title: Dnmt3ab_WT_H3K4me3_rep3

description: Dnmt3DKO.WT_H3K4me3_Me.Unme.domains_RPM.txt

extract_protocol:
The ChIP-seq libraries for all samples were prepared using an ultra-low input native ChIP protocol, as previously described with the several modifications.  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease in prepared digestion buffer, as per recommendations in the Brind’Amour protocol.  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using spri purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads at a 1.8:1 ratio.  Library preparation was completed using the Diagenode MicroPlex Library Preparation kit v2 using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations.
Cells for ChIP-seq were flash frozen in nuclear lysis buffer, cells for PBAT were flash frozen in PBS
The ChIP-seq libraries for all samples were prepared using an ultra-low input native ChIP protocol, as previously described with the several modifications.  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease in prepared digestion buffer, as per recommendations in the Brind’Amour protocol.  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using spri purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads at a 1.8:1 ratio.  Library preparation was completed using the Diagenode MicroPlex Library Preparation kit v2 using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations.
For single oocyte RNA profiling, four GV oocytes from Mll2 KO and WT mice were collected for each genotype. Cells were lysed, RNA reverse transcribed and amplified according to the protocol of SMARTer Ultra Low RNA Kit for Illumina Sequencing (Version 1, Clontech). Subsequently, samples were subjected to NEBNext Ultra DNA library preparation for Illumina using indexed adaptors (New England Biolabs). Resulting libraries were pooled in equimolar quantities for 75-bp single-read sequencing on Illumina HiSeq 2000, resulting in about 15-18 million reads per sample.
Post-bisulfite adaptor tagging (PBAT) was used to generate whole-genome bisulfite sequencing libraries using 100 collected oocytes. Briefly, cells are lysed with 0.5% SDS in EB buffer and bisulfite-treated with one-step modification procedure using the Sigma Imprint DNA Modification kit. The resulting DNA are purified using columns from Zymo EZ DNA Methylation Direct kit. First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 10 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.
ChIP-bisulfite-seq was done on MNase-digested 10% input samples from the ChIP protocol, detailed in the corresponding ChIP-seq samples.  Following DNA purification from chromatin using spri purification with Sera-Mag carboxylate-modified Magnetic SpeedBeads, samples were bisulfite converted using the Zymo EZ DNA Methylation Direct kit.  First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 16-20 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.

value: postnatal day 25

value: Dnmt3a floxed/floxed, Dnmt3b floxed/floxed, Zp3 -ve


title: shNat14_R2

status: Public on Jan 01 2018

type: SRA

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: IUE: Plasmids containing NTC control or Nat14 shRNA were injected into the lateral ventricle of E14.5 mouse brains, which were given an electrical stimulation (34 V with 950 mA). Four days later, mice were sacrificed and embryonic brains were subjected to FAC-sorting.

library_source: transcriptomic

data_processing:
The FASTQ files were aligned human genome (hg19) using TopHat v2.0.8
Samtools v0.1.19 was used for File format conversions (bam to sam)
Reads at transcripts were counted using HTSeq (v0.5.4p1)
Normalization (for library size) was done using DESeq
Differential expression analysis was done using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing normalized logFC

molecule: total RNA

organism: Mus musculus

source_name: cortical cells

extract_protocol:
RNA was isolated using RNeasy Micro Kit (Qiagen, 74004) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using Nextera Illumina protocols

treatment_protocol: Electroporated E 18.5 embryonic brains were isolated, and downstream processing was done in cold HBSS. The cortical region of the brains was micro-dissected and processed for single cell dissociation using Neural Tissue Dissociation Kit (P) (130-092-628) following the manufacturer's instructions. GFP positive live cells were FACS sorted directly into RLT lysis buffer.

tag: cell type

value: cortical cell

tag: source

value: Cells isolated from mouse cortex


title: Mll2_KO_RNA-Seq_rep1

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: RNAseq_groups_oocyte_mRNA_norep_RPKM_corrDNAcont.txt

data_processing:
Raw FastQ sequence files were initially quality and adapter trimmed using Trim Galore v0.4.2 using default parameters (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Mapping of ChIP-Seq data was performed using Bowtie 2 v2.2.9 against the mouse GRCm38 genome assembly. The resulting hits were filtered to remove mappings with a MAPQ scores of < 20. Mapping of RNA-Seq data was performed using HISAT2 v2.0.5 against the mouse GRCm38 genome guided by known splice sites taken from Ensembl v68. Hits were again filtered to remove mappings with MAPQ scores of <20.
For PBAT data, reads were trimmed with Trim Galore using --clip_r1 9 and --clip_r2 9. Trimmed reads were first aligned to the mouse genome in paired-end mode to be able to count overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark v0.16.3 (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output, and methylation from single-end and paired-end mapping were merged into a single Bismark coverage report.
genome build: GRCm38
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
processed data files format and content : "10_5_Domains_75_25_NoOverlap_NoGaps_NoInterm_NoSmall_NoGaps" file contains the GV methylated and unmethylated domains used for analyses in this study.
processed data files format and content : "RNAseq_groups_oocytemRNA_norep_RPKM_corrDNAcont" file contains RNA-seq quantitation for two groups: Mll2 WT oocytes and Mll2 cKO oocytes (each a replicate set of 4 single cell RNA-seq libraries).  RPKM was quantitated in SeqMonk for oocyte transcriptome mRNA annotation (Veselovska et al. 2014) excluding repetitive elements, correcting for DNA contamination
processed data files format and content : "ESC_oocyte_technicaloptimisation_2kbrunning_RPM_nofilters" file contains ChIP-seq quantitation for individual replicates for H3K4me3 in 1000 ESCs and 500 ESCs used for validation of the ULI-nChIP-seq method and the antibody titration for 125ng,and 62.5ng of antibody for H3K27ac and 125ng, 250ng and 500ng of H3K27me3 in GV oocytes (25-day old mice).  Reads per million was quantitated in SeqMonk for 2kb running window probes, with no filters applied.
processed data files format and content : "Dnmt3DKO.WT_H3K4me3_Me.Unme.domains_RPM" file contains ChIP-seq quantitation for H3K4me4 in GV oocytes (25-day old mice) from grouped Dnmt3a/b cDKO (N=4) and Dnmt3a/b WT controls (N=4).  Reads per million was quantitated in SeqMonk for GV methylated and unmethylated domains.
processed data files format and content : "GO_and_Mll2_peaks" file contains peak and seedpeak calls for H3K4me3 in non-growing oocytes (NGO) (5-day old mice), growing oocytes (GO) (10-day old mice), germinal vesicle (GV) oocytes (15-day old mice) and GV oocytes (25-day old mice), Mll2 WT GV oocytes (25-day old mice), and Mll2 KO GV oocytes (25-day old mice) using Chromstar peak calling program.  Temporal peak calling was done using a joint multivariate analysis (parameters: binsize = 1000bp, stepsize = 200bp, mode = differential). A cutoff of 1-10-4 was applied on the peak score (which is defined as the maximum posterior probability anywhere within a peak), to divide the resulting peak set into peaks with high H3K4me3 enrichment and seed-peaks with low H3K4me3 enrichment.
processed data files format and content : "bed_files_combinations_GV" file contains combinatorial peak for H3K4me3, H3K27ac, and H3K27me3 in germinal vesicle (GV) oocytes (25-day old mice) using Chromstar peak calling program.  Combinatorial chromatin states were called using a combined multivariate analysis. A cutoff of 1-10-4 was applied on the posterior probability in each bin to yield a stringent set of peaks.
processed data files format and content : "Epiblast_combinations_and_peaks" file contains combinatorial peak for H3K4me3, H3K27ac, and H3K27me3 in E6.5 epiblast using Chromstar peak calling program.   Combinatorial chromatin states were called using a combined multivariate analysis. A cutoff of 1-10-4 was applied on the posterior probability in each bin to yield a stringent set of peaks.
processed data files format and content : "bivalency_PGC_d05_d25_domains" file contains combinatorial peak for combined replicates for H3K4me3, H3K27me3 in non-growing oocytes (NGO) (5-day old mice), GV oocytes (25-day old mice), E11.5 primordial germ cells (Sachs et al. 2013).  Combinatorial chromatin states were called using a joint multivariate analysis (parameters: binsize = 1000bp, stepsize = 200bp, mode=differential).  A cutoff of 1-10-4 was applied on the peak score to select broad bivalent domains and subsequently only those domains were retained which contained clear enrichment, by applying a cutoff on the posterior probability of 1-10-4.
processed data files format and content : "OocyteH3K27ac_H3K27acGVpeaks_RPMcorrlength" file contains H3K27ac enrichment in grouped d5 NGOs and d25 GV oocytes for H3K27ac peaks called in GV oocytes using Chromstar.  Enrichment was quantitated as reads per million, corrected for probe length.
processed data files format and content : "Oocyte_H3K27ac_5kbrunning_RPM_nofilters" file contains H3K27ac enrichment in grouped d5 NGOs and d25 GV oocytes for running 5kb windows.  Enrichment was quantitated as reads per million.

source_name: Germinal vesicle oocytes

growth_protocol: Ovaries were collected from 5, 10, 15, and 25 day-old C57BL/6Babr or 21 or 25-day-old Mll2Gdf9cKO or 25-day-old Dnmt3a/bZp3cDKO mice and digested using 2mg/mL collagenase and 0.02% trypsin solution, gently agitating at 37°C for 20-30 minutes. Oocytes were hand collected and washed in M2 medium (Sigma), followed by 2 consecutive washes in PBS.

extract_protocol:
For single oocyte RNA profiling, four GV oocytes from Mll2 KO and WT mice were collected for each genotype. Cells were lysed, RNA reverse transcribed and amplified according to the protocol of SMARTer Ultra Low RNA Kit for Illumina Sequencing (Version 1, Clontech). Subsequently, samples were subjected to NEBNext Ultra DNA library preparation for Illumina using indexed adaptors (New England Biolabs). Resulting libraries were pooled in equimolar quantities for 75-bp single-read sequencing on Illumina HiSeq 2000, resulting in about 15-18 million reads per sample.
Cells for ChIP-seq were flash frozen in nuclear lysis buffer, cells for PBAT were flash frozen in PBS
The ChIP-seq libraries for all samples were prepared using an ultra-low input native ChIP protocol, as previously described with the several modifications.  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease in prepared digestion buffer, as per recommendations in the Brind’Amour protocol.  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using spri purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads at a 1.8:1 ratio.  Library preparation was completed using the Diagenode MicroPlex Library Preparation kit v2 using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations.
For single oocyte RNA profiling, four GV oocytes from Mll2 KO and WT mice were collected for each genotype. Cells were lysed, RNA reverse transcribed and amplified according to the protocol of SMARTer Ultra Low RNA Kit for Illumina Sequencing (Version 1, Clontech). Subsequently, samples were subjected to NEBNext Ultra DNA library preparation for Illumina using indexed adaptors (New England Biolabs). Resulting libraries were pooled in equimolar quantities for 75-bp single-read sequencing on Illumina HiSeq 2000, resulting in about 15-18 million reads per sample.
Post-bisulfite adaptor tagging (PBAT) was used to generate whole-genome bisulfite sequencing libraries using 100 collected oocytes. Briefly, cells are lysed with 0.5% SDS in EB buffer and bisulfite-treated with one-step modification procedure using the Sigma Imprint DNA Modification kit. The resulting DNA are purified using columns from Zymo EZ DNA Methylation Direct kit. First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 10 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.
ChIP-bisulfite-seq was done on MNase-digested 10% input samples from the ChIP protocol, detailed in the corresponding ChIP-seq samples.  Following DNA purification from chromatin using spri purification with Sera-Mag carboxylate-modified Magnetic SpeedBeads, samples were bisulfite converted using the Zymo EZ DNA Methylation Direct kit.  First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 16-20 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.

