title: BN68OG

first: Haoran

last: An

address: 17th Qinghua East Road

institute: China Agricultural University

description: Sample 2

data_processing:
Base-calling performed using SOLiD 4 System SETS software.
All sequenced reads were aligned to the genome of B. longum BBMN68 using SOLiD Corona Lite software v4.2.
We used a recursive strategy to improve the usable sequenced reads information as follows: 50 mers reads were firstly mapped to the genome with ≤ 5 color-space mismatches and unmapped reads were progressively trimmed off 5 bases from the 3’ end once, then the trimmed reads were mapped to the genome again until a match was found or unless the read had been trimmed by < 30 bases.
All those uniquely mapped reads were used to calculate the RPKM values (reads per kilobase of exon per million mapped sequenced reads) of genes, which indicated the normalized gene expression level.
Differentially expressed genes (DEGs) from different samples were identified according to an R package DEGseq (http://waprna.big.ac.cn/rnaseq/function/degseq.jsp)
Genome_build: NCBI accession number CP002286
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each gene of sample.

organism: Bifidobacterium longum

source_name: BBMN68 culture_stress

growth_protocol: Volumes of 200 ml of fresh MRSc were inoculated at 1% (v/v) with fresh overnight cultures and incubated in a chamber with an anaerobic atmosphere (5% CO2, 5% H2, and 90% N2) at 37 °C.

extract_protocol:
Total RNA isolation was carried out using TRIzol reagent (Invitrogen) as the manufacturer’s instructions, and purified using a RiboMinus Kit (Invitrogen) to eliminate ribosomal RNA.
The RNA-seq library was constructed using a total RNA-Seq Kit (Applied Biosystems) for SOLiD method according to manufacturer’s introductions.

treatment_protocol: For bile stress treatment, ox-bile (Sigma) was added to a final concentration of 0.75 g/liter. Cultures were harvested when the optical density at mid-exponential phase (OD600 of 0.6).

tag: stress treatment


title: Stimulated OB, mouse 1 (120 min)

status: Public on Jun 27 2014

type: SRA

city: Cambridge

first: Yarden

last: Katz

state: MA

address: 9 Cambridge Center

department: Dept. of Biology and Whitehead Institute

country: USA

institute: MIT

description:
processed data file: rpkm.table.txt
Stim120_1

library_source: transcriptomic

data_processing:
Alignment to mouse genome (mm9) using Bowtie to genome and set of 35-bp splice junctions, followed by calculation of RPKM using constitutive exons of protein-coding (CDS-containing) genes.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values for samples. Contains the gene ID (Ensembl), the read counts in the set of constitutive exons, the length of the region being considered (sum of lengths of constitutive exons), and the RPKM value.

molecule: polyA RNA

organism: Mus musculus

source_name: stimulated_120m_olfactory bulb

extract_protocol:
RNA was extracted using Trizol. RNA was Dnase I-treated and cleaned up on a column using Rneasy kit.
Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.

treatment_protocol: Odorant stimulation (30 min stimulation, 90 min clean air)

tag: strain

tag: developmental stage

value: adult (6-8 weeks or older)

tag: exposed to

value: cocktail of odorants for 30 min followed by clean air for 90min

tag: time point

value: 120 min

tag: tissue

value: olfactory bulb


title: BN68CK

status: Public on Jun 29 2014

city: Beijing

country: China

description: Sample 1

molecule: total RNA

source_name: BBMN68 culture_control


title: Control OB, mouse 2 (clean air)

description:
processed data file: rpkm.table.txt
Control_C2

source_name: control_olfactory bulb

treatment_protocol: Clean air

value: clean air

value: control


title: Stimulated OB, mouse 3 (120 min)

description:
processed data file: rpkm.table.txt
Stim120_4


title: 513

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

data_processing:
The paired-end sequencing reads were aligned against the GRCh37 genome model using TopHat 2.04 with Bowtie 2.03.
The separate alignments were then merged using Cuffmerge with UCSC gene models as a reference.
The resulting files were then analyzed with Cufflinks to test for differential expression.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Cufflinks output showing FPKM values for genes (row) by sample ID (column).

organism: Homo sapiens

source_name: esophageal tissue

extract_protocol:
Total RNA was extracted using the QIAGEN RNEasy or miRNEASY kits.
RNA libraries were prepared for sequencing using standard Illumina protocols at the CCHMC Genetic Variation and Gene Discovery Core.

tag: patient cohort

value: active EoE


title: 713


title: 723


title: 594


title: 692


title: 778


title: 424


title: 334


title: 803


title: Control OB, mouse 3 (clean air)

description:
processed data file: rpkm.table.txt
Control_C5


title: 333


title: 520

value: healthy control


title: SCord_WT

city: Berkeley

first: Francisco

middle: J

last: Herrera

state: CA

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Processed data file: GSE55782_WT_ES_SCord_RNA-seq.txt

data_processing:
RNA-seq samples were mapped to the mouse genome using TopHat, and differentially expressed genes were determined using CuffDiff.
Genome_build: MGSCv37 (UCSC mm9)
Supplementary_files_format_and_content: RNA-seq .txt files: Tab-delimited text files include FPKMs ('value_1' and 'value_2') and differentially expressed genes determined using CuffDiff.
Supplementary_files_format_and_content: ChIP-seq: .bed files include peaks determined using MACS.

source_name: Mouse newborn spinal cord tissue, WT

growth_protocol: mES cells were differentiated into motor neurons using embryoid bodies cultures. See detailed protocol in associated manuscript (Herrera et al.)

extract_protocol:
RNA-seq: Total RNA was isolated and Poly-A libraries were constructed.
Libraries were constructed following Illumina protocols.

tag: strain/background

tag: genotype/variation

value: wild type

tag: cell type

value: newborn spinal cord tissue

tag: cell line

value: JM8 clone


title: Smc1_ChIAPET_rep1

first: Richard

middle: A

last: Young

institute: Whitehead Institute for Biomedical Research

description: ChIA-PET against Smc1 in v6.5 mESCs

library_source: genomic

data_processing:
Images analysis and base calling was done using the solexa pipeline.
The raw sequences were analyzed for linker barcode composition and separated into non-chimeric PET sequences with homodimeric linkers (AA or BB linkers) derived from specific ligation products, or chimeric PET sequences (AB linkers) with heterodimeric linker derived from nonspecific ligation products. We trimmed the 3’ end of PET sequences after a perfect match of the first 10nt of the liner sequences (Linker A with CTGCTGTCCG; Linker B with CTGCTGTCAT). After removing the linkers, only the 5’ ends of the trimmed PET sequences with length of 27bp were retained because the restriction enzyme EcoP151 cuts 27bp away from its recognition sequence.
The sequences of the two ends of PET sequences were separately mapped to the mm9 mouse genome using the bowtie algorithm with the option “-k 1 -m 1 -v 1”.  These criteria retained only the uniquely mapped reads, with at most a single mismatch for further analysis. Aligned reads were paired with mates and were filtered for redundant sequences to avoid bias from PCR amplification in the library preparation procedure. PET sequences with identical genomic coordinates and strand information at both ends were collapsed into a single PET sequence.
Genome_build: mm9
Supplementary_files_format_and_content: BED12 file: The PET sequences were categorized into intrachromosomal PETs, where the two ends of a PET were on the same chromosome, and interchromosomal PETs, where the two ends were on different chromosomes. The unique intrachromosomal PETs are parsed into BED12 format file.

molecule: genomic DNA

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol:
100 million murine ES cell were cross-linked by 1% formaldehyde at RT 10 mintues and were sonicated to solubilize the chromatin. The chromatin complexes contain DNA fragments with an average size of 300-800bp were immunoprecipitated by using murine SMC1a antibody.
After end repair, the blunt end DNA were ligated with biotin labled half-linkers which containing flanking ECOP15i sites.  After eluted chromatin complexes from protein bead A, Proximity ligated was performed at extremely dilute conditions at 16 O/N. The purified DNA which digested by Ecop15I were prepared for sequencing according to a modified version of the pair end  DNA protocol. Fragmented DNA was end repaired and subjected to add "A" at 3' end, ligated with PE adaptor provided by Illumina. Amplified fragment 214bp (representing pair end genomic DNA 52bp, 42nt linker and  and ~120bp of adaptor sequence) were isolated by agarose gel electrophoresis and purified. sequencing was performed on Illumina Hi-Seq 2000 with PE 50 cycles.
Linker A: 3'-GAC GAC AGG CTA TAG CGC CGG-5', 5'-CTG CTG TCC  GAT ATC GC-3'.  Linker B: 3'-GAC GAC AGT ATA TAG CGC CGG-5' 5'-CTG CTG TCA  TAT ATC GC-3'

value: V6.5 Embryonic stem cells

tag: chip antibody

tag: antibody catalog number

value: Bethyl A300-055A


title: EB_Day4_WT

description: Processed data file: EB_D4_WT_KO_RNA-seq.txt

source_name: EB-Day4-neuronal progenitors, WT

value: EB-Day4-neuronal progenitors


title: RNA_Pol2_ChIP

description: anti-Pol2 antibody: clone #8WG16; monoclonal antibody available from different vendors.

data_processing:
ChIP-seq samples were mapped using Bowtie, and peaks were determined using MACS.
Genome_build: MGSCv37 (UCSC mm9)
Supplementary_files_format_and_content: RNA-seq .txt files: Tab-delimited text files include FPKMs ('value_1' and 'value_2') and differentially expressed genes determined using CuffDiff.
Supplementary_files_format_and_content: ChIP-seq: .bed files include peaks determined using MACS.

source_name: EB-Motor neuron, WT, RNA Pol2  ChIP

extract_protocol:
ChIP-seq: EB-MN were fixed with 0.5% PFA and ChIP was performed. See details in associated manuscript (Herrera et al.)
Libraries were constructed following Illumina protocols.

value: EB-Motor neuron

value: RNA Pol2

value: HBG3 clone


title: H3K27ac_ChIPSeq control

status: Public on Jun 30 2014

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
Illumina CASAVA 1.8.2 for basecalling
ELAND mapping
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using MACS1.0, HNF4A ChIP-seq bed files generated using MACS2, H3K27ac Bed files were generated using NPS and BINOCh. The top 1000 scoring regions (indicating most dynamic chromatin between conditions) for each condition used for data analysis were retained in the bed file.

source_name: colonic epithelial cells

growth_protocol: Adult mice, 2-4 months old

extract_protocol:
Colonic epithelial scraping
Tru-seq Illumina Kit according to manufacturer's instructions

treatment_protocol: 3% DSS for 6 days or water only controls

tag: antibody

tag: treatment

value: water only


title: 168


title: EB_Day6_KO

description: Processed data file: EB_D6_WT_KO_RNA-seq.txt

source_name: EB-Day6-Motor neuron, TAF9B KO

value: TAF9B -/-

value: EB-Day6-Motor neuron

value: Taf9b_BG10 clone


title: IgG_ChIP

description: IgG control antibody: Abcam cat#46540.

source_name: EB-Motor neuron, WT, IgG control ChIP

value: IgG


title: SC_NB_WT

description: Processed data file: SC_NB_WT_KO_RNA-seq.txt

source_name: Mouse newborn spinal column tissue, WT

value: newborn spinal column tissue


title: EB_Day6_WT

source_name: EB-Day6-Motor neuron, WT


title: TAF9B_ChIP

description: anti-TAF9B antibody: #G3206; described in the associated manuscript.

