title: Mature testes-3 mRNAseq

city: Changchun

first: Xibi

last: Fang

address: No. 5333 Xian Road

institute: Jilin University

description: Male reproduction

data_processing:
Whole transcriptome libraries preparation and deep sequencing
The sequencing library of each RNA sample was pre- pared by using Ion Total RNA-Seq Kit v2
Raw Data Treatment: Using high-throughput Life technologies Ion Proton Sequencer, the transcript with poly (A)+ RNA of Human were analyzed. Reads sequenced were filtered and mapped to Cattle genome (download from NCBI) using Mapsplice software. The mapped reads was counted to achieve the expression of each gene based on the gene annotation information from NCBI database.
Data Filtering:In order to achieve the best quality of the RNA Sequencing, Novelbio applied the reads filtration to filter the reads with lower quality and short sequence under following criteria: read length > 50; over 30% base quality >13.
Identification of differentially expressed genes :The DE-Seq algorithm was  applied  to  filter  differentially expressed  genes. After  the  significance  analysis  and  FDR  (false discovery  rate)  analysis ,  we  selected  the  differentially expressed  genes  according  to  the FDR threshold set at p < 0.05 and FDR <0.05. And the fold changes of any two groups are more than 2.
All target genes regulated by DERs were predicted by the combination of miRbase (http://www.mirbase.org) and TargetScan (http://www.targetscan.org). All the predicted target genes were intersected with the DEGs obtained by RNA-seq, and then the DEGs and DERs were obtained by a combined analysis.
Genome_build: Btau_5.0.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ..

organism: Bos taurus

source_name: mature bovine testes

growth_protocol: A total of 6 testicular tissues of cattle (3 newborn for 1-day and 3 adult for 24-months-old) were collected from the Agricultural Science Academy of Jilin Province cattle farm (Gongzhuling, China).

extract_protocol:
Total RNA was extracted from the collected testis tissues using trizol reagent (Invitrogen, USA) following the manufacturer’s instructions. Total RNA was treated with DNase I (NEB, Beijing, China). The RNA concentration and integrity quality were detected using an Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA) and the RIN or RNA integrity number was used to determine the RNA integrity quality of extraction.
Six libraries of RNA-seq were constructed and grouped to I and M by source of testicular tissues for subsequent analysis. mRNA was enriched with oligo (dT) beads and fractionized for cDNA synthesis. The cDNA was then amplified to prepare the mRNA library. Two small RNA libraries representing each group (coming from the pooling of testis tissues in 3 newborn for 1-day and 3 adult for 24-months-old cattle) were constructed for Solexa sequencing according to the Illumina® TruSeq™ Small RNA Sample manufacturer’s instructions.

tag: breed

value: Chinese Red Steppes cattle

value: mature testes


title: Mature testes-1 mRNAseq

status: Public on Dec 31 2020

type: SRA

country: China

description: Male reproduction

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: Immature testes miRNAseq

description: Male reproduction

source_name: immature bovine testes

value: immature testes


title: 4C_DM_HS+.rep2

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description: Replica 2

library_source: genomic

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed for adaptor sequences and low quality sequences by cutadapt v. 1.16 using the following options: cutadapt --trim-n --times=5 --minimum-length 20 -q 26 -e 0.15 -g ACTGTTCACGATGAACTTG -g TTCAGTTCACAATCCCAAG -a CTTGGGATTGTGAACTGAA -a CAAGTTCATCGTGAACAGT
Trimmed reads were mapped to dm6.BDGP6.22.96 genome by bwa 0.7.12-r1039 using the mem algorithm. All non-aligned reads were removed from resulting alignment file by samtools 1.6: -b -S -F 4 -@ 10 allalign.sam > aligned.bam
Mapping and alignment results were converted to resulting tables using samtools 1.6 and ad hoc Perl scripts.
Each replica results table was converted to bedGraph file for further processing using reads amount as data value. Intersection file was built by bedtools v. 2.27.1 with the following command line: bedtools intersect -a 4C_dm0.hs.rep1.bedGraph -b 4C_dm0.hs.rep2.bedGraph -wb. Ad hoc Perl script was used to convert bedtools output file back to bedGraph file with averaging in the overlapped regions.
Intersection file was filtered from low complexity regions and transposable elements from the DFAM database by bedtools v. 2.27.1 with the following command line: bedtools intersect -sorted -v -f 1.0 -a 4C_dm0.hs.intersect.bedGraph -b dm6_dfam.hits.bed > 4C_dm0.hs.intersect.hc.txt and ad hoc Perl script.
genome build: Drosophila melanogaster dm6/BDGP.6.22.96 genome build
processed data files format and content: Tab-delimited text file include the following features of each mapping: begin, end, length, coverage, number of reads, sequence. bedGraph files for each replica and intersection are supplied too.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown in GIBCO Drosophila medium with 10% FBS in a humidified incubator at 25°C to 80% confluency. Heat shock treatment was performed by incubation of celles in the medium at 37°C for 1 h and then for 1 h at 27°C.

extract_protocol:
DNA samples were prepared as described before (Dekker et al., 2002; Osborne et al., 2004; http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=3978).  Cross-linking: To suspension containing about 34x106 S2 cells in 4 ml of the GIBCO medium formaldehyde solution was added to final concentration 1.5%. After mixing incubation of cell suspension was performed for 10 min at room temperature with mixing. The quenching with 2.75 ml of 2M glycin (final concentration 0.125M) was performed. After incubation at room temperature for 5 min the suspension was cooled for 15 min in ice bath and then cells were collected by centrifugation for 15 min at 3500 rpm at +2°C.  Lysis: The pellet of cells was resuspended at °C in 1ml of buffer containing 10 mM tris-HCl buffer, pH 8, 10 mM NaCl, 0.2% NP-40 and freshly added protease inhibitors – 0.1 mM PMSF and 1:500 protease inhibitor cocktail (Sigma). After incubation for 15 min cells were homogenized by passing through insulin syringe about 50 times into Eppendorf. Then nuclei were spin down by centrifugation for 5 min at 5000 rpm in Eppendorf centrifuge 5415 R at +2°C.  Digestion with EcoRI: The nuclei pellet was resuspended in 756 microl of solution containing 40 mM tris-HCl buffer, pH 7.4, 50 mM NaCl, 10 mM MgCl2 and 10 mM 2-mercaptoethanol. Then 20% SDS was added to final concentration 0.3% and incubation with shaking was performed for 1 h at +37°C. To sequester SDS 180 l of 10% Triton X-100 was added and the incubation for 1 h at +37°C was performed. Before digestion 1 l of BSA (5 mg/ml) was added with mixing. Then 50 l of EcoRI (10 u/l) was added and after mixing digestion was performed overnight at +37°C.   Ligation: To inactivate the restriction enzyme, 35 l of 20% SDS was added (final concentration 0.7%) and the probe was heated to 65°C for 30 min. Then the mixture was transferred into 15 ml Nunc tube and consequently 375 l of 20% Triton X-100 (to final concentration 1%), 750 l of 10x ligase buffer, 7,5 l of BSA (5 mg/ml), 80 l of 100 mM ATP, and 5241 l of milliQ water  were added and the final 7.5 ml solution was well mixed. Then 10 l of T4 DNA ligase (200 u/l) was added and after mixing incubation was performed for 5 h at +16°C and then for 30 min at room temperature. Usually during ligation DNA concentration was equal to 2 ng/l.    DNA purification: For isolation of DNA 50 l of proteinase K (10 mg/ml) was added (final concentration 50 g/ml) and after mixing incubation was performed at 55°C B1overnight. For RNA digestion 40l of RNase A (10 mg/ml) was added (final concentration 0.5 g/ml) and after mixing incubation was performed for 30 min at +37°C. After extensive extraction with phenol-chloroform extraction (three times with 7 ml each) DNA was precipitated by 2.5 vol. of ethanol after addition of 40 l 10 mg/ml glycogen and 175 l 4M NaCl. The final DNA pellet was washed twice with 70% ethanol and then dissolved in 0.1xTE.   Digestion with FaeI: About 15 g of DNA was digested in 250 microl solution with 75 u of FaeI overnight at +37°C. Then the enzyme was inactivated by heating at 65°C for 30 min. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 100 l of 0.1xTE.   Ligation: For circularization 15 microg of DNA was incubated in 8 ml of T4 DNA ligase buffer containing 400 u of T4 DNA ligase for 5 h at +16°C. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 50 microl of 0.1xTE.
One  round of  PCR was used as described below. The following primers were used: 5' ACTGTTCACGATGAACTTGGAATT 3' and 5' TTCAGTTCACAATCCCAAGCATG 3'. PCR products were purified using QIAqiuck PCR purification kit kit (Quigen). The libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina). The samples were sequenced using HiSeq 1500 (Illumina) following the manufacturer's protocols.

tag: cell type

tag: developmental stage

value: late embryo

tag: genotype

value: wild type

tag: stress

value: heatshock


title: RNASeq_S2.rep1

description: Replica 1

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed from low quality and/or short sequences by trimmomatic v. 0.36 using the following options: LEADING:18 TRAILING:18 SLIDINGWINDOW:4:22 MINLEN:20
Trimmed reads were mapped to BDGP6.22.96 D.melanogaster genome by STAR aligner 2.6.1c with dm6 ENSEMBLE genome map v.98 ftp://ftp.ensembl.org/pub/release-98/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.22.98.gtf.gz. Alignment options were the following:  --outSAMtype BAM SortedByCoordinate --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --twopassMode Basic
Wig files with unique mappings from each replica and strand were converted to bigWig by wigToBigWig tool from UCSC Kent Utilities http://hgdownload.soe.ucsc.edu/admin/exe/ and then averaged by wiggletools 1.2 with the following options: wiggletools write_bg rnaseq.str1.mean.bedGraph mean rnaseq.rep1.str1.bw rnaseq.rep2.str1.bw. The files with mean expression signal for each strand were then converted to bigWig by bedGraphToBigWig tool from UCSC Kent utilities.
Trimmed reads were quantified to dm6 BDGP6.22 genome with ENSEMBLE genome map v.98 by RSEM 1.3.1 using the following options: rsem-calculate-expression --star --output-genome-bam --calc-ci --num-threads 10 --ci-memory 4096 --star-gzipped-read-file. This operation was performed for both replicas separately and both replicas simultaneously.
genome build: Drosophila melanogaster dm6/BDGP6.22.96 genome build. Drosophila melanogaster dm6/BDGP6.22.98 ENSEMBL annotation in GTF format.
processed data files format and content: bigWig files contain normalized (RPM, reads per million) expression signal genomewide for each strand. Results files contain quantified expression values in TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase Million) for each gene.

molecule: polyA RNA

growth_protocol: S2 cells were grown in DMEM with 10% FBS in a humidified incubator at 27°C and 5% CO2 to 80% confluency.

extract_protocol:
Total RNA was extracted from cell lysed with Trisol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA Quality was checked with  BioAnalyser and  RNA 6000 Nano Kit(Agilent). Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion).
Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length.


