HAM_TSP_S13_PBMC

description: HAM/TSP

value: Unknown


title: control.CM023 W00

description: control.CM023-C 00_low;yes


title: control.CM026 W12

description: control.CM026-C 12_


title: control.CM020 W12

description: control.CM020-C 12_


title: control.CM023 W04

description: control.CM023-C 04_


title: control.CM020 W00

description: control.CM020-C 00_low;yes


title: control.CM020 W04

description: control.CM020-C 04_


title: MS_S6_PBMC

description: MS

value: No


title: HAM_TSP_S13_CD4

description: HAM/TSP


title: HAM_TSP_S13_CD8

description: HAM/TSP


title: HAM_TSP_S12_PBMC

description: HAM/TSP


title: HAM_TSP_S12_CD8

description: HAM/TSP


title: MS_S18_PBMC

description: MS


title: HAM_TSP_S12_CD4_T3

description: HAM/TSP


title: control.CM011 W00

description: control.CM011-C 00_low;no


title: HAM_TSP_S12_CD4_T1

description: HAM/TSP


title: HAM_TSP_S12_CD4_T2

description: HAM/TSP


title: HAM_TSP_S11_PBMC

description: HAM/TSP


title: CMIRIS.CM133 W02_ND

description: CMIRIS.CM133-iris 03_ND04

value: IRIS

value: earlyIRIS


title: CMIRIS.CM131 W02_ND

description: CMIRIS.CM131-iris 03_ND04


title: control.CM004 W00

description: control.CM004-C 00_low;no


title: HAM_TSP_S11_CD8

description: HAM/TSP


title: control.CM011 W12

description: control.CM011-C 12_


title: CMIRIS.CM132 W03_ND

description: CMIRIS.CM132-iris 03_ND04


title: CMIRIS.CM132 W00_ND

description: CMIRIS.CM132-iris 00_low;no


title: CMIRIS.CM131 W00_ND

description: CMIRIS.CM131-iris 00_low;no


title: CMIRIS.CM133 W12-ND

description: CMIRIS.CM133-iris 12_


title: control.CM011 W04

description: control.CM011-C 04_


title: HAM_TSP_S11_CD4

description: HAM/TSP


title: CMIRIS.CM133 W00_ND

description: CMIRIS.CM133-iris 00_low;no


title: CMIRIS.CM133 W04_ND

description: CMIRIS.CM133-iris 04_


title: CMIRIS.CM117 W18_ND

description: CMIRIS.CM117-iris 16_ND16

value: LateIRIS


title: control.CM004 W04

description: control.CM004-C 04_


title: CMIRIS.CM117 W04_ND

description: CMIRIS.CM117-iris 04_


title: CMIRIS.CM131 W12_ND

description: CMIRIS.CM131-iris 12_


title: CMIRIS.CM116 W00_ND

description: CMIRIS.CM116-iris 00_low;yes


title: CMIRIS.CM112 W02_ND

description: CMIRIS.CM112-iris 03_ND04


title: CMIRIS.CM112 W04_ND

description: CMIRIS.CM112-iris 04_


title: CMIRIS.CM112 W12_ND

description: CMIRIS.CM112-iris 12_


title: CMIRIS.CM117 W00_ND

description: CMIRIS.CM117-iris 00_low;no


title: CMIRIS.CM112 W00_ND

description: CMIRIS.CM112-iris 00_low;no


title: CMIRIS.CM108 W12_ND

description: CMIRIS.CM108-iris 12_


title: CMIRIS.CM117 W12_ND

description: CMIRIS.CM117-iris 12_


title: HAM_TSP_S10_CD4

description: HAM/TSP


title: HAM_TSP_S9_PBMC

description: HAM/TSP


title: CMIRIS.CM108 W04_ND

description: CMIRIS.CM108-iris 03_ND04


title: CMIRIS.CM116 W02_ND

description: CMIRIS.CM116-iris 03_ND04


title: HAM_TSP_S8_PBMC

description: HAM/TSP


title: HAM_TSP_S7_PBMC_T3

description: HAM/TSP

value: Yes


title: HAM_TSP_S7_PBMC_T2

description: HAM/TSP

value: PBMC


title: HAM_TSP_S7_PBMC_T1

description: HAM/TSP


title: HAM_TSP_S6_PBMC_L3

description: HAM/TSP


title: IMR90_0Gy_24h_3_S9_R1

city: Munich

first: Benjamin

last: Becker

address: Neuherbergstr. 11

department: Genomics II

country: Germany

institute: Bundeswehr Institute for Radiobiology

description:
sham control
hme_diff_RNASeq_2Gy_24h

data_processing:
For differential gene expression analysis we followed the workflow described by Love et al.. In brief, sequence reads were aligned to the human transcriptome (Homo_sapiens.GRCh37.67) with Salmon (version 0.8.1) and counted by means of a python script provided within the RSeqQC package . Resulting data was summarized into matrices using tximport (version 1.4.0) and analyzed for differential gene expression using the default settings of DESeq2 (version 1.16.1). Genes were assumed to be differentially expressed with log2 fold changes of FPKM ratios > 1 (fragments per kilobase per million mapped fragments) and FDR £ 0.1. Results were exported with DESeq2 and the R package “reporting tools” (version 2.1.16.0) .
Results were exported from R to Microsoft Excel and sorted in accordance to their fold changes and significance
Genome_build: hg19
Supplementary_files_format_and_content: xlsx-File, Results table from DESeq2 with gene-symbols

source_name: Human Caucasian fetal lung fibroblast

growth_protocol: Primary human lung fibroblasts (IMR-90, adherent cells) were obtained from Corriell Institute for medical Research (Camden, New Jersey, USA). Cells were cultivated at 37°C / 5% CO2 in RPMI-1640 2mM L-glutamine and Eagle´s Minimum Essential Medium, respectively.

extract_protocol:
RNA isolation was performed with the RNeasy Mini kit (Qiagen, RNeasy Mini Handbook 06/2012) following the manufacturer’s protocol.
RNA Seq library preparation was performed with Illumina TruSeq® Stranded mRNA Sample Preparation Kit (Cat.-No. RS-122-9004DOC, Part # 15031047 Rev. E, 10/13, Index Primers Set 1). Library fragment length was determined with Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and concentration was measured with a Qubit 3.0 Fluorometer (Thermo Scientific, Waltham, MA, USA). Libraries were sequenced with 2 x 75 bp paired end reads following the protocols for the NextSeq500 sequencing platform (NextSeq 500 High Output Kit 2x75bp; NextSeq System Guide; NextSeq Denature and Dilute Libraries Guide; Illumina, San Diego, CA, USA, Document # 15048776 v02, Document # 15046563 v02).

treatment_protocol: For each time-point and dose 10 million cells were irradiated with an x-ray beam at room temperature with 240 kV tube current (YXLON Maxishot; Hamburg, Germany) filtered with 3 mm beryllium. Absorbed dose was measured with a PTW Unidos dosimeter (PTW Freiburg GmbH, Germany). Dose rate was 1 Gy/min at 13 mA. No fresh medium was added to cells after irradiation.