source_name: EB-Motor neuron, WT, TAF9B ChIP


title: mESC KO

description: Processed data file: ES_D1_WT_KO_RNA-seq.txt

source_name: mouse embryonic stem cells (mESC), TAF9B KO

value: mouse embryonic stem cells (mESC)


title: mESC WT

description:
Processed data file: ES_D1_WT_KO_RNA-seq.txt
Processed data file: GSE55782_WT_ES_SCord_RNA-seq.txt

source_name: mouse embryonic stem cells (mESC), WT


title: EB_Day2_WT

description: Processed data file: EB_D2_WT_KO_RNA-seq.txt

source_name: embryoid bodies (EB)-Day 2, WT

value: embryoid bodies (EB)-Day 2


title: 609

value: healthy control


title: 527


title: MEF Suv39h dn Nuclear RNA-seq

status: Public on Jun 26 2014

city: Freiburg im Breisgau

first: Thomas

last: Manke

address: Stuebeweg 51

department: Bioinformatics and Deep-Sequencing Unit

country: Germany

institute: Max-Planck-Institute for Immunobiology and Epigenetics

description:
two biological replicates
Raw files for Rep 1: RNA_MEF_dn_1_GCCAAT_R1_001.fastq.gz ; RNA_MEF_dn_1_GCCAAT_R2_001.fastq.gz
Raw files for Rep 2: RNA_MEF_dn_2_CTTGTA_R1_001.fastq.gz ; RNA_MEF_dn_2_CTTGTA_R2_001.fastq.gz

data_processing:
Illumina Casava 1.7.0 and bcl2fastq 1.8.3 software used for basecalling.
Bowtie version 2.0.0-beta6  with parameters -D 15 -R 2 -N 0 -L 32 -i S,1,0.75 -M 10000 was used to map reads agains the mm9 genome build. The default bowtie2 mapping of multi-reads to one of the possible genomic locations was used. Reads mapping with mismatches were removed.
bigWig RPKM files were generated using bamCoverage from the deepTools package (http://deeptools.github.io). Scores represent the normalized number of reads overlaping bins of 10bp. The normalization scales the original depth of sequencing to RPKM for each 10 bp bin.
Genome_build: mm9

molecule: nuclear RNA

source_name: Mouse Embryonic Fibroblasts

growth_protocol: ES cells were grown on gelatin coated plates with ES medium ( DMEM supplemented with 15% FCS, 1x Pen/strept, L-Glutamine 2mM, ß-mercaptoethanol 0.1 MM, Non Essential amino acids 1x, Sodium piruvate 1mM and LIF). MEFs were grown in DMEM supplemented with 10% FCS, 1x Pen/strept, L-Glutamine 2mM, ß-mercaptoethanol 0.1 MM, Non Essential amino acids 1x, Sodium piruvate 1mM. In vitro differentiation to NPCs was carried out as described before (Bibel et al., 2007)

extract_protocol:
After nuclei isolation, only nuclear-RNA was extracted from 10^6 cells using TRIzol reagent (Invitrogen) and contaminating DNA was digested with Turbo DNase (Ambion).
RNA libraries were prepared for sequencing following standard Illumina protocols (TruSeq®)

value: Mouse Embryonic Fibroblasts

tag: genotype

value: Suv39h double null


title: 11_5_Dup

city: ny

first: mingyan

last: lin

address: 1925 morris park ave

institute: aecom

description: Sample 3

data_processing:
library strategy: Methyl Sensitive Tiny Fragment Enrichment/Massive Parallel Sequencing (MSFE/MPS)
Illumina pipeline software was used to analyzed images generated by the Illumina sequencing and ilitial data processing was performed using a read length of 36bp. Sequenced in which adapter-tags were identified on the 3’end the tag sequence was replaced with a poly(N) sequence of the same length. The Illumina ELAND pipeline was then re-ran with a sequence length of 27bp. Data contained within the ELAND_extended.txt files were used for counting sequences adjacent to ‘ACGT’ (HpyCH4IV) sites annotated in the mm9 Mus musculus genome in the UCSC genome browser. Up to two mismatches were permitted in each sequence and a sequence was allowed to align to a maximum of 10 locations within the genome. In the case of non-unique alignments,  a partial count for each alignment location amounting to 1/n, n representing total number of aligned positions, was assigned to each sequence. Normalization was performed by dividing the number of sequences associated with each HpyCH4IV site by the total number of sequences aligning to all HpyCH4IV sites in the same sample.
Genome_build: mm9
Supplementary_files_format_and_content: wig files

source_name: E11.5_embryonic heart

growth_protocol: ICR (CD-1) wild type mice were bred for timed pregnancies and embryonic hearts were collected at embryonic day (E)11.5 and E14.5

extract_protocol:
High molecular weight genomic DNA extraction PMID:16809668
Five micrograms genomic DNA was digested with methyl-sensitive restriction enzyme HpyCH4IV(NEB), purified by phenol/chloroform extraction and ethanol precipitation. Purification was followed by ligation of a custom adaptor, containing an EcoP15I recognition site and a T7 promoter sequence, using an NEB Quick Ligation Kit. Products were purified using AMpure(Agencort) prior to digestion with EcoP15I (NEB). Resulting restriction fragments were end-repaired and dA tailing was performed followed by ligation of the second adaptor containing an Illumina adapter sequence, again using the NEB Quick Ligation Kit. Products were prufied using the Qiagen MinElute PCR purification kit and then transcribed in vitro using MEGAshortscript  (Ambion). Products were then purified with Qiagen’s RNeasy clean up kit and reverse transcribed using the SuperScript III kit (invitrogen). The first strand cDNA was then amplified by the polymerase chain reaction and the library was purified using the QiaQuick PCR clean up kit (Qiagen). Protocol designed and described by Suzuki et al. 2010, PMID: 20359321.

treatment_protocol: Flash Frozen

value: ICR (CD-1)

value: wild type

value: embryonic heart


title: 11_5_1

description: Sample 1


title: 14_5_1

description: Sample 2

source_name: E14.5_embryonic heart


title: MEF WT Nuclear RNA-seq

description:
two biological replicates
Raw files for Rep 1: RNA_MEF_wt_1_GCCAAT_R1_001.fastq.gz ; RNA_MEF_wt_1_GCCAAT_R2_001.fastq.gz
Raw files for Rep 2: RNA_MEF_wt_2_CTTGTA_R1_001.fastq.gz ; RNA_MEF_wt_2_CTTGTA_R2_001.fastq.gz

value: wt


title: 508

source_name: esophageal tissue


title: NPC Suv39h dn Nuclear RNA-seq

description:
two biological replicates
Raw files for Rep 1: RNA_NPC_dn_1_GCCAAT_R1_001.fastq.gz ; RNA_NPC_dn_1_GCCAAT_R2_001.fastq.gz
Raw files for Rep 2: RNA_NPC_dn_2_CTTGTA_R1_001.fastq.gz ; RNA_NPC_dn_2_CTTGTA_R2_001.fastq.gz

source_name: Neural precursors cells

value: Neural precursors cells


title: MEF Suv39h dn H3K9me3 ChIP-seq

description: two biological replicates were merged; fastq file contains reads for both replicates

data_processing:
Illumina Casava 1.7.0 and bcl2fastq 1.8.3 software used for basecalling.
Bowtie version 2.0.0-beta6  with parameters -D 15 -R 2 -N 0 -L 32 -i S,1,0.75 -M 10000 was used to map reads agains the mm9 genome build. The default bowtie2 mapping of multi-reads to one of the possible genomic locations was used. Reads mapping with mismatches were removed.
For each ChIP-seq the number of reads overlapping a region of 10bp was normalized by the total number of reads sequenced. The difference between the ChIP normalized counts and the Input is reported. The tool bamCompare from the deepTools package (http://deeptools.github.io) was used to compute the differences.
bigWig difference ChIP vs. Input files (-input_merge.bw)  were generated using bamCompare from the deepTools package (http://deeptools.github.io). Scores represent the ChIP-seq normalized number of reads minus the input normalized number of reads overlaping bins of 10bp.
bigWig normalized signal files (-merge.bw) were generated using bamCoverage from the deepTools package (http://deeptools.github.io). Scores represent the normalized number of reads overlaping bins of 10bp. The normalization scales the original depth of sequencing to match a depth of 1x.
Genome_build: mm9

extract_protocol:
For ChIP, double cross-linking with Di(N-succinimidyl)-glutarate and formaldehyde  was used as described (Nowak et al., 2005). After sonication, lysates were incubated with the corresponding antibodies, histones-DNA complexes were immunoprecipitated with dynabeads and DNA was purified using columns.
Libraries were prepared following the standard illumina Pair-end protocol.

value: In house anti-H3K9me3 #4861


title: MEF WT H3K9me3 ChIP-seq


title: EB_Day2_KO

source_name: embryoid bodies (EB)-Day 2, TAF9B KO


title: WT poly-A RNA-seq

description:
three biological replicates
Raw files for Rep 1: tot_wt_A1_R1.fastq.gz ; tot_wt_A1_R2.fastq.gz
Raw files for Rep 2: tot_wt_A2_R1.fastq.gz ; tot_wt_A2_R2.fastq.gz
Raw files for Rep 3: tot_wt_B_R1.fastq.gz ; tot_wt_B_R2.fastq.gz

source_name: Embryonic Stem cells

extract_protocol:
Total RNA was extracted from 10^6 cells using TRIzol reagent (Invitrogen) and contaminating DNA was digested with Turbo DNase (Ambion).
RNA libraries were prepared for sequencing following standard Illumina protocols (TruSeq RNA Sample Prep Kit v2 -Set A)

value: Embryonic Stem cells


title: Suv39h dn Nuclear RNA-seq

description:
two biological replicates
Raw files for Rep 1: Nuc_dn_B1_R1.fastq.gz ; Nuc_dn_B1_R2.fastq.gz
Raw files for Rep 2: Nuc_dn_B2_R1.fastq.gz ; Nuc_dn_B2_R2.fastq.gz


title: TR192 Mac virus Positive rep 3

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 50bpX50bp pair-end! 10 sequencing. Sequencing reads were trimmed at the 3’end to mitigate n effect of C addition by template-switching enzyme used for preparation of small-input libraries. Then, data were aligned using Tophat to mm9 assembly of mouse genome and expression of genes scored by using  Cufflinks. Top 9000 expressed genes (representing stably expressed fraction of  transcriptome) were used to create ranked list ordered by the differential expression  between RFP positive (virus-positive) and RFP negative (virus-negative) macrophages.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file that includes normalized count data for each sample

source_name: peritoneal macrophages

extract_protocol:
Peritoneal cells from 8-10 mice were harvested by lavage, pooled, and blocked with 10% mouse serum. Cells selected with CD11b MicroBeads (Miltenyi Biotec) were analyzed or sorted after staining with antibodies: CD11b-PerCP-Cy5.5 (clone M1/70, BioLegend), F4/80-APCAlexa Fluor 750 (clone BM8, Invitrogen), CD19-PE-Cy7 (clone 1D3, BD Pharmigen). 3 For analysis cells were also stained with CD206-PE (clone C068C2, BioLegend), CD301-Alexa Fluor 647 (clone ER-MP23, AbD Serotec). Cells were sorted into Trizol Reagent (Invitrogen). 1000 to 2000 cells were obtained from each sort. RNA wasquantified using Qubit RNA assay kits (Invitrogen).
All of the RNA from virus-pos cells and 50 ng of RNA from virus-neg cells was prepared for RNA-seq using ScriptSeq v2 RNA-seq library preparation kit (Epicentre). Index Primers (Epicentre) were added and samples underwent Duplex-Specific thermostable nuclease (DSN) (Evrogen) treatment to remove ribosomal RNA. Samples were pooled and sequenced on HiSeq.

