title: Endothelial cells from wildtype kidney tissue_Rep_3

city: Taichung

first: Tien

last: Hsu

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

institute: China Medical University

description: Renal_VhlhKO_ECs (FPKM)_Process Data

data_processing:
The bases with low quality and sequences from adapters in raw data were removed using program Trimmomatic (version 0.39)
The filtered reads were aligned to the reference genomes using Bowtie2 (version 2.3.4.1)
A user-friendly software RSEM (version 1.2.28) was applied for the quantification of the transcript abundance
Differentially expressed genes (DEGs) were identified by EBSeq (version 1.16.0)
The functional enrichment analysis of Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways among gene clusters was implemented in an R package called clusterProfiler (version 3.6.0)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized count of mapped reads (FPKM) for every gene and every sample

source_name: Endothelial cells

extract_protocol:
Using miRNeasy Mini Kit (QIAGEN, #217004)
The purified RNA was used for the preparation of the sequencing library by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 µg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on 3’ ends of DNA fragments, the adaptors were ligated and purified with AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed on the Agilent Bioanalyzer 2100 system and a Real-Time PCR system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan

value: Kidney

value: 3-month old

value: male


title: ChIP_PU1_C57_BMDM_24hIL4_rep1

status: Public on Jun 18 2021

type: SRA

city: La Jolla

first: Christopher

middle: K

last: Glass

state: CA

address: 9500 Gilman Drive

department: CMM

country: USA

institute: University of California, San Diego

description:
processed data file:
ChIP_PU1_C57_BMDM_24hIL4.idr.txt

library_source: genomic

data_processing:
FASTQ files from sequencing experiments were mapped to the custom genome of the corresponding mouse strain using Bowtie2 with default parameters (Langmead and Salzberg, 2012). Mapped data for strains other than C57 were later shifted to the mm10 genome using MMARGE (Link et al., 2018). Human data were mapped to hg38. HOMER was used to convert aligned reads into “tag directories” for downstream quantitative analysis (Heinz et al., 2010).
The reproducible enriched regions (i.e. peaks) were identified by first using HOMER (Heinz et al., 2010) to call unfiltered 200-bp peaks (command “findPeaks -style factor -L 0 -C 0 -fdr 0.9 -size 200”) and then running IDR (Li et al., 2011) on replicates with default parameters.
Normalized tag counts were computated using HOMER annotatePeaks.pl script with parameter "-norm 1e7". Histone markers were counted within +/- 500 bp around peaks, while transcription factor binding tags were counted within +/- 300 bp.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Tab delimited text file containing called peaks in the HOMER peak file format

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Bone marrow was isolated from mice and differentiated for 7 days using media containing M-CSF to bone marrow-derived macrophages (BMDMs) as described previously (Link et al., 2018).

extract_protocol:
For histone marks, PU.1, CEBPb and RNA Pol2 ChIP-seqs, culture media was removed and plates were washed once with PBS and then fixed for 10 minutes with 1% formaldehyde (Thermo Fisher Scientific) in PBS at room temperature and reaction was then quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For STAT6, PPARg, and Egr2 ChIP-seq, cells were cross-linked for 30 minutes with 2mM DSG (Pierce) in PBS at room temperature. Subsequently cells were fixed for 10 minutes with 1% formaldehyde at room temperature and the reaction was quenched with 0.125M glycine. After fixation, cells were washed once with cold PBS and then scraped into supernatant using a rubber policeman, pelleted for 5 minutes at 400xG at 4°C. Cells were transferred to Eppendorf DNA Lobind tubes and pelleted at 700xG for 5 minutes at 4°C, snap-frozen in liquid nitrogen and stored at -80°C until ready for ChIP-seq protocol preparation.Chromatin immunoprecipitation (ChIP) was performed in biological replicates as described previously (Seidman et al., 2020). Samples were sonicated using a probe sonicator in 500 µl lysis buffer (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5mM EGTA, 0.1% deoxycholate, 0.5% sarkozyl, 1 × protease inhibitor cocktail). After sonication, 10% Triton X-100 was added to 1% final concentration and lysates were spun at full speed for 10 minutes. 1% was taken as input DNA, and immunoprecipitation was carried out overnight with 20 µl Protein A Dynabeads (Invitrogen) and 2 µg specific antibodies for PU.1 (Santa Cruz, sc-352X), H3K4me2 (Millipore, 07-030), H3K4me3 (Millipore, 04-745), H3K27ac (Active Motif, 39135), RNA Pol2 (Genetex, GTX102535), STAT6 (Santa Cruz, sc-374021), Egr2 (abcam, ab43020) and CEBP- (Santa Cruz, sc-150). Beads were washed three times each with wash buffer I (20mM Tris/HCl, 150mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA), wash buffer II (10mM Tris/HCl, 250mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, 1mM EDTA), TE 0.2% Triton X-100 and TE 50mM NaCl and subsequently resuspended 25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20 and sequencing libraries were prepared on the Dynabeads as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit (NEB) as previously described (Heinz et al., 2018). DNA was polished, polyA-tailed and ligated after which dual UDI (IDT) or single (Bioo Scientific) barcodes were ligated to it. Libraries were eluted and crosslinks reversed by adding to the 46.5 µl NEB reaction 16 µl water, 4 µl 10% SDS, 4.5 µl 5M NaCl, 3 µl 0.5 M EDTA, 4 µl 0.2M EGTA, 1 µl RNAse (10 mg/ml) and 1 µl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 75C for 30 minutes in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries were cleaned up by adding 2 µl SpeedBeads 3 EDAC (Thermo) in 124 µl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 µl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 12.25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 25 µl reaction volume using NEBNext Ultra II PCR master mix and 0.5 µM each Solexa 1GA and Solexa 1GB primers. Libraries were size selected using TBE gels for 200 – 500 bp and DNA eluted using gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research).

treatment_protocol: Macrophages were left untreated or treated with 20 ng/mL mouse recombinant IL-4 (Peprotech) for 1, 6 or 24 hours

tag: strain

tag: treatment

tag: cell type

value: BMDMs (bone marow-derived macrophages)

tag: chip antibody

value: PU1 (Santa Cruz, sc-352X, lot L2012)


title: Endothelial cells from wildtype kidney tissue_Rep_2

country: Taiwan

description: Renal_VhlhKO_ECs (FPKM)_Process Data

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: age

tag: Sex


title: Endothelial cells from wildtype kidney tissue_Rep_1

description: Renal_VhlhKO_ECs (FPKM)_Process Data


title: ChIP_PU1_C57_BMDM_basal_rep1

description:
processed data file:
ChIP_PU1_C57_BMDM_basal.idr.txt


title: Endothelial cells from Vhlh mutant kidney tissue_Rep_4

description: Renal_VhlhKO_ECs (FPKM)_Process Data


title: ChIP_PU1_C57_BMDM_basal_rep2


title: ChIP_PPARg_SPRET_BMDM_basal_rep1

description:
processed data file:
ChIP_PPARg_SPRET_BMDM_basal.idr.txt

value: SPRET/EiJ

value: PPARg (Santa Cruz, sc-271392 and sc-7273, lots G0210 and J1415)


title: ChIP_PPARg_SPRET_BMDM_24hIL4_rep1

description:
processed data file:
ChIP_PPARg_SPRET_BMDM_24hIL4.idr.txt


title: DIO DMSO-1 intestine

city: San Diego

first: Brian

middle: Patrick

last: James

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Read data was processed in BaseSpace (basespace.illumina.com).
Reads were aligned to to Mus musculus genome (mm10) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Differential transcript expression was determined using the Cufflinks Cuffdiff package (https://github.com/cole-trapnell-lab/cufflinks).
Genome_build: Mus musculus genome mm10
Supplementary_files_format_and_content: Read FPKM and Log2 fold differential expression, and FDR corrected Q-values

source_name: intestine

growth_protocol: 16 weeks old C57BL/6J DIO male mice (cat#380050)

extract_protocol:
Intestine from DMSO or NCT treated mice was removed, flash frozen in liquid nitrogen, and RNA harvested using Trizol reagent.
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).  Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

treatment_protocol: High fat diet mice treated with DMSO or NCT for 2 weeks with intraperitoneal injection.

value: 16weeks old

tag: agent

value: DMSO control


title: Endothelial cells from Vhlh mutant kidney tissue_Rep_2

description: Renal_VhlhKO_ECs (FPKM)_Process Data


title: ChIP_PPARg_PWK_BMDM_24hIL4_rep1

description:
processed data file:
ChIP_PPARg_PWK_BMDM_24hIL4.idr.txt

value: PWK/PhJ


title: ChIP_PPARg_PWK_BMDM_basal_rep1

description:
processed data file:
ChIP_PPARg_PWK_BMDM_basal.idr.txt


title: Endothelial cells from Vhlh mutant kidney tissue_Rep_1

description: Renal_VhlhKO_ECs (FPKM)_Process Data


title: hichip_C57_BMDM_24hIL4_rep1

data_processing:
library strategy: HiChIP
H3K4me3 ChIP-seq fastqs were aligned with bowtie2 (Langmead and Salzberg, 2012) to the mm10 reference genome, and peak calling was done with MACS (Zhang et al., 2008) for each replicate separately. Significant peaks from basal and 24h IL4 were merged using bedtools (Quinlan and Hall, 2010) into a general bed file that was used as corresponding peak-file for the downstream HiChIP data processing with MAPS.
HiChIP-seq data was first trimmed from 75 bp to 42 bp and then processed with MAPS (Juric et al., 2019) at 5000bp resolution as described previously for PLAC-seq (Nott et al., 2019) for all four samples separately, basal and 24h IL-4 duplicate samples combined, and a merge of all four samples.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file containing called peaks

extract_protocol:
For H3K4me3 HiChIP, 10 million formaldehyde crosslinked cells per condition in biological replicates were used. HiChIP was performed as described before (Mumbach et al., 2016). In our experiments, 375 U of MboI (NEB, R0147M) restriction enzyme was used for chromatin digestion. Shearing was performed in three Covaris microtubes per sample and using the following parameters on a Covaris E220 (Fill Level = 6, Duty Cycle = 5, PIP = 140, Cycles/Burst = 200, Time = 200s). H3K4me3 IP was performed using 7.5 μg of antibody (Millipore, 04-745).
Final PCR was performed using NEBNext High-Fidelity PCR MM and Nextera general Primer Ad1 and specific Nextera Primer Ad2.n. PCR product was run on a TBE gel (Invitrogen) and libraries were size selected from 250bp to 700bp and cleaned up using 150 ul gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research). Samples were quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 75bp paired-end sequenced on a NextSeq 500 (Illumina).

treatment_protocol: Macrophages were left untreated or treated with 20 ng/mL mouse recombinant IL-4 (Peprotech) for 24 hours


title: DIO NCT-2 intestine

value: NCT treated 200 mg/kg bid 14 days


title: hichip_C57_BMDM_basal_rep2


title: ChIP_PPARg_NOD_BMDM_basal_rep1

description:
processed data file:
ChIP_PPARg_NOD_BMDM_basal.idr.txt

value: NOD/ShiLtJ


title: ChIP_PPARg_NOD_BMDM_24hIL4_rep1

description:
processed data file:
ChIP_PPARg_NOD_BMDM_24hIL4.idr.txt


title: RNA_LyzMCreEgr2flfl_BMDM_24hIL4_rep2

description: processed data file: RNA_TPM_DESeq2_Egr2KO.tsv

data_processing:
FASTQ files from sequencing experiments were mapped to the custom genome of the corresponding mouse strain using STAR with default parameters (Dobin et al., 2013). Mapped data for strains other than C57 were later shifted to the mm10 genome using MMARGE (Link et al., 2018). F1 data were mapped to both C57 and SPRET genomes, which were represented in separate columns in the processed TPM file. Human data were mapped to hg38. HOMER was used to convert aligned reads into “tag directories” for downstream quantitative analysis (Heinz et al., 2010).
Transcripts were quantified by TPM values generated by the “analyzeRepeats” script of HOMER with the parameters -condenseGenes -count exons -tpm. Differentially expressed genes were identified by feeding raw read counts into DESeq2 (Love et al., 2014) through the “getDiffExpression” script of HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file: table of TPM values and differential gene expression analysis results from DESeq2

