title: B

description: 2PN eggs: Donated oocytes are fertilized with ICSI or IVF to obtain 2PN, a total of 25

source_name: 2PN egg

growth_protocol: Methods of ICSI: ICSI fertilization was performed on oocytes and spermatozoa from the above sources, and the mature egg was selected to remove the egg droplet to the center of the field of view. Hold the egg with the Holding needle, oocyte was transfer to the clearest state under microinjection needle, the polar body is located at 6,7 o'clock or 11,12 o'clock position, so that the injection of quasi-oocyte was in the middle 3 o'clock position.   The sperm were pushed to the tip of the injection needle, injection needle was placed in the oocyte 3 o'clock vertically through the zona pellucida until sperm was pushed within the cytoplasm of the middle of the egg. After the eggs were injected one by one, they were repeatedly rinsed in a pre-prepared G1.5 Plus Petri dish and placed in 37 ° C, 5% CO2, 5% O2, 90% N2 incubators and cultured in G1.5 Plus droplets separately.   For IVF fertilization, GIVF-plus which has been equilibrated overnight was used to prepare fertilized droplets according to the standard of 0.1 ml per microtube droplet per 3 eggs. Then this fertilized droplets were stored in incubator (37 ° C, 6% CO2) with coverage of mineral oil. Moderate amount of sperm was added to prepared fertilized dish under a microscope. And concentration was adjusted to 1.0 × 10 6 / ml. this sperm droplets were stored in incubator (37 ° C, 6% CO2) to wait for fertilization.  After 3-4 hour’s pre-incubation, eggs were transferred to the fertilized dish. 2-3 eggs were added to one semen drop and this fertilized drop was returned to the embryo box for overnight cultivation.  2PN Collection: Prokaryotic cells were observed at 16-20 hours after ICSI or IVF under inverted microscope and fertilization information was recorded. Two circular structures with nucleolar precursors in the cytoplasm were the male and female pronuclei (2PN). Two polar bodies (2PB) can be seen in the perivitelline space when normal fertilization occured. 12 prokaryotic and ICSI-derived prokaryotes from 2PN-derived IVF will be collected to extract DNA. DNA extraction method was identical to oocyte genomic DNA extraction method.  2 prokaryotic embryos were cotinue to culture to D2 at 16-20 hours after ICSI or IVF. And 5 cells which had 4 cells, uniform blastomere size and lower fragments rate (less than 5%) were used in present study. DNA extraction method was identical to oocyte genomic DNA extraction method.

value: immunoprecipitated DNA

value: 2PN egg


title: A

status: Public on Feb 01 2020

type: genomic

city: guangzhou

first: yuling

last: huang

address: No. 250, Changgang East Road, Haizhu District, Guangzhou

country: China

institute: Center for Reproductive Medicine, Third Affiliated Hospital of Guangzhou Medical University

description: 25 MII egg cells, patients give up their own oocyte donation for scientific research or volunteer donation due to special circumstances (mainly);

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner. Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: In order to avoid technical variability and evaluate methylation differences between samples, the log2-ratio getting from raw data value should be normalized. We perform Median-centering, quantile normalization and linear smoothing in this analysis process by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample, it can be used to further peak-finding analysis. so, 'the normalized log2-ratio data' correspond to 'MeDIP/input' log2-ratio data.

molecule: genomic DNA

organism: Homo sapiens

source_name: MII stage egg cell

label_protocol:
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
The immunoprecipitated DNA was eluted and purified by phenol chloroform extraction and ethanol precipitation. The total input and immunoprecipitated DNA were labeled with Cy3- and Cy5-labeled random 9-mers, respectively, and hybridized to NimbleGen Human DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Microarray, which is a multiplex slide with 3 identical arrays per slide, and each array includes 27,728 CpG Islands regions (from about - 2440bp to +610bp of the TSSs) totally covered by ~720,000 probes.

extract_protocol:
Oocyte collection and DNA extraction   Oocyte of patients and ovulation volunteers who assisted in pregnancy treatment in hospitals of Guangyi Hospital from January 2010 to December 2015 were collected. All the volunteers age ranged from 22-40 years.    Under a stereomicroscope, individual eggs were placed in Tyrode's solution (Sage) using a stripping egg (about 140 μm in diameter, Cook). After the disappearance of the zona pellucida observed under a stereomicroscope, (About 0.1 mL / drop), the oocytes were placed in a buffer containing 2 μL of lysis buffer A (10 mM Tris-HCl, 1 mM EDTA, 10% SDS, 1% proteinase K, pH 8.0). After the cells were completely lysed, the cells were placed in a water bath at 37 ° C for about 1 hour to fully lyse the cells. Then the cell were centrifuged at 10,000 rpm for 2 minutes and stored at -80 ° C until use. 2 μl of the last wash droplet were took for PCR reaction blank control.    Sperm collection and DNA extraction   Sperm of patients who accepted IVF treatment in Guangzhou Medical Third Affiliated Hospital from January 2010 to December 2015 were collected. The patient's husband age ranged from 22-40 years, secondary to infertility without any male factor in patients with her husband's semen. Density gradient centrifugation and upstream separation were applied for collection of sperm. The differential lysis method [89] was used, and DNA was extracted by the kit procedure in combination with reagents using Genomic DNA urification Kit (Promega).    2PN and 4 cell embryos collected and DNA extraction    Methods of ICSI: ICSI fertilization was performed on oocytes and spermatozoa from the above sources, and the mature egg was selected to remove the egg droplet to the center of the field of view. Hold the egg with the Holding needle, oocyte was transfer to the clearest state under microinjection needle, the polar body is located at 6,7 o'clock or 11,12 o'clock position, so that the injection of quasi-oocyte was in the middle 3 o'clock position.   The sperm were pushed to the tip of the injection needle, injection needle was placed in the oocyte 3 o'clock vertically through the zona pellucida until sperm was pushed within the cytoplasm of the middle of the egg. After the eggs were injected one by one, they were repeatedly rinsed in a pre-prepared G1.5 Plus Petri dish and placed in 37 ° C, 5% CO2, 5% O2, 90% N2 incubators and cultured in G1.5 Plus droplets separately.   For IVF fertilization, GIVF-plus which has been equilibrated overnight was used to prepare fertilized droplets according to the standard of 0.1 ml per microtube droplet per 3 eggs. Then this fertilized droplets were stored in incubator (37 ° C, 6% CO2) with coverage of mineral oil. Moderate amount of sperm was added to prepared fertilized dish under a microscope. And concentration was adjusted to 1.0 × 10 6 / ml. this sperm droplets were stored in incubator (37 ° C, 6% CO2) to wait for fertilization.  After 3-4 hour’s pre-incubation, eggs were transferred to the fertilized dish. 2-3 eggs were added to one semen drop and this fertilized drop was returned to the embryo box for overnight cultivation.  2PN Collection: Prokaryotic cells were observed at 16-20 hours after ICSI or IVF under inverted microscope and fertilization information was recorded. Two circular structures with nucleolar precursors in the cytoplasm were the male and female pronuclei (2PN). Two polar bodies (2PB) can be seen in the perivitelline space when normal fertilization occured. 12 prokaryotic and ICSI-derived prokaryotes from 2PN-derived IVF will be collected to extract DNA. DNA extraction method was identical to oocyte genomic DNA extraction method.  2 prokaryotic embryos were cotinue to culture to D2 at 16-20 hours after ICSI or IVF. And 5 cells which had 4 cells, uniform blastomere size and lower fragments rate (less than 5%) were used in present study. DNA extraction method was identical to oocyte genomic DNA extraction method.     D3 embryo collection and DNA extraction  After two years of successful transplant, donated embryos were stored via vitrified cryopreservation method. After thawing, there were 7-9 available embryos which had uniform size and lower cell debris rate (less than 20%). And 5 of them were used in present study. DNA extraction method was identical to oocyte genomic DNA extraction method.    morulae collection and DNA extraction  The thawed D3 embryos were continue to cultured in 37 °C, 5% CO2, 5% O2, 90% N2 incubators. After overnight culturing, 6 mulberry embryos which were completely fused and with less than 20% fragmentation were used in present study. DNA extraction method was identical to oocyte genomic DNA extraction method.    Collection of blastocyst ICM and TE and their DNA extraction  The above thawed D3 embryos were cultured to D5 embryos, and high quality blastocysts were screened for this study. Screening of D5 high-quality blastocysts was based on Garden's grading standards: stage of inner cell mass and trophoblast were A or B blastocysts. Separation of ICM and trophoblast blastocyst was performed via mechanical methods, the capillary pipette segregate ICM and trophoblast blastocyst under stereomicroscope bluntly. The isolated ICM and TE were washed for several times in PBS and then these isolated ICM and TE were extracted with reference to the DNA extraction method of the oocyte.
Genomic DNA were extracted according to the manufacturer’s instructions and sonicated to random fragments in size about 200-1000 bp. Immunoprecipitation of methylated DNA was performed using Biomag TM magnetic beads coupled mouse monoclonal antibody against 5-methylcytidine.

tag: fraction

tag: cell type

value: MII stage egg cell

value: input DNA


title: C4-2b enz resistant 1

type: SRA

city: Seoul

first: Kyoung-Hwa

last: Lee

address: 101 Daehak ro

department: Urology

country: South Korea

institute: Seoul National University Hospital

description: prostatic carcinoma

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include EdgeR-normalized values for each sample.

molecule: total RNA

source_name: enzalutamide resistant C4-2b

growth_protocol: Parental and enzalutamide resistant C4-2b cells were cultured in RPMI-1640 medium at 37 °C in 5% CO2, which was supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: parental cell line

value: bone-metastatic LNCaP-derivative


title: D

description: Mulberry embryo: For patients who have ART, the frozen D3 embryos will be abandoned for more than two years, and the mulberry embryos will continue to be cultured after thawing, 6 pieces;

source_name: Mulberry embryo

growth_protocol: Pax5-/- Rag2-/- pro-B cells are an established cell line

value: Mulberry embryo


title: E1

description: Abortion of frozen D3 embryos for more than two years after gestation, and culturing to 5 D5 or D6 high quality blastocysts after thawing, mechanically separating ICM cells;

source_name: Blastocyst inner cell mass

value: Blastocyst inner cell mass


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_7d_Rep2_ERCC78A

city: Bethesda

first: Alexei

last: Arnaoutov

state: MD

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

country: USA

institute: NICHD

data_processing:
We used Illumina Casava1.8.2 for basecalling
Shortreads from RNA-Seq were mapped onto Drosophila Reference Genome 6 (PMID: 25589440) using TopHat 2.1.1 (PMID: 23618408) with -g 1 and -G parameters with FlyBase gene annotation model 6.12.
We used HTSeq 0.6.1p1 (PMID: 25260700) to measure gene-level read counts with the “-s reverse” option.  We provide Cufflinks 2.2.1-generated (PMID: 23222703) FPKM values (Fragments Per Kilobase of transcript per Million mapped reads) in this GEO submission that we prepared.  We used the -G, -u, and -b parameters.
Genome_build: Drosophila Reference Genome Release 6 (Berkeley Drosophila Genome Project)
Supplementary_files_format_and_content: Gene-level expression measurements from HTSeq (read count) and Cufflinks (FPKM values) are provided in a tab-limited text format

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: midgut

growth_protocol: We cultured flies using Jazz-Mix food (Thrermo Fisher Scientific, Waltham, MA) for the samples that we performed 50bp single-end RNA-Seq.  For samples with 76bp single-end RNA-Seq, we cultured files as appeared in Broderick et al 2014 (PMID: 24865556) with minor modifications.

extract_protocol:
We extracted total RNA using 1 ml of Trizol (Thrermo Fisher Scientific, Waltham, MA) as in manufacturer’s guideline.
We prepared stranded RNA libraries using Illumina TruSeq mRNA kit (Illumina, San Diego, CA).

treatment_protocol: We treated 30 flies with 100 ul of autoclaved yeast paste with or without 400 uM deoxyadenosine, deoxyguanosine, or 40mM hydroxyurea.