tag: background strain

tag: time-point in reprogramming

value: postnatal day 21

tag: cell number

value: Germinal vesicle oocytes

tag: antibody amount

tag: genotype

value: Mll2 floxed/floxed, Gdf9 +ve


title: IL9-3 rep1

city: Davis

first: Siobhan

middle: M

last: Brady

state: CA

address: 1 Shields Ave

department: Plant Biology

country: USA

institute: UC Davis

data_processing:
Each pool was sequenced in 50 bp single-end format on a total of 5 lanes of a HiSeq 2000 platform (Illumina Inc. San Diego, CA, USA).  Two replicates were lost during library creation, S. pennellii #3 and IL7-5 #3.
Demultiplexed data and filtered and trimmed bad base calls.  Note that FASTQ files provided to GEO have been demultiplexed but not trimmed.
A chimeric reference was created for each IL by combining parental matched references (SlCDS_ITAG2.3_pseudoGMAP5V80passNoDif.fa and SpCDS_ITAG2.3_pseudoGMAP5V80passNoDif.fa) using the latter pennellii reference in the introgression region obtained from (Chitwood et al. 2013) or if not there then using introgression coordinates obtained by using the sequence data to locate the introgression.
Reads were mapped to chimeric references using BWA with parameters “aln -t 4 -k 1 -l 25 -n 0.1 -e 15 -i 10” and mapped read counts extracted with samtools.
Custom R code was used to combine count files, normalized using R edgeR package function calcNormFactors() method TMM, differentially expressed genes (DEG) called using edgeR.  Custom R code tested DEG for GO and other biological category enrichments and special gene set enrichments and looked for common enrichments in ILs exhibiting QTLs for various root traits.  Gene-gene and gene-trait correlations were done. Co-expression networks were built using partial correlation R package SPACE and using a probabilistic graphical model with bootstrap aggregation with R package DAGBAG.
Genome_build: Matched references from (Koenig et al. 2013) and chimeric references described above, based on International Tomato Annotation Group SL2.40 ITAG 2.3 genome at SolGenomics.net.

organism: Solanum lycopersicum x Solanum pennellii

source_name: Root

growth_protocol: Seedlings of S. lycopersicum (cv. M82), S. pennellii (LA0716), and 75 introgression lines between those parents were grown according to (Ron et al., 2013). Plates were placed vertically in a rack in a randomized block design.

extract_protocol:
The  germination date was monitored for each seed. Immediately prior to harvesting root tissue for RNA-seq, each replicate of each genotype had between 2 and 5 plates, all of which were scanned with a Epson Perfection V700 photo flatbed scanner into 24-bit RGB TIF image files at 300 dpi. Images were analyzed with the imageJ program (Rasband 1997-2014) and custom macros. Based on germination date and scan date, seedling age in days after germination was determined, and primary roots of seedlings that were 3 or 4 days post-germination were traced with the imageJ polyline tool, following the root centerline from the top of the root (at start of hairs and change from green to white) to the tip. The coordinates of the polylines were recorded by the macros in data tables saved as files, along with metadata including genotype, plate ID, plating date, germination day of each seedling, plate harvest date, measurer, and two flags for each root: “collide” was true if the root contacted or crossed another root, and “along” was true if the root contacted another root and grew along it for any distance. The polylines in the vetted data were analyzed to measure root length and angle using multiple traits (Figure 1A). Additional data was calculated from the metadata: root age (days from germination to harvest), “germination age” (days from plating to germination), “plating age” (days from plating to harvest), and biological replicate number (based on plating date; replicates were named REP2 through REP5, and later replicates for fixing genotype errors were named REPN2 through REPN5 and REPX1 through REPX6). Four replicates of each of the 77 genotypes were grown. Plates were opened only once, at harvest time, to ensure the same growth conditions for all seedlings. Sampling occurred mid-afternoon. Between 7 and 14 root tips (1 cm), 3 to 4 days post-germination, from each genotype replicate were cut and immediately placed into a labeled 2ml tube containing silica beads and immersed in liquid nitrogen. Samples were stored at −80ºC until library preparation.
Libraries were created using a modified Kumar et. al. protocol. Library enrichment was done using 12 cycles. Each library was barcoded, using a unique bar code for each IL, but the same barcode for all replicates of an IL.  The libraries of each replicate were pooled, and the four pools were purified with Ampure beads. The library pooling was tested using a Bioanalyzer.

treatment_protocol: The experiments were carried out in a growth chamber with a 16:8 light:dark cycle at 22ºC and 50-75% humidity with a light intensity of 100μE.

tag: solanum pennellii introgression line

tag: tissue

value: Root

tag: solanum lycopersicum cultivar


title: Dnmt3ab_WT_H3K4me3_rep1

library_source: genomic

molecule: genomic DNA


title: Dnmt3ab_WT_H3K4me3_rep2


title: IL9-2-6 rep4


title: Dnmt3ab_DKO_H3K4me3_rep3

value: Dnmt3a floxed/floxed, Dnmt3b floxed/floxed, Zp3 +ve


title: IL9-2-6 rep3


title: d5_NGO_Input_rep1

description:
bivalency_PGC_d05_d25_domains.tar
GO_and_Mll2_peaks.tar

source_name: Non-growing oocytes

value: postnatal day 5

value: Non-growing oocytes


title: IL9-2-6 rep2


title: IL9-2-6 rep1


title: Dnmt3ab_DKO_H3K4me3_rep1


title: IL9-2-5 rep2


title: d5_NGO_H3K4me3_rep1


title: IL9-3-1 rep1


title: IL9-3 rep4


title: IL9-2-5 rep4


title: IL9-2-5 rep3


title: Dnmt3ab_DKO_H3K4me3_rep2


title: IL9-3-1 rep2


title: d5_NGO_H3K27ac_rep2

description:
Oocyte_H3K27ac_5kbrunning_RPM_nofilters.txt
OocyteH3K27ac_H3K27acGVpeaks_RPMcorrlength.txt


title: d5_NGO_H3K27ac_rep1


title: d5_NGO_H3K27me3_rep1


title: IL9-2-5 rep1


title: IL9-3 rep3


title: IL9-2 rep4


title: d25_GV_oocyte_Input_rep3

description:
GO_and_Mll2_peaks.tar
bed_files_combinations_GV.tar.gz
bivalency_PGC_d05_d25_domains.tar


title: IL9-2 rep3


title: d25_GV_oocyte_Input_rep2


title: IL9-2 rep2


title: IL9-1-3 rep4


title: d25_GV_oocyte_Input_rep1


title: d25_GV_oocyte_H3K4me3_rep2


title: IL9-1-3 rep3


title: d25_GV_oocyte_H3K27me3_rep2

description:
bed_files_combinations_GV.tar.gz
bivalency_PGC_d05_d25_domains.tar


title: IL9-1-3 rep2


title: IL9-1-3 rep1


title: d25_GV_oocyte_H3K27me3_rep1


title: d25_GV_oocyte_H3K27me3_500ng

description: ESC_oocyte_technical_optimisation_2kb_running_RPM_nofilters.txt


title: IL9-1-2 rep2


title: d25_GV_oocyte_H3K27me3_250ng


title: IL9-1-2 rep4


title: IL9-1-2 rep1


title: d25_GV_oocyte_H3K27ac_rep2

description:
bed_files_combinations_GV.tar.gz
Oocyte_H3K27ac_5kbrunning_RPM_nofilters.txt
OocyteH3K27ac_H3K27acGVpeaks_RPMcorrlength.txt


title: d25_GV_oocyte_H3K27ac_rep1


title: IL9-1 rep4


title: IL9-1 rep3


title: d25_GV_oocyte_H3K27ac_125ng


title: IL9-1 rep2


title: d15_GV_Input_rep1

value: postnatal day 15


title: d15_GV_H3K4me3_rep1


title: IL9-2 rep1


title: IL9-1 rep1


title: IL10-1-1 rep1


title: d25_GV_oocyte_H3K4me3_rep1


title: IL8-3-1 rep4


title: d10_GO_Input_rep1

source_name: Growing oocytes

value: postnatal day 10

value: Growing oocytes


title: d10_GO_H3K4me3_rep2


title: d10_GO_H3K4me3_rep1


title: IL8-3-1 rep2


title: IL8-3-1 rep1


title: IL8-3 rep4


title: 500_ESC_Input

source_name: Embryonic stem cells

value: Embryonic stem cells


title: IL8-3 rep3


title: 1000_ESC_Input


title: IL8-3 rep2


title: IL8-3 rep1


title: IL8-2-1 rep4


title: 1000_ESC_H3K4me3_2


title: MLL2_WT_GV_oocyte_rep3

description:
library strategy: BS-seq (PBAT)
Processed data files: MLL2_WT_GV_oocyte_rep3.cov.gz

extract_protocol:
Post-bisulfite adaptor tagging (PBAT) was used to generate whole-genome bisulfite sequencing libraries using 100 collected oocytes. Briefly, cells are lysed with 0.5% SDS in EB buffer and bisulfite-treated with one-step modification procedure using the Sigma Imprint DNA Modification kit. The resulting DNA are purified using columns from Zymo EZ DNA Methylation Direct kit. First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 10 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.
Cells for ChIP-seq were flash frozen in nuclear lysis buffer, cells for PBAT were flash frozen in PBS
The ChIP-seq libraries for all samples were prepared using an ultra-low input native ChIP protocol, as previously described with the several modifications.  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease in prepared digestion buffer, as per recommendations in the Brind’Amour protocol.  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using spri purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads at a 1.8:1 ratio.  Library preparation was completed using the Diagenode MicroPlex Library Preparation kit v2 using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations.
For single oocyte RNA profiling, four GV oocytes from Mll2 KO and WT mice were collected for each genotype. Cells were lysed, RNA reverse transcribed and amplified according to the protocol of SMARTer Ultra Low RNA Kit for Illumina Sequencing (Version 1, Clontech). Subsequently, samples were subjected to NEBNext Ultra DNA library preparation for Illumina using indexed adaptors (New England Biolabs). Resulting libraries were pooled in equimolar quantities for 75-bp single-read sequencing on Illumina HiSeq 2000, resulting in about 15-18 million reads per sample.
Post-bisulfite adaptor tagging (PBAT) was used to generate whole-genome bisulfite sequencing libraries using 100 collected oocytes. Briefly, cells are lysed with 0.5% SDS in EB buffer and bisulfite-treated with one-step modification procedure using the Sigma Imprint DNA Modification kit. The resulting DNA are purified using columns from Zymo EZ DNA Methylation Direct kit. First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 10 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.
ChIP-bisulfite-seq was done on MNase-digested 10% input samples from the ChIP protocol, detailed in the corresponding ChIP-seq samples.  Following DNA purification from chromatin using spri purification with Sera-Mag carboxylate-modified Magnetic SpeedBeads, samples were bisulfite converted using the Zymo EZ DNA Methylation Direct kit.  First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 16-20 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.

