title: NSC-6 (miRNA)

city: McAllen

first: Satish

last: Kumar

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

description: iPSC-NSC-miRNA.txt

data_processing:
Raw fastq sequence files were generated and de-multiplexed using the Illumina CASAVA v1.8 pipeline.
After pre-alignment QCs, sequences were aligned to human genome build 19 (hg19) and mapped to UCSC transcripts using Strand NGS software v2.1 (Strand Genomics Inc.). The small RNA reads were also mapped to small RNA annotations as implemented in Strand NGS v2.1 (Strand Genomics Inc.) and reads mapping only to miRNAs were retained for further analysis.
The aligned reads were then filtered based on read quality metrics, so that only perfect alignments were retained and then quantification was performed using NGS software v2.1 (Strand Genomics Inc.).
The expression values (read counts) were log transformed and ‘DESeq’ normalization was applied.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include DESeq normalized abundance measurements for six LCLs-iPSC and six iPSC-NSC pairs, formatted as matrix tables.

source_name: neural stem cell (NSC)

growth_protocol: The six de-identified LCLs were cultured in RPMI 1640 complete media at 37 oC, 5% CO2 and atmospheric O2 for 1-2 passages to obtain the appropriate number of viable cells.

extract_protocol:
smallRNA Sequencing: The Illumina® TruSeq® Small RNA Sample Preparation Kit was used to prepare small RNA sequencing libraries from 1 μg of total RNA.
Total RNA was extracted from cell pellets (~5x106 cells) snap-frozen from LCLs immediately before nucleofection with reprogramming factors; from stable iPSC lines after at least five but less than ten passages; and from validated NSC lines after 3-4 passages.

treatment_protocol: The six LCLs were reprogrammed into iPSCs using episomal plasmids encoding reprogramming factors (i.e. OCT3/4, SOX2, KLF4, L-MYC, LIN28) and mouse p53DD - p53 carboxy-terminal dominant-negative fragment as described in Okita et al., 2012. The reprogrammed iPSCs were then differentiated into neural stem cells (NSC). Both iPSC reprogramming and NSC inductions were confirmed by immunocytochemistry.

value: NSC differentiated from LCL-reprogrammed iPSC


title: NSC-4 (miRNA)

status: Public on Feb 11 2017

type: SRA

state: Texas

country: USA

description: iPSC-NSC-miRNA.txt

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: NSC-5 (miRNA)

description: iPSC-NSC-miRNA.txt


title: D47_55_2

city: Harbin

first: Liu

last: Shanshan

state: Heilongjiang

address: 59 Mucai Street

department: College of Agriculture

country: China

institute: Northeast Agricultural University

data_processing:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.In this step, clean data (clean reads) were obtained by removing reads containing adapter, eads containing ploy-N and low quality reads from raw data
Reference genome and gene model annotation files were downloaded from genome website directly.
Genome_build:
ftp://ftp.ensemblgenomes.org/pub/release_23/plants/fasta/glycine_max/dna/
ftp://ftp.ensemblgenomes.org/pub/release_23/plants/gtf/glycine_max/
Supplementary_files_format_and_content: RPKM / readcount

organism: Glycine max

source_name: normal_55 DAF_seeds

extract_protocol:
Total RNA was extracted from each sample using the improved cetyl trimethylammonium bromide method, used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Dongnong47 (DN47)

tag: genotype/variation

value: parental DN47; normal

tag: age (daf)

value: 55 days after flowering

tag: tissue

value: developing seed


title: D47_55_1


title: NSC-3 (miRNA)

description: iPSC-NSC-miRNA.txt


title: PE_Lhx5_WT_AntNPC

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

description: WT (E14)

library_source: genomic

data_processing:
Library strategy: 4C-seq
Supplementary_files_format_and_content: bedGraph
Reads were assigned to samples based on the first 10 bases of the read. Subsequently, the primer sequence was removed from the read and the remaining sequence was trimmed to 36 bases. These 36 bases were aligned to the mouse reference genome mm9 using Bowtie 0.12.7.
The resulting mapped reads were analyzed with R3C-seq (Thongjuea et al., 2013) in order to generate RPM (reads per million) normalized bedgraph files for downstream visualization and analysis.
Genome_build: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: AntNPC (anterior neural progenitors derived from mESC)

growth_protocol: WT (E14) mESC and EED-/- mESC lines  were cultured on gelatin-coated plates using Knock-out DMEM (KO-DMEM, Life Technologies) supplemented with 15% FBS (Life Technologies) and LIF. These mESC lines were differentiated into AntNPC according to a previously described protocol (Gouti et al., 2014), with slight modifications. Briefly, mESC were plated at a density of 10000 cells/cm2 on gelatin-coated plates and grown for three days in N2B27 medium supplemented with 10 ng/ml bFgf (Life Technologies) and without serum or LIF (Advanced Dulbecco’s Modified Eagle Medium F12 (Life Technologies) and Neurobasal medium (Life Technologies) (1:1), supplemented with 1x N2 (Life Technologies), 1x B27 (Life Technologies), 2 mM L-glutamine (Life Technologies), 40 mg/ml BSA (Life Technologies), 0.1 mM 2-mercaptoethanol (Life Technologies)). Subsequently, cells were grown for another two days in N2B27 medium without bFgf (D3–D5).  Moreover, to improve the homogeneity of the differentiation, from D2-D5 the N2B27 medium was also supplemented with 5μM Xav939 (Sigma), a potent WNT inhibitor (Matsuda and Kondoh, 2014).

extract_protocol:
4C-seq assays were performed as previously described (Splinter et al., 2012; Stadhouders et al., 2013) with slight modifications. 10 million mESC or AntNPC were crosslinked with 1% formaldehyde during 20 minutes and quenched with 0.125M glycine for 10 min. Cells were washed with PBS and resuspended in lysis buffer (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 and 1X protease inhibitors) during 10 min on ice.  Following centrifugation for 5 min at 650g (4 °C), nuclei were re-suspended in 0.5 ml of 1.2X restriction buffer with 0.3% SDS and incubated at 37 °C and 900 rpm for 1h. After that, Triton X-100 was added to a final concentration of 2% followed by 1h incubation at 37 °C and 900 rpm. Afterwards, chromatin was digested overnight at 37 °C and 900 rpm with 400 U of NlaIII (R0125L, NEB). NlaIII was inactivated by adding SDS to a final concentration of 1.6% and incubating the mixture for 20 min at 65 °C while shaking (900 rpm). The digested chromatin was transferred to 50-ml tubes and 6.125 ml of 1.15X ligation buffer (50 mM Tris-HCl pH 7.6, 10 mM MgCl2, 1 mM ATP, 1mM DTT) were added. Triton X-100 was also added to a final concentration of 1% and the resulting solution was incubated for 1 h at 37 °C while shaking gently. After that, digested chromatin was ligated with 100 U of T4 DNA ligase (15224-041, Life Technologies) for 8 h at 16 °C, followed by RNAse A treatment (300 μg, Peqlab) for 45 min at 37 °C. Subsequently, chromatin was de-crosslinked with 300 μg of Proteinase K (Peqlab) and overnight incubation at 65 °C. DNA was then purified by phenol/chloroform extraction followed by ethanol precipitation and re-suspension in 100 μl of water. At this step, the digestion and ligation efficiencies were evaluated by analysing a small fraction of the purified DNAs by agarose electrophoresis. The remaining DNA was digested with 50U of DpnII (R0543M, NEB) in 500 μl of 1x NEBuffer DpnII at 37 °C overnight. DNA samples were purified by phenol/chlorophorm extraction, followed by ethanol precipitation. Once purified, DNA samples were re-suspended in 500 μl of water and a second ligation was performed by adding 200 U of T4 DNA Ligase into a final volume of 14 ml 1X ligation buffer followed by overnight incubation at 16 °C. DNA samples were subjected to another round of phenol/chlorophorm extraction and ethanol precipitation, re-suspended in 100 μl of water and purified with a QIAgen PCR purification column (28104, QIAgen). The efficiencies of the second digestion and ligation were also evaluated by agarose electrophoresis.
4C samples were amplified by inverse PCR using primers located within selected poised enhancers and that included illumina adaptor sequences and short barcodes. The inverse PCRs were performed with the expand long template PCR system (11681842001, Roche) and 30 amplification cycles (94°C 2 min, 30x [94°C 10 sec, 60°C 1 min, 68°C 3 min], 68°C 5 min). The inverse PCR primers were designed as previously described (Stadhouders et al., 2013). Once amplified, 4C-seq libraries were sequenced on the HiSeq2500, generating reads of either 74 or 100 bp in length.

treatment_protocol: EED-/- mESC were previously generated and characterized (Schoeftner et al., 2006).

tag: genotype

value: WT

tag: treatment

value: mESC differentiation into AntNPC


title: PE_Lhx5_WT_mESC

description: WT (E14)

source_name: mESC

value: mESC


title: LCL-4 (miRNA)

description: LCL-iPSC-miRNA.txt

source_name: lymphoblastoid cell line (LCL)

value: EBV-immortalized LCL


title: LCL-3 (miRNA)

description: LCL-iPSC-miRNA.txt


title: LCL-2 (miRNA)

description: LCL-iPSC-miRNA.txt


title: LCL-5 (miRNA)

description: LCL-iPSC-miRNA.txt


title: D47_50_2

source_name: normal_50 DAF_seeds

value: 50 days after flowering


title: PE_Sox1_WT_mESC

description: WT (E14)


title: iPSC-4 (miRNA)

description:
LCL-iPSC-miRNA.txt
iPSC-NSC-miRNA.txt

source_name: induced pluripotent stem cells (iPSC)

value: LCL-reprogrammed iPSC


title: LCL-6 (miRNA)

description: LCL-iPSC-miRNA.txt


title: NSC-1 (miRNA)

description: iPSC-NSC-miRNA.txt


title: iPSC-2 (miRNA)

description:
LCL-iPSC-miRNA.txt
iPSC-NSC-miRNA.txt


title: NSC-2 (miRNA)

description: iPSC-NSC-miRNA.txt


title: iPSC-1 (miRNA)

description:
LCL-iPSC-miRNA.txt
iPSC-NSC-miRNA.txt


title: iPSC-6 (miRNA)

description:
LCL-iPSC-miRNA.txt
iPSC-NSC-miRNA.txt


title: iPSC-5 (miRNA)

description:
LCL-iPSC-miRNA.txt
iPSC-NSC-miRNA.txt


title: iPSC-3 (miRNA)

description:
LCL-iPSC-miRNA.txt
iPSC-NSC-miRNA.txt


title: NSC-6 (mRNA)

description: iPSC-NSC-mRNA.txt

extract_protocol:
mRNA Sequencing: The Illumina® TruSeq® RNA Sample Preparation Kit v2 was used to prepare cDNA sequencing libraries from 1 μg of total RNA.
Total RNA was extracted from cell pellets (~5x106 cells) snap-frozen from LCLs immediately before nucleofection with reprogramming factors; from stable iPSC lines after at least five but less than ten passages; and from validated NSC lines after 3-4 passages.


title: NSC-5 (mRNA)

description: iPSC-NSC-mRNA.txt


title: NSC-3 (mRNA)

description: iPSC-NSC-mRNA.txt


title: D47_50_1


title: D47_35_2

source_name: normal_35 DAF_seeds

value: 35 days after flowering


title: D47_25_1

source_name: normal_25 DAF_seeds

value: 25 days after flowering


title: LCL-1 (miRNA)

description: LCL-iPSC-miRNA.txt


title: PE_Lhx5_EEDnull_mESC

description: EED-/-

value: EED-/-


title: D47_18_2

source_name: normal_18 DAF_seeds

value: 18 days after flowering


title: NSC-2 (mRNA)

description: iPSC-NSC-mRNA.txt


title: NSC-1 (mRNA)

description: iPSC-NSC-mRNA.txt


title: D47_35_1


title: Archer_T47D_FAIRESeq

city: RTP

first: Christopher

last: Lavender

state: NC

address: 111 T. W. Alexander Drive

institute: NIEHS

description:
Genomic DNA
FAIRE-Sseq

data_processing:
FAIRE-Seq: Prior to alignment, FAIRE-Seq reads were filtered based on quality; reads with an average Sanger quality score less than 20 were removed from analysis. Following quality filtering, Cutadapt was used to remove adapter sequences.  Alignment of FAIRE-Seq reads was performed using Bowtie. Aligned FAIRE-Seq reads were then de-duplicated using Picard (version 1.118). FAIRE-Seq fragment lengths were estimated using Homer.  From each uniquely mapped fragment, the fragment was extended based on the estimated length, and the estimated fragment center subsequently identified. Genome-wide coverage of fragment centers is reported in bigWig format.
genome build: hg19
processed data files format and content: FAIRE-Seq: bigWig file describes the coverage of fragment centers. FAIRE-Seq fragment lengths were estimated using Homer.  From each uniquely mapped fragment, the fragment was extended based on the estimated length, and the estimated fragment center subsequently identified.