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from in vitro culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s instructions (Zymo Research).
Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Thermo Fisher Scientific), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primers (3 µg/µL) (Thermo Fisher Scientific), 0.5 µL of Oligo dT primer (50 µM) (Thermo Fisher Scientific), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for one minute. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.5 µL of Superscript III (Thermo Fisher Scientific) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads (Beckman Coulter) according to manufacturer's instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 2.5 hours. The resulting dUTP-marked dsDNA was purified using 28 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen at -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 16 cycles, size selected by gel extraction.

value: LyzM-Cre Egr2 fl/fl


title: hichip_C57_BMDM_basal_rep1


title: Endothelial cells from Vhlh mutant kidney tissue_Rep_3

description: Renal_VhlhKO_ECs (FPKM)_Process Data


title: ChIP_STAT6_SPRET_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_STAT6_SPRET_BMDM_24hIL4.idr.txt

value: STAT6 (Santa Cruz, sc-374021, lot L0916)


title: RNA_LyzMCreEgr2flfl_BMDM_6hIL4_rep1

value: IL-4 6h


title: RNA_LyzMCreEgr2flfl_BMDM_24hIL4_rep1


title: ChIP_PPARg_C57_BMDM_24hIL4_rep1

description:
processed data file:
ChIP_PPARg_C57_BMDM_24hIL4.idr.txt


title: RNA_LyzMCreEgr2flfl_BMDM_basal_rep2


title: ChIP_STAT6_SPRET_BMDM_24hIL4_rep1


title: RNA_Egr2flfl_BMDM_24hIL4_rep2

value: Egr2 fl/fl


title: ChIP_STAT6_PWK_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_STAT6_PWK_BMDM_24hIL4.idr.txt


title: hichip_C57_BMDM_24hIL4_rep2


title: ChIP_STAT6_SPRET_BMDM_basal_rep1

description:
processed data file:
ChIP_STAT6_SPRET_BMDM_basal.idr.txt


title: ChIP_STAT6_SPRET_BMDM_basal_rep2


title: RNA_LyzMCreEgr2flfl_BMDM_1hIL4_rep2

value: IL-4 1h


title: ChIP_STAT6_PWK_BMDM_24hIL4_rep1


title: RNA_Egr2flfl_BMDM_24hIL4_rep1


title: ChIP_STAT6_NOD_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_STAT6_NOD_BMDM_24hIL4.idr.txt


title: ChIP_STAT6_PWK_BMDM_basal_rep1

description:
processed data file:
ChIP_STAT6_PWK_BMDM_basal.idr.txt


title: RNA_Egr2flfl_BMDM_6hIL4_rep1


title: ChIP_STAT6_PWK_BMDM_basal_rep2


title: RNA_Egr2flfl_BMDM_6hIL4_rep2


title: RNA_Egr2flfl_BMDM_1hIL4_rep2


title: ChIP_PPARg_C57_BMDM_basal_rep1

description:
processed data file:
ChIP_PPARg_C57_BMDM_basal.idr.txt


title: RNA_Egr2flfl_BMDM_1hIL4_rep1


title: ChIP_STAT6_NOD_BMDM_24hIL4_rep1


title: ChIP_STAT6_NOD_BMDM_basal_rep2

description:
processed data file:
ChIP_STAT6_NOD_BMDM_basal.idr.txt


title: RNA_LyzMCreEgr2flfl_BMDM_1hIL4_rep1


title: RNA_LyzMCreEgr2flfl_BMDM_basal_rep1


title: RNA_Egr2flfl_BMDM_basal_rep1


title: RNA_Egr2flfl_BMDM_basal_rep2


title: ChIP_CEBPb_LyzMCreEgr2flfl_BMDM_24hIL4_rep1

description:
processed data file:
TF_tagCounts_around_24hIL4inducedEGR2Peaks_EGR2KO.txt

value: CEBPb (Santa Cruz, sc-150, lot D0915)


title: ChIP_STAT6_BALB_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_STAT6_BALB_BMDM_24hIL4.idr.txt

value: BALB/cJ


title: ChIP_STAT6_BALB_BMDM_24hIL4_rep1


title: ChIP_STAT6_NOD_BMDM_basal_rep1


title: ChIP_STAT6_BALB_BMDM_basal_rep2

description:
processed data file:
ChIP_STAT6_BALB_BMDM_basal.idr.txt


title: ChIP_PPARg_BALB_BMDM_24hIL4_rep1

description:
processed data file:
ChIP_PPARg_BALB_BMDM_24hIL4.idr.txt


title: ChIP_PPARg_LyzMCreEgr2flfl_BMDM_24hIL4_rep2


title: ChIP_STAT6_BALB_BMDM_basal_rep1


title: ChIP_CEBPb_Egr2flfl_BMDM_24hIL4_rep1


title: ChIP_PPARg_LyzMCreEgr2flfl_BMDM_basal_rep2


title: ChIP_PPARg_Egr2flfl_BMDM_24hIL4_rep2


title: ChIP_STAT6_C57_BMDM_1hIL4_rep2

description:
processed data file:
ChIP_STAT6_C57_BMDM_1hIL4.idr.txt


title: ChIP_STAT6_C57_BMDM_6hIL4_rep2

description:
processed data file:
ChIP_STAT6_C57_BMDM_6hIL4.idr.txt


title: ChIP_STAT6_C57_BMDM_6hIL4_rep1


title: ChIP_PPARg_SPRET_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_PPARg_SPRET_BMDM_24hIL4.idr.txt


title: ChIP_STAT6_C57_BMDM_1hIL4_rep1


title: ChIP_CEBPb_Egr2flfl_BMDM_basal_rep1


title: ChIP_PPARg_PWK_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_PPARg_PWK_BMDM_24hIL4.idr.txt


title: ChIP_EGR2_SPRET_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_EGR2_SPRET_BMDM_24hIL4.idr.txt


title: ChIP_STAT6_C57_BMDM_basal_rep1

description:
processed data file:
ChIP_STAT6_C57_BMDM_basal.idr.txt


title: ChIP_CEBPb_LyzMCreEgr2flfl_BMDM_basal_rep1


title: ChIP_STAT6_C57_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_STAT6_C57_BMDM_24hIL4.idr.txt


title: ChIP_STAT6_C57_BMDM_basal_rep2


title: ChIP_PPARg_BALB_BMDM_basal_rep1

description:
processed data file:
ChIP_PPARg_BALB_BMDM_basal.idr.txt


title: ChIP_PPARg_NOD_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_PPARg_NOD_BMDM_24hIL4.idr.txt


title: ChIP_STAT6_C57_BMDM_24hIL4_rep1


title: ChIP_PPARg_NOD_BMDM_basal_rep2

description:
processed data file:
ChIP_PPARg_NOD_BMDM_basal.idr.txt


title: ChIP_PPARg_PWK_BMDM_basal_rep2

description:
processed data file:
ChIP_PPARg_PWK_BMDM_basal.idr.txt


title: ChIP_PPARg_BALB_BMDM_24hIL4_rep2


title: ChIP_EGR2_SPRET_BMDM_24hIL4_rep1


title: ChIP_EGR2_SPRET_BMDM_basal_rep2

description:
processed data file:
ChIP_EGR2_SPRET_BMDM_basal.idr.txt


title: ChIP_PPARg_BALB_BMDM_basal_rep2


title: ChIP_EGR2_PWK_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_EGR2_PWK_BMDM_24hIL4.idr.txt


title: ChIP_EGR2_SPRET_BMDM_basal_rep1


title: ChIP_PPARg_Egr2flfl_BMDM_basal_rep2

description:
processed data file:
TF_tagCounts_around_24hIL4inducedEGR2Peaks_EGR2KO.txt


title: ChIP_PPARg_C57_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_PPARg_C57_BMDM_24hIL4.idr.txt


title: 18C fBAT-5 [C18BAT.5]

city: Baton Rouge

first: Ji Suk

last: Chang

state: LA

address: 6400 Perkins Rd.

department: Gene Regulation and Metabolism

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.4.3, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.18.1 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: mouse- GRCm38.84
Supplementary_files_format_and_content: tab-delimited text containing raw or DESeq2 normalized counts

source_name: 18C fBAT

extract_protocol:
RNA was isolated from placenta and fetal BAT (2-3 BAT pooled) using Trizol reagent and Rneasy Plus mini kit.
Lexogen Quant-Seq; indexed and pooled samples, 50bp forward read

treatment_protocol: After detection of plug positivity, BL6 females were housed at 28°C or 18°C during gestation. At E18.5, placenta and fetal brown adipose tissue (BAT) were dissected.

tag: mouse strain

value: not determined

value: Fetal brown adipose tissue (fBAT)

tag: condition

value: housed at 18°C during pregnancy


title: ChIP_EGR2_PWK_BMDM_basal_rep2

description:
processed data file:
ChIP_EGR2_PWK_BMDM_basal.idr.txt

value: BMDMs (bone marow-derived macrophages)


title: 18C fBAT-4 [C18BAT.4]


title: ChIP_EGR2_PWK_BMDM_basal_rep1


title: ChIP_EGR2_NOD_BMDM_24hIL4_rep1

description:
processed data file:
ChIP_EGR2_NOD_BMDM_24hIL4.idr.txt


title: 18C fBAT-6 [C18BAT.6]


title: ChIP_PPARg_SPRET_BMDM_basal_rep2

description:
processed data file:
ChIP_PPARg_SPRET_BMDM_basal.idr.txt

value: SPRET/EiJ

value: PPARg (Santa Cruz, sc-271392 and sc-7273, lots G0210 and J1415)


title: ChIP_EGR2_NOD_BMDM_24hIL4_rep2


title: ChIP_EGR2_NOD_BMDM_basal_rep2

description:
processed data file:
ChIP_EGR2_NOD_BMDM_basal.idr.txt


title: ChIP_EGR2_NOD_BMDM_basal_rep1


title: ChIP_EGR2_BALB_BMDM_24hIL4_rep2

description:
processed data file:
ChIP_EGR2_BALB_BMDM_24hIL4.idr.txt


title: ChIP_EGR2_BALB_BMDM_basal_rep2

description:
processed data file:
ChIP_EGR2_BALB_BMDM_basal.idr.txt


title: 18C fBAT-3 [C18BAT.3]


title: 18C fBAT-1 [C18BAT.1]


title: ChIP_EGR2_BALB_BMDM_24hIL4_rep1


title: ChIP_EGR2_BALB_BMDM_basal_rep1


title: ChIP_EGR2_C57_BMDM_24hIL4_rep1

description:
processed data file:
ChIP_EGR2_C57_BMDM_24hIL4.idr.txt
EGR2_tagCounts_C57_BMDM_timecourse.txt


title: ChIP_EGR2_PWK_BMDM_24hIL4_rep1


title: 18C fBAT-2 [C18BAT.2]


title: 28C fBAT-6 [RT28BAT.6]

source_name: 28C fBAT

value: housed at 28°C during pregnancy


title: 28C fBAT-1 [RT28BAT.1]


title: 28C fBAT-2 [RT28BAT.2]


title: 28C fBAT-5 [RT28BAT.5]


title: ChIP_PPARg_C57_BMDM_basal_rep2

description:
processed data file:
ChIP_PPARg_C57_BMDM_basal.idr.txt


title: 28C fBAT-4 [RT28BAT.4]


title: 28C fBAT-3 [RT28BAT.3]


title: ChIP_EGR2_C57_BMDM_24hIL4_rep2


title: ChIP_EGR2_C57_BMDM_6hIL4_rep2

description:
processed data file:
ChIP_EGR2_C57_BMDM_6hIL4.idr.txt
EGR2_tagCounts_C57_BMDM_timecourse.txt


title: 18C Placenta-6 [C18PL.6]

source_name: 18C Placenta

value: Female

value: Placenta


title: ChIP_EGR2_C57_BMDM_6hIL4_rep1


title: 18C Placenta-5 [C18PL.5]


title: ChIP_EGR2_C57_BMDM_basal_rep2

description:
processed data file:
ChIP_EGR2_C57_BMDM_basal.idr.txt
EGR2_tagCounts_C57_BMDM_timecourse.txt


title: ChIP_EGR2_C57_BMDM_1hIL4_rep1

description:
processed data file:
ChIP_EGR2_C57_BMDM_1hIL4.idr.txt
EGR2_tagCounts_C57_BMDM_timecourse.txt


