title: SD rep 3

city: La Jolla

first: Felipe

last: Barreto

state: California

address: 8750 Biological Grade

department: Marine Biology Research Division

institute: Scripps Institution of Oceanography

description: This is duplicated sample record of GSM945350 for the convenient retrieval of the complete raw data from SRA

data_processing:
Raw forward fastq reads were imported into CLC Genomics Workbench v5.1, where adapters were trimmed and reads were trimmed based on base quality (Phred = 30).  After initial trimming, only reads with length > 60 bp were retained.
Remaining high-quality reads were then mapped to a ‘mixed assembly’ that contained the transcriptome assemblies of San Diego (TSA accession: GBSZ00000000) and Santa Cruz (GBTC00000000).  Mapping parameters in CLC Genomics Workbench were: length fraction = 0.8; similarity fraction = 0.95.  For each gene, the read count was the sum of reads mapping to each ortholog (i.e., San Diego + Santa Cruz).
Expression levels were estimated within each sample by normalizing the number of mapped reads for each gene by contig length and total number of mapped reads in the sample (RPKM).
Supplementary_files_format_and_content: For each sample, the file contains a tab-delimited matrix listing contig ID (specific to the Burton Lab) and GenBank Accessions for San Diego and Santa Cruz transcriptomes, BLAST gene product, and normalized expression levels (RPKM).

molecule: polyA RNA

organism: Tigriopus californicus

source_name: SD parental

growth_protocol: Parental (SD and SCN) copepods were maintained in large population beakers (400 mL) and kept in incubators at 20C and 12-hr light:dark cycle.   Hybrids were generated by crossing virgin females from one population to adult males from the other. F1 hybrids were then allowed to mate to produce F2 hybrids, and these allowed to mate to produce F3 hybrids.

extract_protocol:
Total RNA was extracted using standard Tri-reagent protocol and then purified in QIAGEN RNeasy columns.
Groups of samples were sequenced on different runs but always on the same lane, with samples barcoded as needed.   Libraries were grouped and sequenced as follows:
run 1: SD rep 1 + SCN rep 1
run 2: SD rep 2
run 3: SD rep 3 + SCN rep 2
run 4: SDf x SCNm rep 1
run 5: SDf x SCNm rep 2 + SCNf x SDm rep1 + SCNf x SDm rep2

treatment_protocol: For each RNA-seq sample, 400-500 copepods were placed in a 50 mL tube and immersed in 20C water bath for two hours.  Total RNA was then extracted.

value: San Diego

tag: developmental stage

value: all pooled

tag: tissue

value: pool of 400-500 individuals


title: T032(ST)BHI

status: Public on Jan 05 2015

type: SRA

city: Braunschweig

first: Diego

last: Chaves-Moreno

address: inhoffenstrasse 7

department: Department of Medical Microbiology (MMIK)

country: Germany

institute: Helmholtz Centrum for Infection Research

library_source: transcriptomic

data_processing:
Base calls for the  GAIIx were done using the GA II x  CASAVA-1.8.1 pipeline and for the MISeq was performed using MiSeq RTA 1.14.23 pipeline
Filtering and trimming with the following parameters: Q ≥ 15, Seq. length ≥ 80nt, Homopolymers ≤ 8nt and N's = 0.
Two sequencing events were done for all in vitro S. aureus samples. After quality filtering, libraries were merged into one file and collapsed into representative reads
From the In vivo sample (Metatranscriptome) human reads were removed using BLAT against a human genome repository downloaded from NCBI ftp site. Sequences with >70% identity were removed
Ribosomal sequences were removed using HMMER (V3.0) using as a database models build with alignments of the Ribosomal fractions (5S,16S, and 23S) and BLASTN against a database of Ribosomal proteins of S. aureus genomes
Reads were assigned as belonging to S. aureus via blastn using a database of 25 concatenated genomes
Remaining reads were blasted (RPS-BLASTN) against a reference database of Position Scoring Matrices (PSM) build from a comparison of 25 Genomes of S. aureus
Read counts were down-sampled by a random resampling using an in-house script written in perl
A rank-ordering (from highest to lowest expression) of all genes in each sample was performed
Supplementary_files_format_and_content: text file with abundance (by counting the number of transcripts) for each gene (groups of genes, OG) within each condition

molecule: total RNA

organism: Staphylococcus aureus

source_name: Nasal isolate from Northern Germany

growth_protocol: Two S. aureus strains (USA300 and T032) were grown in rich (BHI) and minimun media (SNM) and harvested at different phases (mid-log and stationary). The in vivo sample was taken from the anterior nares of a human nose known to be an S. aureus carrier.

extract_protocol:
RNA was extracted using Qiagen's Rneasy Mini Kit following manufacturer's instructions, the where the samples were treated by beat beating in a solution of RLT Buffer (Qiagen) and 1% of β-mercaptoethanol.
Enriched mRNA fractions were amplified using the MessageAMP II-Bacteria RNA amplification according to manufacturer's instructions. Amplified samples were converted to ds-cDNA using SuperScript Double-Stranded cDNA Synthesis Kit and purified using GeneClean Turbo for PCR Kit (MP Biomed).
Paired-End DNA Sample Prep Kit (Illumina, San Diego, USA) according to manufacturer's instructions

treatment_protocol: Stabilization of the RNA in the samples was performed by incubating with RNAprotect for 30 mins before proceeding with the RNA isolation.

tag: strain

tag: media

value: BHI

tag: harvest phase

value: Stationary

tag: sequence events

tag: specific host


title: input_Serum_ChIPSeq

city: Kansas City

first: Joan

last: Conaway

state: MO

country: USA

institute: Stowers Institute

description: Input DNA from whole cell extract of serum activated HCT116 cells

library_source: genomic

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
Nascent-seq alignments were done using TopHat v2.0.9 with bowtie1 v0.12.9, using -g 1 option and allowing up to two mismatches.
ChIP-seq: Alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Nascent-seq: Reads were aligned using Ensembl 67 GTF human annotations using TopHat v2.0.9 and Bowtie v0.12.9.  Alignments were not extended.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

molecule: genomic DNA

organism: Homo sapiens

source_name: Colon cancer cell line

growth_protocol: HCT116 cells were grown in DMEM supplemented with 10% FBS.

extract_protocol:
For ChIP-seq, HCT116 cells were crosslinked with 1% paraformaldehyde for 10 minutes at room temperature with gentle rotation, and then quenched by 0.125 M glycine solution. After washing, nuclei were sonicated on a Misonix Sonicator 3000 Ultrasonic Cell Disruptor, and the supernatant was used for immunoprecipitation with the indicated antibody. ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit. For nascent RNA-seq, HCT116 cells was harvested and washed 3 times with cold PBS, then suspended in 10 ml Buffer A (10 mM HEPES at pH=7.9, 10 mM KCl, 2 mM MgCl2, 1 mM DTT, 1× Complete protease inhibitors [Roche]). After incubating on ice for 15 minutes, the cells were homogenized in pre-cooled 15 ml Dounce tissue homogenizer for 15 times. Nuclei were then washed twice with Buffer B (10 mM HEPES at pH=7.9, 250 mM Sucrose, 1 mM DTT, 1× Complete protease inhibitors). The pellet was vigorously suspended with 1 ml NUN buffer (20 mM HEPES at pH=7.9, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% v/v Nonidet P40, 1 mM DTT, 20 U/ml SUPERase.In RNase Inhibitor [Ambion]) that was freshly prepared. The chromatin was then washed twice more with 5 ml NUN buffer each time. The supernatant was removed and TRIzol reagent (Invitrogen) was added to the pellet for purification of RNA. The RNA was subjected to polyA depletion with Oligo(dT) magnetic beads (Invitrogen) and DNase I treatment (NEB) for 20 minutes, and then was re-purified. For sequencing, 2 μg of resulting RNA was used for ribosomal RNA depletion with the RiboZero kit (Epicenter) and libraries were made with the TruSeq RNA sample Prep Kit (Illumina).
ChIP-seq and Nascent-RNA-seq libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: human colon cancer cell

tag: antibody

tag: serum

value: activated


title: Pol_II_shScr_starved_rep2_ChIPSeq

description: Chromatin IP of Pol II in starved HCT116 cells targeted by scramble shRNA

value: RNAPII rabbit polyclonal N20 (Santa Cruz, sc-899)

value: starved

tag: targeted by

value: scramble shRNA


title: input_starved_rep2_ChIPSeq

description: Input DNA from whole cell extract of starved HCT116 cells


title: Pol_II_shScr_starved_rep1_ChIPSeq


title: SCN rep 2

description: This is duplicated sample record of GSM945352 for the convenient retrieval of the complete raw data from SRA

source_name: SCN parental

value: Santa Cruz


title: Pol_II_Serum_24min_TPL_ChIPSeq

description: Chromatin IP of Pol II in HCT116 cells activated by serum for 24 minutes and treated with TPL for 1 hour

tag: treatment

value: TPL for 1 hour


title: USA300(ST)BHI

source_name: Reference Strain


title: USA300(EX)BHI

value: Exponential


title: input_starved_rep1_ChIPSeq


title: SCNf x SDm rep2

source_name: SDf x SCNm hybrid

value: San Diego x Santa Cruz hybrid


title: Pol_II_Serum_24min_DMSO_ChIPSeq

description: Chromatin IP of Pol II in HCT116 cells activated by serum for 24 minutes and treated with DMSO for 1 hour

value: DMSO for 1 hour


title: Pol_II_Serum_8min_TPL_ChIPSeq

description: Chromatin IP of Pol II in HCT116 cells activated by serum for 8 minutes and treated with TPL for 1 hour


title: SCNf x SDm rep1


title: Nascent_RNA_starved_rep2

description:
Ribosomal RNA-depleted total RNA
library strategy: nascent-seq
nascent RNA in starved HCT116 cells


title: SDf x SCNm rep 2


title: Pol_II_Serum_8min_DMSO_ChIPSeq

description: Chromatin IP of Pol II in HCT116 cells activated by serum for 8 minutes and treated with DMSO for 1 hour


title: Pol_II_Starved_TPL_rep2_ChIPSeq

description: Chromatin IP of Pol II in starved HCT116 cells treated with TPL for 1 hour


title: RNASeq_htz1-rrp6-del_rep1

city: Cambridge

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: University of Cambridge

description: Strand-specific mRNA-seq of htz1Δrrp6Δ, replicate 1

data_processing:
Sequence reads were mapped to the S. cerevisiae genome assembly sacCer1 using Bowtie version 0.12.9, allowing up to 2 mismatches and no ambiguously mapped reads.Mapped reads were then converted to WIG files.
Genome_build: sacCer1
Supplementary_files_format_and_content: BedGraph (WIG)

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae grown in SD medium

growth_protocol: Yeast cells were grown in SD medium to mid-log phase before harvesting for ChIP or RNA extraction.

extract_protocol: Total RNA was purified using the Ribopure Purification Kit (Life Technologies) and contaminating genomic DNA was removed by DNaseI digestion. Illumina TruSeq stranded mRNA sample preparation kits were used for library preparation.

