title: RA-MTX (not receiving methotrexate)

value: RA-MTX (not receiving methotrexate)


title: Healthy control subject

status: Public on Apr 11 2017

type: SRA

city: Nashville

first: Charles

middle: F

last: Spurlock III

state: Tennessee

address: 1161 21st Avenue South

department: Medicine

country: USA

institute: Vanderbilt University School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.9 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: text file, FPKM table

molecule: total RNA

organism: Homo sapiens

source_name: peripheral whole blood draw

extract_protocol:
Peripheral whole blood was collected into PaxGene tubes. RNA was isolated per the manufacturer's supplied protocol.
Total RNA isolated from PaxGene tubes was purified with the RNeasy MinElute Cleanup kit (Qiagen) using an on-column DNAse treatment to ensure absence of genomic DNA contamination according to the manufacturer’s supplied protocol.
Libraries were constructed using the Illumina TruSeq Stranded mRNA kit (Cat. No. RS-122-2101) following the manufacturer's supplied protocol.

tag: type

value: Healthy control subject


title: CIS-MS

value: CIS-MS


title: atg7-2_dehydration3

city: Ames

first: Yanhai

last: Yin

state: IA

address: 1035D Roy J. Carver Co-Lab

department: Genetic Development and Cell Biology

institute: Iowa State University

description: Sample name: 12

data_processing:
Quality Control
Alignment using GSNAP
Differential expression using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: comma seperated files including RPM values and statistical significance for each sample calculated using DESeq2

organism: Arabidopsis thaliana

source_name: leaf tissue

extract_protocol:
RNA was then extracted using Trizol, followed by DNAse digestion and RNA cleanup using Qiagen RNeasy kit. Purified RNA was subject to quality control on an Agilent 2100 Bioanalyzer.
Library preparation and RNA sequencing were performed by BGI Americas using an Illumina HiSeq 2000 with 50bp single-end reads and ~30 million reads per sample.

tag: tissue

value: leaf

tag: genotype

tag: treatment

value: Dehydration

tag: replication


title: K326_ShootApex_ZT0_R3

city: Cambridge

first: Kieron

middle: David

last: Edwards

state: Cambridgeshire

address: GR&D Cambridge, 210 Cambridge Science Park

department: Plant Biotechnology

country: United Kingdom

institute: British American Tobacco

data_processing:
Basecalls performed using HiSeq Control Software 2.2.38
Deconvolution of multiplexed reads was carried out using Casava 1.9.4
Data were filtered and multiplex adaptors trimmed from reads using fastq-mcf  1.04.803 with the following configurations: -q 30 -l 50 -P 30
Reads were aligned to Nitab4.5 gene models and quantified using rsem 1.2.7 and bowtie 1.1.0
Genome_build: nitab45_transcripts.fasta
Supplementary_files_format_and_content: tab-delimited text files including gene model, TPM and FPKM were produced for each sample

organism: Nicotiana tabacum

growth_protocol: Plants were grown under long day conditions (18h light, 6h dark) at 23 degrees.

extract_protocol:
Total RNA was extracted using QIAzol followed by clean up, including on-column DNase treatment, using Qiagen RNeasy spin columns. RNA was QC'd using Bioanalyzer RNAnano protocol. RNA with RIN>=8.0 was used in library preparation
Random primed cDNA-libraries were prepared at GATC Biotech (Konstanz, Germany) using propritary methods

treatment_protocol: Tissue was harvested at ZT0, 6, 12 and 18

tag: cultivar

value: ShootApex

tag: timepoint

tag: age (days)

tag: photoperiod

tag: replicate


title: K326_ShootApex_ZT0_R1


title: Celiac disease

value: Celiac disease


title: K326_ShootApex_ZT0_R2


title: Fibromyalgia syndrome

value: Fibromyalgia syndrome


title: K326_Root_ZT6_R1

value: Root


title: Irritable bowel syndrome

value: Irritable bowel syndrome


title: K326_Root_ZT6_R2


title: K326_Shoot_ZT0_R3

value: Shoot


title: Crohn's disease

value: Crohn's disease


title: K326_Shoot_ZT6_R2


title: K326_Shoot_ZT0_R2


title: Ulcerative colitis

value: Ulcerative colitis


title: K326_Shoot_ZT0_R1


title: Rpo21 glucose to no glucose time course 2 time point 1

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

description:
UV cross-linked RNA
CRAC library
processed data file: Rpo21_timecourse_2_glu_to_noglu.txt

data_processing:
Library strategy: CRAC-seq
CRAC data processing steps: All processing steps were performed using the pyCRAC package version 1.2.2.6. Demultiplexing was performed using pyBarcodeFilter.py (version 2.3.4). 3' adapter removal and 3' end quality trimming (min Phred = 30) was performed using FlexBar (version 2.5). Reads were collapsed using random nucleotides present in 5' barcodes using pyFastqDuplicateRemover.py (version 0.0.2). Reads were mapped to the S. cerevisiae geneome (EF.64; source ENSEMBL) using novoalign (version 2.0.4) and feature counts were generated using pyReadCounters (version 0.5.3).
We scaled the FPKM values of all transcripts within each time point by a constant factor such that the sum of FPKMs for all time points and all experimental replicates is the same. This was done for all data sets that were analysed simultaneously, e.g. Nab3 and Pol II data sets (see below). For all data sets, the same time points were used (on a few occasions, temporally close time points were deemed identical for experimental purposes). Finally, for all analysed data sets, we divided each time series of each experimental replicate by its steady state value before the imposition of stress (at 0 minutes after the nutrient shift). This way, all time series start at the same normalised binding value of 1 a.u. before the nutrient shift and the other values for later time points are relative to the background binding signal. We only keep those transcripts for the analysis that have real values for all time points in all experimental replicates after all steps of the normalisation procedure.
The scaled FPKM values are provided in the processed data files.
Genome gtf and fasta files are also included
Genome_build: EF64
Supplementary_files_format_and_content: text files containing normalized FPKM values for each time-series

organism: Saccharomyces cerevisiae

growth_protocol: For an 8 time-points time-course, 8L of cells were grown in synthetic medium with glucose (SD-TRP) to exponential phase (OD600 ~0.5) at 30ºC. For time-point zero, 1L of cells were cross-linked in the Vari-X-linker using the high-output 254nm lamps for 12 seconds and then harvested by rapidly passing the cells through a 0.8 µm filter (Millipore) using a home-made vacuum filtration device (contact UVO3 for information and prices). The remaining 7L of cells were harvested on filters and quickly resuspended in S-TRP (no glucose samples) or SD-TRP (glucose control samples) and maintained at 30oC. For each time-point 1L of cells were cross-linked in the Vari-X-linker and harvested by filtration as above. This yielded ~1g of cells for each time-point.

extract_protocol:
Cells were lysed in 1V/w of TN150 (50 mM Tris pH 8.0, 150 mM NaCl, 0.1% NP-40, 5 mM b-mercaptoethanol) and 3V of Zirkonia beads (0.5 mm; Thistle Scientific) as previously described (Granneman et al. PNAS 2009). For the Nab3 anchor-away nuclear depletion experiments (Haruki et al., Mol Cell 2008), cells were incubated with 1µg/ml rapamycin (Sigma) for 1 hour before the cells were shifted.  For the Pol II (Rpo21-HTP) cCRAC experiments, cells were lysed in 1V/w TMn150 (50 mM Tris-HCl pH 8.0, 10 mM MnCl2, 0.1% NP-40, 5 mM b-mercaptoethanol, 150 mM NaCl, Roche Midi protease inhibitors; 1 ml per gram of cells). Subsequently, 1V/w of TMn150 was added containing 1U/ml of RQ1 RNase-free DNAse (Promega) and the suspension was incubated for half an hour on ice to degrade the chromatin. Three milliliter of lysis buffer was added and extracts were clarified by centrifugation (20 min at 4,500 g and 20 min at 20,000 g at 4 °C). Extracts were incubated with 250 µl of equilibrated IgG Sepharose beads (GE Healthcare) for 2h at 4 °C.
linker ligations were performed as previously described (Granneman et al., PNAS 2009) using adapters provided in the Supplementary Information of the manuscript. Cross-linked protein-RNA complexes were resolved on 1mm thick 4-12% NuPAGE gels (Thermo Fisher Scientific), transferred to nitrocellulose membranes and visualized by autoradiography. Bands corresponding to the size of the protein of interest, including a region 0.5 cm above the band, were cut from the nitrocellulose membrane and pooled in a single 2 ml tube. Radiolabeled RNA was extracted by incubating the membrane slices with 200 µg of proteinase K in 800 µl of wash buffer II containing 1% SDS and 5 mM EDTA. The solution was transferred to a new tube and the RNA was subsequently phenol-chloroform-extracted and ethanol-precipitated. Reverse transcription with SuperScript III was performed as per manufacturer's procedures (Thermo Fisher Scientific) using the reverse transcription primer listed in Table S2. The cDNAs were purified using the Zymo DNA Clean & Concentrator 5 kit and eluted into a final volume of 10 µl. Five µl of cDNA was PCR amplified using Pfu polymerase (Promega) for 20-24 cycles (95ºC 30s, 52ºC 30s and 72ºC 1min) using PCR oligonucleotides listed in Table S2. PCR products were resolved on 2% Metaphor agarose gels (Lonza) and 160-300 bp fragments were gel purified using the miniElute kit (Qiagen) according to manufacturer’s procedures. Paired-end sequencing (50 bp) was performed by Edinburgh Genomics using the Illumina HiSeq 2500 and 4000 platforms.

value: BY4741:MATa; his3delta_1; leu2delta_0; met15delta_0; ura3delta_0


title: Rpo21 glucose to no glucose time course 2 time point 14


title: K326_Root_ZT0_R3


title: K326_Root_ZT0_R2


title: Wapl MEFs - 2 (Peters Lab ID: 10506)

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description:
Peters Lab ID: 10506
processed data file: RPKM_values_RNA-seq.txt

data_processing:
Basecalling software: Illumina RTA
Alignment: TopHat 1.3.1. for samples 85, 86, 89, 90, 93, 94 (RNA-Seq), reads are mapped uniquely to genome with 0 to 2 errors
Alignment: TopHat 1.4.1. for all other RNA-Seq samples, reads are mapped uniquely to genome with 0 to 2 errors
Alignment: Alignment: Bowtie 0.12.5 and 1.0.0 for ChIP-Seq and GRO-Seq data, reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq MACS peak calling version 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS 1.4.2 with output switches [-w -S] and represent genomic distribution of the factors as described in the paper.
Supplementary_files_format_and_content: RPKM and TPM values are generated according to standard formulas after read counting using 'bedtools coverage' and 'htseq-count' methods resp. as described.

organism: Mus musculus

source_name: mouse embryonic fibroblasts (E13.5d)

growth_protocol: Quiescent, non-proliferating MEFs were used in all experiments.

