title: OS15_MspI

status: Public on Jan 18 2015

city: Valhall

first: Jeremy

last: Rosenblum

address: 40 Sunshine Cottage Rd, Skyline Office 1N-H13

institute: New York Medical College

data_processing:
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions ELAND - 1.7.0).
Initial data processing was performed using the default read length of 37 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length, and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).
The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.
Genome_build: hg19
Supplementary_files_format_and_content: Hcount files are the result of the data processing described above.  Column 1 is the ID assignment for each HpaII/MspI site in the GRCh37/hg19 assembly of the human genome.  Columns 2 and 3 are the chromosome and position within the chromosome for each HpaII/MspI site.  Columns 4 and 5 are the counts of the HpaII tiny fragments aligned from the 27 base pairs before and after the HpaII/MspI site respectively.  Column 6 is the total number of reads aligned at a given HpaII/MspI site (Column 4 + Column 5).

source_name: Human Osteosarcoma Biopsy

extract_protocol:
Cell lysis with proteinase K and RNAse A.  DNA concentration either via ethanol precipitation or dialysis with SSC.
HELP tagging: 500 ng of genomic DNA digested with either MspI or HpaII.  Custom Illumina adapter also containing an EcoP15I restriction site and a T7 transcription promoter was ligated to both ends.  Following digestion with EcoP15I, end repair, and dA tailing a second Illumina adapter containing the Illumina sequencing primer, which also contains the multiplex barcode was added.  After transcription, reverse transcription, and PCR, the libraries were gel extracted and sequenced.

value: Osteosarcoma tumor

tag: response to neoadjuvant chemotherapy

value: Good

tag: 5 year efs

value: Relapse

tag: 5 year os

value: Alive

tag: metastasis

value: No

tag: dna concentration method

value: Dialysis


title: OS14_MspI

type: SRA

state: NY

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: gender

value: Female

value: No Relapse

value: Yes

value: Ethanol precipitation


title: H1047R 12hr rep1

status: Public on Jan 19 2015

city: La Jolla

first: Jonathan

middle: Ross

last: Hart

state: CA

address: 10550 North Torrey Pines Road, BCC239

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

description: Breast Epithelial cell line

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version v1.8.2
Trimmed reads with fastx_quality_trimmer 0.0.13 with a quality treshhold of 18 and a length of 20
Aligned with Bowtie 2.1.0 and Tophat 2.0.10 using Gencode v19 junctions
Samtools 0.1.19-44428cd to make a bam, sort, index
Raw counts were generated using htseq_count 0.6.1 using the UCSC HG19 known gene transcripts from Illumina iGenomes
edgeR 3.2.4 in R 3.1.0 were used to normalize counts between samples and to make comparisons between groups.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized reads in CPM for each detected gene along with differential gene expression log2 (fold change) and p-values for each time point

molecule: total RNA

source_name: H1047R 12hr rep1

growth_protocol: 500k Cells were seeded in 10cm petri dishes in DMEM/F12 growth medium.  After 24 hours, medium was changed to MCDB-170 serum free media.  Cells were allowed to grow an additional 24 hours.  Medium was changed once more and cells harvested at 0, 6, 12, 24 hours post medium exchange.

extract_protocol:
Total RNA was extracted using Trizol following standard protocol.  1mL Trizol was added directly to cells, RNA was separated from protein and DNA using 200uL chloroform.  Aqueous layer was removed and total RNA was precipitated using 500uL isopropanol precipitation.    This precipitate was redissolved and precipitated with 250uL DEPC treated water folled by 750uL anhydrous ethanol.  Pellet was redissolved in 200uL DEPC treated water. Residual DNA was eliminated using Ambion Dneasy kits.
Nugen Ovation protocol

treatment_protocol: No drug treatments

tag: cell line

tag: time


title: OS13_MspI

value: Male

value: Dead


title: OS13_HpaII


title: OS12_MspI

value: Poor


title: OS10_HpaII


title: OS9_HpaII


title: OS15_HpaII


title: OS9_MspI


title: OS8_HpaII


title: OS12_HpaII


title: OS8_MspI


title: OS7_HpaII


title: OS10_MspI


title: OS4_MspI


title: OS5_HpaII


title: OS6_MspI


title: OS4_HpaII


title: OS3_HpaII


title: OS3_MspI


title: OS5_MspI


title: OS11_HpaII


title: OS11_MspI


title: OS2_HpaII


title: OS14_HpaII


title: OS1_MspI


title: OS2_MspI


title: OS1_HpaII


title: JT_18_RNA-seq

city: Los Angeles

first: John

last: Tower

state: California

address: 1020 Childs Way, RRI213

department: Biological Sciences

institute: University of Southern California

description: processed data file: males_gene_exp.diff

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data was trimmed using Trimmomatic.
Differential expression was estimated using Tophat and Cufflinks following Trapnell et al. 2012. Nature Protoc 7:562-78
Genome_build: Ensembl BDGP5.25
Supplementary_files_format_and_content: Cuffdiff output, normalized expression values

organism: Drosophila melanogaster

growth_protocol: Males of strain w[1118]; p53B[6] were crossed to virgins of w[1118]; rtTA(3)E2 and progeny males and virgins were collected over 48 hours.  One half of the virgins were mated to w[1118] males at ratio of 1:1 virgins to males for 4 days.  Mated females were then separated from the w[1118] males.

extract_protocol:
Total fly RNA was isolated from 20 animals per sample using Trizol reagent and purified using Qiagen RNAeasy kit.
Sequencing libraries were prepared from total RNA using the KAPA Stranded RNA-Seq Library Preparation Kit for Illumina platforms (KAPA Biosystems). Isolation of mRNA was done using the Dynabeads® mRNA purification kit (Invitrogen Dynal AS, Oslo, Norway), following the Appendix A in the KAPA kit protocol. All 18 libraries were indexed using standard Illumina TruSeq indexes, and sequenced altogether in one lane of a high-output paired-end 100 bp run using an Illumina HiSeq 2500. A second high-output paired-end 100 bp run of all 18 libraries was performed to increase coverage. The library preparation and the sequencing were done at the UPC Genome Core facility at the University of Southern California (Los Angeles, CA).

treatment_protocol: The mated females, males and virgins females were then maintained at approximately 20 flies per vial, on food with and without supplementation with 160ug/ml mifepristone for 12 days.

tag: strain background

value: male w[1118]; p53B[6] crossed to virginw[1118]; rtTA(3)E2

tag: strain/sex

value: progeny male

tag: mating status

value: males

tag: treated with

value: 160ug/ml mifepristone for 12 days

value: whole animal


title: JT_17_RNA-seq


title: JT_16_RNA-seq


title: JT_15_RNA-seq

value: none (control)


title: JT_14_RNA-seq


title: OS6_HpaII

value: Osteosarcoma tumor

value: Good


title: JT_12_RNA-seq

description: processed data file: mated_gene_exp.diff

source_name: mated females_mifepristone

value: progeny virgin

value: mated females


title: JT_13_RNA-seq


title: JT_6_RNA-seq

description: processed data file: virgin_gene_exp.diff

source_name: virgin females_mifepristone

value: virgin females


title: JT_9_RNA-seq

source_name: mated females_control


title: JT_11_RNA-seq


title: JT_10_RNA-seq


title: JT_7_RNA-seq


title: JT_4_RNA-seq


title: JT_5_RNA-seq


title: JT_8_RNA-seq


title: JT_3_RNA-seq

source_name: virgin females_control


title: JT_1_RNA-seq


title: sample4a

status: Public on Jan 16 2015

city: West Lafayette

first: Stephen

middle: R

last: Lindemann

state: IN

address: 745 Agriculture Mall Drive

department: Food Sciences

institute: Purdue University

description: rRNA depleted

data_processing:
Measurement of gene expression was performed in RNA-Seq experiments conducted across the two conditions of normal oxygen (20% O2, normal aerobic) and low oxygen (8.5% O2, anoxic). Three technical replicates were done for sample1 (aerobic) and three for sample4 (anoxic), for a total of six RNA-Seq runs on a Life Technologies SOLiD 4 sequencer, following rRNA depletion. Runs were performed on two additional anoxic samples (sample5 and sample6) with separate library preparations as technical duplicates and with rRNA depletion (four runs total). Two additional aerobic samples (sample2 and sample3) were each run four times, twice after rRNA depletion, and twice using total RNA (eight runs total). These 12 additional runs were performed on a SOLiD 5500xl sequencer. The 50-base short read sequences produced by the SOLiD 4 sequencer were mapped in color space using the Life Technologies BioScope software version 1.3. The 75-base reads produced by the SOLiD 5500xl sequencer were similarly mapped using the Life Technologies LifeScope software version 2.5, using the same reference genome (The reference genome and called genes are from Shewanella oneidensis strain MR-1 (RefSeq Assembly ID GCF_000146165.2). ). The default settings were used in the Life Technologies BioScope and LifeScope software.
Filtering: For sample1 and sample4, BioScope was given a filtering file that included 28 rRNA sequences for Shewanella oneidensis, in addition to the adapter and bar code sequences. This file was used filter out reads that mapped to such sequences, before mapping the remaining short reads to the reference genome (The reference genome and called genes are from Shewanella oneidensis strain MR-1 (RefSeq Assembly ID GCF_000146165.2). ). LifeScope was given the same filter file to use in the second set of SOLiD 5500xl RNA-Seq runs that employed total RNA. For those SOLiD 5500xl runs done after rRNA depletion, a simpler filter file consisting of only adapter and bar code sequences was employed.
Genome_build: ASM14616v2
Supplementary_files_format_and_content: tab-delimited gene rollup text files listing the gene counts, and (for LifeScope output) listing RPKM values, for each sample

organism: Shewanella oneidensis MR-1

source_name: 8.5% oxygen, chemostat culture of S. oneidensis MR-1

growth_protocol: A 15-liter New Brunswick Bioflow 3000 reactor operated at a 7 liter working volume at 30 1C was used to grow chemostat cultures of S. oneidensis MR-1 in modified M1 media supplemented with 18 mM lactate. The gas flow rate and agitation were kept at 3.5 L min 1 and 350 rpm, respectively, and the dissolved oxygen tension (DOT) was maintained at 20% or 8.5% by automatically changing the ratio of N2 and air in the gas mix. The  pH was maintained at 7.0.Culture growth was constantly monitored by measuring and recording optical density. Continuous cultures were started by pumping medium of the same composition at desired dilution rate. Samples for further analysis were taken after at least five volume changes at steady-state conditions.