value: MATalpha can1-delta::STE2pr-SP_his5 lyp1-delta his3-delta-1 ura3-delta-0 met15-delta-0 htz1-delta::HpH rrp6-delta::KanMX


title: SDf x SCNm rep 1


title: RNASeq_rrp6-del_rep1

description: Strand-specific mRNA-seq of rrp6Δ, replicate 1

value: MATalpha can1-delta::STE2pr-SP_his5 lyp1-delta his3-delta-1 ura3-delta-0 met15-delta-0 HTZ1-HpH rrp6-delta::KanMX


title: RNASeq_WT_rep1

description: Strand-specific mRNA-seq of wild type S.cerevisiae, replicate 1

value: MATalpha can1-delta::STE2pr-SP_his5 lyp1-delta his3-delta-1 ura3-delta-0 met15-delta-0 HTZ1-HpH


title: Pol_II_Starved_DMSO_rep2_ChIPSeq

description: Chromatin IP of Pol II in starved HCT116 cells treated with DMSO for 1 hour


title: Pol_II_Starved_TPL_rep1_ChIPSeq


title: SD rep 2

value: San Diego

value: all pooled


title: Pol_II_Starved_DMSO_rep1_ChIPSeq


title: SCN rep 1

value: pool of 400-500 individuals


title: pSCR(pSCRBRI1)_8h_rep2

status: Public on Jan 04 2015

city: Haifa

first: Sigal

last: Savaldi-Goldstein

address: Technion City

country: Israel

institute: Technion

data_processing:
Illumina Casava1.8.2 software used for basecalling.
FASTQC v0.10.1 was used for quality control
The last base of all reads was trimmed, generating 50bp reads.
Reads were mapped to the TAIR10 genome using TopHat2 v.2.0.9 with the parameters: -N 3 --min-intron-length 10 --max-intron-length 11000 --b2-sensitive
The numbers of reads per gene were estimated using HTSeq v0.5.3p3
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files, containing  raw counts values of all samples

organism: Arabidopsis thaliana

source_name: endodermis (BRI1 in endodermis in bri1), 8 hours BL (100 nM)

growth_protocol: re stratified in the dark, at 4°C for 2 days, and then transferred to 22°C in continuous light (~70 μmol m−2 s−1), for 6 days.

extract_protocol:
Immunopurification of FLAG-tagged polysomes from root cells was performed as described in Mustroph A, et al. 2009, with few modifications.
RNA libraries were prepared for sequencing using TruSeq RNA v2 (Illumina)

treatment_protocol: 100 nM BL was added to 6-day-old roots, at the indicated time points.

tag: ecotype and background

value: root

tag: age


title: T032(EX)BHI

value: BHI


title: pSCR(pSCRBRI1)_8h_rep1

description: Please note: 51-base reads were sequenced. The quality of the last base was low for all the samples, thus it was trimmed out from all the reads before mapping to the reference genome. Fastq files marked as trimmed include the reads after trimming.


title: pGL2(pSCRBRI1)_8h_rep2

source_name: epidermis (BRI1 in endodermis in bri1), 8 hours BL (100 nM)


title: pSCR(pSCRBRI1)_3h_rep2

source_name: endodermis (BRI1 in endodermis in bri1), 3 hours BL (100 nM)


title: pSCR(pSCRBRI1)_0h_rep2

source_name: endodermis (BRI1 in endodermis in bri1), 0 BL


title: pSCR(pSCRBRI1)_0h_rep1


title: pSCR(pSCRBRI1)_3h_rep1


title: pGL2(pSCRBRI1)_8h_rep1


title: pGL2(pSCRBRI1)_3h_rep2

source_name: epidermis (BRI1 in endodermis in bri1), 3 hours BL (100 nM)


title: pGL2(pSCRBRI1)_0h_rep2

source_name: epidermis (BRI1 in endodermis in bri1), 0 BL


title: pGL2(pSCRBRI1)_0h_rep1


title: pGL2(pSCRBRI1)_3h_rep1


title: pGL2(pGL2BRI1)_8h_rep1

source_name: epidermis (BRI1 in epidermis, in bri1), 8 hours BL (100 nM)


title: pGL2(pGL2BRI1)_3h_rep2

source_name: epidermis (BRI1 in epidermis, in bri1), 3 hours BL (100 nM)


title: pGL2(pGL2BRI1)_8h_rep2


title: pGL2(pGL2BRI1)_3h_rep1


title: RNASeq_htz1-del_rep1

description: Strand-specific mRNA-seq of htz1Δ, replicate 1

value: MATalpha can1-delta::STE2pr-SP_his5 lyp1-delta his3-delta-1 ura3-delta-0 met15-delta-0 htz1-delta::HpH


title: pGL2(pGL2BRI1)_0h_rep2

source_name: epidermis (BRI1 in epidermis, in bri1), 0 BL


title: pGL2(pGL2BRI1)_0h_rep1


title: pSHR_8h_rep2

source_name: stele, 8 hours BL (100 nM)


title: pSHR_8h_rep1


title: SD rep 1

source_name: SD parental


title: pSHR_3h_rep1

source_name: stele, 3 hours BL (100 nM)


title: pSHR_0h_rep1

source_name: stele, 0 BL


title: pSHR_0h_rep2


title: pSCR_8h_rep2

source_name: endodermis, 8 hours BL (100 nM)


title: pSCR_3h_rep1

source_name: endodermis, 3 hours BL (100 nM)


title: pSCR_3h_rep2


title: pSCR_0h_rep2

source_name: endodermis, 0 BL


title: pSCR_0h_rep1


title: pGL2_8h_rep2

source_name: epidermis, 8 hours BL (100 nM)


title: pBRN2_8h_rep1

source_name: lateral root cap/columalla, 8 hours BL (100 nM)


title: pBRN2_0h_rep2

source_name: lateral root cap/columalla, 0 BL


title: pGL2_3h_rep2

source_name: epidermis, 3 hours BL (100 nM)


title: pBRN2_3h_rep1

source_name: lateral root cap/columalla, 3 hours BL (100 nM)


title: pGL2_3h_rep1


title: pBRN2_8h_rep2


title: 35S_8h_rep2

source_name: whole root, 8 hours BL (100 nM)


title: pBRN2_0h_rep1


title: 35S_8h_rep1


title: pSHR_3h_rep2


title: 35S_3h_rep2

source_name: whole root, 3 hours BL (100 nM)


title: 35S_0h_rep2

source_name: whole root, 0 BL


title: 35S_3h_rep1


title: 35S_0h_rep1


title: pSCR_8h_rep1


title: P12_ANT

status: Public on Jan 03 2015

city: Shanghai

first: Hong

last: Zhang

address: Ming Dao Building  138 Yi Xue Yuan Road

department: Institute for Biomedical Sciences

country: China

institute: Fudan University

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2.0.9
The aligned read files processed by TopHat were then processed by Cufflinks2.1.1, which uses the normalized RNA-seq fragment counts to measure the relative abundances of the transcripts. The unit of measurement is Fragments Per Kilobase of exon per Million fragmentsmapped (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Hepatocellular Carcinoma

extract_protocol:
Total RNA was extracted from ANT and HCC tissues with TRIzol according to the manufacturer's protocol (Invitrogen).
We used Illumina standard kit according to the TruSeq RNA Sample Prep Guide (Illumina).

value: Adjacent non-tumor

tag: tumor type

value: HCC

tag: tumor stage

value: III


title: P11_HCC

value: Hepatocellular carcinoma primary tumor


title: P10_HCC


title: P9_ANT


title: P8_HCC


title: pGL2_0h_rep2

source_name: epidermis, 0 BL


title: pGL2_8h_rep1


title: pGL2_0h_rep1


title: pBRN2_3h_rep2


title: P7_HCC


title: P8_ANT


title: P7_ANT


title: P6_HCC


title: P5_HCC


title: P3_HCC


title: P4_ANT


title: P3_ANT


title: P6_ANT


title: P12_HCC


title: P2_HCC


title: P2_ANT


title: P10_ANT


title: P1_HCC


title: P1_ANT


title: Ring1BG53

status: Public on Jan 02 2015

city: Montreal

first: Soizik

last: Berlivet

state: Quebec

address: 110, avenue des Pins Ouest

country: Canada

institute: Institut de Recherches Cliniques de Montreal

data_processing:
The sequencing data was processed through a Torrent 5C data transformation pipeline on Galaxy (https://main.g2.bx.psu.edu/). The data was mapped against a customized reference file with TMAP.  The reference file contained a list of all possible contacts between Forward and Reverse 5C primers covering our regions.
The data was then filtered to remove low-quality reads (MAQ quality score of lower than 30), reads aligning more than two nucleotides away from the reference sequence start site, and reads which do not contain EcoRI restriction sites. This analysis generates a matrix text file containing the interaction frequencies.
5C data was normalized by dividing the number of reads of each 5C contact by the total number of reads from the corresponding sequence run multiplied by 103.
Genome_build: mm9

organism: Mus musculus

source_name: Ring1B KO mouse ES cells

extract_protocol:
3C libraries were denatured and annealed to 5C primers. 5C oligonucleotide were designed upstream (FORWARD) or downstream (REVERSE) EcoRI restriction sites. Annealing was followed by ligation with Taq DNA ligase. Ligated 5C primers were then amplified with the A-key and P1-key primers to generate the 5C libraries. 5C libraries were then prepared for sequencing onto Ion 316™ Chips with an Ion PGM™ Sequencer following either the Ion Xpress™ Template Kit v2.0, and Ion Sequencing Kit v2.0 protocols, or the Ion PGM™ Template OT2 200 Kit, and Ion PGM™ Sequencing 200 Kit v2.0 protocols as recommended by the manufacturer’s instructions (Life TechnologiesTM).
Libraries were prepared according to Ion Torrent's instructions

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperature. Crosslinking was stopped with glycine (125 mM final concentration), and incubated for 5 min at room temperature followed by 15 min on ice.  Cells were centrifuged at 400 g for 10 min at 4°C.  Supernatants were removed and cell pellets were flash frozen on dry ice.

tag: growth

value: ESCs were cultured were grown on mitomycin C-treated primary embryonic fibroblasts (PEFs) derived from E12.5 mouse embryos in DMEM supplemented with 15% fetal calf serum (FCS) , 1,000 units/ml LIF, nonessential amino acids, sodium pyruvate, 2-mecaptoethanol, L-glutamine, and Penicillin/Streptomycin.

value: ES cell

tag: genotype

value: Ring1B KO


title: P11_ANT

tag: tissue


title: Ring1B-/-_replicate2


title: Ring1B-/-_replicate1


title: Ring1BGWT_replicate


title: P9_HCC


title: Ring1BGWT


title: EED-/-_replicate

source_name: EED KO mouse ES cells

value: EED KO


title: Ring1B_WT_replicate

source_name: WTF18 ES cells


title: EED-/-


title: Ring1B-/-


title: P5_ANT


title: P4_HCC


title: Ring1B_WT


title: 72a2Hox_replicate

source_name: Mesenchymal cell lines derived from Immortomouse E10.5 anterior distal forelimb buds

value: Mesenchymal cell lines derived from the anterior (A2) and posterior (P2) distal forelimb buds of E10.5 day Immortomouse embryos were plated into 6-well plates in DMEM, 10% foetal calf serum, 20 ng/ml γ-Interferon (Peprotech) and grown at 33°C.

value: Mesenchymal cell


title: 74fp2Hox_replicate

source_name: Mesenchymal cell lines derived from Immortomouse E10.5 posterior distal forelimb buds


title: 74fp2Hox


title: OS25_D3_replicate

source_name: OS25 ES cells

value: OS25 ES cells were cultured and differentiated for 3 days (2 days with RA). Differentiation was induced by plating the cells at low density without LIF or hyg for 1 day. Retinoic acid (RA) 5×10-6 M was then added.


