title: KO2

city: Cleveland

first: Xiaodong

last: Bai

address: 10900 Euclid Avenue

department: Center for RNA Molecular Biology

institute: Case Western Reserve University

data_processing:
Base-calling was performed using the Illumina pipeline software ELAND v1.7
Data were processed and aligned with the University of California-Santa Cruz (UCSC) mouse genome assembly and transcript annotation (mm9) using Genomic Short-read Nucleotide Alignment Program (GSNAP),.
The raw read counts for mouse RefSeq genes were extracted using HTSeq-count program and used for calculations of reads per kilobase per million mapped reads (RPKM) values
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample

extract_protocol:
Mice were euthanized by cervical dislocation. Eyes were enucleated and immediately placed in RNAlater stabilization reagent (Qiagen, Valencia, CA, USA) to preserve RNA content and integrity.
Two mouse retinas were homogenized at once and passed through a QIAShredder column (Qiagen) as per manufacturer’s directions to further homogenize the  tissues. Total RNA was then purified by using the RNeasy Mini Kit (Qiagen) with on column DNase treatment (Qiagen) as per manufacturer’s directions. Poly(A) RNA was isolated with the Oligotex kit (Qiagen) as per the manufacturer’s instructions. Pooled total RNA samples of 4 mice 4 weeks of age were used for each retina library preparation.
For first strand cDNA synthesis, instructions from the SuperScript III kit protocol (Invitrogen) were followed. About 400-450 ng of isolated poly(A) RNA was mixed with 50 ng of random primers and 1 mM deoxyribonucleotide triphosphate (dNTP), incubated at 65°C for 5 min and then placed on ice for 5 min. A reaction mixture comprising 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT, and 200 U SuperScript III reverse transcriptase was added to the initial mix to achieve a total volume of 20 µL. The mixture was incubated at 25°C for 10 min, followed by 50 min at 50°C. The reaction was terminated at 85°C for 5 min and then chilled on ice for 10 min. At this point, 2 U RNase H was added and the mix was incubated at 37°C for 20 min. The first strand cDNA synthesis reaction was immediately used for second strand synthesis. To the first strand product, 300 µM dNTP, E. coli DNA polymerase I buffer, and water was added to obtain a total volume of 95 µL and allowed to incubate on ice for 10 min. Then, 0.05 U E. coli DNA polymerase I (New England Biolabs, Beverly, MA, USA) was added and the mixture was incubated at 16°C for 2.5 h. The resulting double stranded cDNA was purified with the Wizard SV Gel and PCR Clean-up System (Promega, Madison, WI, USA) and eluted in 100 µL nuclease-free water and then fragmented by the Covaris S2 instrument (Woburn, MA, USA) to generate ~200 bp fragments as follows: 10% duty cycle, intensity of 5, 100 cycles per burst, with a bath temperature of 7.7°C and an acoustic power of 24 W.
The Illumina library was prepared according to the manufacturer’s instructions and purified using the Wizard SV Gel and PCR Clean-up System (Promega). Overhangs were converted into blunt ends with T4 DNA polymerase and Klenow DNA polymerase by incubating the mixed sample at 20°C for 30 min. cDNA was purified and eluted in 32 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The purified sample was then mixed with Klenow fragment (3’ to 5’ exo minus) and incubated at 37°C for 30 min to add an ‘A’ base to the 3’ end of the blunt phosphorylated DNA fragments. The cDNA was then purified and eluted in 23 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). Eluted DNA was mixed with Illumina Adapter Oligo mix and T4 DNA ligase and incubated at room temperature for 15 min to ligate adapters to the ends of the DNA fragments to prepare them for hybridization to the flow cell. cDNA then was purified and eluted in 10 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). cDNAtemplates were purified by running samples on a 1% agarose gel at 120 V for 60 min and excising the region of the gel in the 200 bp range. The 200 bp cDNA enriched fragments were purified and eluted in 30 µL of nuclease free water with the Wizard PlusMinipreps DNA purification system (Promega). cDNA in the library was then amplified by a 15 cycle PCR with two primers that annealed to the ends of the adapters. The amplified cDNA was purified and eluted in 30 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The size, purity and concentration of the final library was checked with the Bio-Rad Experion DNA specific chip. Each library was sequenced as one lane on an Illumina HiScan instrument.

tag: strain background

value: RHO_KO; Rhodopsin knockout

tag: age

value: 4 Weeks

value: eye


title: KO3

status: Public on Dec 31 2016

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype/variation

tag: tissue


title: Expt5_FU1-Vs-05_a103_rip

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: TOE1 expression induced to be roughly equal to endogenous levels

data_processing:
Demultiplexing: Reads were demultiplexed based on the presence of the gene-specific primer at the beginning of R2, and a random-mer was extracted off of the beginning of R1.
Read trimming: Reads were trimmed at the 3' end using the cutadapt program, with options "--discard-untrimmed flag -a Gene_Specific_Primer"
Tail counting: Non-PCR duplicate reads were counted by summing reads with the same sequence that did not have the same randommer sequence as any other read. Counts were performed for unique only (hamming distance > 0), as well as randommers at least 1 nt apart (hamming distance >1)
Genome_build: Analysis was done on raw reads without genome mapping
Supplementary_files_format_and_content: Processed files are tab-delimited files, with each line containing the sample ID, trimmed sequence, total number of observed reads for that sequence,  number of non-PCR duplicate reads for that sequence (hamming distance > 0), and number of non-PCR duplciate reads for that sequence (hamming distance > 1)

organism: Homo sapiens

source_name: HEK 293

extract_protocol:
One 10 cm dish of stable cell lines expressing FLAG-TOE1 variants was transfected twice with 20 nM siRNA targeting either luciferase or the 3’UTR of TOE1 using siLentFect (Bio-Rad) according to the manufacturer’s recommendations 72 h and 24 h before harvest. At ~50% confluency, cells were induced for 24 hours with tetracycline at 1 ng/ml. Cells were harvested in PBS and lysed in isotonic lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0.2 mM EDTA, 0.1% Triton X-100, 1 mM PMSF, 2 μg/mL aprotinin, 2 μg/mL leupeptin, 0.1 μg/ml yeast total RNA, 80 U/mL RNaseOUT (Invitrogen)) for 10 minutes on ice. Lysates were cleared at 20K x g for 15 min at 4°C. FLAG peptide was added to 1 μg/ml and lysates were incubated for 2 h with Anti-FLAG M2 beads (Sigma) at 4°C. Beads were then washed 8 times with NET2 (10 mM Tris, pH 7.5, 150 mM NaCl, 0.1% Triton X-100). One-fifth of the beads were eluted in protein loading buffer, and four-fifths of the beads were resuspended in Trizol (Life Technologies). RNA was extracted according to manufacturer’s protocol.
RNA adapters containing bar-codes and 10-11 nucleotide randomers were ligated to the 3’ ends of total and eluted RNA with T4 RNA ligase (NEB) at 16°C for 16 hours. Ligated RNA samples were treated with RQ1 RNase-free DNase (Promega) for 30 minutes at 37°C and extracted with PCA (Affymetrix). cDNA was generated from AR-17 primer with Superscript III (Life Technologies). 3’ ends were amplified by Q5 High-Fidelity DNA Polymerase (NEB) first, using snRNA gene-specific primers and AR-17, and then with primers D501 and D702 (Illumina). Libraries were purified on AMPure XP magnetic beads (Beckman), and validated by 2200 Tape Station Instrument (Agilent). Libraries were pooled at 4 nM, denatured with NaOH and diluted in HT1 buffer (Illumina) to 7 pM before sequencing with MiSeq Reagent Kit V2 Nano configuration (Illumina).

tag: cell line

value: HEK 293

tag: sirna

tag: rip antibody

value: Mouse anti-FLAG (Sigma)

value: A103 addback

value: NNNNNNNNNNNCT


title: polII-48hours-ChIPseq

city: Barcelona

first: Chris

last: van Oevelen

state: Catalunya

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

country: Spain

institute: Centre for Genomic Regulation (CRG)

library_source: genomic

data_processing:
Images obtained from high throughput sequencing were processed using the Illumina pipeline to generate raw sequence files, which were subsequently aligned to the mouse genome (mm9) using either the Illumina Eland alignment tool or Bowtie (cmd: bowtie -n 0 -l 28 -m 1 mm9 INPUT OUTPUT, Langmead et al, 2009, PMID: 19261174) without mismatches. Aligned sequences were further filtered to remove identical sequence tags and sequence tags that do not align uniquely to the mouse genome
To detect regions enriched for factor  binding relative to background, we used HOMER (http://biowhat.ucsd.edu/homer/ngs/index.html) (Heinz et al, 2010, PMID: 23064439) with the peak localization/shape option set to region and the style option set to factor.
Genome_build: mm9
Supplementary_files_format_and_content: USCS bed format: chr start end strand

molecule: genomic DNA

source_name: Haftl pre-B cells

growth_protocol: C10 cells were grown in RPMI 1640 without phenol red (Lonza) supplemented with 10% charcoal/dextran-treated FBS (Hyclone) and 50 μM 2-mercaptoethanol (GIBCO), incubated at 37°C in 5% CO2

extract_protocol: ChIP experiments were performed as described previously (van Oevelen et al, 2008, PMID:20956564). DNA libraries of C/EBPa and C/EBPb enriched chromatin fragments were prepared using Illumina's reagents and instructions. All other libraries were prepared according to manufacturer’s instructions with some modifications (Asp et al, 2011, PMID: 21551099). All libraries were sequenced on the Illumina 2AAIIx sequencer except C/EBPa and PU.1 libraries generated 10, 30 and 60 minutes post induction and pax5 (0 hours) and Foxo1 (0 hours) that were sequenced using the Illumina Hiseq2000 sequencer.

treatment_protocol: C10 cells were induced by the addition 100 nM of β-estradiol (Calbiochem) and grown with 10 nM of IL-3 and CSF-1 (Peprotech). Control cells were treated with 0.1% ethanol (solvent)

tag: cell type

value: haftl derived C10 cells

tag: time after induction

value: 48 hours

tag: chip antibody

value: Pol II (sc-899x, Santa Cruz)


title: polII-24hours-ChIPseq

value: 24 hours


title: Expt3_input-U5-DEaddback-siCaf1z


title: polII-12hours-ChIPseq

value: 12 hours


title: polII-3hours-ChIPseq

value: 3 hours


title: Expt3_input-U5-WTaddback-siCaf1z


title: KO1


title: Expt3_elu-U4-DEaddback

value: DEaddback


title: Expt3_elu-U4-WTaddback

value: WTaddback

value: NNNNNNNNNNCT


title: Expt3_input-U4-DEaddback-siCaf1z


title: polII-0hours-ChIPseq

value: 0 hours


title: Expt3_elu-U5-DEaddback


title: E2A-0hours-ChIPseq


title: Expt8_PATFIB_U1_ATCC

source_name: Primary Fibroblast

value: Primary Fibroblast


title: 310_SS

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
sRNAbench: expression profiling of microRNAs based on genome mappings generated by Bowtie aligner
sRNAde: differntially expressed microRNA identification, differentially expressed microRNA were defined from edgeR output table
miRNAconsTargets: consensus microRNA target prediction, using miRNAda and PITA
Functional anlaysis for target genes with Ingenuity Pathway Anlaysis
Genome_build: BosTau7
Supplementary_files_format_and_content: excel file, content is normalized expressional abundance (counts per million) of each microRNA from each animal

organism: Bos taurus

source_name: rectal tissue_Super-shedders

extract_protocol:
Two 2 cm^2 biopsies 3-5 cm proximal to the rectal-anal junction were collected from each animal and immediately flash frozen in liquid nitrogen within 10 min after death of the animal. Samples were stored at -80 °C until RNA was extracted. 100 mg of powdered rectal tissue was used for RNA extraction using a mirVana total RNA Isolation Kit
Illumina TruSeq Small RNA Sample Preparation kit

