title: E75Exe_WGBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using using bsmap(v 2.89) with parameter “--s 16 -v 0.1 -n 1 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters, and output bed format files are transformed to tab-delimited text files using custom python scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG site.

extract_protocol:
For MII oocyte and cleavage-stage embryos, the zona pellucida of embryos was removed by 0.5% pronase E (Sigma). Then the embryo was incubated in Ca2+ free CZB for 5 min. Polar bodies were removed by gentle pipetting using an inner diameter of 120 μm fire polished glass needle. For ICM and TE isolation, the zona pellucida of blastocysts was removed by 0.5% pronase E (Sigma). They were then incubated for 20 min in Ca2+ free CZB，the tight junctions TE cells and ICM cells were separated by gently pipetting in a pipette with a diameter of 40-60 μm.For epiblast (Epi) and extraembryonic ectoderm (Exe) isolation, embryos were cuttted at the embryonic/extraembryonic boundary using properly sharpened forceps. A fire-polished glass needle whose inner diameter is silghtly smaller than the width of the embryonic/extraembryonic fragment was used for separating epiblast or extraembryonic ectoderm from the visceral endoderm, and the epiblast or extraembryonic ectoderm were then incubated in Ca2+-free CZB for 10 min. Single cells were separated by gentle pipetting using a fire-polished glass needle with an inner diameter of 15-20 μm.100-200 cells were washed three times in 0.5% BSA-PBS solution for one reaction。
Libraries were prepared according to Pico Methyl-Seq™ Library Prep Kit (Zymo Research, D5456) following the manufacturer’s instructions


title: E65Exe_WGBS

status: Public on Apr 13 2018

type: SRA

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

country: China

institute: Tongji University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryo

tag: tissue

value: 6.5 day embyo extraembryonic ectoderm

tag: strain

value: C57BL/6 x DB/2


title: E65Exe H3K27me3 rep1_ChIP-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bwa mem command, reads that have map quality score less than 30 were removed from downstream analysis.
Peaks were called using macs14(v1.4.2) with the parameters "macs14 -g mm --nomodel --nolambda --shiftsize=73" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 callpeak function and normlized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

extract_protocol:
For MII oocyte and cleavage-stage embryos, the zona pellucida of embryos was removed by 0.5% pronase E (Sigma). Then the embryo was incubated in Ca2+ free CZB for 5 min. Polar bodies were removed by gentle pipetting using an inner diameter of 120 μm fire polished glass needle. For ICM and TE isolation, the zona pellucida of blastocysts was removed by 0.5% pronase E (Sigma). They were then incubated for 20 min in Ca2+ free CZB，the tight junctions TE cells and ICM cells were separated by gently pipetting in a pipette with a diameter of 40-60 μm.For epiblast (Epi) and extraembryonic ectoderm (Exe) isolation, embryos were cuttted at the embryonic/extraembryonic boundary using properly sharpened forceps. A fire-polished glass needle whose inner diameter is silghtly smaller than the width of the embryonic/extraembryonic fragment was used for separating epiblast or extraembryonic ectoderm from the visceral endoderm, and the epiblast or extraembryonic ectoderm were then incubated in Ca2+-free CZB for 10 min. Single cells were separated by gentle pipetting using a fire-polished glass needle with an inner diameter of 15-20 μm.500 cells were washed three times in 0.5% BSA-PBS solution. Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to KAPA Hyper Prep Kit for illumina platform (kk8504)

treatment_protocol: For gene knockdown，small interference RNAs (siRNAs) against mouse Chaf1a, Sumo2, Setdb1, Ube2i and Zfp809 were diluted in nuclease-free water to 20 μM. The siRNAs for a given gene were mixed for knock-down, with a working concentration of 5 μM. Oocytes were injected with approximately 10 pL of siRNAs using a Piezo-driven micromanipulator. Allow oocytes to recover for at least 1 h in the incubator prior to Intracytoplasmic sperm injection (ICSI). The sperm head was then injected into the oocyte according to the method described previously (Kimura and Yanagimachi, 1995). The injected embryos were observed and summarized from the 2-cell stage to blastocyst stage.

tag: chip antibody

value: H3K27me3(Diagnode, pAb-069-050)


title: E75Epi_WGBS

value: 7.5 day embyo epiblast


title: ESC H3K27me3 rep1_ChIP-seq

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells

value: mouse ES cell R1


title: ESC H3K9me3 rep2_ChIP-seq


title: ESC H3K27me3 rep2_ChIP-seq


title: E65Epi_WGBS

value: 6.5 day embyo epiblast


title: E65Epi H3K9me3 rep2_ChIP-seq


title: E65Exe H3K4me3 rep2_ChIP-seq

value: H3K4me3(Cell signaling Technology, #9727)


title: TE_WGBS

value: trophoblast


title: ESC H3K4me3 rep2_ChIP-seq


title: ICM_WGBS

value: inner cell mass


title: ESC H3K4me3 rep1_ChIP-seq


title: morula_WGBS

value: morula embro


title: TE H3K9me3 rep2_ChIP-seq


title: E65Epi H3K4me3 rep2_ChIP-seq


title: TE H3K9me3 rep1_ChIP-seq


title: 8-cell_WGBS

value: 8-cell embryo


title: ICM H3K9me3 rep2_ChIP-seq


title: 4-cell_WGBS

value: 4-cell embryo


title: Late 2-cell_WGBS

value: late 2-cell embryo


title: ICM H3K9me3 rep1_ChIP-seq


title: Early 2-cell_WGBS

value: early 2-cell embryo


title: morula H3K9me3 rep2_ChIP-seq

value: morula embryo


title: Zygote_WGBS

value: zygote


title: 8-cell H3K9me3 rep2_ChIP-seq


title: 4-cell H3K9me3 rep2_ChIP-seq


title: 8-cell H3K9me3 rep1_ChIP-seq


title: 72_1_2

city: Panajim

first: vishal

last: gupta

state: Goa

address: Dona Paula

department: Biological Oceanography

country: India

institute: CSIR-National Institute of Oceanography

library_source: transcriptomic

data_processing:
FASTQ quality check through base quality score distribution, average base content per read and GC distribution in the read
Illumina adapters were removed, reads with average quality score less than 20 were fileterd, removed non-coding RNAs and mtRNA and 5' end were trimmed by Cutadapt, Sickle and Bowtie2
Reads were assembeled by Trinity2.0.6
Transcripts with FPKM>1 were taken into account for differential expression studies
Reads were aligned to assembled transcriptome using Bowtie2 and differential gene expression analysis was carried out using DESeq
Genome_build: Assembly.fasta
Supplementary_files_format_and_content: fold change, p value and read count

molecule: total RNA

organism: Ulva lactuca

source_name: Ulva lactuca thalli

growth_protocol: The algal thalli were desiccated for 24 h, 36 h and 72 h at a moisture condition of 20%. Afterwards, the thalli were resubmerged to seawater. The transcriptome profile was carried out at each time point of desiccation and resubmergence.

extract_protocol:
RNA was extracted following the protocol of commercial kit from SIGMA for Plant RNA extraction
Library were constructed by True-seq kit

treatment_protocol: Desiccation and submergence

value: thalli

tag: treatment

value: Resubmerg for 1 h after desiccation period of 72 h


title: 4-cell H3K9me3 rep1_ChIP-seq


title: 2-cell H3K9me3 rep2_ChIP-seq

value: 2-cell embryo


title: 2-cell H3K9me3 rep1_ChIP-seq


title: zygote H3K27me3 rep2_ChIP-seq

value: H3K27me3(Diagnode, pAb-069-050)


title: zygote H3K9me3 rep2_ChIP-seq


title: zygote H3K27me3 rep3_ChIP-seq


title: zygote H3K9me3 rep1_ChIP-seq


title: zygote H3K4me3 rep2_ChIP-seq


title: zygote H3K4me3 rep1_ChIP-seq


title: zygote H3K27me3 rep1_ChIP-seq


title: zygote Input


title: 36_1_2

value: Resubmerg for 1 h after desiccation period of 36 h


title: 72_0

value: Desiccation for 72 h


title: 24_1_2

value: Resubmerg for 1 h after desiccation period of 24 h


title: 24_6

value: Control (always submerg)


title: 36_0

value: Desiccation for 36 h


title: morula H3K9me3 rep1_ChIP-seq


title: 24-0

value: Desiccation for 24 h


title: sperm Input

source_name: sperm

value: sperm


title: MII Oocyte H3K9me3 rep1_ChIP-seq

source_name: MII Oocyte

value: MII Oocyte


title: MII Oocyte H3K9me3 rep2_ChIP-seq


title: sperm H3K9me3 rep2_ChIP-seq


title: sperm H3K9me3 rep1_ChIP-seq


title: EM3016_2

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
RNA-seq reads were mapped to the Salmonella_enterica genome (GI:16763390, NC_003197.1) using the Stampy aligner with default settings.
Differential expression was estimated using the R library DESeq
Genome_build: ASM694v1
Supplementary_files_format_and_content: The processed file in .txt format include gene IDs, gene names and reads per gene for each of the samples

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: S. Typhimurium planktonic culture, ΔrfaL

growth_protocol: LB medium at 37°C and 140 rpm until OD600=2.0.

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012).

treatment_protocol: Cells from 2 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation. The RNA was stored at -70°C.

tag: genotype/variation

value: {delta}rfaL


title: WT_2

source_name: S. Typhimurium planktonic culture, wildtype

value: Wild-type


title: WT_1


title: EM3092_1

source_name: S. Typhimurium planktonic culture, ΔrfaG

value: {delta}rfaG


title: EM3094_1

source_name: S. Typhimurium planktonic culture, ΔrfaD

value: {delta}rfaD


title: EM3016_1


title: EM3092_2


title: EM3094_2


title: Non-granuloma-associated crypt sort-372

status: Public on Apr 12 2018

city: San Francisco

first: Adam

middle: K

last: Savage

state: CA

address: 513 Parnassus Ave

country: USA

institute: University of California San Francisco

data_processing:
Sequence alignment and splice junction estimation was performed using STAR_2.4.0j
Mappings were restricted to those that were uniquely assigned to the mouse transcriptome, as provided by Ensembl (Flicek, et al., 2014) and aggregated on a per-gene basis
Variance and differential expression assessed using DESeq2 (Anders and Huber, 2010)
Genome_build: Ensembl Mouse GRCh38.78
Supplementary_files_format_and_content: Tab separated values

molecule: polyA RNA

source_name: Sorted intestinal crypt epithelium

extract_protocol:
Five wild-type mice were infected with H. polygyrus and six days later 1 mm punch biopsies from granuloma and non-granuloma tissue were taken, pooled by tissue, digested, and sorted for DAPI(lo) CD45(–) EpCAM(+) CD44(+) crypt epithelial cells. Total RNA from sorted cells was prepared using the Qiagen RNeasy Mini kit. RNA quality was assessed using a Bioanalyzer and submitted for downstream processing.
Illumina Truseq Stranded mRNA Library Prep Kit

treatment_protocol: ~200 H. polygyrus L3 larvae delivered i.g. 6 days prior to analysis.