tag: time point (h)

tag: dose x-ray (gy)


title: IMR90_0Gy_24h_2_S8_R1

description:
sham control
hme_diff_RNASeq_2Gy_24h


title: CMIRIS.CM075 W00_ND

description: CMIRIS.CM075-iris 00_low;yes


title: CMIRIS.CM075 W12_ND

description: CMIRIS.CM075-iris 12_


title: CMIRIS.CM070 W04_ND

description: CMIRIS.CM070-iris 03_ND04


title: CMIRIS.CM104 W00_ND

description: CMIRIS.CM104-iris 00_low;no


title: CMIRIS.CM101 W00_ND

description: CMIRIS.CM101-iris 00_low;no


title: CMIRIS.CM075 W04_ND

description: CMIRIS.CM075-iris 03_ND04


title: HAM_TSP_S6_PBMC_L2

description: HAM/TSP


title: CMIRIS.CM101 W04_ND

description: CMIRIS.CM101-iris 04_


title: CMIRIS.CM104 W03_ND

description: CMIRIS.CM104-iris 03_ND04


title: CMIRIS.CM070 W12_ND

description: CMIRIS.CM070-iris 12_


title: CMIRIS.CM058 W22_ND

description: CMIRIS.CM058-iris 16_ND16


title: HAM_TSP_S10_CD8

description: HAM/TSP

value: CD8 T cell


title: CMIRIS.CM108 W00_ND

description: CMIRIS.CM108-iris 00_low;no


title: CMIRIS.CM101 W03_ND

description: CMIRIS.CM101-iris 03_ND04


title: CMIRIS.CM063 W00_ND

description: CMIRIS.CM063-iris 00_low;yes


title: CMIRIS.CM063 W04_ND

description: CMIRIS.CM063-iris 03_ND04


title: CMIRIS.CM070 W00_ND

description: CMIRIS.CM070-iris 00_low;no


title: CMIRIS.CM058 W12_ND

description: CMIRIS.CM058-iris 12_


title: CMIRIS.CM054 W15_ND

description: CMIRIS.CM054-iris 16_ND16


title: CMIRIS.CM054 W12_ND

description: CMIRIS.CM054-iris 12_


title: CMIRIS.CM058 W00_ND

description: CMIRIS.CM058-iris 00_low;no


title: CMIRIS.CM058 W04_ND

description: CMIRIS.CM058-iris 04_


title: HAM_TSP_S10_PBMC

description: HAM/TSP


title: HAM_TSP_S6_PBMC_L1

description: HAM/TSP


title: HAM_TSP_S4_PBMC

description: HAM/TSP


title: IMR90_2Gy_24h_3_S12_R1

description:
treatment
hme_diff_RNASeq_2Gy_24h


title: IMR90_0Gy_6h_1_S1_R1

description:
sham control
hme_RNASeq_2Gy_Vs_0Gy_6h


title: IMR90_0Gy_6h_3_S3_R1

description:
sham control
hme_RNASeq_2Gy_Vs_0Gy_6h


title: HAM_TSP_S3_PBMC_L2

description: HAM/TSP


title: HAM_TSP_S3_PBMC_L1

description: HAM/TSP


title: HAM_TSP_S3_PBMC_L3

description: HAM/TSP


title: HAM_TSP_S5_PBMC

description: HAM/TSP


title: IMR90_0Gy_24h_1_S7_R1

description:
sham control
hme_diff_RNASeq_2Gy_24h


title: HAM_TSP_S2_PBMC

description: HAM/TSP


title: IMR90_0Gy_6h_2_S2_R1

description:
sham control
hme_RNASeq_2Gy_Vs_0Gy_6h


title: IMR90_2Gy_24h_2_S11_R1

description:
treatment
hme_diff_RNASeq_2Gy_24h


title: IMR90_2Gy_24h_1_S10_R1

description:
treatment
hme_diff_RNASeq_2Gy_24h


title: IMR90_2Gy_6h_3_S6_R1

description:
treatment
hme_RNASeq_2Gy_Vs_0Gy_6h


title: HAM_TSP_S1_PBMC

description: HAM/TSP


title: CMIRIS.CM052 W00_ND

description: CMIRIS.CM052-iris 00_High;yes


title: CMIRIS.CM053 W04_ND

description: CMIRIS.CM053-iris 03_ND04


title: CMIRIS.CM052 W12_ND

description: CMIRIS.CM052-iris 12_


title: CMIRIS.CM053 W00_ND

description: CMIRIS.CM053-iris 00_low;yes


title: CMIRIS.CM054 W04_ND

description: CMIRIS.CM054-iris 04_


title: HC_S20_PBMC

description: HC

value: HC


title: IMR90_2Gy_6h_2_S5_R1

description:
treatment
hme_RNASeq_2Gy_Vs_0Gy_6h


title: CMIRIS.CM052 W22_ND

description: CMIRIS.CM052-iris 16_ND16

value: peripheral blood


title: CMIRIS.CM050 W04_ND

description: CMIRIS.CM050-iris 04_


title: CMIRIS.CM054 W00_ND

description: CMIRIS.CM054-iris 00_low;no


title: HC_S20_CD8

description: HC


title: CMIRIS.CM053 W12_ND

description: CMIRIS.CM053-iris 12_


title: CMIRIS.CM048 W01_ND

description: CMIRIS.CM048-iris 03_ND04


title: CMIRIS.CM050 W12_ND

description: CMIRIS.CM050-iris 12_


title: CMIRIS.CM052 W04_ND

description: CMIRIS.CM052-iris 04_


title: IMR90_2Gy_6h_1_S4_R1

description:
treatment
hme_RNASeq_2Gy_Vs_0Gy_6h


title: HC_S20_CD4

description: HC


title: CMIRIS.CM050 W13_ND

description: CMIRIS.CM050-iris 16_ND16


title: CMIRIS.CM050 W00_ND

description: CMIRIS.CM050-iris 00_low;no


title: CMIRIS.CM048 W04_ND

description: CMIRIS.CM048-iris 04_


title: 2Gy_120h_P18_S5

description:
treatment data
annotation_hme_diff_2Gy_120h.txt

data_processing:
FastQ files were aligned to reference genome hg19 (human_g1k_v37.fasta) using BWA MEM (version 0.7.15) and the resulting .bam files were indexed with samtools (version 1.5). Reads not matching quality criteria (QC score 30) were excluded from further analysis with samtools before sorting.
Peak calling was performed using MACS2 default settings for paired end reads following the workflow of Zhang et al.. Resulting .narrowpeak files were annotated and analyzed with ChIPseeker using R (version 3.4.2).
Differential peak calling between samples were assessed using the bdgdiff command in MACS2. Resulting peak files were further analyzed and annotated with ChIPseeker.
Genome_build: hg19
Supplementary_files_format_and_content: txt file, annotated hydroxymethylated regions identified by differential peak calling with macs2, annotation performed with r package chipseeker