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; GRO-Seq: Nuclei were isolated and global run-on was preformed in the presence of BrU analog. RNA was fragmented and isolated by a BrU immunoprecipitation. Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step; RNA-Seq: Total RNA was extracted from MEFs via the RNA Easy Plus kit and PolyA containing mRNAs were isolated using Dynabeads. The mRNA was fragmented and reversely transcribed with Superscript III followed by second strand synthesis.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols; GRO-Seq: see extract protocol

treatment_protocol: The deletion of the Smc3 and Wapl gene was induced in quiescent MEFs by activating an inducible Cre recombinase with 4'-hydroxytamoxifen; The deletion of the Ctcf gene alone or in the combination with the Wapl gene was induced by the expression Cre recombinase from an adenovirus.

tag: cell type

value: Mouse embryonic fibroblasts

tag: strain

value: Rosa26(CreER/+) Wapl(fl/-); clone 2

value: 10d resting

tag: assayed molecule

value: mRNA


title: Wapl MEFs - 1 (Peters Lab ID: 9935)

description:
Peters Lab ID: 9935
processed data file: RPKM_values_RNA-seq.txt

value: Rosa26(CreER/+) Wapl(fl/-); clone 1

value: 2-3d 4'hydroxytamoxifen and 10d resting


title: Rpo21 glucose to no glucose time course 2 time point 8


title: Rpo21 glucose to no glucose time course 1 time point 1

description:
UV cross-linked RNA
CRAC library
processed data file: Rpo21_timecourse_1_glu_to_noglu.txt


title: Rpo21 glucose to no glucose time course 2 time point 2


title: Wapl MEFs - 1 (Peters Lab ID: 9934)

description:
Peters Lab ID: 9934
processed data file: RPKM_values_RNA-seq.txt


title: Wapl MEFs - 2 (Peters Lab ID: 10507)

description:
Peters Lab ID: 10507
processed data file: RPKM_values_RNA-seq.txt


title: Smc3 MEFs - 4 (Peters Lab ID: 10504)

description:
Peters Lab ID: 10504
processed data file: RPKM_values_RNA-seq.txt

value: Rosa26(CreER/+) Smc3(fl/-); clone 4


title: Rpo21 glucose to no glucose time course 1 time point 4


title: Rpo21 glucose to no glucose time course 2 time point 0


title: Rpo21 glucose to no glucose time course 1 time point 14


title: Smc3 MEFs - 3 (Peters Lab ID: 9930)

description:
Peters Lab ID: 9930
processed data file: RPKM_values_RNA-seq.txt

value: Rosa26(CreER/+) Smc3(fl/-); clone 3


title: Rpo21 glucose to no glucose time course 1 time point 0


title: Smc3 MEFs - 2 (Peters Lab ID: 10503)

description:
Peters Lab ID: 10503
processed data file: RPKM_values_RNA-seq.txt

value: Rosa26(CreER/+) Smc3(fl/-); clone 2


title: Smc3 MEFs - 3 (Peters Lab ID: 9931)

description:
Peters Lab ID: 9931
processed data file: RPKM_values_RNA-seq.txt


title: Rpo21 glucose to no glucose time course 1 time point 8


title: Rpo21 glucose to glucose time course 1 time point 1

description:
UV cross-linked RNA
CRAC library
processed data file: Rpo21_timecourse_1_glu_to_glu.txt


title: Rpo21 glucose to no glucose time course 1 time point 2


title: Rpo21 glucose to glucose time course 1 time point 14


title: Rpo21 glucose to no glucose time course 2 time point 4


title: Smc3 MEFs - 1 (Peters Lab ID: 9612)

description:
Peters Lab ID: 9612
processed data file: RPKM_values_RNA-seq.txt

value: Rosa26(CreER/+) Smc3(fl/fl); clone 1


title: Smc3 MEFs - 1 (Peters Lab ID: 9611)

description:
Peters Lab ID: 9611
processed data file: RPKM_values_RNA-seq.txt


title: K326_Root_ZT0_R1


title: Rpo21 glucose to no glucose time course 2 time point 20


title: bes1_dehydration1

description: Sample name: 26

value: leaf

value: Dehydration


title: CTCF ChIP (Peters Lab ID: 9149)

description:
Peters Lab ID: 9149
processed data file: 9149+27722.wig

library_source: genomic

molecule: genomic DNA

value: Rosa26(CreER/+) Wapl(fl/-)

tag: chip antibody

value: CTCF (Upstate 07-729)


title: Rpo21 glucose to glucose time course 1 time point 0


title: CTCF ChIP (Peters Lab ID: 9147)

description:
Peters Lab ID: 9147
processed data file: 9147+27719.wig

value: wild-type


title: Rpo21 glucose to glucose time course 1 time point 8


title: Smc3 MEFs - 4 (Peters Lab ID: 10505)

description:
Peters Lab ID: 10505
processed data file: RPKM_values_RNA-seq.txt


title: Rpo21 glucose to no glucose time course 1 time point 20


title: Rpo21 glucose to glucose time course 1 time point 2


title: Rpo21 glucose to no glucose anchor away strain time point 14

description:
CRAC library
Rpo21_glu_to_noglu_14
processed data file:
Rpo21_RAP_no_RAP_0_14_control_exp_data.txt

data_processing:
CRAC data processing steps: All processing steps were performed using the pyCRAC package version 1.2.2.6. Demultiplexing was performed using pyBarcodeFilter.py (version 2.3.4). 3' adapter removal and 3' end quality trimming (min Phred = 30) was performed using FlexBar (version 2.5). Reads were collapsed using random nucleotides present in 5' barcodes using pyFastqDuplicateRemover.py (version 0.0.2). Reads were mapped to the S. cerevisiae geneome (EF.64; source ENSEMBL) using novoalign (version 2.0.4) and feature counts were generated using pyReadCounters (version 0.5.3).
We scaled the FPKM values of all transcripts within each time point by a constant factor such that the sum of FPKMs for all time points and all experimental replicates is the same. This was done for all data sets that were analysed simultaneously, e.g. Nab3 and Pol II data sets (see below). For all data sets, the same time points were used (on a few occasions, temporally close time points were deemed identical for experimental purposes). Finally, for all analysed data sets, we divided each time series of each experimental replicate by its steady state value before the imposition of stress (at 0 minutes after the nutrient shift). This way, all time series start at the same normalised binding value of 1 a.u. before the nutrient shift and the other values for later time points are relative to the background binding signal. We only keep those transcripts for the analysis that have real values for all time points in all experimental replicates after all steps of the normalisation procedure.
The scaled FPKM values are provided in the processed data files.
Genome gtf and fasta files are also included
Genome_build: EF64
Supplementary_files_format_and_content: text files containing normalized FPKM values for each time-series

value: HHY168:MATalpha; tor1-1; fpr1::NAT PMA1-2xFKBP12::TRP

tag: molecule subtype

value: UV cross-linked RNA


title: Nab3 glucose to no glucose time course 2 time point 4

description:
UV cross-linked RNA
CRAC library
processed data file: Nab3_timecourse_2_glu_to_noglu.txt

value: BY4741:MATa; his3delta_1; leu2delta_0; met15delta_0; ura3delta_0


title: Nab3 glucose to no glucose time course 2 time point 16


title: Rpo21 glucose to no glucose anchor away strain time point 0

description:
CRAC library
Rpo21_glu_to_noglu_0
processed data file:
Rpo21_RAP_no_RAP_0_14_control_exp_data.txt


title: Smc3 MEFs - 2 (Peters Lab ID: 10502)

description:
Peters Lab ID: 10502
processed data file: RPKM_values_RNA-seq.txt

value: Mouse embryonic fibroblasts


title: Rpo21 glucose to no glucose anchor away strain rapamycin time point 0

description:
CRAC library
Rpo21_glu_to_noglu_0_RAP
processed data file:
Rpo21_RAP_no_RAP_0_14_control_exp_data.txt


title: Nab3 glucose to no glucose time course 2 time point 8


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 2 time point 2

description:
UV cross-linked RNA
CRAC library
processed data file: Rpo21_Nab3-FRB_RAP_time_course_2_glu_to_noglu.txt

value: HHY168:MATalpha; tor1-1; fpr1::NAT RPL13A-2xFKBP12::TRP


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 2 time point 14


title: Nab3 glucose to no glucose time course 2 time point 45


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 2 time point 1


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 2 time point 20


title: Nab3 glucose to no glucose time course 2 time point 22


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 2 time point 0


title: Nab3 glucose to no glucose time course 2 time point 28


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 2 time point 4


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 2 time point 8


title: Nab3 glucose to no glucose time course 2 time point 0


title: Nab3 glucose to no glucose time course 1 time point 1

description:
UV cross-linked RNA
CRAC library
processed data file: Nab3_timecourse_1_glu_to_noglu.txt


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 2 time point 40


title: Rpo21 glucose to no glucose anchor away strain rapamycin time point 14

description:
CRAC library
Rpo21_glu_to_noglu_14_RAP
processed data file:
Rpo21_RAP_no_RAP_0_14_control_exp_data.txt


title: Rpo21 glucose to glucose time course 1 time point 20


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 1 time point 18

description:
UV cross-linked RNA
CRAC library
processed data file: Rpo21_Nab3-FRB_RAP_time_course_1_glu_to_noglu.txt


title: Nab3 glucose to no glucose time course 1 time point 14


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 1 time point 4


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 1 time point 1


title: Nab3 glucose to no glucose time course 1 time point 20


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 1 time point 40


title: Nab3 glucose to no glucose time course 2 time point 1


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 1 time point 10


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 1 time point 2


title: Nab3 glucose to no glucose time course 1 time point 2


title: Nab3 glucose to no glucose time course 1 time point 8


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 1 time point 0


title: Rpo21 glucose to no glucose anchor away strain rapamycin time course 1 time point 28


title: Nab3 glucose to glucose time course 1 time point 1

description:
UV cross-linked RNA
CRAC library
processed data file: Nab3_timecourse_1_glu_to_glu.txt


title: K0 Control_Exome-seq

city: New York

first: Liang

last: Liu

state: NY

address: 1150 St. Nicholas Avenue

institute: Columbia University

data_processing:
Library strategy: Exome-Seq
For Exome-Seq, reads were mapped to the NCBI/build37.2 genome using the BWA algorithm. Mapped reads were sorted and indexed using the Samtools program. UV-induced somatic mutations between the paired UV-4h vs. control or UV-72h vs. control were called using Samtools mpileup and bcftools.
genome build: NCBI/build37.2
processed data files format and content: For Exiome-Seq, vcf files include the genetic variants that are different between the UVR-treated versus no-UVR control samples.

source_name: neonatal foreskin

growth_protocol: Primary human keratinocytes were isolated from neonatal foreskins and were cultured in 154CF medium supplemented with human keratinocyte growth supplement (Life Technologies, Grand Island, NY)

extract_protocol:
Genomic DNA was isolated from UV-irradiated and control samples using the Wizard Genomic DNA Purification Kit (Promega).
Exome-Seq was performed at the Columbia Genome Center following standard Illumina TruSeq multiplexing protocol to generate targeted number of reads with more than 85% coverage of the targeted regions by ≥15 reads and 90% covered by ≥10 reads.

treatment_protocol: Cells were irradiated in approximately 0.5 ml PBS in each 10 cm dish with 30 mJ/cm2 UV. Control and irradiated cells were collected at 4 or 72 hours after UV radiation.

value: neonatal foreskin

value: Cultured primary keratinocytes

value: no UVR

tag: uv dose (time/dose)


title: Nab3 glucose to glucose time course 1 time point 14


title: K3D, UV, 72h/30 mJ/cm2 (time/dose)_RNA-seq

data_processing:
For RNA-Seq, we used RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We mapped the reads to the human reference genome (NCBI/build37.2) using Tophat (version 2.0.4). We calculated the relative gene expression level using cufflinks (version 2.0.2) with default settings. We determined differentially expressed genes under various conditions using the DEseq software.
genome build: NCBI/build37.2
processed data files format and content: csv files include normalized gene expression values and differential gene expression levels in the UVR-treated versus no-UVR control samples from DESeq

extract_protocol:
Total RNA was isolated from cultured keratinocytes using the QIAGEN RNeasy Kit.
RNA libraries were prepared for sequencing using TruSeq RNA prep kit

value: UVR


title: K4H, UV, 4h/30 mJ/cm2 (time/dose)_RNA-seq


title: Rpo21 glucose to no glucose anchor away strain time course 2 time point 14

description:
UV cross-linked RNA
CRAC library
processed data file: Rpo21_Nab3-FRB_time_course_2_glu_to_noglu.txt


title: Nab3 glucose to glucose time course 1 time point 4


title: K0 Control_RNA-seq


title: Nab3 glucose to glucose time course 1 time point 0


title: Rpo21 glucose to no glucose anchor away strain time course 2 time point 1


title: Rpo21 glucose to no glucose anchor away strain time course 2 time point 40


title: Nab3 glucose to glucose time course 1 time point 8


title: Nab3 glucose to no glucose time course 1 time point 4


title: Nab3 glucose to glucose time course 1 time point 20


title: Nab3 glucose to no glucose time course 1 time point 0


title: Rpo21 glucose to no glucose anchor away strain time course 2 time point 8


title: Nab3 glucose to glucose time course 1 time point 2


title: Rpo21 glucose to no glucose anchor away strain time course 2 time point 4


title: K4H, UV, 4h/30 mJ/cm2 (time/dose)_Exome-seq

description: processed data file: K4HvsK0_EXOMESEQ.vcf


title: Mclr-2Δsah-2 replicate 3

city: Berkeley

first: Lina

last: Qin

state: California

address: 2151 Berkeley way

institute: University of Carlifornia

data_processing:
Illumina Casava1.8 software used for base calling
Sequence reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) with HiSat2 v2.0.5 with the parameters --max-intronlen 5000 --rna-strandness R --dta-cufflinks
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cufflinks v2.2.1 with the parameters --library-type fr-firststrand -u -b -G --compatible-hits-norm --max-bundle-frags=10000000
Genome_build: N. crassa OR74A genome (v12)
Supplementary_files_format_and_content: fpkm_tracking

organism: Neurospora crassa

source_name: Mycelia

growth_protocol: Vogel’s minimal medium (VMM)(38) was used to grow N. crassa. Conidia were inoculated into 100 mL liquid media at 10^6 conidia/mL and grown at 25°C on a rotary shaker (200 rpm) for 16 hrs and than transfer into anothrer 100mL fresh VMM media for 24 hrs.