tag: tissue

value: midgut

tag: developmental stage

value: adult

tag: age

value: 7 day

tag: growth condition

value: normal

tag: Sex

value: Female

tag: treatment

tag: genotype

value: deltaIRBIT+gene

tag: replicate number

tag: ercc spikein


title: Putamen, MSA3-2

city: Copenhagen NW

first: Rasmus

last: Rydbirk

state: Please Select

address: Nielsine Nielsens Vej 6B, stair 11B, 2nd Floor

department: Department of Neurology

country: Denmark

institute: Bispebjerg-Frederiksberg Hospital

data_processing:
Data were trimmed using Trimmomatic v. 0.38 in paired-end mode (PE) including clipping Illumina adapter sequences (ILLUMINACLIP) using the following specifications: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed data were aligned to GRCh38 release 94, thereby creating BAM files, using STAR v. 2.5.3a with genome index created using --sjdbOverhang 100
A count table was produced for aligned data using summarizeOverlaps from GenomicAlignments in R v. 3.5.0 using the following specifications: mode="Union", singleEnd=FALSE, ignore.strand=FALSE, fragments=TRUE
Genome_build: GRCh38 rel. 94
Supplementary_files_format_and_content: A tab-delimited text file containing raw gene counts per sample.

source_name: Putamen

extract_protocol:
Whole brains were slabbed and frozen at -80 °C. RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen; #80224).
300 ng RNA per sample was used as inpt for library preparation using TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold rRNA Removal Kit (Illumina; #RS-122-2303).

tag: disease state

value: multiple system atrophy

value: brain (putamen)

tag: pmi

tag: rin


title: K

description: D2 embryos obtained by ICSI or IVF fertilization of donated oocytes, a total of 5;

source_name: 4 cell cleavage stage embryo

value: 4 cell cleavage stage embryo


title: Putamen, MSA3-1


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_7d_Rep1_ERCC78A


title: Putamen, MSA2-2


title: C4-2b control 2

description: prostatic carcinoma

source_name: parental C4-2b


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_40d_Rep3_ERCC78B

value: 40 day


title: Putamen, MSA2-1


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_40d_Rep2_ERCC78B


title: C4-2b control 1

description: prostatic carcinoma


title: Putamen, MSA1-2


title: GIC Replica 2 - RNASeq

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

data_processing:
ChIPSeq: Adaptor sequence and other artefacts were removed from sequence reads using Trimgalore. After trimming and quality control, reads were aligned using Bowtie v2.3.4, allowing up to 1 mismatch per read and discarding multi-mapped reads.
Peak Calling: MACS2 was used to call H3K27me3 peaks (subroutine callpeak) with broad mark option. The shifting model and the dynamic lambda were both disabled. A minimum fold enrichment of 2 was selected with an FDR (--broad-cut-off) of 0.05.
RNASeq: Adaptor sequence and other artefacts were removed from sequence reads using Trimgalore. After trimming and quality control, reads were aligned using STAR with the following parameters: --outSAMstrandField intronMotif --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ChIPSeq: *_peaks.broadPeak; For each sample, a bed file with enrichment scores for each genomic region is provided.
Supplementary_files_format_and_content: RNASeq: *ReadsPerGene.out.tab; For each sample, a tab file with raw counts per gene is provided.

organism: Mus musculus

source_name: Glioblastoma initiating cells

extract_protocol:
Chromatin was extracted and sonicated to get fragments of 100 to 500 bp, then immunoprecipitated with 10 µL of anti-H3K27me3 (Active Motif, #39155). ChIPSeq libraries were prepared following the Illumina protocol and ligated to standard PE adaptors and sequenced on a HiSeq2000.
Total RNA was extracted using Mini RNeasy kit (Qiagen) according to the manufacturer’s instructions. For RNASeq, 200 ng of total RNA was used to prepare RNASeq libraries using the TruSeq RNA kit from Illumina following the instructions provided in the supplier's manual, and sequenced on HiSeq2000.

tag: genotype/variation

value: Glioblastoma initiating cells


title: Mnase_0.8U

city: RTP

first: Takashi

last: Shimbo

address: 111 TW Alexander Dr.

institute: NIH/NIEHS

library_source: genomic

data_processing:
Reads were filtered based on a mean base quality score >20. Reads were mapped to hg19 genome using Bowtie 0.12.8
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
Non-duplicate, uniquely mapped paired-end reads were converted to a single fragment. BedGraph files contain genome coverage information
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

growth_protocol: Cells were grown on 15 cm plates in DMEM medium with 10% FBS

extract_protocol: Libraries were constructed from Mnase digested DNA using NEXTflex Rapid Illumina DNA-Seq Library Prep Kit(Bioo)

treatment_protocol: To inhibit pol II, MCF7 cells were treated 1µM triptolide or 1µM flavopiridol for 30min

value: Breast

tag: cell line

tag: agent


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_40d_Rep1_ERCC78B


title: Mnase_0.4U


title: GIC Replica 1 - RNASeq

tag: cell type


title: C4-2b control 3

description: prostatic carcinoma

tag: parental cell line


title: Putamen, MSA1-1

tag: tissue


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_axenic_7d_Rep3_ERCC78A

tag: developmental stage

value: axenic

value: deltaIRBIT


title: NSC Bmi1over Replica 2 - RNASeq

source_name: Neural stem cells

value: Neural stem cells


title: PD10-2

value: Brain

tag: age

value: Male


title: NSC Bmi1over Replica 1 - RNASeq


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_axenic_7d_Rep2_ERCC78A

value: midgut

tag: growth condition


title: PD10-1

tag: Sex


title: Mnase_0.1U


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_axenic_7d_Rep1_ERCC78A

value: adult

tag: treatment


title: Mnase_4U


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_axenic_40d_Rep3_ERCC78B

tag: genotype


title: PD9-1


title: GIC - ChiPSeq

description: Chromatin

tag: chip antibody


title: Mnase_8U


title: Control NSC Replica 1 - RNASeq

value: Wild type


title: PD9-2


title: Mnase_1.6U


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_axenic_40d_Rep2_ERCC78B

tag: replicate number

tag: ercc spikein


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_axenic_40d_Rep1_ERCC78B


title: NSC Bmi1over - ChiPSeq

description: Chromatin


title: Mnase_16U


title: PD8-2

tag: pmi


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_7d_Rep3_ERCC78B

value: 7 day

value: normal


title: Mnase_0.2U


title: Trp_treated_Hi-Mnase_rep_2

value: triptolide


title: PD7-2

value: Female

tag: rin


title: PD7-1


title: FP_treated_Hi-Mnase_rep_2

value: flavopiridol


title: Trp_treated_Hi-Mnase_rep_1


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_7d_Rep2_ERCC78B


title: mouse_testis

city: Shanghai

first: Li

last: Feng

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology, CAS

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw fastq data was pre-processed using a common procedure. After quality filtering, sequencing reads were clipped from the 3’ adaptor allowing a minimum match of 10nt. Reads unable to match the 3' adaptor sequence or with lengths shorter than 17 bp were discarded.
The useful reads were mapped to the mouse genome by bowtie (bowite options –v 0 –k 100) (Langmead et al. 2009). The mapped genome sequences were further aligned to known miRNAs, tRNAs, rRNAs, snoRNAs and snRNAs by bowtie. The remaining 25~32 nt sequences were used to identify piRNAs following the method described previously (Inuk Jung et al 2014) with slight modifications. The clustering parameters were determined as MinReads = 4 and Eps = 2500 bp by running a series of k-dist analysis with different Eps and MinReads in our own data. After clustering all remaining 25~32nt sequences with the determined parameters, all candidate clusters were considered as piRNA clusters without any further scoring and filtering.
Only the reads that exactly matched the 5’ start site of annotated miRNAs and has ≤2 nt deletions or additional sequences derived from pri-miRNAs at the 3’ ends were counted as miRNAs. The count of each miRNAs, piRNAs and tRNA, rRNA, snRNA-derived sequences was normalized to the count of methylated spike-in. The small RNAs were mapped in the following order: miRNA, tRNA, rRNA, snoRNA, snRNA and piRNA
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: tab-delimited text files include useful reads count for each sample.

source_name: mouse testis

growth_protocol: BxPC-3 cells were cultured in DMEM (GIBCO) with 10% FBS (GIBCO) and 1% penicillin/streptomycin according to the manufacturer’s instructions.

extract_protocol:
Total cellular RNA was extracted using a TRIzol reagent (Takara).
Approximately 1 µg of total cellular RNA was used to construct a small RNA library according to the Illumina protocol
High-throughput RNA sequencing was performed using a Hi-Seq 2000 with 50 running circles (Genergy Biotechnology)

treatment_protocol: Zero point five microliters of mixture of RNA and spike-in was transferred to a new tube and added with 1 μl of 0.25 μM 3' adapter and 3.5 μl DEPC water as a no oxidation control. The 6.5 μl mixture of RNA and spike-in was used for oxidization experiment by adding 2 μl of 5× borate buffer (150mM borax,150mM boric acid, pH 8.6) and 1.5 μl of freshly dissolved 100mM NaIO4 (Sigma, USA). The reaction mixture was incubated in the dark for 30 min at room temperature and then precipitated using 100% ethanol with 25 μg linear acrylamide and 30 μl sodium acetate (3 M, pH 5.2) and stored at −30 °C for 30 min before centrifugation.

tag: strain

value: testis

value: wild type


title: mouse_testis_NaIO4

source_name: mouse testis NaIO4 added


title: PD6-2


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_40d_Rep3_ERCC78A

value: 40 day


title: INPUT_BMAL1

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
The raw reads (single-end, 100 bp) were aligned to mouse reference genome mm9 using bowtie (v1.1.0) allowing up to one mismatch.
Genome_build: mm9
Supplementary_files_format_and_content: Peak calling was performed using MACS (v1.4.2) with the default cutoff of P ≤ 1 × 10-8. Clonal reads were automatically removed by MACS.

source_name: Mouse embryonic fibroblast (MEF)

growth_protocol: DMEM supplemented with 10% FBS and antibiotics.

extract_protocol:
ChIP-Seq for H3K4me3 was performed according to the Ren Lab ChIP protocol (http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf). ChIP-seq for BMAL1 was performed using the ChIP-IT high Sensitivity Kit (#53040, Active Motif) according to the manufacturer’s instructions. Library construction was performed using the PrepX Illumina ChipSeq kit and the PrepXComplete ILMN DNA barcodes on the Apollo324 System. The resulting library was cleaned with AMPure XP beads and quantified by qPCR with Kapa Sybr Fast universal for Illumina Genome Analyzer kit. The library size was determined by analysis using the Bioanalyzer 2100 DNA High Sensitivity Chip and libraries were sequenced on the HiSeq 4000 Sequencer (100 bp, single-end reads).
ChIP–seq samples were sequenced using the Illumina HiSeq 4000 .

treatment_protocol: Cells were were synchronized with 100nM dexamethasone for 1 hour and treated with either vehicle (DMSO) or 10 mM Dznep.