extract_protocol:
DNA was isolated from cell pellets using a phenol-free approach (Qiagen Genomic DNA Isolation Kit Mini for Blood and Tissue, Version 04/12).
DNA was randomly sheared using the Covaris M220 according to the manufacturers’ protocol (Covaris protocol truChIP™ Chromatin Shearing Reagent Kit, PN 010179, Rev C 15 August 2013). Sequencing libraries were prepared with the IDeal Library preparation kit (Diagenode, including Primer Set 1, Version 1 / 11_14, Cat. No. C05010020) and hydroxymethylated DNA was selected using hMeDIP kit (Diagenode, monoclonal mouse antibody, Version 2 09.10, Cat. No. C02010031). 5-hmC monoclonal antibody was used for specific selection of hydroxymethylated DNA and washed using IPure kit (Diagneode, Version 2 I 07.15, Cat. No.C03010015). For library amplification we run 12 PCR-cycles in accordance to the manufacturers protocol.
hydroxymethylation-Seq


title: 2Gy_120h_P15_S5


title: HC_S19_CD8

description: HC


title: HC_S19_CD4

description: HC


title: HC_S19_PBMC

description: HC


title: CMIRIS.CM037 W10_ND

description: CMIRIS.CM037-iris 03_ND04


title: CMIRIS.CM034 W12_ND

description: CMIRIS.CM034-iris 12_


title: CMIRIS.CM048 W00_ND

description: CMIRIS.CM048-iris 00_High;yes


title: CMIRIS.CM037 W00_ND

description: CMIRIS.CM037-iris 00_low;no


title: 2Gy_24h_P15_S4

description:
treatment data
annotation_hme_diff_2Gy_24h.txt


title: HC_S18_CD8

description: HC


title: CMIRIS.CM037 W12_ND

description: CMIRIS.CM037-iris 12_


title: CMIRIS.CM034 W07_ND

description: CMIRIS.CM034-iris 03_ND04


title: HC_S18_CD4

description: HC


title: CMIRIS.CM032 W02_ND

description: CMIRIS.CM032-iris 03_ND04


title: CMIRIS.CM032 W00_ND

description: CMIRIS.CM032-iris 00_low;no


title: CMIRIS.CM031 W12_ND

description: CMIRIS.CM031-iris 12_


title: CMIRIS.CM034 W00_ND

description: CMIRIS.CM034-iris 00_low;no


title: 2Gy_1h_P18_S2

description:
treatment data
annotation_hme_diff_2Gy_1h.txt


title: 2Gy_6h_P15_S3

description:
treatment data
annotation_hme_diff_2Gy_6h.txt


title: HC_S17_PBMC

description: HC


title: 2Gy_24h_P18_S4


title: 2Gy_6h_P18_S3


title: HC_S18_PBMC

description: HC


title: CMIRIS.CM030 W16_ND

description: CMIRIS.CM030-iris 16_ND16


title: CMIRIS.CM030 W12_ND

description: CMIRIS.CM030-iris 12_


title: HC_S17_CD8

description: HC


title: CMIRIS.CM032 W04_ND

description: CMIRIS.CM032-iris 04_


title: CMIRIS.CM031 W00_ND

description: CMIRIS.CM031-iris 00_low;no


title: CMIRIS.CM029 W12_ND

description: CMIRIS.CM029-iris 12_


title: 05Gy_120h_P15_S8

description:
treatment data
annotation_hme_diff_05Gy_120h.txt


title: CMIRIS.CM030 W00_ND

description: CMIRIS.CM030-iris 00_low;yes


title: CMIRIS.CM031 W04_ND

description: CMIRIS.CM031-iris 03_ND04


title: CMIRIS.CM030 W04_ND

description: CMIRIS.CM030-iris 04_


title: HC_S17_CD4

description: HC


title: HC_S16_PBMC

description: HC


title: 2Gy_1h_P15_S2


title: 05Gy_24h_P14_S15

description:
treatment data
annotation_hme_diff_05Gy_24h.txt


title: HC_S16_CD8

description: HC


title: 05Gy_24h_P15_S7


title: 05Gy_120h_P14_S16


title: CMIRIS.CM029 W02_ND

description: CMIRIS.CM029-iris 03_ND04


title: HC_S16_CD4

description: HC


title: CMIRIS.CM019 W04_ND

description: CMIRIS.CM019-iris 03_ND04


title: 05Gy_6h_P15_S6

description:
treatment data
annotation_hme_diff_05Gy_6h.txt


title: CMIRIS.CM019 W00_ND

description: CMIRIS.CM019-iris 00_low;no


title: CMIRIS.CM029 W04_ND

description: CMIRIS.CM029-iris 04_


title: 05Gy_6h_P14_S14


title: seCLIP GG Ago2 SM_input

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University

data_processing:
Library strategy: seCLIP
seCLIP libraries were analyzed by Illumina HiSeq 2000.
Identification of seCLIP clusters enriched against size-matched input (SMinput) were performed as previously described (Van Nostrand, E. L. et al., Nature methods 13, 508-514, (2016)). First, obtained sequences were processed for adaptor removal, and reads mapping to the repetitive elements were removed. Remaining reads were aligned to the mm9 reference genome assembly using STAR (v2.5.1b), and seCLIP clusters for IP samples were identified using CLIPper peak calling algorithm (https://github.com/yeolab/eclip) with the following parameters: --bonferrroni --superlocal --threshold binomial (Lovci, M. T. et al. Nat Struct Mol Biol 20, 1434-1442 (2013)). Finally, peak normalization vs SMinput was performed, and enriched seCLIP clusters were extracted.
Genome_build: mm9
Supplementary_files_format_and_content: Summary txt file includes the information of enriched seCLIP clusters above SM_input, including chromosome, start, end, log10(p-value seCLIP vs SMInput), log2(fold-enrichment in seCLIP vs SMInput), and strand.

source_name: primary chondrocytes

growth_protocol: Mouse primary rib chondrocytes were isolated from the frontal part of the lib cage of 7 day-old mice and cultured in standard culture conditions.

extract_protocol:
Mouse primary rib chondrocytes were UV-crosslinked and harvested.
seCLIP were performed in mouse wild-type and mutant primary chondrocytes using Ago2 and Ybx1 antibodies, as previously described (Van Nostrand, E. L. et al., Nature methods 13, 508-514, (2016)., Van Nostrand, E. L. et al. Methods Mol Biol 1648, 177-200, (2017).). Anti-Ago2 antibody (2D4), and anti-Ybx1 antibody (D2A11, #9744S) were from Wako and Cell Signaling Technology, respectively.