extract_protocol:
The RNA was extracted using Invitrogen TRIzols reagent followed by genomic DNA removal and clean up using Qiagen RNase-Free DNase Set kit and Qiagen Mini RNeasyt kit. The Agilent 2100 Bioanalyzer was used to assess the integrity of the RNA samples.
For rRNA depleted samples, Invitrogen’s RiboMinusTM Eukaryote kit for RNA-Seq and bacterial probe from Invitrogen’s RiboMinus TM Transcriptome Isolation Kit (Bacteria) were used to remove the 16s and 23s rRNA. The SOLiD Total RNA-Seq Kit was used to construct template cDNA for RNA-Seq and this was performed accordingly to the protocol recommended by Applied Biosystems. The mRNA was fragmented using chemical hydrolysis followed by ligation with strand-specific adapters and reverse transcribed to generate cDNA. Fragments of cDNA between 150 to 250 bp were subsequently isolated by electrophoresis in 6% urea-TBE acrylamide gel. The gel-isolated cDNA went through 15 cycles of amplification to produce enough templates for the SOLiD TM EZ Bead TM system to generate template bead library for ligation base sequencing on the SOLiD TM instruments.

tag: culture

value: steady state in chemostat

tag: oxygen level


title: JT_2_RNA-seq


title: sample1c

description: rRNA depleted

source_name: 20% oxygen, chemostat culture of S. oneidensis MR-1


title: sample4c

description: rRNA depleted


title: Zfp407 siRNA #2 Sample 1

city: Cleveland

first: David

last: Buchner

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Reads were aligned to the mouse genome using TopHat v2.0.5, SamTools v0.1.18.0, and Bowtie2 v2.0.0.7
Gene expression was analyzed using Cufflinks v2.0.2
Genome_build: Ensembl m38.69, GenBank Assembly ID GCA_000001635.2
Supplementary_files_format_and_content: excel file containing all FPKM values for each sample

organism: Mus musculus

source_name: Adipocyte cell line

extract_protocol:
RNA was collected using the QIAshredder and the RNeasy mini kit (Qiagen, Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Differentiated 3T3-L1 adipocytes were electroporated with 0.75 nmol siRNAs per ~1.5x107 cells  2 days after differentiation

tag: cell type

value: 3T3-L1 cells


title: Zfp407 siRNA #2 Sample 2


title: sample1b

description: rRNA depleted


title: Zfp407 siRNA #2 Sample 3


title: Zfp407 siRNA #1 Sample 2


title: sample4b

description: rRNA depleted


title: Zfp407 siRNA #1 Sample 3


title: Zfp407 siRNA #1 Sample 1


title: sample1a

description: rRNA depleted


title: Control siRNA Sample 6


title: Control siRNA Sample 4


title: Control siRNA Sample 5


title: Control siRNA Sample 3


title: Control siRNA Sample 1


title: QC-Y-27

city: Badalona

first: Miguel

middle: A

last: Peinado

state: Barcelona

address: Ctra. de Can Ruti, camí de les escoles, s/n

country: Spain

institute: IGTP

description:
AIMS-Seq
SmaI/XmaI digested DNA ampified after adaptors ligation
Whole tissue

data_processing:
Data filtering; The global low quality reads were filtered out and the 5’ or 3’ end of the remaining reads were trimmed according to the quality.
Adaptor trimming
Read alignment softweare: Bowtie alignment program (v0.11.3)
Data filtering; only reads mapping uniquely inside amplicons between 20 and 2,000 base pairs were considered for further analysis.
Normalization:Mapped reads of each sample were normalized using total-sum scaling method and respect the sample with the lowest number of mapped reads
Differential methylation comparisons between samples were done with the amplicons with at least one read in at least one sample using the DESeq R package.
Genome_build: mm9

source_name: Skeletal muscle 1

growth_protocol: Primary myoblast were cultured in growth medium (GM: Ham’s F-10 plus 20% FBS, 5 ng/ml bFGF, 100 U/ml penicillin and 100 µg/ml streptomycin) on 100 mg Collagen I rat tail (Becton and Dickinson) coated tissue culture dishes

extract_protocol:
Differential methylation libraries were generated using a next generation sequencing adaptation of the Amplification of Inter-Methylated Sites (AIMS). AIMS-seq is a methyl-sensitive restriction enzyme based approach that combines the consecutive use of two neoisoschizomer enzymes, SmaI and XmaI, which recognize the same cleavage site (5’-CCCGGG-3’) but present different methylation sensitivities and generate distinct end-fragments: SmaI digests unmethylated DNA leaving blunted ends, whereas XmaI digests DNA regardless methylation state and generates cohesive ends. Genomic DNA was extracted with a standard phenol-chloroform protocol.Following 1 microgram genomic DNA digestion with both enzymes (SmaI from Roche, 6 hours digestion at 25ºC; XmaI from NEB, 6 hours digestion at 37ºC), cohesive adaptors were ligated specifically to XmaI products (5’CCGGTCAGAGCTTTGCGAAT and 5’CCGAATTCGCAAAGCTCTGA were the adaptor sequences), allowing the amplification of intermethylated fragments by conventional PCR
The amplified products were next-gen sequenced using Illumina GA2 platform at the Genomics Unit of Center for Genomic Regulation (Barcelona-Spain), and the high quality reads were mapped to the mm9 mouse genome

treatment_protocol: To induce myotube formation, confluent proliferating primary myoblasts were grown on matrigel coated culture dishes (Basement Membrane Matrix, Becton and Dickinson) and switched to differentiation medium next day (DM: DMEM plus 2% horse serum, 100 U/ml penicillin and100 µg/ml streptomycin (Life technologies)) for 1,2 and 4 days.

tag: genotype

value: male

value: skeletal muscle


title: Qc-BL6

source_name: Skeletal muscle 3


title: ScQ

description:
AIMS-Seq
SmaI/XmaI digested DNA ampified after adaptors ligation
Muscle precursor cells not cultured, freshly isolated

source_name: Primary myoblasts passage zero freshly isolated

value: primary myoblast


title: QC-Y40

source_name: Skeletal muscle 2


title: SC26-AP

description:
AIMS-Seq
SmaI/XmaI digested DNA ampified after adaptors ligation
Muscle precursor cells in proliferation conditions at passage 0

source_name: Primary myoblasts passage zero replicate 1


title: ScA

description:
AIMS-Seq
SmaI/XmaI digested DNA ampified after adaptors ligation
Muscle precursor cells not cultured, freshly isolated  3 days post CTX injury

source_name: Primary myoblasts passage zero freshly isolated after injury


title: MPC26-D2

description:
AIMS-Seq
SmaI/XmaI digested DNA ampified after adaptors ligation
Muscle precursor cells in differentiation conditions at day 2

source_name: Primary myotubes differentiatd for 2 days replicate 3

value: primary myotube


title: OS7_MspI

value: Female

tag: response to neoadjuvant chemotherapy

value: No Relapse

value: Alive

value: No

value: Dialysis


title: MPC26-D4

description:
AIMS-Seq
SmaI/XmaI digested DNA ampified after adaptors ligation
Muscle precursor cells in differentiation conditions at day 4

source_name: Primary myotubes differentiatd for 4 days replicate 3


title: MPC26-D1

description:
AIMS-Seq
SmaI/XmaI digested DNA ampified after adaptors ligation
Muscle precursor cells in differentiation conditions at day 1

source_name: Primary myotubes differentiatd for 1 day replicate 3


title: MPC27-D1

source_name: Primary myotubes differentiatd for 1 day replicate 2


title: MPC26-P

description:
AIMS-Seq
SmaI/XmaI digested DNA ampified after adaptors ligation
Muscle precursor cells in proliferation conditions at passage 8-10

source_name: Primary myoblasts in proliferation replicate 3


title: MPC_wt_21_D4

source_name: Primary myotubes differentiatd for 4 days replicate 1


title: sample6b

description: rRNA depleted


title: sample6a

description: rRNA depleted


title: MPC27-D2

source_name: Primary myotubes differentiatd for 2 days replicate 2


title: MPC27-P

source_name: Primary myoblasts in proliferation replicate 2


title: MPC_wt_21_D1

source_name: Primary myotubes differentiatd for 1 day replicate 1


title: sample5a

description: rRNA depleted

source_name: 8.5% oxygen, chemostat culture of S. oneidensis MR-1


title: MPC_wt_21_P

source_name: Primary myoblasts in proliferation replicate 1


title: MPC27-D4

source_name: Primary myotubes differentiatd for 4 days replicate 2


title: sample5b

description: rRNA depleted


title: Control siRNA Sample 2

source_name: Adipocyte cell line


title: SC27-AP

source_name: Primary myoblasts passage zero replicate 2


title: RD1

description:
AIMS-Seq
SmaI/XmaI digested DNA ampified after adaptors ligation
Embryonic stem cell line

source_name: Embryonic stem cell line replicate 2

value: embryonic cell line


title: E14Tg2

source_name: Embryonic stem cell line replicate 3


title: sample3c

description: total RNA

source_name: 20% oxygen, chemostat culture of S. oneidensis MR-1


title: CGR8_r2

source_name: Embryonic stem cell line technical replicate 1


title: sample3b

description: rRNA depleted


title: sample3a

description: rRNA depleted


title: Adult

city: Shanghai

first: Yun

last: Bai

state: Shanghai

address: Building 10#, No 1278, Baode Road

department: Central Laboratory

country: China

institute: Shanghai Skin Disease Hospital

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequences using miRExpress, and removed duplicated sequences, then mapped to E granulosus genome sequences using bowtie v0.12.5 with parameters -f -n 0 -e 80 -l 18 -a -m 5 --best --strata
New miRNAs were predicted using an improved version of the miRDeep software (miRDeep 2.0), and the read counts were calculated using the quantifier module of miRDeep2.
Genome_build: E. granulosus genome (APAU00000000) in GeneBank
Supplementary_files_format_and_content: Sequence count file, small RNAs ranging from 18-30 nucleotides

organism: Echinococcus granulosus

source_name: Adult worm

extract_protocol:
Samples of the 3 different life cycle stages of E. granulosus were homogenized in lysis buffer and total RNA was extracted using mirVana miRNA isolation kits (Ambion, Austin, TX, USA)
We constructed each small RNA library using Illumina Small RNA v1.5 Sample Preparation Kits (Illumina, San Diego, CA). Briefly, total RNA (5µg) of each sample was resolved on denaturing polyacrylamide gel electrophoresis (PAGE) gels, and then fractions of 18 to 30 nt in size were collected. The isolated small RNAs were sequentially ligated to 3ˈadapters, using T4 RNA ligase 2 (New England Biolabs, Ipswich, MA, USA), and 5ˈadapters using T4 RNA ligase (New England Biolabs, Ipswich, MA, USA). The ligation products were reverse transcribed using SuperScript Reverse Transcriptase II (Life Technologies, Gaithersburg, MD, USA) and amplified with 12 PCR cycles. Then, 6% (w/v) PAGE was used to purify the amplification products.

