title: 1440307_H3K4me1_H2-D3

description: ChIP-seq


title: C28

status: Public on Feb 04 2021

type: genomic

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

description: Already submitted as GSM4602896(GSE152089)

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina).

data_processing: Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP (release 2.8.9) package (Morris TJ et al., 2014) implemented R environment (version 3.6.2). ChAMP pre-processing module appears more suitable in preventing biases due to genetic variations in downstream analyses by filtering an increased number of probes. Sites with a detection p-value above 0.01 (n=4706) and a bead count <3 in at least 5% of samples (n=226) were removed. Moreover, also non-GpG probes (n=3025), potentially SNP affected probes (n=57699) (Zhou Wet al., 2017) probes aligning to multiple locations (n=11) (Nordlund J et al., 2013) and of X and Y chromosomes (n=9705) were filtered out. As a final outcome of the filtering procedures, a total of 410140 CpG sites were retained. Quantile normalization was performed through preprocessCore package (release 1.38.1).

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Control

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from peripheral blood lymphocytes of probands and their parents (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).

tag: disease state

value: control

tag: tissue

value: Peripheral Blood

tag: Sex

value: female

tag: epigenetic age


title: C29

description: Already submitted as GSM4602897(GSE152089)

value: male


title: C25

description: Already submitted as GSM4602890(GSE152089)


title: C26

description: Already submitted as GSM4602894(GSE152089)


title: Cxxc1null-H2AK119ub

type: SRA

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

country: China

institute: Life Sciences Institute, Zhejiang University

library_source: genomic

data_processing:
ChIP-seq data analysis.ChIP-seq reads were trimmed to 50 bp and aligned to the mouse genome build mm9 using  bowtie2 (v2.3.4.1) with default parameters. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. H3K4me3 peaks were called using MACS2 (v 2.1.1.20160309) with the parameters “--nomodel --nolambda --broad -B --SPMR -g mm” and signal tracks for each sample were generated with “wigToBigWig” from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
WGBS data analysis. Raw reads were trimmed using TrimGalore (v 0.4.4) with default parameters. Then the reads were mapped to converted mm9 reference using bismark (v0.19.0) with parameters “--bowtie2 --non_directional”. PCR duplicates were removed. The cytosine was distinguished as CpG, CHG and CHH and the methylation levels were calculated separately.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

organism: Mus musculus

source_name: Cxxc1fl/fl;Gdf9-Cre mouse GV oocytes

growth_protocol: in vivo

extract_protocol: STAR ChIP-seq was performed according to a protocol described previously (Zhang et al., 2016). Briefly, samples were directly lysed and fragmented by micrococcal nuclease (MNase) at 37 °C for 5 min before being incubated with the primary antibody overnight with rotation at 4 °C. The next day, 100 μg Dynabeads Protein A (Thermo Fisher Scientific) was added to each sample and incubated for 2–3 h with rotation at 4 °C. The beads were washed five times with 150 μl radioimmunoprecipitation assay buffer (RIPA) and once with 150 μl lithium chloride buffer. For each sample, beads were resuspended with 27 μl deionized H2O and 1 μl 10× Ex-Taq buffer (Takara, RR006B); 1 μl proteinase K (catalog no. 10910000; Roche) was added to each sample and incubated at 55 °C for 90 min to elute DNA from the beads. After incubation at 80 °C for 40 min to inactivate the proteinase K, the sample was subjected to TELP (tailing, extension, ligation and PCR) library preparation without DNA purification.

treatment_protocol: 4 week mouse treated by  PMSG 44 h

tag: stain

tag: antibody


title: 1324306_Hudep2_KLF1_rep1

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

country: USA

institute: St. Jude Children’s Research Hospital

description: ChIP-seq

data_processing:
FASTQ files were mapped to hg19 by using BWA mem (v0.7.16a).  Bigwiggle files were generated using DeepTools (v3.2.0)
ChIP-seq peaks were called by using MACS2 (v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle

growth_protocol: Approximately 2.5 × 107 cells were used for each immunoprecipitation. Cells were cross-linked with 1% formaldehyde for 10 min at room temperature with rotation, and the reaction was quenched with glycine at a final concentration of 125 mM. Cross-linked cells were then lysed and resuspended in 2 mL of RIPA buffer and sonicated for 12 cycles with a Branson 250 sonifier (10 s on/90 s off for a total of 2 min of pulses with 20% output from the micro-tip) to obtain fragments of chromatin approximately 200–300 bp in size. Supernatants were precleared by incubation with 200 µL of protein A/G agarose bead slurry (Thermo Fisher Scientific, cat. #15918014) overnight at 4°C with rotation. Meanwhile, 12.5 µg of IP antibody was incubated with 50 µL of protein A/G agarose bead slurry in 1 mL of PBS overnight at 4°C with rotation. Saved precleared chromatin (20 µL) was used as the input sample. Precleared chromatin was incubated with the antibody–bead complex for 7 h at 4°C with rotation. Cross-linking of DNA was reversed by incubation with RNase A (1 µg/µL), proteinase K (0.2 mg/mL), and 0.25 M NaCl overnight at 65°C.

extract_protocol:
Immunoprecipitated DNA was purified using the Qiagen PCR Extraction Kit and eluted with 20 µL of EB elution buffer. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, cat. #E7645) with homemade TruSeq adaptors. Libraries were sequenced using an Illumina HiSeq 4000 system.
NA

tag: cell line


title: Cxxc1null-H3K36me3-rep2


title: C32

description: Already submitted as GSM4602900(GSE152089)


title: C37

description: Already submitted as GSM4602905(GSE152089)


title: 1324305_Hudep2_KLF1_rep2_ChIP

description: ChIP-seq


title: Cxxc1null-H3K36me3-rep1


title: 1482928_Hudep2_D0_TAL1_rep2

description: ChIP-seq


title: C22

description: Already submitted as GSM4602887(GSE152089)


title: C21

description: Already submitted as GSM4602886(GSE152089)


title: C19

description: Already submitted as GSM4602884(GSE152089)


title: Cxxc1null-H3K27me3-rep2


title: 1482927_Hudep2_D0_TAL1_rep1

description: ChIP-seq


title: 1267112_RFC924_Hudep2_LDB1

description: ChIP-seq


title: C33

description: Already submitted as GSM4602901(GSE152089)


title: Cxxc1null-H3K27me3-rep1


title: Cxxc1null-H3K4me3-rep2


title: C23

description: Already submitted as GSM4602888(GSE152089)


title: 1267111_RFC923_Hudep2_LDB1

description: ChIP-seq


title: C34

description: Already submitted as GSM4602902(GSE152089)


title: Cxxc1null-H3K4me3-rep1


title: 1151779_Hudep2_GATA1_rep2

description: ChIP-seq


title: C20

description: Already submitted as GSM4602885(GSE152089)


title: WT-H2AK119ub

source_name: WT mouse GV oocytes


title: C24

description: Already submitted as GSM4602889(GSE152089)


title: 1151778_Hudep2_GATA1_rep1

description: ChIP-seq


title: WT-H3K36me3-rep2


title: C17


title: C18

description: Already submitted as GSM4602891(GSE152089)


title: WT-H3K36me3-rep1


title: BN-Lx  rat 3

city: Aurora

first: Laura

middle: Maren

last: Saba

state: CO

address: 12850 East Montview Blvd.

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

library_source: transcriptomic

data_processing:
Reads were trimmed to remove adapters and low-quality base calls using cutadapt
Trimmed reads were aligned to strain-specific rn6 rat genomes (available at http://phenogen.org) using HISAT2
StringTie (v.1.3.5) was used to reconstruct the transcriptome from the RNA-Seq data. Ensembl(v.99) reference annotation from the rat was provided to guide the StringTie reconstruction. The StringTie reconstruction was further augmented for identification of active polyadenylation sites using aptardi (https://github.com/luskry/aptardi).
Individual isoforms and genes from the stringtie/aptardi transcriptome were quantitated using RSEM.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include estimated read counts, TPM, and FPKM values for each Sample (standard RSEM output)
Supplementary_files_format_and_content: estimated count matrices with genes or isoforms as rows and Samples as columns
Supplementary_files_format_and_content: GTF file for reconstructed transcriptome

molecule: polyA RNA

organism: Rattus norvegicus

source_name: whole brain

extract_protocol:
RNA was extracted from whole brain of three naïve male rats per strains using the the miRNeasy Mini and RNeasy MinElute Cleanup Kits (Qiagen, Valencia, CA, USA).
Sequencing libraries were constructed using the Illumina TruSeq RNA Sample Preparation kit from 1 ug RNA according to manufacturer's instructions.
Library quality was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Samples were sequenced (2x100 paired-end reads) on the Illumina HiSeq2000. Samples were multiplexed over 3 lanes of the flowcell (2 lanes with 3 samples each and 1 lane with all 6 samples).

value: brain

tag: strain

value: BN-Lx/CubPrin


title: C16

description: Already submitted as GSM4602883(GSE152089)


title: BN-Lx  rat 2


title: BN-Lx  rat 1


title: WT-H3K27me3-rep1


title: SHR rat 3

value: SHR/OlaIpcvPrin


title: WT-H3K4me3-rep2


title: WT-H3K27me3-rep2


title: C15

description: Already submitted as GSM4602882(GSE152089)


title: SHR rat 1


title: Ambra1_KPTC

city: Stanford

first: Chuan

last: Li

state: CA

address: 327 Campus Drive

department: Biology

institute: Stanford University

description: barcode sequencing from 4 mice

data_processing:
Each read is expected to contain an 8-nucleotide sgID region followed by a 30-nucleotide barcode (BC) region (GCNNNNNTANNNNNGCNNNNNTANNNNNGC), and each of the 20 Ns represent random nucleotides with roughly equal representation of A, T, G and C.
The sgID region identifies the putative tumour suppressor gene being targeted, for which we require perfect match between the sequence in the forward read and one of the 102 forward sgIDs with known sequences.
We require the forward and reverse read to agree completely within the 30 nucleotide sequence to be further processed. Any “tumours” that are within a Hamming distance of two from a larger tumour is assigned as “spurious tumours”, which are likely to be resulting from sequencing or PCR error, and are removed from subsequent analysis.
The tumour size (number of neoplastic cells) is calculated by normalizing the number of reads to the three benchmarks “spike-in” cell lines (5x105 cells for each benchmark cell line) added to each sample prior to lysis of the lung and DNA extraction step.
Supplementary_files_format_and_content: Txt files showing the tumor sgRNA, barcode and tumor size for each identified tumor

source_name: Lung epithelial cell

growth_protocol: All experiments were performed in accordance with Stanford University Institutional Animal Care and Use Committee guidelines.

extract_protocol:
Genomic DNA was isolated from bulk tumour-bearing lung tissue from each mouse. Three benchmark control cell lines of 500,000 cells were added to each mouse lung sample prior to lysis to enable the calculation of the absolute number of neoplastic cells in each tumour from the number of sgID-BC reads.
Q5 High-Fidelity 2x Master Mix (New England Biolabs, M0494X) was used to amplify the sgID-BC region from 32 µg of genomic DNA using unique dual-indexed primers.