value: small intestine duodenum

value: wild-type

value: H. polygyrus day 6

tag: location

value: Non-granuloma


title: Non-granuloma-associated crypt sort-359


title: Granuloma-associated crypt sort-359

value: Granuloma


title: Non-granuloma-associated crypt sort-336


title: Granuloma-associated crypt sort-372


title: Granuloma-associated crypt sort-316


title: Non-granuloma-associated crypt sort-361


title: Granuloma-associated crypt sort-336


title: Non-granuloma-associated crypt sort-316


title: RNAseq_cKit_WT_rep1

city: Cincinnati

first: Satoshi

last: Namekawa

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
Briefly, reads were mapped to the hg19 genome and RefSeq-based transcriptome using RNA-STAR (v. 2.4.2a and assigned to the RefSeq genes  using the BioWardrobe algorithm.
For ChIP-Seq, reads were mapped using BowTie and islands were identified using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes RPKM values for each sample

source_name: c-Kit+ spermatogonia

extract_protocol:
none provided by the submitter
none provided by the submitter

value: testis

tag: age

tag: genotype

value: wild type

tag: biowardrobe ides


title: Input_RS_Scml2KO_rep2

source_name: Round spermatides

value: adult


title: RNAseq_cKit_WT_rep2


title: Input_RS_WT_rep1


title: Input_RS_WT_rep2


title: Input_Thy1_WT_rep1

source_name: Thy1+ spermatogonia


title: Input_Thy1_WT_rep2


title: Input_PS_WT_rep2

source_name: Pachyten spermatocytes


title: Input_RS_Scml2KO_rep1


title: Input_PS_WT_rep1


title: H3K4me3_RS_Scml2KO_rep2


title: Input_PS_Scml2KO_rep1


title: Input_PS_Scml2KO_rep2


title: H3K4me3_RS_WT_rep2


title: H3K4me3_RS_WT_rep1


title: H3K4me3_cKit_WT_rep1


title: H3K4me3_RS_Scml2KO_rep1


title: H3K4me3_PS_WT_rep2


title: H3K4me3_Thy1_WT_rep2


title: H3K4me3_Thy1_WT_rep1


title: H3K4me2_RS_Scml2KO_rep2


title: H3K4me2_RS_WT_rep1


title: H3K4me2_PS_Scml2KO_rep1


title: H3K4me2_RS_Scml2KO_rep1


title: H3K4me2_PS_Scml2KO_rep2


title: H3K4me2_cKit_WT_rep1


title: H3K4me2_Thy1_WT_rep2


title: H3K27me3_RS_Scml2KO_rep1


title: H3K4me2_Thy1_WT_rep1


title: H3K4me3_PS_Scml2KO_rep2


title: H3K4me3_PS_WT_rep1


title: H3K27me3_RS_WT_native


title: H3K27me3_PS_Scml2KO_native


title: H3K27me3_PS_Scml2KO_rep1


title: H3K4me2_RS_WT_rep2


title: H3K27me3_PS_Scml2KO_rep2


title: H3K27me3_RS_WT_rep2


title: H3K27me3_RS_Scml2KO_native


title: H3K27me3_RS_Scml2KO_rep2


title: H3K27me3_PS_WT_rep1


title: H3K27me3_Thy1_WT_rep2


title: H3K27me3_PS_WT_native


title: H3K4me2_PS_WT_rep2


title: H3K4me3_PS_Scml2KO_rep1


title: H3K27me3_PS_WT_rep2


title: H3K27me3_cKit_WT_rep1


title: H3K27me3_Thy1_WT_rep1


title: H3K4me2_PS_WT_rep1


title: H3K27me3_RS_WT_rep1


title: AMA MII - 4

city: Davis

first: Pablo

middle: Juan

last: Ross

address: 1 Shields Avenue

department: Animal Science Department

institute: UC Davis

description:
Sample 18
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv

data_processing:
Illumina Casava software used for basecalling.
Raw reads were imported into CLC Genomics Workbench (CLC, v7.5.1; Qiagen, USA) and trimmed for the Clontech IS PCR primer (5'-AAGCAGTGGTATCAACGCAGAGTAC-3’). The remaining reads for each sample were mapped to the annotated human genome (GRCh38.82) using the RNA-Seq tool within CLC with one modification to the default settings: reads mapping as broken pairs were included in mapped read counts. CLC calculated expression values for each gene as total exon reads per kilobase of transcript per million mapped reads (RPKM). Genes with an RPKM greater than 0.4 in at least three of five replicates for a minimum of one sample type were considered expressed.
Differentially expressed genes were determined in R with the DESeq2 package (v1.10.1; (Love, et al., 2014)) by analyzing total exon reads exported from CLC for only expressed genes. Library size factors for DESeq2 were manually calculated using total gene reads. Experimental designs for different comparisons included stage (GV and MII), age (YNG and AMA), day of library preparation (day 1, 2, and 3), and potential interactions: overall GV vs. MII (age + stage + prep + age:prep + stage:prep + age:stage), YNG GV vs. AMA GV, YNG MII vs. AMA MII, YNG GV vs. YNG MII, and AMA GV vs. AMA MII (stage_age + prep + stage_age:prep). Genes exhibiting an adjusted p < 0.05 and log2 fold change > 1 between different stages (GV vs. MII) irrespective of age, or an adjusted p < 0.1 and log2 fold change > 1 between age groups (YNG vs. AMA) within stage (GV or MII) were considered differentially expressed genes (DEGs).
Following variance stabilizing transformation of total exon reads data using DESeq2, a heatmap was generated for all expressed genes and for overall DEGs between GV and MII oocytes using the heatmap3 package in R (v1.1.1; (Zhao, et al., 2015)). Gene Ontology enrichment was conducted on the DEGs using Ingenuity Pathway Analysis software (IPA) with an FDR cutoff of 0.05 (Qiagen, USA). For DEGs detected between AMA and YNG MII oocytes, Gene Ontology enrichment was also examined using DAVID Bioinformatics (v6.7; (Huang da, et al., 2009, Huang da, et al., 2009)).
Variance stabilized transformed data for expressed genes from GV and MII samples were separately analyzed using the WGCNA package (Langfelder and Horvath, 2008). The following parameters were set for the blockwiseConsensusModules function within WGCNA to construct gene modules as described above: maxBlockSize = 40000, power = 19 and 17 for GV and MII samples respectively, networkType = “signed”, TOMType = “signed”, minModuleSize = 30, mergeCutHeight = 0.45, reassignThreshold = 1E-6. In addition, correspondence between gene modules and traits were then determined and significant (p < 0.05) cases were examined by IPA. Biological function and canonical pathway enrichment analysis (IPA) significance was set at a Benjamini-Hochberg multiple testing correction p-value (FDR) < 0.05.
Annotated 3’UTR sequences in the human genome were exported from CLC for each gene. Genes containing a hexanucleotide polyadenylation signal (Hex, a.k.a. PAS) within the last 30bp were analyzed for potential CP activity using the predictive tool developed by Pique et al. (2008). Predictions are determined based on presence, position, and distribution of transcript 3’UTR motifs that include the cytoplasmic polyadenylation element, Pumilio binding element, and Hex. For genes with multiple 3’UTR, results for the longest Hex-containing 3’UTR were retained unless none of the gene 3’UTR contained a Hex, in which case the longest overall 3’UTR was used.
Genome_build: GRCh38.82
Supplementary_files_format_and_content: csv files include differentially expressed genes and RPKM values (Differentially Expressed Genes and RPKM Values.csv), total gene reads for all genes (Total Gene Reads - All Genes.csv), and total exon reads for expressed genes only (Total Exon Reads - Expressed Genes Only.csv) for each Sample.

organism: Homo sapiens

source_name: AMA MII_oocyte

growth_protocol: A single verified GV and a single in vitro matured MII oocyte were collected for each of the five YNG and five AMA patients, which were subsequently processed as individual oocytes for library preparation (total single oocyte libraries = 20). GV oocytes were either processed immediately as individual GV samples, or placed into maturation medium for 24 hours (6% CO2, 5% O2, 37°C). Maturation medium was supplemented with human recombinant BDNF (3 ng/mL; Sigma Aldrich, USA), human recombinant FSH (0.1 IU/mL, Gonal F; EMD Serono, USA), estradiol (1 µg/mL; Sigma Aldrich, USA), human recombinant EGF (10 ng/mL; Sigma Aldrich, USA), human recombinant BMP15 (100 ng/mL; R&D Systems, USA), and human serum albumin (5 mg/mL; Cooper Surgical, USA). After incubation, oocytes were examined for the presence of a polar body to confirm maturation and then processed individually as MII samples.

extract_protocol:
Individual GV and MII human oocytes were exposed to hyaluronidase (80 units/ml; Sigma Aldrich, USA) and manipulated with a Stripper (Origio, USA) tip to remove all remaining cumulus cells, and then washed three times in Dulbecco’s phosphate buffered saline with 0.01% PVP (Sigma Aldrich, USA). Samples were stored in PicoPure RNA extraction buffer (10 µL), heated to 42°C for 30 minutes, and subsequently stored at -80°C until total RNA purification as per manufacturer’s protocol (Thermo Fisher Scientific, USA), which included RNAse-free DNAse treatment (Qiagen, USA).
RNA eluate (9 µL/sample) was used as input for cDNA synthesis and amplification with the SMARTer Ultra Low Input RNA HV kit (Clontech, USA) following manufacturer recommendations with 13 cycles of PCR amplification. Following cDNA fragmentation with a Covaris S2 sonicator (Duty%: 10, Intensity: 5, Burst cycle: 200, Time: 5 min, Mode: frequency sweeping; Covaris, USA), the cDNA was isolated and eluted into 10 µL with the DNA Clean and Concentrator - 5 kit (Zymo Research, USA). All material isolated (3.9 ± 0.5 ng/sample) was used as input for the Thruplex DNA-seq kit (Rubicon Genomics, USA) and processed per manufacturer’s recommendations, which included 9 library amplification cycles. Illumina paired-end 100 bp sequencing was performed on a HiSeq2500 apparatus (Illumina, USA).

tag: age category

value: advanced maternal age

tag: maternal age

value: oocyte

tag: developmental stage

value: metaphase II


title: AMA GV - 5

description:
Sample 19
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv

source_name: AMA GV_oocyte

value: germinal vesicle


title: YNG MII - 5

description:
Sample 14
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv

source_name: YNG MII_oocyte

value: young


title: YNG GV - 5

description:
Sample 13
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv

source_name: YNG GV_oocyte


title: AMA GV - 3

description:
Sample 15
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: AMA MII - 2

description:
Sample 12
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: AMA MII - 3

description:
Sample 16
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: AMA GV - 4

description:
Sample 17
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: AMA GV - 2

description:
Sample 11
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: YNG MII - 4

description:
Sample 10
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: YNG GV - 4

description:
Sample 09
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: YNG MII - 3

description:
Sample 06
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: YNG GV - 3

description:
Sample 05
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: AMA GV - 1

description:
Sample 07
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: AMA MII - 1

description:
Sample 08
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: YNG MII - 1

description:
Sample 02
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: YNG GV - 2

description:
Sample 03
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: AMA MII - 5

description:
Sample 20
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: YNG MII - 2

description:
Sample 04
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: YNG GV - 1

description:
Sample 01
processed data file:
Differentially Expressed Genes and RPKM Values.csv
Total Exon Reads - Expressed Genes Only.csv
Total Gene Reads - All Genes.csv


title: asynchronous

city: Oxford

first: Hannah

middle: E

last: Mischo

address: South Parks Road

department: Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: nascent RNA

data_processing:
Library strategy: NET-seq
Libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net).
The linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.
Data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read.
88p0ldyj0e
NET-seq data have been normalized by uniquelly mapping million mapped reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph, Chromosome, Start, End, Score