title: Tet2-/- control, Rep1 [6neg]

city: MARSEILLE

first: erinn

last: soucie

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

data_processing:
Sequencing quality control was done with FastQC v.0.10.1.
Reads were mapped with the TopHat v2.0.11 software to the UCSC mouse (mm10) or human (GRCh38/hg38) reference genome, with on average 20 million aligned reads/sample (mouse, 25 million human).
Biological quality control and summarization were done with RSeQC v2.4, PicardTools v1.92 and SamTools v0.1.18 respectively.
Read coverages were determined to be uniform and the percentage of mRNA bases was on average 64%. The percentage of ribosomal bases was less than 5%.
The count data, prepared with HTSeq v.0.6.1p1 (htseq-count, default parameters).
The raw count data are filtered. We filtered out very lowly expressed genes, keeping genes that are expressed at a reasonable level. Since the group size average is 2, we kept genes that achieved 10 counts in at least 2 samples: genes 23,420 – 11,821 = 11,599 expression values for each sample- ~49% (mouse); 23,710- 14,298 = 9,412 - ~40% (human).
The normalization and differential expression analysis was performed with the R/Bioconductor edgeR package v.3.4.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw and normalized counts for all samples

organism: Mus musculus

source_name: Tet2-/- control

growth_protocol: Primary mast cells were derived from bone marrow of either Tet2+/+ or Tet2-/- C57BL/6J Tet2LacZ

extract_protocol:
RNA was isolated from sorted cell fractions using the RNAeasyPlus kit (Qiagen) for sequencing
8- indexed libraries were prepared using the Illumina TrueSeq protocol following ribodepletion and 100 single-end reads were run on a HiSeq2500 from Illumina

treatment_protocol: mice, isolated and cultured in OptiMEM/10% FCS (Life Technologies) media supplemented with 10 ng/ml IL3 (Peprotech), 50ug/ml Penicillin/streptomycin, and 1% beta-mercaptoethanol (both Life Technologies) on tissue culture treated plastic, at 37°C, 5% CO2. Non-adherent cells were selected for 15 days under these conditions, at which point cultures were infected with lenti-virus carrying the KitD816V allele and GFP (ires). For infection, we used a single 2h spinoculation in the presence of 6μg/ml polybrene. Infected cells were further expanded for 15 days, for a total of 30 days of in vitro culture, and then GFP-negative and positive fractions (cultures were 40-80% GFP-positive) were FACS sorted on FACSAria using DIVATM (Becton- Dickinson) software for direct lysis and RNA isolation.

tag: strain

value: C57BL/6J Tet2LacZ

tag: genotype/variation

value: Primary murine mast cells derived from bone marrow


title: RNASeq_S2.hs.rep1

description: Replica 1

treatment_protocol: RNA-Seq procedure was used for analysis of expression in S2 cells. Heat shock treatment was performed for 1 h at 37°C. Then heat-shock treated S2 cells were incubated for 1 h at 27°C. Then cells of each replicate were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with  BioAnalyser and  RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 10 millions of reads were generated for each sample.


title: Immature testes-2 mRNAseq

description: Male reproduction


title: Mature testes-2 mRNAseq

description: Male reproduction


title: Immature testes-3 mRNAseq

description: Male reproduction


title: Mature testes miRNAseq

description: Male reproduction


title: 4C_DM_HS-.rep2

description: Replica 2

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed for adaptor sequences and low quality sequences by cutadapt v. 1.16 using the following options: cutadapt --trim-n --times=5 --minimum-length 20 -q 26 -e 0.15 -g ACTGTTCACGATGAACTTG -g TTCAGTTCACAATCCCAAG -a CTTGGGATTGTGAACTGAA -a CAAGTTCATCGTGAACAGT
Trimmed reads were mapped to dm6.BDGP6.22.96 genome by bwa 0.7.12-r1039 using the mem algorithm. All non-aligned reads were removed from resulting alignment file by samtools 1.6: -b -S -F 4 -@ 10 allalign.sam > aligned.bam
Mapping and alignment results were converted to resulting tables using samtools 1.6 and ad hoc Perl scripts.
Each replica results table was converted to bedGraph file for further processing using reads amount as data value. Intersection file was built by bedtools v. 2.27.1 with the following command line: bedtools intersect -a 4C_dm0.rep1.bedGraph -b 4C_dm0.rep2.bedGraph -wb. Ad hoc Perl script was used to convert bedtools output file back to bedGraph file with averaging in the overlapped regions.
Intersection file was filtered from low complexity regions and transposable elements from the DFAM database by bedtools v. 2.27.1 with the following command line: bedtools intersect -sorted -v -f 1.0 -a 4C_dm0.intersect.bedGraph -b dm6_dfam.hits.bed > 4C_dm0.intersect.hc.bedGraph and ad hoc Perl script.
genome build: Drosophila melanogaster dm6/BDGP.6.22.96 genome build
processed data files format and content: Tab-delimited text file include the following features of each mapping: begin, end, length, coverage, number of reads, sequence. bedGraph files for each replica and intersection are supplied too.

growth_protocol: S2 cells were grown in GIBCO Drosophila medium with 10% FBS in a humidified incubator at 25°C to 80% confluency.

extract_protocol:
DNA samples were prepared as described before (Dekker et al., 2002; Osborne et al., 2004; http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=3978).  Cross-linking: To suspension containing about 34x106 S2 cells in 4 ml of the GIBCO medium formaldehyde solution was added to final concentration 1.5%. After mixing incubation of cell suspension was performed for 10 min at room temperature with mixing. The quenching with 2.75 ml of 2M glycin (final concentration 0.125M) was performed. After incubation at room temperature for 5 min the suspension was cooled for 15 min in ice bath and then cells were collected by centrifugation for 15 min at 3500 rpm at +2°C.  Lysis: The pellet of cells was resuspended at °C in 1ml of buffer containing 10 mM tris-HCl buffer, pH 8, 10 mM NaCl, 0.2% NP-40 and freshly added protease inhibitors – 0.1 mM PMSF and 1:500 protease inhibitor cocktail (Sigma). After incubation for 15 min cells were homogenized by passing through insulin syringe about 50 times into Eppendorf. Then nuclei were spin down by centrifugation for 5 min at 5000 rpm in Eppendorf centrifuge 5415 R at +2°C.  Digestion with EcoRI: The nuclei pellet was resuspended in 756 microl of solution containing 40 mM tris-HCl buffer, pH 7.4, 50 mM NaCl, 10 mM MgCl2 and 10 mM 2-mercaptoethanol. Then 20% SDS was added to final concentration 0.3% and incubation with shaking was performed for 1 h at +37°C. To sequester SDS 180 l of 10% Triton X-100 was added and the incubation for 1 h at +37°C was performed. Before digestion 1 l of BSA (5 mg/ml) was added with mixing. Then 50 l of EcoRI (10 u/l) was added and after mixing digestion was performed overnight at +37°C.   Ligation: To inactivate the restriction enzyme, 35 l of 20% SDS was added (final concentration 0.7%) and the probe was heated to 65°C for 30 min. Then the mixture was transferred into 15 ml Nunc tube and consequently 375 l of 20% Triton X-100 (to final concentration 1%), 750 l of 10x ligase buffer, 7,5 l of BSA (5 mg/ml), 80 l of 100 mM ATP, and 5241 l of milliQ water  were added and the final 7.5 ml solution was well mixed. Then 10 l of T4 DNA ligase (200 u/l) was added and after mixing incubation was performed for 5 h at +16°C and then for 30 min at room temperature. Usually during ligation DNA concentration was equal to 2 ng/l.    DNA purification: For isolation of DNA 50 l of proteinase K (10 mg/ml) was added (final concentration 50 g/ml) and after mixing incubation was performed at 55°C B1overnight. For RNA digestion 40 l of RNase A (10 mg/ml) was added (final concentration 0.5 g/ml) and after mixing incubation was performed for 30 min at +37°C. After extensive extraction with phenol-chloroform extraction (three times with 7 ml each) DNA was precipitated by 2.5 vol. of ethanol after addition of 40 l 10 mg/ml glycogen and 175 l 4M NaCl. The final DNA pellet was washed twice with 70% ethanol and then dissolved in 0.1xTE.   Digestion with FaeI: About 15 g of DNA was digested in 250 microl solution with 75 u of FaeI overnight at +37°C. Then the enzyme was inactivated by heating at 65°C for 30 min. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 100l of 0.1xTE.   Ligation: For circularization 15 g of DNA was incubated in 8 ml of T4 DNA ligase buffer containing 400 u of T4 DNA ligase for 5 h at +16°C. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 50 l of 0.1xTE.
One  round of  PCR was used as described below. The following primers were used: 5' ACTGTTCACGATGAACTTGGAATT 3' and 5' TTCAGTTCACAATCCCAAGCATG 3'. PCR products were purified using QIAqiuck PCR purification kit kit (Quigen). The libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina). The samples were sequenced using HiSeq 1500 (Illumina) following the manufacturer's protocols.


title: ATM_KO_2

city: New York

first: Xiaobin

middle: Summer

last: Wang

state: NEW YORK

address: 1130 Siant Nicholas Ave, Room 501

department: Institute for Cancer Genetics

country: USA

institute: Columbia University Medical Center

data_processing:
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 genome (mm9sr) with IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6 replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3 using Bowtie2. The best-path searching algorithm (related to YAHA; ref. 50) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads are then filtered to exclude mispriming events, germ-line (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. To plot all of the S-region junctions, including those in the repeats but unequivocally mapped to an individual switch region, we combined the ones filtered by a mappability filter but unequivocally mapped to S regions with “good” reads passing both the mappability (both deduplicated) filters (please see ref. 28 for simulation and details on plotting). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait and prey-break site. Blunt junctions are considered to have no MHs or insertions.
Mutation rate was calculated by custom Excel integrated VBA script. Mutations were determined by comparing the actual bait sequence of each IgH junction with the germ-line bait sequence based on the IgH sequence from 129/Sv strain (NCBI gene accession no. AJ851868.3). Only true mismatches (no insertion or deletion within 7 nt) were counted as a mutation.
Genome_build: mm9sr (to customized mm9 genome (mm9sr) with IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6 replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3)
Supplementary_files_format_and_content: .xlsx files generated from tab-delimited text files after analysis for reads distribution and mutation rates.

source_name: B cells

growth_protocol: Purified splenic B (CD43-) cells from mice were cultured in RPMI mediume with cytokines (anti-CD40 (1 ng/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)).

extract_protocol:
Genomic DNA was extracted from day 4 cultured B cells.
Libraries were prepared according to protocol in (Hu J, et al. Nat Protoc 11:853–871.(2016)) Linear amplifications were performed using Sμ-specific biotin primer  5′/5BiosG/CAGACCTGGGAATGTATGGT3′) and followed by nesting PCR with (5′CACACAAAGACTCTGGACCTC3′)  AflII is used to remove germ-line sequence.
high-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v

treatment_protocol: Cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

value: anti-CD40 and Il4 activated B cells

value: ATM-/-


title: ATM_RX_2

value: ATM RX/RX


title: ATM_KO_1


title: wildtype_2 (ATM control)


title: Experiment_02_g2G3_M

city: Las Vegas

first: Martin

last: Schiller

state: NV

address: 4505 S Maryland Pkwy

department: Nevada Institute of Personalized Medicine

institute: University of Nevada, Las Vegas

description:
Hela cells with blocking both C-NHEJ and A-NHEJ pathways in Experiment_02
all_sample_human_RNA_max.txt

data_processing:
Sequenced reads were imported into CLC Genomics Workbench 12.0 (https://www.qiagenbioinformatics.com/) and trimmed for adaptor sequence using quality limit of 0.05 calculated from a modified-Mott trimming algorithm, read through adapter trimming, and trimming of ambiguous bases from read regions with more than 2 ambiguous reads.
RNA seq analysis was performed with the RNA Seq Analysis tool in Genomics Workbench which is based upon the ENRAGE pipeline2.  Default settings were used including a mismatch cost of 2, insertion and deletion cost of 3.
Read 1 and read 2 from pairs could be processed independently as technical replicates.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each raw read file

organism: Homo sapiens

source_name: human cell line

growth_protocol: HeLa (ATCC® CCL-2™) cells obtained from the ATCC and LentiX293T (Clonetech) were grown in Dulbecco modified Eagle’s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (HyClone). To assess DNA repair, HeLa cells (0.6 million) were seeded and after one day, co-transfected with a NHEJ reporter plasmid with either pairs of TALEN reporter constructs. Media was changed after 6 hours and cultured in complete media (DMEM+ 10% FBS), with or without mirin.

extract_protocol:
The cells post 48 hours transfection were harvested and RNA was extracted using Zymogen RNA prep kit (Zymogen).
The RNA sample library preparation and sequencing on the Illumina platform PE150 was performed at Novagene Corporation Inc.

