title: Normal sample

city: Taipei

first: Moloya

last: Gohain

state: Taipei

address: 128, SEC.2 ACADEMIA ROAD, NANGANG DISTRICT

department: INSTITUTE OF PLANT AND MICROBIAL BIOLOGY

country: Taiwan

institute: ACADEMIA SINICA

description: Reduced representation bisulfite sequencing data

data_processing:
The data were preprocessed for duplicate reads, adapter trimmed, filtered and aligned to H19 version of human genome. Post-alignment, CG-maps were generated using the model-based and non-model based and single-cell algorithms. Wiggle files were generated to visualise the data on Integrated Genome Viewer (IGV). Methylation heteogeneity were estimated from each algorithm and resulting scores were compared to assess the efficiency of proposed methods versus commonly reported methods like methylation entropy.
Genome_build: Human genome (hg19)
Supplementary_files_format_and_content: RRBS data from normal and tumor samples in fastq.gz files and processed wiggle files using model-basd, non-model based and single-cell based approaches for estimation of DNA methylation heterogeneity.

source_name: Oral Cavity

extract_protocol:
Normal and tumor tissue were collected from head and neck cancer patients. Genomic DNA was isolated and used for preparation of RRBS libraries.
Genomic DNA was isolated from normal and tumor samples and digested separately by methylation-insensitive restriction enzyme MspI to generate short fragments that contain CpG dinucleotides at the ends. After end-repair, A-tailing and ligation to methylated Illumina adapters, the CpG-rich DNA fragments (40–220 bp) are size selected, subjected to bisulfite conversion, PCR amplified and end sequenced on an Illumina Genome Analyzer.

value: oral cavity

value: Somatic cells

tag: diagnosis

value: healthy


title: JURKAT_siRNA1_2h

status: Public on Sep 15 2017

type: SRA

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

library_source: transcriptomic

data_processing:
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with TopHat2
count reads with htseq-count
Genome_build: Drosophila Melanogaster (dm6), Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts

molecule: total RNA

organism: Homo sapiens

source_name: JURKAT cell line

extract_protocol:
Maxwell 16 LEV simplyRNA Cells Kit according to manufacturers instructions (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: 2h after Actinomycin D

tag: cell line

value: JURKAT

tag: genotype/variation

value: CNOT3 knockdown with si328


title: JURKAT_Ctrl3_2h

value: control sample


title: Head and Neck Cancer (HNC) sample

library_source: genomic

molecule: genomic DNA

tag: tissue

tag: cell type

value: head and neck cancer


title: JURKAT_Ctrl2_2h


title: JURKAT_siRNA3_0h

value: 0h after Actinomycin D


title: JURKAT_Ctrl1_2h


title: JURKAT_siRNA2_0h


title: JURKAT_siRNA1_0h


title: JURKAT_Ctrl3_0h


title: INPUT_DNA

city: Madrid

first: Luis

last: del Peso

state: Madrid

address: Arzobispo Morcillo

department: Biochemistry

country: Spain

institute: Universidad Autonoma de Madrid

data_processing:
Illumina adaptor sequences were trimmed from the ChIP-seq reads using Trimgalore and the reads were then aligned to Genome Reference Consortium GRCh37 (hg19) using BWA  ChIP-seq: Low quality mapping was removed (MapQ < 15) using SAMtools
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: wig files were generated using genomeCoverageBed (v2.25.0) and wigToBigWig tools.

source_name: HUVEC cells

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVEC) were purchased from Lonza (Lonza, C2519A) and grown in Endothelial Medium Bullet Kit (EGM‐2, Lonza, CC‐3162).

extract_protocol:
HUVEC cells  fixed and protein‐DNA complexes crosslinked by treatment with 1% formaldehyde, and then quenched with glycine (125mM). Next, cells were washed 3 times with ice‐cold PBS, collected using a cell scraper and resuspended in ice‐cold lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris‐HCl pH 8.1). DNA was sheared by using a sonicator (Diagenode Bioruptor, Belgium). Samples were diluted 1/10 with dilution Buffer (0.01% SDS, 1.1% Triton X‐100, 1.2 mM EDTA, 16.7 mM Tris‐HCl pH 8.1, 167 mM NaCl) and then precleared with Salmon Sperm DNA/Protein A agarose 50% slurry (Fast Flow, Millipore, 16‐156.) Sample were immunoprecipitated with different antibodies at 4°C rocking overnight; HIF1A (PM14), EPAS1 (PM9), [57] ARNT (Novus NB‐100‐110) and pre‐immune serum  used as negative control.Immunocomplexes were recovered by addition of Salmon Sperm DNA/Protein A agarose 50% slurry. Then samples were sequentially washed in Low Salt Wash Buffer (0.1% SDS, 1% Triton X‐100, 2 mM EDTA, 20 mM Tris‐HCl pH 8.1, 150 mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X‐100, 2 mM EDTA, 20 mM Tris‐HCl pH 8.1, 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP‐40, 1% NaDesoxycholate, 1 mM EDTA, 10 mM Tris‐HCl pH 8.1), and twice in TE buffer (10 mM Tris‐HCl pH 8, 1 mM EDTA). Elution of protein‐bound DNA was performed using 500 μl of fresh elution buffer (1% SDS, 0.1 M NaHCO3). Next crosslinking of all samples was reversed by the overnight incubation with 200 mM NaCl at 65°C. Next day, proteins were removed by the addition of 10 μl of 0.5 M EDTA, 20 μl Tris‐HCl pH 6.5 and proteinase K (40 μg/sample). Then immunoprecipitated DNA was purified by Phenol:Chloroform:Isoamyl alcohol extraction and ethanol precipitation (UltraPure™  phenol:Chloroform:Isoamyl Alcohol 25:24:1, Invitrogen, 15593‐031).
Libraries were prepared according to Illumina ChIP‐Seq kit's intructions (Illumina, IP‐202‐1012).

treatment_protocol: Cells were exposed 16h to hypoxia  in a 1% O2, 5% CO2, 94% N2 gas mixture in a Whitley Hypoxystation H35 (Don Withley Scientific).

value: HUVEC

tag: chip antibody

tag: passagges

value: from 4 to 6


title: ARNT_ChIPSeq

value: ARNT (Novus, NB-100-110)


title: EPAS1_ChIPSeq

value: EPAS1 (PM9)


title: HIF1A_ChIPSeq

value: HIF1A (PM14)


title: Repeat Treated Timepoint 12

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

country: USA

institute: Michigan State University

data_processing:
Data QC using FastQC, and reads trimmed 13 from the left and 27 from the right
Trimmed paired reads mapped using Tophat 2.0.13 (using --no-coverage-search --library-type fr-firststrand)
Mapped files quantitated using Cufflinks (--no-effective-length-correction, using hg19 annotation)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample corresponding to Cufflinks output.

source_name: B-Lymphoblastoid Cell Line

growth_protocol: The B-LCL MS1 cells were grown to a a density of 0.6-0.8 x 10^6/mL in 15% fetal bovine serum and 1% antibiotic-antimycotic.

extract_protocol:
For RNA-Seq, total RNA was extracted using the Qiagen RNeasy kit (Qiagen) and treated with RNAse-free DNase (Qiagen). RNA from ~2 million cells was extracted, with concentration measured on a Qubit (Life Technologies). Additionally, RNA integrity was checked on a Bioanalyzer (Agilent, Santa Clara CA) and only RNA with an RNA integrity number (RIN) of > 8.5 was used for subsequent library construction.
Libraries were constructed using Illumina's TruSeq kits with Ribo-Zero following the manufacturer's protocol. cDNA was quantitated on a Qubit (Life Technologies) and additionally the library quality was evaluated on a Bioanalyzer (Agilent)

treatment_protocol: In the first experiment, cells were grown together and separated into two flasks at the beginning of the time course (corresponding to a “treated” and an “untreated” condition). Both flasks were sampled simultaneously every hour over 24 hours (24 time points). The difference between the conditions occurs at time point 8 where, after taking a sample, the cells corresponding to the “treated” condition were treated with Rituximab at a concentration of 20 micrograms/ml.  In the validation repeat experiment, cells were grown under the same conditions and separated into two flasks at the start of the timecourse experiment again corresponding to a “treated and “untreated” condition. The validation sampled time point 8 (pre-treatment for treated line) and timepoint 9,10,12,15 and 23.

tag: sample type

value: repeat treated

tag: timepoint


title: Repeat Treated Timepoint 15


title: Repeat Treated Timepoint 23


title: JURKAT_Ctrl2_0h


title: Repeat Treated Timepoint 10


title: Repeat Treated Timepoint 9


title: JURKAT_Ctrl1_0h


title: CCRFCEM_ActD_4h_si328_3

source_name: CCRF-CEM cell line

value: 4h after Actinomycin D

value: CCRF-CEM


title: Repeat Treated Timepoint 8

description: treatment after sampling


title: JURKAT_siRNA3_2h


title: Repeat Untreated Timepoint 23

value: repeat untreated


title: CCRFCEM_ActD_4h_si328_2


title: CCRFCEM_ActD_4h_si328_1


title: Repeat Untreated Timepoint 15


title: CCRFCEM_ActD_4h_si326_3

value: CNOT3 knockdown with si326


title: Repeat Untreated Timepoint 12


title: Repeat Untreated Timepoint 10


title: CCRFCEM_ActD_4h_si326_2


title: CCRFCEM_ActD_4h_si326_1


title: CCRFCEM_ActD_4h_CTRL3


title: Treated Timepoint 24

value: treated


title: Repeat Untreated Timepoint 8


title: CCRFCEM_ActD_4h_CTRL2


title: CCRFCEM_ActD_4h_CTRL1


title: Treated Timepoint 23


title: CCRFCEM_ActD_2h_si328_3

value: 2h after Actinomycin D


title: CCRFCEM_ActD_2h_si328_2


title: CCRFCEM_ActD_2h_si326_3


title: CCRFCEM_ActD_2h_si328_1


title: Treated Timepoint 21


title: Treated Timepoint 19


title: Treated Timepoint 22


title: CCRFCEM_ActD_2h_si326_1


title: Treated Timepoint 18


title: Treated Timepoint 20


title: Treated Timepoint 15


title: Treated Timepoint 17


title: Repeat Untreated Timepoint 9


title: Treated Timepoint 14


title: CCRFCEM_ActD_2h_CTRL1


title: CCRFCEM_ActD_0h_si328_3


title: CCRFCEM_ActD_2h_CTRL3


title: Treated Timepoint 16


title: Treated Timepoint 11


title: Treated Timepoint 12


title: Treated Timepoint 13


title: CCRFCEM_ActD_0h_si328_1


title: Treated Timepoint 10


title: CCRFCEM_ActD_0h_si326_3


title: Treated Timepoint 9


title: CCRFCEM_ActD_0h_si328_2


title: CCRFCEM_ActD_0h_si326_2


title: Treated Timepoint 8

description: treatment after sampling


title: CCRFCEM_ActD_2h_si326_2


title: Treated Timepoint 7


title: CCRFCEM_ActD_0h_CTRL3


title: CCRFCEM_ActD_0h_CTRL1


title: Treated Timepoint 6


title: CCRFCEM_ActD_0h_CTRL2


title: Treated Timepoint 5


title: CCRFCEM_ActD_2h_CTRL2


title: Treated Timepoint 4


title: donor 2 RNA-seq

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v1.3.1)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v1.3.1)
barcode processing, Cell Ranger Single Cell Software Suite (v1.3.1)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v1.3.1)
alignment, Cell Ranger Single Cell Software Suite (v1.3.1)
Genome_build: UCSC hg19

molecule: polyA RNA

source_name: CD14+ monocytes

extract_protocol:
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) according to manufacturer’s protocol
Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3’ v2 Reagent Kit, following these steps: (1) fragmentation, end repair and A-tailing; (2) size selection with SPRI select; (3) adaptor ligation; (4) post ligation cleanup with SPRI select; (5) sample index PCR and cleanup with SPRI select beads.