tag: infection

value: γ-herpesvirus

value: macrophage

value: peritoneal macrophages


title: TR192 Macrophage virus Negative rep 3


title: TR192 Mac virus Positive rep 2


title: WT Nuclear RNA-seq

description:
two biological replicates
Raw files for Rep 1: Nuc_wt_B1_R1.fastq.gz; Nuc_wt_B1_R2.fastq.gz
Nuc_wt_B2_R1.fastq.gz; Nuc_wt_B2_R2.fastq.gz


title: 14_5_Dup

description: Sample 4


title: SC_NB_KO

source_name: Mouse newborn spinal column tissue, TAF9B KO

value: TAF9B -/-

value: Taf9b_BG10 clone


title: TR192 Mac virus Positive rep 1


title: Input_MEF_d5

description:
two biological replicates
Raw files for Rep 1: D5_input_NoIndex_L001_R1_001.fastq.gz ; D5_input_NoIndex_L001_R2_001.fastq.gz
Raw files for Rep 2: D5_input_NoIndex_L005_R1_001.fastq.gz ; D5_input_NoIndex_L005_R2_001.fastq.gz

value: none (Input)


title: Input_MEF_w8

description:
two biological replicates
Raw files for Rep 1: W8_input_NoIndex_L003_R1_001.fastq.gz ; W8_input_NoIndex_L003_R2_001.fastq.gz
Raw files for Rep 2: W8_input_NoIndex_L007_R1_001.fastq.gz ; W8_input_NoIndex_L007_R2_001.fastq.gz


title: Input_NPC

description: one biological replicate


title: NPC Suv39h dn H3K9me3 ChIP-seq

description:
two biological replicates
Raw files for Rep 1: 110705_HWUSI-EAS616_00016_FC_3_1.fq.gz ; 110705_HWUSI-EAS616_00016_FC_3_2.fq.gz
Raw files for Rep 2: 110705_HWUSI-EAS616_00016_FC_8_1.fq.gz; 110705_HWUSI-EAS616_00016_FC_8_2.fq.gz


title: NPC WT H3K9me3 ChIP-seq

description:
two biological replicates
Raw files for Rep 1: 110705_HWUSI-EAS616_00016_FC_1_1.fq.gz; 110705_HWUSI-EAS616_00016_FC_1_2.fq.gz
Raw files for Rep 2: 110705_HWUSI-EAS616_00016_FC_2_1.fq.gz ; 110705_HWUSI-EAS616_00016_FC_2_2.fq.gz


title: Suv39h2-HA/FLAG ChIP-seq

description:
two biological replicates
Raw files for Rep 1: 100921_HWUSI-EAS616_00004_FC_7_1.fq ; 100921_HWUSI-EAS616_00004_FC_7_2.fq
Raw files for Rep 2: 100921_HWUSI-EAS616_00004_FC_8_1.fq; 100921_HWUSI-EAS616_00004_FC_8_2.fq

value: α-HA (Roche 3F10) and α-DYKDDDDK (Biozol)

value: Suv39h2-HA/Flag Knock in


title: TR192 Macrophage virus Negative rep 2


title: Suv39h dn H3K9me3 ChIP-seq

description:
two biological replicates
Raw files for Rep 1: 100302_HWUSI-EAS616_0002_6_1.fq ; 100302_HWUSI-EAS616_0002_6_2.fq
Raw files for Rep 2: 100302_HWUSI-EAS616_0002_8_1.fq; 100302_HWUSI-EAS616_0002_8_2.fq


title: WT H3K9me3 ChIP-seq

description:
two biological replicates
Raw files for Rep 1: 100921_HWUSI-EAS616_00004_FC_2_1.fq; 100921_HWUSI-EAS616_00004_FC_2_2.fq
Raw files for Rep 2: 100921_HWUSI-EAS616_00004_FC_6_1.fq; 100921_HWUSI-EAS616_00004_FC_6_2.fq


title: Suv39h1-HA/FLAG ChIP-seq

description:
two biological replicates
Raw files for Rep 1: 100921_HWUSI-EAS616_00004_FC_3_1.fq; 100921_HWUSI-EAS616_00004_FC_3_2.fq
Raw files for Rep 2: 100921_HWUSI-EAS616_00004_FC_4_1.fq; 100921_HWUSI-EAS616_00004_FC_4_2.fq

extract_protocol:
For ChIP, double cross-linking with Di(N-succinimidyl)-glutarate and formaldehyde  was used as described (Nowak et al., 2005). After sonication, lysates were incubated with the corresponding antibodies, histones-DNA complexes were immunoprecipitated with dynabeads and DNA was purified using columns. Libraries were prepared following the standard illumina Pair-end protocol.
Libraries were prepared following the standard illumina Pair-end protocol.

value: Suv39h1-HA/Flag Knock in


title: Culex pipiens quinquefasciatus

first: Chunxiao

last: Li

address: 20 Dongdajie, Fengtai District

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
The Cx. pipiens quinquefasciatus genome and gene information were downloaded from the quinquefasciatus Genome Annotation Project (https://www.vectorbase.org/organisms/culex-quinquefasciatus, GenBank accession number: AAWU00000000.1).
The remaining reads were aligned to the mosquito genome using SOAPaligner/soap2.
ERANGE software (version 4.0) (http://woldlab.caltech.edu/gitweb/) was used to calculate normalized gene locus expression levels by assigning reads to their site of origin and counting them. The expression level of a gene from RNA-Seq was normalized by the RPKM (reads per kilo bases per million reads) value.
The R package DEGseq was applied to identify DEGs with a random sampling model based on the read count for each gene in each mosquito population.
Genome_build: AAWU00000000.1
Supplementary_files_format_and_content: text files include RPKM values for each sample

organism: Culex quinquefasciatus

source_name: mosquito females

extract_protocol:
Total RNA of 30 mosquito females of each was extracted using the TRIzol. Total RNA samples were pooled and 10 mg from each pool was used to isolate poly(A) mRNA and to prepare non-directional Illumina RNA-Seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: laboratory strain

tag: gender

value: female


title: Culex pipiens molestus

organism: Culex pipiens molestus

tag: strain


title: WT_SOLID_313

status: Public on Jun 25 2014

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Rec12-associated DNA oligonucleotides

data_processing:
Base calls were made using 454 gsRunBrowser for samples run on 454, and SOLiD Analysis Tools (SAT) for those run on SOLID.
Sequenced reads were trimmed for adaptor sequence, then mapped to S. pombe whole genome using SHRiMP 2.2.2 gsmapper-cs with options -E --strata --global -o 10000 -V -n 1 -g -100 -e -100. Mapping was done in three steps: Step (1) Reads longer than 15bp;  Default Seeds for gsmapper-cs; (2) Reads between 11 and 15bp: -s 1111101111 (ie seed values were reset); (3) Reads shorter than 11bp: -s 1111111
Maps of 5' ends of uniquely mapping sequence reads were compiled and analyzed in R
For reads that mapped to multiple locations, imputed maps ("multimap") were calculated by fractionally assigning each multi-mapper to each of its map positions in proportion to the density of uniquely mapped reads within +/- 250 bp
Genome_build: Sanger Center S. pombe genome, Aug 7, 2010 version
Supplementary_files_format_and_content: plain tab-delimited text files include raw Rec12 oligo counts for each sample at each non-zero base position in the genome

organism: Schizosaccharomyces pombe

source_name: meiotic culture

growth_protocol: Synchronized meiotic cultures were prepared at 30°C and harvested at 4.5 hr.

extract_protocol:
Based on Milman et al. 2009 Mol Cell Biol 29: 5998-6005 and Pan et al. 2011 Cell 144:719-731. Whole cell extracts were prepared by grinding cells with glass beads and extracting in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to immunoprecipitation of Rec12-flag with anti-flag antibodies. Protein was digested with proteinase K and Rec12-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell 144:719-731. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add 454 or SOLiD adapters.

tag: epitope tag

tag: ploidy

value: diploid


title: TR192 Macrophage virus Negative rep 1


title: Input DNA

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

country: Italy

institute: Italian National Cancer Institute "Regina Elena"

data_processing:
Base-calling and quality-control was performed using the Illumina pipeline Casava
ChIP-Seq reads were aligned to the human hg18 using Bowtie.
Peak calling was done by MACS 1.4. The setting for peak calling was tsize=36, bw=200, mfold=10,30, p-value at least 1e-5.
Genome_build: hg18
Supplementary_files_format_and_content: wig files were generated using BedTools and BEDGRAPH

growth_protocol: SKBr3 breast cancer cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-glutamine and penicillin/streptomycin.

extract_protocol:
Chromatin was isolated from the nuclei of formaldehyde cross-linked cells, sonicated and immunoprecipated with anti-H3K4me3 antibody.
ChIP-Seq libraries were constructed from 10ng immunoprecipitated or original input chromatin using the ChIP-Seq Sample Prep Kit from Illumina, following the manufacturer's instructions.

treatment_protocol: The cells were treated for 2h with 100nM 1α,25(OH)2D3 or vehicle as control.

value: breast cancer epithelial cells


title: HP1α-EGFP ChIP-seq

description:
two biological replicates
Raw files for Rep 1: wt_HP1_4_NoIndex_L003_R1_001.fastq.gz ; wt_HP1_4_NoIndex_L003_R2_001.fastq.gz
Raw files for Rep 2: wt_HP1_11_NoIndex_L004_R1_001.fastq.gz ; Raw files for Rep 2: wt_HP1_11_NoIndex_L004_R2_001.fastq.gz

value: α-EGFP (invitrogen, A11122)

value: EGFP tagged


title: H3K4me3_Ctrl_ChIP-Seq

value: H4K4me3 (Abcam, ab1012)

value: control


title: WT Control

city: Seattle

first: Akhilesh

middle: K

last: Singh

state: WA

department: Center for Immunity and Immunotherapies

institute: Seattle Childrens Research Institute

data_processing:
base-calling - Illumina OLB version 1.9.3
demultipexing- Python custom program
alignment-CLCBIO- version 6.5
Genome_build: mm8
Supplementary_files_format_and_content: RPKM- Genes - tab-delimited file

source_name: Wild type mouse colon

extract_protocol:
C. rodentium infected mice colons were harvested at day and cleaned with ice cold PBS. Colon samples were homogenized and total RNA was purified by using RNeasy mini kit (Qiagen)
Libraries were prepared for sequencing using Illumina's instructions accompanying the TrueSeq RNA sample preparation V2.

treatment_protocol: Mice Infected with C. rodentium

value: colon

tag: phenotype

value: DOCK8 wild type

tag: infectious agent

value: Citrobacter rodentium


title: H3K4me3_1α,25(OH)2D3_ChIP-Seq


title: KO2 RNA

status: Public on Jun 24 2014

city: Frederick

first: Scott

last: Durum

state: MD

address: Building 560, Room 31-71

department: CCR

institute: National Cancer Institute

data_processing:
ChIP-seq, RTA 1.8.70.0 software was used for basecall analysis and aligned to the reference genome was performed at a mismatch error rates =<0.05%. CASAVA1.8.2 (Eland_extended used for mapping)
Tag density was performed using IGV tool at a window of 5kb and selected at an FDR<0.0001 for autosomes only.
RNA-seq, RTA 1.12.4.2 software was used for basecall analysis and aligned to the reference genome was performed at a mismatch error rates =<0.05%. CASAVA1.8.2   (Both eland_pair and eland_rna module were used for mapping)
To evaluate the abundance of transcripts, each set of WT and KO MEF samples and their biologic replica were analyzed independently using Partek Genomics Suite software. Reads per kilobase of exon per million mapped reads (rpkm) were calculated for all murine genes.
Reads that mapped to multiple locations in the genome were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files with tag density for ChIP-seq data, txt with RPKM for RNA-seq data.

source_name: KO MEF

growth_protocol: Lsh WT and Lsh KO MEFs were maintained in DMEM supplemented with 10% (vol/vol) FBS (Gibco), 2 mM Glutamax (Invitrogen), and 1% penicillin and streptomycin (Invitrogen).

extract_protocol:
Total RNA was isolated from cell pellets of WT (Lsh+/+) MEFs and KO (Lsh-/-) MEFs and their biologic replica using the RNeasy Mini Kit (Qiagen) and treated with DNaseI (Roche) for 10 min at room temperature. rRNAs were removed from 5 μg of total RNA by RiboMinus (Life Technologies) as per the manufacturer’s instructions.
Cells were cross-linked with formaldehyde and nuclear DNA was sonicated with 200-300bp,  then the H3K4me1-DNA complexes were isolated with antibody.
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. After purification and PCR amplification the final cDNA library was generated based on the mRNA-seq Library Preparation Protocol from Illumina.
ChIP DNA libraries were made following Illumina ChIP-Seq library preparation kit and subjected to Solexa sequencing (Illumina) at the CCR-Sequencing Facility, National Cancer Institute. Sequencing was performed on Illumina Genome Analyzer IIx.

treatment_protocol: Primary  MEF cells were derived from the body of E13.5 C57Bl/6 mouse embryos and genotyping was performed to select Lsh WT and Lsh KO.