tag: developmental stage

value: Adult


title: CGR8_r1

source_name: Embryonic stem cell line replicate 1


title: Oshsfa2e-WW-2

city: Fayetteville

first: Andy

last: Pereira

state: AR

address: 115 Plant Science Building,

department: Crop, Soil and Environmental Sciences (CSES)

institute: University of Arkansas,

data_processing:
Trapnell et. al, Nature Protocols 7, 562–578 (2012) pipeline was used for analyses. The reads were Mapped with tophat v2.05 on MSU rice genome v7 information
Transcript Assembly was done with cufflinksv2.0.2
Transcript merge with cuffmerge
Cuffdiff used for Differencial expression
Genome_build: MSU rice genome v7 information
Supplementary_files_format_and_content: Cuffdiff output gene_exp.exp file was used for further analyses

organism: Oryza sativa Japonica Group

source_name: Leaf tissue

growth_protocol: Rice plants were grown in the greenhouse conditions with 26o C ± 1 day /22o C ± 1 night temperature, 600 mmol/m2/s light intensity and 14 h light and 10 h dark cycles. All pots, filled with Redi-earth potting mix (Sun Gro Horticulture Distribution Inc., Bellevue, WA, USA), were placed in water-filled trays to simulate flooded condition and fertilized every week with 24-8-16 Miracle-Gro (Scotts Miracle-Gro Products, Inc., Marysville, OH, USA) until used for the experiment.

extract_protocol:
Total RNA was isolated using TRIZol reagent (Invitrogen) following the manufacturer's instructions. Total RNA was treated with RNase-free DNase I (Promega) and passed through RNeasy spin columns (Qiagen) to remove DNA and other contaminants. The concentration, quality and integrity of the RNA were analysed using the Agilent 2100 bioanalyzer (Bio-Rad) and NanoDrop™ ND-1000 (Thermo Scientific). Samples with RNA Quality Indicator (RQI) of > 8.0 were used for RNA-sequencing.
Libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Plant kit according to Illumina's instructions accompanying the Kit
TruSeq Stranded Total RNA with Ribo-Zero

treatment_protocol: Controlled drought stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Well-watered plants were maintained at 100% FC.

value: OsHSFA2e loss-of-function

tag: cultivar

value: Nipponbare

value: leaf

tag: treatment

value: control


title: Germ

source_name: Germ layer

value: Germ


title: MPC_wt_21_D2

source_name: Primary myotubes differentiatd for 2 days replicate 1


title: sample2d

description: total RNA

value: steady state in chemostat


title: Oshsfa2e-WW-1


title: Oshsfa2e-DR-2

value: drought


title: Northern_Rep3

city: Jinan

first: Liu

last: Dasheng

state: Shandong

address: Lishan Lu 50

institute: Shandong Institute of Environmental Science

data_processing:
Raw sequence reads were checked for quality using the FastQC0.10.0 program and quality trimmed using the Sickle-quality-base-triming program in the iPlant discovery environment with the parameters minimum quality = 20 and minimum number of bases = 70.
The trimmed reads from each end for all six samples (from both populations) were concatenated and the two files (one from each paired end) were kmer normalized using the Trinity_normalize_by_kmer_coverage (Grabherr et al. 2011) in the iPlant DE with parameters of 30 reads per kmer. The resulting two files were assembled using the program Trinity (Robertson et al. 2011) in the iPlant DE using the default parameters. The assembled contigs were checked for quality by assessing contig length and coverage and for completeness using the program CEGMA (Parra et al. 2007) in the iPlant DE.
The program Bowtie (Langmead et al., 2009) was used to map thetrimmed reads from the individual samples back to the Trinity assembled reference contig file. Likewise, the reads were also mapped separately to the Trinity assembled reference files for both the central and northern populations accordingly. Differential expression analysis was accomplished using the program RSEM (Li and Dewey 2011) with the program EBseq to identify differentially expressed genes (Leng et al. 2013). Programs were run on the iPlant Atmosphere resource using an Ubuntu 12.04.5 - iPlant Base interface
Genome_build: Trinity assembled contig database
Supplementary_files_format_and_content: The differentially expressed genes and contigs were additionally annotated by BlastX against the non-redundant database using the Blast 2.26 stand-alone program (McGinnis and Madden 2004).
Supplementary_files_format_and_content: : Expression values are normalized Transcripts Per Million based on RSEM mapping to componants (not contigs which is why the expression values are identical for all contigs represented by a given componant) and EBseq normalization of trimmed reads mapped to the trinity-assembled transcriptome using Bowtie1.
Supplementary_files_format_and_content: : Raw reads were trimmed using Sickle-quality-base-trimming in iPlant with a minimum quality score or 20 and a minimum length of 70. Trimmed reads from each paired end of the six samples were combined and kmer reduced to a maximum of 30 kmers using Trinity normalize_by_kmer_coverage. The resulting two files (one for each paired end) were assembled using Trinity in the iplant discovery environment using the default parameters.

organism: Alternanthera philoxeroides

source_name: The top 2-3 leaf pairs per individual

growth_protocol: Plants were collected from the wild from rivers either near Shanghai or Jinan in November of 2013 and established in a common garden plot of greenhouse in Jinan, Shandong,China. Plants were grown in the 67×43×7 cm pots containing potting soil and watered every 2-3 days with 50% concentration Hoagland’s solution. Plants were allowed to grow in the greenhouse with night and day temperatures of 16-31C respectively under natural light condition and photoperiod for 4 weeks prior to treatment.

extract_protocol:
tissue collection: top 2-3 leaves were excised between 10:00 am-12:00 am and immediately frozen in liquid nitrogen for future RNA extraction and sequencing library construction.
RNA extraction was performed by grinding approximately 0.1 grams of frozen tissue in liquid nitrogen to a fine powder, and adding 1 ml Trizol reagent (Ambion/Life Technologies). Chloroform:Isoamyl (24:1) was added to the Trizol/tissue mixture, centrifuged, and RNA was extracted from the resulting supernatant using an RNeasy Plant Mini kit (Qiagen). Quality control was assessed using a nanodrop bioanalyzer on the RNA setting.
Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Plants were first subjected to 2 day of interim temperatures (11-19C night/day), and then were subjected to 2 week of cold temperatures (daytime 6-13 C, nighttime 4-9 C) with natural light condition and photoperiod.

value: wild

tag: location

value: Jinan

tag: normal growing conditions in the wild

value: The average annual temperature in Jinan is 14.7 C with an average of -0.4 C in January and 27.5 C in July.


title: sample3d

description: total RNA


title: sample2c

description: total RNA


title: WT-WW-2 (OsHSFA2e control)

value: wild type

tag: tissue


title: Mouse siRNA EPAS1 knockdown rep2

city: New York

first: Seungyeul

last: Yoo

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequence reads are mapped and aligned to human (hg19) and mouse (mm10) genome assembly for HUVEC and C166, respectively, and then quantified in terms of FPKM using Cufflinks.
Genome_build: hg19 for HUVEC and mm10 for C166
Supplementary_files_format_and_content: tab-delimited text file including FPKM values of each gene for each Sample

source_name: Endothelial

growth_protocol: The cell lines of HUVEC (Lonza, MD, USA) and C166 (American Type Culture Collection, VA, USA) were cultured in the appropriate media at 37°C with 5% CO2. The cells were transfected with EPAS1 siRNA and non-targeting negative control siRNA (Life Technologies, CA, USA) using Lipofectamine RNAiMAX as recommended transfection protocols by the manufacturer.

extract_protocol:
After the treatments with 5nM Silencer® Select siRNA (s4700 for EPAS1, s65525 for Epas1; Life Technologies, USA) for 48 hours, the total RNA was purified with RNeasy Mini Kit (QIAGEN, Germany). The efficiencies of knocked down the EPAS1 expression were assessed by qPCR with 1.4% for HUVEC, 3.2% for C166.
Approximately 250 ng of total RNA per sample were used for library construction by the TruSeq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument with 100nt single read setting according to the manufacturer's instructions.

tag: cell line

value: siRNA EPAS1 knockdown

value: Yolk sac


title: Mouse siRNA EPAS1 knockdown rep3


title: sample2b

description: rRNA depleted


title: Northern_Rep1

growth_protocol: Plants were collected from the wild from rivers either near Shanghai or Jinan in November of 2013 and established in a common garden plot of greenhouse in Jinan,Shandong,China. Plants were grown in the 67×43×7 cm pots containing potting soil and watered every 2-3 days with 50% concentration Hoagland’s solution. Plants were allowed to grow in the greenhouse with night and day temperatures of 16-31C respectively under natural light condition and photoperiod for 4 weeks prior to treatment.