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: samples 1-3 were grown in minimal complete media and arrested with 0.15 µg/ml alpha factor (sample 2) or 15 µg/ml nocodazole (sample 3) for 2-2.5hrs, prior to harvest and processing according to the NET-seq protocol. Samples 4 and 5 were induced for 3.5 hrs with 2% galactose prior to harvest and processing according to teh NET-seq protocol.

extract_protocol:
For NET-seq frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004).
For NET-seq a preadenylated RNA linker was ligated onto the 3’ end of the immunoprecipitated RNA. Fragmentation of the ligated samples by alkaline hydrolysis followed by a size selection after electrophoresis on a polyacrylamide gel allowed for the final DNA library to contain inserts of a narrow range. cDNA synthesis by reverse transcription (SuperScriptsIII (Invitrogen)) was performed with a long 5’ phosohorylated primer split by two 18 carbon spacers. Circularization of the RT product was performed with CircLigase (Epicentre) according to the manufacturer’s directions. The PCR was performed directly on the circularized product resulting in DNA with Illumina cluster generation sequences on each end and a sequencing primer binding site positioned so that sequencing would start at the 3’ end. DNA was purified from a PCR reaction that had not reached saturation (~8-10 cycles) by band extraction from a polyacrylamide gel. DNA was sequenced on the Illumina NextSeq 500 according to the manufacturer’s instructions in 75 base pair reads.

tag: cell type

value: asynchronous


title: G1- alpha Factor

description: nascent RNA


title: G2/M- nocodazole

description: nascent RNA


title: Vector

description: nascent RNA

value: vector


title: Low plane of nutrition-D76

city: Co. Meath

first: Anne-Marie

last: English

address: Dunsany

department: Department of Animal Bioscience

country: Ireland

institute: Teagasc Grange

description: Low plane of nutrition - an overall growth rate of 0.5 kg/day

data_processing:
Basecalls performed using CASAVA version 1.4
RNAsq reads were then aligned to the bovine reference genome (UMD4.0) using Spliced Transcripts Alignment to a Reference (STAR) aligner
Raw counts were enumerated using HTSEQ-count (settings: mode = union)
The raw read counts were normalized using scaling factors estimated by the Trimmed mean of M-Values (TMM) method implemented the edgeR software package. The normalised values represent read counts per million mapped reads, adjusted for sample library size.
Genome_build: Bos_taurus_UMD_4.0
Supplementary_files_format_and_content: Tab delimited txt files. First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene

organism: Bos taurus

source_name: Subcutaneous Adipose

extract_protocol:
Total RNA was extracted from frozen subcutaneous adipose tissue by homogenisation in Trizol. RNA was extracted using RNeasy Lipid Tissue Mini Kit spin columns. RNA was purified using the RNA Clean & Concentrator.
Single-end mRNA-seq libraries were constructed using the Illumina Truseq sample prep kit.

tag: breed

value: Holstein Friesian

tag: Sex

value: male

tag: diet

value: Low plane of nutrition

value: Subcutaneous Adipose


title: Sen1

description: nascent RNA


title: Low plane of nutrition-D77


title: Low plane of nutrition-D70


title: Low plane of nutrition-D68


title: High plane of nutrition-D75

description: High plane of nutrition - an overall growth rate of 1.08  kg/day

value: High plane of nutrition


title: Low plane of nutrition-D67


title: Low plane of nutrition-D66


title: Low plane of nutrition-D79


title: High plane of nutrition-D74


title: High plane of nutrition-D73


title: miR-125a-5p transfected, sample 3

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: monocytic cell line

growth_protocol: THP-1 cells were grown in RPMI+10% FBS

extract_protocol:
RNA extracted with trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with negative control microRNA mimic or miR-125a-5p mimic

value: THP-1 monocytic cells

value: transfected with miR-125a-5p mimic


title: Low plane of nutrition-D78


title: Negative control transfected, sample 3

value: transfected with negative control microRNA mimic


title: High plane of nutrition-D63


title: High plane of nutrition-D62


title: Negative control transfected, sample 2


title: Low plane of nutrition-B20

source_name: Testes

extract_protocol:
Total RNA was extracted from frozen arcuate, anterior pituitary and testes  tissue by homogenisation in Trizol. RNA was extracted using RNeasy Universal plus Kit spin columns. RNA was purified using the RNA Clean & Concentrator.
Single-end mRNA-seq libraries were constructed using the Illumina Truseq sample prep kit.

value: Testes


title: High plane of nutrition-D64


title: miR-125a-5p transfected, sample 1


title: High plane of nutrition-D71


title: High plane of nutrition-D65


title: High plane of nutrition-D61


title: Low plane of nutrition-D69


title: Negative control transfected, sample 1


title: Low plane of nutrition-B31


title: Low plane of nutrition-B15


title: Low plane of nutrition-B26


title: Low plane of nutrition-B7


title: Low plane of nutrition-B21


title: Low plane of nutrition-B50


title: High plane of nutrition-D72


title: High plane of nutrition-B38


title: miR-125a-5p transfected, sample 2


title: High plane of nutrition-B5


title: High plane of nutrition-B49


title: High plane of nutrition-B54


title: High plane of nutrition-B12


title: High plane of nutrition-B30


title: High plane of nutrition-B32


title: NHP_12_DPI_0

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Sequenced on a HiSeq 2500 with paired-end 100bp reads in dual-index format
Reads were filtered with FASTX Toolkit v0.0.14
Aligned to Genome using Bowtie 2 v2.2.6 and Tophat v2.1.0
Count Tables Generated using HTSeq v0.5.4 and Python v.2.7.3
Genome_build: Cynomolgus Macques Genome v5.0
Supplementary_files_format_and_content: Text files with raw count values from HTSeq

organism: Macaca fascicularis

source_name: Whole Blood

extract_protocol:
500ul whole blood mixed with 500 ul of TRIzol LS and purified using the PureLink RNA MiniKit
Constructed on a Sciclone G3 Liquid Handling Robot with TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: 12 Cynomolgus Macaques infected with EBOV-Makona through intranasal routes

value: Whole Blood

tag: agent

value: Ebola virus Makona

tag: route

value: IN MAD

tag: dpi


title: NHP_12_DPI_6

tag: tissue


title: NHP_11_DPI_41


title: NHP_12_DPI_10


title: NHP_11_DPI_35


title: NHP_11_DPI_28


title: Low plane of nutrition-C33

source_name: Arcuate Nucleus of the Hypothalamus

value: Arcuate Nucleus of the Hypothalamus


title: High plane of nutrition-B42


title: High plane of nutrition-A48


title: Low plane of nutrition-B2


title: NHP_11_DPI_21


title: Low plane of nutrition-C13


title: NHP_11_DPI_14


title: Low plane of nutrition-C24


title: NHP_11_DPI_3


title: NHP_11_DPI_6


title: NHP_11_DPI_0


title: Low plane of nutrition-C8


title: NHP_11_DPI_10


title: NHP_10_DPI_10


title: High plane of nutrition-B17


title: Low plane of nutrition-C43


title: NHP_12_DPI_3


title: Low plane of nutrition-C28


title: NHP_10_DPI_0


title: NHP_9_DPI_21


title: Low plane of nutrition-C55


title: NHP_10_DPI_6


title: NHP_9_DPI_14


title: NHP_9_DPI_10


title: Low plane of nutrition-C34


title: Low plane of nutrition-C41


title: Low plane of nutrition-C6


title: NHP_9_DPI_6


title: NHP_8_DPI_12


title: NHP_9_DPI_0


title: High plane of nutrition-C16


title: NHP_8_DPI_10


title: NHP_8_DPI_6


title: NHP_8_DPI_3


title: High plane of nutrition-C3


title: NHP_8_DPI_0


title: NHP_10_DPI_3


title: High plane of nutrition-C44


title: NHP_7_DPI_41


title: High plane of nutrition-C22


title: NHP_7_DPI_28


title: NHP_7_DPI_14


title: NHP_7_DPI_21


title: High plane of nutrition-C37


title: NHP_7_DPI_35


title: NHP_7_DPI_10


title: NHP_7_DPI_3


title: High plane of nutrition-C60


title: High plane of nutrition-C25


title: NHP_7_DPI_0


title: NHP_7_DPI_6


title: High plane of nutrition-C9


title: High plane of nutrition-C59


title: Low plane of nutrition-A47

source_name: Anterior Pituitary

value: Anterior Pituitary


title: NHP_6_DPI_10

value: IN Pipette


title: NHP_6_DPI_14


title: Low plane of nutrition-A35


title: Low plane of nutrition-A10


title: NHP_6_DPI_6


title: NHP_6_DPI_3


title: NHP_9_DPI_3


title: Low plane of nutrition-A40


title: Low plane of nutrition-A19


title: NHP_6_DPI_0


title: NHP_5_DPI_15


title: Low plane of nutrition-A4


title: NHP_5_DPI_14


title: NHP_5_DPI_10


title: Low plane of nutrition-A14


title: Low plane of nutrition-A46


title: Low plane of nutrition-A52


title: NHP_5_DPI_3


title: Low plane of nutrition-A27


title: H3_Sox9_2

city: Chicago

first: Christopher

last: Futtner

state: Il

address: 303 E. Superior St, Lurie 7-220

department: Endocrinology

institute: Northwestern University

description: We are submitting the data corresponding only to the Sox9 locus, including the Sox9 gene body and the 2Mb gene desert upstram of the TSS (chr11:110525649-112884857).

data_processing:
Files were trimmed for quality using trim_galore with a stringency setting of 5
Reads were aligned to the mm9 genome with bowtie using the parameters -m 1 and --best
Unmapped reads were eliminated with samtools view using -F 4 settings
Peaks were called using MACS2/2.1.0. For ATAC-seq: the --nomodel and --broad settings were used. For ChIP-seq: the --broad setting was used, H3K27ac was used as treament (-t) and H3 as control (-c)
bigwig files were created from .bdg files using BedGraphToBigWig for visualization on the UCSC genome browser. For optimal visualization, ChIP-seq replicates were concatenated to increase number of reads.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig and bedGraph files contain tracks for visualization on the UCSC genome browser

source_name: FACS-sorted Sertoli cells

extract_protocol:
Embryonic gonads were micro-dissected at according stage, removed from the mesonephros and incubated in 0.05% trypsin for 5 minutes at 37C. Gonads were then mechanically dissasociated in PBS/3% BSA and passed through a filter cap to obtain a single cell suspension. Fluorescently-labeled cells were collected by Fluorescence Activated Cell Sorting (FACS). For ATAC-seq, 60K cells were collected per replicate. For ChIP-seq, 100K cells were collected per replicate.
ATAC-seq libraries were prepared according to Buenrostro et al.2013. ChIP-seq libraries were prepared according Van Galen et al., 2016.

tag: embryonic stage

tag: sex chromosome

value: XY

tag: transgenic line

tag: chip-antibody

value: H3 Active Motif 39763


title: H3K27ac_Sox9_2

value: H3K27ac Active Motif 39133


title: NHP_6_DPI_20


title: H3K27ac_Sox9_1


title: H3_TESm_2

source_name: FACS-sorted granulosa cells

value: XX

value: TESm-CFP


title: NHP_5_DPI_0


title: High plane of nutrition-A36

value: Holstein Friesian

value: male


title: NHP_4_DPI_21


title: High plane of nutrition-A18

value: High plane of nutrition


title: NHP_4_DPI_14


title: H3_TESm_1


title: LPS treatment replicate 3

first: Xiao-Di

last: Tan

state: IL

address: 2430 N Halsted St

department: Stanley Manne Children's Research Institute

institute: Ann & Robert H. Lurie Children's Hospital of Chicago

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 GENCODE M11 whole genome using HISAT2 with default parameters
Raw counts for each gene was calculated with HT-Seq package
Normalized counts for each gene was estimated with DESeq2 software.
Genome_build: GENCODE M11
Supplementary_files_format_and_content: Comma seperated CSV files include normalized counts for each gene exported from DESeq2

source_name: small intestine

extract_protocol:
Mouse small intestine was flushed with cold PBS, and total RNA was extracted by Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were injected intraperitoneally with lipopolysaccharide (LPS, 2 mg/kg) for 24 hours. Control mice were given with saline instead.