title: ChIP_EGR2_C57_BMDM_basal_rep1


title: ChIP_EGR2_C57_BMDM_1hIL4_rep2


title: 28C Placenta-5 [RT28PL.5]

source_name: 28C Placenta


title: 18C Placenta-4 [C18PL.4]


title: 18C Placenta-3 [C18PL.3]


title: 18C Placenta-2 [C18PL.2]


title: 28C Placenta-2 [RT28PL.2]


title: ChIP_H3K4me2_SPRET_BMDM_24hIL4_rep2

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_SPRET_BMDM.txt


title: 28C Placenta-1 [RT28PL.1]


title: 28C Placenta-6 [RT28PL.6]


title: Salm_N_3

city: Philadelphia

first: De'Broski

last: Herbert

state: PA

address: 3900 Spruce Street

department: Pathobiology

institute: University of Pennsylvania

data_processing:
fastq files were aligned to version 81 of mouse reference genome GRCm38 using the STAR aligner
BAM files resulting from the alignments were summarized to genes using htseq-count, using the union mode for read overlap resolution
Genes with group average counts of less than 5 were removed from the dataset in R, and expression count data was normalized, and differential genes assessed using DESeq2 in R
Genome_build: version 81 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes counts for each sample, csv file includes output from the DESeq2 analysis consisting of Log2FoldChange Benjamini-Hochberg adjusted p-values for group pairwise comparisons, and normalized expression values for each sample

source_name: 2W-Salmonella-infected Peyer's patches, mesenteric lymph node cells

growth_protocol: Cells were isolated directly from infected mice prior to sorting and sequencing

extract_protocol:
FACS sorted cells were directly sorted into lysis and cDNA synthesis buffer
cDNA was prepared with the Clonetech Smartseq v4 Ultra Low Input kit (Takara Bio), and libraries were made with the Illumina NexteraXT kit, following manufacturer’s instructions

treatment_protocol: See samples section for infection treatments. All cells were stained with I-A(b) mouse 2W1S tetramer from the NIH Tetramer Core Facility to label 2W1S-specific CD4+ T cells prior to sorting.

value: Naive, 2W1S-CD62Lhi CD4+ T cells (N)

tag: genotype

value: Wild-type

value: 5x109 CFU 2W-Salmonella given 2 times orally on days 0, 2 and 1x105 CFU 2W-Salmonella given 1 time intraperitoneally on day 2 of experiment


title: 18C Placenta-1 [C18PL.1]


title: ChIP_H3K4me2_SPRET_BMDM_basal_rep1


title: ChIP_H3K4me2_SPRET_BMDM_24hIL4_rep1


title: ChIP_H3K4me2_SPRET_BMDM_basal_rep2


title: Salm_N_1


title: ChIP_H3K4me2_PWK_BMDM_24hIL4_rep2

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_PWK_BMDM.txt

value: PWK/PhJ


title: 28C Placenta-3 [RT28PL.3]


title: 28C Placenta-4 [RT28PL.4]


title: ChIP_H3K4me2_PWK_BMDM_24hIL4_rep1


title: Salm_2W_2

value: 2W1S+CD62Llo CD4+ T cells (2W)


title: ChIP_H3K4me2_PWK_BMDM_basal_rep2


title: RNA_LyzMCreEgr2flfl_BMDM_6hIL4_rep2

description: processed data file: RNA_TPM_DESeq2_Egr2KO.tsv

value: LyzM-Cre Egr2 fl/fl

value: IL-4 6h


title: ChIP_H3K4me2_NOD_BMDM_basal_rep2

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_NOD_BMDM.txt

value: NOD/ShiLtJ


title: ChIP_H3K4me2_PWK_BMDM_basal_rep1


title: Hulk_N_2

source_name: Hulk S. ratti-infected lung, mediastinal lymph node cells

value: 1000 iL3 Hulk S. ratti given 3 times subcutaneously on days 0, 5, 10 of experiment


title: Salm_N_2


title: ChIP_H3K4me2_NOD_BMDM_24hIL4_rep2


title: Salm_2W_3


title: ChIP_H3K4me2_NOD_BMDM_24hIL4_rep1


title: Hulk_N_3


title: ChIP_H3K4me2_BALB_BMDM_24hIL4_rep2

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_BALB_BMDM.txt

value: BALB/cJ


title: ChIP_H3K4me2_BALB_BMDM_basal_rep2


title: Salm_2W_1


title: Hulk_N_1


title: PBT003 PUS7 sg 2-CMC_rep 3

city: San Francisco

first: Kailin

last: Yin

state: California

address: 1650 Owens street

institute: Gladstone Institutes

data_processing:
For Small RNA DM-Ψ-seq data analysis, only reads 2 in raw sequencing data were used to further analysis, which were demultiplexed to each sample according to their barcode information.
Next, the adapter sequences were trimmed by Cutadapt (Version 1.18). The parameters were set as “cutadapt --times 1  -e 0.1  -O 3  --quality-cutoff 25 -m 15 -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCT”.
The remaining reads were mapped to the small RNA annotation index with Bowtie aligner (Version 1.2.2), the parameters were set as “bowtie -v 1 -m 200 -k 20”.
Site-calling of small RNA DM-Ψ-seq were performed by custom scripts.
Genome_build: hg19
Supplementary_files_format_and_content: The file includes FPKM values and site calling for each group of samples.

organism: Homo sapiens

growth_protocol: GSCs were derived from patients with newly diagnosed grade IV GBM. The GSCs were maintained in sphere cultures as previously described (Cui et al., 2017; Cui et al., 2016). Briefly, GSCs were cultured in DMEM-F12 medium (Omega Scientific) supplemented with 2 mM L-glutamine (Media Tech), 27.4 mM HEPES (Fisher Scientific), B27 (Gibco) and growth factors including 20 ng ml-1 EGF (PeproTech), 20 ng ml-1 FGF (PeproTech) and 5 μg ml-1 heparin (Sigma). All cultures were confirmed for no contamination of mycoplasma using MycoAlert PLUS Mycoplasma Detection Kit (Lonza).

extract_protocol:
Small RNA was extracted with MEGAclear Transcription Clean-Up Kit (Invitrogen) according to manufacturer’s instructions. RNA sample was brought to 100 μl with nuclease-free water, and then mixed gently. 350 μl binding solution concentrate was added to each sample, followed by gently mixing. 250 μl 100% ethanol was then added to each sample. Small RNA fraction was separated through Filter Cartridge, followed by ethanol precipitation.
For small RNA library preparation for DM-Ψ-seq, briefly, small RNA fraction was demethylated by AlkB protein, recovered by phenol chloroform extraction, labeled by CMC and then treated with Na2CO3.  For CMC labeling, RNA (small RNA) was labeled with CMC as previously described (Li et al., 2015) with some modifications. Briefly, 10 μg RNA samples were fragmented into 150-200 nt fragments in RNA fragmentation buffer (NEB) at 94 ℃ for 4 min, placed on ice immediately, added with RNA fragmentation stop solution (NEB), and then followed by ethanol precipitation. Fragmented RNA was dissolved in nuclease-free water, denatured at 80 ℃ for 5 min by adding 2 μl 50 mM EDTA, placed on ice immediately. 5 μg denatured RNA was added to 100 μl BEU buffer (50 mM Bicine, pH 8.5, 4 mM EDTA, 7 M urea) containing 0.2 M CMC (sigma) as the "CMC+" group; or added to 100 μl BEU buffer without CMC as the "CMC-" group. The CMC reaction was carried out at 37 ℃ for 20 min at 800 rpm, followed by ethanol precipitation. Recovered RNA (CMC+ and CMC-) was dissolved in 50 μl Na2CO3 buffer (50 mM sodium carbonate, 2 mM EDTA, pH 10.4), incubated at 37 ℃ for 6 h at 800 rpm, followed by ethanol precipitation.  Library preparation was performed according to eCLIP protocol as previously described (Van Nostrand et al., 2016) with some modifications. RNA samples were dephosphorylated with CIP (NEB), recovered by phenol chloroform extraction and ethanol precipitation. 3’ adaptor ligation was performed with RNA T4 ligase 2 truncated KQ (NEB), followed by 5’ deadenylase (NEB) and RecJf (NEB) treatment, and then recovered by ethanol precipitation. Reverse transcription was performed with Superscript III reverse transcriptase (Invitrogen), and cDNA was further treated with RNase H (NEB), quenched by adding 1 μl 0.5 M EDTA, 7 μl 1 M NaCl and 1.8 μl nuclease-free water, recovered with Myone silane beads. 5’ linker ligation was performed with T4 RNA ligase 1 high concentration (NEB), followed by silane beads recovery. The cDNA was amplified by PCR with index primer (NEB) and universal primer (NEB) in high-fidelity 2× PCR mix (NEB). PCR products were purified with XP beads recovery, 6% native page separation, ethanol precipitation, and then sequenced on Illumina Hiseq 2000.

treatment_protocol: Lentiviruses were prepared using 293T cells as described (Shi et al., 2004). To transduce GSCs, cells were dissociated for overnight culture and then incubated with lentivirus and 4 μg ml-1 polybrene (AmericanBio) for 24 h.

tag: cell line

value: PUS7 KD

tag: label

value: CMC


title: ChIP_H3K4me2_NOD_BMDM_basal_rep1

value: BMDMs (bone marow-derived macrophages)


title: ChIP_H3K4me2_C57_BMDM_basal_rep2

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_C57_BMDM.txt


title: PBT003 PUS7 sg 2-CMC_rep 1


title: Hulk_2W_3


title: ChIP_H3K4me2_C57_BMDM_basal_rep1


title: ChIP_H3K4me2_C57_BMDM_24hIL4_rep1


title: Hulk_2W_2


title: ChIP_H3K4me2_C57_BMDM_24hIL4_rep2


title: ChIP_H3K4me3_SPRET_BMDM_24hIL4_rep2

value: SPRET/EiJ


title: PBT003 PUS7 sg 2-CMC_rep 2


title: ChIP_H3K4me3_PWK_BMDM_24hIL4_rep2


title: ChIP_H3K4me3_SPRET_BMDM_24hIL4_rep1


title: ChIP_H3K4me2_BALB_BMDM_basal_rep1


title: PBT003 PUS7 sg 1-CMC_rep 2


title: PBT003 ctrl sg-CMC_rep 3

value: WT


title: ChIP_H3K4me3_PWK_BMDM_basal_rep1


title: ChIP_H3K4me3_SPRET_BMDM_basal_rep1


title: ChIP_H3K4me2_BALB_BMDM_24hIL4_rep1


title: ChIP_H3K4me3_NOD_BMDM_24hIL4_rep1


title: PBT003 PUS7 sg 1-CMC_rep 1


title: ChIP_H3K4me3_PWK_BMDM_basal_rep2


title: ChIP_H3K4me3_PWK_BMDM_24hIL4_rep1


title: ChIP_H3K4me3_NOD_BMDM_basal_rep1


title: PBT003 ctrl sg-CMC_rep 1


title: PBT003 PUS7 sg 1-CMC_rep 3


title: PBT003 PUS7 sg 2-BEU_rep 3

value: BEU


title: ChIP_H3K4me3_NOD_BMDM_basal_rep2


title: Hulk_2W_1


title: PBT003 PUS7 sg 1-BEU_rep 2


title: PBT003 PUS7 sg 1-BEU_rep 3


title: ChIP_H3K4me3_BALB_BMDM_24hIL4_rep1


title: ChIP_H3K4me3_BALB_BMDM_24hIL4_rep2


title: PBT003 PUS7 sg 1-BEU_rep 1


title: PBT003 PUS7 sg 2-BEU_rep 2


title: PBT003 ctrl sg-BEU_rep 1


title: PBT003 ctrl sg-BEU_rep 3


title: ChIP_H3K4me3_NOD_BMDM_24hIL4_rep2


title: ChIP_H3K4me3_BALB_BMDM_basal_rep2


title: ChIP_H3K4me3_BALB_BMDM_basal_rep1


title: PBT003 ctrl sg-BEU_rep 2


title: ChIP_H3K4me3_C57_BMDM_24hIL4_rep2


title: ChIP_H3K4me3_C57_BMDM_24hIL4_rep1


title: ChIP_H3K4me3_C57_BMDM_basal_rep1


title: SIRT1-ChIPseq

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
Basecalls performed using CASAVA version 1.4
The high quality reads were mapped to the Human genome of Ensembl by using Bowtie(version 0.12.8) with the default parameter.
Data were filtered using the following specification:A Perl program was used to filter of low quality sequences from raw sequencing data. The quality of each base was checked from the first base of each read. Once a low-quality base (quality<10) was  found,  it was removed together with following sequences. For paired-end reads, if one read was less than 30 bases after the trimming of low quality bases, the whole paired-end reads were  removed."
The expression peaks were detected by MACS(Model-based Analysis for ChIP-Seq) using the parameter:-f BOWTIE -g hs -n C_Ip -w.
Genome_build: hg 19
Supplementary_files_format_and_content: tab-delimited text files were generated using MACS2 and The R programming language-ChIPseeker