tag: background strain

tag: antibody


title: DMSO_treated_Hi-Mnase_rep_2

value: Breast

tag: cell line

tag: agent

value: DMSO


title: PD6-1

tag: tissue


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_40d_Rep2_ERCC78A

tag: developmental stage

value: deltaIRBIT


title: FP_treated_Hi-Mnase_rep_1


title: INPUT_H3K4me3


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_40d_Rep1_ERCC78A

tag: age


title: PD8-1


title: PD5-2


title: PD5-1


title: DMSO_treated_Hi-Mnase_rep_1


title: CT24.2_DZnep_H3K4me3

value: DZnep

tag: circadian time

value: circadian time (CT) 24

value: H3K4me3, Active Motif #39915


title: Control NSC - ChiPSeq

description: Chromatin

tag: genotype/variation

tag: cell type

value: Neural stem cells


title: RNA-Seq_50bp_SE_Male_WholeAnimal_yw_dGuo_7d_Rep3

source_name: WholeAnimal

value: WholeAnimal

value: adult

tag: growth condition

tag: Sex

value: Male

tag: treatment

value: dGuo

tag: genotype

value: yw


title: Trp_treated_Lo-Mnase_rep_2

value: triptolide


title: PD4-2

value: Brain

value: Female

tag: pmi


title: RNA-Seq_50bp_SE_Male_WholeAnimal_yw_dGuo_7d_Rep2

value: 7 day

value: normal

tag: replicate number

tag: ercc spikein


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_7d_Rep1_ERCC78B

value: midgut


title: CT24.2_DZnep_BMAL1

tag: background strain

value: BMAL1, Abcam ab93806


title: CT24.2_DMSO_H3K4me3

value: DMSO

tag: antibody


title: Trp_treated_Lo-Mnase_rep_1

value: Breast

tag: cell line


title: Control NSC Replica 2 - RNASeq

value: Wild type


title: PD4-1

tag: rin


title: FP_treated_Lo-Mnase_rep_2

tag: tissue

tag: agent

value: flavopiridol


title: RNA-Seq_50bp_SE_Male_WholeAnimal_yw_dGuo_7d_Rep1

tag: developmental stage

tag: age


title: PD3-2


title: CT24.2_DMSO_BMAL1

tag: circadian time

value: circadian time (CT) 24


title: CT24.1_DZnep_H3K4me3

value: DZnep

value: H3K4me3, Active Motif #39915


title: PD3-1

value: Male


title: RNA-Seq_50bp_SE_Male_WholeAnimal_yw_dAdo_7d_Rep2

value: WholeAnimal

value: adult

value: dAdo


title: DMSO_treated_Lo-Mnase_rep_2


title: CT24.1_DZnep_BMAL1


title: RNA-Seq_50bp_SE_Male_WholeAnimal_yw_dAdo_7d_Rep1

value: yw


title: DMSO_treated_Lo-Mnase_rep_1


title: RNA-Seq_50bp_SE_Male_WholeAnimal_yw_7d_Rep3


title: PD2-2

value: Brain


title: PD2-1


title: 33_L1.D709: Nlrp3 KI_ASK1 Inhibitor liver #4P

city: Foster City

last: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

data_processing:
Illumina software (CASAVA v. 1.8.2)
remove residual Illumina adapter sequence and low quality bases from the ends of reads
STAR software version 2.4
RSEM version 1.2.14
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RSEM values for each Sample

source_name: Liver

extract_protocol:
total RNA was isolated from fresh frozen tissue using the Qiagen miRNeasy Mini Kit
Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103)

value: Liver

tag: genotype/variation

value: M


title: CT24.1_DMSO_BMAL1


title: CT24.1_DMSO_H3K4me3


title: PD1-2

value: Female


title: 32_L1.D708: Nlrp3 KI_ASK1 Inhibitor liver #3P

value: F


title: CT12.2_DZnep_H3K4me3

value: circadian time (CT) 12


title: RNA-Seq_50bp_SE_Male_WholeAnimal_yw_7d_Rep2

value: 7 day

tag: growth condition

value: normal


title: FP_treated_Lo-Mnase_rep_1

value: Breast

value: flavopiridol


title: RNA-Seq_50bp_SE_Male_WholeAnimal_yw_7d_Rep1

tag: Sex


title: CT12.2_DZnep_BMAL1

value: DZnep

value: BMAL1, Abcam ab93806


title: RNA-Seq_50bp_SE_Male_WholeAnimal_yw_dAdo_7d_Rep3

value: Male

tag: treatment


title: PD1-1


title: 31_L1.D707: Nlrp3 KI_ASK1 Inhibitor liver #2P


title: 30_L1.D706: Nlrp3 KI_ASK1 Inhibitor liver #1P


title: CT12.2_DMSO_H3K4me3

value: DMSO

value: H3K4me3, Active Motif #39915


title: RNA-Seq_50bp_SE_Male_WholeAnimal_IRBIT_HU_7d_Rep3

value: WholeAnimal

value: adult

value: Hydroxyurea

tag: genotype

value: deltaIRBIT


title: CT12.2_DMSO_BMAL1


title: 29_L1.D705: Nlrp3 KI_con diet liver #1P

value: Liver

value: Control chow+placebo

value: M


title: CT12.1_DZnep_H3K4me3

value: circadian time (CT) 12


title: RNA-Seq_50bp_SE_Male_WholeAnimal_IRBIT_HU_7d_Rep1

value: 7 day


title: 28_L1.D704: WT_ASK1 Inhibitor liver #2P

value: WT

value: F


title: RNA-Seq_50bp_SE_Male_WholeAnimal_IRBIT_gene_7d_Rep3

value: normal

value: deltaIRBIT+gene


title: CT12.1_DZnep_BMAL1

value: DZnep

value: BMAL1, Abcam ab93806


title: CT12.1_DMSO_H3K4me3

value: DMSO


title: 27_L1.D703: WT_ASK1 Inhibitor liver #1P


title: CT12.1_DMSO_BMAL1


title: RNA-Seq_50bp_SE_Male_WholeAnimal_IRBIT_HU_7d_Rep2

value: Male


title: 24_L8.D712: Nlrp3+GS  liver 6


title: 25_L8.D701: WT_con diet liver #1P


title: RNA-Seq_50bp_SE_Male_WholeAnimal_IRBIT_gene_7d_Rep2

value: WholeAnimal


title: RNA-Seq_50bp_SE_Male_WholeAnimal_IRBIT_gene_7d_Rep1

value: adult


title: RNA-Seq_50bp_SE_Male_WholeAnimal_IRBIT_7d_Rep3


title: 23_L8.D711: Nlrp3+GS  liver 5


title: 26_L8.D702: WT_con diet liver #2P


title: RNA-Seq_50bp_SE_Male_WholeAnimal_IRBIT_7d_Rep2


title: RNA-Seq_76bp_SE_Female_Gut_IRBIT_gene_axenic_40d_Rep3_ERCC78A

value: midgut

value: 40 day

value: axenic

value: Female


title: 22_L8.D710: Nlrp3+GS  liver 4

value: Liver


title: 21_L8.D709: Nlrp3+GS  liver 3

value: M


title: RNA-Seq_50bp_SE_Female_WholeAnimal_yw_dAdo_7d_Rep3

value: 7 day

value: dAdo

value: yw


title: RNA-Seq_50bp_SE_Female_WholeAnimal_yw_dAdo_7d_Rep2

value: normal


title: 19_L7.D707: Nlrp3+GS  liver 1


title: 20_L8.D708: Nlrp3+GS  liver 2


title: HUVEC MIR-335 GFP LENTI 1

type: RNA

city: New Haven

first: hyung

last: chun

state: CT

address: 300 George St Room 770H

department: Internal Medicine

institute: Yale University

description:
SAMPLE 3
5965581003_F.AVG_Signal

hyb_protocol: Samples were hybridized onto beadchips according to gene expression profiling protocol from Illumina.

scan_protocol: The Illumina BeadArray Reader and BeadScan software were used to scan and extract raw intensity values.

data_processing: Background subtraction and quantile normalization were performed.

source_name: HUVEC MIR-335 GFP LENTI

label_protocol: Samples were labeled according to gene expression profiling protocol from Illumina

growth_protocol: HUVECs grown in EGM-2 (Lonza)

extract_protocol: Qiagen miRNeasy per manufacturer's protocol

treatment_protocol: Transduced with lentivirus overexpressing microRNA

tag: cell type

value: HUVEC

value: MIR-335 GFP LENTI

value: miR-335 overexpression


title: RNA-Seq_50bp_SE_Male_WholeAnimal_IRBIT_7d_Rep1

value: deltaIRBIT

tag: replicate number


title: HUVEC GFP LENTI CONTROL 1

description:
SAMPLE 1
5965581003_B.AVG_Signal

source_name: HUVEC GFP LENTI CONTROL

value: GFP LENTI CONTROL

value: control


title: HUVEC MIR-335 GFP LENTI 2

description:
SAMPLE 4
5965581003_H.AVG_Signal


title: 18_L7.D706: Nlrp3+con liver 4

value: Control chow+placebo


title: RNA-Seq_50bp_SE_Female_WholeAnimal_yw_dAdo_7d_Rep1

value: WholeAnimal

value: adult

tag: ercc spikein


title: RNA-Seq_50bp_SE_Female_WholeAnimal_yw_7d_Rep2


title: 17_L7.D705: Nlrp3+con liver 3


title: HUVEC GFP LENTI CONTROL 2

description:
SAMPLE 2
5965581003_D.AVG_Signal


title: RNA-Seq_50bp_SE_Female_WholeAnimal_yw_7d_Rep3


title: RNA-Seq_50bp_SE_Female_WholeAnimal_yw_7d_Rep1


title: RNA-Seq_50bp_SE_Female_WholeAnimal_yw_1d_Rep3

value: 1 day


title: Mutant Atring1a Atring1b 7-day-old seedlings Replicate 1

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

description: Biological replicate 1 of mutant Atring1a Atring1b seedlings

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction. Signal intensity were normalized using Quantile method. Signal : raw Cy3 signal intensity ; Log2NormSignal : Log2 transformed Normalized Signal

organism: Arabidopsis thaliana

source_name: Atring1ab seedlins

label_protocol: 2 µg of total RNA were labeled according Aligent's instructions. Please see manufacture’s web site at http://www.aligent.com/

growth_protocol: Plants were grown in the greenhouse under 16h light and 8h dark at 22°C.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up according to manufacturer's instructions.

tag: ecotype

value: Columbia ecotype

tag: organ

value: seedlings


title: 16_L7.D704: Nlrp3+con liver 2

value: Liver

value: M


title: biopsy healthy inactive; sHT57.1

city: Cork

first: Rachel

middle: Siobhain

last: Fitzgerald

state: Cork

address: College Road

department: BIOSCIENCES INSTITUTE

country: Ireland

institute: University College Cork

hyb_protocol: Four µl of bisulphite-converted DNA were used for hybridization, following the Illumina Infinium HD Methylation protocol. This consisted of a whole genome amplification step followed by enzymatic end-point fragmentation, precipitation and resuspension. The resuspended samples were hybridized on Human Methylation 450 BeadChips at 48°C for 16 h – 24h. Then unhybridized and non-specifically hybridized DNA was washed away, followed by a single nucleotide primer extension using the hybridized bisulphite-treated DNA as a template

scan_protocol: The Illumina iScan scanner is a two-colour laser (532 nm-658 nm) fluorescent scanner with a 0.53 µm spatial resolution capable of exciting the fluorophores.

data_processing: Normalized using BMIQ

label: biotin

source_name: biopsy healthy inactive

label_protocol: The nucleotides incorporated were labelled with biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP). After the single base extension, repeated rounds of staining were performed with a combination of antibodies that differentiated DNP and biotin by fixing them different fluorophores. The nucleotides incorporated were labelled with biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP). After the single base extension, repeated rounds of staining were performed with a combination of antibodies that differentiated DNP and biotin by fixing them different fluorophores. The nucleotides incorporated were labelled with biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP). After the single base extension, repeated rounds of staining were performed with a combination of antibodies that differentiated DNP and biotin by fixing them different fluorophores

extract_protocol: Genomic DNA was extracted from colonic biopsies using AllPrep DNA/RNA mini kit (Qiagen) and following manufacturer's instructions. Sample homogenization was done by two cicles of 15 min at 6500 rpm in a MagnaLyser.

