title: 2C_sRNA-seq

description: sRNA-seq

source_name: Replicate 2 Control No challenge sRNA-sq


title: Bcl11b_DP_2

status: Public on Feb 20 2018

type: SRA

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

country: USA

institute: West Virginia University

library_source: genomic

data_processing:
Basecalls performed using CASAVA 1.8.4
Sequence reads were mapped to the mouse (mm9) genomes with bowtie (v2-2.0.2; default parameters; PMID 3322381). Only pair-end tags (PETs) mapped with high quality score (MAPQ > 10) were include for the analysis of chromatin interaction. For ChIP-Seq and scDNase-Seq analysis, if multipe reads were mapped to the same genomic site, only one read  was kept.
The HOMER (PMID 20513432) package was employed to partition the genome into A and B compartment, at a resolution of 20K bps, with compartment signal across the genome corresponding to the cooridantes of the first principal obtained from PCA analysis on the normalized interaction matrix. Interaction matrices at a resolution of 20Kb were normalized by ICE (PMID 22941365). The  gross intearcion of a gene is measured by the PETs with at least one end originated from the gene. PETs with distance less than 4K and longer than 2M were excluded. Also, FitHi-C (PMID: 24501021) was used to filtered PETs potentially orignated from background; potential interactions between any pairs of 2Kb bins were called under p<0.05 and an minimal of 2PETs. Potential HSs from DNase-Seq data were called by SICER (PMID 19505939), with a window size of 100 bps, E-value = 0.001 and no gap. Bcl11b binding sites from ChIP-Seq data were also called by SICER (PMID 19505939) with a window size of 200 bps, E-value = 1, and gap = 400 bps. Gene expression from RNA-Seq was quantified by RPKM with in-house script and RefSeq gene annotation. Nucleosome positioning was called by Danpos (v2.2.1, -m 1, quantile normalization, others default; PMID 23193179).
genome build: mm9
processed data files format and content: file name ending with "rpkm.txt": plan text file. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.
processed data files format and content: file name ending with "scoreisland": plan text output from SICER. Columns from right to left are for chr, start, end, score.
processed data files format and content: file name ending with "positions.xls": plan text file; prediction of nucleosome position from Danpos. Columns from left to right denote chr, start, end, sumit_pos, sumit_value_quantile_normalized, and fuzziness_score.
processed data files format and content: file name ending with "PC1.bedGraph.sort" or "PCA.bedgraph.sort": plan text file; compartment score output from HOMER (PMID 20513432). Columns from left to right include: "chr     start   end  PC1". The file was sorted into the "bedgraph" format acceptable by WahsU epigenome browser (PMID 23629413).
processed data files format and content: file name ending with "mtx.normICE.washU.sort": plain text file recording the number of interacting PETs between pairs of 20K bins, transformed into "longrange" format acceptable by WashU epigenome browser (PMID 20513432). Columns from left to right denotes "chr start end information_about_the_interacting_region ID  relative_direction_of_the_interacting_region" (http://wiki.wubrowse.org/Long-range).
processed data files format and content: file name ending with "sbsmp.iii.genWashU.sort": plain text file recording the number of gross interacting PETs of genes, transformed into "longrange" format acceptable by WashU epigenome browser (PMID 20513432). Columns from left to right denotes "chr start end information_about_the_interacting_region ID  relative_direction_of_the_interacting_region" (http://wiki.wubrowse.org/Long-range).

molecule: genomic DNA

organism: Mus musculus

source_name: DP

extract_protocol:
For Hi-C, five thousands to millions cells were stained with Biotin anti-CD45.2 antibody. Cells were bound to biotin binder (Dynabeads Biotin Binder, Cat#11047, Invitrogen) and cross-link with 1% formaldehyde.  Biotin binders were blocked by 0.5mM biotin solution. Cells were lysed and digested with CviQ I + CviA II + Bfa I for 20min. For DNase-Seq, 1000 purified cells were lysed in 32ul of lysis buffer (10mM Tris-Cl, pH7.5, 10mM NaCl, 3mM MgCl2) and digested with 8ul of DNase I for 5 min at 37°C. The reaction was stopped by adding 40ul of stop buffer containing 10mM Tris-Cl, pH7.5, 10mM NaCl, 10mM EDTA, 2% SDS, 0.5mg/ml Proteinase K, and 1ng/ul of circular carrier DNA), followed by incubation at 65°C for 1 hour. For MNase-Seq, 100 purified cells were lysed in 32ul of lysis buffer (10mM Tris-Cl, pH7.5, 10mM NaCl, 2mM CaCl2) and digested with 8ul of MNase I for 5 min at 37°C. The reaction was stopped by adding 40ul of stop buffer containing 10mM Tris-Cl, pH7.5, 10mM NaCl, 10mM EGTA, 2% SDS, 0.5mg/ml Proteinase K, and 1ng/ul of circular carrier DNA), followed by incubation at 65°C for 1 hour. For RNA-Seq, 2ng of total RNA were extracted miRNeasy Micro Kit (50) from Qiagen (Cat # 217084).
The Hi-C samples were processed following the Hi-C protocol (PMID 19815776) with modifications briefly described as follows: DNA end were marked by biotin-14-dATP with Klenow(larg) for 1hrs at 37°C. Blunt-end DNA were ligated with T4 DNA Ligase for overnight at 16°C. DNA were reverse cross-linked and purified by phenol/chloroform extraction. Biotin were removed from unligated DNA-ends by T4 DNA polymerase for 2hrs at 12°C. DNA were purified by phenol/chloroform. DNA were sheared to 300-500bps by sonication and flowed by DNA-end repair and add”A”34. Biotin labeled DNA were pull-downed by streptavidin beads and then flowed by illumine adapter ligation and PCR amplification. Library construction protocals for DNase-Seq, MNase-Seq and RNA-Seq follow that described in (PMID 26605532), (PMID 18329373) and (PMID 24056875), respectively.

tag: strain

tag: tissue

value: Thymus

tag: dilution setting

tag: antibody

value: Bethyl (Cat# A300-385A)


title: worGal4_Dam_1

city: London

first: Gabriel

last: Aughey

address: Imperial college road

country: United Kingdom

institute: Imperial College London

description: E.Coli Dam methylase expressed in neural stem cells for detection of open chromatin regions - First replicate

data_processing:
Library strategy: DamID-seq / CATaDa
The forward sequencing reads were mapped to release 6 of the Drosophila genome using Bowtie2 _see PMID: 26112292 for details of the damidseq_pipeline_
Reads were extended to adjacent GATC sites and binned for each GATC fragment
GATC fragments without any reads were excluded.
Data was rpm normalised.
Genome_build: BDGP6
Supplementary_files_format_and_content: GFF files for rpm normalised reads mapped to GATC fragments

organism: Drosophila melanogaster

source_name: Larval CNS

growth_protocol: Flies were maintained on standard fly media.

extract_protocol:
Genomic DNA was isolated,RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors _Marshall et al., 2016_.
Libraries were generated using the Illumina Truseq Library Kit

treatment_protocol: Animals were raised at 18 degrees, then shifted to 29 degrees 24 h before DNA extraction

tag: cell type

value: Neural stem cells

tag: enzyme

value: Dam methylase


title: 2O_sRNA-seq

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

state: MD

address: 910 Light Street, Apartment 2

department: Biology

institute: The Johns Hopkins Univeristy

description: sRNA-seq

library_source: transcriptomic

data_processing:
The program trim galore was used with base settings to trim adapter sequences from reads and to filter out low phred score reads (<20).
The reference-based alignments were assembled into transcriptomes using the program stringtie in order to build full-length transcripts, calculate coverage and expression values (TPM). The assembly was guided by a gene annotation file from the H. volcanii DS2 (NCBI refseq taxid 2246) genome to build transcripts and annotate them either as a gene or novel transcript.
gffcompare under default options was used to compare the assembled transcriptomes against the gene annotation file from H. volcanii DS2 (NCBI refseq taxid 2246) to annotate transcripts as genes or non-coding RNA (antisense or intergenic).
The program featureCounts was used to rapidly count reads and was run with strand-specific options on, paired-end mode on, multi-mapping off.
The read counts were then used in the R differential expression software package DESeq2 to calculate differential expression of sRNAs and mRNAs.
Genome_build: ASM2568v1 GCF_000025685.1

molecule: total RNA

organism: Haloferax volcanii DS2

source_name: Replicate 2 Oxidative Stress sRNA-sq

growth_protocol: H. volcanii auxotrophic strain H53 (Δpyre2, ΔtrpA) was used for all experiments. Culturing in liquid and solid media was done in rich medium (Hv-YPC), at 42°C and with shaking at 220 rpm (Amerix Gyromax 737).[31] Uracil and tryptophan were added to a final concentration of 50 µg/mL, each.

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Miniprep kit with the following modifications: after addition of RNA lysis buffer to the frozen cell pellets, cells were processed with a 23 G needle and syringe to insure complete cell lysis. H. volcanii liquid culture is slimy and viscous thus to increase cellular lysis a 23 G needle and syringe was used to suck up and break down the cell pellet. Total RNA was then extracted following the standard kit protocol.
Total RNA, for each biological replicate and condition, was size-selected using denaturing polyacrylamide gel electrophoresis. 20 µg of total RNA was loaded onto a 7% denaturing urea polyacrylamide gel (SequaGel, National Diagnostics) in 0.5 x TBE buffer and ran at constant power of 30 W until bromophenol blue bands reached the bottom of the gel. The gel was stained with SYBR Gold, visualized on a blue light box, and bands in the 50-500 nucleotide range, as indicated by the RNA Century Marker plus ladder (ThermoFisher), were excised. Small RNAs (sRNA) were eluted by rotating overnight in 1.2 mL 0.3 M NaCl, ethanol precipitated, and DNase I (NEB) treated (37 °C for 2 hours) as previously described. Strand-specific libraries were prepared using the SMART-seq Ultralow RNA input kit (Takara), insert sizes checked with the Bioanalyzer RNA pico kit (Agilent), and paired-end sequencing (2 x 150 bp) was carried out on the Illumina HiSeq 2500 platform at the Johns Hopkins University Genetic Resources Core Facility (GRCF). Library preparation and sequencing was as described above, omitting the size-selection by denaturing gel electrophoresis.

treatment_protocol: We exposed 5 biological replicates of H. volcanii strain H53 liquid cultures to the oxidative stress agent H2O2. Initially, cultures were grown in 80 mL of Hv-YPC under optimal conditions to an OD of 0.4 (mid exponential phase). To ensure homogeneity, each replicate was subsequently split into two 40 mL cultures, one used for the non-challenged (control) condition and the other for the oxidative stress condition. For the latter condition, 2 mM H2O2  (80% survival rate, previously determined) was directly added to the cultures followed by an hour incubation at 42 °C with shaking at 220 rpm. Cultures were then rapidly cooled down, centrifuged at 8000 rpm  for 5 minutes and the pellets resuspended in 18% sea water. The cell suspensions were then transferred to a 1 mL tube and centrifuged at 8000 rpm  for 3 minutes, the pellets were flash frozen and stored at -80 °C until ready for RNA extraction. Control non-challenged culture replicates were processed in the same manner without the addition of H2O2.