source_name: PANC-1 cells

extract_protocol:
Approximately 5 x 107 cells were used for each ChIP-Seq assay. The chromatin DNA precipitated by polyclonal antibodies against SIRT1 and CUL4B. The DNA was purified with a Qiagen PCR purification kit.
A Vazyme TruePrep DNA Library Prep Kit V2 for Illumina ® (Vazyme Biotech) was used for DNA library construction. Briefly,the kit uses a new-type transposasea for DNA fragmentation and ligation  of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell treatment method

value: untreated


title: Input DNA


title: ChIP_PolII_SPRET_BMDM_24hIL4_rep3

value: PolII (Genetex, GTX102535, lot 39918)


title: PBT003 PUS7 sg 2-BEU_rep 1


title: ChIP_PolII_SPRET_BMDM_24hIL4_rep2


title: ChIP_PolII_SPRET_BMDM_24hIL4_rep1


title: ChIP_PolII_SPRET_BMDM_basal_rep2


title: RKO, DMSO-2

city: Oslo

first: Martin

middle: Frank

last: Strand

address: Prinsensgate 7

country: Norway

institute: Høyskolen Kristiania

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
8-DEGs.txt
8_2

data_processing:
Clean reads were mapped to the reference gene set using SOAPaligner/SOAP2, with no more than 2 mismatches allowed in the alignment.
Gene expression level was calculated using RPKM (Reads Per kb per Million reads).
Genome_build: Homo sapiens (UCSC hg19)
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample, normalized counts, and Differentially expressed gene (DEGs)

source_name: RKO

growth_protocol: ABC-1 and RKO were grown in Eagle's Minimum Essential Medium (EMEM, 30-2003, ATCC) while COLO 320DM, OVCAR-4, UO-31 and HCT-8 were grown in RPMI-1640 medium (R8758, Sigma Aldrich). Both mediums contained 10% Fetal Bovine Serum (FBS, 10270-106, Gibco lot 42F9164K) and 1% Penicillin-Streptomycin (P4333, Sigma Aldrich). Cells were grown at 37 oC in humidified cell incubators with 5% CO2. Cells were routinely monitored for Mycoplasma with MycoAlert Mycoplasma detection kit (Lonza).

extract_protocol:
Total RNA was isolated using GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma Aldrich). mRNA was then treated with DNase I (AMPD1-1KT, Sigma Aldrich) before 4 µg mRNA was sent to BGI Tech Solutions Co (Hong Kong) for RNA sequencing according to their standard protocol. Briefly, total RNA samples were treated with DNase I, and enriched using oligo(dT) magnetic beads, before fragmentation (about 200 bp). Then double strand cDNA was synthetized and purified, before end reparation, ligation of sequencing adaptors and enrichment by PCR amplification.
Quality control and quantification was performed using Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System, prior to library sequencing via Illumina HiSeq™ 2000.

treatment_protocol: all cell lines were treated with 1 µM G007-LK or 0.01% DMSO (two biological replicates) for 24 hours

value: Colorectal adenocarcinoma

tag: cellosaurus identifier (cvcl code)

value: RKO

value: DMSO


title: RKO, DMSO-1

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
8-DEGs.txt
8_1


title: OVCAR-4, G007-LK-2

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
4-DEGs.txt
4_4

value: High grade ovarian serous ademocarsinoma


title: ChIP_PolII_SPRET_BMDM_basal_rep1


title: OVCAR-4, DMSO-2

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
4-DEGs.txt
4_2


title: OVCAR-4, G007-LK-1

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
4-DEGs.txt
4_3


title: ChIP_PolII_PWK_BMDM_24hIL4_rep3

value: PWK/PhJ


title: ChIP_PolII_SPRET_BMDM_basal_rep3


title: CUL4B-ChIPseq


title: ChIP_PolII_PWK_BMDM_24hIL4_rep1


title: UO-31, G007-LK-2

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
3-DEGs.txt
3_4

value: Renal cell carsinoma


title: ChIP_H3K4me3_C57_BMDM_basal_rep2


title: ChIP_PolII_PWK_BMDM_24hIL4_rep2


title: ChIP_PolII_PWK_BMDM_basal_rep3


title: UO-31, G007-LK-1

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
3-DEGs.txt
3_3


title: OVCAR-4, DMSO-1

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
4-DEGs.txt
4_1


title: RKO, G007-LK-2

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
8-DEGs.txt
8_4


title: ChIP_PolII_PWK_BMDM_basal_rep2


title: UO-31, DMSO-2

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
3-DEGs.txt
3_2


title: UO-31, DMSO-1

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
3-DEGs.txt
3_1


title: ChIP_PolII_NOD_BMDM_24hIL4_rep2

value: NOD/ShiLtJ


title: RKO, G007-LK-1

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
8-DEGs.txt
8_3


title: ChIP_PolII_NOD_BMDM_24hIL4_rep1


title: ChIP_H3K4me3_SPRET_BMDM_basal_rep2

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_SPRET_BMDM.txt


title: ABC-1, DMSO-1

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
2-DEGs.txt
2_1

value: Lung adenocarsinoma


title: ChIP_PolII_NOD_BMDM_basal_rep2

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_NOD_BMDM.txt


title: ABC-1, DMSO-2

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
2-DEGs.txt
2_2


title: ChIP_PolII_BALB_BMDM_basal_rep3

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_BALB_BMDM.txt

value: BALB/cJ


title: ABC-1, G007-LK-2

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
2-DEGs.txt
2_4


title: ChIP_PolII_BALB_BMDM_basal_rep2


title: ChIP_PolII_NOD_BMDM_basal_rep1


title: PBT003 ctrl sg-CMC_rep 2


title: ChIP_PolII_C57_BMDM_24hIL4_rep3

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_C57_BMDM.txt
histone_tagCounts_around_1000bpATACpeaks_C57_BMDM_timecourse.txt


title: COLO320DM, DMSO-2

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
1-DEGs.txt
1_2


title: COLO320DM, G007-LK-2

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
1-DEGs.txt
1_4


title: ChIP_PolII_BALB_BMDM_basal_rep1


title: ChIP_PolII_C57_BMDM_24hIL4_rep2


title: COLO320DM, DMSO-1

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
1-DEGs.txt
1_1


title: ChIP-seq MCF10Ashy PCNA 1.2

city: Malmö

first: Maria

middle: Alvarado

last: Kristensson

address: 59 Jan Waldenströms street

country: Sweden

institute: Lund University

data_processing:
Basecalls performed using the software Torrent Suite v5.0.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie version 1.0.0 with parameter -m 1
peaks were called using MACS2 version 2.1.1 with the following setting: FDR threshold (0.05)
Differential peak analysis was performed using the bggdiff tool as part of MACS2 Chip-seq analysis package
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using genomeCoverageBed version 2.17.0; Scores represent -log10 (FDR)

source_name: ChIP-seq MCF10Ashy PCNA

growth_protocol: MCF10A cells were grown in DMEM/F12 medium (Hyclone) supplemented with 5% horse serum, 1% PEST, 20 ng/ml EGF, 0.5 ug/ml hydrocortisone, 100 ng/ml cholera toxin and 10 ug/ml insulin. Cells were grown in a p150 plate to 90 % confluency (typically 12-15 x106 cells).

extract_protocol:
Nuclei were lysed and sonicated. The sonicated nuclei were cleared and gamma-tubulin-DNA-complexes or PCNA-DNA-complexes were isolated with antibody.
Library Builder System (ThermoFisher)

treatment_protocol: Cells were subjected to dubble thymidine syncronization and released for 1h or 2 h prior to harvest.

tag: tissue source

value: Mammary gland; breast

value: Breast epithelial cell

tag: stable transfection

value: gamma-tubulin shRNA

tag: selection

value: 100 ug/ml Zeocin

tag: time from release to harvest


title: ChIP-seq MCF10Ashy PCNA 2.2

tag: cell type


title: ChIP-seq MCF10Ashy PCNA 2.1

tag: chip antibody


title: ChIP_PolII_BALB_BMDM_24hIL4_rep1

tag: strain

tag: treatment

value: BMDMs (bone marow-derived macrophages)


title: ChIP_PolII_PWK_BMDM_basal_rep1

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_PWK_BMDM.txt


title: ChIP_PolII_C57_BMDM_6hIL4_rep1

description:
processed data file:
histone_tagCounts_around_1000bpATACpeaks_C57_BMDM_timecourse.txt

value: IL-4 6h


title: ChIP-seq MCF10A PCNA 2.2

source_name: ChIP-seq MCF10A PCNA


title: ChIP_PolII_C57_BMDM_24hIL4_rep1


title: ChIP_PolII_C57_BMDM_1hIL4_rep1

value: IL-4 1h


title: COLO320DM, G007-LK-1

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
1-DEGs.txt
1_3

tag: tissue


title: ChIP_PolII_C57_BMDM_basal_rep4

value: PolII (Genetex, GTX102535, lot 39918)


title: ChIP-seq MCF10A PCNA 1.2


title: ChIP-seq MCF10Ashy PCNA 1.1


title: ChIP_PolII_C57_BMDM_basal_rep2


title: ChIP_PolII_C57_BMDM_basal_rep1


title: ABC-1, G007-LK-1

description:
Normalized_RPKM.txt
all.gene.rpkm.xlsx
2-DEGs.txt
2_3


title: sRNA Retina P17

city: Wenzhou

first: Gang

last: Chen

address: 270 Xueyuan Road

country: China

institute: Eye Hospital of Wenzhou Medical University

data_processing:
Quality of raw data was controlled by Fast QC and paired-end reads were trimmed using Trimmomatic. The ribosomal RNAs were further removed according to RNA central Database and clean data were obtained.
lncRNA reads were mapped to reference genome mm10 by Hisat2. HTSeq was used to count the reads numbers mapped to each gene. The sRNA reads were aligned by BWA and miRNAs were identified by miRDeep2. For circular transcriptome, two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. Only circRNAs that were detected by both methods will be considered as identified cirRNAs.
The expression values of lncRNAs, mRNAs were normalized by RPKM, while circRNAs and miRNAs were normalized by reads per million (RPM)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Retina

growth_protocol: C57BL/6J mice were obtained from Vital River Laboratory (Beijing, China) and were kept in a pathogen-controlled environment in standard cages and were fed ad libitum. All animal experiments were performed strictly according to the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research and approved by the Animal Care and Use Committee of Wenzhou Medical University.

extract_protocol:
Retinas were dissected from mice in six developmental periods: embryonic day (E) 14.5, postnatal day (P) 1, 7, 12, 17 and adult. Briefly, the mice were euthanized, and retinas were isolated from eyes and moved into the RNA-Solv Reagent (Omega Bio-tek, Norcross, GA, United States). T10 basic S25 ULTRA-TURRAX Disperser (IKA, China) was used to homogenize retinas. Total RNA was extracted by miRNA Kit (Omega Bio-tek) according to the manufacturer’s instructions. RNA quantity was assessed by Agilent 2100 Bioanalyzer (Santa Clara, CA).
Three RNA libraries were constructed individually to fully characterize the complex transcriptome of developing retina. Libraries of lncRNA were prepared after removed rRNA using the Ribo-ZeroTM kit (Epicentre, Madison, WI) and sequenced with pair-end 150bp using Illumina HiSeq 3000 platform. Similarly, sRNA libraries were pooled and sequenced in Illumina HiSeq 2500 sequencing platform at RiboBio (Guangzhou, China). In term of circRNA library, the rRNAs were depleted from total RNA using Ribo-ZeroTM kit. Then, RNA was treated with RNase R (Epicentre, Madison, WI) to remove liner transcripts and fragmented to approximately 200bp. The purified RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation according to instructions of NEB Next Ultra TM RNA Library Prep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0 (Life Technologies, USA) and sequenced on HiSeq 3000 with pair-end 150 bp mode.