title: OS25_UD


title: OS25_UD_replicate


title: forsk_Input

city: New York

first: Li

last: Shen

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Bowtie 1.0.1 -p 1 -q -m 1 -v 3 --sam --best --strata mm9
diffReps 1.54 -mo p -fr 250
diffRepeats 1.54 defaults (https://github.com/shenlab-sinai/diffRepeats)
Genome_build: mm9
Supplementary_files_format_and_content: TAB delimited text file of chromatin differential sites
Supplementary_files_format_and_content: TAB delimited text file of repeat elements enrichment

source_name: Primary culutured mouse cortical neurons (DIV 8)

extract_protocol:
ChIPs for H3K9me3S10ph and Atrx were performed with approximately 2x107 neurons per sample in biological triplicates/group. Primary cortical neurons +/- isotonic KCl stimulation (5 hr) were crosslinked with 1% paraformaldehyde (PFA) for 12 min at room temperature and then quenched for five min with 0.125 M glycine. Pelleted cells were washed 5X with 1X PBS containing protease inhibitors before being subjected to lysis, sonication, IP (7.5 μg antibody per sample was used) and DNA purification, as previously described.
Following DNA purification, ChIP-seq libraries were prepared according to the Illumina protocol and sequenced with the HiSeq 2000.

treatment_protocol: Control and KCl plates were pre-treated with 100 µM D-AP5 (Tocris) and 1 µM Tetrodotoxin (Tocris) for one hr at 37 °C. For plates to be stimulated, 1/3 of the media was removed and saved. To collected media, 170 mM KCl, 2 mM CaCl2, 1 mM MgCl2 and 10 mM HEPES, pH, 7.9 were added. The isotonic KCl-containing media was then restored to each plate at 1X, and neurons were incubated in a cell culture incubator for five hrs at 37 °C. Control plates underwent media exchanges without addition of isotonic components. For application of pharmacological activators or inhibitor, cultured neurons were treated for 5 hrs with 30 mM Forskolin (Cell signaling).

value: Forskolin stimulated (30 uM)

tag: strain


title: con_Input

value: Non-stimulated control


title: con_H3K9S10

tag: antibody vendor/catalog

value: Millipore (05-809)


title: K3_Atrx_Lib_NoIndex_L007_R1_001

value: Atrx

value: Santa Cruz (sc-15408)

value: KCl stimulated (Isotonic KCl, 55 mM)


title: K2_Atrx_Lib_NoIndex_L006_R1_001


title: K1_Atrx_Lib_NoIndex_L005_R1_001


title: C3_Atrx_Lib_NoIndex_L003_R1_001


title: C1_Atrx_Lib_NoIndex_L001_R1_001


title: C2_Atrx_Lib_NoIndex_L002_R1_001


title: -N rep2

city: New Brunswick

first: Orly

last: Levitan

state: NJ

address: 71 Dudley Road

institute: Rutgers university

description:
Sample 5
WT minusN replicat 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, then mapped to Phaeodactylum tricornutum's filtered models genes (10,402) using CLC genomic workbench v6.0.2 alowing a maximum of 3 mismatches. Only unique matching reads were counted for differential expression analysis.
The R package DESeq v1.10.1 was used for calling differentially expressed genes.
Genome_build: Phatr2 (http://genome.jgi.doe.gov/Phatr2/Phatr2.home.html)
Supplementary_files_format_and_content: tab-delimited text file, DESeq output with 8 columns: gene id, baseMean, baseMeanA (WT+),  baseMeanB (WT-),  foldChange (WT-/WT+), log2FoldChange,  pval and padj (FDR).

organism: Phaeodactylum tricornutum

source_name: whole cells

growth_protocol: Axenic culture of Phaeodactylum tricornutum (accession Pt1, 8.6) were maintained in sterile artificial sea water enriched with F/2 nutrients. The nitrogen source used was 0.88 mM NaNO3. A set of three biologically independent cultures were maintained under exponential growth conditions at 18 °C and 200 µmol photons m-2s-1 continuous white LED light, and aerated through 0.2 µm filters. Cultures were cultivated using an exponentially growing inoculum to keep them optically thin and to make sure that the sampling is done during exponential growth phase.

extract_protocol:
For total RNA extraction we have used the RNAeasy plant mini kit (Qiagen) following manufacturer's instructions. Used oligo dt to extract mRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Exponentially grown cells werespun down for 5 minutes at 5,000 g  set to 18 °C, and the pellets were washed (re-suspended and centrifuged) twice using an N-free ASW-based F/2. Following the washes, each original culture was separated into two cultures with cell concentration of 2x105 cells/mL, one with 0.88 mM of NaNO3 (N-replete) and one without any N source (N-starved). Cultures were grown for 48 hours and then harvested for the different analysis.

tag: growth protocol

value: :-nitrogen


title: +N rep3

description:
Sample 3
WT plusN replicat 3

value: :+nitrogen


title: -N rep3

description:
Sample 6
WT minusN replicat 3


title: -N rep1

description:
Sample 4
WT minusN replicat 1


title: VCaP_SUMO2/3_R1881_rep1

city: Kuopio

first: Sari

last: Toropainen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description:
Chromatin IP against SUMO2/3 in VCaP cells
processed data file: VCaP_SUMO2_3_R1881_rep1_rep2.bedGraph.gz

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.7) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
Individual background was generated for each AR, PIAS1 and FOXA1 ChIP-seq sample. The read ration of IgG/ChIP-seq sample was set to same for all ChIP-seq samples by randomly removing IgG reads.
The peak detection was done by using HOMER software (4.1). Binding sites were determined with findPeaks command (using -factor or -histone mode and individual IgG samples as a background).
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks (foun in both replicates). regions.bed file contain information of H3K4me2 promoter and intergenic regions. bedGraph files are done using HOMER software (tags normalized to 1e7) combining two replicates.

growth_protocol: The cells were grown in DMEM containing 10% (v/v) defined FBS, 25 U/ml penicillin and 25 mg/ml streptomycin in a 5% CO2 atmosphere at 37 C.

extract_protocol:
Lysates were derived from sonicated nuclei and AR-, PIAS1-, FOXA1-, Pol2-, SUMO2/3- and H3K4me2-DNA complexes were isolated with 1 ug (one microgram) of antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocol, as utilized at the Functional Genomics Unit, Helsinki, Finland, BGI Tech Solutions, Shenzhen, China or at the Gene Core in EMBL, Heidelberg, Germany.

treatment_protocol: ChIP-seq samples transfected by reverse transfection with siNON or siPIAS1 were seeded onto plates in DMEM (10% US defined FBS). After three days of plating the cells, the medium was changed to transfection medium (DMEM containing 2.5% charcoal-stripped FBS) and cells were exposed to vehicle (EtOH) or R1881 (10 nM) for 2 h after 48 h from medium change.

tag: cell line

value: Vertebral Cancer of Prostate (VCaP)

tag: cell line origin

value: bone metastasis of prostate cancer

tag: exposed to

value: 10 nM R1881 for 2hrs

tag: chip antibody

value: Anti-SUMO-2/3 mAb

tag: chip antibody vendor

value: MBL International Corporation

tag: chip antibody cat. #


title: VCaP_FOXA1_R1881_rep1

description:
Chromatin IP against FOXA1 in VCaP cells
processed data file: VCaP_FOXA1_R1881_rep1+2_peaks.bed

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.7) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
Individual background was generated for each AR, PIAS1, FOXA1 and H3K4me2 ChIP-seq sample. The read ration of IgG/ChIP-seq sample was set to same for all ChIP-seq samples by randomly removing IgG reads.
The peak detection was done by using HOMER software (4.1). Binding sites were determined with findPeaks command (using -factor or -histone mode and individual IgG samples as a background).
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed files contain information of the statistically significant peaks (foun in both replicates). regions.bed file contain information of H3K4me2 promoter and intergenic regions. bedGraph files are done using HOMER software (tags normalized to 1e7) combining two replicates.

growth_protocol: The cells were grown in DMEM containing 10% (v/v) defined FBS, 25 U/ml penicillin and 25 µg/ml streptomycin in a 5% CO2 atmosphere at 37 °C.

tag: treated with

value: 10nM R1881 for 2hr

value: Abcam


title: +N rep2

description:
Sample 2
WT plusN replicat 2


title: VCaP_FOXA1_R1881_rep2


title: VCaP_Pol2_R1881_rep1

description: Chromatin IP against Pol2 in VCaP cells

source_name: VCaP cells

value: Covance


title: VCaP_FOXA1_EtOH_rep1

description:
Chromatin IP against FOXA1 in VCaP cells
processed data file: VCaP_FOXA1_EtOH_rep1+2_peaks.bed

value: Ethanol for 2hr


title: VCaP_PIAS1_R1881_rep2

description:
Chromatin IP against PIAS1 in VCaP cells
processed data file: VCaP_PIAS1_R1881_rep1+2_peaks.bed


title: VCaP_SUMO2/3_R1881_rep2


title: forsk_H3K9S10

tag: antibody

tag: treatment

value: Forskolin stimulated (30 uM)


title: +N rep1

description:
Sample 1
WT plusN replicat 1


title: VCaP_Pol2_R1881_rep2

description: Chromatin IP against Pol2 in VCaP cells


title: VCaP_PIAS1_R1881_rep1


title: VCaP_AR_R1881_rep2

description:
Chromatin IP against AR in VCaP cells
processed data file: VCaP_AR_R1881_rep1+2_peaks.bed

value: rabbit antiserum against AR


title: VCaP_PIAS1_EtOH_rep2

description:
Chromatin IP against PIAS1 in VCaP cells
processed data file: VCaP_PIAS1_EtOH_rep1+2_peaks.bed


title: 72a2Hox

value: Mesenchymal cell lines derived from the anterior (A2) and posterior (P2) distal forelimb buds of E10.5 day Immortomouse embryos were plated into 6-well plates in DMEM, 10% foetal calf serum, 20 ng/ml γ-Interferon (Peprotech) and grown at 33°C.

tag: cell type

value: Mesenchymal cell


title: VCaP_PIAS1_EtOH_rep1


title: OS25_D3

value: ESCs were cultured were grown on mitomycin C-treated primary embryonic fibroblasts (PEFs) derived from E12.5 mouse embryos in DMEM supplemented with 15% fetal calf serum (FCS) , 1,000 units/ml LIF, nonessential amino acids, sodium pyruvate, 2-mecaptoethanol, L-glutamine, and Penicillin/Streptomycin.

value: OS25 ES cells were cultured and differentiated for 3 days (2 days with RA). Differentiation was induced by plating the cells at low density without LIF or hyg for 1 day. Retinoic acid (RA) 5×10-6 M was then added.