treatment_protocol: Tumors were initiated by intratracheal delivery of 60 µl of lentiviral pools.

tag: viral pool

tag: weeks after tumor initiation

tag: genotype


title: C14

description: Already submitted as GSM4602881(GSE152089)


title: SHR rat 2


title: WT-H3K4me3-rep1


title: Ambra1_KTC

description: barcode sequencing from 9 mice


title: C13

description: Already submitted as GSM4602880(GSE152089)


title: p58

city: Philadelphia

first: Mathieu

last: Wimmer

state: PA

address: 1701 N 13th Street

institute: Temple University

data_processing:
Evaluating quality of samples with FastQC ver  0.11.9
Remove adapters and unpaired reads using Trimmomatic ver 0.39
Mapping to the geonome by HISAT 2.2.0 release 2/6/2020
Making sorted bam files using SAMtools ver 1.11
Counting number of reads by Stringtie v2.1.2
Finding diffrenetinally expressed genes applying Deseq2 ver 1.28.1
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: gtf file

source_name: Nucleus accumbens brain tissue

extract_protocol:
Nucleus accumbens tissue was dissected and flash frozen on dry ice. RNA was extracted using trizol reagent followed by the Qiagen micro RNAeasy kit
Library preps were created using the NEBNext Ultra library prep kit for illumina

value: Long-evans

value: M

tag: treatment

value: LBN


title: Ambra1_KT

description: barcode sequencing from 4 mice

value: KT


title: C12

description: Already submitted as GSM4602879(GSE152089)


title: KTC_sg-85-Pool_26Wks

description: barcode sequencing from 41 mice

extract_protocol:
Genomic DNA was isolated from bulk tumour-bearing lung tissue from each mouse. Twelve benchmark control cell lines (3 cell lines of 500,000 cells each, 3 cell lines of 50,000 cells, 3 cell lines of 5,000 cells, and 3 cell lines of 500 cells) were added to each mouse lung sample prior to lysis to enable the calculation of the absolute number of neoplastic cells in each tumour from the number of sgID-BC reads.
Q5 High-Fidelity 2x Master Mix (New England Biolabs, M0494X) was used to amplify the sgID-BC region from 32 µg of genomic DNA using unique dual-indexed primers.


title: p55

value: F

value: Control


title: p50


title: p46


title: KT_sg-85-Pool_Ctrl for 26Wks

description: barcode sequencing from 6 mice at 15 weeks, serving as the control for KTC_sg-85-Pool_26Wks data, which were transfected with the same viral pool


title: KTC_sg-85-Pool_15Wks

description: barcode sequencing from 10 mice


title: C11

description: Already submitted as GSM4602878(GSE152089)


title: p43


title: p68


title: KT_sg-85-Pool_Ctrl for 15Wks

description: barcode sequencing from 6 mice at 15 weeks, serving as the control for KTC_sg-85-Pool_15Wks data, which were transfected with the same viral pool


title: C08

description: Already submitted as GSM4602874(GSE152089)


title: C10

description: Already submitted as GSM4602877(GSE152089)


title: C06

description: Already submitted as GSM4602872(GSE152089)


title: p325


title: KT_sg-102-Pool_15Wks

description: barcode sequencing from 12 mice at 15 weeks, serving as the control for KTC_sg-102-Pool_15Wks data, which were transfected with the same viral pool


title: p323


title: p34


title: C09

description: Already submitted as GSM4602875(GSE152089)


title: Neuro-2A_SUPT16_posCtrl

city: Irvine

first: Pawel

middle: Michal

last: Switonski

state: California

address: 1001 Health Sciences Road

department: Department of Pathology & Laboratory Medicine

institute: University of California, Irvine

data_processing:
Library strategy: LAM-HTGTS
For QC analysis, FASTQ files for each barcode were processed in R using vmatchPattern function in Biostrings.  The pattern aligned to was: “AACCGCTTCAGCTTGGTGTAGACGGTGTGCAAGCCCCCCA”, which contains the nested primer, 20 bp downstream genomic sequence, and is 63 bp upstream of  the CRISPR-Cas9 cleavage site, allowing up to 3 mismatches
To determine indels, we only counted reads that contained the sequence “TGGCCCCTCTCAGATCCACCATTTTGCACTCATTATTCTG” and were not isogenic to the reference sequence in length.  This sequence allows for up to 15 bp deletion indels distal to the cut site (up to 63+15bp total indel), since the sequence begins 15 bp distal to the cut site.
Reads which were not indels were separately saved, trimmed by 110 bp (the  region containing the nested primer up to the CRISPR-Cas9 cut site), and then end-end aligned to mm10 using Bowtie2 in Galaxy
Aligned BAM files were converted to BED files using BAM to BED in Galaxy.  All reads within 50 kb of the bait Cas9 cleavage site were designated “local”  translocations, and all reads on other chromosomes or >50 kb from the bait site were considered  “distal” translocations.
For the 10Q vs 92Q ATXN7 analysis, FASTQ files were similarly processed.  For site 1 analysis, the initial vmatchPattern alignment was “GTTGAAGACCTCAGAGGTGATGCTGGCTGCTTTCTTCATC”, which contains the nested primer, 20 bp downstream genomic sequence, and is 40 bp upstream of the CRISPR-Cas9 cut site.
To determine indels, we counted reads that contained the sequence “TGTCTACCTGTAGCAAGGTGATGCATTTCTACTACACACA” and were not isogenic to the reference sequence in length.  As for site 2, this sequence allows for up to 15 bp deletion indels distal to the cut site (up to 40+15bp total indel), since the sequence begins 15 bp distal to the cut site
The remainder of the analysis was identical to the QC analysis with translocations defined as “distal”, i.e. >50 kb away from cut site translocations.
To determine overlap with mm10 annotations BED files for each, corresponding annotation was downloaded from the UCSC genome browser (exons, intron, ChIP-Seq hit genes) or supplemental data files.  Any discrepancy from mm9 and mm10 genomes was first converted using the LiftOver function of the UCSC genome browser.  To create a randomized control “expect” rate, BED locations were permuted 1000x over the mm10 chromosomal genome.
Genome_build: mm10
Supplementary_files_format_and_content: Peak text files

source_name: Neuroblast cells

extract_protocol:
5 million murine Neuro2a cells were transfected with 10QATXN7 or 92Q-ATXN7 and co-transfected with a plasmid expressing sgRNA to a designated target site on Chromosome 14 (site 1: GGTAGACATCAGCGCTGTTG, site 2: CTCGCAGCCCTCCACCGTAA), along with CRISPR-Cas9 and a constitutive GFP reporter.  For the quality control experiment, only the CRISPR-Cas9 plasmid co-expressing site 2 targeted sgRNA or non-targeted sgRNA were used.  48 hrs after transfection, cells were trypsinized for 5 min, rinsed in PBS, and three replicates were pooled. 1 million GFP positive cells per pooled condition were sorted by flow cytometry.  Cells were then resuspended in 200 μl PBS and 20 μl NEB Proteinase K (800U/mL) and incubated for 30 min at 56°C.  Proteinase K was inactivated by heating at 95°C for 5 min and then 5 µl RNaseA (8mg/ml) was added and incubated for 30 min at 37°C.  Treated lysate was purified using the Qiagen Blood and Tissue DNA Kit using the manufacturer’s protocol, with the final elution performed twice with 100 µl AE buffer.
A Diagenode Bioruptor Pico was used to shear DNA to 750 bp fragments.  Each sample was then bait-amplified using using Phusion DNA polymerase (ThermoFisher #F530L) in standard reactions containing biotinylated bait primers (site 1: /5Biosg/ACTAAAAAGAGCGCCCCTCTTTC, site 2: /5Biosg/GGTTTCCCCTCCGCTCTTTA). The Invitrogen PureLink PCR Cleanup Kit was used to remove excess RNA and biotinylated primer.  50 µl 5M NaCl and 2.5 µl 0.5M EDTA pH 8 were added to each sample.  Biotinylated bait DNA was then purified using magnetic C1 Streptavidin Dynabeads (ThermoFisher #11205D).  Bead-DNA complexes were washed and resuspended in water and then the following was added for an on-bead ligation reaction: 10 µl 10X T4 ligase buffer, 5 µl 20mM hexamine cobalt III chloride (Sigma #481521), 5 µl bridge adapters as per reference, 5 µl3U/µl T4 DNA ligase (NEB #M0202S), and 30 µl 50% PEG8000 (Promega #V3011) in water.  A thermal cycler was used for the ligation reaction using settings of 1 hr at 25°C, 1 hr at 22°C, a manual pipette resuspension step, 1 hr at 22°C, and 16 hrs at 16°C.  Ligation product was then washed by first adding 100 µl 2X B&W buffer per sample, captured on magnets, and then washing with 200 µl 1X B&W buffer twice followed by a 200 µl water wash.  LpnPI digestion was performed on indicated samples using beads resuspended in 23.5 µl water, 3 µl 10X NEB Cutsmart buffer, 0.5 µl of 100 µM 5-Cytosine methylated primer (site 1: TTTGGGAAGAGC/iMe-dC/TGAGCATTCTGAG, site 2: TCAACCCCGTCCC/iMedC/AGTGGAAAACACCC), 0.5µl LpnPI enzyme (NEB #R0663S), 1 µl 30X enzyme activator, at  running conditions of 37°C for 4 hrs, then 65°C heat inactivation for 20 min.  LpnPI digested  samples were washed with 600 µl B&W buffer 5x, then once with 1 mL water, and resuspended in 200 µl water. For Illumina adapter inclusion and barcoding, resuspended samples were split into 8 PCR reactions consisting of 10 µl 5X Phusion buffer, 4 µl 2.5mM dNTPs, 2 µl 10µM I5 nested primer, 2 µl 10µM I7 primer, 0.5 µl Phusion polymerase, 25 µl bead-DNA complex, and 6.5 µl water. Reaction was run using 95°C 30 sec, 18 cycles of 95°C 15 sec, 60°C 30 sec, 72°C 1 min, then 72°C 6min, and ending with 4°C until removed from thermal cycler.  PCR products were pooled and   removed of beads by extraction of supernatant on magnet followed by centrifugation at 15,000g for 5 min at RT.  Supernatant was transferred to a new tube and purified using the Invitrogen PureLink PCR Cleanup Kit with Buffer 2 conditions and eluted with 60 µl water.  Final Illumina binding adapters were added by 4 PCR reactions of P5-I5 and P7-I7 adapter primers, using the following conditions: 15 µl DNA products, 16.5 µl water, 10 µl 5X Phusion buffer, 4 µl 2.5mM dNTPs, 2 µl of each 10 µM P5-I5 and P7-I7 primer, 0.5 µl Phusion polymerase, with running conditions of 95°C 3min, 16 cycles of 95°C 15 sec, 62°C 30 sec, 72°C 1 min, then 72°C 6 min, and 4°C until removal from thermal cycler.  Final purification of library prior to NGS steps was performed by running on a 1X TBE gel containing GelRed stain (VWR #89139-134), excised in the 350-1,250bp range (directly above primer-dimer band), and extracted using a Qiagen gel purification kit.  Additional purification was performed from the gel purification by a second purification through the Invitrogen PureLink PCR Cleanup Kit with Buffer 2 conditions and eluted with 30 µl water.  Library concentration was estimated using a NanoDrop, and library pools were created using equimolar DNA per sample.  Finally, libraries were run on an Illumina MiSeq at 300 bp depth (QC reads, P5-I5-end only) or 250bp depth (experimental reads, P5-I5 end only).