source_name: T-47D cells

growth_protocol: T-47D cells were cultured in DMEM containing 10% FBS.  Prior to harvest, cells were cultured in medium supplemented with 5% charcoal dextran-treated serum for at least 24 hours.

extract_protocol:
FAIRE-Seq: FAIRE-seq experiments were performed as previously described (Burd et al., Mol Cell Biol 2012).
FAIRE-Seq: Libraries were constructed as previously described (Burd et al., Mol Cell Biol 2012).

tag: cell line


title: D47_18_1


title: iPSC-6 (mRNA)

description:
LCL-iPSC-mRNA.txt
iPSC-NSC-mRNA.txt


title: a_N_55_2

source_name: α-subunit-null_55 DAF_seeds

value: cgy-2-NIL (near-isogenic line for alpha-subunit null)


title: D47_25_2


title: NSC-4 (mRNA)

description: iPSC-NSC-mRNA.txt


title: Archer_T47D_MNaseSeq

description:
Genomic DNA
MNase-Seq

data_processing:
MNase-Seq: Prior to alignment, MNase-Seq reads were filtered based on quality; reads with an average Sanger quality score less than 20 were removed from analysis. Following quality filtering, Cutadapt was used to remove adapter sequences. Alignment of MNase-Seq read pairs was performed using Bowtie.  From each uniquely mapped fragment, the fragment center was found. Genome-wide coverage of fragment centers is reported in bigWig format.
genome build: hg19
processed data files format and content: MNase-Seq: bigWig file describes the coverage of fragment centers. From each uniquely mapped fragment, the fragment center was found.

extract_protocol:
MNase-Seq: Nuclei were harvested from T-47D cells and digested for 5 minutes at 37C with a range of MNase (Worthington) concentrations. Reactions were stopped by addition of EDTA and then treated with RNase and proteinase K. Digested DNA was isolated by phenol/chloroform extraction and ethanol precipitation.
MNase-Seq: Libraries were constructed using an Illumina TruSeq sample preparation kit.


title: Archer_T47D_StartSeq_rep1

description:
Nascent RNA
Start-Seq

data_processing:
Library strategy: Start-seq
Start-Seq: Start-Seq reads were first filtered by quality score; reads with an average Sanger score less than 20 were removed from analysis. Following quality filtering, Cutadapt (version 1.2.1) was used to remove adapter sequences. Alignment of Start-Seq reads was performed using Bowtie (version 0.12.8) to the hg19 genome assembly. From each uniquely mapped Start-Seq fragment, the 5? end was taken forward into the TSS calling procedure. TSSs were called using the higher depth Replicate 1 and validated by Replicate 2. Gene TSS and uaTSS calling procedures were described previously (Scruggs et al., Mol Cell 2015).  To call daTSS positions, a method analogous to uaTSS identification was used. daTSS search space was defined as 1 to 2000 nt downstream of an obsTSS in the antisense orientation.  To ensure that identified daTSSs were not simply mis-called gene TSSs or uaTSSs, additional criteria were used to filter daTSS calls. A daTSS call was filtered if (1) it was within 1000 nt upstream of the daTSS there was a genomic position with Start-Seq reads greater than or equal to 10% of reads at the TSS, implicating the daTSS as a potential uaTSS for an uncalled TSS, or (2) it was within 1000 nt of an annotated TSS on the same strand, implicating the daTSS as a potential gene TSS.
genome build: hg19
processed data files format and content: Start-Seq: bigWig files describe the stranded coverage of the 5’ end of Start-Seq reads. For each uniquely mapped Start-Seq read, the 5’ end of the alignment was considered.  TSS calls from the Start-Seq data are reported as BED files.  The TSS calling procedure has been described previously (Scruggs et al., Mol Cell 2015). All calls are compiled in a XLSX spreadsheet, annotated by Start-Seq read coverage and RNA-Seq FPKM values for associated genes.

extract_protocol:
Start-Seq: Start-Seq experiments were performed as previously described (Nechaev et al., Science 2010).
Start-Seq: Libraries were constructed as previously described (Nechaev et al., Science 2010) using an Illumina TruSeq small RNA kit.


title: a_N_50_1

source_name: α-subunit-null_50 DAF_seeds


title: iPSC-5 (mRNA)

description:
LCL-iPSC-mRNA.txt
iPSC-NSC-mRNA.txt


title: a_N_35_1

source_name: α-subunit-null_35 DAF_seeds


title: iPSC-2 (mRNA)

description:
LCL-iPSC-mRNA.txt
iPSC-NSC-mRNA.txt


title: a_N_55_1


title: iPSC-4 (mRNA)

description:
LCL-iPSC-mRNA.txt
iPSC-NSC-mRNA.txt


title: LCL-5 (mRNA)

description: LCL-iPSC-mRNA.txt


title: iPSC-3 (mRNA)

description:
LCL-iPSC-mRNA.txt
iPSC-NSC-mRNA.txt


title: LCL-6 (mRNA)

description: LCL-iPSC-mRNA.txt


title: a_N_25_2

source_name: α-subunit-null_25 DAF_seeds


title: a_N_25_1


title: LCL-4 (mRNA)

description: LCL-iPSC-mRNA.txt


title: a_N_18_2

source_name: α-subunit-null_18 DAF_seeds


title: LCL-2 (mRNA)

description: LCL-iPSC-mRNA.txt


title: LCL-1 (mRNA)

description: LCL-iPSC-mRNA.txt


title: Archer_T47D_StartSeq_Rep2

description: Start-Seq

data_processing:
Library strategy: Start-seq
Start-Seq: Start-Seq reads were first filtered by quality score; reads with an average Sanger score less than 20 were removed from analysis. Following quality filtering, Cutadapt (version 1.2.1) was used to remove adapter sequences. Alignment of Start-Seq reads was performed using Bowtie (version 0.12.8) to the hg19 genome assembly. From each uniquely mapped Start-Seq fragment, the 5’ end was taken forward into the TSS calling procedure. TSSs were called using the higher depth Replicate 1 and validated by Replicate 2. Gene TSS and uaTSS calling procedures were described previously (Scruggs et al., Mol Cell 2015).  To call daTSS positions, a method analogous to uaTSS identification was used. daTSS search space was defined as 1 to 2000 nt downstream of an obsTSS in the antisense orientation.  To ensure that identified daTSSs were not simply mis-called gene TSSs or uaTSSs, additional criteria were used to filter daTSS calls. A daTSS call was filtered if (1) it was within 1000 nt upstream of the daTSS there was a genomic position with Start-Seq reads greater than or equal to 10% of reads at the TSS, implicating the daTSS as a potential uaTSS for an uncalled TSS, or (2) it was within 1000 nt of an annotated TSS on the same strand, implicating the daTSS as a potential gene TSS.
RNA-Seq: Prior to alignment, RNA-Seq reads were filtered based on quality; reads with an average Sanger quality score less than 20 were removed from analysis. Following quality filtering, Cutadapt was used to remove adapter sequences. Insert lengths were estimated by transcriptome alignment using Bowtie.  Sequence alignment was then performed using TopHat (version 2.0.4) [35]. Following de-duplication by Picard, alignments from individual replicates were merged. FPKM values were calculated using Cufflinks (version 2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: Start-Seq: bigWig files describe the stranded coverage of the 5’ end of Start-Seq reads. For each uniquely mapped Start-Seq read, the 5’ end of the alignment was considered.  TSS calls from the Start-Seq data are reported as BED files.  The TSS calling procedure has been described previously (Scruggs et al., Mol Cell 2015). All calls are compiled in a XLSX spreadsheet, annotated by Start-Seq read coverage and RNA-Seq FPKM values for associated genes.
Supplementary_files_format_and_content: RNA-Seq: Gene FPKM values are reported in CSV format. FPKM values were calculated using Cufflinks (version 2.2.1).

extract_protocol:
Start-Seq: Start-Seq experiments were performed as previously described (Nechaev et al., Science 2010). RNA-Seq: Total RNA was harvested using an RNeasy kit (Qiagen) with on-column DNase treatment.  RNA quality was validated by Bioanalyzer (Agilent). Paired-end strand-specific poly-A enriched RNA-seq libraries were generated by the NIH Intramural Sequencing Center (NISC). MNase-Seq: Nuclei were harvested from T-47D cells and digested for 5 minutes at 37C with a range of MNase (Worthington) concentrations. Reactions were stopped by addition of EDTA and then treated with RNase and proteinase K. Digested DNA was isolated by phenol/chloroform extraction and ethanol precipitation. FAIRE-Seq: FAIRE-seq experiments were performed as previously described (Burd et al., Mol Cell Biol 2012).
Start-Seq: Libraries were constructed as previously described (Nechaev et al., Science 2010) using an Illumina TruSeq small RNA kit. RNA-Seq: Libraries were constructed using an Illumina TruSeq Stranded mRNA kit. MNase-Seq: Libraries were constructed using an Illumina TruSeq sample preparation kit. FAIRE-Seq: Libraries were constructed as previously described (Burd et al., Mol Cell Biol 2012).
RNA-Seq: Prior to alignment, RNA-Seq reads were filtered based on quality; reads with an average Sanger quality score less than 20 were removed from analysis. Following quality filtering, Cutadapt was used to remove adapter sequences. Insert lengths were estimated by transcriptome alignment using Bowtie. Sequence alignment was then performed using TopHat (version 2.0.4) [35]. Following de-duplication by Picard, alignments from individual Replicates were merged. FPKM values were calculated using Cufflinks (version 2.2.1).

tag: molecule subtype

value: Nascent RNA


title: WT

city: Upton

first: Chang-Jun

last: Liu

state: NY

address: 50 Bell Avenue

department: Biology Department

institute: Brookhaven National Lab

data_processing:
Sequencing was done using the Illumina HiSeq2500 platform via 100-bp single-end reads of multiplexed RNA samples
RNA-Seq reads first were aligned to the ribosomal RNA database (http://www.arb-silva.de/no_cache/download/archive/current/Exports/) using Bowtie and those mapped were excluded for downstream analysis. The resulting cleaned reads were aligned to the Populus trichocarpa genome downloaded from the PlantGDB (http://www.plantgdb.org) using TopHat allowing one mismatch.
Raw counts for each poplar gene were derived and normalized to reads per kilobase of exon model per million mapped reads (RPKM)
Genome_build: Populus trichocarpa (black cottonwood) genome Poptr2_0
Supplementary_files_format_and_content: ods file was generated, including RPKM values for both Samples

organism: Populus tremula x Populus alba

source_name: WT, Young stem

growth_protocol: The coppiced hybrid aspen of WT and MOMT4-0 transgenic lines grew in a greenhouse for about 2 months.  The 1st to 15th internodes from the top were harvested and, their barks were removed.

extract_protocol:
About 100 mg stem samples pooled from 2~3 individual transgenic and control plants, respectively, were grounded to fine powder under liquid nitrogen. Total RNAs were extracted using Qiagen RNeasy Plant Mini Kit
The assessment of purity and concentration of each RNA sample, and the strand-specific RNA-Seq library construction were conducted by using the Polar Genomics (Ithaca, NY) service, using standard Illumina protocols

value: young stem


title: MOMT4 transgenic line

source_name: MOMT4 transgenic, Young stem

value: MOMT4 transgenic line


title: a_N_18_1

value: Dongnong47 (DN47)


title: LCL-3 (mRNA)

description: LCL-iPSC-mRNA.txt


title: iPSC-1 (mRNA)

description:
LCL-iPSC-mRNA.txt
iPSC-NSC-mRNA.txt


title: QM9414 WT Sophorose 2

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

description: Sample 5

data_processing:
Illumina Casava1.8.2 software used for base-calling.
The Illumina HiSeq 2000 system was used to sequence the mutant transcriptome, yielding approximately 76 million 100-bp paired-end reads. These sequences were firstly quality-filtered and mapped to the Trichoderma reesei 2.0 reference genome available the JGI Genome Portal (http://genome.jgi-psf.org/Trire2/Trire2.home.html) using the Bowtie aligner version 0.12.8 (Li, Durbin, 2009), allowing two mismatches and only unique alignments.
After alignment, Samtools version 0.1.18 (Li et al., 2009) was used to process the alignments files which were visualized using the Integrative Genomics Viewer (Thorvaldsdottir et al., 2012).
Bioconductor DESeq package version 1.10.1 (Anders, Huber, 2010) was employed to differential expression analysis, using two-fold change, i.e., log2 fold change ≥ 1 or ≤ -1 and adjusted p-value ≤ 0.05 as thresholds.
Genome_build: http://genome.jgi-psf.org/Trire2/Trire2.home.html
Supplementary_files_format_and_content: Processed data files are presented in tab delimited txt format. Raw and normalized count data are presented, expressed as follows: "Protein ID (JGI Trichoderma reesei v2.0)", "sample ID".
Supplementary_files_format_and_content: Gene expression results are expressed as log2 Fold change between indicated samples and the respective adjusted p-value calculated by DESeq.