tag: donor number

value: donor 2

value: CD14+ monocytes


title: Treated Timepoint 2


title: donor 1 RNA-seq

value: donor 1


title: Treated Timepoint 22

data_processing:
Data QC using FastQC.  150bp long reads were trimmed 15bp from both ends. 125bp long reads were trimmed 12bp from the left and 10bp from the right. 100bp long reads were trimmed 12bp from the left and 15bp from the right.
Trimmed paired reads mapped using Tophat 2.1.0 (using --no-coverage-search --library-type fr-firststrand)
Mapped files quantitated using Cufflinks (--no-effective-length-correction, using hg38 annotation)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample corresponding to Cufflinks output.

growth_protocol: A BLCL line (Donor 165/Astarte Biologics) cells were grown to a a density of 0.6-0.8 x 10^6/mL in 15% fetal bovine serum and 1% antibiotic-antimycotic.

extract_protocol:
For RNA-Seq, total RNA was extracted using the Qiagen RNeasy kit (Qiagen) and treated with RNAse-free DNase (Qiagen). RNA from ~2 million cells was extracted, with concentration measured on a Qubit (Life Technologies). Additionally, RNA integrity was checked on a Bioanalyzer (Agilent, Santa Clara CA) and only RNA with an RNA integrity number (RIN) of > 7  was used for subsequent library construction.
Libraries were constructed using Illumina's TruSeq kits with Ribo-Zero following the manufacturer's protocol. cDNA was quantitated on a Qubit (Life Technologies) and additionally the library quality was evaluated on a Bioanalyzer (Agilent). Libraries  for the repeat experiment were constructed through Novogene, also using Illumina protocols.

treatment_protocol: In the first experiment, cells were grown together and separated into two flasks at the beginning of the time course (corresponding to a “treated” and an “untreated” condition). Both flasks were sampled simultaneously every half hour over 12 hours (24 time points). The difference between the conditions occurs at time point T7 where, after taking a sample, the cells corresponding to the “treated” condition were treated with Everolimus at a concentration of 50nM.  In the validation repeat experiment, cells were grown under the same conditions and separated into two flasks at the start of the timecourse experiment again corresponding to a “treated and “untreated” condition. The validation sampled time points 0, 7, 10, 13, 16, and 22.


title: Treated Timepoint 23


title: Untreated Timepoint 24

value: untreated


title: Untreated Timepoint 23


title: Treated Timepoint 18


title: Untreated Timepoint 22


title: Treated Timepoint 21


title: Untreated Timepoint 21


title: CCRFCEM_ActD_0h_si326_1

value: 0h after Actinomycin D


title: Untreated Timepoint 19


title: Untreated Timepoint 20


title: Treated Timepoint 17


title: Treated Timepoint 16


title: Treated Timepoint 15


title: Untreated Timepoint 18


title: Treated Timepoint 3


title: Treated Timepoint 14


title: Treated Timepoint 13


title: Treated Timepoint 12


title: Untreated Timepoint 15


title: Untreated Timepoint 16


title: Treated Timepoint 1


title: Untreated Timepoint 13


title: Untreated Timepoint 14


title: Untreated Timepoint 12


title: Treated Timepoint 19


title: Treated Timepoint 10


title: Treated Timepoint 9


title: Treated Timepoint 8


title: Treated Timepoint 20


title: Untreated Timepoint 11


title: Untreated Timepoint 10


title: Treated Timepoint 7

description: treatment after sampling


title: Treated Timepoint 6


title: Untreated Timepoint 8


title: Untreated Timepoint 9


title: Treated Timepoint 4


title: Untreated Timepoint 7


title: Treated Timepoint 5


title: Treated Timepoint 3


title: Untreated Timepoint 17


title: Treated Timepoint 2


title: Untreated Timepoint 6


title: Treated Timepoint 11


title: Treated Timepoint 1


title: Untreated Timepoint 4


title: Untreated Timepoint 3


title: Untreated Timepoint 5


title: Untreated Timepoint 2


title: Treated Timepoint 0


title: Untreated Timepoint 22


title: Untreated Timepoint 1


title: Untreated Timepoint 20


title: Untreated Timepoint 18


title: Untreated Timepoint 21


title: Untreated Timepoint 19


title: Untreated Timepoint 17


title: Untreated Timepoint 15


title: Untreated Timepoint 14


title: Untreated Timepoint 16


title: Untreated Timepoint 11


title: Untreated Timepoint 12


title: Untreated Timepoint 13


title: Untreated Timepoint 10


title: Untreated Timepoint 7


title: Untreated Timepoint 9


title: Untreated Timepoint 6


title: Untreated Timepoint 8


title: Untreated Timepoint 23


title: Untreated Timepoint 5


title: Untreated Timepoint 2


title: Untreated Timepoint 4


title: Untreated Timepoint 1


title: shMXI1_Hyp

data_processing:
Primary analysis was performed using Illumina’s CASAVA software package.
The resulting reads were aligned to the GRCh37/hg19 assembly of the human genome using TopHat with the default parameters
The gene expression level was calculated as the number of reads per gene, computed using HTSeq and gene features as defined in the GRCh37.75 release of the human genome (gtf file) and expressed as RPKMs.  Feature coordinates and associated HGNC gene symbols were extracted with biomaRt package for R. Differential gene expression analysis was performed with the Bioconductor edgeR package for the R statistical Software
Genome_build: GRCh37/hg19

extract_protocol:
Total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen; 74106)
Integrity and quantity of each RNA samples was determined by Advanced Analytical Technologies Fragment AnalyizerTM.  PolyA+ fractions were purified and randomly fragmented. After first strand cDNA synthesis using random primers, the second strand synthesis is performed.  The ends of the double stranded cDNA fragments are repaired and dATP ligated to the blunt ended fragments. Then, the sequencing adapters are ligated to the DNA fragments. Determination of size distribution and quantification of the sequencing was accomplished on the Advanced Analytical Technologies Fragment AnalyzerTM. The libraries were also measured on the Invitrogen QubitR Fluorometer. The results of these measurements were integrated to accurately determine the appropriate sequencing dilution.

treatment_protocol: Cells were exposed 16h to hypoxia  in a 1% O2, 5% CO2, 94% N2 gas mixture in a Whitley Hypoxystation H35 (Don Withley Scientific). Lentiviral vector pGIPz (Open Biosystems) were produced and tittered in 293t cells, and used for at a multiplicity of infection (MOI) of 10 for 8h  to silence the mRNA expression of HIF1A (V2LHS_132150) EPAS1 (V2LHS_113753) as well as a Non-silencing lentiviral shRNA Control (NS; RHS4346), resulting in more than 95% transduced cells after 72h.

tag: normoxia/hypoxia

value: Hypoxia

tag: lentiviral infection

value: shMXI1_pGIPz (V3LHS_408351)


title: shMXI1_Nx


title: Untreated Timepoint 0


title: CBM1

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 with flag --b2-sensitive from 2 fastq files generated one aligment bam
cuffdiff with flag -u
Genome_build: mm9 for coding genes
Supplementary_files_format_and_content: The processed file is in tab delimined format with the gene counts for the individual samples

organism: Mus musculus

source_name: male embryo from cross between CAST/EiJ female X  C57BL/6J male

growth_protocol: Blastocysts were cultured individually and used to establish single, independent cell lines. Each line was maintained in Leukemia Inhibitory Factor (LIF) on inactivated mouse embryonic fibroblasts (MEFs) on gelatin-coated tissue culture plates in a 5% CO2 humid incubator at 37°C.

extract_protocol:
RNA isolation was performed using Roche’s High Pure RNA Isolation kit for the undifferentiated lines following two consecutive 60 minute MEF-depletion steps
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)

treatment_protocol: Cells were distinguished by sex chromosome complement- either XX, XY, or XO.

value: ES cells

tag: strain

value: C57BL/6J x CAST/EiJ

tag: genotype

tag: x chromosome complement

value: XY


title: CBM3


title: Untreated Timepoint 3


title: CBM2


title: CBF3

source_name: female embryo from cross between CAST/EiJ female X  C57BL/6J male

value: XX


title: BCO2

source_name: XO embryo from cross between C57BL/6J female X CAST/EiJ male

value: XO


title: CBF1


title: shSIN3a_Hyp_2

data_processing:
Primary analysiswas performed using Illumina’s CASAVA software package.
The resulting reads were aligned to the GRCh37/hg19 assembly of the human genome using TopHat with the default parameters
The gene expression level was calculated as the number of reads per gene, computed using HTSeq and gene features as defined in the GRCh37.75 release of the human genome (gtf file) and expressed as RPKMs.  Feature coordinates and associated HGNC gene symbols were extracted with biomaRt package for R. Differential gene expression analysis was performed with the Bioconductor edgeR package for the R statistical Software
Genome_build: GRCh37/hg19

treatment_protocol: Cells were exposed 16h to hypoxia  in a 1% O2, 5% CO2, 94% N2 gas mixture in a Whitley Hypoxystation H35 (Don Withley Scientific). Lentiviral vector pGIPz (Open Biosystems) were produced and tittered in 293t cells, and used for at a multiplicity of infection (MOI) of 10 for 8h  to silence the mRNA expression of SIN3A (V3LHS_343545) as well as a Non-silencing lentiviral shRNA Control (NS; RHS4346), resulting in more than 95% transduced cells after 72h.

value: HUVEC

value: shSIN3a_pGIPZ (V3LHS_343545)

tag: biological replicate

value: HUVEC pool 2


title: shSIN3a_Nx_2

value: Normoxia


title: NS_Hyp_2

value: Non Silencing_pGIPZ (RHS4346)


title: NS_Nx_2


title: BCO1


title: BCM3

source_name: male embryo from cross between C57BL/6J female X CAST/EiJ male


title: shSIN3a_Hyp_1

value: HUVEC pool 1


title: BCM1


title: shSIN3a_Nx_1


title: BCF3

source_name: female embryo from cross between C57BL/6J female X CAST/EiJ male


title: BCF2


title: shEPAS_Hyp

value: shEPAS_pGIPz (V2LHS_113753)


title: NS_Nx_1


title: CBF4


title: shHIF_Hyp

value: shHIF1A_pGIPz (V2LHS_132150)


title: NS_Hyp


title: Control, CO_007

city: Berlin

first: Josef

last: Priller

address: Charitéplatz 1

department: Department of Neuropsychiatry

country: Germany

institute: Charité - Universitätsmedizin Berlin

data_processing:
reads were mapped to reference genome hg19 using tophat (v2.0.9) and bowtie2 (v2.1.0) with following parameters for tophat: --min-anchor-length=8, --splice-mismatches=1, --min-intron-length=40, --max-intron-length=1000000, --mate-inner-dist=150, --solexa1.3-quals, --coverage-search
mapped reads were subjected to differential gene analysis using cufflinks (v2.1.1) using default parameters and UCSC hg19 reference gene annotation
Genome_build: hg19
Supplementary_files_format_and_content: the expression matrix of FPKM values

source_name: normal control

extract_protocol:
Fresh blood was collected (3 x 10 ml) from patients with HD and controls in tubes containing EDTA. All samples were extracted and analyzed separately and not pooled.  The LeukoLOCKTM total RNA isolation system was used for RNA extraction according to the manufactures’ protocol (Ambion, Austin, TX). Briefly, each 10 ml blood sample was passed through a LeukoLOCKTM filter, followed by flushing the filter with 3 ml phosphate-buffered saline (PBS) and subsequently with 3 ml RNAlater®. After removing the residual RNAlater® from the LeukoLOCKTM filter, the filter was flushed with 2.5 ml pH-adjusted Lysis/Binding solution. The lysate was collected in 15 ml tubes containing 2.5 ml Nuclease-free water, followed by adding 25 µl Proteinase K and shaken for 5 min on a roto-rack. For RNA isolation 50 µl RNA binding Beads and 2.5 ml 100% isopropanol were added, incubated at room temperature for 5 min and centrifuged at 2000 x g for 3 min. Supernatant was discarded. RNA binding beads were washed with 1.2 ml wash solution and transferred in a 1.5 ml reaction tube. The samples were centrifuged at 16,000 x g for 30 sec and the supernatant was discarded. The RNA binding beads were washed two times with 750 µl wash solution 2/3; and the pellet was air dried. RNA was removed from the RNA binding beads with 100 µl elution solution. After centrifugation at 16,000 x g for 2 min the supernatant containing the RNA was transferred to a new nuclease-free reaction tube and stored at -80°C. The quality and the yield of extracted RNA was analyzed on a total eukaryote RNA nano chip by the 2100 Bioanalyzer (Agilent Technologies, Germany) and by UV spectrography using Nanodrop 1000 (Thermo Scientific, Germany).
Poly(A)+ selected RNA libraries were prepared following a previously published protocol and preserving the strand information (Parkhomchuk et al. 2009. Nucl. Acids Res. 37, e123).