value: colonic biopsy

tag: patient

tag: condition

value: healthy

tag: status

value: Non-inflamed

value: Male

tag: smoking

value: No


title: 15_L7.D703: Nlrp3+con liver 1

tag: tissue

value: F


title: Mutant Atring1a Atring1b 7-day-old seedlings Replicate 3

description: Biological replicate 3 of mutant Atring1a Atring1b seedlings

hyb_protocol: Please see manufacture’s web site at http://www.aligent.com/

tag: age


title: Mutant Atring1a Atring1b 7-day-old seedlings Replicate 2

description: Biological replicate 2 of mutant Atring1a Atring1b seedlings


title: biopsy healthy inactive; sHT48.1


title: Wild-type 7-day-old seedlings Replicate 2

description: Biological replicate 2 of Col0 seedlings

source_name: Col0 seedlings

value: wild type


title: biopsy healthy inactive; sHT52.1

value: Female


title: 14_L7.D702: WT+GS liver 7

value: WT


title: Wild-type 7-day-old seedlings Replicate 1

description: Biological replicate 1 of Col0 seedlings


title: biopsy healthy inactive; sHT47.1


title: RNA-Seq_50bp_SE_Female_WholeAnimal_yw_1d_Rep1

tag: developmental stage

value: normal

value: yw


title: biopsy healthy inactive; sHT53.1


title: 13_L7.D701: WT+GS liver 6

tag: genotype/variation


title: RNA-Seq_50bp_SE_Female_WholeAnimal_IRBIT_gene_7d_Rep3

value: WholeAnimal

value: adult

value: 7 day

tag: growth condition

value: deltaIRBIT+gene


title: biopsy healthy inactive; sHT50.1

tag: Sex


title: biopsy healthy inactive; sHT43.1


title: RNA-Seq_50bp_SE_Female_WholeAnimal_yw_1d_Rep2

value: 1 day

tag: treatment


title: 12_L6.D712: WT+GS liver 5

value: Liver


title: Mutant clf flower buds Replicate 1

description: Biological replicate 1 of mutant clf flower buds

source_name: clf flower buds

value: Columbia ecotype

value: whole flower buds

value: before developmental stage 8

value: clf


title: biopsy healthy inactive; sHT44.2

value: colonic biopsy

value: healthy

value: Non-inflamed

value: No


title: biopsy healthy inactive; sHT45.1

value: Male


title: RNA-Seq_50bp_SE_Female_WholeAnimal_IRBIT_7d_Rep3

value: normal

value: Female

tag: genotype

value: deltaIRBIT


title: biopsy healthy inactive; sHT34.1


title: 11_L6.D711: WT+GS liver 4

value: WT

value: M


title: 10_L6.D710: WT+GS liver 3


title: RNA-Seq_50bp_SE_Female_WholeAnimal_IRBIT_gene_7d_Rep2

value: WholeAnimal

value: adult

value: 7 day

value: deltaIRBIT+gene


title: Mutant Atring1a Atring1b flower buds Replicate 2

description: Biological replicate 2 of mutant Atring1a Atring1b flower buds

source_name: Atring1ab flower buds

value: Columbia ecotype

value: whole flower buds


title: 9_L6.D709: WT+GS liver 2

value: Liver


title: biopsy healthy inactive; sHT17.2

value: colonic biopsy


title: biopsy healthy inactive; sHT46.1

value: healthy


title: biopsy healthy inactive; sHT24.1

value: Non-inflamed

value: Yes


title: biopsy healthy inactive; sHT30.1

value: Male

value: No


title: 8_L6.D708: WT+con liver 8

value: Control chow+placebo


title: biopsy healthy inactive; sHT41.1

value: Female


title: biopsy healthy inactive; sHT14.1


title: RNA-Seq_50bp_SE_Female_WholeAnimal_IRBIT_7d_Rep2

value: normal

value: deltaIRBIT


title: Wild-type 7-day-old seedlings Replicate 3

description: Biological replicate 3 of Col0 seedlings

value: seedlings

value: wild type


title: Mutant lhp1 flower buds Replicate 2

description: Biological replicate 2 of mutant lhp1 flower buds

source_name: lhp1 flower buds

value: before developmental stage 8


title: RNA-Seq_50bp_SE_Female_WholeAnimal_IRBIT_7d_Rep1

value: WholeAnimal

value: adult

value: 7 day


title: 7_L6.D707: WT+con liver 7

value: Liver

value: WT

value: F


title: RNA-Seq_50bp_SE_Female_WholeAnimal_IRBIT_1d_Rep3

value: 1 day


title: Aedes_Diro.Be.d3.3

city: Philadelphia

first: Michael

last: Povelones

state: PA

address: 3800 Spruce St.

department: Pathobiology

institute: University of Pennsylvania School of Veterinary Medicine

data_processing:
Fastq files were mapped to the Aedes aegypti Liverpool strain transcriptome (version AGWG AaegL5.1) using Kallisto or Dirofilaria immitis transcriptome (PRJEB1797 version nDi.2.2) using Kallisto, version 0.44.0
abundance data were read into the R/bioconductor environment using the TxImport package, version 1.0.2
For analysis of Aedes transcripts, transcripts with low/no read counts in three of the cultured samples or any of the mosquito samples were eliminated
data was normalized using the calcNormFactors function from Limma (3.34.4), using the TMM method
precision weights were applied to expression data using the Limma/VOOM function
Genome_build: differentially expressed genes (0.05 adjusted Pval and 2 fold change) for Ae. aegypti transcripts were identified using linear modeling and Bayesian statistics using the Limma package

organism:
Dirofilaria immitis
Aedes aegypti

source_name: Malpighian tubules of Aedes aegypti

growth_protocol: Blood containing Dirofilaria immitis microfilariae was obtained from an experimentally infected dog. Blood used to infect Ae. aegypti(S) to generate L3i to establish the dog was obtained from a shelter in Charleston, NC. The average microfilaremia during these experiments was approximately 50,000 mf/mL. All animal studies were performed under Institutional Animal Care and Use Committee approved protocols and in accordance with the guidelines of the Institutional Animal Care and Use Committee of the University of Pennsylvania (IACUC, protocol 805059). Blood was diluted with the appropriate volume of heparinized sheep blood (Hemostat) to a concentration of 3000-4000 mf/mL. Blood containing microfilariae was heated to 37 ºC placed in an artificial membrane feeder consisting of the indentation in the bottom of a 300 mL plastic baby bottle (Advent, Phillips) filled with 37 ºC water. The blood was then covered with thinly-stretched Parafilm. The bottle was inverted, placed on top of netted mosquito cups, and removed after 20 minutes. The indentation holds approximately 3.5 mL of blood resulting in an average uptake of 14 mf/mosquito (range 5-24 mf/mosquito) for D. immitis  at the concentration used. Immediately following the feed, blood fed mosquitoes were separated using CO2 anesthesia.

extract_protocol:
Malpighian tubules were dissected into PBS by pulling at the last abdominal segment with forceps until the hindgut emerges. Next, the abdomen is opened where it joins the thorax and the midgut was separated from the thorax. The hindgut, midgut, and Malpighian tubules are removed from the posterior abdomen by pulling again on the previously separated posterior segment with forceps. The hindgut and midgut were separated, leaving a set of tubules. Tubules from five mosquitoes were transferred together to a tube containing Trizol (Life Technologies) and stored at -80 ºC until processing according to the manufacturer’s instructions. Purified total RNA was resuspended in water and treated with Turbo DNA-free (Invitrogen) to remove potentially contaminating genomic DNA. The RNA concentration and quality were assayed using a NanoDrop (ThermoFisher), 4200 TapeStation (Agilent) and Qubit 3 Fluorometer (ThermoFisher). Overall, 23 libraries were generated from the 24 conditions, as one replicate of Ae. aegyptiS control did not yield a sufficient quantity of RNA for library production
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit according to the 9 manufacturer’s instructions. Samples were run on Illumina NextSeq 500 using a two High Output v2 kit flow cells to generate 75-base pair, single-end reads.

treatment_protocol: Malpighian tubules from susceptible "Blackeye" strain of Ae. aegypti (S) and the "Liverpool" refractory strain of Ae. aegypti (R) mosquitoes were isolated at day 1, day 2, and day 3 following infection by D. immitis and from sugar fed controls. Ae. aegypti (S),  Blackeye Liverpool (NR-48921 BEI Resources) is a D. immitis and B. malayi susceptible strain. Ae. aegypti (R) Liverpool Strain (LVP-IB12; MRA-735, contributed by David W. Severson to BEI Resouces) is a D. immitis and B. malayi refractory strain.

value: Malpighian tubules

tag: strain

value: Blackeye

tag: infection

value: Yes

tag: timepoint (day)

tag: biological replicate


title: 6_L6.D706: WT+con liver 6

value: Control chow+placebo


title: Mutant lhp1 flower buds Replicate 1

description: Biological replicate 1 of mutant lhp1 flower buds

tag: ecotype

value: Columbia ecotype

tag: organ

value: whole flower buds


title: RNA-Seq_50bp_SE_Female_WholeAnimal_IRBIT_1d_Rep2

value: normal

value: Female

value: deltaIRBIT

tag: replicate number

tag: ercc spikein


title: Mutant clf flower buds Replicate 2

description: Biological replicate 2 of mutant clf flower buds

value: before developmental stage 8

value: clf


title: Wild-type flower buds Replicate 1

description: Biological replicate 1 of Wild-type flower buds

source_name: Col0 flower buds

value: wild type


title: RNA-Seq_50bp_SE_Female_WholeAnimal_IRBIT_1d_Rep1

value: WholeAnimal

value: adult


title: 4_L6.D704: WT+con liver 4

value: Liver

value: WT


title: RNA-Seq_50bp_SE_Female_WholeAnimal_IRBIT_gene_7d_Rep1

value: 7 day

value: deltaIRBIT+gene


title: RNA-Seq_50bp_SE_Female_Gut_yw_HU_7d_Rep3

source_name: midgut

value: midgut

value: Hydroxyurea

value: yw


title: 5_L5.D705: WT+con liver 5

value: Control chow+placebo

value: F


title: Aedes_Diro.Lvp.d3.3

value: Malpighian tubules

value: Liverpool

value: Yes


title: 3_L5.D703: WT+con liver 3


title: biopsy Crohn's inactive; sCD60i

source_name: biopsy Crohn's inactive

value: colonic biopsy

tag: patient

tag: condition

value: Crohn's Disease

tag: status

value: Non-inflamed

value: Female

tag: smoking

value: No


title: RNA-Seq_50bp_SE_Female_Gut_yw_HU_7d_Rep2

tag: tissue

tag: developmental stage

value: adult

tag: age

value: normal


title: biopsy Crohn's inactive; sCD62i

tag: Sex


title: 2_L5.D702: WT+con liver 2

value: Liver

tag: genotype/variation

value: WT

tag: treatment


title: biopsy Crohn's active; sCD63a

source_name: biopsy Crohn's active

value: Inflamed


title: Wild-type flower buds Replicate 2

description: Biological replicate 2 of Wild-type flower buds

value: Columbia ecotype

value: whole flower buds

value: before developmental stage 8

value: wild type


title: Aedes_Diro.Be.d2.3

value: Malpighian tubules

tag: strain

value: Blackeye

tag: infection


title: biopsy Crohn's active; sCD62a

value: Yes


title: Aedes_Diro.Lvp.d1.3

value: Liverpool

tag: timepoint (day)

tag: biological replicate


title: RNA-Seq_50bp_SE_Female_Gut_yw_HU_7d_Rep1

value: midgut

value: 7 day

tag: growth condition

value: Hydroxyurea

tag: genotype

value: yw


title: 1_L5.D701: WT+con liver 1

value: Control chow+placebo

value: F


title: Aedes_Diro.Lvp.d2.3


title: RNA-Seq_50bp_SE_Female_Gut_yw_dAdo_7d_Rep3

value: adult

value: normal

value: Female

value: dAdo

tag: replicate number

tag: ercc spikein


title: biopsy healthy inactive; sHT16.1

value: colonic biopsy

tag: patient

tag: condition

value: healthy

value: Non-inflamed

value: No


title: Aedes_Diro.Be.d3.2

value: Malpighian tubules

value: Blackeye


title: RNA-Seq_50bp_SE_Female_Gut_yw_dAdo_7d_Rep2


title: Lewis Lung Carcinoma cells, UROD KD-3

city: Dallas

first: Shruthy

last: Suresh

state: Texas

address: 6000 Harry Hines Blvd NA6.300

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Illumina Hiseq 2500 used for basecalling
Reads were trimmed to remove low-quality regions in the ends
Trimmed reads were mapped to the mouse genome (mm10) using TopHat v2.0.1227 guided by iGenomes GTF file. Alignments with mapping quality less than 10 were discarded.
Expression abundance estimation and differential expression analysis were carried out using Cufflinks/Cuffdiff (v2.1.1) software
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include Normalized Counts, fold changes in expression and statistics results of Scrambled vs UROD-KD generated with cuttdiff

source_name: Mouse lung cancer cells

growth_protocol: Lewis Lung Carcinoma cells were cultured in DMEM with 10% FBS and 1% anti-anti.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) including a DNAse column digestion step (Qiagen)
Four micrograms of total DNAse treated RNA were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Poly-A RNA is purified and fragmented before strand specific cDNA synthesis.  cDNA were A-tailed and indexed adapters were ligated. Samples were PCR amplified and purified with AmpureXP beads and validated on the Agilent 2100 Bioanalyzer. Before being normalized and pooled, samples were quantified by Qubit (Invitrogen). Sequencing was performed on a Illumina Hiseq 2500 to generate 51-bp single-end reads. Four g of total DNAse treated RNA was prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina.   Poly-A RNA was purified and fragmented before strand specific cDNA synthesis.  cDNA was A-tailed and indexed adapters were ligated.  Samples were PCR amplified and purified with AmpureXP beads and validated on the Agilent 2100 Bioanalyzer.  Samples were quantified by Qubit (Invitrogen) prior to normalization and pooling.  Sequencing was performed on an Illumina Hiseq 2500 to generate 51-bp single-end reads.  Reads were trimmed to remove low-quality regions in the ends.  Trimmed reads were mapped to the mouse genome (mm10) using TopHat v2.0.1227 guided by iGenomes GTF file (https://ccb.jhu.edu/software/tophat/igenomes.shtml).  Alignments with mapping quality less than 10 were discarded.  Expression abundance estimation and differential expression analysis were carried out using Cufflinks/Cuffdiff (v2.1.1) software.