treatment_protocol: Cattle with two phenotypes, control group was cattle negative for E. coli O157, experimental group was cattle shedding > 10^4 CFU E. coli O157/g of feces

value: rectum

tag: phenotype

value: Super-shedders


title: 299_SS


title: Expt3_input-U4-WTaddback-siCaf1z

value: HEK 293


title: Expt3_elu-U2-WTaddback

value: Mouse anti-FLAG (Sigma)


title: Expt3_elu-U2-DEaddback


title: 294_SS


title: 274_SS


title: Expt3_input-U4-FLAGonly-siLuc

value: siControl

value: FLAG


title: Expt3_input-U4-FLAGonly-siCaf1z


title: 287_SS


title: CLOCK_ChIPSeq_NIH3T3_22h

city: Lausanne

first: Jonathan

middle: Aryeh

last: Sobel

state: Vaud

address: EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

description:
Chromatin
Processed data file: CLOCK_NIH3T3_filtered_withannot.bed

data_processing:
The obtained fastq raw sequence files were mapped to the mm9 genome using Bowtie allowing for three mismatches, but only one hit on the genome (Langmead et al., 2009). Mapped reads files were handled and manipulated using SAMtools (Li et al., 2009). Peaks were called using the MACS algorithm (Zhang et al., 2008; shift = 75, bandwidth = 150, genome size = 2.4 Gb) providing the input sample as background and deconvolved to find the center of the peak and a more refined binding site using custom scripts (Rey et al., 2011). These scripts were also used to quantify peaks and annotate binding sites to the closest Ensembl TSS (Curwen et al., 2004). This pipeline has been turned into an automated web-based station (http://htsstation.epfl.ch (David et al., 2014)), that was used for analysis of the 18-38h after-Dex time courses of anti-BMAL1 and anti-CLOCK ChIP-seq samples in NIH3T3 cells.
For anti-BMAL1 and anti-CLOCK ChIP-seq data binding sites were refiltered after obtaining the initial list of peaks, using custom criteria that take into account not only the area of the detected binding site but also the individual chromatin environment as assessed by including 20 background regions 1 kb up- and downstream of the peak.
1) ChIP signal needs to be three-fold enriched over input.
2) The site has to have higher tag density +2SD (standard deviations) than the mean of the neighboring regions.
3) The site has to have higher enrichment over input than the mean of the neighboring regions +2SD.
The binding sites in BED format were handled and manipulated using BEDTools (Quinlan and Hall, 2010). Quantification of the signal at binding sites was performed with a script based on the code provided by Rey et al., 2011, which counts tags mapped to the genome in a given window (usually ±250bp around the center of the binding site as determined by deconvolution) and normalized to total number of tags.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Wig: enrichment score over input; Bed: chromosome, start, end, closest gene symbol (if present in file), distance to TSS (if present in file).

source_name: NIH3T3 cells, 22h, CLOCK ChIP

growth_protocol:
NIH3T3 fibroblasts were kept in DMEM high glucose medium (Life Technologies) supplemented with 1% Penicilling/Streptomycin/Glutamate (PGS; Sigma Aldrich) solution and 10% fetal calf serum (FCS, Sigma Aldrich). They were split using trypsin (Tryple Express, Life Technologies) as detaching and dissociation agent as necessary depending on experimental conditions or when reaching confluency. For synchronization with dexamethasone (Dex; Sigma Aldrich), cells were incubated for 30 minutes with 100 nM Dex solution (stock 100µM in ethanol), then washed once with PBS and supplied with fresh medium.
Mice: C57/BL6, 12-14 wk-old, 12h/12h LD, food ad libitum.

extract_protocol:
Anti-BMAL1 and anti-CLOCK antibodies were kindly provided by Prof. Michael Brunner (University of Heidelberg). For chromatin preparation, medium of two confluent 15 cm dishes (approximately 10,000,000 cells each) per timepoint was removed, 6 ml PBS+1% fresh formaldehyde were added and cells were placed for 5' at 37°C in the incubator. Cells were washed twice with ice cold PBS and the reaction was stopped with 1.5 ml stop solution (125 mM glycine or 100 mM Tris pH 9.4, 10 mM DTT). Cells were scraped off the dish, transfered to 2 ml tubes, kept on ice for 15', then at 30°C for 15' and vortexed. Lysates were spun down 1' at 2500 rpm, 4°C, supernatant was removed. 500 µl sol II (10 mM EDTA, 1 mM EGTA, 10 mM HEPES pH 6.8, 0.25% Tx-100) were added, tubes were vortexed to resuspend and spun down 5' at 2500 rpm, 4°C. Supernatant was removed, 500 µl solIII (1mM EDTA, 1mM EGTA, 10 mM HEPES pH 6.8, 200 mM NaCl) were added. Tubes were vortexed to resuspend, spun down 5' at 2500 rpm, 4°C and supernatant was removed.
The nuclei from the two plates per sample were united in 300 µl nuclei resuspension buffer (22 mM Tris pH 7.4, 165 mM NaCl, 2.2 mM EDTA) + 1% SDS and sonicated 20 min (30" on/off cycles) in a Bioruptor ultrasonicator 4°C water bath (Diagenode) to obtain a fragment size of approx. 250 bp. Chromatin was diluted in 2700 µl chromatin dilution buffer (20 mM Tris pH 7.4, 150 mM NaCl, 2 mM EDTA, 1.1% Tx-100) and aliquoted (500 µl per IP + 5 µl Input).
To submit DNA purified from ChIP samples for sequencing, we pooled several IPs to collect 10ng of DNA. We precipitated the DNA using standard sodium acetate precipitation to resuspend it in a small volume and measured the amount of DNA on a Qubit 2.0 fluorometer (Life Technologies). Sample DNA as well as input DNA as control were submitted for Illumina deep sequencing at the Lausanne Genomic Facility (University of Lausanne).
A total of 5-10 ng DNA were used for the preparation of the library. Libraries for ultra-high-throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.

treatment_protocol: NIH3T3 cells were synchronized by dexamethasone.

tag: treatment

value: dexamethasone synchronized

tag: time post-dex synchronization

value: anti-CLOCK


title: 242_NS

source_name: rectal tissue_negative for E. coli O157

value: negative for E. coli O157


title: Expt3_input-U2-FLAGonly-siCaf1z


title: Expt3_input-U2-WTaddback-siCaf1z

value: NNNNNNNNNNNCT


title: 152_NS


title: 108_NS


title: Expt3_input-U2-DEaddback-siCaf1z


title: 165_NS


title: Expt3_elu-U1-Deaddback


title: Expt3_elu-U1-WTaddback


title: Expt3_input-U2-FLAGonly-siLuc


title: Expt3_input-U1-DEaddback-siCaf1z


title: RL1A

city: Haerbin

first: Chunmei

last: wang

address: 59 MuCai Street

country: China

institute: Northeast Agricultural University

data_processing:
We use software developed by BGI to deal with the data from HiSeq sequencing
Map the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome using Bos_taurus.UMD3.1.74.dna.toplevel.fa.
Align small RNA to the miRNA precursor of corresponding species (mature miRNA if there is no precursor information of that species in miRBase18) to obtain the miRNA count as well as base bias on the first position of identified miRNAs with certain length and on each position of all identified miRNAs respectively.
Small RNAs including miRNA, siRNA, piRNA, rRNA, tRNA, snRNA, snoRNA，repeat associated sRNA and degraded tags of exon or intron. using a protocol from Hafner et al.,Methods 44(1): 3-12,2008
Annotate the small RNA tags for rRNA, scRNA, snoRNA, snRNA and tRNA from Genbank and get rid of matched tags from unannotated tags.
Genome_build: Bos taurus.UMD3.1.74
Supplementary_files_format_and_content: tar archive of .txt files with abundance measurements for each type of gene feature

source_name: mammary gland

extract_protocol:
Mammary gland  were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat# RS-122-2001) was used with 1 ug of small RNA for the construction of sequencing libraries. miRNA and ncRNA libraries were sequenced using BGI Small RNA Solexa Sequencing protocol

value: mammary gland

tag: 305d matured equivalency

tag: milk fat percentage

tag: milk protein percentage

tag: dry  matter milk content

tag: somatic cell sore


title: RH1A


title: RP1A


title: Expt3_input-U1-FLAGonly-siCaf1z


title: pr67

city: Milan

first: Chiara

last: Ronchini

address: Via Adamello, 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

description: processed data files: reads_uniq_mapped_133871.txt, RISs.bed, CISc.bed

data_processing:
De-multiplexing of data: retroviral insertions were amplified, primed and sequenced such that the 4-bp leukemia-identifying barcode always appeared at the beginning of the sequence (read). We scanned via R positions 1-4 of all reads for the presence of the leukemia barcode not allowing mismatches since the barcodes might differ by only 1 bp (an N or an error in the 4-bp tag). We successfully assigned 98.5% of all reads to a leukemia-code (the unassigned sequences (~1.54% of all reads (4384/283331) were not processed further).
Identification of genomic inserts: in order to identify and remove the viral sequences, we applied EMBOSS fuzznuc (Rice P et al. Trends in Genetics, 2000) to match the 25 bp SupF allowing 3 mismatches (12.5% of the SupF). We sequentially attempted to match the 50 bp LTR sequence using BLASTN in both sense and antisense orientations. For each read the longest identified sequence was trimmed. Rare unexpected patterns (multiple SupFs or inverted orientations) were inspected manually. Reads with none genomic insert after SupF and LTR removal were not processed further.
Identification of retroviral integration sites (RISs): we mapped the RISs to the mouse genome (NCBI Build 37), using BLAT with the requirement to match at least 96% identity. Multiple alignments were excluded. Each genomic insert had to match unequivocally one position on the genome.
Identification of common integration sites (CISs): we applied two independent statistical approaches: Monte Carlo simulations (Mikkers et al., 2002) and Gaussian kernel convolution (de Ridder et al., 2006).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include all sequence reads univocally mapped onto the mouse genome, with their genomic coordinates and orientation and the leukemia they belong to.
Supplementary_files_format_and_content: BED files for RISs and CISs alignments to the mouse genome

source_name: Leukemic spleens

extract_protocol:
Genomic DNA was isolated from leukemic spleen cells using Genomic DNA isolation kit (QIAGEN) according to the manufacturer’s instructions.
The genomic DNA flanking the viral site of integration was cloned using the Inverse PCR (IPCR) technique. Briefly, the DNA (2 mg) was digested with TaqIa restriction enzyme and ligated at low concentration (20 ng) with T4 DNA ligase, in order to obtained circularized fragments. 5 ng of ligated DNA was amplified by two subsequent rounds of PCR, using primers specific for the LTR and the SupF viral sequences and containing the short adaptors required for sequencing with the GeneFlex technology. A 4-bp barcode (tag) in the Nested primer LTR allowed multiplexing and sequencing of 48 tumors in 4 pools of 12 leukemias each.

treatment_protocol: PML/RAR KI newborn mice were injected i.p. with viral supernatant containing high titer MLV. At signs of disease mice were sacrificed and underwent necropsy. Infiltrated organs were collected and frozen.