tag: cell types

value: primary mouse embryonic fibroblasts E13.5

value: Lsh KO

tag: passage


title: 461

tag: patient cohort

value: healthy control


title: KO1 RNA


title: Lsh KO3 H3K27me3

value: Millipore, 07-449


title: Lsh KO H3K4me3

value: Abcam, ab8580


title: WT1 RNA

source_name: WT MEF

value: wild type


title: WT3 H3K27me3


title: WT H3K4me3


title: WT_SOLID_310

description: Rec12-associated DNA oligonucleotides


title: NPC WT Nuclear RNA-seq

description:
two biological replicates
Raw files for Rep 1: RNA_NPC_wt_1_GCCAAT_R1_001.fastq.gz; RNA_NPC_wt_1_GCCAAT_R2_001.fastq.gz
Raw files for Rep 2: RNA_NPC_wt_2_CTTGTA_R1_001.fastq.gz; RNA_NPC_wt_2_CTTGTA_R2_001.fastq.gz

tag: cell type

value: Neural precursors cells

value: wt


title: Lsh KO2 Pol II

value: Santa Cruz, sc-899x


title: WT2 H3K27me3


title: Lsh KO1 Pol II


title: Lsh KO2 H3K27me3


title: WT1 H3K27me3


title: WT1 Pol II


title: Lsh KO1 H3K27me3


title: DOCK8 KO

source_name: DOCK8 KO mouse colon

tag: tissue

value: DOCK8 knock-out


title: WT_454

description: Rec12-associated DNA oligonucleotides

value: haploid


title: WT2 RNA


title: WT2 Pol II

tag: chip antibody


title: WT3 input


title: Lsh KO2 input


title: Lsh KO3 input


title: Lsh KO1 input


title: EB_Day4_KO

description: Processed data file: EB_D4_WT_KO_RNA-seq.txt

source_name: EB-Day4-neuronal progenitors, TAF9B KO

tag: strain/background

tag: genotype/variation

value: TAF9B -/-

value: EB-Day4-neuronal progenitors

tag: cell line

value: Taf9b_BG10 clone


title: XH

city: Guangzhou

first: Xuenong

last: Zhu

state: Guangdong

address: Wushan street 483

department: College of Animal Science

institute: South China Agricultural University

description: Sample 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data received from Illumina sequencing were first managed to filter out the reads containing adaptors, the reads which have over 10% of N, and the low quality reads in which the number of bases with quality value Q ≤ 10 was over 50%.
The residual rRNA was removed by blasting to rRNA database (http://www.arb-silva.de/) using SOAP before the following analysis. Clean data was gained and then was mapped to the chicken reference genome (ftp://ftp.ensembl.org/pub/release-73/fasta/gallus_gallus/dna/) by TopHat 2.0.8. The mapped reads were retained to construct transcripts by Cufflinks 2.0.2.
These transcripts were blasted to non-coding RNA database (Gallus_gallus.Galgal4.73.ncrna.fa.gz) and the transcripts with identity > 0.9 & coverage > 0.8 were selected. The annotated transcripts were described as known non-coding RNA. The transcripts unmapped to non-coding RNA database were filtered by blasted to KEGG, NR, COG, SWISSPROT database according to identity > 0.9 & coverage > 0.8, and the annotated transcripts were regarded as mRNA. The transcripts unmapped to the above protein database were distinguished as coding or non-coding sequences by CPC to operate SVM prediction according to framefinder, value, coverage of ORF, whether the transcripts were started with initiation codon and ended with termination codon, the length and score of transcripts blasted to protein, and whether the mapped fragment was in the same ORF. The non-coding transcripts were described as novel non-coding RNA.
Genome_build: Gallus_gallus.Galgal4.73
Supplementary_files_format_and_content: Expression amounts of novel lncRNAs were calculated according to the sequences of predicted lncRNAs using RPKM method (Reads Per kb per Million reads).

organism: Gallus gallus

source_name: Breast muscle

growth_protocol: WRR (a chicken strain with fast growth rate) and XH ( a Chinese native chicken strain with slow growth rate) were obtained from South China Agricultural University, Guangdong, China. All chickens were raised in the same space but different cages and with the same feed diet. They were free to get water and fed with 16.5% CP and 2,800 kcal of ME/kg. According to the body weight (BW) records at 7 weeks of age, 4 female broilers from each of the two strains that had average body weight were selected then two sample groups named WRR and XH were generated. The BW values were 625.3 ± 12.0 and 328.5 ± 10.6 g in WRR and XH group, respectively.

extract_protocol:
Total RNA of 8 breast muscles was isolated using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the protocol of manufacture.
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, total RNA from 4 birds within each group was mixed in equal amounts to generate a pooled sample using Agilent 2000. Ribosomal RNA was removed from total RNA. Subsequently, the RNA was sonicated to produce RNA fragments ranging from 200-500 nt. The RNA fragments were used to generate the first strand cDNA synthesis with normaldNTPs. Then, the second strand cDNA synthesis was obtained with dTTP changed to dUTP. After purifying with QIAquick Gel Extraction Kit (Qiagen, Valencia, CA, USA), the addition of EB buffer solution, end repairing, the addition of single “A” base to 3’ terminal and Y-adaptor ligation, and the degradation of the second strand cDNA synthesis by Uracil-N-Glycosylase enzyme, qualified RNA was excised from the gel by fragment size selection and then used for PCR amplification. Following library qualification, RNA libraries were sequenced on the Illumina Hiseq 2000 (Illumina, San Diego, CA, USA)

treatment_protocol: Breast muscle tissues of the 8 individuals were collected immediately after death, snap frozen in liq nitrogen, then stored at -80°C until DNA extraction.

value: Xing Hua

value: Breast muscle

value: slow-growing

tag: age

value: 7 weeks old


title: WRR

description: Sample 1

value: White Recessive Rock

value: fast-growing


title: TA FNP

city: Evanston

first: Carole

last: LaBonne

state: IL

address: 2220 Campus Drive

department: Molecular Biosciences

institute: Northwestern University

data_processing:
BAM files were loaded into GeneSpring Version 12.5-GX-NGS for NGS, Whole Genome RNA-seq analysis
The chicken reference genome was selected (WASHU2, Ensembl 4/9/12) as well as parameters for Immumina Single end sequencing
Data Interpretation was set to program defaults
Quality inspection was performed and data proved of good quality
For qunatification, reads were considered and the detection of novel genes and exons was allowed for. Counts were normalized to one, with the baseline median to all samples. All entities were filtered on expression (3.0-8607.81) in the NRPKM with at least one out of six samples having a value within the defined range
The Audic Claverie test (no correction) was used to identify differentially expressed genes in between control and ta2 facial prominences with a p-value ≤ 0.05.
Genome_build: Gallus_gallus-2.1
Supplementary_files_format_and_content: .txt file, as exported from Genespring, all available parameters for export were included

source_name: Frontonasal Prominence

growth_protocol: Fertilized eggs (control and mutant) were incubated at 99.5C until embryos reached developmental stage HH 25.

extract_protocol:
Facial promiences were manually harvested and pooled.  RNA was extracted using Trizol reagent. RNA was processed according to llumina TruSeq and Nugen Ovation RNA-Seq System V2 methods.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: HH St. 25

tag: genotype

value: Frontonasal Prominence


title: WT2 input

value: primary mouse embryonic fibroblasts E13.5

tag: strain

value: wild type


title: TA MNP

source_name: Mandibular Prominence

value: Mandibular Prominence


title: CTL FNP

value: control embryo


title: TA MXP

source_name: Maxillary Prominence

value: Maxillary Prominence


title: T1682

city: Washington

first: Krithika

last: Bhuvaneshwar

state: DC

address: 2115 Wisconsin Ave NW

institute: Georgetown University

data_processing:
FASTQ files were obtained directly from the sequencing machine programmed to automatically trim the adaptors and barcode sequences. The reads were mapped to the reference genome using TopHat 28. Quality of the RNA sequencing results was assessed using CollectRnaSeqMetrics available in Picard tools and with FASTQC software
Gene expression was estimated from the mapped reads using Cufflinks algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file that includes RPKM values for each sample

source_name: Thymoma

extract_protocol:
From FFPE blocks, 4 and 10μm slices were cut using a microtome. 4μm slides were stained with Haematoxylin and Eosin and a pathologist (G.F.) confirmed the tumor diagnosis and selected the tumor material. 10μm slides were deparaffinized using Histochoice Clearing Agent (Sigma-Aldrich, St. Louis, MO) and rehydrated through alcohol series. Thereafter, the stained and the 10μm slides, from the same block, were matched and the selected regions rich in tumor cells were macro-dissected by scraping from the rehydrated slides. Samples were annotated with pathologist’s estimation of tumor cellularity. DNA was extracted using DNeasy Blood and Tissue kit (Qiagen) according to vendor’s protocol but with an extended proteinase K digestion of at least 16h at 70oC. Patient’s blood (5mL) were collected in EDTA tubes and frozen at -80oC. DNA was extracted from the whole blood using QiAamp DNA Blood Maxi Kit (Qiagen).
Transcriptome sequencing was conducted at the NCI sequencing facility according to the Illumina mRNA sample preparation kit (Illumina, San Diego, CA). Briefly, using poly-T-bound magnetic beads, poly-A mRNAs were captured from total RNA. First and second strand cDNA were serially synthetized. Overhanging fragments’ ends were repaired using T4 DNA and Klenow DNA polymerases and adaptors linked using T4 DNA Ligase. Ligation products were run on an agarose gel, the 200 bp band was excised and used for DNA extraction. cDNA libraries were generated from the purified products and subsequently validated with the 2100 Agilent bioanalyzer (Agilent). According to the instructions, cDNA libraries were hybridized to a flow cell, amplified, linearized and denatured using Illumina Cluster Station, in order to generate pair-end clusters ready for sequencing. Genome Analyzer II or HiSeq2000 were used for sequencing

tag: sample type

value: Cell Line

tag: who histotype

tag: Stage

value: uk

tag: final gtf2i mutation status

value: WT


title: CTL MNP


title: N-Thy010

value: Frozen

value: IVA

tag: age at diagnosis

tag: Sex

value: F


title: P-Thy037

value: A

value: IIA

value: M

value: MUT


title: P-Thy041


title: N-Thy002

source_name: Thymic Carcinoma

value: IVB


title: P-Thy034

value: IIB


title: P-Thy031


title: P-Thy027


title: P-Thy018


title: P-Thy019


title: total small RNAs in WT with L4440

city: Worcester

first: Craig

last: Mello

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
WT with L4440 food
5' barcode: (A) TGAC and 3' linker: 1 CTGTAGGCACCATCAAT

data_processing:
Remove 5' barcode and 3' barcode (or called linker)
Map the reads to WS215 genome and annotation
A custom PERL pipeline is used to summarize reads and generate histogram at single nt level.
Generic genome browse is used to visualize the data
Genome_build: WormBase WS215
Supplementary_files_format_and_content: Tab delimited txt format file containing sequence and read number used in the analysis with the first line as header

organism: Caenorhabditis elegans

source_name: N2 with L4440

growth_protocol: C. elegans worm grown at 20 degree

extract_protocol: Small RNAs of 18-40nt from total RNAs were resolved on a 15% polyacrylamide/7M Urea Gel, along with 2 picomoles of RNA standard (18- and 40-nt) in separate lanes. SYBR gold staining was used to visualize the RNA standards. A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and isopropanol-precipitated with 20mg of glycogen as the carrier. The gel purified RNA was incubated with 0.25 U/µl TAP (Epicentre) and  1U/µl SuperRNaseIN (Ambion) in 10µl reaction containing 1X buffer at 37 oC for 1 hr, followed by phenol-chloroform extraction and isopropanol precipitation. The TAP-treated samples were then incubated with 5µM of 3’-end linker (miRNA cloning linker1 from IDT DNA Technologies), 1 Unit/µl of SuperRNaseIN, 10% DMSO and 1 U/µl T4 RNA ligase (Takara) in 10µl ligation buffer (50mM Tris-Cl pH7.5, 10mM MgCl2,10mg/mL BSA, 10mM DTT) at 15 oC for 2 hrs and then at 4 oC overnight. The 3’ ligated products were gel purified, eluted, precipitated and then incubated with 5 µM of 5’ adapter oligonucleotide with 4nt barcode at the 3'  end, 1 Unit/µl SuperRNaseIN (Ambion) and 2 U/µl of T4 RNA ligase in ligation buffer (50mM Tris-HCI pH7.5), 10mM MgCI2, 10mM DTT, 1mM ATP) and 10% DMSO at 15 oC for 8 hrs  and then at 4 oC overnight. The ligated products were gel purified and reverse transcribed in a standard 20µl reaction (SuperScript III, Invitrogen). The cDNA was amplified by PCR and purified using a 8% polyacrylamide gel. PCR products generated for all the samples were sequenced on a Solexa sequencing GAIIx platform (Illumina, Inc.) and single-end 36 nt reads were obtained.