treatment_protocol: Cells were treated with 2ug/mL doxycycline for 4 days to induce shRNA expression andthen RNA was isolated.

tag: cell type

value: Lewis Lung Carcinoma cells

value: Urod knockdown


title: Lewis Lung Carcinoma cells, UROD KD-2


title: Aedes_Diro.Be.d2.2

tag: tissue

value: Yes


title: Mutant Atring1a Atring1b flower buds Replicate 1

description: Biological replicate 1 of mutant Atring1a Atring1b flower buds

tag: ecotype

value: Columbia ecotype

tag: organ

value: whole flower buds

value: before developmental stage 8


title: RNA-Seq_50bp_SE_Female_Gut_yw_dAdo_7d_Rep1

value: midgut

tag: developmental stage

tag: age

value: 7 day

tag: Sex

value: yw


title: Lewis Lung Carcinoma cells, UROD KD-1


title: Aedes_Diro.Be.d1.2

tag: strain


title: biopsy Crohn's inactive; sCD63i

value: Crohn's Disease

tag: status

value: Female

tag: smoking


title: Lewis Lung Carcinoma cells, SCRAMBLED-3

value: Urod wildtype


title: RNA-Seq_50bp_SE_Female_Gut_yw_7d_Rep3

value: adult

value: normal

tag: treatment


title: RNA-Seq_50bp_SE_Female_Gut_yw_7d_Rep2

tag: growth condition


title: biopsy Crohn's inactive; sCD59i

value: colonic biopsy

value: Non-inflamed

value: No


title: Lewis Lung Carcinoma cells, SCRAMBLED-1

value: Lewis Lung Carcinoma cells

tag: genotype


title: Aedes_Diro.Lvp.d2.2

value: Malpighian tubules

value: Liverpool

tag: infection

tag: timepoint (day)

tag: biological replicate


title: biopsy Crohn's inactive; sCD58i

tag: patient

tag: condition

value: Ex


title: biopsy Crohn's active; sCD60a

tag: tissue

value: Inflamed


title: Aedes_Diro.Lvp.d1.2

value: Yes


title: RNA-Seq_50bp_SE_Female_Gut_yw_40d_Rep3

value: midgut

value: 40 day

tag: replicate number

tag: ercc spikein


title: RNA-Seq_50bp_SE_Female_Gut_yw_7d_Rep1

tag: developmental stage

value: 7 day

value: yw


title: Lewis Lung Carcinoma cells, SCRAMBLED-2

tag: cell type


title: Aedes_Diro.Be.d3.1

value: Blackeye


title: 72h rep2

city: Chengdu

first: Wanxin

last: Tang

state: Sichuan

address: No.37, Guoxue alley, Department of nephrology, West China Hospital, Sichuan University,

description: circRNA/linear RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2
Reads mapping using TopHat2 software
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using Cufflinks software
circRNA prediction using CIRI software
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel files include FPKM values for each Sample ...

source_name: Renal Tubule tissues

extract_protocol:
Renal cortex were removed to isolate proximal tubular cells and lysed with Trizol immediately. Total RNA was prepared using epicentre Ribo-Zero kit to remove rRNA.
Libraries were prepared according to NEB Next®Ultra™ small RNA Sample Library Prep Kit for Illumina®

treatment_protocol: Male C57BL/6 mice induced AKI with intraperitoneal injections of cisplatin at a dose of 30 mg/kg

value: Renal Tubule tissues

tag: development stage

value: After cisplatin injection 72h


title: biopsy Crohn's active; sCD59a

value: Crohn's Disease

tag: age

tag: Sex

value: Female


title: Aedes_Diro.Lvp.d3.2

tag: strain


title: Aedes_Diro.Be.d1.3


title: Aedes_Diro.Be.d2.1


title: RNA-Seq_50bp_SE_Female_Gut_yw_40d_Rep2

value: adult

value: normal

tag: treatment


title: biopsy Crohn's active; sCD55i

value: colonic biopsy

tag: status

value: Non-inflamed

tag: smoking


title: RNA-Seq_50bp_SE_Female_Gut_yw_40d_Rep1

tag: growth condition

tag: genotype


title: biopsy Crohn's active; sCD58a


title: 72h rep1

institute: Department of nephrology, West China Hospital, Sichuan University

description: circRNA/linear RNA


title: 48h rep2

description: circRNA/linear RNA

value: After cisplatin injection 48h


title: Aedes_Diro.Be.d1.1

value: Malpighian tubules

tag: infection

tag: timepoint (day)

tag: biological replicate


title: Aedes_Diro.Lvp.d3.1

tag: tissue

value: Liverpool


title: RNA-Seq_50bp_SE_Female_Gut_yw_1d_Rep2

value: 1 day

tag: replicate number


title: Aedes_Diro.Lvp.d2.1

value: Yes


title: biopsy Crohn's inactive; sCD57.1

tag: patient

tag: condition

value: Inflamed

value: Male

value: No


title: biopsy Crohn's active; sCD54a


title: Aedes_Diro.Lvp.d1.1


title: 24h rep1

description: circRNA/linear RNA

value: After cisplatin injection 24h


title: RNA-Seq_50bp_SE_Female_Gut_yw_1d_Rep1

value: midgut

tag: developmental stage

value: yw

tag: ercc spikein


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_HU_7d_Rep3

tag: age

value: 7 day

value: Hydroxyurea

value: deltaIRBIT


title: 48h rep1

description: circRNA/linear RNA

value: Renal Tubule tissues

tag: development stage


title: RNA-Seq_50bp_SE_Female_Gut_yw_1d_Rep3

value: adult

value: normal

tag: Sex

value: Female


title: 0h rep2

description: circRNA/linear RNA

tag: strain


title: HTM141-S1

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cell Biology and Anatomy

institute: Medical College of Georgia

hyb_protocol: Purified and labeled target/probe complexes were hybridized to the manufactuer supplied cartridge, according to the manufactuer's instructions.

scan_protocol: The cartridges were digitally imaged and analyzed using the nCounter Digital Analyzer.

data_processing: The raw miRNA counts were normalized based on RNA content using the trimmed geometric mean, using the miRNAs with the median 40% of the counts, and the geometric mean of the positive control probes using the nSolver 3.0 software. After normalization, data was imported into R, and batch effects were adjusted for using the limma package.

label: not provided

source_name: HTM Cells

label_protocol: RMA were hybridized to color codes and washed using a two step-magnetic bead method, according to the manufactuer's instructions.

growth_protocol: Human primary TM cells were cultured at 37˚C in 5% CO2 in low glucose Dulbecco’s Modified Eagle Medium (DMEM) with L-glutamine, 110 mg/ml sodium pyruvate, 10% fetal bovine serum, 100 µM non-essential amino acids, 100 units/ml penicillin, and 100 µg/ml streptomycin

extract_protocol: Total RNA was isolated from the samples using the miRCURY RNA Isolation Kit for Cell and Plant (Exiqon, Woburn, MA), according to the manufacturer’s instructions.

treatment_protocol: Stretched HTM cells underwent 15% cyclic mechanical stretch at a rate of 1 cylce/second for 24 hours, while controls were grown in the absence of mechanical stretch.

tag: cell line

tag: cell type

value: Human Trabecular Meshwork Cells


title: biopsy Crohn's inactive; sCD51i

value: colonic biopsy

value: Crohn's Disease

tag: status

value: Non-inflamed

tag: smoking


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_HU_7d_Rep2

tag: growth condition

tag: treatment

tag: genotype


title: HTM136-S2


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_gene_7d_Rep3

tag: tissue

value: deltaIRBIT+gene


title: biopsy Crohn's inactive; sCD50i


title: biopsy Crohn's active; sCD51a

value: Inflamed


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_HU_7d_Rep1

tag: replicate number


title: SAS-3.4/GFP_3

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National cancer center research institute

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Agilent SureScan G4900DA

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: GFP overexpressed SAS-3.4 cells

label_protocol: The miRNA Complete Labeling and Hyb Kit (Agilent Technologies)

growth_protocol: SAS cells were obtained from the Japanese Collection of Research Bioresources Cell Bank. SAS cells were cultured in Dulbecco’s modified Eagle medium (DMEM; Invitrogen, CA, USA) supplemented with 10% heat-inactivated FBS, 1% AA and 10mg/mL Puromicine at 37 °C in 5% CO2.

extract_protocol: Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: The gene was overexpressed in SAS-3.4 cells and cultured for 48 hours. After 48 hours, total RNA of SAS cells was extracted.

value: oral squamous cancer cell line

tag: genotype/variation

value: GFP overexpression

tag: molecule subtype

value: miRNA


title: HTM126-S3


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_gene_7d_Rep1

value: midgut

tag: developmental stage


title: SAS-3.4/GFP_1


title: 0h rep1

description: circRNA/linear RNA


title: HTM141-C1


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_gene_7d_Rep2

value: 7 day

tag: ercc spikein


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_dAdo_7d_Rep3

tag: age

value: dAdo


title: biopsy Crohn's inactive; sCD49i

tag: patient

tag: condition

value: No


title: SAS-3.4/CD44s_3

source_name: CD44s overexpressed SAS-3.4 cells

value: CD44s overexpression


title: HTM136-C2


title: biopsy Crohn's active; sCD49a

tag: Sex


title: HTM126-S1

tag: cell line


title: SAS-3.4/CD44s_2

tag: cell type


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_dAdo_7d_Rep2

value: adult

value: deltaIRBIT


title: biopsy Crohn's active; sCD47a

tag: status

value: Female


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_dAdo_7d_Rep1

value: normal


title: HTM126-C1

value: Human Trabecular Meshwork Cells


title: SAS-3.4/CD44s_1


title: biopsy Crohn's inactive; sCD44i

value: colonic biopsy

value: Crohn's Disease

tag: smoking

value: Yes


title: biopsy Crohn's active; sCD45a

value: Inflamed


title: biopsy Crohn's inactive; sCD47i

value: Non-inflamed


title: Injected with Shiga toxin-24hr [ST24c]

city: Cincinnati

first: Alison

middle: A

last: Weiss

state: Ohio

address: 231 Albert Sabin Way

department: COM Molecular Genetics

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: organoid_injected with Shiga toxin-24hr

growth_protocol: Organoids were grown in Gut Media for 24 days before being microinjected. Medium was changed every 2 days.

extract_protocol:
Organoids were snap frozen in liquid nitrogen and Total RNA was extracted 4 hour post injection following the Qiagen RNeasy plus mini kit protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Organoids were microinjected with 30 ng Shiga toxin and sterile PBS in 100 nL volume.