value: retina

tag: age


title: ChIP-seq MCF10A PCNA 1.1


title: ChIP-seq MCF10A PCNA 2.1


title: sRNA Retina P12


title: ChIP_H3K27ac_SPRET_BMDM_24hIL4_rep1

value: SPRET/EiJ


title: sRNA Retina P7


title: ChIP_PolII_C57_BMDM_6hIL4_rep2


title: ChIP_H3K27ac_SPRET_BMDM_basal_rep2


title: Control-2

data_processing:
SOAPnuke (version: v1.5.2) was used for filter reads, parameters: -1 15 -q 0.5 -n 0.1.
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
HISAT (version: v2.0.4) was used to align clean reads to the mouse genome, parameters: -p 8 --phred64 --sensitive -I 1 -X 10000.
RSEM (version: v1.2.12) was used for abundance measurement, parameters: default.
FPKM method was used in calculated expression level.
Genome_build: hg 19
Supplementary_files_format_and_content: tab-delimited text files ChIPseeker

source_name: Human pancreatic cancer cell line

extract_protocol:
Total RNA was extracted from the PANC-1 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard BGI protocols

value: Control


title: sRNA Retina P1


title: siSIRT1-1


title: ChIP_H3K27ac_SPRET_BMDM_basal_rep1


title: ChIP_PolII_BALB_BMDM_24hIL4_rep2


title: CUTTag_RHOX10_3

first: Kun

last: Tan

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

data_processing:
Library strategy: CUT&Tag
CUT&Tag: Reads were filtered for quality and aligned with bowtie2 (v2.2.5) against Mus musculus (mm10) genome, with options: –local–very-sensitive-local–no-unal–no-mixed–no-discordant–phred33 -I 10 -X 700. Following alignment, multiple-aligned reads were discarded and reads duplicates were removed by samtools rmdup. Normalization to GC-content was performed using Homer, and peak calling was performed using Homer findPeaks function with “-style factor” mode. Motif finding and annotation were performed using Homer findMotifsGenome.pl and annotatePeaks.pl functions, respectively.
genome build: Mus musculus (mm10) genome.
Peak annotation file

source_name: testis

growth_protocol: For both CUT&Tag and iSLAMseq, mouse germline stem (GS) cells were dissociated from neonatal (P0-P1) testes and cultured in IMDM/SFM medium.

extract_protocol:
CUT&Tag was performed as previously described (Kaya-Okur et al., 2019).
CUT&Tag was performed as previously described (Kaya-Okur et al., 2019).

treatment_protocol: CUT&Tag: Endogenous RHOX10 was knocked-down using an shRNA lentivirus and purified on the basis of GFP fluorescence by FACS. A HA-tagged Rhox10 lentivirus (unsensitive to this shRNA; expresses mCHERRY reporter) was used to induce a control level of exogenous Rhox10 expression. 1 million GS cells were used per sample and three biological replicates were performed. The negative IgG controls were performed using Rhox10-kd;HA-tagged Rhox10 GS cells.  Samples from Rhox10-kd; HA-tagged empty vector GS cells served as another control (Ctrl).

tag: group

value: germline stem cells

value: testis

tag: cut&tag antibody

value: HA (Novus Biologicals, NB600-363)


title: Control-1


title: Vector-3

data_processing:
SOAPnuke (version: v1.5.2) was used for filter reads, parameters: -1 15 -q 0.5 -n 0.1.
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
HISAT (version: v2.0.4) was used to align clean reads to the mouse genome, parameters: -p 8 --phred64 --sensitive -I 1 -X 10000.
RSEM (version: v1.2.12) was used for abundance measurement, parameters: default.
FPKM method was used in calculated expression level.
Genome_build: hg 19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Tumor tissue

extract_protocol:
Total RNA was extracted from tumor samples 4 weeks after injection using Trizol reagent (Invitrogen, USA).  Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.
RNA libraries were prepared for sequencing using standard BGI protocols

tag: mouse strain

value: NOD/SCID

tag: injected cell line

value: lentivirus overexpressing Vector


title: sRNA Retina E14.5


title: CUTTag_RHOX10_2


title: Vector-2


title: ChIP_H3K27ac_PWK_BMDM_24hIL4_rep2

value: PWK/PhJ


title: Vector-1


title: sRNA Retina Adult

value: Adult


title: SIRT1-3

value: lentivirus overexpressing SIRT1


title: SIRT1-1


title: ChIP_H3K27ac_SPRET_BMDM_24hIL4_rep2


title: ChIP_PolII_C57_BMDM_basal_rep3


title: SIRT1-2


title: siSIRT1-2


title: G13_CMC_rep 2 rRNA

description:
G13_CMC_rep 2
rRNA

extract_protocol:
Small RNA was extracted with MEGAclear Transcription Clean-Up Kit (Invitrogen) according to manufacturer’s instructions. RNA sample was brought to 100 μl with nuclease-free water, and then mixed gently. 350 μl binding solution concentrate was added to each sample, followed by gently mixing. 250 μl 100% ethanol was then added to each sample. Small RNA fraction was separated through Filter Cartridge, followed by ethanol precipitation.
For small RNA library preparation for DM-Ψ-seq, briefly, small RNA fraction was demethylated by AlkB protein, recovered by phenol chloroform extraction, labeled by CMC and then treated with Na2CO3.  For CMC labeling, RNA (small RNA) was labeled with CMC as previously described (Li et al., 2015) with some modifications. Briefly, 10 μg RNA samples were fragmented into 150-200 nt fragments in RNA fragmentation buffer (NEB) at 94 ℃ for 4 min, placed on ice immediately, added with RNA fragmentation stop solution (NEB), and then followed by ethanol precipitation. Fragmented RNA was dissolved in nuclease-free water, denatured at 80 ℃ for 5 min by adding 2 μl 50 mM EDTA, placed on ice immediately. 5 μg denatured RNA was added to 100 μl BEU buffer (50 mM Bicine, pH 8.5, 4 mM EDTA, 7 M urea) containing 0.2 M CMC (sigma) as the "CMC+" group; or added to 100 μl BEU buffer without CMC as the "CMC-" group. The CMC reaction was carried out at 37 ℃ for 20 min at 800 rpm, followed by ethanol precipitation. Recovered RNA (CMC+ and CMC-) was dissolved in 50 μl Na2CO3 buffer (50 mM sodium carbonate, 2 mM EDTA, pH 10.4), incubated at 37 ℃ for 6 h at 800 rpm, followed by ethanol precipitation.  Library preparation was performed according to eCLIP protocol as previously described (Van Nostrand et al., 2016) with some modifications. RNA samples were dephosphorylated with CIP (NEB), recovered by phenol chloroform extraction and ethanol precipitation. 3’ adaptor ligation was performed with RNA T4 ligase 2 truncated KQ (NEB), followed by 5’ deadenylase (NEB) and RecJf (NEB) treatment, and then recovered by ethanol precipitation. Reverse transcription was performed with Superscript III reverse transcriptase (Invitrogen), and cDNA was further treated with RNase H (NEB), quenched by adding 1 μl 0.5 M EDTA, 7 μl 1 M NaCl and 1.8 μl nuclease-free water, recovered with Myone silane beads. 5’ linker ligation was performed with T4 RNA ligase 1 high concentration (NEB), followed by silane beads recovery. The cDNA was amplified by PCR with index primer (NEB) and universal primer (NEB) in high-fidelity 2× PCR mix (NEB). PCR products were purified with XP beads recovery, 6% native page separation, ethanol precipitation, and then sequenced on Illumina Hiseq 2000.
Small RNA DM-Ψ-seq

tag: genotype

value: G13 treatment

tag: label

value: CMC


title: ChIP_H3K27ac_PWK_BMDM_24hIL4_rep1

value: BMDMs (bone marow-derived macrophages)


title: ChIP_H3K27ac_PWK_BMDM_basal_rep2


title: G13_CMC_rep 1 rRNA

description:
G13_CMC_rep 1
rRNA


title: ChIP_H3K27ac_PWK_BMDM_basal_rep1


title: CUTTag_Ctrl_3

value: Ctrl


title: ChIP_H3K27ac_NOD_BMDM_24hIL4_rep1

value: NOD/ShiLtJ


title: ChIP_H3K27ac_NOD_BMDM_24hIL4_rep2


title: CUTTag_Ctrl_2


title: ctrl_CMC_rep 2 rRNA

description:
ctrl_CMC_rep 2
rRNA

value: WT


title: CUTTag_IgG_3

value: IgG

value: IgG (Antibodies-Online, ABIN101961)


title: G13_BEU_rep 2 rRNA

description:
G13_BEU_rep 2
rRNA

value: BEU


title: G13_BEU_rep 1 rRNA

description:
G13_BEU_rep 1
rRNA


title: ctrl_BEU_rep 2 rRNA

description:
ctrl_BEU_rep 2
rRNA


title: ctrl_BEU_rep 1 rRNA

description:
ctrl_BEU_rep 1
rRNA


title: ChIP_H3K27ac_NOD_BMDM_basal_rep2


title: ctrl_CMC_rep 1 rRNA

description:
ctrl_CMC_rep 1
rRNA


title: CUTTag_RHOX10_1

value: germline stem cells


title: CUTTag_Ctrl_1

value: testis


title: NSC_CMC_rep 2 small RNA

description:
NSC_CMC_rep 2
small RNA


title: CUTTag_IgG_1


title: NSC_CMC_rep 3 small RNA

description:
NSC_CMC_rep 3
small RNA


title: CUTTag_IgG_2


title: ChIP_H3K27ac_NOD_BMDM_basal_rep1


title: NSC_CMC_rep 1 small RNA

description:
NSC_CMC_rep 1
small RNA


title: ChIP_H3K27ac_BALB_BMDM_24hIL4_rep1

value: BALB/cJ


title: ChIP_H3K27ac_BALB_BMDM_24hIL4_rep2


title: ctrl_CMC_rep 3 small RNA

description:
ctrl_CMC_rep 3
small RNA


title: G13_CMC_rep 3 small RNA

description:
G13_CMC_rep 3
small RNA


title: ctrl_CMC_rep 2 small RNA

description:
ctrl_CMC_rep 2
small RNA


title: M KO striatum PFF d90 SAM24378227

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from brain region tissue

extract_protocol: Tissue was rapidly frozen and stored until a full collection was obtained. RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.