extract_protocol:
Mycelia was filtered and frozen in liquid nitrogen, and RNA was harvested using Trizol reagent and purified using Qiagen RNeasy Mini Kit (Cat # 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FGSC 2489

tag: genotype/variation


title: Mclr-2Δsah-2 replicate 1


title: Nab3 Vari-X-linker Megatron data 2

description:
UV cross-linked RNA
CRAC library
processed data file: Megatron_vs_Nab3_merged_hittable.txt

source_name: Nab3 Vari-X-linker Megatron data 2


title: Rpo21 glucose to no glucose anchor away strain time course 2 time point 2


title: Mclr-2Δsah-2 replicate 2


title: Rpo21 glucose to no glucose anchor away strain time course 2 time point 20


title: Rpo21 glucose to no glucose anchor away strain time course 1 time point 20

description:
UV cross-linked RNA
CRAC library
processed data file: Rpo21_Nab3-FRB_time_course_1_glu_to_noglu.txt


title: Nab3 Vari-X-linker glucose data

source_name: Nab3 Vari-X-linker glucose data


title: Rpo21 glucose to glucose time course 1 time point 4

description:
UV cross-linked RNA
CRAC library
processed data file: Rpo21_timecourse_1_glu_to_glu.txt


title: Mclr-2 replicate 2


title: Rpo21 glucose to no glucose anchor away strain time course 1 time point 2


title: Total RNA sequencing glucose to no glucose time point 30

description:
rRNA depleted total RNA
Total RNA-seq library
processed data file: RNASeq_time_course_1_glu_to_noglu.txt


title: Mclr-2 replicate 1


title: Total RNA sequencing glucose to no glucose time point 40


title: Rpo21 glucose to no glucose anchor away strain time course 1 time point 1


title: Δsah-2 replicate 3


title: Rpo21 glucose to no glucose anchor away strain time course 1 time point 18


title: Total RNA sequencing glucose to no glucose time point 14


title: Δsah-2 replicate 2


title: Rpo21 glucose to no glucose anchor away strain time course 1 time point 0


title: Total RNA sequencing glucose to no glucose time point 4


title: Δsah-2 replicate 1


title: Rpo21 glucose to no glucose anchor away strain time course 1 time point 8


title: Treated mutant

city: Hangzhou

first: Tao

last: Li

state: Zhejiang

address: Kaixuan road

department: Institute of Nuclear-Agricultural Sciences

country: China

institute: zhejiang 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 R1 whole genome using Rockhopper 1.20 with default parameters
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: Deinococcus radiodurans R1; ASM856v1
Supplementary_files_format_and_content: RPKM values

organism: Deinococcus radiodurans

source_name: mazEF mutant

growth_protocol: D. radiodurans strains were grown in TGY media and 10 µg/ml Streptomycin was used for the mutant strain.

extract_protocol:
Total RNA was extracted using the TRIzol method. Then, Dnase I was used to digest the DNA and Ribo-Zero Magnetic Kit was used to remove the rRNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: D.radiodurans wild-type and ΔmazEF-dr cells were grown to OD600 of 0.6, and then each culture was divided in half; one half was treated with a sub-lethal MMC (15 μg/ml for 30 min) and the other untreated half was used as a control.

value: mazEF mutant

tag: treated with

value: 15 μg/ml MMC for 30 min


title: Nab3 Vari-X-linker Megatron data 1

source_name: Nab3 Vari-X-linker Megatron data 1


title: Mutant

value: none (untreated control)


title: Treated wild-type

source_name: wild type

value: wild type


title: Mclr-2 replicate 3


title: Total RNA sequencing glucose to no glucose time point 8


title: Rpo21 glucose to no glucose anchor away strain time course 1 time point 4


title: Wild type replicate 3

value: wildtype


title: Total RNA sequencing glucose to no glucose time point 1


title: Total RNA sequencing glucose to no glucose time point 0


title: Wild type replicate 1


title: Wild type replicate 2


title: SW900 transfected with 25 nM of miR-193a-3p mimic

status: Public on Apr 10 2017

city: Beijing

first: Cheng

address: No.5 Yiheyuan Road

institute: Peking University

description: total RNA without small RNA

data_processing:
Quality control was conducted by fastQC version 0.11.4
Reads were mapped by Tophat and differential expression analyses were conducted by cufflinks and customized scripts written in  R.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include p-value and log2(fold change) for comparison between two samples

source_name: Lung, Squamous cell carcinoma

extract_protocol:
48 hours post-transfection, total RNA was isolated using Ambion mirVana miRNA isolation kit without enrichment for small RNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100,000 SW900 cells were transfected with 25 nM of miR-193a-3p mimic or 25 nM of negative miRNA control (Negative control #2, Ambion).

value: Lung, Squamous cell carcinoma

tag: cell line


title: SW900 transfected with 25 nM of negative miRNA control

description: total RNA without small RNA


title: mouse_ES_RNASeq

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Drive MC 0412

department: Bioengineering

institute: University of California, San Diego

data_processing:
RNA-Seq data were mapped using TopHat with default parameters
Data were filtered to keep reads with mapping quality higher than 50
Gene expression levels were computed using cufflinks
genome build: mm9
processed data files format and content: gene expression levels in text format (Cuffdiff output)

source_name: Embryonic stem cells

growth_protocol: Undifferentiated mouse ES cells E14 was cultured under feeder-free condition, were plated onto gelatin-coated dishes in Dulbecco's modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM -mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Millipore ESG1107) in incubator set at 37 ºC in 5% CO2.

extract_protocol:
Cells were scraped off dishes and collected by centrifuge. Cross-linked chromatin complexes were isolated from the Nuclei lysis buffer and then sonicated to obtain fragments in a size range between 350-500bp. H3R26Cit antibody (ab19847) were incubated with solubilized DNA fragments overnight at 4°C. Protein A/G agarose beads (Pierce, Rockford, IL) were used to capture the antibody-chromatin complex followed by washes and elution with 1% SDS. The DNA was recovered by reversing the cross-links with 20 mM NaCl at 65°C overnight. DNA was purified by QIAquick PCR Purification Kit (Qiagen 28106) and dissolving in a final volume of 30ul per immunoprecipitation.
The Protocol of KAPA High-Throughput Library Preparation Kit (Cat. No. KK8234)

treatment_protocol: Cells were cross-linked with 1% formaldehyde for 10 min at room temperature. Fixation was subsequently inactivated by the addition of 125mM glycine.

value: Embryonic stem cells

value: ES maintianence-feeder free

tag: chip-antibody


title: KD_E14_H3K27Ac_ChIP-seq

data_processing:
Paired-end ChIP-Seq data were aligned to the mm9 genome assembly using Bowtie2 version 2.1.0 with maximum fragment length = 1,000; single-end ChIP-Seq data were mapped using bowtie2 with default parameters
Data were filtered to remove PCR duplicates using samtools rmdup
Data were filtered to keep reads with mapping quality higher than 5.
Paired end data were filtered to keep reads mapped in proper pair.
Peaks were called using MACS14 (1.4.0beta) with default parameters. IgG data for peak calling: GSM881345.
genome build: mm9
processed data files format and content: peak files in BED format

tag: treatment

value: Smarcad1 RNAi


title: mouse_ES_Smarcad1_KD_RNASeq


title: PADI_inhibition_H3K9me3_ChIP-Seq

value: CI-Amidine treatment


title: Liver

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the mm10 genome using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

source_name: Hepatic Kupffer cells

extract_protocol:
The cells were FACS-sorted as CD11b+F4/80+Ly6G-Ly6C- cells.  Total RNA purified from sorted cardiac macrophages, liver Kupffer cells, and renal macrophages was amplified using SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech).
RNA-seq libraries were prepared according to the manufacturer's protocol (Illumina).

tag: age

value: 8 weeks old


title: Heart

source_name: Cardiac tissue macrophages


title: Kidney

source_name: Renal tissue macrophages


title: female_Smarcad1_ChIP-Seq

data_processing:
Paired-end ChIP-Seq data were aligned to the mm9 genome assembly using Bowtie2 version 2.1.0 with maximum fragment length = 1,000; single-end ChIP-Seq data were mapped using bowtie2 with default parameters
Data were filtered to remove PCR duplicates using samtools rmdup
Data were filtered to keep reads with mapping quality higher than 5.
Paired end data were filtered to keep reads mapped in proper pair.
Peaks were called using MACS14 (1.4.0beta) with default parameters. IgG data for peak calling: GSM881345
genome build: mm9
processed data files format and content: peak files in BED format

value: OCT4-deltaPE-GFP x C57BL/6


title: KD_Smarcad1_ChIP-Seq


title: mouse_Blastocyst_RNA-seq

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The ChIP-seq data were mapped back into mm9 genome by Bowtie 0.12.7, with unique alignment and ≤ 1 mismatch
Raw RNA-seq data were aligned to mouse (mm9) genome using Tophat with unique alignment and ≤ 1 mismatch.  Cufflinks with default parameters was used to estimate the expression levels.
Raw MNase-seq data were mapped to mouse (mm9) and human(hg19) genome using Bowtie 0.12.7 allowing 2 mis-matches and unique alignment only.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: BED files for mapped data of Mnase-seq and ChIP-seq experiment;

source_name: Mouse Blastocyst

growth_protocol: Cells are maintained in standard mouse stem cells medium with Lif. Purimycin was added to the medium for transfected cells.

extract_protocol:
Cells are lysed in 1% SDS lysis buffer and sonicated for ChIP analysis. RNA extraction and amplification from preimplantation embryos and ICM were carried out as described before (Xie et al., 2010).
For ChIP-seq, the libraries were prepared with Illumina's 'TruSeq DNAseq Sample Prep kit'. The libraries were then pooled and quantitated by qPCR. Each pool each was sequenced on one lane for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3. For RNA-seq of ICM and blastocyst, there are two-round of RNA Amplification. The amplified RNAs were subjected to sequencing using Illumina’s small sample RNA-seq protocol.

treatment_protocol: For ChIP-seq, Cells are fixed in 1% Formaldehyde and stoped by lysine. For Mnase-seq, Chromatin was processed by optimizing a previously published protocol (Ozsolak et al., 2007) with 200 units of MNase (Worthington Biochemical Corp.) and incubation at 25 degree for 5 min, which typically yielded 80-90% mononucleosomal DNA.

value: Blastocyst


title: PADI_inhibition_Smarcad1_ChIP-Seq


title: E14_Smarcad1_ChIP-seq


title: Pmch_AAV5_vTRAP_input_rep3

first: Eric

last: Schmidt

address: 1230 York Avenue

institute: The Rockefeller University

description:
AN305_GCCAAT_L001_R1_001
Processed data file: MCH_AAV5_vTRAP_IPvInput.txt

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Differential expression was calculated by DESeq2 v1.4.5 using default settings.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include data output from DESeq2 on all genes for each sample in the analysis including: entrezID, RefSeq ID, geneName (symbol), chromosome, strand, txStart position, txEnd position, Description, normalized counts for each sample, baseMean, log2FoldChange (IP/input), lfcSE, stat, pvalue, padj.

source_name: Whole hypothalamus input RNA pooled from five mice with viral expression of EGFPL10a

extract_protocol:
Cortex or hypothalamus was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol. Total RNA from "input" samples was purified from the pre-IP tissue homogenates using the Agilent Nanoprep kit.
15 ng total RNA from TRAP IP or input was amplified using the NuGEN Ovation RNA-Seq System V2 and libraries were prepared from 10 ug amplified RNA using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer's protocols.