treatment_protocol: 18-40 nt small RNAs from total RNAs were resolved on a 15% PAGE/7M Urea gel, along with 2 picomoles of RNA standard (18- and 40-nt) in separate lanes visualized using SYBR gold (invitrogen). A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and isopropanol-precipitated with 20mg of glycogen as the carrier. The gel purified RNA was incubated with 0.25 U/µl TAP (Epicentre) and  1U/µl SuperRNaseIN (Ambion) in 10µl reaction containing 1X buffer at 37 oC for 1 hr, followed by phenol-chloroform extraction and isopropanol precipitation.


title: total small RNAs in rde-12 with cpsf-2 RNAi food

description:
rde-12 with cps-2 food
5' barcode: (D) ATCA and 3' linker: 1 CTGTAGGCACCATCAAT

source_name: rde-12 with cpsf-2 RNAi food

value: rde-12 mutant


title: total small RNAs in WT with cpsf-2 RNAi food

description:
WT with cpsf-2 food
5' barcode: (B) CAGT and 3' linker: 1 CTGTAGGCACCATCAAT

source_name: N2 with cpsf-2 RNAi food

value: wild type


title: total small RNAs in rde-12 with L4440

description:
rde-12 with L4440 food
5' barcode: (C) GCTG and 3' linker: 1 CTGTAGGCACCATCAAT

source_name: rde-12 with L4440


title: TY82


title: N-Thy011


title: CTL MXP

value: HH St. 25


title: T1889


title: WT1 input

tag: cell types

value: primary mouse embryonic fibroblasts E13.5

tag: passage


title: N-Thy009


title: N-Thy008


title: N-Thy001


title: P-Thy015


title: P-Thy009

value: AB


title: P-Thy003

value: III


title: P-Thy002


title: P-Thy021


title: P-Thy025


title: TF18-Pink rep1

status: Public on Jun 23 2014

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

country: Japan

institute: National Food Research Institute

data_processing:
Illumina CASAVA software (ver.1.8.1) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the predicted protein-coding sequences (CDS) of tomato genes provided the International Tomato Annotation Group (ITAG, version2; available at http://solgenomics.net/organism/Solanum_lycopersicum/genome) using bowtie2 with parameters -q -p 4.
Reads Per Kilobase of exon per Million mapped reads (RPKM) were calculated for all tomato predicted genes.
Genome_build: ITAG2_cds
Supplementary_files_format_and_content: A tab-delimited text file includes RPKM values for each sample.

organism: Solanum lycopersicum

source_name: Tomato fruits

growth_protocol: Plants were grown in a glasshouse under 16-h light at 26°C and 8-h dark at 20°C conditions, and the fruits were harvested at 35 and 45 DAP.

extract_protocol:
The frozen fruits were powdered with moter and pestle. Total RNA samples were prepared from fruits of wild type, a FUL1/FUL2 suppressed line (TF18) and rin mutant at 35 DAP (G stage) and 45 DAP (P-stage) by SDS-phenol extraction and following elimination of polysaccharides with 2-botoxyethanol. The RNAs were further purified with the RNeasy Plus Kit (Qiagen). The quality of the RNAs was confirmed using a 2100 Bioanalyzer (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The harvested fruits were sliced and immediately frozen in liquid nitrogen and stored at -80°C.

tag: type

value: FUL1/FUL2-suppressed transgenic line TF18

value: Ailsa Craig cultivar

value: 45 DAP


title: TF18-Pink rep3


title: TF18-Green rep3

value: 35 DAP


title: rin-Pink rep3

value: rin mutant

value: LA3754 (Ailsa Craig background)


title: TF18-Green rep1


title: TF18-Pink rep2


title: TF18-Green rep2


title: rin-Pink rep2


title: rin-Green rep3


title: AC-Pink rep2

value: Wild type


title: rin-Pink rep1


title: rin-Green rep2


title: rin-Green rep1


title: AC-Green rep3


title: AC-Pink rep3


title: P-Thy008

value: Frozen

value: IIA

value: M


title: AC-Pink rep1


title: AC-Green rep2


title: P-Thy016

value: F

value: WT


title: B6_18_rep3

city: Bar Harbor

first: Cheryl

last: Ackert-Bicknell

state: ME

address: 600 Main Street

institute: The Jakcson Laboratory

data_processing:
All the reads were aligned to NCBIM37 reference transcriptome using bowtie version 0.12.9 with parameters -q, -a, -v 3, --all, --best, --strata.
Abundance estimation was performed using RSEM version 1.2.8 with the parameters of --fragment-length-mean 280 and --fragment-length-sd 50. RSEM outputs the normalized expression level in TPM (transcripts per million) so we can compare levels at different time points.
Genome_build: NCBIM37 reference transcriptome
Supplementary_files_format_and_content: Tab-delimited text files that contain the expression abundance in TPM (Transcripts Per Million)

source_name: neonatal calvaria

growth_protocol: Calvaria were collected from neonatal mice of 5 to 9 days of age.  The calvaria were subjected to four rounds of digestion with an enzyme mixture containing 0.05% trypsin and 1.5U/ml collagenase P.  Digestions 2 through 4 were collected and the cells plated in DMEM contain 10% Fetal Bovine Serum.  Cells were allowed to grow for 4 days, after which they were removed from culture and subjected to FACS.  Cells expressing Cyan Florecent Protein were collected and returned to culture.

extract_protocol:
Cells were washed with PBS and scraped directly into Trizol for RNA extration.
RNA was conveted to cDNA using a NuGEN Ovation aplification step and libraries were contructed using the Illumina TruSeq method.

treatment_protocol: After FACS sorting, the cells were grown in aMEM containing 50 mg/ml Ascorbic Acid, 4 mM beta-glycerol phosphate, 10% fetal bovine serum and 1X pen/strep.

value: C57BL/6J-Col3.6 CFP

tag: cell type

value: osteoblast

tag: time (days post differentiation)


title: AC-Green rep1


title: B6_16_rep3


title: P-Thy001


title: B6_18_rep2


title: B6_16_rep1


title: B6_14_rep3


title: B6_16_rep2


title: B6_14_rep2


title: B6_14_rep1


title: B6_12_rep1


title: B6_12_rep2


title: B6_10_rep3


title: ECFC_L2_3

first: Terri

last: DiMaio

address: 750 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
perform image analysis and base calling with Illumina's RTA v1.17 Software
demultiplex and generate files in FASTQ format, using Illumina's CASAVA v1.8.2 Software
remove reads that didn't pass Illumina's base call quality threshold
align reads, using TopHat v2.08b ( http://tophat.cbcb.umd.edu/ ) along with Bowtie 1.0.0 ( http://bowtie-bio.sourceforge.net/index.shtml ), using Ensembl's GRCh37 release 70 as the reference genome.
generate counts for each gene using htseq-count v0.5.3p9 (using the intersection-strict overlapping mode)
Genome_build: Ensembl's GRCh37 release 70
Supplementary_files_format_and_content: tab-delimited text file includes CPM (counts per million reads) for each sample

source_name: whole peripheral blood

extract_protocol:
RNA was isolated using the RNA isolation kit by Macherey-Nagel. Samples were cleaned and concentrated, where necessary, using Zymogen kit
RNA-seq libraries were generated using Illumina TruSeq RNA Sample Prep Kit v2 following the manufactures protocol.

value: lymphatic endothelial colony forming cells


title: B6_12_rep3


title: ECFC_L2_1


title: B6_8_rep3


title: B6_10_rep2


title: B6_10_rep1


title: B6_8_rep1


title: ECFC_B2_2

value: blood endothelial colony forming cells


title: B6_18_rep1


title: B6_6_rep2


title: ECFC_B2_1


title: ECFC_B1_3


title: ECFC_B1_2


title: B6_6_rep1


title: B6_8_rep2


title: ECFC_B2_3


title: B6_6_rep3


title: B6_2_rep3


title: ECFC_L1_3


title: ECFC_B1_1


title: B6_4_rep1


title: B6_4_rep2


title: ECFC_L1_2


title: Suv39h dn poly-A RNA-seq

description:
three biological replicates
Raw files for Rep 1: tot_dn_A1_R1.fastq.gz ; tot_dn_A1_R2.fastq.gz
Raw files for Rep 2: tot_dn_A2_R1.fastq.gz ; tot_dn_A2_R2.fastq.gz
Raw files for Rep 3: tot_dn_B_R1.fastq.gz ; tot_dn_B_R2.fastq.gz

source_name: Embryonic Stem cells

extract_protocol:
Total RNA was extracted from 106 cells using TRIzol reagent (Invitrogen) and contaminating DNA was digested with Turbo DNase (Ambion). RNA libraries were prepared for sequencing following standard Illumina protocols (TruSeq RNA Sample Prep Kit v2 -Set A,
RNA libraries were prepared for sequencing following standard Illumina protocols (TruSeq RNA Sample Prep Kit v2 -Set A)

value: Embryonic Stem cells

value: Suv39h double null


title: ECFC_L2_2


title: B6_2_rep1


title: ECFC_L1_1


title: Runx3_CD4DC_CHIP_Runx3_IP1

status: Public on Jun 22 2014

city: Rehovot

first: Yoram

last: Groner

state: istael

department: Molecular genetics

country: Israel

institute: Weizmann institute of science

data_processing:
Basecalls performed using CASAVA version 1.8
For data analysis 70 million Runx3 IP and 74 million whole genome extract sequences were aligned uniquely to the mouse genome (mm9) using bowtie. Bound regions of merged biological replicates were detected using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file containing 15121 peaks detected by MACS2.

source_name: Splenic CD4+ dendritic cells

growth_protocol: Two biological replicate ChIP-Seq experiments were conducted for detection of Runx3-bound genomic regions using in-house anti Runx3 Ab and 30x106 positive CD11c MACS isolated (Miltenyi Biotec) DC. These cells were further purified by FACS to CD11chiMHCII+CD4+ cDC subset, collected from approximately 15 mice. DC were freshly sorted, fixed and frozen -80c.

extract_protocol:
Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 40ul of anti-Runx3 Ab were added to 15 mL of diluted, fragmented chromatin; whole cell extract fragmented chromatin served as control. DNA was purified using QIAquick spin columns (QIAGEN).
For ChIP-seq analysis, indexed CiHP-seq libraries were prepared as published Blecher-Gonen et al. Nature Protocols 8, 539–554 (2013).  Illumina sequencing of short reads (50 bp) was performed in one lane of Hiseq 2000 using v3 clustering and sequencing reagents.

value: Splenic CD4+ dendritic cells

tag: passages

value: Collected from approximately 15 mice. DC were freshly sorted, fixed and frozen -80c

tag: chip antibody

value: Runx3poly clonal home made


title: input DNA

status: Public on Jun 21 2014

city: Singapore

first: Shawn

last: Hoon

address: 61 Biopolis Street

country: Singapore

institute: Agency for Science Technology and Research

data_processing: The sequenced reads were filtered based on the quality score of each read and alignments. Reads with phred score < 20 were removed. Reads were mapped to the human reference genome (hg19) using bowtie version 0.12.7 with settings (-m 1 --chunkmbs 256 --best -p 8 -S hg19). Aligned reads were analyzed by the MACS peak finder program with detault settings to identify 15,436 peaks (FDR 10% cutoff) corresponding to putative PDX1-bound sites. Only reads which uniquely mapped to the human genome were used.