value: brain

tag: Sex

value: M

value: KO

tag: region

value: striatum

value: PFF

tag: days


title: G13_CMC_rep 1 small RNA

description:
G13_CMC_rep 1
small RNA

value: G13 treatment


title: ChIP_H3K27ac_BALB_BMDM_basal_rep1


title: ChIP_H3K27ac_BALB_BMDM_basal_rep2


title: M WT midbrain mono d90 SAM24378239

value: midbrain

value: mono


title: NSC_BEU_rep 1 small RNA

description:
NSC_BEU_rep 1
small RNA


title: ChIP_H3K27ac_C57_BMDM_24hIL4_rep2

value: BMDMs (bone marow-derived macrophages)


title: ChIP_H3K27ac_C57_BMDM_24hIL4_rep1


title: NSC_BEU_rep 3 small RNA

description:
NSC_BEU_rep 3
small RNA


title: F WT midbrain PFF d90 SAM24378260

value: F


title: F KO striatum PFF d90 SAM24378222


title: G13_BEU_rep 3 small RNA

description:
G13_BEU_rep 3
small RNA


title: G13_CMC_rep 2 small RNA

description:
G13_CMC_rep 2
small RNA

value: CMC


title: G13_BEU_rep 2 small RNA

description:
G13_BEU_rep 2
small RNA


title: M KO midbrain mono d90 SAM24378243


title: ChIP_H3K27ac_C57_BMDM_6hIL4_rep1

value: IL-4 6h


title: M WT striatum PFF d60 SAM24378232

value: WT


title: ChIP_H3K27ac_C57_BMDM_6hIL4_rep2


title: F WT midbrain mono d90 SAM24378234


title: G13_BEU_rep 1 small RNA

description:
G13_BEU_rep 1
small RNA

value: BEU


title: ctrl_BEU_rep 3 small RNA

description:
ctrl_BEU_rep 3
small RNA


title: ctrl_BEU_rep 2 small RNA

description:
ctrl_BEU_rep 2
small RNA


title: NSC_BEU_rep 2 small RNA

description:
NSC_BEU_rep 2
small RNA


title: ChIP_H3K27ac_C57_BMDM_1hIL4_rep2

value: IL-4 1h


title: ctrl_CMC_rep 1 small RNA

description:
ctrl_CMC_rep 1
small RNA


title: ctrl_BEU_rep 1 small RNA

description:
ctrl_BEU_rep 1
small RNA


title: PUS7 sg 2-CMC_rep 1 poly A+ RNA

description:
PUS7 sg 2-CMC_rep 1
poly A+ RNA

value: PUS7 KD


title: M WT brainstem PFF d90 SAM24378296

value: brainstem


title: PUS7 sg 1-CMC_rep 2 poly A+ RNA

description:
PUS7 sg 1-CMC_rep 2
poly A+ RNA


title: PUS7 sg 2-CMC_rep 2 poly A+ RNA

description:
PUS7 sg 2-CMC_rep 2
poly A+ RNA


title: ctrl sg-CMC_rep 3 poly A+ RNA

description:
ctrl sg-CMC_rep 3
poly A+ RNA


title: ChIP_H3K27ac_C57_BMDM_basal_rep2


title: M KO midbrain PFF d90 SAM24378266

value: brain


title: M WT brainstem PFF d60 SAM24378285

value: M


title: ChIP_H3K27ac_C57_BMDM_1hIL4_rep1


title: F KO brainstem PFF d60 SAM24378280

value: KO


title: ctrl sg-CMC_rep 1 poly A+ RNA

description:
ctrl sg-CMC_rep 1
poly A+ RNA


title: PUS7 sg 2-CMC_rep 3 poly A+ RNA

description:
PUS7 sg 2-CMC_rep 3
poly A+ RNA


title: PUS7 sg 1-CMC_rep 3 poly A+ RNA

description:
PUS7 sg 1-CMC_rep 3
poly A+ RNA


title: M KO brainstem PFF d90 SAM24378299


title: M KO striatum PFF d90 SAM24378229

value: striatum


title: PUS7 sg 1-CMC_rep 1 poly A+ RNA

description:
PUS7 sg 1-CMC_rep 1
poly A+ RNA


title: ChIP_input_PWK_BMDM_24hIL4

value: PWK/PhJ

value: input


title: PUS7 sg 2-BEU_rep 1 poly A+ RNA

description:
PUS7 sg 2-BEU_rep 1
poly A+ RNA


title: M WT brainstem mono d90 SAM24378275


title: ChIP_input_SPRET_BMDM_basal

value: SPRET/EiJ


title: F KO midbrain PFF d90 SAM24378257

value: midbrain

value: PFF


title: ChIP_input_PWK_BMDM_basal

value: BMDMs (bone marow-derived macrophages)


title: ChIP_H3K27ac_C57_BMDM_basal_rep1


title: ChIP_input_SPRET_BMDM_24hIL4


title: PUS7 sg 2-BEU_rep 3 poly A+ RNA

description:
PUS7 sg 2-BEU_rep 3
poly A+ RNA


title: M KO striatum PFF d90 SAM24378231


title: ctrl sg-CMC_rep 2 poly A+ RNA

description:
ctrl sg-CMC_rep 2
poly A+ RNA

value: CMC


title: PUS7 sg 2-BEU_rep 2 poly A+ RNA

description:
PUS7 sg 2-BEU_rep 2
poly A+ RNA


title: PUS7 sg 1-BEU_rep 3 poly A+ RNA

description:
PUS7 sg 1-BEU_rep 3
poly A+ RNA


title: PUS7 sg 1-BEU_rep 2 poly A+ RNA

description:
PUS7 sg 1-BEU_rep 2
poly A+ RNA


title: PUS7 sg 1-BEU_rep 1 poly A+ RNA

description:
PUS7 sg 1-BEU_rep 1
poly A+ RNA


title: ctrl sg-BEU_rep 3 poly A+ RNA

description:
ctrl sg-BEU_rep 3
poly A+ RNA


title: M KO brainstem PFF d60 SAM24378288


title: ctrl sg-BEU_rep 1 poly A+ RNA

description:
ctrl sg-BEU_rep 1
poly A+ RNA


title: RNAseq of Camelus dromedarius: adult male kidney / medulla rehydration 4

city: Bristol

first: Fernando

last: Alvira Iraizoz

address: Dorothy Hodgkin Building, University of Bristol, Whitson Street

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

description:
ArabianC_kidney_MR4
29.MR4N
RNAseq polyA selection

data_processing:
Merge fastq files (Linux command line).
Sort fastq files (Linux command line).
Trim adapter regions (Linux command line).
Align reads against reference genome (Linux command line; Rsubread package).
Run QC of the alignments (Linux command line).
Run feature counts (Linux command line).
Run QC of feature counts (Linux command line).
Analyse differential gene expression (DESeq2 1.31.18 in Rstudio 1.3.1073).
Genome_build: CamDro2 (Camelus_dromedarius.CamDro2.dna.toplevel.fa.gz)
Supplementary_files_format_and_content: FeatureCountsCamelKidneyRsubread.txt: Tab-delimited text file includes Feature counts for all transcripts identified in the analysis.
Supplementary_files_format_and_content: CamKidRNA_DESeq2NormalisedExpressionDataWithGeneInfo.csv: Comma-separated text file includes raw data of differential gene expression for all identified genes.

organism: Camelus dromedarius

source_name: Kidney medulla

extract_protocol:
Total RNA was extracted from fresh frozen kidney medulla and cortex of 5 control, 5 dehydrated and 5 rehydrated camels (for a total of 30 samples). These 15 animals were randomly selected out of the 19 animals included in the experimental set up while the remaining 4 were used for preliminary analyses only. Frozen tissue was added to a pre-cooled mortar containing a small volume of liquid nitrogen. Tissue was then grounded to a fine powder using a pestle and the nitrogen was allowed to evaporate. The powdered tissue was placed into pre-chilled tubes on dry ice and stored at -80°C. For RNA extraction, 1ml of Qiazol (79306, Qiagen) was added to 100mg of powdered tissue, then immediately vortexed for 2 minutes, then incubated on ice for 10 minutes. Lysed samples were spun at 12000xg for 10 minutes at 4°C and the supernatant was transferred to a new tube. 1/5 volume Chloroform (22711.244, VWR) was added to each sample and vortexed for 15 seconds. Samples were then spun at 12000xg for 15 minutes at 4°C. 350ml of the upper phase was removed and mixed with an equal volume of absolute ethanol. RNA was extracted using ZymoTM Direct-Zol RNA miniprep (Zymo Research) as per the manufacturer’s instructions. Total RNA concentration and 260/280 ratios were measured using a Nanodrop 2000c (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The camels were supplied with alfalfa hay as feed and ranch-housed in the United Arab Emirates. Veterinary supervision was provided throughout the experimental period and no signs of distress or illness were identified. After a short adaptive period, the camels were divided into 3 groups, control (n=5), dehydrated (n=8) and rehydrated (n=6). The control group had free access to food and water during the entire experimental period. The dehydrated group was water-deprived but had ad libitum access to food for 20 days. Meanwhile the rehydrated group was subjected to the same protocol as the dehydrated animals followed by ad libitum water supply for 3 additional days. After the experimental period, the camels were sacrificed in the local central abattoir for human consumption in April 2016. Kidney samples were harvested within 1 hour after killing the animals, immediately frozen in liquid nitrogen and kept at -80°C for later physiological, histological, morphological and molecular analysis. Samples were shipped frozen on dry ice to the University of Bristol under the auspices of a DEFRA Import Licence (TARP/2016/063). This study was approved by the Animal Ethics Committee of the United Arab Emirates University (approval ID: AE/15/38) and the University of Bristol Animal Welfare and Ethical Review Board.

value: Kidney medulla

value: 4-5 years

value: Male

value: 20 days dehydration + 3 days rehydration

tag: individual


title: ChIP_input_BALB_BMDM_24hIL4

extract_protocol:
For histone marks, PU.1, CEBPb and RNA Pol2 ChIP-seqs, culture media was removed and plates were washed once with PBS and then fixed for 10 minutes with 1% formaldehyde (Thermo Fisher Scientific) in PBS at room temperature and reaction was then quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For STAT6, PPARg, and Egr2 ChIP-seq, cells were cross-linked for 30 minutes with 2mM DSG (Pierce) in PBS at room temperature. Subsequently cells were fixed for 10 minutes with 1% formaldehyde at room temperature and the reaction was quenched with 0.125M glycine. After fixation, cells were washed once with cold PBS and then scraped into supernatant using a rubber policeman, pelleted for 5 minutes at 400xG at 4°C. Cells were transferred to Eppendorf DNA Lobind tubes and pelleted at 700xG for 5 minutes at 4°C, snap-frozen in liquid nitrogen and stored at -80°C until ready for ChIP-seq protocol preparation.Chromatin immunoprecipitation (ChIP) was performed in biological replicates as described previously (Seidman et al., 2020). Samples were sonicated using a probe sonicator in 500 µl lysis buffer (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5mM EGTA, 0.1% deoxycholate, 0.5% sarkozyl, 1 × protease inhibitor cocktail). After sonication, 10% Triton X-100 was added to 1% final concentration and lysates were spun at full speed for 10 minutes. 1% was taken as input DNA, and immunoprecipitation was carried out overnight with 20 µl Protein A Dynabeads (Invitrogen) and 2 µg specific antibodies for PU.1 (Santa Cruz, sc-352X), H3K4me2 (Millipore, 07-030), H3K4me3 (Millipore, 04-745), H3K27ac (Active Motif, 39135), RNA Pol2 (Genetex, GTX102535), STAT6 (Santa Cruz, sc-374021), Egr2 (abcam, ab43020) and CEBP- (Santa Cruz, sc-150). Beads were washed three times each with wash buffer I (20mM Tris/HCl, 150mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA), wash buffer II (10mM Tris/HCl, 250mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, 1mM EDTA), TE 0.2% Triton X-100 and TE 50mM NaCl and subsequently resuspended 25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20 and sequencing libraries were prepared on the Dynabeads as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit (NEB) as previously described (Heinz et al., 2018). DNA was polished, polyA-tailed and ligated after which dual UDI (IDT) or single (Bioo Scientific) barcodes were ligated to it. Libraries were eluted and crosslinks reversed by adding to the 46.5 µl NEB reaction 16 µl water, 4 µl 10% SDS, 4.5 µl 5M NaCl, 3 µl 0.5 M EDTA, 4 µl 0.2M EGTA, 1 µl RNAse (10 mg/ml) and 1 µl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 75C for 30 minutes in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries were cleaned up by adding 2 µl SpeedBeads 3 EDAC (Thermo) in 124 µl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 µl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 12.25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 25 µl reaction volume using NEBNext Ultra II PCR master mix and 0.5 µM each Solexa 1GA and Solexa 1GB primers. Libraries were size selected using TBE gels for 200 – 500 bp and DNA eluted using gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research).