tag: strain background

tag: mouse model

value: PML/RAR KI transgenic mice infected with Moloney Murine Leukemia Virus (MLV)

value: Spleen

tag: tumor stage

value: Full leukemia


title: Expt3_input-U1-FLAGonly-siLuc

tag: cell line

value: NNNNNNNNNNCT


title: pr68

tag: tissue


title: pr65


title: pr61


title: pr63


title: pr60


title: Expt2_elu-U6-DEaddback

tag: sirna

tag: rip antibody

value: DEaddback


title: Expt2_elu-U6-Wtaddback

value: WTaddback


title: pr59


title: Expt2_input-U6-WTaddback-siCaf1z


title: pr56


title: pr57


title: Expt2_input-U6-FLAGonly-siLuc


title: Expt2_input-U6-FLAGonly-siCaf1z


title: Expt2_elu-U5-WTaddback


title: pr55


title: Expt3_input-U1-WTaddback-siCaf1z


title: Expt2_input-U5-DEaddback-siCaf1z


title: Expt2_input-U5-WTaddback-siCaf1z


title: pr53


title: pr54


title: Expt2_elu-U4-WTaddback


title: Expt2_input-U4-DEaddback-siCaf1z


title: Expt2_input-U4-WTaddback-siCaf1z


title: pr49


title: pr47


title: Expt2_input-U6-DEaddback-siCaf1z


title: pr48


title: pr46


title: Expt2_elu-U5-DEaddback


title: pr51


title: Expt2_input-U4-FLAGonly-siLuc


title: Expt2_input-U4-FLAGonly-siCaf1z


title: Expt2_elu-U2-WTaddback


title: pr39


title: pr44


title: Expt2_input-U2-DEaddback-siCaf1z


title: Expt2_input-U2-FLAGonly-siCaf1z


title: pr42


title: pr38


title: Expt2_elu-U4-DEaddback


title: Expt2_input-U2-FLAGonly-siLuc


title: pr52


title: Expt2_elu-U1-DEaddback


title: pr58


title: pr37


title: Expt2_elu-U1-WTaddback


title: pr35


title: Expt2_input-U1-DEaddback-siCaf1z


title: Expt2_elu-U2-DEaddback


title: pr45


title: pr34


title: Expt2_input-U1-FLAGonly-siCaf1z


title: Expt2_input-U1-WTaddback-siCaf1z


title: pr29


title: pr28


title: pr31


title: pr33


title: Expt1_elu-U2-WTaddback

value: CAGCTTNNNNT


title: Expt2_input-U1-FLAGonly-siLuc


title: Expt1_elu-U2-Deaddback


title: pr27


title: pr24


title: pr23


title: Expt2_input-U2-WTaddback-siCaf1z


title: Expt1_input-U2-WTaddback-siCaf1z


title: Expt1_input-U2-FLAGonly-siCaf1z


title: pr22


title: pr36


title: pr21


title: Expt1_elu-U1-DEaddback


title: Expt1_input-U2-FLAGonly-siLuc


title: pr17


title: Expt1_elu-U1-WTaddback


title: pr16


title: pr15


title: pr11


title: Expt1_input-U1-DEaddback-siCaf1z


title: Expt1_input-U1-FLAGonly-siCaf1z


title: Expt1_input-U1-WTaddback-siCaf1z


title: Expt1_input-U1-FLAGonly-siLuc


title: pr8


title: Expt5_FU1-Vs-15_de_tot


title: Expt1_input-U2-DEaddback-siCaf1z


title: pr6


title: pr4


title: pr7


title: pr5


title: pr1


title: wildtype larvae replicate 2

city: Providence

first: Hua

state: RI

address: 34 Olive St, BMC502

department: EEB

institute: Brown University

data_processing:
MiSeq Imaging and Base Calling Script
Galaxy-FastQ trimmer. Offset from 5' end:9 bp. Offset from 3' end: 5 bp.
Galaxy-Tophat2: Mapping the reads against a reference genome
Galaxy-Cufflinks: Reconstructing Transcripts
Galaxy-Cuffmerge: Merge together several Cufflinks assemblies
Genome_build: Galaxy-Cuffdiff: Find significant changes in transcript expression
Supplementary_files_format_and_content: List of differential expressed gene

organism: Drosophila melanogaster

source_name: wildtype larvae

growth_protocol: Flies were maintained at 25°C, 40% relative humidity and 12-hour light/dark. Adults were reared on agar-based diet with 0.8% cornmeal, 10% sugar, and 2.5% yeast

extract_protocol:
Message RNAs were extracted using Poly-A mRNA isolation kit (Promega) from wildtype and kr-h1[7] homozygous 3rd instar larvae at 100 hr AEL. After fragmentation, message RNAs were reverse transcribed to cDNA following be double-stranded DNA synthesis.
Libraries made using PrepX library prep kits with double-stranded cDNA (sheared to 320 bp insert using Covaris shearing) and ligated to Illumina adapter and indices (see below) using the WaferGen Apollo 324 robot (end repair, a-tailing, adapter/index ligation, and size-selection using Ampure XP beads) and PCR enrichment and cleanup of the final library.
NextGen sequencing was performed using Illumina MiSeq paired-end sequencing, and MiSeq v2 300-cycle kit.

tag: Stage

value: 100 hr after egg laying

tag: genotype/variation

value: wild type

value: whole larvae


title: wildtype larvae replicate 1


title: LL miRNA-Seq

city: Beijing

first: Zhixiu

last: Wang

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

data_processing:
The Fastx (FastX_Toolkit v. 0.0.13.2) was applied to obtain clear reads from the raw data by removing the joint sequences, low-quality fragments, and sequences of <18 nucleotides (nt) in length.
The CLC Genomics Workbench 5.5 software was used to align the sequences to the Sanger miRBase v19.0, and during this process, no mismatch was allowed.
In addition, other noncoding RNA databases such as ncRNA, piRNA, and Rfam databases were used for alignment, and two base mismatches or the shortening or extension of both ends by two bases was permitted in the target sequences. The clear sequence reads were aligned with miRBase v19.
Genome_build: miRBase v19.0
Supplementary_files_format_and_content: tab-delimited text files include reads count and expression values  for DSP TP LL YY. Expression values in columns such as "DSP_expression"  were calculated as expression value=(read count *1,000,000)/total_ read number

organism: Sus scrofa

source_name: Longissimus dorsi muscle of pig

extract_protocol:
Longissimus dorsi muscle were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. “Balancer NGS Library Preparation Kit for small /micro RNA Guide"  was used with 1 ug of total RNA for the construction of sequencing libraries.
Balancer NGS Library Preparation Kit for small /micro RNA Guide

tag: pig breed

value: Landrace

tag: pig type

value: introduced pig breed

value: Longissimus dorsi muscle


title: kr-h1 mutant larvae replicate 2

description: kr-h1 mutant-2

source_name: kr-h1 mutant larvae

value: kr-h1 mutant


title: kr-h1 mutant larvae replicate 1

description: kr-h1 mutant-1


title: pr2


title: TP miRNA-Seq

value: Tibetan pig

value: indigenous Chinese pig breed


title: DSP miRNA-Seq

value: Diannan Small Ear pig


title: YY miRNA-Seq

value: Yorkshire


title: YY RNA-Seq

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using CLC Genomics Workbench(version:4.8)
Clean reads were aligned onto the whole reference genome (Sus scrofa 10.2)  using TopHat
The number of fragments per kilobase of exon length million mapped reads (FPKM) analyzed by Cufflink (version 2.0.2) was used as the value of the normalized gene expression.
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for DSP TP LL YY

extract_protocol:
Longissimus dorsi muscle were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq RNA Sample Preparation Guide (Part#15008136 Rev.A, Illumina)  was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: LL RNA-Seq


title: TP RNA-Seq


title: Ovary rep 3

city: Palmerston North

first: Andre

last: Sim

address: Tennent Dr

department: Institute of Fundamental Sciences

country: New Zealand

institute: Massey University

data_processing:
Quality control with fastq-mcf, DynamicTrim (-h 20) and Lengthsort
Mapping with Tophat with library type set as "fr-firststrand"
Read counts generated with Htseq-count against Nasonia vitripennis OGS2
Differential analysis with DESeq
Genome_build: GCF_000002325.3
Supplementary_files_format_and_content: Deseq output table showing normalized read counts and fold change (>1 fold change is up in VG)

organism: Nasonia vitripennis

source_name: Ovary

extract_protocol:
Venom gland (VG) and ovary tissue was dissected under aseptic conditions and placed immediately into ice cold Trizol. Each replicate contained VG or ovaries tissue pooled from between 40-50 individual 1-3 day old mated and host exposed female wasps. RNA was extracted using the modified trizol plus kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Lab II

value: Ovary


title: Venom Gland rep 3

source_name: Venom Gland

value: Venom Gland


title: Ovary rep 2


title: Venom Gland rep 1


title: Ovary rep 1


title: Venom Gland rep 2


title: Reaeration day 4, replicate 2

city: Newark

first: Lanbo

last: Shi

state: NJ

address: 185 South Orange

institute: Rutgers University

description:
day4.2
D4-2
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt

data_processing:
Base-calling, QC and adapter removal were performed by BGI.
Alignment performed by BOWTIE2 with H37Rv reference genome.
Read counts and normalization done by HTSeq and DESeq package in R.
Differential expression was called by DESeq.
Genome_build: M. tuberculosis H37Rv (NC_018143.2)
Supplementary_files_format_and_content: normalizedCounts.txt: Tab-delimited text file contains a table where genes are in rows and samples are in columns. Each cell is normalized counts for a gene in a sample.

organism: Mycobacterium tuberculosis H37Rv

source_name: bacteria, reactivation, day 4

growth_protocol: Mid-logarithmic M. tuberculosis cultures of H37Rv WT were grown in Dubos Tween Albumin (DTA) medium and subjected to the Wayne low oxygen model for 25 days.

extract_protocol:
Regrowth cultures were harvested by centrifugation after treatment with RNAprotect Bacteria Agents (Qiagen) for 15 minutes to stabilize RNA, and RNA was extracted with Trizol.
rRNAs were first removed from total RNAs using the Ribo-zero rRNA removal kit (Epicenter, Applied Systems); after mRNA fragmentation, first strand cDNA synthesis was carried out using Super Script II (Invitrogen) reverse transcription system; after the second strand cDNA synthesis, the double strand (ds) cDNAs were repaired and their 3' end adenylated for adapter ligation; after ligating multiple indexing adapters, the dsDNA library was enriched by PCR and validated; the qualified library was amplified and sequenced with 90 bp pair-end reads.

treatment_protocol: Regrowth was initiated by reaeration.

tag: strain/background

value: WT

tag: growth condition

value: reaeration

tag: timepoint

value: day 4


title: Reaeration day 4, replicate 3

description:
day4.3
D4-3
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt


title: Reaeration day 4, replicate 1

description:
day4.1
D4-1
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt


title: Reaeration day 3, replicate 1

description:
day3.1
D3-1
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt

source_name: bacteria, reactivation, day 3

value: day 3


title: Reaeration day 3, replicate 3

description:
day3.3
D3-3
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt


title: DOA10 delete 90hrs

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

department: School of Engineering

country: Israel

institute: The Hebrew University of Jerusalem

description: plasmid insert sequence

data_processing:
Illumina bcl2fastq to extract read pairs
Filter read pairs, retaining only ones that contained the flanking signature sequences from the plasmid, and if the sequence frame relative to the URA was positively identified
Reads were aligned to the yeast genome using bowtie2
Fragments were counted to bins according to their frame relative to the URA protein, and their sequence.
Genome_build: sacCer3
Supplementary_files_format_and_content: CSV file describing the location of the fragement, and their counts in each of the libraries

organism: Saccharomyces cerevisiae

extract_protocol:
Plasmids were purified from yeast pellets equivalent to 10OD using AccuPrep Plasmid MiniPrep DNA Extraction Kit (Bioneer; Republic of Korea).
Sequencing Library preparation consisted of two amplification steps. The first step (18 cycles) was performed using primers flanking the peptide, with overhangs complementary to Illumina adapters. A primer mix was used to increase library complexity for downstream NGS step. The second step was performed with the standard N-series Illumina barcoded adapters (12 cycles). Sequences were size selected to 200-800bp using Ampure XP beads for next generation sequencing (Agencourt). Instrument models used: Illumina MiSeq and Illumina NextSeq 500.