treatment_protocol: For vTRAP, AAV-FLEX-EGFP virus was stereotaxically injected into cortex or lateral hypothalamus of Ntsr1-Cre or Pmch-Cre mice, respectively. TRAP was performed 3-4 weeks after virus injections.

tag: strain/background

tag: tissue

value: Brain

tag: brain region

value: Hypothalamus

value: MCH neurons

tag: injection site

value: Lateral hypothalamus

tag: aav serotype

tag: rna

value: Whole tissue input


title: Pmch_AAV5_vTRAP_input_rep2

description:
AN304_TGACCA_L001_R1_001
Processed data file: MCH_AAV5_vTRAP_IPvInput.txt

tag: cell type


title: Rpo21 glucose to no glucose anchor away strain time course 1 time point 51

tag: genotype

value: HHY168:MATalpha; tor1-1; fpr1::NAT RPL13A-2xFKBP12::TRP


title: Pmch_AAV5_vTRAP_input_rep1

description:
AN302_CGATGT_L001_R1_001
Processed data file: MCH_AAV5_vTRAP_IPvInput.txt


title: Pmch_AAV5_vTRAP_IP_rep1

description:
AN307_CAGATC_L001_R1_001
Processed data file: MCH_AAV5_vTRAP_IPvInput.txt

source_name: TRAP IP RNA of pooled hypothalami from five mice with viral expression of EGFPL10a

value: TRAP IP


title: Pmch_AAV5_vTRAP_IP_rep2

description:
AN308_CTTGTA_L001_R1_001
Processed data file: MCH_AAV5_vTRAP_IPvInput.txt


title: Pmch_AAV5_vTRAP_IP_rep3

description:
AN310_CCGTCC_L001_R1_001
Processed data file: MCH_AAV5_vTRAP_IPvInput.txt


title: Wild-type

tag: strain

value: wild type

value: none (untreated control)


title: Ntsr1_AAV9_vTRAP_input_rep2

description:
659_Ntsr1_aav9TRAP_input_Rep2_GCCAAT_L008_R1_001
Processed data file: Ntsr1_AAV9_vTRAP_IPvInput.txt

source_name: Whole cortex input RNA pooled from three mice with viral expression of EGFPL10a

value: Cortex

value: Layer 6 Ntsr1 neurons

value: Sensorimotor cortex


title: Ntsr1_AAV9_vTRAP_IP_rep3

description:
657_Ntsr1_aav9TRAP_IP_Rep3_GTGAAA_L007_R1_001
Processed data file: Ntsr1_AAV9_vTRAP_IPvInput.txt

source_name: TRAP IP RNA of pooled cortices from three mice with viral expression of EGFPL10a


title: Ntsr1_AAV9_vTRAP_IP_rep2

description:
656_Ntsr1_aav9TRAP_IP_Rep2_CAGATC_L007_R1_001
Processed data file: Ntsr1_AAV9_vTRAP_IPvInput.txt


title: Ntsr1_AAV5_vTRAP_input_rep3

description:
780_Ntsr1_AAV5_input_Rep3_ATGTCA_L008_R1_001
Processed data file: Ntsr1_AAV5_vTRAP_IPvInput.txt


title: Ntsr1_AAV9_vTRAP_input_rep1

description:
658_Ntsr1_aav9TRAP_input_Rep1_ACAGTG_L008_R1_001
Processed data file: Ntsr1_AAV9_vTRAP_IPvInput.txt


title: Ntsr1_AAV5_vTRAP_input_rep2

description:
779_Ntsr1_AAV5_input_Rep2_GCCAAT_L008_R1_001
Processed data file: Ntsr1_AAV5_vTRAP_IPvInput.txt


title: Ntsr1_AAV5_vTRAP_input_rep1

description:
778_Ntsr1_AAV5_input_Rep1_ACAGTG_L008_R1_001
Processed data file: Ntsr1_AAV5_vTRAP_IPvInput.txt


title: Ntsr1_AAV5_vTRAP_IP_rep1

description:
772_Ntsr1_AAV5_IP_Rep1_ACAGTG_L006_R1_001
Processed data file: Ntsr1_AAV5_vTRAP_IPvInput.txt


title: Ntsr1_AAV5_vTRAP_IP_rep3

description:
774_Ntsr1_AAV5_IP_Rep3_ATGTCA_L006_R1_001
Processed data file: Ntsr1_AAV5_vTRAP_IPvInput.txt


title: Ntsr1_AAV5_vTRAP_IP_rep2

description:
773_Ntsr1_AAV5_IP_Rep2_GCCAAT_L006_R1_001
Processed data file: Ntsr1_AAV5_vTRAP_IPvInput.txt


title: Ntsr1_AAV2_vTRAP_input_rep2

description:
776_Ntsr1_AAV2_input_Rep2_CAGATC_L007_R1_001
Processed data file: Ntsr1_AAV2_vTRAP_IPvInput.txt


title: Ntsr1_AAV2_vTRAP_IP_rep1

description:
769_Ntsr1_AAV2_IP_Rep1_CGATGT_L008_R1_001
Processed data file: Ntsr1_AAV2_vTRAP_IPvInput.txt


title: FAIRE-seq, EpRas, siControl, untreated, 4 days

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

data_processing:
FAIRE-seq reads were aligned to the mm10 genome assembly using bowtie
MACS2 (version 2.1.0) was used to identify significantly enriched FAIRE-positive regions at q < 10e-4.
Genome_build: mm10
Supplementary_files_format_and_content: bed and bedgraph files were generated by MACS2.

growth_protocol: EpRas cells were obtained from Dr. Sabine Maschler (Research Institute of Molecular Pathology, Vienna, Austria) (Maschler et al., 2005; Oft et al., 1996) and cultured in 4% fetal bovine serum (FBS), 50 units/ml penicillin, and 50 ug/ml streptomycin. All cells were maintained in a 5% CO2 atmosphere at 37°C.

extract_protocol:
FAIRE samples were obtained based on a protocol as described previously (Giresi and Lieb, 2009; Waki et al., 2011). In brief, cells were fixed with final 1% formaldehyde for 5 min at room temperature and stopped the fixation by adding 2.5 M glycine (final 125 mM) for 5 min at room temperature. After washing fixed cells with cold phosphate-buffered saline (PBS) twice, cells were scraped with 1 ml cold PBS and centrifuged. Collected cells were lysed in 800 ul of MC lysis buffer (10 mM NaCl, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 0.5% NP-40) and incubated on ice for 10 min. After centrifuged at 8,000 rpm at 4°C for 4 min, the pellet of cells was re-suspended in 400 ul of sodium dodecyl sulfate (SDS) lysis buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, protease inhibitor [P8304; Sigma-Aldrich]) and incubated on ice for 10 min. Next, DNAs in cell lysate were sonicated 15 cycles for 30 sec each time at intervals of 30 sec with Bioruptor UCW-201 (Cosmo Bio). After centrifuged at 14,000 rpm 4°C for 10 min, we added 200 ul of ChIP dilution buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 Complete EDTA-free protease inhibitors (Roche)). Samples were centrifuged at 8,000 rpm at 4°C for 4 min. After removal of a control aliquot, supernatants were purified by phenol/chloroform extraction and reverse-crosslinked by overnight incubation at 65°C. Genomic DNA was purified by ethanol precipitation and extracted by RNase-free water after elution with a PCR purification kit (Qiagen).
Libraries were made using Ion Fragment Library Kit (Thermo Fisher Scientific) and sequenced with Ion Proton (Thermo Fisher Scientific)

treatment_protocol: Cells were transfected with Etv4 and Etv5 siRNAs and treated with 1 ng/ml of TGF-beta3 for 4 days or left untreated (culture medium supplemented with TGF-beta was changed every other day).

value: EpRas

tag: active h-ras expression

value: yes

tag: histology

value: mammary gland epithelial cells

tag: tgfb treatment

value: no

tag: sirna transfection

value: control siRNA (12935-112, Thermo Fisher Scientific)


title: Ntsr1_AAV2_vTRAP_IP_rep3

description:
771_Ntsr1_AAV2_IP_Rep3_GTGAAA_L008_R1_001
Processed data file: Ntsr1_AAV2_vTRAP_IPvInput.txt

value: Brain


title: Ntsr1_bacTRAP_input_rep2

description:
34_Cortex_Input_2_CAGATC_L005_R1_001
Processed data file: Ntsr1_bacTRAP_IPvInput.txt

source_name: Whole cortex input RNA pooled from three mice with transgenic expression of EGFPL10a


title: Ntsr1_AAV2_vTRAP_IP_rep2

description:
770_Ntsr1_AAV2_IP_Rep2_CAGATC_L008_R1_001
Processed data file: Ntsr1_AAV2_vTRAP_IPvInput.txt


title: FAIRE-seq, EpRas, siEtv4/5 set 1, TGF-beta treated, 4 days

source_name: FAIRE-seq_EpRas_siEtv4/5 set_TGF-beta treated_4 days

tag: cell line

value: Etv4 and Etv5 siRNAs set 1 (MSS237548 and MSS272298, Thermo Fisher Scientific)


title: Ntsr1_AAV2_vTRAP_input_rep1

description:
775_Ntsr1_AAV2_input_Rep1_CGATGT_L007_R1_001
Processed data file: Ntsr1_AAV2_vTRAP_IPvInput.txt


title: FAIRE-seq, EpRas, siControl, TGF-beta treated, 4 days


title: Ntsr1_bacTRAP_IP_rep1

description:
661_Ntsr1_bacTRAP_IP_Rep1_CGATGT_L003_R1_001
Processed data file: Ntsr1_bacTRAP_IPvInput.txt

source_name: TRAP IP RNA of pooled cortices from three mice with transgenic expression of EGFPL10a


title: Ntsr1_AAV9_vTRAP_IP_rep1

description:
655_Ntsr1_aav9TRAP_IP_Rep1_CGATGT_L007_R1_001
Processed data file: Ntsr1_AAV9_vTRAP_IPvInput.txt


title: Ntsr1_bacTRAP_IP_rep2

description:
662_Ntsr1_bacTRAP_IP_Rep2_CAGATC_L003_R1_001
Processed data file: Ntsr1_bacTRAP_IPvInput.txt


title: Ntsr1_AAV9_vTRAP_input_rep3

description:
660_Ntsr1_aav9TRAP_input_Rep3_ATGTCA_L008_R1_001
Processed data file: Ntsr1_AAV9_vTRAP_IPvInput.txt


title: Ntsr1_bacTRAP_input_rep1

description:
33_Cortex_Input_1_CGATGT_L004_R1_001
Processed data file: Ntsr1_bacTRAP_IPvInput.txt


title: FAIRE-seq, EpRas, TGFB treated, 8 days, replicate 2

data_processing:
FAIRE-seq reads were aligned to the mm10 genome assembly using bowtie2
MACS2 (version 2.0.9) was used to identify significantly enriched FAIRE-positive regions at p < 10e-5.
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated by MACS2. wig files were generated using CisGenome v2.0.

source_name: EpRas

growth_protocol: The EpH4 mouse mammary gland epithelial cells and their H-Ras-transformed derivative EpRas cells were obtained from Dr. Sabine Maschler (Research Institute of Molecular Pathology, Vienna, Austria) (Maschler et al., 2005; Oft et al., 1996) and cultured in F12/DMEM containing 10% (for EpH4) or 4% (for EpRas) fetal bovine serum (FBS), 50 units/ml penicillin, and 50 ug/ml streptomycin. All cells were maintained in a 5% CO2 atmosphere at 37°C.

treatment_protocol: Cells were treated with 1 ng/ml of TGF-beta3 for 8 days or left untreated (culture medium supplemented with TGF-beta was changed every other day and cells were split every 4 days).