organism: Trichoderma reesei

source_name: mycelia

growth_protocol: The mutant strain was grown in MEX medium at 28°C for 7-10 days for complete sporulation. For gene expression assays, a spore suspension containing approximately 107 cells mL-1 was inoculated into 200 mL of Mandels-Andreotti medium (Schmollet al. 2009) containing 1mM of sophorose as the carbon source.

extract_protocol:
Total RNA was extracted using the TRIzol kit (Invitrogen) according to manufacture's instructions.
RNA-seq libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit.

value: wild type

value: mycelia

tag: carbon source

value: Sophorose


title: NDGA_replicate 2

city: Hangzhou

first: Wangshu

last: Mou

state: Zhejiang

address: Yuhangtang Road 866

department: College of Bio-engineering and Food Science

institute: Zhejiang University

data_processing:
Tophat version 2.0.9 was unsed to align the qualified reads to S. lycopersicum genome
The mapped reads were assembled by cufflinks version 2.1.1
Cumerge was applied to comerge all transcripts of the three samples to generate unique transcripts
Cuffdiff reestimates the abundance of the transcripts and concurrently test for different expression. The genes expression level in each treatment was all expressed as the average of the two biological replicates.

organism: Solanum lycopersicum var. cerasiforme

source_name: tomato fruit

extract_protocol:
Total RNA samples were prepared using the Total RNA Purication Kit, TRK1001 (LC Science, Houston, TX), treated with RNase-free DNaseI following the manufacturer's procedure to remove contaminated genomic DNA. The quantity and purity of total RNA were analysed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA).Equal quantities of high-quantity RNA of each sample were blended for cDNA library construction.
The poly (A) messgener RNA was isolated from the total RNA samples with oligo (dT) attached magnetic beads (Invitrogen). The mRNA was frangmented into short pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to the first-strand cDNAs by random hexamer primers. Then the second-strand cDNAs were synthesized to construct the final cDNA library according to the instruction of mRNA-Seq sample preparation kit (Illumina, San Diego, USA) and the paired-end cDNA with a length of 300 bp (±50 bp). After that, the cDNA libraries were sequenced on the Illumina HiSeqTM 2000 platform at the LC-BIO (Hangzhou, China) following the manufacturer’s recommendations.

treatment_protocol: For each group, 25 μL each of ABA (10 mM), NDGA (1 mM) solutions and control (distilled water) was injected into the fruits with the same depth from the pedicle by microsyringe, respectively

tag: time point

value: post-harvest

value: pericarp

value: 25 μL NDGA (1 mM)


title: a_N_35_2

value: developing seed


title: ABA_replicate 2

value: 25 μL ABA (10 mM)


title: NDGA_replicate 1


title: Δcre1 Sophorose 3

value: mutant


title: QM9414 WT Sophorose 3

description: Sample 6


title: QM9414 WT Sophorose 1

description: Sample 4


title: CK_replicate 1

value: 25 μL distilled water


title: Δcre1 Sophorose 2


title: Δcre1 Sophorose 1


title: CK_replicate 2


title: Sample_txyD

city: Nanjing

first: ZHANG

last: chunhua

address: Xuanwu road

institute: Jiangsu Academy of Agricultural Sciences

data_processing:
Library strategy: Parallel analysis of RNA ends (PARE-Seq)
Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software
Sequencing image was analyzed  by Pipeline Firecrest Module.
Base-calling was done by Pipeline Bustard Module
CleaveLand3.0 was used for alignment, filtering, peak-calling and so on.
Genome_build: http://www.ncbi.nlm.nih.gov/genome/388?genome_assembly_id=28754:assembly Prupe1_0
Supplementary_files_format_and_content: Profiles of Peach miRNAs.xls, miRNA sequence and expression data, Degradome_Targets_prediction.xlsx, miRNA target prediction results,target position and degradome fragments abundance on cleavage position

organism: Prunus persica

source_name: Peach

growth_protocol: Six-year old ‘Troubador’ peach trees grown under standard field conditions at the National Peach Germplasm Repository in Nanjing, China.

extract_protocol:
Total RNA was extracted from the fruit samples using Trizol reagent and subsequently treated with DNaseI (Takara Biotechnology Co., Ltd, Dalian, China) per the manufacturer’s instructions to remove contamination by genomic DNA.
sRNA fractions of 18 to 30 nt in length were first purified from the low-molecular weight RNA by excision from 15% denaturing polyacrylamide gels and then ligated to 3’ and 5’ adaptors using T4 RNA ligase according to the manufacturer’s instructions. The sRNAs ligated with 3’ and 5’ adaptors were purified and reverse transcribed to cDNA with the reverse transcription primers for 17 cycles according to the protocol. Eventually, the PCR products were further purified and subjected to sequencing using the Illumina Genome Analyzer. The image files obtained from the analyzer were then evaluated and used to form a large repertoire of digital data suitable for bioinformatics analysis. Degradome library was constructed following with methods previously described by Ma et al.(2010).  CleaveLand3.0  program was used to detect potentially sliced targets of known and novel miRNA.

treatment_protocol: Collect fruit at 35, 55, 75, 90, 105 days after full bloom,respectively

value: Troubador

tag: development

value: Sampling at 35, 55, 75, 90, 105 days after full bloom

value: Fruit

tag: flesh color

value: Yellow flesh


title: a_N_50_2

value: cgy-2-NIL (near-isogenic line for alpha-subunit null)

value: 50 days after flowering


title: TBD-623

data_processing:
Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software
Sequencing image was analyzed  by Pipeline Firecrest Module.
Base-calling was done by Pipeline Bustard Module
CleaveLand3.0 was used for alignment, filtering, peak-calling and so on.
Genome_build: http://www.ncbi.nlm.nih.gov/genome/388?genome_assembly_id=28754:assembly Prupe1_0
Supplementary_files_format_and_content: Profiles of Peach miRNAs.xls, miRNA sequence and expression data, Degradome_Targets_prediction.xlsx, miRNA target prediction results,target position and degradome fragments abundance on cleavage position


title: input_H3K4me3_PC3 shCHD1

status: Public on Feb 10 2017

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

institute: MD Anderson Cancer Center

data_processing:
Raw reads were aligned using bowtie (version 1.1.2) (Langmead B et.al., 2009) to build version hg19 of the human genome retaining only uniquely mapped reads.
MACS1.4 (Zhang et al., 2008) was used to call peaks in using Input ChIP-seq as control sample using default p value cut-off of 1e-5.
bamCoverage from deeptools (Ramírez Fet.al., 2016) was used to make RPKM normalized bigwig track extending the reads to 200bp fragment length.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig

source_name: Prostate cancer cell line

growth_protocol: PC-3 was cultured in Ham's F-10 Nutrient Mixture medium with 10% fetal bovine serum (FBS).

extract_protocol:
chromatin from formaldehyde-fixed cells (control and CHD1 knockdown PC-3 cells, 10 x106 cells for CHD1 antibody and 1x106 cells for H3K4me3 antibody) were cross-linked using 1% paraformaldehyde for 10 minutes and reactions were quenched by 0.125 M glycine for 5 minutes at room temperature. Cells were lysed with ChIP lysis buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA [pH 8.0], 140 mM NaCl, 1% Triton X-100, 0.2% SDS, 0.1% deoxycholic acid) for 30 minutes on ice. Chromatin fragmentation was performed using a Diagenode Bioruptor®Pico sonicator (30 secs on and 30 secs off for 45 cycles) to achieve a DNA shear length of 200 to 500 basepairs. Solubilized chromatin was then incubated overnight with their respective antibody-Dynabead (Life Technologies) mixture (CHD1 antibody: Bethyl, #A301-218A; H3K4me3 antibody: Abcam #ab8580). Immune complexes were then washed 3 times with RIPA buffer, once with RIPA-500 (RIPA with 500 mM NaCl), and once with LiCl wash buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% deoxycholic acid). Elution and reverse crosslinking were performed in direct elution buffer (10 mM Tris-Cl [pH 8.0], 5 mM EDTA, 300 mM NaCl, 0.5% SDS) with proteinase K (20 mg/ml) at 65°C overnight.
Libraries were prepared using NEBNext Ultra DNA Library kit (E7370) from NEB.

treatment_protocol: Recombinant lentiviral particles were produced by transient transfection of 293T cells. Briefly, 8 μg of the shRNA plasmid, 4 μg of PsPAX2 plasmid, and 2 μg of pMD2.G plasmid were transfected using Lipofectamine 2000 into 293T cells plated in 100 mm dishes. Viral supernatant was collected 48 h and 72 h after transfection and filtered. PC-3 cells were infected twice in 48 h with viral supernatant containing 10 μg/mL polybrene, and then selected using 2 μg/mL puromycin and tested for CHD1 expression by immunoblot.

tag: anitbody

value: input


title: input_H3K4me3_PC3 Ctrl


title: input_CHD1_PC3 Ctrl


title: PC3 shCHD1_H3K4me3_2

value: H3K4me3 antibody:Abcam #ab8580


title: PC3 shCHD1_CHD1_Bethyl_2

value: CHD1 antibody:Bethyl, #A301-218A


title: PC3 shCHD1_H3K4me3_1


title: PC3 shCHD1_CHD1_Bethyl_1


title: PC3 Ctrl_H3K4me3_1


title: PC3 Ctrl_CHD1_Bethyl_2


title: PC3 Ctrl_CHD1_Bethyl_1


title: PC3 Ctrl_H3K4me3_2


title: ABA_replicate 1


title: input_CHD1_PC3 shCHD1


title: Human_d14.3

city: Madison

middle: A

last: Barry

state: WI

address: 330 N. Orchard St.

department: Regenerative Biology

institute: Morgridge Institute for Research

description:
H1 teratoma day d14 rep3
Teratoma.RSEM.xlsx

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 1.0 --seed-length 28 "
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Excel Spreadsheets containing RSEM-calculated Gene Expression Estimates in both Expected Counts (EC) and Transcripts Per Million (TPM)

source_name: Teratoma time course

growth_protocol: In vitro cells were differentiated in DF3S+N2 supplement + B27 supplement + 100 ng/mL Noggin.  EGFP-positive cells for tertomas were injected in a 1.8:1 ratio of either TSS:Matrigel+3uM Y-27632 (mEpiSC) or E8:Matrigel (H1).  Dissected teratomas were digested with Dispase/Collagenase (Roche) for single cell suspensions for FACS sort.

extract_protocol:
RNA was extracted using the Rneasy plus mini kit (Qiagen)
cDNA libraries were prepped using the LM-Seq protocol described in  Hou et al 2015 (PMID 25831155).

treatment_protocol: Each sample was lysed in RLT plus buffer and stored at -80C until multiple samples could be processed in parallel.