value: Mll2 floxed/floxed, Gdf9 -ve


title: 1000_ESC_H3K4me3_1


title: MLL2_WT_GV_oocyte_rep2

description:
library strategy: BS-seq (PBAT)
Processed data files: MLL2_WT_GV_oocyte_rep2.cov.gz


title: IL8-2-1 rep2


title: IL8-2-1 rep3


title: IL8-3-1 rep3


title: IL8-2 rep4


title: IL8-2-1 rep1


title: MLL2_KO_GV_oocyte_rep3

description:
library strategy: BS-seq (PBAT)
Processed data files: MLL2_KO_GV_oocyte_rep3.cov.gz


title: MLL2_KO_GV_oocyte_rep2

description:
library strategy: BS-seq (PBAT)
Processed data files: MLL2_KO_GV_oocyte_rep2.cov.gz


title: mm1179KO_replicate_04_input

city: Berkeley

first: Diane

last: Dickel

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

description: H3K27ac profiling in mouse embryonic limbs

data_processing:
Basecalls performed using CASAVA bcl2fastq_v2.17
Reads were filtered cutadapt v1.1 with parameter "-m 25 -q 25" and aligned to the mm9 genome assembly using bowtie v0.12.8, then peaks were called by MACS v1.4.2 with parameter "--mfold=10,30 -nomodel -p 0.0001"
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: pooled forelimbs from mm1179 enhancer-null mouse embryos at e11.5

growth_protocol: Mice were maintained in an animal facilty under standard conditions.

extract_protocol:
Forelimbs from embryos at E11.5 were dissected and cells were disaggregated using a 2ml glass douncer. Nuclei were crosslinked with 1% formaldehyde for 5 minutes and quenched with Glycine (1mM final). Nuclear pellets were sonicated to a fragment range of 200-400bp using a Diagenode Bioruptor Sonicator. Sonicated extracts were precleared for 1 hour at 4˚C and incubated with anti-H3K27ac antibodies for 2 hours at 4˚C. Dynabeads (1:1 mixture of Protein A and G) were then incubated with the antibody-chromatin complexes for 30 minutes at 4˚C and ChIP-immune complexes were pulled down using a magnet.
Illumina Truseq DNA sample prep kit

treatment_protocol: None.  WT and KO mice were not subjected to any treatment.

tag: strain

value: FVB

value: Forelimb

tag: developmental stage

value: embryonic day 11.5

value: mm1179 KO

tag: chip antibody

value: Input


title: IL8-2 rep3


title: MLL2_KO_GV_oocyte_rep1

value: postnatal day 21


title: IL8-2 rep2


title: 500_ESC_H3K4me3


title: IL8-2 rep1


title: IL8-1-5 rep4


title: Wt_replicate_04_input

source_name: pooled forelimbs from wild-type mouse embryos at e11.5

value: wild-type


title: hs72KO_replicate_01_input

source_name: pooled forelimbs from hs72 enhancer-null mouse embryos at e11.5

value: hs72 KO


title: IL8-1-5 rep3

value: Root


title: hs72KO_replicate_02_input


title: IL8-1-5 rep2


title: IL8-1-5 rep1


title: IL8-1-1 rep3


title: hs72KO_replicate_02_ChIP_H3K27ac

value: anti-H3K27ac (Active Motif cat no. 39133)


title: Wt_replicate_03_input


title: hs72KO_replicate_01_ChIP_H3K27ac


title: IL8-1-1 rep2


title: mm1179KO_replicate_03_ChIP_H3K27ac


title: mm1179KO_replicate_03_input


title: Wt_replicate_04_ChIP_H3K27ac


title: Wt_replicate_03_ChIP_H3K27ac


title: mm1179KO_replicate_01_input


title: IL8-1 rep4


title: IL8-1 rep3


title: mm1179KO_replicate_02_input


title: Wt_replicate_02_input


title: IL8-1-1 rep1


title: IL8-1 rep1


title: IL8-1 rep2


title: IL7-5-P75 rep4


title: Wt_replicate_01_input


title: mm1179KO_replicate_04_ChIP_H3K27ac


title: IL8-1-1 rep4


title: mm1179KO_replicate_02_ChIP_H3K27ac


title: mm1179KO_replicate_01_ChIP_H3K27ac


title: IL7-5-P75 rep2


title: IL7-5-P75 rep1


title: IL7-5-P5 rep3


title: Wt_replicate_01_ChIP_H3K27ac


title: Irf4Het Chronic d30 REP4

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
RNA sequencing reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped reads were retained. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included.
Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least one library. Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. P values from Bayes moderated t-tests were adjusted to control the global false discovery rate (FDR) across all comparisons with the ‘global’ option of the limma package. Genes were called differentially expressed if they achieved a FDR of 0.1 or less and had an expression change of 1.5 folds or greater. The called differentially expressed genes must also have at least 8 RPKMs (reads per kilobase of exon length per million mapped reads) in one or both of the two cell types being compared.
Genome_build: mm10
Supplementary_files_format_and_content: space-delimited text files include normalized log2-RPKM values for each sample

source_name: spleens and lymph nodes

growth_protocol: P14 CD8 T cell (wildtype [WT] or Irf4+/- [Irf4Het] or Batf+/- [BatfHet]) were transferred into congenically marked host mice, which were subsequently infected with LCMV WE (acute) or LCMV Docile (chronic). Donor P14 cell were sorted from infected mice on either day 8 or day 30 post infection and used for RNA sequencing. Naive (CD62L+, CD44-) CD8 T cells were used as controls.

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNAeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: celltype

value: P14 CD8+ T cells

value: Irf4 Het

tag: infection

value: Chronic

tag: time

value: 30 days


title: MLL2_WT_GV_oocyte_rep1

description:
library strategy: BS-seq (PBAT)
Processed data files: MLL2_WT_GV_oocyte_rep1.cov.gz

value: Germinal vesicle oocytes


title: IL7-5-P5 rep2


title: IL7-5-P5 rep4


title: Irf4Het Chronic d30 REP3


title: WT Acute d30 REP4

value: WT

value: Acute


title: Irf4Het Chronic d8 REP2

value: 8 days


title: WT Chronic.PDL1 d30 REP3


title: BatfHet Chronic d8 REP5

value: Batf Het


title: IL7-5-P5 rep1


title: IL7-5-P75 rep3


title: BatfHet Chronic d8 REP4


title: IL7-5-5 rep3


title: IL7-5-1 rep4


title: BatfHet Chronic d8 REP3


title: IL7-5-5 rep1


title: IL7-5-5 rep2


title: BatfHet Acute d8 REP2


title: IL7-5-1 rep3


title: IL7-5-1 rep2


title: BatfHet Acute d8 REP1


title: Wt_replicate_02_ChIP_H3K27ac

value: FVB

value: Forelimb

value: embryonic day 11.5


title: IL7-5-1 rep1


title: IL7-5 rep4


title: Irf4Het Acute d8 REP2


title: IL7-5-5 rep4


title: WT Chronic d8 REP4


title: IL7-5 rep3


title: IL7-4-1 rep4


title: IL7-4-1 rep3


title: WT Acute d8 REP3


title: 8-cell_embryo_MAST-seq_8b

city: Beijing

first: YangLu

last: Yang

state: Beijing

address: Beijing Xicheng District Yongan Road NO.95

country: China

institute: Beijing Friendship Hospital, Capital Medical University

description:
sequenced on Illumina
Sample 58

data_processing:
library strategy: MAST-seq (Measure a single cell twice by RNA-Seq)
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling. For data from Ion Proton, base calls were collected using Ion Torrent Suite v4.3 software.
Adaptor contamination and low-quality reads were discarded from the raw data.
For Illumina paired-end reads, TopHat (version 2.0.10) were used for sequence alignment, and FPKM values were generated by Cufflinks (version 2.1.1). For Ion Proton RNA-Seq reads, 2-step alignment method which combined STAR (version 2.3.0) and bowtie2 (version 2.1.0) was applied. Unmapped reads produced by STAR were re-mapped with bowtie2 in the “very-sensitive-local” mode, and merged bam files were taken as input by Cufflinks.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly mm10.
Supplementary_files_format_and_content: FPKM table generated by cufflinks

molecule: polyA RNA

growth_protocol: Isolation of zygotes, 2-cell, 4-cell, 8-cell embryos, inner cell mass (ICM) and trophectoderm (TE). 6- to 8-weeks old ICR female mice were injected with 7.5IU human chorionic gonadotropin (hCG) 46~48h after injection of 7.5IU pregnant mare serum gonadotrophin (PMSG). 2-cell, 4-cell and 8-cell stage embryos were collected from the oviduct of mated mice at 48, 56 and 70h post-hCG, respectively. The embryos were treated with Acid Tyrode’s solution to remove the zona pellucida and then were transferred to trypsin-EDTA and incubated at 37°C for 5 minutes. Then the embryos were washed with PBS-BSA buffer gently to dissociate the embryos into individual blastomeres. ICM and TE were isolated from mouse E3.5 blastocysts (Yan et al. 2013). The trophectoderm was isolated from the blastocysts with zona pellucida removed under a microscope by mechanically cut using a 30G needle. The exposed ICM was gently scraped from the trophectoderm. These two types of cells were then treated with Accutase or 0.005% trypsin at 37 °C for dissociated into single cell. Cell lines. Mouse embryonic fibroblast (MEF) was derived from E13.5 embryos of ICR strain. Mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatinized tissue culture plates and were passaged every two days.

extract_protocol:
The RNA of single mESC was extracted by the MAST-Seq protocol which was developed from the single cell RNA-Seq technique we previously developed (Tang et al. 2010b).
For the library constructed for Illumina sequencing platform, 10-100ng amplified cDNA was fragmentized to about 200bp fragments by Covaris S2, and purified with DNA Clean & Concentrator™-5. Then NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, Catalog #E7370L) was used to construct the cDNA library. The cDNA libraries were sequenced on Illumina HiSeq 2000 and 2500 instrument with 100bp reads and pair-end parameter. For the libraries constructed for Thermo Fisher Proton sequence platform, First, 10-100ng amplified cDNA was fragmentized to about 250bp fragments by Covaris S2, and purified with DNA Clean & Concentrator™-5. The Ion XpressTM Plus Fragment Library Kit (ThermoFisher, cat. no. 4471269) and Ion XpressTM Barcode Adapters 1-16 Kit (Thermo Fisher, cat. No. 4471250) were used to construct the library. Then, sequencing was performed using PI chips with the Ion PI Sequencing 200 kit v3 on Ion PI Proton system.