value: BALB/cJ


title: RNAseq of Camelus dromedarius: adult male kidney / medulla rehydration 3

description:
ArabianC_kidney_MR3
28.MR3
RNAseq polyA selection


title: RNAseq of Camelus dromedarius: adult male kidney / medulla rehydration 5

description:
ArabianC_kidney_MR5
30.MR5N
RNAseq polyA selection


title: ChIP_input_NOD_BMDM_24hIL4

value: NOD/ShiLtJ


title: ChIP_input_C57_BMDM_6hIL4

value: IL-4 6h


title: RNAseq of Camelus dromedarius: adult male kidney / medulla dehydration 4

description:
ArabianC_kidney_MD4
24.MD4N
RNAseq polyA selection

value: 20 days dehydration


title: RNAseq of Camelus dromedarius: adult male kidney / medulla rehydration 1

description:
ArabianC_kidney_MR1
26.MR1N
RNAseq polyA selection


title: RNAseq of Camelus dromedarius: adult male kidney / medulla dehydration 3

description:
ArabianC_kidney_MD3
23.MD3
RNAseq polyA selection


title: F WT brainstem mono d90 SAM24378272

value: brain

value: F

value: WT

value: brainstem

value: mono


title: RNAseq of Camelus dromedarius: adult male kidney / medulla control 5

description:
ArabianC_kidney_MC5
20.MC5N
RNAseq polyA selection

value: control


title: F WT striatum PFF d90 SAM24378221

value: striatum

value: PFF


title: F WT striatum mono d90 SAM24378199


title: ChIP_input_NOD_BMDM_basal

value: BMDMs (bone marow-derived macrophages)

value: input


title: ATAC_LyzMCreEgr2flfl_BMDM_24hIL4_rep3

data_processing:
FASTQ files from sequencing experiments were mapped to the custom genome of the corresponding mouse strain using Bowtie2 with default parameters (Langmead and Salzberg, 2012). Mapped data for strains other than C57 were later shifted to the mm10 genome using MMARGE (Link et al., 2018). Human data were mapped to hg38. HOMER was used to convert aligned reads into “tag directories” for downstream quantitative analysis (Heinz et al., 2010).
The reproducible enriched regions (i.e. peaks) were identified by first using HOMER (Heinz et al., 2010) to call unfiltered 200-bp peaks (command “findPeaks -style factor -L 0 -C 0 -fdr 0.9 -size 200”) and then running IDR (Li et al., 2011) on replicates with default parameters.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Tab delimited text file containing called peaks in the HOMER peak file format

extract_protocol:
Approximately 80k cells were lysed in 50 μL room temperature ATAC lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), 2.5 μL DNA Tagmentation Enzyme mix (Nextera DNA Library Preparation Kit, Illumina) was added. The mixture was incubated at 37°C for 30 minutes and subsequently purified using the ChIP DNA purification kit (Zymo Research) as described by the manufacturer.
DNA was amplified using the Nextera Primer Ad1 and a unique Ad2.n barcoding primers using NEBNext High-Fidelity 2X PCR MM for 8-14 cycles. PCR reactions were size selected using TBE gels for 175 – 350 bp and DNA eluted using gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research). Samples were quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 75bp single-end sequenced on HiSeq 4000 or NextSeq 500 (Illumina).

value: LyzM-Cre Egr2 fl/fl


title: F WT striatum PFF d60 SAM24378214


title: ctrl sg-BEU_rep 2 poly A+ RNA

description:
ctrl sg-BEU_rep 2
poly A+ RNA

value: BEU


title: RNAseq of Camelus dromedarius: adult male kidney / medulla rehydration 2

description:
ArabianC_kidney_MR2
27.MR2N
RNAseq polyA selection

value: Kidney medulla

value: 4-5 years

value: Male

value: 20 days dehydration + 3 days rehydration


title: RNAseq of Camelus dromedarius: adult male kidney / cortex rehydration 3

description:
ArabianC_kidney_CR3
13.CR4N
RNAseq polyA selection

source_name: Kidney cortex

value: Kidney cortex


title: F KO brainstem PFF d60 SAM24378279

value: brain

value: KO


title: ATAC_LyzMCreEgr2flfl_BMDM_basal_rep3


title: RNAseq of Camelus dromedarius: adult male kidney / cortex rehydration 1

description:
ArabianC_kidney_CR1
11.CR2N
RNAseq polyA selection


title: RNAseq of Camelus dromedarius: adult male kidney / medulla dehydration 5

description:
ArabianC_kidney_MD5
25.MD6N
RNAseq polyA selection

value: 20 days dehydration


title: M KO striatum PFF d60 SAM24378216

value: M


title: RNAseq of Camelus dromedarius: adult male kidney / medulla dehydration 2

description:
ArabianC_kidney_MD2
22.MD2N
RNAseq polyA selection


title: M KO brainstem mono d90 SAM24378273

value: brainstem

value: mono


title: ATAC_LyzMCreEgr2flfl_BMDM_24hIL4_rep2


title: RNAseq of Camelus dromedarius: adult male kidney / medulla dehydration 1

description:
ArabianC_kidney_MD1
21.MD1N
RNAseq polyA selection


title: F WT midbrain mono d90 SAM24378237

value: F

value: WT

value: midbrain


title: ChIP_input_C57_BMDM_1hIL4

data_processing:
FASTQ files from sequencing experiments were mapped to the custom genome of the corresponding mouse strain using Bowtie2 with default parameters (Langmead and Salzberg, 2012). Mapped data for strains other than C57 were later shifted to the mm10 genome using MMARGE (Link et al., 2018). Human data were mapped to hg38. HOMER was used to convert aligned reads into “tag directories” for downstream quantitative analysis (Heinz et al., 2010).
The reproducible enriched regions (i.e. peaks) were identified by first using HOMER (Heinz et al., 2010) to call unfiltered 200-bp peaks (command “findPeaks -style factor -L 0 -C 0 -fdr 0.9 -size 200”) and then running IDR (Li et al., 2011) on replicates with default parameters.
Normalized tag counts were computated using HOMER annotatePeaks.pl script with parameter "-norm 1e7". Histone markers were counted within +/- 500 bp around peaks, while transcription factor binding tags were counted within +/- 300 bp.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Tab delimited text file containing called peaks in the HOMER peak file format

value: IL-4 1h

value: BMDMs (bone marow-derived macrophages)

value: input


title: F KO brainstem mono d90 SAM24378271


title: ATAC_LyzMCreEgr2flfl_BMDM_basal_rep1

value: LyzM-Cre Egr2 fl/fl


title: F KO brainstem mono d90 SAM24378268


title: RNAseq of Camelus dromedarius: adult male kidney / cortex dehydration 1

description:
ArabianC_kidney_CD1
6.CD1
RNAseq polyA selection

value: 4-5 years


title: RNAseq of Camelus dromedarius: adult male kidney / cortex rehydration 4

description:
ArabianC_kidney_CR4
14.CR5
RNAseq polyA selection

value: Male


title: RNAseq of Camelus dromedarius: adult male kidney / medulla control 4

description:
ArabianC_kidney_MC4
19.MC4N
RNAseq polyA selection

value: Kidney medulla

value: control


title: RNAseq of Camelus dromedarius: adult male kidney / medulla control 3

description:
ArabianC_kidney_MC3
18.MC3R
RNAseq polyA selection


title: ChIP_input_C57_BMDM_basal


title: RNAseq of Camelus dromedarius: adult male kidney / cortex control 5

description:
ArabianC_kidney_CC5
5.CC5
RNAseq polyA selection

value: Kidney cortex


title: RNAseq of Camelus dromedarius: adult male kidney / cortex control 4

description:
ArabianC_kidney_CC4
4.CC4
RNAseq polyA selection


title: RNAseq of Camelus dromedarius: adult male kidney / medulla control 2

description:
ArabianC_kidney_MC2
17.MC2N
RNAseq polyA selection


title: RNAseq of Camelus dromedarius: adult male kidney / medulla control 1

description:
ArabianC_kidney_MC1
16.MC1N
RNAseq polyA selection


title: M WT midbrain PFF d90 SAM24378261

value: brain

value: PFF


title: ATAC_Egr2flfl_BMDM_24hIL4_rep3

value: Egr2 fl/fl


title: ChIP_input_BALB_BMDM_basal

value: BALB/cJ


title: RNAseq of Camelus dromedarius: adult male kidney / cortex rehydration 5

description:
ArabianC_kidney_CR5
15.CR6
RNAseq polyA selection

value: 20 days dehydration + 3 days rehydration


title: RNAseq of Camelus dromedarius: adult male kidney / cortex control 2

description:
ArabianC_kidney_CC2
2.CC2
RNAseq polyA selection


title: M KO brainstem PFF d90 SAM24378300

value: M

value: KO

value: brainstem


title: RNAseq of Camelus dromedarius: adult male kidney / cortex rehydration 2

description:
ArabianC_kidney_CR2
12.CR3N
RNAseq polyA selection


title: ATAC_LyzMCreEgr2flfl_BMDM_24hIL4_rep1


title: M WT striatum mono d90 SAM24378204

value: WT

value: striatum

value: mono


title: RNAseq of Camelus dromedarius: adult male kidney / cortex dehydration 5

description:
ArabianC_kidney_CD5
10.CD6
RNAseq polyA selection

value: 20 days dehydration


title: Replicate B R1 + pRADgro-MS2Dsr2, MS2-coimmunoprecipitation

city: Austin

first: Lydia

last: Contreras

state: Texas

address: 200 E Dean Keeton St

institute: University of Texas at Austin

data_processing:
Trimming adaptors with cutadapt (1.14, -q 30 - m 22)
Alignment to reference D. radiodurans genome (GenBank accession numbers NC_001263.1 and NC_001264.1) with Bowtie2 aligner (2.3.2, -local-very-sensitive)
Convert from sam to bam files (samtools (1.10) view) and sort (samtools sort -n)
Read counts obtained using htseq-count (0.9.1) union settings (-m union -s no -a 10)  using gff file that had D. radiodurans sRNAs manually added
Differential gene expression determined using DESeq2 (1.30.1) in R (4.0.2)
Genome_build: GenBank accession numbers NC_001263.1 and NC_001264.1
Supplementary_files_format_and_content: Processed data is tab-deliminated text file from Htseq-count that lists the gene number in one column and the count in the other column

organism: Deinococcus radiodurans

growth_protocol: D. radiodurans R1 (WT) or PprSKD,or WT cells expressing pRADgro-MS2-PprS or pRADgro-MS2only plasmids were grown to late exponential phase cultures (OD600 0.8) in TGY media at 32˚C before IR treatment with 2hr recovery (for WT and KD samples) and collection for RNAseq library preparation (or MS2 co-immunoprecipitation for the MS2 strains).

extract_protocol:
RNA was extracted using Trizol reagent and bead beating. The cDNA libraries were prepared from total RNAs using NEBNext RNA First Strand Synthesis Module (NEB E7525L) and NEBNext DNA Library Prep Master Mix Set for Illumina (NEB E6040L)
cDNA libraries were prepared using NEBNext RNA First Strand Synthesis Module (NEB E7525L) according to standard protocols without any modification. Single-end reads were analyzed with Illumina NextSeq 500 single-end platform

treatment_protocol: D. radiodurans R1 and PprSKD cultures were irradiated with 10 kGy acute ionizing radiation by a 10-MeV, 18-kW linear accelerator (LINAC) β-ray source (250 Gy/s) at the National Center for Electron Beam Research, Texas A&M University. Samples were kept static on dry ice during transport to and from the irradiator (~2 hr each way). Samples were recovered for 2hrs after IR exposure before RNA processing

value: Wild-type

tag: plasmid

value: unirradiated


title: Replicate A R1 + pRADgro-MS2Dsr2, MS2-coimmunoprecipitation


title: Replicate C R1 + pRADgro-MS2only, MS2-coimmunoprecipitation


title: RNAseq of Camelus dromedarius: adult male kidney / cortex dehydration 4

description:
ArabianC_kidney_CD4
9.CD4N
RNAseq polyA selection

value: 4-5 years

value: Male


title: F KO striatum PFF d60 SAM24378213

value: F


title: RNAseq of Camelus dromedarius: adult male kidney / cortex dehydration 3

description:
ArabianC_kidney_CD3
8.CD3
RNAseq polyA selection

value: Kidney cortex


title: M WT midbrain mono d90 SAM24378242

value: brain

value: midbrain


title: RNAseq of Camelus dromedarius: adult male kidney / cortex dehydration 2

description:
ArabianC_kidney_CD2
7.CD2
RNAseq polyA selection


title: ATAC_LyzMCreEgr2flfl_BMDM_basal_rep2

value: LyzM-Cre Egr2 fl/fl

tag: cell type

value: BMDMs (bone marow-derived macrophages)


title: Replicate B wild-type (R1) strain, irradiated with 10 kGy IR (2hr post-IR recovery)

source_name: wild-type (R1)_irradiated with 10 kGy IR (2hr post-IR recovery)

value: irradiated (10 kGy)