tag: gender

value: female

tag: age (yrs)

tag: number of htt polyq repeats

value: not tested

value: peripheral blood


title: Control, CO_008


title: shEPAS_Nx

tag: cell line


title: shHIF_Nx


title: Huntington's Disease, HD_003

source_name: Huntington's disease patient

value: male

tag: tissue


title: NS_Nx


title: BCM2

tag: cell type

value: ES cells


title: Huntington's Disease, HD_006


title: Huntington's Disease, HD_011


title: Huntington's Disease, HD_009


title: Huntington's Disease, HD_012


title: Huntington's Disease, HD_010


title: NS_Hyp_1

value: Hypoxia


title: Huntington's Disease, HD_015


title: Huntington's Disease, HD_014


title: Huntington's Disease, HD_013


title: BCF1

value: C57BL/6J x CAST/EiJ


title: Control, CO_004


title: Control, CO_002


title: Control, CO_006


title: Huntington's Disease, HD_001


title: 60 min post-light stimulation

city: Princeton

first: Jared

middle: E

last: Toettcher

address: Washington Road

department: Molecular Biology

institute: Princeton University

description: Constant light 60

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
All reads from the same index were pooled from all 3 lanes, resulting in ~30-50 million reads per condition.
Ribosomal/tRNA reads were excluded by first using Bowtie to map to an rRNA/tRNA genome, and discarding any successfully-mapped reads.
Non-ribosomal/tRNA reads were then mapped using Tophat using the mm9 genome and genome annotation file (GTF) from Illumina's iGenomes page.
Cufflinks/Cuffcompare was then used to generate a tracking file to compare FPKM data across all samples. The tracking file is included as OptoSOS_transcript_abundance.tabular.
Genome_build: mm9
Supplementary_files_format_and_content: OptoSOS_transcript_abundance.tabular

source_name: NIH3T3 OptoSOS cells

growth_protocol: NIH3T3 cells were grown in DMEM + 10% FBS + GlutaMAX + penicillin/streptomycin.

extract_protocol:
After treatment, total RNA was extracted by TRIzol treatment according to the manufacturer's instructions.
A cDNA library was constructed using the Illumina TruSeq library preparation kit.

treatment_protocol: Cells were starved in DMEM + 20mM HEPES overnight, incubated with 10 µM phycocyanobilin (to render the OptoSOS system functional), and treated for the appropriate time with 100 ng/mL PDGF or red light from an LED light source.

value: Fibroblast cell line

tag: transgene 1

value: Phy-mCherry-CAAX

tag: transgene 2


title: 0 min unstimulated control 3

description: untreated 3


title: 120 min post-PDGF stimulation

description: PDGF 120


title: 120 min post-light stimulation

description: Constant light 120


title: Huntington's Disease, HD_005


title: 60 min post-PDGF stimulation

description: PDGF 60


title: 30 min post-PDGF stimulation

description: PDGF 30


title: Control, CO_003


title: RNA_shCTL_R2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. RNAseq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. Cufflinks (PubMed ID 22383036) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIPseq profiles were produced by MACS in BedGraph format. Peaks were reported in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP_HA-Cbx6_R1.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_HA-Cbx6_R2.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_HA-Cbx6_Control.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_Cbx7.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_Cbx7_IgG.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_Ring1b.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_Ring1b_IgG.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_HA-Cbx6_R1_peaks.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: ChIP_HA-Cbx6_R2_peaks.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: ChIP_Cbx7_peaks.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: ChIP_Ring1b_peaks.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: RPKMs_shCtlR1R2-shCbx6R1R2.txt (RPKM values control r1, control r2, shCbx6 r1, shCbx6 r2.)

source_name: mouse ESCs

growth_protocol: Wild-type (E14Tg2A) ESCs were cultured feeder-free in plates coated with 0.1% gelatin. Coating was achieved by covering the plates with gelatin 15 min at 37°C. After removing any remaining gelatin, ESCs were cultured with Glasgow minimum essential medium (Sigma) supplemented with β-mercaptoethanol, sodium pyruvate, penicillin-streptomycin, non-essential amino acids, GlutaMAX, 20% fetal bovine serum (Hyclone) and leukemia inhibitory factor (LIF).

extract_protocol:
RNA was extracted with the RNeasy mini kit (Qiagen) following manufacturer's instruction. Genomic DNA for the HA and Cbx7 ChIPs was extracted using the ChIP-IT High sensitivity kit, from Active Motif. Genomic DNA for the Ring1B ChIP was extracted according to the protocol in the Materials and Methods. IP buffer + sonication. IP buffer = (1   volume SDS buffer [100 mM NaCl, 50 mM Tris-HCl, pH 8., 5 mM EDTA, pH 8, and 2% SDS] and 0.5 volume Triton dilution buffer (100 mM NaCl, 50 mM Tris-HCl, pH 8.6, 5 mM EDTA, pH 8 and 5% Triton X-100]) with proteinase inhibitors
Libraries were prepared according to Illumina instructions.

treatment_protocol: Two 15-cm plates for each cell line to be tested were prepared at 70–80% confluency. Cells were trypsinized and crosslinked in 1% formaldehyde for 10 min at room temperature in a shaker. To stop the fixation reaction, 0.125 M glycine was added to the existing culture media and incubated for 5 min. Sample pellets were then washed twice with PBS 1× at room temperature. After aspirating PBS completely, crosslinked pellets were resuspended in 1.3 ml ice-cold IP buffer (1× volume SDS buffer [100 mM NaCl, 50 mM Tris-HCl, pH 8., 5 mM EDTA, pH 8, and 2% SDS] and 0.5 volume Triton dilution buffer (100 mM NaCl, 50 mM Tris-HCl, pH 8.6, 5 mM EDTA, pH 8 and 5% Triton X-100]) with proteinase inhibitors. Samples were sonicated for 12 min (30 sec ON/30 sec OFF) in a Bioruptor (Diagenode) at maximum output. After sonication, samples were centrifuged at 4°C at maximum speed for 20 min. To check chromatin size, 20 µl of the supernatant was mixed with 80 µl of 1× PBS and de-crosslinked for 3 h at 65°C in a shaker (1000 rpm), followed by PCR purification kit (Qiagen). DNA was eluted in 30 µl of water and quantified by Nanodrop. Around 800 ng were loaded in a 1% agarose gel. If chromatin was between 200–500 bp, 40 µg of chromatin was used to ChIP proteins.


title: RNA_shCbx6_R1


title: RNA_shCTL_R1


title: DN-2

city: Shanghai

first: Shuangshuang

last: Wang

state: Shanghai / 上海

address: 2005 Songhu Road

country: China

institute: Fudan 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 TAIR10 whole genome
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: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Arabidopsis thaliana

source_name: anther

growth_protocol: Arabidopsis thaliana plants were grown on soil in greenhouse conditions (21℃) under long-day conditions (16-h of light/8-h of dark)

extract_protocol:
More than 1000 stage 4-10 anthers from the WT and mutant plants were collected and immediately frozen in the liquid nitrogen. Total RNA was extracted and purified using the ZR plant RNA Miniprep™ kit (Zymo Research, Irvine, USA). 2 μg total RNA of each sample was used for deep sequencing .
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: anther


title: DN-1


title: ChIP_Ring1b_IgG

description: chromatin IP against IgG

tag: chip antibody

value: Rabbit pAb Abcam ab46540


title: ChIP_Ring1b

description: chromatin IP against Ring1b

value: Rabbit pAb In-house


title: OX-1


title: ChIP_HA-Cbx6_R1

description: chromatin IP against Cbx6

value: Rabbit pAb BioLegend 902301


title: OX-2


title: ChIP_Cbx7

description: chromatin IP against Cbx7

value: Rabbit pAb Abcam ab21873


title: 0 min unstimulated control 1

description: untreated 1


title: ChIP_Cbx7_IgG

description: chromatin IP against IgG


title: ChIP_HA-Cbx6_Control

description: chromatin IP against HA-NEO


title: 30 min post-light stimulation

description: Constant light 30


title: Control, CO_005


title: RNA_shCbx6_R2


title: ChIP_HA-Cbx6_R2

description: chromatin IP against Cbx6


title: C24-2

value: wild type C24


title: mRNA from div-1 mutant worms biological replicate 3

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

data_processing:
Reads mapped using tophat v2.1.0 -T
Assigning reads to genes using featureCounts v1.5.0 -s 2 -t exon -g gene_name -M -O --fraction
Counts normalization by total mapped small RNAs using DESeq2 v1.8.1.
Genome_build: C. elegans genome assembly WS215 from WormBase and annotation from Ensembl release 70 with the vector transgene as an additional chromosome
Supplementary_files_format_and_content: Matrix of scaled reads per gene

organism: Caenorhabditis elegans

source_name: mRNA from div-1 mutant worms

growth_protocol: Synchronized populations of worms grown on multiple OP50 plates at 20C were bleached, washed 3x with M9 and the larvae let to hatch o/n in M9 at 20 ºC. The L1 larvae were washed with M9 and RNA was extracted.

extract_protocol:
RNA was extracted using TRIzol® extraction protocol (Portman, D.S. (2006). Profiling C. elegans gene expression with DNA microarrays. WormBook : the online review of C elegans biology, 1-11.)
1 microgram of total RNA was treated with Antarctic phosphatase (ref. M0289S, NEB) and subsequently with T4 PNK (3' phosphatase minus) (ref. M0236S, NEB) in order to make the 5’ and 3’ ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. Briefly, 3’ adapters and subsequently 5’ adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3’ RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, libraries were size selected using 6% Novex® TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 18 to 36 bp were cut from the gel, and DNA was precipitated and eluted in 10 µl EB. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot. Libraries were pooled and loaded at a concentration of 10 pM onto the flowcell, and were sequenced 1 x 50 on Illumina’s HiSeq 2000.

treatment_protocol: Worms grown on regular NGM plates seeded with OP50 bacteria.

tag: strain background

tag: strain genotype

value: BCN6101 (EU548+pdaf-21::mCherry)

value: whole multiple worms


title: mRNA from N2 wild type worms biological replicate 2

source_name: mRNA from N2 wild type worms

value: BCN1050 (pdaf-21::mCherry)


title: Control, CO_009

value: not tested


title: mRNA from N2 wild type worms biological replicate 1


title: C24-1


title: 0 min unstimulated control 2

description: untreated 2


title: mRNA from div-1 mutant worms biological replicate 2


title: Col0-2

value: wild type Col-0


title: mRNA from N2 wild type worms biological replicate 3


title: mRNA from div-1 mutant worms biological replicate 1


title: Col0-1


title: Pre-existent_RNA_Nx_3

data_processing:
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files showing reads per feature (gene)

extract_protocol:
Exponentially growing HUVEC cells were exposed to 21% or 1% oxygen for 8 hours and pulse‐labeled with 4-thiouridine (400 µM, 4sU, Sigma, T4509) during the last two hours of treatment. After treatment, total cellular RNA was isolated from cells using TRI-reagent (Ambion, AM9738). 100 µg of total RNA was subjected to a biotinylation reaction to label the newly transcribed RNA containing the 4sU moiety (Pierce, EZ-Link Biotin-HPDP, 21341). Then, RNA was purified using Ultrapure TM Phenol:Chloroform:Isoamylalcohol (Invitrogen, 15593‐031) and labeled RNA  was isolated from the total RNA by affinity chromatography using streptavidin coated magnetic beads (μMacs Streptavidin Kit; Miltenyi, 130‐074‐101). The three fractions corresponding to total RNA, pre-existent RNA and Newly Tr RNA were sequenced by RNA-seq
1 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 9.2 to 9.6 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fractions were purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by 9 cycles of PCR with Illumina PE primers. The resulting purified cDNA library of template molecules of known strand origin was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

treatment_protocol: Cells were exposed for 8h to hypoxia  in a 1% O2, 5% CO2, 94% N2 gas mixture in a Whitley Hypoxystation H35 (Don Withley Scientific).