tag: strain

value: small intestine

tag: genotype

value: wild type


title: High plane of nutrition-A39


title: Control replicate 3


title: NHP_4_DPI_10


title: H3K27ac_TESm_2


title: H3K27ac_TESm_1


title: High plane of nutrition-A29


title: LPS treatment replicate 2


title: NHP_4_DPI_6


title: Control replicate 2


title: NHP_5_DPI_6


title: High plane of nutrition-A51


title: H3_Sox9_1


title: NHP_4_DPI_0


title: High plane of nutrition-A23


title: NHP_4_DPI_3


title: ATAC_SertoliDM16


title: LPS treatment replicate 1


title: Control replicate 1


title: ATAC_SertoliDM10


title: ATAC_SertoliDM15


title: High plane of nutrition-A11


title: High plane of nutrition-A1


title: NHP_3_DPI_3


title: ATAC_GranulosaDM14


title: High plane of nutrition-A57


title: ATAC_GranulosaDM12


title: NHP_3_DPI_10


title: NHP_2_DPI_3


title: NHP_2_DPI_0


title: NHP_2_DPI_10


title: NHP_2_DPI_6


title: NHP_1_DPI_9


title: NHP_1_DPI_6


title: NHP_1_DPI_3


title: 4dpi_C_Zebrafish_Retina_RNA-seq

city: Mohali

first: Rajesh

last: Ramachandran

state: Punjab

address: Knowledge city, Sector 81, SAS Nagar, Manauli

department: Department of Biological Sciences

institute: Indian Institute of Science Education and Research, Mohali

data_processing:
Base calling: bowtie2 (version 2.2.2)
Read alignment software: Tophat program (Version 2.1.0)
cufflinks program (version 2.2.1)
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text files contain comparison of gene expression levels between different time points or treatment.

organism: Danio rerio

source_name: cyclopamine treated 4dpi retina

growth_protocol: Zebrafish were maintained at 26-28 degree C before or after retinal injury with 14-10 hours light-dark cycles.

extract_protocol:
Retinae were disected out and taken into 250uL of TRIzol reagent, and homogenised followed by aquous phase seperation by adding chloroform. RNA was precipitated from aquous phase by isopropanol mediated chilling. Finally it was solubilised in appropriate volume of water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cyclopamine treatment, post retinal imjury, fish were dipped in 10uM cyclopamine for 4days.

tag: age

value: 10 months

value: Retina

value: cyclopamine


title: NHP_3_DPI_6

value: Whole Blood

value: Ebola virus Makona


title: 4dpi_Zebrafish_Retina_RNA-seq

source_name: 4dpi retina


title: 12hpi_Zebrafish_Retina_RNA-seq

source_name: 12hpi retina


title: ATAC_GranulosaDM13


title: Uninjured_Zebrafish_Retina_RNA-seq

source_name: uninjured retina


title: sf3b4 knockdown k562 replicate 1

status: Public on Apr 11 2018

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: featureCounts_hg19_mirnas_only_mirbase_features_batch2.txt

data_processing:
Sequencing reads from small RNA-seq libraries were first trimmed of adapters using cutadapt
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the hg19 genome (UCSC assembly) using bowtie version 1.1.1 with parameters -p 8 -k 1 -m 10 -l 25 --best --chunkmbs 128
counts of reads for each miRNA were calculated from featureCounts using miRBase annotations
Genome_build: hg19
Supplementary_files_format_and_content: count file, txt

growth_protocol: cell lines were grown as previously described (Van Nostrand, 2016)

extract_protocol:
small RNAs were isolated using the mirvana kit, following manufacturer protocol for isolation of small RNAs
Illumina TruSeq small RNA sample preparation kit

treatment_protocol: shRNAs were delivered to cells via lentivirus to deplete the RBP of interest

tag: lentivirus

value: shRNA sf3b4

tag: cell line


title: sf3b4 knockdown k562 replicate 2


title: NHP_3_DPI_0

value: IN Pipette


title: ATAC_BiMaleDM22

source_name: FACS-sorted gonadal progenitor cells

value: XY


title: ATAC_BiMaleDM17


title: ATAC_BiFemaleDM25


title: ATAC_BiFemaleDM24


title: ATAC_BiMaleDM20


title: ATAC_BiMaleDM21


title: ATAC_BiFemaleDM19


title: ptbp1 knockdown k562 replicate 1

value: shRNA ptbp1


title: prpf8 knockdown k562 replicate 2

value: shRNA prpf8


title: NHP_1_DPI_0


title: ilf3 knockdown k562 replicate 2

value: shRNA ilf3


title: non-targeting control k562 replicate 4 set 2

value: shRNA non-targeting


title: hnrnpm knockdown k562 replicate 1

value: shRNA hnrnpm


title: hnrnpm knockdown k562 replicate 2


title: ATAC_BiFemaleDM23

value: XX


title: ilf3 knockdown k562 replicate 1


title: non-targeting control k562 replicate 2 set 2


title: non-targeting control k562 replicate 1 set 2


title: non-targeting control k562 replicate 3 set 2


title: High plane of nutrition-C53

value: Holstein Friesian

value: male

value: High plane of nutrition

value: Arcuate Nucleus of the Hypothalamus


title: ptbp1 knockdown hepg2 replicate 2


title: sf3b4 knockdown hepg2 replicate 2


title: ptbp1 knockdown k562 replicate 2


title: ptbp1 knockdown hepg2 replicate 1


title: ilf3 knockdown hepg2 replicate 1


title: ilf3 knockdown hepg2 replicate 2


title: prpf8 knockdown k562 replicate 1


title: prpf8 knockdown hepg2 replicate 1


title: prpf8 knockdown hepg2 replicate 2


title: non-targeting control hepg2 replicate 3 set 2


title: non-targeting control hepg2 replicate 1 set 2


title: non-targeting control hepg2 replicate 2 set 2


title: non-targeting control hepg2 replicate 4 set 2


title: lin28b knockdown k562 replicate 1

description: featureCounts_hg19_mirnas_only_mirbase_features.txt

value: shRNA lin28b


title: sltm knockdown k562 replicate 1

value: shRNA sltm


title: larp7 knockdown k562 replicate 2

value: shRNA larp7


title: larp4 knockdown k562 replicate 2

value: shRNA larp4


title: rbfox2 knockdown k562 replicate 1

value: shRNA rbfox2


title: sltm knockdown k562 replicate 2


title: rbfox2 knockdown k562 replicate 2


title: lin28b knockdown k562 replicate 2


title: larp7 knockdown k562 replicate 1


title: larp4 knockdown k562 replicate 1


title: dkc1 knockdown k562 replicate 2

value: shRNA dkc1


title: non-targeting control k562 replicate 4


title: ddx3x knockdown k562 replicate 2

value: shRNA ddx3x


title: bud13 knockdown k562 replicate 1

value: shRNA bud13


title: dkc1 knockdown k562 replicate 1


title: bud13 knockdown k562 replicate 2


title: ddx3x knockdown k562 replicate 1


title: sltm knockdown hepg2 replicate 2


title: non-targeting control k562 replicate 3


title: non-targeting control k562 replicate 2


title: sltm knockdown hepg2 replicate 1


title: sf3b4 knockdown hepg2 replicate 1

value: shRNA sf3b4


title: hnrnpm knockdown hepg2 replicate 2


title: non-targeting control k562 replicate 1


title: lin28b knockdown hepg2 replicate 1


title: rbfox2 knockdown hepg2 replicate 2


title: lin28b knockdown hepg2 replicate 2


title: larp7 knockdown hepg2 replicate 2


title: rbfox2 knockdown hepg2 replicate 1


title: larp4 knockdown hepg2 replicate 1


title: ddx3x knockdown hepg2 replicate 2


title: dkc1 knockdown hepg2 replicate 2


title: hnrnpm knockdown hepg2 replicate 1


title: ddx3x knockdown hepg2 replicate 1


title: larp7 knockdown hepg2 replicate 1


title: non-targeting control hepg2 replicate 3


title: dkc1 knockdown hepg2 replicate 1


title: non-targeting control hepg2 replicate 4


title: larp4 knockdown hepg2 replicate 2


title: non-targeting control hepg2 replicate 2


title: non-targeting control hepg2 replicate 1


title: bud13 knockdown hepg2 replicate 2


title: bud13 knockdown hepg2 replicate 1


title: Svi3_3_2

city: Uppsala

first: Dan

middle: I.

last: Andersson

address: Box 582

department: Department of Medical Biochemistry and Microbiology

country: Sweden

institute: Uppsala University

data_processing:
BGI inhouse software “filter_fq” for basecalling and trimming
Read-mapping was done with soap2.21. Mapping towards genes was done by the following parameters -m 0 -x 1000 -s 28 -l 32 -v 5 -r 2 -p 3
The gene expression values were calculated as RPKM (reads per kilobase transcriptome per million mapped reads) by the inhouse BGI pipeline.
Genome_build:  NC_000913
Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli MG1655 / Svi3-3 comp.

growth_protocol: Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics.

extract_protocol:
The cells for RNA extraction were immediately mixed with RNA Protect Bacterial reagent® (Qiagen) and processed by the RNAeasy Mini Kit (Qiagen) according to the manufacturers instructions. The cells for whole cell proteomics were chilled in ice-slush, pelleted at 14000 rpm, 4°C and the media was aspirated.  The cells were washed with 3×1.5 mL PBS with pelleting at as above in between. The final pellet was stored at -80°C until being shipped to the Proteomics Core Facility at University of Gothenburg for processing. The RNA was shipped to BGI for total RNA sequencing.
TruSeq

tag: replicates

value: Svi3-3 replicate 2 / not induced


title: Svi3_3_1

treatment_protocol: The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics.