extract_protocol:
tissue collection: top 2-3 leaf pairs were excised between 10:00 am-12:00 pm and immediately frozen in liquid nitrogen for future RNA extraction and sequencing library construction.
RNA extraction was performed by grinding approximately 0.1 grams of frozen tissue in liquid nitrogen to a fine powder, and adding 1 ml Trizol reagent (Ambion/Life Technologies). Chloroform:Isoamyl (24:1) was added to the Trizol/tissue mixture, centrifuged, and RNA was extracted from the resulting supernatant using an RNeasy Plant Mini kit (Qiagen). Quality control was assessed using a nanodrop bioanalyzer on the RNA setting.
Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: Mouse siRNA EPAS1 knockdown rep1


title: central_Rep3

value: Shanghai

value: The average annual temperature in Shanghai is 16.6 C with an average of 4.7 C in January and 28.0 C in July.


title: Northern_Rep2

extract_protocol:
tissue collection: top 2-3 leaf pairs were excised between 10:00 am-12:00 am and immediately frozen in liquid nitrogen for future RNA extraction and sequencing library construction.
RNA extraction was performed by grinding approximately 0.1 grams of frozen tissue in liquid nitrogen to a fine powder, and adding 1 ml Trizol reagent (Ambion/Life Technologies). Chloroform:Isoamyl (24:1) was added to the Trizol/tissue mixture, centrifuged, and RNA was extracted from the resulting supernatant using an RNeasy Plant Mini kit (Qiagen). Quality control was assessed using a nanodrop bioanalyzer on the RNA setting.
Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.


title: Mouse siRNA control rep3

value: siRNA control


title: PSC

source_name: Protoscolex

value: PSC


title: central_Rep2

growth_protocol: Plants were collected from the wild from rivers either near Shanghai or Jinan in November of 2013 and established in a common garden plot of greenhouse in Jinan, Shandong, China. Plants were grown in the 67×43×7 cm pots containing potting soil and watered every 2-3 days with 50% concentration Hoagland’s solution. Plants were allowed to grow in the greenhouse with night and day temperatures of 16-31C respectively under natural light condition and photoperiod for 4 weeks prior to treatment.


title: Mouse siRNA control rep2


title: WT-DR-2 (OsHSFA2e control)


title: central_Rep1


title: Mouse siRNA control rep1


title: Osbhlh148-WW-2

value: OsbHLH148 loss-of-function

value: Vegetative stage


title: Oshsfa2e-DR-1

value: OsHSFA2e loss-of-function

value: Nipponbare

value: leaf


title: Human endothelial siRNA EPAS1 knockdown rep2

value: HUVEC

value: umbilical vein/vascular endothelium


title: Osbhlh148-DR-1

value: drought


title: Human endothelial siRNA EPAS1 knockdown rep3


title: HelaS3_GRO-seq

city: Berlin-Buch

first: Scott

middle: Allen

last: Lacadie

address: Robert-Rössle-Str. 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: run-on RNA

data_processing:
Two replicates of 5’end sequenced reads from the 5’-GRO-seq or traditional GRO-seq protocols were trimmed for adapters using cutadapt (Martin, 2011)  and mapped together to the hg19 human genome using Bowtie2 with default settings (Langmead and Salzberg, 2012). Reads that did not map uniquely and reads overlapping rRNA loci were removed
bedGraph signal files were generated for 5'-GRO-seq and GRO-seq by counting the number of read 5'ends that aligned to a given genomic coordinate, and then separating into two files by strand
5'-GRO-seq clusters were identified according to the strategy  described in Ni et al. (Ni et al., 2010).  Briefly, a kernel density estimate (KDE) of the 5’ end positions of the mapped reads was calculated across the genome.  Any region exceeding the genome-wide average KDE that contained at least 10 reads was identified as a cluster and used in subsequent analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files are split by strand and scores represent the number of read 5'ends that aligned at that coordinate. .bed cluster file represent 5'-GRO-seq peak coordinates where column 3 is a unique identifier and column 4 is the coordinate of the position in the cluster containing the most reads (cluster mode)

extract_protocol:
5’GRO-seq was performed as described previously (Lam et al., 2013). 10^7 HeLa S3 nuclei were used for run-on with BrU-labelled NTPs. Fragmented transcripts were incubated with polynucleotide kinase (PNK, NEB) to remove 3’ phosphates. BrU-labelled nascent transcripts were subsequently immunoprecipitated with anti-BrdU agarose beads (Santa Cruz Biotech).
For 5’GRO-seq, immunoprecipitated RNA was dephosphorylated with calf intestinal phosphatase (NEB). Then 5′ capped fragments were de-capped with tobacco acid pyrophosphatase (Epicentre). Illumina TruSeq adapters were ligated to the RNA 3′ and 5′ ends with truncated mutant RNA ligase 2 (K227Q) and RNA ligase 1 (NEB), respectively. Reverse transcription was performed with Superscript III (Invitrogen) followed by PCR amplification for 12 cycles. Final libraries were size selected on PAGE/TBE gels to 175–225 bp. GRO-seq was essentially performed as 5’GRO-seq but the immunoprecipitated RNA was directly de-capped with tobacco acid pyrophosphatase (Epicentre) and subsequently kinased with PNK (NEB) prior to adapter ligation.


title: HelaS3_5'-GRO-seq

description: run-on RNA


title: Osbhlh148-WW-1

value: control


title: Osbhlh148-DR-2


title: Human endothelial siRNA control rep3


title: WT-DR-2 (OsbHLH148  control)


title: Human endothelial siRNA control rep2


title: Human endothelial siRNA EPAS1 knockdown rep1


title: WT-WW-1 (OsbHLH148  control)


title: WT-WW-2 (OsbHLH148  control)


title: WT-WW-1 (OsHSFA2e control)


title: Col-0_flg22-6h

city: Paris

first: Emmanuelle

last: Lastrucci

address: 46 rue d'Ulm

country: France

institute: Institut de Biologie de l’Ecole Normale Supérieure

description: Poly A transcript profiling.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence («AGATCGGAAGAGCGGTTCAG» ) and mapped to the TAIR10 version of the A. thaliana genome using Bowtie (2 mismatches allowed).
The reads were normalized in reads per million.
Genome_build: TAIR10
Supplementary_files_format_and_content: all_unnormalized_count_flg22_water.txt: tab-delimited text file with unnormalized counts for the flg22 treated (T) and mock (N) conditions.

organism: Arabidopsis thaliana

source_name: 5-week-old leaves, flg22, 6h

extract_protocol:
Total RNA was extracted using the RNeasy Plant mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Syringe infiltrated with either water or flg22 at 1-μM concentration for 6h.

tag: ecotype

tag: age

value: 5 weeks

value: leaves

value: flg22 for 6h


title: WT-WW-2


title: TF-1 ZRSR2 shRNA2 experiment 2

status: Public on Jan 15 2015

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Mapped the sequenced reads to the reference transcript in the database obtained from Refseq, Ensemble and UCSC known genes using bowtie.
Unmapped or poorly mapped reads were realigned to human reference genome (hg19) with the Blat software.
The mapped reads were organized into five different libraries 1) exon read library, 2) intron read library, 3) exon-intron junction read library, 4) exon-exon junction read library, and 5) intergenic read library. The gene classification was done using all known Refseq transcripts.
Differential splicing analysis.
Classification of introns.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized bigwig for each sample

source_name: TF-1 cell line

extract_protocol:
cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina). 1 μg of total RNA was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease

value: erythroleukemia

tag: gender

value: Male


title: WT-WW-1


title: Human endothelial siRNA control rep1


title: untreated

city: ChiaYi

first: Chin

last: Li

address: 168 University Road, Minhsiung

department: Life Science

country: Taiwan

institute: National Chung Cheng University

data_processing:
Basecalls performed using CASAVA version 1.7
The adaptor sequences were removed and data were Q20 filtered
RPKM was calculated using CLC genomic workbench 3.0
Filtered data was also aligned to database using Tophat 1.2 with parameters set to default
Genome_build: hg19

source_name: HeLa/TO-SmN untreated

growth_protocol: HeLa/TO-SmN was grown in DMEM medium with tetracycline-free 10% FBS

extract_protocol:
Total RNA was extracted by TRIZOL reagent
Libraries were prepared using TruSeq Stranded Total Sample Preparation kit (Illumina, RS-122-2201). The standard protocol was followed.

treatment_protocol: Expression of SmN was induced by 10 ng/ml doxycycline.

value: HeLa


title: WT-DR-1


title: TF-1 control shRNA experiment 2


title: TF-1 ZRSR2 shRNA1 experiment 2


title: doxycycline treated

source_name: HeLa/TO-SmN doxycycline treated


title: WT-DR-1 (OsbHLH148  control)

value: wild type


title: WT-DR-1 (OsHSFA2e control)


title: TF-1 control shRNA experiment 1


title: TF-1 ZRSR2 shRNA2 experiment 1


title: WT-DR-2


title: Normal bone marrow 2

source_name: bone marrow

value: normal


title: Normal bone marrow 4


title: ZRSR2 wild type MDS 4

value: myelodysplastic syndrome (MDS)


title: ZRSR2 wild type MDS 2


title: ZRSR2 wild type MDS 3

value: Female


title: TF-1 ZRSR2 shRNA1 experiment 1


title: ZRSR2 wild type MDS 1


title: Normal bone marrow 1


title: Col-0_water-6h

description: Poly A transcript profiling.