value: ES cell


title: VCaP_AR_R1881_rep1


title: VCaP_IgG

description: Chromatin IP against IgG in VCaP cells

value: 10nM R1881 and EtOH for 2hr

value: normal rabbit IgG

value: Santa Cruz Biotechnology


title: VCaP_SUMO2/3_EtOH_rep1

description:
Chromatin IP against SUMO2/3 in VCaP cells
processed data file: VCaP_SUMO2_3_EtOH_rep1_rep2.bedGraph.gz

value: Vertebral Cancer of Prostate (VCaP)

value: bone metastasis of prostate cancer

value: vehicle (EtOH) for 2hrs


title: VCaP_FOXA1_siNON_R1881_rep2

description:
Chromatin IP against FOXA1 in VCaP cells
processed data file: VCaP_FOXA1_siNON_R1881_rep1+2_peaks.bed

value: 10nM R1881 for 2hr


title: VCaP_FOXA1_EtOH_rep2

value: Abcam


title: VCaP_SUMO2/3_EtOH_rep2

value: Anti-SUMO-2/3 mAb

value: MBL International Corporation


title: VCaP_FOXA1_siNON_R1881_rep1


title: VCaP_H3K4me2_R1881

description: Chromatin IP against H3K4me2 in VCaP cells


title: VCaP_FOXA1_siPIAS1_R1881_rep2

description:
Chromatin IP against FOXA1 in VCaP cells
processed data file: VCaP_FOXA1_siPIAS1_R1881_rep1+2_peaks.bed


title: VCaP_AR_siPIAS1_R1881_rep2

description:
Chromatin IP against AR in VCaP cells
processed data file: VCaP_AR_siPIAS1_R1881_rep1+2_peaks.bed


title: s9470_16C

status: Public on Jan 01 2015

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description:
PolyA RNA
s9470_16C_122310-27_GTAT

data_processing:
Sequences were assigned to barcodes using custom python scripts (adapted from Gan et al. 2011. Nature, 477:419-23). For a read to be assigned to a corresponding library, the first four bases of the sequence were required to exactly match one of the four barcode sequences. Further, to eliminate mis-assignments resulting from low sequence quality, we further required that two of the first three bases have a quality scores >= 30, and that each of the first three bases have quality scores >= 25. For the T at the 4th base of our barcode sequences (shared among all barcodes and required for cloning during Illumina library construction), we further required a quality score >= 20. The submitted FASTQ files retain the barcodes as part of the sequence read (a consequence of the position of the barcode in our modification of the Illumina library construction method).
For read alignment, RNA-Seq reads from each accession were trimmed of barcode bases (the first 4nt) and mapped with the PALMapper aligner22 against the TAIR10 reference genome while taking a set of known variants into account (these variants were detected from the sequencing of the genomes of the accessions as described by Long et al. 2013. Nature Genetics, 45:884-90; for a description of PALMapper, see Jean et al. 2010. Curr Protoc Bioinformatics Chapter 11:Unit 11.6). To account for reads ambiguously mapping to multiple locations, we used a custom python script to remove all reads that showed at least one additional mapping to the best hit with the same edit distance. Additional hits were only assigned as ambiguous and subjected to removal if they differed by more than 3nt in start and stop coordinates to the best hit.
During alignment we used a feature of PALMapper that takes known variants into account to improve RNA-seq alignments. This was used to reduce allelic biases in read alignments to genomes with intraspecific polymorphisms. We first created a set of variants from two different sources: 1) single nucleotide variants (SNV) and structural variants (SV) from genome sequencing and 2) SNVs and SVs called in an initial alignment round of the RNA-Seq reads to the TAIR10 reference genome with PALMapper (relevant parameters: -M 4 -G 4 -E 6 -I 25000 -NI 1 -S). For both sources of variants we applied stringent filter criteria to reduce false calls: 1) genome variants had to appear in at least 40 strains with a minor allele count of at least 5 strains, 2) RNA-Seq variants had to be confirmed by at least 2 alignments within the same strain and had to have less than a factor of 2-fold non-confirming alignments within the same strain. Variants from both sources were integrated into one file that was used for a second, variant-aware alignment round with PALMapper (relevant parameters: -M 2 -G 0 -E 2 -I 5000 -NI 0 -S). In variant-aware alignment mode, PALMapper builds an implicit representation of the reference genome that reflects all possible variant combinations that exist for a genomic region. The output is automatically projected to the TAIR10 coordinate system.
We used a total of 499 RNA-Seq libraries for RNA-Seq expression quantification. Next, we merged libraries (e.g., technical and biological replicates) based on their ecotype and environment, yielding 323 unique merged RNA-Seq samples for each unique ecotype and environment (160 in 10C, 163 in 16C). We quantified gene expression by counting the number of reads with alignments longer than 24 bp and that mapped to genes on all non-chloroplast and non-mitochondrial chromosomes. Our gene set includes all of the annotated TAIR10 features including genes, transposable element sequence, and newly identified genes reported in Gan et al (2011; Nature, 477:419-23). To obtain a stable quantification, we applied a number of filters to the sequence mappings: 1) we only used those reads which were uniquely mapped into the exonic regions of genes, 2) we required that the reads did not map completely into regions where two genes overlap in order to avoid mixing quantifications of different genes, and 3) we excluded regions spanning structural variants (reads that start in an insertion or deletion and their two neighboring bases), alternative splicing (regions that are not contained in all transcripts of a gene), and repetitive sequences (repetitive based on a 50 bp window) that could all bias gene expression quantification.
After filtering the mapped reads, we generated expression results using 1) raw read counts and 2) RPKM estimates for each of the 323 samples. For RPKM estimates, we followed the low level normalization approach proposed by Anders and Huber (2010. Genome Biol 11:R106), jointly applied to the set of expression estimates across ecotypes and environmental backgrounds. First, we estimated effective library sizes as the median expression estimates across all genes. Based on this, we derived correction factors to adjust individual libraries for differences in size. Library-size adjusted raw counts were then used to obtain standard read counts per million expression estimates for each gene.
Genome_build: TAIR10
Supplementary_files_format_and_content: Each processed, tab-delimited data file contains the TAIR10 gene id (column 1), the raw read counts for the indicated sample (column 2), and the RPKM measures for the sample (column 3). Samples represent RNA-Seq estimates for each unique accession and temperature treatment.

source_name: whole rosette, 9-leaf stage, 16C, 9470

growth_protocol: A diverse set of 163 Swedish accessions were sown on soil and stratified for 3 days at 4 C in the dark. They were then transferred to environmentally controlled growth chambers under long day conditions (04:00-20:00 hours corresponding to light) and individual seedlings were transplanted to single pots after one week. When plants attained the 9-true-leaf stage of development, whole rosettes were collected between 15:00 and 16:00 hours into the light cycle and flash frozen in liquid nitrogen.

extract_protocol:
For each accession, 3 plants were pooled and total RNA was extracted by TRIzol (Invitrogen 15596-018), DNase treated and mRNA purified with oligo dT Dynabeads (Life Technology).
RNA was fragmented using Ambion Fragmentation buffer and first and second strand cDNA synthesis was carried out using Invitrogen kit 18064-071. The ends of sheared fragments were repaired using Epicentre kit ER81050. After A-tailing using exo- Klenow fragment (New England Biolabs, MA, NEB M0212L), barcoded adaptors were ligated with Epicentre Fast-Link DNA Ligation Kit (Epicentre LK6201H). Adaptor-ligated DNA was resolved on 1.5% low melt agarose gels for 1 hour at 100V. DNA in the range of 200-250 bp was excised from the gel and purified with the Zymoclean Gel DNA recovery kit (Zymo Research). The libraries were amplified by PCR for 15 cycles with Illumina PCR primers 1.1 and 1.2 with Phusion polymerase (NEB F-530L). Single-end 36-40 bp sequencing was performed at the University of Southern California Epigenome Center on an Illumina GAIIx instrument using 4-fold multiplexing. Barcodes were introduced into adaptors such that the first 4 bases of the respective Illumina sequence reads corresponded to one of the adaptor sequences (the custom barcodes were: ACGT, CATT, GTAT, and TGCT).

treatment_protocol: The Arabidopsis accessions were reared at either 10C or 16C.

tag: accession number

tag: accession name

tag: growth temperature

value: whole rosette

tag: develomental stage

value: 9-leaf stage


title: s9454_16C

description:
PolyA RNA
s9454_16C_121110-23_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 9454

value: Ste 3

tag: tissue


title: VCaP_AR_siPIAS1_R1881_rep1

value: rabbit antiserum against AR


title: s9481_10C

description:
PolyA RNA
s9481_10C_120210-28_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9481


title: s9470_10C

description:
PolyA RNA
s9470_10C_111510-28_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9470


title: s9436_16C

description:
PolyA RNA
s9436_16C_121010-26_CATT

source_name: whole rosette, 9-leaf stage, 16C, 9436


title: s9437_16C

description:
PolyA RNA
s9437_16C_010511-6_CATT

source_name: whole rosette, 9-leaf stage, 16C, 9437


title: s9481_16C

description:
PolyA RNA
s9481_16C_013111-16_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9481


title: s9454_10C

description:
PolyA RNA
s9454_10C_010511-24_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9454


title: s9452_10C

description:
PolyA RNA
s9452_10C_092710-23_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 9452

value: Spro 3


title: Grouper_spleen

city: Guangzhou

first: Yang

last: Yan

address: West Xingang Road

institute: South China Sea Institute of Oceanology Chinese Academy of Sciences

data_processing:
small RNA reads were produced by Illumina Genome Analyzer and base-calling was processed with Illumina pipeline versions 1.4.
Raw sequencing data were filtered by eliminating low quality reads and triming adaptor contaminants.
After filtering, the usable reads were aligned against zebrafish genome using SOAP v1.11 (Short Oligonucleotide Alignment Program) (http://soap.genomics.org.cn).
Genome_build: zebrafish(Zv9/danRer7)
Supplementary_files_format_and_content: sequence length and read count of sequences

organism: Epinephelus coioides

source_name: grouper spleen cells

growth_protocol: Grouper spleen (GS) cells were grown in Leibovitz' s L-15 medium that contained 10% FBS at 25 °C.

extract_protocol:
After growth for 48 h, the GS cells were harvested and total RNA was extracted using TRIzol reagent,with a little modification. After addition of isopropanol, the RNA extract was incubated at -20°C  for 2 h to acquire more low-molecular-weight RNAs.
After electrophoresing on 15% polyacrylamide–8 M urea gel, the small RNAs with about 30 nt were extracted, and a pair of Solexa proprietary adaptors as PCR primer was ligated to both 5′ and 3′ ends of the RNAs. After reverse transcription reaction from the RNAs, the resulting cDNA was amplified to produce sequencing libraries.