treatment_protocol: To create a XRCC4(-/-) cell line to block cNHEJ, a gXRCC4 sequence targeting the XRCC4 gene (NCBI RefSeq: NC_000005.10) was annealed, phosphorylated with T4 Polynucleotide Kinase (New England Biolabs) and cloned into the BsmBI digested LenticrisprV2 plasmid (Addgene). The plasmid was delivered into HeLa cells by lentiviral transduction.

value: Hela cells

tag: treatment

value: XRCC4 knockout with Mirin

tag: experiment


title: Experiment_02_gSCR_M

description:
Hela cells with only blocking A-NHEJ pathway by mirin treatment in Experiment_02
all_sample_human_RNA_max.txt

value: scrambled gRNA with Mirin


title: wildtype_1 (ATM control)


title: Experiment_02_gSCR

description:
Hela cells as controls in Experiment_02
all_sample_human_RNA_max.txt

value: scrambled gRNA control


title: Experiment_01_gSCR_M

description:
Hela cells with only blocking A-NHEJ pathway by mirin treatment in Experiment_01
all_sample_human_RNA_max.txt


title: Experiment_02_g2G3

description:
Hela cells with only blocking C-NHEJ pathway by XRCC4 knockout in Experiment_02
all_sample_human_RNA_max.txt

value: XRCC4 knockout


title: Immature testes-1 mRNAseq

description: Male reproduction


title: Experiment_01_g2G3

description:
Hela cells with only blocking C-NHEJ pathway by XRCC4 knockout in Experiment_01
all_sample_human_RNA_max.txt


title: F11KO+shLuc Ctrl-2 (RNA-seq)

city: Memphis

first: Mitch

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Hematology

institute: st jude children's research hospital

description:
RNA.count.all.txt.gz
F11KO+shLuc_Ctrl-2

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were aligned and counted by RNA-seq pipeline(WARDEN) at https://www.stjude.cloud/tools.html
Briefly, paired-end reads were aligned to hg19 by STAR and counted by HTSEQ.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each gene for each sample

growth_protocol: Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.

extract_protocol:
HUDEP-2 cells' RNA was harvested using RLT reagent (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: erythroblast cells

value: Umbilical Cord blood derived

value: FBXO11 -/-  +shLuc


title: F11KO+B1sh1-1 (RNA-seq)

description:
RNA.count.all.txt.gz
F11KO+B1sh1-1

value: FBXO11 -/-  +BAHD1KD


title: Clone-F11KO-2 (RNA-seq)

description:
RNA.count.all.txt.gz
Clone_F11KO_2


title: F11KO+B1sh1-2 (RNA-seq)

description:
RNA.count.all.txt.gz
F11KO+B1sh1-2


title: Clone-F11KO-3 (RNA-seq)

description:
RNA.count.all.txt.gz
Clone_F11KO_3


title: Clone-WT-3 (RNA-seq)

description:
RNA.count.all.txt.gz
Clone_WT_3


title: Drosophila wing disc Sce RNAi Ubx-GAL4>DamPc rep2

city: Melbourne

first: Michael

middle: Joseph

last: Murray

state: VIC

address: Parkville

department: School of BioSciences

country: Australia

institute: University of Melbourne

description: DNA amplicon

data_processing:
Base calling and quality scoring was performed by the Real Time Analysis (v2.4.6) software.  The FASTQ file generation and de-multiplexing for the samples was performed by the bcl2fastq conversion software (v2.15.0.4).
Sequencing data was mapped to release 6.03 of the Drosophila genome and Dampol/Dam bedgraph ratio files created using damidseq_pipeline (Marshall and Brand, 2015,Bioinformatics 31:3371).
Drosophila genome annotation release 6.03
Genome_build: Drosophila genome annotation release 6.03
Supplementary_files_format_and_content: CTL1_DamPc.gatc.bedgraph: DamPc vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: CTL2_DamPc.gatc.bedgraph: DamPc vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: CTL3_DamPc.gatc.bedgraph: DamPc vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: CTL_DamPc.scaled.average.gatc.bedgraph: average of three CTL replicates scaled by dividing by standard deviation
Supplementary_files_format_and_content: SceIR1_DamPc.gatc.bedgraph: DamPc vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: SceIR2_DamPc.gatc.bedgraph: DamPc vs Dam log2 ratio bedgraph files
Supplementary_files_format_and_content: SceIR_DamPc.scaled.average.gatc.bedgraph: average of two SceIR replicates scaled by dividing by standard deviation

source_name: third instar wing imaginal disc

growth_protocol: wing discs dissected out of wandering third instar larvae raised at 29C

extract_protocol:
30 wing discs were dissected in 1xPBS, were frozen at -80˚C, thawed, 40ul of 500mM EDTA, 180ul of ATL buffer, and 20ul Proteinase K added, mixed gently and incubated for 56˚C overnight, cooled to RT and 20ul of RNAase (12.5ul/ul) added and incubated for 2 mins. 400ul of a 1:1 mix of Buffer AL and 100% ethanol was added and mixed gently, before processing through the DNeasy kit spin columns. The genomic DNA was then digested overnight with DpnI, cleaned up with a Qiagen PCR Purification kit, and DamID Adapters blunt ligated with T4 ligase, digested again with DpnII, and then adapter-ligated fragments PCR amplified using DamID primers and Advantage PCR kit DNA polymerase (Clontech). Adapters were then removed with AlwI digestion,
An input of 100ng of genomic DNA was prepared and indexed for illumina sequencing using the TruSeq DNA sample Prep Kit (illumina) as per manufacturer’s instruction.  The library was quantified using the Agilent Tapestation and the Qubit™ RNA assay kit for Qubit 2.0® Fluorometer (Life technologies).  The indexed libraries were then prepared and diluted to 1.5pM for single end (1x 86 base) sequencing on a NextSeq500 instrument using the 75 cycle kit v2 chemistry (illumina) as per manufacturer’s instructions.

value: TaDaG-Polycomb (attP2)

value: third instar wing imaginal disc


title: F11KO+shLuc Ctrl-1 (RNA-seq)

description:
RNA.count.all.txt.gz
F11KO+shLuc_Ctrl-1


title: Clone-F11KO-1 (RNA-seq)

description:
RNA.count.all.txt.gz
Clone_F11KO_1


title: ATM_RX_1


title: Drosophila wing disc Sce RNAi Ubx-GAL4>DamPc rep1

description: DNA amplicon


title: Clone-WT-1 (RNA-seq)

description:
RNA.count.all.txt.gz
Clone_WT_1

value: wild type


title: Experiment_01_gSCR

description:
Hela cells as controls in Experiment_01
all_sample_human_RNA_max.txt


title: Drosophila wing disc Sce RNAi Ubx-GAL4>Dam rep1

description: DNA amplicon

value: TaDaG-Dam (attP2)


title: Drosophila wing disc Control Ubx-GAL4>DamPc rep3

description: DNA amplicon


title: Drosophila wing disc Sce RNAi Ubx-GAL4>Dam rep2

description: DNA amplicon


title: H. parainfluenzae monoculture rep2

city: Kingston

first: Dasith

last: Perera

state: Rhode Island

address: Flagg Rd

institute: University of Rhode Island

data_processing:
paired end alignment using bowtie2
counts generated using htseq-count with parameters -rev -a 1 -m intersection-nonempty
normalization and differential expression analysis carried out using DESeq2
automated workflow can be found at https://github.com/dasithperera-hub/RNASeq-analysis-toolkit
Genome_build: H. parainfluenzae ATCC 33392
Supplementary_files_format_and_content: csv file

organism: Haemophilus parainfluenzae

source_name: Bacterial culture

growth_protocol: H. parainfluenzae grown in mono or coculture with mitis aerobically for 22 hours on BHI-YE HP at 37.C, 5% CO2, transferred to fresh media for 4 hours

extract_protocol:
Beadbeating and trizol
RNAtag-Seq (Shishkin AA, Giannoukos G, Kucukural A, et al. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods. 2015;12(4):323-5.)

value: H. parainfluenzae ATCC 33392


title: Drosophila wing disc Control Ubx-GAL4>DamPc rep2

description: DNA amplicon


title: H. parainfluenzae monoculture rep1


title: Drosophila wing disc Control Ubx-GAL4>Dam rep3

description: DNA amplicon


title: Hsh-A

city: Nanjing

first: Xiannan

last: Meng

address: Hankou Road 22

institute: Nanjing University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from MM10. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Mapping reads to mature miRNA and hairping which recorded in miRBase (release 21) to identiy known-miRNA. After excluded the reads mapped to known miRNA/ncRNA/repeat region/mRNA region, the remaining reads were used to predict novel miRNA, the keys of prediction is hairping structure and stability. The software for identification and prediction is miRDeep2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: sperm

extract_protocol:
Sperm were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（ #E7530L， NEB） was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina

value: Balb/c

value: post natal month 8

tag: shRNA

value: Hsp90aa1 shRNA


title: Sample_139325: Empty_Vector_rep3_RNAseq

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

data_processing:
Sequencing/Basecalls/demultiplexing performed using Illumina NovaSeqControlSoftware 1.6.0 / RTA 3.4.4 / Bcl2fastq v2.20.0.422
Trimmed using Trim Galore 0.6.0 / Cutadapt 1.15
Aligned to GRCm38 using STAR 2.7.2b and standard gencode options for the version
Count read using featureCounts function from Rsubread 1.34.6 and Ensembl GRCm38.p6/gencode.vM23.annotation.gtf as reference
Normalization (TMM), quantitation and differential expression analysis using EdgeR
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited file of counts after featureCounts command

source_name: Primary forebrain neuronal cultures

growth_protocol: Perinatal neuronal culture

extract_protocol:
TRIzol isolation + RNeasy Purification
Samples were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (catalog number E7760L) Ribo depletion Module NEBNext rRNA Human/Mouse/Rat (catalog number E6310X) and NEBNext Multiplex Oligos for Illumina Unique dual (catalog number E6440L) (NEB, Ipswitch, MA). Where 100ng of total RNA was ribosomal depleted using rRNA Depletion module. The rRNA-depleted RNA is then fragmented 10 minutes determined by RIN (RNA Integrity Number) of input RNA as per protocol, and copied into first strand cDNA using reverse transcriptase and dUTP mix. Samples undergo end repair and dA-Tailing step followed by ligation of NEBNext adapters. The products are purified and enriched by 12 cycles PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA)

treatment_protocol: Lentiviral vector transduction

value: Primary forebrain neuronal cultures


title: Clone-WT-2 (RNA-seq)

description:
RNA.count.all.txt.gz
Clone_WT_2


title: Drosophila wing disc Control Ubx-GAL4>Dam rep1

description: DNA amplicon


title: Drosophila wing disc Control Ubx-GAL4>Dam rep2

description: DNA amplicon


title: Heat-Recovery-3

status: Public on Dec 30 2020

city: YangLin

first: WANG

middle: QI

last: QI

address: No.3，TaiCheng Road

institute: Northwest A&F University

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with default parameters
Clean reads were separately aligned to reference genome with orientation mode using TopHat  software
To identify DEGs (differential expression genes) between two different samples, the expression level for each transcript was calculated using the fragments per kilobase of exon per million mapped reads (FPKM) method.Cuffdiff  was used for differential expression analysis.
Genome_build: Current Tomato Genome version SL4.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Solanum lycopersicum

source_name: Solanum lycopersicum:heat stress

growth_protocol: Seeds of the tomato (S. lycopersicum cv. M82) were obtained from the Tomato Genetic Resource Center, University of California, Davis, CA, USA. Seeds were evenly sown per pot (7 x 7cm pots) with stroma (Nutritive soil :Vermiculite: Perlite=3:1:1) in artificial climate chambers. The climate conditions included: 16/8 h day/night photoperiod, 25°C air temperature, 800 μmol/m2/s1 light intensity, and 70% humidity. Plants were watered daily to meet the optimal water requirement before stress treatment.