value: ICR

tag: tissue/cell type

value: mouse 8-cell embryo


title: WT Acute d8 REP4


title: IL7-4-1 rep1


title: IL7-4-1 rep2


title: 8-cell_embryo_MAST-seq_8a

description:
sequenced on Illumina
Sample 57


title: 8-cell_embryo_MAST-seq_7a

description:
sequenced on Illumina
Sample 55


title: IL7-4 rep3


title: Irf4Het Chronic d8 REP1


title: IL7-4 rep1


title: IL7-4 rep4


title: IL7-4 rep2


title: 8-cell_embryo_MAST-seq_6a

description:
sequenced on Illumina
Sample 53


title: IL7-3 rep3


title: 8-cell_embryo_MAST-seq_7b

description:
sequenced on Illumina
Sample 56


title: IL7-3 rep2


title: IL7-3 rep4


title: Irf4Het Acute d8 REP1


title: IL7-5 rep1


title: 8-cell_embryo_MAST-seq_5b

description:
sequenced on Illumina
Sample 52


title: IL7-3 rep1


title: IL7-2 rep4


title: WT Chronic d8 REP3


title: 8-cell_embryo_MAST-seq_4b

description:
sequenced on Illumina
Sample 50


title: 8-cell_embryo_MAST-seq_5a

description:
sequenced on Illumina
Sample 51


title: 8-cell_embryo_MAST-seq_4a

description:
sequenced on Illumina
Sample 49


title: IL7-2 rep3


title: IL7-2 rep2


title: 8-cell_embryo_MAST-seq_3b

description:
sequenced on Illumina
Sample 48


title: 8-cell_embryo_MAST-seq_6b

description:
sequenced on Illumina
Sample 54


title: 8-cell_embryo_MAST-seq_3a

description:
sequenced on Illumina
Sample 47


title: IL7-2 rep1


title: IL7-1 rep3


title: 8-cell_embryo_MAST-seq_2a

description:
sequenced on Illumina
Sample 45


title: 8-cell_embryo_MAST-seq_1b

description:
sequenced on Illumina
Sample 44


title: IL7-1 rep2


title: IL7-1 rep1


title: 8-cell_embryo_MAST-seq_1a

description:
sequenced on Illumina
Sample 43


title: IL6-4 rep2


title: Eigth_mESC_1f

description:
sequenced on Illumina
Sample 24

value: mouse embryonic stem cell


title: Eigth_mESC_1g

description:
sequenced on Illumina
Sample 25


title: IL6-4 rep3

value: Root


title: IL6-4 rep4


title: IL6-4 rep1


title: IL6-3 rep3


title: IL6-3 rep4


title: Eigth_mESC_1d

description:
sequenced on Illumina
Sample 22


title: Eigth_mESC_1c

description:
sequenced on Illumina
Sample 21


title: Eigth_mESC_1e

description:
sequenced on Illumina
Sample 23


title: Eigth_mESC_1b

description:
sequenced on Illumina
Sample 20


title: Eigth_mESC_1a

description:
sequenced on Illumina
Sample 19


title: IL6-3 rep1


title: 8-cell_embryo_MAST-seq_2b

description:
sequenced on Illumina
Sample 46


title: Quarter_mESC_1d

description:
sequenced on Illumina
Sample 18


title: IL6-2 rep4


title: IL7-1 rep4


title: Quarter_mESC_1c

description:
sequenced on Illumina
Sample 17


title: IL6-3 rep2


title: Eigth_mESC_1h

description:
sequenced on Illumina
Sample 26


title: Half-mESC_2b

description:
sequenced on Illumina
Sample 14


title: Quarter_mESC_1b

description:
sequenced on Illumina
Sample 16


title: IL6-2 rep2


title: IL6-2 rep1


title: Quarter_mESC_1a

description:
sequenced on Illumina
Sample 15


title: IL6-2 rep3


title: IL6-1 rep4


title: Half-mESC_2a

description:
sequenced on Illumina
Sample 13


title: IL6-1 rep3


title: Half_mESC_1b

description:
sequenced on Illumina
Sample 12


title: IL6-1 rep2


title: Half_mESC_1a

description:
sequenced on Illumina
Sample 11


title: Single_mESC_6

description:
sequenced on Illumina
Sample 6


title: IL6-1 rep1


title: IVF-2

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The number of raw reads mapped to genes was calculated by RSEM(rsem-1.2.4), the reference genome using Sscrofa11.1, then put all the samples results together and normalized by EDAseq(1.99.1),  genes expression fold change were calculated using normalized raw reads.
Genome_build: Sscrofa11.1/susScr11
Supplementary_files_format_and_content: Each files contain RSEM output, including raw counts, TPM and RPKM, all_samples_tpm file contains all samples normalized tpm value.

organism: Sus scrofa

source_name: in vitro blastocysts

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (Cat# E7770) was used with 1 ug of fetuses total RNA for the construction of sequencing libraries.Embryo RNA was conveted into cDNA then NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat# E7645) was used with 100 ng of embryo cDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: in vitro day6

value: blastocysts

tag: Sex

value: pooled male and female


title: IVF-1


title: IL5-5 rep4


title: Single_mESC_5

description:
sequenced on Illumina
Sample 5


title: XIST-KO-2

value: male


title: IL5-5 rep2


title: Single_mESC_3

description:
sequenced on Illumina
Sample 3


title: WT-1


title: WT-2


title: Single_mESC_4

description:
sequenced on Illumina
Sample 4


title: XIST-KO-1


title: IL5-4 rep4


title: IL5-5 rep1


title: IL5-4 rep3


title: IL5-4 rep2


title: WT+Kdm4A-1


title: Single_mESC_1

description:
sequenced on Illumina
Sample 1


title: WT+Kdm4A-2


title: Single_mESC_2

description:
sequenced on Illumina
Sample 2


title: day35-NF-1

description: naturally fertilized (NF)

source_name: fetus tissue

value: embryonic day35

value: body tissue


title: day35-NF-2

description: naturally fertilized (NF)


title: day35-normal-3


title: IL5-3 rep3


title: IL5-5 rep3


title: JQ1+  (UJ006)

city: Shenyang

first: Guoxin

last: Liang

state: Liaoning

address: No.155 Nanjing North street

department: AIDS research center

institute: China Medical University

data_processing:
55 TO 60 MILLION 2x100 BP PAIRED END RAW PASSING FILTERS READS SEQUENCED ON ILLUMINA HISEQ 2000 V3 INSTRUMENT
map reads onto reference genome mm9
estimate normalized expression level (RPKM/FPKM) of known genes and transcripts
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Spleen

growth_protocol: all cells were cultured in RPMI1640 medium plus LPS+ IL4 for 3 days

extract_protocol:
total RNA was extracted with Trizol, rRNA was depleted with the Ribo-Zero rRNA removal kit (Epicentre)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated with Control, JQ1+(80nM) and Flavopiridol (30nM) for 3 days

tag: cell type

value: B cells

tag: subset

tag: culture

value: LPS+ IL4 plus DMSO stimulated B cells for 3 days

tag: treatment


title: Flavopiridol (UJ007)

value: Flavopiridol


title: IL5-3 rep4


title: day35-normal-2


title: IL5-3 rep2


title: day35-normal-1


title: OSK-D3_minus_GSK3i

description: Extracting total RNA at D3 after OSK transfection for 2 days, medium do not contain CHIR-99021 and LiCl

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The number of raw reads mapped to genes was calculated by RSEM(rsem-1.2.4), the reference genome using mm10, then put all the samples results together and normalized by EDAseq(1.99.1), genes expression fold change were calculated using normalized raw reads.
Genome_build: mm10
Supplementary_files_format_and_content: Each files contain Rsem output, including TPM and FPKM.

extract_protocol:
Total RNA was extracted by Trizol-based protocol.
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)

tag: passage


title: OSK-D7_minus_GSK3i

description: Extracting total RNA at D7 after OSK transfection for 2 days, medium do not contain CHIR-99021 and LiCl


title: OSK-D7_minus_vc

description: Extracting total RNA at D7 after OSK transfection for 2 days, medium do not contain Vitamin C


title: IL5-3 rep1


title: IL5-2 rep4


title: DMSO (UJ005)

value: DMSO


title: IL5-2 rep3


title: day35-abnormal-2


title: day35-abnormal-1


title: OSK-D3_minus_bFGF

description: Extracting total RNA at D3 after OSK transfection for 2 days, medium do not contain bFGF


title: OSK-D7_minus_bFGF

description: Extracting total RNA at D7 after OSK transfection for 2 days, medium do not contain bFGF


title: IL5-4 rep1


title: day30-NF-2

description: naturally fertilized (NF)

value: embryonic day30

value: female


title: IL5-2 rep2


title: IL5-2 rep1


title: day30-NF-1

description: naturally fertilized (NF)


title: IL5-1 rep4


title: day30-normal-2


title: GFP-D5

description: Extracting total RNA at D5 after GFP transfection for 2 days


title: GFP-D3

description: Extracting total RNA at D3 after GFP transfection for 2 days


title: day30-normal-1


title: OSK-D3_minus_vc

description: Extracting total RNA at D3 after OSK transfection for 2 days, medium do not contain Vitamin C


title: IL5-1 rep2


title: OSK-D7

description: Extracting total RNA at D7 after OSK transfection for 2 days


title: IL5-1 rep1


title: day30-abnormal-2


title: day30-abnormal-1


title: GFP-D7

description: Extracting total RNA at D7 after GFP transfection for 2 days


title: IL4-4 rep4


title: PP flower and fruit RNA-seq

first: Xia

last: Cui

address: 12 Zhongguancun Nandajie

institute: Chinese Academy of Agricultural Sciences

data_processing:
The RNA-seq reads were aligned to the tomato genome (ITAG2.4) using tophat-2.0.11 (Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis.
Genome_build: ITAG2.4
Supplementary_files_format_and_content: bigWig

organism: Solanum pimpinellifolium

source_name: 5DPA, 20DPA, mature green, break stage and red ripen fruits and -2DPA flower from Solanum pimpinellifolium PI365967 (PP)

growth_protocol: the tomato plants were grown in greenhouse on soil

extract_protocol:
the flowers and fruits from different stages were collected. The total RNA was extracted using TRIZOL reagent (Invitrogen Cat#15596026).
Strand-specific RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina Hiseq 2500.

treatment_protocol: No treatment

tag: cultivar

value: fruit/flower

tag: Stage


title: IL4-4 rep3

tag: solanum pennellii introgression line

tag: tissue


title: OSK-D1

description: Extracting total RNA at D1 after OSK transfection for 2 days

tag: strain


title: OSK-D0

description: Extracting total RNA at D0 after OSK transfection for 2 days


title: IL4-4 rep2

tag: solanum lycopersicum cultivar


title: OSK-D3

description: Extracting total RNA at D3 after OSK transfection for 2 days


title: day30-normal-3

tag: developmental stage


title: OvSvK-D4

description: Extracting total RNA at D4 after OvSvK transfection for 2 days


title: IL4-4 rep1


title: OvSvK-D3

description: Extracting total RNA at D3 after OvSvK transfection for 2 days


title: IL4-3-2 rep4


title: IL4-3-2 rep3


title: GFP-D1

description: Extracting total RNA at D1 after GFP transfection for 2 days


title: MNase-Seq kay RNAi replicate 2

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

data_processing:
Paired-end reads were mapped to D. melanogaster genome assembly dm3 excluding the scaffold Uextra. We used Bowtie v1.1.1 with “-X 750” parameter setting.
Dyad coverage vectors were obtained by size-selecting fragments of length >=120 and <=200 bp and resizing their length to 50 bp fixed at the fragment center
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph files with dyad coverage

organism: Drosophila melanogaster

source_name: BG3-c2 cell line

growth_protocol: BG3-c2 cells were cultured at 26°C in Schneider’s Drosophila Medium (Gibco) including 10% fetal calf serum (FCS), Penicillin-Streptomycin and 10 µg/ml human insulin.