value: fibroblast cell

value: spleen


title: s9427_16C

description:
PolyA RNA
s9427_16C_121610-12_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9427

value: Näs 2


title: s9436_10C

description:
PolyA RNA
s9436_10C_010511-8_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9436


title: s9427_10C

description:
PolyA RNA
s9427_10C_110410-27_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 9427


title: s9437_10C

description:
PolyA RNA
s9437_10C_010511-9_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 9437


title: VCaP_FOXA1_siPIAS1_R1881_rep1


title: s9421_16C

description:
PolyA RNA
s9421_16C_121010-8_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9421

value: Lan 1


title: s9416_16C

description:
PolyA RNA
s9416_16C_121610-2_CATT

source_name: whole rosette, 9-leaf stage, 16C, 9416


title: s9434_10C

description:
PolyA RNA
s9434_10C_120210-13_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 9434

value: Öde 2


title: s9412_16C

description:
PolyA RNA
s9412_16C_092710-28_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9412

value: Kor 3


title: s9413_10C

description:
PolyA RNA
s9413_10C_012111-25_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 9413

value: Kor 4


title: s9402_16C

description:
PolyA RNA
s9402_16C_121010-7_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 9402


title: s9413_16C

description:
PolyA RNA
s9413_16C_121710-13_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 9413


title: s9402_10C

description:
PolyA RNA
s9402_10C_110410-25_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 9402


title: s9452_16C

description:
PolyA RNA
s9452_16C_121610-11_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 9452


title: s9395_16C

description:
PolyA RNA
s9395_16C_121010-20_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9395


title: s9399_16C

description:
PolyA RNA
s9399_16C_013111-15_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 9399


title: s9394_10C

description:
PolyA RNA
s9394_10C_110410-23_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 9394


title: s9394_16C

description:
PolyA RNA
s9394_16C_121610-16_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9394


title: s9392_16C

description:
PolyA RNA
s9392_16C_122310-26_CATT

source_name: whole rosette, 9-leaf stage, 16C, 9392


title: s9391_10C

description:
PolyA RNA
s9391_10C_012111-24_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9391


title: s9392_10C

description:
PolyA RNA
s9392_10C_092710-22_CATT

source_name: whole rosette, 9-leaf stage, 10C, 9392


title: s9391_16C

description:
PolyA RNA
s9391_16C_121710-21_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 9391


title: s9395_10C

description:
PolyA RNA
s9395_10C_110410-24_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9395


title: s9390_10C

description:
PolyA RNA
s9390_10C_012111-23_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 9390


title: s9383_16C

description:
PolyA RNA
s9383_16C_111210-12_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9383

value: Fri 3


title: s9416_10C

description:
PolyA RNA
s9416_10C_120210-23_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 9416


title: s9390_16C

description:
PolyA RNA
s9390_16C_010511-5_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 9390


title: s9383_10C

description:
PolyA RNA
s9383_10C_090210-4_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9383


title: s9412_10C

description:
PolyA RNA
s9412_10C_110410-26_CATT

source_name: whole rosette, 9-leaf stage, 10C, 9412


title: s9382_16C

description:
PolyA RNA
s9382_16C_090210-23_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 9382

value: Fri 2


title: s9434_16C

description:
PolyA RNA
s9434_16C_121610-23_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 9434


title: s9382_10C

description:
PolyA RNA
s9382_10C_090210-11_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 9382


title: s9380_16C

description:
PolyA RNA
s9380_16C_013111-14_CATT

source_name: whole rosette, 9-leaf stage, 16C, 9380

value: FlyA 3


title: s9381_10C

description:
PolyA RNA
s9381_10C_111510-22_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9381

value: Fri 1


title: s9381_16C

description:
PolyA RNA
s9381_16C_121610-28_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9381


title: s9380_10C

description:
PolyA RNA
s9380_10C_111510-21_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 9380


title: s9369_10C

description:
PolyA RNA
s9369_10C_012111-21_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 9369

value: EkS 2


title: s9363_16C

description:
PolyA RNA
s9363_16C_121610-8_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9363

value: EdJ 2

value: whole rosette


title: s9371_10C

description:
PolyA RNA
s9371_10C_092710-21_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 9371

value: FäL 1

value: 9-leaf stage


title: s9369_16C

description:
PolyA RNA
s9369_16C_122310-15_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 9369


title: s9353_10C

description:
PolyA RNA
s9353_10C_110410-22_CATT

source_name: whole rosette, 9-leaf stage, 10C, 9353

value: Död 3


title: s9353_16C

description:
PolyA RNA
s9353_16C_121710-20_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9353


title: s9339_16C

description:
PolyA RNA
s9339_16C_121610-22_CATT

source_name: whole rosette, 9-leaf stage, 16C, 9339

value: Böt 1


title: s9352_10C

description:
PolyA RNA
s9352_10C_110410-21_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 9352

value: Död 2


title: s9352_16C

description:
PolyA RNA
s9352_16C_121010-6_CATT

source_name: whole rosette, 9-leaf stage, 16C, 9352


title: s9363_10C

description:
PolyA RNA
s9363_10C_111510-20_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9363


title: s9336_16C

description:
PolyA RNA
s9336_16C_121610-4_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9336

value: Bön 1


title: s9332_10C

description:
PolyA RNA
s9332_10C_110410-20_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9332

value: Bar 1


title: s9332_16C

description:
PolyA RNA
s9332_16C_121010-3_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 9332


title: s9323_16C

description:
PolyA RNA
s9323_16C_090210-27_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 9323

value: Ådal 3


title: s9323_10C

description:
PolyA RNA
s9323_10C_090210-18_CATT

source_name: whole rosette, 9-leaf stage, 10C, 9323


title: s9058_10C

description:
PolyA RNA
s9058_10C_FlowCell1_25_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 9058

value: Västervik


title: s9058_16C

description:
PolyA RNA
s9058_16C_FlowCell2_8_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9058


title: s9057_16C

description:
PolyA RNA
s9057_16C_121710-4_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 9057

value: Vinslöv


title: s9057_10C

description:
PolyA RNA
s9057_10C_111210-26_CATT

source_name: whole rosette, 9-leaf stage, 10C, 9057


title: s8422_16C

description:
PolyA RNA
s8422_16C_122310-2_CATT

source_name: whole rosette, 9-leaf stage, 16C, 8422


title: s9399_10C

description:
PolyA RNA
s9399_10C_120210-25_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 9399


title: s8426_10C

description:
PolyA RNA
s8426_10C_120210-11_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 8426


title: s9371_16C

description:
PolyA RNA
s9371_16C_121110-22_CATT

source_name: whole rosette, 9-leaf stage, 16C, 9371


title: s8426_16C

description:
PolyA RNA
s8426_16C_122310-9_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 8426


title: s8387_10C

description:
PolyA RNA
s8387_10C_012111-20_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 8387


title: s8422_10C

description:
PolyA RNA
s8422_10C_092710-19_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 8422


title: s8376_16C

description:
PolyA RNA
s8376_16C_FlowCell2_22_CATT

source_name: whole rosette, 9-leaf stage, 16C, 8376


title: s8387_16C

description:
PolyA RNA
s8387_16C_121010-18_CATT

source_name: whole rosette, 9-leaf stage, 16C, 8387


title: s8369_10C

description:
PolyA RNA
s8369_10C_111210-16_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 8369


title: s9339_10C

description:
PolyA RNA
s9339_10C_010511-20_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9339


title: s8351_10C

description:
PolyA RNA
s8351_10C_112210-11_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 8351


title: s8334_16C

description:
PolyA RNA
s8334_16C_FlowCell2_14_CATT

source_name: whole rosette, 9-leaf stage, 16C, 8334


title: s8335_16C

description:
PolyA RNA
s8335_16C_111210-10_CATT

source_name: whole rosette, 9-leaf stage, 16C, 8335

value: Lund


title: s8369_16C

description:
PolyA RNA
s8369_16C_010511-3_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 8369


title: s8351_16C

description:
PolyA RNA
s8351_16C_FlowCell2_17_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 8351


title: s8335_10C

description:
PolyA RNA
s8335_10C_112210-13_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 8335


title: s9336_10C

description:
PolyA RNA
s9336_10C_120210-12_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 9336


title: s8283_16C

description:
PolyA RNA
s8283_16C_090210-19_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 8283


title: s8258_16C

description:
PolyA RNA
s8258_16C_FlowCell2_13_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 8258


title: s8258_10C

description:
PolyA RNA
s8258_10C_032511-5_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 8258


title: s8283_10C

description:
PolyA RNA
s8283_10C_010511-22_CATT

source_name: whole rosette, 9-leaf stage, 10C, 8283


title: s8259_10C

description:
PolyA RNA
s8259_10C_092710-17_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 8259


title: s8256_16C

description:
PolyA RNA
s8256_16C_FlowCell2_15_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 8256


title: s8259_16C

description:
PolyA RNA
s8259_16C_121710-11_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 8259


title: s8376_10C

description:
PolyA RNA
s8376_10C_112210-10_CATT

source_name: whole rosette, 9-leaf stage, 10C, 8376


title: s8256_10C

description:
PolyA RNA
s8256_10C_112210-2_CATT

source_name: whole rosette, 9-leaf stage, 10C, 8256


title: s8241_10C

description:
PolyA RNA
s8241_10C_092710-16_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 8241

value: Liarum


title: s8247_16C

description:
PolyA RNA
s8247_16C_032511-11_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 8247


title: s8240_16C

description:
PolyA RNA
s8240_16C_121110-20_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 8240


title: s8242_10C

description:
PolyA RNA
s8242_10C_112210-23_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 8242


title: s8334_10C

description:
PolyA RNA
s8334_10C_120210-10_CATT

source_name: whole rosette, 9-leaf stage, 10C, 8334


title: s8249_10C

description:
PolyA RNA
s8249_10C_FlowCell1_26_CATT

source_name: whole rosette, 9-leaf stage, 10C, 8249

value: Vimmerby


title: s8249_16C

description:
PolyA RNA
s8249_16C_FlowCell2_10_CATT

source_name: whole rosette, 9-leaf stage, 16C, 8249


title: s8247_10C

description:
PolyA RNA
s8247_10C_090210-16_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 8247


title: s8237_16C

description:
PolyA RNA
s8237_16C_122310-1_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 8237


title: s8234_16C

description:
PolyA RNA
s8234_16C_111210-7_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 8234


title: s8234_10C

description:
PolyA RNA
s8234_10C_090210-15_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 8234


title: s8237_10C

description:
PolyA RNA
s8237_10C_010511-14_CATT

source_name: whole rosette, 9-leaf stage, 10C, 8237


title: s8326_16C

description:
PolyA RNA
s8326_16C_111210-9_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 8326


title: s8227_10C

description:
PolyA RNA
s8227_10C_120210-21_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 8227

value: THÖ 03


title: s8230_16C

description:
PolyA RNA
s8230_16C_122310-22_CATT

source_name: whole rosette, 9-leaf stage, 16C, 8230

value: Algutsrum


title: s8222_10C

description:
PolyA RNA
s8222_10C_112210-22_CATT

source_name: whole rosette, 9-leaf stage, 10C, 8222


title: s8227_16C

description:
PolyA RNA
s8227_16C_122310-7_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 8227


title: s7519_10C

description:
PolyA RNA
s7519_10C_112210-18_CATT

source_name: whole rosette, 9-leaf stage, 10C, 7519


title: s8241_16C

description:
PolyA RNA
s8241_16C_121710-6_CATT

source_name: whole rosette, 9-leaf stage, 16C, 8241


title: s7517_10C

description:
PolyA RNA
s7517_10C_112210-19_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 7517


title: s7519_16C

description:
PolyA RNA
s7519_16C_FlowCell2_12_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 7519


title: s7516_10C

description:
PolyA RNA
s7516_10C_111210-5_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 7516


title: s7517_16C

description:
PolyA RNA
s7517_16C_111210-6_CATT

source_name: whole rosette, 9-leaf stage, 16C, 7517


title: s8240_10C

description:
PolyA RNA
s8240_10C_110410-19_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 8240


title: s7516_16C

description:
PolyA RNA
s7516_16C_FlowCell2_9_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 7516


title: s8222_16C

description:
PolyA RNA
s8222_16C_FlowCell2_18_CATT

source_name: whole rosette, 9-leaf stage, 16C, 8222


title: s6973_10C

description:
PolyA RNA
s6973_10C_FlowCell1_27_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6973


title: s6973_16C

description:
PolyA RNA
s6973_16C_FlowCell2_16_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6973