extract_protocol:
Total RNA of these samples were extracted using the TRIzol reagent, according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Thirty-eight days after sowing (DAS), plants of the same stage with maximum water holding capacity of soil were subjected to 42°C heat stress conditions with 90% relative humidity for 0h (Heat-0h), 2h (Heat-2h), 4h (Heat-4h), 12h (Heat-12h), 24h (Heat-24h) and put back into the optimal conditions mentioned above for 1 d after Heat-24h (Heat-Recovery).When the quality of each nutrient pot is reduced by about 1/5 (i.e. the soil water capacity is about 80%), then it will be counted as the drought treatment control 0d. After this time point, tomato plants of 0d (D-0d), 1d (D-1d), 2d (D-2d), 3d (D-3d), 4d (D-4d), 5d (D-5d) and re-watered and grew in the optimal conditions mentioned above for another 1d (D-Recovery) were respectively selected for drought treatment.

tag: cultivar

value: leaves

value: Thirty-eight days old seedings

value: Heat-Recovery


title: Heat-Recovery-2


title: Heat-Recovery-1


title: Heat-24h-3


title: Drosophila wing disc Control Ubx-GAL4>DamPc rep1

description: DNA amplicon


title: Heat-24h-1


title: Heat-12h-1


title: Heat-4h-3


title: Heat-12h-3


title: Heat-4h-1


title: Heat-2h-3


title: Heat-24h-2


title: E165_NSC_WT_2

city: Basel

first: Verdon

last: Taylor

address: Mattenstrasse 28

department: Department of Biomedizin

country: Switzerland

institute: University of Basel

description:
mRNA
Forebrain NSC at stage E165, replicate 2
processed data file: gene_tpm_BULK_WT.txt.gz

data_processing:
Reads mapped to the transcriptome (GENCODE Release M2 GRCm38.p2) with kallisto 0.43.0 with option --single -l 200.0 -s 100.0 –pseudobam. Last option is to obtain pseudoalignments to transcriptome in BAM files.
The reads mapping to multiple transcripts are uniformly distributed.
Expression per transcript normalized by first dividing the number of reads mapping to each transcript by the length of the transcript in nucleotides and then transform the length-normalized read counts in transcript per million (TPM).
Gene expression was obtained by summing for each gene the TPM of the transcripts corresponding to the gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_tpm_BULK_WT.txt: Tab-delimited text file, TPM table, genes in rows and samples in columns.

source_name: dorsal cerebral cortex

extract_protocol:
Total RNA was isolated from FAC-sorted GFP positive cells from Hes5::GFP and Tbr2::GFP transgenic lines using TRIzol reagent. A time course was performed with NSCs, BPs and NBNs isolated at each time point during development from E10.5 to postnatal day 1 (PN). Samples were analyzed for their integrity and concentration using Agilent 2100 Bioanalyzer and Quant-IT RiboGreen RNA Assay Kit. Sequencing libraries were prepared with the Illumina TruSeq RNA Library Prep Kit v2 according to Illumina’s instructions.
After quality control (Fragment Analyzer, AATI) libraries were pooled and loaded on an Illumina flow cell for cluster generation (HiSeq SR Cluster Kit v4 cBot). Libraries were sequenced SR50 on the HiSeq 2500 system (HiSeq SBS Kit V4) following the manufacturer’s protocols.

treatment_protocol: Dorsal cortices from embryonic day E10.5 to postnatal day 1 (PN) were micro-dissected and dissociated into single cell suspensions using Papain and Ovo-mucoid mix (Giachino et al, 2009). Cells were washed with L15 medium and FAC-sorted for GFP positive NSCs using FACSariaIII (BD Biosciences) derived from Hes5::GFP transgenic embryos for NSCs and Tbr2::GFP transgenic embryos for BPs and NBNs.

tag: strain/background

tag: isolate

value: Wild-type

value: Forebrain

value: Neural stem cell

tag: Sex

value: Female

tag: age


title: Experiment_01_g2G3_M

description:
Hela cells with blocking both C-NHEJ and A-NHEJ pathways in Experiment_01
all_sample_human_RNA_max.txt

value: Hela cells

value: XRCC4 knockout with Mirin


title: Heat-2h-2


title: Heat-2h-1


title: Heat-0h-1


title: Heat-0h-3


title: Heat-0h-2


title: D-Recovery-2

source_name: Solanum lycopersicum:drought

value: drought-Recovery


title: D-Recovery-3


title: Heat-12h-2


title: D-5d-3


title: D-4d-2


title: D-Recovery-1


title: D-4d-3


title: D-5d-2


title: D-3d-3


title: D-4d-1


title: D-3d-2


title: Heat-4h-2


title: D-3d-1


title: D-2d-1


title: D-1d-3


title: D-2d-3


title: D-1d-1


title: D-0d-2


title: D-0d-3


title: D-0d-1


title: Terc-/-ESC PDL800times

city: suwon

first: DAEUN

last: KIM

address: World cup-ro

country: South Korea

institute: Ajou university

data_processing:
Library strategy: long-read Iso-Seq
The library was sequenced with the PacBio Sequel System then the circular consensus sequences were analyzed using SMRT Link v6.0
The reads were aligned to the mm10 reference genome using the minimap2 aligner (version 2.14-r894-dirty)
Genome_build: mm10

source_name: mESC

growth_protocol: The Terc targeting construct (TR-10) was transfected into E14 mESC by electroporation to exchange the first Terc allele. The targeting plasmid included PGK-neo gene flanked by loxP sites. The transfected cells were selected with G418 (200 mg/ml) and Ganciclovir (1 mM). The resistant Terc+/- cells were picked after eight days. The neo gene was removed by infection with the adenovirus of Cre recombinase. The Terc+/- cells were re-targeted with TR-10. Two lines of Terc-/- ESC, DKO301 and DKO741 were recovered. Both of DKO301 and DKO741 produced survivors with rare frequencies. We got those ALT survivor cells at each PDL timing (PD100, PD350, PD400, PD450) with control (Terc+/+) cells. For mESC maintenance and stock preparation, mouse embryonic fibroblast (MEF) cells were used as feeder cells. Feeder-free mESCs were used for all experiments including nucleic acids extraction, protein extraction, immunostaining, and fluorescent in situ hybridization.

extract_protocol:
RNA was extracted using chloroform and isopropanol precipitation
Library was constructed using the SMATer PCR cDNA Synthesis kit and DNA Template prep kit 1.0

treatment_protocol: Cells were longitudinally harvested at 100 and 800 passage

value: mouse Embryonic Stem Cell


title: D-5d-1


title: Wild Type

city: Tel-Aviv

first: Katherine

last: Domb

address: Haim Levanon st.

department: Gray Faculty of Medical and Health Sciences

country: Israel

institute: Tel Aviv University

data_processing:
Identical duplicate reads and low-quality reads were filtered out using Prinseq-lite software v0-20-4
Custom Perl scripts were used to convert all the Cs in the ‘forward’ reads and reference sequence to Ts, and all the Gs in the ‘reverse’ reads and reference sequence to As
Reads were aligned to the reference genome using Bowtie2.0
Custom Perl scripts were used to recover the original sequence information and, for each C (on either strand), to count the number of times it was sequenced as a C or a T.
For each sequence context (CG, CHG, CHH),  the genomic averaged fractional methylation as well as fractional methylation within a 50 bp sliding window that were used in downstream analyses were calculated.
Genome_build: Ppatens v3.0
Supplementary_files_format_and_content: Separate gff files for each methylation context (CG, CHG and CHH), each entry represents one citosine. Scores represent methylation level for each position, column 9 contains numbers of times each cytosine was sequenced as either C or T, as well as total reads coverage of the given citosine.
Supplementary_files_format_and_content: Separate gff files for each methylation context (CG, CHG and CHH), each entry represents 50-bp window. Scores represent methylation level for each window, column 9 contains numbers of times cytosines within the given window were sequenced as either C or T, as well as total reads coverage of citosines within the window.

organism: Physcomitrium patens

source_name: protonema

growth_protocol: 7 days on BCDAT media, 25 °C,  16-h light and 8-h dark regime

extract_protocol:
Genomic DNA was extracted from 7 days old protonema using DNeasy Plant Mini Kit (Qaigen) according to manufacturer’s instructions
Genomic DNA was isolated from protonema, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adaptors. Adaptor-ligated libraries were subjected to bisulfite conversion treatment using the Methylation-Gold kit (ZYMO) as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR and gel purified (~350-400 bp size range) prior to quantification with a Bioanalyzer (Agilent).

value: WT

value: Grandsen

value: 7 days


title: D-2d-2


title: Terc-/-ESC PDL100times


title: D-1d-2


title: F+RVT 3

type: RNA

city: Barcelona

first: Christian

middle: Griñán

last: Ferré

state: Barcelona

address: Joan XIII, s/n

department: Pharmacology, Toxicology and Therapeutic Chemistry

country: Spain

institute: University of Barcelona

description:
Fructose Resveratrol Treated 3
SAMPLE 9

data_processing:
We normalized using the SignArraysR analysis tool from (Any Genes, Paris, France).
mRNA expression was calculated using the recommended 2-ΔΔCt method

label: SYBR Green

organism: Rattus norvegicus

source_name: liver, Fructose Resveratrol Treated

label_protocol: The expression of 84 mature mRNAs was analyzed using Array Template (AnyGenes)

growth_protocol: RNA from liver of Sprague-Dawley rats were converted to cDNA thorugh a reverse transcription reaction using using StaRT Reverse Transcriptase kit (StaRT-50)

extract_protocol: Total RNA was isolated from liver by using the Trizol® reagent (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s instructions. NucleoSpin RNA Clean-Up (Macherey-Nagel, Düren, Germany) was used for RNA purification. RNA concentration was determined by measuring absorbance at 260 nm, and the absorbance ratio 260/280 nm was used to analyze RNA quality

treatment_protocol: Liver extraction by using Trizol Reagent

value: Sprague-Dawley

value: Fructose Resveratrol

value: liver


title: FRC 3

description:
Fructose Treated 3
SAMPLE 6

source_name: liver, Fructose Treated

value: Fructose


title: F+RVT 2

description:
Fructose Resveratrol Treated 2
SAMPLE 8


title: FRC 1

description:
Fructose Treated 1
SAMPLE 4


title: F+RVT 1

description:
Fructose Resveratrol Treated 1
SAMPLE 7


title: FRC 2

description:
Fructose Treated 2
SAMPLE 5


title: CT 1

description:
Control 1
SAMPLE 1

source_name: liver, Control

value: Control


title: CT 2

description:
Control 2
SAMPLE 2


title: 65-4 N matched non-cancerous tissue

city: Shenyang City

first: Zhenning

address: 155 North Nanjing Street

department: Department of Surgical Oncology and General Surgery

institute: The First Affiliated Hospital of China Medical University

data_processing:
Target gene signals normalized to housekeeping genes: 2-ΔΔCt,[ΔCt (group 1) = average Ct – average of house-keeping genes’ Ct for group 1 array, ΔCt (group 2) = average Ct – average of house-keeping genes’ Ct for group 2 array, ΔΔCt = ΔCt (group2) - ΔCt (group1)]
Fold Change worksheet reports test/control

source_name: matched non-cancerous tissue

label_protocol: RNAs were then pretreated with rtStar™ tRF&tiRNA Pretreatment Kit (Cat# AS-FS-005, Arraystar) and reverse-transcribed with rtStar™ First-Strand cDNA Synthesis Kit. Quantitative real-time PCR were performed (ABI 7900) with 40 cycles at 95 ℃ for 10 seconds and 60 ℃ for 60 seconds.

growth_protocol: All tissue samples were put into liquid nitrogen immediately after separation and then transferred to −80℃ for long-term storage.

extract_protocol: Total RNA was extracted with trizol reagent.