source_name: hESCs differentiated into pancreatic lineage

growth_protocol: hESCs were plated onto fibronectin-coated transwell plates (Corning) and cultured in hESC medium for two days. They were induced to differentiate into DE using differentiation medium (RPMI-1640, 2 % B-27® Supplement, 2 mM L-Glutamine and 1 x MEM NEAA (no beta mercap?)) supplemented with 50 ng/ml Activin A (R & D Systems) and 50 ng/ml BMP4 (R & D Systems) for three days. The cells were then induced with 50 ng/ml Activin A for another two days. Thereafter, pancreatic differentiation was initiated (and maintained) with 50 ng/ml FGF2, 3 µM all-trans-retinoic acid (RA) and 10 mM nicotinamide (Nic) for five days, 50 ng/ml FGF2, 3 µM RA, 10 mM Nic and 20 µM DAPT for four days, and 50 ng/ml FGF2, 10 mM Nic and 20 µM DAPT for three days.

extract_protocol:
Two 6-well transwell plates of day 17 differentiated hESCs were sonicated for 2 min x 90 % pulse x 5 times using Ultrasonic 3000 Ultrasonic homogenizer (Biologics, Inc).
For ChIP-seq, libraries were prepared using the Solexa ChIP-seq DNA Sample Prep Kit (IP102-1001). After amplification, DNA fragments between 180 and 400 bp were gel extracted and sent for sequencing. Libraries were sequenced by the Genome Institute of Singapore using the Illumina Genome Analyzer II as single-end 35 bp reads

tag: age

value: day 17

tag: antibody


title: Runx3_CD4DC_CHIP_Runx3_IP2


title: B6_4_rep3


title: Runx3_CD4DC_CHIP_Sample_input2

value: Input control


title: Runx3_CD4DC_CHIP_Sample_input1


title: Control replicate 4

status: Public on Jun 20 2014

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

data_processing:
CASAVA 1.8.2 was used for base calling
Reads were aligned to hg19 using TopHat 2.0.6 with BowTie 0.12.8.
Gene-level counts for genes in the ensembl database were generated using Rsamtools using script makeCounts.Rscript (supplemental file)
Normalization was performed using DESeq
Samples were clustered using the top 30 expressing genes and outliers eliminated
The bottom 40% of genes by total expression over all samples were removed from analysis
Differentially expressed genes were identified using DESeq with a false discovery rate of 10%
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file containing counts for each gene for each sample

source_name: Breast cancer cells

growth_protocol: Human MCF-7 breast cancer cells (ATCC (Manassas, VA)) were maintained in DMEM, 10% FBS, .01 µg/mL bovine insulin (Cell Applications, Inc.) and 1% penicillin/streptomycin (P/S).

extract_protocol:
Total RNA was isolated using RNA purification columns (Qiagen) and DNase treated (Qiagen)
RNA libraries were prepared for sequencing using Illumina TruSeq RNA preparation protocols

treatment_protocol: 200,000 MCF-7 cells seeded in 35 mm plates were transfected with 50 nM of cRNAi or AHR-siRNA #2 in phenol red-free DMEM supplemented with 10% charcoal treated FBS and 2 µL of Dharmafect transfection reagent (#1) for 36 hr

tag: cell line

tag: treatment

value: Non-specific control RNA


title: Control replicate 6


title: MCF7_PMA_PKC_ChIP_Seq

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

data_processing:
Adapters stripped using cutadapt
Reads mapped with Bowtie2 using local alignment. Only uniquely mapped reads used.
Duplicates removed using Picard
Wig files from HTSEQ, reads extended 200bp.
Peaks called for PKC against TI for MCF7 stimulated sample, called with ZINBA (pvalue < 0.05) and BayesPeaks (cut-off 0.999) and MACS2 (parameters --keep-dup all   -g hs -s 50 --bw 200 -q 0.05 then qvalue filtered to be < 0.01) or just ZINBA and BayesPeak (ZINBA_BP.bed).
Genome_build: hg19
Supplementary_files_format_and_content: wig files show tag densities for the different treatments (NS and ST) for antibody (PKC) and Total Input (TI). Bed files are peaks for PKC in Stimulated MCF7 (against TI).

source_name: MCF7 cell line

growth_protocol: Cells were cultured at 37C in low glucose DMEM (Gibco) and supplemented with 10% FCS, 2mM L-glutamine, and 0.1% PSN antibiotics.

extract_protocol:
ChIP samples were prepared with anti-PKC-theta (sc-212, SantaCruz), according to the protocol supplied by Upstate Biotechnology.
10ng of PKC-theta immunoprecipitated ChIP-DNA, and the corresponding total input (TI), were used to prepare the ChIP-seq DNA library using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (New England BioLabs Inc, NEB#E6240L) according to the manufacturer’s instructions. ChIP-DNA size was selected with AMPure XP beads (Beckman Coulter, Inc., Part #: A63881). The selected DNA was repaired with NEBNext End Repair Enzyme Mix and Buffer, followed by treatment with Klenow fragment (3’à5’ exo-) to generate “A” base overhangs. Subsequent adaptor ligation of the dA-tailed DNA was performed with 1.5μM NEBNext adaptor primers, Quick Ligation Reaction Buffer, and Quick T4 DNA ligase. AMPure beads were used to isolate library fragments ranging between 175 and 225bp in size and the purified DNA was combined with the NEBNext High-Fidelity 2X PCR Master mix, 25μM Universal PCR primer, and 25μM index primer for multiplexing purposes (New England BioLabs Inc, NEBNext® Multiplex Oligos for Illumina®, NEB#E7335L). A total of 15 cycles were used for PCR amplification of the adaptor-ligated DNA. The resultant ChIP-DNA library was subjected to DNA purification with AMPure beads. The quality of the ChIP-DNA library was assessed on a Bioanalyzer. A total of 2nM was captured on the Illumina flow cell for cluster generation

treatment_protocol: Cells were left untreated or stimulated with PMA (0.65ng/ml) for 60h.

value: PMA

value: PKCtheta (sc-212, SantaCruz)


title: Control replicate 2


title: MCF7_Total_Input

value: Total input


title: AHR knockdown replicate 4

value: Short interfering RNA against the AHR


title: MCF7_PKC_ChIP_Seq


title: PDX1_ChIPSEQ

value: hESCs differentiated into pancreatic lineage


title: Control replicate 3


title: AHR knockdown replicate 1


title: Control replicate 5


title: AHR knockdown replicate 2


title: AHR knockdown replicate 3


title: Control replicate 1


title: MCF7_PMA_Total_Input


title: B6_2_rep2

tag: strain

value: C57BL/6J-Col3.6 CFP


title: unassigned reads II

city: Norwich

first: Ghanasyam

last: Rallapalli

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

description: library strategy: Tag-seq

data_processing: This Sample is a placeholder for runs containing unassigned reads. See the GSM1251235_README_unassigned_reads_info.txt.gz and GSE51720_barcode_info.txt.gz supplementary files.

organism: Arabidopsis thaliana

source_name: Leaf discs

growth_protocol: Arabidopsis thaliana (Col-0, ein2-5, jar1-1 and npr1-1) plants were grown under short-day conditions (8 hr light/16 hr dark cycles at 20°C).

extract_protocol:
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.
Typically 5 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Ilumina flowcell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity – 5, Duty cycle – 20%, Cycles/Burst – 200, Duration – 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library

treatment_protocol: Leaf discs from 5-week-old Col-0, ein2-5, jar1-1 and npr1-1 plants were prepared 2 hours after start of light period and vacuum-infiltrated with water for 1 min. Leaf discs were placed in water in 50 mm petri dishes and left in the same growing conditions for ~20 h. A day after leaf disc generation the water in the petri dishes was replaced with water or 100 nm of flg22 and samples were harvested at 8 minutes incubation in water and 8, 15, 30, 45, 60, 120 & 180 minutes incubation in flg22 for total RNA extraction.

tag: ecotype

value: Columbia (Col-0)


title: Rep3_npr1-1_060min_flg22

description: library strategy: Tag-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Read qualities are converted from Illumina fastq to sanger fastq format. Illumina sequence library is quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50 and reads containing “N” are discarded.
EXPRSS libraries are separated using perfect match to the barcode (at 5' end). Each sub-library is quality filtered (-q20 and -p50) and artefact filtered using FASTX-toolkit.
Quality filtered library was aligned to the Arabidopsis thaliana Col-0 genome sequences (TAIR10) using Bowtie version 0.12.8 (-a -m 10 --best --strata) and selected reads with up to 10 reportable alignments. Unaligned reads from previous step are used to align to transcript sequences of Arabidopsis using Bowtie version 0.12.8 (-a -m 100 --best --strata). Tag to gene association is carried out using following considerations. Reads aligning in sense orientation with in each gene limits are assigned to that gene. A read aligning to all splice variant of a gene is counted once, and the reads uniquely aligning to various splice variants of a gene are pooled. Reads aligning to genes with overlapping gene limits are split equally between them. Reads aligning to more than 10 genes are discarded. Reads aligning to up to 10 genes are split equally between them. Reads aligning on the anti-sense strand of any gene are tested for if the read falls within 500bp from 3’ end of another gene in sense direction. Otherwise reads are assigned as antisense tags for the specific gene. The tag assignment process was implemented in perl and scripts are available on request. Differential expression analysis was performed using the R statistical language version 2.15.3 with the Bioconductor package baySeq version 1.12.0 using 10000 iterations to estimate empirical distribution on the parameters of the Negative Binomial distribution
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files containing each genes tag counts for individual samples

tag: genotype

tag: timepoint

value: 60 minutes


title: Rep3_npr1-1_180min_flg22

description: library strategy: Tag-seq

value: 180 minutes


title: Rep3_npr1-1_120min_flg22

description: library strategy: Tag-seq

value: 120 minutes


title: Rep3_npr1-1_045min_flg22

description: library strategy: Tag-seq

value: 45 minutes


title: Rep3_npr1-1_030min_flg22

description: library strategy: Tag-seq

value: 30 minutes


title: Rep3_npr1-1_008min_flg22

description: library strategy: Tag-seq

value: 8 minutes


title: Rep3_npr1-1_015min_flg22

description: library strategy: Tag-seq

value: 15 minutes


title: Rep3_npr1-1_008min_water

description: library strategy: Tag-seq


title: AHR knockdown replicate 5


title: Rep3_jar1-1_180min_flg22

description: library strategy: Tag-seq


title: Rep3_jar1-1_060min_flg22

description: library strategy: Tag-seq


title: Rep3_jar1-1_045min_flg22

description: library strategy: Tag-seq


title: Rep3_jar1-1_120min_flg22

description: library strategy: Tag-seq


title: Rep3_jar1-1_008min_flg22

description: library strategy: Tag-seq


title: Rep3_jar1-1_030min_flg22

description: library strategy: Tag-seq


title: Rep3_ein2-5_060min_flg22

description: library strategy: Tag-seq


title: Rep3_jar1-1_015min_flg22

description: library strategy: Tag-seq


title: Rep3_ein2-5_045min_flg22

description: library strategy: Tag-seq


title: Rep3_ein2-5_120min_flg22

description: library strategy: Tag-seq


title: P90_C-DGCR8 KO cones, replicate 2 [RNA-seq]

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

data_processing:
Individual reads were assigned to their sample based on the TruSeq barcode using the Illumina software Casava v1.8.0.
RNA sequencing reads, obtained for the wild type and C-DGCR-KO conditions at each time point, were aligned to the mm10 mouse genome assembly using the QuasR Bioconductor package (http://www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) and SpliceMap (Au et al., 2010) from the Rbowtie package (http://www.bioconductor.org/packages/2.12/bioc/html/Rbowtie.html) using the default parameters except for "splicedAlignment=TRUE".
A table with the number of alignments per gene was produced by counting alignments starting in annotated exons on the same strand of a gene using the QuasR's qCount function and gene models from the TxDb.Mmusculus.UCSC.mm10.knownGene Bioconductor package (version 2.9.0).
Counts were first normalized by the length of the gene locus and then to raw count levels to housekeeping genes.
We used the mean of the two independent samples as data for further analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file with counts normalized to gene locus length and housekeeping genes.

source_name: FACS-sorted cones, P90 C-DGCR8 KO mice

growth_protocol: The animals were maintained under a 12-hour light-dark cycle. Conditional DGCR8 knockout mice were crossed to the cone-specific Cre recombinase driver line D4-cre resulting in C-DGCR8 KO mice. To visualize cones, C-DGCR8 KO line mice were crossed to the floxed tdTomato reporter line Ai9. D4-cre or D4-cre/Ai9 animals served as wild type controls.