tag: plasmid type

value: cytosolic

tag: genetic background


title: Hypoxia nongrowing, replicate 3

description:
day0.3
D0-3
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt

source_name: bacteria, persistence, day 0

value: hypoxia

value: day 0


title: Reaeration day 2, replicate 1

description:
day2.1
D2-1
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt

source_name: bacteria, reactivation, day 2

value: day 2


title: Reaeration day 1, replicate 3

description:
day1.3
D1-3
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt

source_name: bacteria, reactivation, day 1

value: day 1


title: Reaeration day 1, replicate 2

description:
day1.2
D1-2
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt


title: DOA10 delete 96hrs

description: plasmid insert sequence


title: DOA10 delete 78hrs

description: plasmid insert sequence


title: Reaeration day 2, replicate 3

description:
day2.3
D2-3
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt


title: Hypoxia nongrowing, replicate 1

description:
day0.1
D0-1
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt


title: Reaeration day 1, replicate 1

description:
day1.1
D1-1
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt


title: DOA10 delete 64hrs

description: plasmid insert sequence


title: DOA10 delete 46hrs

description: plasmid insert sequence


title: Hypoxia nongrowing, replicate 2

description:
day0.2
D0-2
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt


title: DOA10 delete 0hrs

description: plasmid insert sequence


title: DSP RNA-Seq

value: Longissimus dorsi muscle


title: DOA10 delete 72hrs

description: plasmid insert sequence


title: Nuclear 24hrs

description: plasmid insert sequence

value: nuclear


title: Reaeration day 3, replicate 2

description:
day3.2
D3-2
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt


title: Nuclear 0hrs

description: plasmid insert sequence


title: Cytosolic 48hrs

description: plasmid insert sequence


title: Reaeration day 2, replicate 2

description:
day2.2
D2-2
RNA fractions
Paired end, strand-specific
Processed data file: normalizedCounts.txt


title: Cytosolic 0hrs

description: plasmid insert sequence


title: Cytosolic 24hrs

description: plasmid insert sequence


title: Nuclear 72hrs

description: plasmid insert sequence


title: Morocco-MCCFC_96h-rep1

city: Manhattan

first: William

middle: Brock

last: Rutter

state: KS

address: 1712 Claflin Road

department: Plant Pathology

institute: Kansas State University

description: Biological replicate 1

data_processing:
Basecalls were performed using Illumina CASAVA software
Raw sequencing reads were pre-processed. adapters were removed and each read was quality trimmed and filtered to a minimum quality score of 15, a minimum length of 30bp (cutadapt v1.1 and fastx_toolkit v0.0.13 ). Low quality reads with less 80% of their bases having quality scores of at least 15 were removed
Tritticum aestivum reads were aligned using Tophatv2.0.10 with maximum read segment mismatch=1 and the defaults for all other parameters.  Puccinia gramminis reads were aligned using default Tophatv2.0.10 parameters
Aligned reads from both the fungal isolates and wheat were analyzed separately and FPKM values were calculated using the tuxedo pipeline as described in the Cufflinks2 manual
Genome_build: NZ_AAWC00000000.1, FAOM00000000.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Triticum aestivum

source_name: Infected Wheat Leaf tissue

growth_protocol: wheat was grown in a controlled growth chamber environment (16hours light, 8hours dark,  22C) for 14 days before inoculation with fungus

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life Technologies) according to manufacturer’s guidelines
mRNA specific sequencing libraries were constructed using the TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer’s protocol

treatment_protocol: Plants were inoculated by suspending 5 mg urediniospores per mL Soltrol 170 (Philips 66, Bartlesville, OK) and spraying onto leaves using an atomizer at 40 psi. Following inoculation, plants were incubated in a dew chamber at 100% humidity for 24h at 18C. Plants were then moved back into growth chambers.

tag: host cultivar

value: Morocco

tag: host tissue

value: Leaf

tag: treatment (inoculation of host)

value: Puccinia graminis isolate 59KS19

tag: time (hours post inoculation)


title: Morocco-MCCFC_96h-rep2

description: Biological replicate 2


title: Morocco-MCCFC_48h-rep3

description: Biological replicate 3


title: Cao-1

city: Alicante

first: Angel

last: Barco

address: Ramon y Cajal

department: Neuro Plasticity

institute: NeuroSciences Institute of Alicante CSIC

data_processing:
reads quality was checked with FastQC
adapters were eliminated cutting 10bp with trimmomatic v0.32
paired end reads were mapped to TAIR10 genome with tophat v2.010, default options
counts mapping in genes were counted in bam files using Htseq using the TAIR10.gff annotation
counts mapping in introns present in the first isoform of genes annotated in TAIR10  were counted in bam files using Htseq and a intron.gff file derived form TAIR10.gff
counts were further processed in R. Batch effect was corrected using the RUVseq package. Differential gene expression and differential intron abundance analyses were performed in RUVseq-corrected counts with the package DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: gene_count.tsv file generated with HTseq contains RNA counts in whole genes acording to TAIR10 annotation
Supplementary_files_format_and_content: intron_count.tsv file generated with HTseq contains RNA counts in introns from the first isoform acording to TAIR10 annotation

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: wt and mutant plants were grown in parallel at SD conditions for 15 days. Samples were harvested 1h before dark.

extract_protocol:
RNA was extracted from rosette leaves using TRIzol Reagent according to manufactures recommendations (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols, Truseq SBS Kit v3. RIbosomal RNA was removed using the Ribo-Zero Magnetic kit Plant leaf (cat# MRZPL116, EpiCentre) starting with 1.5μg total RNA. Sequencing libraries were generated from the rRNA depleted RNA using the ScriptSeq v2 RNAseq library prep kit (cat# SSV21124, EpiCentre).

tag: ecotype

value: cao mutant

tag: tissue

value: rosette leaves

tag: biological replicate


title: Morocco-MCCFC_96h-rep3

description: Biological replicate 3


title: Col-1

value: wild type


title: Cao-2


title: Morocco-MCCFC_72h-rep2

description: Biological replicate 2


title: Cao-3


title: Morocco-MCCFC_48h-rep1

description: Biological replicate 1


title: Morocco-MCCFC_72h-rep1

description: Biological replicate 1


title: Col-2


title: Morocco-MCCFC_72h-rep3

description: Biological replicate 3


title: Col-3


title: WT_C10 [smallRNA]

city: Ann Arbor

first: Yifan

last: lIU

state: Michigan

address: 1301 Cathrine street

institute: University of Michigan

description:
Size selected total RNA (length<200bp)
processed data files: scnRNA_reads_counts.txt, siRNA_reads_counts.txt
Small RNA-Seq

data_processing:
small RNA-Seq reads were firstly trimmed the adaptor sequence (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG) using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html), and all the reads belong to the rRNAs, tRNA, snRNAs and the mitochondrial genome were removed. Then, the reads were selected by its length and divided into two category: 1) 22-24nt corresponding to the siRNA reads; 2) 27-31nt corresponding to the scnRNA reads. The reads in two categories were mapped using the BWA requiring perfect alignment. All the unique mapped reads are used.
Reads number in IES or transcripts (transcribed loci) were counted using Subread program. For RPKM (Reads Per Kilobase per Million mapped reads) value was used to normalization, and the total sequenced reads numbers were used for normalization.
Genome_build: T. thermophila MIC (v2) genome (http://www.broadinstitute.org/annotation/genome/Tetrahymena/GenomeDescriptions.html#Tetra_therm_V2)
Supplementary_files_format_and_content: Reads counts table matrix

organism: Tetrahymena thermophila

source_name: Conjugation cells

growth_protocol: Tetrahymena thermophila cells were grown in SPP medium at 30 oC. For conjugation, log-phase growing cells (~200k cells/ml) of two different mating types were washed, starved (~12 hrs) and mixed in 10 mM Tris (pH 7.5) or Dryl’s buffer (2 mM sodium citrate, 1 mM NaH2PO4, 1 mM Na2HPO4, 1.5 mM CaCl2, pH 6.8) at 30°C.

extract_protocol:
Total RNA was extracted using the RNeasy Protect Cell Mini Kit (Qiagen, Valencia, CA,  cat. # 74624) according to the protocol  in TetraFGD (http://tfgd.ihb.ac.cn/index/smphelp).
RNA libraries were prepared for sequencing using standard Illumina protocols. Size selected total RNA (<200bp) in C3, C6 and C10 of WT, ∆EZL1 and ∆DCL1 cells were used to the starting materials. Small RNA libraries were constructed using the Illimuna TruSeq Small RNA Sample Prep Kit (RS-200-0012). Total RNA was ligated with 3’ adaptor and 5’ adaptor respectively, and then first strand was synthesized for PCR amplification. The PCR amplification products with library insert size corresponding to ~22nt and ~30nt were selected by gel. Single-end (50X1) sequencing was performed.

tag: genotype

value: WT

tag: time point

value: Conjugation 10 hours


title: DCL1KO_C10 [smallRNA]

value: Strain from reference PMID:16199890

value: DCL1 germline Knock out


title: EZL1KO_C10 [smallRNA]

value: EZL1 Knock out


title: Nuclear 48hrs

description: plasmid insert sequence


title: Nuclear 12hrs

description: plasmid insert sequence


title: Morocco-MCCFC_24h-rep3

description: Biological replicate 3


title: Morocco-MCCFC_24h-rep2

description: Biological replicate 2


title: Cytosolic 12hrs

description: plasmid insert sequence

value: cytosolic


title: Cytosolic 72hrs

description: plasmid insert sequence


title: EZL1KO_C6 [smallRNA]

value: Conjugation 6 hours


title: WT_C6 [smallRNA]


title: Morocco-MCCFC_24h-rep1

description: Biological replicate 1


title: Morocco-MCCFC_12h-rep3

description: Biological replicate 3


title: Morocco-MCCFC_48h-rep2

description: Biological replicate 2


title: EZL1KO_C3 [smallRNA]

value: Conjugation 3 hours


title: Morocco-MCCFC_12h-rep2

description: Biological replicate 2


title: Morocco-MCCFC_12h-rep1

description: Biological replicate 1


title: EZL1KO_C10[mRNA]

description: Strand specific RNA-Seq

data_processing:
mRNA-Seq data processing: RNA-Seq reads of each sample were firstly mapped to the MIC genome assembly of Tetrahymena thermophila (http://www.broadinstitute.org/annotation/genome/Tetrahymena/MultiHome.html) using TopHat allowing  2 edit distances (including mismatch and indels). To assemble the transcripts, the mapping results of all the samples were independently assembled in both strands using the Cufflinks program, and then merged the assemblies using cuffmerge.
Reads number in IES or transcripts (transcribed loci) were counted using Subread program
Genome_build: T. thermophila MIC (v2) genome (http://www.broadinstitute.org/annotation/genome/Tetrahymena/GenomeDescriptions.html#Tetra_therm_V2)
Supplementary_files_format_and_content: Reads counts table matrix

growth_protocol: Tetrahymena thermophila cells were grown in SPP medium at 30 oC.  For conjugation, log-phase growing cells (~200k cells/ml) of two different mating types were washed, starved (~16 hrs) and mixed in Dryl’s buffer (2 mM sodium citrate, 1 mM NaH2PO4, 1 mM Na2HPO4, 1.5 mM CaCl2, pH 6.8) at 30°C.

extract_protocol:
Total RNA was extracted using the RNeasy Protect Cell Mini Kit (Qiagen, Valencia, CA,  cat. # 74624) according to the protocol  in TetraFGD (http://tfgd.ihb.ac.cn/index/smphelp).
RNA libraries were prepared for sequencing using standard Illumina protocols. First strand specific libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (RS-122-2101). The Poly-A tailed mRNA as purified using the Sera‐Mag Magnetic Oligo(dT) Beads. The mRNA fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, A tailing, adaptor ligation and PCR amplification were performed according to the stranded mRNA sample preparation guide of the kit.  Sequencing (Single-end (52X1) for C3 and C6, Paired-end (101x2) FOR C10) was performed using an Illumina HiSeq 2000 sequencer (DNA Sequencing Core of University of Michigan).