value: chondrocytes

tag: genotype and drug

value: miR-140 G/G

tag: chip antibody


title: HC_S15_PBMC

description: HC

tag: diagnosis

tag: cell type


title: HC_S14_PBMC

description: HC

tag: technical replicate

tag: biological replicate


title: HC_S13_PBMC

description: HC

value: M


title: 05Gy_1h_P15_S5

description:
treatment data
annotation_hme_diff_05Gy_1h.txt


title: CMIRIS.CM009 W00_ND

description: CMIRIS.CM009-iris 00_low;no

tag: group

tag: group description


title: CMIRIS.CM009 W02_ND

description: CMIRIS.CM009-iris 03_ND04


title: CMIRIS.CM009 W12_ND

description: CMIRIS.CM009-iris 12_


title: CMIRIS.CM009 W04_ND

description: CMIRIS.CM009-iris 04_


title: CMIRIS.CM029 W00_ND

description: CMIRIS.CM029-iris 00_High;yes


title: 05Gy_1h_P14_S13


title: CMIRIS.CM001 W04_ND

description: CMIRIS.CM001-iris 04_


title: 0Gy_120h_P15_S4

description:
sham control
annotation_hme_diff_0Gy_120h_2GyExp.txt


title: HC_S11_PBMC

description: HC

tag: longitudinal replicate

tag: gender

value: Caucasian


title: 0Gy_24h_P15_S3

description:
sham control
annotation_hme_diff_0Gy_24h_2GyExp.txt


title: 0Gy_120h_P14_S12

description:
sham control
annotation_hme_diff_0Gy_120h_05GyExp.txt


title: HC_S10_PBMC

description: HC

tag: race

tag: age


title: HC_S12_PBMC

description: HC

value: F


title: 0Gy_24h_P14_S11

description:
sham control
annotation_hme_diff_0Gy_24h_05GyExp.txt

tag: cell line


title: seCLIP WT Ago2 SM_input

value: miR-140 WT


title: HC_S9_PBMC_L3

description: HC


title: HC_S9_PBMC_L2

description: HC


title: seCLIP GG Ybx1 SM_input


title: CMIRIS.CM001 W00_ND

description: CMIRIS.CM001-iris 00_low;no


title: 0Gy_6h_P15_S2

description:
sham control
annotation_hme_diff_0Gy_6h_2GyExp.txt


title: 0Gy_6h_P14_S10

description:
sham control
annotation_hme_diff_0Gy_6h_05GyExp.txt


title: 0Gy_1h_P15_S1

description:
sham control
annotation_hme_diff_0Gy_1h_2GyExp.txt


title: CMIRIS.CM001 W02_ND

description: CMIRIS.CM001-iris 03_ND04


title: seCLIP WT Ybx1 SM_input


title: HC_S8_PBMC

description: HC


title: 0Gy_1h_P14_S9

description:
sham control
annotation_hme_diff_0Gy_1h_05GyExp.txt


title: HC_S9_PBMC_L1

description: HC


title: HC_S7_PBMC

description: HC

value: African-American


title: HC_S6_PBMC

description: HC


title: 0Gy_120h_INP_P18_S11

description:
Input data
used for all processed files


title: 0Gy_120h_INP_P15_S11

description:
Input data
used for all processed files


title: 0Gy_0h_INP_P18_S10

description:
Input data
used for all processed files


title: 0Gy_0h_INP_P15_S10

description:
Input data
used for all processed files


title: HC_S4_PBMC

description: HC


title: HC_S5_PBMC

description: HC


title: HC_S3_PBMC_L3

description: HC


title: HC_S3_PBMC_L1

description: HC


title: HC_S2_PBMC

description: HC


title: HC_S3_PBMC_L2

description: HC


title: p53+/+_no-dox_0h

city: Tokyo

first: Koichi

last: Matsuda

address: 4-6-1, Shirokanedai, Minato-ku

institute: The University of Tokyo

description: Gene expression in non-treated wild-type p53 cells

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction containing Agilent Fragmentation Buffer and Gene Expression Blocking Agent following the manufacturers instructions. Hi-RPM Hybridization Buffer was added to stop the fragmentation. Samples were hybridized to SurePrint G3 Human Gene Expression 8x60K Microarrays for 17 hours at 65°C with rotation. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 and 1 minute with 37°C pre-warmed Gene Expression Wash Buffer 2.

scan_protocol: Slides were scanned on the Agilent Microarray Scanner using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, 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 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: HCT116 p53+/+, control, 0 h.

label_protocol: The fluorescent cRNA using cyanine 3-labelled (Cy3) targets was generated following the Agilent’s One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp labeling) protocol. The Cy3-labeled cRNA was purified by Rneasy Mini Kit (Qiagen) and quantified by Nanodrop-2000 Spectrophotometer.

extract_protocol: Total RNA was isolated from the cells using RNeasy Plus Universal Mini Kits (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: HCT116 p53+/+ and HCT116 p53−/− cells were treated with 2 μg/mL of doxorubicin for 2 hours. The cultures were incubated for 0, 12, 24, or 48 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: genotype

tag: treatment

value: no

tag: time to harvest

value: 0 hour


title: p53+/+_dox_12h

description: Gene expression after 12h in doxorubicin-treated wild-type p53 cells

source_name: HCT116 p53+/+, doxorubicin, 12 h.

value: doxorubicin

value: 12 hours


title: p53-/-_dox_12h

description: Gene expression after 12h in doxorubicin-treated p53-null cells

source_name: HCT116 p53−/− , doxorubicin, 12 h.


title: p53+/+_dox_24h

description: Gene expression after 24h in doxorubicin-treated wild-type p53 cells

source_name: HCT116 p53+/+, doxorubicin, 24 h.

value: 24 hours


title: p53-/-_dox_24h

description: Gene expression after 24h in doxorubicin-treated p53-null cells

source_name: HCT116 p53−/− , doxorubicin, 24 h.


title: NP_SAD3.1

description: Gene expression data from SAD3.1 NPs

hyb_protocol: Hybridizations were performed in the Genechip hybridization oven 640 (60 rpm) for 16 hrs at 45ºC on U133 Plus 2.0 arrays. The probe arrays were then washed, stained in the GeneChip Fluidics Station 400 operated by GeneChip software following the appropriate fluidics protocols.

scan_protocol: Arrays were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The scanned digital intensity values were stored as image data files (*.dat) and then converted into cell intensity files (*.cel) using Affymetrix Microarray Suite 5.0.

source_name: neural progenitor cells, sporadic Alzheimer's disease

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

growth_protocol: NPs were grown to 80-95% confluency on polyornithine and laminin in medium containing Neurobasal medium with 1x B-27 without vitamin A, 1 mM L-glutamine, 10 ng/ml bFGF, 10 ng/ml LIF, 50 U/ml penicillin, and 50 mg/ml streptomycin.

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were directly harvested.

value: neural progenitor cells

tag: subject

value: sporadic Alzheimer's disease

tag: clone

value: Clone 1

tag: coriell #


title: FSGS_Tub_7

city: Nanjing

first: Hao

last: Bao

state: Jiangsu

address: 305 East Zhong Shan Road

department: National Clinical Research Center of Kidney Diseases, Jinling Hospital

institute: Nanjing university

description: expression value derived from Expression Console software

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing: Raw data were processed with Expression Console software (Affymetrix) for background correction and normalization.

source_name: FSGS

label_protocol: Total RNA was amplified, labeled and purified by Ovation® Pico WTA System V2(Cat#3302, NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200, NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Tissues were kept in RNAlater at 4°C.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Microdissection of tubulointerstitial tissues was performed manually under a stereomicroscope using two dissection needle holders in RNAlater at 4°C.

tag: tissue

value: renal tubulointerstitial tissue

tag: disease state

value: FSGS


title: FSGS_Tub_6


title: FSGS_Tub_8


title: p53-/-_no-dox_0h

description: Gene expression in non-treated p53-null cells

source_name: HCT116 p53−/−, control, 0 h.