value: H1 (WA01) NIH Registration#0043

tag: cell type source

value: Human Intestinal Organoid

value: induced plueropotent embryonic stem cell

value: 30 ng Shiga toxin

tag: time post injection

value: 24 hours post injection


title: biopsy Crohn's active; sCD50a

value: No


title: HTM122-S3


title: SAS-3.4/GFP_2

value: oral squamous cancer cell line

value: GFP overexpression

value: miRNA


title: biopsy Crohn's inactive; sCD45i

value: Female


title: biopsy Crohn's inactive; sCD42i

value: Male


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_7d_Rep3

value: midgut

value: adult

value: 7 day

tag: growth condition

value: normal

tag: treatment

tag: genotype

value: deltaIRBIT


title: Injected with Shiga toxin-24hr [ST24b]


title: HTM122-C3

value: Human Trabecular Meshwork Cells


title: 24h rep2

description: circRNA/linear RNA

tag: strain

tag: tissue

value: Renal Tubule tissues

tag: development stage

value: After cisplatin injection 24h


title: biopsy Crohn's active; sCD42a

value: colonic biopsy

value: Crohn's Disease

value: Inflamed


title: biopsy Crohn's inactive; sCD54i

value: Non-inflamed

value: No


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_7d_Rep2

tag: developmental stage

tag: replicate number

tag: ercc spikein


title: biopsy Crohn's inactive; sCD22i

tag: patient

tag: condition

tag: age


title: Injected with Shiga toxin-24hr [ST24a]

tag: cell line

value: H1 (WA01) NIH Registration#0043

value: Human Intestinal Organoid

tag: cell type

value: induced plueropotent embryonic stem cell

value: 30 ng Shiga toxin

value: 24 hours post injection


title: HTM93-S2


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_7d_Rep1

value: midgut

value: adult

tag: Sex

value: Female


title: Injected with PBS as control-24hr [PB24c]

source_name: organoid_injected with PBS as control-24hr

tag: cell type source

value: PBS


title: biopsy Crohn's inactive; sCD24i

tag: status

tag: smoking


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_1d_Rep3

value: 1 day

tag: growth condition

value: normal

tag: treatment

value: deltaIRBIT


title: HTM93-C1

value: Human Trabecular Meshwork Cells


title: biopsy Crohn's active; sCD24a

value: colonic biopsy

value: Crohn's Disease


title: Adult-femalepool-HATTseq

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

description: This library was not used in expression table, rather it was used to confirm data.

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Xenopus tropicalis genome using the aligner torrent mapper version 3.4.1. The ends of mapped reads within 24bp of each other on the same strand were clustered to detect poly(A) sites.
Genome_build: Xenopus tropicalis v9.1
Supplementary_files_format_and_content: .txt files reporting the poly(A) sites and  transcriptional start sites

organism: Xenopus tropicalis

source_name: Whole body

extract_protocol:
HATT-seq library was constructed based on our protocols. The HATT-seq method includes several major steps: poly(A)+ RNA enrichment, 1st strand cDNA synthesis, fragmentation,circularization,size selection and PCR amplification
Total RNA was harvested using Trizol reagent.

value: Whole body

value: Adult


title: Injected with PBS as control-24hr [PB24b]

value: H1 (WA01) NIH Registration#0043

tag: time post injection


title: Adult-male5-WTTSseq

extract_protocol:
WTTS-seq libraries were constructed based on our protocols. The WTTS-seq method includes several major steps: fragmentation, poly(A)+ RNA enrichment, 1st strand cDNA synthesis, size selection and PCR amplification
Total RNA was harvested using Trizol reagent.

tag: tissue


title: Injected with PBS as control-24hr [PB24a]

value: Human Intestinal Organoid


title: Adult-male4-WTTSseq


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_1d_Rep1

city: Bethesda

last: Arnaoutov

address: 49 Convent Dr, Bldg 49 Room 5A10

institute: NICHD

data_processing:
We used Illumina Casava1.8.2 for basecalling
Shortreads from RNA-Seq were mapped onto Drosophila Reference Genome 6 (PMID: 25589440) using TopHat 2.1.1 (PMID: 23618408) with -g 1 and -G parameters with FlyBase gene annotation model 6.12.
We used HTSeq 0.6.1p1 (PMID: 25260700) to measure gene-level read counts with the “-s reverse” option.  We provide Cufflinks 2.2.1-generated (PMID: 23222703) FPKM values (Fragments Per Kilobase of transcript per Million mapped reads) in this GEO submission that we prepared.  We used the -G, -u, and -b parameters.
Genome_build: Drosophila Reference Genome Release 6 (Berkeley Drosophila Genome Project)
Supplementary_files_format_and_content: Gene-level expression measurements from HTSeq (read count) and Cufflinks (FPKM values) are provided in a tab-limited text format

extract_protocol:
We extracted total RNA using 1 ml of Trizol (Thrermo Fisher Scientific, Waltham, MA) as in manufacturer’s guideline.
We prepared stranded RNA libraries using Illumina TruSeq mRNA kit (Illumina, San Diego, CA).

tag: genotype


title: Adult-male3-WTTSseq

tag: developmental stage


title: RNA-Seq_50bp_SE_Female_Gut_IRBIT_1d_Rep2

tag: replicate number


title: Injected with Shiga toxin-4hr [ST4b]

source_name: organoid_injected with Shiga toxin-4hr

value: induced plueropotent embryonic stem cell

value: 4 hours post injection


title: Adult-male2-WTTSseq


title: Injected with Shiga toxin-4hr [ST4a]

value: 30 ng Shiga toxin


title: Injected with PBS as control-4hr [PB4c]

source_name: organoid_injected with PBS as control-4hr


title: Adult-male1-WTTSseq


title: Adult-female6-WTTSseq


title: HTM126-C2


title: Injected with PBS as control-4hr [PB4b]


title: Adult-female5-WTTSseq


title: Injected with PBS as control-4hr [PB4a]


title: MTO_2

city: shenzhen

first: Guanyu

last: Ji

state: GuangDong

address: 14th of middle jinxiu road

department: R&D

institute: GENEDOHEALTH

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BosTau6 whole genome using bwa-0.7.7 with default parameters.
enrich information of peaks was analysised using MACS2
Genome_build: Angus cattle(BosTau8,A two-week-old female calf was referred to the Clinic for Ruminants at the Vetsuisse Faculty, University of Bern, Switzerland,Genome infomation can be downloaded from ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/bigZips/chromFa.tar.gz)
Supplementary_files_format_and_content: tab-delimited text files include peaks information of Angus cattle.

organism: Bos taurus

source_name: Angus cattle

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA purification kit (Promega, Madison, WI). DNA concentrations were measured by the Qubit dsDNA Broad-Range Assay (Invitrogen, Carlsbad, CA). The MBD-seq method was used to identify methylated DNA regions and elution of the captured methylated DNA was done using three salt gradients, namely low, medium and high concentrations as our previous report [48]. MethylCap kit (Diagenode，Denville, NJ) was used to obtain DNA containing methylated CpGs. Briefly, DNA was extracted and dissolved to reach 0.1μg/μl for a final volume of 40 μl in a 1.5 ml tube. The DNA was sheared into 300-500 bp fragments using the Bioruptor® Sonicator (Diagenode) and visualized on an agarose gel to verify the size of the resultant segments. A 141.8 μl capture reaction mix containing 12 μl of sheared DNA and lacking the MethylCap protein was prepared. From this preparation, 119 μl of capture reaction mix was incubated with 1 μl of diluted MethylCap protein at 40 rpm on a rotating wheel for 2 hours and at 4°C to allow the interaction.  The remaining solution (22.8 μl) was used as an input sample. Magnetic beads captured methylated DNA. Unbound DNA was washed off and the eluted DNA collected. For the elution, 150 μl of low, medium, and high concentration elution buffer was used serially per capture. These three elutions are corresponding to high, medium, and low methylation parts of the whole genome, respectively [37]. All fractions and input were purified using the MiniElute PCR Purification Kit (QIAGEN, Valencia, CA). Quantitative PCR (qPCR) (iCycler iQ PCR system, Bio-Rad, Hercules, CA) was performed in duplicate for each sample to test the enrichment efficiency. Method 2-∆∆Ct was applied to determine relative fold enrichments and compared enrichment values of a positive TGFB3 to a negative primer pair MON2, between experimental (methyl DNA) and reference (input DNA) samples.
The sequencing libraries  were constructed as follows: NEBNext® End Repair Module (NEB, Ipswich, MA) was used for the end repair of the fragmented methylated DNA, a 3’ A was added using DNA Polymerase I, Large (Klenow) Fragment (NEB), then a pair of Solexa adaptors (Illumina, San Diego, CA) was ligated to the repaired ends by T4 ligase (Promega). Filtration in a 2% agarose gel was used to select fragments (DNA plus adaptors) from 200 to 500bp. PCR enriched purified DNA templates were amplified by Phusion® Hot Start High-Fidelity DNA Polymerase (NEB). After purification, DNA quality was examined. The DNA library was diluted and the concentration double-checked using the Qubit assay (Life Technology). A total of 12 libraries were constructed for three gradient-eluted DNA from two replicates of two groups. Sequencing analysis was performed in the Solexa 1G Genome Analyzer (Illumina) according to manufacturer protocols.Finally, the libraries identified by the 6-bp index were sequenced at 50 bp squence read using an IlluminaHiSeq 2000 sequencer.

value: longissimus dorsi

tag: library construction elute

value: middle gradient

tag: beef toughness

value: tough


title: Adult-female3-WTTSseq


title: biopsy Crohn's inactive; sCD18i

tag: patient

tag: condition

value: Non-inflamed

value: Male

value: No


title: biopsy Crohn's active; sCD18a

value: Inflamed

tag: age


title: biopsy Crohn's active; sCD22a


title: MTO_1


title: MTE_2

value: tender


title: Adult-female1-WTTSseq


title: Input DNA WT3

city: Oxford

first: Satish

last: Adhikari

state: MS

address: 415 Shoemaker Hall

institute: University of Mississippi

data_processing:
FastQC v0.10.1
Trimmomatic 0.35
Bowtie2 version 2.2.9
IGVtools and bamCompare
MACS2
Supplementary_files_format_and_content: bw, peaks, bed