extract_protocol:
After 6 days cells were harvested and 1/10 volume of fixing solution (1 M NaCl, 0.5 M HEPES pH 8, 10 mM EDTA, 5 mM EGTA, 11% FA) directly added to the medium. After an incubation of 10 min at 18°C, glycine was added to 125 mM and cells collected by centrifugation. To isolate the nuclei, cells were washed in 10 ml of cold PBS and resuspended in 1 ml PBS (containing protease inhibitor cocktail (PIC, Roche) and 0.5% Triton X-100) per 1 x 108 cells and rotated for 15 min at 4°C. Nuclei were then washed in 10 ml PBS and resuspended in 1 ml RIPA buffer (incl. PIC) per 1 x 108 cells and CaCl2 was added to 2 mM f.c.. Aliquots of 600 µl were treated with 1.2 U of MNase for 20 min at 37°C, then 13 µl of 0.5 M EGTA and 400 µl RIPA were added. The chromatin was sheared in a Covaris sonicator in a 12x12 fiber tube at 50 W, 20% output for 8 min. After a centrifugation at 17,000 x g for 20 min, the supernatant was used for subsequent H3 ChIP.
Recovered DNA was quantified using the Qubit® dsDNA HS Assay Kit (Life Technologies, Cat.no.Q32851) and sequencing libraries were prepared using the MicroPlex Library Preparation kit (Diagenode, Cat. No. C05010011) starting with 2 ng DNA whenever possible. PCR amplification was monitored by quantifying amplified libraries (maximum 19 cycles).

treatment_protocol: For each knockdown condition, two 250 ml flasks of cells were prepared. 1.5 x 106 cells in 4 ml medium (containing antibiotics and insulin but no FCS) were seeded per flask and 50 µg of dsRNA added. After gentle shaking for 1 hr at room temperature (RT), 16 ml of medium (+FCS/+antibiotics/+insulin) was added to the cells.

tag: cell line

tag: RNAi knockdown

value: kay

tag: replicate


title: MNase-Seq GST RNAi replicate 3

value: GST


title: MNase-Seq mod(mdg4) RNAi replicate 2


title: OvSvK-D2

description: Extracting total RNA at D2 after OvSvK transfection for 2 days


title: OvSvK-D1

description: Extracting total RNA at D1 after OvSvK transfection for 2 days


title: OvSvK-D0

description: Extracting total RNA at D0 after OvSvK transfection for 2 days


title: MNase-Seq GST RNAi replicate 2


title: IL4-3-2 rep1

value: Root


title: MNase-Seq Q9VQ77 RNAi replicate 2


title: MNase-Seq ACF1 RNAi replicate 1


title: IL4-3 rep3


title: IL4-3 rep4


title: MNase-Seq yw replicate 1

source_name: 2-8 hour embryos

extract_protocol:
Eggs laid during a 6 hr period were collected and aged for a further two hours at 25°C. Subsequently, one gram embryos were dechorinated in 120 ml 1:5 diluted sodium hypochloride (VWR, Cat.no. 301696S) for 3 min, thoroughly washed and fixed in 10 ml fixing solution [0.1 M NaCl, 0.05 M HEPES pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1.8% Formaldehyde (FA; Sigma, Cat. No F1635) added to 30 ml n-Heptane (VWR, Cat. No. 8.22332.1000)] for 15 min at 16-18°C on a rotating wheel. Fixation was quenched by adding 125 mM glycine. The embryos were subsequently washed with PBS (including 0.01% Triton-X100) for 10 min and stored at -80°C. For nuclei isolation, embryos were slowly thawed and dounced using a glass homogenizer (Schubert, Cat.no. 9164693) with 20 strokes each of the A and B pestles in ice-cold NX-I buffer [15 mM HEPES pH 7.6, 10 mM KCl, 2 mM MgCl2, 0.5 mM EGTA, 0.1 mM EDTA, 350 mM sucrose, 1 mM DTT, 0.2 mM PMSF, Protease inhibitors Leupeptin, Pepstatin and Aprotinin (10 µg/ml)]. The lysate was filtered through Miracloth and nuclei were pelleted at 3,500 rpm, 10 min at 4°C. For MNase digestion, the nuclei were resuspended in the MNase digestion buffer. About 80 mg of nuclei were digested with 13 units of MNase (Sigma, Cat.no N5386) for 15 min, 37°C while shaking at 500 rpm. The reaction was stopped by adding 20 µl of 0.5 M EDTA, pH 8.0 and the tubes were quickly transferred to ice for 1 min. Nuclei were spun at 12,500 rpm, 10 min at 4°C. The supernatants containing most of the DNA were collected and the buffer composition was aDJ.gzusted to RIPA [1% Triton X-100, 0.1% Na deoxycholate, 140 mM NaCl, 10 mM Tris pH 8.0, 1 mM EDTA, 0.1% SDS, 1mM PMSF]. The digestion predominantly yielded mononucleosomes.
Recovered DNA was quantified using the Qubit® dsDNA HS Assay Kit (Life Technologies, Cat.no.Q32851) and sequencing libraries were prepared using the MicroPlex Library Preparation kit (Diagenode, Cat. No. C05010011) starting with 2 ng DNA whenever possible. PCR amplification was monitored by quantifying amplified libraries (maximum 19 cycles).

value: 2-8 hour embryos

tag: genotype

value: yw


title: MNase-Seq yw replicate 2


title: IL4-3 rep2


title: IL4-3 rep1


title: MNase-Seq W1118 replicate 3


title: OSK-D5

description: Extracting total RNA at D5 after OSK transfection for 2 days


title: IL4-2 rep4


title: IL4-2 rep3


title: MNase-Seq ACF1 replicate 3


title: IL4-3-2 rep2


title: MNase-Seq ACF1 replicate 1


title: MNase-Seq ACF1 replicate 2


title: IL4-2 rep2


title: IL5-1 rep3


title: IL4-1 rep4


title: MNase-Seq W1118 replicate 1


title: MNase-Seq W1118 replicate 2


title: MNase-Seq GST RNAi replicate 1


title: IL4-1 rep3


title: H2A.C ChIP

data_processing:
Alignment to dm3 without chromosome Uextra using bowtie version 1.1.1 (parameter -m 1)
Read extension to 200 bp and coverage vector calculation, bedGraph files were generated from coverage vectors using export.bedGraph (bioconductor package 'rtracklayer')
Peak calling with Homer. CTCF called over input (parameters: -style factor -size 200 -fragLength 200 -inputFragLength 200). H2A.V callled over H3 ChIP (parameters: -style histone)
Genome_build: dm3
Supplementary_files_format_and_content: bedgraph files of coverage and bed files of ChIP-peaks

source_name: unstaged embryos

extract_protocol:
Unstaged embryos (1 g) were dechorinated in 120 ml, 1:5 diluted, sodium hypochloride (VWR, Cat.no. 301696S) for 3 min. The embryos were thoroughly washed and fixed in the fixing solution [10 ml, 0.1 M NaCl, 0.05 M HEPES pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 3.7% Formaldehyde (Sigma, Cat. No F1635) added to 30 ml n-Heptane (VWR, Cat. No. 8.22332.1000)] for 15 min at 16-18°C on a rotating wheel. Fixation was quenched by adding 125 mM glycine. The embryos were subsequently washed with PBS (including 0.01% Triton-X100) for 10 min and stored at -80°C until further use.   For nuclei isolation, embryos were slowly thawed and dounced using a glass homogenizer (Schubert, Cat.no. 9164693) with 20 strokes each of the A and B pestles in ice-cold NX-I buffer [15 mM HEPES pH 7.6, 10 mM KCl, 2 mM MgCl2, 0.5 mM EGTA, 0.1 mM EDTA, 350 mM sucrose, 1 mM DTT, 0.2 mM PMSF, Protease inhibitors Leupeptin, Pepstatin and Aprotinin (10 µg/ml)]. The lysate was filtered through Miracloth and nuclei were pelleted at 3500 rpm, 10 min, 4°C. The pellet was washed in NX-I buffer. Finally, the nuclei were resuspended in RIPA [1% Triton X-100, 0.1% Sodium deoxycholate, 140 mM NaCl, 10 mM Tris pH 8.0, 1 mM EDTA, 0.1% SDS, 1 mM PMSF] and washed 3 times. Nuclei were then counted and frozen at -80°C in aliquots of ~109 nuclei/ml.  For shearing and ChIP, thawed nuclei were adjusted to ~2x108/ml by dilution in RIPA and sheared with a Covaris S220 system (Covaris Inc. MA, USA) at 110 Watts, 20% duty factor and 200 cycles per burst for 25 min. Chromatin was pre-cleared using protein a A+G bead (1:1) mix for 1h at 4°C. Immunoprecipitations were set up overnight at 4°C with 200 µl chromatin and 4 µl of the respective antibody adjusted to 500 µl with RIPA. RIPA-equilibrated protein A+G (1:1) mix was then added to precipitate the immune-complexes for 3 h at 4°C. Beads were washed subsequently 5 times for 10 min each in 1 ml RIPA buffer. Residual RNA was digested by RNase A (10 µg/100 µl, Sigma, Cat. No. R4875) at 37°C for 20 min. Subsequent protein digestion (25 µg/100 µl, Proteinase K, Genaxxon, Cat.no. M3036.0100) and reversal of cross-linking were performed together at 68°C for 2 hours. DNA was purified using GenElute™ PCR Clean-Up Kit (Sigma, Cat.no NA1020)
ChIP DNA was quantified using the Qubit® dsDNA HS Assay Kit (Life Technologies, Cat.no.Q32851) and sequencing libraries were prepared using the MicroPlex Library Preparation kit (Diagenode, Cat. No. C05010011) starting from 2 ng DNA, whenever possible. PCR amplification was monitored by quantifying amplified libraries (maximum 19 cycles).

value: embryos

value: wt

tag: chip-antibody

value: H2A.V (custom AB)


title: IL4-1 rep2


title: MNase-Seq ACF1 RNAi replicate 2


title: IL4-1 rep1


title: H3 ChIP

value: H3 (Abcam Cat.# ab1791)


title: CTCF ChIP


title: IL3-5 rep4


title: IL3-5 rep3


title: IL3-5 rep2


title: input


title: Fibroblast rep2

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequenced reads were aligned to the mm9 mouse genome assembly using STAR
Uniquely aligned reads were quantified at exons of annotated genes and normalized to sequence depth and gene length using HOMER. The number of reads per kilobase per million mapped (RPKM) for all RefSeq annotated genes were calculated
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for all annotated genes for each sample

source_name: Lewis lung carcinomas

growth_protocol: For generation of fluorescently tagged Lewis Lung carcinoma cells , cultured cells were transfected with a dTomato-containing pCEFL expression vector and subjected to FACS-sorting for dTomato-positive cells.  The sorted cells were subsequently maintained in culture media supplemented with 2 mg/ml G418. Cells (5×10^5 per injection) were injected subcutaneously in both flanks of mice.

extract_protocol:
Cells were sorted into cold media, and RNA was isolated by cell lysis with Trizol (Invitrogen), phase separation with chloroform, and subsequent purification of RNA from the aqueous phase using an RNA micro purification kit (Qiagen).
RNA quality was assessed using the Agilent 2100 Bioanalyzer. Total RNA (200 ng) was prepared for sequencing using polydT-mediated cDNA synthesis according to the manufacturer´s (Illumina) instructions. Subsequent library preparation was performed using the NEBNext RNA library preparation kit for Illumina. Library quality was assessed using the Fragment Analyzer (AATI) followed by library quantification (Illumina library quantification kit). Sequencing was carried out on a HiSeq1500 platform (Illumina) with a read length of 50 bp.

treatment_protocol: Alexa 647-collagen was injected into Lewis lung carcinomas formed by subcutaneous inoculation of dTomato-expressing Lewis lung carcinoma cells into transgenic Col1a1-GFP mice. 24 h later, single-cell suspensions were prepared, FC receptor-blocked, and stained with Zombie aqua and anti-F4/80 antibody. Cells were sorted into dTomato+ cells (Lewis lung carcinoma cells), GFP+ cells (fibroblasts), and dTomato-;GFP-;F4/80+;collagen+ cells (M2-TAMs).