title: NP_SAD5.1

description: Gene expression data from SAD5.1 NPs

tag: cell type

tag: diagnosis


title: p53-/-_dox_48h

description: Gene expression after 48h in doxorubicin-treated p53-null cells

source_name: HCT116 p53−/− , doxorubicin, 48 h.

value: 48 hours


title: Control_Tub_8

source_name: Control

value: Control


title: NP_NL1.1

description: Gene expression data from NL1.1 NPs

source_name: neural progenitor cells, normal

value: normal


title: NP_SAD4.1

description: Gene expression data from SAD4.1 NPs


title: Neuron_SAD5.1

description: Gene expression data from SAD5.1 neurons

source_name: neurons, sporadic Alzheimer's disease

growth_protocol: Neurons were grown for 6 weeks on polyornithine and laminin in medium containing Neurobasal medium with 1x B-27, 1 mM L-glutamine, 50 U/ml penicillin, and 50 mg/ml streptomycin.

value: neurons


title: NP_NL6.1

description: Gene expression data from NL6.1 NPs


title: FSGS_Tub_5


title: FSGS_Tub_2


title: p53+/+_dox_48h

description: Gene expression after 48h in doxorubicin-treated wild-type p53 cells

source_name: HCT116 p53+/+, doxorubicin, 48 h.


title: Control_Tub_7


title: NP_NL2.1

description: Gene expression data from NL2.1 NPs


title: NP_SAD2.1

description: Gene expression data from SAD2.1 NPs


title: NP_SAD1.1

description: Gene expression data from SAD1.1 NPs


title: NP_NL3.1

description: Gene expression data from NL3.1 NPs


title: NP_NL4.1

description: Gene expression data from NL4.1 NPs


title: FSGS_Tub_3


title: FSGS_Tub_1


title: FSGS_Tub_4


title: Control_Tub_6


title: Control_Tub_5


title: Neuron_NL4.1

description: Gene expression data from NL4.1 neurons

source_name: neurons, normal


title: Neuron_SAD3.1

description: Gene expression data from SAD3.1 neurons


title: Control_Tub_4


title: Neuron_SAD2.1

description: Gene expression data from SAD2.1 neurons


title: Neuron_NL5.2

description: Gene expression data from NL5.2 neurons

value: Clone 2


title: iPSC_SAD5.1

description: Gene expression data from SAD5.1 iPSCs

source_name: induced pluripotent stem cells, sporadic Alzheimer's disease

growth_protocol: iPSCs were grown on inactivated mouse embryonic fibroblasts (iMEFs) in medium containing DMEM/F-12 medium with 20% knockout serum, 10 ng/ml bFGF, 1 mM L-glutamine, 100 µM non-essential amino acids, 100 µM 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin.

treatment_protocol: iPSCs were manually dissected to separate from iMEFs.

value: induced pluripotent stem cells


title: G. oxydans, 4hr, Furfural, replicate 2

city: Shanghai

first: Jie

address: 130 Meilong Road

institute: East China University of Science and Technology

description:
258001210003_1_1
Gene expression with furfural treatment
151581A&150948A_F2

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner (G2565CA) with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing:
Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software V13 (Agilent) was used to calculate the difference of gene expression and statistical significance p value
The normalized value of 75 percentile was calculated (log2).  Note: Normalization is done using the Percentile75 method (the ratio is obtained by dividing the 75 bits value of the data expressed by each chip itself), and then the value generated after the logarithm of the log2 is taken.

organism: Gluconobacter oxydans

source_name: G. oxydans, 4hr, Furfural

label_protocol: Cyanine-3 (Cy3) (GE Healthcare Cat. No. PA53021) labeled cRNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.

growth_protocol: G. oxydans was cultured in a 3 L bioreactor (Baoxing Biotech Co., Shanghai, China) containing one liter seed medium (80 g of sorbitol, 20 g of yeast extract, 0.5 g of MgSO4·7H2O, 1.5 g of KH2PO4, 1.5 g of (NH4)2SO4 per liter of deionized water) at 30 ºC, pH 5.5, 2.5 vvm and 500 rpm to OD₆₀₀ reached 5.0. Then the seed broth was inoculated at 10% (v/v) ratio into 250 mL flask containing 45 mL synthetic fermentation medium (80 g of glucose, 20 g of yeast extract, 0.5 g of MgSO4·7H2O, 1.5 g of KH2PO4, 1.5 g of (NH4)2SO4 per liter of deionized water) with the addition of 1.2 g/L furfural, 1.5 g/L of HMF, 0.8 g/L of HBA, 0.9 g/L of syringaldehyde or 0.8 g/L of vanillin, respectively at 30 ºC, 220 rpm.

extract_protocol: RNA was prepared using the Trizol (Invitrogen, Gaithersburg, MD, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The cells were harvested at 4 h by centrifugation at 10,000 rpm, 4 oC for 10 min, then quenched by liquid nitrogen and stored at -80 oC freezer for RNA extraction.

tag: strain

tag: agent

value: Furfural


title: Neuron_NL3.1

description: Gene expression data from NL3.1 neurons


title: Control_Tub_3


title: Control_Tub_2


title: G. oxydans, 4hr, Furfural, replicate 1

description:
258001210002_2_4
Gene expression with furfural treatment
151581A&150948A_F1


title: iPSC_SAD4.1

description: Gene expression data from SAD4.1 iPSCs


title: G. oxydans, 4hr, Furfural, replicate 3

description:
258001210003_1_2
Gene expression with furfural treatment
151581A&150948A_F3


title: Neuron_NL2.1

description: Gene expression data from NL2.1 neurons


title: Neuron_NL1.1

description: Gene expression data from NL1.1 neurons


title: Neuron_NL6.1

description: Gene expression data from NL6.1 neurons


title: G. oxydans, 4hr, HMF, replicate 3

description:
258001210002_2_3
Gene expression with HMF treatment
151581A&150948A_HMF3

source_name: G. oxydans, 4hr, HMF

value: HMF


title: G. oxydans, 4hr, HMF, replicate 2

description:
258001210002_2_2
Gene expression with HMF treatment
151581A&150948A_HMF2


title: iPSC_SAD2.1

description: Gene expression data from SAD2.1 iPSCs


title: iPSC_NL4.1

description: Gene expression data from NL4.1 iPSCs

source_name: induced pluripotent stem cells, normal


title: iPSC_NL6.1

description: Gene expression data from NL6.1 iPSCs


title: iPSC_SAD3.1

description: Gene expression data from SAD3.1 iPSCs


title: iPSC_NL3.1

description: Gene expression data from NL3.1 iPSCs


title: iPSC_NL2.1

description: Gene expression data from NL2.1 iPSCs


title: iPSC_NL5.1

description: Gene expression data from NL5.1 iPSCs


title: G. oxydans, 4hr, HMF, replicate 1

description:
258001210002_2_1
Gene expression with HMF treatment
151581A&150948A_HMF1


title: Control_Tub_1


title: iPSC_NL1.1

description: Gene expression data from NL1.1 iPSCs


title: clf_K27 input

status: Public on Jan 28 2019

first: YUHAI

last: CUI

state: ON

address: 1391 Sandford Street

department: London Research and Development Centre

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using Bowtie2
Mapped reads were filted by removing PCR duplications and unmapped reads
unique mapped reads were converted to bed file by bedtools2
BigWig file for each replicates was genearted using MACS2 with 100 bp extended reads
Reads were mapped to genome using TopHat v2.0.4 with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 4000 bp were used. Calculations to identify differentially expressed genes were carried out as described (Trapnell et al., 2012)
Genome_build: TAIR10
Supplementary_files_format_and_content: WIG, bigwig, txt

organism: Arabidopsis thaliana

source_name: clf K27

growth_protocol: Arabidopsis seedlings were growth on 1/2 MS plates for 10 days under 16h light/ 8h dark condition, the somatic embyos were  growth on 1/2 MS plates for 30 days under 16h light/ 8h dark condition.