tag: strain/background

tag: treatment

value: 2 mM H2O2

tag: target molecule

value: size-selected 50-500 nt


title: 1O_sRNA-seq

description: sRNA-seq

source_name: Replicate 1 Oxidative Stress sRNA-sq


title: smallRNA X^YYohio testis Replica 2

city: Boston

first: Bernardo

last: Lemos

state: MA

address: 655 Huntington Avenue

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

description: Replica 2

data_processing:
Reads were trimmed using Trimgalore under default quality parameters (-q 30 --phred33)
Reads  from 19 to 27 bps were selected, and  mapped onto Drosophila reference genome, as well as a list of interested elements (including Suste, 45S rDNA, satellite repeats, transposable elements, telomeric sequences, snoRNA, mtDNA and tRNA genes) with bowtie v1.1.1 by requiring 0 mismatches (-v 0 -k 50 --best).
Since small RNA reads are strand-specific, reads mapped onto both strands of each element were counted separately, and normalized against total reads mapped to the whole genome. Specifically, in either female or male, the sample with fewest totally mapped reads was assigned with library size of 1; and then the others were calculated accordingly. After normalization, ANOVA was used to decide whether each element is differentially expressed among groups in each sex.
Genome_build: dmel_r6.08_FB2015_05 (ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.08_FB2015_05/)
Supplementary_files_format_and_content: Text files, contain normalized reads numbers, and P values from ANOVA

source_name: Testis

growth_protocol: Molasses medium was prepared in house with 850 mL of distilled water, 5 g of agar, 27.5 g of torula yeast, 52 g of corn meal, 55 g of dextrose, and 40 mL of unsulfured molasses. The food was stirred until boiling on a heat block. After 10 minutes of boiling, the heat source was turned off and the food left at room temperature with constant stir until reaching 65oC. At this point 5 mL of phosphoric acid and 8 mL of 10% tegosep (w/v) diluted in ethanol were added to the mix. All strains were reared at 23oC and 14-hour light cycle.

extract_protocol:
Total RNA was isolated with Trizol. In order to check the quality of the RNA extracts, samples were run in an 1% TAE-Agarose gel and integrity of the sample was estimated based on the sharpness of the ribosomal RNA bands. Samples that did not meet this quality control were re-extracted. Concentration of all samples was accessed with Qubit 3.0 Fluorometer (Thermo Fisher Scientific).
Samples with intact RNA were subjected to library synthesis using the automated Apollo 324™ NGS Library Prep system set to the parameters for smallRNA libraries using the kit PrepX RNA-Seq kit (Wafergen). Final product of each library was subjected to 15 cycles of PCR enrichment following the program suggested by the manufacturer of the kit. Each PCR reaction was carried out with one barcode. Final libraries were purified with magnetic beads and checked with Agilent 2200 TapeStation (Agilent Technologies). Samples were normalized with Qubit 3.0 Fluorometer, and twelve libraries were combined in a single mix. Multiplexed mix was submitted to 50 cycles of single-end sequencing using HiSeq 2500 (Illumina). Two biological replicates were sequenced for each sample.

treatment_protocol: Genetic manipulation for generation of Y-chromosome aneuploidy strains

value: Testis

tag: age

tag: genotype

value: X^Y/Yohio

tag: gender

value: male


title: smallRNA X^YYcongo testis Replica 2

description: Replica 2

value: X^Y/Ycongo


title: 8A_MG+PMA_t10

city: Athens

first: Stephen

middle: Patrick

last: LaVoie

state: Ga

address: 527 Biological Sciences Bldg.

department: Microbiology

institute: University of Georgia

description:
rRNA-depleted total RNA
MG1655 + 3µM PMA at t10 (biological rep. 1)

data_processing:
Quality control processing of sequence data was performed using Galaxy (https://galaxyproject.org). The FASTX tools in Galaxy (http://hannonlab.cshl.edu/fastx_toolkit) were used for filtering by quality (80% of sequence > quality score of 20), then reads were trimmed at both 5’ and 3’ ends using a window and step size of 1 with quality score > 20.
Forward- and reverse-read mate-pairs were assembled and aligned to the Escherichia coli MG1655 K-12 genome using Bowtie2 (Langmead and Salzberg, 2012, Nat Methods). SAMtools (Li et al., 2009, Bioinformatics) was used to convert Bowtie2 output (.bam file) to SAM format.
The number of sequence reads that aligned to features in annotation file (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf from http://bacteria.ensembl.org) were tabulated from the resulting SAM alignment files using the HTSeq-count program (Anders et al., 2015, Bioinformatics) with intersection non-empty mode.
Mapped read counts were analyzed for differential expression (false discovery rate of < 0.01, fold-change > 2) using the baySeq package in R (Hardcastle and Kelly, 2010, BMC Bioinformatics). Within baySeq, two-way comparisons using quantile normalization were made for all three biological replicate transcriptomes over time for HgCl2 exposure or PMA exposure versus the unexposed control.
Genome_build: ASM584v2 (Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.24.gtf )
Supplementary_files_format_and_content: raw read counts as determined by HTseq-Count, provided in .csv format

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

source_name: E. coli

growth_protocol: For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm.

extract_protocol:
One cell pellet from each condition and sampling time was thawed on ice; total RNA was isolated by RNAsnap™ (Stead et al., 2012, Nucleic Acids Res). DNA contamination was removed by two treatments with Turbo-DNase (Ambion; Life Technologies). Ribosomal RNA depletion was performed with the Ribo-Zero™ rRNA removal kit for Gram-negative bacteria (Epicentre) and concentrated using RNA Clean and Concentrator™ -5 columns (Zymo Research) following the manufacturer’s instructions.
The quality and quantity of rRNA-depleted RNA was assessed on a 2100 Bioanalyzer RNA pico chip (Agilent Technologies) using manufacturer’s recommendations. Next generation sequencing (NGS) libraries were prepared using the Kapa biosystems NGS stranded library prep kit for RNA-Seq with dual indexed Illumina adapters. The mode library insert size was ~150 bp, as determined by high sensitivity NGS fragment analysis kit for Fragment Analyzer™ (Advanced Analytical Technologies) using manufacturer’s instructions. Quantification of each library was done by qPCR and all 30 libraries were pooled in equal concentrations.

treatment_protocol: When cultures reached OD595 ≈ 0.470 (~ 200 min), two cultures were made 3 µM mercuric chloride (HgCl2) or 3 µM phenylmercuric-acetate (PMA) and the third was left as an unexposed control. Duplicate 1 ml aliquots of each culture were collected at 0 (unexposed control only), 10, 30, 60 min after mercurial exposure and immediately centrifuged at 21 krpm, for 3 min at 4°C. Spent medium was aspirated and cell pellets were frozen at -70°C within 5 min after collection.

value: MG1655 + 3µM PMA at t10


title: 1C_sRNA-seq

description: sRNA-seq

source_name: Replicate 1 Control No challenge sRNA-sq

value: No challenge


title: HiC_DP_r5

description:
DPv2_20k_Reg.chrA.mtx.norm.washu.sort
DP_KZ621KZ761GA9929GA9930GA9932.Bin1kMin1kMax2000m.sbsmp.iii.genWashU.sort

data_processing:
Library strategy: Hi-C
Basecalls performed using CASAVA 1.8.4
Sequence reads were mapped to the mouse (mm9) genomes with bowtie (v2-2.0.2; default parameters; PMID 3322381). Only pair-end tags (PETs) mapped with high quality score (MAPQ > 10) were include for the analysis of chromatin interaction. For ChIP-Seq and scDNase-Seq analysis, if multipe reads were mapped to the same genomic site, only one read  was kept.
The HOMER (PMID 20513432) package was employed to partition the genome into A and B compartment, at a resolution of 20K bps, with compartment signal across the genome corresponding to the cooridantes of the first principal obtained from PCA analysis on the normalized interaction matrix. Interaction matrices at a resolution of 20Kb were normalized by ICE (PMID 22941365). The  gross intearcion of a gene is measured by the PETs with at least one end originated from the gene. PETs with distance less than 4K and longer than 2M were excluded. Also, FitHi-C (PMID: 24501021) was used to filtered PETs potentially orignated from background; potential interactions between any pairs of 2Kb bins were called under p<0.05 and an minimal of 2PETs. Potential HSs from DNase-Seq data were called by SICER (PMID 19505939), with a window size of 100 bps, E-value = 0.001 and no gap. Bcl11b binding sites from ChIP-Seq data were also called by SICER (PMID 19505939) with a window size of 200 bps, E-value = 1, and gap = 400 bps. Gene expression from RNA-Seq was quantified by RPKM with in-house script and RefSeq gene annotation. Nucleosome positioning was called by Danpos (v2.2.1, -m 1, quantile normalization, others default; PMID 23193179).
Genome_build: mm9
Supplementary_files_format_and_content: file name ending with "rpkm.txt": plan text file. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.
Supplementary_files_format_and_content: file name ending with "scoreisland": plan text output from SICER. Columns from right to left are for chr, start, end, score.
Supplementary_files_format_and_content: file name ending with "positions.xls": plan text file; prediction of nucleosome position from Danpos. Columns from left to right denote chr, start, end, sumit_pos, sumit_value_quantile_normalized, and fuzziness_score.
Supplementary_files_format_and_content: file name ending with "PC1.bedGraph.sort" or "PCA.bedgraph.sort": plan text file; compartment score output from HOMER (PMID 20513432). Columns from left to right include: "chr     start   end  PC1". The file was sorted into the "bedgraph" format acceptable by WahsU epigenome browser (PMID 23629413).
Supplementary_files_format_and_content: file name ending with "mtx.normICE.washU.sort": plain text file recording the number of interacting PETs between pairs of 20K bins, transformed into "longrange" format acceptable by WashU epigenome browser (PMID 20513432). Columns from left to right denotes "chr start end information_about_the_interacting_region ID  relative_direction_of_the_interacting_region" (http://wiki.wubrowse.org/Long-range).
Supplementary_files_format_and_content: file name ending with "sbsmp.iii.genWashU.sort": plain text file recording the number of gross interacting PETs of genes, transformed into "longrange" format acceptable by WashU epigenome browser (PMID 20513432). Columns from left to right denotes "chr start end information_about_the_interacting_region ID  relative_direction_of_the_interacting_region" (http://wiki.wubrowse.org/Long-range).