value: Svi3-3 replicate 1 / not induced


title: WT2_IPTG

source_name: E. coli MG1655 / pCA24N, -gfp

tag: induction

value: induced 50 µM IPTG

value: WT replicate 2 / induced


title: Pf-3D7-t25, dirRNAseq

city: Nijmegen

first: Christa

last: Toenhake

state: Netherlands

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
For dirRNAseq: libraries were sequenced on a NextSeq 500 system to obtain 75bp single-end reads (TruSeq SR Cluster Kit v2) according to standard protocols of the manufacturer (Illumina). Single-end reads were mapped against the annotated P. falciparum 3D7 transcriptome from PlasmoDB release 26 using BWA samse (version 0.7.12-r1039). Single-end reads were filtered to mapping quality >= 15 (samtools version 1.2) and only uniquely mapped reads (between 9.2 and 11.6 million per library) were used for further analysis. To visualize RNA-seq data in the UCSC Genome browser, 75bp reads were additionally mapped against the annotated P. falciparum 3D7 genome from PlasmoDB version 26, filtered for uniquely mapped reads and mapping quality >= 15. Reads were separated according to the strand they mapped to (sense strand FLAG16, antisense strand FLAG0) and normalized to the number of mapped reads per million (RPM). Bedgraph files were generated (bedtools v2.20.1) and visualized in the UCSC genome browser.
The ATAC-seq libraries were sequenced for 75 bp, paired-end on a NextSeq500 system (Illumina) using NextSeq500/550 HighOutput kit V2 (75 cycles) reagents (Illumina). Raw fastq reads were first evaluated using FastQC before continuing ((Andrew, 2010) and reads obtained from the two gDNA control libraries were combined after sequencing. Paired-end libraries were mapped with BWA-mem (version 0.7.10; (Li, 2013)) against the P. falciparum 3D7 reference genome (PlasmoDB release 26; (Aurrecoechea et al., 2009; Logan-Klumpler et al., 2012)) and filtered for mapping quality >= 30 ((samtools version 1.3.1; (Li et al., 2009)). Duplicate reads were removed using Picard tools (version 1.139; (BroadInstitute)) and reads mapping to the apicoplast and mitochondrial DNA were removed as well as supplementary alignments (FLAG 2048). Finally, an in silico size selection was performed to select for read pairs with insert sizes between 50 and 150 bp (or different when indicated) and these libraries were used for further analysis (between 5.9M-9.7M reads for replicate 1; between 3.6M-6.4M per library for replicate 2; and 36.9M for the merged gDNA control library). For visualization, these libraries were converted to bedgraph files using bedtools genomecov (version 2.20.1; (Quinlan and Hall, 2010)) with the option "-pc" for paired end data and scaled per million reads (RPM). Alternatively, for genomic DNA-corrected tracks, the coverage in each of the t05 to t40 libraries (with an offset of +0.1) was divided by the coverage in the merged gDNA library (with an offset of +0.1). Bedgraph files were visualized in the UCSC genome browser (Kent et al., 2002).
ATAC-seq mapping and generation of tracks *ATAC-seq_50-150_gDNAcorr.bedGraph.gz:(01) mapping with bwa mem agains PlasmoDB release 26 of Pfalciparum 3D7 genome (02) filter for mapq => 30 with samtools view (03) remove duplicates with "picard-tools-1.139/picard.jar MarkDuplicates" with settings REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=STRICT QUIET=true (04) remove supplementary alignments (-F 2048) and select reads mapping to chromosomes using samtools view (05) manually select reads between 150 and 50 bp using awk (06) generate bedgraph file scaled per million reads using bedtools genomeCoverage with options -bga -pc -scale xx (07) generate one file with per-million-reads-coverage of ATAC library and gDNA control library using "bedtools unionbedg" with options -g $genome_noMito_NoApi -filler (08) manually calculate ratio of ATAC library over gDNA control library coverage with offset of 0.1 using awk
For MACS2 peak calling on ATAC-seq data: Step (01) till (05) of generation of *ATAC-seq_50-150_gDNAcorr.bedGraph.gz tracks, followed by:(09) manually split bam file in increments of 5bp insertsizes from 5<=50 till 145<=150 using "awk" (10) shift reads with in-house script in each sub-bamfile with +4 bp for reads aligning to plus strand and -5bp for those aligning to the minus strand (11) for every sub-bamfile generate pileup file using "macs2-2.7 pileup" with options -f BAM and --extsize [half of the original mean insert size of sub file] (12) sum coverage in from all sub-bamfiles using "bedtools unionbedg" and "awk" (13) manually scale coverage to 1M reads using "awk" (14) add offset of 0.1 to every positiong in per-million-coverage using "awk" (15) use "bdgcmp" with pe-million-coverage in gDNA control track as control (-c) and -qpois (16) call peaks using "macs2 bdgpeakcall" on output from (15) with options -c 3.0 -g 150 -l 100
Genome_build: Plasmodium falciparum 3D7 PlasmoDB release 26
Supplementary_files_format_and_content: *ATACseq_50-150_gDNAcorr.bedGraph.gz: coverage of filtered, 50-150 bp insert size ATAC-seq libraries that were prepared as replicate 1, corrected for coverage in gDNA.
Supplementary_files_format_and_content: *ATACseq_rep2_50-150_gDNAcorr.bedGraph.gz: coverage of filtered, 50-150 bp insert size ATAC-seq libraries that were prepared as replicate 2, corrected for coverage in gDNA.
Supplementary_files_format_and_content: *[alltp|tp]*peaks.bed: genomic locations of peaks for specific time point or merged over time points ("alltps"), called using MACS2 subcommand on 50-150 bp insert size, shifted ATAC-seq libraries with gDNA as control.
Supplementary_files_format_and_content: *[alltp|tp]*summits.bed: genomic locations of peak summits for specific time point or the highest scoring peak summit for merged time points, called using MACS2 subcommand on 50-150 bp insert size, shifted ATAC-seq libraries with gDNA as control.
Supplementary_files_format_and_content: *.minus_strand_bedGraph.gz: RNA-seq coverage for minus strand normalized to complete (plus and minus) library after filtering.
Supplementary_files_format_and_content: *.plus_strand_bedGraph.gz: RNA-seq coverage for plus strand normalized to complete (plus and minus) library after filtering.

organism: Plasmodium falciparum

source_name: red blood cell stage, 17-25 hours post invasion

growth_protocol: 3D7 Plasmodium falciparum blood-stage parasites obtained from the Swiss Tropical and Public Health Institute (Basel, Switzerland - a kind gift from Dr. T. Voss) were cultured RPMI medium supplemented with 10% human serum, 0.2% NaHCO3 and 2.5% human O+ red blood cells. Cultures were selected for var2csa expression (Fraschka et al., 2016) and expanded and synchronized with multiple rounds of sorbitol treatments. After a final Percoll gradient centrifugation human red blood cells, pre-filtered twice over sterile PlasmoPure (EuroProxima) filters to remove human white blood cells, were added 1.5 h later to prevent ?premature? invasion and therefore ensure better synchronicity of the culture. The time of adding blood was set as time point zero (0 hours post invasion (hpi)) and this procedure resulted in a synchronicity window of 7 h (i.e. 7h difference between the first and last invasion) for >90% of parasites. Medium was changed every ten hours but not less than ten hours before collection. Cultures were mixed with every medium change and after 20 hpi kept at 1.25% hmt. Native nuclei (for ATAC-Seq) and RNA (for dirRNA-Seq) were collected every 5 hours.

extract_protocol:
Native nuclei and RNA were collected from the pooled culture flasks of the same batch of synchronized parasites for each time point to ensure complete matching between ATAC-seq and dirRNA-seq.
ATAC-seq: Native parasite nuclei were isolated as in (Bartfai et al., 2010). In short, after lysis of RBCs by 0.05% saponin treatment and separating nuclei from parasite debris using a cell lysis buffer (CLB: 10 mM Tris-HCL pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.2% NP-40) with 0.25 M sucrose cushion. A 10 ul sized nuclei pellet was resuspended with a cut-off pipet tip in 337.5 ul CLB and for ATAC-seq replicate 1 69 ul of nuclei was used for t05 to t20 and 23 ul of nuclei was used for t25 to t40 (these volumes were based on previous tests using a dilution series of nuclei). For ATAC-seq replicate 2 we had to optimize the amount of nuclei again due to the use of a kit from a different lot and this led us to use 466 ul of nuclei for t05 and t10 and 155 ul for t15 and t20. Nuclei were brought to 10.5 ul in CLB and used in a 25 ul ATAC reaction based on (Lara-Astiaso et al., 2014) with 2 ul Tn5 transposase and 12.5 ul TD buffer (Nextera DNA Library Prep Kit, #FC-121-1030, Illumina, USA). Reactions were incubated for 1 h in a 37°C heat block. Nuclei were kept in suspension by gently tapping the tube every 10 minutes. The reaction was stopped by addition of 5 ul clean up buffer (900 mM NaCl, 300 mM EDTA), 2 ul 5% SDS and 2 ul proteinase K (Sigma-Aldrich #P6556) and incubated for 30 min at 40°C. Tagmentated DNA fragments were isolated using 2.4 sample volume of Agencourt AMPure XP beads (Beckman Coulter, #A63882, Inc. USA).
RNA isolation: Parasite cultures were immediately placed on ice and washed once with ice-cold PBS. Pelleted cultures were resuspended in RLT buffer (Qiagen, #74106) supplemented with 1% beta-mercaptoethanol and snap-frozen in liquid nitrogen. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, #74106; including RNA clean-up and two on-column DNase treatments) and PolyA-selected using the Oligotex mRNA Mini Kit (Qiagen, #70022) according to manufacturer's instructions. Subsequently, 2000ng of PolyA-selected total RNA equivalent were fragmented by alkaline hydrolysis (40mM Tris acetate pH 8.2, 100mM potassium acetate,30mM magnesium acetate) for 1min 45sec at 85°C in a 150Âµl volume and precipitated as previously described in (Hoeijmakers et al., 2013). Next, PolyA-selected RNA was cleaned from remaining genomic DNA (detected by qPCR) by two additional TURBO DNase treatments (Ambion, #AM2238).
ATAC-seq libraries: Half of the isolated DNA was used for library preparation (the other half was stored as back-up) starting with a size selection using 0.85x volumes of AMPure XP beads to enrich for fragments of 500 bp and smaller. Size-selected fragments were amplified using the KAPA HiFi HotStart ready-mix (KAPA Biosystems, #KK2602, US) and Nextera index primers (Nextera DNA Sample Preparation Index Kit, #FC-121-1012) under the following conditions: 98°C for 2 min; 16 cycles of 98°C for 20 sec, and 62°C for 3 min; 62°C for 5 min. Libraries were purified using 1x volumes Agencourt AMPure XP beads. The fragment size distribution of the libraries was evaluated in a High-Sensitivity Bioanalyzer run (Agilent, #5067-4626, US) and the size selection was repeated when there was a large proportion of fragments longer than 500 bp (t05_69.66u, t05_23.22u, t15_69.66u, t30_23.22u, t35_23.22u, t40_23.22u). To control for sequence bias, the same ATAC protocol was applied to genomic DNA from synchronous wild type 3D7 P. falciparum ring stage parasites using 547.0 ng or 60.8 ng of input DNA. All ATAC-seq libraries were KAPA quantified (KAPA Library Quantification Kit, #KR0405).
Strand-specific RNA-seq libraries: Strand-specific RNA-seq was performed as in (Kensche et al., 2015). Accordingly, first strand cDNA synthesis was performed with AT-corrected Random N9 primers (76% AT) in the presence of 0.2ug Actinomycin D (Thermo 446 Fisher Scientific). During second strand synthesis dTTPs were substituted with dUTPs to preserve strand-specific information. Next, 10 ng of each double stranded cDNA library was end repaired, extended with 3Ã¢â‚¬â„¢ A-overhangs, barcoded with NextFlex adapters (Bio Scientific, #514122) and treated with USER enzyme (NEB, #M5505L) to specifically degrade the dUTP-containing second strand. Libraries were amplified by PCR (98°C for 2min; 4 cycles of 98°C for 20sec, 62°C for 3min; 62°C for 5 min) using KAPA HiFi HotStart ready mix (KAPA Biosystems, #KM2602) and NEXTflex primer mix (Bio Scientific, #514122) and subsequently gel size-selected for 300 - 400 bp using 2% E-Gel Size Select agarose gels (Invitrogen, #G6610-02). After an additional eight cycles of amplification (see above), libraries were purified and adapter dimers depleted using 1x volume of Agencourt AMPure XP beads (Beckman Coulter, #A63880).