tag: cell type

value: Neuro-2a cells

value: Transfected with plasmids encoding spCas9 and sgRNA for site 2 from PX458


title: C04

description: Already submitted as GSM4602870(GSE152089)


title: C07

description: Already submitted as GSM4602873(GSE152089)


title: C05

description: Already submitted as GSM4602871(GSE152089)


title: p30


title: C01

description: Already submitted as GSM4602867(GSE152089)


title: Neuro-2A_SUPT16_92Q

value: Transfected with plasmids encoding ataxin-7 92Q, spCas9 and sgRNA for site 2 from PX458


title: C03

description: Already submitted as GSM4602869(GSE152089)


title: C02

description: Already submitted as GSM4602868(GSE152089)


title: Neuro-2A_SUPT16_10Q

value: Transfected with plasmids encoding ataxin-7 10Q, spCas9 and sgRNA for site 2 from PX458


title: p241


title: p28


title: p202


title: Neuro-2A_DACH1_posCtrl

value: Transfected with plasmids encoding spCas9 and sgRNA for site 1 from PX458


title: KTC_sg-102-Pool_15Wks

description: barcode sequencing from 47 mice


title: OAVS45

source_name: Case

value: Oculo-auriculo-vertebral spectrum

value: Peripheral Blood


title: OAVS40

value: female


title: OAVS44

value: male


title: p116


title: Neuro-2A_DACH1_92Q

value: Transfected with plasmids encoding ataxin-7 92Q, spCas9 and sgRNA for site 1 from PX458


title: Neuro-2A_DACH1_10Q

value: Transfected with plasmids encoding ataxin-7 10Q, spCas9 and sgRNA for site 1 from PX458


title: p16

value: Long-evans


title: p107


title: Neuro-2A_DACH1_non_targeting

value: Transfected with plasmids encoding spCas9 and non-targeting sgRNA from PX458


title: OAVS46


title: OAVS43


title: p90

value: LBN


title: OAVS37


title: OAVS35


title: Fasted Control 10

type: RNA

city: Edmonton

first: René

middle: L

last: Jacobs

state: Alberta

address: Li Ka Shing Centre for Health Research

department: Agriculture, Food and Nutritional Science; Biochemistry

country: Canada

institute: University of Alberta

description: Gene expression data from mouse intestines without PC synthesis in the fasted state

hyb_protocol: 16-18 hours at 45 degrees Celcius as descibed in Affymetrix protocol.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Expression Console 1.4.1.46 using RMA normalization; TAC 3

label: Biotin

molecule: total RNA

source_name: Mouse intestines without PC synthesis in the fasted state

label_protocol: Biotin labeled cRNA were prepared according to the standard Affymetrix WT Plus Kit Protocol from 400ng total RNA.

growth_protocol: Pcyt1aLoxp/LoxP;VilcreERT2 mice were treated with tamoxifen for 5 days to induce Cre recombinase, and LoxP/LoxP control mice were also treated with tamoxifen.

extract_protocol: Trizol extraction folllowed by RNeasy column clean-up.

treatment_protocol: The mice were placed on a high fat diet for 4 days before being fasted overnight. Intestines were excised and opened longitudinally. 3 cm was removed from the geometric middle of the small intetsine (jejunum) and stored in liquid nitrogen.

value: Intestine

tag: age

value: 10-12 weeks


title: p80

value: F

value: Control


title: OAVS36


title: OAVS47


title: OAVS34


title: OAVS41


title: Fasted Control 9


title: 0x_B

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

data_processing:
Raw data were analyzed using the TopHat2.0.4 aligner with stand-specific settings  and Perkinsus marinus genomic reference sequence (GCA_000006405.1 JCVI_PMG_1.0).
Differential gene expression was analyzed using the DESeq R package (Bioconductor) and the negative binomial model
Criteria for significant differences in gene expression were (1) false discovery rate (FDR) <0.05, (2) expression level >10th percentile, and (3) ≥ 2-fold change.
Genome_build: Perkinsus marinus(GCA_000006405.1 JCVI_PMG_1.0)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Perkinsus marinus

source_name: Perkinsus marinus cells

growth_protocol: P. marinus cells (monoclonal sample of ATCC 50439/D3 were kindly provided by Chris Dungan of the Maryland Department of Natural Resources) and cultivated as described (Dungan and Hamilton 1995) at 27°C.  Growth and confluence were checked daily with a light microscope at 10X, and cell concentration was measured spectrophotometrically at an OD of 600.

extract_protocol:
P. marinus cells were harvested from day 11 lipid replete and lipid deplete media for each biological replicate. Cells were pelleted at 3,900 RPM for 10 minutes at 4 C° using an Eppendorf 5810R Centrifuge. P. marinus total RNA was extracted per manufacturer’s protocol using the Qiagen RNeasy mini- kit; RNA quality was verified on a 1% percent agarose gel and visualized using a UV transilluminator.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For analysis of growth in defined DME media (Dungan and Hamilton, 1995), week old log phase P. marinus cell cultures were adjusted to an OD .100 and subsequently split into two groups consisting of three biological replicates: lipid replete- medium containing a 1X solution of lipid concentrate and lipid deplete -medium without lipid concentrate. Lipid replete and lipid deplete cells were exponentially grown until day 11

value: log phase Perkinsus marinus cells

value: Perkinsus marinus monoclonal sample  of ATCC 50439/D7

value: without lipids


title: OAVS42


title: OAVS39


title: OAVS33


title: Fasted Control 8


title: 0x _A

value: Perkinsus marinus monoclonal sample  of ATCC 50439/D6


title: p101


title: 0x_D

value: Perkinsus marinus monoclonal sample  of ATCC 50439/D8


title: p76

value: M


title: Control_D

value: Perkinsus marinus monoclonal sample  of ATCC 50439/D5

value: with lipids


title: OAVS29

value: Oculo-auriculo-vertebral spectrum

value: Peripheral Blood

value: female


title: Control_B

value: Perkinsus marinus monoclonal sample  of ATCC 50439/D4


title: Control _A

value: Perkinsus marinus monoclonal sample  of ATCC 50439/D3


title: Fasted Control 6

value: Intestine


title: Fasted Knockout 5

value: 10-12 weeks


title: OAVS26


title: Fasted Control 7


title: CS_seedlings_DNaseI_seq

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

data_processing:
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 using BWA 0.7.5a-r405  for ChIP-seq,  HISAT2 2.1.020 for RNA-seq data, all with default settings.
For ChIP-seq, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–5 and fold-change >32.  ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
For DAP-seq, MACS2.2.6 was used to identify protein binding sites (peaks). TF peaks which overlap with Halo peaks were removed. The top 6,000 peaks, ranked first by -log10(qvalue), then by fold enrichment, were used to discover novel DNA-binding motifs by MEME-ChIP in MEME software toolkit.
For DNase-seq,  MACS2.2.5 was used to identify read-enriched regions (peaks) with combined criteria: q value < 1e5.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files and bigwig files were provided; In lncRNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided. In DAP-seq, peak files  and bigwig files were provided.

organism: Triticum aestivum

source_name: Triticum aestivum 12-days-old seedlings

growth_protocol: 16h light, 8h dark, 22°C

extract_protocol:
Chromatin or RNA was extracted from 14-days-old seedlingss, using standard protocols. 2μg total RNA (rRNA depleted) were used to prepare lncRNA-seq，2.2 μg DNA extracted from the harvested seedlings were used to prepare ChIP-seq. For DAP-seq, genomic DNA was extracted from leaves (14-days-old). 5μg gDNA was used to prepare DAP-seq library.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 2000/2500 system (Illumina) to produce 150-bp paired-end reads.
For DAP-seq, genomic DNA was extracted from wheat leaves using Plant DNAzol Reagent (invitrogen) and fragmented. DNA was then end repaired using the End-It kit (Lucigen) and A-tailed using Klenow (3′–5′ exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase (Promega).

treatment_protocol: For hormone and NaCl treatments, germinated seeds were grown in Hoagland solution at 22 °C under long-days conditions for 7 days. The 7-day-old seedlings in Hoagland were treated with 100μm ABA, 100μm MeJA, 500μm SA and 150mM NaCl, respectively, followed by incubation for 7 days.

value: 12-days-old seedlings

tag: cultivar

value: Chinese Spring


title: OAVS27


title: CS_seedlings_H3K9ac_ChIP_seq_rep2

data_processing:
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 using BWA 0.7.5a-r405  for ChIP-seq,  HISAT2 2.1.020 for RNA-seq data, all with default settings.
For ChIP-seq, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–5 and fold-change >32.  ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
For DAP-seq, MACS2.2.6 was used to identify protein binding sites (peaks). TF peaks which overlap with Halo peaks were removed. The top 6,000 peaks, ranked first by -log10(qvalue), then by fold enrichment, were used to discover novel DNA-binding motifs by MEME-ChIP in MEME software toolkit.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files were provided; In lncRNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided. In DAP-seq, peak files were provided.

value: 14-days-old seedlings

tag: chip antibody

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #


title: Fasted Knockout 3

tag: tissue


title: Fasted Knockout 2

tag: Sex


title: Fasted Knockout 1


title: OAVS24

tag: disease state

value: male

tag: epigenetic age


title: Fasted Knockout 4


title: CS_seedlings_H3K9ac_ChIP_seq_rep1


title: Neuro-2A_SUPT16_non_targeting

value: Neuro-2a cells

value: Transfected with plasmids encoding spCas9 and non-targeting sgRNA from PX458


title: OAVS32


title: CS_seedlings_H3K4me3_ChIP_seq_Rep2

source_name: Triticum aestivum 14-days-old seedlings


title: OAVS23


title: CS_seedlings_H3K4me3_ChIP_seq_Rep1


title: CS_seedlings_H3K27me3_ChIP_seq_Rep2


title: OAVS22


title: OAVS28


title: Fed Control 5

description:
Gene expression data from mouse intestines with PC synthesis in the re-fed state
Pcyt1aLoxp/LoxP;VilcreERT2 mice were treated with tamoxifen for 5 days to induce Cre recombinase, and LoxP/LoxP control mice were also treated with tamoxifen.

source_name: Mouse intestines with PC synthesis in the re-fed state

treatment_protocol: The mice were placed on a high fat diet for 3 days before being fasted overnight and re-fed a high fat diet for 2 hours. Intestines were excised and opened longitudinally. 3 cm was removed from the geometric middle of the small intetsine (jejunum) and stored in liquid nitrogen.