extract_protocol:
Cones were isolated by FACS from wild type and C-DGCR8 KO mice at different time points (P30, P40, P50, P60, and P90). RNA extraction was performed with Trizol or Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) according to the manufacturer's instructions. Quantitative and qualitative analysis was performed using 2100 Bioanalyzer.
Total RNA from isolated cones (150 ng) was processed using the ScriptSeq Complete (Human/Mouse/Rat) Low Input kit according to the manufacturer's instructions (Epicentre/Illumina).
Libraries were pooled equimolarly in batches of 4, and 12 pM of each pool were sequenced on one lane of the HiSeq 2000 instrument using RTA 1.13.48.

tag: strain/background

tag: genotype/variation

value: C-DGCR8 KO (D4-cre/DGCR8 KO/Ai9 tdTomato)

tag: tissue

value: retina

value: cone photoreceptors

value: postnatal day P90


title: P60_C-DGCR8 KO cones, replicate 1 [RNA-seq]

source_name: FACS-sorted cones, P60 C-DGCR8 KO mice

value: postnatal day P60


title: Rep3_ein2-5_180min_flg22

description: library strategy: Tag-seq


title: Rep3_jar1-1_008min_water

description: library strategy: Tag-seq


title: P50_C-DGCR8 KO cones, replicate 2 [RNA-seq]

source_name: FACS-sorted cones, P50 C-DGCR8 KO mice

value: postnatal day P50


title: Rep3_ein2-5_008min_water

description: library strategy: Tag-seq


title: P50_C-DGCR8 KO cones, replicate 1 [RNA-seq]


title: P60_C-DGCR8 KO cones, replicate 2 [RNA-seq]


title: P90_C-DGCR8 KO cones, replicate 1 [RNA-seq]


title: Rep3_ein2-5_015min_flg22

description: library strategy: Tag-seq


title: Rep3_ein2-5_008min_flg22

description: library strategy: Tag-seq


title: Rep3_Col-0_120min_flg22

description: library strategy: Tag-seq

value: Wild type


title: Rep3_Col-0_060min_flg22

description: library strategy: Tag-seq


title: P40_C-DGCR8 KO cones, replicate 1 [RNA-seq]

source_name: FACS-sorted cones, P40 C-DGCR8 KO mice

value: postnatal day P40


title: Rep3_Col-0_045min_flg22

description: library strategy: Tag-seq


title: P30_C-DGCR8 KO cones, replicate 2 [RNA-seq]

source_name: FACS-sorted cones, P30 C-DGCR8 KO mice

value: postnatal day P30


title: Rep3_Col-0_180min_flg22

description: library strategy: Tag-seq

value: Columbia (Col-0)


title: Rep3_ein2-5_030min_flg22

description: library strategy: Tag-seq


title: Rep3_Col-0_030min_flg22

description: library strategy: Tag-seq


title: P90_wt cones, replicate 2 [RNA-seq]

source_name: FACS-sorted cones, P90 wild type mice

value: wild type (D4-cre/Ai9 tdTomato)


title: P90_wt cones, replicate 1 [RNA-seq]


title: Rep3_Col-0_008min_water

description: library strategy: Tag-seq


title: P60_wt cones, replicate 1 [RNA-seq]

source_name: FACS-sorted cones, P60 wild type mice


title: Rep3_Col-0_008min_flg22

description: library strategy: Tag-seq


title: Rep2_npr1-1_180min_flg22

description: library strategy: Tag-seq

value: 180 minutes


title: Rep2_npr1-1_120min_flg22

description: library strategy: Tag-seq

value: 120 minutes


title: P40_C-DGCR8 KO cones, replicate 2 [RNA-seq]


title: P50_wt cones, replicate 2 [RNA-seq]

source_name: FACS-sorted cones, P50 wild type mice


title: Rep2_npr1-1_060min_flg22

description: library strategy: Tag-seq

value: 60 minutes


title: Rep2_npr1-1_045min_flg22

description: library strategy: Tag-seq

value: 45 minutes


title: P40_wt cones, replicate 1 [RNA-seq]

source_name: FACS-sorted cones, P40 wild type mice


title: Rep2_npr1-1_030min_flg22

description: library strategy: Tag-seq

value: 30 minutes


title: P50_wt cones, replicate 1 [RNA-seq]


title: Rep2_npr1-1_008min_flg22

description: library strategy: Tag-seq

value: 8 minutes


title: P30_wt cones, replicate 1 [RNA-seq]

source_name: FACS-sorted cones, P30 wild type mice


title: Rep2_npr1-1_008min_water

description: library strategy: Tag-seq


title: P30_C-DGCR8 KO cones, replicate 1 [RNA-seq]

value: C-DGCR8 KO (D4-cre/DGCR8 KO/Ai9 tdTomato)


title: Rep3_Col-0_015min_flg22

description: library strategy: Tag-seq

value: 15 minutes


title: Rep2_jar1-1_060min_flg22

description: library strategy: Tag-seq


title: Mutant + kan

city: Atlanta

first: Mentewab

last: Ayalew

state: GA

address: 350 Spelman Lane

department: Biology Department

institute: Spelman College

description: mRNA

data_processing:
Processed GSE58662_READs using FASTX clipper version 0.0.6 to remove adapter sequences and keep sequences of 36 mer.
Processed GSE58662_READs were aligned to the Arabidopsis thaliana reference genome (TAIR10, ENSEMBL 14) using TopHat version 2.0.5. The minimum GSE58662_READ length was set to 18 and up to 2 mismatches were tolerated.
Mapped GSE58662_READs were assembled and merged using Cufflinks version 2.0.2 and Cuffmerge 2.0.2.
Transcript abundance and differential expression was analyzed using Cuffdiff version 1.3.0. Statistical significance was only tested when a minimum of 10 GSE58662_READs were mapped on a given transcript.
Genome_build: TAIR10
Supplementary_files_format_and_content: .xls file with RPKM values for each sample and p value generated by Cuffdiff; gene descriptions and GO classifications were obtained from The Arabidopsis Information Resource (TAIR). Section and column definitions are in the GSE58662_README.txt file.

source_name: Five-day-old seedlings, wbc19 mutant, kanamycin

growth_protocol: Control (SALK_064816C) and wbc19 mutant (SALK_107731) lines were used. SALK_064816C mutants served as controls as they carry a T-DNA insertion that does not disrupt a gene. The T-DNA insertion is located in the vicinity of the TRANSPARENT TESTA 4 gene, 260 bp upstream of the start codon and the mutants have no visible phenotype. After stratification (3 days at 4°C), plates were transferred to a controlled-environment cabinet (23°C, 16 h light; 18°C, 8 h dark) and plant material was harvested and flash frozen 5 days later.

extract_protocol:
Total RNA was extracted using a Plant RNeasy Mini Kit (Qiagen) and poly(A) mRNA isolated using oligo(dT) DynaBeads (Life Technologies).
Messenger RNA fragmentation and RNA-seq library generation were according to Guo et al., 2010 (Nature 466: 835-840). Briefly, after alkaline fragmentation of mRNA, ~25-45 mer fragments were gel purified on a 10% denaturing polyacrylamide-urea gel. After 3'-dephosphorylation with polynucleotide kinase (PNK, New England Biolabs), a 3' adaptor was ligated to the fragments. Following a second gel purification step, the fragments were 5' phosphorylated with PNK and the 5' adapter ligated. Each library was then amplified for 21 cycles and gel purified on a 90% formamide, 8% acrylamide denaturing gel.
RNA-seq: single-end sequencing on the Illumina GAII high-throughput sequencing platform.

treatment_protocol: Homozygous seeds were plated under sterile conditions on MS media with or without kanamycin 50mg/l.

tag: line

value: wbc19 mutant

value: 5 days

value: seedling

tag: growth media

value: MS + 50mg/l kanamycin


title: Rep2_jar1-1_045min_flg22

description: library strategy: Tag-seq


title: Rep2_jar1-1_120min_flg22

description: library strategy: Tag-seq


title: Mutant

description: mRNA

source_name: Five-day-old seedlings, wbc19 mutant, no kanamycin

value: MS


title: P60_wt cones_rep2 [miRNA-seq]

data_processing:
Individual reads were assigned to their sample based on the TruSeq barcode using the Illumina software Casava v1.8.0.
The 3' adapter sequence was removed by aligning it to the read, allowing one or two mismatches in prefix alignments of at least 7 or 10 bases, respectively. Low complexity reads were filtered out based on their dinucleotide entropy. All reads shorter than 14 nt were removed.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file with raw read counts per miRBase entry.

growth_protocol: The animals were maintained under a 12-hour light-dark cycle. To visualize cones, D4-cre mice, expressing the cone-specific Cre recombinase, were crossed to the floxed tdTomato reporter line Ai9. D4-cre/Ai9 tdTomato animals served as wild type.

extract_protocol:
Cones were isolated by FACS from D4-cre/Ai9 tdTomato (wild type) mice at P60. RNA extraction was performed with Trizol according to the manufacturer's instructions. Quantitative and qualitative analysis was performed using 2100 Bioanalyzer.
Small RNA (15-30 nt in length) libraries were prepared from 1 µg of total RNA using TruSeq Small RNA Sample Prep Kit according to the manufacturer's protocol.
Samples were multiplexed and 13 pM of the multiplexed libraries were sequenced on one lane of the HiSeq 2000 instrument using RTA 1.13.48. Each sample was prepared from FACS-sorted cones from 20 retinas.

value: retina

tag: cell type

value: cone photoreceptors

value: postnatal day 60


title: Rep2_jar1-1_180min_flg22

description: library strategy: Tag-seq

value: Columbia (Col-0)


title: P60_wt cones [miRNA-seq]

value: wild type (D4-cre/Ai9 tdTomato)


title: Control

description: mRNA

source_name: Five-day-old seedlings, control line, no kanamycin

value: control


title: Control + kan

description: mRNA

source_name: Five-day-old seedlings, control line, kanamycin


title: Rep2_ein2-5_180min_flg22

description: library strategy: Tag-seq

value: 180 minutes


title: Rep2_jar1-1_015min_flg22

description: library strategy: Tag-seq


title: Rep2_ein2-5_045min_flg22

description: library strategy: Tag-seq

value: 45 minutes


title: Rep2_ein2-5_120min_flg22

description: library strategy: Tag-seq

value: 120 minutes


title: Rep2_jar1-1_008min_flg22

description: library strategy: Tag-seq

value: 8 minutes


title: P60_wt cones, replicate 2 [RNA-seq]

value: postnatal day P60


title: Rep2_ein2-5_030min_flg22

description: library strategy: Tag-seq

value: 30 minutes


title: Rep2_ein2-5_060min_flg22

description: library strategy: Tag-seq

value: 60 minutes


title: Rep2_ein2-5_008min_flg22

description: library strategy: Tag-seq


title: P40_wt cones, replicate 2 [RNA-seq]

value: postnatal day P40


title: Rep2_npr1-1_015min_flg22

description: library strategy: Tag-seq

value: 15 minutes


title: P30_wt cones, replicate 2 [RNA-seq]