tag: cell type

value: Conjugation cells


title: Morocco-RKQQC_96h-rep2

description: Biological replicate 2

value: Puccinia graminis isolate 99KS76A-1


title: Morocco-RKQQC_96h-rep3

description: Biological replicate 3


title: WT_C10[mRNA]

description: Strand specific RNA-Seq


title: DCL1KO_C3 [mRNA]

description: Strand specific RNA-Seq


title: WT_C6 [mRNA]

description: Strand specific RNA-Seq


title: EZL1KO_C3 [mRNA]

description: Strand specific RNA-Seq


title: Morocco-RKQQC_72h-rep2

description: Biological replicate 2


title: Morocco-RKQQC_96h-rep1

description: Biological replicate 1


title: Morocco-RKQQC_72h-rep3

description: Biological replicate 3


title: WT_C3 [smallRNA]


title: WT_C3 [mRNA]

description: Strand specific RNA-Seq


title: Morocco-RKQQC_48h-rep2

description: Biological replicate 2


title: Morocco-RKQQC_24h-rep3

description: Biological replicate 3


title: Morocco-RKQQC_48h-rep3

description: Biological replicate 3


title: DCL1KO_C6 [mRNA]

description: Strand specific RNA-Seq


title: Morocco-RKQQC_24h-rep1

description: Biological replicate 1


title: Morocco-RKQQC_72h-rep1

description: Biological replicate 1


title: Morocco-RKQQC_12h-rep3

description: Biological replicate 3


title: EZL1KO_C6 [mRNA]

description: Strand specific RNA-Seq


title: Morocco-RKQQC_24h-rep2

description: Biological replicate 2


title: Morocco-RKQQC_12h-rep1

description: Biological replicate 1


title: Morocco-RKQQC_48h-rep1

description: Biological replicate 1


title: Morocco-RKQQC_12h-rep2

description: Biological replicate 2


title: B-Brain

city: shanghai

first: hygine

last: lin

address: siping road 1239

institute: tongji unversity

data_processing:
Illumina Off-Line Basecaller(OLB) 1.9.4 software used for basecalling.
Sequenced reads mapped to rhesus whole genome(MMUL_1.73) using Tophat(vision 1.3.2) with default parameters and max-multihits=10 ,min-anchor-length=5
Fragment Per Kilobase of exon model per Million mapped reads (FPKM) were calculated using Cufflinks (version 2.0.2). 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: MMUL_1.73
Supplementary_files_format_and_content: The "fpkm" file includes FPKM values for each Sample
Supplementary_files_format_and_content: The "cvrg" file contain transcript coverage calculated by Cufflinks.

organism: Macaca mulatta

source_name: Brain

extract_protocol:
All kinds of tissue from the two aborted male rhesus monkeys were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

value: Brain


title: B-Spleen

source_name: Spleen

value: Spleen


title: DCL1KO_C10[mRNA]

description: Strand specific RNA-Seq

tag: strain


title: B-Heart

source_name: Heart

value: Heart


title: B-Head

source_name: Head

value: Head


title: B-Tail

source_name: Tail

value: Tail


title: Morocco_0h-rep3

description: Biological replicate 3

value: Morocco

value: Leaf

value: Mock


title: Morocco_0h-rep2

description: Biological replicate 2


title: B-Ribs

source_name: Ribs

value: Ribs


title: Morocco_0h-rep1

description: Biological replicate 1


title: B-Spine

source_name: Spine

value: Spine


title: ND20

city: tyuo-ku

first: noriko

last: nishi

state: Tokyo

address: 5-11 hakozaki 5F Yunibasaru Bldg

country: Japan

institute: Axiohelix Co. Ltd.

data_processing:
Sequenced reads were mapped to mm10 whole genome using Torrent Suite Software version 4.0.2.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using AvadisNGS1.5 Software.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files were generated using bedtools version 2.17.0; tab-delimited text files include RPKM values, count of tags, and total exon length for each gene;

source_name: gastric epithelial cells

extract_protocol:
Total RNA was prepared from sorted cells by using an AllPrep DNA/RNA Micro Kit (Qiagen), and then treated with DNase I. Ribosomal RNA (rRNA) was removed from total RNA using Low Input RiboMinus Eukaryote System v2 (Life Technologies).
RNA-seq libraries were prepared for sequencing using Ion Total RNA-Seq Kit v2 without Barcoding according to the manufacturer’s instructions.

value: stomach

value: gastric epithelial cells


title: B-Kidney

source_name: Kidney

value: Kidney


title: B-Liver

source_name: Liver

value: Liver


title: B-Intestinal

source_name: Intestinal

value: Intestinal


title: ND15.17.18


title: ND16


title: B-Leg

source_name: Leg

value: Leg


title: A-Liver

value: male


title: HFD27


title: A-Brain

value: Brain


title: HFD23


title: A-Right Kidney

source_name: Right Kidney

value: Right Kidney


title: HFD22


title: A-Spine


title: A-Arm

source_name: Arm

value: Arm


title: A-Heart

value: Heart


title: A-Spleen

value: Spleen


title: A-Ribs


title: A-Left Kidney

source_name: Left Kidney

value: Left Kidney


title: A-Tail

value: Tail


title: A-Lung

source_name: Lung

value: Lung


title: A-Leg


title: A-Intestinal


title: Sharbati_grain [AFG1]

city: Kolkata

first: Avijit

last: Das

state: West Bengal

address: 12 Regent Park

department: Quality Evaluation and Improvement

country: India

institute: NIRJAFT

description: grain transcriptome of Sharbati cultivar

data_processing:
Cluster generation and sequencing: RNA-Seq was performed using Illumina HiSeq2000 instrument. Amplified products were loaded on sample loading port of eight tube strip on cBOT for cluster generation and further subjected to 100 cycles of paired-end (2 × 100 bp) sequencing on HiSeq 2000. Approximately, 30 million reads were generated per sample. The processing of fluorescent images into sequences, base-calling and quality value calculations were performed using the Illumina data processing pipeline (version 1.8).
Read mapping: Rice genome and gene information for reference cultivar Nipponbare (Oryza sativa L. subsp. japonica) was downloaded from ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/ Further, raw reads were filtered to obtain high-quality reads by removing low-quality reads with Q < 25. After trimming low-quality reads and adaptor sequences, the resulting high-quality reads were mapped onto the downloaded reference genome.  Sequencing reads from all 4 transcriptome libraries were first pooled and mapped to the rice genome sequence scaffolds using the Bowtie (V 0.12.9) and TopHat (V 1.3.3) with default parameters. The resulting alignment (in BAM file format) was used to generate transcript annotations (in gene feature file or GFF format) with the Cufflinks (V 1.3.0).  The Ensembl reference annotation in GFF format was used to provide established junctions via the ‘–G’ option. These read counts were used in statistical tests of differential expression between test and reference for differential gene expression [PMID:22383036; PMID: 22853646].
Assessment of differentially expressed genes (DEGs): Differences in gene expression between different samples were tested with Cuffdiff package of Cufflinks using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) from reference-guided mapping. Genes expressed at very low levels (read counts < 10 across all six libraries) were not used in analysis of differential gene expression. Significance tests for differential expression were based on a modified exact test. A false discovery rate (FDR) of 0.05 and p-value ≤0.05 was used for identifying differentially expressed genes. The CuumeRbund, a package of R was used to generate the heatmaps of differentially expressed genes [PMID:22383036; PMID: 22853646].
Genome_build: Rice genome and gene information for reference cultivar Nipponbare (Oryza sativa L. subsp. japonica) was downloaded from ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/

Supplementary_files_format_and_content: MS Excel, Supplementary file 1: Number of genes that are differentially expressed in the roots and developing grains of the cultivars Sharbati and Lalat. Gene with FPKM values obtained by Cufflink v.1.3.0 higher than zero was considered as expressed genes.
Supplementary file 2: List of Gene ontology terms that are enriched for genes expressed in four samples. P-value less than 0.05 were considered as significant.
Supplementary file 3: List of differential expressed genes enriched in pathway analysis performed by KAAS online pathway annotation.
Supplementary file 4: List of transcription factors analysed by BlastX search against rice transcription factor database
Supplementary file 5: Complete list of rice novel transcripts that are expressed and their putative functions in AFR1 in the roots and developing grains of the cultivars Sharbati and Lalat.

organism: Oryza sativa

source_name: Central Rice Research Institute Gene Bank

growth_protocol: Seeds were surface sterilized by immersing them in a 4% solution of commercial sodium hypochlorite solution for 10 min, followed by repeated washing with glass-distilled water. Treated seeds were allowed to germinate at 30oC in darkness in a petri dish lined with two layers of moistened filter paper discs. One week old seedlings were transferred to plastic pots filled soil and farm yard manure in 3:1 ratio and grown in the net house under ambient conditions till maturity. Fifteen days after  panicle emergence (mid-grain-filling stage) roots and developing grains were collected, washed in sterile nanopure water, blotted, dipped in RNA stabilizer solution in a falcon tube and stored in refrigerator for 24h. The tubes were sifted to -80oC ultra freezer for until future use.

extract_protocol:
Total RNA was extracted from roots and developing rice grains (sampled 15 days after panicle emergence) using Plant RNA miniprep kit (Xcerlis Genomis, India) as per standard protocol provided with the kit. The yield and purity of RNA were assessed by determination of the absorbance at 260 and 280 nm. Further, RNA quality was checked using RNA 6000 Nano Assay Kit and Agilent Bioanalyzer 2100. RNA Integrity Number (RIN) values were >8.5 for all samples. The pair end Sequencing libraries were prepared using Illumina TruSeq® RNA Library Preparation Kit as per manufacturer's protocol (Illumina®, San Diego, CA).
Total RNA (4µg) from each sample was used to isolate poly(A) mRNA. Steps involved in library preparation were mRNA fragmentation, first strand cDNA synthesis followed by second strand cDNA synthesis and adaptor ligation, 200-bp cDNA fragments isolation and amplification by 18 cycles of PCR. Library quality control and quantification were performed on Caliper LabChip GX using HT DNA High Sensitivity Assay Kit. The libraries of all samples were of 285 bp to 303 bp range.

tag: cultivar

value: Sharbati

tag: grain iron conc.

value: higher concentration (24.88 ppm) of Fe in the grain

tag: crop duration

value: Long slender rice grain


title: Lalat_root [AFR2]

description: root transcriptome of Lalat cultivar

value: Lalat

value: lower concentration (7.80 ppm) of Fe in the grain

value: root


title: Lalat_grain [AFG2]

description: grain transcriptom of Lalat cultivar


title: ND19

value: stomach

value: gastric epithelial cells


title: hns_1

city: Shanghai

first: Baoshan

last: Wan

state: Shanghai

address: Rm 710, Bldg 5, 280 S. Chongqing Rd

department: Department of Microbiology and Immunology

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
All raw FastQ files generated were filtered using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Reads per kilobase of exon model per million mapped reads (RPKM) was used as a normalized metric to present the gene expression levels.(Nature methods 2008, 5: 621-628)
Transcripts evaluation of differential expression were accomplished using MARS (MA-plot-based method with Random sampling model) in DEGseq package.(Bioinformatics 2010, 26: 136-138)
Genome_build: NC_002655.2
Supplementary_files_format_and_content: RPKM

organism: Escherichia coli O157:H7 str. EDL933

source_name: Enterohemorrhagic Escherichia coli O157:H7 strain EDL933

growth_protocol: Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8.

extract_protocol:
RNA extraction was performed using RiboPure-BacteriaTM Bacteria kit according to the manufacturer's protocol (Ambion, Life Technologies). DNase I treatment was applied to eliminate genomic DNA contamination as per the manufacturer's recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The bacteria were centrifuged at 4000×g at 4°C for 5 min and then washed with PBS.