title: Dnase_DN2_2

value: Dnase 1:20 dilution


title: smallRNA X^Y (control) testis Replica 2

description: Replica 2

value: X^Y


title: worGal4_Dam_2

description: E.Coli Dam methylase expressed in neural stem cells for detection of open chromatin regions - second replicate


title: smallRNA X^Y (control) testis Replica 1

description: Replica 1


title: smallRNA X^XYcongo ovary Replica 1

description: Replica 1

source_name: Ovary

value: Ovary

value: X^X/Ycongo

value: female


title: smallRNA X^XYohio ovary Replica 1

description: Replica 1

value: X^X/Yohio


title: smallRNA X^X (control) ovary Replica 2

description: Replica 2

value: X^X


title: G00266

status: Public on Feb 19 2018

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

data_processing:
Sequence reads were trimmed for adapters using the software Trimmomatic (version 0.36) and mapped to the GRCm38 genome using tophat (version 2.0.14)
Expression counts of genes were estimated using htseq
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with expression counts  for each sample

extract_protocol:
Tumor tissue and surrounding unaffected tissue of Apc Min/+ and Apc Min/+ ::ADAM17 ex/ex mice were prepared freshly. To isolate total RNA from animal tissue for RNA sequencing, the RNeasy Mini Kit from Qiagen (Hilden, Germany) was used according to supplier’s instructions including a QIAshredder column from Qiagen.
Individual strand-specific sequencing libraries were prepared with the TruSeq stranded mRNA kit (Illumina) from 500 ng total RNA.

value: Surrounding Non-tumor intestinal tissue

value: Apc Min/+ ::ADAM17 ex/ex


title: smallRNA X^X (control) ovary Replica 1

description: Replica 1


title: smallRNA X^XYcongo ovary Replica 2

description: Replica 2


title: smallRNA X^YYcongo testis Replica 1

description: Replica 1


title: G00264

value: Intestinal tumor tissue


title: G00267


title: G00262


title: G00261


title: G00260


title: smallRNA X^YYohio testis Replica 1

description: Replica 1


title: G00258


title: G00263


title: G00259


title: G00265


title: G00255


title: G00253


title: G00254


title: G00252


title: G00256


title: smallRNA X^XYohio ovary Replica 2

description: Replica 2


title: G00250


title: G00249


title: G00246


title: G00245


title: G00248


title: G00247


title: G00251


title: G00243

value: Apc Min/+


title: G00242


title: G00241


title: G00240


title: G00239


title: T KO, iPSC, MS081Y29

status: Public on Feb 21 2018

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description:
Sample 36
Transcriptome of amplified cDNA from PGCLC induction of T-/-#27 line, harvested at iPSC, non-sorted

data_processing:
Samples were sequenced by four separate runs with different conditions, 3 runs on NextSeq 500 and 1 run on HiSeq 2500 with length between 76 and 134 bases (detail available on GEO records). For equal comparison between these samples, all bases longer than 76 bases from read data were trimmed from 3'-end by trimmomatic v0.35 (Bolger et.al., 2014).
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the human genome hg19 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and hg19 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

organism: Homo sapiens

source_name: iPSC, from 585B1 hiPSC line

growth_protocol: 585B1 hiPSCs (XY) was cultured with AK03N medium on iMatrix coated plate as reported previously (Sasaki and Yokobayashi et al., 2015).

extract_protocol:
The cells were pelleted down and snap frozen until use.  RNA samples were extracted with RNeasy kit following manufacturer's protocol.
For 3'-seq analysis, cDNA synthesis / amplification from RNA samples and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60].

treatment_protocol:
The iMeLC induction was induced from iPSC cultured in above condition, passaged to fibronectin coated plate with Activin A (50 ng/ml), CHIR99021 (3µM) and Y27632 (10µM) in GMEM containing 15% KSR, and cultured for 44 to 48 hours.
Above iMeLCs were then dissociated and replated to low-adherent V-bottom plates to form aggregates with BMP4 (200 ng/ml), SCF (100 ng/ml), EGF (50 ng/ml), LIF(1000U/ml), and Y27632 (10µM) in GMEM containing 15% KSR, until the harvest day.

tag: sampled time point

value: iPSC

tag: cell line

tag: transgenes

tag: genotype/variation

tag: differentiation series

value: Series 2, TFAP2C KO and T KO


title: G00244

tag: strain


title: G00236

tag: tissue


title: G00235


title: G00234


title: G00231


title: G00230


title: G00233


title: G00238


title: Brx82_1_SC2_051613

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: circulating cells in lysis buffer

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). See platform.xls for a description of the IDs in readCounts.xls

source_name: CTCs

extract_protocol:
RNA was extracted as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535).
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.
RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

value: circulating tumor cells

tag: patient

tag: progression

value: Bone (+)


title: Brx61_1_SC3_032012

description: circulating cells in lysis buffer

tag: cell type

value: Visceral (+)


title: Brx74_1_SC1_032813

description: circulating cells in lysis buffer


title: G00257


title: BrTr08_1_SC2_012913

description: circulating cells in lysis buffer


title: BrTr11_CL3_022513

description: circulating cells in lysis buffer


title: G00237


title: ebs1-delta_rep3

city: Paris

first: Marine

last: Dehecq

address: 25 rue du docteur roux

country: France

institute: Institut Pasteur

description:
sample 15
Sample 9, 12, 15, 18 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt

data_processing:
reads were first reverse using seqtk (version 1.0-r31)
sequences were trimmed using AlienTrimmer (version 0.4.0) and the default parameter (-k 10 -l 15 -m 5 -q 20 -p 0 (Phred+33). This step removes illumina adapters and filtrate reads depending on their quality.
sequences were mapped on the Saccharomyces cerevisiae S288c genome (version R64-2-1). For the mapping, we use the software STAR (version STAR-STAR_2.4.2a), it allows to map reads on intron notably. We use the default parameters except for these three: --alignIntronMax 1500 --alignMatesGapMax 1500 --alignSJoverhangMin 25 . The outfile is in BAM format.
BAM files were converted to wiggle files using STAR.
For the reads counting per features, we have used the function featureCounts of the subread package (version Subread-1.5.0-p3-Linux-x86_64). Annotation file is specific to our study, it contains pervasive transcript, dubious ORF, intron, etc. We have used default parameter except -s 0 -0.
Genome_build: Saccharomyces cerevisiae S288c genome (version R64-2-1) were indexed and prepared by STAR genomeGenerate.
Supplementary_files_format_and_content: There are two wig files by sample for positive (str1) and negative strands (str2). Counts of all samples prepared by CP experimenter were aggregated in count_3RNASeq_GB_BY4741_delNAM7.txt. Counts of all samples prepared by MD experimenter were aggregated in count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt.

organism: Saccharomyces cerevisiae

source_name: exponential state cells

growth_protocol: yeast cells growed until exponential phase DO 0.6 in YPD media at 30°C.

extract_protocol:
After collection, RNA are extracted by hot acid phenol/chloroform method, precipitate with Ammonium acetate and ethanol. Samples were treated with DNaseI.
Samples were treated by ribozero and libraries were prepared using TruSeq Stranded mRNA LT Kit. We strictly followed the protocol except that we started directly at the fragmentation step after the ribozero and we adjusted the number of cycle required to amplified libraries.

tag: genetic background

value: Saccharomyces cerevisiae S288 BY4741

tag: illumina tag

value: TruSeq Index 05:ACAGTG

tag: sexual type

value: mat a

tag: experimenter

value: MD


title: BrTr11_SC1_022513

description:
circulating cells in lysis buffer
same sample as GSM1253397


title: BrTr11_CL2_022513

description:
circulating cells in lysis buffer
same sample as GSM1253399


title: nmd4-ebs1-delta_rep2

description:
sample 17
Sample 8, 11, 14, 17 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt

value: Saccharomyces cerevisiae S288 BY4742

value: TruSeq Index 06:GCCAAT

value: mat alpha


title: ebs1-delta_rep1

description:
sample 13
Sample 7, 10, 13, 16 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt


title: BrTr11_SC2_022513

description: circulating cells in lysis buffer


title: nmd4-ebs1-delta_rep3

description:
sample 18
Sample 9, 12, 15, 18 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt


title: nmd4-delta_rep3

description:
sample 12
Sample 9, 12, 15, 18 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt

value: TruSeq Index 02:CGATGT


title: G00232


title: nmd4-ebs1-delta_rep1

description:
sample 16
Sample 7, 10, 13, 16 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt


title: BrTr11_CL1_022513

description:
circulating cells in lysis buffer
same sample as GSM1253398


title: BrTr08_1_SC1_012913

description:
circulating cells in lysis buffer
same sample as GSM1253377


title: G00229


title: Brx53_SC2_010313

description:
circulating cells in lysis buffer
same sample as GSM1253376


title: Brx09_1_011513

description: circulating cells in lysis buffer


title: nmd4-delta_rep2

description:
sample 11
Sample 8, 11, 14, 17 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt


title: ebs1-delta_rep2

description:
sample 14
Sample 8, 11, 14, 17 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt


title: BY4741_rep1

description:
sample 7
Sample 7, 10, 13, 16 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt

value: TruSeq Index 07:CAGATC


title: nmd4-delta_rep1

description:
sample 10
Sample 7, 10, 13, 16 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt


title: upf1-delta_rep3

description:
sample 6
In parallel with sample 3
count_3RNASeq_GB_BY4741_delNAM7.txt

value: TruSeq Index 22:CGTACG

value: CP


title: upf1-delta_rep2

description:
sample 5
In parallel with sample 2
count_3RNASeq_GB_BY4741_delNAM7.txt

value: TruSeq Index 10:TAGCTT


title: BY4741_rep2

description:
sample 8
Sample 8, 11, 14, 17 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt


title: upf1-delta_rep1

description:
sample 4
In parallel with sample 1
count_3RNASeq_GB_BY4741_delNAM7.txt

value: TruSeq Index 21:GTTTCG


title: BY4741_GB_rep1

description:
sample 1
In parallel with sample 4
count_3RNASeq_GB_BY4741_delNAM7.txt

value: TruSeq Index 01:ATCACG


title: Mnase_ChIP-Seq_H3_16min

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq reads were aligned to the dm6 genome using bowtie2 v2.2.9 with parameters -t -p 8 --local
Genome_build: FB2017_02 Dmel Release 6.15
Supplementary_files_format_and_content: Wig files were generated using Spp v1.11 and converted to bigWig using wigToBigWig v4. Scores represent number of reads normalized by the size of the library.

source_name: S2 Schneider cells

growth_protocol: Drosophila Schneider line 2 (S2) cells were maintained at 25°C in the ecdysone-free Schneider’s insect medium (Sigma) containing 10% FBS (HyClone).

extract_protocol:
Crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 10 ?g of antibodies and 8 ?L of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 ?L per 500 ?L sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 ?L of proteinase K and 5 ?L of 0.5M EDTA per 500 ?L sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation. Mnase-ChIP seq was performed with the same protocol except one stage. Step of chromatin sonication was change to treatment with Micrococcal nuclease (ThermoScientific) for 5 min at 37°C and for 30 min at 4°C.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 0.3 µM 20-hydroxyecdysone (Sigma, http://www.sigmaaldrich.com/catalog/product/sigma/h5142) to induce the ecdysone cascade.