tag: genotpye

tag: age and sex

value: 10-12 week old female


title: Fed Control 2


title: Fed Control 4


title: P20190717 UCEC

city: Beijing

first: Sijin

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Science

institute: Peking University

description:
UCEC_normalized_expression.csv.gz
UCEC_metadata.csv.gz
cDC2_normalized_expression.csv.gz
cDC2_metadata.csv.gz

data_processing:
Cell Ranger 3.0.0 was used to quantify gene expression level.
Scanpy 1.4.3 was used to conduct the scRNA-seq analysis.
Genome_build: GRCh38

source_name: UCEC

extract_protocol:
Tumors and adjacent normal tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single cell suspensions were stained with antibodies against CD45 and 7AAD for FACS sorting, performed on a BD Aria SORP instrument. Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul. Cells were loaded between 7,000 and 15,000 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3 barcoding chemistry) according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.
10x Chromium Single cell 5’ Library

value: Non-cancer, Tumor

tag: patient id


title: P20190910 UCEC


title: OAVS30


title: P20190625 UCEC


title: OAVS20


title: Fed Knockout 4

description:
Gene expression data from mouse intestines without PC synthesis in the re-fed state
Pcyt1aLoxp/LoxP;VilcreERT2 mice were treated with tamoxifen for 5 days to induce Cre recombinase, and LoxP/LoxP control mice were also treated with tamoxifen.

source_name: Mouse intestines without PC synthesis in the re-fed state


title: Fed Control 1


title: Fed Knockout 5


title: Fed Knockout 2


title: Fed Knockout 3


title: OAVS15


title: P20190305 UCEC


title: OAVS16


title: OAVS21


title: TOX3_2

city: Jinan

first: Yuanyuan

last: Man

state: Shandong

address: No.157, Jingliuweiwu Road

department: Center for Reproductive Medicine

institute: Shandong University

data_processing:
The sequencing data were filtered with SOAPnuke by removing reads containing sequencing adapters
Reads whose low-quality base ratio, i.e., a base quality less than or equal to 5, was above 20%
Reads whose unknown base ('N' base) ratio was more than 5%, after which clean reads were obtained and stored in the FASTQ format.
Genome_build: RefSeq hg38
Supplementary_files_format_and_content: The expression levels were calculated using RNA-Seq by Expectation Maximization

source_name: Ovarian granulosa cells

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F12) (Hyclone Corporation, South Logan, UT, USA) supplemented with 10% fetal bovine serum (Hyclone Corporation) and 100 U/mL penicillin (Hyclone Corporation) and 100 mg/mL streptomycin (Hyclone Corporation) at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted by removing the culture medium and lysing the remaining cells using TRIzol™ Reagent (Takara Bio, Beijing, CHN) according to the manufacturer’s instructions. RNA concentration and integrity number were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control (lentiviral-control, LV-CON) and TOX3 (lentiviral-TOX3, LV-TOX3) overexpression lentiviruses (Genechem Company, Shanghai, CHN) carrying the puromycin resistance gene were synthesized. Lentiviruses were added at a ratio of 1:200 into the cell culture medium when cell fusion reached 60–70%. Positive cells were screened using 2 mg/mL of puromycin for two passages.

tag: cell line

value: KGN

value: Ovarian granulosa cells

tag: genotype/variation

value: TOX3 overexpression


title: Fed Control 3


title: TOX3_1


title: Fed Knockout 1


title: P20181211 UCEC


title: W2

city: WuHan

first: wang

middle: rui

last: rui

address: District fruit lake street

department: Medical Research Institute

institute: WuHanUniversity

description: AllSamplesFPKMValue.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mus_musculus.GRCm38.94
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Mammary basal cell

growth_protocol: mammary basal cells were routinely sorted by flow cytometer cell sorting experiment after stained with antibodies

extract_protocol:
mammary basal cells were routinely sorted by flow cytometer ,cells was immediately lysated into 1ul specific smart seq reagent,and RNA was harvested using Trizol reagent.RNA sequencing libraries were generated using the KAPA Stranded RNA-Seq Kit for illumina with multiplexing primers, according to the manufacturer’s protocol. Then sequencing was performed on illumina Nova sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: singel cell preparation

tag: strain

value: mammary gland

value: 8 weeks old

tag: genotype

value: wild type


title: CON_2

tag: cell type

value: control


title: W1

description: AllSamplesFPKMValue.txt

tag: age


title: P20181122 UCEC


title: OAVS18

value: Oculo-auriculo-vertebral spectrum

value: Peripheral Blood


title: P20190911 UCEC


title: OAVS19


title: CON_1


title: OAVS12

value: female


title: P20190312 UCEC


title: P20190816 THCA

description:
THCA_normalized_expression.csv.gz
THCA_metadata.csv.gz
cDC2_normalized_expression.csv.gz
cDC2_metadata.csv.gz

source_name: THCA


title: Lung, Sp140-/- rep1

city: Boston

first: Daisy

last: Ji

state: Massachusetts

address: 665 Huntington Avenue, Building 1, Room 811

institute: Harvard University School of Public Health

data_processing:
Base calling was performed using bcl2fastq2 v2.20
Sequence reads were aligned to mm10 genome using Kallisto version 0.46.0 using standard parameters.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files include raw counts and normalized TPM (transcript per million) values for each sample.
matrix file containing raw counts for each sample and each gene.

source_name: Lung

extract_protocol:
Lungs were preserved in RNAlater and frozen in -80ºC. Samples were homogenized in TRIzol reagent, extracted with chloroform and further cleaned using E.Z.N.A Total RNA kit I (Omega Bio-tek). Total RNA was treated with Dnase I.
Illumina-compatible library construction was performed by the QB3 Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley. PolyA selection was performed. Standard size libraries were constructed using Kapa Biosystems library preparation kits.

treatment_protocol: Mice were infected with low dose of wildtype M. tuberculosis Erdman via the aerosol route. Samples were harvested at 25 days post-infection.

value: Sp140-/- on C57BL/6J background

value: lung

tag: infection

value: M. tuberculosis for 25 days


title: Lung, Sp110-/- rep2

value: Sp110-/- on C57BL/6J background


title: Iso rep2

city: Hong Kong

first: Nancy

middle: Y.

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

data_processing:
The transcript-level expression analysis was performed as previously described (Pertea et al, Nat Protoc 11, 1650-1667, 2016). Briefly, quality control was first accomplished using FastQC and RSeQC. The FASTQ files were aligned to human GRCh38.91 reference genome using HISAT2 alignment program. The aligned files were assembled into potential transcripts using StringTie assembler program. Next, the potential transcripts were passed to the prepDE program to generate read counts. Minimal pre-filtering with row counts greater than 10 reads was performed. Differential gene expression analysis was performed using DESeq2 from Bioconductor version 3.10
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: iPSC-derived neurons

extract_protocol:
RNA was extracted using the NucleoSpin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: isogenically-corrected (Iso)


title: Lung, Sp140-/- rep2


title: Iso rep1

institute: Hong Kong University of Science and Technology


title: OAVS14


title: Lung, Sp110-/- rep1


title: Iso rep3


title: Lung, B6.Sst1S rep2

value: B6J.C3-Sst C3HeB/FeJKrmn


title: OAVS10

value: male


title: APP rep3

value: APP duplication (APP)


title: P20190213 UCEC

value: Non-cancer, Tumor


title: Lung, B6.Sst1S rep1


title: P20190612 THCA


title: APP rep2


title: P20190621 THCA


title: APP rep1


title: P20190730 THCA


title: Lung, B6 rep2


title: P20190125 THCA


title: OAVS08


title: OAVS13


title: OAVS07


title: OAVS03


title: P20190122 THCA


title: Lung, B6 rep1


title: RPM_TAM_WT_1

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 (Version25.06.2015) whole genome using STAR aligner.
differential expression analyses of read counts was perforemed using EdgeR
the read counts were scaled with the use of the trimmed mean of M-values (TMM) method proposed by Robinson and Oshlack (Robinson & Oshlack, 2010).
Supplementary_files_format_and_content: the text file (.txt), the processed data file includes Gene Identifier, gene name, description, normalized count (between-sample-normalization, TMM)

source_name: Red pulp macrophage

extract_protocol:
Tissues were removed, cell were FACS sorted and 1000 cells were collected into lysis buffer. oligo-dT primers and dNTPs were added to lysed cells and hybridization of the primer to poly(A) tails
PCR products were purified with AMPure XP beads (Beckman Coulter) and 1 ng of the product was tagmented by using the Nextera XT DNA sample preparation kit (Illumina)

value: WT

value: spleen

tag: developmental stage

value: adult


title: RPM_TAM_WT_3


title: Hudep2_ABEmax_RNA_seq_rep2

description: RNA-seq

data_processing:
Gene expression profiles were quantified using Kallisto (v0.43.1) on hg19 Ensembl v75 cDNA annotation.
Gene expression correlation was calculated based on TPM values.
Genome_build: hg19
Supplementary_files_format_and_content: tsv

extract_protocol:
RNA was extracted from 1 million HUDEP-2 cells, using the RNeasy Mini Kit (Qiagen).
The TruSeq Stranded mRNA Library Prep Kit (Illumina) was used to enrich for polyA+ RNA and to create libraries for HiSeq2000 sequencing (Illumina).


title: NDC rep2

value: nondemented control (NDC)


title: NDC rep3


title: P20181226 THCA


title: RPM_TAM_CreERT2_4


title: P20190118 THCA


title: Hudep2_ABEmax_RNA_seq_rep1

description: RNA-seq


title: NDC rep1


title: OAVS09

data_processing: Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP (release 2.8.9) package (Morris TJ et al., 2014) implemented R environment (version 3.6.2). ChAMP pre-processing module appears more suitable in preventing biases due to genetic variations in downstream analyses by filtering an increased number of probes. Sites with a detection p-value above 0.01 (n=4706) and a bead count <3 in at least 5% of samples (n=226) were removed. Moreover, also non-GpG probes (n=3025), potentially SNP affected probes (n=57699) (Zhou Wet al., 2017) probes aligning to multiple locations (n=11) (Nordlund J et al., 2013) and of X and Y chromosomes (n=9705) were filtered out. As a final outcome of the filtering procedures, a total of 410140 CpG sites were retained. Quantile normalization was performed through preprocessCore package (release 1.38.1).

extract_protocol: DNA was extracted from peripheral blood lymphocytes of probands and their parents (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).


title: OAVS02


title: P20190925 KIDNEY

description:
KIDNEY_normalized_expression.csv.gz
KIDNEY_metadata.csv.gz
cDC2_normalized_expression.csv.gz
cDC2_metadata.csv.gz

source_name: KIDNEY


title: RPM_TAM_CreERT2_5


title: P20190703 THCA


title: P20190108 THCA


title: RPM_TAM_CreERT2_2


title: OAVS05


title: P20190923 KIDNEY


title: PARP 7 KD with SiRNA 3 Replicate 2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
PARP7_SiRNA3_R2
polyA-RNA-seq
processed data file: SiRNA3.Forward.bw
processed data file: SiRNA3.Reverse.bw