tag: normoxia/hypoxia

value: Normoxia

tag: rna fraction

value: Pre-existent

value: HUVEC

tag: treatment

value: normoxia

tag: labelled fraction

value: non-labelled

value: HUVEC pool 3


title: Pre-existent_RNA_Nx_2

tag: biological replicate

value: HUVEC pool 2


title: Total_RNA_Hyp_2

value: Hypoxia

value: Total

value: hypoxia

value: total RNA


title: Newly_Tr_RNA_Hyp_2

value: Newly Tr

value: newly transcribed RNA


title: Pre-existent_RNA_Hyp_2


title: Total_RNA_Nx_3


title: mix

city: changsha

first: Gang

last: Gao

address: No. 348, West Xianjiahu Road,

institute: Institue of bast fiber crops,Chinese academy of agricultural science

data_processing:
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence to get clean read. And then perform the de novo assembly with clean reads to get unigenes.
With functional annotation, Unigene that best mapped to functional databases in a priority order of NR,SwissProt,KEGG,COG  was selected and displayed from 5' to3' in FASTA fromat for functional annotation. Unigenes that can't be aligned to any database mentioned above were predicted by ESTScan with Blast-predicted CDS as model.
RPKM of each unigene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Boehmeria nivea

source_name: ramie roots

growth_protocol: The ramie tender was respectively cultivated in  soil or  hydroponic environment  for roots induction and development.

extract_protocol:
Ramie roots were collected, flash frozen on dry ice, and total RNA was extracted using Trizol reagent according to  the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pooled aquatic and terrestrial developmental stages

value: root pool


title: Total_RNA_Nx_2

source_name: HUVEC cells


title: Total_RNA_Nx_1

value: HUVEC pool 1


title: Newly_Tr_RNA_Nx_1


title: Pre-existent_RNA_Hyp_1


title: Newly_Tr_RNA_Hyp_3


title: Total_RNA_Hyp_3


title: S5_BoEMZ2

city: Gif-sur-Yvette

first: Karine

last: Alix

address: Chemin du Moulon

institute: GQE - Le Moulon

data_processing:
FastQC (Version 0.10.1) was used for quality control of the high throughput sequence data.
Sequences of adaptors, empty reads, low complexity reads and reads smaller than 18-nt and bigger than 26-nt, as well as transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) (using de novo predictions of Brassica-specific tRNAs and rRNAs that were made locally with tRNAscan-SE 1.21 and RNAmmer 1.2) were removed by using Filter Tool from the UEA sRNA toolkit.
Each small RNA library was analyzed individually; Each library was searched for known miRNAs using miRProf (from the UEA sRNA toolkit, Moxon et al. 2008) that identifies sequence reads matching already registered miRNAs in miRBase (version 19, database: plant_mature, with the options:1 missmatch maximum,  group-organisms, group-family and collapse-match-groups were enabled; Griffiths-Jones 2004)
Supplementary_files_format_and_content: miRNA profiling against mirBase (: plant_mature, number of allowed mismatches: 1). CSV file format : Each line contains : "matching miRNAs","raw count","weighted count","normalised weighted count".

organism: Brassica napus

source_name: stem

extract_protocol:
Total RNAs were extracted from stems of adult plants (grown under controlled conditions: 18°C during 8h night and 21°C during 16h) using the TRIzol® reagent following the manufacturer’s protocol (Invitrogen), with addition of 0.2 µl/ml beta-mercapto-ethanol to TRIzol® extemporarily.
RNA quality of all samples was verified using a Bioanalyzer. Cloning and sequencing of small RNAs were performed by ImaGenes GmbH (Berlin, Germany) using the standard Illumina protocol: small RNAs (18-32 nt long) were size selected, purified, and ligated with TruSeq adaptors. A total of eleven sRNA libraries of size-selected RNAs from the eleven plant samples were prepared by reverse-transcription PCR, followed by PCR. High-throughput multiplex sequencing of the libraries was performed on the Illumina Genome Analyzer GAII. Barcodes: HDEM-1: CTCA; HDEM-2: CCAT;  Z1-1: GAGA; Z1-2: CTTA; HDEM+Z1: CTAC; S1_BoEMZ1: CGCC; S1_BoEMZ2: TCAA; S1_BoEMZ5: AGTA; S5_BoEMZ1: CGTA; S5_BoEMZ2: CGAT; S5_BoEMZ5: ACTA.

tag: plant

value: resynthesized B. napus CCAA

tag: ploidy

value: tetraploid 4x

tag: generation


title: Pre-existent_RNA_Hyp_3

value: Pre-existent

tag: cell line


title: Pre-existent_RNA_Nx_1

value: Normoxia

value: HUVEC


title: S5_BoEMZ5


title: S1_BoEMZ1


title: S1_BoEMZ5


title: Newly_Tr_RNA_Hyp_1


title: S5_BoEMZ1


title: Maple sap N. crassa 360min rep 3

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description:
replicate 3
Ncrassa_Maple_lox.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. For each read, we trimmed the first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 using in-house scripts.  If, after trimming, the read was shorter than 45-bp, the whole read was discarded.
Trimmed reads were aligned to Neurospora crassa OR74A v12 genome using Tophat v.2.0.12 (Trapnell et al., 2009) using the very-sensitive preset and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results. We used the default settings for all other Tophat options. We tallied reads aligning to exons of genes with the program HTSeq v0.6.1p1.
LOX v1.8 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals.
Genome_build: Neurospora crassa OR74A v12
Supplementary_files_format_and_content: tab-delimited text files provides relative gene expression levels standardized by the lowest sample and their confident intervals. Output from LOX software. In the processed data files, 1,2,3,4 represent 15, 120, 240, and 360 minutes respectively.

organism: Neurospora crassa

source_name: conidia germination_maple sap

growth_protocol: CULTURES were performed by applying 2 ml of the suspension of  conidia in 1.5% Tween 60 (105 - 106 conidia/ml) to the surface of medium plates that were covered with cellophane membranes. Conidia germination were monitored with microscope, and roughly over 70% individual conidia showing same development stage were used to decide the sampling time points

extract_protocol:
RNA was isolated from homogenized mycelia with TRI REAGENT (Invitrogen) and mRNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen)
Twenty-four sequencing libraries, 3 replicates per condition, were produced from purified total RNA samples by the Illumina TruSeq stranded protocol. The libraries underwent 76bp pair-end sequencing using Illumina HiSeq 2500 according to Illumina protocols.

treatment_protocol: For transcriptomic analysis, all tissues and perithecia were immediately and rapidly frozen in liquid nitrogen as they were sampled, then stored at -80°C

tag: strain

tag: timepoints

value: 360 minutes after inoculation

tag: sample type

value: monokaryotic


title: Maple sap N. crassa 360min rep 1

description:
replicate 1
Ncrassa_Maple_lox.txt


title: Newly_Tr_RNA_Nx_3

value: normoxia

value: HUVEC pool 3


title: Newly_Tr_RNA_Nx_2

value: HUVEC pool 2


title: Maple sap N. crassa 240min rep 2

description:
replicate 2
Ncrassa_Maple_lox.txt

value: 240 minutes after inoculation


title: Maple sap N. crassa 240min rep 1

description:
replicate 1
Ncrassa_Maple_lox.txt


title: Maple sap N. crassa 120min rep 3

description:
replicate 3
Ncrassa_Maple_lox.txt

value: 120 minutes after inoculation


title: Maple sap N. crassa 120min rep 2

description:
replicate 2
Ncrassa_Maple_lox.txt


title: Maple sap N. crassa 120min rep 1

description:
replicate 1
Ncrassa_Maple_lox.txt


title: Maple sap N. crassa 15min rep 3

description:
replicate 3
Ncrassa_Maple_lox.txt

value: 15 minutes after inoculation


title: Bird N. crassa 360min rep 2

description:
replicate 2
Ncrassa_Bird_lox.txt

source_name: conidia germination_Bird


title: Bird N. crassa 240min rep 3

description:
replicate 3
Ncrassa_Bird_lox.txt


title: Bird N. crassa 360min rep 1

description:
replicate 1
Ncrassa_Bird_lox.txt


title: Bird N. crassa 240min rep 1

description:
replicate 1
Ncrassa_Bird_lox.txt


title: Maple sap N. crassa 240min rep 3

description:
replicate 3
Ncrassa_Maple_lox.txt


title: Bird N. crassa 360min rep 3

description:
replicate 3
Ncrassa_Bird_lox.txt


title: Bird N. crassa 120min rep 3

description:
replicate 3
Ncrassa_Bird_lox.txt


title: Total_RNA_Hyp_1

value: Hypoxia

value: Total

value: hypoxia

value: total RNA


title: 48 h PI fed

city: Pune

first: Ashok

middle: P

last: Giri

address: Pashan road, pune

country: India

institute: NCL

data_processing:
Raw sequencing reads from 12 libraries (6 different time intervals each for AD and rCanPI-7 fed larvae) were submitted to miRDeep2 and data from each library were separately analyzed
miRDeep2 pre-processed raw sequencing reads by removing the 3' adapter sequence and discarding reads shorter than 18 nucleotides, before aligning reads to the Bombyx mori (silkworm) genome
H. armigera was designated as the related species and the known miRNA input was from miRBase 20.0 to analyze sequenced miRNAs
Supplementary_files_format_and_content: text file of identified miRNA sequences using miRDeep software; html file is output from miRDeep2.

organism: Helicoverpa armigera

source_name: Whole insect tissue

growth_protocol: H. armigera larvae were maintained on artificial diet (AD) at optimum growth conditions (27±2 °C, 60±5% relative humidity and a photoperiod of 14h L and 10h D).

extract_protocol:
Total RNA was isolated from the whole-body homogenates of insect tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA) based on the manufacturer's protocol
Small RNA library was prepared using Tru Seq Small RNA sample preparation kit v2 (Illumina, San Diego, CA, USA) following manufacturer’s specified protocols. Total RNA (1 μg) was taken and adapters were ligated to the 5’ phosphate and 3’ hydroxyl groups that are specific to miRNAs according to manufacturer’s instructions. Reverse transcription PCR was done based on manufacturer’s protocol to make cDNA constructs that would enrich the fragments that have adapter molecule on both ends. A size selection targeting miRNA’s in the range of 20 to 35 nucleotides was performed (The adapter is around 125 bases in length).

treatment_protocol: First instar larvae were allowed to feed for 48h on AD and AD incorporated with rCanPI-7

tag: tissue

value: whole body

value: larvae

tag: diet

value: artificial diet with recombinant Capsicum annuum PI-7


title: 12 h AD fed

tag: developmental stage

value: artificial diet


title: 48 h AD fed


title: 24 h AD fed


title: Bird N. crassa 240min rep 2

description:
replicate 2
Ncrassa_Bird_lox.txt


title: 6 h PI fed


title: 12 h PI fed


title: Bird N. crassa 120min rep 2

description:
replicate 2
Ncrassa_Bird_lox.txt


title: Maple sap N. crassa 360min rep 2

description:
replicate 2
Ncrassa_Maple_lox.txt


title: Maple sap N. crassa 15min rep 2

description:
replicate 2
Ncrassa_Maple_lox.txt


title: 2 h PI fed


title: Bird N. crassa 15min rep 3

description:
replicate 3
Ncrassa_Bird_lox.txt


title: 6 h AD fed


title: Bird N. crassa 15min rep 2

description:
replicate 2
Ncrassa_Bird_lox.txt


title: Bird N. crassa 15min rep 1

description:
replicate 1
Ncrassa_Bird_lox.txt


title: 0.5 h PI fed


title: 24 h PI fed


title: S1_BoEMZ2

value: resynthesized B. napus CCAA

value: tetraploid 4x


title: 0.5 h AD fed


title: INPUT_Nx

data_processing:
FASTQ files were aligned to the hg19 version of human reference genome usin Bowtie 2 (version 2.1.0). The resulting BAM files were filtered to remove PCR duplicates (picard tools, version 1.87). Bound regions and peaks were identified with macs (version 1.4.2) using default parameters.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedGraphBig files were generated usibedtools genomecovols (version 2.25) without scaling.