title: FAIRE-seq, EpRas, untreated, 8 days, replicate 2


title: FAIRE-seq, EpRas, TGFB treated, 8 days, replicate 1


title: FAIRE-seq, EpH4, TGFB treated, 8 days, replicate 2


title: Ntsr1_AAV2_vTRAP_input_rep3

description:
777_Ntsr1_AAV2_input_Rep3_GTGAAA_L007_R1_001
Processed data file: Ntsr1_AAV2_vTRAP_IPvInput.txt


title: FAIRE-seq, EpRas, siEtv4/5 set 2, TGF-beta treated, 4 days

value: Etv4 and Etv5 siRNAs set 2 (MSS237550 and custom-made (5'-UUAAAUUCCAUGCCUCGGCCAGUCC-3'), Thermo Fisher Scientific)


title: FAIRE-seq, EpH4, untreated, 8 days, replicate 2


title: WT_P0_Cochlea_SensoryEpithelium_3

city: Tel Aviv

first: Karen

middle: B

last: Avraham

address: Levanon St.

department: Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

description: Total RNA  from at least 20 cochleae were pooled and hybridized.

data_processing:
Paired-end alignment with tophat2 (v2.1.0).
Sorting BAM by read names using samtools program (v0.1.18).
Counting reads with htseq-count (v0.5.4p5) with parameters: "-s no -a 10".
Filtering only the genes that have one read per million in three or more of the samples.
Calculating RPKM using edgeR (v3.4.2). Gene length was calculated as the sum of lengths of all exons, from the genome build's GTF file.
Genome_build: Mus_musculus.GRCm38.74
Supplementary_files_format_and_content: *.count - Count data for each sample.; expression_matrix.csv - RPKM values for all filtered genes across all samples.

source_name: Mouse P0 cochlear sensory epithelium

extract_protocol:
Sensory epithelia from 20 cochlea or 20 vestibule were removed and RNA was harvested using QIAgen’s RNeasy micro kit.
Illumina TruSeq® Stranded mRNA Sample Preparation Kit (Cat# RS-122-2101) was used with 450 ng of total RNA for the construction of sequencing libraries.

tag: Sex

value: pooled male and female

value: newborns (P0)

value: cochlear sensory epithelium


title: WT_P0_Cochlea_SensoryEpithelium_2


title: FAIRE-seq, EpH4, TGFB treated, 8 days, replicate 1


title: WT_P0_Vestibule_SensoryEpithelium_3

description: Total RNA  from at least 20 vestibules were pooled and hybridized.

source_name: Mouse P0 vestibular sensory epithelium

value: vestibular sensory epithelium


title: WT_P0_Cochlea_SensoryEpithelium_1


title: WT_P0_Vestibule_SensoryEpithelium_1


title: RNA-seq, EpRas, si Etv4_1 and Etv5_1, 48 h

data_processing:
RNA-seq reads were trimmed down to 80 bp and Tophat2 (2.0.11) and Bowtie2 (2.2.2.2) were used. Parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G.
FPKM calculation was performed by using Cuffdiff (cufflinks version 2.2.0 with options -m 200 -u).
Genome_build: mm10
Supplementary_files_format_and_content: Expression data of the samples were summarized into two processed files by Cuffdiff. Gene-level expressions of siRNA-untransfected samples are in genes.fpkm_tracking_9-16_80.txt and that of siRNA-transfected samples were in genes.fpkm_tracking_3-8-80.txt.

molecule: polyA RNA

extract_protocol:
Total RNAs were extracted from EpH4 and EpRas cells using the RNeasy Mini Kit (Qiagen) and Dnase-treated.
siRNA-untransfected samples and siRNA-transfected samples were processed independently. mRNA was purified using Dynabeads mRNA DIRECT Purification Kit. Libraries were made using Ion Total RNA-Seq Kit v2 and directionally sequenced with the Ion Proton using Ion PI chip v2, Ion Proton IC200 kit, as described (Isogaya et al., Cell Res, 2014; Mizutani et al., 2016, Oncogene).

treatment_protocol: Cells were treated with 1 ng/ml of TGF-beta3 for 48 h or left untreated.

tag: sirna

value: Etv4/5 siRNAs (MSS237548 and MSS272298, Thermo Fisher Scientific)

tag: tgf-beta treatment

value: mammary gland epithelial cell


title: RNA-seq, EpRas, si Etv4_2 and Etv5_2, TGFB treated, 48 h

value: Etv4/5 siRNAs (Etv4:MSS237550, Etv5:custum made(5'-UUAAAUUCCAUGCCUCGGCCAGUCC-3'), Thermo Fisher Scientific)


title: RNA-seq, EpRas, si Negative control, TGFB treated, 48 h


title: RNA-seq, EpRas, si Etv4_2 and Etv5_2, 48 h


title: FAIRE-seq, EpH4, untreated, 8 days, replicate 1


title: RNA-seq, EpRas, si Etv4_1 and Etv5_1, TGFB treated, 48 h


title: FAIRE-seq, EpRas, untreated, 8 days, replicate 1


title: E14 H3R26Cit ChIP-Seq

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.1.0 with maximum fragment length = 1,000
Data was filtered to remove PCR duplicates using samtools rmdup
Data was filtered to keep read mapped in proper pair
Peaks were called using MACS14 (1.4.0beta) with p-value=1e-4. IgG data for peak calling: GSM881345.
Genome_build: mm9
Supplementary_files_format_and_content: peak file in BED format.

value: Embryonic stem cells

tag: treatment

tag: chip antibody

value: H3R26Cit antibody (ab19847)


title: RNA-seq, EpRas, si Negative control, 48 h

value: EpRas


title: RNA-seq, EpRas, TGFB treated, 48 h, replicate 1

value: yes


title: RNA-seq, EpH4, TGFB treated, 48 h, replicate 2


title: WT_P0_Vestibule_SensoryEpithelium_2

tag: age

tag: tissue


title: RNA-seq, EpRas, untreated, 48 h, replicate 1


title: RNA-seq, EpH4, TGFB treated, 48 h, replicate 1


title: RNA-seq, EpRas, TGFB treated, 48 h, replicate 2


title: RNA-seq, EpRas, untreated, 48 h, replicate 2


title: Etv5 ChIP-seq, EpRas cells

description: ChIP antibody: Etv5

data_processing:
ChIP-seq reads were trimmed down to 36 bp and aligned to the mm10 genome assembly using bowtie.
One-sample analysis of CisGenome v2 was used for peak calling (sliding window length: 300 bp, p < 0.1).
Genome_build: mm10
Supplementary_files_format_and_content: bed (peak positions at p<0.1) and wig format files.

growth_protocol: EpRas cells were obtained from Dr. Sabine Maschler (Research Institute of Molecular Pathology, Vienna, Austria) and cultured in F12/DMEM containing 4% (for EpRas) fetal bovine serum (FBS), 50 units/ml penicillin, and 50 ug/ml streptomycin. All cells were maintained in a 5% CO2 atmosphere at 37C.

extract_protocol:
ChIP were performed as described (Koinuma et al, Mol Cell Biol 29: 172-186, 2009). Etv4/Etv5-DNA complexes were isolated with anti-Etv4/Etv5 antibodies. Rabbit polyclonal anti-Etv4 antibody, previously used for ChIP-seq by Hollenhorst et al. Genes Dev 25, 2011, was from AVIVA Systems Biology (ARP32263, San Diego, CA, USA), and mouse monoclonal anti-Etv5 antibody (MAB7107) was from R&D Systems. Lot number not available.
Libraries were prepared as described (Murai et al, Cell Discovery 1: 15026, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

treatment_protocol: Cells were treated with 1 ng/ml of TGF-beta3 for 1.5 h.


title: RNA-seq, EpH4, untreated, 48 h, replicate 2


title: RNA-seq, EpH4, untreated, 48 h, replicate 1


title: Etv4 ChIP-seq, EpRas cells

description: ChIP antibody: Etv4


title: n3122 60 DPA rep1

city: Shanghai

first: Lei

last: Gao

address: Dongchuan Road No. 800

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava software used for basecalling.
Raw reads were screened by FASTX-Toolkit to remove adaptor sequences and low-quality regions. The remaining high-quality reads were mapped to tomato reference genome (ITAG2.3) using TopHat (version 2.0)
fragments per kilobase of exon per million fragments mapped (FPKM) calculated by Cufflinks (http://cufflinks.cbcb.umd.edu/).
Genome_build: Solanum lycopersicum reference genome (ITAG2.3); http://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample  in each pairwise comparison (the gene locus can be traceable in Sol Genomics Network (https://solgenomics.net/search/locus)

organism: Solanum lycopersicum

source_name: n3122 60 DPA_fruit pericarps

growth_protocol: Plants were grown in a greenhouse at at Pujiang experimental base, Shanghai Jiao Tong University, Shanghai, China.

extract_protocol:
RNA was extracted using  RNAprep pure Plant Kit (Cat#DP441). Sequencing libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar background

tag: developmental stage

value: 60 DPA

tag: genotype/variation

value: Mutant

tag: phentoype

value: yellow-fruited mutant

value: fruit pericarps


title: n3122 54 DPA rep2

source_name: n3122 54 DPA_fruit pericarps

value: 54 DPA


title: n3122 54 DPA rep1


title: n3122 60 DPA rep2


title: n3122 35 DPA rep1

source_name: n3122 35 DPA_fruit pericarps

value: 35 DPA


title: M82 54 DPA rep2

source_name: M82 54 DPA_fruit pericarps

value: Wild Type

value: red-fruited tomato


title: n3122 47 DPA rep2

source_name: n3122 47 DPA_fruit pericarps

value: 47 DPA


title: M82 47 DPA rep2

source_name: M82 47 DPA_fruit pericarps


title: M82 35 DPA rep2

source_name: M82 35 DPA_fruit pericarps


title: M82 54 DPA rep1


title: M82 47 DPA rep1


title: Liver T3 2

city: Querétaro

first: Aurea

last: Orozco Rivas

state: Querétaro

address: Boulevard Juriquilla 3001

department: Neurobiología Celular y Molecular

country: Mexico

institute: Instituto de Neurobiología, UNAM

data_processing:
Quality Control (QC) of raw reads was performed using FASTQC software and contamination and adapter removal was carried out using in-house Perl scripts.
QC’ed reads were mapped using the Bowtie 1.1.2 aligner to the Oreochromis_niloticus (Orenil1.0.cds.all) coding sequences downloaded using BioMart from Ensembl repository database.
Quantification and repetitiveness was carried using eXpress software 1.5). Total effective counts for each sample were merged; a matrix was generated using the “abundance_estimates_to_matrix.pl” Perl script included in the Trinity pipeline.
DEG analysis was performed using R Bioconductor tool edgeR through the “run_DE_analysis.pl” script from Trinity and the merged count matrix. Pairwise comparisons among each sample type (Control vs T2 or Control vs T3, each with its respective biological replicate) were performed. To determine DEG, a False Discovery Rate (FDR) of adjusted p < 0.05 was used.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oreochromis niloticus

source_name: Liver T3 2

extract_protocol:
Total RNA was extracted from brain regions and liver tissues with TRIzol (Invitrogen)
Libraries were generated using Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s instructions

treatment_protocol: All fish treatments were performed following an immersion protocol and treatment conditions were 25 nM of T2 or T3 and 12 h of exposure

value: Liver

value: Juvenil (4 month)


title: mouse_ICM_RNA-seq

source_name: Mouse Inner Cell Mass

tag: cell type

value: Inner Cell Mass


title: M82 35 DPA rep1


title: Liver T2 2

source_name: Liver T2 2


title: Liver Control 2

source_name: Liver Control 2

value: Control (non treated)


title: Liver T2 1

source_name: Liver T2 1


title: Thalamus-pituitary T3 1

source_name: Thalamus-pituitary T3 1

value: Thalamus-pituitary


title: Thalamus-pituitary T3 2

source_name: Thalamus-pituitary T3 2


title: Liver T3 1

source_name: Liver T3 1


title: 275aM (P/sf) P1 Hamster

city: Antwerp

first: Hideo

last: Imamura

state: Antwerp

address: Nationalestraat 155

country: Belgium

institute: Institute of Tropical Medicine, Antwerp

data_processing:
Standard Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to the Leishmania donovani reference using smalt 7.4
Reads per gene was extracted from read depth: ploidy normalization was performed based on median read depth
Deseq was used for the differential expression analysis
Genome_build: Leishmania donovani BPK282
Supplementary_files_format_and_content: tab-delimited text files include read count per gene values for each sample in one file

organism: Leishmania donovani

source_name: Leishmania donovani

extract_protocol: RNASeq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep kit according to the manufacturer’s standard protocol apart from the PCR amplification, which was performed using KAPA Hifi Polymerase. 75 base pair paired-end reads were generated on the HiSeq 2000 v4 according to the manufacturer’s standard sequencing protocol.