value: matched non-cancerous tissue


title: 303-3 N matched non-cancerous tissue


title: 290-4 N matched non-cancerous tissue


title: 310-3 N matched non-cancerous tissue


title: 313-3 N matched non-cancerous tissue


title: 309-3 N matched non-cancerous tissue


title: 286-3 N matched non-cancerous tissue


title: 98-3 CA matched non-cancerous tissue


title: 302-3 N matched non-cancerous tissue


title: 299-3 CA gastric cancer tissue

source_name: gastric cancer tissue

value: gastric cancer tissue


title: 302-3 CA gastric cancer tissue


title: 299-3 N matched non-cancerous tissue


title: 290-4 CA gastric cancer tissue


title: 313-3 CA gastric cancer tissue


title: 98-3 N matched non-cancerous tissue


title: 286-3 CA gastric cancer tissue


title: 65-4 CA gastric cancer tissue


title: 303-3 CA gastric cancer tissue


title: CT 3

description:
Control 3
SAMPLE 3


title: 310-3 CA gastric cancer tissue


title: 301-HMO-2

city: Amherst

first: Ezgi

last: Ozcan

state: MASSACHUSETTS

address: 424 Chenoweth Lab, 102 Holdsworth Way

institute: University of Massachusetts Amherst

data_processing:
Sequence reads were automatically trimmed for adaptor sequence by Illumina. Adaptor trimmed reads were obtained from Illumina BaseSpace.
Reads from each lane were concatenated as left and right sequences. Left and right reads were then checked for low-quality reads, bacteria 16S, 23S and 5S rRNA contamination. B. infantis 23S rRNA region was removed using bbduk in bbmap (v38.34).
The resultant reads were concatenated to create a reference genome. The overall reads were then subject to de novo assembly using Trinity using parameters --CPU 10 --bflyCPU 6 --bflyHeapSpaceMax 2G. The statistics and the quality of the resultant transcriptome was determined by mapping the transcriptome to the raw reads using bowtie2 v2.3.4.3 using parameters -p 8 and using TrinityStats.pl function.
The estimated abundance for each sample was calculated using RSEM (v1.3.3)  The quality of biological replicates and samples were determined with the PtR function in trinity and sample correlation matrix were generated using built-in pheatmap function in R (v3.6.2)
The resultant isoform count matrix was subject to differential analysis with a built-in function in Trinity using EdgeR method (25) in R (v.3.4.0) and differentially expressed genes within strains and across strains were identified paratemeter with p<0.05; log2 fold change >2, with minimum row sum of 10 raw counts)
Genome_build: Bifidobacterium longum subsp. infantis ATCC 15697
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every strain
Supplementary_files_format_and_content: Normalized diffferential expression measurements from edgeR
Supplementary_files_format_and_content: Transcript fasta files

organism: Bifidobacterium longum subsp. infantis

source_name: human infant feces

growth_protocol: Bifidobacterium infantis  strains were routinely propagated in De Man Rogosa Sharp medium supplemented with 0.05 % (m/v) L-cysteine hydrochloride at 37°C under anaerobic conditions. Cells then transferred into modified MRS medium (no carbohydrate source, no acetate). Carbohydrate source is replaced with either 2% w/v lactose,  pooled human milk oligosaccharides, lacto-N-tetraose, lacto-N-neotetraose. The cells were grown under same conditions.

extract_protocol:
Cell pellets stored in RNAlater were centrifuged at 14,000 × g for 3 min and cell pellets were washed with 1 mL cold 1X PBS buffer. Total RNA was extracted using Ambion RNAqeous kit with slight modifications. Accordingly, cells were suspended in 600 μL lysis buffer in beadbeating tubes using a FastPrep 24 bead beader (MP Biomedicals, USA). Total RNA, then,  were subjected to DNase treatment using the Ambion Turbo DNA-free kit. The RNA was evaluated for genomic DNA contamination using qRT-PCR. ribosomal RNA is depleted via RiboMinus kit with Magnetic Bead Clean up Module using the custom Pan-Prokaryote Probe Mix to target bacterial rRNA. Purified mRNA was used to asseses for quality and used for RNA-seq library preparation.
mRNA enriched library preparation was performed with the NEBNext Ultra II Directional kit following the manufacturer's instructions

treatment_protocol: lactose, pooled human milk oligosaccharides (HMOs), lacto-N-tetraose (LNT), lacto-N-neotetrraose (LNnT)

value: pooled human milk oligosaccharides


title: 301-HMO-1


title: 301-LAC-2

value: lactose


title: 301-LNnT-2

value: lacto-N-neotetraose


title: 301-LNnT-1


title: 301-LNT-1

value: lacto-N-tetraose


title: 300-HMO-2


title: 309-3 CA gastric cancer tissue


title: 300-LNnT-2


title: 300-HMO-1


title: 300-LNnT-1


title: Lung_Air_1wk_Rat178

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

state: MD

address: 2900 Ricketts Point Rd

institute: USAMRICD

description: Rat 178 1wk Air Lu

hyb_protocol: The complimentary RNA (cRNA) produced from the isolated total RNA was then fragmented and hybridized to GeneChip HT RG-230PM array plates (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: The HT RG-230PM array plates were scanned using an Affymetrix GeneTitan system.

data_processing:
Raw data (CEL files) were imported into Partek Genomic suite v6.6 (Partek Incorporated, St. Louis, MO) and normalized using robust multiarray averaging (RMA)
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HT_Rat230_PM
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

label_protocol: The isolated RNA was amplified and biotinylated using the GeneChip 3’ in vitro transcription (IVT) Plus reagent kit (Affymetrix; Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: Male Sprague-Dawley rats (300-400 g, Charles-River Laboratories, Wilmington, MA) were individually housed under standard conditions (12 hour light/dark cycle) with standard rodent chow and water provided ad libitum.

extract_protocol: Following eutanasia (ketamine (90 mg/kg) and xylazine (10 mg/kg)  by im followed by exsanguination), tissues were flash frozen in liquid nitrogen and stored at -80 until processing. Tissues were cryopulverized and total RNA isolated using RNeasy Plus mini kits (Qiagen; Germantown, MD) according to manufacturer's instructions with a DNase digestion step. Blood samples were collected via heart stick. RNA was isolated from collected blood samples and processed using the RNeasy Protect Animal Blood System (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Whole-body PH3 inhalation exposures were conducted as described in Wong et al., 2017. PH3 concentrations was 15,480 ppm x minute (387 ppm x 40 minutes) and represents a “low” concentration Ct.

value: male

value: adult

tag: treatment/exposure

value: Air

tag: treatment/exposure info

value: 0 ppm x 40 min (0 ppm x min)

tag: time point

value: 1 week

value: Lung


title: Kidney_Air_1hr_Rat168

description: Rat 168 1hr Air K

value: Sprague-Dawley

value: 1 Hour

tag: tissue

value: Kidney


title: Heart_Air_1hr_Rat168

description: Rat 168 1hr Air H

value: Heart


title: Kidney_Air_1hr_Rat163

description: Rat 163 1hr Air K


title: Brain_Air_1hr_Rat168

description: Rat 168 1hr Air Br

value: Brain


title: Brain_Air_6hr_Rat156

description: Rat 156 6hr Air Br

value: 6 Hour


title: Liver_Air_6hr_Rat156

description: Rat 156 6hr Air Li

value: Liver


title: 301-LNT-2


title: Lung_Air_1wk_Rat185

description: Rat 185 1wk Air Lu


title: 300-LNT-2


title: Brain_Air_1hr_Rat163

description: Rat 163 1hr Air Br


title: Heart_Air_6hr_Rat156

description: Rat 156 6hr Air H


title: Kidney_Air_6hr_Rat156

description: Rat 156 6hr Air K


title: Lung_PH3_24Hhr_Rat155

description: Rat 155 24hr PH3 Lu

value: 387 ppm  x 40 min (15,480 ppm x min)

value: 24 Hour


title: Lung_Air_1wk_Rat179

description: Rat 179 1wk Air Lu


title: Lung_PH3_3Hr_Rat152

description: Rat 152 3hr PH3 Lu

value: 3 Hour


title: Kidney_PH3_3Hr_Rat152

description: Rat 152 3hr PH3 K


title: 301-LAC-1

value: lactose


title: Lung_PH3_3Hr_Rat154

description: Rat 154 3hr PH3 Lu

value: male


title: 300-LNT-1

value: lacto-N-tetraose


title: Heart_Air_1hr_Rat163

description: Rat 163 1hr Air H

value: adult

value: Air


title: 300-LAC-2


title: 300-LAC-1


title: 299-HMO-2

value: pooled human milk oligosaccharides


title: Brain_PH3_3Hr_Rat152

description: Rat 152 3hr PH3 Br


title: 299-LNT-2


title: 299-LNnT-1

value: lacto-N-neotetraose


title: 299-LNT-1


title: 299-LNnT-2


title: Lung_Air_3hr_Rat150

description: Rat 150 3hr Air Lu

value: Sprague-Dawley

value: 0 ppm x 40 min (0 ppm x min)

value: Lung


title: Heart_Air_3hr_Rat150

description: Rat 150 3hr Air H

value: Heart


title: Heart_PH3_3Hr_Rat152

description: Rat 152 3hr PH3 H


title: Kidney_Air_3hr_Rat150

description: Rat 150 3hr Air K

value: Kidney


title: 272-HMO-1


title: 272-LNnT-2


title: 299-LAC-2


title: 299-LAC-1


title: 272-HMO-2


title: 272-LNnT-1


title: 272-LNT-2


title: 299-HMO-1


title: Lung_Air_24hr_Rat151

description: Rat 151 24hr Air Lu


title: 272-LNT-1


title: Lung_PH3_24Hhr_Rat149

description: Rat 149 24hr PH3 Lu


title: Lung_PH3_3Hr_Rat147

description: Rat 147 3hr PH3 Lu


title: Brain_PH3_24Hhr_Rat149

description: Rat 149 24hr PH3 Br

value: Brain


title: Lung_PH3_3Hr_Rat148

description: Rat 148 3hr PH3 Lu


title: 272-LAC-2


title: Kidney_Air_24hr_Rat145

description: Rat 145 24hr Air K


title: 272-LAC-1


title: Heart_Air_24hr_Rat145

description: Rat 145 24hr Air H


title: Lung_Air_24hr_Rat145

description: Rat 145 24hr Air Lu


title: Cg_Gal4_abdA_rep3

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

country: India

institute: CSIR Centre for Cellular and Molecular biology

data_processing:
Base-calling was performed using bcl2fastq of Illumina
Quality control was performed on the FASTQ read files using FastQC v0.11.7.
The reads were aligned to the reference genome using STAR-2.5.2 with the parameters STAR --runThreadN 16 --runMode alignReads --readFilesCommand zcat --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM
Read counts were calculated using HTSeq v0.11.2. using the parameters htseq-count -c -n
Differential expression between the two conditions were performed using DESeq2
Genome_build: dm6
Supplementary_files_format_and_content: File containing read count values

source_name: Hemolymph

growth_protocol: Flies were cultured in standard cornmeal and sucrose agar. The wild-type flies used in this study were Canton-S. Flies were maintained at 25 °C. For all experiments, flies laid eggs for 6 hours before being transferred to a fresh vial. Larvae were dissected at 96-102 hours post egg laying, before the onset of metamorphosis.