source_name: 5-week-old leaves, water, 6h

value: water for 6h


title: ZRSR2 mutant MDS 6


title: ZRSR2 mutant MDS 4


title: ZRSR2 mutant MDS 5


title: Normal bone marrow 3


title: ZRSR2 mutant MDS 3


title: ZRSR2 mutant MDS 1


title: PBB17_input

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
Sequencing tags from FAIRE- and ChIP-Seq were aligned to the reference genome (build GRCh37/hg19) with Novoalign
MACS was used to identify FAIRE or ChIP peaks by comparison of matched treatment to input samples using the following changes to the default settings: --nomodel --shiftsize=150 (ChIP-Seq), --nomodel --shiftsize=50 (FAIRE-Seq)
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using MACS and converted to bigWig

source_name: CD19+ B cells

extract_protocol:
ChIP-Seq: Cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed with ice-cold PBS and lysed in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for 20 min on ice. The crosslinked chromatin was sheared to an average size of less than 300 bp using a BiorupterTM sonicator (Diagenode). 5 µg of antibody was incubated with Dynabeads ProteinA beads (Invitrogen at 4C for 2-4 hours .  Sonicated lysates were subjected to immunopreciptation overnight at 4°C with acetylated H3 (Millipore, #06-599, Lot#2277850), acetylated H3K27 (Abcam,#ab4739, Lot#GR144577-1), or isotype control antibodies conjugated to Dynabeads (Invitrogen, USA) coated with Protein-A.  After incubation, the immune complexes were collected by centrifugation and washed with the following buffers each for 3 min at 4C;low salt (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and TE (10 mM Tris pH8.0, 1 mM EDTA). The protein-DNA complexes were eluted from the beads in 250 µl elution buffer (1% SDS, 100 mM NaHCO3) at 65C overnight followed by the addition of proteinaseK to 500 µg/ml and incubaton at 56C for 1 hour. Genomic DNA was isolated using QIAquick PCR purification column.
ChIP-seq: At least 3 ng of ChIP or input DNA was used for library preparation according to the Illumina ChIP-seq protocol. After end-repair and indexed adapter ligation, fragments were size-selected (average 250 bp) using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) prior to amplification. The size-selected and amplified fragment libraries were verified on a 2100 Bioanalyzer (Agilent) prior to being pooled (7-10 per lane) and sequenced.
FAIRE-Seq:  Cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min.  Crosslinked chromatin was lysed for 10 minutes sequentially in L1 buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 5% NP40 and 0.25% Triton X-100) followed by L2 buffer (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 1M and Tris pH 8.0). The pellets were resuspended in 300ul of buffer L3 (1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 1M Tris pH 8.0, 100mM NaCl, 0.1% Na-deoxycholate and 5mg/ml N-lauroyl sarcosine) and subjected to sonication using a Bioruptor to an average size of 500bp. The soluble DNA fraction was isolated by performing two consecutive phenol:chloroform:isoamylalcohol (25:24:1, pH 8) extractions followed by a chloroform-isoamyl alcohol (24:1) extraction. Precipitated DNA was resuspended in 10mM Tris-HCl (pH 7.4) and incubated with 10 g of RNase A for 1hr. Genomic DNA was isolated using QIAquick PCR purification column.
FAIRE-seq: The same protocol was used with the exception that size selected fragments averaged 90 bp.

value: peripheral blood

tag: tumor

value: male

tag: previously treated for nhl

value: no

value: peripheral blood B cells

tag: chip antibody

value: input


title: PBBA4_H3K27ac

value: Activated (IL4, anti-CD40, IgM, and IgD) peripheral blood

value: female

tag: cell type

value: acetylated H3K27 (Abcam, catalog# ab4739, lot# GR144577-1)


title: PBBA4_input


title: PBB5_input

value: yes


title: PBB5_H3K27ac


title: PBBA3_FAIRE

extract_protocol:
FAIRE-Seq:  Cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min.  Crosslinked chromatin was lysed for 10 minutes sequentially in L1 buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 5% NP40 and 0.25% Triton X-100) followed by L2 buffer (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 1M and Tris pH 8.0). The pellets were resuspended in 300ul of buffer L3 (1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 1M Tris pH 8.0, 100mM NaCl, 0.1% Na-deoxycholate and 5mg/ml N-lauroyl sarcosine) and subjected to sonication using a Bioruptor to an average size of 500bp. The soluble DNA fraction was isolated by performing two consecutive phenol:chloroform:isoamylalcohol (25:24:1, pH 8) extractions followed by a chloroform-isoamyl alcohol (24:1) extraction. Precipitated DNA was resuspended in 10mM Tris-HCl (pH 7.4) and incubated with 10 g of RNase A for 1hr. Genomic DNA was isolated using QIAquick PCR purification column.
FAIRE-seq: The same protocol was used with the exception that size selected fragments averaged 90 bp.
FAIRE-Seq:  Cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min.  Crosslinked chromatin was lysed for 10 minutes sequentially in L1 buffer (50mM Hepes KOH pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 5% NP40 and 0.25% Triton X-100) followed by L2 buffer (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 1M and Tris pH 8.0). The pellets were resuspended in 300ul of buffer L3 (1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 1M Tris pH 8.0, 100mM NaCl, 0.1% Na-deoxycholate and 5mg/ml N-lauroyl sarcosine) and subjected to sonication using a Bioruptor to an average size of 500bp. The soluble DNA fraction was isolated by performing two consecutive phenol:chloroform:isoamylalcohol (25:24:1, pH 8) extractions followed by a chloroform-isoamyl alcohol (24:1) extraction. Precipitated DNA was resuspended in 10mM Tris-HCl (pH 7.4) and incubated with 10 g of RNase A for 1hr. Genomic DNA was isolated using QIAquick PCR purification column.
FAIRE-seq: The same protocol was used with the exception that size selected fragments averaged 90 bp.


title: PBBA2_input


title: ZRSR2 mutant MDS 8


title: ZRSR2 mutant MDS 7


title: sample2a

description: rRNA depleted

source_name: 20% oxygen, chemostat culture of S. oneidensis MR-1

tag: culture

value: steady state in chemostat

tag: oxygen level


title: PBB17_H3K27ac


title: ZRSR2 mutant MDS 2

value: Male


title: CC2_FAIRE

source_name: CD19+/CD10+/CD44low/CXCR4- B cells

value: Tonsil

value: centrocyte


title: CC2_H3K27ac


title: CC4_input


title: PBBA1_FAIRE


title: PBBA1_H3ac

value: acetylated H3 (Millipore, catalog# 06-599, lot# 2277850)


title: CC2_input


title: CC5_H3K27ac


title: CC3_H3K27ac


title: CC3_FAIRE


title: PBBA1_H3K27ac


title: CC3_H3ac


title: CC3_input


title: PBBA2_H3ac


title: CC1_input


title: CC1_H3ac


title: CC1_FAIRE


title: CC4_H3K27ac


title: CC2_H3ac


title: PBBA1_input


title: CC5_input


title: PBBA2_H3K27ac


title: PBBA2_FAIRE


title: CB5_input

source_name: CD19+/CD10+/CD44low/CXCR4+ B cells

value: centroblast


title: CB4_H3K27ac


title: CB4_input


title: CC1_H3K27ac


title: CB3_input


title: CB5_H3K27ac


title: CB3_FAIRE


title: CB3_H3K27ac


title: CB3_H3ac


title: CB2_input


title: CB2_H3ac


title: CB2_H3K27ac


title: FL18_H3ac

value: LN

value: follicular lymphoma


title: CB1_input


title: FL17_H3K27ac


title: CB1_H3K27ac


title: FL17_input


title: FL16_FAIRE


title: CB2_FAIRE


title: CB1_H3ac


title: FL18_input


title: FL14_H3K27ac


title: CB1_FAIRE


title: FL16_H3ac


title: FL14_input


title: FL16_input


title: FL15_FAIRE


title: FL13_FAIRE


title: FL14_FAIRE


title: FL16_H3K27ac


title: FL10_input


title: FL11_input


title: FL11_FAIRE


title: FL14_H3ac


title: FL12_FAIRE


title: FL11_H3ac


title: FL10_H3K27ac


title: FL9_input


title: FL9_H3ac


title: FL7_FAIRE


title: FL8_FAIRE


title: FL8_H3K27ac


title: FL8_H3ac


title: FL11_H3K27ac


title: FL5_H3ac


title: FL4_H3ac


title: FL3_input


title: FL4_input


title: FL2_FAIRE


title: FL3_H3ac


title: FL2_input


title: FL3_FAIRE


title: FL6_FAIRE


title: FL1_input


title: FL2_H3ac


title: FL1_H3K27ac


title: FL10_H3ac


title: PBBA4_RNAseq

description: Gene expression profiles of in vitro activated B cells generated from RNA-Seq.

data_processing:
RNA-Seq data were aligned to the transcriptome and reference genome (EnsemblRef_67) with TopHat 2.0.9
Peaks were called using MACS version 1.4.2 with default settings
Genome_build: hg19
Supplementary_files_format_and_content: bw files report peaks

extract_protocol:
RNA was purified using Qiagen RNeasy Kits.
RNA-seq libraries were prepared from rRNA-depleted samples (Ribo-Zero, Epicentre) using TruSeq RNA Sample kits with indexed adaptors (Illumina), pooled (3 libraries), and subjected to 101bp paired-end sequencing using an Illumina HiSeq2000 (San Diego, CA, USA).


title: CC3_RNAseq

description: Gene expression profiles of CC generated from RNA-Seq.


title: CC2_RNAseq


title: FL8_input


title: FL5_input


title: PBBA3_RNAseq


title: FL5_FAIRE


title: FL5_H3K27ac


title: FL17_RNAseq

description: Gene expression profiles and sequence variants of FL generated from RNA-Seq.


title: FL16_RNAseq


title: FL2_H3K27ac


title: FL10_RNAseq


title: FL11_RNAseq


title: FL9_RNAseq


title: FL14_RNAseq


title: FL1_H3ac


title: FL8_RNAseq


title: FL2_RNAseq


title: FL1_RNAseq


title: HCC1419_untreated2

city: San

first: Mia

last: Grifford

address: 1156 High Street

institute: UCSC

data_processing:
The input Illumina fastq files consisted of paired end reads with each end containing 100 bp, which were reduced to 80x80bp by trimming 20bp from the 3' end of each read to improve mapping of fragments shorter than 100nt.
Fragments that mapped to elements in the repeatMasker human library, using Bowtie2, were removed.
Bowtie2 was used to map the remaining fragments against a version of the human transcriptome derived from the UCSC Known Genes track of the GRCh37hg19 human assembly by using the target generation script supplied with RSEM.
Only mappings with both read ends aligned were kept.
Potential PCR duplicates (mappings of more than one fragment with identical positions for both read ends) were removed with the samtools “rmdup” function, keeping only one of any potential duplicates.
The final set of mapped paired end reads for a sample were converted to transcript and gene expression estimates using RSEM.
For input to DESeq all genes with non-zero counts in any sample were considered.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RSEM expression estimates and DESeq results

growth_protocol: HCC1419 cells (ATCC, CRL-2326, purchased 1/31/11) were grown in RPMI containing 1% penicillin streptomycin (PenStrep) and 10% Gibco certified fetal bovine serum (FBS) (Invitrogen) (RPMI-complete) conditioned with mouse embryonic fibroblasts (MEF). Media was changed every 3 days.