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using TopHat a fast splice junction mapper for RNA-Seq reads using the ultra high-throughput short read aligner Bowtie (Langmead et al, 2009).
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and bigwig files were generated to for presentation as browser tracks using custom R scripts.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.bw: BigWig files

source_name: PARP 7 KD with siRNA 3

growth_protocol: OVCAR4 cells were purchased from the American Type Cell Culture (ATCC). They were maintained in RPMI (Sigma-Aldrich, R8758) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Fresh cell stocks were regularly replenished from original stocks and tested for mycoplasma.

extract_protocol:
Two biological replicates of total RNA were isolated from each siRNA-mediated knockdown. Total RNA was isolated using the RNeasy kit (Qiagen, 74106) according to the manufacturer’s instructions. The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen).
The polyA+ RNA was then used to generate strand-specific RNA-seq libraries as described previously (Zhong et al., 2011). The RNA-seq libraries were subjected to QC analyses (final library yield, and the size distribution of the final library DNA fragments) and sequenced using an Illumina HiSeq 2000.

treatment_protocol: OVCAR4 cells were transfected with control or PARP7-specific siRNAs at a final concentration of 30 nM in 10 cm diameter culture dishes. Twenty-four hours later, the cells were collected and plated at a density of 20,000 cells per well in a 24-well plate.

tag: sirna

value: PARP7 siRNA3


title: RPM_TAM_CreERT2_1


title: RPM_d7_Spic_WT_3

value: pup D7


title: Hudep2_RNA_seq_rep1

description: RNA-seq


title: OAVS04

city: Cusano Milanino

first: Luciano

address: Via Zucchi 18

institute: IRCCS Istituto Auxologico Italiano

value: Oculo-auriculo-vertebral spectrum

value: Peripheral Blood


title: RPM_d7_Spic_WT_2


title: Hudep2_RNA_seq_rep2

description: RNA-seq


title: OAVS01


title: P20181224 KIDNEY


title: RPM_d7_Spic_WT_1


title: PARP 7 KD with SiRNA 2 Replicate 2

description:
PARP7_SiRNA2_R2
polyA-RNA-seq
processed data file: SiRNA2.Forward.bw
processed data file: SiRNA2.Reverse.bw

source_name: PARP 7 KD with siRNA 2

value: PARP7 siRNA2


title: P20190919 KIDNEY


title: PARP 7 KD with SiRNA 3 Replicate 1

description:
PARP7_SiRNA3_R1
polyA-RNA-seq
processed data file: SiRNA3.Forward.bw
processed data file: SiRNA3.Reverse.bw


title: PARP 7 KD with SiRNA 2 Replicate 1

description:
PARP7_SiRNA2_R1
polyA-RNA-seq
processed data file: SiRNA2.Forward.bw
processed data file: SiRNA2.Reverse.bw


title: P20190918 KIDNEY


title: RPM_d7_Spic_KO_2


title: P20190909 PAAD

description:
PAAD_normalized_expression.csv.gz
PAAD_metadata.csv.gz
cDC2_normalized_expression.csv.gz
cDC2_metadata.csv.gz

source_name: PAAD

value: Tumor


title: P20181217 KIDNEY


title: RPM_d7_Spic_KO_1


title: PARP 7 KD with SiRNA 1 Replicate 1

description:
PARP7_SiRNA1_R1
polyA-RNA-seq
processed data file: SiRNA1.Forward.bw
processed data file: SiRNA1.Reverse.bw

source_name: PARP 7 KD with siRNA 1

value: PARP7 siRNA1


title: PARP 7 KD with SiRNA 1 Replicate 2

description:
PARP7_SiRNA1_R2
polyA-RNA-seq
processed data file: SiRNA1.Forward.bw
processed data file: SiRNA1.Reverse.bw


title: P20190515 PAAD


title: P20190306 PAAD


title: P20190225 PAAD


title: Negative KD Control Replicate 2

description:
PARP7_SiRNANeg_R2
polyA-RNA-seq
processed data file: SiRNANeg.Forward.bw
processed data file: SiRNANeg.Reverse.bw

source_name: Negative KD Control

value: PARP7 siRNANeg


title: Negative KD Control Replicate 1

description:
PARP7_SiRNANeg_R1
polyA-RNA-seq
processed data file: SiRNANeg.Forward.bw
processed data file: SiRNANeg.Reverse.bw


title: P20181128 PAAD


title: P20181121 PAAD


title: P20190304 OV-FTC

description:
OV-FTC_normalized_expression.csv.gz
OV-FTC_metadata.csv.gz
cDC2_normalized_expression.csv.gz
cDC2_metadata.csv.gz

source_name: OV-FTC


title: CD62L-low GMP rep-3

city: Shinjuku-ku

first: Yusuke

last: Ito

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology

country: Japan

institute: Keio University

data_processing:
Base calling was performed by Illumina RTA software in sequencer, further demultiplexing was performed by Illumina bcl2fastq software.
Adaptor trimming, mapping and acquiring read count data were performed by Trim-Galore, Hisat2 and Htseq.
bulk CMP rep-2 was removed from analysis due to low mapping rate.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample

source_name: murine hematopoietic progenitor cells

extract_protocol:
Mononuclear cells were extracted from bone marrow cells, then each subset was sorted by flow cytometry and RNA was extracted.
RNA libraries were prepared for sequencing using SMARTer Stranded RNA-Seq Kit.

value: hematopoietic progenitors from bone marrow

tag: cell subset

value: CD62L-low GMP


title: CD62L-high GMP rep-1

value: CD62L-high GMP


title: CD62L-high GMP rep-2


title: CD62L-low GMP rep-2


title: P20181225 OV-FTC

tag: tissue


title: CD62L-low GMP rep-1


title: CD62L-neg GMP rep-3

value: CD62L-neg GMP


title: P20190322 MYE

description:
MYE_normalized_expression.csv.gz
MYE_metadata.csv.gz
cDC2_normalized_expression.csv.gz
cDC2_metadata.csv.gz

source_name: MYE

value: Blood, Tumor


title: P20190306 MYE


title: KPPF;Col1smaKO mouse PDAC 3 [7-13-10]

city: Houston

first: Yang

last: Chen

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

description: Each biological sample includes 8 Fastq files

data_processing:
Fastq files from the Illumina platform were aligned to the reference genome mm10 using the Spliced Transcripts Alignment to a Reference (STAR) algorithm
HTSeq-count was then utilized to generate the raw counts for each gene
Raw counts were then analyzed by DESeq2 for data processing, normalization, and differential expression analysis according to standard procedures.
Genome_build: Raw sequencing data from the Illumina platform were converted into Fastq files and aligned to the reference genome mm10 using the Spliced Transcripts Alignment to a Reference (STAR) algorithm
Supplementary_files_format_and_content: txt

source_name: KPPF;Col1smaKO mouse PDAC

growth_protocol: Mice with standard housing conditions

extract_protocol:
Direct-zol RNA extraction kit (Zymo)
Illumina TrueSeq stranded mRNAseq Library

treatment_protocol: Mice received no treatment

tag: detailed genotype

value: pancreatic tumor


title: CD62L-neg GMP rep-2


title: CD62L-neg GMP rep-1


title: KPPF;Col1smaKO mouse PDAC 2 [7-13-9]


title: P20190122 MYE


title: KPPF;Col1smaKO mouse PDAC 1 [7-13-7]


title: CD62L-high GMP rep-3


title: bulk GMP rep-3

value: bulk GMP


title: P20181219 MYE


title: KPPF mouse PDAC 3 [7-18-12]

source_name: KPPF mouse PDAC

value: KPPF


title: P20190301 LYM

description:
LYM_normalized_expression.csv.gz
LYM_metadata.csv.gz
cDC2_normalized_expression.csv.gz
cDC2_metadata.csv.gz

source_name: LYM


title: KPPF mouse PDAC 2 [7-18-11]


title: bulk GMP rep-1


title: KPPF;Col1smaKO mouse PDAC 4 [7-13-11]


title: P20181123 LYM


title: KPPF mouse PDAC 1 [7-18-9]


title: rat-NS-NS challenge-1 rep

first: Hui

address: 27th Taiping Road

institute: Beijing Key Laboratory of Neuropsychopharmacology

hyb_protocol: the labeled RNA targets were hybridized to the Rat Whole Genome OneArray® (ROA 1.1) (Phalanx Biotech Group) according to the Phalanx hybridization protocol.

scan_protocol: The slides were scanned using an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
The Cy5 fluorescence intensity of each spot was analyzed using GenePix pro software (Molecular Devices).
The signal intensity of each spot was loaded into the Rosetta Resolver System® (Rosetta Biosoftware) for data analysis.

source_name: total mRNA from PFC NS-NS group

label_protocol: the amplified RNA argets were labeled with dye (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: The fluorescently amplified RNA targets were prepared from 2.5 μg of total RNA samples using the OneArray® Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group)。

treatment_protocol: The rats were administrated with METH (5 mg/kg, s.c.) or normal saline (NS) (1 ml/kg, s.c.) once daily in acute phase or for 7 days in development phase. On d8-14, the rats were housed in home cages, and nothing was injected in withdrawal phase. On d15, METH (1 mg/kg, s.c.) was used to challenge in the rats that were administrated with NS or METH in development phase, and then the locomotor activity was recorded for 60 min in challenge phase.

value: Sprague-Dawley

value: prefrontal cortex

tag: gender

value: male


title: CD62L-high CMP rep-3

value: CD62L-high CMP


title: rat-NS-METH challenge-1 rep

source_name: total mRNA from PFC METH-NS group


title: P20190404 LYM


title: CD62L-high CMP rep-2


title: P20190401 LYM


title: CD62L-high CMP rep-1


title: P20190916 ESCA

description:
ESCA_normalized_expression.csv.gz
ESCA_metadata.csv.gz
cDC2_normalized_expression.csv.gz
cDC2_metadata.csv.gz

source_name: ESCA

value: Non-cancer, Tumor


title: CD62L-low CMP rep-3

value: CD62L-low CMP


title: rat-H4-NS-METH challenge-1 rep

description: Adult male Sprague-Dawley rats weighing 160-180 g were used in this study.