extract_protocol:
RNA profiles were compared between Cg-Gal4>CS and Cg-Gal4>UAS-abd-A larvae. Larvae were dissected in 4mm wells with 20uL PBS. After each dissection, the hemolymph and PBS were transferred into a microfuge tube on ice. The hemolymph of 20 larvae was thus collected, pelleted and resuspended in 20uL of TRIzol. TRIzol containing hemocytes were snap frozen and stored at -80°C till processed. The hemolymph in TRIzol  was pooled and 1/5th the volume of chloroform was added. The mixture was vortexed for 15s and incubated at room temperature for about 2-3 minutes. The mixture was centrifuged at 4°C for 15min at 12,000*g. The aqueous phase was taken and added to half the volume of isopropyl alcohol at room temperature and incubated for about 10min. The RNA was precipitated by centrifuging this mixture at 12,000*g for 10min at 4°C. The supernatant was discarded and washed twice with 75% ethanol. The RNA was then resuspended in DEPC water.
500ng of total RNA was utilized for mRNA isolation, fragmentation and priming. First strand synthesis was carried out in the presence of Actinomycin D followed by second strand synthesis. The obtained double stranded cDNA was purified using magnetic beads, end-repaired, adenylated and ligated to Illumina multiplex barcode adapters as per the NEBNext Ultra Directional RNA Library Prep Kit protocol. The adapter ligated cDNA was purified using magnetic beads and was subjected to 12 cycles of Indexing-PCR with the following conditions: 37˚C for 15mins, denaturation at 98˚C for 30s, 12 cycles of 98˚C for 10s and 65˚C for 75s, followed by a final extension of 65˚C for 5min to enrich the adapter-ligated fragments. The sequencing library thus obtained by PCR was purified with magnetic beads, followed by library quality control checks. The sequencing library was quantified by Qubit fluorometer. An Agilent 2200 TapeStation was used to analyze fragment size distribution. Finally, Kapa Library Quantification Kit was used to quantify the sequencing library by quantitative PCR.

treatment_protocol: For the overexpression of abd-For the over-expression of abdA, the UAS-Gal4 binary system was used. Homozygous Cg-Gal4 females were mated with homozygous UAS-abd-A males. Experimental crosses were set between Cg-Gal4 and UAS-abd-A at a density of 12 females and 6 males for each cross. Egg lay was allowed for 6 hours and progeny were collected after 96 hours post egg lay, at the L3F stage.

value: Canton-S

tag: developmental stage

value: larva

tag: genotype

value: abdA overexpression


title: Cg_Gal4_abdA_rep2

tag: strain


title: Cg_Gal4_abdA_rep1


title: Lung_PH3_1wk_Rat143

description: Rat 143 1wk PH3 Lu

value: 387 ppm  x 40 min (15,480 ppm x min)

value: 1 week


title: Cg_Gal4_CS_rep2

value: Control


title: Cg_Gal4_CS_rep1


title: Brain_Air_3hr_Rat150

description: Rat 150 3hr Air Br

value: male

value: 3 Hour


title: Kidney_PH3_24Hhr_Rat149

description: Rat 149 24hr PH3 K

value: adult

value: 24 Hour


title: Brain_Air_24hr_Rat145

description: Rat 145 24hr Air Br

value: Air


title: RATT_255

first: Kelly

last: Bakulski

address: 1415 Washington Heights

department: Department of Epidemiology

data_processing:
Quality control metrics on raw fastq files for the 32 samples were examined using fastQC (version 0.11.5) (40) and multiQC (version 0.9)
The first 11 base pairs were trimmed for all samples using Trimmomatic (version 0.36)
Reads were mapped to a sheep reference genome (Oar_rambouillet_v1.0) using the Spliced Transcripts Alignment to a Reference (STAR) (version 2.6.0c) program
featureCounts (version 1.6.1) was used to quantify aligned reads mapping to exons
Processed data were analyzed in R statistical software (version 3.6.3) with the DESeq2 package (version 1.24.0)
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: matrix of raw gene counts for each sample

organism: Ovis aries

source_name: perirenal adipose tissue

growth_protocol: All animal studies were conducted under Institutional Animal Care and Use Committee of the University of Michigan approved protocols at the University of Michigan Sheep Research Facility (Ann Arbor, MI) and met the requirements of National Institutes of Health Guide for Use and Care of Animals. All experimental animals from both control and prenatal testosterone-treated group were housed together, provided maintenance diet to prevent them from becoming obese.

extract_protocol:
The four adipose depots were collected with VAT obtained from the mesenteric fat surrounding the ventral sac of the rumen, SAT from under the skin in the sternal region, PRAT from around the kidney and ECAT from between the myocardium and the serous/visceral layer. Each adipose depot was immediately flash-frozen and stored at -80°C until processing. To isolate total RNA, adipose tissue was homogenized with liquid nitrogen and dissolved in Trizol reagent (Life Technologies, Carlsbad, CA) and RNA isolated as per manufacturer’s recommendations. RNA was then purified and DNAse-treated on a column using the RNAeasy kit (Qiagen, Germantown, MD) according to manufacturer's instructions.
RNA purity and integrity were measured using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA with RNA integrity values ≥ 7.0 were converted into cDNA by using QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen, Greenland, NH) according to manufacturer's instructions and libraries compatible for Illumina sequencing were generated.

treatment_protocol: Pregnant ewes with similar body conditions were randomly assigned to two treatment groups: control (C), and T-treated (T). Gestational T-treatment consisted of twice weekly intramuscular administration of 100mg T propionate (1.2 mg/kg; Millipore Sigma, St. Louis, MO) suspended in 2 ml corn oil from 30 to day 90 of gestation. Only one female offspring was used in any given treatment group when the dam had more than one offspring in the same pregnancy. To prevent confounding effects from differing steroid background, all animals were ovariectomized at the end of the second breeding season and the four adipose depots collected during artificial follicular phase. Early follicular phase levels of estradiol was achieved by inserting a 1 cm estradiol implant subcutaneously. An artificial luteal phase of the estrus cycle was initiated by placing two controlled internal drug-releasing implants containing progesterone (CIDR-G; InterAg, Hamilton, New Zealand) subcutaneously. After 14 days, progesterone implants were removed, four 30-mm estradiol implants inserted subcutaneously to mimic follicular phase and 18 hours later animals were euthanized by barbiturate overdose (Fatal Plus; Vortech Pharmaceuticals, Dearborn, MI).

value: testosterone

tag: sheep id

value: perirenal adipose tissue


title: CATT_255

source_name: epicardial adipose tissue

tag: treatment

value: epicardial adipose tissue


title: SATT_255

source_name: subcutaneous adipose tissue

value: subcutaneous adipose tissue


title: Heart_PH3_6Hr_Rat141

description: Rat 141 6hr PH3 H

value: Sprague-Dawley

value: 6 Hour

value: Heart


title: SATC_098

value: control


title: Liver_PH3_6Hr_Rat141

description: Rat 141 6hr PH3 Li

value: Liver


title: Lung_PH3_1wk_Rat142

description: Rat 142 1wk PH3 Lu

value: 387 ppm  x 40 min (15,480 ppm x min)

value: Lung


title: VATC_201

source_name: visceral adipose tissue

value: visceral adipose tissue


title: Liver_PH3_6Hr_Rat140

description: Rat 140 6hr PH3 Li

value: male


title: CATT_233


title: CATT_185


title: CATT_048


title: Kidney_PH3_6Hr_Rat140

description: Rat 140 6hr PH3 K

value: Kidney


title: Brain_PH3_6Hr_Rat141

description: Rat 141 6hr PH3 Br

value: adult

value: Brain


title: Lung_Air_3hr_Rat144

description: Rat 144 3hr Air Lu

value: Air

value: 0 ppm x 40 min (0 ppm x min)

value: 3 Hour


title: RATC_098

value: perirenal adipose tissue


title: CATC_201

value: epicardial adipose tissue


title: CATC_132


title: Heart_PH3_6Hr_Rat140

description: Rat 140 6hr PH3 H

value: Sprague-Dawley


title: Brain_PH3_6Hr_Rat140

description: Rat 140 6hr PH3 Br

value: 6 Hour


title: Kidney_PH3_6Hr_Rat141

description: Rat 141 6hr PH3 K


title: Liver_Air_6hr_Rat138

description: Rat 138 6hr Air Li


title: Brain_Air_6hr_Rat138

description: Rat 138 6hr Air Br


title: Kidney_Air_6hr_Rat138

description: Rat 138 6hr Air K


title: Lung_PH3_1wk_Rat137

description: Rat 137 1wk PH3 Lu

value: 1 week


title: SATT_233

value: testosterone

value: subcutaneous adipose tissue


title: Heart_Air_6hr_Rat138

description: Rat 138 6hr Air H

value: Heart


title: CATC_098

value: control


title: Liver_PH3_6Hr_Rat134

description: Rat 134 6hr PH3 Li

value: 387 ppm  x 40 min (15,480 ppm x min)

value: Liver


title: SATT_185


title: Kidney_PH3_6Hr_Rat134

description: Rat 134 6hr PH3 K

value: male

value: Kidney


title: Brain_PH3_6Hr_Rat135

description: Rat 135 6hr PH3 Br

value: adult

value: Brain


title: Heart_PH3_6Hr_Rat134

description: Rat 134 6hr PH3 H


title: SATC_201


title: SATT_048


title: Lung_Air_1wk_Rat133

description: Rat 133 1wk Air Lu

value: Air

value: 0 ppm x 40 min (0 ppm x min)

value: Lung


title: Liver_Air_6hr_Rat132

description: Rat 132 6hr Air Li


title: Kidney_Air_6hr_Rat132

description: Rat 132 6hr Air K


title: SATC_132


title: SATC_131


title: RATT_233

value: perirenal adipose tissue


title: Heart_Air_6hr_Rat132

description: Rat 132 6hr Air H

value: Sprague-Dawley


title: RATT_185


title: RATT_048


title: RATC_131


title: RATC_201


title: RATC_132


title: Liver_PH3_6Hr_Rat128

description: Rat 128 6hr PH3 Li

value: 6 Hour


title: CATC_131

value: epicardial adipose tissue


title: VATT_255

value: testosterone

value: visceral adipose tissue


title: VATT_185


title: VATT_048


title: VATC_132


title: Kidney_PH3_6Hr_Rat128

description: Rat 128 6hr PH3 K


title: VATT_233


title: Kidney_Air_6hr_Rat126

description: Rat 126 6hr Air K


title: VATC_131


title: Heart_PH3_6Hr_Rat128

description: Rat 128 6hr PH3 H

value: Heart


title: Heart_Air_6hr_Rat126

description: Rat 126 6hr Air H


title: Brain_Air_3hr_Rat120

description: Rat 120 3hr Air Br

value: 3 Hour


title: Heart_PH3_3Hr_Rat122

description: Rat 122 3hr PH3 H

value: 387 ppm  x 40 min (15,480 ppm x min)


title: Heart_Air_3hr_Rat120

description: Rat 120 3hr Air H


title: Kidney_Air_3hr_Rat120

description: Rat 120 3hr Air K


title: Kidney_PH3_1Hr_Rat115

description: Rat 115 1hr PH3 K

value: 1 Hour


title: Liver_PH3_3Hr_Rat122

description: Rat 122 3hr PH3 Li

value: male

value: Liver


title: VATC_098

value: control


title: Brain_PH3_6Hr_Rat128

description: Rat 128 6hr PH3 Br

value: adult

value: Brain


title: Kidney_PH3_3Hr_Rat122

description: Rat 122 3hr PH3 K

value: Kidney


title: 6095_Luteal_2018-06-27 (batch 2)

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

institute: University of Washington

hyb_protocol: standard as recommended by Illumina, except that hybridization was performed at 48C

scan_protocol: standard Illumina protocol using Illumina iScan system

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 10 samples were included in the analysis.