extract_protocol:
Trizol + RNEasy cleanup, followed by ribozero rRNA depletion
Strand-specific dUTP followed by TruSeq DNA library prep kit

value: untreated

tag: sample id


title: HCC1419_DTEP_L1P7

value: 1μM Lapatinib indefinitely


title: HCC1419_DTP2

value: 1μM Lapatinib 9 days


title: HCC1419_untreated1


title: HCC1419_DTEP_L1P12


title: HCC1419_DTEP_L2P6


title: AA-treated_2

city: Dalian

first: Zhiguang

state: Liaoning

address: 9 Lvshun Road South

department: Institute of Cancer Stem Cell, Cancer Center

institute: Dalian Medical University

description: The 6 week-old male Big Blue rats were treated with AA as its sodium salt at 10.0 mg/kg body weight by gavage (4 ml/kg body weight) 5 times a week for 13 weeks, a treatment protocol that induces tumors in rat kidney.

data_processing:
Illumina Casava software 1.7 used for basecalling.
We used the miRanalyzer webserver for the detection of known microRNAs expression from miRNA-seq (http://www.mirbase.org/). The required input in read/count format was generated by means of the provided groupReads.pl perl script. In both analysis steps, (i) conversion of fastq to read/count and (ii) the microRNA expression profiling we used the default parameters of the programs.
Genome_build: We use miRNA release 16 from Sanger miRBase for miRNA-seq mapping.
Supplementary_files_format_and_content: The provided data table includes the hits of miRNA by sequenced reads.

organism: Rattus norvegicus

source_name: Aristolochic Acid-treated kidney

growth_protocol: Same as Stratagene (La Jolla, CA)

extract_protocol:
40-50 mg tissue was cut and mechanically minced using Tissue Tearor (Biospec Products Inc, OK).  Total RNA was isolated using a small RNA-retaining protocol that employed an organic extraction followed by glass-fiber immobilization (Ambion, TX).  RNA concentration was determined by Nandrop1000 spectrophotometer (Thermo Scientific, DE).
Samples were prepared using illumina small RNA sample Prep kit with the small RNA v1.5 sample preparation guide.  Approximately 10 µg of total RNA was used for small RNA library construction. The v1.5 sRNA 3’ and SRA 5’ adaptors (Illumina, USA) were added to both ends of the small RNA. The 3’ and 5’ Ligated RNAs were used as templates for reverse transcription followed by PCR amplification.  The enriched cDNA constructs were loaded to 6% TBE PAGE gel and the bands containing the 22-30 nt RNA fragments (93-100 nt in length with both adapters) were cut and purified. The concentrations of the libraries were determined using a NanoDrop ND-1000 Spectrophotometer and the size and purity were determined using an Agilent 2100 Bioanalyzer in combination with the Agilent DNA 1000 Kit. The purified DNA was used directly for cluster generation and sequence analysis using the Illumina Genome Analyzer II (Illumina, San Diego, CA, USA) according to the manufacturer's instructions (36 cycle single read cluster kit v4 and sequence kit v4).

treatment_protocol: Groups of four 6 week-old male Big Blue rats were treated with AA as its sodium salt at 10.0 mg/kg body weight by gavage (4 ml/kg body weight) 5 times a week for 12 weeks, a treatment protocol that induces tumors in rat kidney.  The rats  treated with 0.9% sodium chloride on the same schedule were used as control. All animals were sacrificed 1 day after the last treatment.  The kidneys were isolated, frozen quickly in liquid nitrogen and stored at −80 ◦C.

value: 18 weeks

tag: strain

value: Fisher 344

tag: genotype/variation

value: Big Blue Transgenic


title: AA-treated_3

description: The 6 week-old male Big Blue rats were treated with AA as its sodium salt at 10.0 mg/kg body weight by gavage (4 ml/kg body weight) 5 times a week for 14 weeks, a treatment protocol that induces tumors in rat kidney.


title: Control_4

description: The 6 week-old male Big Blue rats treated with 0.9% sodium chloride 5 times a week for 15 weeks were used as control.

source_name: Control kidney


title: AA-treated_1

description: The 6 week-old male Big Blue rats were treated with AA as its sodium salt at 10.0 mg/kg body weight by gavage (4 ml/kg body weight) 5 times a week for 12 weeks, a treatment protocol that induces tumors in rat kidney.


title: Control_2

description: The 6 week-old male Big Blue rats treated with 0.9% sodium chloride 5 times a week for 13 weeks were used as control.


title: Control_3

description: The 6 week-old male Big Blue rats treated with 0.9% sodium chloride 5 times a week for 14 weeks were used as control.


title: Control_1

description: The 6 week-old male Big Blue rats treated with 0.9% sodium chloride 5 times a week for 12 weeks were used as control.


title: 35_SusScrofa

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

data_processing:
Alignment: STAR
Filtering: SAM flag 1792 (not primary alignment, read fails platform/vendor quality checks, read is PCR or optical duplicate)
Count reads: HTSeq
Library size factor estimation: DESeq
Normalization of reads: voom (limma), samples were corrected for gender
Filter of reads with expression lower than 5
Genome_build: SScrofa10.2.72
Supplementary_files_format_and_content: comma seperated files with raw and normalized counts

organism: Sus scrofa

source_name: subcuteneous adipose tissue

extract_protocol:
Rneasy lipid Mini kit
TruSeq RNA Sample Prep (Illumina)

value: subcuteneous adipose

value: High

tag: Sex

value: m


title: 36_SusScrofa


title: 32_SusScrofa


title: v6.5

city: Rochester

first: Paul

middle: L.

last: Boutz

address: 601 Elmwood Ave.

department: Biochemistry & Biophysics

institute: University of Rochester School of Medicine

data_processing:
Read Mapping: Paired-end reads were mapped with Bowtie (1.0.0, allowing up to 2 mismatches; unique mapping was enforced using the --best –strata mode.  Reads were also mapped using Tophat (2.0.9) with default settings, against a custom junctions file. In both cases reads mapping to repetitive regions were eliminated using a repeat RNA mask. Bowtie mapped reads were further depleted of microRNAs, pseudogenes, and single exon ribosomal protein genes using bedTools intersectBed.  Each lane of sequencing was mapped all together, then the individual samples were sorted by barcode using Samtools (0.1.19) and awk.
BedGraphs: Tophat-mapped reads for each sample in .bam format were converted to bedGraphs using bedTools (2.17.0) genomeCoverageBed, normalized by the total mapped read counts per sample as determined by Cufflinks (2.1.1).  Strand-specific reads were filtered using Samtools (0.1.19), requiring properly paired and mapped mates, and outputting a separate bedGraph for each strand.
DESeq: Reads uniquely mapped by Bowtie and filtered for repeats, small RNA, and pseudogenes were processed using bedTools intersectBed | coverageBed to count the number of reads falling within each intron.  Exon-intron junction spanning reads were required to have a minimum of 10 nucleotides overlapping the intron to be counted.  For determining introns that are more abundant than expected by chance, all expressed introns in v6.5 cells (determined by Tophat junction mapping) that had a minimum threshold of 10 counts across all samples considered (22,228 introns-- these are the rows of table “IntronQuantificationDESeqProcessedData.txt”) were run through the DESeq module (1.16.0) in R (2.15.3), comparing expected coverage (considers mappability, read length, null distribution, total intronic reads/gene) with actual observed coverage per intron in a sample with 2 biological replicates. DMSO vs. CB19 treatments were compared the same way for each intron.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraphs show normalized read density genome-wide and can be visualized using genome browsers such as the Broad IGV or UCSC Genome Browser.  The two biological replicates for each sample were combined to produce each bedGraph, and reads originating from each strand are separated into the plus- and minus- files to enable strand-specific visualization.  DMSO treated samples are shown in blue, and CB19 in orange.  Read density per nucleotide was normalized to millions of mapped reads, so the scale of the bedGraph is equivalent to FPKM, and is initially set to 1 FPKM to emphasize intronic reads.  The scale can be adjusted depending on the expression level of the transcript for better visualization.  The intron quantification data is provided in tab-delimited text that can be opened with Excel.  Rows are introns that met the minimum read coverage threshold for our DESeq pipeline.  Columns: intron id and genomic location are provided (columns 1-5). Columns 6-13 are the normalized mean read counts (average between 2 biological replicates) that are expected under the null model and the number actually observed, followed by log2-fold change (observed/expected), and the FDR-adjusted p-value for the difference.  This is provided for DMSO ( 6-9) and then CB19 (10-13) at time zero.  Columns 14-17 are the normalized mean read counts (average between 2 biological replicates) for DMSO 2 hour treatment, CB19 2 hour treatment, the log2-fold change (CB19/DMSO), and the FDR-adjusted p-value for the difference. Column 18 indicates detained introns that were spliced more (More, CB19<DMSO,p-adj < 0.05), less (Less, CB19>DMSO, p-adj < 0.05) or no change (NC, CB19~DMSO, p-adj >0.05).  Column 19 indicates which introns met the cutoff for detained introns (DI), log2fc obs/exp & p-adj < 0.01 for DMSO 0 or CB19 0.