tag: cell type

value: Fibroblast


title: TAM rep 1

value: M2 tumor-associated macrophages


title: IL3-5 rep1


title: IL4-2 rep1


title: LLC rep2

value: Lewis lung carcinoma cells


title: IL3-4 rep2


title: IL3-4 rep1


title: IL3-4 rep4


title: LLC rep1


title: Total tumor rep2

value: Total tumor


title: Fibroblast rep1


title: Total tumor rep1


title: IL3-1 rep4


title: IL3-1 rep3


title: TAM rep 2


title: IL3-2 rep2


title: IL3-2 rep3


title: IL3-2 rep1


title: IL3-2 rep4


title: IL3-1 rep1


title: IL3-1 rep2


title: Plectus sambesii

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

description: Bisulfite sequencing

data_processing:
Processing and alignment to genome was performed using Bismark using non-directional mode to generate bam files
CG methylation extracted from bam files using MethylExtract with default parameters
Genome_build: P. sambesii: BioSample SAMN07227113; R. culicivorax, T. spiralis and T. muris all from Wormbase Parasite release 4 (WBPS4)
Supplementary_files_format_and_content: All CG sequences genome-wide with >10 total reads.  Bed files tab delimited: chr, start, stop, methyl C reads, total reads

organism: Plectus sambesii

source_name: Psambesii

extract_protocol:
DNA extracted using Qiagen blood/tissue kit according to manufacturer's instructions
Pico-methylseq kit (Zymo) according to manufacturer's instructions

value: Adult


title: IL2-6-5 rep3

source_name: Root


title: IL2-6-5 rep4


title: IL2-6-5 rep1


title: IL3-4 rep3


title: Tlr2-/-_PBS_12

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

data_processing:
The RNAseq data were mapped on zebrafish genome (GRCz10 version) and tag counts were performed by Bowtie 2 using GeneTiles software (http://www. genetiles. com)
Then, we performed normalization and gene expression analysis using the R package and DESeq2
Genome_build: GRCz10
Supplementary_files_format_and_content: Yang_genes_mapped_27-6-2017_DEseq2.xlsx

organism: Danio rerio

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Life Technologies) and purified using RNeasy MinElute Cleanup Kit (Qiagen, the Netherlands). The concentration and quality of RNAs were evaluated by NanoDrop 2000 (Thermo Scientific, the Netherlands).
RNAseq was performed using Illumina Hi-Seq 2500
RNAseq was performed using Illumina Hi-Seq 2500

tag: line

value: Tlr2 fish line

value: whole embryos

tag: age

value: 5 days post fertilization

tag: infection

value: PBS injection


title: HAT3-1_ChIPSeq

city: Frederiksberg C

first: Daniel

address: Thorvaldsensvej 40

department: Plant and Environmental Sciences

institute: University of Copenhagen

data_processing:
Standard Illumina base calling software
Read mapping and coverage analysis were done using SHORE ver. 0.8unstable (rev. 2316.a00f) (Ossowski et al., 2008)
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph

organism: Arabidopsis thaliana

source_name: whole plant

growth_protocol: plants were grown in liquid MS medium for 10 days

extract_protocol:
ChIP experiments were carried out as described by "Kwon, C.S., Chen, C. and Wagner, D. (2005) WUSCHEL is a primary target for transcriptional regulation by SPLAYED in dynamic control of stem cell fate in Arabidopsis. Genes Dev. 19, 992–1003. " except that anti-FLAG M2 magnetic beads (Sigma) were used and immunoprecipitations were only performed for 2 h.
Illumina® TruSeq® ChIP Sample Preparation Kit

value: Columbia

tag: chip antibody

value: anti-FLAG M2 magnetic beads (Sigma, catalog# A2220)


title: IL2-6 rep3

value: Root


title: IL2-6 rep4


title: Tlr2-/-_PBS_11


title: Col-WT-1_Coverage

value: none (input)


title: Sm_PZQ_46_3

city: Albuquerque

first: Charles

last: Cunningham

state: New Mexico

address: 1 University of New Mexico

department: Biology

institute: University of New Mexico

data_processing:
Raw read data was demultiplexed (segregated by library index) using Illumina CASAVA version 1.8.2.
Thereafter, NCGR's custom contaminant filtering pipeline removed anomalous sequences. These aberrant sequences include Illumina Phix control, library adapters, primer dimers and library indexes not part of the experiment.  NCGR's contaminant filtering pipeline ensures only the highest quality data goes into downstream analyses.
Sequenced reads were mapped to Ensembl Mouse release 75 (GRCm38) whole genome using Tophat2 v.2.0.12 using default settings.
Genome_build: Ensembl Mouse release 75 (GRCm38)
Supplementary_files_format_and_content: A matrix of the samples in a tab-delimited text file with the FPKM values.
Supplementary_files_format_and_content: A matrix of the samples in a tab-delimited text file with the raw count of the sequence reads.

source_name: Liver

extract_protocol:
Livers were removed, placed in RNA at 4°, and RNA was harvested using RNA Maxi Kit (Qiagen #75162).  RNA was tested on nanodrop and Bioanalzer. Illumina TruSeq RNA Library Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
TRUSEQ RNA Library Preparation on the Sciclone NGS Liquid Handler

treatment_protocol: Mice were gavaged at 32-35 days post infection with either Vehicle (Cremophor EL(250 mg/kg)) or Praziquantel (250 mg/kg).

value: Swiss Webster (CFW)

value: liver

tag: days post infection

value: 46 days

tag: treatment

value: Praziquantel (250 mg/kg)


title: Tlr2-/-_PBS_4


title: Tlr2-/-_Mm20_13

value: M. mariunum injection


title: IL2-5 rep4

extract_protocol:
The  germination date was monitored for each seed. Immediately prior to harvesting root tissue for RNA-seq, each replicate of each genotype had between 2 and 5 plates, all of which were scanned with a Epson Perfection V700 photo flatbed scanner into 24-bit RGB TIF image files at 300 dpi. Images were analyzed with the imageJ program (Rasband 1997-2014) and custom macros. Based on germination date and scan date, seedling age in days after germination was determined, and primary roots of seedlings that were 3 or 4 days post-germination were traced with the imageJ polyline tool, following the root centerline from the top of the root (at start of hairs and change from green to white) to the tip. The coordinates of the polylines were recorded by the macros in data tables saved as files, along with metadata including genotype, plate ID, plating date, germination day of each seedling, plate harvest date, measurer, and two flags for each root: “collide” was true if the root contacted or crossed another root, and “along” was true if the root contacted another root and grew along it for any distance. The polylines in the vetted data were analyzed to measure root length and angle using multiple traits (Figure 1A). Additional data was calculated from the metadata: root age (days from germination to harvest), “germination age” (days from plating to germination), “plating age” (days from plating to harvest), and biological replicate number (based on plating date; replicates were named REP2 through REP5, and later replicates for fixing genotype errors were named REPN2 through REPN5 and REPX1 through REPX6). Four replicates of each of the 77 genotypes were grown. Plates were opened only once, at harvest time, to ensure the same growth conditions for all seedlings. Sampling occurred mid-afternoon. Between 7 and 14 root tips (1 cm), 3 to 4 days post-germination, from each genotype replicate were cut and immediately placed into a labeled 2ml tube containing silica beads and immersed in liquid nitrogen. Samples were stored at −80ºC until library preparation.
Libraries were created using a modified Kumar et. al. protocol. Library enrichment was done using 12 cycles. Each library was barcoded, using a unique bar code for each IL, but the same barcode for all replicates of an IL.  The libraries of each replicate were pooled, and the four pools were purified with Ampure beads. The library pooling was tested using a Bioanalyzer.

tag: solanum pennellii introgression line


title: IL2-6 rep2

tag: tissue


title: IL2-5 rep3


title: IL2-6 rep1


title: Tlr2-/-_Mm20_9


title: MP_rep4

city: Marburg

first: Pengfei

last: liu

department: Department of Biogeochemistry

institute: Max-Planck-Institute for terrestrial microbiology

description:
mRNA were enriched for sequencing
processed data file: Raw_reads_counts_M.txt, Raw_reads_counts_P.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to reference genomes (CP003243 for M. conradii and AP009389 for P. thermopropionicum) using the function BWA-MEM of program bwa version 0.7.5a-r405 (Li and Durbin, 2009) with parameters: -t 4. Unique mapped reads were filtered by using samtools-0.1.19 (Li et al., 2009), with parameters: -f 0×2, -q 30, -F 0×100, NM≤5. Reads belonging to 16S/23S rRNA, reads that matched more than one segment of a genome, and reads with more than 5 mismatches were discarded. To exclude reads that may align ambiguously (that is, to either genome), we did a cross reference alignment by using the parameter described above (Fig. S3). Briefly, we firstly aligned reads from M and P to the opposing genome.
Unique mapped reads were analyzed and assigned to individual CDSs by HTSeq (Anders et al., 2014) according to the genome annotation provided by GenBank (M. conradii: NC_017034 and P. thermopropionicum: NC_009454).
Genome_build: CP003243 for M. conradii and AP009389 for P. thermopropionicum
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each samples calculated by HTSeq

organism:
Pelotomaculum thermopropionicum
Methanocella conradii

growth_protocol:
Methanocella conradii strain HZ254 was grown in monoculture (abbreviated as M) in strictly anaerobic medium with H2:CO2 (4:1, 1.7 atm ) as previously described (Liu et al., 2014, Appl Environ Microbiol, 80:4668-4676; Lü and Lu, 2012, PLoS One, 7:e35279 )
Pelotomaculum thermopropionicum strain SI was grown in monoculture (abbreviated as P) in the same strictly anaerobic medium as M. conradii with N2:CO2 (4:1, 1.7 atm) and 20 mM pyruvate as previously described (Liu et al., 2014, Appl Environ Microbiol 80:4668-4676& Imachi et al., 2002, Int J Syst Evol Microbiol 52:1729-1735 )
Methanocella conradii and Pelotomaculum thermopropionicum coculture (abbreviated as MP) were grown in the same strictly anaerobic medium as M. conradii with N2:CO2 (4:1, 1.7 atm) and 20 mM propionate as previously described (Liu et al., 2014, Appl Environ Microbiol 80:4668-4676 )

extract_protocol:
Total RNA were extracted using AllPrep DNA/RNA Mini Kit (Qiagen, Germany) according to the manufacture’s instruction. RLT plus buffer was supplemented with 2% v/v 2 M DTT (Sangon Biotech, China). 600 µl RLT Plus buffer was added to each cell pellet. Cell pellets of P and MP were homogenized for 120 s in total (5.0 m/s, 3×40 s with 2 min intervals on ice) in a FastPrep-24 (MP Biomedicals, USA) with 0.5 g RNase free beating beads (0.1 mm, Sigma, USA). Cell pellets of M were homogenized at 5.0 m/s for 20 s without beating beads. Residue DNA digestion, verification of DNA absence and RNA purification were carried out as previously described (Liu et al., 2014, Applied and environmental microbiology 80:4668-4676;). RNA was finally dissolved in 75 µl RNase free H2O. RNA integrity values (RIN) were determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) according to the manufacturer’s instruction
mRNA enrichment was carried out by using the Ribo-Zero™ Magnetic Kit for Bacteria (Epicenter, USA) and RNA libraries were prepared for strand specific sequencing using protocols as previously described (Parkhomchuk et al., 2009, Nucleic Acids Res, 37:e123)