tag: strain

tag: parasite developmental stage

value: Amastigotes

tag: host cell type

value: spleen extract

tag: genotype


title: 275ProM (I) R33

value: Promastigotes

value: cell culture


title: Thalamus-pituitary T2 1

source_name: Thalamus-pituitary T2 1


title: 275ProM (P) Sandfly 2


title: n3122 47 DPA rep1

value: Mutant


title: Thalamus-pituitary T2 2

source_name: Thalamus-pituitary T2 2


title: Liver Control 1

source_name: Liver Control 1


title: Thalamus-pituitary Control 1

source_name: Thalamus-pituitary Control 1


title: Thalamus-pituitary Control 2

source_name: Thalamus-pituitary Control 2


title: aM (P/sf) P1 Hamster


title: Cerebellum T3 2

source_name: Cerebellum T3 2

value: Cerebellum


title: ProM (P) Sandfly 3


title: Cerebellum T3 1

source_name: Cerebellum T3 1


title: ProM (A) R10


title: Cerebellum T2 2

source_name: Cerebellum T2 2


title: aM P4 Hamster


title: Cerebellum Control 1

source_name: Cerebellum Control 1


title: WT_xylose_3

status: Public on Apr 09 2017

first: Yi

last: Xiong

address: 341A Koshland Hall

department: Plant and Microbial Bioloby

institute: UC berkeley

data_processing:
The sequencing reads that passed filtering from the CASAVA 1.8 FASTQ files from Illumina sequencer were subjected to quality score checking using the FASTX-Toolkit. Only reads with all bases scoring greater than 22 were used to map against predicted transcripts from the N. crassa OR74A genome v12 with Tophat v2.0.4. (Tophat options :-N --max-intron-length 1000 -u -G -b)
For differential gene expression analysis, the bam files were first processed using the HTSeq package v0.6.0 to generate raw counts (option: --stranded=no).
The raw counts are subjected to differential analysis using the DESeq2 package version 1.10.1
Genome_build: N. crassa: OR74A version 12 from the Broad Institute
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: wild type_xylose_mycelia

growth_protocol: N. crassa strains were innoculated in 3 mL VMM with 2% sucrose, grown 16 hours at 25ºC 200 rpm and constant light. Mycelia were washed twice in media with VMM-NC and resuspended in VMM-NC, then grown for an additional 4 hours at 25ºC with shaking at 200 rpm and constant light.

extract_protocol:
Mycelia were harvested by filtration and flash frozen in liquid nitrogen. Total RNA was extracted by bead-beating in TRIZOL reagent and purified with RNeasy kit from Qiagen.
Total RNA starting material was 1 µg per sample and 10 cycles of PCR was used for library amplification. The prepared libraries were then quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. The quantified libraries were then multiplexed into pools of 9 libraries, and the pool was then prepared for sequencing on the Illumina HiSeq2000 sequencer.

value: FGSC 2489

value: wild type

tag: carbon source

value: xylose

value: mycelia


title: ProM (I) R20


title: WT_xylose_2


title: aM P3 Hamster


title: Cerebellum Control 2

source_name: Cerebellum Control 2


title: WT_xylose_1


title: WT_xyloglucan_3

source_name: wild type_xyloglucan_mycelia

value: xyloglucan


title: WT_trehalose_3

source_name: wild type_trehalose_mycelia

value: trehalose


title: KD_E14_H3K4me3_ChIP-seq

source_name: E14 cells with SMARCAD1 knockdown

value: Embryonic stem cells

tag: cell line

value: shRNA targeting Smarcad1 mRNA

tag: antibody

value: H3K4me3 (Abcam, Ab8580)


title: WT_trehalose_2


title: WT_trehalose_1


title: WT_sorbose_3

source_name: wild type_sorbose_mycelia

value: sorbose


title: WT_sorbose_2


title: n3122 35 DPA rep2

source_name: n3122 35 DPA_fruit pericarps

value: 35 DPA

value: yellow-fruited mutant

value: fruit pericarps


title: ProM (A) R3

source_name: Leishmania donovani

value: Promastigotes


title: WT_mannose_2

source_name: wild type_mannose_mycelia

value: mannose


title: Cerebellum T2 1

source_name: Cerebellum T2 1

value: Juvenil (4 month)


title: RB1-/- B-derived Teratoma (2)

city: Jerusalem

first: Yishai

last: Avior

state: Israel

address: Edmond J. Safra Campus, Givat Ram

department: Genetics

institute: Hebrew University of Jeursalem

data_processing:
Reads were mapped to the human reference genome (GRCh38/hg38) using Tophat (version 2.0.4)
Human embryonic stem cell expression values were obtained and normalized using HTSeq (Anders et al., 2015) and DESeq2 (Love et al., 2014). Batch-effect removal was performed using SVseq2.
In the teratoma-derived data, fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated using Cufflinks (version 2.0.2)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: hESC data: Tab-delimited text file includes FPKM values for each sample; Teratoma data: Tab-delimited text file includes relative expression values for each sample

source_name: Teratoma

extract_protocol:
RNA was isolated using NucleoSpin RNA Plus kit (Macherey-Nageland). For RNA sequencing analysis, poly(A) pull-down was used to enrich mRNAs from total RNA samples (200 ng–1 µg per sample, RIN > 9)
Libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina)

tag: group


title: KD_E14_H3K9me3_ChIP-seq

tag: treatment

value: H3K9me3 (Abcam, ab8898)


title: WT_sorbose_1

value: FGSC 2489


title: RB1-/- B-derived Teratoma (1)


title: WT_maltose_3

source_name: wild type_maltose_mycelia

value: wild type

value: maltose


title: WT_xyloglucan_2

value: mycelia


title: RB1-/- A-derived Teratoma


title: Control B-derived Teratoma

value: Control


title: Control A-derived Teratoma


title: WT_maltose_1


title: WT_glycerol_3

source_name: wild type_glycerol_mycelia

value: glycerol


title: RB1-/- A

source_name: Human embryonic stem cells


title: WT_maltose_2


title: Control B (CSES7, Cas9 No guide)


title: WT_glycerol_2


title: RB1-/- B


title: RB1-/- C


title: Control A (CSES7)


title: WT_mannose_3


title: WT_glycerol_1


title: WT_fructose_3

source_name: wild type_fructose_mycelia

value: fructose


title: WT_mannose_1


title: WT_fructose_2


title: IL-1R8-/-_Anakinra_3_L2

city: San Joan d'Alacant

first: Jose

middle: P

last: Lopez-Atalaya

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias

country: Spain

institute: CSIC-UMH

data_processing:
Sequencer: Illumina HiSeq 2500 (SND00104). Basecalling pipeline: HiSeq Control Software 2.2.38; RTA 1.18.61.0; CASAVA 1.8.2.
Run: Mode HiSeq High-Output (HO) Version 4. Number of cycles: 2x125+7; Number of lanes: 2; Flow cell version: HiSeq Flow Cell v4; Kit version: TruSeq SBS Kit v4. Yield (Gb): 55; Error rate: 1.5%; Q30: 80%.
Sequenced reads were trimmed for adapter sequence using Trimmomatic v0.32, and then mapped to the mouse genome (build GRCm38/mm10) using bowtie 2 v2.0.5 and TopHAT v2.0.6. SAM/BAM files were further processed using SAMTOOLS v1.2
Read count quantitations were obtained using Seqmonk (0.26.0). Normalization of read counts and differential expression analysis between genotypes was carried out using DESeq2 R package from Bioconductor (Release 2.13).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include Ensmbl gene identifiers (ENSMUSG) and raw counts.

source_name: cerebral cortical tissue of adult mice

extract_protocol:
Total cortical RNA was extracted with TRI reagent (Sigma) and subsequently treated with DNaseI (Qiagen) and precipitated using potassium acetate. To prepare each sample equal amounts of purified total RNA from 3 mice were pooled together. 3 samples (biological replicates) per genotype were sequenced in HiSeq 2500 apparatus (Illumina). Service provided by Fasteris S.A.
Paired-End stranded RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Prep Kit). Service provided by Fasteris S.A.

value: Anakinra (25 mg/kg per day for 3 consecutive days, i.p. administration)

tag: flow cell lane

value: lane 2

value: Adult mice (3-month-old)


title: WT_fructose_1


title: WT_cellobiose_2

source_name: wild type_cellobiose_mycelia

value: cellobiose


title: IL-1R8-/-_Anakinra_1_L2

tag: age


title: IL-1R8-/-_Anakinra_2_L2


title: WT_cellobiose_3

tag: tissue


title: WT_xyloglucan_1

value: xyloglucan


title: WT_cellobiose_1


title: IL-1R8-/-_NT_3_L2

value: Non-treated


title: WT_avicel_3

source_name: wild type_avicel_mycelia

value: avicel


title: WT_avicel_2


title: IL-1R8-/-_NT_2_L2


title: IL-1R8-/-_NT_1_L2


title: WT_IL1b_3_L2

value: Wild-type

value: IL1b (200 ng/mouse, 14h)


title: WT_avicel_1


title: WT_IL1b_2_L2


title: WT_IL1b_1_L2


title: WT_NT_2_L2


title: [delta]col-26 maltose #2

description: HiSeq-2000 1x50, barcode CTTGTA

source_name: mycelia

growth_protocol: N. crassa strains were innoculated in 3 mL VMM-2% cellobiose, grown 28 hours at 25ºC 200 rpm and constant light. Mycelia were washed once with VMM-NC followed by a 18-hour grown in VMM-NC, then resuspend in VMM-2% maltose and grown for 5.5 hours at 25ºC with shaking at 200 rpm and constant light.

tag: media


title: WT_NT_3_L2


title: WT amylopectin #3

growth_protocol: N. crassa strains were innoculated in 3 mL VMM with 2% sucrose, grown 16 hours at 25ºC 200 rpm and constant light. Mycelia were washed twice in media with VMM-NC and resuspended in VMM-1% amylopectin, then grown for an additional 4 hours at 25ºC with shaking at 200 rpm and constant light.

value: amylopectin


title: [delta]col-26 maltose #3

description: HiSeq-2000 1x50, barcode CATTTT


title: [delta]col-26 maltose #1

description: HiSeq-2000 1x50, barcode GCCAAT


title: WT amylopectin #2

value: FGSC 2489


title: WT_NT_1_L2


title: GEK90

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Vernicia fordii

source_name: mature seeds

growth_protocol: fruits from V. fordii plants growth in an open environment were collected at 100-120 (mature seeds) days after flower opening (DAF). Seeds were dissected from fruits and immediately frozen in liquid nitrogen and stored at -80 °C.

extract_protocol: Total RNA was isolated from the seed material using Trizol (Invitrogen, CA, USA) according to the manufactures’ protocol, and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing and sequencing by Illumina HiSeq2000. Three libraries were generated from immature, intermediate and mature seeds. Briefly, the polyadenylated transcript sequencing (mRNA-seq) was performed using the following successive steps: Poli-A purification, cDNA synthesis using Poli-T primer shotgun to generate inserts of 500 nt, 3p and 5p adapters ligations, pre-amplification, colony generation and sequencing. The Illumina output data were sequence tags of 100 bases.

tag: sample

value: pool

tag: daf


title: WT amylopectin #1

value: wild type


title: WT amylose #3

growth_protocol: N. crassa strains were innoculated in 3 mL VMM with 2% sucrose, grown 16 hours at 25ºC 200 rpm and constant light. Mycelia were washed twice in media with VMM-NC and resuspended in VMM-1% amylose, then grown for an additional 4 hours at 25ºC with shaking at 200 rpm and constant light.

value: amylose


title: WT amylose #2


title: IL-1R8-/-_Anakinra_2_L1

value: lane 1


title: IL-1R8-/-_NT_3_L1


title: IL-1R8-/-_Anakinra_1_L1


title: WT amylose #1


title: K3D, UV, 72h/30 mJ/cm2 (time/dose)_Exome-seq

description: processed data file: K3DvsK0_EXOMESEQ.vcf

data_processing:
Library strategy: Exome-Seq
For Exome-Seq, reads were mapped to the NCBI/build37.2 genome using the BWA algorithm. Mapped reads were sorted and indexed using the Samtools program. UV-induced somatic mutations between the paired UV-4h vs. control or UV-72h vs. control were called using Samtools mpileup and bcftools.
genome build: NCBI/build37.2
processed data files format and content: For Exiome-Seq, vcf files include the genetic variants that are different between the UVR-treated versus no-UVR control samples.