molecule: polyA RNA

source_name: v6.5_Subconfluent ESCs

growth_protocol: v6.5 mouse embryonic stem  cells were cultured in DMEM/HEPES(Life Technologies) supplemented with 2mM L-glutamine & 1X Non-essential amino-acids (Life Technologies), 15% FBS (Hyclone), 1000U/ml ESGRO (Chemicon) on gelatinized flasks.

extract_protocol:
Total RNA from V6.5 mESCs was treated with Turbo DNase (Life Technologies) and poly(A) selected (Poly(A)Purist MAG, Life Technologies).  Poly(A)+ RNA was then digested with 5' exonuclease (Terminator, Epicentre) to further enrich for capped mRNAs.  2 ug poly(A)+ RNA was shattered under alkaline conditions in the presence of Mg++ for 80 seconds  (Mortazavi et al., 2009).    A 3' linker containing both priming sites and a 6 nucleotide random 3' overhang was ligated by splint-ligation using T4 DNA Ligase (NEB), reverse transcribed at 60° C (SuperScript III, Life Technologies), treated with RNaseH/A (Life Technologies, NEB) to remove RNA, and the cDNAs size selected on a 10% PAGE gel under denaturing conditions.  The extracted DNA was circularized (CircLigase II, Epicentre) and amplified using 18 cycles (Phusion Polymerase, NEB).  The resulting product was again purified on a 2% agarose gel followed by standard paired-end sequencing (2x36 nucleotides, Illumina Genome Analyzer IIx).
Cells were lysed in Trizol (Life Technologies) and processed according to manufacturer's protocol.  Total extracted RNA was digested with TurboDNase (Life Technologies), acid-phenol/chloroform extracted, and ethanol precipitated.   The resulting purified RNA was assessed for RNA integrity using a Bioanalyzer 2100 (ABI) nano-RNA chip.

treatment_protocol: Subconfluent v6.5 mouse embryonic stem cells were harvested in in Trizol (Life Technologies).

value: mouse embryonic stem cells

tag: treated with

value: none (untreated control)

tag: barcode

tag: rna integrity (rin)


title: FL5_RNAseq

tag: tissue

value: male

value: yes


title: 30_SusScrofa


title: HCC1419_DTP1

tag: cell line

tag: treatment


title: 28_SusScrofa


title: 27_SusScrofa

value: f


title: 31_SusScrofa


title: 29_SusScrofa


title: 26_SusScrofa


title: AA-treated_4

description: The 6 week-old male Big Blue rats were treated with AA as its sodium salt at 10.0 mg/kg body weight by gavage (4 ml/kg body weight) 5 times a week for 15 weeks, a treatment protocol that induces tumors in rat kidney.

tag: gender

value: Male

tag: age


title: 25_SusScrofa


title: 22_SusScrofa

value: Mean


title: 23_SusScrofa


title: 18_SusScrofa


title: 19_SusScrofa


title: 20_SusScrofa


title: 33_SusScrofa


title: 34_SusScrofa


title: 21_SusScrofa


title: 16_SusScrofa


title: 17_SusScrofa


title: 14_SusScrofa


title: 13_SusScrofa


title: 12_SusScrofa

value: Low


title: 15_SusScrofa


title: Control rep2

first: Yuheng

last: Lu

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Paired-end RNA-Seq reads were first processed with Trimmomatic to remove TruSeq adaptor sequences and bases with quality scores below 20, and reads with less than 30 remaining bases were discarded.
Trimmed reads were then aligned to mm9 genome with the STAR aligner.
The number of uniquely mapped reads overlapping with each RefSeq gene was counted with HTSeq.
We used DESeq to evaluate the differences in expression between Msi2 KO and control samples, which were represented with log2 fold change and Benjamini-Hocheberg corrected p-values.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including gene-wise read counts for each sample

source_name: c-Kit high leukemic cell

extract_protocol:
RNA was extracted using Trizol and RNeasy RNA extraction kit.
Samples were prepared with a standard Illumina kit using the TruSeq RNA SamplePrep Guide.
mRNA fragments with a length of 200–300 bp were selected for library construction. Sequencing was performed on a Hiseq2000 platform using a standard paired-end protocol.

value: Msi2 flox/flox

value: c-Kit high leukemic cell


title: 11_SusScrofa


title: Control rep1


title: 24_SusScrofa


title: Msi2 knock-out rep1


title: Msi2 knock-out rep2


title: 10_SusScrofa


title: CB19_2H_replicate_two

description:
processed data file: IntronQuantificationDESeqProcessedData.txt
processed data file: CB19_2H_plus-strand.bedgraph.gz
processed data file: CB19_2H_minus-strand.bedgraph.gz

extract_protocol:
Libraries for the CB19 experiment were prepared using the Illumina TruSeq stranded library kit with 2 passes over oligo-dT beads, following manufacturer's instructions with minor modifications.  Two independent biological replicates were prepared for each condition (DMSO and CB19) at time zero and 2 hours after drug treatment and each was made into a separate, barcoded library.  Input was 4 mg total RNA/replicate, fragmentation time was decreased to 5 minutes to produce longer insert length, and samples were size-selected on a 2% agarose gel following PCR amplification.  Barcoded samples were paired-end sequenced (2x100 nucleotides) in multiplex on an Illumina HiSeq 2000 instrument.
Cells were lysed in Trizol (Life Technologies) and processed according to manufacturer's protocol.  Total extracted RNA was digested with TurboDNase (Life Technologies), acid-phenol/chloroform extracted, and ethanol precipitated.   The resulting purified RNA was assessed for RNA integrity using a Bioanalyzer 2100 (ABI) nano-RNA chip.

treatment_protocol: KH-CB19 (CalBioChem) was disolved in DMSO and added to cells to a final concentration of 10mM.  An equal volume of dimethyl sulfoxide (DMSO, Sigma) was added to the negative control cells. Immediately following drug treatment (0) or 2 hours following addition of drugs to culture medium (2H), culture medium was removed and cells harvested in Trizol (Life Technologies).

value: Clk kinase inhibitor KH-CB19

tag: harvest time point

value: 2 hrs after treatment (2h)

value: AGTTCC


title: 9_SusScrofa


title: 7_SusScrofa


title: pol2-4 rnh201 (KK-107)

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

data_processing:
UMIs were processed from the reads (first 8 bases)
Trimmed reads were aligned to the S. cerevsiiae genome (sacCer2) with bowtie in `uniq` (-m 1) and `all` (--all) modes.
Coverage in bedGraph was calculated with BEDTools (`genomecov -ibam <bam> -5 -strand [pos|neg]
Genome_build: sacCer2
Supplementary_files_format_and_content: bedgraph = bedGraph files containing sites of ribonucleotides and their counts from sequencing

organism: Saccharomyces cerevisiae

source_name: Genomic DNA

growth_protocol: Cells were grown to stationary phase in YEPD for 2 days.

extract_protocol:
Genomic DNA from S. cerevisiae cells grown in liquid rich medium containing yeast extract, peptone, and 2% (w/v) dextrose (YPD) for 2 days to stationary phase was extracted following the protocol “Preparation of Yeast Samples” in QIAGEN Genomic DNA Handbook (Valencia, CA, U.S.A.). Genomic-tip 500/G (QIAGEN), Genomic DNA Buffer Set (QIAGEN), Proteinase K (QIAGEN), RNase A (QIAGEN), and Lyticase (Sigma-Aldrich, St. Louis, MO, U.S.A.) were used to extract genomic DNA from S. cerevisiae cells.
Extracted genomic DNA was digested with SspI, DraI, and EcoRV (NEB, Ipswich, MA, U.S.A.) overnight at 37 °C. Following confirmation of digestion by Experion Automated Electrophoresis System (BIO-RAD, Hercules, CA, U.S.A.), the fragments were tailed with dAMP (Sigma-Aldrich) by Klenow fragment (exo-) (NEB) for 30 min at 37 °C. The resulting products were purified by spin-column (QIAGEN) and then ligated to preannealed double-stranded (ds) adaptors (Adaptor.L/Adaptor.S) that contain single dT overhangs and a randomized 8-base molecular index, UMI, by T4 DNA ligase (NEB) overnight at 15 °C. The products were purified using AMPure XP beads (Beckman Coulter, Brea, CA, U.S.A.). All subsequent purifications were done using AMPure XP beads. The adaptor-ligated DNA fragments were incubated in 0.3 M NaOH for 2 hr at 55 ˚C to expose 2′,3′-cyclic phosphate and 2′-phosphate termini of DNA at rNMP sites, followed by neutralization and purification. The resulting single-stranded (ss) fragments were incubated in 50 mM Tris-HCl, pH 7.5, 40 mM NaCl, 5 mM MgCl2, 1 mM DTT, 30 µM ATP, and 1 µM AtRNL (Schutz et al., 2010) for 1 hr at 30 °C, followed by purification. The products and remaining fragments of DNA were treated with T5 exonuclease (NEB) for 2 hr at 37 °C to degrade the background of unligated, linear ss DNA, leaving self-ligated ss DNA circles intact. Treatment with the 1 µM Tpt1 (Schutz et al., 2010) in 20 mM Tris-HCl, pH 7.5, 5 mM MgCl2, 0.1 mM DTT, and 0.4% Triton X-100 for 1 hr at 30 °C was used to remove the 2′-phosphate remaining at the ligation junction. After purification and resuspension, the libraries were PCR-amplified with one of the bar-coded primers, PCR.1.Index1-4, and PCR.2 using either Phusion High-Fidelity DNA Polymerase (NEB) or EconoTaq DNA Polymerase (Lucigen, Middleton, WI, U.S.A.), purified, and pooled for analysis by Illumina sequencing.