tag: time of 20h-ecdysone treatment

value: 16 min

tag: 20h-ecdysone concentration

tag: chip antibody

value: Abcam antibodies against Histone H3 (Ab1791)


title: BY4741_rep3

description:
sample 9
Sample 9, 12, 15, 18 in parallel
count_3RNAseq_MD_BY4741_delNMD4_delEBS1_deldel.txt


title: Mnase_ChIP-Seq_H3_12min

value: 12 min


title: Mnase_ChIP-Seq_H3_08min

value: 8 min


title: Mammary Gland 2

city: Austin

first: Christopher

last: Sullivan

state: Texas

address: 2506 Speedway Stop A5000

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
cutadapt,1.4.2,(HC11 Samples:-m 16 -a TGGAATTCTCGGGTGCCAAGGAACT,Others:-m 16 -a AGATCGGAAGAGCACACGTCTGAAC)
SHRIMP2,2.2.3,-N 8 -h 90% --qv-offset=33
mirUtils,1.0.0-r27,mbaseMirStats --organism=mmu
Genome_build: miRBase Release 21 (GRCm38) and MMTV reference sequences ((HYB MTV (Shackleford and Varmus, 1988) clone sequenced in-house for in vivo samples or C3H provirus sequence AF228552.1 for cell culture experiments), MTV-6_X64554.1, MTV-8_M22028.1, MTV-8_X05400.1, MTV-8_X74073.1, MTV-8_M74713.1, MTV-9_M29600.1, MTV-9_M21800.1).
Supplementary_files_format_and_content: tsv, mirUtils mature microRNA counts

source_name: Mammary gland

extract_protocol:
Trizol
TruSeq Small RNA Library Prep Kit

value: BALB/c

value: gland

tag: infection

value: uninfection


title: PolII_Ser5(Phospho)_0h

value: sham-treated

value: 0 uM

value: Active motif antibodies against Rpb1 (phosphoS5)(39097)


title: PolII_Ser5(Phospho)_1h

value: 1 hour


title: AL2045-3

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

description: ribosomal depleted mRNA

data_processing:
Alignment with Bowtie 2.1.0 against reference Aba_6009v5
Quantification using counts from nesoni 0.113
Genome_build: Aba_6009v5.gff
Supplementary_files_format_and_content: csv file with raw counts for each sample

organism: Acinetobacter baumannii

source_name: bacterial cell

growth_protocol: Isolates were grown in triplicate in cation adjusted Mueller-Hinton broth (no antibiotics) to an OD600 of 0.5±0.05.

extract_protocol:
Cell pellets were treated with RNA later and stored at -80C.  Total RNA was purified from each sample using Qiagen RNA purification columns and protocol. Residual DNA was removed using the Qiagen RNase-free DNA set according to manufacturers instructions. Ribosome RNA was depleted using the Ribozero rRNA depletion kit using standard methods
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA sample prep kit v2

tag: resistance

value: high colistin resistance

tag: isolate


title: AL2045-1

description: ribosomal depleted mRNA


title: Mammary Gland 1


title: PolII_Rpb3_1h

value: Custom-made (against 1-275 aa of dRpb3)


title: Sample_33775

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

institute: University of Pennsylvania

data_processing:
Illumina Casava 1.8.2 was used for basecalling
Low confidence nucleotides (with Phred score less than 20) were treated as unknown and replaced with Ns. Unknown nucleotides (Ns) at the ends of reads were trimmed. Poly-A and method-specific adapter sequences were trimmed from the 3’ end of reads using in-house software. Reads were aligned to the danio rerio reference genome, build GRCz10, and to spike-in transcript sequences using STAR (Spliced Transcripts Alignment to a Reference) aligner version 2.4.0. We provided STAR with GRCz10 annotations to generate a splice-junction loci database for use in alignment. We retained reads that aligned to at least 40% (paired-end) of trimmed length or 30bp, whichever was greater. In addition, we discarded reads with greater than 30% mismatched positions in trimmed length.
Uniquely aligned reads were assigned to GRCz10 gene annotations and to spike-in transcripts using Verse which functions identically to HTSeq's htseq-counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non-empty method.
Genome_build: GRCz10
Supplementary_files_format_and_content: all data files are tab-delimited text files containing gene abundence measurements

molecule: polyA RNA

organism: Danio rerio

source_name: OMP positive bulk cells

extract_protocol:
Cells were isolated on a C1 Fluidigm platform
libraries made using Illumina's Nextera kit

value: Tu/TLF

tag: spike-in

value: ERCC

tag: single-cell amplification protocol used

value: Clontech SMARTer Ultralow RNA kit


title: PolII_Ser2(Phospho)_1h

value: Abcam antibodies against Rpb1 (phosphoS2) (Ab5095)


title: PolII_Rpb3_0h


title: Mnase_ChIP-Seq_H3_00min


title: PolII_Ser2(Phospho)_0h


title: AL2045-2

description: ribosomal depleted mRNA


title: Sample_23574

source_name: OMP positive cell

tag: strain


title: Sample_33773


title: AL2044-3

description: ribosomal depleted mRNA

value: low/intermediate colistin resistance


title: AL2044-1

description: ribosomal depleted mRNA


title: AL2044-2

description: ribosomal depleted mRNA


title: BY4741_GB_rep2

description:
sample 2
In parallel with sample 5
count_3RNASeq_GB_BY4741_delNAM7.txt

value: Saccharomyces cerevisiae S288 BY4741

value: TruSeq Index 11:GGCTAC

value: mat a

value: CP


title: Sample_33774


title: BY4741_GB_rep3

description:
sample 3
In parallel with sample 6
count_3RNASeq_GB_BY4741_delNAM7.txt

value: TruSeq Index 20:GTGGCC


title: Sample_23575


title: Sample_23572


title: Sample_23564


title: Sample_23562


title: Sample_23561


title: Sample_23569


title: LOUCY_JQ1_Exp2_Rep1

city: Oxford

last: Booth

state: Oxfordshire

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing:
FASTQ files were aligned to the human genome (hg38) using STAR version 2.5.1b.
Reads mapping to gene exons were counted using the Subread (version 1.4.5-p1) featureCounts tool and the hg38 annotation.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR (version 3.10.5). Only genes detected at greater than 1 count per million (cpm) in at least 4 samples were included for analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Table of RPKM values for all samples for all genes expressed at greater than 1 cpm in at least 4 samples

source_name: Leukemia cell line

growth_protocol: Cells were grown in RPMI-1640 (Gibco) supplemented with 10% FCS (HyClone) and 1% penicillin/streptomycin (PAA Laboratories)

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen).
Libraries were constructed using the Smart-seq2 method (Picelli et al., Full-length RNA-seq from single cells using Smart-seq2. Nat Protocols 2014). cDNA was generated using SuperScript II (Invitrogen) and oligo-dT30VN primers (Biomers.net), pre-amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and purified using Agencourt AMPure XP (Beckman Coulter). Tagmentation and library preparation was performed using the Nextera XT DNA Library Preparation Kit (Illumina).

tag: cell line

value: LOUCY

tag: treatment

value: 24 hr 250 nM JQ1

tag: experiment number


title: LOUCY_DMSO_Exp2_Rep1


title: Sample_23571


title: Sample_23567


title: Sample_23565


title: LOUCY_IBET151_Exp2_Rep2


title: Sample_23568


title: Sample_23555


title: JURKAT_Untreated_Exp2_Rep2

value: JURKAT

value: Untreated


title: JURKAT_Untreated_Exp2_Rep3


title: LOUCY_IBET151_Exp2_Rep1


title: Sample_23556


title: Sample_23563


title: Sample_23560


title: Sample_23570


title: Sample_23566


title: Sample_23559


title: LOUCY_JQ1_Exp2_Rep2


title: Sample_23553


title: Sample_23573


title: LOUCY_DMSO_Exp2_Rep2


title: Sample_23558


title: Sample_23554


title: JURKAT_Untreated_Exp2_Rep1


title: Sample_23552


title: LOUCY_Untreated_Exp2_Rep3


title: Sample_23548


title: LOUCY_JQ1_Exp1_Rep2


title: LOUCY_IBET151_Exp1_Rep1


title: Sample_23545


title: LOUCY_DMSO_Exp1_Rep2


title: LOUCY_Untreated_Exp2_Rep2


title: HC11 Uninfected

source_name: HC11 cell culture

value: BALB/c

tag: tissue

value: cell line

value: uninfection


title: Sample_23551

value: Tu/TLF


title: Sample_23543

value: ERCC


title: LOUCY_Untreated_Exp2_Rep1


title: Sample_23550

value: Clontech SMARTer Ultralow RNA kit


title: Sample_23549


title: LOUCY_IBET151_Exp1_Rep2


title: Sample_20566

value: Fluidigm


title: Sample_23547


title: Sample_20595


title: LOUCY_Untreated_Exp1_Rep2


title: Sample_20565


title: LOUCY_DMSO_Exp1_Rep1


title: Sample_23544


title: LOUCY_JQ1_Exp1_Rep1


title: Sample_23546


title: LOUCY2_input

data_processing:
FASTQ files were aligned to the mouse (mm10) or human (hg38) genomes using Bowtie2 (version 2.2.5) and default parameters.
Peak calling was performed using Macs2 (version 2.0.10) and default parameters (human samples) or the broad peak calling parameter (mouse samples).
Genome browser tracks normalised to input were produced using the Macs2 (version 2.0.10) bdgcmp function and the ppois method.
Genome_build: mm10 (mouse samples); hg38 (human samples)
Supplementary_files_format_and_content: Macs2 peak calling output: text files containing all peaks called.
Supplementary_files_format_and_content: Genome browser tracks: Bigwig files for display of signal tracks normalised using input controls

source_name: LOUCY leukemia cell line

extract_protocol:
5 million cells were used per sample. Cells were fixed with 1% formaldehyde for 10 min. Fixed chromatin was fragmented using an S220 Focused-ultrasonicator (Covaris) to an average size of 200-500 bp. Immunoprecipitation was then performed using a mixture of Protein A and Protein G Dynabeads (Life Technologies). Fragmented Drosophila melanogaster DNA was added at the immunoprecipitation step at a ratio of DNA from 1 Drosophila cell to 4 mouse/human cells, for the purpose of normalization (Orlando et al., Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. Cell Rep 2014). However, reads mapping to the Drosophila melanogaster genome were not used for analysis.
The NEBNext Ultra II DNA Library Prep Kit for Illumina, with NEBNext Multiplex Oligos for Illumina (New England BioLabs) was used to prepare DNA samples for sequencing as directed. Sequencing was performed using the Illumina NextSeq 500 platform.