value: {delta}hns

tag: phase

value: logarithmic phase


title: hns_2


title: wt_2

value: wild type


title: wt_1


title: HFD26


title: Seedling_salt

city: Taichung

first: Hungchen

middle: Emilie

last: Yen

address: 250 Kuo Kwang Rd

department: Life Sciences

country: Taiwan

institute: National Chung Hsing University

data_processing:
Analysis of small-RNA reads was based on Motameny et al. Genes, 2010. Raw sequences of small RNAs from control and salt treated seedlings were parsed by removing the adaptor sequences, sequence lengths outside 18-25 nt, sequences containing ambiguous nucleotides, and t/r RNA contamination.
The filtered unique reads were compared to known mature plant miRNA deposited in the miRBase database using the miRProf tool (UEA sRNA toolkit) with no more than two mismatches allowed.
To identify the conserved and novel miRNAs in ice plant, unique sequences were aligned to unigenes in the poly (A)+ RNA library using the sequence alignment program (UEA sRNA toolkit) with only perfect matches.
Aligned sequences were used as anchors to extend 200 nt upstream or downstream of unigenes to predict their miRNA precursors. Precursor prediction was achieved using the miRCat program (UEA sRNA toolkit) and the secondary structure was analyzed by the mfold program
A sequence was considered as a valid miRNA candidate if its secondary structure met the following criteria according to Meyers et al. Plant cell, 2008.
Supplementary_files_format_and_content: tab-delimited text files include Raw read and RPM values for each Sample ...

organism: Mesembryanthemum crystallinum

growth_protocol: Sterile ice plant (Mesembryanthemum crystallinum L.) seeds were sown in 1X Murashige & Skoog basal medium with vitamins (PhytoTechnology Laboratories) and maintained in a vertical position under conditions of 16 h 100 micromol m-2s-1 light/8h dark at 25oC (light grown) or continuous darkness at 25oC (dark grown).

extract_protocol:
Total RNA was extracted using TRIzol® (Invitrogen) according to the manufacturer’s instructions.
Small RNA fractions of 15-30 nt were purified using 15% denaturing acrylamide gel. The sequences were obtained using the Illumina Hiseq 2000 platform

treatment_protocol: Three-day-old dark-grown ice plant seedlings were immersed in water (control) or 200 mM NaCl (salt) for 6 h.

tag: developmental stage

value: three-day-old dark-grown seedlings

tag: treatment

value: 200 mM NaCl treatment for 6 h


title: MG4-PBMC RNA-Seq

city: Bangalore

first: Ramesha

middle: P.

last: Kerekoppa

state: Karnataka

address: Adugodi

institute: ICAR-NDRI

description: Transcriptome profiling of peripheral blood mononuclear cells from Bos indicus Malnad Gidda breed

data_processing:
CASAVA for base calling
Adaptor trimming and quality trimming using 'cutadapt-1.4.1' and 'fastx-0.0.13 toolkit'
Alignment using TopHat-2.0.11 and Bowtie2-2.2.3
Assembly and quantification using Cufflinks-2.2.1
Genome_build: Bos_taurus_UMD_3.1
Supplementary_files_format_and_content: BI-MG4-PBMC_RNA-Seq.transcripts.gtf [Transcript assembly as GTF using the B.taurus UMD3.1 annotations (Ensembl release 77) as reference using Cufflinks]
Supplementary_files_format_and_content: BI-MG4-PBMC_RNA-Seq.combined.gtf [Transcript assembly as GTF combined with the B.taurus UMD3.1 annotations (Ensembl release 77) as reference using cuffcompare]
Supplementary_files_format_and_content: Ensembl GTF format:  1. Sequence/reference name, 2. Source - name of the program, 3. Feature type - Gene, mRNA, exon, CDS etc, 4. Start, 5. End, 6. Score, 7. Strand, 8. Frame, 9. Attributes - gene_id, transcript_id, gene_name etc.
Supplementary_files_format_and_content: BI-MG4-PBMC_RNA-Seq.cuffcmp.tracking [TAB delimited tracking file of identified transcripts compared to B.taurus UMD3.1 Ensembl 77 annotations using cuffcompare]
Supplementary_files_format_and_content: Cufflink (cuffcmp) result file format:  1. Transfrag ID, 2. Locus ID, 3. Reference gene name|transcript ID, 4. Class code, 5. qJ:<gene_id>|<transcript_id>|<FMI>|<FPKM>|<conf_lo>|<conf_hi>|<cov>|<len>.

organism: Bos indicus

source_name: PBMC isolated from blood

extract_protocol:
Total RNA was isolated using RNeasy Mini kit (Qiagen, Venlo, The Netherlands).  RNA was quantitated by 260 nm absorbance with a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies Inc, DE, USA) as well as by measuring fluorescence using Qubit 2.0 (Life Technologies, NY, USA). The quality of RNA was further determined using capillary electrophoresis with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). RNA sample was rRNA depleted using Epicentre Ribo-Zero™ kit to enrich the sample for mRNA and non-coding RNA.
Enriched RNA samples is further  processed to generate RNA library using the TruSeq RNA Sample Preparation v2 kit following the manufactures guide. Paired-end 100bp read sequencing of RNA library was carried out on Illumina HiSeq 2000 platform.

tag: breed

value: Malnad Gidda

value: Blood

value: Peripheral Blood Mononuclear Cells (PBMC)


title: Rsv1_SMV-G7_degradome-seq

city: London

first: Hui

last: Chen

state: Ontario

address: 1391 Sandford St.

institute: Agriculture and Agri-Food Canada

data_processing:
Library strategy: degradome-seq
For RNA-seq analysis, the raw sequences were aligned to the soybean reference transcriptome (Glyma1, Ensembl genes and transcripts) using the Strand NGS software (Strand Life Sciences, version 2.1) following RNA alignment and RNA-seq analysis pipeline with standard parameters.
For sRNA-seq analysis, after the low quality reads and the adapter sequences were trimmed, the sequences were mapped to the Glycine max reference genome (Glyma1, Ensembl) and aligned to the known miRNA gene of Glycine max (miRBase 21) using the Strand NGS software (Strand Life Sciences, version 2.1) following small RNA alignment and small RNA analysis pipeline with standard parameters.
For degradome-seq analysis, the adaptor sequences, tRNA/rRNA sequences and low complexity sequences were removed from raw reads, then the length of degradome sequences and small RNA sequences were trimmed to 20-21 nt and 19-24 nt, respectively. Any sequences without a match to the soybean genome (Glyma1, Ensembl) were also removed from further analysis. The potential targets of small RNAs were identified and validated using the UEA small RNA workbench following the PAREsnip pipeline under a high stringency setting with the Glycine max reference genome (Glyma1, Ensembl) and the known miRNAs of Glycine max (miRBase 21).
Genome_build: Soybean reference transcriptome (Glyma1, Ensembl) and soybean known miRNA (miRBase 21)
Supplementary_files_format_and_content: The txt files of alignment reports were geneated using the Strand NGS software (Strand Life Sciences, version 2.1) following various alignment and analysis pipeline with standard parameters.

organism: Glycine max

source_name: leaves tissues

growth_protocol: Soybeans were grown in a growth chamber under a 16 h light at 22°C and 8 h dark at 18°C.

extract_protocol:
Total RNA and small RNA fractions (≤ 200 nt) were extracted from the leaves inoculated by SMV-L, SMV-G7 and Mock using a mirVana miRNA isolation kit (Ambion) and the Poly (A)+ RNA was isolated using the NucleoTrap@ mRNA purification kits (Machery-Nagel) according to the instructions of the supplier.
RNA-seq and sRNA-seq libraries were prepared following the manufacturer's instructions using Illumina TruSeq Stranded Total RNA Sample Prep Kit (Cat#RS-122-2501) and TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012),respectively. Degradome-seq libraries were constructed as previously described using Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0024)(German, M. A. et al., Nature Biotechology, 2008; German et al., Nature Protocols, 2009; Zhai et al., 2014).

treatment_protocol: Leaves were mechanically inoculated  by SMV-L, SMV-G7 and Mock (buffer) after germination at 10 days.

tag: cultivar type

value: Rsv1-genotype soybean

tag: cultivar id

tag: innoculation

tag: age

value: 14 days post-inoculation


title: Rsv1_Mock_degradome-seq

value: Mock


title: Rsv1_SMV-G7_sRNA-seq

description: Small RNA fractions (≤ 200 nt)

data_processing:
For RNA-seq analysis, the raw sequences were aligned to the soybean reference transcriptome (Glyma1, Ensembl genes and transcripts) using the Strand NGS software (Strand Life Sciences, version 2.1) following RNA alignment and RNA-seq analysis pipeline with standard parameters.
For sRNA-seq analysis, after the low quality reads and the adapter sequences were trimmed, the sequences were mapped to the Glycine max reference genome (Glyma1, Ensembl) and aligned to the known miRNA gene of Glycine max (miRBase 21) using the Strand NGS software (Strand Life Sciences, version 2.1) following small RNA alignment and small RNA analysis pipeline with standard parameters.
For degradome-seq analysis, the adaptor sequences, tRNA/rRNA sequences and low complexity sequences were removed from raw reads, then the length of degradome sequences and small RNA sequences were trimmed to 20-21 nt and 19-24 nt, respectively. Any sequences without a match to the soybean genome (Glyma1, Ensembl) were also removed from further analysis. The potential targets of small RNAs were identified and validated using the UEA small RNA workbench following the PAREsnip pipeline under a high stringency setting with the Glycine max reference genome (Glyma1, Ensembl) and the known miRNAs of Glycine max (miRBase 21).
Genome_build: Soybean reference transcriptome (Glyma1, Ensembl) and soybean known miRNA (miRBase 21)
Supplementary_files_format_and_content: The txt files of alignment reports were geneated using the Strand NGS software (Strand Life Sciences, version 2.1) following various alignment and analysis pipeline with standard parameters.


title: Rsv1_Mock_sRNA-seq

description: Small RNA fractions (≤ 200 nt)


title: Rsv1_SMV-L_RNA-seq

value: SMV-L


title: Rsv1_SMV-G7_RNA-seq


title: Rsv1_SMV-L_sRNA-seq

description: Small RNA fractions (≤ 200 nt)


title: NCDS001181

status: Public on Dec 30 2016

city: Cambridge

first: Hugues

last: Bernard

state: MA

address: 35 Landsdowne St.

department: Molecular Pathology

institute: Millennium: The Takeda Oncology company

data_processing:
OSA v4 (http://omicsoft.com/osa) was used to align the reads to the Dog genome (CanFam3.1) and to MiRBase (v.21) [44] allowing for two mismatches and excluding any reads that aligned to greater than 10 genomic locations
Expression levels were quantified by counting the number of reads aligned to mature miRNA region
Genome_build: Dog genome (CanFam3.1)

organism: Canis lupus familiaris

source_name: Plasma (2 mL in K2EDTA)

extract_protocol:
Total RNA was isolated by Asuragen from tissue homogenate with KingFisher Pure RNA Tissue Kit (Thermo Scientific).
Isolation of miRNA from 50 μM tissue samples used a lysis buffer (RLT [Qiagen] + 1% β  mercaptoethanol) and a rotor-stator homogenizer
A TruSeq Small RNA Library Kit (Illumina) was used for library construction of dog miRNA

treatment_protocol: No Treatment

tag: tissue

value: Plasma (2 mL in K2EDTA)

value: Untreated

value: Beagle

tag: prep type

value: Qiagen RNeasy_96

tag: Sex

value: Male


title: NCDS001180

source_name: Bone Marrow (2 mL)

value: Bone Marrow (2 mL)


title: Rsv1_SMV-L_degradome-seq


title: NCDS001179


title: NCDS001182


title: Sharbati_root [AFR1]

description: root transcriptome of Sharbati cultivar

value: Sharbati

value: higher concentration (24.88 ppm) of Fe in the grain

value: root


title: Placenta

source_name: Placenta

value: Placenta


title: Seedling_control

value: three-day-old dark-grown seedlings

value: water treatment for 6 h


title: NCDS001177


title: NCDS001176


title: Necrotic stem tissues

city: Thiverval Grignon

first: Julie

last: Gervais

address: Avenue Lucien Brétignières

department: BIOGER

country: France

institute: INRA

description: RNA-seq pilot project

data_processing:
The sofwtware CLC worckbench v7.5.1 (Qiagen, Venlo, Netherlands) was used for data processing.
Sequenced reads were trimmed with the following parameters: ambiguous limit: 2, quality limit: 0.05, maximum number of nucleotides in reads: 50, minimum number of nucleotides in reads: 15. Short reads were discarded.
Reads were mapped on the genomes of L. maculans and B. napus with the following parameters: maximum number of mismatches allowed: 2, minimum lenght fraction: 0.80, Minim fraction of similarity: 0.8, unspecific match limit: 30
Expression values of fungal genes was measured with the RPKM.
Genome_build: Brassica napus (annotation release:100) (Chalhoub et al., 2014)
Genome_build: Leptosphaeria maculans JN3 (Rouxel et al., 2011)
Supplementary_files_format_and_content: Text files include RPKM (Reads Per Kilobase of exon per Megabase) values and number of aligned reads for each fungal gene.