tag: time course


title: Human_d21.2

description:
H1 teratoma day d21 rep2
Teratoma.RSEM.xlsx


title: Human_d14.2

description:
H1 teratoma day d14 rep2
Teratoma.RSEM.xlsx


title: Human_d2.2

description:
H1 teratoma day d2 rep2
Teratoma.RSEM.xlsx


title: Human_d42.1

description:
H1 teratoma day d42 rep1
Teratoma.RSEM.xlsx


title: Human_d11.3

description:
H1 teratoma day d11 rep3
Teratoma.RSEM.xlsx


title: Human_d36.1

description:
H1 teratoma day d36 rep1
Teratoma.RSEM.xlsx


title: Human_d8.2

description:
H1 teratoma day d8 rep2
Teratoma.RSEM.xlsx


title: Human_d11.2

description:
H1 teratoma day d11 rep2
Teratoma.RSEM.xlsx


title: Human_d0.2

description:
H1 teratoma day d0 rep2
Teratoma.RSEM.xlsx


title: Human_d28.2

description:
H1 teratoma day d28 rep2
Teratoma.RSEM.xlsx

value: EpiSC


title: Human_d2.3

description:
H1 teratoma day d2 rep3
Teratoma.RSEM.xlsx


title: Human_d16.1

description:
H1 teratoma day d16 rep1
Teratoma.RSEM.xlsx


title: Human_d23.1

description:
H1 teratoma day d23 rep1
Teratoma.RSEM.xlsx


title: Human_d21.1

description:
H1 teratoma day d21 rep1
Teratoma.RSEM.xlsx


title: Human_d14.1

description:
H1 teratoma day d14 rep1
Teratoma.RSEM.xlsx


title: Human_d8.1

description:
H1 teratoma day d8 rep1
Teratoma.RSEM.xlsx


title: Human_d2.1

description:
H1 teratoma day d2 rep1
Teratoma.RSEM.xlsx


title: Human_d0.1

description:
H1 teratoma day d0 rep1
Teratoma.RSEM.xlsx


title: Human_d10.2

description:
H1 teratoma day d10 rep2
Teratoma.RSEM.xlsx


title: H1Rosa7_d42

description:
47853_H1 day 42 in vitro
mEpiVH1.RSEM.xlsx

source_name: In Vitro Neural Differentiation


title: H1Rosa7_d40

description:
47852_H1 day 40 in vitro
mEpiVH1.RSEM.xlsx


title: Human_d10.1

description:
H1 teratoma day d10 rep1
Teratoma.RSEM.xlsx


title: H1Rosa7_d38

description:
47851_H1 day 38 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d36

description:
47850_H1 day 36 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d34

description:
47849_H1 day 34 in vitro
mEpiVH1.RSEM.xlsx


title: Human_d28.1

description:
H1 teratoma day d28 rep1
Teratoma.RSEM.xlsx


title: Human_d18.1

description:
H1 teratoma day d18 rep1
Teratoma.RSEM.xlsx


title: H1Rosa7_d32

description:
47848_H1 day 32 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d30

description:
47847_H1 day 30 in vitro
mEpiVH1.RSEM.xlsx


title: Human_d11.1

description:
H1 teratoma day d11 rep1
Teratoma.RSEM.xlsx


title: H1Rosa7_d20

description:
47842_H1 day 20 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d21

description:
47843_H1 day 21 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d8

description:
47836_H1 day 8 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d24

description:
47845_H1 day 24 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d22

description:
47844_H1 day 22 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d5

description:
47833_H1 day 5 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d18

description:
47841_H1 day 18 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d7

description:
47835_H1 day 7 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d26

description:
47846_H1 day 26 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d4

description:
47832_H1 day 4 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d14

description:
47839_H1 day 14 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d6

description:
47834_H1 day 6 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d16

description:
47840_H1 day 16 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d10

description:
47837_H1 day 10 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d3

description:
47831_H1 day 3 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d0

description:
47828_H1 day 0 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d1

description:
47829_H1 day 1 in vitro
mEpiVH1.RSEM.xlsx


title: H1Rosa7_d2

description:
47830_H1 day 2 in vitro
mEpiVH1.RSEM.xlsx


title: ATB_0

city: Hannover

first: Aravind

last: Tallam

state: Lower Saxony

address: Feodor-Lynen str. 7

department: BIOM

institute: TWINCORE

data_processing:
The below briefly described steps for library preparation, sequencing, pre-processing and mapping, were performed at the Genome Analytics facilities of the Helmholtz Zentrum für Infektionsforschung (Braunschweiger/Germany).
The sequencing was performed following the standard protocols on Illumina HiSeq® 2500 Sequencing System (Illumina, San Diego, CA) running 100 bp paired-end reads (PE100) and generating approximately 30 million reads passing filter for each sample to produce the mRNA reads.
Sequenced reads were trimmed for adaptor sequence using TrimGalore with the trimming mode as paired-end, and masked (hemoglobins, rRNA, tRNA and chromossome M mRNAs) for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2.
After mapping, the aligned transcripts were assembled using Cufflinks (v2.1.1) standard parameters. To calculate the expression values and test the statistical difference in the mRNA expression we used the Cuffdiff tool.
Venn diagram analysis was performed to identify mRNAs differently expressed (q < 0.01, p < 0.05) in the blood of TB patients compared to both control and LTBI groups. Then, AUROC (area under the receiver operating characteristics curve) analysis was used for the selection of target-gene candidates
Genome_build: hg19
Supplementary_files_format_and_content: Expresison data matrix file with the normalised expression value of each gene (ENSEMBL)

molecule: polyA RNA

source_name: Whole blood

extract_protocol:
Approximately 2.5mL of venous blood were collect from all participants using Paxgene RNA collection scheme (PreAnalytiX, Hombrechtikon, Switzerland). Further, the total RNA was isolated by PAXgene Blood miRNA Kit (PreAnalytiX, Hombrechtikon, Switzerland) which is indicated for the isolation and purification of the total RNA longer than 18 nucleotides (nt) from the whole blood collected with the Paxgene tubes. The manufacturer’s instructions were strictly followed at both blood collection and RNA purification stages.
The samples were submitted to a previous mRNA isolation step by Magnetic mRNA isolation kit. Which is designed to isolate intact polyadenosine (poly A) RNA. Then, the purified mRNA was used as input for the sequencing library preparation using the ScriptSeqTM V2 RNA-Seq library preparation kit (Epicenter) as per the manufacturer’s instructions.Subsequently, the sequencing was performed following the standard protocols on Illumina HiSeq® 2500 Sequencing System (Illumina, San Diego, CA) running 100 bp paired-end reads (PE100) and generating approximately 30 million reads passing filter for each sample to produce the mRNA reads.

tag: clinical information

value: Active Tuberculosis

value: whole blood


title: ATB_1


title: H1Rosa7_d12

description:
47838_H1 day 12 in vitro
mEpiVH1.RSEM.xlsx


title: Ctrl_BCG_0

value: Control - BCG - vaccinated


title: ATB_3


title: LTBI_BCG_1

value: Latent Tuberculosis - BCG - vaccinated


title: LTBI_BCG_0


title: Ctrl_BCG_1


title: LTBI_Unvac_0

value: Latent Tuberculosis - BCG - Unvaccinated


title: ATB_2


title: Ctrl_Unvac_0

value: Control - BCG - Unvaccinated


title: LTBI_BCG_2


title: Ctrl_BCG_3


title: Ctrl_Unvac_2


title: LTBI_BCG_3


title: Ctrl_Unvac_1


title: Ctrl_BCG_5


title: LTBI_BCG_5


title: Ctrl_BCG_4


title: LTBI_BCG_4


title: LTBI_Unvac_1


title: Ctrl_BCG_6


title: LTBI_Unvac_2


title: Treated_ATB_0

value: Treated Active Tuberculosis


title: LTBI_BCG_6


title: LTBI_BCG_7


title: LTBI_Unvac_3


title: ATB_4


title: Ctrl_BCG_7


title: LTBI_BCG_8


title: Ctrl_BCG_2


title: LTBI_BCG_9


title: LTBI_BCG_10


title: Treated_ATB_1


title: LTBI_Unvac_4


title: ATB_5


title: Ctrl_Unvac_3


title: Pf_DCJ_H33Ty1_T30_dirRNAseq

city: Nijmegen

first: Sabine

last: Fraschka

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

data_processing:
Illumina Casava 1.8.2 software for basecalling.
Data were mapped with BWA samse (Version: 0.7.10-r789) to the P. falciparum 3D7 reference genome from PlasmoDB version 6.1 (http://www.plasmodb.org).
Sam files were converted to bam files, q15 filtered and filtered for unique reads
Normalized bedGraph files were generated using bedtools genomecov with the option –bga (regions with zero coverage are also reported) and normalized using the option -scale and the scaling factor ‘1000000/amount of unique reads’. These normalized files were used to generate log2 PfH3.3-ChIP-over-H3core-ChIP ratio tracks.
Genome_build: PlasmoDB Plasmodium falciparum 3D7 release 6.1
Supplementary_files_format_and_content: ratio bedGraph.gz files show the coverage as log2-ratio of PfH3.3-ChIP-over-PfH3core-ChIP  calculated using normalized bedGraph files (T*_H33_H3core.Bedgraph.gz) (unique reads only, normalized to tag counts per million)

organism: Plasmodium falciparum

source_name: red blood cell stage, trophozoites (30hpi)

growth_protocol: Parasites were cultured in standard RPMI medium supplemented with 10% human serum (AB), 0.2% NaHCO3 and 2.5% human O+ red blood cells. Culturing occurred in 250 ml tissue culture ﬂasks placed in candle jars or in an incubator with a gas composition of 3% O2, 4% CO2 and 93% N2 and incubated at 37°C.

extract_protocol:
directional RNA-seq protocol to extract and prepare the material: Parasite cultures used for RNA extraction were immediately placed and processed on ice (4°C).  The preparation of strand-specific RNA-seq libraries was performed as in (Kensche et al., 2015). In short, after total RNA isolation (with on-column DNase treatment) and oligo-dT-selection (Hoeijmakers et al., 2013a) PolyA-selected RNA was further treated with DNase (TURBO DNase, Ambion) to remove remaining genomic DNA.  Subsequently, 1.2µg PolyA-selected total RNA equivalent (see (Hoeijmakers et al., 2013a) for details) for 10hpi and 2µg for 20hpi, 30hpi and 40hpi were fragmented by means of alkaline hydrolysis (5x fragmentation buffer: 200mM Tris acetate pH 8.2, 500mM potassium acetate, 150mM magnesium acetate) for 2min at 85°C in 250µl volume. RNA was precipitated overnight and checked for genomic DNA contamination using qPCR, followed by - if needed - another DNase treatment and RNA precipitation for clean-up. Remaining material was processed for strand-specific RNA-seq as in (Kensche et al., 2015). To prevent unwanted DNA-dependent second strand cDNA synthesis - a major source of artificial antisense ‘transcripts’ (Perocchi et al., 2007) - 0.2µg Actinomycin D was included into the first strand synthesis reaction, which was followed by a 15 min 70 °C enzyme deactivation step and QIAquick MinElute purification (Qiagen). During second strand synthesis replacement of dTTP with dUTPs resulted in incorporation of U-bases into the second cDNA strand.
Sequencing libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification
2ng double stranded cDNA were used for each sequencing library which were prepared as described in (Hoeijmakers et al., 2011) and (Kensche et al., 2015) with a few adjustments: after adaptor ligation samples were treated with USER enzyme (New England Biolabs) for 15min at 37°C that resulted in dUTP-dependent second strand-specific degradation, followed by a first amplification cycle (4 cycles: 98°C for 2min; 4 cycles of 98°C for 20sec, 62°C for 3min; 62°C for 5 min), using 2x KAPA HiFi HotStart ready-mix (KAPA Biosystems) and NextFlex primers, size-selection for 300-400bp fragments using 2% E-Gel Size Select Agarose Gels (Thermo Fisher Scientific), a second amplification cycle (9 cycles) and Agencourt AMPure XP Beads purification  (1:1 library beads ratio).

treatment_protocol: Prior to collection parasites were selected for var2CSA expression by affinity purification as in (Noviyanti et al., 2001). For the collection parasites were synchronized with sorbitol treatments and Percoll gradient centrifugations as described previously (Bártfai et al., 2010). During collections, medium was changed every 10 hours, but not less than 10 hours before collection to ensure optimal parasite growth. After 20 hours post invasion (hpi), medium volume was doubled. During each medium change parasite cultures were mixed to minimize growth differences within single culture flasks. Early ring, late ring, trophozoite and schizont stages were collected (10, 20, 30 or 40 hpi respectively).