extract_protocol:
Lysates were clarified from sonicated nuclei and the associated complexes were isolated with antibodies.
5 ng of ChIP DNA immuoprecipitated by corresponding antibodies was used for ChIP-seq library construction.

value: seedlings

tag: developmental

value: 10 days

tag: antibody


title: G. oxydans, 4hr, Vanillin, replicate 3

description:
258001210002_1_1
Gene expression with vanillin treatment
151581A&150948A_V3

source_name: G. oxydans, 4hr, Vanillin

value: Vanillin


title: G. oxydans, 4hr, Vanillin, replicate 2

description:
258001210001_2_4
Gene expression with vanillin treatment
151581A&150948A_V2


title: G. oxydans, 4hr, 4-Hydroxybenaldehyde, replicate 2

description:
258001210002_1_3
Gene expression with 4-hydroxybenaldehyde treatment
151581A&150948A_4H2

source_name: G. oxydans, 4hr, 4-Hydroxybenaldehyde


title: G. oxydans, 4hr, Vanillin, replicate 1

description:
258001210001_2_3
Gene expression with vanillin treatment
151581A&150948A_V1


title: G. oxydans, 4hr, 4-Hydroxybenaldehyde, replicate 3

description:
258001210002_1_4
Gene expression with 4-hydroxybenaldehyde treatment
151581A&150948A_4H3


title: G. oxydans, 4hr, Syringaldehyde, replicate 1

description:
258001210001_1_4
Gene expression with syringaldehyde treatment
151581A&150948A_S1

source_name: G. oxydans, 4hr, Syringaldehyde

value: Syringaldehyde


title: G. oxydans, 4hr, 4-Hydroxybenaldehyde, replicate 1

description:
258001210002_1_2
Gene expression with 4-hydroxybenaldehyde treatment
151581A&150948A_4H1


title: swn_K27 rep1

source_name: swn K27


title: clf swn_K27 rep1

source_name: clf

value: somatic embryo

value: 30 days


title: clf swn_K27 rep2


title: clf_K27 rep2


title: clf_K27 rep1


title: clf swn_K27 input


title: 35S_GFP (input)

source_name: 35S GFP

value: anti-GFP


title: WT_K27 input

source_name: WT K27

value: Col-0 (wild type)


title: G. oxydans, 4hr, 0 aldehyde, replicate 3

description:
258001210001_1_3
Gene expression without treatment
151581A&150948A_C3

source_name: G. oxydans, 4hr, 0 aldehyde

value: control (0 aldehyde)


title: G. oxydans, 4hr, Syringaldehyde, replicate 3

description:
258001210001_2_2
Gene expression with syringaldehyde treatment
151581A&150948A_S3


title: G. oxydans, 4hr, 0 aldehyde, replicate 2

description:
258001210001_1_2
Gene expression without treatment
151581A&150948A_C2


title: SWN-GFP Rep2

source_name: SWN-GFP


title: G. oxydans, 4hr, 0 aldehyde, replicate 1

description:
258001210001_1_1
Gene expression without treatment
151581A&150948A_C1


title: G. oxydans, 4hr, Syringaldehyde, replicate 2

description:
258001210001_2_1
Gene expression with syringaldehyde treatment
151581A&150948A_S2


title: swn_K27 rep2


title: swn_K27 input


title: SWN-GFP Rep1


title: WT_K27 rep2


title: WT_K27 rep1


title: H9KC

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drive, CCSR 2145c

department: Dermatology

institute: Stanford University

description: hESC_lineH9_Differentiation_mature keratinocyte (KC)

data_processing:
Alignment was called using tophat. FPKM values were called using cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file. FPKM values

source_name: mature ketatinocyte from hESC-epidermal differentiation

growth_protocol: In vitro differentiation of hESC into keratinocyte :H9 hESCs were passed on to Matrigel coated plate and maintained in Essential 8 media. To induce differentiation into keratinocyte, the cells were first fed with “differentiation medium 1” containing 5ng/ml BMP4 and 1 μM RA in Essential 6 media (Life Technologies) for seven days; thus forming surface ectodermal progenitor cells. After seven days, the medium was changed to “differentiation medium 2”, i.e. Defined Keratinocyte Serum Free Medium (DKSFM) with growth supplements containing EGF and FGF (Life Technologies), and the cells underwent selection and expansion for 2 months to get maturation into keratinocyte. The resulting keratinocyte colonies were passed onto Corning PureCoat™ ECM Mimetic 6-well Collagen I Peptide Plate (Corning) and expanded in DKSFM medium.

extract_protocol:
RNA extraction was performed using RNeasy Plus (Qiagen) from the samples reported in this research. Ribosomal RNA was removed from each RNA extraction using Ribo-Zero Gold rRNA Removal kit (Illumina).
The RNA-seq libraries were constructed by TruSeq Stranded mRNA Library Prep kit (Illumina).

value: mature keratinocyte differentiated from hESC

value: Differentiation from wild type hESC

tag: treatment and stage

value: mature keratinocyte from terminal differentiation


title: CLF-GFP Rep2

source_name: CLF-GFP


title: CLF-GFP Rep1


title: D45c

source_name: progenitor cells from hESC-epidermal differentiation

value: Epidermal differentitation at Day 45

value: Differentiaiton at Day 45


title: D45b

value: Differentiation at Day 45


title: D14b

value: Epidermal differentitation at Day 14

value: Differentiation at Day 14


title: D21b

value: Epidermal differentitation at Day 21

value: Differentiation at Day 21


title: H9a

source_name: undifferentiated human embryonic stem cell line H9

value: hESC line H9, differentiation at Day 0

value: Differentiation at Day 0


title: H9KC_1 [ATAC-Seq]

description:
hESC_lineH9_Differentiation_mature keratinocyte (KC)
Differentiation from wild type hESC
genomic DNA from open chromatin region
H9KC.fdr0.01.pks.bed

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie2, duplicate fragments were then removed using Picard.
peaks called using HOTSPOT
Genome_build: hg19
Supplementary_files_format_and_content: bed file, peaks

extract_protocol:
Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

tag: originating cell line


title: ipsD7_1: iPSC_Differentiation_D7 (ATAC-Seq)