organism:
Brassica napus
Plenodomus lingam

source_name: Stem

growth_protocol: Plants were grown in grown chambers at 16°C (night) and 24°C (day), with a 12h photoperiod.

extract_protocol:
Total RNA was extracted from infected cotyledon and stem tissues, using the TRIzol reagent (Invitrogen,Cergy Pontoise, France) according to the manufacturer’s protocol. Total RNA was treated with DNase I RNase-Free (New England Biolabs, Ipswich, MA, U.S.A.).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: l.maculans strain

tag: brassica napus cultivar

value: Eurol

tag: inoculation protocol

value: Adult plants of the susceptible cultivar Eurol were inoculated 22 days after sowing at the three leaves development stage. The petiole of the second leaf was cut off at 1 cm from the leaf insertion and 10µl of inoculum (107 pycnidiospores/ml) was placed over the wound.Inoculated plants were incubated in darkness for 48h at room temperature under saturated humidity, and then transferred to a growth chamber at 16°C (night) and 24°C (day), with a 12h photoperiod. 24 days after inoculation necrotic stem tissues were sampled.


title: Below necrosis stem tissues

description: RNA-seq pilot project

value: Adult plants of the susceptible cultivar Eurol were inoculated 22 days after sowing at the three leaves development stage. The petiole of the second leaf was cut off at 1 cm from the leaf insertion and 10µl of inoculum (107 pycnidiospores/ml) was placed over the wound.Inoculated plants were incubated in darkness for 48h at room temperature under saturated humidity, and then transferred to a growth chamber at 16°C (night) and 24°C (day), with a 12h photoperiod. 24 days after inoculation below necrosis stem tissues were sampled.


title: Symptomless stem tissues

description: RNA-seq pilot project

value: Adult plants of the susceptible cultivar Eurol were inoculated 22 days after sowing at the three leaves development stage. The petiole of the second leaf was cut off at 1 cm from the leaf insertion and 10µl of inoculum (107 pycnidiospores/ml) was placed over the wound.Inoculated plants were incubated in darkness for 48h at room temperature under saturated humidity, and then transferred to a growth chamber at 16°C (night) and 24°C (day), with a 12h photoperiod. 24 days after inoculation stem tissues of symptomless plants were sampled.


title: NCDS001175


title: NCDS001174


title: NCDS001172

source_name: Colon

value: Colon


title: NCDS001173

value: Plasma (2 mL in K2EDTA)


title: Inoculated cotyledons (NzT4)

description: RNA-seq pilot project

source_name: Cotyledons

value: Darmor-bzh

value: Ten days-old seedling of the susceptible cultivar Darmor-bzh were inoculated with 10µl of inoculum (107 pycnidiospores/ml) at a needle puncture. Inoculated plants were incubated in darkness for 48h at room temperature under saturated humidity, and then transferred to a growth chamber at 16°C (night) and 24°C (day), with a 12h photoperiod. 7 days after infection,  cotyledons were sampled.


title: Inoculated cotyledons (JN3)

description: RNA-seq pilot project


title: Rsv1_Mock_RNA-seq

value: Rsv1-genotype soybean

value: Mock

value: 14 days post-inoculation


title: NCDS001171

source_name: Pancreas

value: Pancreas

value: Untreated

value: Beagle

value: Qiagen RNeasy_96

value: Male


title: NCDS001170

source_name: Ileum

value: Ileum


title: Inoculated stems rep1

description: validation RNA-seq project

value: Adult plants of the susceptible cultivar Darmor-bzh were inoculated 22 days after sowing at the three leaves development stage. The petiole of the second leaf was cut off just under the leaf blade and 10µl of inoculum was placed over the wound.Inoculated plants were incubated in darkness for 48h at room temperature under saturated humidity, and then transferred to a growth chamber at 16°C (night) and 24°C (day), with a 12h photoperiod. 14 days after inoculation stem tissues were sampled.


title: Inoculated stems rep2

description: validation RNA-seq project


title: NCDS001169

source_name: Jejunum

value: Jejunum


title: NCDS001168

source_name: Duodenum

value: Duodenum


title: Inoculated cotyledons rep2

description: validation RNA-seq project


title: NCDS001166

source_name: Brain

value: Brain


title: NCDS001178

value: Bone Marrow (2 mL)


title: Inoculated cotyledons rep1

description: validation RNA-seq project


title: y6-5SA-C

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

data_processing:
reads were aligned in single-end mode to dog genome (canFam3, http://www.ensembl.org/Canis_familiaris/) using STAR (version 2.3.1n) aligner using default settings.
Mapped data were converted in gene level counts using HTSeq-count 0.6.0 and the ENSEMBL annotation (canFam3.1, http://www.ensembl.org/Canis_familiaris/).
Differential expression was evaluated using DESeq2 Bioconductor package 1.4.5.
Genome_build: canFam3.1
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

source_name: (YAP5SA) YAP expression

growth_protocol: TR-T10 cells, as well as retroviral and lentiviral 293 packaging cells, were all propagated in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was isolated from 1x106 cells using RNeasy kit (Qiagen).  RNA integrity was analyzed on an Agilent Technologies 2100 Bioanalyzer using the Agilent RNA 6000 Nano kit (Agilent Technologies) and only samples with an RNA integrity number (RIN) above 9.5 was used for further analysis.
cDNA and libraries were prepared using 1 µg total RNA and the TruSeq mRNA sample preparation kit according to the manufacturer’s instructions (Illumina).  Library quality was analysed on an Agilent Technologies 2100 Bioanalyzer using the Agilent DNA 1000 kit (Agilent Technologies).  Library samples were quantified using the Qubit dsDNA BR assay kit (Invitrogen) and diluted to 10 nM before single read sequencing on an Illumina HiSeq 2000 sequencing platform, performed at the National High-throughput DNA Sequencing Centre, University of Copenhagen.

treatment_protocol: To permit inducible knockdown of p190A and or p190B expression, TR-T10 cells were transduced with retrovirus encoding p190A shRNA or p190B shRNA and cells then selected in hygromycin (p190A shRNA) or puromycin (p190B shRNA).  To generate TR-T10 cells with combined knockdown of p190A and p190B, p190B-kd cells were transduced with retrovirus encoding p190A shRNA and cells were selected in hygromycin.  To induce knockdown of gene expression, cells were plated at subconfluent density and cultured for 3 days in the presence of 4 µg/ml of doxycycline.  Cells were then harvested and replated at subconfluent or confluent density for another 3-5 days prior to experimentation.

tag: cell line

tag: confluence

value: confluent

tag: genotype/variation

value: (YAP5SA) YAP expression and p190A and B shRNAs

tag: experiment


title: y5-5SA-C


title: y4-5SA-C


title: NCDS001163

source_name: Skeletal Muscle:  Quadraceps

value: Skeletal Muscle: Quadraceps


title: NCDS001162

source_name: Lung

value: Lung


title: aby12-AB-S94A-C

source_name: (YAP5SA+S94A) YAP expression and p190A and B shRNAs


title: aby11-AB-S94A-B

value: (YAP5SA+S94A) YAP expression and p190A and B shRNAs


title: NCDS001161

source_name: Testis

value: Testis


title: NCDS001160

source_name: Heart

value: Heart


title: Inoculated cotyledons (G06E-107)

description: RNA-seq pilot project

value: Darmor-bzh

value: Ten days-old seedling of the susceptible cultivar Darmor-bzh were inoculated with 10µl of inoculum (107 pycnidiospores/ml) at a needle puncture. Inoculated plants were incubated in darkness for 48h at room temperature under saturated humidity, and then transferred to a growth chamber at 16°C (night) and 24°C (day), with a 12h photoperiod. 7 days after infection,  cotyledons were sampled.


title: NCDS001159

source_name: Liver

value: Liver

value: Untreated

value: Beagle

value: Qiagen RNeasy_96


title: aby10-AB-S94A-A


title: NCDS001158

value: Colon

value: Male


title: ab7-AB-A

source_name: p190A and B shRNAs

value: p190A and B shRNAs


title: ab8-AB-B


title: sB2

source_name: p190B shRNA

value: sub-confluent

value: p190B shRNA


title: NCDS001157

value: Pancreas


title: NCDS001155

value: Jejunum


title: sAB2


title: NCDS001152

value: Brain


title: NCDS001165

source_name: Thymus

value: Thymus


title: NCDS001164

source_name: Kidney

value: Kidney


title: sB1


title: NCDS001156

value: Ileum


title: sA1

source_name: p190A shRNA

value: p190A shRNA


title: NCDS001154

value: Duodenum


title: NCDS001150


title: sAB1


title: NCDS001151


title: sA2


title: ab9-AB-C

value: confluent


title: s1

source_name: wild type cell

value: wild type


title: c3-T10C


title: s2


title: NCDS001146

value: Heart

value: Untreated

value: Beagle


title: NCDS001147

value: Testis

value: Qiagen RNeasy_96

value: Male


title: c2-T10B


title: NCDS001149

value: Skeletal Muscle: Quadraceps


title: cB2

value: p190B shRNA


title: c1-T10A


title: NCDS001145

value: Liver


title: cB1


title: NCDS001144

source_name: Colon

value: Colon


title: NCDS001143

source_name: Pancreas

value: Pancreas


title: NCDS001142

source_name: Ileum


title: cAB2

value: p190A and B shRNAs


title: NCDS001141

source_name: Jejunum

value: Jejunum


title: NCDS001140

source_name: Duodenum


title: cA2

value: p190A shRNA


title: cAB1


title: cA1


title: c2


title: NCDS001138

source_name: Brain

value: Brain


title: NCDS001139

source_name: Sciatic Nerve

value: Sciatic Nerve


title: NCDS001148

source_name: Lung

value: Lung


title: NCDS001136

value: Kidney


title: NCDS001137

value: Thymus

value: Untreated


title: NCDS001135

source_name: Skeletal Muscle:  Quadraceps

value: Beagle


title: c1

value: confluent

value: wild type


title: Cut_and_Run_H3K27me3_size_selected_(20161206_PS_HsDm_H30ss1121)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
antibody: anti H3K27me3 Millipore 07-449
Cut-and-Run H3K27me3 30 min digestion time on ice size selected fragments

data_processing:
Genome_build: UCSC hg19
Genome_build: FlyBase r6.06
1. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the same paired-end 25bp reads to dm6 version of  the D.melanogaster genomic sequence obtained from UCSC. 3. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> (Supplementary file .bed). 4. We counted the properly paired reads from the D.melanogaster alignments. 5. We used the bedtools 2.21.0 genomecov command with a scaling factor of (10000/number of fragments mapped to D.melanogaster) to create a normalized human track file (Supplementary file .spikenorm.bedgraph).

organism: Homo sapiens

source_name: Chromatin immunocleavage and release

value: human K562 cells


title: Cut_and_Run_no_antibody_size_selected_(20161206_PS_HsDm_neg_30_1201)

description:
antibody: no antibody
Cut-and-Run no antibody 30 min digestion time on ice size selected fragments


title: Cut-and-Run_Sth1_No1o_Total_2_(20161123_SH_ScDm_Sth1no1_1107)

description:
Cut-and-Run Sth1 No primary antibody 30 min digestion time Ampure selected Total
experiment: 3xFLAG-tagged Sth1

data_processing:
Genome_build: YeastBase V64
Genome_build: FlyBase r6.06
1. We used Novoalign 2.08.03 (http://www.novocraft.com) with options "-F STDFQ -a -r Random -o SAM" to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC.  2. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the same paired-end 25bp reads to release 6.06 (Jul 2015) of D.melanogaster genomic sequence obtained from FlyBase. This release corresponds to release dm6 from UCSC.  3. We extracted properly paired reads from both alignments (Supplementary files .bed.gz .DM.bed.gz). 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000/(number of fragments mapped to D.melanogaster) to create a normalized yeast track file (Supplementary file .bedgraph.gz).