tag: strain

value: NF54 - DCJ clone

tag: genomic modification

value: endogenous PfH3.3 (PF3D7_0617900) C-terminally tagged with Ty1 by single cross-over homologous recombination

tag: development stage

value: trophozoites


title: Pf_DCJ_H33Ty1_T10_dirRNAseq

source_name: red blood cell stage, early rings (10hpi)

value: early rings


title: Pf_DCJ_H33Ty1_T40_H3core_xLCHIP

source_name: red blood cell stage, schizonts (40hpi)

extract_protocol:
xl anti-histone H3 ChIP (H3.3 and H3) protocol to extract and prepare the material:  Parasite cultures used for cross-linked ChIP were immediately treated with 1% formaldehyde (final concentration) and incubated at 37°C for 10 min while shaking. Crosslinking reaction was quenched by adding 0.125M glycine (final concentration). After erythrocyte and parasite lysis using 0.05% saponin and a hypotonic buffer (10 mM Tris pH 8.0, 3 mM MgCl2 , 0.2%  NP-40, Roche Protease Inhibitor Cocktail) respectively, formaldehyde-cross-linked nuclei were separated from cell debris using a 0.25 M sucrose buffer cushion as described in (Bártfai et al., 2010). Subsequent, crosslinked chromatin was prepared as described in (Kensche et al., 2015) with a few adjustments. In short, for generation of genome-wide PfH3.3 profiles, enzymatic MNase digestion of cross-linked chromatin was performed using digestion buffer (50mM Tris pH7.4, 4mM MgCl2, 1mM CaCl2, 0.075% NP40, Roche Protease Inhibitor Cocktail) with 0.5 U MNase (Worthington Biochemicals Corporation) in 150μl aliquots at 37 ºC. Optimal digestion times were empirically determined for each stage by test-digestion of a nuclear aliquot for varying times, to obtain primarily mono-nucleosomal DNA fragments. Digestion reactions were stopped by adding 150μl quenching solution (2% Triton X100, 0.6% SDS, 300 mM NaCl, 6 mM EDTA, Roche Protease Inhibitor Cocktail) and placing the samples on ice. Subsequently, digested chromatin was sonicated for 6 x 10 sec (setting low, BioruptorTM Next Gen, Diagenode) to free cross-linked chromatin from nuclear membranes. Approximately 200 ng of digested DNA-containing cross-linked chromatin was incubated in ChIP buffer (150mM NaCl, 20mM Tris pH 8.0, 2mM EDTA, 1% Triton X-100, 0.1% SDS, Roche Protease Inhibitor Cocktail ) with the respective antibody overnight at 4°C while rotating, followed by the addition of 10µl ProtA/G beads (Life Technologies, 10008D and 10009D) and further incubation at 4°C for 2 h. For the anti-histone H3 antibody (capturing histone PfH3 and PfH3.3) one ChIP reaction was performed per life cycle stage (1 µg antibody/ChIP).After washing with three different buffers (buffer1, 1x: 20mM Tris pH 8.0, 2mM EDTA, 1% Triton-X100, 0.1% SDS, 150mM NaCl; buffer 2, 2x: 20mM Tris pH 8.0, 2mM EDTA, 1% Triton-X100, 0.1% SDS, 500mM NaCl and buffer 3, 2x: 10mM Tris pH 8.0, 1mM EDTA) immunoprecipitated chromatin was eluted using 1% SDS and 0.1M NaHCO3. Immunoprecipitated chromatin was de-cross-linked (1% SDS, 0.1M NaHCO3, 1M NaCl) overnight at 45 °C shaking, followed by DNA isolation via QIAquick column purification (Qiagen).
Sequencing libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification
For each sequencing library generated from endogenously PfH3.3-Ty1 expressing DCJ P. falciparum parasites 3 ng of ChIP DNA were end repaired, extended with 3’  A-overhangs, and ligated to barcoded NextFlex adapters (Bio Scientific) (Hoeijmakers et al., 2011). Subsequent library amplification was performed under similar conditions as described previously (Kensche et al., 2015) with a few adjustments: First, 2x KAPA HiFi HotStart ready-mix (KAPA Biosystems) and NextFlex primers were used for 4 cycles of PCR amplification (98°C for 2min; 4 cycles of 98°C for 20sec, 62°C for 3min; 62°C for 5 min). Subsequently, amplified libraries were size selected for 270 bp (mono-nucleosomes + ~125bp NextFlex adapter) using 2% E-Gel Size Select Agarose Gels (Thermo Fisher Scientific) and again amplified as described above for 9 cycles. To deplete adapter dimers and clean-up the DNA, libraries were subsequently purified with Agencourt AMPure XP bead (Beckman Coulter) (1:1 library beads ratio) before sequencing.

value: schizonts

tag: chip antibody

value: polyclonal anti-histone H3 (Abcam Ab1791)


title: Pf_DCJ_H33Ty1_T40_dirRNAseq


title: Pf_DCJ_H33Ty1_T20_dirRNAseq

source_name: red blood cell stage, late rings (20hpi)

value: late rings


title: Pf_DCJ_H33Ty1_T10_BB2_xLCHIP

extract_protocol:
xl anti-Ty ChIP (H3.3) protocol to extract and prepare the material:  Parasite cultures used for cross-linked ChIP were immediately treated with 1% formaldehyde (final concentration) and incubated at 37°C for 10 min while shaking. Crosslinking reaction was quenched by adding 0.125M glycine (final concentration). After erythrocyte and parasite lysis using 0.05% saponin and a hypotonic buffer (10 mM Tris pH 8.0, 3 mM MgCl2 , 0.2%  NP-40, Roche Protease Inhibitor Cocktail) respectively, formaldehyde-cross-linked nuclei were separated from cell debris using a 0.25 M sucrose buffer cushion as described in (Bártfai et al., 2010). Subsequent, crosslinked chromatin was prepared as described in (Kensche et al., 2015) with a few adjustments. In short, for generation of genome-wide PfH3.3 profiles, enzymatic MNase digestion of cross-linked chromatin was performed using digestion buffer (50mM Tris pH7.4, 4mM MgCl2, 1mM CaCl2, 0.075% NP40, Roche Protease Inhibitor Cocktail) with 0.5 U MNase (Worthington Biochemicals Corporation) in 150μl aliquots at 37 ºC. Optimal digestion times were empirically determined for each stage by test-digestion of a nuclear aliquot for varying times, to obtain primarily mono-nucleosomal DNA fragments. Digestion reactions were stopped by adding 150μl quenching solution (2% Triton X100, 0.6% SDS, 300 mM NaCl, 6 mM EDTA, Roche Protease Inhibitor Cocktail) and placing the samples on ice. Subsequently, digested chromatin was sonicated for 6 x 10 sec (setting low, BioruptorTM Next Gen, Diagenode) to free cross-linked chromatin from nuclear membranes. Approximately 200 ng of digested DNA-containing cross-linked chromatin was incubated in ChIP buffer (150mM NaCl, 20mM Tris pH 8.0, 2mM EDTA, 1% Triton X-100, 0.1% SDS, Roche Protease Inhibitor Cocktail ) with the respective antibody overnight at 4°C while rotating, followed by the addition of 10µl ProtA/G beads (Life Technologies, 10008D and 10009D) and further incubation at 4°C for 2 h. For PfH3.3 (anti-Ty1) four ChIP reactions were performed in parallel per life cycle stage to ensure sufficient amount of DNA for subsequent ChIP-seq (2 µg antibody /ChIP). After washing with three different buffers (buffer1, 1x: 20mM Tris pH 8.0, 2mM EDTA, 1% Triton-X100, 0.1% SDS, 150mM NaCl; buffer 2, 2x: 20mM Tris pH 8.0, 2mM EDTA, 1% Triton-X100, 0.1% SDS, 500mM NaCl and buffer 3, 2x: 10mM Tris pH 8.0, 1mM EDTA) immunoprecipitated chromatin was eluted using 1% SDS and 0.1M NaHCO3. Immunoprecipitated chromatin was de-cross-linked (1% SDS, 0.1M NaHCO3, 1M NaCl) overnight at 45 °C shaking, followed by DNA isolation via QIAquick column purification (Qiagen).
Sequencing libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification
For each sequencing library generated from endogenously PfH3.3-Ty1 expressing DCJ P. falciparum parasites 3 ng of ChIP DNA were end repaired, extended with 3’  A-overhangs, and ligated to barcoded NextFlex adapters (Bio Scientific) (Hoeijmakers et al., 2011). Subsequent library amplification was performed under similar conditions as described previously (Kensche et al., 2015) with a few adjustments: First, 2x KAPA HiFi HotStart ready-mix (KAPA Biosystems) and NextFlex primers were used for 4 cycles of PCR amplification (98°C for 2min; 4 cycles of 98°C for 20sec, 62°C for 3min; 62°C for 5 min). Subsequently, amplified libraries were size selected for 270 bp (mono-nucleosomes + ~125bp NextFlex adapter) using 2% E-Gel Size Select Agarose Gels (Thermo Fisher Scientific) and again amplified as described above for 9 cycles. To deplete adapter dimers and clean-up the DNA, libraries were subsequently purified with Agencourt AMPure XP bead (Beckman Coulter) (1:1 library beads ratio) before sequencing.

value: monoclonal anti-Ty1 antibody (BB2)


title: Pf_DCJ_H33Ty1_T20_BB2_xLCHIP


title: Pf_DCJ_H33Ty1_T40_BB2_xLCHIP


title: Pf_DCJ_H33Ty1_T10_H3core_xLCHIP


title: normal 2

city: Taian

first: Yuqian

last: Wang

address: Daizong Street No. 61

institute: Shandong Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low quality reads, reads without 3’ primer, reads with 5’ primer contaminants, reads without the inserted tag, reads with poly(A), reads shorter than 18 nt or low-quality sequence, then mapped to Ovis aries genome using SOAPv1.11 software
Genome_build: NCBI, 2012, RGSC Rnor 5.0/rn5
Supplementary_files_format_and_content: micro RNA sequences and counts

organism: Rattus norvegicus

source_name: Rat liver tissue

extract_protocol: Wistar rat liver tissues were obtained by surgery and immediately frozen in liquid nitrogen. RNA was harvested using Trizol reagent. Illumina/Solexa RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.

tag: disease state

value: control

value: Wistar

tag: age

value: 4 months

value: liver tissue


title: NAFLD 3

value: NAFLD

tag: tissue


title: NAFLD 2


title: Pf_DCJ_H33Ty1_T30_BB2_xLCHIP


title: NAFLD 1


title: normal 3


title: normal 1


title: Pf_DCJ_H33Ty1_T20_H3core_xLCHIP


title: ABA_tolerant_ONSEN_line2_polIV_2

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

data_processing:
Basecalls were performed using standard tools equipped with ABI SOLiD4 sequencer.
Each sequences were aligned on TAIR9 genome using bowtie (version 0.12.8).
Sequences mapped on a subtype of retrotransposon (ONSEN) were collected and mapped regions of their pairs were evaluated.
Genome_build: TAIR9
Supplementary_files_format_and_content: An Excel file containing sequence IDs and their inserted positions and a file having summerized genomic locations where the retrotransposon were inserted.

organism: Arabidopsis thaliana

source_name: Plant

growth_protocol: for two weeks at 21C on MS medium agar plate. Light:24h.

extract_protocol:
Qiagen plant DNA purification kit
pair-endo sequencing libraries using SOLiD fragment library construction kit (Life Technologies)
50bp-35bp pair-end sequencing for SOLiD4 sequencer (accoding to manufacturers instructions)

treatment_protocol: A parent plant was shift to 37C for 24h.

tag: developmental stage

value: 1 week old

tag: genotype

tag: ecotype

tag: treatment

value: A progeny of a non-stressed parent


title: ABA_tolerant_ONSEN_lines_6_13_7

value: A progeny of a heat-stressed parent


title: ABA_tolerant_ONSEN_lines_6_16_1


title: ABA_tolerant_ONSEN_lines_6_14_1


title: ABA_tolerant_ONSEN_lines_6_13_8


title: 44hAPF_R1

city: Chapel Hill

first: Daniel

last: McKay

address: 250 Bell Tower Drive

department: Biology and Genetics

institute: University of North Carolina, Chapel Hill

description: RNA-seq on wing tissue  at 44hAPF - replicate 1

data_processing:
Sequenced reads were mapped to the dm3 whole genome using Tophat2 v2.1.0., supplementing a dm3 version transcript annotation file and using library-type fr-firststrand
The resulting bam file was indexed and sorted using samtools v1.2
htseq-count v0.6.1 was used to count reads mapping to genes, using the parameters -s reverse -a 10 -t exon -i gene_name -f bam -r pos
RPKMs were calculated from the resulting count files using EdgeR
Genome_build: dm3
Supplementary_files_format_and_content: Count files generated using htseq-count and a single matrix table in the form of a csv file contains RPKMs for genes at all the timepoints

organism: Drosophila melanogaster

source_name: Wing

extract_protocol:
Forty wings for each stage were manually dissected and RNA was isolated using Trizol.
RNA libraries were prepared for sequencing using stranded mRNA sequencing kit from KAPA Biosystems (catalog # KK8421).