extract_protocol:
HUVEC cells  fixed and protein‐DNA complexes crosslinked by treatment with 1% formaldehyde, and then quenched with glycine (125mM). Next, cells were washed 3 times with ice‐cold PBS, collected using a cell scraper and resuspended in ice‐cold lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris‐HCl pH 8.1). DNA was sheared by using a sonicator (Diagenode Bioruptor, Belgium). Samples were diluted 1/10 with dilution Buffer (0.01% SDS, 1.1% Triton X‐100, 1.2 mM EDTA, 16.7 mM Tris‐HCl pH 8.1, 167 mM NaCl) and then precleared with Salmon Sperm DNA/Protein A agarose 50% slurry (Fast Flow, Millipore, 16‐156.) Sample were immunoprecipitated with the antibodies SIN3A (ab3479) at 4°C rocking overnight. Immunocomplexes were recovered by addition of Salmon Sperm DNA/Protein A agarose 50% slurry. Then samples were sequentially washed in Low Salt Wash Buffer (0.1% SDS, 1% Triton X‐100, 2 mM EDTA, 20 mM Tris‐HCl pH 8.1, 150 mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X‐100, 2 mM EDTA, 20 mM Tris‐HCl pH 8.1, 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP‐40, 1% NaDesoxycholate, 1 mM EDTA, 10 mM Tris‐HCl pH 8.1), and twice in TE buffer (10 mM Tris‐HCl pH 8, 1 mM EDTA). Elution of protein‐bound DNA was performed using 500 μl of fresh elution buffer (1% SDS, 0.1 M NaHCO3). Next crosslinking of all samples was reversed by the overnight incubation with 200 mM NaCl at 65°C. Next day, proteins were removed by the addition of 10 μl of 0.5 M EDTA, 20 μl Tris‐HCl pH 6.5 and proteinase K (40 μg/sample). Then immunoprecipitated DNA was purified by Phenol:Chloroform:Isoamyl alcohol extraction and ethanol precipitation (UltraPure™  phenol:Chloroform:Isoamyl Alcohol 25:24:1, Invitrogen, 15593‐031).
Libraries were prepared according to TruSeq DNA library kit.

value: HUVEC

tag: stress

tag: passagges

value: from 4 to 6

tag: chip antibody


title: SIN3A_Nx

value: normoxia


title: DOCK8 KO 1  activated

city: Melbourne

first: Conor

last: Kearney

address: Grattan Street

country: Australia

institute: Peter MacCallum cancer Centre

description: Voomnormalizedcounts.csv

data_processing:
Demultiplexing of the reads was performed using CASAVAv1.8.2
low-quality reads Q<30 were removed
Cutadapt (v1.9) was used to trim poly-A derived sequences and biased 3’ reads resulting from random hexamer priming
HISAT2 was used to map the resulting reads to the human reference genome
Read counting was performed using featureCounts, which is part of the subread package
Genome_build: hg19
Supplementary_files_format_and_content: Comma Seperated File Containing Voom Normalised Counts

source_name: KHYG1 cells

growth_protocol: 10% FCS in RPMI, 5% CO2

extract_protocol:
KHYG1 cells were cultured as indicated prior to stimulation with anti-Nkp30 (duplicate samples). After 90 minutes, cell pellets were collected and total RNA was extracted using the Nucleospin® RNA extraction kit (Macherey-Nagel).
RNA quality was checked on the Agilent 4200 Tapestation and RNA with RIN values > 9 were used for the subsequent analysis. Sequencing libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturers instructions using 200ng total RNA input. Single-end 75bp RNA-sequencing was performed on the NextSeq 500 (Illumina).

treatment_protocol: 10 ug/ml anti-NKp30 for 90 minutes

tag: genotype

value: DOCK8 KO

tag: activation status

value: activated


title: DOCK8 KO 2 not activated

description: Voomnormalizedcounts.csv

value: not activated


title: SIN3A_Hp


title: control 2  activated

description: Voomnormalizedcounts.csv

value: control


title: DOCK8 KO 1 not activated

description: Voomnormalizedcounts.csv


title: control 1  activated

description: Voomnormalizedcounts.csv


title: Newly_Tr_RNA_shEPAS_Hyp

data_processing:
Basecalls performed using RTA software from sequencer. Demultiplexing with bcl2fastq
The resulting reads were aligned to the GRCh37/hg19 assembly of the human genome using TopHat with the default parameters
The gene expression level was calculated as the number of reads per gene, computed using HTSeq and gene features as defined in the GRCh37.75 release of the human genome (gtf file). Feature coordinates and associated HGNC gene symbols were extracted with biomaRt package for R. Differential gene expression analysis was performed with the Bioconductor edgeR package for the R statistical Software
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files showing reads per feature (gene)

extract_protocol:
Exponentially growing HUVEC cells were exposed to 21% or 1% oxygen for 8 hours and pulse‐labeled with 4-thiouridine (400 µM, 4sU, Sigma, T4509) during the last two hours of treatment. After treatment, total cellular RNA was isolated from cells using TRI-reagent (Ambion, AM9738). 100 µg of total RNA was subjected to a biotinylation reaction to label the newly transcribed RNA containing the 4sU moiety (Pierce, EZ-Link Biotin-HPDP, 21341). Then, RNA was purified using Ultrapure TM Phenol:Chloroform:Isoamylalcohol (Invitrogen, 15593‐031) and labeled RNA  was isolated from the total RNA by affinity chromatography using streptavidin coated magnetic beads (μMacs Streptavidin Kit; Miltenyi, 130‐074‐101, ).
Libraries were prepared following the instructions of Ultra Directional RNA Library Prep Kit (New England Biolabs, Cat no. E7420S) without Actinomycin D.

treatment_protocol: Cells were exposed 8h to hypoxia  in a 1% O2, 5% CO2, 94% N2 gas mixture in a Whitley Hypoxystation H35 (Don Withley Scientific). Lentiviral vector pGIPz (Open Biosystems) were produced and tittered in 293t cells, and used for at a multiplicity of infection (MOI) of 10 for 8h  to silence the mRNA expression of EPAS1 (V2LHS_113753) as well as a Non-silencing lentiviral shRNA Control (NS; RHS4346), resulting in more than 95% transduced cells after 72h.

tag: normoxia/hypoxia

value: Hypoxia

tag: lentiviral infection

value: shEPAS_pGIPz (V2LHS_113753)

tag: rna fraction

value: Newly Tr RNA


title: INPUT_Hp

value: hypoxia


title: Bird N. crassa 120min rep 1

description:
replicate 1
Ncrassa_Bird_lox.txt

value: 120 minutes after inoculation

value: monokaryotic


title: Newly_Tr_RNA_NS_Hyp

value: Non Silencing_pGIPZ (RHS4346)


title: Newly_Tr_RNA_shEPAS_Nx

value: Normoxia


title: Total_RNA_shEPAS_ Hyp

value: total RNA


title: Total_RNA_shEPAS_ Nx


title: Newly_Tr_RNA_NS_Nx


title: 2 h AD fed

value: whole body

value: larvae

value: artificial diet


title: control 2 not activated

description: Voomnormalizedcounts.csv


title: Total_RNA_NS_ Hyp

value: HUVEC


title: control 1 not activated

description: Voomnormalizedcounts.csv


title: Total_RNA_NS_ Nx


title: Z1-2

organism: Brassica rapa subsp. oleifera

value: Brassica rapa ssp. oleifera

tag: plant

value: progenitor AA

tag: ploidy

value: diploid 2x

value: parent


title: 2011_0028

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

data_processing:
A mean of 52±10 million passing illumina quality filter reads was obtained for each of all the samples. We performed RNA-seq analysis using the Eoulsan pipeline.
Only read1 was considered for the further analyses.
Before mapping, poly N read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded.
Reads were then aligned against the T. reesei genome (version 2 from the JGI website) using the Bowtie mapper (version 0.12.7).
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools.
To compute gene expression, the T. reesei genome annotation from JGI (version 2) was used. All overlapping regions between alignments and referenced exons were counted. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3.
A threshold of 2 for the log2 ratios with an adjusted p-value <0.001 were used to identify genes differentially expressed (DE).
Gene functions were identified by the aid of a manually annotated T. reesei genome database proprietary to IFPEN.
Genome_build: T. reesei genome (version 2 from the JGI website)
Supplementary_files_format_and_content: DESeq 1.8.3 normalized counts

organism: Trichoderma reesei

source_name: T. reesei QM6a, T48h Lactose

growth_protocol: 50 mL of minimal media (5 g/L (NH4)2SO4, 5 g/L KH2PO4,  11.7 g/L Trisodium Citrate,  0.6 g/L MgSO4, 0.6 g CaCl2, 20 g/L glucose) were prepared in a 250 mL Erlenmeyer flask. The medium was supplemented with the following trace elements: 0.5 mL/L FeSO4·7H2O, 2 mL/L CoCl2, 0.16 mL/L MnSO4, and 0.14 mL/L ZnSO4 in a 1 wt % aqueous solution. Prior to sterilization, the pH of the medium was adjusted to 5.4.  Strains QM6a and QM9978 were inoculated in duplicate with approx. 100 conidia / mL. Cultivation was carried out at 30°C at 150 rpm. When the glucose was close to depletion (<3 g/L), 5 mL of a lactose solution was added (25 g/L lactose, 6 g/L (NH4)2SO4, 5 g/L Trisodium Citrate). Glucose concentration was assessed by enzymatic reaction using an Analox Glucose analyser GM10 (Imlab). Extracellular protein concentration was measured against a BSA strandard (0 to 1.5 g/L range with second-order regression) by using the Quick Start Bradford Protein Assay kit (Bio-Rad).

extract_protocol:
At each time point, 5 mL culture medium containing mycelia was filtrated on 1.2 µL GF/C glass microfiber membranes and flash frozen in liquid nitrogen. Frozen mycelia were disrupted and homogenized in Lysing Matrix C (Fast RNA Pro Red Kit, MP Bio) in the presence of 700 µL Lysis buffer RLT (RNeasy Mini Kit, Qiagen) complemented with 7 µL of β-mercaptoethanol on a rotor-stator homogenizer (FastPrep, MP Bio, Santa Ana, CA, USA). After centrifugation, the lysate was transferred on a Qiashredder spin column (Qiagen) and centrifuged for 2 min. to eliminate all cell debris. The flow-through was then mixed with 0.5 volumes of pure ethanol and transferred to an RNeasy spin column. All further steps, including an on-column DNAse digestion, were realized following the manufacturer’s instructions. RNA quantification was performed with Qubit 2.0 (Life Technologies, Carlsbad, CA, USA). The quantity and quality of the total RNA was determined using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, USA) and by electrophoresis on 1 % agarose gel. An additional quality control was performed on the Bioanalyzer 2100 system (Agilent, Santa Clara, USA).
Library preparation and Illumina sequencing were performed at the Ecole normale superieure Genomic Platform (Paris, France). Messenger (polyA+) RNAs were purified from 1 µg of total RNA using oligo(dT) primer. Libraries were prepared using the strand non-specific RNA-Seq library preparation TruSeq RNA Sample Prep Kits v1 (Illumina). Libraries were multiplexed by 4 on one single flowcell lane and subjected to 50 bp paired-end read sequencing on a HiSeq 2000 device

tag: growth

value: T48h Lactose

tag: phenotype

value: wild type


title: 2011_0030

tag: strain


title: unstimulated T-blast

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
Library strategy: Dnase-Seq
DNAse-seq reads were aligned to the hg19 genome assembly using Bowtie 2 to BAM to stdoutput using --very-sensitive-local | samtools view -S - -b -o <bam_file>
SAM to BAM conversion (samtools view -S stdinput -b -o stdoutput/bam file)
Optional BAM merging for SOLiD and Illumina datasets (samtools merge)
Tag shift (macs14)
Wig coverage track generation (macs14)
Peak detection (macs14)
Genome_build: hg19
Supplementary_files_format_and_content: Variable step 10bp wig files depincting DNaseI hypersensitivity coverage