source_name: Endocervical cytobrush from participant 6095 at the Luteal on 2018-06-27

label_protocol: Labeling was performed using 25 ng total RNA and the NuGEN Ovation PicoSL WTA System V2 and Encore BiotinIL kits.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Plus mini kit

tag: studyid

tag: date

tag: index

value: P

tag: rin

tag: enrollment

tag: status

value: LTFU

value: Positive

tag: progesterone

tag: bv

value: N

tag: visit

value: Luteal

tag: drop

value: Don't drop

tag: batch


title: Kidney_PH3_1Hr_Rat116

description: Rat 116 1hr PH3 K

value: Sprague-Dawley

tag: Sex

tag: age

tag: treatment/exposure

tag: treatment/exposure info

tag: time point

tag: tissue


title: Liver_Air_6hr_Rat126

description: Rat 126 6hr Air Li

tag: strain

value: Air

value: 0 ppm x 40 min (0 ppm x min)

value: 6 Hour


title: Brain_PH3_1Hr_Rat116

description: Rat 116 1hr PH3 Br

value: 387 ppm  x 40 min (15,480 ppm x min)

value: 1 Hour


title: Brain_PH3_3Hr_Rat122

description: Rat 122 3hr PH3 Br

value: male

value: 3 Hour


title: Brain_Air_6hr_Rat126

description: Rat 126 6hr Air Br

value: adult


title: Heart_PH3_1Hr_Rat116

description: Rat 116 1hr PH3 H

value: Heart


title: 6095_Follicular_2018-07-11 (batch 2)

source_name: Endocervical cytobrush from participant 6095 at the Follicular on 2018-07-11

tag: studyid

tag: date

value: Q

value: Follicular


title: 6087_Luteal_2018-03-23 (batch 2)

source_name: Endocervical cytobrush from participant 6087 at the Luteal on 2018-03-23

tag: index

value: O

tag: rin

value: Withdrawn


title: 6087_Follicular_2018-03-09 (batch 2)

source_name: Endocervical cytobrush from participant 6087 at the Follicular on 2018-03-09

value: N

tag: enrollment

tag: status

value: Positive


title: Brain_Air_6hr_Rat132

description: Rat 132 6hr Air Br

value: Brain


title: S5-8

city: Guangzhou

first: Gan

last: Xihui

address: School of Life Sciences Building 438, No. 132 Waihuan East Rd., Guangzhou University City, Panyu District

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Illumina CASAVA 1.8 software used for basecalling.
Qualified reads were obtained after removing raw reads with adapters or of low quality and then aligned to the mouse genome by HISAT with default parameters.
RSeQC was used to measured gene expression abundance as reads per kilobase per million mapped reads (RPKM).
Differential expression analysis of two samples was performed using the previous statistics model. The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. P-value <0.05 were assigned as differentially expressed gene.

source_name: late_Hind limb unloading_10dbA_normal air pressure_hypothalamus cells

extract_protocol:
RNA was extracted with Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: three-month-old

tag: period

value: late

tag: progress of activity

value: Hind limb unloading

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure

value: Hypothalamus


title: S1-8


title: 6083_Follicular_2017-12-28 (batch 2)

source_name: Endocervical cytobrush from participant 6083 at the Follicular on 2017-12-28

value: J

value: Negative

tag: progesterone

tag: bv

tag: visit

tag: drop

value: Don't drop

tag: batch


title: S21-8

tag: age


title: S17-8

tag: tissue


title: Brain_PH3_1Hr_Rat115

description: Rat 115 1hr PH3 Br

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment/exposure

tag: treatment/exposure info

value: 387 ppm  x 40 min (15,480 ppm x min)

tag: time point

value: 1 Hour


title: Heart_PH3_1Hr_Rat115

description: Rat 115 1hr PH3 H

value: Heart


title: S13-8


title: Brain_PH3_3Hr_Rat111

description: Rat 111 3hr PH3 Br

value: 3 Hour


title: Kidney_PH3_3Hr_Rat111

description: Rat 111 3hr PH3 K

value: Kidney


title: Heart_PH3_3Hr_Rat111

description: Rat 111 3hr PH3 H


title: S9-8


title: Liver_PH3_3Hr_Rat111

description: Rat 111 3hr PH3 Li

value: Liver


title: Kidney_PH3_1Hr_Rat109

description: Rat 109 1hr PH3 K


title: S5-7

source_name: late_Free moving_10dbA_normal air pressure_hypothalamus cells

value: three-month-old

value: Free moving


title: Heart_Air_3hr_Rat108

description: Rat 108 3hr Air H

value: Air

value: 0 ppm x 40 min (0 ppm x min)


title: Brain_Air_3hr_Rat108

description: Rat 108 3hr Air Br

value: Brain


title: Heart_PH3_1Hr_Rat109

description: Rat 109 1hr PH3 H


title: 6091_Luteal_2018-05-02 (batch 2)

source_name: Endocervical cytobrush from participant 6091 at the Luteal on 2018-05-02

tag: studyid

tag: date

tag: index

value: W

tag: rin

tag: enrollment

value: Active

value: Positive

value: N

value: Luteal


title: Heart_Air_1hr_Rat107

description: Rat 107 1hr Air H

value: Sprague-Dawley

value: male

value: adult


title: Brain_PH3_1Hr_Rat109

description: Rat 109 1hr PH3 Br

value: 387 ppm  x 40 min (15,480 ppm x min)

value: 1 Hour


title: 6091_Ring_2018-08-02 (batch 2)

source_name: Endocervical cytobrush from participant 6091 at the Ring on 2018-08-02

value: X

tag: status

tag: progesterone

value: Ring

value: Don't drop


title: Kidney_Air_1hr_Rat107

description: Rat 107 1hr AirK

value: Kidney


title: 6091_Follicular_2018-05-14 (batch 2)

source_name: Endocervical cytobrush from participant 6091 at the Follicular on 2018-05-14

value: U

tag: bv

tag: visit

value: Follicular


title: S21-7

value: three-month-old

tag: period

value: late

tag: progress of activity

value: Free moving

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure

value: Hypothalamus


title: 6079_Luteal_2017-12-12 (batch 2)

source_name: Endocervical cytobrush from participant 6079 at the Luteal on 2017-12-12

value: E

value: Active

value: Negative

value: N

value: Luteal

tag: drop

tag: batch


title: Kidney_Air_3hr_Rat108

description: Rat 108 3hr Air K

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

tag: age

value: adult

tag: treatment/exposure

value: Air

value: 0 ppm x 40 min (0 ppm x min)

value: 3 Hour

tag: tissue


title: 6079_Ring_2018-02-23 (batch 2)

source_name: Endocervical cytobrush from participant 6079 at the Ring on 2018-02-23

tag: studyid

tag: date

tag: index

value: M

value: Ring

value: Don't drop


title: Brain_Air_1hr_Rat107

description: Rat 107 1hr Air Br

tag: treatment/exposure info

tag: time point

value: 1 Hour

value: Brain


title: 6083_Luteal_2017-12-12 (batch 2)

source_name: Endocervical cytobrush from participant 6083 at the Luteal on 2017-12-12

value: F

tag: rin

tag: enrollment

tag: status

value: Withdrawn

tag: progesterone

tag: bv


title: patient 3 (tumor)

city: Tianjin

first: Jie

last: Li

address: Wei Jin Road Nankai District No. 94

department: Department of Cell Biology and Genetics

institute: Nankai University

data_processing:
Transcript alignment, counting, and inter-library normalization were performed using the Cell Ranger pipeline (10x Genomics, default settings, Version 2.1.1).
Using the Seurat R package for downstream analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output files (matrix.mtx, genes.tsv, barcodes.tsv)

source_name: human colorectal cancer

extract_protocol:
Single-cell suspension in PBS with 0.04% BSA was mixed with RT-PCR master mix
Single Cell 3’ Gel Beads and Partitioning Oil into a Single Cell 3’ Chip according to the manufacturer’s instructions.
cDNA molecules were pre-amplified, fragmented, end repaired and ligated with Illumina adapters to generate a single multiplexed library.

value: tumor


title: Kidney_PH3_3Hr_Rat105

description: Rat 105 3hr PH3 K

value: 387 ppm  x 40 min (15,480 ppm x min)

value: Kidney


title: S1-7

value: three-month-old

tag: period

value: late

tag: progress of activity

value: Free moving

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure

value: Hypothalamus


title: 6079_Follicular_2017-11-30 (batch 2)

source_name: Endocervical cytobrush from participant 6079 at the Follicular on 2017-11-30

value: C

value: Active

value: Negative

value: N

tag: visit

value: Follicular

tag: drop

tag: batch


title: S13-7

tag: strain

tag: age

tag: tissue


title: patient 3 (normal)

value: normal


title: 6071_Ring_2018-02-07 (batch 2)

source_name: Endocervical cytobrush from participant 6071 at the Ring on 2018-02-07

tag: studyid

tag: date

tag: index

value: L

value: Complete

value: Ring

value: Don't drop


title: S9-7


title: Brain_PH3_3Hr_Rat105

description: Rat 105 3hr PH3 Br

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment/exposure

tag: treatment/exposure info

value: 387 ppm  x 40 min (15,480 ppm x min)

tag: time point

value: 3 Hour

value: Brain


title: Heart_PH3_1H_Rat98

description: Rat 98 1hr PH3 H

value: 1 Hour

value: Heart


title: BIN67_BRG1_ATACseq_Rep3

city: Chapel Hill

first: Bernard

middle: E.

last: Weissman

state: NC

address: 450 West Drive

department: Pathology and Laboratory Medicine

institute: University of North Carolina at Chapel Hill

data_processing:
Fastq files from both sequencing lanes were merged with cat (unix) command and then initially analyzed by fastqc (v0.11.5).
Adaptor sequences were trimmed from reads using trimgalore (v0.6.2) with –nextera argument.
Reads were aligned with Bowtie2 (v2.3.2) to UCSC hg38 using –x 2000.
Aligned mitochondrial reads were eliminated.
Aligned reads were sorted with samtools (v1.9) and duplicates were removed using picard (v2.10.3).
Subsequently, hg38 blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) and BRG1 plasmid reads were removed using bedtools (v2.26.0) intersect.
Biological replicates for each condition were merged using samtools merge (v1.9).
Peaks were called on the merged replicates using MACS (v2.1.0) without model (--nomodel).
Called peaks from both control and BRG1 conditions were merged into a union peak set using bedtools merge (v.2.26.0).
Reads under the union peak set in each biological sample were counted using featureCounts (subread v1.6.3).
Differential peak analysis was performed using DESeq2 (v1.22.2). Peak annotation was performed with HOMER (v4.10).
IGV tracks (bigwig) for the merged biological replicates were generated by deeptools (v3.2.) bamCoverage with a binsize of 30 and normalized using RPKMs.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig = normalized RPKM signal tracks of merged samples
Supplementary_files_format_and_content: TXT files = genomic locations of differentially accesible peaks.
Supplementary_files_format_and_content: narrowPeak = peaks called from merged replicate samples per condition

source_name: Cell Line

growth_protocol: BIN67 cells were cultured in RPMI-1640 (Gibco #11875-093) supplemented with 10% FBS and maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Four biological replicates were processed for ATAC-seq following standard protocol (Buenrostro, J. D., et al, (2013) Nature Methods ) with modifications:  increasing the cell number per sample to 100,000 cells, the use of Zymo ChiP DNA Clean & Concentrator Kit (Zymo Cat #D5205) in place of Qiagen MinElute, and lastly size selected with AMPure XP Beads (1.8x volume; Agencourt #A63880). For each biological replicate, samples were done in technical triplicate and run on 6% TBE gel to assay for nucleosome banding. The technical sample with the most pronounced nucleosome banding within each biological sample was selected for future studies and were then analyzed by Agilent Tapestation for molarity content. Samples were equimolar pooled paired end sequenced across two lanes on a Illuminia HiSeq2500 (Paired end x 50 bp).
Libraries were prepared following standard protocol (Buenrostro, J. D., et al, (2013) Nature Methods)

treatment_protocol: Four biological replicates of BIN67 cells were co-transfected (FuGENE 6, Promega #E269A) with either control (pCMV-neo or pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2 µg/ml puromycin for 3 days and then harvested for ATAC-seq.