value: Leukemia cell line


title: JURKAT_Untreated_Exp1_Rep3


title: Sample_20599


title: JURKAT2_input

source_name: JURKAT leukemia cell line

value: Jurkat


title: JURKAT_Untreated_Exp1_Rep2


title: LOUCY2_H3K27me3

value: H3K27me3 (Merck Millipore, 07-449)


title: Sample_20535


title: DKOITD48_input

organism: Mus

source_name: Total bone marrow

growth_protocol: Cells were harvested directly from mouse bone marrow

value: bone marrow

tag: genotype

value: Ezh2(fl/fl) Runx1(fl/fl) Rag1(Cre/+) Flt3(ITD/+)


title: Sample_20534


title: LOUCY_Untreated_Exp1_Rep3


title: LOUCY_Untreated_Exp1_Rep1


title: Sample_20556


title: Sample_18931


title: Sample_20545


title: Sample_18930


title: Sample_20544


title: WT1_input

source_name: Bone marrow enriched for Kit-expressing cells using CD117 microbeads and LS columns (Miltenyi Biotec)

value: Ezh2(fl/fl) Runx1(fl/fl) Rag1(+/+) Flt3(+/+)


title: DKOITD185_H3K27ac

value: H3K27ac (Diagenode, C15410196)


title: LOUCY1_H3K27me3

value: LOUCY


title: LOUCY2_H3K27ac


title: Sample_18926


title: DKOITD53e_H3K27ac


title: JURKAT_Untreated_Exp1_Rep1

value: JURKAT


title: Sample_18927


title: Sample_23557


title: DKOITD52_H3K27me3


title: LOUCY1_H3K27ac


title: DKOITD83_H3K27me3


title: JURKAT2_H3K27ac


title: DKOITD53e_H3K27me3


title: shCON CDT Rep 2

last: McNair

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

data_processing:
alignment to hg19 with STAR
Generate count table using Homer
Differential expression using EdgeR
Genome_build: hg19
Supplementary_files_format_and_content: Count matrix

source_name: LNCaP Cell Line

growth_protocol: LNCaP cells (either shCON or shRB) were cultured in hormone proficient media unless otherwise indicated.

extract_protocol:
RNA Seq was prepared as previously described (Xu et al 2016)
RNA-Seq libraries were constructed using TruSeq RNA Sample Prep Kit v2 (Illumina, #RS-122-2001)

treatment_protocol: Cells were treated with CDT for 72 hours prior to harvest

tag: cell cycle arrest treatment

value: 72 hour CDT

tag: knockdown

value: shCON


title: DKOITD83_H3K27ac


title: JURKAT1_H3K27me3


title: DKOITD48_H3K27ac


title: shCON CDT Rep 3


title: JURKAT1_H3K27ac


title: DKOITD185_H3K27me3


title: DKOITD52_H3K27ac


title: WT3_H3K27me3


title: shRB CDT Rep 1

value: shRB


title: shCON CDT Rep 1


title: WT3_H3K27ac


title: WT2_H3K27me3


title: JURKAT2_H3K27me3


title: Mammary Tumor 2

organism:
Mus musculus
Mouse mammary tumor virus

source_name: Mammary tumor

value: BALB/c, HYB-MTV

value: tumor

value: HYB-MTV


title: WT1_H3K27me3


title: WT2_H3K27ac


title: HC11 Infected

value: BALB/c, C3H-MMTV

value: cell line


title: WT1_H3K27ac


title: shRB CDT Rep 2


title: DKOITD48_H3K27me3


title: H3.3swap-3

status: Public on Feb 18 2018

city: Madison

first: Xuehua

last: Zhong

state: WI

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

description:
Genomic DNA isolated from immnuoprecipitated chromatin using FLAG antibody
H3.3H87S L90A mutation replicate 3

data_processing:
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10 genome, with default parameters. Reads mapping to identical positions in the genome  were collapsed into one read.
Samtools and Bedtools were used to generate bed file and bedGraph file
Bigwig file generated by UCSC "bedGraphToBigWig" scipts
Genome_build: TAIR10 for Arabidopsis
Supplementary_files_format_and_content: bigwig file

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Arabidopsis plants were grown on soil at 21 degree under continuous light for 3 weeks.

extract_protocol:
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850
ChIP library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330)

tag: ecotype

value: leaf

value: H3.3H87S L90A mutation


title: H3.3swap-2

description:
Genomic DNA isolated from immnuoprecipitated chromatin using FLAG antibody
H3.3H87S L90A mutation replicate 2


title: H3.3swap-1

description:
Genomic DNA isolated from immnuoprecipitated chromatin using FLAG antibody
H3.3H87S L90A mutation replicate 1


title: H3.1

description: Genomic DNA isolicated from immnuoprecipitated chromatin using FLAG antibody

data_processing:
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.bedtools was used to generate bedGraph file; UCSC "bedGraphToBigWig" scipt was used to generate bigwig file.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: ChIP-seq(BigWig file)

growth_protocol: Arabidopsis plants were grown on soil at 21 degree under continuous light.

extract_protocol:
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850.
ChIP library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330).

tag: tag


title: H3.1swap

description:
Genomic DNA isolated from immnuoprecipitated chromatin using FLAG antibody
H3.1S87H A90L mutation

value: H3.1S87H A90L mutation


title: H3.1F41Y-1

description:
Genomic DNA isolated from immnuoprecipitated chromatin using FLAG antibody
H3.1F41Y mutation replicate 1

value: H3.1F41Y mutation


title: H3.3


title: shRB CDT Rep 3


title: H3.3Y41F

description:
Genomic DNA isolated from immnuoprecipitated chromatin using FLAG antibody
H3.3Y41F mutation

value: H3.3Y41F mutation


title: H3.3T31A

description:
Genomic DNA isolated from immnuoprecipitated chromatin using FLAG antibody
H3.3T31A mutation

value: H3.3T31A mutation


title: 4su03

city: New York

middle: R

last: Hawley

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

description:
processed data file: 5kb_genes_byabundance.bed
4sU-enriched total RNA. Biological repeat 3

data_processing:
(small RNA) Removal of 3' adapter sequence TGGAATTCTCGGGTGCCAAGG using cutadapt v1.11. The adapters used contained 4 random nucleotides at the ligating ends, so cutadapt was also used to remove 4 nt from each end of adapter trimmed reads.
(small RNA) Alignment to hg38 using Bowtie2 v2.29.0
(small RNA) Alignment to miRBase release 21 human miRNA hairpins using Bowtie2 v2.29.0. Unaligned reads extracted and used downstream.
(small RNA) Further removal of small non-coding RNA (sncRNA) gene reads using samtools v1.3.1 to exclude small RNA as annotated by DASHR 1.0 and those annotated Y_RNA and sRNA in GRCh38.85
(small RNA) Counting of non-miRNA/sncRNA small RNA reads in regions -/+5kb of all AsiSI recognition motifs (GCGATCGC) in chromosomes 1-22&X. HTSeq-count v0.6.1p1.
(small RNA) Differential expression of htseq count tables using DESeq2 v1.12.4. Conditions from 0 h to 24 h (time) were imported, and a DE design looked for differences over time (~ time) with and without likelihood ratio tests to observe any differences over time or at any time.
(small RNA) Small RNA read coverage determined using bedtools coverage v2.26.0 in 10 bp windows in 5kb regions around AsiSI cut sites, as well as control sites as determined from 4sU-seq.
(4sU RNA) Pseudoalignment to GRCh38.85 using kallisto v0.43.0. TPM values used to randomly sample comparable transcriptional activity genes to AsiSI cut genes.
(DRIP) Alignment to hg38 using Bowtie v2.29.0
(DRIP) Per-base coverage calculated using bedtools coverage v2.26.0 around AsiSI cut sites.
Genome_build: hg38
Supplementary_files_format_and_content: Binned genomic coverage counts at loci of interest (AsiSI recognition sites) for all non-annotated small RNA and DRIP. TPM values (>0) for all genes (greater than 5kb in genomic length) from 4sU-seq as determined by kallisto.

extract_protocol:
Illumina TruSeq stranded kit omitting polyA selection step on 4sU-containing RNAs enriched from total RNA.
Small RNA and 4sU-incorporated RNA extracted from cells using Trizol. DNA for DRIP-seq obtained by extracting the nuclear fraction and treating with protease, fragmented by in vitro AsiSI digestion plus sonication, then DNA:RNA fragments isolated by S9.6 antibody

treatment_protocol: Induction of damage by addition of 300 nM 4-OHT. This translocates the AsiSI enzyme to the nucleus to cut.

tag: cell type

tag: sirna

tag: ip antibody


title: DRIP02

description:
processed data file: DRIPs_perbase_byrepair_Rtable_melt.tsv
Cells transfected with control siRNA and treated for 2 hours with 4-OHT. Genomic fragments containing DNA:RNA hybrids are immunoprecipitated by the S9.6 antibody. The DNA is then sequenced.

extract_protocol:
Libraries constructed using the NEBNext Ultra II kit following the manufacturer protocol. 1ng of DRIP sample was used. 8 PCR cycles were used and an additional 0.85X volume clean-up using the supplied sample purification beads.
Small RNA and 4sU-incorporated RNA extracted from cells using Trizol. DNA for DRIP-seq obtained by extracting the nuclear fraction and treating with protease, fragmented by in vitro AsiSI digestion plus sonication, then DNA:RNA fragments isolated by S9.6 antibody

value: control


title: H3.1A31T

description:
Genomic DNA isolated from immnuoprecipitated chromatin using FLAG antibody
H3.1A31T mutation

value: H3.1A31T mutation


title: DRIP03

description:
processed data file: DRIPs_perbase_byrepair_Rtable_melt.tsv
Cells transfected with Drosha siRNA and treated for 2 hours with DMSO. Genomic fragments containing DNA:RNA hybrids are immunoprecipitated by the S9.6 antibody. The DNA is then sequenced.

value: Drosha

value: DMSO


title: DRIP04

description:
processed data file: DRIPs_perbase_byrepair_Rtable_melt.tsv
Cells transfected with Drosha siRNA and treated for 2 hours with 4-OHT Genomic fragments containing DNA:RNA hybrids are immunoprecipitated by the S9.6 antibody. The DNA is then sequenced.


title: DRIP01

description:
processed data file: DRIPs_perbase_byrepair_Rtable_melt.tsv
Cells transfected with control siRNA and treated for 2 hours with DMSO. Genomic fragments containing DNA:RNA hybrids are immunoprecipitated by the S9.6 antibody. The DNA is then sequenced.