source_name: Blast-cultured PBMC PHA-stimulated T-cells

growth_protocol: T cells were prepared from 20- or 50-ml peripheral blood samples obtained from healthy volunteers as follows. Mononuclear cells were purified by gradient centrifugation over Lymphoprep (Gibco) and cultured for 2 to 3 days in the presence of 2 μg of phytohemagglutinin per ml at a density of between 0.5 and 2 × 106 cells/ml. Nonadherent cells were then spun down and cultured for 4 to 7 days in fresh medium in the presence of 10 U of recombinant human IL-2 (Boehringer Mannheim) per ml at a density of 0.5 × 106 to 1.5 × 106/ml. Purity was assessed by staining for CD3. Under these conditions, we typically obtained cultures of approximately 97% CD3-positive T cells. Human peripheral blood T cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, 25 mM HEPES, 50 μM β-mercaptoethanol, 10 mM sodium pyruvate (Gibco), penicillin and streptavidin at 500 U/ml each (Gibco), 2 mM l-glutamine, 0.2% glucose, and minimal essential medium (MEM) essential amino acids and nonessential amino acids (Gibco)

extract_protocol:
NP-40 permeabilised cells were digested with DNase I for 3 minutes at 22oC as previously described (Bert et al). A range of DNase I concentrations was used to get the optimal digestion, the initial amounts varied depending on the cell type. Following DNA purification, samples were analysed by qPCR comparing the amount of PCR product generated between regions expected to be DNase I hypersensitive (e.g. TBP promoter) and regions which should not be cleaved (e.g. a gene desert region of chromosome 1). Optimally digested samples gave a ratio of ~0.7. DNA fragments (80-300bp) were isolated from favourable samples by agarose gel extraction and further validated by qPCR analysis before library preparation.
Libraries were prepared from approximately 10ng DNA from DNaseI samples. Libraries for sequencing on the Illumina were prepared using the Kapa HyperPrep library preparation kit. Samples were sequenced using 75bp reads on an Illumina NextSeq 500 sequencer

treatment_protocol: Cells were stimulated with 20ng/ml phorbol myristate acetate (PMA) and 2uM Calcium Ionophore (CaI) at a concentration of 1x106 cells/ml for up to 180 mins.

value: peripheral blood mononuclear cells (PBMCs)

tag: pma treatment

value: 0 min

tag: dnasei origin

value: Worthington


title: PMA/I 180 min stimulated T-blast

tag: tissue

value: 180 min


title: DOCK8 KO 2  activated

description: Voomnormalizedcounts.csv

value: DOCK8 KO

value: activated


title: 2011_0026

source_name: T. reesei QM6a, T24h Lactose

value: T24h Lactose


title: 2011_0029


title: HDEM-1

organism: Brassica oleracea var. botrytis

value: Brassica oleracea var. botrytis italica

value: progenitor CC

tag: generation


title: 2011_0027

source_name: T. reesei QM6a, T0 Glucose

value: T0 Glucose


title: ARO_YFB_S_R3

first: Balazs

last: Balint

state: Csongrad

address: Vallalkozok street

country: Hungary

institute: Seqomics Ltd

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 9.5.2). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package 2.1 of CLC Genomics Workbench Tool (v. 9.5.2) allowing intergenic mapping.  Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8.  mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Linear modeling with empirical Bayes moderation was built in limma. Package: limma, Version: 3.18.13
Genome_build: Reference sequence file: p3_i2_t47428_Arm_ostoy_v2.scaf (fasta file containing assembled reference genome for Armillaria ostoyae).  GFF3 annotation file: p3_i2_t47428_Arm_ostoy_v2.gff (gff3 annotation file containing genome annotation data for Armillaria ostoyae).
Supplementary_files_format_and_content: [*.CLC.RNA_Seq.csv.gz] Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool
Supplementary_files_format_and_content: [ARO_RPKM_22Nov2016.csv.gz] Supplementary file containing RPKM gene expression data matrix for all samples

organism: Armillaria ostoyae

source_name: young fruiting body, stipe

growth_protocol: RSTO medium  was prepared in 720 ml jars and inoculated with A. ostoyae C18, incubated for 28 days at 24 °C in the dark, then placed in a growth chamber at 15 °C with a 10/14 hour light/dark cycle. Light intensity: 11 µE / (m2*s).

extract_protocol:
Vegetative mycelia, rhizomorphs, stage I and II primordia, young and mature fruiting bodies were harvested. RNA was extracted by using the RNEasy Midi kit (QIAGEN, Cat.Num.: 75144) following the manufacturer’s instructions
PolyA RNA-Seq library was generated using TrueSeq RNA Library Preparation Kit v2 (Illumina, Cat.Num.: RS-122-2001 according to the manufacturer’s instructions.

tag: developmental stage (group)


title: 2011_0025


title: 2011_0038

source_name: T. reesei QM9978, T0 Glucose

value: cellulase negative


title: 2011_0042

source_name: T. reesei QM9978, T48h Lactose


title: 2011_0041


title: ARO_YFB_C_R2

source_name: young fruiting body, cap


title: ARO_YFB_C_R3


title: ARO_YFB_S_R1


title: ARO_YFB_S_R2


title: HDEM-2


title: 2011_0039

source_name: T. reesei QM9978, T24h Lactose


title: ARO_YFB_C_R1


title: ARO_VM_R3

source_name: vegetative mycelium

value: VM


title: ARO_VM_R2


title: ARO_VM_R1


title: 2011_0040


title: 2011_0037


title: ARO_RMA_R3

source_name: rhizomorp

value: RMA


title: Z1-1

value: Brassica rapa ssp. oleifera

value: progenitor AA

value: diploid 2x


title: ARO_RMA_R1


title: ARO_P2_S_R3

source_name: stage II primordium, stipe


title: ARO_RMA_R2


title: ARO_P2_S_R1


title: HDEM+Z1

description: 1:1 parental RNA mix used as a technical replicate to represent the additivity hypothesis

organism:
Brassica rapa
Brassica oleracea

source_name: stem

tag: sample type

value: Brassica oleacea + rapa mix

value: technical mix CC+AA

value: parent


title: ARO_P2_C_R3

source_name: stage II primordium, cap


title: ARO_P2_S_R2


title: GSF946-P23-G-3

city: Gary

first: Taeok

last: Bae

state: IN

address: 3400 Broadway

department: Microbiology & Immunology

institute: IU School of Medicine

data_processing:
Bases were called using bcl2fasta v2.16.0.10
Reads were quality and adapter trimmed using Trimmomatic v0.33 using default parameters, Illumina adapters, and a minimum read length of 30bps
Mapping was accomplished with bowtie2 version 2.1.0 by mapping to chromosome NC_007793
Counts were determined for genes and 100bp intergenic intervals using a custom perl script
Differential gene expression was identified using the program DESeq2 with default parameters
Genome_build: NC_008533.1
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest including genes and intergenic regions for each fastq file; intergenic regions are identified as follows Inter.<molecule>.<strand>.<basepair_begin>.<basepair_end>

organism: Staphylococcus aureus subsp. aureus USA300

growth_protocol: Cultures of strains USA300_P23 and USA300_P23_ ∆ftsH grown late-exponentially in TSB media at 37ºC. Starter cultures were used to inoculate 3 mL cultures of TSB broth in 15 mL test tubes.

extract_protocol:
To isolate RNA for RNA-sequencing, overnight culture in TSB was diluted 100 times in a fresh TSB and incubated in a shaking incubator at 37°C for 8 h.  After immediate stabilization of RNA in all samples by RNAprotect Bacteria Reagent (Qiagen), cells were collected by centrifugation, suspended in TE buffer (10 mM Tris HCl, pH 8.0, 1 mM EDTA) and treated with lysostaphin (50 µg/mL final concentration) at 37°C for 10 min. The resulting protoplasts were collected by centrifugation and RNA isolation was done using RNeasy Mini Kit (Qiagen), including on-column treatment with DNase I (Qiagen), according to the manufacturer’s recommendations. The amount and purity of all RNA samples isolated were assessed by NanoDrop spectroscopy (Thermo Fisher) and sent to the Center for Genomics and Bioinformatics at Indiana University. Sequencing libraries were constructed using the ScriptSeq Complete Kit for Bacteria (Epicentre).
cDNA libraries were prepared from total RNA by the Indiana University Center for Genomics and Bioinformatics. mRNA was enriched from one microgram total RNA using RiboZero rRNA Removal (Bacteria) Kit (Illumina, Inc., San Diego, CA, USA). rRNA-depleted mRNA samples were purified by Agencourt AMPure® XP beads (Beckman Coulter, Indianapolis IN, USA) and viewed using Agilent High Sensitivity RNA ScreenTape (Agilent Technologies, Inc., Santa Clara, CA, USA). Double stranded cDNA synthesis was performed using Illumina TruSeq Stranded mRNA Library Prep Kit in accordance with the manufacturer’s standard protocol. Enriched mRNA was fragmented using divalent cations via incubation for 8 min at 94oC. The first strand of cDNA was synthesized by reverse transcription using random-sequence primers. Second-strand synthesis was performed by subsituting dTTP with dUTP followed by digestion using Uracil-DNA-Glycosylase (UDG). A-tailing and adapter ligation was performed  followed by PCR amplification for 12 cycles using polymerase provided in kit. This step generated the second strand of cDNA and completed the addition of Illumina adapter sequences incorporating a user-defined barcode. The amplified libraries were purified using Agencourt AMPure® XP beads. Quality and quantity were assessed using an Agilent DNA1000 ScreenTape (Agilent Technologies, Inc., Santa Clara, CA, USA) and Picogreen assay kit (Invitrogen, Carlsbad, California, USA), respectively. Libraries were made single-stranded and diluted to 1.8pM, as per Illumina manufacturer's instructions. Cluster generation and sequencing was performed on an Illumina NextSeq500 using NextSeq 500/550 High Output v2 kit (75 cycles).
Single-end 80bp sequencing was performed on an Illumina NextSeq500 using NextSeq 500/550 High Output v2 kit (75 cycles).

value: Late-exponentially grown cells

tag: genotype/variation

value: ftsH mutant


title: ARO_P2_C_R1


title: ARO_P2_C_R2


title: GSF946-P23-G-2


title: ARO_P1_R2

source_name: stage I primordium


title: terrestrial-3

source_name: ramie roots

tag: developmental stage

value: terrestrial root at 30-day-old seedling

value: terrestrial root


title: GSF946-P23-2

value: ftsH wild-type


title: ARO_P1_R3


title: GSF946-P23-1


title: GSF946-P23-3


title: terrestrial-2


title: ARO_P1_R1


title: late-stage-3

value: late stage of aquatic root induction at 30-day-old seedling

value: aquatic root


title: late-stage-1


title: ARO_FB_S_R1

source_name: fruiting body, stipe


title: late-stage-2


title: ARO_FB_S_R2


title: terrestrial-1


title: Maple sap N. crassa 15min rep 1

description:
replicate 1
Ncrassa_Maple_lox.txt

source_name: conidia germination_maple sap

tag: timepoints

value: 15 minutes after inoculation

value: monokaryotic


title: ARO_FB_L_R3

source_name: fruiting body, lamella


title: ARO_FB_S_R3


title: ARO_FB_L_R1


title: ARO_FB_L_R2


title: early-stage-1

value: early stage of aquatic root induction at 5-day-old seedling


title: early-stage-2


title: early-stage-3


title: ARO_FB_C_R3

source_name: fruiting body, cap


title: GSF946-P23-G-1


title: HF Recovery

city: Singapore

first: Lee Lee

last: Wong

address: 14 Medical Drive, 08-01

department: Medicine

country: Singapore

institute: National University of Singapore

description: Biological pool sample from 4 HF-R, heart tissue harvasted after additional 14 days of dicontinuation of pacing