treatment_protocol: Cultivation was carried out at 55 °C in the dark without agitation and all cultures were harvested for transcriptomic analysis at the middle to late exponential-growth phases

tag: strain

value: HZ254; SI

tag: growth stage

value: middle exponential-growth phases


title: Tlr2+/-_PBS_8

value: Tlr2 fish line x ABTL

tag: developmental stage


title: Tlr2-/-_Mm20_3


title: MP_rep3


title: IL2-5 rep2

tag: solanum lycopersicum cultivar


title: IL2-5 rep1


title: Tlr2+/-_PBS_7


title: IL2-4 rep4


title: IL2-6-5 rep2


title: IL2-4 rep3


title: MP_rep1


title: 11225X18

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

institute: University of Utah

description:
Af_Elephant_NT_5h_rep1
3_NT5h0

data_processing:
Reference Creation: p53 retrogenes not present in Ensembl annotation were added manually. USeq_8.8.9beta MakeTranscriptome was to create splices.  Set max splices to 10K. Created index using novoindex 2.08.03.
Reads were aligned to the LoxAfr3 transcriptome index using pysano
Spliced alignments were converted back to genomic space using USeq's SamTranscriptomeParser
Normalized coverage tracks were created using USeq's Sam2USeq and USeq2UCSCExe application
Differential expression was determined using USeq's DefinedRegionDifferentialSeq application
Genome_build: loxAfr3
Supplementary_files_format_and_content: TXT, Differential expression

organism: Loxodonta africana

source_name: Blood

extract_protocol:
PureLink RNA mini kit, RNeasy MinElute Cleanup Kit
Illumina TruSeq Stranded RNA Kit with Ribo Zero Gold

tag: agent

value: Untreated

tag: time point


title: 11225X20

description:
Af_Elephant_2Gy_24h_rep1
7_2Gy24h0

value: Irradiated


title: MP_rep2


title: 11225X16

description:
Af_Elephant_2Gy_24h_rep2
7_2Gy24h1


title: Tlr2+/-_PBS_2

value: whole embryos


title: IL2-4 rep2

data_processing:
Each pool was sequenced in 50 bp single-end format on a total of 5 lanes of a HiSeq 2000 platform (Illumina Inc. San Diego, CA, USA).  Two replicates were lost during library creation, S. pennellii #3 and IL7-5 #3.
Demultiplexed data and filtered and trimmed bad base calls.  Note that FASTQ files provided to GEO have been demultiplexed but not trimmed.
A chimeric reference was created for each IL by combining parental matched references (SlCDS_ITAG2.3_pseudoGMAP5V80passNoDif.fa and SpCDS_ITAG2.3_pseudoGMAP5V80passNoDif.fa) using the latter pennellii reference in the introgression region obtained from (Chitwood et al. 2013) or if not there then using introgression coordinates obtained by using the sequence data to locate the introgression.
Reads were mapped to chimeric references using BWA with parameters “aln -t 4 -k 1 -l 25 -n 0.1 -e 15 -i 10” and mapped read counts extracted with samtools.
Custom R code was used to combine count files, normalized using R edgeR package function calcNormFactors() method TMM, differentially expressed genes (DEG) called using edgeR.  Custom R code tested DEG for GO and other biological category enrichments and special gene set enrichments and looked for common enrichments in ILs exhibiting QTLs for various root traits.  Gene-gene and gene-trait correlations were done. Co-expression networks were built using partial correlation R package SPACE and using a probabilistic graphical model with bootstrap aggregation with R package DAGBAG.
Genome_build: Matched references from (Koenig et al. 2013) and chimeric references described above, based on International Tomato Annotation Group SL2.40 ITAG 2.3 genome at SolGenomics.net.


title: Tlr2+/-_Mm20_6

value: 5 days post fertilization


title: IL2-4 rep1


title: 11225X13

description:
Af_Elephant_2Gy_5h_rep2
6_2Gy5h1


title: Tlr2+/-_Mm20_5


title: 11225X11

description:
Af_Elephant_NT_5h_rep2
3_NT5h1


title: Tlr2+/-_Mm20_1


title: IL2-3 rep4


title: 11225X10

description:
Af_Elephant_2Gy_24h_rep3
7_2Gy24h2


title: IL2-3 rep3


title: Sphere treated, frozen at seen somite stage; denoted Sphere/Somite in processed data file

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

data_processing:
Aligned to RefSeq mRNA (downloaded from NCBI May 2014) using NCBI's blastn, E-value cutoff of 10^(-5)
Differential expression evaluated using DESeq v.1.6.1 and the Benjamini-Hochberg method with an FDR of 0.05 after filtering for at least 50% mean change and at least 100 mapped reads
Supplementary_files_format_and_content: NormalizedCountsDrerioLiang.xls, Excel spreadsheet

source_name: Embryonic tissue

extract_protocol:
30-60 embryos were frozen per sample; treated with SB505124, later frozen with liquid nitrogen; RNA was isolated using the Qiagen RNeasy Mini Kit
Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

value: seven somite stage


title: 11225X17

description:
Af_Elephant_2Gy_5h_rep3
6_2Gy5h2


title: IL11-4-1 rep3


title: 11225X9

description:
Af_Elephant_NT_24h_rep1
4_NT24h0


title: Sphere treated, frozen at tailbud stage; denoted Sphere/Tailbud in processed data file

value: tailbud stage


title: 11225X6

description:
Af_Elephant_NT_5h_rep3
3_NT5h2


title: IL2-3 rep2


title: 30% Epiboly treated, frozen at seven somite stage; denoted Epiboly/Somite in processed data file


title: 11225X8

description:
Af_Elephant_NT_24h_rep3
4_NT24h2


title: 11225X15

description:
Af_Elephant_2Gy_5h_rep1
6_2Gy5h0


title: IL2-2 rep3


title: IL2-3 rep1


title: 30% Epiboly treated, frozen at shield stage; denoted Epiboly/Shield in processed data file

value: shield stage


title: IL2-2 rep4

value: Root


title: 11225X4

description:
Af_Elephant_NT_24h_rep2
4_NT24h1


title: IL2-2 rep1


title: SC_cAMP-2_IN

city: Provo

first: David

middle: Wayne

last: Sant

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

description:
Input DNA
Counts of reads within each peak investigated
Single-read fastq file

data_processing:
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the rn6 transcriptome using STAR
RNA-seq counts were generated during alignment using STAR
hMeDIP-seq reads and Unprecipitated Input reads were aligned to the rn6 genome assembly using BWA
Peak calling was performed with MACS2
Peaks were filtered using the IDR pipeline from the Encode Project with an IDR cutoff of 0.02.
Number of reads in peaks were counted using HTSeq-count.
Genome_build: rn6
Supplementary_files_format_and_content: Count files were generated using either STAR or HTSeq-count.

organism: Rattus norvegicus

source_name: Unprecipitated Input Controls

extract_protocol:
Qiagen RNEasy or Qiagen DNA Mini
Active Motif hMeDIP or TruSeq RNA Prep kit v2

treatment_protocol: 100 mM cAMP

value: Primary cultured schwann cells

tag: passage

value: 3 to 5


title: IL2-2 rep2

first: Siobhan

institute: UC Davis


title: IL2-1-1 rep4


title: xpo1-1 mex67-5 rep2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Basecalling and adapter trimming has been performed using Illumina's bcl2fastq v2.17
Reads were aligned to the S. cerevisiae genome (assembly R64-1-1) using STAR 2.5 and up to 2 mismatches in 50 bp.
Counting of reads mapping to intronic or exonic regions was performed using the featureCounts software with annotation from Ensembl. Intronic region annotation was downloaded from UCSC using the table browser and converted to GTF exon annotation format.
Normalization of read counts and differential expression analysis was conducted with the DeSeq2 package (v1.8.2)
Candidates for differential intron usage were identified by comparing the exon-/intron-specific fold change information.
Genome_build: R64-1-1 (GCA_000146045.2)
Supplementary_files_format_and_content: count files were generated with featureCounts as described above and processed with awk to contain tab-delimited exon-/intron-specific raw read counts

organism: Saccharomyces cerevisiae

growth_protocol: over night at 25 °C

extract_protocol:
Cells were harvested at 1*10^7 cells/ml after 1h 37 °C, total RNA was extracted with Macherey-Nagel nucleospin RNA extraction Kit
RNA-samples were prepared with the "TruSeq RNA Sample Prep Kit v2" according to the manufacturer's protocol (Illumina). Single read (50 bp) sequencing was conducted using a HiSeq 2000 (Illumina).

treatment_protocol: 1h 37°C

tag: genotype/variation

tag: cultivated at

tag: temperature shift

value: 1h 37 °C


title: Wild type rep2

source_name: Wild type

value: Wild type


title: IL2-1-1 rep2

city: Davis

last: Brady

address: 1 Shields Ave


title: SC_Control-3_IN

tag: cell type


title: SC_cAMP-1_IN


title: Sphere treated, frozen at shield stage; denoted Sphere/Shield in processed data file


title: Wild type rep1


title: IL2-1-1 rep1


title: SC_Control-1_IN


title: SC_Control-2_IN


title: 30% Epiboly treated, frozen at tailbud stage; denoted Epiboly/Tailbud in processed data file


title: SC_cAMP-3_IP

description:
Anti-5hmC Immunoprecipitated
Counts of reads within each peak investigated
Single-read fastq file

source_name: hMeDIP-seq


title: IL2-1 rep4


title: SC_cAMP-1_IP


title: SC_cAMP-2_IP


title: IL2-1 rep2


title: IL2-1 rep3


title: IL2-1 rep1


title: SC_Control-3_IP


title: SC_cAMP-3_IN


title: IL1-4-18 rep3


title: IL1-4-18 rep4


title: SC_Control-2_IP


title: SC_plate3

city: Berkeley

first: Maureen

last: Berg

address: 3040 Valley Life Sciences Building # 3140

institute: UC Berkeley

description:
mRNA to cDNA
Processed data file: kallisto_RNAseq_count_table_isoforms.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to WBcel235 genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were aligned, and transcript counts were estimated using Kallisto.
Genome_build: WBcel235
Supplementary_files_format_and_content: kallisto_RNAseq_count_table_isoforms.txt: Tab-delimited text file includes a count matrix for all samples.

organism: Caenorhabditis elegans

source_name: C. elegans, synthetic community

growth_protocol: Synthetic community was comprised of 30 gut isolates; soil was autoclaved before inoculating with either E. coli or the soil microbiota; worms were harvested for mRNA after 3 days of growth (day 1 adults).

extract_protocol:
RNA was extracted using a modified CTAB protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: food

value: Synthetic community

tag: environment

value: Plate

value: whole body

tag: age

value: day 1 adult

tag: truseq index #


title: OP_plate3

source_name: C. elegans, E.coli

value: E. coli


title: IL1-4-18 rep2

tag: solanum pennellii introgression line


title: SC_Control-1_IP


title: xpo1-1 mex67-5 rep1


title: Soil3

source_name: C. elegans, soil microbiota

value: Soil microbiota

value: Soil

tag: tissue


title: IL2-1-1 rep3


title: Soil2


title: mikatae rapa-treated

city: Santa Cruz

first: Jason

last: Talkish

address: 1156 High St.