source_name: neonatal foreskin

extract_protocol:
Genomic DNA was isolated from UV-irradiated and control samples using the Wizard Genomic DNA Purification Kit (Promega).
Exome-Seq was performed at the Columbia Genome Center following standard Illumina TruSeq multiplexing protocol to generate targeted number of reads with more than 85% coverage of the targeted regions by ≥15 reads and 90% covered by ≥10 reads.

value: neonatal foreskin

value: Cultured primary keratinocytes

value: UVR

tag: uv dose (time/dose)


title: WT maltose #3

description: HiSeq-2000 1x50, barcode ACAGTG

value: maltose


title: IL-1R8-/-_NT_1_L1

value: Adult mice (3-month-old)


title: WT Sucrose #3

growth_protocol: N. crassa strains were innoculated in 3 mL VMM with 2% sucrose, grown 16 hours at 25ºC 200 rpm and constant light. Mycelia were washed twice in media with VMM-NC and resuspended in VMM-2% sucrose, then grown for an additional 4 hours at 25ºC with shaking at 200 rpm and constant light.

value: sucrose


title: WT_IL1b_3_L1


title: WT_IL1b_2_L1


title: WT_IL1b_1_L1


title: WT Sucrose #1


title: WT_NT_3_L1


title: IL-1R8-/-_Anakinra_3_L1

value: Anakinra (25 mg/kg per day for 3 consecutive days, i.p. administration)


title: [delta]col-26 amylose #3


title: P6

city: Guangzhou

first: Zhi

last: Xie

address: 54 South Xianlie Road, Guangzhou, China

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

data_processing:
The PA-seq sequencing reads of 42 bp in length were mapped to the Mus musculus genome (mm10, downloaded from UCSC) using BWA (version 0.7.5a-r405) allowing a maximum of two mismatches and no gaps.
The duplicated reads were discarded, and the alignments with mapping quality ≥20 were kept.
The F-seq was applied to find pA peaks with a feature length of 30 bp and a fragment length of 1 bp.
The peak sites were filtered with a minimum enrichment score of 3 and a minimum number of tags of 40.
In order to remove the effects of internal priming, the number of As in the downstream 20-nucleotide (nt) region of the identified sites were counted and the sites with fewer than 12 As were kept.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each pA sites at each developmental stage.

source_name: retina tissue

extract_protocol:
Total RNA was extracted from collected retinas using the TRIzol reagent (Invitrogen) according to the manufacturer’s instruction.
DNA-free total RNA was sheared into 200–300 nt fragments by heating (94°C for 3 minutes) with magnesium. Sheared RNA was precipitated by ethanol with GlycoBlue (Ambion) as a carrier. Reverse transcription was carried out using a modified oligo(dT) primer (5'-bio-TTTTTTTTTTTTTTTTdUT TTVN-3', ‘bio’ denotes duo biotin group, ‘dU’ stands for deoxyuricile, ‘V’ represents any nucleotide except T and ‘N’ denotes any nucleotide). Incubate the reverse transcription reaction at 42°C for 2 min before adding Superscript reverse transcriptase II (Invitrogen) to increase specificity. After second strand synthesis, Dynabeads MyOne C1 (Invitrogen) was used to pull down the resulting dsDNA. Incubate the beads with APex Heat-Labile Alkaline Phosphatase (Epicentre) to remove phosphate group, which enables strand specificity at the later PCR step since only the bottom strand cDNA can be ligated and thus amplified. To release dsDNA from MyOne beads, USER enzyme (NEB) was added. The released dsDNA was then end repaired, followed by adding an ‘A’ base at the ends. Illumina paired-end Y linker was ligated and size selected. A 16- cycle PCR was then carried out with Phusion Hot Start High-Fidelity DNA Polymerase (Finnzymes) to generate the final PA-seq libraries.

value: retina

tag: developmental stage

value: Postnatal day P6


title: [delta]col-26 amylose #2

tag: strain


title: WT No Carbon #3

value: no carbon


title: P21

value: Postnatal day P21


title: WT_NT_1_L1

value: Wild-type

value: Non-treated


title: WT No Carbon #1

value: FGSC 2489


title: E18.5

value: Embryonic day 18.5


title: WT_NT_2_L1


title: TRZT22_2; ZT22, total RNA, rep2

status: Public on Apr 08 2017

city: Lausanne

first: David

last: Gatfield

address: Genopode

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

description:
total RNA
total RNA

data_processing:
Base-calling: Casava 1.82
Adapter trimming: Adapter sequences were removed using cutadapt utility with following options: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --match-read-wildcards -m 6
Insert size filtering: Trimmed read sequences were filtered by their size using an in-house Python script with following inclusive ranges: [26,35] for footprints, [21,60] for total RNA
Alignment: Trimmed and filtered insert sequences were mapped sequentially to following databases: mouse rRNA, human rRNA, mt-tRNA, mouse tRNA, mouse cDNA (Ensembl.v.75) and mouse genome (GRCm38.p2). All but last one were mapped using bowtie (version 2.2.1) using following parameters: -p 2 -L 15 -k 20 –no-unal. Mapping against genomic sequence was performed using tophat (v2.0.11) with following parameters: --transcriptome-index=Mmusculus.GRCm38.75.dna.ensembl_data -p 2. After each alignment, only reads that were not aligned were used in the following mapping. For further analysis (processed data files), only alignments against mouse cDNA were used. Separately from this alignment strategy, each query set was also directly aligned against mouse genome using tophat with similar parameters (“global tophat”).
Post-alignment filtering: For each query sequence, only alignments with maximum score were kept. The output of “global tophat” alignment was used to estimate expressed transcript models using cufflinks (v2.2.1) with following parameters: --GTF Mus_musculus.GRCm38.75.gtf --frag-len-mean 37 --frag-len-std-dev 8 --compatible-hits-norm --multi-read-correct --upper-quartile-norm --frag-bias-correct Mmusculus.GRCm38.75.dna.ensembl.fa -p 3. Transcript FPKM estimates from all samples were merged using cuffcompare with following parameters: -r Mus_musculus.GRCm38.75.gtf -R -V. Resulting FPKM tracking information was parsed with an in-house Python script to filter out transcripts which were not found to have an FPKM > 0.1, a LOW95 > 0.05 and a FMI > 2.0 in at least 3 samples. A database of expressed transcripts was used in further analysis.
Abundance measurement: mRNA and RPF (ribosome protected fragment) levels were estimated per locus. An in-house Python script was used to count uniquely (by gene) mapped reads within each annotation feature (5'UTR, CDS, 3'UTR). For multi-isoform loci, preference order used was CDS, 5'UTR, 3'UTR.
Normalization: Read counts of total RNA and RPF were normalized with upper quantile method of R package edgeR. Prior to normalization, transcripts which did not have at least 10 counts in at least one fourth of the samples were removed from the datasets.
Normalization: RPKM values were calculated as the number of counted reads per 1000 mappable and countable bases per geometric mean of normalized read counts per million.
Genome_build: Genome Reference Consortium GRCm38.p2 (mm10)
Supplementary_files_format_and_content: rpkm files were generated with R; gene IDs are ENSEMBL-IDS

source_name: kidney

extract_protocol:
Kidneys were homogenized in 3 volumes of lysis buffer (150 mM NaCl, 20 mM Tris-HCl pH7.4, 5 mM MgCl2, 5 mM DTT, 100 μg ml-1 cycloheximide, 1% Triton X-100, 0.5% Sodium deoxycholate, complete EDTA-free protease inhibitors (Roche) and 40 U ml-1 RNasin plus (Promega)) using a Teflon homogenizer. Lysates were incubated for 10 min on ice and cleared by centrifugation at 1000 x g, 4°C for 3 min in a tabletop centrifuge. Supernatants were flash-frozen and stored in liquid nitrogen. Lysates of two mice per timepoint were pooled. Total RNA-seq libraries were generated from the lysate pool. For ribosome profiling libraries, lysate pools (15 OD260) were digested with 650 U RNase I (Ambion) for 45 min at room temperature and passed over size exclusion columns for ribosome purification prior to RNA extraction and library preparation.
Sequencing libraries for total RNA and ribosome protected RNA were generated using Ribo-Zero (Epicentre) and ARTseq ribosome profiling kits (Epicentre).

tag: Sex

value: male

value: 11-12 weeks

tag: timepoint


title: WT No Carbon #2

tag: genotype

value: wild type


title: IL-1R8-/-_NT_2_L1

value: lane 1


title: WT maltose #1

description: HiSeq-2000 1x50, barcode CGATGT


title: ProM (A) Sandfly 3

tag: parasite developmental stage

value: Promastigotes

tag: host cell type

value: cell culture


title: WT Sucrose #2


title: WT maltose #2

description: HiSeq-2000 1x50, barcode TGACCA

value: maltose


title: [delta]col-26 amylose #1

value: amylose


title: TRZT22_1; ZT22, total RNA, rep1

description:
total RNA
total RNA


title: TRZT18_1; ZT18, total RNA, rep1

description:
total RNA
total RNA


title: TRZT16_2; ZT16, total RNA, rep2

description:
total RNA
total RNA


title: E13.5

value: Embryonic day 13.5


title: P0

value: retina

value: Postnatal day 0


title: TRZT20_1; ZT20, total RNA, rep1

description:
total RNA
total RNA


title: TRZT18_2; ZT18, total RNA, rep2

description:
total RNA
total RNA


title: TRZT16_1; ZT16, total RNA, rep1

description:
total RNA
total RNA


title: TRZT14_1; ZT14, total RNA, rep1

description:
total RNA
total RNA


title: TRZT12_2; ZT12, total RNA, rep2

description:
total RNA
total RNA


title: TRZT14_2; ZT14, total RNA, rep2

description:
total RNA
total RNA


title: TRZT12_1; ZT12, total RNA, rep1

description:
total RNA
total RNA


title: E15.5

value: Embryonic day 15.5


title: TR_ZT8_2; ZT8, total RNA, rep2

description:
total RNA
total RNA


title: TRZT10_2; ZT10, total RNA, rep2

description:
total RNA
total RNA


title: TRZT10_1; ZT10, total RNA, rep1

description:
total RNA
total RNA


title: TR_ZT8_1; ZT8, total RNA, rep1

description:
total RNA
total RNA


title: TR_ZT6_1; ZT6, total RNA, rep1

description:
total RNA
total RNA


title: TR_ZT6_2; ZT6, total RNA, rep2

description:
total RNA
total RNA


title: TRZT20_2; ZT20, total RNA, rep2

description:
total RNA
total RNA


title: TR_ZT4_1; ZT4, total RNA, rep1

description:
total RNA
total RNA


title: TR_ZT2_2; ZT2, total RNA, rep2

description:
total RNA
total RNA


title: TR_ZT2_1; ZT2, total RNA, rep1

description:
total RNA
total RNA


title: TR_ZT0_2; ZT0, total RNA, rep2

description:
total RNA
total RNA


title: TR_ZT0_1; ZT0, total RNA, rep1

description:
total RNA
total RNA


title: RPZT22_2; ZT22, ribosome footprint, rep2

description:
ribosome protected RNA
ribosome footprint


title: RPZT22_1; ZT22, ribosome footprint, rep1


title: RPZT20_2; ZT20, ribosome footprint, rep2


title: RPZT20_1; ZT20, ribosome footprint, rep1


title: RPZT14_2; ZT14, ribosome footprint, rep2


title: RPZT18_2; ZT18, ribosome footprint, rep2


title: RPZT16_1; ZT16, ribosome footprint, rep1


title: RPZT18_1; ZT18, ribosome footprint, rep1


title: RPZT14_1; ZT14, ribosome footprint, rep1


title: RPZT12_1; ZT12, ribosome footprint, rep1


title: RPZT10_2; ZT10, ribosome footprint, rep2


title: RP_ZT8_1; ZT8, ribosome footprint, rep1


title: RP_ZT6_2; ZT6, ribosome footprint, rep2


title: TR_ZT4_2; ZT4, total RNA, rep2

description:
total RNA
total RNA


title: RPZT10_1; ZT10, ribosome footprint, rep1


title: RP_ZT4_1; ZT4, ribosome footprint, rep1


title: RP_ZT6_1; ZT6, ribosome footprint, rep1


title: RP_ZT8_2; ZT8, ribosome footprint, rep2


title: RP_ZT4_2; ZT4, ribosome footprint, rep2


title: RP_ZT2_1; ZT2, ribosome footprint, rep1


title: RP_ZT0_1; ZT0, ribosome footprint, rep1


title: RP_ZT2_2; ZT2, ribosome footprint, rep2


title: H_VBV24

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description:
experimental
RawCounts.csv
RPKMedgeR.csv