organism: Brevundimonas subvibrioides

source_name: Input DNA WT3

growth_protocol: PYE medium at 30 degree Celcius

extract_protocol:
Wild-type cells were grown to mid-log stage and molecular crosslinking was performed by adding 10 mM sodium phosphate (pH 7.6) and 1% formaldehyde at room temperature for 10 min, followed by incubation on ice for 30 min. Crosslinking was stopped by adding glycine to final concentration of 100 mM and incubated for 5 mins at room temperature followed by 15 min on ice. Cells were centrifuged at 5000 x g at 4oC for 5 mins. The supernatant was removed, and cells were resuspended in 1 ml of 1X phosphate buffered saline (PBS, pH 7.4). This step was repeated 2 more time and cells were finally resuspended in 500 µL of TES buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 100 mM NaCl) to which 2 µL of 20,000 U/µL lysozyme was added and the solution was then incubated for 15 min at room temperature. ChIP buffer (16.7 mM Tris-HCl (pH 8.1), 167 mM NaCl, 1.1% Triton X-100, 1.2 mM EDTA) containing Protease inhibitors (Roche cOmplete EDTA-free tablets) solution (prepared as per manufacture’s instruction) was prepared and 500 µL was added. After incubating for 10 mins at 37°C, the lysates were sonicated on ice to generate DNA fragments of 0.3–0.5 kbp (assessed by agarose gel electrophoresis) followed by centrifugation at 14000 x g for 5 mins at 4oC. Supernatant was collected and the protein concentration in the supernatant was measured by Pierce BCA protein assay kit (Thermo Scientific). A protein solution containing 500 µg was diluted to a final volume of 1 mL using ChIP buffer (containing protease inhibitor) with 0.01% SDS, and pre-cleared with 80 µL of Protein-A agarose (Invitrogen)(pre-blocked with 100 µg bovine serum albumin (BSA) overnight) for 1 hr at 4oC in a shaking platform. After centrifugation (3000 x g, 1 min), supernatant was collected and 10% of the supernatant was stored at -80 °C and used as total chromatin input DNA. Anti-GcrA sera (1:500 dilution) was added to the remaining supernatant with 80 µl of protein-A agarose (Invitrogen) (pre-blocked with 100 µg BSA overnight) and incubated at 4°C overnight. The pellet was washed with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl) followed by centrifugation (5000 x g, 2 mins) at 4oC and the supernatant was discarded. This washing step was repeated with high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)) and finally twice with TE buffer (10 mM Tris-HCl (pH 8.1),1 mM EDTA). Elution was performed twice from the beads with 250 µL of freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3) followed by addition NaCl to a final concentration of 300 mM as well as 2 µl of RNase A (10mg/ml) (Thermo scientific). Reverse crosslinking was done overnight by incubating at 65 °C. Samples were then incubated at 45 °C for 2 hr with 5 µL of Proteinase-K (20 mg/ml) in the presence of 40 mM EDTA (pH 8.0) and 40 mM Tris-HCl (pH 6.8). Phenol:chloroform:isoamyl alcohol (25:24:1) was used for DNA extraction which was followed by addition of 1/10 volume of 3M sodium acetate (pH 5.2), 100 µg glycogen and 1 volume of cold isopropanol. The solution was stored -20°C overnight. Next day, centrifugation (16000 x g, 2 min) was done to pellet glycogen containing DNA and washed with 75% ethanol followed by centrifugation (16000 x g, 2 min) twice and finally resuspended in 100 µl of TE buffer (pH 8.0).
The raw Illumina 2x75bp pair-end reads were quality checked using FastQC v0.10.1, followed by adapter trimming and quality clipping by Trimmomatic 0.35. Any reads with start, end or the average quality within 4 bp windows falling below quality scores 18 were trimmed. The clean reads were aligned to the reference genome Brevundimonas subvibrioides ATCC 15264  by Bowtie 2 version 2.2.9.  Library insert size was checked by Picard Tool (https://broadinstitute.github.io/picard/). Library complexity was checked by NRF (nonredundancy fraction), defined as the number of unique start positions of uniquely mappable reads divided by number of uniquely mappable reads. IGVtools and bamCompare from deepTools were employed for comparing two BAM files based on the number of mapped reads. First the genome is partitioned into bins of equal size and then the number of reads in each bin is counted. The log2 value for the ratio of number of reads per bin of each sample was reported for IGV visualization and compared between each pair. With 95% correlation, three biological replicates were combined for peak identification. MACS2 was used for peaks calling with 0.05 FDR cutoff.

tag: strain

value: WT

tag: fraction

value: Before IP

tag: antibody

value: Absent


title: Input DNA WT2

source_name: Input DNA WT2


title: Adult-femalepoolR2-WTSSseq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Xenopus tropicalis genome using the aligner torrent mapper version 3.4.1. The starts of mapped reads within 20bp of each other on the same strand were clustered for transcriptional start sites detection.
Genome_build: Xenopus tropicalis v9.1
Supplementary_files_format_and_content: .txt files reporting the poly(A) sites and  transcriptional start sites

extract_protocol:
WTSS-seq libraries were constructed based on our protocols. The WTSS-seq method includes several major steps: rRNA depletion, 1st strand cDNA synthesis, size selection and PCR amplification
Total RNA was harvested using Trizol reagent.

value: Whole body

value: Adult


title: LTO_2

value: low gradient


title: MTE_1


title: Adult-femalepoolR1-WTSSseq


title: Hypoxia day 10 rep 2 [5-hmC]

city: Chicago

first: Lucy

last: Godley

state: IL

address: 5841 S. Maryland Ave. MC 2115

institute: University of Chicago

data_processing:
fastq reads were aligned to hg19 reference genome with BWA/0.7.17
Peaks were called by MACS2 for each sample using input as control
Numbers of reads in each peak quantified by Htseq-count
Counts normalized to FPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files containing peak positions and calculated FPKM value of each peak

source_name: Bone marrow derived HSPCs

growth_protocol: Human primary erythroblasts were generated by culturing CD34+ early hematopoietic stem and progenitor cells initially isolated from growth factor-mobilized peripheral blood (purchased from ALL Cells, Inc.) using a CliniMacs device. The culture contained 15% fetal bovine serum, 15% human serum, Isocove’s modified Dulbecco’s medium (IMDM), 10 ng/ml interleukin-3, 2 units/ml EPO, and 50 ng/ml SCF. During the initial 8 days of culture, cells were fed on days 3 and 6 by adding equal volumes of fresh culture media supplemented with growth factors. However, no new interleukin-3 was added after the initial addition on day 0, and the amount of SCF added to the fresh media was gradually decreased at each feeding (day 3, 25 ng/ml; day 6, 10 ng/ml; day 8, 2 ng/ml). The amount of EPO added was 2 units/ml during each feeding until d8 of culture. Cells were fed one more time on day 10 of culture by adding equal volumes of fresh media with only EPO (2 units/ml) during this final feeding. Cells were collected at various time points during the culture and stained with benzidine and hematoxylin  and Flow cytometry was done with CD71 and GlyA  to monitor the differentiation program.

extract_protocol:
DNA was from cell pellets were sheared to 300bp. 5-hmC was labeled with UDP-6'-azide-glucose by T4 glucosyltransferase, then biotin-S-S-DBCO via Click reaction. 5-hmC containing DNA fragments were then captured using streptavidin beads, washed, released from beads by DTT cleavage of S-S bond, and purified for sequencing
Library was prepared with standard Illumina protocol by the University of Chicago Sequencing Core

treatment_protocol: normoxia (21% O2) vs hypoxia (1% O2)

tag: time point

value: Day 10

value: 1% oxygen


title: Adult-female4-WTTSseq


title: Input DNA WT1

source_name: Input DNA WT1


title: LTO_1


title: Hypoxia day 10 rep 1 [5-hmC]


title: Adult-female2-WTTSseq


title: Adult-male6-WTSSseq


title: Hypoxia day 7 rep 2 [5-hmC]

value: Day 7


title: IP/WT3

value: After IP

value: 1:500 dilution of Anti GcrA antibody


title: LTE_1

value: longissimus dorsi


title: LTE_2


title: IP/WT2


title: Injected with Shiga toxin-4hr [ST4c]

tag: cell line

value: H1 (WA01) NIH Registration#0043

tag: cell type source

value: Human Intestinal Organoid

tag: cell type

value: induced plueropotent embryonic stem cell

value: 30 ng Shiga toxin

value: 4 hours post injection


title: IP/WT1

value: WT


title: Adult-male5-WTSSseq


title: Hypoxia day 7 rep 1 [5-hmC]

tag: treatment


title: ccrM3

data_processing:
FASTQC
Trimmomatic
Bowtie2
DEseq2
Supplementary_files_format_and_content: countstable.txt, DEGList

extract_protocol:
Total RNA from mid log stage cells was extracted using Max Bacterial Enhancement Reagent (Ambion) with TRIzol reagent (Ambion) and PureLink RNA Mini Kit (Invitrogen). The concentration was measured using a Nanodrop 2000 and sent for sequencing at the Center for Genomics and Bioinformatics at Indiana University, Bloomington. RNA integrity was assessed by an Agilent 2100 Bioanalyzer (Agilent Technologies). Messenger RNA enrichment was done by removing rRNA using MICROBExpress rRNA removal kit (Ambion). Before library preparation, cDNA was synthesized complementary to mRNA using random primers and Reverse Transcriptase. Second strands complementary to newly synthesized strands were synthesized, creating a double stranded DNA from the mRNA template.
cDNA was used for library preparation using Nextera XT DNA Library Prep Kit (Illumina) followed by Illumina sequencing and analysis. After sequencing, raw reads were viewed by FASTQC, followed by adapter trimming and quality clipping by Trimmomatic and low-quality reads were discarded. Good quality reads were mapped to B. subvibrioides genome using Bowtie2. Differential gene expression analysis was performed using DEseq2 package.

value: ccrM mutant


title: Adult-male4-WTSSseq

tag: tissue


title: biopsy Crohn's active; sCD13a

value: colonic biopsy

value: Crohn's Disease

tag: status

value: Inflamed

tag: Sex

value: Female

tag: smoking

value: No


title: Hypoxia day 3 rep 2 [5-hmC]

value: Day 3

value: 1% oxygen

tag: genotype


title: Adult-male3-WTSSseq

value: Whole body

tag: developmental stage

value: Adult


title: HTO_1

value: longissimus dorsi

tag: library construction elute

value: high gradient

tag: beef toughness

value: tough


title: biopsy Crohn's inactive; sCD13i

source_name: biopsy Crohn's inactive

tag: patient

tag: condition

value: Non-inflamed

tag: age


title: ccrM2


title: Hypoxia day 3 rep 1 [5-hmC]


title: Adult-male2-WTSSseq


title: biopsy Crohn's inactive; sCD09i

value: Male

value: Yes


title: HTE_2

value: tender


title: ccrM1

value: ccrM mutant


title: biopsy Crohn's inactive; sCD03i

value: colonic biopsy


title: biopsy Crohn's active; sCD14a

source_name: biopsy Crohn's active

value: Crohn's Disease


title: Adult-male1-WTSSseq


title: Normoxia day 10 [5-hmC]

value: Day 10

value: 21% oxygen

value: WT


title: biopsy Crohn's active; sCD02i

value: Female

value: No


title: gcrA3

value: gcrA mutant


title: biopsy Crohn's active; sCD09a

value: Inflamed


title: Normoxia day 7 [5-hmC]

value: Day 7


title: biopsy Crohn's active; sCD05a


title: Adult-female6-WTSSseq

value: Whole body

value: Adult


title: gcrA2


title: biopsy Crohn's inactive; sCD14i

value: Non-inflamed


title: biopsy Crohn's active; sCD20a

value: Male


title: biopsy Crohn's inactive; sCD07i

value: Yes


title: Adult-female5-WTSSseq


title: gcrA1


title: biopsy Crohn's inactive; sCD05i


title: Adult-female4-WTSSseq


title: biopsy Crohn's inactive; sCD20i


title: Normoxia day 0 [5-hmC]

value: Day 0


title: biopsy Crohn's active; sCD03a


title: WT3


title: input  [5-hmC]


title: Adult-female3-WTSSseq


title: HTO_2

value: longissimus dorsi

value: high gradient

value: tough


title: Adult-female2-WTSSseq


title: Hypoxia day 10 rep 2

data_processing:
Sequence reads aligned to reference genome and transcriptome by Tophat2/Bowtie2
Initial quantification by Cufflinks
Statistical test by Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing genes and FPKM quantification

extract_protocol:
RNA was extracted by Trizol.
mRNA library was prepared by KAPA mRNA HyperPrep Kit.

value: Day 10

value: 1% oxygen


title: WT1

value: WT


title: Adult-female1-WTSSseq


title: biopsy Crohn's active; sCD07a

value: colonic biopsy

value: Crohn's Disease


title: Hypoxia day 7 rep 2


title: Normoxia day 3 [5-hmC]

value: Day 3

value: 21% oxygen


title: anaerobic 3

city: Helsinki

first: Hans

middle: K

last: Mattila

address: Viikinkaari 9

department: Microbiology department

country: Finland

institute: University of Helsinki

description:
DeSeq2.tsv
Phlrad1_GeneCatalog_genes_20181020.gff

data_processing:
Pre-processing of the reads was performed with Cutadapt version 1.7.1. Adapters were removed and reads were quality trimmed from the 3′ ends. Only reads that fulfilled the pairing criteria and were >50 bp in length were included in the analysis.
Data processing for samples 9-14 was conducted by BGI sequencing services
The following data processing steps were done for all samples: RNA-seq reads were mapped against the reference genome by STAR aligner version 2.4.1b guided by the genomic coordinates of gene models predicted by the BRAKER1 software.
Resulting alignment files were cleaned using Bamtools with parameters -mapQuality 255, -isMateMapped true, -isProperPair true, -insertSize "<800" and -insertSize ">-800"
Aligned reads were counted using HTSeq software. Differential expression was analyzed with DESeq2.
Genome_build: reference sequence
Supplementary_files_format_and_content: tab delimited DESeq2 file contains  raw counts and DESeq2 analysis of all 12017 differentially expressed genes of Phlebia radiata. GTF files are respective to reference genome

organism: Phlebia radiata

source_name: agar plug from P. radiata

growth_protocol: P. radiata was cultivated on 2% malt agar plates for 7-9 days. A 6 mm agar plug from P. radiata plates were transferred into cultivation flasks.