tag: cell line

tag: transfected vector


title: Kidney_PH3_1H_Rat98

description: Rat 98 1hr PH3 K

value: Kidney


title: BIN67_BRG1_ATACseq_Rep4


title: S5-6

source_name: late_Hind limb unloading_85dbA_low air pressure_hypothalamus cells

value: three-month-old

tag: period

value: late

tag: progress of activity

value: Hind limb unloading

value: 85dbA,0.9 atmospheric

value: Hypothalamus


title: BIN67_BRG1_ATACseq_Rep2


title: S17-7

value: Free moving

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure


title: Heart_PH3_3Hr_Rat105

description: Rat 105 3hr PH3 H


title: 6071_Follicular_2017-11-27 (batch 2)

source_name: Endocervical cytobrush from participant 6071 at the Follicular on 2017-11-27

value: B

tag: rin

tag: enrollment

tag: status

value: Complete

value: Negative

tag: progesterone

tag: bv

value: N

tag: visit

value: Follicular

tag: drop

value: Don't drop


title: S1-6

tag: strain

tag: age

tag: tissue


title: BIN67_BRG1_ATACseq_Rep1


title: 6071_Follicular_2017-12-14 (batch 2)

source_name: Endocervical cytobrush from participant 6071 at the Follicular on 2017-12-14

tag: studyid

tag: date

tag: index

value: I

value: Y

value: Don't drop:luteal changed to follicular

tag: batch


title: S21-6

tag: period


title: Liver_PH3_3Hr_Rat105

description: Rat 105 3hr PH3 Li

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment/exposure

tag: treatment/exposure info

value: 387 ppm  x 40 min (15,480 ppm x min)

tag: time point

value: 3 Hour

value: Liver


title: S17-6

value: three-month-old

value: late

tag: progress of activity

value: Hind limb unloading

tag: noise intensity and atmospheric pressure

value: 85dbA,0.9 atmospheric

value: Hypothalamus


title: BIN67_Control_ATACseq_Rep4

tag: cell line

tag: transfected vector

value: Control


title: Brain_PH3_1H_Rat98

description: Rat 98 1hr PH3 Br

value: 1 Hour

value: Brain


title: Kidney_Air_3hr_Rat97

description: Rat 97 3hr Air K

value: Air

value: 0 ppm x 40 min (0 ppm x min)

value: Kidney


title: BIN67_Control_ATACseq_Rep3


title: 6062_Follicular_2017-07-10 (batch 2)

source_name: Endocervical cytobrush from participant 6062 at the Follicular on 2017-07-10

tag: rin

tag: enrollment

tag: status

value: Complete

value: Negative

tag: progesterone

tag: bv

value: N

tag: visit

value: Follicular

tag: drop

value: Don't drop


title: S13-6

tag: strain

tag: age

tag: tissue


title: BIN67_Control_ATACseq_Rep2


title: Heart_Air_1hr_Rat96

description: Rat 96 1hr Air H

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment/exposure

value: Heart


title: Heart_Air_3hr_Rat97

description: Rat 97 3hr Air H

tag: treatment/exposure info

tag: time point

value: 3 Hour


title: Brain_Air_3hr_Rat97

description: Rat 97 3hr Air Br


title: 6068_Follicular_2017-10-23 (batch 2)

source_name: Endocervical cytobrush from participant 6068 at the Follicular on 2017-10-23

tag: studyid

tag: date

tag: index

value: K

value: Positive

value: Y

tag: batch


title: 6068_Follicular_2017-10-12 (batch 2)

source_name: Endocervical cytobrush from participant 6068 at the Follicular on 2017-10-12

tag: rin

tag: enrollment

value: Don't drop:luteal changed to follicular


title: BIN67_Control_ATACseq_Rep1

tag: cell line

tag: transfected vector

value: Control


title: 6068_Ring_2017-12-14 (batch 2)

source_name: Endocervical cytobrush from participant 6068 at the Ring on 2017-12-14

value: H

tag: status

tag: progesterone

tag: bv

tag: visit

value: Ring


title: 6062_Luteal_2017-07-26 (batch 2)

source_name: Endocervical cytobrush from participant 6062 at the Luteal on 2017-07-26

value: Complete

value: Luteal

tag: drop


title: S5-5

source_name: late_Free moving_85dbA_low air pressure_hypothalamus cells

tag: strain

tag: age

value: three-month-old

tag: period

value: late

tag: progress of activity

value: Free moving

tag: noise intensity and atmospheric pressure

value: 85dbA,0.9 atmospheric

tag: tissue

value: Hypothalamus


title: Kidney_Air_1hr_Rat96

description: Rat 96 1hr Air K

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment/exposure

value: Air

tag: treatment/exposure info

value: 0 ppm x 40 min (0 ppm x min)

tag: time point

value: 1 Hour

value: Kidney


title: 6062_Ring_2017-11-03 (batch 2)

source_name: Endocervical cytobrush from participant 6062 at the Ring on 2017-11-03

tag: studyid

tag: date

tag: index

value: A

tag: rin

tag: enrollment

value: Negative

value: N

value: Don't drop

tag: batch


title: S1-5


title: Nrf2 KO mice 2 months after MAC infection 3

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

country: Japan

institute: Tsukuba university

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 7.5.1; Qiagen, Redwood City, CA).
Genome_build: mm10
Supplementary_files_format_and_content: TRS_007_4group_N3_TotalCount_quantile_normlaized_ANOVA_FDR_pVal_005_2x_2659genes.xlsx

source_name: Lung tissue

extract_protocol:
Lung tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 500 ng total RNA was used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420). Poly-A purification: Poly-T column kit (NEB, E7490), followed by NEB kit (E7420). Illumina NextSeq500 was used for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Balb/c

tag: genotype

value: Nrf2 KO


title: Brain_Air_1hr_Rat96

description: Rat 96 1hr Air Br

tag: strain

value: Brain


title: Kidney_PH3_24Hr_Rat91

description: Rat 91 24hr PH3 K

tag: age

value: 387 ppm  x 40 min (15,480 ppm x min)

value: 24 Hour


title: Heart_PH3_24Hr_Rat91

description: Rat 91 24hr PH3 H

value: Heart


title: 6068_Follicular_2017-10-12 (batch 1)

tag: status

value: Active

value: Positive

tag: progesterone

tag: bv

tag: visit

value: Follicular

tag: drop

value: Drop for microarray:rerun in batch 2


title: Brain_PH3_24Hr_Rat91

description: Rat 91 24hr PH3 Br

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment/exposure

tag: tissue


title: S21-5

value: three-month-old

tag: period

value: late

tag: progress of activity

value: Free moving

tag: noise intensity and atmospheric pressure

value: 85dbA,0.9 atmospheric

value: Hypothalamus


title: 6015_Follicular_2016-05-25 (batch 1)

source_name: Endocervical cytobrush from participant 6015 at the Follicular on 2016-05-25

tag: studyid

tag: date

tag: index

tag: rin

value: Withdrawn

value: Negative

value: N

value: Don't drop


title: Nrf2 KO mice 2 months after MAC infection 1

tag: strain

value: Balb/c

tag: genotype

value: Nrf2 KO


title: S9-6

tag: age

value: Hind limb unloading


title: Nrf2 KO mice 2 months after MAC infection 2


title: Kidney_Air_24hr_Rat90

description: Rat 90 24hr Air K

value: Air

tag: treatment/exposure info

value: 0 ppm x 40 min (0 ppm x min)

tag: time point

value: 24 Hour

value: Kidney


title: S13-5


title: WT mice 2 months after MAC infection 3

value: WT


title: WT mice 2 months after MAC infection 2


title: 6062_Luteal_2017-07-26 (batch 1)

tag: enrollment

tag: status

value: Active

tag: progesterone

tag: bv

tag: visit

value: Luteal

value: Drop for microarray:rerun in batch 2

tag: batch


title: 6025_Follicular_2016-06-14 (batch 1)

source_name: Endocervical cytobrush from participant 6025 at the Follicular on 2016-06-14

value: LTFU

value: Positive

value: Follicular

tag: drop


title: Kidney_Air_24hr_Rat89

description: Rat 89 24hr Air K

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment/exposure

tag: tissue


title: WT mice 2 months after MAC infection 1

value: Balb/c


title: S5-4

source_name: early_Hind limb unloading_10dbA_normal air pressure_hypothalamus cells

value: two-month-old

tag: period

value: early

tag: progress of activity

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure

value: Hypothalamus


title: Nrf2 KO mice control 3

tag: strain

tag: genotype

value: Nrf2 KO


title: S1-4

tag: age

value: Hind limb unloading


title: 6055_Follicular_2017-05-31 (batch 1)

source_name: Endocervical cytobrush from participant 6055 at the Follicular on 2017-05-31

tag: studyid

tag: date

tag: index

tag: rin

value: Negative

value: N

value: Don't drop


title: Brain_Air_24hr_Rat89

description: Rat 89 24hr Air Br

value: Air

tag: treatment/exposure info

value: 0 ppm x 40 min (0 ppm x min)

tag: time point

value: 24 Hour

value: Brain


title: 6055_Luteal_2017-06-19 (batch 1)

source_name: Endocervical cytobrush from participant 6055 at the Luteal on 2017-06-19

tag: enrollment

tag: status

value: LTFU

tag: progesterone

tag: bv

tag: visit

value: Luteal

tag: batch


title: S17-5

value: three-month-old

tag: period

value: late

tag: progress of activity

value: Free moving

value: 85dbA,0.9 atmospheric

tag: tissue


title: S21-4

tag: strain

value: two-month-old

value: early

tag: noise intensity and atmospheric pressure

value: 10dbA,normal atmospheric pressure


title: 6048_Luteal_2017-01-10 (batch 1)

source_name: Endocervical cytobrush from participant 6048 at the Luteal on 2017-01-10

tag: studyid

value: Withdrawn

value: Positive

tag: drop


title: S17-4

tag: age

value: Hind limb unloading

value: Hypothalamus


title: Nrf2 KO mice control 1

value: Balb/c

tag: genotype

value: Nrf2 KO


title: S9-5


title: WT mice control 3

value: WT


title: WT mice control 2


title: S9-4


title: Nrf2 KO mice control 2


title: Lung_PH3_24Hr_Rat87

description: Rat 87 24hr PH3 Lu

value: Sprague-Dawley

tag: Sex

value: male

value: adult

tag: treatment/exposure

tag: treatment/exposure info

value: 387 ppm  x 40 min (15,480 ppm x min)

value: 24 Hour

value: Lung


title: S5-3

source_name: early_Free moving_10dbA_normal air pressure_hypothalamus cells

value: Free moving


title: WT mice control 1


title: S1-3

value: two-month-old


title: met/dnmt3b_rep3

data_processing:
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Alignment to the reference genome and counting reads per gene/TE in the supplied annotation file, using STAR v2.7.0f
Genome_build: Ppatens v3.0
Supplementary_files_format_and_content: tab-delimited text file with raw read counts assigned to each of the annotated features (gene or transposable element), in each sample

source_name: protonema

extract_protocol:
Total RNA was extracted from 7 days old protonema using SV Total RNA Isolation System (Promega, USA) and DNase treatment (Thermo Fisher Scientific, USA).
The polyA fraction (mRNA) was purified from 500 ng of total input RNA, followed by fragmentation and the generation of double-stranded cDNA. Then, Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent).

tag: cultivar

value: Grandsen

value: 7 days


title: S13-4

value: early

value: 10dbA,normal atmospheric pressure


title: met/dnmt3b_rep2


title: S21-3


title: 6030_Follicular_2016-09-29 (batch 1)

source_name: Endocervical cytobrush from participant 6030 at the Follicular on 2016-09-29

tag: date

tag: index

tag: rin

tag: enrollment

tag: status

value: LTFU

value: Atypical

tag: progesterone

value: N

value: Follicular

value: Drop for all:Hsv2 ambiguous


title: Heart_PH3_24Hr_Rat85

description: Rat 85 24hr PH3 H

value: Sprague-Dawley

tag: time point

tag: tissue

value: Heart


title: Heart_Air_24hr_Rat84

description: Rat 84 24hr Air H

tag: strain

value: male

value: adult

value: Air

value: 0 ppm x 40 min (0 ppm x min)


title: Brain_PH3_24Hr_Rat85

description: Rat 85 24hr PH3 Br

value: 387 ppm  x 40 min (15,480 ppm x min)

value: 24 Hour

value: Brain


title: met/dnmt3b_rep1

value: Grandsen

value: 7 days


title: Kidney_PH3_24Hr_Rat85

description: Rat 85 24hr PH3 K

value: Kidney


title: cmt_rep2

value: cmt