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie2, duplicate fragments were then removed using Picard.
peaks called using HOTSPOT
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, bed

source_name: progenitor cells from iPSC-epidermal differentiation

growth_protocol: The iPSC line was derived by sendai virus vector-mediated reprogramming in human fibroblast from Invitrogen (Macarthur et al., Stem Cells Int 2012, 564612.). The cells were differentiated into keratinocyte using a protocol revised from Sebastiano et al. 2014 (Science translational medicine 6, 264ra163). Briefly, the iPSCs were first formed into embryo bodies, using AggreWell 400 plates and AggreWell medium (STEMCELL Technologies) supplemented with 1mg/ml RA and 10 mM ROCK inhibitor (STEMCELL Technologies) for 24 hours. Embryoid bodies were collected and cultured in suspension for 2 days and then plated onto gelatin-coated dishes in FAD medium (Itoh et. al. 2011, Proc. Natl. Acad. Sci. U.S.A. 108, 8797–8802) for 4 days and then in N2 medium (Metallo et. al. 2008, Stem Cells 26(2):372-80) for 3 days. During this 7-day differentiation, the media were supplemented with RA (1 mg/ml) and human recombinant BMP4 (25 ng/ml). The medium was then changed to either N2 or DKSFM (Life Technologies), and the cells underwent selection and expansion for 2 months. The resulting keratinocyte colonies were passed onto Corning PureCoat™ ECM Mimetic 6-well Collagen I Peptide Plate (Corning) and expanded in DKSFM medium.

extract_protocol:
Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed by following the published ATAC-seq protocols (NHK samples: Buenrostro et al., 2013, Nat Methods 10, 1213-1218;  iPSC samples: Corces et. al. Nat Methods 14, 959-962.) using a modified version of the Illumina Nextera DNA Sample prep kit.

value: Epidermal differentiation at Day 7

value: Differentiation from wild type iPSC

tag: Stage

value: Differentiation at Day 7


title: NHK_1: Normal Human Keratinocytes (ATAC-Seq)

source_name: keratinocyte from normal skin tissue

value: keratinocyte from normal skin tissue

tag: genotype

value: Normal keratinocytes


title: H9KC_2 [ATAC-Seq]

value: mature keratinocyte differentiated from hESC


title: ipsKC_2: iPSC_Differentiation_mature keratinocytes(KC) (ATAC-Seq)

source_name: mature keratinocyte from iPSC-epidermal differentiation

value: mature keratinocyte differentiated from iPSC


title: NHK_2: Normal Human Keratinocytes (ATAC-Seq)


title: D21a

value: Differentiation from wild type hESC


title: H9b


title: D7b

value: Epidermal differentitation at Day 7


title: ipsD7_2: iPSC_Differentiation_D7 (ATAC-Seq)


title: D7a


title: D43_2 [ATAC-Seq]

description:
hESC_lineH9_Differentiation_D43
Differentiation from wild type hESC
genomic DNA from open chromatin region
D43.fdr0.01.pks.bed

value: Epidermal differentitation at Day 43

value: Differentiaiton at Day 43


title: H9KCa

value: mature keratinocyte from terminal differentiation


title: D43_1 [ATAC-Seq]

value: Differentiation at Day 43


title: D21_2 [ATAC-Seq]

description:
hESC_lineH9_Differentiation_D21
Differentiation from wild type hESC
genomic DNA from open chromatin region
D21.fdr0.01.pks.bed

value: Epidermal differentitation at Day 21


title: D21_1 [ATAC-Seq]

value: Differentiation at Day 21


title: D14a

value: Epidermal differentitation at Day 14

value: Differentiation at Day 14


title: ipsKC_1: iPSC_Differentiation_mature keratinocytes(KC) (ATAC-Seq)


title: D14_1 [ATAC-Seq]

description:
hESC_lineH9_Differentiation_D14
Differentiation from wild type hESC
genomic DNA from open chromatin region
D14.fdr0.01.pks.bed


title: D14_2 [ATAC-Seq]


title: D7_1 [ATAC-Seq]

description:
hESC_lineH9_Differentiation_D7
Differentiation from wild type hESC
genomic DNA from open chromatin region
D7.fdr0.01.pks.bed


title: D7_2 [ATAC-Seq]


title: H9_1 [ATAC-Seq]

description:
hESC_lineH9_Differentiation_D0
Differentiation from wild type hESC
genomic DNA from open chromatin region
H9.fdr0.01.pks.bed

value: hESC line H9, differentiation at Day 0

value: Differentiation at Day 0


title: H9_2 [ATAC-Seq]


title: AP2Cd7Off_2 (RNA-Seq)

description:
total RNA with ribosomal RNA depleted
RNA-seq

data_processing:
Alignment was performed using tophat. RPKM values were called using cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: TetO-TFAP2C hESC differentiation at Day7 without Dox

growth_protocol: In vitro differentiation of TetO-TFAP2C H9 hESCs: To study the function of TFAP2C in surface ectoderm differentiation, TetO-TFAP2C H9 hESCs were induced with 2 mg/ml Doxycycline(Dox) in E6 medium without RA/BMP4 for 7 days. The resulting cells were imaged and collected for subsequent analysis. To study long term epidermal differentiation ability, TetO-TFAP2C H9 hESCs were first induced into surface ectodermal cells by activation of TFAP2C expression with Dox in E6 medium for 7 days; and then were transitioned to DKSFM with Dox for 14 days and then maintained in DKSFM only until keratinocyte colony was formed. The differentiated keratinocytes were passed and maintained onto collagen coated plates (CELLstar) in DKSFM, and collected for additional analysis.

value: early epidemal differentiated cell

value: early differentiaiton without Dox for 7 days


title: AP2Cd7On_2 (RNA-Seq)

source_name: TetO-TFAP2C hESC differentiation at Day7 with Dox

value: early differentiaiton with Dox for 7 days


title: D21-AP2C+p63KO rep1

description: ATAC-seq

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.
Peaks were called usign the HOTSPOT algorithm
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file

source_name: epidermal differentiaiton from hESC at D21

value: immature epidermal progenitor cell

value: Differentiation at D21


title: APKC_1 (RNA-Seq)

source_name: mature keratinocyte from TetO-TFAP2C hESC differentiation

value: mature kerationcyte

value: late differentiation into mature keratinocyte


title: D21-AP2C+p63KO rep2

description: ATAC-seq


title: APKC_2

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.
Peaks were called using the HOTSPOT algorithm.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig file

source_name: mature keratinocyte from hESC differentiation

growth_protocol: In vitro differentiation of TetO-TFAP2C H9 hESCs: To study the function of TFAP2C in surface ectoderm differentiation, TetO-TFAP2C H9 hESCs were induced with 2 mg/ml Doxycycline (Dox) in E6 medium without RA/BMP4 for 7 days. The resulting cells were imaged and collected for subsequent analysis. To study long term epidermal differentiation ability, TetO-TFAP2C H9 hESCs were first induced into surface ectodermal cells by activation of TFAP2C expression with Dox in E6 medium for 7 days; and then were transitioned to DKSFM with Dox for 14 days and then maintained in DKSFM only until keratinocyte colony was formed. The differentiated keratinocytes were passed and maintained onto collagen coated plates (CELLstar) in DKSFM, and collected for additional analysis.