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on a NimbleGen MS 200 Microarray Scanner per manufacturer's protocol (http:// www.nimblegen.com/products/instruments/ under Literature).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: H4 hyperacetylation ChIP DNA from PFC METH-NS group

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: prefrontal cortex tissues were crosslinked with 1% formaldehyde at 37°C for 10 min, and then glycine was added to a final concentration of 0.125 M and incubated for 5 min to stop the crosslinking. Samples were centrifuged at 800 g at 4°C for 10 min to pellet tissues. The PFC tissues were sonicated on wet ice in 300 μl of nuclear lysis buffer using a sonicator (Sonics Vibra-cellTM, Sonics & Materials Inc., Newtown, Connecticut, USA). The sonication conditions were used: amplitude 70%, pulse 10 sec, and pause 59 sec for 9 cycles. The supernatant was collected as described in the instructions of a chromatin immunoprecipitation kit (Millipore, Cat. No. 17408). The lysate was precipitated with antibodies against acetyl-histone H3 (Millipore, Cat. No. 06599) and acetyl-histone H4 (Millipore, Cat. No. 06866).

tag: chip antibody

source_name: Input DNA from PFC H4-METH-NS group

value: none, input DNA


title: rat-H4-NS-NS challenge-1 rep

source_name: H4 hyperacetylation ChIP DNA from PFC NS-NS group

source_name: Input DNA from PFC H4-NS-NS group


title: rat-METH-METH challenge-1 rep

source_name: total mRNA from PFC METH-METH group


title: P20190613 ESCA


title: P20181123 ESCA


title: P20181114 ESCA


title: rat-H4-METH-METH challenge-1 rep

source_name: H4 hyperacetylation ChIP DNA from PFC METH-METH group

source_name: Input DNA from PFC H4-METH-METH group


title: CD62L-low CMP rep-1


title: rat-H3-NS-NS challenge-1 rep

source_name: H3 hyperacetylation ChIP DNA from PFC NS-NS group

source_name: Input DNA from PFC H3-NS-NS group


title: bulk GMP rep-2

source_name: murine hematopoietic progenitor cells


title: P20190411 ESCA


title: bulk CMP rep-3

value: bulk CMP


title: rat-H3-NS-METH challenge-1 rep

source_name: H3 hyperacetylation ChIP DNA from PFC METH-NS group

source_name: Input DNA from PFC H3-METH-NS group


title: bulk CMP rep-2


title: P20190410 ESCA


title: rat-H3-METH-METH challenge-1 rep

source_name: H3 hyperacetylation ChIP DNA from PFC METH-METH group

source_name: Input DNA from PFC H3-METH-METH group


title: mouse_control_rep1

first: sun

middle: tong

last: xin

address: xinjunhuanlu

institute: oebiotech

description: Gene expression  in mouse cell

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE V2.0 Microarray(8*60K)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 by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k 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 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Mus musculus control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

tag: agent

value: DMSO


title: mouse_case_rep1

description: Gene expression  in mouse cell

source_name: Mus musculus case


title: P20190404 ESCA

last: Cheng

source_name: ESCA


title: bulk CMP rep-1

value: hematopoietic progenitors from bone marrow


title: CD62L-low CMP rep-2


title: E.timonensis-GABA B3

status: Public on Feb 03 2021

city: Cambridge

first: Lauren

middle: Julia

last: Rajakovich

state: MA

address: 12 Oxford Street

department: Chemistry & Chemical Biology

institute: Harvard University

data_processing:
Reads were identified based on their associated barcode using custom scripts, allowing one mismatch in the barcode
Barcode sequences were removed from the first read as were terminal G's from the second read
Reads were alignmed using BWA
Reads were assigned to genes and other genomic features using custom scripts
Differential expression analysis was performed using DESeq2
Genome_build: Reference genome FLKM00000000.1
Supplementary_files_format_and_content: normalized abundance measurements (RPKM)

organism: Emergencia timonensis

source_name: bacterial culture

growth_protocol: E. timonensis SN18 cultures (15 mL) were grown under anaerobic conditions in PYG-modified medium at 37 °C.

extract_protocol:
Cultures were centrifuged and cell pellets were resuspended in cold Trizol reagent, followed by flash freezing in liquid nitrogen. Total RNA was isolated by bead beating using 0.1 mm dia. Zirconia/Silica Beads at 10 m/s for 90 s, then using the Zymo Resarch Direct-Zol RNA MiniPrep Plus Kit.
Illumina cDNA libraries were generated using a modified version of the RNAtag-Seq protocol (63). Briefly, 500 ng of total RNA was fragmented, depleted of genomic DNA, and dephosphorylated prior to its ligation to DNA adapters carrying 5ʹ-AN8-3ʹ barcodes with a 5ʹ phosphate and a 3ʹ blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (Epicentre, Madison, WI). These pools of barcoded RNAs were converted to Illumina cDNA libraries in three main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcoded adaptor; (ii) addition of a second adapter on the 3’ end of the cDNA during reverse transcription using SmartScribe RT (Clontech Biotechnologies, Mountain View, CA) as previously described (63); (iii) PCR amplification using primers that target the constant regions of the 3’ and 5’ ligated adaptors and contain the full sequence of the Illumina sequencing adaptors.

treatment_protocol: At OD=0.7 (trial A) or OD=0.5 (trial B), 1 mM of gamma-butyrobetaine, DL-carnitine, gamma-aminobutyric acid, or 1x PBS (vehicle) were added and cultures were grown for additional 45 min.

tag: treatment

value: gamma-aminobutyric acid

tag: trial

value: B


title: E.timonensis-GABA B1


title: E.timonensis-carnitine B2

value: dl-carnitine


title: E.timonensis-gbb B3

value: gamma-butyrobetaine


title: E.timonensis-gbb B1


title: E.timonensis-vehicle B3

value: vehicle


title: E.timonensis-carnitine B1


title: E.timonensis-vehicle B2


title: ChIP-Seq_TrcR_WTRm1021_S.meliloti_PYERif100

city: Geneva 4

first: Patrick

last: Viollier

address: Rue Michel Servet 1

department: Microbiology and Molecular Medicine

institute: University of Geneva UNIGE

data_processing:
Base calling: HiSeq Control Software 2.2.58, RTA 1.18.64.0, CASAVA-1.8.2
Alignment: Map with Bowtie for illumina (Galaxy Version 1.2.0), SAM-to-BAM (Galaxy Version 2.1.1)
Peak calling and refinement: MACS2 Callpeak (Galaxy Version 2.1.1.20160309.6)
Peak annotation: SeqMonk Software v1.46 (Braham Bionformatics Institute)
Genome_build: Caulobacter crescentus : NC_011916.1, Sinorhizobium meliloti chromosome : NC_020528.1, Sinorhizobium meliloti pSymA: NC_020527.1 and Sinorhizobium meliloti pSymB: NC_020560.1
Supplementary_files_format_and_content: The xls file reporting TrcR, RpoD and RNAP ChIP-Seq peaks was generated by MACS2 software. The sheet is organized in columns as follows: column 1: Peak # (order on chromosome); column 2: Peak start coordinates (bp); column 3: Peak end coordinates (bp); column 4: Peak length coordinates (bp); column 5: Peak summit coordinates (bp); column 6: Peak pileup; column 7: -LOG10(pvalue); column 8: Fold enrichment; column 9: -LOG10(qvalue). Common peaks between TrcR, RNAP, RpoD and CdnL are highlighted.

organism: Sinorhizobium meliloti 2011

source_name: Sinorhizobium meliloti 2011

growth_protocol: Mid-log phase C. crescentus cells were cultured in PYE and S. meliloti cells cultured in LB supplemented with CaCl2 2.5 mM and MgSO4 2.5 mM or with an extra 10 minutes treatment with antibiotics (Rifampicin 30 μg/ml for C. crescentus and 100 μg/ml for S. meliloti ; Nalidixic Acid 20 μg/ml).

extract_protocol:
Cells were lysed in a Ready-Lyse lysozyme solution (Epicentre Technologies) according to manufacturer’s instructions and lysates were sonicated (Bioruptor® Pico) in an ice-water bath for 15 cycles 30 seconds ON and 30 seconds OFF, to shear DNA fragments to an average length of 0.3-0.5 kbp and cleared by centrifugation at 14,000 g for 2 minutes at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 mL using ChIP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl (pH 8.1), 167 mM NaCl plus protease inhibitors (Roche, Switzerland) and pre-cleared with 80 μL of protein-A (rabbit antibodies) or –G (mouse antibodies) agarose (Roche) and 100 μg BSA. Ten percent of the supernatant was removed and used as total chromatin input DNA as described before (Delaby et al., 2019).Two microliters of polyclonal antibodies to TrcR, or of a mix of RNA polymerase from a monoclonal antibody sampler kit (ratio 1:1:1:1, Biolegend), or of monoclonal antibodies to σ70 (BioLegend, Mouse IgG2b) were added to the remains of the supernatant, incubated overnight at 4 °C with 80 μL of protein-A or -G agarose beads pre-saturated with BSA, washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 150 mM NaCl), high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 500 mM NaCl) and LiCl buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)), and twice with TE buffer (10 mM Tris-HCl (pH 8.1) and 1 mM EDTA). The protein DNA complexes were eluted in 500 μL freshly prepared elution buffer (1% SDS and 0.1 M NaHCO3), supplemented with NaCl to a ﬁnal concentration of 300 mM and incubated overnight at 65 °C to reverse the crosslinks. The samples were treated with 2 μg of Proteinase K for 2 h at 45 °C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol precipitated using 20 μg of glycogen as carrier and resuspended in 100 μL of water.
Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer’s instructions.

treatment_protocol: Cells were cross-linked in 10 mM sodium phosphate (pH 7.6) and 1% formaldehyde at room temperature for 10 minutes and on ice for 30 minutes thereafter and washed three times in phosphate-buffered saline (PBS).

value: Wild type


title: E.timonensis-vehicle B1


title: ChIP-Seq_TrcR_WTRm1021_S.meliloti_PYE


title: E.timonensis-gbb A2

value: A


title: E.timonensis-gbb A3


title: E.timonensis-vehicle A1


title: E.timonensis-vehicle A2


title: E.timonensis-vehicle A3


title: E.timonensis-GABA B2


title: E.timonensis-carnitine B3


title: E.timonensis-gbb B2


title: AtWW_G_mRNA

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

description:
mRNA-seq processed data.xlsx
AtWW_G

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

organism: Triticum turgidum subsp. durum

source_name: Developing grain tissue

growth_protocol: Durum wheat variety DBA Artemis plants were grown in controlled glasshouse conditions as previously described (Liu et al., 2019). The standard growing conditions were 22°C/12°C (day/night) with a 12h photoperiod.