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed with adaptor sequence using cutadapt v1.2.1  and mapped to GRCh38.p7 reference build with GENCODE GTF annotation version 25 using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 and RPKM estimation using edgeR_3.12.1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with counts and RPKM values of each sample

source_name: LNCaP

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

tag: experiment

tag: condition

value: androgen


title: RP_ZT0_2; ZT0, ribosome footprint, rep2


title: H_VBV8

description:
control
RawCounts.csv
RPKMedgeR.csv

value: ETOH

tag: group


title: H_VBV12

description:
control
RawCounts.csv
RPKMedgeR.csv


title: H_VBV16


title: H_VBV23


title: H_VBV4

description:
control
RawCounts.csv
RPKMedgeR.csv


title: RPZT16_2; ZT16, ribosome footprint, rep2


title: H_VBV15


title: RPZT12_2; ZT12, ribosome footprint, rep2


title: H_VBV7

description:
control
RawCounts.csv
RPKMedgeR.csv

value: DMSO/Vehicle


title: H_VBV22


title: H_VBV18


title: H_VBV19


title: H_VBV10

description:
control
RawCounts.csv
RPKMedgeR.csv


title: H_VBV3

description:
control
RawCounts.csv
RPKMedgeR.csv


title: H_VBV11

description:
control
RawCounts.csv
RPKMedgeR.csv


title: H_VBV6

description:
control
RawCounts.csv
RPKMedgeR.csv


title: H_VBV2

description:
control
RawCounts.csv
RPKMedgeR.csv


title: H_VBV17


title: H_VBV1

description:
control
RawCounts.csv
RPKMedgeR.csv

value: siCtrl/Vehicle


title: H_VBV9

description:
control
RawCounts.csv
RPKMedgeR.csv


title: H_VBV21


title: H_VBV14


title: H_VBV20


title: H_VBV13


title: WT-TM_B

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

institute: Weizmann Institute of Science

data_processing:
Reads were aligned to the tomato genome sequence SL2.50 (downloaded from the sol genomics network http://solgenomics.net/organism/Solanum_lycopersicum/genome) using Tophat (v2.0.10).
Counting reads on ITAG2.4 genes (downloaded from sol genomics network) was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Genome_build: SL2.50
Supplementary_files_format_and_content: Excel file includes the normalized counts

source_name: WT tomato shoot apical meristem (SAM)

growth_protocol: Seedlings were grown in a greenhouse for 2-12 days.

extract_protocol:
RNeasy kit, QIAGEN, Cat. #74004
Truseq RNA Sa prep-Illumina V2 Guide, Part # 15026495

treatment_protocol: Seedlings were fixed in acetone and shoot apical meristems were dissected

value: WT

tag: Stage

value: transitional meristem


title: WT-TM_A


title: WT-6 Leaves_D

value: vegetative meristem after the production of 6 leaves


title: ltm-6 Leaves_B

source_name: ltm tomato shoot apical meristem (SAM)

tag: genotype/variation

value: ltm mutant


title: ltm-6 Leaves_A


title: ltm-4 Leaves_A


title: ltm-4 Leaves_B


title: WT-6 Leaves_B


title: WT-6 Leaves_A


title: WT-4 Leaves_A


title: WT-4 Leaves_B


title: Myl7_RNASeq_Nuclear_26hpf_1

status: Public on Apr 07 2017

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

description: Myl7 promoter driving biotin ligase.

data_processing:
ATAC-seq reads were trimmed for quality using sickle (v 1.33) and mapped using bowtie (v.1.0.0). Smoothened bigWig files were generated using an enhanced Perl script courtesy of Jim Hughes.
RNA-seq reads were mapped using STAR (v.2.4.2a).
BAM files incorporating reads belonging to either DNA strand were generated using custom python script.
Genome_build: danRer7 (Zv9)
Supplementary_files_format_and_content: bigWig files

organism: Danio rerio

extract_protocol:
Nuclei isolation using biotin-tagged outer nuclear envelope, adapted from INTACT procedure. Polyribosome isolation using biotin-tagged Rpl10 protein, adapted from TRAP procedure. FACS procedure using cell-specific fluorescent marker, following gentle dissociation of embryonic tissue. ATAC procedure adapted from Buenostro et al., 2013, adapted for FACS-sorted embryonic cells.
RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non-directional sequencing libraries after polyA-selection of RNA transcripts (NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEB) were built using NEBnext Ultra RNA library kit for Illumina (NEB). Following ribodepletion using Ribo-ZeroTM Magnetic Kit (Epicentre), directional RNA-seq libraries were constructed using Stranded RNA-Seq Library Preparation Kit (KAPABiosystems).

tag: strain/background

value: AB/TU

tag: tissue

value: myocardium

tag: assay

value: RNA-seq stranded

value: nuclear

tag: ribodepleted

value: ribodepleted

value: InVivoBiotinylatedNuclei

tag: strand

value: reverse


title: H_VBV5

description:
control
RawCounts.csv
RPKMedgeR.csv


title: Myl7_RNASeq_Nuclear_26hpf_2

description: Myl7 promoter driving biotin ligase.


title: Sox10_RNASeq_Whole_Cell_18ss

description: Sox10 BAC driving mCherry expression for FACS.

value: neural crest and otic

value: whole cell

value: FACS


title: Sox10_RNASeq_Nuclear_16ss_1

description: Sox10 BAC driving biotin ligase.


title: Bactin_RNASeq_Ribo_16ss_1

description: Bactin promoter driving biotin ligase.

value: embryonic structure

value: polyribosome-associated

value: InVivoBiotinylatedPolysomes


title: ChlamyBabeni2-2

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

institute: University of Geneva

description:
Sample name: C8_Site2
Sample 8_Cr
Processed data file: normalized_counts_edgeR_cpm_Chlamy.xlsx
Processed data file: DEG_Site2_vs_Site1_FDR5_FC2.xlsx

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
The reads were mapped using BWA v.0.7.10 to a de novo Elodea nuttalii transcriptome.
The reads were mapped with TopHat v.2.0.11 on the Chlamydomonas renhardtii 236 genome.
The gene features were counted with HTSeq v0.5.3p9 (htseq-count). Normalization and differential expression analysis were performed with the statistical analysis R/Bioconductor package edgeR v. 3.4.2.
Genome_build: de novo transcriptome Elodea nuttallii (Nicole Regier, Rebecca Beauvais-Flück, Vera I. Slaveykova, Claudia Cosio. Mercury exposure under enhanced ultraviolet radiation in Elodea nuttallii: effects on bioaccumulation, transcriptome, pigment content and oxidative stress endpoints. Aquatic toxicology under review.)
Genome_build: Chlamydomonas reinhardtii 236 (Phytozome v.9.1)
Supplementary_files_format_and_content: normalized*: Excel file with normalized counts in cpm (count per million) for each Sample.
Supplementary_files_format_and_content: DEG*: Excel file with significantly differentially expressed genes with a fold change 2 threshold and FRD 5% correction.
Supplementary_files_format_and_content: Elodea_muttallii.fasta: FASTA file of the de novo Elodea nuttallii transcriptome assembly.

organism: Chlamydomonas reinhardtii

source_name: ChlamyBabeni2-2 whole cells

growth_protocol: Up to middle exponential phase (~1x10^6 cells·ml-1) in a (4x) diluted tris-acetate-phosphate (TAP) medium.

extract_protocol:
TRI-Reagent
The libraries were prepared with 300 ng of total RNA as starting material and processed with the Illumina TruSeq mRNA stranded kit according to the manufacturer instructions.

treatment_protocol: 2h in situ exposure in the River Olt.


title: Sox10_RNASeq_Nuclear_18s

description: Sox10 BAC driving biotin ligase.


title: ChlamyBabeni1-3

description:
Sample name: C6_Site1
Sample 6_Cr
Processed data file: normalized_counts_edgeR_cpm_Chlamy.xlsx
Processed data file: DEG_Site2_vs_Site1_FDR5_FC2.xlsx

source_name: ChlamyBabeni1-3 whole cells


title: WT-6 Leaves_C

value: WT


title: Bactin_RNASeq_Ribo_16ss_2

description: Bactin promoter driving biotin ligase.


title: ChlamyValcea2

description:
Sample name: C2_control
Sample 2_Cr
Processed data file: normalized_counts_edgeR_cpm_Chlamy.xlsx
Processed data file: DEG_Site1_vs_Control_FDR5_FC2.xlsx
Processed data file: DEG_Site2_vs_Control_FDR5_FC2.xlsx

source_name: ChlamyValcea2 whole cells


title: ChlamyValcea1

description:
Sample name: C1_control
Sample 1_Cr
Processed data file: normalized_counts_edgeR_cpm_Chlamy.xlsx
Processed data file: DEG_Site1_vs_Control_FDR5_FC2.xlsx
Processed data file: DEG_Site2_vs_Control_FDR5_FC2.xlsx

source_name: ChlamyValcea1 whole cells


title: ChlamyValcea3

description:
Sample name: C3_control
Sample 3_Cr
Processed data file: normalized_counts_edgeR_cpm_Chlamy.xlsx
Processed data file: DEG_Site1_vs_Control_FDR5_FC2.xlsx
Processed data file: DEG_Site2_vs_Control_FDR5_FC2.xlsx

source_name: ChlamyValcea3 whole cells


title: Ng2/Cspg4 f/f sarcoma2

city: Durham

first: Claire

last: Hsu

address: 305 research drive

institute: Duke University

description: Sample 5 (S5)

data_processing:
Base calling was done using RTA 2.7.3 and bcl files were converted into fastq files using bcl2fastq v2.17.1.14
Reads were processed with TrimGalore to remove adapter sequences and low quality bases from the 3' end of the reads
Reads were aligned to the GRCm38v68 version of the mouse genome and transcriptome using the STAR alignment tool
Read counts per gene were calculated using HTSeq
Genes with fewer than 10 reads in any one condition were removed
DESeq2 was used to normalize the data
Genome_build: GRCm38v68

source_name: sarcoma cells

extract_protocol:
Qiagen RNAeasy Micro kits were used for RNA isolation from sarcoma tissues
Illumina HiSeq 4000 libraries and/or sequencing

value: sarcoma


title: ChlamyBabeni2-3

description:
Sample name: C9_Site2
Sample 9_Cr
Processed data file: normalized_counts_edgeR_cpm_Chlamy.xlsx
Processed data file: DEG_Site2_vs_Site1_FDR5_FC2.xlsx

source_name: ChlamyBabeni2-3 whole cells


title: ChlamyBabeni2-1

description:
Sample name: C7_Site2
Sample 7_Cr
Processed data file: normalized_counts_edgeR_cpm_Chlamy.xlsx
Processed data file: DEG_Site2_vs_Site1_FDR5_FC2.xlsx

source_name: ChlamyBabeni2-1 whole cells


title: ChlamyBabeni1-1

description:
Sample name: C4_Site1
Sample 4_Cr
Processed data file: normalized_counts_edgeR_cpm_Chlamy.xlsx
Processed data file: DEG_Site2_vs_Site1_FDR5_FC2.xlsx

source_name: ChlamyBabeni1-1 whole cells


title: WT sarcoma1

description: Sample 2 (S2)


title: WT sarcoma2

description: Sample 3 (S3)


title: Ng2/Cspg4 f/f sarcoma3

description: Sample 6 (S6)


title: Ng2/Cspg4 f/f sarcoma1

description: Sample 4 (S4)