title: 4su02

description:
processed data file: 5kb_genes_byabundance.bed
4sU-enriched total RNA. Biological repeat 2


title: srna10_hr6_rep2

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced at 6 hours following DNA damage by 4-OHT induction in AsiSI transfected U2OS cells. Biological repeat 2

extract_protocol:
Adapted small RNA-seq protocol as in Xu P et al., Methods in Next Generation Sequencing, 2015. Importantly, 3' and 5' adapters have 4 nucleotide degeneracy at the ligating ends to reduce ligation biases.
Small RNA and 4sU-incorporated RNA extracted from cells using Trizol. DNA for DRIP-seq obtained by extracting the nuclear fraction and treating with protease, fragmented by in vitro AsiSI digestion plus sonication, then DNA:RNA fragments isolated by S9.6 antibody


title: 4su01

description:
processed data file: 5kb_genes_byabundance.bed
4sU-enriched total RNA. Biological repeat 1


title: Sample_18928

value: Tu/TLF

value: Fluidigm

value: Clontech SMARTer Ultralow RNA kit


title: srna11_hr12_rep2

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced at 12 hours following DNA damage by 4-OHT induction in AsiSI transfected U2OS cells. Biological repeat 2


title: srna05_hr12_rep1

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced at 12 hours following DNA damage by 4-OHT induction in AsiSI transfected U2OS cells. Biological repeat 1


title: srna06_hr24_rep1

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced at 24 hours following DNA damage by 4-OHT induction in AsiSI transfected U2OS cells. Biological repeat 1


title: srna07_EV_rep2

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced in empty vector (EV) transfected U2OS cells. This sample represents the background small RNA profile. Biological repeat 2


title: srna03_hr1_rep1

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced at 1 hour following DNA damage by 4-OHT induction in AsiSI transfected U2OS cells. Biological repeat 1


title: srna08_hr0_rep2

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced at time point 0 (i.e. uninduced) in AsiSI transfected U2OS cells. Biological repeat 2


title: srna02_hr0_rep1

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced at time point 0 (i.e. uninduced) in AsiSI transfected U2OS cells. Biological repeat 1


title: srna01_EV_rep1

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced in empty vector (EV) transfected U2OS cells. This sample represents the background small RNA profile. Biological repeat 1


title: Mammary Tumor 1

value: BALB/c, HYB-MTV

value: tumor

tag: infection


title: srna04_hr6_rep1

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced at 6 hours following DNA damage by 4-OHT induction in AsiSI transfected U2OS cells. Biological repeat 1


title: H3.1F41Y-2

description:
Genomic DNA isolated from immnuoprecipitated chromatin using FLAG antibody
H3.1F41Y mutation replicate 2


title: Msm/pMV261-ydeH(E208,209A) rep2

city: Wuhan

first: Weihui

last: Li

address: 1 str Sizisan

country: China

institute: Huazhong Agricultural University

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 Mycobacterium_smegmatis_MC2_155_uid57701 whole genome using bowtie2 v2-2.0.5
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mycobacterium_smegmatis_MC2_155_uid57701
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mycolicibacterium smegmatis

source_name: strain

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNeasy Mini Kit (Cat#74106, Qiagen) 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: overexpression


title: srna12_hr24_rep2

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced at 24 hours following DNA damage by 4-OHT induction in AsiSI transfected U2OS cells. Biological repeat 2


title: WT heart 20dpa

city: Pittsburgh

first: Michael

last: Tsang

address: 3501 Fifth Ave

department: Developmental Biology

institute: University of Pittsburgh

data_processing:
fastq files were analyzed using CLC genomics workbench 9.0
sequence reads were mapped onto Danio rerio GRC.z10
EDGE test was performed usng CLC genomics workbench. Uninjured WT and Dusp6 mutant hearts were merged to represent uninjured baseline heart transcriptome. For differential gene analysis, this merged group was compared to WT at 20 days post amputation and to Dusp6 mutant at 20 dpa.
Genome_build: GRC.z10
Supplementary_files_format_and_content: Excel file with EDGE output.

source_name: Adult heart_WT_20dpa

growth_protocol: Zebrafish adult at 6months-1year of age.

extract_protocol:
Ventricles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit (Cat# 74004).
TS RNA

treatment_protocol: Adults hearts were injured through ventricular resection and allowed to recover until 20 days post amputation.

value: AB*

value: heart ventricle

tag: age

value: 6 months to 1 year


title: Dusp6 mutant heart uninjured

source_name: Adult heart_Dusp6_uninjured

value: dusp6 pt30a/pt30a


title: Msm/pMV261-ydeH(E208,209A) rep3


title: srna09_hr1_rep2

description:
processed data file: 5kb_wins_allsamples_Rtable_melt.tsv
Small RNA sequenced at 1 hour following DNA damage by 4-OHT induction in AsiSI transfected U2OS cells. Biological repeat 2


title: Msm/pMV261-ydeH rep3

value: ydeH


title: Msm/pMV261-ydeH rep1


title: Msm/pMV261-ydeH(E208,209A) rep1


title: Msm/pMV261-ydeH rep2


title: H2

city: Shanghai

first: lili

last: zhang

address: 2901 Beidi Rd

institute: Shanghai Academy of Agricultural Sciences

data_processing:
The raw reads were first processed through in-house Perl scripts, which removed reads containing the sequencing adapters, reads with over 10% ambiguous ‘N’ nucleotides, and reads with over 50% of bases with a quality score lower than 5. The remaining clean reads from each library were assembled using a combined de novo transcriptome assembly strategy. De novo assembly of transcripts was performed using Trinity software as previously described for de novo transcriptome assembly without a reference genome
Unigene function was annotated using NCBI BLAST 2.2.28+ with an E-value threshold of 10-5 for the NCBI non-redundant protein (Nr) database, the NCBI non-redundant nucleotide sequences database (Nt), the Swiss-Prot protein database, and the Clusters of Orthologous Groups of proteins database (COG), and the Kyoto Encyclopedia of Genes and Genomes database (KEGG).
Blast2GO v2.5 was used to obtain Gene Ontology (GO) annotation of unigenes based on BLASTX hits against the Nr database with a cut-off E-value of 10^-5
The FPKM method (Fragments Per kb per Million fragments) was used to calculate the transcript expression levels
The method of Audic and Claverie was applied to determine the P-value, which corresponds to the differential transcript expression of the contigs. The false discovery rate (FDR) is used to determine the P-value threshold in multiple tests. FDR ≤0.05 and the absolute value of log2Ratio ≥1 were used as the threshold to judge the significance of differential gene expression.
Supplementary_files_format_and_content: Files include FPKM values and annotations for each unigene and differentially expressed unigenes between two samples

organism: Lactuca sativa

source_name: Aerial part

growth_protocol: seedlings were grown on soil/vermiculite (3:1, v/v) at 25 °C in an environment controlled chamber at a light intensity of 120 μmol photons m−2 s−1 and a 14/10 h light/dark photoperiod.

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen Life Technologies, USA) following the manufacturer’s instructions and was treated with RNase-free DNase I (Takara, Japan) to avoid genomic DNA contamination.For each time point, RNA was extracted from 6 randomly selected seedlings (as one biological replicate). Two replicates were conducted for RNA extraction for each time point.
The poly (A) mRNA was isolated from the total RNA samples using oligo (dT) attached magnetic beads (Invitrogen) and was fragmented into short pieces using divalent cations under elevated temperature. First- and second-strand cDNA was generated using mRNA-Seq sample preparation (Illumina Inc., San Diego, CA, USA) and random hexamer primers. The double-stranded cDNA fragments were subjected to end repair, and sequencing adapters were ligated to both ends. The final cDNA library was selectively enriched by PCR and purified using the AMPure XP system (Beckman Coulter, Beverly, USA).

treatment_protocol: Four week-old healthy seedlings were exposed to UV-B radiation (310 nm light-emitting diode, T9E31C, Seoul Optodevice, 0.3Wm-2). Devices for supplemental UV-B radiation were suspended above and perpendicular to the planted rows (rows oriented in an east-west direction to minimize shading).

tag: cultivar

value: shenxuan 5

tag: developmental stage

value: 4-week-old seedlings

tag: number of plants

value: 6 seedlings

tag: stress

value: UV-B treatment

tag: time

value: 12 h of recovery after 24 h of UV-B treatment


title: h24_1


title: H1


title: h24_2


title: h6_2

value: 6 h


title: h6_1


title: h0_2

value: control

value: 0 h


title: h0_3


title: Fibroblast LMNA rep2

status: Public on Feb 17 2018

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

data_processing:
For RNA: Reads aligned with tophat v2.1.0 with parameters -M, -G and –-b2-very-sensitive
For RNA: Transcript abundance estimated with cufflinks v2.2.1 with parameters -G, -b, -u
For RNA: Reference gtf with cuffmerge v2.2.1 with parameters -g, -s
For RNA: Quantification using cuffquant v2.2.1 with parameters -b, -u
For RNA: Normalization of quantification using cuffnorm v2.2.1
For RNA: Differential expression analysis using cuffdiff v2.2.1 with parameters -b, -u
For RNA: Bed files created from genes_fpkm.tracking file
For ChIP: Reads were trimmed to a length of 75 bp using fastx toolkit
For ChIP: Only left mates were aligned to reference hg19 using bowtie2 version 2.2.6
For ChIP: bigWig files were generated by getting a ratio of IP over Input in 1 kb bins
For ChIP: Peaks called using Enriched Domain Detector
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: For RNA: bed with 5 columns – chromosome, start co-ordinate, end-co-ordinate, gene symbol, expression (fpkm).
Supplementary_files_format_and_content: For ChIP: bed with 4 columns – chromosome, start co-ordinate, end-co-ordinate, score.

source_name: Skin fibroblasts with endogenous LMNA p.R482W mutation, lamin A/C ChIP

growth_protocol: iPS cells (iPSCs) were cultured in mTeRS1 medium (Stem Cells) on Matrigel coated dishes (Corning). Medium was replaced every day. Skin fibroblasts were cultured in DMEM/F12.

extract_protocol:
For RNA-seq, total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation.
For ChIP, fibroblasts (10e7 per ChIP) were cross-linked in suspension for 10 min in PBS containing 1% formaldehyde before quenching with 1.25 mM glycine. Cells were lysed for 30 min at 4oC on a rotator in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 1 mM PMSF, 1x protease inhibitor cocktail) adjusted to 1% SDS, and sonicated for 3 times 15 min in a Bioruptor (Diagenode) with 30 sec ON/OFF at high power to generate chromatin fragments of 200-400 base pairs (bp). After sedimentation, chromatin (supernatant from 10e7 cell-equivalents) was diluted 10 times in RIPA buffer without SDS, and incubated on a rotator overnight at 4oC with the primary antibody. For "LMNA ChIPs", 20 µg anti-lamin A/C antibody (Santa Cruz, cat# sc-7292 ) was used and pre-coupled to magnetic Dynabeads Protein G (Invitrogen). For "LMNB1 ChIPs", an anti-lamin B1 antibody was used (Abcam, cat# 16048; rabbit polyclonal) and pre-coupled to magnetic Dynabeads Protein G (Invitrogen). The ChIP material was collected and washed 3 times in 1 ml of ice-cold RIPA buffer without protease inhibitors. The crosslink was reversed and DNA eluted for 6 h on a shaker at 37oC in elution buffer (50 mM NaCl, 20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 1% SDS) containing 0.5 µg/ml RNase A and 2 µg/ml Proteinase K. DNA was purified as described, processed for library preparation.
RNA-seq library was prepared according to the Illumina protocol, and sequenced on an Illumina NextSeq500 at the Norwegian Sequencing Center.
ChIP-seq libraries were prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq4000 at the Norwegian Sequencing Center.

treatment_protocol: Endothelial differentiation was induced in iPS cells on day 0 (D0) in STEMPro34 with 2 mM GlutaMAX (Thermofisher Scientific), 50 µg/ml ascorbic acid (Sigma-Aldrich), 10 ng/mL BMP4 (BMP4, R&D Systems), 25ng/ml activin A (R&D Systems), and 5 ng/mL of FGF2 (Peprotech). Medium was renewed on Day 2 and cells cultured further up to Day 4. On Day 4, cells were harvested and processed for RNA isolation and/or chromatin immunoprecipitation as described under "extraction protocol".