value: postnatal day P30


title: Rep2_ein2-5_008min_water

description: library strategy: Tag-seq


title: Rep2_jar1-1_030min_flg22

description: library strategy: Tag-seq


title: Rep2_Col-0_060min_flg22

description: library strategy: Tag-seq

value: Wild type


title: Rep2_Col-0_045min_flg22

description: library strategy: Tag-seq


title: Rep2_Col-0_120min_flg22

description: library strategy: Tag-seq


title: Rep2_Col-0_180min_flg22

description: library strategy: Tag-seq


title: Rep2_Col-0_030min_flg22

description: library strategy: Tag-seq


title: Rep2_Col-0_015min_flg22

description: library strategy: Tag-seq


title: Rep2_Col-0_008min_water

description: library strategy: Tag-seq


title: Rep2_Col-0_008min_flg22

description: library strategy: Tag-seq


title: Rep1_npr1-1_180min_flg22

description: library strategy: Tag-seq


title: Rep1_npr1-1_060min_flg22

description: library strategy: Tag-seq


title: Rep1_npr1-1_045min_flg22

description: library strategy: Tag-seq


title: Rep1_npr1-1_120min_flg22

description: library strategy: Tag-seq


title: Rep1_npr1-1_030min_flg22

description: library strategy: Tag-seq


title: Rep1_npr1-1_015min_flg22

description: library strategy: Tag-seq


title: Rep2_ein2-5_015min_flg22

description: library strategy: Tag-seq


title: Rep1_jar1-1_060min_flg22

description: library strategy: Tag-seq


title: Rep1_jar1-1_180min_flg22

description: library strategy: Tag-seq


title: Rep1_npr1-1_008min_flg22

description: library strategy: Tag-seq


title: Rep1_jar1-1_045min_flg22

description: library strategy: Tag-seq


title: Rep1_npr1-1_008min_water

description: library strategy: Tag-seq


title: Rep1_jar1-1_030min_flg22

description: library strategy: Tag-seq


title: Rep1_ein2-5_180min_flg22

description: library strategy: Tag-seq


title: Rep1_ein2-5_120min_flg22

description: library strategy: Tag-seq


title: Rep1_ein2-5_060min_flg22

description: library strategy: Tag-seq


title: Rep1_ein2-5_045min_flg22

description: library strategy: Tag-seq


title: Rep1_ein2-5_008min_water

description: library strategy: Tag-seq


title: Rep1_jar1-1_008min_water

description: library strategy: Tag-seq


title: Rep1_jar1-1_120min_flg22

description: library strategy: Tag-seq


title: Rep1_ein2-5_015min_flg22

description: library strategy: Tag-seq


title: Rep1_Col-0_060min_flg22

description: library strategy: Tag-seq


title: Rep1_Col-0_015min_flg22

description: library strategy: Tag-seq


title: Rep1_Col-0_045min_flg22

description: library strategy: Tag-seq


title: Rep1_Col-0_008min_flg22

description: library strategy: Tag-seq


title: Rep1_Col-0_120min_flg22

description: library strategy: Tag-seq


title: Rep1_jar1-1_008min_flg22

description: library strategy: Tag-seq


title: Rep1_ein2-5_030min_flg22

description: library strategy: Tag-seq


title: Rep1_ein2-5_008min_flg22

description: library strategy: Tag-seq


title: Rep1_Col-0_030min_flg22

description: library strategy: Tag-seq


title: Rep1_jar1-1_015min_flg22

description: library strategy: Tag-seq


title: Rep2_jar1-1_008min_water

description: library strategy: Tag-seq


title: NlaIII-DGE_Col-0_1hr_flg22_BioRep1

description:
Tag-seq
Barcode sequence: GTCA
Barcode position: 3' end of the read followed by Adapter sequence TCGTATGCCGTCTTC

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina sequence library is quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50 and reads containing “N” are discarded. Read qualities are converted from Illumina fastq to sanger fastq format
EXPRSS:  EXPRSS libraries are separated using perfect match to the barcode (at 5' end). Each sub-library is quality filtered (-q20 and -p50) and artefact filtered using FASTX-toolkit.
NlaIII-DGE:  For NlaIII-DGE, FASTX Toolkit fastx_clipper is used to trim 3’ adapter sequence (parameters used -a TCGTATGCCGTCTTC -l 18 –c) and libraries are separated using barcodes (at 3' end) allowing up to 1 mismatch. Each sub-library is quality filtered (-q20 and -p50) and artefact filtered using FASTX-toolkit. For NlaIII-DGE libraires NlaIII recognition site (CATG) was added at 5’ end of each tag sequence and “FFFF” as fastq quality.
Quality filtered library was aligned to the Arabidopsis thaliana Col-0 genome sequences (TAIR10) using Bowtie version 0.12.8 (-a -m 10 --best --strata) and selected reads with up to 10 reportable alignments. Unaligned reads from previous step are used to align to transcript sequences of Arabidopsis using Bowtie version 0.12.8 (-a -m 100 --best --strata). Tag to gene association is carried out using following considerations. Reads aligning in sense orientation with in each gene limits are assigned to that gene. A read aligning to all splice variant of a gene is counted once, and the reads uniquely aligning to various splice variants of a gene are pooled. Reads aligning to genes with overlapping gene limits are split equally between them. Reads aligning to more than 10 genes are discarded. Reads aligning to up to 10 genes are split equally between them. Reads aligning on the anti-sense strand of any gene are tested for if the read falls within 500bp from 3’ end of another gene in sense direction. Otherwise reads are assigned as antisense tags for the specific gene. The tag assignment process was implemented in perl and scripts are available on request. Differential expression analysis was performed using the R statistical language version 2.15.3 with the Bioconductor package baySeq version 1.12.0 using 10000 iterations to estimate empirical distribution on the parameters of the Negative Binomial distribution
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files containing each genes tag counts for individual samples

growth_protocol: Arabidopsis thaliana (Col-0) plants were grown under short-day conditions (8 hr light/16 hr dark cycles).

extract_protocol:
Library preparation was carried out with 5 µg of total RNA as mentioned previously [Morrissy et al., Genome Research 2009, 19(10):1825-1835], with our modifications. Ligation of biotinylated Adapter1, harbouring methylated adenine, was carried out in the presence of NlaIII and T4 DNA ligase at 37 oC as described previously [So et al., Nucleic Acids Research 2004, 32(12):e96]. After Adapter2 (which contains barcode) ligation, streptavidin magnetic beads (Promega) were used to capture ligated constructs and which were taken forward for PCR enrichment as in the default protocol.
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.

treatment_protocol: Leaf discs from 5-week-old Col-0 plants were prepared 2 hours after start of light period and vacuum-infiltrated with water for 1 min. Leaf discs were placed in water in 50 mm petri dishes and left in the same growing conditions for ~20 h. A day after leaf disc generation the water in the petri dishes was replaced with water or 100 nm flg22 and samples were harvested 1 h after incubation.

value: Leaf

value: 5 weeks old

value: 100nM flg22


title: Rep1_Col-0_180min_flg22

description: library strategy: Tag-seq

value: Columbia (Col-0)


title: Unassigned reads

description:
Tag-seq
This Sample represents the unassigned sequences from GSM1121342-GSM1121365.

GSM1121342-GSM1121345 were sequenced in one lane.
GSM1121342 barcode sequence: AACT
GSM1121343 barcode sequence: GTAT
GSM1121344 barcode sequence: CGAT
GSM1121345 barcode sequence: TCGT
SRR825609 is the SRA accession that includes the sequences unassigned to any barcode.

GSM1121346-GSM1121349 were sequenced in one lane.
GSM1121346 barcode sequence: AACT
GSM1121347 barcode sequence: GTAT
GSM1121348 barcode sequence: CGAT
GSM1121349 barcode sequence: TCGT
SRR825610 is the SRA accession that includes sequences unassigned to any barcode.

GSM1121350-GSM1121357 were sequenced in one lane.
GSM1121350 barcode sequence: AGCT
GSM1121351 barcode sequence: GCTCT
GSM1121352 barcode sequence: CATACGT
GSM1121353 barcode sequence: TTGGAT
GSM1121354 barcode sequence: TCGT
GSM1121355 barcode sequence: GTACT
GSM1121356 barcode sequence: AACAGAT
GSM1121357 barcode sequence: CGAGAT
SRR825611 is the SRA accession that includes the sequences unassigned to any barcode.

GSM1121358-GSM1121365 were sequenced in one lane.
GSM1121358 barcode sequence: ATGC
GSM1121359 barcode sequence: TAGC
GSM1121360 barcode sequence: TGCA
GSM1121361 barcode sequence: CAGT
GSM1121362 barcode sequence: GTCA
GSM1121363 barcode sequence: GCAT
GSM1121364 barcode sequence: ACTG
GSM1121365 barcode sequence: ATCG
SRR825612 is the SRA accession that includes the sequences unassigned to any barcode.

extract_protocol:
EXPRSS: Typically 5 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Ilumina flowcell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity – 5, Duty cycle – 20%, Cycles/Burst – 200, Duration – 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library
NlaIII-DGE: Library preparation was carried out with 5 µg of total RNA as mentioned previously [Morrissy et al., Genome Research 2009, 19(10):1825-1835], with our modifications. Ligation of biotinylated Adapter1, harbouring methylated adenine, was carried out in the presence of NlaIII and T4 DNA ligase at 37 oC as described previously [So et al., Nucleic Acids Research 2004, 32(12):e96]. After Adapter2 (which contains barcode) ligation, streptavidin magnetic beads (Promega) were used to capture ligated constructs and which were taken forward for PCR enrichment as in the default protocol.
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.

value: water, 100nM flg22


title: NlaIII-DGE_Col-0_1hr_water_BioRep2

description:
Tag-seq
Barcode sequence: TAGC
Barcode position: 3' end of the read followed by Adapter sequence TCGTATGCCGTCTTC

value: water


title: NlaIII-DGE_Col-0_1hr_water_BioRep3

description:
Tag-seq
Barcode sequence: TGCA
Barcode position: 3' end of the read followed by Adapter sequence TCGTATGCCGTCTTC


title: NlaIII-DGE_Col-0_1hr_flg22_BioRep2

description:
Tag-seq
Barcode sequence: GCAT
Barcode position: 3' end of the read followed by Adapter sequence TCGTATGCCGTCTTC


title: NlaIII-DGE_Col-0_1hr_flg22_BioRep3

description:
Tag-seq
Barcode sequence: ACTG
Barcode position: 3' end of the read followed by Adapter sequence TCGTATGCCGTCTTC


title: EXPRSS_Col-0_1hr_flg22_BioRep4

description:
Tag-seq
Barcode sequence: CGAGAT
Barcode position: 5' end of the read

extract_protocol:
Typically 5 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Ilumina flowcell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity – 5, Duty cycle – 20%, Cycles/Burst – 200, Duration – 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.


title: NlaIII-DGE_Col-0_1hr_water_BioRep1

description:
Tag-seq
Barcode sequence: ATGC
Barcode position: 3' end of the read followed by Adapter sequence TCGTATGCCGTCTTC


title: NlaIII-DGE_Col-0_1hr_water_BioRep4

description:
Tag-seq
Barcode sequence: CAGT
Barcode position: 3' end of the read followed by Adapter sequence TCGTATGCCGTCTTC


title: EXPRSS_Col-0_1hr_flg22_BioRep3

description:
Tag-seq
Barcode sequence: AACAGAT
Barcode position: 5' end of the read


title: EXPRSS_Col-0_1hr_flg22_BioRep2

description:
Tag-seq
Barcode sequence: GTACT
Barcode position: 5' end of the read


title: Rep1_Col-0_008min_water

description: library strategy: Tag-seq


title: NlaIII-DGE_Col-0_1hr_flg22_BioRep4

description:
Tag-seq
Barcode sequence: ATCG
Barcode position: 3' end of the read followed by Adapter sequence TCGTATGCCGTCTTC


title: EXPRSS_Col-0_1hr_flg22_BioRep1

description:
Tag-seq
Barcode sequence: TCGT
Barcode position: 5' end of the read


title: EXPRSS_Col-0_1hr_water_BioRep1

description:
Tag-seq
Barcode sequence: AGCT
Barcode position: 5' end of the read


title: EXPRSS_Col-0_1hr_water_BioRep2

description:
Tag-seq
Barcode sequence: GCTCT
Barcode position: 5' end of the read


title: EXPRSS_Col-0_1hr_flg22_TechRep4


title: EXPRSS_Col-0_1hr_water_BioRep3

description:
Tag-seq
Barcode sequence: CATACGT
Barcode position: 5' end of the read


title: EXPRSS_Col-0_1hr_flg22_TechRep2

description:
Tag-seq
Barcode sequence: GTAT
Barcode position: 5' end of the read


title: EXPRSS_Col-0_1hr_flg22_TechRep1

description:
Tag-seq
Barcode sequence: AACT
Barcode position: 5' end of the read


title: EXPRSS_Col-0_1hr_water_TechRep3

description:
Tag-seq
Barcode sequence: CGAT
Barcode position: 5' end of the read


title: EXPRSS_Col-0_1hr_water_TechRep2


title: EXPRSS_Col-0_1hr_water_TechRep1