data_processing:
The raw NGS reads were subjected to data quality control via measurement of the quality score (Q-score, a prediction of the probability of an incorrect base-call) and filtered to remove background signals (short reads of <15 nucleotides [nts]). The remaining sequences with lengths between 15 to 30 nts were analyzed.
The sequence analyzing pipeline was carried out by performing alignment with known miRNAs in miRBase v21 with Blast
Mapping to the sheep genome with Bowtie Oar v4.0. NGS sequences with at least 10 counts and homology >70% (read length over miRNA length) were included.
Combining all three libraries, examine into sequence mapped to ovine genome and miRBase database
Genome_build: GCF_000298735.2_Oar_v4.0
Supplementary_files_format_and_content: each data files contained the mapping alignment to sheep genome and miRNAs sequence with counts provided

organism: Ovis aries

source_name: Left ventricular heart tissue

extract_protocol:
Total RNA were extracted from the frozen homogenized LV tissue using TRIzol® Reagent (Ambion, Austin, TX, USA) according to the manufacturer’s protocol. RNA concentration was determined by an ND-1000 Spectrophotometer (Nanodrop™, Wilmington, DE, USA), with OD260/OD280 and OD260/OD230 ratios ³1.90 required. The integrity of RNA was verified using the Bioanalyzer 2100 (Agilent Technology, CA, USA) with RNA integrity numbers (RINs) ≥6.5 required. All RNA samples were stored at −80°C until further processing.
Three RNA groups were generated from the pooling of 4 Cont, 6 HF and 4 HF-R samples, and 100 ng of total RNA from each group converted into three small RNA libraries using a NEBNEXT library generation kit (New England Biolabs Inc., Ipswich, MA, USA) according to the manufacturer’s instructions. Each pooled RNA sample was ligated with adaptors to its 3’ and 5’ ends and converted into cDNA before pre-amplification with specific primers containing sample-specific indexes. After 15 cycles, pre-PCR cDNA was purified on QiaQuick columns (Qiagen, Hombrechtikon, Switzerland) and the insert efficiency evaluated by the 2100 Bioanalyzer on high sensitivity DNA chips (Agilent Inc., Waldbronn, Germany). The miRNA cDNA were size fractionated (LabChip XT, Caliper Inc., Hopkintin, MA, USA) and bands representing adaptors and 15-50 base pair (bp) inserts were excised and collected. Based on quality of the inserts and the concentration measurements the 3 libraries were assembled in equal concentrations. The libraries were finally quantified again with qPCR and sequenced on the Illumina NextSeq 500 system (Illumina Inc., San Diago, CA, USA).

value: Left ventricular heart tissue-HF-R

value: Coopworth ewes

tag: treatment

value: sampled 26 days following cessation of pacing


title: Paced-induced HF

description: Biological pool sample from 6 HF, heart tissue harvested after 14 days of pacing at 225 bpm

value: Left ventricular heart tissue-HF

value: subjected to rapid LV pacing at ~220bpm for 13 days


title: Normal Control

description: Biological pooled sample from 4 Normal Control, heart tissue harvesteds

value: Left ventricular heart tissue-CONT

value: No treatment


title: ARO_FB_C_R1


title: Benta 6-1

status: Public on Sep 14 2017

city: Bethesda

first: Andrew

middle: L

last: Snow

state: Maryland

address: 4301 Jones Bridge Road, C-2013

department: Pharmacology & Molecular Therapeutics

institute: Uniformed Services University of the Health Sciences

data_processing:
Base calling was performed using Illumina bcl2fastq 2.17
Sequencing reads were aligned using TopHat Alignment v1.0 and hg19 human reference build
Transcript abundance counting and differential expression analysis was performed using Cufflinks Assembly & DE v1.1.0 on BaseSpace Onsite
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each sample

source_name: Blood

growth_protocol: Naive B cells cultured in Iscove’s modified Dulbecco medium + 10% fetal bovine serum + penicillin/streptomycin

extract_protocol:
Control and patient B cell pellets were harvested for total RNA isolation using the Qiagen RNeasy Mini Plus Kit
Total RNA input of 75 ng was used for library preparation using the Illumina Neoprep Stranded mRNA Library Preparation Kit
Stranded mRNA

treatment_protocol: Stimulated for 4 days with 10 ?g/ml of Affinipure F(ab’2) –fragment specific goat anti-human IgM + 1 ?g/ml anti-CD40 Ab + 100 ng/ml IL-21 and 20 U/ml IL-2 + 1:10,000 DMSO

tag: cell type

value: Naive B cells

value: IL-2 stimulation

tag: duration

value: 4 days


title: Control 2-2


title: Benta 2-2


title: Benta 4-2


title: Control 3-2


title: Control 4-2


title: Benta 4-1


title: Control 6-2


title: Control 4-1


title: Control 2-1


title: Benta 6-2


title: ARO_FB_C_R2


title: Benta 3-1


title: Control 6-1


title: Control 3-1


title: Benta 2-1


title: 8101: wt_ASO1_15wk_rep7

city: Carlsbad

first: Sagar

middle: S

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

data_processing:
demultiplexing and base-calling was performed by Illumina bcl2fastq2 software (version 2.17.1.14)
reads were associated to transcripts using a quasi-mapping based mode of Salmon  (version 0.7.2)
gene-level TPM was computed by normalizing number of reads mapped per transcript by number of mapped reads, using gene models from mouse ensembl build 81
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: comma-separated files containing gene symbol and TPM for genes

source_name: sciatic nerve

extract_protocol:
Standard Trizol RNA extraction method was used to extract RNA. RNA quantity and quality were determined using the Agilent Bioanalyzer. All samples RIN were > 8.
Digital gene expression (DGE) was performed by sequencing fragment libraries from purified total RNA as described previously (Patro et al., Nat Methods, 2017) using the QuantSeq 3' mRNA-Seq Library Prep Kit from Lexogen

treatment_protocol: For 5 wk-old mice, sciatic nerves were collected and immediately frozen for susequent RNA extraction. For 15 wk-old mice, mice were treated weekly with subcutaneous injection of PBS or ASO at 100 mg/kg for 9 weeks; mice were sacrificed at 2 days after the last dose.

value: sciatic nerve

tag: concentration

value: 100 mg/kg

tag: age (weeks)

tag: genotype

value: wt


title: 8098: wt_ASO1_15wk_rep4


title: 8103: wt_baseline_5wk_rep1

value: 0 mg/kg


title: 8096: wt_ASO1_15wk_rep2


title: 8105: wt_baseline_5wk_rep3


title: 8095: wt_ASO1_15wk_rep1


title: 8099: wt_ASO1_15wk_rep5


title: 8104: wt_baseline_5wk_rep2


title: 8097: wt_ASO1_15wk_rep3


title: Benta 3-2


title: 8094: wt_baseline_15wk_rep8

value: PBS


title: 8093: wt_baseline_15wk_rep7


title: 8088: wt_baseline_15wk_rep2


title: 8091: wt_baseline_15wk_rep5


title: 8089: wt_baseline_15wk_rep3


title: 8087: wt_baseline_15wk_rep1


title: 8090: wt_baseline_15wk_rep4


title: 8102: wt_ASO1_15wk_rep8


title: 7281: c22_ASO1_15wk_rep8


title: 8100: wt_ASO1_15wk_rep6


title: 7278: c22_ASO1_15wk_rep5


title: 7275: c22_ASO1_15wk_rep2


title: 7274: c22_ASO1_15wk_rep1


title: 7279: c22_ASO1_15wk_rep6


title: 7276: c22_ASO1_15wk_rep3


title: 7273: c22_PBS_15wk_rep8


title: 7272: c22_PBS_15wk_rep7


title: 7271: c22_PBS_15wk_rep6


title: 7262: c22_baseline_5wk_rep5


title: 7264: c22_baseline_5wk_rep7


title: 7265: c22_baseline_5wk_rep8


title: 7266: c22_PBS_15wk_rep1


title: 7269: c22_PBS_15wk_rep4


title: 7270: c22_PBS_15wk_rep5


title: 7267: c22_PBS_15wk_rep2


title: 7260: c22_baseline_5wk_rep3


title: 7263: c22_baseline_5wk_rep6


title: 7280: c22_ASO1_15wk_rep7


title: 7261: c22_baseline_5wk_rep4


title: 7277: c22_ASO1_15wk_rep4


title: 8092: wt_baseline_15wk_rep6


title: shNup153_D5_Atac_2

city: Dresden

first: Tomohisa

last: Toda

address: Tazberg 41

institute: German Center for Neurodegenerative Diseases

description:
TT_Atac_mNPC_shNup_D5_5_S5
TF peaks (150 bp or 300bp) called: TT_Atac_mNPC_shNup_D5_5_S5_R1_001_mm10_150_75_peaks.txt

data_processing:
ChIP/Atac-sequencing reads were trimmed for low base-quality using SolexaQA++ dynamic trim, v.3.1.3 and aligned to mm10 using bowtie2 version 4.8.4 --end-to-end --very-sensitive
RNA-sequencing reads were trimmed for low base-quality using SolexaQA++ dynamic trim, v.3.1.3 and aligned to mm10 using RSEM rsem-calculate-expression ( v.1.2.18) with bowtie2 version 4.8.4 expected counts (counts) and normalized transcripts per million (TPM) were calculated using RSEM
peaks were called with Homer v4.8.3 using either --style histone, or --style factor or size=300/minDist=75 o size=150/minDist=75 or size=500/minDist=500. IgG files or input file were used as controls where appropriate
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited regions files have the peaks called from homer using histone settings, peak files have the peaks called using transcription factor settings, the counts file is the raw RNA-seq file, and the tpm file is the normalized RNA-seq data.

source_name: Neural progenitor cells

growth_protocol:
The mouse NeuPC cell line from adult mouse hippocampus was cultured in DMEM/F-12 supplemented with N2 and B27 (Invitrogen) in the presence of FGF2 (20 ng/ml), EGF (20 ng/ml), and heparin (5 µg/ml).
The mouse NeuPC cell line from adult mouse hippocampus was cultured in DMEM/F-12 supplemented with N2 and B27 (Invitrogen) in the presence of FGF2 (20 ng/ml), EGF (20 ng/ml), and heparin (5 µg/ml).

extract_protocol: 50,000 mouse NeuPCs treated with plasmids harboring shRNA-GFP were sorted into ice-cold PBS, and the transposition reaction was performed. A DNA library was generated using NEBNext High-Fidelity 2x PCR Master Mix and Nextera custom primers. qPCR was used to estimate the number of PCR cycles required to determine the number of PCR cycles for 25% saturation and 10-12 cycles in total were used. The library was analyzed on Tape station analyzer (Agilent Technologies) and followed by deep sequencing with the Illumina’s NextSeq 500 at PE42.