value: 44 (h APF)


title: 36hAPF_R2

description: RNA-seq on wing tissue  at 36hAPF - replicate 2

value: 36 (h APF)


title: 36hAPF_R1

description: RNA-seq on wing tissue  at 36hAPF - replicate 1


title: 24hAPF_R2

description: RNA-seq on wing tissue  at 24hAPF - replicate 2

value: 24 (h APF)


title: Pf_DCJ_H33Ty1_T30_H3core_xLCHIP

value: NF54 - DCJ clone

value: endogenous PfH3.3 (PF3D7_0617900) C-terminally tagged with Ty1 by single cross-over homologous recombination

value: trophozoites


title: 6hAPF_R1

description: RNA-seq on wing tissue  at 6hAPF - replicate 1

value: 6 hours after puparium formation (h APF)


title: 6hAPF_R2

description: RNA-seq on wing tissue  at 6hAPF - replicate 2

value: 6 (h APF)


title: 24hAPF_R1

description: RNA-seq on wing tissue  at 24hAPF - replicate 1


title: 18hAPF_R2

description: RNA-seq on wing tissue  at 18hAPF - replicate 2

value: 18 (h APF)


title: 18hAPF_R1

description: RNA-seq on wing tissue  at 18hAPF - replicate 1


title: ABA_tolerant_ONSEN_line2_polIV_1


title: 0hAPF_R1

description: RNA-seq on wing tissue  at 0hAPF - replicate 1

value: wandering 3rd instar larvae


title: MAGIC490

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

data_processing:
Illumina sequencing was performed at the Oxford Genomics Centre (Oxford, UK) to produce 100 bp paired-end reads using a HiSeq 2000 instrument and the TruSeq V3 chemistry. Reads from each library were aligned to the TAIR10 reference genome using PALMapper v0.6512 following a variation-aware alignment approach. Genome variants collected from the 19 founder strains (Gan et al., 2011; PMID: 21874022) as well as variants reported for a diverse natural population (Long et al., 2013; PMID: 23793030) were integrated and provided to the aligner as a set of known variants. Briefly, the mapper used this set of variants in alignments to prevent reference biases in RNA-seq read mapping. To facilitate accurate alignments, we further provided splice junction information collected in an earlier study with the founder strains (Gan et al., 2011; PMID: 21874022) as well as junction information extracted from the TAIR10 genome annotation. The full alignment parameter set for PALMapper was: -M 3 -G 0 -E 3 -l 12 –L 14 -K 12 -C 14 -I 5000 -NI 1 -SA 5 -UA 50 -CT 50 -JA 15 -JI 1 -z 10 -S -seed-hit-truncate-threshold 100 -report-map-read -report-spliced-read -report-map region -report-splice-sites 0.9 -filter-max-mismatches 0 -filter-max-gaps 0 -filter-splice-region 5 -min-spliced-segment-len 1 -qpalma-use-map-max-len 10 -f bam -qpalma-prb-offset-fix -junction-remapping <junction_file> -score-annotated-splice-sites <junction_file> -max-dp-deletions 2 -use-variants-editop-filter -use-variants <variant_file> -filter-variants-minuse 1 –merge-variant-source-ids -use-iupac-snp-variants -filter-variants-map-window 20 -iupac-genome -filter-variants-maxlen 100 -index-precache.
From the aligned reads per sample, gene expression quantification was performed using custom Python scripts that counted the number of reads overlapping with at least one exonic position of an annotated gene feature. For each read only the best alignment as assessed with the PALMapper aligner was considered for counting. An alignment was excluded from being counted towards the expression of a gene if (i) at least one position in the alignment overlapped to an annotated intron, (ii) the alignment fell entirely into a region where two or more annotated genes overlap, and (iii) the alignment did not start at a position that is part of an exon in all annotated isoforms. For each gene feature the total number of reads passing these filters was used to calculate Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and RANKSUM expression values (briefly, for the latter a rank transformation was applied in which the gene expression levels were ranked across samples and then transformed values were sampled from an inverse Gaussian CDF based on the ranks). Genes included in the expression quantification were from the TAIR10 annotation and a set of novel genes reported in an earlier study (Gan et al., 2011; PMID: 21874022).
The 209 MAGIC lines included in this analysis are part of a larger set of nearly 500 lines for which the genomic intervals derived from the 19 founder accessions of the MAGIC cross were imputed using Illumina genomic sequencing of both the MAGIC founders and the derived lines. The imputed genomes of each MAGIC line as assessed from genomic DNA sequences are publically available at the respective genome project site (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/magic.html). An analogous imputation using variants inferred from the RNA-seq alignments gave similar imputations for nearly all lines -- a prerequisite for using the RNA-seq data with the genomic imputations for genotype-phenotype studies -- with a small number of exceptions that included MAGIC lines 4, 10, 88, 105, 108, 152, 198, 298, 423 and 432. In some of these cases, differences may reflect regions of lines that were not fixed by inbreeding (the seed stocks used in the current RNA-seq study were from a different batch than used for genomic DNA imputation), and the result should be factored into specific downstream analyses with this subset of lines.
Genome_build: TAIR 10
Supplementary_files_format_and_content: FPKM and RANKSUM normalized expression values as separate text files.

source_name: aerial seedling

growth_protocol: A subset of MAGIC lines were obtained from the Nottingham Arabidopsis Stock Centre (NASC). Briefly, 209 of the MAGIC lines were grown at 20°C in Percival environmental chambers (Perry, IA, USA) and total RNA was prepared as previously described for an earlier study with the MAGIC parental founders (twenty aerial rosettes from seedlings at the fourth true leaf stage were pooled per single biological replicate per line; Gan et al., 2011; PMID: 21874022).

extract_protocol:
Pools of aerial seedlings per MAGIC line were ground in liquid nitrogen using a mortar and pestle and RNA was isolated using PureLink Plant RNA Reagent (#12322-012, Invitrogen, Carlsbad, CA, USA) following the manufacturers instructions. Precipitated RNA was resuspended in RNAsecure Resuspension Solution (#AM7010, Ambion; Life Technologies, Carlsbad, CA, USA) following manufacturers guidelines to prevent RNA degradation. Contaminating genomic DNA was removed by incubating samples with Turbo DNase (#AM2238, Ambion) for 15 min at 37°C. Finally, RNA was precipitated using 2.5 vol 100% ethanol, 0.1 volume 5M Ammonium Acetate and 1µl glycogen (5 mg/ml) and resuspended in RNase-free water.
Non-strand specific RNA-seq libraries were constructed using the Illumina method at the Oxford Genomics Centre (Oxford, UK). Poly-A selection was employed in the library construction.

value: 4th true leaf stage

tag: accession

value: MAGIC Line 490

tag: growth temperature


title: MAGIC310

value: MAGIC Line 310


title: MAGIC265

value: MAGIC Line 265


title: MAGIC241

value: MAGIC Line 241


title: MAGIC499

value: MAGIC Line 499


title: MAGIC237

value: MAGIC Line 237


title: MAGIC295

value: MAGIC Line 295


title: MAGIC434

value: MAGIC Line 434


title: MAGIC433

value: MAGIC Line 433


title: MAGIC198

value: MAGIC Line 198


title: MAGIC388

value: MAGIC Line 388


title: MAGIC494

value: MAGIC Line 494


title: MAGIC423

value: MAGIC Line 423


title: 44hAPF_R2

description: RNA-seq on wing tissue  at 44hAPF - replicate 2

value: 44 (h APF)