title: s6974_16C

description:
PolyA RNA
s6974_16C_FlowCell2_6_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6974


title: s8242_16C

description:
PolyA RNA
s8242_16C_FlowCell2_19_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 8242


title: s6913_16C

description:
PolyA RNA
s6913_16C_FlowCell2_1_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6913


title: s6917_10C

description:
PolyA RNA
s6917_10C_012111-19_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6917


title: s6974_10C

description:
PolyA RNA
s6974_10C_112210-16_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6974


title: s6909_16C

description:
PolyA RNA
s6909_16C_FlowCell2_20_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6909


title: s6901_16C

description:
PolyA RNA
s6901_16C_FlowCell2_2_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6901


title: s6909_10C

description:
PolyA RNA
s6909_10C_092710-24_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6909


title: s6913_10C

description:
PolyA RNA
s6913_10C_090210-5_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6913


title: s6413_16C

description:
PolyA RNA
s6413_16C_121110-19_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6413


title: s6413_10C

description:
PolyA RNA
s6413_10C_120210-8_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6413


title: s6276_16C

description:
PolyA RNA
s6276_16C_121110-18_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6276


title: s6901_10C

description:
PolyA RNA
s6901_10C_112210-8_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6901


title: s6252_10C

description:
PolyA RNA
s6252_10C_013111-4_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6252


title: s6244_16C

description:
PolyA RNA
s6244_16C_090210-26_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6244

value: TRÄ 01


title: s6276_10C

description:
PolyA RNA
s6276_10C_111510-16_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6276

value: whole rosette


title: s6258_10C

description:
PolyA RNA
s6258_10C_012111-18_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6258


title: s6252_16C

description:
PolyA RNA
s6252_16C_121710-24_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6252


title: s6242_16C

description:
PolyA RNA
s6242_16C_121110-17_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6242


title: s6242_10C

description:
PolyA RNA
s6242_10C_110410-18_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6242


title: s6238_16C

description:
PolyA RNA
s6238_16C_090210-25_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6238

value: TOM 04


title: s6244_10C

description:
PolyA RNA
s6244_10C_090210-10_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6244

value: 9-leaf stage


title: s6243_16C

description:
PolyA RNA
s6243_16C_121010-13_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6243


title: s6238_10C

description:
PolyA RNA
s6238_10C_090210-1_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6238


title: s6243_10C

description:
PolyA RNA
s6243_10C_092710-15_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6243


title: s6237_10C

description:
PolyA RNA
s6237_10C_110410-17_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6237

value: TOM 03


title: s6240_16C

description:
PolyA RNA
s6240_16C_121110-16_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6240

value: TOM 06


title: s6917_16C

description:
PolyA RNA
s6917_16C_013111-12_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6917


title: s6231_10C

description:
PolyA RNA
s6231_10C_012111-17_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6231

value: TNY 04


title: s6235_16C

description:
PolyA RNA
s6235_16C_121110-14_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6235

value: TOM 01


title: s6235_10C

description:
PolyA RNA
s6235_10C_120210-20_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6235


title: s6221_10C

description:
PolyA RNA
s6221_10C_111210-15_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6221

value: TGR 02


title: s6231_16C

description:
PolyA RNA
s6231_16C_122310-14_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6231


title: s6210_10C

description:
PolyA RNA
s6210_10C_110410-15_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6210

value: TEDEN 03


title: s6203_16C

description:
PolyA RNA
s6203_16C_122310-18_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6203


title: s6209_16C

description:
PolyA RNA
s6209_16C_010511-4_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6209

value: TEDEN 02


title: s6209_10C

description:
PolyA RNA
s6209_10C_010511-16_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6209


title: s6203_10C

description:
PolyA RNA
s6203_10C_110410-14_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6203


title: s6210_16C

description:
PolyA RNA
s6210_16C_121710-9_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6210


title: s6202_10C

description:
PolyA RNA
s6202_10C_010511-17_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6202


title: s6202_16C

description:
PolyA RNA
s6202_16C_122310-5_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6202


title: s6194_16C

description:
PolyA RNA
s6194_16C_013111-9_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6194


title: s6195_10C

description:
PolyA RNA
s6195_10C_012111-16_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6195


title: s6193_16C

description:
PolyA RNA
s6193_16C_122310-4_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6193


title: s6195_16C

description:
PolyA RNA
s6195_16C_121710-15_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6195


title: s6191_16C

description:
PolyA RNA
s6191_16C_121710-2_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6191


title: s6192_16C

description:
PolyA RNA
s6192_16C_111210-4_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6192


title: s6221_16C

description:
PolyA RNA
s6221_16C_121610-19_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6221


title: s6216_10C

description:
PolyA RNA
s6216_10C_110410-16_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6216

value: TFÄ 06


title: s6216_16C

description:
PolyA RNA
s6216_16C_012111-28_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6216


title: s6189_16C

description:
PolyA RNA
s6189_16C_121710-17_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6189


title: s6189_10C

description:
PolyA RNA
s6189_10C_111210-14_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6189


title: s6191_10C

description:
PolyA RNA
s6191_10C_012111-14_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6191


title: s6237_16C

description:
PolyA RNA
s6237_16C_121110-15_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6237


title: s6192_10C

description:
PolyA RNA
s6192_10C_090210-9_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6192


title: s6188_10C

description:
PolyA RNA
s6188_10C_120210-5_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6188


title: s8326_10C

description:
PolyA RNA
s8326_10C_090210-17_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 8326


title: s6184_16C

description:
PolyA RNA
s6184_16C_122310-25_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6184

value: TBÖ 01


title: s6184_10C

description:
PolyA RNA
s6184_10C_110410-13_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6184


title: s6180_16C

description:
PolyA RNA
s6180_16C_013111-8_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6180

value: TÄL 07


title: s6188_16C

description:
PolyA RNA
s6188_16C_122310-20_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6188


title: s6173_16C

description:
PolyA RNA
s6173_16C_121010-11_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6173

value: TÅD 05


title: s6172_16C

description:
PolyA RNA
s6172_16C_121710-7_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6172

value: TÅD 04


title: s6173_10C

description:
PolyA RNA
s6173_10C_092710-14_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6173


title: s6172_10C

description:
PolyA RNA
s6172_10C_111510-15_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6172


title: s6193_10C

description:
PolyA RNA
s6193_10C_012111-15_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6193


title: s6151_16C

description:
PolyA RNA
s6151_16C_121610-3_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6151


title: s6153_10C

description:
PolyA RNA
s6153_10C_110410-11_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6153

value: TAA 03


title: s6151_10C

description:
PolyA RNA
s6151_10C_010511-25_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6151


title: s6150_16C

description:
PolyA RNA
s6150_16C_121610-14_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6150


title: s6150_10C

description:
PolyA RNA
s6150_10C_111510-27_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6150


title: s6149_10C

description:
PolyA RNA
s6149_10C_092710-13_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6149


title: s6258_16C

description:
PolyA RNA
s6258_16C_122310-11_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6258


title: s6147_16C

description:
PolyA RNA
s6147_16C_111210-3_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6147


title: s6147_10C

description:
PolyA RNA
s6147_10C_090210-8_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6147


title: s6142_10C

description:
PolyA RNA
s6142_10C_010511-23_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6142


title: s6136_16C

description:
PolyA RNA
s6136_16C_111210-1_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6136


title: s6142_16C

description:
PolyA RNA
s6142_16C_111210-2_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6142


title: s6132_10C

description:
PolyA RNA
s6132_10C_120210-4_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6132


title: s6131_16C

description:
PolyA RNA
s6131_16C_121610-13_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6131


title: s6180_10C

description:
PolyA RNA
s6180_10C_012111-13_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6180


title: s6128_10C

description:
PolyA RNA
s6128_10C_110410-7_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6128


title: s6128_16C

description:
PolyA RNA
s6128_16C_032511-7_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6128


title: s6136_10C

description:
PolyA RNA
s6136_10C_092710-26_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6136


title: s6132_16C

description:
PolyA RNA
s6132_16C_121610-24_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6132


title: s6126_16C

description:
PolyA RNA
s6126_16C_121110-12_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6126


title: s6131_10C

description:
PolyA RNA
s6131_10C_092710-12_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6131


title: s6127_16C

description:
PolyA RNA
s6127_16C_121610-1_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6127


title: s6125_16C

description:
PolyA RNA
s6125_16C_010511-2_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6125


title: s6127_10C

description:
PolyA RNA
s6127_10C_092710-10_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6127


title: s6122_10C

description:
PolyA RNA
s6122_10C_092710-8_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6122


title: s6118_16C

description:
PolyA RNA
s6118_16C_121110-11_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6118


title: s6124_16C

description:
PolyA RNA
s6124_16C_121610-6_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6124


title: s6114_16C

description:
PolyA RNA
s6114_16C_121110-28_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6114


title: s6122_16C

description:
PolyA RNA
s6122_16C_121610-26_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6122


title: s6124_10C

description:
PolyA RNA
s6124_10C_111210-23_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6124


title: s6115_16C

description:
PolyA RNA
s6115_16C_121010-15_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6115


title: s6113_16C

description:
PolyA RNA
s6113_16C_121010-10_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6113


title: s6112_10C

description:
PolyA RNA
s6112_10C_111210-21_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6112


title: s6112_16C

description:
PolyA RNA
s6112_16C_121010-16_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6112


title: s6109_16C

description:
PolyA RNA
s6109_16C_121110-10_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6109


title: s6126_10C

description:
PolyA RNA
s6126_10C_092710-9_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6126


title: s6125_10C

description:
PolyA RNA
s6125_10C_012111-11_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6125


title: s6109_10C

description:
PolyA RNA
s6109_10C_010511-28_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6109


title: s6113_10C

description:
PolyA RNA
s6113_10C_111510-26_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6113


title: s6108_16C

description:
PolyA RNA
s6108_16C_121710-1_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6108


title: s6108_10C

description:
PolyA RNA
s6108_10C_092710-7_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6108


title: s6104_16C

description:
PolyA RNA
s6104_16C_121110-27_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6104


title: s6105_16C

description:
PolyA RNA
s6105_16C_121010-9_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6105


title: s6149_16C

description:
PolyA RNA
s6149_16C_121610-25_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6149


title: s6105_10C

description:
PolyA RNA
s6105_10C_111510-12_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6105


title: s6104_10C

description:
PolyA RNA
s6104_10C_090210-7_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6104


title: s6115_10C

description:
PolyA RNA
s6115_10C_110410-5_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6115


title: s6118_10C

description:
PolyA RNA
s6118_10C_110410-6_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6118


title: s6102_16C

description:
PolyA RNA
s6102_16C_121110-9_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6102


title: s6102_10C

description:
PolyA RNA
s6102_10C_111210-20_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6102


title: s6114_10C

description:
PolyA RNA
s6114_10C_090210-22_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6114


title: s6100_16C

description:
PolyA RNA
s6100_16C_122310-8_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6100


title: s6100_10C

description:
PolyA RNA
s6100_10C_111210-19_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6100


title: s6092_16C

description:
PolyA RNA
s6092_16C_121610-21_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6092


title: s6092_10C

description:
PolyA RNA
s6092_10C_092710-5_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6092


title: s6090_16C

description:
PolyA RNA
s6090_16C_121110-7_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6090


title: s6090_10C

description:
PolyA RNA
s6090_10C_092710-4_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6090


title: s6088_16C

description:
PolyA RNA
s6088_16C_FlowCell2_3_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6088