department: Molecular, Cellular, and Developmental Biology

institute: University of California, Santa Cruz

data_processing:
RNAseq 1a: the 100x100bp pairedEnd reads for cerevisiae samples were not trimmed.
RNAseq 1b: the 51x51bp pairedEnd reads for mikatae and bayanus samples were not trimmed.
RNAseq 2: reads mapping (by bowtie2) to cerevisiae rRNA, tRNA elements defined by Ensembl,  or to Ty elements defined in SGD, were discarded.
RNAseq 3a: cerevisiae reads were mapped to sacCer3 by STAR 2.4.1d, with "twopass" mode.
RNAseq 3b: mikatae reads were mapped to sacMik2 by STAR 2.4.0h with "twopass" mode
RNAseq 3c: bayanus reads were mapped to sacBay2 by STAR 2.4.0h with "twopass" mode
RNAseq 4: duplicate read mappings of the same start and end position were discarded
Ratios involving three coverage numbers were generated for each of the samples and each splice junction. A splice junction coverage was the number of reads that contained the splice junction. The intron coverage was generated from the coverage data using the average across the whole intron. When introns overlapped, a minimal length intron was used such that start of the intron was the maximal start of any of the overlapping introns and the end of the minimal length intron was the minimal end of any overlapping intron. Exon2 coverage was the average coverage for 100 bases of the following exon. Log2-transformed ratios were calculated for the three comparisons: intron/exon2, junction/exon2, intron/junction. Final scores were generated by subtracting the timepoint zero score for each timepoint. Separately intron splice sites and branch points are classified. Given an intron position the splice sites are extracted with conservation scores and a most likely branch point is found using several heuristics. The likely branch points are prioritized 1.)ACTAA, 2.)PYTPAYP, 3.)YTPAY. It must be 45 or more bases away from the 5' splice site and the one closest to the 3' splice site is chosen. Conservation is then calculated around the adenosine branch point. Details and scripts are at: http://exon.ucsc.edu/intron_bp_generator/
Genome_build: sacCer3 (UCSC Apr 2011 )
Genome_build: sacMik2 (sequences obtained in Feb 2015 from the Saccharomyces sensu stricto database)
Genome_build: sacBay2 (sequences obtained in Feb 2015 from the Saccharomyces sensu stricto database)
Supplementary_files_format_and_content: Intron_master_list.xls: junction coordinates and counts, splice site identification and conservation, bp prediciton,  intron and exon2 coverage and log2 ratios, change in log2 ratios after rapamycin treatment, splicing efficiency
Supplementary_files_format_and_content: Deseq_Log2_0vs60.xls: DEseq log2 ratios of expression changes in s. cerevisiae after treatment with rapamycin.

organism: Saccharomyces mikatae

source_name: yeast culture

growth_protocol: Yeast were grown in YEPD to early log phase (OD600 about 0.25 to 0.3) at 30°C (S. cerevisiae) or 26°C (S. mikatae, S. bayanus)

extract_protocol:
RNA was isolated as described in Rio et al. (RNA: A Laboratory Manual, CSH Press)
RNA was treated using the RiboZero kit to remove ribosomal RNAs and then RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated cells were harvested by centrifugation after growth, or after growth plus 1 hour treatment with 200 uM rapamycin as per Munding et al. (2013) Mol. Cell 51: 338-48.

value: haploid, vegetative

tag: strain

value: JRY9177, derived from IFO 1815T, MATa hoD::KanMX his3D::HygMX ura3D::HygMX


title: IL1-4-18 rep1


title: IL1-4 rep4


title: mikatae untreated


title: Soil1


title: IL1-4 rep3


title: OP_soil3


title: IL1-4 rep2


title: OP_soil2


title: OP_soil1


title: IL1-4 rep1


title: IL1-3 rep4


title: SC_plate2


title: SC_plate1


title: IL1-3 rep1


title: Af H2O2-treated 3

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
CASAVA software was used for pass filtering and demultiplexing process
Reads were aligned to A fumigatus (Af293) genome using tophat (version 2.0.9) with parameters "-no-coverage-search -max-multihits 1 -p 1"
Calculation of FPKM values at the gene level and differential gene expression testing was performed using cuffdiff (version 2.2.1) with parameters "-labels "control,Festarv,H2O2,combined" -num-threads 4 -library-type fr-unstranded  -library-norm-method geometric -dispersion-method pooled -no-update-check"
Genome_build: A fumigatus (Af293) genome (Genome: http://www.aspergillusgenome.org/download/sequence/A_fumigatus_Af293/current/A_fumigatus_Af293_version_s03-m05-r04_chromosomes.fasta.gz; Genome features file (GFF): http://www.aspergillusgenome.org/download/gff/A_fumigatus_Af293/A_fumigatus_Af293_version_s03-m05-r04_features_with_chromosome_sequences.gff.gz)
Supplementary_files_format_and_content: Excel file containing the FPKM values and data on differential expression

organism: Aspergillus fumigatus

source_name: hyphae

growth_protocol: Modified Barrat’s minimal nitrate broths (100 ml in 500 ml flasks) were inoculated with freshly isolated conidia and were incubated at 37 ºC and 3.7 Hz shaking frequency. The modified Barrat’s minimal nitrate broth differed to the standard Barrat’s minimal nitrate media in the applied trace element solution which did not contain EDTA and iron.

extract_protocol:
Total RNA was isolated from lyophilized mycelia according to Chomczynski (1993). (Chomczynski P (1993) Biotechniques 1993, 15:536-537; see also Emri, T., Zalka, A. and Pócsi, I. (2017) Mycotoxigenic Fungi: Methods and Protocols (Moretti, A. and Susca, A., Eds.), Springer Science+Business Media, New York, pp. 345-365.)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control and H2O2 treated cultures were supplemented with 30 mM FeCl3. Mild oxidative stress was induced by addition of H2O2 (at 3 mM final concentration) to the cultures 1 h our before sample taking.


title: Af H2O2-treated 2


title: Af Fe-starved and H2O2-treated 1


title: IL1-3 rep3


title: OP_plate2


title: IL1-1-4 rep4


title: Af Fe-starved 2


title: bayanus rapa-treated

organism: Saccharomyces bayanus

value: JRY9189, derived from CBS 7001, MATa hoD::NatMX


title: OP_plate1


title: Af Fe-starved 3


title: Af Fe-starved and H2O2-treated 3


title: Af Fe-starved 1


title: IL1-1-4 rep3


title: Af Fe-starved and H2O2-treated 2


title: Af control 3


title: Af control 2


title: bayanus untreated


title: IL1-1-4 rep2


title: IL1-1-4 rep1


title: D3_K_3_sRNA

city: Shanghai

first: jianfei

last: lu

address: No.999, Huchenghuan Rd

department: Freshwater Fishery Germplasm Resources

institute: Shanghai Ocean University

data_processing:
For the miRNA analyze, data processing followed the procedures as described in a previous study (Li. M, 2010) provided by LC Sciences Service. Brieﬂy, the raw reads were subjected to the Illumina pipeline ﬁlter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18-26 nucleotide were mapped to speciﬁc species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3. and 5. ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to speciﬁc species mature miRNAs in hairpin arms were identiﬁed as known miRNAs. The unique sequences mapping to the other arm of known speciﬁc species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of speciﬁc species) in miRBase 20.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the speciﬁc species genomes to determine their genomic locations. The above two we deﬁned as known miRNAs. The unmapped sequences were BLASTed against the speciﬁc genomes, and the hairpin RNA structures containing sequences were predicated from the ﬂank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (<=12) (2) number of base pairs in the stem region of the predicted hairpin =16) (3) cutoﬀ of free energy (kCal/mol <=15) (4) length of hairpin (up and down stems + terminal loop >=50) (5) length of hairpin loop (<=20). (6) number of nucleotides in one bulge in mature region (<=8) (7) number of biased errors in one bulge in mature region(<=4) (8) number of biased bulges in mature region (<=2) (9) number of errors in mature region (<=7) (10) number of base pairs in the mature region of the predicted hairpin (>=12) (11) percent of mature in stem (>=80).
Genome_build: none de novo sequencing
Supplementary_files_format_and_content: 1_Expressed_miRNA.xlsx, 2_gene_expression.xlsx,3_Trinity_gene.fasta, format and content :fasta,xlsx, assembly sequences and expression data.

organism: Carassius gibelio

source_name: treated sample,were inoculated by intraperitoneal injection with Cyhv-2 suspended in PBS at a dose of 1 ×106 TCID50/g which was applied and verified by previous challenge experiments after seven days of acclimation, fish

growth_protocol: Healthy silver crucian carp for the present experiment (approximately 10 cm in body length) were obtained from the SHOU experimental fish breeding farm. Initially, fish were temporarily reared in at 23 °C for adaptation.

extract_protocol: RNA preparation, library construction and high-throughput sequencing were performed by LC Sciences (Houston, TX, USA). The experimental procedure is introduced as follows: total RNAs were extracted using Trizol reagent (Invitrogen, CA, USA) following the instruction of the product manual. The total RNA quantity and purity were analyzed by using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number higher than 7.0. The total RNA with lowest quality was not used for further study from the pre-receptive endometrium samples and receptive endometrium samples, respectively. For sRNA-seq experiment, approximately 1 μ g of total RNA was subjected to construct sRNA library according to the protocol of TruSeq™ Small RNA Sample Prep Kits (Illumina, San Diego, USA). Then, single-end sequencing (50 bp) was performed on the Illumina Hiseq2500 platform following the vendor’s recommended protocol. For RNA-seq experiment, approximately 10 μ g of total RNA was used to enrichment of poly (A)-tailed mRNAs with poly-Toligo attached magnetic beads (Invitrogen, MA, USA). Following purification, the mRNAs were fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to produce the final cDNA library according to the protocol of the mRNA-seq sample preparation kit (Illumina, San Diego, USA). Each PE and RE library was constructed by pooling 9 homogenized total RNAs from the endometrium samples. Then, paired-end sequencing of the PE and RE libraries was performed on the Illumina Hiseq2500 (LC Sciences, USA) following the vendor’s recommended protocol. The length of the reads was 100 bp, and the average insert size for the paired-end libraries was 179 bp (the length of the adapter was 121 bp). Pre-treatment of the sRNA-seq. First, the sequencing adapters were removed and the short reads containing ambiguous base “N” were discarded. Then, in order to allow cross-library comparison, read count normalization was performed. Specifically, the normalized read count (in RPM, reads per million) of a short sequence from a sequencing library was calculated by dividing the raw count of this sequence by the total counts of the library, and then multiplied by 10^6.

treatment_protocol: After seven days of acclimation, fish were inoculated by intraperitoneal injection with Cyhv-2 suspended in PBSat a dose of 1 ×106 TCID50/g which was applied and verified by previous challenge experiments5. As control, fish were injected with PBS at the same dosage. After the injection, all the fish were fostered under the same and suitable condition, fed with a diet according to standard feeding scheme, and continuously observed for collecting moribund animals.

value: kidney

tag: development

value: one year old


title: Af control 1


title: IL1-1-3 rep4

value: Root


title: IL1-3 rep2


title: Af H2O2-treated 1


title: D3_K_2_sRNA


title: M_rep4

description:
mRNA were enriched for sequencing
processed data file: Raw_reads_counts_M.txt

organism: Methanocella conradii

source_name: M. conradii_anaerobic_monocultures

tag: growth stage

value: middle exponential-growth phases


title: IL1-1-3 rep3

organism: Solanum lycopersicum x Solanum pennellii

tag: solanum lycopersicum cultivar


title: O_K_3_sRNA

source_name: control sample, were injected with PBS at the same dosage as treated sample.


title: IL1-1-3 rep2