tag: cell type

value: yeast


title: Cut-and-Run_Sth1_3m_Total_2_(20161123_SH_ScDm_Sth13m_1107)

description:
Cut-and-Run Sth1 3 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged Sth1


title: Cut-and-Run_Sth1_5s_Total_(20161123_SH_ScDm_Sth15s_1104)

description:
Cut-and-Run Sth1 5 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Sth1


title: NCDS001133

source_name: Testis

value: Testis

tag: treatment

value: Qiagen RNeasy_96

value: Male


title: Cut-and-Run_Sth1_No1o_Total_1_(20161123_SH_ScDm_Sth1No1_1104)

description:
Cut-and-Run Sth1 No primary antibody 10 min digestion time Ampure selected Total
experiment: 3xFLAG-tagged Sth1


title: Cut_and_Run_Max_size_selected_(20161206_PS_HsDm_Max_30_1201)

description:
antibody: anti Max Santa Cruz Biotechnology sc-197 X
Cut-and-Run Max 30 min digestion time on ice size selected fragments


title: Cut_and_Run_Myc_size_selected_(20161206_PS_HsDm_Myc_30_1201)

description:
antibody: anti Myc Cell Signalling D3N8F 13987
Cut-and-Run Myc 30 min digestion time on ice size selected fragments


title: Cut_and_Run_H3K27me3_liberated_(20161206_PS_HsDm_H30_npc1121)

description:
antibody: anti H3K27me3 Millipore 07-449
Cut-and-Run H3K27me3 30 min digestion time on ice liberated fragments

extract_protocol:
Cut_and_Run_human.rtf
PMID 25827087


title: Cut_and_Run_CTCF_9min_(20160628_PS_HsDm_CTCF_0602_E)

description:
antibody: anti CTCF Millipore 07-729
Cut-and-Run CTCF 9 min digestion time on ice


title: Cut_and_Run_CTCF_5s_(20160628_PS_HsDm_CTCF_0602_A)

description:
antibody: anti CTCF Millipore 07-729
Cut-and-Run CTCF 5 s digestion time on ice


title: NCDS001132

source_name: Heart

value: Heart

tag: breed


title: Cut-and-Run_Sth1_3m_Total_1_(20161123_SH_ScDm_Sth13m_1104)


title: Cut-and-Run_Sth1_30m_Total_(20161123_SH_ScDm_Sth130m_1107)

description:
Cut-and-Run Sth1 30 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged Sth1


title: NCDS001131

source_name: Liver

value: Liver


title: NCDS001130

value: Colon


title: Cut_and_Run_CTCF_15s_(20160628_PS_HsDm_CTCF_0602_B)

description:
antibody: anti CTCF Millipore 07-729
Cut-and-Run CTCF 15 s digestion time on ice


title: NCDS001134


title: Cut-and-Run_Sth1_1m_Total_2_(20161123_SH_ScDm_Sth11m_1107)

description:
Cut-and-Run Sth1 1 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged Sth1


title: Cut-and-Run_Sth1_20s_Total_1_(20161123_SH_ScDm_Sth120s_1104)

description:
Cut-and-Run Sth1 20 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Sth1


title: Native_Input_low_MNase_(20151207_PS_Hs_Input_E_ss)

description:
experiment: input chromatin
Native input low Mnase digestion size selected

data_processing:
Genome_build: UCSC hg19
1. We used Novoalign 2.08.03 (http://www.novocraft.com) with options "-F STDFQ -a -r Random -o SAM" to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC.  2. We extracted properly paired reads (Supplementary file .bed.gz). 3. We separated mapped fragments into two length categories, 21-120bp and 151-max bp. 4. We counted  the number of reads mapped to each base pair in the two length categories and normalized the counts by computing the fraction of total counts at each base pair and multiplying by the size of the yeast genome (Supplementary files .21-120.bedgraph.gz and .151-max.bedgraph.gz).

source_name: Native ChIP


title: Native_Input_medium_MNase_(20151207_PS_Hs_Input_D_ss)

description:
experiment: input chromatin
Native input medium Mnase digestion size selected


title: NCDS001129

value: Pancreas


title: Native_ChIP_CTCF_high_MNase_2_(20151104_PS_Hs_N_CTCF_C)

description:
experiment: anti CTCF Millipore 07-729
Native ChIP CTCF high Mnase digestion, biological replicate 2


title: Native_ChIP_CTCF_high_MNase_1_(20150925_PS_Hs_N_CTCF_C)

description:
experiment: anti CTCF Millipore 07-729
Native ChIP CTCF high Mnase digestion, biological replicate 1


title: NCDS001128

value: Ileum


title: Native_ChIP_CTCF_medium_MNase_2_(20151104_PS_Hs_N_CTCF_D)

description:
experiment: anti CTCF Millipore 07-729
Native ChIP CTCF medium Mnase digestion

source_name: Native ChIP, biological replicate 2


title: NCDS001127

value: Jejunum


title: Cut-and-Run_Sth1_1m_Total_1_(20161123_SH_ScDm_Sth11m_1104)


title: Native_ChIP_CTCF_low_MNase_2_(20151104_PS_Hs_N_CTCF_E)

description:
experiment: anti CTCF Millipore 07-729
Native ChIP CTCF low Mnase digestion, biological replicate 2


title: NCDS001126

value: Duodenum


title: Cut-and-Run_Sth1_10m_Total_2_(20161123_SH_ScDm_Sth110m_1107)

description:
Cut-and-Run Sth1 10 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged Sth1


title: Cut_and_Run_CTCF_45s_(20160628_PS_HsDm_CTCF_0602_C)

description:
antibody: anti CTCF Millipore 07-729
Cut-and-Run CTCF 45 s digestion time on ice


title: NCDS001125

value: Sciatic Nerve


title: Native_ChIP_CTCF_medium_MNase_1_(20150925_PS_Hs_N_CTCF_D)

source_name: Native ChIP, biological replicate 1


title: Cut_and_Run_CTCF_27min_(20160628_PS_HsDm_CTCF_0602_F)

description:
antibody: anti CTCF Millipore 07-729
Cut-and-Run CTCF 27 min digestion time on ice


title: Cut-and-Run_Reb1_4s_Total_(20160909_SH_ScDm_Re_4A0829)

description:
Cut-and-Run Reb1 4 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Reb1


title: Cut_and_Run_CTCF_45min_(20160401_PS_HsDm_CTCF_45)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 45 min digestion time on ice

data_processing:
Genome_build: UCSC hg19
Genome_build: FlyBase r6.06
1. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the same paired-end 25bp reads to dm6 version of  the D.melanogaster genomic sequence obtained from UCSC. 3. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> (Supplementary file .bed). 4. We counted the properly paired reads from the D.melanogaster alignments. 5. We used the bedtools 2.21.0 genomecov command with a scaling factor of (hg19 genome size/number of mapped fragments to hg19) create a normalized human track file (Supplementary file .stdnorm.bedgraph). 6. We used the bedtools 2.21.0 genomecov command with a scaling factor of (10000/number of fragments mapped to D.melanogaster) to create a normalized human track file (Supplementary file .spikenorm.bedgraph).


title: SCZ rep19

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

description: processed data column: T41

data_processing:
RNA libraries sequenced on theSOLiDv4 platform (Life Technologies, Carlsbad, CA, USA)
Sequenced reads werer mapped to the human genome (hg19) using TopHat2 (v 2.0.4) calling the Bowtie aligner (v 0.12.8) using the default parameters.
HTSeq-count (Python package HTSeq, python v 2.7.3) was used to generate counts of reads uniquely mapped to annotated genes using the Ensembl annotation file GRCh37.66_chr.gtf
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with read count for each sample.

source_name: DLPFC

extract_protocol:
Tissue from dorsal lateral prefrontal cortex (DLPFC) was pulverized over dry ice. Approximately 300 mg was weighed while frozen and stored at 80°C until extraction. Total RNA was extracted with TRIzol Reagent (Invitrogen Life Science, Cat. No. 15596-018, Mount Waverley, Victoria), using a polytron. Total RNA pellets were re-suspended in DEPC treated water. The yield of total RNA was then analysed using a spectrophotometer (Nanodrop ND-1000, Thermo Scientific). Total RNA was not further purified through a column. The quality of extracted total RNA was determined by high resolution capillary electrophoresis using the Agilent Bioanalyzer 2100.
Twelve micrograms of RNA from each of the samples was used in creation of the library for sequencing. RNA was DNase treated using TURBO DNA-free (Ambion, Austin TX, USA) before the depletion of ribosomal RNA using the Ribominus kit (Invitrogen, Carlsbad, CA, USA). The resulting RNA was fragmented and the SOLiD library prepared using the Total RNA-Seq kit (Invitrogen). Quality control of the library was assessed by size (480% and within 200--300 bp) using a bioanalyser.
Samples were run with four individuals per slide on the SOLiDv4 (Life Technologies, Carlsbad, CA, USA). Reads were unpaired and 50nt in length. Average reads per individual were 135 355 990 (±32 081 820) and did not differ between diagnostic groups.

value: Post-mortem brain (DLPFC) tissue

tag: condition

value: SCZ

tag: batch


title: Cut_and_Run_CTCF_3min_(20160628_PS_HsDm_CTCF_0602_D)

description:
antibody: anti CTCF Millipore 07-729
Cut-and-Run CTCF 3 min digestion time on ice


title: Native_Input_high_MNase_(20151207_PS_Hs_Input_C_ss)

description:
experiment: input chromatin
Native input high Mnase digestion size selected


title: SCZ rep18

description: processed data column: T1


title: Cut-and-Run_Sth1_20s_Total_2_(20161123_SH_ScDm_Sth120s_1107)


title: NCDS001124

value: Brain

value: Untreated

value: Beagle


title: Cut_and_Run_CTCF_30min_(20160401_PS_HsDm_CTCF_30)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 30 min digestion time on ice

value: human K562 cells


title: Cut-and-Run_Reb1_4s_3_(20160909_SH_ScDm_Re_4s0829)

description:
Cut-and-Run Reb1 4 second digestion time
experiment: 3xFLAG-tagged Reb1

value: yeast


title: SCZ rep17

description: processed data column: T83


title: NCDS001123

source_name: Thymus

value: Thymus

value: Qiagen RNeasy_96


title: Cut-and-Run_Reb1_20s_(20160909_SH_ScDm_Re_20s0829)

description:
Cut-and-Run Reb1 20 second digestion time
experiment: 3xFLAG-tagged Reb1


title: Cut_and_Run_CTCF_8min_(20160414_PS_HsDm_CTCF_8m)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 8 min digestion time at room temp


title: Cut_and_Run_CTCF_15min_(20160401_PS_HsDm_CTCF_15)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 15 min digestion time on ice


title: Cut-and-Run_Sth1_10m_Total_1_(20161123_SH_ScDm_Sth110m_1104)


title: Cut-and-Run_Reb1_20s_Total_(20160909_SH_ScDm_Re_20A0829)

description:
Cut-and-Run Reb1 20 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Reb1


title: Native_ChIP_CTCF_low_MNase_1_(20150925_PS_Hs_N_CTCF_E)

description:
experiment: anti CTCF Millipore 07-729
Native ChIP CTCF low Mnase digestion, biological replicate 1


title: NCDS001122

source_name: Kidney

value: Kidney

value: Male


title: Cut-and-Run_Mot1_No1o_Total_(20161123_SH_ScDm_Mot1No1_1107)

description:
Cut-and-Run Mot1 No primary antibody 10 min digestion time Ampure selected Total
experiment: 3xFLAG-tagged Mot1