title: s6088_10C

description:
PolyA RNA
s6088_10C_112210-14_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6088


title: s6076_16C

description:
PolyA RNA
s6076_16C_122310-19_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6076


title: s6085_10C

description:
PolyA RNA
s6085_10C_092710-3_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6085


title: s6085_16C

description:
PolyA RNA
s6085_16C_121010-14_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6085


title: s6153_16C

description:
PolyA RNA
s6153_16C_121610-10_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6153


title: s6074_16C

description:
PolyA RNA
s6074_16C_121710-10_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6074


title: s6076_10C

description:
PolyA RNA
s6076_10C_120210-17_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6076


title: s6074_10C

description:
PolyA RNA
s6074_10C_092710-2_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6074


title: s6098_16C

description:
PolyA RNA
s6098_16C_121110-8_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6098


title: s6094_16C

description:
PolyA RNA
s6094_16C_013111-7_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6094


title: s6094_10C

description:
PolyA RNA
s6094_10C_010511-26_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6094


title: s6098_10C

description:
PolyA RNA
s6098_10C_092710-6_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6098


title: s6040_16C

description:
PolyA RNA
s6040_16C_121710-14_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6040


title: s6042_16C

description:
PolyA RNA
s6042_16C_122310-24_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6042


title: s6043_10C

description:
PolyA RNA
s6043_10C_112210-9_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6043


title: s6070_16C

description:
PolyA RNA
s6070_16C_013111-6_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6070


title: s6069_16C

description:
PolyA RNA
s6069_16C_121110-5_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6069


title: s6043_16C

description:
PolyA RNA
s6043_16C_FlowCell2_4_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6043


title: s6070_10C

description:
PolyA RNA
s6070_10C_010511-12_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6070


title: s6073_10C

description:
PolyA RNA
s6073_10C_010511-15_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6073


title: s6042_10C

description:
PolyA RNA
s6042_10C_013111-2_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6042


title: s6071_10C

description:
PolyA RNA
s6071_10C_111510-10_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6071


title: s6040_10C

description:
PolyA RNA
s6040_10C_111210-17_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6040


title: s6046_16C

description:
PolyA RNA
s6046_16C_FlowCell2_5_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6046


title: s6071_16C

description:
PolyA RNA
s6071_16C_121110-6_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6071


title: s6069_10C

description:
PolyA RNA
s6069_10C_012111-9_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6069


title: s6073_16C

description:
PolyA RNA
s6073_16C_010511-1_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6073


title: s6039_16C

description:
PolyA RNA
s6039_16C_121010-22_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6039


title: s6039_10C

description:
PolyA RNA
s6039_10C_092710-1_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6039


title: s6046_10C

description:
PolyA RNA
s6046_10C_112210-15_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6046


title: s6034_10C

description:
PolyA RNA
s6034_10C_112210-26_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6034


title: s6036_10C

description:
PolyA RNA
s6036_10C_112210-27_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6036


title: s6034_16C

description:
PolyA RNA
s6034_16C_122310-21_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6034


title: s6030_16C

description:
PolyA RNA
s6030_16C_121110-3_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6030


title: s6030_10C

description:
PolyA RNA
s6030_10C_120210-16_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 6030


title: s6021_16C

description:
PolyA RNA
s6021_16C_121010-5_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 6021


title: s6023_10C

description:
PolyA RNA
s6023_10C_090210-13_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6023


title: s6023_16C

description:
PolyA RNA
s6023_16C_112210-24_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6023


title: s6021_10C

description:
PolyA RNA
s6021_10C_111510-9_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6021


title: s6016_16C

description:
PolyA RNA
s6016_16C_FlowCell2_7_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6016


title: s6016_10C

description:
PolyA RNA
s6016_10C_112210-1_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 6016


title: s5867_16C

description:
PolyA RNA
s5867_16C_121010-21_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 5867


title: s6012_10C

description:
PolyA RNA
s6012_10C_111510-6_CATT

source_name: whole rosette, 9-leaf stage, 10C, 6012


title: s6013_16C

description:
PolyA RNA
s6013_16C_121110-2_CATT

source_name: whole rosette, 9-leaf stage, 16C, 6013


title: s5856_16C

description:
PolyA RNA
s5856_16C_121010-1_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 5856


title: s5856_10C

description:
PolyA RNA
s5856_10C_111510-23_CATT

source_name: whole rosette, 9-leaf stage, 10C, 5856


title: s5867_10C

description:
PolyA RNA
s5867_10C_111510-5_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 5867


title: s6011_10C

description:
PolyA RNA
s6011_10C_111510-24_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6011


title: s1552_10C

description:
PolyA RNA
s1552_10C_012111-6_CATT

source_name: whole rosette, 9-leaf stage, 10C, 1552


title: s5865_16C

description:
PolyA RNA
s5865_16C_121610-18_CATT

source_name: whole rosette, 9-leaf stage, 16C, 5865


title: s5832_10C

description:
PolyA RNA
s5832_10C_111510-3_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 5832


title: s6012_16C

description:
PolyA RNA
s6012_16C_121010-27_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 6012


title: s6036_16C

description:
PolyA RNA
s6036_16C_121110-4_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6036


title: s1317_16C

description:
PolyA RNA
s1317_16C_121010-25_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 1317


title: s6011_16C

description:
PolyA RNA
s6011_16C_122310-16_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 6011


title: s1552_16C

description:
PolyA RNA
s1552_16C_122310-17_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 1552


title: s5832_16C

description:
PolyA RNA
s5832_16C_121610-27_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 5832


title: s1317_10C

description:
PolyA RNA
s1317_10C_010511-10_CATT

source_name: whole rosette, 9-leaf stage, 10C, 1317


title: s1257_10C

description:
PolyA RNA
s1257_10C_013111-1_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 1257


title: s1158_16C

description:
PolyA RNA
s1158_16C_121710-8_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 1158


title: s1158_10C

description:
PolyA RNA
s1158_10C_012111-3_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 1158


title: s1074_10C

description:
PolyA RNA
s1074_10C_010511-11_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 1074


title: s6013_10C

description:
PolyA RNA
s6013_10C_111510-7_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 6013


title: s1137_10C

description:
PolyA RNA
s1137_10C_110410-1_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 1137


title: s1074_16C

description:
PolyA RNA
s1074_16C_121710-5_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 1074


title: s1137_16C

description:
PolyA RNA
s1137_16C_121010-2_CATT

source_name: whole rosette, 9-leaf stage, 16C, 1137


title: s5865_10C

description:
PolyA RNA
s5865_10C_111510-4_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 5865


title: s1254_16C

description:
PolyA RNA
s1254_16C_090210-20_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 1254


title: s1070_10C

description:
PolyA RNA
s1070_10C_012111-2_CATT

source_name: whole rosette, 9-leaf stage, 10C, 1070


title: s1063_10C

description:
PolyA RNA
s1063_10C_012111-1_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 1063


title: s1062_10C

description:
PolyA RNA
s1062_10C_112210-25_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 1062


title: s1062_16C

description:
PolyA RNA
s1062_16C_122310-3_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 1062


title: s992_16C

description:
PolyA RNA
s992_16C_121710-16_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 992


title: s1063_16C

description:
PolyA RNA
s1063_16C_121010-19_GTAT

source_name: whole rosette, 9-leaf stage, 16C, 1063


title: s1061_16C

description:
PolyA RNA
s1061_16C_121010-4_TGCT

source_name: whole rosette, 9-leaf stage, 16C, 1061


title: s1257_16C

description:
PolyA RNA
s1257_16C_122310-10_CATT

source_name: whole rosette, 9-leaf stage, 16C, 1257


title: s992_10C

description:
PolyA RNA
s992_10C_010511-19_GTAT

source_name: whole rosette, 9-leaf stage, 10C, 992


title: s1254_10C

description:
PolyA RNA
s1254_10C_012111-4_TGCT

source_name: whole rosette, 9-leaf stage, 10C, 1254


title: hua2 hulk1 seedling, biological replicate 2

description:
hua2_hulk1_biol_rep_2
HUA2 HULK1 T-DNA insertions (Col-0 background)
PolyA RNA
Barcode for sample: CATT

data_processing:
Read data was acquired from an Illumina Genome IIx sequencer using the SR_Amplification_Linearization_Blocking_PrimerHyb_v7 protocol. Base calling was performed with the Illumina version SCS2.6 software. For the "Real Time Analysis (RTA)" that is implemented in the SCS control software, we used "per lane" parameters for basecalling.
Barcode splitting was performed as described by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
Reads from FASTQ files that were the output of the Illumina SCS analysis pipeline were aligned to the genome and processed with TopHat/Bowtie (parameters: -a 5, -i 5, -I 32000, --solexa1.3-quals, -g 1, --segment-mismatches 3, -p 5) for calculation of gene expression levels determined as reads aligned to exons using the TAIR10 annotation.
Genome_build: TAIR10
Supplementary_files_format_and_content: A single tab-delimited text file per sample with Gene IDs and RPM values.

source_name: Seedling, emergence of fourth true leaf, HUA2 HULK1 T-DNA insertions

growth_protocol: Plants were germinated on soil and grown until emergence of the fourth true leaf (16 hours light, 8 hours dark, at 20C).

extract_protocol:
Aerial seedling tissue was frozen in liquid nitrogen, ground to a fine power in liquid nitrogen, and RNA was extracted with the Plant Reagent (Invitrogen using the manufacturer's recommendations). Specific details are as given in Gan et al. 2011. Nature, 477:419-23; see Supplementary Information Section 7.
Illumina non-strand-specific (a minor adaptation of the Illumina mRNA-seq methods as reported by Gan et al. 2011. Nature, 477:419-23; see Supplementary Information Section 7).

tag: strain/background

tag: genotype/variation

value: HUA2 HULK1 T-DNA insertions

value: seedling

tag: developmental stage

value: emergence of fourth true leaf


title: hua2 hulk1 hulk2 seedling, biological replicate 1

description:
hua2_hulk1_hulk2_biol_rep_1
HUA2 HULK1 HULK2 T-DNA insertions (Col-0 background)
PolyA RNA
Barcode for sample: TGCT

source_name: Seedling, emergence of fourth true leaf, HUA2 HULK1 HULK2 T-DNA insertions

value: HUA2 HULK1 HULK2 T-DNA insertions


title: s991_10C

description:
PolyA RNA
s991_10C_111510-1_ACGT

source_name: whole rosette, 9-leaf stage, 10C, 991

value: whole rosette

value: 9-leaf stage


title: hua2 hulk1 seedling, biological replicate 1

description:
hua2_hulk1_biol_rep_1
HUA2 HULK1 T-DNA insertions (Col-0 background)
PolyA RNA
Barcode for sample: CATT


title: Col-0 seedling, biological replicate 2

description:
Col-0_biol_rep_2
Col-0 accession (wild type control)
PolyA RNA
Barcode for sample: GTAT

source_name: Seedling, emergence of fourth true leaf, wild type

value: wild type


title: hua2 seedling, biological replicate 2

description:
hua2_biol_rep_2
HUA2 T-DNA insertion (Col-0 background)
PolyA RNA
Barcode for sample: ACGT

source_name: Seedling, emergence of fourth true leaf, HUA2 T-DNA insertion

value: HUA2 T-DNA insertion


title: hua2 hulk1 hulk2 seedling, biological replicate 2

description:
hua2_hulk1_hulk2_biol_rep_2
HUA2 HULK1 HULK2 T-DNA insertions (Col-0 background)
PolyA RNA
Barcode for sample: TGCT


title: Col-0 seedling, biological replicate 1

description:
Col-0_biol_rep_1
Col-0 accession (wild type control)
PolyA RNA
Barcode for sample: GTAT


title: hua2 seedling, biological replicate 1

description:
hua2_biol_rep_1
HUA2 T-DNA insertion (Col-0 background)
PolyA RNA
Barcode for sample: ACGT


title: N2Y6-M (DGE)

city: Hangzhou

first: bo

last: shen

address: Cangqian  road

institute: Hangzhou normal university

description:
Sample 8
Sample name: BSA2
processed data file: Table  S6.xls

data_processing:
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for miRNA sequencing data analysis (Li et al. 2010; Wei et al. 2011). ACGT101_DGE was used for DGE sequencing data analysis. A Public software package, CleaveLand3.0 was used for analyzing Degradome sequencing data.
Genome_build: MSU Release 7.0 (http://www.phytozome.net/rice.php), miRbase20.0
Supplementary_files_format_and_content: xls format and mRNA abundance measurements

organism: Oryza sativa

source_name: N2Y6 rice

extract_protocol: Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions. Small RNA libraries were generated from the two samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by Ma et al.(2010).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.