title: MAGIC346

value: MAGIC Line 346


title: MAGIC361

value: MAGIC Line 361


title: MAGIC320

value: 4th true leaf stage

value: MAGIC Line 320


title: MAGIC314

value: MAGIC Line 314


title: MAGIC304

value: MAGIC Line 304


title: MAGIC299

value: MAGIC Line 299


title: 0hAPF_R2

description: RNA-seq on wing tissue  at 0hAPF - replicate 2

value: wandering 3rd instar larvae


title: MAGIC324

value: MAGIC Line 324


title: MAGIC291

value: MAGIC Line 291


title: MAGIC234

value: MAGIC Line 234


title: MAGIC250

value: MAGIC Line 250


title: MAGIC206

value: MAGIC Line 206


title: MAGIC278

value: MAGIC Line 278


title: MAGIC227

value: MAGIC Line 227


title: MAGIC498

value: MAGIC Line 498


title: MAGIC328

value: MAGIC Line 328


title: MAGIC298

value: MAGIC Line 298


title: MAGIC231

value: MAGIC Line 231


title: MAGIC420

value: 4th true leaf stage

value: MAGIC Line 420


title: MAGIC266

value: MAGIC Line 266


title: MAGIC432

value: MAGIC Line 432


title: MAGIC313

value: MAGIC Line 313


title: MAGIC354

value: MAGIC Line 354


title: MAGIC221

value: MAGIC Line 221


title: MAGIC496

value: MAGIC Line 496


title: MAGIC319

value: MAGIC Line 319


title: MAGIC205

value: MAGIC Line 205


title: MAGIC491

value: MAGIC Line 491


title: MAGIC325

value: MAGIC Line 325


title: MAGIC296

value: MAGIC Line 296


title: MAGIC311

value: MAGIC Line 311


title: MAGIC303

value: MAGIC Line 303


title: MAGIC261

value: MAGIC Line 261


title: MAGIC286

value: MAGIC Line 286


title: MAGIC247

value: 4th true leaf stage

value: MAGIC Line 247


title: MAGIC229

value: MAGIC Line 229


title: MAGIC220

value: MAGIC Line 220


title: MAGIC199

value: MAGIC Line 199


title: MAGIC485

value: MAGIC Line 485


title: MAGIC430

value: MAGIC Line 430


title: MAGIC493

value: MAGIC Line 493


title: MAGIC353

value: MAGIC Line 353


title: MAGIC366

value: MAGIC Line 366


title: MAGIC395

value: MAGIC Line 395


title: MAGIC283

value: MAGIC Line 283


title: MAGIC294

value: MAGIC Line 294


title: MAGIC301

value: MAGIC Line 301


title: MAGIC308

value: MAGIC Line 308


title: MAGIC197

value: MAGIC Line 197


title: MAGIC424

value: MAGIC Line 424


title: MAGIC363

value: 4th true leaf stage

value: MAGIC Line 363


title: MAGIC317

value: MAGIC Line 317


title: MAGIC351

value: MAGIC Line 351


title: MAGIC323

value: MAGIC Line 323


title: MAGIC484

value: MAGIC Line 484


title: MAGIC255

value: MAGIC Line 255


title: MAGIC253

value: MAGIC Line 253


title: MAGIC495

value: MAGIC Line 495


title: MAGIC322

value: MAGIC Line 322


title: MAGIC236

value: MAGIC Line 236


title: MAGIC224

value: MAGIC Line 224


title: MAGIC213

value: MAGIC Line 213


title: MAGIC196

value: MAGIC Line 196


title: MAGIC492

value: MAGIC Line 492


title: MAGIC191

value: MAGIC Line 191


title: MAGIC293

value: MAGIC Line 293


title: MAGIC414

value: 4th true leaf stage

value: MAGIC Line 414


title: MAGIC327

value: MAGIC Line 327


title: MAGIC157

value: MAGIC Line 157


title: MAGIC115

value: MAGIC Line 115


title: MAGIC83

value: MAGIC Line 83


title: MAGIC307

value: MAGIC Line 307


title: MAGIC312

value: MAGIC Line 312


title: MAGIC483

value: MAGIC Line 483


title: MAGIC96

value: MAGIC Line 96


title: MAGIC230

value: MAGIC Line 230


title: MAGIC201

value: MAGIC Line 201


title: MAGIC292

value: MAGIC Line 292


title: MAGIC305

value: MAGIC Line 305


title: MAGIC321

value: MAGIC Line 321


title: MAGIC362

value: MAGIC Line 362


title: MAGIC235

value: MAGIC Line 235


title: MAGIC300

value: 4th true leaf stage

value: MAGIC Line 300


title: MAGIC280

value: MAGIC Line 280


title: MAGIC251

value: MAGIC Line 251


title: MAGIC175

value: MAGIC Line 175


title: MAGIC125

value: MAGIC Line 125


title: MAGIC114

value: MAGIC Line 114


title: MAGIC194

value: MAGIC Line 194


title: MAGIC212

value: MAGIC Line 212


title: MAGIC95

value: MAGIC Line 95


title: MAGIC105

value: MAGIC Line 105


title: MAGIC90

value: MAGIC Line 90


title: MAGIC297

value: MAGIC Line 297


title: MAGIC81

value: MAGIC Line 81


title: MAGIC264

value: MAGIC Line 264


title: MAGIC316

value: MAGIC Line 316


title: MAGIC74

value: MAGIC Line 74


title: MAGIC63

value: 4th true leaf stage

value: MAGIC Line 63


title: MAGIC41

value: MAGIC Line 41


title: MAGIC222

value: MAGIC Line 222


title: MAGIC55

value: MAGIC Line 55


title: MAGIC35

value: MAGIC Line 35


title: MAGIC174

value: MAGIC Line 174


title: MAGIC123

value: MAGIC Line 123


title: MAGIC13

value: MAGIC Line 13


title: MAGIC104

value: MAGIC Line 104


title: MAGIC94

value: MAGIC Line 94


title: MAGIC54

value: MAGIC Line 54


title: MAGIC226

value: MAGIC Line 226


title: MAGIC34

value: MAGIC Line 34


title: MAGIC25

value: MAGIC Line 25


title: MAGIC73

value: MAGIC Line 73


title: MAGIC11

value: MAGIC Line 11


title: MAGIC180

value: 4th true leaf stage

value: MAGIC Line 180


title: MAGIC170

value: MAGIC Line 170


title: MAGIC120

value: MAGIC Line 120


title: MAGIC103

value: MAGIC Line 103


title: MAGIC72

value: MAGIC Line 72


title: MAGIC88

value: MAGIC Line 88


title: MAGIC62

value: MAGIC Line 62


title: MAGIC52

value: MAGIC Line 52


title: MAGIC138

value: MAGIC Line 138


title: MAGIC187

value: MAGIC Line 187


title: MAGIC32

value: MAGIC Line 32


title: MAGIC21

value: MAGIC Line 21


title: MAGIC89

value: MAGIC Line 89


title: MAGIC113

value: MAGIC Line 113


title: MAGIC40

value: MAGIC Line 40


title: MAGIC10

value: MAGIC Line 10


title: MAGIC118

value: 4th true leaf stage

value: MAGIC Line 118


title: MAGIC168

value: MAGIC Line 168


title: MAGIC101

value: MAGIC Line 101


title: MAGIC77

value: MAGIC Line 77


title: MAGIC86

value: MAGIC Line 86


title: MAGIC71

value: MAGIC Line 71


title: MAGIC135

value: MAGIC Line 135


title: MAGIC50

value: MAGIC Line 50


title: MAGIC9

value: MAGIC Line 9


title: MAGIC61

value: MAGIC Line 61


title: MAGIC80

value: MAGIC Line 80


title: MAGIC161

value: MAGIC Line 161


title: MAGIC116

value: MAGIC Line 116


title: MAGIC92

value: MAGIC Line 92


title: MAGIC97

value: MAGIC Line 97


title: MAGIC84

value: MAGIC Line 84


title: MAGIC76

value: 4th true leaf stage

value: MAGIC Line 76


title: MAGIC108

value: MAGIC Line 108


title: MAGIC27

value: MAGIC Line 27


title: MAGIC37

value: MAGIC Line 37


title: MAGIC93

value: MAGIC Line 93


title: MAGIC60

value: MAGIC Line 60


title: MAGIC4

value: MAGIC Line 4


title: MAGIC16

value: MAGIC Line 16


title: MAGIC188

value: MAGIC Line 188


title: MAGIC31

value: MAGIC Line 31


title: MAGIC106

value: MAGIC Line 106


title: MAGIC45

value: MAGIC Line 45


title: MAGIC127

value: MAGIC Line 127


title: MAGIC91

value: MAGIC Line 91


title: MAGIC75

value: MAGIC Line 75


title: MAGIC26

value: MAGIC Line 26


title: MAGIC57

value: 4th true leaf stage

value: MAGIC Line 57


title: MAGIC36

value: MAGIC Line 36


title: MAGIC14

value: MAGIC Line 14


title: MAGIC179

value: MAGIC Line 179


title: hRBCs 24 hpi replicate 3

city: Stockholm

first: S Noushin

last: Emami

address: Svante Arrhenius väg 20C

country: Sweden

institute: Stockholm University

description: total RNA

data_processing:
Paired-end reads obtained from each sample were aligned to the A. gambiae reference genome (AgamP4.2, VectorBase, 22 August 2014) using TopHat (42, 43). All HMBPP cohorts were cross-compared to control cohorts.
The Cufflinks program (Cuffdiff, Version 2.1., 11 April 2013) was used to assemble individual transcripts from the mapped reads and to quantify the expression level of each transcript using a Linux coding strategy and RNA-Rocket software (v.2013, Galaxy.org, USA).
Differential transcript expression analysis was additionally conducted using the Cuffdiff program. Unadjusted p-values and fold-change cut-offs were used for interpretation. Genes with read abundances less than 1 FPKM (average fragments per kilobase of transcript per million fragments mapped) were removed from the analysis.
The functional gene annotation and signalling pathways were analysed and highlighted using the bioinformatics resources DAVID, BioMart and Qlucore Omics Explorer (Version 3.1. trial Qlucore, Sweden)
Data were explored and visualised using CummeRbund v.2.0.0 (http://compbio.mit.edu/cummeRbund/) and R scripts (RStudio software v.3.1.0, http://www.r-project.org/).
Genome_build: AgamP4.2, VectorBase, 22 August 2014
Supplementary_files_format_and_content: .xlsx file include calculated fold changes based on RPKM values between control and treatment. See Emami et al. 2017 for details.

organism: Anopheles gambiae

source_name: Whole body

growth_protocol: Standard rearing conditions. See Emami et al. 2017.

extract_protocol:
Trizol extraction. See Emami et al. 2017.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HMBPP was added RBCs immediately prior to feeding (final concentration: 10 microM). A corresponding volume of MilliQ H2O was added to control feedings. Replicate experiments were performed in parallel.

tag: line

value: Keele colony

value: 5-7 days old females

tag: time point

value: 24 hpi

tag: agent

value: hmbRBCs


title: MAGIC44

value: MAGIC Line 44


title: RBCs 24 hpi replicate 3

description: total RNA

value: RBCs


title: hRBCs 24 hpi replicate 2

description: total RNA


title: MAGIC67

value: MAGIC Line 67


title: RBCs 24 hpi replicate 2

description: total RNA


title: MAGIC176

value: MAGIC Line 176


title: MAGIC256

value: MAGIC Line 256


title: MAGIC130

value: MAGIC Line 130


title: RBCs 24 hpi replicate 1

description: total RNA


title: hRBCs 24 hpi replicate 1

description: total RNA


title: hRBCs 6 hpi replicate 3

description: total RNA

value: 6 hpi


title: MAGIC117

value: MAGIC Line 117


title: RBCs 6 hpi replicate 3

description: total RNA


title: hRBCs 6 hpi replicate 1

description: total RNA


title: MAGIC66

value: 4th true leaf stage

value: MAGIC Line 66


title: MAGIC107

value: MAGIC Line 107


title: hRBCs 6 hpi replicate 2

description: total RNA


title: MAGIC152

value: MAGIC Line 152


title: RBCs 6 hpi replicate 2

description: total RNA


title: hRBCs 3 hpi replicate 3

description: total RNA

value: 3 hpi


title: MAGIC85

value: MAGIC Line 85


title: RBCs 6 hpi replicate 1

description: total RNA

value: Keele colony

value: 5-7 days old females


title: MAGIC70

value: MAGIC Line 70


title: RBCs 3 hpi replicate 2

description: total RNA


title: MAGIC49

value: MAGIC Line 49


title: hRBCs 3 hpi replicate 1

description: total RNA

value: hmbRBCs


title: RBCs 3 hpi replicate 1

description: total RNA

value: RBCs


title: MAGIC39

value: MAGIC Line 39


title: MAGIC165

value: MAGIC Line 165


title: hRBCs 1 hpi replicate 3

description: total RNA

value: 1 hpi


title: RBCs 1 hpi replicate 3

description: total RNA


title: MAGIC30

value: MAGIC Line 30


title: hRBCs 1 hpi replicate 2

description: total RNA


title: hRBCs 1 hpi replicate 1

description: total RNA


title: MAGIC17

value: MAGIC Line 17


title: MAGIC6

value: 4th true leaf stage

value: MAGIC Line 6


title: MAGIC99

value: MAGIC Line 99


title: Day 40 Week Control Pituitary 1578

city: Newark

first: Carl

last: Schmidt

state: DE

address: 601 Sincock Ln

institute: University of Delaware

data_processing:
Bowtie
TopHat
Cufflinks
Genome_build: Gallus gallus ver 4

organism: Gallus gallus

source_name: Pituitary Gland Tissue

growth_protocol: Birds were raised following grower standards outlined by our AACUC protocol (#(27)03-12-14R). Briefly, birds were raised on litter with ad libitum access to feed and water. First week house temperature: 35 degrees C with 5 degrees C decrease each week until 25 degrees celsius was reached. Thermoneutral/Control house maintained this temperature through completion of the trial while heat stress (experimental) house began a cyclical heat stress scheme detaield below through completion of the trial at day 42 (typical market age). Both houses received 23 hours of light and 1 hour of dark for the entirety of the study. Necropsies were performed on Day 21 (prior to treatment), Day 22 (8 hours of treatment), Day 26 (2 hours acute treatment), Day 32 (4 hours acute treatment) and Day 42 (3 weeks of cyclical heat stress). Matched controls were collected at each time point.

extract_protocol:
Birds were euthanized via cervical dislocation and necropsied on each day listed above. Whole pituitary glands were collected and flash frozen with liquid nitrogen.
Libraries were constructed using the Illumina Stranded RNA-seq kit according to manufacturers instructions.

treatment_protocol: Temperature in the experimental house was increased each day from 25 degrees celsius to approximately 35-37 degrees celsius from 7 am to 3 pm each day starting on day 21. This cyclical heat stress scheme continued through day 42, completion of the trial.

value: Pituitary


title: RBCs 1 hpi replicate 2

description: total RNA


title: Day 40 Week Control Pituitary 1579


title: RBCs 1 hpi replicate 1

description: total RNA


title: MAGIC24

value: MAGIC Line 24


title: MAGIC501

value: MAGIC Line 501


title: MAGIC254

value: MAGIC Line 254


title: hRBCs 3 hpi replicate 2

description: total RNA

value: Keele colony

value: 5-7 days old females

value: 3 hpi


title: MAGIC18

value: MAGIC Line 18


title: Day 40 Week Heat Stress Pituitary 1576


title: Day 40 Week Heat Stress Pituitary 1575


title: Day 40 Week Control Pituitary 1577


title: Day 21 Control Pituitary 1573


title: Day 40 Week Heat Stress Pituitary 1574


title: RBCs 3 hpi replicate 3

description: total RNA

value: RBCs


title: Day 21 Control Pituitary 1571


title: Day 21 Control Pituitary 1572


title: MAGIC51

value: MAGIC Line 51


title: Day 21 Control Pituitary 1570


title: Day 21 Control Pituitary 1568


title: MAGIC1

value: MAGIC Line 1


title: Day 21 Control Pituitary 1569


title: MAGIC43

value: MAGIC Line 43


title: Day 21 Control Pituitary 1567


title: Day 21 Control Pituitary 1566


title: Day 21 Control Pituitary 1565


title: MAGIC513

value: MAGIC Line 513


title: MAGIC42

value: MAGIC Line 42


title: Day 21 Control Pituitary 1564


title: Day 21 Control Pituitary 1562


title: Day 21 Control Pituitary 1561


title: Day 22 Heat Stress Pituitary 1559


title: MAGIC505

value: 4th true leaf stage

value: MAGIC Line 505


title: Day 22 Heat Stress Pituitary 1558


title: MAGIC504

value: MAGIC Line 504


title: Day 22 Heat Stress Pituitary 1556

value: Pituitary


title: Day 22 Heat Stress Pituitary 1555


title: MAGIC503

value: MAGIC Line 503


title: Day 22 Control Pituitary 1551


title: Day 22 Heat Stress Pituitary 1549


title: Day 22 Control Pituitary 1552


title: Day 22 Control Pituitary 1525


title: Day 22 Heat Stress Pituitary 1557


title: MAGIC502

value: MAGIC Line 502


title: Day 22 Control Pituitary 1523


title: Day 22 Control Pituitary 1550


title: Day 22 Control Pituitary 1524


title: Day 22 Control Pituitary 1526


title: Day 22 Heat Stress Pituitary 1522


title: Day 22 Heat Stress Pituitary 1521


title: Day 40 Week Control Pituitary 1516


title: Day 22 Heat Stress Pituitary 1519


title: Day 21 Control Pituitary 1560


title: Day 22 Heat Stress Pituitary 1520


title: Day 22 Heat Stress Pituitary 1517


title: Day 26 2 Hour Control Pituitary 1514


title: Day 26 2 Hour Control Pituitary 1513


title: Day 26 2 Hour Control Pituitary 1512


title: Day 26 2 Hour Heat Stress Pituitary 1511


title: Day 22 Control Pituitary 1553


title: HEK293T tRNA Untreated

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description: library strategy: DM-tRNA-Seq