tag: selection

tag: developmental stage

value: late trophozoite


title: Pf-3D7-t40, dirRNAseq

source_name: red blood cell stage, 32-40 hours post invasion

value: late schizont


title: Pf-3D7-t20, dirRNAseq

source_name: red blood cell stage, 12-20 hours post invasion

value: early trophozoite


title: Pf-3D7-t35, dirRNAseq

source_name: red blood cell stage, 27-35 hours post invasion

value: medium schizont


title: Svi3_3_1_IPTG

value: Svi3-3 replicate 1 / induced


title: ORF1_2

source_name: E. coli MG1655 / pORF1

value: ORF1 replicate 2 / not induced


title: Pf-3D7-t30, dirRNAseq

source_name: red blood cell stage, 22-30 hours post invasion

value: early schizont


title: Pf-3D7-t15, dirRNAseq

source_name: red blood cell stage, 7-15 hours post invasion

value: late ring stage


title: Pf-3D7-t05, dirRNAseq

source_name: red blood cell stage, 40-5 hours post invasion

value: early ring stage


title: RRBS-Bisulfite-100bp-animal3

city: Montreal

first: Lisa

last: Boureau

state: QC

address: Sir William Osler Promenade

department: Pharmacology

country: Canada

institute: McGill University

description:
genomic DNA - double enzymatic digestion
bisulfite sequencing
[processed data files:]
CG_sites_methylation_status&RNApolII_enrichment.txt
average_methylation_level_in_H3K4me1_peaks.txt
CG_sites_differentially_methylated.txt
RRBS-Peaks-all-animals.bedgraph.txt

data_processing:
RRBS reads were aligned to cavPor3 genome using BSMap version 2.74
Duplicates were removed with Samtools  version 1.1, then the 3 alignments corresponding to the 3 independant animals were merge in one unique bam file.
Methylation level was determined for CpG sites using MethylKit
genome build: cavPor3
processed data files format and content: CG_sites_methylation_status_and_RNApolII_enrichment.txt: tab-delimited text files include genomic location of CG sites, methylation state (from RRBS, H3K4me1 ChIP-seq and RNapolII PS5 ChIP-seq)
processed data files format and content: average_methylation_level_in_H3K4me1_peaks.txt: tab-delimited text files include average methylation of CG sites in H3K4me1 peaks from RRBS and H3K4me1ChIP seq
processed data files format and content: CG_sites_differentially_methylated.txt: tab-delimited text files include the list of all CG sites differentially methylated between RRBS and H3K4me1 ChIP seq analyses
processed data files format and content: RRBS-Peaks-all-animals.bedgraph: Bedgraph file include number of reads for peaks detected with BSMap from RRBS analysis

organism: Cavia porcellus

source_name: Hippocampus

extract_protocol:
Genomic DNA was extracted from frozen and ground hippocampi using the Qiagen kit, AllPrep DNA/RNA/miRNA Universal Kit. Then, DNA was double disgested with MspI and ApeKI.
DNA librairies were prepared using TruSeq DNA Low Throughput Protocol (Illumina).

value: hippocampus

tag: Sex

value: male

value: wild type

tag: bisulfite treatment

value: Bisulfite treatement

tag: chip antibody


title: RRBS-Bisulfite-100bp-animal2

tag: tissue


title: Pf-3D7-gDNA-b, ATACseq

source_name: genomic DNA red blood cell stage, 0-20 hours post invasion

value: ring stage

tag: input

value: 60.8 ng of genomic DNA


title: Pf-3D7-gDNA-a, ATACseq

source_name: red blood cell stage, 0-20 hours post invasion

value: 547.0 ng genomic DNA


title: ORF1_1

value: ORF1 replicate 1 / not induced


title: RRBS-Bisulfite-100bp-animal1


title: RRBS-Bisulfite-50bp-animal2


title: WT1_IPTG

value: induced 50 µM IPTG

value: WT replicate 1 / induced


title: RRBS-Bisulfite-50bp-animal1


title: RRBS-Bisulfite-50bp-animal3


title: Svi3_3_2_IPTG

value: Svi3-3 replicate 2 / induced


title: Pf-3D7-t40, ATACseq

value: late schizont


title: RRBS-animal3

description:
genomic DNA - double enzymatic digestion
DNA sequencing (control for RRBS)
[processed data files:]
RRBS-Peaks-all-animals.bedgraph.txt

data_processing:
RRBS reads were aligned to cavPor3 genome using BSMap version 2.74
Duplicates were removed with Samtools  version 1.1, then the 3 alignments corresponding to the 3 independant animals were merge in one unique bam file.
Methylation level was determined for CpG sites using MethylKit
genome build: cavPor3
processed data files format and content: RRBS-Peaks-all-animals.bedgraph: Bedgraph file include number of reads for peaks detected with BSMap from RRBS analysis


title: RRBS-animal2


title: Pf-3D7-t10, dirRNAseq

source_name: red blood cell stage, 2-10 hours post invasion

value: medium ring stage


title: Pf-3D7-t35, ATACseq

value: medium schizont


title: RRBS-animal1


title: H3K4me1 ChIPBisulfite-seq-animal2

description:
genomic DNA - sonicated
ChIP bisulfite sequencing
[processed data files:]
CG_sites_methylation_status_and_RNApolII_enrichment.txt
average_methylation_level_in_H3K4me1_peaks.txt
CG_sites_differentially_methylated.txt
H3K4me1-MACS2Peaks-Score.bedgraph.txt

data_processing:
ChIP-Bisulfite sequencing reads were aligned to cavPor3 genome using Bismark version 0.12.5.
Duplicates were removed with Samtools  version 1.1, then the 3 alignments corresponding to the 3 independant animals were merge in one unique bam file.
Methylation level was determined for CpG sites using MethylKit
genome build: cavPor3
processed data files format and content: CG_sites_methylation_status_and_RNApolII_enrichment.txt: tab-delimited text files include genomic location of CG sites, methylation state (from RRBS, H3K4me1 ChIP-seq and RNapolII PS5 ChIP-seq)
processed data files format and content: average_methylation_level_in_H3K4me1_peaks.txt: tab-delimited text files include average methylation of CG sites in H3K4me1 peaks from RRBS and H3K4me1ChIP seq
processed data files format and content: CG_sites_differentially_methylated.txt: tab-delimited text files include the list of all CG sites differentially methylated between RRBS and H3K4me1 ChIP seq analyses
processed data files format and content: H3K4me1-MACS2Peaks-Score.bedgraph: Bedgraph file include score values of peaks detected with MACS2 from H3K4me1 ChIP-seq
processed data files format and content: RNApolII-HomerPeaks-Score-all-animals.bedgraph: Bedgraph file include score values of peaks detected with Homer from RNApolII PS5-ChIP seq

extract_protocol:
Frozen hippocampi were ground in liquid nitrogen, fixed  (0.5% formaldehyde) and DNA extracted was sonicated then immuno-precipitated with the ChIP-IT ® Sensitivity kit (Active Motif) using antibody against H3K4me1 or RNApoII-PS5.
DNA librairies were prepared using TruSeq DNA Low Throughput Protocol (Illumina). Bisulfite treatment were performed using  the EZ DNA Methylation-Gold Kit (Zymo Research).

value: H3K4me1 (Abcam, ab8895)


title: ChIP-RNApolII-PS5-animal2

description:
genomic DNA - sonicated
ChIP sequencing
[processed data files:]
CG_sites_methylation_status_and_RNApolII_enrichment.txt
RNApolII-HomerPeaks-Score-all-animals.bedgraph.txt
CG_sites_differentially_methylated.txt

data_processing:
ChIP-seq reads were aligned to the cavPor3 guinea pig genome assembly using Bowtie2 version 2.2.3.
Duplicates were removed with Samtools  version 1.1, then the 3 alignments corresponding to the 3 independant animals were merge in one unique bam file.
H3K4me1 peaks were detected using MACS2 and RNApoII-PS5 peaks were detected using Homer version 4.6.
All peaks were annotated using Homer version 4.6.
genome build: cavPor3
processed data files format and content: CG_sites_methylation_status&RNApolII_enrichment.txt: tab-delimited text files include genomic location of CG sites, methylation state (from RRBS, H3K4me1 ChIP-seq and RNapolII PS5 ChIP-seq)
processed data files format and content: CG_sites_differentially_methylated.txt: tab-delimited text files include the list of all CG sites differentially methylated between RRBS and H3K4me1 ChIP seq analyses
processed data files format and content: RNApolII-HomerPeaks-Score-all-animals.bedgraph: Bedgraph file include score values of peaks detected with Homer from RNApolII PS5-ChIP seq

value: RNA PolII CTD phosphorylated in serine 5 [4H8] (Abcam, ab5408)


title: ChIP-RNApolII-PS5-animal3


title: Pf-3D7-t30, ATACseq

value: early schizont


title: ORF1_2_IPTG

value: ORF1 replicate 2 / induced


title: Intermittent Calorie Restriction IC

city: Istanbul

first: Nehir

last: Ozdemir Ozgenturk

address: Davutpasa/Esenler

department: Mol. Bio. and Genetics

country: Turkey

institute: Yildiz Technical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 mouse genome using TopHat2
Gene expression levels were quantified by Cufflinks 2.2.1 and normalized by the fragments per kilobase of transcript per milion fragments mapped method (FPKM) (Trapnell et al. 2010)
The differential expressed genes (DEGs) were identified with Cuffdiff
MMTV-TGF- α female mice

source_name: thymus

extract_protocol:
Thymus tissues were removed, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MMTV-TGF-alpha

value: thymus


title: Calorie Restriction CC


title: H3K4me1 ChIPBisulfite-seq-animal3

value: hippocampus

value: male

value: wild type

value: Bisulfite treatement


title: Ad libitum AL


title: H3K4me1 ChIPBisulfite-seq-animal1


title: Pf-3D7-t25, ATACseq

value: late trophozoite


title: Pf-3D7-t20, ATACseq

value: early trophozoite


title: H3K4me1 ChIP-seq-animal3

description:
genomic DNA - sonicated
ChIP sequencing
[processed data files:]
H3K4me1-MACS2Peaks-Score.bedgraph.txt

data_processing:
ChIP-seq reads were aligned to the cavPor3 guinea pig genome assembly using Bowtie2 version 2.2.3.
Duplicates were removed with Samtools  version 1.1, then the 3 alignments corresponding to the 3 independant animals were merge in one unique bam file.
H3K4me1 peaks were detected using MACS2 and RNApoII-PS5 peaks were detected using Homer version 4.6.
All peaks were annotated using Homer version 4.6.
genome build: cavPor3
processed data files format and content: H3K4me1-MACS2Peaks-Score.bedgraph: Bedgraph file include score values of peaks detected with MACS2 from H3K4me1 ChIP-seq


title: H3K4me1 ChIP-seq-animal2


title: Pf-3D7-t10, ATACseq


title: ORF1_1_IPTG

value: induced 50 µM IPTG

value: ORF1 replicate 1 / induced


title: Mtb_STR_24hrs_rep2

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description: Mtb.counts.txt

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
Quality trimmed read sequences were mapped to M. tuberculosis H37Rv Areference genomes using BWA (Cole et al. 1998; Stinear et al. 2008; Li et al. 2009). Gene expression estimates were made as raw read counts using the Pyhton script ‘HTSeq- count’ (model type – union). Counts data were converted to counts per million (cpm) and genes were filtered if they failed to achieve a cpm value of 1 in at least 30% of libraries per conditions.
Normalization of raw read counts and differential expression analysis was performed using DeSeq2
Genome_build: M. tuberculosis H37Rv
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Mycobacterium tuberculosis H37Rv