title: ChIP_input_C57_BMDM_24hIL4

tag: chip antibody

value: input


title: Replicate A wild-type (R1) strain, unirradiated

source_name: wild-type (R1)_unirradiated

tag: strain


title: F KO midbrain PFF d60 SAM24378248

value: KO

tag: treatment

value: PFF


title: ATAC_PWK_BMDM_24hIL4_rep1

value: PWK/PhJ


title: Replicate A wild-type (R1) strain, irradiated with 10 kGy IR (2hr post-IR recovery)


title: F WT brainstem PFF d90 SAM24378293

tag: tissue

value: WT

value: brainstem


title: ATAC_PWK_BMDM_24hIL4_rep2


title: M KO midbrain mono d90 SAM24378241

value: M

value: mono


title: RNAseq of Camelus dromedarius: adult male kidney / cortex control 3

description:
ArabianC_kidney_CC3
3.CC3N
RNAseq polyA selection

tag: age

value: 4-5 years

value: control


title: M KO midbrain PFF d60 SAM24378251


title: ATAC_Egr2flfl_BMDM_24hIL4_rep2

value: Egr2 fl/fl


title: RNAseq of Camelus dromedarius: adult male kidney / cortex control 1

description:
ArabianC_kidney_CC1
1.CC1
RNAseq polyA selection

value: Kidney cortex

value: Male


title: circRNA Retina P17

value: retina


title: ATAC_Egr2flfl_BMDM_24hIL4_rep1


title: F WT striatum mono d90 SAM24378202

value: brain

value: F

value: striatum


title: circRNA Retina P12


title: M WT brainstem PFF d90 SAM24378298


title: ATAC_Egr2flfl_BMDM_basal_rep3

value: BMDMs (bone marow-derived macrophages)


title: ATAC_NOD_BMDM_24hIL4_rep2

value: NOD/ShiLtJ


title: ATAC_Egr2flfl_BMDM_basal_rep2


title: Replicate B PprS (Dsr2) knockdown strain, irradiated with 10 kGy IR (2hr post-IR recovery)

source_name: PprS (Dsr2) knockdown_irradiated with 10 kGy IR (2hr post-IR recovery)

value: PprSKD

value: irradiated (10 kGy)


title: Replicate A R1 + pRADgro-MS2only, MS2-coimmunoprecipitation

value: Wild-type

value: unirradiated


title: ATAC_NOD_BMDM_24hIL4_rep1


title: F KO striatum PFF d60 SAM24378209

value: KO

value: PFF


title: Replicate C wild-type (R1) strain, irradiated with 10 kGy IR (2hr post-IR recovery)


title: ATAC_Egr2flfl_BMDM_basal_rep1


title: Replicate C R1 + pRADgro-MS2Dsr2, MS2-coimmunoprecipitation


title: Replicate C wild-type (R1) strain, unirradiated


title: M WT brainstem PFF d60 SAM24378289

value: M

value: WT

value: brainstem


title: ATAC_NOD_BMDM_basal_rep1


title: circRNA Retina E14.5


title: lncRNA Retina Adult

value: Adult


title: Replicate B wild-type (R1) strain, unirradiated


title: Replicate B R1 + pRADgro-MS2only, MS2-coimmunoprecipitation


title: F KO midbrain PFF d60 SAM24378245

value: midbrain


title: circRNA Retina Adult

value: retina


title: lncRNA Retina P17


title: ATAC_BALB_BMDM_basal_rep2

value: BALB/cJ


title: ATAC_PWK_BMDM_basal_rep2

value: PWK/PhJ


title: M WT striatum PFF d90 SAM24378226

value: brain

value: striatum


title: Replicate C PprS (Dsr2) knockdown strain, irradiated with 10 kGy IR (2hr post-IR recovery)


title: tonsil_lymphoid_stroma_subject4

type: RNA

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description:
tonsil lymphoid stroma from patient 4
L4

hyb_protocol: The biotin-labeled single-strand DNA was hybridized to Illumina HT-12 V4.0 expression beadchips following Illumina’s protocols but with the hybridization temperature at 48°C.

scan_protocol: Signal was detected with streptavidin-Cy3 and all signal intensity quantification was performed using an Illumina iScan high speed scanner, using the standard Illumina scanning protocol.

data_processing:
For each sample, a single intensity (expression) value for each Illumina probe on the array was obtained using
Illumina GenomeStudio software with standard settings and no background correction.
For the data matrices, the ID_REF is the Illumina Probe_ID, and the Detection Pval is as provided by the Illumina software.
Detection Pvalues < 0.01 were taken to indicate Present  (i.e., the corresponding expression level was considered to be above background).
Normalization of the expression values in each sample was done by scaling: for each sample all its expression values were
multiplied by the constant which made the median of the expression values for that sample equal to 256. The scaled values
were then log base 2 transformed. Two group comparisons of expression levels were done for each Illumina probe using the paired
t-test since samples from the 3 tonsil compartments were obtained from each of the 4 patients.
Note due to the processing of the RNA described above (Total RNA was first converted to 1st-strand cDNA using special primers), the
material hybridized to the Illumina HT-12 V4.0 expression beadchips only contained oligonucleotides corresponding to a subset of the
probes on this beadchip.  Hence the appropriate GEO platform is GPL13369 (which contains the proper subset of the
probes for the Illumina HT-12 V4.0 expression beadchip, whose GEO platform is GPL10558).

label: biotin

source_name: tonsil lymphoid stroma

label_protocol:
Total RNA was first converted to 1st-strand cDNA using special primers and linear amplication was done following 2nd-strand cDNA synthesis,
as detailed in the manuscript. Amplified single strand DNA was then biotinylated using
the Encore (TM) BiotinIL Module following the manufacturer's instructions.

extract_protocol: Sample acquisition and RNA isolation from tonsil specimens were performed as described in the reference above.

tag: tonsil tissue compartment

value: lymphoid stroma containing chronic inflammatory cells with germinal centers


title: ATAC_PWK_BMDM_basal_rep1

value: BMDMs (bone marow-derived macrophages)


title: F KO brainstem PFF d90 SAM24378292

value: F


title: M WT striatum PFF d60 SAM24378217


title: lncRNA Retina P1


title: circRNA Retina P7


title: Replicate B PprS (Dsr2) knockdown strain, unirradiated

source_name: PprS (Dsr2) knockdown_unirradiated

value: PprSKD


title: F KO striatum mono d90 SAM24378201

value: mono


title: tonsil_surface_epithelium_subject4

description:
tonsil surface epithelium from patient 4
S4

source_name: tonsil surface epithelium

value: PD-L1 negative squamous surface epithelium


title: Replicate C PprS (Dsr2) knockdown strain, unirradiated

value: unirradiated


title: circRNA Retina P1


title: Replicate A PprS (Dsr2) knockdown strain, irradiated with 10 kGy IR (2hr post-IR recovery)

value: irradiated (10 kGy)


title: lncRNA Retina P7


title: lncRNA Retina E14.5


title: M KO striatum PFF d60 SAM24378218

value: M

value: KO

value: PFF


title: ATAC_SPRET_BMDM_timecourse_24hIL4_rep2

value: SPRET/EiJ


title: M WT midbrain PFF d60 SAM24378250

value: WT

value: midbrain


title: Replicate A PprS (Dsr2) knockdown strain, unirradiated


title: ATAC_BALB_BMDM_24hIL4_rep2

value: BALB/cJ


title: F WT striatum PFF d60 SAM24378212

value: brain


title: ATAC_NOD_BMDM_basal_rep2

value: NOD/ShiLtJ


title: RNAseq_DIDO3_MUT2_rep2

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using BWA-MEM 0.7.15 with parameters mem -M -t 4 mm10bwaidx file_1.fastq file_2.fastq
Transcripts per Million of library size (TPM) were calculated using StringTie version 1.3.3 with parameters -e -v -p 32 -G knownGene_UCSC_mm10_3UTR_2kb.gtf
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cov, FPKM, and TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with TPM values for every transcript and every sample

source_name: mouse embryonic stem cell

growth_protocol: All mouse embryonic stem cells were cultured in KO-DMEM (Gibco, Invitrogen) supplemented with 20% fetal calf serum, GlutaMAX (Gibco, Invitrogen), non-essential amino acids, 2-mercaptoethanol, antibiotics and mouse leukemia inhibitory factor (LIF) (Millipore) on a layer of mitomycin C-treated mouse embryonic fibroblasts (MEF) or gelatinized tissue culture plates.

extract_protocol:
Total RNA was performed with a SPLIT RNA extraction kit (Lexogen, Austria) using the manufacturer´s protocol and approximately 2.5x10^6 cells. Triplicate RNA probes from wild-type mESC, DIDO3_exon16, and DIDO3_dCT+HADIDO3 were sent to Centro Nacional de Análisis Genómico (CNAG-CRG) in Barcelona, Spain.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cell

tag: source

value: cell culture

value: DIDO3_dCT+HADIDO3 mutant


title: ATAC_SPRET_BMDM_timecourse_6hIL4_rep1

value: IL-4 6h

value: BMDMs (bone marow-derived macrophages)


title: M WT striatum PFF d60 SAM24378215

value: striatum


title: ATAC_SPRET_BMDM_timecourse_1hIL4_rep2

value: IL-4 1h


title: ATAC_BALB_BMDM_24hIL4_rep1


title: M KO midbrain PFF d90 SAM24378262


title: RNAseq_DIDO3_MUT1_rep3

value: DIDO3_exon16 mutant


title: F WT midbrain PFF d60 SAM24378247

value: F


title: M WT midbrain PFF d60 SAM24378252

value: M


title: lncRNA Retina P12

value: retina


title: F WT brainstem PFF d90 SAM24378291

value: brainstem

value: PFF


title: ATAC_BALB_BMDM_basal_rep1


title: F KO striatum PFF d90 SAM24378224

value: KO


title: F KO midbrain PFF d60 SAM24378244

value: midbrain


title: tonsil_crypt_subject4

description:
tonsil crypt tissue from patient 4
C4

source_name: tonsillar crypts

value: PD-L1 positive crypt epithelium with associated immune cells


title: RNAseq_DIDO3_WT_rep4

value: wild type


title: tonsil_crypt_subject1

description:
tonsil crypt tissue from patient 1
C1


title: tonsil_lymphoid_stroma_subject3

description:
tonsil lymphoid stroma from patient 3
L3

value: lymphoid stroma containing chronic inflammatory cells with germinal centers


title: tonsil_lymphoid_stroma_subject1

description:
tonsil lymphoid stroma from patient 1
L1


title: ATAC_SPRET_BMDM_timecourse_24hIL4_rep1

value: SPRET/EiJ


title: RNAseq_DIDO3_MUT1_rep1

value: embryonic stem cell

value: cell culture


title: tonsil_crypt_subject3

description:
tonsil crypt tissue from patient 3
C3


title: RNAseq_DIDO3_MUT2_rep3

value: DIDO3_dCT+HADIDO3 mutant


title: ATAC_SPRET_BMDM_timecourse_6hIL4_rep2

value: IL-4 6h

value: BMDMs (bone marow-derived macrophages)


title: RNAseq_DIDO3_WT_rep2


title: M KO brainstem PFF d90 SAM24378301

value: brain


title: ATAC_C57_BMDM_timecourse_6hIL4_rep2


title: tonsil_surface_epithelium_subject3

description:
tonsil surface epithelium from patient 3
S3

value: PD-L1 negative squamous surface epithelium


title: M KO striatum mono d90 SAM24378203

value: M

value: striatum

value: mono


title: F KO brainstem PFF d90 SAM24378294

value: F

value: brainstem

value: PFF


title: RNAseq_DIDO3_MUT2_rep1


title: tonsil_lymphoid_stroma_subject2

description:
tonsil lymphoid stroma from patient 2
L2


title: ATAC_SPRET_BMDM_timecourse_1hIL4_rep1

value: IL-4 1h


title: ATAC_SPRET_BMDM_timecourse_basal_rep2


title: tonsil_crypt_subject2

description:
tonsil crypt tissue from patient 2
C2

value: PD-L1 positive crypt epithelium with associated immune cells


title: F KO midbrain mono d90 SAM24378236

value: KO

value: midbrain


title: ATAC_SPRET_BMDM_timecourse_basal_rep1

value: SPRET/EiJ


title: RNAseq_DIDO3_MUT1_rep2

value: embryonic stem cell

value: cell culture

value: DIDO3_exon16 mutant