data_processing:
Raw reads were processed using Trimmomatic v 0.32n and custom Python scripts to fully remove traces of adapter.
Processed reads were aligned in Bowtie 1.0 according to the parameters of -t -v 3 -m 10 --best --strata -p 12
Fragments shorter than 18 base pairs during alignment were removed during subsequent analysis.
Further processing using custom C and Python scripts were used to map reads onto tRNA isodecoders/rRNAs for visualization and modification index analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Individual alignment files mapping tRNA to isodecoder with read counts

extract_protocol:
Total RNA was isolated by using mirVana miRNA Isolation Kit (Life Technologies). Purified total RNA was deacylated by incubating in 0.1 M tris-HCl, pH 9 at 37°C for 45 min. When necessary, total tRNA was subsequently isolated using a denaturing 10% polyacrylamide gel followed by passive gel elution and ethanol precipitation.
Homemade protocol based on Illumina protocols. Deacylated RNAs with or without the demethylation were first treated with T4 Polynucleotide Kinase (Epicentre) at 37C° for 30 min to further warrant a free 3' hydroxyl group for template switching. Template-switching reactions were performed as described7. Briefly, we used an initial template-primer substrate consisting of a 41-nt RNA oligonucleotide (5’-AGA UCG GAA GAG CAC ACG UCU AGU UCU ACA GUC CGA CGA UC/3SpC3/-3’) that contains Illumina Read1 and Read2 primer-binding sites and a 3’ blocking group (three carbon spacer; IDT) annealed to a complementary 32P-labeled DNA primer with a single-nucleotide 3’ overhang, T, which facilitates the template switch to full-length tRNA that mostly contain a 3’ CCA end. For g2RT template-switching reactions, average 100 ng of demethylated tRNAs or 1 μg of demethylated total RNA were mixed with the initial template-primer substrate (100 nM) and g2RT (1 μM of TeI4cΔEn or 500 nM of GsI-IIC RT) in reaction medium containing 450 mM NaCl, 5 mM MgCl2, 20 mM Tris-HCl, pH 7.5, and DTT (1 mM for TeI4cΔEn or 5 mM for GsI-IIC RT). For template-switching with TeI4cΔEn RT, the reactions were pre-incubated at room temperature for 30 min, initiated by adding 25 mM dNTPs to a final concentration of 1 mM and incubating at 60°C for 30 min. For template-switching with GsI-IIC RT, the pre-incubation step is not required. The reactions were terminated by adding 5 M NaOH to a final concentration of 0.25 M, incubating at 95°C for 3 min, and neutralizing with 5M HCl. The cDNAs resulting from template switching were analyzed in a denaturing 6% polyacrylamide gel, electroeluted using a D-tube Dialyzer Maxi with MWCO of 6-8 kDa (EMD Millipore), and ethanol precipitated with 0.3 M sodium acetate in the presence of 25 µg of linear acrylamide (Life Technologies). The purified cDNAs were then circularized with CircLigase II (Epicentre) using manufacture’s protocol with extended incubation time of 5 hours at 60°C, phenol-CIA extracted, ethanol precipitated and amplified with Phusion-HF (Thermo Scientific) using Illumina multiplex (5’- AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG TTC AGA GTT CTA CAG TCC GAC GAT C -3’) and barcode (5’- CAA GCA GAA GAC GGC ATA CGA GAT BARCODE GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T -3’) primers for 12 cycles of 98°C for 5 sec, 60°C for 10 sec and 72°C for 10 sec. The PCR products were sequenced on Illumina HiSeq 1000 system.

treatment_protocol: Human HEK293T cell line was cultured in DMEM (Thermo) media supplemented with 10% FBS and 1% 100 × Pen Strep (Gibco)

value: no AlkB-derived enzyme mixture

tag: cell line

tag: molecule

value: tRNA


title: HeLa tRNA Untreated

description: library strategy: DM-tRNA-Seq

source_name: HeLa

value: HeLa


title: HEK293T tRNA Treated

description: library strategy: DM-tRNA-Seq

value: AlkB-derived enzyme mixture


title: Day 42 Heat Stress Pituitary 1438


title: small RNA/rRNA Treated

description: library strategy: DM-tRNA-Seq

value: small RNA/rRNA


title: Day 42 Heat Stress Pituitary 1435


title: Day 22 Control Pituitary 1432


title: Day 22 Control Pituitary 1437


title: Day 42 Heat Stress Pituitary 1434


title: Day 42 Control Pituitary 1420


title: Day 42 Heat Stress Pituitary 1436


title: Day 42 Control Pituitary 1419


title: Day 26 2 Hour Heat Stress Pituitary 1431


title: Day 42 Heat Stress Pituitary 1433


title: Day 42 Heat Stress Pituitary 1418


title: Day 42 Control Pituitary 1417


title: Day 42 Control Pituitary 1414


title: Day 42 Heat Stress Pituitary 1413


title: Day 40 Week Heat Stress Pituitary 1515


title: Day 42 Heat Stress Pituitary 1319


title: B108208

city: Honolulu

first: Yanghua

last: He

state: HI

address: 1955 East West Road

department: Human Nutrition, Food and Animal Sciences

institute: University of Hawaii at Manoa

description: S. aureus culture status: No exist

data_processing:
ChIP-seq reads were aligned to the bosTau4 genome assembly using SOAP 2.21 with the less than two mismatch
Data were filtered using the following specifications…
peaks were called using MACS 1.4.0 with the following setting: bandwidth of 200 bp, mfold of 30, p-value of 1.00e-05 under a FDR cutoff of 1%
Genome_build: bosTau4
Supplementary_files_format_and_content: wig files

organism: Bos taurus

source_name: Peripheral blood lymphocytes

growth_protocol: Peripheral blood lymphocytes were isolated by Lymphocytes Separation Medium (TBDsciences, Tianjin, China, PN.LTS1086) according to the manufacturer’s instructions.

extract_protocol:
Lymphocytes from peripheral blood were digested with MNase (TAKARA, D2910) to generate mainly mononucleosomes with a minor fraction of dinucleosomes for histone modification mapping. Chromatin from 5×10^7 cells were used for ChIP experiment and antibodies against histone H3K27me3 (millipore, Cat. #17–622) were used, that yielded approximately 30 ng of DNA.
The ChIP DNA fragments were blunt-ended and ligated to the Solexa adaptors (Paired-End DNA Sample Prep kit, Illumina, Cat. #PE-102–1001), the ChIP DNA was then amplified using the adaptor primers for 15 cycles and the fragments around 100–300 bp (mononucleosome + adaptors) were isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Hiseq2000 following manufacturer protocols.

value: blood

tag: cell type

value: lymphocytes

tag: days in milk

tag: parity


title: B108157

description: S. aureus culture status: No exist


title: Day 32 4 Hour Control Pituitary 1315


title: Day 26 2 Hour Heat Stress Pituitary 1510


title: B108076

description: S. aureus culture status: Exist


title: Day 42 Control Pituitary 1415


title: Day 26 2 Hour Heat Stress Pituitary 1312


title: Day 32 4 Hour Control Pituitary 1314


title: Day 26 2 Hour Heat Stress Pituitary 1313


title: B108074

description: S. aureus culture status: Exist


title: Day 32 4 Hour Control Pituitary 1309


title: Day 42 Control Pituitary 1416


title: Day 32 4 Hour Control Pituitary 1308


title: Day 32 4 Hour Heat Stress Pituitary 1307


title: Day 32 4 Hour Heat Stress Pituitary 1305


title: B105213

description: S. aureus culture status: Exist


title: Day 32 4 Hour Heat Stress Pituitary 1306


title: B106117

description: S. aureus culture status: No exist


title: Day 32 4 Hour Heat Stress Pituitary 1303


title: Day 22 Heat Stress Pituitary 1283


title: Day 42 Heat Stress Pituitary 1317


title: Day 22 Heat Stress Pituitary 1282


title: Day 40 Week Control Pituitary 1279


title: Day 21 Control Pituitary 1281


title: Day 32 4 Hour Control Pituitary 1277


title: Day 40 Week Heat Stress Pituitary 1278


title: Day 21 Control Pituitary 1280


title: Day 32 4 Hour Heat Stress Pituitary 1276


title: Day 32 4 Hour Control Pituitary 1310


title: Day 42 Heat Stress Pituitary 1077


title: Day 26 2 Hour Control Pituitary 1078


title: Day 42 Heat Stress Pituitary 1015


title: Day 42 Control Pituitary 1011


title: Day 42 Control Pituitary 1012


title: Day 42 Control Pituitary 1013


title: Day 42 Heat Stress Pituitary 1014


title: Day 32 4 Hour Heat Stress Pituitary 1304


title: Day 42 Heat Stress Pituitary 1010


title: Day 42 Heat Stress Pituitary 995


title: Day 42 Heat Stress Pituitary 1008


title: small RNA/rRNA Untreated

description: library strategy: DM-tRNA-Seq


title: Day 42 Heat Stress Pituitary 984


title: Day 42 Control Pituitary 993


title: Day 42 Heat Stress Pituitary 982


title: Day 42 Heat Stress Pituitary 983


title: Day26 2 Hour Control Pituitary 845


title: Day26 2 Hour Control Pituitary 847


title: mut_cyt

city: Beijing

first: Shouyu

last: Yan

address: 5#, Yiheyuan Road

department: Institution of Molecular Medicine

institute: Peking University

data_processing:
raw reads were aligned by Tophat v2.0.8
RPKM values were calculated by in-house perl scripts
Genome_build: danRer7
Supplementary_files_format_and_content: chromosome, start, end, RefseqID,  RPKM Values, strand, geneName, Number of Mapped Reads, Total Length of Exon

organism: Danio rerio

source_name: zebrafish embryo

extract_protocol:
Cytoplasmic RNA was generated from 36hpf embryos by PARIS™ Kit (Life)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: TL

tag: library type

value: unstranded

tag: subcellular component

value: cytoplasm


title: hUC-HM1

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: hg19
Supplementary_files_format_and_content: TPM

source_name: urine derived cells

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

tag: cell line/strain

value: primary cell

value: urine derived epithelium


title: mutant_rep2

extract_protocol:
Total RNA of 36 hpf embryos were isolated by Trizol reagent (Sigma).  Each sample contained 30 embryos.
A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed.

tag: genotype

value: strand-specific, dUTP protocal

value: whole cell


title: sib_nuc

extract_protocol:
Nucleus RNA was generated from 36hpf embryos by PARIS™ Kit (Life)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nucleus


title: mutant_rep1


title: wt_sibling_rep2


title: sib_cyt


title: wt_sibling_rep1


title: EGFP_1

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Paired-end sequencing (150 x 2) was performed using a Nextseq-500 (Illumina).
Reference genome sequence data from Rattus norvegicus were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: rn4). The reference genome index was built using SAMtools (v. 0.1.19) and the Bowtie2-build component of Bowtie2 (v. 2.1.0). Reads were mapped to the reference genome using Tophat2 (v. 2.0).
The number of fragments per kilobase per million mapped reads (fpkm) for each gene of 17,066 RefSeq (UCSC rn4) gene models was calculated using Cufflinks (v. 2.2.1).
Heat maps were constructed using Mev (v. 4.9.0). Statistical analyses and graph construction were performed using R (v. 3.1.0) and PYTHON (v. 2.7.6).
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.

source_name: EGFP, hippocampus from E18 embryos

growth_protocol: Hippocampal neuron cultures were prepared from E18 Sprague-Dawley (SD) rat embryos and maintained for 14-15 days in vitro (DIV) in Neurobasal media containing B27 supplements.

extract_protocol:
Total RNA was isolated from the infected cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.
The sequencing library was prepared using the Illumina TruSeqStranded mRNA Sample Preparation Kits (Illumina).

treatment_protocol: Cultured hippocampal neurons were infected with lentivirus expressing EGFP, CCNY-WT-EGFP or CCNY-shRNA-EGFP at DIV5 or 6.

value: Sprague-Dawley

tag: age

value: primary culture of hippocampal neurons

tag: genotype/variation

value: control


title: mut_nuc


title: wt_control_rep2

value: wildtype


title: CCNY-WT_2

source_name: CCNY-WT, hippocampus from E18 embryos

value: CCNY overexpression


title: CCNYshRNA_1

source_name: CCNYshRNA, hippocampus from E18 embryos

value: CCNY knockdown