value: keratinocytes derived from TFAP2C induced progenitor

tag: genotype/variation


title: AP2Cd7On_1 (RNA-Seq)


title: D21-AP2C rep2

description: ATAC-seq


title: APKC_1


title: AP2Cd7Off_2

source_name: early surface ectoderm differentiation from hESC

value: control ES without specific differentiation

value: Dox- for 7 days


title: AP2Cd7Off_1


title: AP2Cd7On_1

value: surface ectoderm progenitor cells

value: Dox+ for 7 days


title: D4_siSPRR5_2

city: Regensburg

first: Christian

last: Ziegler

address: Universitaetsstrasse 31

institute: University Regensburg

description:
biological replicate 2
processed data file: counts_D4_SPRR5KD.txt

data_processing:
(I) Preprocessing: Quality of sequencing data from the RNA-Seq libraries was examined using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and size, adapter and quality trimming was performed using Trimmomatic (ver. 0.32, ILLUMINACLIP:TruSeq_s tranded_SE.fa:2:30:10 HEADCROP:0 TRAILING:26 LEADING:26 SLIDINGWINDOW:4:15 MINLEN:25). Trimmed reads were aligned to the Homo sapiens genome (ftp://ftp.ensembl.org/pub/release-85/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz) combined with ERCC sequence information using STAR. The mapped reads were then assessed on the gene level using featureCounts from the Rsubread R-library based on annotation information from ensemble (GRCh38.p7 release-85). Following alignment, further quality control was performed using QoRTs.
(II) Differential expression analysis: Count data at the gene level was analyzed with DESeq2 using ERCC spike-ins for library size normalization. All treatment comparisons were performed and corrected for multiple testing using FDR. Genes that met the indicated log2(fold change) restraint and a false discovery rate <0.05 (“padj”) were considered significant differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files for the individual days contain a matrix table of counts per gene with respect to the corresponding samples. Data is formatted as csv.

molecule: polyA RNA

source_name: Organotypic human epidermis

growth_protocol: Pooled primary human keratinocytes from different donors were obtained from PromoCell (Lot.No.: 1020401, 1040101 and 407Z001) or Lonza (Lot.No.:0000402834) and grown in a 1:1 mixture of KSF-M (Gibco) and Medium 154 for keratinocytes (Gibco), supplemented with Human Keratinocyte Growth Supplement, epidermal growth factor, bovine pituitary extract and 1x Antibiotic-Antimycotic (all supplements from Gibco). Cells were cultured at 37 °C in a humidified chamber with 5% CO2. For the generation of organotypic human epidermal tissue, 500,000 human keratinocytes that have been nucleofected with siRNAs were seeded onto a devitalized dermal matrix and raised to the air–liquid interface to initiate stratification and differentiation, as described by Truong et al. (2006, Genes Dev) and Sen et al. (2010, Nature).

extract_protocol:
RNA from the obtained organotypic epidermis was extracted with the QIAGEN RNeasy Plus Mini Kit according to the manufacturer's instructions.
Library preparation and mRNA sequencing were carried out according to the Illumina TruSeq Stranded mRNA Sample Preparation Guide, the Illumina HiSeq 1000 System User Guide (Illumina), and the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Kapa Biosystems), with minor modifications. In brief, mRNA molecules were purified using oligo-dT probes immobilized on magnetic beads starting with 250 ng of total RNA supplied with ERCC spike-Ins. Chemical fragmentation of the mRNA to an average insert size of 200-400 bases was performed using divalent cations under elevated temperature (94°C, 4 minutes). First strand cDNA was produced by reverse transcription with random primers. Actinomycin D was added to improve strand specificity by preventing spurious DNA-dependent synthesis. Blunt-ended second strand cDNA was synthesized using DNA Polymerase I, RNase H and dUTP nucleotides. The resulting cDNA fragments were adenylated at the 3' ends, the indexing adapters were ligated and subsequently specific cDNA libraries were created by PCR enrichment. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit. Equimolar amounts of each library were used for cluster generation on the cBot (TruSeq SR Cluster Kit v3). The sequencing run was performed on a HiSeq 1000 instrument using the indexed, 1x50 cycles single end protocol and TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in .bcl files, which were converted into .fastq files by the CASAVA1.8.2 software.

treatment_protocol: Nucleofection with siRNA targeting the gene of interest or a non-targeting control

value: Organotypic human epidermis

tag: treatment

value: siPool for efficient knockdown of SPRR5

tag: day of differentiation

value: day 4

value: pooled primary human keratinocytes


title: D4_siSPRR5_3

description:
biological replicate 3
processed data file: counts_D4_SPRR5KD.txt


title: D4_siSPRR5_1

description:
biological replicate 1
processed data file: counts_D4_SPRR5KD.txt


title: D4_siSPRR5_4

description:
biological replicate 4
processed data file: counts_D4_SPRR5KD.txt


title: D4_siCtrl_4

value: Control siPool


title: D4_siCtrl_5

description:
biological replicate 5
processed data file: counts_D4_SPRR5KD.txt


title: D4_siCtrl_2


title: D4_siCtrl_3


title: APKC_2 (RNA-Seq)


title: AP2Cd7Off_1 (RNA-Seq)

value: early epidemal differentiated cell


title: D4_siCtrl_1


title: D3_siSPRR5_4

description:
biological replicate 4
processed data file: counts_D3_SPRR5KD.txt

value: day 3


title: D3_siSPRR5_3

description:
biological replicate 3
processed data file: counts_D3_SPRR5KD.txt


title: D21-AP2C rep1

description: ATAC-seq


title: AP2Cd7On_2


title: D3_siSPRR5_2

description:
biological replicate 2
processed data file: counts_D3_SPRR5KD.txt


title: D3_siCtrl_2


title: D3_siLINC00941_4

description:
biological replicate 4
processed data file: D3_CountTable_LINC00941KD.txt

value: siPool for efficient knockdown of LINC00944


title: D3_siLINC00941_2

description:
biological replicate 2
processed data file: D3_CountTable_LINC00941KD.txt

value: siPool for efficient knockdown of LINC00942


title: D3_siLINC00941_3

description:
biological replicate 3
processed data file: D3_CountTable_LINC00941KD.txt

value: siPool for efficient knockdown of LINC00943


title: D3_siCtrl_1

description:
biological replicate 1
processed data file: counts_D3_SPRR5KD.txt


title: D3_siControl_5

description:
biological replicate 5
processed data file: D3_CountTable_LINC00941KD.txt


title: D3_siControl_4


title: D3_siLINC00941_1

description:
biological replicate 1
processed data file: D3_CountTable_LINC00941KD.txt

value: siPool for efficient knockdown of LINC00941


title: D3_siControl_2


title: D2_siLINC00941_3

description:
biological replicate 3
processed data file: D2_CountTable_LINC00941KD.txt

value: day 2


title: D2_siLINC00941_4

description:
biological replicate 4
processed data file: D2_CountTable_LINC00941KD.txt


title: D2_siLINC00941_5

description:
biological replicate 5
processed data file: D2_CountTable_LINC00941KD.txt

value: siPool for efficient knockdown of LINC00945


title: D3_siControl_3


title: D3_siSPRR5_1


title: D2_siControl_4


title: D2_siControl_3


title: D2_siLINC00941_1

description:
biological replicate 1
processed data file: D2_CountTable_LINC00941KD.txt


title: D2_siControl_5