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

treatment_protocol: The treatment groups are: AtCC (DBA Artemis control group parents, progenies treated with control), AtCW (DBA Artemis control group parents, progenies treated with water-deficit stress), AtWC (DBA Artemis water-deficit stress group parents, progenies treated with control), AtWW (DBA Artemis water-deficit stress group parents, progenies treated with water-deficit stress). L represents flag leaf libraries, G represents developing grain libraries. All plants were well-watered from germination to booting. Water-deficit stress was applied by maintaining the soil water content at 6% (half of the field capacity) from booting until harvest. Flag leaf and developing grain samples were collected at 5 DPA (days post anthesis).

value: DBA Artemis

tag: origin of the parental plants

value: Water-deficit stress group parents

tag: progeny treatment

value: Water-deficit stress group


title: E.timonensis-gbb A1

tag: strain


title: AtWC_G_mRNA

description:
mRNA-seq processed data.xlsx
AtWC_G

tag: genotype

value: Control group


title: AtWW_L_mRNA

description:
mRNA-seq processed data.xlsx
AtWW_L

source_name: Flag leaf tissue


title: AtCC_G_mRNA

description:
mRNA-seq processed data.xlsx
AtCC_G

value: Control group parents


title: AtCW_G_mRNA

description:
mRNA-seq processed data.xlsx
AtCW_G


title: AtWC_L_mRNA

description:
mRNA-seq processed data.xlsx
AtWC_L


title: AtCC_L_mRNA

description:
mRNA-seq processed data.xlsx
AtCC_L


title: AtCW_L_mRNA

description:
mRNA-seq processed data.xlsx
AtCW_L


title: ChIP-Seq_GcrA_WT_C.crescentus_PYERif30

organism: Caulobacter vibrioides NA1000

source_name: C. crescentus cells


title: ChIP-Seq_GcrA_WT_C.crescentus_PYE


title: Adeno-Cre infected mouse primary keratinocyte from Sos1/2 DKO mice, biological rep 2

city: SALAMANCA

first: FERNANDO

middle: C

last: BALTANAS

state: SALAMANCA

address: CAMPUS MIGUEL DE UNAMUNO

country: Spain

institute: CANCER RESEARCH CENTER

description: DKO.E

hyb_protocol: Protocol was developed following GeneChip® WT PLUS Reagent Kit userguide.

scan_protocol: Affymetrix GeneChip Command Console 3.2

data_processing:
R version 3.6.3 was used for statistical analyses along with Python version 3.9 for text file processing. Signal intensity values were obtained from expression microarray CEL files after robust multichip average (RMA)
Differentially expressed genes were identified using linear models for microarray data (Limma). Adjusted P-values for multiple comparisons were calculated applying the Benjamini-Hochberg correction (FDR)

label_protocol: Fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded cDNA is required for fragmentation and labeling

growth_protocol: Mice were kept, managed and sacrificed in the NUCLEUS animal facility of the University of Salamanca according with current European and Spanish legislations

extract_protocol: RNA from GFP-Adeno-Cre-treated 2D-cultured primary keratinocytes of the four relevant genotypes (WT, Sos1 KO, Sos2 KO and Sos1/2 DKO) was extracted with Nyzol and QIAGEN RNeasy Mini kit (74104, QIAGEN) following manufacturer’s recommendations

treatment_protocol: P0-P2 neonates from the four relevant genotypes (WT, Sos1 KO, Sos2 KO and Sos1/2 DKO) were euthanized and their skin removed and incubated in Keratinocyte-SFM (10725-018, Gibco) containing dispase (250 U/ml, 04942078001, Gibco) and antibiotics (penicillin/streptomicyn), for 16h at 4°C. Next, the epidermis was mechanically separated from the dermis and placed over 400 ml of accutase (Cnt-Accutase-100, CELLnTEC) for 1 h at 37°C. The keratinocytes were then mechanically extracted and cultured as indicated. For 2D-cultures, primary keratinocytes (1.5 x 106 cells) were seeded on 10-cm dishes with KSFM-medium supplemented with human recombinant EGF, bovine pituitary extract (Gibco and antibiotics (penicillin/streptomicyn) and 0.02M CaCl2. Sos1 depletion in Sos1 KO and Sos1/2 DKO primary keratinocytes was achieved by infecting the cells with GFP-Adeno-Cre (Ade5CMVCre-eGFP; VVC-U Iowa-1174; MOI=2) for 72 h. To avoid off-target effects of the GFP-Adeno-Cre, both WT and Sos2 KO cells were also infected with the adenovirus under the same conditions.

tag: strain background

tag: genotype/variation

value: Sos1/2 DKO

value: skin

tag: cell type

value: primary keratinocytes


title: RNA-Seq_DeltatrcRrep2

data_processing:
sequencing quality control: FastQC v.0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Alignment: BWA aligner v.0.7.15 (Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60)
The table of counts with the number of reads mapping to each gene feature of the NCBI C. crescentus NA1000 was prepared with HTSeq v0.6p1 (htseq-count, http://www-huber.embl.de/users/anders/HTSeq/).
The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v.3.18.1 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140). Briefly, the counts were normalized according to the library size and filtered. The genes having a count above 1 count per million reads (cpm) in at least 2 samples were kept for the analysis.
The differentially expressed genes tests were done with exact Test using a negative binomial distribution. The differentially expressed genes p-values are corrected for multiple testing error with a 5% FDR (false discovery rate). The correction used is Benjamini-Hochberg (BH).
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: Supplementary_Table1 - RNA-Seq analysis summarizes all the differentially expressed genes, the 2 fold changed genes, the -log(FDR) and the normalized count cpm.

source_name: Caulobacter crescentus NA1000

growth_protocol: Two independent biological replicates of WT and ΔtrcR cells were grown to an OD660 of 0.4 in PYE.

extract_protocol:
First, cells were lysed in a Ready-Lyse lysozyme solution (Epicentre Technologies) according to manufacturer’s instructions and lysates were homogenized through QiaShredder columns (Qiagen, 79654). RNA was then purified on RNEasy kit column. To remove DNA from samples, a first treatment using the On-column DNase I digestion kit (Qiagen, 79254) was performed and RNA was extracted according to manufacturer’s instructions. Extracted RNA were subjected to a second DNase treatment Using Promega RQ1 at 1 unit/mg RNA. After phenol/chloroform/isoamyl (Sigma) extraction and ethanol precipitation, the total extracted RNA was submitted to the iGE3 sequencing facility at the Genomics Platform in the CMU (University of Geneva, Faculty of Medicine) for library preparation, next generation sequencing and differential expression analysis.
The total extracted RNA was submitted to the iGE3 sequencing facility at the Genomics Platform in the CMU (University of Geneva, Faculty of Medicine) for library preparation, next generation sequencing and differential expression analysis.The total RNA subjected to library preparation using TruSeq ribodepleted Stranded mRNA (SR100-Illumina Hiseq4000) according to manufacturer’s protocols.

treatment_protocol: Total RNA was extracted using the RNA extraction kit (Qiagen).

value: trcR mutant


title: Adeno-Cre infected mouse primary keratinocyte from Sos2 KO mice, biological rep 2

value: Sos2 KO


title: Adeno-Cre infected mouse primary keratinocyte from Sos2 KO mice, biological rep 4


title: Adeno-Cre infected mouse primary keratinocyte from Sos1/2 DKO mice, biological rep 1

description: DKO.C


title: Adeno-Cre infected mouse primary keratinocyte from Wild-Type mice, biological rep 3

description: WT.C

value: Wild-Type


title: AtWC_G_sRNA

description:
sRNA-seq processed data.xlsx
AtWC_G


title: AtWW_G_sRNA

description:
sRNA-seq processed data.xlsx
AtWW_G


title: Adeno-Cre infected mouse primary keratinocyte from Sos2 KO mice, biological rep 1


title: Adeno-Cre infected mouse primary keratinocyte from Sos2 KO mice, biological rep 3


title: Adeno-Cre infected mouse primary keratinocyte from Sos1 KO mice, biological rep 3

value: Sos1 KO


title: Adeno-Cre infected mouse primary keratinocyte from Sos1 KO mice, biological rep 4


title: Adeno-Cre infected mouse primary keratinocyte from Sos1 KO mice, biological rep 2


title: Adeno-Cre infected mouse primary keratinocyte from Wild-Type mice, biological rep 1

description: WT.A


title: Adeno-Cre infected mouse primary keratinocyte from Sos1 KO mice, biological rep 1


title: Adeno-Cre infected mouse primary keratinocyte from Wild-Type mice, biological rep 2

description: WT.B


title: AtCW_G_sRNA

description:
sRNA-seq processed data.xlsx
AtCW_G


title: RNA-Seq_WTrep2


title: miR-204-3p mimics_rep3 [MiR-204-3p-3]

city: Guangzhou

first: Si-Jia

last: Liang

state: Guangdong

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Zhongshan School of Medicine, Sun Yat-Sen University

data_processing:
Quality control.Clean datas were obtained by removing low quality reads with Fastp.
Reads mapping.Clean reads were mapped to human  reference genome GRCh38 by hisat2.
Differential expression analysis of two conditions/groups was performed using the feartureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx

source_name: miR-204-3p mimics

growth_protocol: Human peripheral blood mononuclear cells were isolated from healthy volunteer donors by Percoll density gradient centrifugation, and were then differentiated into HMDMs in RPMI-1640 medium supplemented with 10% fetal calf serum, 1% HEPES, 1% penicillin/streptomycin, and 100 ng/ml of macrophage colony-stimulating factor.

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: HMDMs were transfected with miRNA mimics negative control or miRNA-204-3p mimics for 24 h.

value: human monocyte-derived macrophages

value: transfected with miR-204-3p mimics


title: miR-204-3p mimics_rep4 [MiR-204-3p-4]


title: RNA-Seq_DeltatrcRrep1


title: AtCC_G_sRNA

description:
sRNA-seq processed data.xlsx
AtCC_G


title: AtWW_L_sRNA

description:
sRNA-seq processed data.xlsx
AtWW_L


title: Adeno-Cre infected mouse primary keratinocyte from Wild-Type mice, biological rep 4

description: WT.E


title: RNA-Seq_WTrep1


title: Total-Input_C.crescentus


title: AtWC_L_sRNA

description:
sRNA-seq processed data.xlsx
AtWC_L


title: AtCW_L_sRNA

description:
sRNA-seq processed data.xlsx
AtCW_L


title: miR-204-3p mimics_rep1 [MiR-204-3p-1]


title: AtCC_L_sRNA

description:
sRNA-seq processed data.xlsx
AtCC_L


title: ChIP-Seq_RpoD_DtrcR_rpoBxP642L_C.crescentus_PYE

value: DtrcR rpoB*P642L


title: miRNA mimics negative control_rep4 [NC-m-4]

source_name: miRNA mimics negative control

value: transfected with mimics negative control


title: ChIP-Seq_RpoD_DtrcR_C.crescentus_PYE


title: miRNA mimics negative control_rep3 [NC-m-3]


title: RNA-seq-HPPT_untreated_rep1

city: Bethesda

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples

source_name: human primary proximal tubule cells

growth_protocol: Primary Human Renal Proximal Tubule Epithelial Cells (ATCC® PCS-400-010™) were cultured in low-serum medium consisting of Renal Epithelial Cell Basal Medium (ATCC® PCS-400-030™) with Renal Epithelial Cell Growth Kit (ATCC® PCS-400-040™), Penicillin-Streptomycin-Amphotericin B Solution (ATCC® PCS-999-002™) and Phenol Red (ATCC® PCS-999-001™) added.

extract_protocol:
Total RNA was isolated from the cytokine-stimulated cells using PureLink™ RNA Mini Kit (Invitrogen) and libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301).
Libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: human primary proximal tubule (HPPT) cells were stimulated with IFNα, IFNβ, IFNγ, TNFα, IL-6 and IL-1β for 12 hours in concentration of 10 ng/ml.