extract_protocol:
RNA was extracted with CsCl density-gradient ultracentrifugation process. Extracted RNA was purified with Nucleospin RNA clean up kit.
For samples 1-8 library was constructed with TruSeq Stranded mRNA Library Prep Kit and paired-end sequencing was done using MiSeq and NextSeq 500 sequencers (Illumina). Library construct for samples 9-14 was conducted by BGI sequencing services as followed: total RNA was treated with DNase I, magnetic beads with Olig o (dT ) were used to isolate mRNA. mRNA was fragmented with fragmantation buffer. cDNA was synthesized using the mRNA fragments as templates. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. Fragments were connected with adapters. The suitable fragments were amplified with PCR. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR system were used in quantification and qualification of the sample library. At last, the library was sequenced using Illumina HiSeq 4000.

treatment_protocol: Spare liquid was sucked out of the substrate by vacuum suction. Lignocellulose including the fungal mycelium was freezed with liquid nitrogen and ground into powder with a mortar and pestle.

tag: time (days)

tag: atmosphere

value: anaerobic

tag: carbon source

value: Spruce wood and core board


title: Testis_Transgenic_REP1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Gene expression data from transgenic (DREAM) testis cells replicate 1

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Mouse Genome 430 2.0 Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45C . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: testis, transgenic

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Freshly dissected testis from adult wild-type or DREAM transgenic mice

extract_protocol: RNA was prepared using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was quantified and the RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies

tag: strain background

value: C57BL/6 x CBA hybrid

value: constitutively active DREAM mutant

value: testis


title: Testis_Transgenic_REP2

description: Gene expression data from transgenic (DREAM) testis cells replicate 2


title: WT2


title: Testis_WildType_REP3

description: Gene expression data from wild type testis cells replicate 3

source_name: testis, wild type

value: Wild Type


title: BS-seq replicate2 of ER stage 2

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing:
For RNA-seq analysis, HISAT (v0.1.6) was used to map clean reads to rice reference genome (RGAP version 7.0). Cufflinks (v2.2.1) and Cuffdiff (v2.2.1) were used to splice transcripts and find differential expressed genes. A strict criteria (fold change>4, q value<0.01) was used to filter differentially expressed genes. For BS-seq analysis, clean reads were mapped to rice reference genome (RGAP version 7.0) by BS-seeker2 (v2.1.8). MethylKit (v3.6) was used to identify differentially methylated regions (DMRs) with win.size equal to 1000 and step.size equal to 100. To avoid bins with few cytosines, we selected bins with at least four cytosines and covered by at least ten reads. Q value less than 0.01 as well as absolute methylation difference of 0.7, 0.5, and 0.1 for CG, CHG, and CHH, respectively, were selected as Tan et al. (2016) suggested. Adjacent bins with overlapping were merged into one DMR.
Genome_build: RGAP version 7.0
Supplementary_files_format_and_content: bed files are tab-delimited text files containing gene expression profile information
Supplementary_files_format_and_content: diff.txt files are blank-delimited text files containing differentially methylated region information

organism: Oryza sativa Japonica Group

source_name: rice embryonic root initials

growth_protocol: Rice (Oryza sativa spp japonica) material used in this study is from ‘Hwayoung’ (HY) background. For germination culture, seeds were surface-sterilized and germinated in medium containing 0.8% agar supplemented with 3% (w/v) sucrose at 28°C (in light) and 24°C (in dark) with a 14-h-light/10-h-dark cycle. For growth in field, germinated rice seedling was transferred to greenhouse at 25–30 °C under 14-h-light followed by 10-h-dark.

extract_protocol:
Twelve µm sections of crown, lateral, and embryonic root initials tissues were put onto RNase-free PEN membrane glass slide (Carl Zeiss, 415190-9041-000). Lasser catpture microdissection (LCM) was performed using the ZEISS PALM MicroBeam system.The RNA of dissected tissues was isolated with RNeasy Plus Micro Kit (Qiagen, 74034). The DNA of dissected tissues was isolated with DNA Micro Kit (Qiagen, 56304).
For RNA-seq library construction, Smart-seq v4 Ultra Low Input RNA Kit (Takara, 091817) was used for amplifying purified mRNA. The amplified DNA was sheared to 200-500 bp range by sonication and purified with AMPure XP beads. 1 μg DNA was used for following library construction. Purified DNA was end repaired, added with adenylate in the 3’ ends, ligated with adapters, and amplified with PCR for 7-8 cycles with the reagents from TruSeq® ChIP Sample Preparation Kit (Illumina). For BS-seq library construction, Bisulfite conversion was performed by utilizing Zymo EZ Methylation Direct Kit (Zymo, D5020). Converted DNA was purified with PureLink PCR Purification Column Kit (Invitrogen, K210012) with minor modification (add M-Desulphonation Buffer to the column and hold for 15 mins before washing) as Clark et al. (2017) suggested. The converted ssDNA was then used for following BS-seq libraries construction with TruSeq® DNA Methylation Kit (Illumina).

value: stage 2 of embryonic root initials

tag: genotype/variation

value: Hwayoung cultivar


title: Testis_WildType_REP2

description: Gene expression data from wild type testis cells replicate 2


title: HUVEC SIMVASTATIN 3

city: New Haven

last: chun

address: 300 George St Room 770H

institute: Yale University

description:
SAMPLE 6
5010241025_K.AVG_Signal

hyb_protocol: Samples were hybridized onto beadchips according to microRNA expression profiling protocol from Illumina.

data_processing: Background subtraction and quantile normalization were performed using the Illumina GenomeStudio package.

source_name: HUVEC SIMVASTATIN

label_protocol: Samples were labeled according to microRNA expression profiling protocol from Illumina.

extract_protocol: Qiagen miRNeasy per manufacturer's protocol

treatment_protocol: Treated with simvastatin for 24 hours

tag: cell type

value: HUVEC

tag: treatment

value: SIMVASTATIN


title: Hypoxia day 7 rep 1

tag: time point

value: Day 7


title: Hypoxia day 3 rep 2

value: 1% oxygen


title: anaerobic 1


title: BS-seq replicate1 of ER stage 2

tag: tissue


title: aerobic 3

value: aerobic


title: Hypoxia day 3 rep 1

value: WT


title: BS-seq replicate1 of ER stage 1

value: stage 1 of embryonic root initials


title: HUVEC SIMVASTATIN 2

description:
SAMPLE 5
5010241025_I.AVG_Signal


title: aerobic 2


title: Normoxia day 10

value: Day 10


title: Hypoxia day 10 rep 1


title: HUVEC SIMVASTATIN 1

description:
SAMPLE 4
5010241025_G.AVG_Signal


title: BS-seq replicate2 of ER stage 0

value: globular embryo  (stage0)


title: HUVEC CONTROL 3

description:
SAMPLE 3
5010241025_E.AVG_Signal

source_name: HUVEC CONTROL

value: CONTROL


title: anaerobic 2

value: anaerobic

value: Spruce wood and core board


title: Normoxia day 7

value: 21% oxygen


title: BS-seq replicate1 of ER stage 0


title: HUVEC CONTROL 2

description:
SAMPLE 2
5010241025_C.AVG_Signal


title: aerobic 1


title: Testis_Transgenic_REP3

description: Gene expression data from transgenic (DREAM) testis cells replicate 3

value: C57BL/6 x CBA hybrid

value: constitutively active DREAM mutant

value: testis


title: BS-seq replicate2 of ER stage 1

value: Hwayoung cultivar


title: Testis_WildType_REP1

description: Gene expression data from wild type testis cells replicate 1

value: Wild Type


title: Spruce 4w2

value: Spruce wood saw dust


title: Normoxia day 3

value: Day 3


title: Spruce 4w1


title: PDAC-2

city: Shanghai

first: Li

last: Feng

address: 320 Yue Yang Road

institute: Institute of Biochemistry and Cell Biology, CAS

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw fastq data was pre-processed using a common procedure. After quality filtering, sequencing reads were clipped from the 3’ adaptor allowing a minimum match of 10nt. Reads unable to match the 3' adaptor sequence or with lengths shorter than 17 bp were discarded.
The useful reads were mapped to the mouse genome by bowtie (bowite options –v 0 –k 100) (Langmead et al. 2009). The mapped genome sequences were further aligned to known miRNAs, tRNAs, rRNAs, snoRNAs and snRNAs by bowtie. The remaining 25~32 nt sequences were used to identify piRNAs following the method described previously (Inuk Jung et al 2014) with slight modifications. The clustering parameters were determined as MinReads = 4 and Eps = 2500 bp by running a series of k-dist analysis with different Eps and MinReads in our own data. After clustering all remaining 25~32nt sequences with the determined parameters, all candidate clusters were considered as piRNA clusters without any further scoring and filtering.
Only the reads that exactly matched the 5’ start site of annotated miRNAs and has ≤2 nt deletions or additional sequences derived from pri-miRNAs at the 3’ ends were counted as miRNAs. The count of each miRNAs, piRNAs and tRNA, rRNA, snRNA-derived sequences was normalized to the count of methylated spike-in. The small RNAs were mapped in the following order: miRNA, tRNA, rRNA, snoRNA, snRNA and piRNA
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: tab-delimited text files include useful reads count for each sample.

extract_protocol:
Total cellular RNA was extracted using a TRIzol reagent (Takara).
Approximately 1 µg of total cellular RNA was used to construct a small RNA library according to the Illumina protocol
High-throughput RNA sequencing was performed using a Hi-Seq 2000 with 50 running circles (Genergy Biotechnology)

tag: cell line

value: PDAC

value: wild type


title: PDAC-1

tag: genotype


title: BS-seq replicate2 of LR stage 1

source_name: rice lateral root initials

value: stage 1 of lateral root initials


title: PDAC-2_NaIO4

source_name: PDAC-sample2 NaIO4 added


title: BS-seq replicate2 of LR stage 2

value: stage 2 of lateral root initials


title: Spruce 2w3

value: aerobic


title: Hypoxia #2

source_name: K562 cells

growth_protocol: RPMI 1640 with 10% FBS

extract_protocol:
Fixed chromatin was sheared for HIF-1alpha ChIP. ChIPed DNA was reverse-crosslinked and purified for sequencing
Library was prepared with standard Illumina protocol by the University of Chicago Sequencing Core

treatment_protocol: normoxia (21% O2) vs hypoxia (1% O2) for 72 hours

value: erythroid leukemia

value: 1% oxygen

tag: treatment length

value: 72 hours

tag: antibody

value: Rabbit polyclonal to HIF-1 alpha

tag: antibody catalog number

value: ab2185 (Abcam)


title: Spruce 2w2


title: Normoxia day 0

value: Day 0

value: 21% oxygen

value: WT


title: PDAC-1_NaIO4

source_name: PDAC-sample1 NaIO4 added


title: HUVEC CONTROL 1

first: hyung

description:
SAMPLE 1
5010241025_A.AVG_Signal

value: HUVEC

value: CONTROL


title: Normoxia #2


title: BS-seq replicate1 of LR stage 1

value: Hwayoung cultivar


title: Spruce 2w1

value: Spruce wood saw dust


title: Malt extract 3

value: semi-aerobic

value: malt extract


title: Normoxia #1


title: Hypoxia #1


title: BS-seq replicate1 of LR stage 0

value: cell layer from where lateral root initiates  (stage0)


title: Malt extract 2


title: input

tag: antibody catalog number:


title: BS-seq replicate1 of LR stage 2

value: stage 2 of lateral root initials


title: Malt extract 1


title: BS-seq replicate2 of CR stage 2

source_name: rice crown root initials

value: stage 2 of crown root initials


title: BS-seq replicate1 of CR stage 2