treatment_protocol: The flag leaves at early, middle and late stages of grain-filling of two hybrid rice, N2Y6 and LYP9 (named as N2Y6-E, N2Y6-M, N2Y6-L, LYP9-E, LYP9-M and LYP9-L, respectively), were collected, respectively.

tag: hybrid

value: Nei-2-You 6 (N2Y6, age-resistant rice)

value: leaf

value: middle stage of grain-filling


title: LYP9-M (miRNA)

description:
Sample 5
Sample name: BSB2
processed data file: Table  S1.xls
processed data file: Table  S2.xls

data_processing:
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for miRNA sequencing data analysis (Li et al. 2010; Wei et al. 2011). ACGT101_DGE was used for DGE sequencing data analysis. A Public software package, CleaveLand3.0 was used for analyzing Degradome sequencing data.
Genome_build: MSU Release 7.0 (http://www.phytozome.net/rice.php), miRbase20.0
Supplementary_files_format_and_content: xls format and miRNAs and targets prediction results

source_name: LYP9 rice

value: Liang-You-Pei 9 (LYP9, age-sensitive rice)


title: LYP9_mixture of E, M, L (targets)

description:
Sample 14
Sample name: BS02
processed data file: Table  S4.xls

value: mixture of early,middle and late stage of grain-filling of leaves


title: LYP9-M (DGE)

description:
Sample 11
Sample name: BSB2
processed data file: Table  S6.xls


title: N2Y6-E (DGE)

description:
Sample 7
Sample name: BSA1
processed data file: Table  S6.xls

value: early stage of grain-filling


title: LYP9-L (DGE)

description:
Sample 12
Sample name: BSB3
processed data file: Table  S6.xls

value: late stage of grain-filling


title: LYP9-L (miRNA)

description:
Sample 6
Sample name: BSB3
processed data file: Table  S1.xls
processed data file: Table  S2.xls


title: N2Y6-L (DGE)

description:
Sample 9
Sample name: BSA3
processed data file: Table  S6.xls


title: N2Y6_mixture of E, M, L (targets)

description:
Sample 13
Sample name: BS01
processed data file: Table  S4.xls


title: LYP9-E (DGE)

description:
Sample 10
Sample name: BSB1
processed data file: Table  S6.xls


title: s1061_10C

description:
PolyA RNA
s1061_10C_111510-2_CATT

source_name: whole rosette, 9-leaf stage, 10C, 1061


title: LYP9-E (miRNA)

description:
Sample 4
Sample name: BSB1
processed data file: Table  S1.xls
processed data file: Table  S2.xls


title: s991_16C

description:
PolyA RNA
s991_16C_121610-9_ACGT

source_name: whole rosette, 9-leaf stage, 16C, 991


title: N2Y6-L (miRNA)

description:
Sample 3
Sample name: BSA3
processed data file: Table  S1.xls
processed data file: Table  S2.xls


title: N2Y6-M (miRNA)

description:
Sample 2
Sample name: BSA2
processed data file: Table  S1.xls
processed data file: Table  S2.xls


title: N2Y6-E (miRNA)

description:
Sample 1
Sample name: BSA1
processed data file: Table  S1.xls
processed data file: Table  S2.xls


title: SW872 D7

city: Doha

first: Andrea

last: Guennoun

address: PO Box 24144

department: Genetic Medicine

country: Qatar

institute: Weill Cornell Medical College in Qatar

data_processing:
Base calling was performed using OverviewThe Off-Line Basecaller (OTB) software
Raw reads were filtered to remove the sequence of adapter, high content of unknown bases and low quality reads
Clean reads are mapped to the human RefSeq database (ftp://ftp.ncbi.nih.gov/refseq) using SOAPaligner/SOAP2 software
Gene expression levels are calculated by using the RPKM method (Reads per kilobase transcriptome per million mapped reads) according to Mortazavi, A., B. A. Williams, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 2008.5(7): 621-8.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: files include RPKM values for each sample

source_name: human mature adipocyte

growth_protocol: All culture and differentiation media were changed every two days and cell cultures were carried out at 37 °C under 5% CO2

extract_protocol:
mRNA was extracted using the Qiagen Rneasy mini kit for lipid tissue according to manufactorer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: adipocyte

tag: passages

tag: differentiation days

tag: culture media

value: Oleic acid was added at a final concentration of 100 μM to initiate differentiation


title: EpiSC_FAIRE-Rep1

first: Matthew

last: Murtha

address: 550 First Ave

department: Microbiology

institute: NYU School of Medicine

data_processing:
Sequencing was performed using the Illumina GAIIx genome analyzer and FASTQ files were generated using CASAVA 1.8
FAIRE-seq and control genomic DNA reads were aligned to the mouse genome (mm9) using ELAND
Peak calling was performed with Qeseq using default parameters
Genome_build: mm9
Supplementary_files_format_and_content: processed data presented as bed files containing the locations of all peaks as well as wig files showing peak location and intensity.

source_name: FAIRE-seq of mEpiSC chromatin

growth_protocol: E14 Mouse embryonic stem cells (ES-E14Tg2a, ATCC #CRL-1821) were maintained on gelatin-coated tissue culture plates in N2/B27 medium (DMEMF12 (Gibco) and Neurobasal (Gibco) in a 1:1 ratio supplemented with N2 (home-made or StemCells), B27 (Invitrogen), L-glutamine and β-mercaptoethanol) containing 1uM MEK inhibitor PD032590 and 3 uM GSK3 inhibitor CH99021 (Axon Medchem BV, The Netherlands) And 10^3 U/ml LIF (Millipore). E3 Epiblast Stem cells were a gift from Boris Greber (Max Planck Institute, Muenster, Germany) and were expanded on a feeder layer of mitomycin C-treated MEFs in MEF-conditioned medium supplemented with 5ng/ml FGF2 (Peprotech). Two days prior to formaldehyde crosslinking, the expanded EpiSC cultures were enzymatically isolated from the MEF feeder layer using Dispase digestion (1mg/ml, 15 minutes) and transferred onto 15 cm fibronectin-coated plates for further feeder-free culture in MEF-conditioned medium supplemented with FGF-2. Neural Stem cells were  maintained in N2B27 medium supplemented with 10ng/ml each of FGF-2 and EGF (Peprotech). Mouse Embryo Fibroblasts were derived from E16.5 embryos and maintained in DMEM and 10% FBS.

extract_protocol:
FAIRE was performed as described (Giresi et al. 2007; Giresi and Lieb 2009) DNA fragments are prepped for sequencing using the recommended protocol except that samples are amplified prior to gel extraction. Adaptor-ligated DNA fragments amplified using PCR and ranging from 150 to 400 bp were subsequently purified from agarose gels (Qiagen Gel Extraction kit).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~150-400 bp were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: epiblast stem cells


title: NSC_FAIRE-Rep2

source_name: FAIRE-seq of mNSC chromatin

value: ES-derived neural progenitor cells


title: MEF_FAIRE-Rep1

value: embryonic fibroblasts


title: PAZ6 D0

source_name: human pre-adipocyte

value: pre-adipocyte

value: PAZ6 pre-adipocytes were cultured in DMEM/F12 medium enriched with 8% FCS, 15mM Hepes and 1% penicillin/streptomycin


title: EpiSC_FAIRE-Rep2


title: GenomicControlRep2

source_name: FAIRE-seq of sheared purified gDNA

value: sheared purified gDNA


title: NSC_FAIRE-Rep1


title: GenomicControlRep1


title: ESC_FAIRE-Rep1

source_name: FAIRE-seq of mESC chromatin

value: embryonic stem cells


title: PAZ6 D14

value: At full confluency differentiation was propagated by addition of 5% FCS, 15mM Hepes, 33 μM biotin, 17 μM panthotenat, 1nM T3, 100nM dexamethasone, 1 μM rosiglitazone and 1% pen-strep to DMEM/F12 medium. Additionally, for the initial four days 0.25 mM IBMX was added to the differentiation medium


title: SW872 D0

value: SW872 cells were cultured in DMEM/F12 medium enriched with 8% FCS, 15mM Hepes and 1% penicillin/streptomycin


title: ESC_FAIRE-Rep2


title: SGBS D28

value: SGBS

value: DMEM/F12 supplemented with transferrin (0.01 mg/ml), insulin (20nM), cortisol (100nM), and triiodothyronine (T3, 0.2 nM). For the initial four days, the differentiation medium was additionally supplemented with dexamethasone (25nM), IBMX (250 μM) and rosiglitazone (2 μM).


title: SGBS D0

value: SGBS pre-adipocytes were grown in DMEM/F12 medium supplemented with 10% fetal calf serum (FCS), 1.7 mM panthotenat, 3.3 mM biotin and 1% penicillin/streptomycin


title: SGBS D14


title: MEF_FAIRE-Rep2


title: Donor2-YAP(S127A)-biological replicate 2

city: Cincinnati

first: Alexander

last: Lange

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Reseach Foundation

data_processing:
Sequences were aligned to the reference genome with TopHat
Sample were independently processed with Cufflinks to generate an initial transcriptome.
Cuffmerge was used to merge the transcriptomes into a single reference and annotate known genes and extend partial transcripts.  This common transcriptome was used in a second pass with Cufflinks to quantify transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: Tables include raw counts and FPKM values

source_name: Human airway tissue, hYAP lentivirus

growth_protocol: A single cell suspension of passage 2 primary Human Bronchial Epithelial Cells (HBECs) that were transduced with hYAP(S127A) lentivirus or control lentivirus was grown in a 50-50 mixture of ALI medium-Cultrex BME reduced growth factor (RGF) (Trevigen Inc.) and cultures were maintained for 18-20 days.

extract_protocol:
Total RNA was isolated using a RNeasy Micro Kit (Qiagen)
Sequencing library was constructed using the Nextera XT DNA Sample Preparation Kit (Illumina)

tag: etiology

value: Non-smoker

value: human bronchiolar epithelial cells


title: Donor1-YAP(S127A)-biological replicate 1

value: Smoker


title: Donor2-Control- biological replicate 2

source_name: Human airway tissue, control lentivirus