value: skin fibroblast

tag: passages

value: Cells in passages 5-8

tag: differentiation stage

value: Cultured in proliferative state

tag: chip antibody

value: anti-lamin A/C (Santa Cruz sc-7292)


title: Fibroblast LMNB1 rep2

source_name: Skin fibroblasts with endogenous LMNA p.R482W mutation, lamin B1 ChIP

value: anti-lamin B1 (rabbit polyclonal; Abcam, cat# 16048)


title: WT heart uninjured

source_name: Adult heart_WT_uninjured

tag: genotype

value: AB*

tag: tissue

value: heart ventricle


title: CD14+ 14 dpi

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
For the CD14+ cells, the MARS-seq pipeline scripts with a genome of hg19 + TB40/E were used.
For the CD34+ cells, CellRanger software was used.
The fastq files, include in the header, the barcodes and the quality of the barcodes coming from the other read.
For the CD14+ it is the batch barcode, the well / cell barcode and the read UMI.
For the CD34+ it is the well / cell barcode and the read UMI.
Genome_build: hg19 + TB40/E (NCBI accession EF999921.1)
Supplementary_files_format_and_content: tab-delimited text files. Include number of umis for all genes, per cell, and a TOC for CD14+ cells, with the cell name, batch, dpi,  etc.

source_name: CD14+ infected with TB40/E 14 dpi

growth_protocol: Purified human CD14+ and CD34+ cells were maintained in X-vivo-15 media (Lonza) supplemented with 2.25mM L-glutamine.

extract_protocol:
For MARS-seq: single cells were sorted into lysis buffer in 384 well plates and RT was carried out with oligo dT primers. For 10x: cells were loaded for Gel Bead-in-Emulsion (GEM) generation and barcoding
MARS-seq protocol as desdribed at Jaitin et al., 2014 and Chromium Single Cell 3’ protocol (10x Genomics, CA, USA) according to manufacturer’s instractions

treatment_protocol: Cells were infected with HCMV strain TB40E with an SV40-GFP tag

tag: time point

value: 14 dpi


title: CD14+ 7 dpi

source_name: CD14+ infected with TB40/E 7 dpi

tag: cell type

value: 7 dpi


title: CD34+ 4 dpi

source_name: CD34+ infected with TB40/E 4 dpi

value: 4 dpi


title: Fibroblast LMNB1 rep1


title: CD14+ 6 dpi

source_name: CD14+ infected with TB40/E 6 dpi

value: 6 dpi


title: CD14+ 5 dpi

source_name: CD14+ infected with TB40/E 5 dpi

value: 5 dpi


title: CD14+ 4 dpi

source_name: CD14+ infected with TB40/E 4 dpi


title: Fibroblast LMNA rep1


title: CD14+ 3 dpi

source_name: CD14+ infected with TB40/E 3 dpi

value: 3 dpi


title: iPSC FPLD D1

source_name: iPSCs, derived from LMNA p.R482W fibroblasts, submitted to an endothelial differentiation protocol, day 1

value: iPSC

value: Cells in passages 30 to 40

value: Endothelial differentiation protocol, day 1


title: iPSC FPLD D2

source_name: iPSCs, derived from LMNA p.R482W fibroblasts, submitted to an endothelial differentiation protocol, day 2

value: Endothelial differentiation protocol, day 2


title: c-iPSC FPLD D4

source_name: TALEN-corrected iPSC, derived from LMNA p.R482W iPSC, submitted to an endothelial differentiation protocol, day 4

value: TALEN-corrected iPSC

value: Endothelial differentiation protocol, day 4


title: iPSC FPLD D0

source_name: iPSCs, derived from LMNA p.R482W fibroblasts, pluripotent stage

value: Pluripotent


title: c-iPSC FPLD D3

source_name: TALEN-corrected iPSC, derived from LMNA p.R482W iPSC, submitted to an endothelial differentiation protocol, day 3

value: Endothelial differentiation protocol, day 3


title: c-iPSC FPLD D2

source_name: TALEN-corrected iPSC, derived from LMNA p.R482W iPSC, submitted to an endothelial differentiation protocol, day 2


title: c-iPSC FPLD D0

source_name: TALEN-corrected iPSC, derived from LMNA p.R482W iPSC


title: 01106 tox rep 2

status: Public on Feb 16 2018

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

country: South Korea

institute: Pusan National University

data_processing:
The filtered reads of raw data were processed using the BWA-MEM algorithm with default parameters.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by Bamtoreadcount.
Reads per kilobase of exon per million mapped sequence reads were calculated for normalization.
Genome_build: Fusarium graminearum PH-1 ASM24013v3
Supplementary_files_format_and_content: gene information, raw count, and RPKM for each Sample

organism: Fusarium graminearum

source_name: ∆GzC2H008_toxoflavin condition

extract_protocol:
Fusarium graminearum wild-type strain GZ03639 and three toxoflavin-sensitive mutant strains (∆GzZC190, ∆GzC2H008, ∆GzbZIP005) were grown in 50 ml of complete medium at 25°C with shaking at 200 rpm for 72 h. The filtrated mycelia were incubated in 50 ml of minimal medium with presence of toxoflvin 100 mg l-1 for 24 h at 200 rpm. The mycelia were grinding in liquid nitrogen and total RNAs were extracted with NucleoSpin RNA Plant Kit (Machey-Nagel GmbH & Co. KG) according to the manufacturer’s protocol.
RNA-sequencing libraries were prepared using an Illumina TruSeqTM RNA sample prep kit (Illumina), according to the manufacturer’s protocols. Sequencing was performed on an Illumina HiSeq2000 instrument at the National Instrumentation Center for Environmental Management (NICEM).

tag: strain background

tag: genotype/variation

value: {delta}GzC2H008 (FGSG_01106 deletion mutant)

tag: cultured condition

value: 100 mg l-1 toxoflavinfor 24 h


title: 02939 tox rep 1

source_name: ∆GzbZIP005_toxoflavin condition

value: {delta}GzbZIP005 (FGSG_02939 deletion mutant)


title: 02939 tox rep 2


title: 01106 tox rep 1


title: TF tox rep 2

source_name: ∆GzZC190_toxoflavin condition

value: {delta}GzZC190 (FGSG_07589 deletion mutant)


title: TF tox rep 1


title: WT tox rep 2

source_name: wild-type_toxoflavin condition

value: wild-type


title: 02939 rep 1

source_name: ∆GzbZIP005_minimal media

value: minimal media


title: WT tox rep 1


title: 01106 rep 2

source_name: ∆GzC2H008_minimal media


title: 01106 rep 1


title: iPSC FPLD D4

source_name: iPSCs, derived from LMNA p.R482W fibroblasts, submitted to an endothelial differentiation protocol, day 4


title: TF rep 1

source_name: ∆GzZC190_minimal media


title: iPSC FPLD D3

source_name: iPSCs, derived from LMNA p.R482W fibroblasts, submitted to an endothelial differentiation protocol, day 3


title: TF rep 2


title: WT rep 1

source_name: wild-type_minimal media


title: IL4 23

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

country: Italy

institute: OSR - San Raffaele Scientific Institute

data_processing:
mapping with STAR v2.5.3a with softclipping -allowedmismatches 14
gene abundances with featureCounts (not multimapping) from Rsubread_1.16.1
differential expression with DESeq2_1.6.3
Genome_build: mm10 (M13 from GeneCode - Primary Assembly) ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M13/GRCm38.primary_assembly.genome.fa.gz
Supplementary_files_format_and_content: xlsx from deseq2::results function on IL4 vs GFP contrast

source_name: CD45lowCD11b+ microglia

growth_protocol: Microglia fractions were sorted by flow cytometry of CD45low/CD11b+ cells from freshly dissociated  spinal cords.

extract_protocol:
RNA samples were extracted by flow cytometry sorting CD45low/CD11b+ cells from spinal cords of mice. Total RNA was extracted using Micro-RNeasy kit according manufacture’s guidelines.
QuantSeq 3′ mRNA-Seq Reverse (FWD) Library Prep Kit (Lexogen advertise article, Nature Methods 11 2014) according to manufacturer's instruction

treatment_protocol: Lentivirus encoding IL-4 (107 P.F.U.) were injected in the 4th ventricle of the CNS through a single injection.

value: spinal cord

tag: strain

tag: genotype & treatment

value: wild type receiving 30 days of IL4-gene therapy


title: IL4 21


title: c-iPSC FPLD D1

source_name: TALEN-corrected iPSC, derived from LMNA p.R482W iPSC, submitted to an endothelial differentiation protocol, day 1


title: GFP 15


title: IL4 1


title: GFP 8


title: GFP 12


title: Parental clone_untreated_replicate 2

city: London

first: Caroline

middle: S

last: Hill

address: 1 Midland Road

department: Developmental Signalling

institute: Francis Crick Institute

description:
Parental_Clone_untreated_R2
Processed data file: GEO_RSEM_normalised_data.txt

data_processing:
The RSEM package (version 1.2.31) in conjunction with the STAR alignment algorithm (version 2.5.2a) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl mouse GRCm.38.86 version genes.
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.2.3).
Genome_build: Ensembl mouse GRCm.38.86
Supplementary_files_format_and_content: GEO_RSEM_normalised_data.txt: Tab-delimited text file containing TMM normalised data. Rows represent Ensembl mouse genes and columns represent individual samples.

source_name: Parental clone, untreated

growth_protocol: DMEM, 10% FCS, 10mg/mL insulin. Treatment with TGF-b was done in OptiMEM with 10mg/mL insulin.

extract_protocol:
RNA was extracted with Trizol, DNase I treated and then cleaned up on RNeasy columns.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Untreated or treated with 2 ng/mL TGF-b for 48 hours.