value: Neural progenitor cell

tag: passage

tag: shRNA


title: 7259: c22_baseline_5wk_rep2


title: shCont_Atac_2

description:
TT_Atac_mNPC_Cont_2_S12
TF peaks (150 bp or 300bp) called: TT_Atac_mNPC_Cont_2_S12_R1_001_mm10_150_75_peaks.txt

tag: strain


title: shCont_Atac_3

description:
TT_Atac_mNPC_Cont_4_S2
TF peaks (150 bp or 300bp) called: TT_Atac_mNPC_Cont_4_S2_R1_001_mm10_150_75_peaks.txt


title: shNup153_D5_Atac_1

description:
TT_Atac_mNPC_shNup_D5_4_S4
TF peaks (150 bp or 300bp) called: TT_Atac_mNPC_shNup_D5_4_S4_R1_001_mm10_150_75_peaks.txt


title: 7258: c22_baseline_5wk_rep1


title: shNup153_D3_Atac_1

description:
TT_Atac_mNPC_shNup_1_S13
TF peaks (150 bp or 300bp) called: TT_Atac_mNPC_shNup_1_S13_R1_001_mm10_150_75_peaks.txt


title: shNup153_D3_Atac_2

description:
TT_Atac_mNPC_shNup_2_S14
TF peaks (150 bp or 300bp) called: TT_Atac_mNPC_shNup_2_S14_R1_001_mm10_150_75_peaks.txt


title: shNup153_D3_Atac_3

description:
TT_Atac_mNPC_shNup_D3_3_S3
TF peaks (150 bp or 300bp) called: TT_Atac_mNPC_shNup_D3_3_S3_R1_001_mm10_150_75_peaks.txt


title: shCont_Atac_1

description:
TT_Atac_mNPC_Cont_1_S11
TF peaks (150 bp or 300bp) called: TT_Atac_mNPC_Cont_1_S11_R1_001_mm10_150_75_peaks.txt


title: 7268: c22_PBS_15wk_rep3


title: Newborn_96hr_Chuong505

city: Los Angeles

first: Mingxing

last: Lei

state: California

address: 2011 Zonal Ave HMR 304A

institute: University of Southern California

data_processing:
The RNA-Seq alignment was performed by STAR 2.4.1d.  Mouse mm9 downloaded from the UCSC Genome Browser.
The quantification was performed by htseq-count 0.6.0 using the union mode
Genome_build: mm9
Supplementary_files_format_and_content: txt files including raw counts of sequencing reads for refGene produced by htseq-count

source_name: Newborn, 96 hrs

growth_protocol: 37℃ with 5% CO2 in incubator

extract_protocol:
Total RNA of dissociated culture cells were extracted using Trizol reagent
Illumina TruSeq RNA Sample Preparation V2

treatment_protocol: Reconstitution and in vitro culture

value: Balb/C

value: Newborn

value: cultured dorsal skin dissociated cells

tag: culture time

value: 96 hrs


title: YoungAdult_48hr_Chuong513

source_name: YoungAdult, 48 hrs

value: Young adult

tag: age

value: about 2 months

value: 48 hrs


title: YoungAdult_6hr_Chuong507

source_name: YoungAdult, 6 hrs

value: 6 hrs


title: Newborn_24hr_Chuong503

source_name: Newborn, 24 hrs

value: 24 hrs


title: YoungAdult_24hr_Chuong508

source_name: YoungAdult, 24 hrs


title: shNup153_D5_Atac_3

description:
TT_Atac_mNPC_shNup_D5_6_S6
TF peaks (150 bp or 300bp) called: TT_Atac_mNPC_shNup_D5_6_S6_R1_001_mm10_150_75_peaks.txt


title: YoungAdult_24hr_Chuong512


title: YoungAdult_0hr_Chuong506

source_name: YoungAdult, 0 hrs

value: 0 hrs


title: YoungAdult_48hr_Chuong509


title: Newborn_48hr_Chuong499

source_name: Newborn, 48 hrs


title: YoungAdult_0hr_Chuong510


title: Newborn_96hr_Chuong500


title: Newborn_6hr_Chuong497

source_name: Newborn, 6 hrs


title: YoungAdult_6hr_Chuong511


title: Newborn_6hr_Chuong502


title: Newborn_48hr_Chuong504


title: Newborn_0hr_Chuong496

source_name: Newborn, 0 hrs


title: Newborn_0hr_Chuong501


title: Newborn_24hr_Chuong498


title: shCont_RbSox2_1

description:
shNTC_RbSox2_1_S3
TF peaks (150 bp or 300bp) called: shNTC_RbSox2_1_S3_R1_001_mm10_peaks.txt

data_processing:
Library strategy: ChIP-mentation
ChIP/Atac-sequencing reads were trimmed for low base-quality using SolexaQA++ dynamic trim, v.3.1.3 and aligned to mm10 using bowtie2 version 4.8.4 --end-to-end --very-sensitive
RNA-sequencing reads were trimmed for low base-quality using SolexaQA++ dynamic trim, v.3.1.3 and aligned to mm10 using RSEM rsem-calculate-expression ( v.1.2.18) with bowtie2 version 4.8.4 expected counts (counts) and normalized transcripts per million (TPM) were calculated using RSEM
peaks were called with Homer v4.8.3 using either --style histone, or --style factor or size=300/minDist=75 o size=150/minDist=75 or size=500/minDist=500. IgG files or input file were used as controls where appropriate
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited regions files have the peaks called from homer using histone settings, peak files have the peaks called using transcription factor settings, the counts file is the raw RNA-seq file, and the tpm file is the normalized RNA-seq data.

extract_protocol: First, plasmids harboring shRNA-GFP were transfected into mouse NeuPCs, and GFP-positive cells were sorted into 10% FBS/PBS. Subsequently, cells were cross-linked with 1% formaldehyde at room temperature for 10 min. After sonicating cells by a M220 Focused-ultrasonicator (Covaris), lysate containing about 350,000 cells was aliquoted.　Chromatin was incubated withα-Sox2 (Cell Signaling) antibody at 4℃ overnight. Subsequently, protein A Dynabeads were transferred to tubes and incubated at 4℃ for 2 hours, and beads were washed. Beads were resuspended in tagmentation reaction solution, incubated for 10 min at 37℃, then cooled on ice. Beads were washed, chromatin was decross-linked, and DNA was extracted and purified by Ampure XP beads (Beckman). A DNA library was generated using 2xKapa HiFi HotStart Ready Mix and Nextera custom primers. qPCR was used to determine the number of PCR cycles, and 11-12 cycles in total were used. The library was analyzed on Tape station analyzer (Agilent Technologies) and followed by deep sequencing with the Illumina’s Hiseq2500 at SE50.

value: shControl

tag: chip antibody


title: shCont_RbSox2_2

description:
shNTC_RbSox2_2_S11
TF peaks (150 bp or 300bp) called: shNTC_RbSox2_2_S11_R1_001_mm10_peaks.txt


title: shNTC_Input

value: None (input)


title: shNup153_RbSox2_1

description:
shNup153_RbSox2_1_S4
TF peaks (150 bp or 300bp) called: shNup153_RbSox2_1_S4_R1_001_mm10_peaks.txt


title: shNup153_RbSox2_2

description:
shNup153_RbSox2_2_S12
TF peaks (150 bp or 300bp) called: shNup153_RbSox2_2_S12_R1_001_mm10_peaks.txt


title: mNPC_shNup153_3_3

description: mNPC_shNup153_3_3_TT-709-8-CGGCTA_CGGCTA_L008

extract_protocol: Three days after electroporation of plasmids encoding shRNA-EGFP using mouse NeuPCs, GFP-positive cells were sorted directly into Trizol-LS (Invitrogen). RNA was isolated according to the manufacturer’s instructions and digested with TURBO DNase (Life Technologies). RNA integrity numbers (RIN) were assessed using the Agilent Tape Station before library preparation. Poly(A)+ RNA was selected and fragmented to prepare sequencing libraries using the Illumina TruSeq Stranded RNA sample preparation kit. Libraries were sequenced single-end 50 bp (SE50) using an Illumina HiSeq 2500 sequencer at the Next Generation Sequencing (NGS) core at the Salk Institute according to manufacturer’s instructions (Illumina).


title: mNPC_shNup153_3_2

description: mNPC_shNup153_3_2_TT-708-8-TAATGC_TAATGC_L008


title: NFIA fl/fl; Pdx1-cre 1

city: Houston

first: Malgorzata

last: Borowiak

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
NextSeq Control Software v2.0 used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using TopHat Alignment v1.0.0
Fragment per kilobase million of library size (FPKM) were calculated using Cufflinks Assembly & DE v1.1.0
Genome_build: RefSeq mm10
Supplementary_files_format_and_content: control_vs_nfia.gene_exp.diff
Supplementary_files_format_and_content: control_vs_nfia.isoform_exp.diff

source_name: pancreas

extract_protocol:
phenol-chloroform with TRIzol
TruSeq Stranded mRNA kit

value: Mix, C57BL/6, 129SvEv, FvB

tag: tissue

value: pancreas

value: NFIA fl/fl; Pdx1-cre


title: NFIA fl/fl; Pdx1-cre 2


title: control 2

value: control (wildtype, NFIA fl/+, NFIA fl/fl)


title: control 1


title: mNPC_shNup153_2_2

description: mNPC_shNup153_2_2_TT-705-8-ATTCAG_ATTCAG_L008

value: Neural progenitor cell


title: mNPC_shCont_2

description: mNPC_shCont_2_TT-702-8-TCCGGA_TCCGGA_L008


title: mNPC_shCont_3

description: mNPC_shCont_3_TT-703-8-CGCTCA_CGCTCA_L008


title: NPC_RbIgG_1

extract_protocol: Approximately 3 x106 cells were cross-linked with 2.5 mM DSG and 1% formaldehyde at room temperature for 15 min. After quenching with 125 mM glycine, samples were briefly sheared by sonication and the concentration of DNA was measured by Nanodrop. Twenty µg of chromatin were treated with Micrococcal Nuclease (1 U/µl, Worthington), and chromatin was incubated with antibodies at 4℃ overnight. Immunoprecipitated complexes were collected using Dynabeads conjugated with anti-rabbit IgG (Life Technologies). Subsequently, beads were washed and DNA was extracted and purified by Ampure XP beads (Beckman). A DNA library was generated using NEBNext Ultra DNA library prep kit for Illumina and Bioo Illumina barcodes followed by deep sequencing with the Illumina’s Hiseq2500 at SE50.

value: RbIgG


title: mNPC_shNup153_2_3

description: mNPC_shNup153_2_3_TT-706-8-GAATTC_GAATTC_L008


title: NPC_RbNup153_1

description:
NPC_RbNup153_1--6-CGATGT_CGATGT_L006
Histone peaks called: NPC_RbNup153_1--6-CGATGT_regions.txt
TF peaks (150 bp or 300bp) called: NPC_RbNup153_1--6-CGATGT_peaks.txt
500bp called


title: mNPC_shNup153_2_1

description: mNPC_shNup153_2_1_TT-704-8-GAGATT_GAGATT_L008


title: mNPC_shNup153_3_1

description: mNPC_shNup153_3_1_TT-707-8-CTGAAG_CTGAAG_L008


title: Aged uterus rep1

city: Cambridge

first: Laura

last: Woods

address: Babraham Hall

country: United Kingdom

institute: The Babraham Institute

description: Sample 32

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.8, default parameters;  www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to the Mus musculus GRCm38 genome assembly using TopHat v2.0.12. Raw counts for DESeq2 analysis were generated at mRNA level using SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts RNA-Seq data files are tab-delimited and contain the following  columns: (1) Gene ID; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description; (7-40) Raw Counts for each sample

source_name: Uterus

growth_protocol: C57BL/6Babr mice were used throughout this study. Virgin females were caged in groups up to 5 until they had reached the desired age as indicated. All animal experiments were conducted in full compliance with UK Home Office regulations and with approval of the local animal welfare committee at The Babraham Institute, and with the relevant project and personal licences in place. Timed matings were set up with standard C57BL/6Babr stud males of 8-16 weeks of age, counting the morning of the vaginal plug as E0.5.

extract_protocol:
Total RNA was extracted using the Allprep DNA/RNA Mini kit (Qiagen 80204) followed by DNase treatment using the TURBO DNA-free kit (Life Technologies AM1907)
mRNA was isolated from total DNA-free RNA (350ng) using the Dynabeads mRNA purification kit (Life Technologies 61006). Indexed, strand specific libraries were prepared using the ScriptSeq v2 RNA-Seq Library Preparation kit (Epicentre SSV21106) according to the manufacturer's instructions. Libraries were quantified/assessed using both the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent). Indexed libraries were pooled and sequenced with a 100bp single-end protocol on an Illumina HiSeq2500 sequencer.

value: Uterus


title: Young uterus rep3

description: Sample 31


title: Nup153_RbFLAG_1

description:
Nup153_RbFLAG_1_S1
Histone peaks called: Nup153_RbFLAG_1_regions.txt
TF peaks (150 bp or 300bp) called: Nup153_RbFLAG_1_peaks.txt
500bp called

value: RbFLAG


title: Young uterus rep2

description: Sample 30


title: Cont_RbFLAG_1

description:
Cont_RbFLAG_1_S3
Histone peaks called: Cont_RbFLAG_1_regions.txt


title: Aged uterus rep2

description: Sample 33


title: Young timecourse E12.5 rep1

description: Sample 26

source_name: Decidua

value: Decidua


title: Young timecourse E12.5 rep2

description: Sample 27


title: Young uterus rep1

description: Sample 29


title: Young timecourse E11.5 rep1

description: Sample 23


title: Young timecourse E11.5 rep3

description: Sample 25


title: Young timecourse E12.5 rep3

description: Sample 28


title: Young timecourse E9.5 rep2

description: Sample 18


title: Young timecourse E10.5 rep1

description: Sample 20


title: Young timecourse E10.5 rep2

description: Sample 21