source_name: M. tuberculosis H37Rv

extract_protocol:
RNA isolation was performed with a NucleoSpin® RNA kit (Machery Nagel). In total 25 OD units were spun down and used for isolation per sample. Isolation was performed with a biological triplicate. There was one deviation to the first step of the protocol to lyse the mycobacterial cells. Cells were disrupted by 0.1 mm zirconium beads in 500 μL Buffer RA1 and 5 μL ß-mercaptoethanol for 1 minute. Subsequent steps were according to protocol provided by the manufacturer. After RNA isolation, RNA concentrations were measured. RNA integrity numbers (RIN) were determined with a bioanalyzer 2100 expert (Agilent). The RIN value was measured for one sample per triplicate. All RIN values were >9. As ribosomal RNA comprises the vast majority of the extracted RNA population, depletion of these molecules through RiboMinus-based rRNA depletion was used in efforts to increase the coverage of mRNA and to reduce rRNA reads. For this mRNA enrichment, the Invitrogen's RiboMinusTM Prokaryotic kit was used according to manufacturer's instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA sequence-specific 5′-biotin labeled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinusTM concentrate module according to the manufacturer's protocol.
The final RiboMinusTM RNA sample was subjected to thermal mRNA fragmentation using Elute, Prime, and fragment Mix from the Illumina TruSeqTM RNA sample preparation kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer's protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III Reverse Transcriptase (Invitrogen) and SRA RT primer (Illumina). The cDNA was further converted into double stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer’s instructions. A small aliquot (1 µl) was analyzed on Invitrogen Qubit and Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled together in equal concentrations in one pool before sequencing on Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with the Illumina Pipeline Software v1.82.

tag: treatment

value: streptomycin

tag: time point


title: Mtb_RIF_24hrs_rep2

description: Mtb.counts.txt

value: rifampicin


title: Mtb_EMB_24hrs_rep2

description: Mtb.counts.txt

value: ethambutol


title: Mtb_STR_24hrs_rep3

description: Mtb.counts.txt


title: Mtb_EMB_24hrs_rep1

description: Mtb.counts.txt


title: Mtb_EMB_24hrs_rep3

description: Mtb.counts.txt


title: Mtb_INH_24hrs_rep3

description: Mtb.counts.txt

value: isoniazid


title: Mtb_RIF_24hrs_rep1

description: Mtb.counts.txt


title: Mtb_RIF_24hrs_rep3

description: Mtb.counts.txt


title: Mtb_STR_24hrs_rep1

description: Mtb.counts.txt


title: Pf-3D7-t05, ATACseq

value: early ring stage


title: H3K4me1 ChIP-seq-animal1

value: H3K4me1 (Abcam, ab8895)


title: ChIP-RNApolII-PS5-animal1

value: RNA PolII CTD phosphorylated in serine 5 [4H8] (Abcam, ab5408)


title: Mtb_CIP_24hrs_rep3

description: Mtb.counts.txt

value: ciprofloxacin


title: Mtb_INH_24hrs_rep1

description: Mtb.counts.txt


title: Mtb_CIP_24hrs_rep1

description: Mtb.counts.txt


title: Mtb_INH_24hrs_rep2

description: Mtb.counts.txt


title: Mtb_RIF_4hrs_rep3

description: Mtb.counts.txt


title: Mtb_Ctrl_24hrs_rep1

description: Mtb.counts.txt

value: control


title: Mtb_Ctrl_24hrs_rep2

description: Mtb.counts.txt


title: Mtb_CIP_24hrs_rep2

description: Mtb.counts.txt


title: Mtb_STR_4hrs_rep3

description: Mtb.counts.txt


title: Mtb_STR_4hrs_rep2

description: Mtb.counts.txt


title: Mtb_RIF_4hrs_rep1

description: Mtb.counts.txt


title: Mtb_RIF_4hrs_rep2

description: Mtb.counts.txt


title: Mtb_STR_4hrs_rep1

description: Mtb.counts.txt


title: Mtb_EMB_4hrs_rep2

description: Mtb.counts.txt


title: Mtb_EMB_4hrs_rep1

description: Mtb.counts.txt


title: Mtb_CIP_4hrs_rep3

description: Mtb.counts.txt


title: Mtb_INH_4hrs_rep1

description: Mtb.counts.txt


title: 2% DSS + ER-464195-01_3

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

data_processing:
Reads were mapped on mm10 mouse reference genome and quantified using CLC Genomics Workbench version 9.5.1 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 9.5.1.
Filtering characteristics of fold-change -2 to 2 (false discovery rate (FDR) at P < 0.05) were used to identify the DEGs.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Intestine_2% DSS + ER-464195-01

extract_protocol:
Intestines were removed, flash frozen on dry ice, and total RNA was extracted from colon of mice using TRIZOL Reagent (Life Technologies). 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Balb/c

value: Intestine

value: 7 weeks


title: 2% DSS + ER-464195-01_5

value: male


title: Mtb_INH_4hrs_rep2

description: Mtb.counts.txt


title: 2% DSS + ER-464195-01_2


title: Mtb_INH_4hrs_rep3

description: Mtb.counts.txt


title: 2% DSS + ER-464195-01_4


title: Mtb_Ctrl_24hrs_rep3

description: Mtb.counts.txt


title: Mtb_CIP_4hrs_rep2

description: Mtb.counts.txt


title: Mtb_CIP_4hrs_rep1

description: Mtb.counts.txt


title: Mtb_Ctrl_4hrs_rep2

description: Mtb.counts.txt


title: 2% DSS + ER-464195-01_1


title: SET-2_pSTAT1-2

city: Cambridge

first: Ioana

middle: Ilinca

last: Nitulescu

state: MA

address: 12 Oxford St

institute: Harvard University

description:
matched input: SET2_pSTAT1-2.fastq.gz
SET-2_pSTAT1_peaks.narrowPeak

data_processing:
Basecalls performed using CASAVA version 1.4
FastQC v.0.10.1 was used to check read quality metrics.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.1 with flags -n 1 -m 1 --best --strata
Duplicate reads were removed with MarkDuplicates (picard tools v.1.88)
SPP was used both for cross-correlation analysis and for peak finding using default parameters or FDR < 0.05. MACS2 was used either with default parameters or using --shiftsize to set the strand shift to match the SPP peak cross-correlation size. Regions on chrM or overlapping repeat elements (RepeatMasker bed file downloaded from UCSC 16 Nov. 2012) by > 70% were routinely excluded.
Genome_build: hg19
Supplementary_files_format_and_content: peak

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for Illumina sequencing were prepared using the KAPA Hyper Prep Kit for Illumina and ligated to unique Bioo Scientific NEXTflex barcode adaptors. Following ligation, libraries were amplified with 8-12 cycles of PCR and were then size-selected using a 2% gel cassette in the Pippin Prep System from Sage Science. DNA fragments of size 200-500bp were captured. Libraries were quantified by qPCR utilizing the KAPA Biosystems Illumina Library Quantification kit.

tag: cell type

value: essential thrombocythemia

tag: treatment protocol

value: untreated

tag: chip epitope

value: STAT1 pS727

tag: chromatin prep#

tag: growth protocol

value: SET2 cells were grown in RPMI-1640 supplemented with 20% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.


title: 2% DSS_5

source_name: Intestine_2% DSS

tag: strain

tag: age


title: 2% DSS_4


title: Pf-3D7-t15, ATACseq

value: late ring stage


title: SET-2_pSTAT1-1_input

description: input for : SET2_pSTAT1-1.fastq.gz

value: input


title: SET-2_pSTAT1-1

description:
matched input: SET2_pSTAT1-1.fastq.gz
SET-2_pSTAT1_peaks.narrowPeak


title: Mtb_Ctrl_4hrs_rep1

description: Mtb.counts.txt


title: Mtb_EMB_4hrs_rep3

description: Mtb.counts.txt

value: ethambutol


title: 2% DSS_3


title: DS203

city: London

first: Rocio Teresa

last: Martinez-Nunez

state: Greater London

address: 5th Floor Tower Wing, Guy’s Campus

department: Infectious Diseases

institute: King's College London

description:
Cytoplasmic RNA
CM4005823

data_processing:
CASAVA software version 1.8.4 was used for de-multiplexing, removal of low quality reads, and production of FASTQ sequence files
The FASTX (http://hannonlab.cshl.edu/fastx_toolkit/index.html) application was used to trim the 3’-end of sequence reads in order to remove the 3’ adaptor sequence (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC). Sequences without any 3’ adapter sequence as well as sequences of less than 17 nucleotides after trimming were removed. A perl script was used to remove sequences with any amount of 5’ –adapter sequence. (AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC). FASTX was also used to collapse identical reads into single entries retaining the read count for each unique sequence
To filter out any sequencing errors, only sequence reads that occurred ≥ 5 were retained for further analysis. Non-redundant sequences were then aligned to genomic (hg19) and mRNA sequence (hg19) using bowtie 2 (35); sequences with perfect-match and 1nt mismatch alignments were retained for further analysis.
Mature miRNA RPM values were normalized using the following formula: raw count / perfectly matched miRNA reads X 1,000,000
Tables were filtered to retain a list of annotated RNAs having a minimum of 10 mapped reads (Detection Threshold) in 25% of samples; for these filtered read tables, missing values were replaced with the average RPM value equivalent to 1 read
Genome_build: miRBase 21.0
Supplementary_files_format_and_content: Text files containing RPM for matched microRNA reads

source_name: Bronchial Epithelial Cells

growth_protocol: Epithelial brushings were collected using disposable, sheathed bronchial brushes (Olympus cytology brushes BC-202D-2010, KeyMed [Medical & Industrial Equipment] Ltd OLYMPUS Group Company), with 4 separate sets of brushings from the central airways. Brushings were placed in a sterile universal tube with 5 ml PBS and washed with 10mL of RPMI medium (PAA, GE Healthcare LifeSciences) supplemented with penicillin/streptomycin (Thermo Fisher Scientific). Brushings were spun at 1200 rpm for 10 minutes, medium was discarded and cells were resuspended in complete BEGM (Lonza). BECs were cultured in collagen (Thermo Fisher Scientific)-coated T25 flasks in BEGM complete medium and passaged onto 15cm2 collagen-coated dishes when 80% confluent. Cells were harvested at passage 1.

extract_protocol:
Cytoplasmic extracts were prepared as described previously (Sterne-Weiler et al. 2013; Martinez-Nunez and Sanford 2016) with the addition of 500g/mL cycloheximide (Sigma-Aldrich UK) in the lysis buffer.
NEBNext Small RNA-Seq Library Preparation Kit (New England Biolabs- Ipswich, USA). The purified libraries were electrophoresed through a freshly cast 8% native polyacrylamide gel. The library fragments of appropriate size (~134-152 nt) were excised and recovered by agitation of the fragments overnight at 37°C at 200 rpm in elution buffer, passage of the eluate through a 0.45μm filter, and ethanol precipitation.
miRNA-seq. Run across two lanes (L001 and L002).