tag: cell line

value: NMuMG

value: Parental

tag: treatment

value: Untreated


title: Parental clone_untreated_replicate 3

description:
Parental_Clone_untreated_R3
Processed data file: GEO_RSEM_normalised_data.txt


title: Parental clone_untreated_replicate 1

description:
Parental_Clone_untreated_R1
Processed data file: GEO_RSEM_normalised_data.txt


title: Parental clone_48 hr TGF beta_replicate 2

description:
Parental_Clone_48hr_TGFbeta_R2
Processed data file: GEO_RSEM_normalised_data.txt

source_name: Parental clone, TGF-beta

value: TGF-b, 48 hr


title: Parental clone_48 hr TGF beta_replicate 3

description:
Parental_Clone_48hr_TGFbeta_R3
Processed data file: GEO_RSEM_normalised_data.txt


title: 02939 rep 2


title: DSMAD1/5 Clone 1_48 hr TGF beta, replicate 2

description:
deltaSMAD1.5_Clone1_48hr_TGFbeta_R2
Processed data file: GEO_RSEM_normalised_data.txt

source_name: DSMAD1/5 Clone 1, TGF-beta

value: SMAD1/5 deletion


title: DSMAD1/5 Clone 1_untreated_replicate 1

description:
deltaSMAD1.5_Clone1_untreated_R1
Processed data file: GEO_RSEM_normalised_data.txt

source_name: DSMAD1/5 Clone 1, untreated


title: DSMAD1/5 Clone 1_48 hr TGF beta, replicate 3

description:
deltaSMAD1.5_Clone1_48hr_TGFbeta_R3
Processed data file: GEO_RSEM_normalised_data.txt


title: DSMAD1/5 Clone 1_48 hr TGF beta, replicate 1

description:
deltaSMAD1.5_Clone1_48hr_TGFbeta_R1
Processed data file: GEO_RSEM_normalised_data.txt


title: WT rep 2


title: A3

city: Cincinnati

first: Keri

middle: Anne

last: Drake

state: Ohio

address: 3333 Burnet Avenue

department: Nephrology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Strand NGS 2.6 software was used for gene alignment, quantification, normalization (RPKM), and differential gene expression analysis
Bam files were generated using mouse build mm10. Data was filtered on read quality metrics standard in Strand NGS 2.6 software, including removal of reads aligning to more than one position in the genome, average base quality < 20, failure of vendor quality control, as well as expression level, requiring at least 5 NRPKM in 2 of 6 samples.
Genome_build: mm10
Supplementary_files_format_and_content: txt; complete gene list of normalized signal values

source_name: kidney

extract_protocol:
Whole kidneys were removed from transgenic and control mice, cut in half, and snap frozen. RNA was isolated using RNeasy Miniprep kit (Qiagen; Cat#74134); 100-300 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB/N

tag: developmental stage

value: Adult

value: Transgenic


title: B1

value: Control


title: A1


title: B2


title: B3


title: A2


title: UVB poly, rep2

city: Indianapolis

first: Ann

last: Collier

state: IN

address: 635 N Barnhill Dr MS4067

institute: Indiana University School of Medicine

description:
mRNA-Seq
UV2-poly
Processed data file: Percent_shift_calculations.xlsx

data_processing:
FASTQ format converted using FASTQgroomer (Galaxy version 1.0.4).
Reads mapped to genome using Tophat (Galaxy version 2.1.0).
FPKM calculated using Cufflinks (Galaxy version 2.2.1.0).
Transcript assemblies merged using Cuffmerge (Galaxy version 2.2.1.0).
Differential expression for total RNA performed on total samples using Cuffdiff an Cuffmerge assembly (Galaxy version 2.2.1.3).
Percent shifts for polysome fractions calculated by difference in percent total of polysome fractions between each treatment group. i.e. polysome FPKM for NT divided by the sum of the polysome and monosome FPKMs for that sample. Then subtract NT by UVB for each replicate to get a shift.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *total_cufflinks.xls: Excel files include FPKMs for the 'total' samples.
Supplementary_files_format_and_content: Percent_shift_calculations.xlsx: Excel file includes FPKMs for the fractionated samples
Supplementary_files_format_and_content: Total_RNA_cuffdiff.xlsx: Excel file includes differential expression for total RNA.

source_name: Human skin

growth_protocol: N-TERT keratinocytes (Dickson et al., 2000) were cultured in EpiLife media (Invitrogen, Carlsbad, CA) supplemented with human keratinocyte growth supplement (HKGS, Invitrogen) and 1000U Penicillin-Streptomycin (Roche, Indianapolis, IN).

extract_protocol:
RNA was isolated using Trizol followed by phenol/chloroform extraction. The concentration and quality of total RNA samples were first assessed using Agilent 2100 Bioanalyzer. A RIN (RNA Integrity Number) of five or higher was required to pass the quality control.
The samples are first spiked-in with ERCC Mix 1 to no treatment and Mix 2 to all treated. Then five hundred nanograms of RNA per sample were used to prepared dual-indexed strand-specific cDNA library using TruSeq Stranded mRNA Library PrepKit (Illumina). The resulting libraries were assessed for its quantity and size distribution using Qubit and Agilent 2100 Bioanalyzer. One and a half pico molar pooled libraries were sequenced with 2x75bp paired-end configuration on NextSeq500 (Illumina) using NextSeq 500/550 High Output Kit. A Phred quality score (Qscore) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

treatment_protocol: UVB irradiation of N-TERT keratinocytes was carried out using Philips FS20T12 UVB broadband light sources as described previously (Lewis et al., 2010). A IL1700 radiometer and a SED240 UVB detector (International Light, Newburyport, MA) were used to measure UVB intensity prior to each experiment using a distance of 8cm from the light source to the culture dish. Cells were always irradiated in EpiLife media, which eliminates any UVC wavelengths, followed by normal incubation settings (37°C and 5% CO2).

value: N-TERT

value: keratinocytes

value: 100 J/m2 UVB + 8hr incubation

tag: fraction

value: Polysome


title: UVB poly, rep3

description:
mRNA-Seq
UV3-poly
Processed data file: Percent_shift_calculations.xlsx


title: DSMAD1/5 Clone 1_untreated_replicate 3

description:
deltaSMAD1.5_Clone1_untreated_R3
Processed data file: GEO_RSEM_normalised_data.txt


title: UVB mono, rep2

description:
mRNA-Seq
UV2-mono
Processed data file: Percent_shift_calculations.xlsx

value: Monosome


title: Parental clone_48 hr TGF beta_replicate 1

description:
Parental_Clone_48hr_TGFbeta_R1
Processed data file: GEO_RSEM_normalised_data.txt


title: UVB mono, rep3

description:
mRNA-Seq
UV3-mono
Processed data file: Percent_shift_calculations.xlsx


title: UVB mono, rep1

description:
mRNA-Seq
UV1-mono
Processed data file: Percent_shift_calculations.xlsx


title: DSMAD1/5 Clone 1_untreated_replicate 2

description:
deltaSMAD1.5_Clone1_untreated_R2
Processed data file: GEO_RSEM_normalised_data.txt


title: UVB total, rep2

description:
mRNA-Seq
UV2
Processed data file: Total_RNA_cuffdiff.xlsx

value: Whole Cell Lysate


title: UVB total, rep3

description:
mRNA-Seq
UV3
Processed data file: Total_RNA_cuffdiff.xlsx


title: No Treatment poly, rep3

description:
mRNA-Seq
NT3-poly
Processed data file: Percent_shift_calculations.xlsx

value: 0 J/m2 UVB + 8hr incubation


title: No Treatment poly, rep2

description:
mRNA-Seq
NT2-poly
Processed data file: Percent_shift_calculations.xlsx


title: UVB total, rep1

description:
mRNA-Seq
UV1
Processed data file: Total_RNA_cuffdiff.xlsx


title: No Treatment mono, rep2

description:
mRNA-Seq
NT2-mono
Processed data file: Percent_shift_calculations.xlsx


title: No Treatment mono, rep1

description:
mRNA-Seq
NT1-mono
Processed data file: Percent_shift_calculations.xlsx


title: No Treatment total, rep1

description:
mRNA-Seq
NT1
Processed data file: Total_RNA_cuffdiff.xlsx


title: No Treatment total, rep3

description:
mRNA-Seq
NT3
Processed data file: Total_RNA_cuffdiff.xlsx


title: LM3-Z3

city: Los Angeles

first: Meng

state: CA

address: 2003 Zonal Avenue

institute: University of Southern California

data_processing:
Basecalls generated on Nextseq 500 by RTA v2
Raw data files in FASTQ format was analyzed with Partek Flow v4
FASTQ files were trimmed with Quality Score method
Trimmed reads were mapped with Star 2.4.1d to human hg38 genome build with Gencode v23 as guidance
Mapped reads were quantificed to Gencode v23 uisng Partek E/M method
Quantified reads were normalized by Upper Quartile method
Normalized reads were analzyed for differentially expression using Partek's Gene Specific Analysis method
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file includes normalized read counts (upper quartile normalization with offset 1) for genes in all samples

source_name: Unfixed Fresh Frozen Human Liver

growth_protocol: Not applicable

extract_protocol:
Unfixed fresh frozen liver tissue embedded in OCT compound were cryo-cut followed by tissue collection via Laser Captured Microdissection methods. The RNA was extracted with RNeasy Micro Kit (QIAGEN).
1ng of RNA per sample was subjected to first-stranded cDNA synthesis followed by PCR amplification (11 cycles) using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). Then, the amplified cDNA was used for the establishement of libraries using standard Illumina protocols.

treatment_protocol: Not applicable

tag: patient

tag: zone

tag: gender

value: Female


title: LM3-Z2


title: LM3-Z1


title: LM2-Z3


title: LM2-Z2


title: LM3-WL

value: Whole Liver


title: LM2-Z1


title: LM2-WL


title: LM1-Z3

value: Male


title: LM1-Z2


title: UVB poly, rep1

description:
mRNA-Seq
UV1-poly
Processed data file: Percent_shift_calculations.xlsx


title: LM1-WL


title: No Treatment mono, rep3

description:
mRNA-Seq
NT3-mono
Processed data file: Percent_shift_calculations.xlsx


title: No Treatment poly, rep1

description:
mRNA-Seq
NT1-poly
Processed data file: Percent_shift_calculations.xlsx


title: im-nc_hen2-4_rep3

city: College Station

first: Akihito

last: Fukudome

address: Dept. Horticultural Sciences MS2133 Texas A&M Univ.

institute: Texas A&M University

description:
im-ncRNA-seq_hen2-4(3)
im-nc_samtools_bedcov.txt

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings. Sequencer .bcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl.
Raw sequenced reads (.fastq files) were uploaded to Galaxy (https://usegalaxy.org/). The following data processing was done using Galaxy.
Sequenced reads were trimmed for adapter and low-quality sequences by using Trim Galore! (v0.4.0), then mapped with Tophat (v2.0.14) against reference assembly Ensembl TAIR10 from Illumina iGenome, using default parameters except -i/--min-intron-length 60 -I/--max-intron-length 6000.
Coverage depth of regions of interest was calculated by SAMtools_BedCov (v1.2).
Genome_build: Arabidopsis TAIR10 (Ensembl)
Supplementary_files_format_and_content: im-nc_samtools_bedcov.txt file includes raw coverage counts (a sum of coverage depth per base in each region of interest) for each sample, computed by SAMtools_BedCov.

source_name: im-nc_hen2-4, 7-day-old seedling

growth_protocol: 7-day-old seedlings horizontally grown on ¼ MS media containing 0.5% sucrose.

extract_protocol:
Seedling roots were flash frozen immediately after harvesting and subjected to total RNA extraction using miRNeasy Plant Mini kit (QIAGEN).
The total RNA was submitted to Texas A&M AgriLife Genomics & Bioinformatics Service for RNA-seq analysis (paired-end, 125-bp). After validating the integrity and purity of total RNA using Nanodrop, sequencing libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Plant kit.  To enrich intermediate non-coding RNA (im-ncRNA), fragmentation step was omitted, and library cDNA with 100-500nt were purified using Pippin (Sage Science) prior to sequencing by Illumina HiSeq (125 nt, paired-end).

tag: ecotype

value: Colombia

tag: age

value: root


title: im-nc_hen2-4_rep1

description:
im-ncRNA-seq_hen2-4(1)
im-nc_samtools_bedcov.txt

tag: genotype

tag: tissue


title: im-nc_Col_rep2

description:
im-ncRNA-seq_Col(2)
im-nc_samtools_bedcov.txt

source_name: im-nc_Col, 7-day-old seedling

value: wild-type