value: untreated

value: primary proximal tubule cells


title: RNA-seq-HPPT_untreated_rep2


title: RNA-seq-HPPT_untreated_rep3


title: RNA-seq-HPPT_IL1b_rep2


title: ChIP-Seq_RpoD_WT_C.crescentus_PYE_2

value: Wild type


title: miRNA mimics negative control_rep2 [NC-m-2]


title: ChIP-Seq_RpoD_WT_C.crescentus_PYERif30


title: miRNA mimics negative control_rep1 [NC-m-1]


title: miR-204-3p mimics_rep2 [MiR-204-3p-2]


title: RNA-seq-HPPT_IFNg_rep2

value: IFNg


title: RNA-seq-HPPT_IFNg_rep3


title: RNA-seq-HPPT_IFNb_rep3

value: IFNb


title: RNA-seq-HPPT_IFNb_rep2


title: RNA-seq-HPPT_IFNg_rep1


title: RNA-seq-HPPT_IFNb_rep1


title: ChIP-Seq_RpoD_WT_C.crescentus_PYE


title: ChIP-Seq_RNAP_WT_C.crescentus_PYERif30


title: ChIP-Seq_RNAP_WT_C.crescentus_PYE


title: RNA-seq-HPPT_IFNa_rep3

value: IFNa


title: ChIP-Seq_TrcR_DtrcR_C.crescentus_PYE


title: RNA-seq-HPPT_IFNa_rep1


title: RNA-seq-HPPT_IFNa_rep2


title: RNA-seq-HPPT_IL1b_rep3


title: Sample 11-con [TN1802R1292]

city: Seoul

first: PI EN

last: CHANG

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Department of Orthodontics

country: South Korea

institute: Yonsei University College of Dentistry

description:
20180214_24_TN1802R1292
processed data file: 10expression.genes

data_processing:
Base calling was performed by bcl2fastq 2.0
The read length Hiseq2500 platform 100PE was used to put fastqc files.
Total Bases of sequencing statistics in raw data divided by Total Reads (=101): Progress with Hiseq2500 platform 100PE
Genome_build: GRCh37(hg19)
Supplementary_files_format_and_content: FPKM

source_name: adult PDL_untreated

extract_protocol:
PDL cells were washed with cold PBS after gentle scrapping from the extracted premolar. Total RNA was extracted from PDL cells using TRIzol Reagent. The RNA was stored at −70 °C and measured at an optical density of 260 nm. The mixtures of total RNA were incubated with Oligo dT. Real-time PCR was performed for the selected upregulated and downregulated genes to verify RNA-seq results.
The library was constructed, sequenced using an Illumina HiSeq2500 sequencer, and the data obtained through RNA-seq.

treatment_protocol: To stimulate the PDL, orthodontic force was applied to the first or second premolar on one side for 3 weeks, whereas the tooth on the other side was left untreated.

tag: age

value: adult tooth premolar periodontal ligment (PDL)


title: Sample 10-exp [TN1802R0683 ]

description:
20180202_24_TN1802R0683
processed data file: 10expression.genes

source_name: adult PDL_orthodontic force stimulate

value: orthodontic force stimulate for 3 wks


title: RNA-seq-HPPT_IL1b_rep1


title: ChIP-seq-HPPT_untreated_Pol2_rep2

description: RNA polymerase II (Abcam, ab5408)

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Quality filtering and alignment of the raw reads was done using Trimmomatic27 (version 0.36) and Bowtie28 (version 1.2.2) and Samtools29 (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome hg19. Homer30 (version 4.8.2) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer31 (version 2.5.3) was used for visualization.  (Langmead et al., Nature methods, 2012)  with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools (Broad Institute. Picard, http://broadinstitute.github.io/picard/.) to remove duplicates. Homer software (Heinz et al., Mol. Cell, 2010) was applied  for the generation of bedGraph files.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph of ChIP-seq

extract_protocol:
Cells were washed twice with PBS and fixed with 0.75% formaldehyde in DMEM for 10 minutes in room temperature. Next, glycine was added to quench fixation in a final concentration of 125 mM and plates were incubated in room temperature for another 10 minutes. Cells were then scraped and centrifuged at 4oC, 1 minute, 3000 rpm, then washed twice with cold PBS. Pellets were re-suspended in 2 ml Farnham Lysis Buffer with protease inhibitors and incubated on ice for 10 minutes. Then, the cells were pelleted again at 4oC, 5 minutes, 3500 rpm, and re-suspended in TE buffer with protease inhibitors. Chromatin was sonicated for 3 minutes, with 20 seconds on and off intervals, at 50% amplitude. Finally, after centrifugation at 4oC, 13000 g for 10 minutes, supernatant was used to prepare ChIP-seq libraries. Briefly, 600-1000 µg chromatin was incubated with antibody-coated Dynabeads™ Protein A (Invitrogen) at 4oC overnight. The beads were then washed with RIPA, high-NaCl RIPA, LiCl buffer and PBS. Next, DNA was eluted from the beads and reverse-crosslinked by incubating with proteinase K at 65oC overnight. DNA was then purified with MinElute PCR Purification Kit (Quiagen) and library preparation was performed according to manufacturer’s instructions for NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biotechnology).
Libraries for sequencing were prepared using standard Illumina protocols.

value: RNA polymerase II (Abcam, ab5408)


title: Sample 10-con [TN1802R0682]

description:
20180209_14_TN1802R0682
processed data file: 10expression.genes


title: Sample 11-exp [TN1802R1291]

description:
20180214_14_TN1802R1291
processed data file: 10expression.genes


title: ChIP-Seq_TrcR_WT_C.crescentus_PYENal20


title: ChIP-seq-HPPT_untreated_H3K27ac_rep1

description: H3K27ac (Active Motif, 39133)

value: H3K27ac (Active Motif, 39133)


title: Sample 9-con2 [TN1802R0184]

description:
2018_02_02_44
processed data file: 9expression.genes


title: ChIP-seq-HPPT_untreated_H3K27ac_rep2

description: H3K27ac (Active Motif, 39133)


title: ChIP-seq-HPPT_untreated_Pol2_rep1

description: RNA polymerase II (Abcam, ab5408)


title: Sample 9-exp2 [TN1802R0183]

description:
2018_02_02_34
processed data file: 9expression.genes


title: ChIP-seq-HPPT_untreated_H3K4me1_rep2

description: H3K4me1 (Active Motif, 39297)

value: H3K4me1 (Active Motif, 39297)


title: ChIP-seq-HPPT_untreated_H3K4me3_rep2

description: H3K4me3 (Millipore, 07-473)

value: H3K4me3 (Millipore, 07-473)


title: ChIP-Seq_TrcR_WT_C.crescentus_PYE


title: ChIP-seq-HPPT_IFNb_Pol2_rep1

description: RNA polymerase II (Abcam, ab5408)


title: ChIP-seq-HPPT_untreated_H3K4me3_rep1

description: H3K4me3 (Millipore, 07-473)


title: ChIP-seq-HPPT_IFNb_H3K27ac_rep1

description: H3K27ac (Active Motif, 39133)


title: Sample 9-exp1 [TN1802R0182]

description:
2018_02_02_24
processed data file: 9expression.genes


title: ChIP-seq-HPPT_untreated_H3K4me1_rep1

description: H3K4me1 (Active Motif, 39297)


title: Sample 8-con2 [TN1801R4093]

description:
34_20180117
processed data file: 8expression.genes


title: 293T_Input1_Norm_

city: Granada

first: Juan

middle: Manuel

last: Marti

address: Avda. del Conocimiento 17

institute: CSIC

data_processing:
Quality assessment and sample alignment were performed using the miARma-Seq pipeline (Andres-Leon, Nunez-Torres et al. 2016).
fastqc were applied to gather the overall sequence quality and possible adapter accumulation.
Then, all samples were aligned to the reference Human GRCH38 genome from the GENCODE portal, version 28.
All samples were aligned using Burrows-Wheeler Aligner software (Li and Durbin 2009).
PCR duplicates were removed using samtools markdup with options –s –r (Li, Handsaker et al. 2009). Peak calling was performed using MACS2 (Zhang, Liu et al. 2008) with option –f BAM –g hs –s 75 –B –SPMR –nomodel.
Genome_build: Human GRCH38 genome from the GENCODE portal, version 28
Supplementary_files_format_and_content: Processed data is presented using wig format.

source_name: HEK293T WT cells

growth_protocol: Cells were cultured on DMEM high glucose growth medium supplemented with FBSi 10%.

extract_protocol:
Cellular lysates were treated with micrococcal nuclease in order to digest genomic DNA. HIF-1α-DNA complexes were isolated with antibody.
Library preparation and Illumina sequencing were performed by the IPBLN Genomics Core Facility (CSIC, Granada, Spain). ChIP-seq libraries were generated from 30 ng of DNA using the NEBNext Ultra II DNA library preparation kit for Illumina (NEB), and following manufacturer´s instructions with some modifications. A 10-fold dilution of adaptor was used in ligation reaction and no size selection was applied to the adaptor-ligated DNA clean up step, as recommended for Micrococcal Nuclease digested chromatin ChIP assays. A total of 5 cycles of amplification were used to complete adaptor sequences and introduce unique indices for sample multiplexing. Final libraries were quantified on the Qubit® fluorometer (Thermo) and run on a Bioanalyzer HS DNA chip to verify quality and size distribution. Equimolecular library pool was prepared, then diluted and denatured as recommended by Illumina NextSeq 500 library preparation guide. The 75 nt single-end sequencing was conducted on a NextSeq 500 sequencer (Illumina). An average of 24 million reads per sample was obtained.

treatment_protocol: Cells were exposed to hypoxia using a sealed hypoxic workstation (Ruskinn, Bridgend, UK). Cells exposed to 1% O2, 5% CO2 at 37ºC. Hypoxic duration is 4 hours.

tag: cell line

value: human embryonic kidney cells

tag: passages

value: WT

tag: condition

value: Normoxia


title: ChIP-seq-HPPT_IFNb_H3K4me3_rep1

description: H3K4me3 (Millipore, 07-473)


title: ChIP-seq-HPPT_IFNb_H3K4me1_rep1

description: H3K4me1 (Active Motif, 39297)


title: 293T_Input1_Hyp_

value: Hypoxia


title: Sample 8-con1 [TN1801R4092]

description:
24_180117
processed data file: 8expression.genes

tag: tissue


title: 293T_Chip2_Hyp_

value: Anti-HIF-1 alpha antibody - ChIP Grade (ab2185)


title: Sample 9-con1 [TN1802T0181]

description:
2018_02_02_14
processed data file: 9expression.genes

value: untreated


title: ChIP-Seq_TrcR_WT_C.crescentus_PYERif30


title: 293T_Chip1_Norm_


title: 293T_Chip1_Hyp_


title: Sample 8-exp2 [TN1801R4094]

description:
44_2018.01.17
processed data file: 8expression.genes