tag: seq name

tag: disease status

value: HC


title: 2% DSS_1


title: SET-2_pSTAT1-2_input

description: input for : SET2_pSTAT1-2.fastq.gz


title: Mtb_Ctrl_4hrs_rep3

description: Mtb.counts.txt


title: Normal water_5

source_name: Intestine_normal water


title: Normal water_4


title: DS205

description:
Cytoplasmic RNA
CM4005813

value: SA


title: DS197

description:
Cytoplasmic RNA
CM4005807


title: Normal water_3


title: DS198

description:
Cytoplasmic RNA
CM4005809


title: DS187

description:
Cytoplasmic RNA
CM4005801


title: DS191

description:
Cytoplasmic RNA
CM3919819


title: Normal water_1


title: Normal water_2


title: DS194

description:
Cytoplasmic RNA
CM3919821


title: DS200

description:
Cytoplasmic RNA
CM3919811


title: DS158

description:
Cytoplasmic RNA
CM3919805


title: DS189

description:
Cytoplasmic RNA
CM3919803


title: SA3_P

description:
Polyribosome-bound RNA
V10532/DS205_Poly_L2

data_processing:
Base call files were converted into FASTQ files using Illumina Software (CASAVA)
Sequencing adapters and other low quality bases were clipped. Reads were aligned to External RNA Controls Consortium (ERCC) sequences to assess the success of library construction and sequencing. A subset (~1M reads) was aligned to other spiked-in control sequences (PhiX and other Illumina controls used during library preparation), residual sequences (globin and ribosomal RNA), and poly-A/T sequences that persisted after clipping. The reads were also aligned to a sampling of intergenic regions to assess the level of DNA contamination level
RSEM v1.2.0 was used to quantify and compute estimated counts by genes and transcripts (Li and Dewey 2011) using the UCSC knownGene. To determine the origin of all reads as a method of quality control, the unaligned reads were aligned to the full genome (not transcriptome) using BWA 0.6.2 (Li and Durbin 2009)
Upper Quartile normalization was used to normalize between different samples with different read depths for both aggregate gene expression and isoform analysis. Each sample was scaled to that the Upper Quartile of counts was equal to 1000. All 77k isoforms defined by UCSC hg19 were considered as initial candidates. 12,485 isoforms are associated with only one gene, and thus were not considered further. Over 12k isoforms had 0 or nearly 0 counts for all subjects. Only genes and isoforms with median counts of 10 or more on each group (Total or Polysome) were taken into account
PROC-GLM was used to perform preliminary statistical analysis
Genome_build: hg19
Supplementary_files_format_and_content: Text files containing non-normalized annotated gene counts and isoform counts for each sample

growth_protocol: Epithelial brushings were collected using disposable, sheathed bronchial brushes (Olympus cytology brushes BC-202D-2010, KeyMed [Medical & Industrial Equipment] Ltd OLYMPUS Group Company), with 4 separate sets of brushings from the central airways. Brushings were placed in a sterile universal tube with 5 ml PBS and washed with 10mL of RPMI medium (PAA, GE Healthcare LifeSciences) supplemented with penicillin/streptomycin (Thermo Fisher Scientific). Brushings were spun at 1200 rpm for 10 minutes, medium was discarded and cells were resuspended in complete BEGM (Lonza). BECs were cultured in collagen (Thermo Fisher Scientific)-coated T25 flasks in BEGM complete medium and passaged onto 15cm2 collagen-coated dishes when 80% confluent. Polyribosome preparation and validations were performed in passage 1 cells

extract_protocol:
Polyribosome profiling was done as described previously (Sterne-Weiler et al. 2013; Martinez-Nunez and Sanford 2016) with the addition of 500g/mL cycloheximide (Sigma-Aldrich UK) in the lysis buffer
TrueSeq Stranded mRNA Library Prep Kit

tag: fraction

value: Polysome


title: HC5_T

description:
Cytoplasmic RNA
V10532/DS190_Total_L6

value: Total


title: 2% DSS_2

tag: Sex


title: HC5_P

description:
Polyribosome-bound RNA
V10532/DS190_Poly_L1


title: DS171

description:
Cytoplasmic RNA
CM4005825


title: HC1_P

description:
Polyribosome-bound RNA
V10532/DS191_Poly_L7


title: R78-9

city: Avignon

first: Cédric

last: Alaux

address: Domaine Saint-Paul

department: UMR 406 Abeilles et Environnement

country: France

institute: INRA

description: pool of 10 varroa

data_processing:
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2).
The read quality of the RNA-seq libraries was evaluated using FastQC. Cleaned and filtered reads were de novo assembled using DRAP version 1.7 and filtered with at least one FPKM.
The resulting contigs were aligned with NCBI blast (blastx program, version 2.2.26) on Refseq protein, Swissprot and Ensembl protein reference files to retrieve the corresponding annotations. The contigs were also processed with rnammer (version 1.2) to find ribosomal genes, with repeatmasker (version open-4-0-3) to list the contained repeats and with interproscan (version 4.8) for gene ontology and structural annotation. Reads have been realigned back to contigs with bwa (version 0.7.12). The resulting sam files were compressed, sorted and indexed with samtools (version 1.1).
The contig expression counts have been generated from the bam files with samtools (idxstats program, version 1.1) and merged with unix commands. The alignment files have then been filtered for duplicates with samtools (rmdup program, version 1.1) before variant calling. The resulting bam files have been processed with GATK (version v3.0-0-g6bad1c6).
The assembly quality has been assessed in several ways. First, the read on contig re-alignment rate has been calculated for every sample using the bam files presented in the previous section. Second, the 308 Varroa destructor proteins found in NCBI protein database have been realigned using blat version  v. 35x1 on the contigs to retrieve their match coverage and similarity. Third, coverage and similarity have been calculated for the 12,035 NCBI Metaseiulus occidentalis proteins in the same way as for Varroa destructor proteins. Last, the contigs where processed with BUSCO (version 2) using the insecta_odb9 database.
Genome_build: de novo assembly contigs.fa
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample.

organism: Varroa destructor

source_name: whole body

growth_protocol: Phoretic mites: capped brood frames of each colony were removed to prevent any mite being released from emerging brood cells. Four days later, one frame of bees was removed from the colony and phoretic mites were sampled directly on adult bees.  Phoretic mites artificially reared: An additional 20 mites were sampled together with the bees they were standing on and placed in a Pain cage, with 10 other non-infested bees. Cages were kept for 4 days in an incubator (28°C) before mites were sampled.   All subsequent stages were sampled from brood frames removed from the colonies and dissected in the laboratory.  Arresting mites: these mites were collected in unsealed L5 brood cells, as mites seen immobile at the bottom of the cells, immersed in larval food.  Pre-laying mites: these mites were collected from sealed brood cells containing moving larvae. These mites displayed an inflated ventral side due to activation of the ovaries.  Laying mites: these mites were collected from sealed brood cells containing pre-pupae and at least one mite egg (but no mite protonymph).  Post-laying mites: these mites were collected from capped brood cells containing purple-eye and white-body pupae (P5). Female mites were sampled if they were accompanied by at least one male and one female deutonymphs.  Non-reproducing mites: these mites were also collected from P5 brood cells, but identified as female mites with no offspring, i.e. in reproduction failure.  Emerging mites: these mites were collected from capped brood cells containing developing bees almost ready to emerge (but with an intact cell cap – P8 to P9).  Young mites: these mites were also collected from P8 to P9 cells, but identified thanks to their lighter body coloration as compared to founder females. These mites should have been just mated, but have yet to undergo their first phoretic and reproducing stages.  Male mites: these mites were also collected from P8 to P9 cells and identified thanks to their striking sexual dimorphism as compared to females. Males exhibit a yellow tan and a round-body shape.

extract_protocol:
Varroa were flash frozen in dry ice. RNA was extracted from pool of 10 varroas using Trizol reagent and the Qiagen RNeasy Mini Kit (QIagen)
Illumina TruSeq Stranded mRNA Sample Preparation kit was used with 200 ng of total RNA for the construction of sequencing libraries.

treatment_protocol: No treatment

tag: life cycle stage

value: phoretic mites artificially reared in cages with adult bees

value: whole body

value: adult

tag: colony


title: DS159

description:
Cytoplasmic RNA
CM4005815


title: HC4_T

description:
Cytoplasmic RNA
V10532/DS171_Total_L5


title: R78-7

description: pool of 10 varroa

value: males (collected from P8 to P9 brood cells)

tag: tissue


title: synthetic mtDNA, 60 min

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

data_processing:
Although reads were paired-end, only the 1st reads (R1) were used for mapping due to low sequencing quality of the 2nd reads (R2).
Low quality sequences (Q < 30) were removed from the 3' end of the reads by trimGalore.
The trimed reads were mapped to the appropriately converted mouse (mm10) and lambda phage (internal control) genomic sequences by bismark.
Using these mapping results, methylation at individual C sites were determined by bismark-methylation-extractor.
The methylation levels at these cytosine sites were analyzed with discrimination of H and L strands.
Genome_build: mm10
Supplementary_files_format_and_content: The csv files contain methylation levels of individual C sites: position, strand, methylation level (%), the number of reads covering the cytosine site.

source_name: bisulfite-treated mtDNA (and lambda DNA)

extract_protocol:
Mitochondrial nucleic acid containing mitochondrial DNA (mtDNA) was prepared from the purified mitochondria by protease K treatment, phenol extraction, chloroform/isoamyl-alcohol extraction and ethanol precipitation, followed by linearization of mtDNA by restriction enzyme digestion.
The mtDNA and spike-in lambda DNA were treated with 9.2M bisulfite, and used for PBAT library preparation as a template.

treatment_protocol: Highly purified mitochondrial fraction was prepared from cells/tissues by homogenization, washing, ultracentrifugation and benzonase treatment.

value: PCR-generated mtDNA

value: bisulfite-treated for 60 min


title: R78-6

description: pool of 10 varroa

value: young mites (collected from P8  to P9 brood cells)


title: HC4_P

description:
Polyribosome-bound RNA
V10532/DS171_Poly_L4


title: synthetic mtDNA, 15 min

value: bisulfite-treated for 15 min


title: synthetic mtDNA, 40 min

value: bisulfite-treated for 40 min


title: DS190

description:
Cytoplasmic RNA
CM3919817


title: R78-4

description: pool of 10 varroa

value: non-reproducing mites (collected from P5 brood cells, but without offspring)


title: R78-3

description: pool of 10 varroa

value: laying mites (collected from sealed brood cells containing pre-pupae)


title: R78-5

description: pool of 10 varroa

value: emerging mites (collected from P8 to P9 brood cells)


title: SA8_T

description:
Cytoplasmic RNA
H33389/DS198_Total_L1.D706_506


title: R78-2

description: pool of 10 varroa

value: pre-laying mites (collected from sealed brood cells containing moving larva)


title: synthetic mtDNA, 5min

value: bisulfite-treated for 5 min


title: R41-10

description: pool of 10 varroa

value: post-laying mites (collected from capped brood cells containing purple-eye and white-body pupae P5)


title: SA7_T

description:
Cytoplasmic RNA
H33389/DS197_Total_L1.D704_506

value: SA


title: R41-9

description: pool of 10 varroa


title: R78-1

description: pool of 10 varroa

value: arresting mites (collected in unsealed L5 brood cells)


title: R78-10

description: pool of 10 varroa


title: R78-8

description: pool of 10 varroa

value: phoretic mites (collected on adult bees)


title: ESC (embryonic stem cells) biological rep3, 90 min

value: mitocondoria purified from embryonic stem cell line E14

value: bisulfite-treated for 90 min


title: SA7_P

description:
Polyribosome-bound RNA
H33389/DS197_Poly_L1.D705_506

value: Polysome