tag: genotype


title: pol3-5DV rnh201 (KK-120)


title: CB19_2H_replicate_one

tag: cell type

value: AGTCAA


title: 8_SusScrofa

value: subcuteneous adipose


title: DMSO_2H_replicate_two

description:
processed data file: IntronQuantificationDESeqProcessedData.txt
processed data file: DMSO_2H_plus-strand.bedgraph.gz
processed data file: DMSO_2H_minus-strand.bedgraph.gz

value: DMSO (negative control)

value: CTTGTA


title: 5_SusScrofa

value: m


title: 4_SusScrofa


title: pol2-M644G rnh201 (KK-170)


title: DMSO_2H_replicate_one

value: mouse embryonic stem cells

value: CAGATC


title: rnh1 rnh201 (KK-125)


title: CB19_0_replicate_one

description:
processed data file: IntronQuantificationDESeqProcessedData.txt
processed data file: CB19_0_plus-strand.bedgraph.gz
processed data file: CB19_0_minus-strand.bedgraph.gz

value: immediately after treatment (0h)

value: ACAGTG


title: CB19_0_replicate_two

value: GCCAAT


title: rnh1 rnh201 ung1 (KK-164)

value: rnh1 rnh201 ung1 (KK-164)


title: 3_SusScrofa

value: Low

value: f


title: 1_SusScrofa


title: DMSO_0_replicate_two

description:
processed data file: IntronQuantificationDESeqProcessedData.txt
processed data file: DMSO_0_plus-strand.bedgraph.gz
processed data file: DMSO_0_minus-strand.bedgraph.gz

value: TGACCA


title: rnh1 rnh201 (KK-174)


title: DMSO_0_replicate_one

value: CGATGT


title: rnh201 (KK-30)


title: 2_SusScrofa


title: rnh201 (KK-100, EconoTaq)

value: rnh201 (KK-100, EconoTaq)


title: USV101 tagged capsule inducing input

status: Public on Jan 14 2015

city: Saint Louis

first: Ezekiel

middle: John

last: Maier

address: 4444 Forest Park Ave

department: Computer Science

institute: Washington University

description: ChIP-seq input control: USV101 tagged capsule inducing

data_processing:
Sequenced reads were aligned to the C. neoformans H99 reference sequence (v2) using Bowtie version 0.12.8
Peak calling was performed with MACS (v1.4.0) by comparing tagged IP reads as the treatment sample and input, mock, and untagged IP reads as the control samples.
For NRG1 analysis, tagged IP treatment replicates 2 & 3 were compared with the untagged wildtype IP control. Any gene falling completely or partially within 1,000 bp on either side of a peak’s summit was considered ChIP positive for that IP-control pair. Only genes that were ChIP-positive for both IP-control pairs were considered NRG1 bound. For Usv101, ChIP-positive genes were called separately for cells grown in capsule-inducing and non-inducing conditions. In each condition, the tagged IP treatment was compared the tagged input and mock controls, and the untagged wildtype IP control. Any gene falling completely or partially within 1,000 bp on either side of a peak’s summit was considered ChIP positive for that IP-control pair. Only genes that were ChIP-positive for all three IP-control pairs were considered USV101 bound.
Genome_build: C. neoformans H99 reference sequence (Cryptococcus neoformans var. grubii H99 Sequencing Project)
Supplementary_files_format_and_content: bed (peaks): Peak calling was performed with MACS (v1.4.0). Each line a peaks bed file gives the coordinates and score (-10log10(pval)) of a MACS identified peak.

organism: Cryptococcus neoformans

source_name: cultured cells

growth_protocol: Wild-type and HA-tagged strains were cultured overnight in YPD to a density of 1-2 OD600.

extract_protocol:
The cells were fixed with formaldehyde, lysed by mechanical bead-beating, and the cell debris was  removed by centrifugation. The supernatant fraction, containing isolated chromatin, was sheared by sonication, cleared again by centrifugation, and an aliquot was reserved as ‘input’. The remaining material was incubated with rabbit IgG anti-HA antibody (Abcam) tethered to protein A sepharose (‘IP’) or sepharose alone (‘mock’) overnight at 4°C. The beads were then washed, incubated at 65°C to reverse DNA-DNA and DNA-protein crosslinks, and the DNA recovered by phenol/chloroform/isoamyl alcohol (25:24:1) extraction, ethanol precipitation, and resuspension in nuclease-free water.
ChIP-DNA for for all samples was end-repaired with Klenow DNA Polymerase and the DNA was purified with AMPure XP System beads (Beckman Coulter Genomics) and modified with A-tails using Klenow exo- before ligation to adapters to incorporate 7-base index sequences using T4 DNA ligase (Enzymatics). Adapter addition was confirmed on an Agilent 2100 bioanalyzer, and the DNA was PCR-amplified and then gel purified to remove adapter dimers and select sizes optimal for high-throughput sequencing (150 to 300 bp). Samples were submitted to the Washington University Genome Technology Access Center for library preparation and multiplex sequencing.

treatment_protocol: Cells were transfered to grow for 90 minutes in either capsule-inducing (DMEM, 37 °C, 5% CO2) or capsule non-inducing (YPD, 30 °C) conditions

tag: chip antibody

tag: condition description

value: capsule-inducing

tag: condition

value: 37°C + CO2 for 90mins


title: Wildtype capsule inducing mock

description: ChIP-seq mock control: wildtype capsule inducing

tag: strain

value: wildtype

value: rabbit IgG anti-HA antibody


title: Wildtype capsule inducing ip

description: ChIP-seq IP control: wildtype capsule inducing


title: USV101 tagged capsule non-inducing input

description: ChIP-seq input control: USV101 tagged capsule non-inducing

value: capsule non-inducing

value: 30°C + YPD


title: rnh201 (KK-100)


title: Wildtype capsule inducing input

description: ChIP-seq input control: wildtype capsule inducing


title: USV101 tagged capsule inducing ip

description: ChIP-seq IP: USV101 tagged capsule inducing


title: USV101 tagged capsule inducing mock

description: ChIP-seq mock control: USV101 tagged capsule inducing


title: USV101 tagged capsule non-inducing mock

description: ChIP-seq mock control: USV101 tagged capsule non-inducing


title: 6_SusScrofa

value: subcuteneous adipose


title: Wildtype capsule non-inducing ip

description: ChIP-seq IP control: wildtype capsule non-inducing


title: Wildtype capsule non-inducing mock

description: ChIP-seq mock control: wildtype capsule non-inducing


title: Wildtype capsule non-inducing input

description: ChIP-seq input control: wildtype capsule non-inducing


title: 05420-37C.CO2.90m-2-09.13.13-10.08.13-421

description: USV101(CNAG_05420)Δ in 37°C + CO2 for 90mins

data_processing:
Sequenced reads were aligned to the C. neoformans H99 reference sequence (v2) using TopHat version 2.0.4 and Bowtie version 0.12.8
Reads that aligned uniquely to the reference sequence were considered for gene expression quantification with Cufflinks version 2.0.2. Gene boundaries were defined using the current C. neoformans genome annotation provided by the Broad institute. Gene expression was normalized using the Cufflinks provided option for quartile normalization.
After gene expression quantification, samples not passing the following quality control filters were removed from consideration. The expression of the deleted gene in mutant expression profiles was required to be less than 10% of its expression in WT. The mean and median expression of the deleted genes were 0.7% and 0% of the WT levels respectively. The low levels of expression that remained for some samples were likely the result of errors in the sequencing process itself, either due to contamination between samples or a low level of error in matching barcodes for multiplexed samples to reads. Wild-type samples were required to express the resistance marker at less than 10% of its median level in all mutant expression profiles. In addition, to maximize the power to detect differentially expressed genes, a quality control filter was established to ensure that replicate expression profiles were in agreement. Specifically, within a replicate set the median of all gene coefficients of variation (CoV), defined as the standard deviation of gene expression over mean gene expression, was required to be less than or equal to 0.2. Any replicate set which did not pass this CoV filter was not used for differential expression analysis, and the mutant expression profiles were remade. However, replicate sets were rescued if the median CoV could be lowered below 0.2 by removing an outlier expression profile replicate.
Differential expression analysis comparing matched mutant and wild type expression profile replicate sets was performed with Cuffdiff using a 5% false discovery rate. If multiple replicate sets of a mutant passed the quality control standards, only the replicate set with the lowest CoV was used for differential expression analysis.
Genome_build: C. neoformans H99 reference sequence (Cryptococcus neoformans var. grubii H99 Sequencing Project)
Supplementary_files_format_and_content: cuff: Gene expression was quantified processing tophat produced bam alignments with Cufflinks v0.9.3 with the current H99 annotation (v2) provided by the Broad institute's Fungal Genome initiative. Expression was normalized by applying the Cufflinks supplied quartile normalization routine.

growth_protocol: All strains were constructed in the C. neoformans KN99α background. Cells were cultured overnight in YPD to a density of 1-2 OD600.

extract_protocol:
For RNA isolation, the culture was treated with ice-cold stop solution (5% Tris-saturated phenol in ethanol) to prevent RNA degradation and then collected by centrifugation. The cells were suspended in TRIzol reagent (Life Technologies) and lysed by mechanical bead-beating at 4°C with 0.5-mm silica-zirconia beads (4 cycles of 3 min of beating followed by 2 min on ice). Following lysis, total RNA was extracted according to the manufacturer’s instructions. Residual DNA was removed from the RNA preparation with the TURBO DNA-free kit (Life Technologies).
Poly(A) RNA was selected from the total using the mRNA Catcher Plus Kit (Life Technologies) with an epMotion 5075 automated pipettor (Eppendorf). The poly(A) RNA was subsequently sheared by incubating in TURBO DNA-free buffer at 75°C for 10 minutes and purified with the QIAquick PCR Purification Kit (Qiagen). First strand cDNA synthesis was performed using random hexameric primers and SuperScript III Reverse Transcriptase, followed by treatment with E. coli DNA ligase, DNA polymerase I, and RNase H for second-strand synthesis, all using standard methods. The cDNA libraries were end-repaired with a Quick Blunting kit and A-tailed using Klenow exo- with dATP (New England Biolabs). Illumina adapters were ligated to the cDNA and fragments ranging from 150-250 bp in size were selected using gel electrophoresis. The libraries were enriched and indexed in a 10-cycle PCR using Phusion Hot Start II High-Fidelity DNA (Fermentas), purified, and pooled in equimolar ratios for multiplex sequencing on an Illumina HiSeq 2500 at the Genome Technology Access Center.

treatment_protocol: Cells were transfered to grow for 90 minutes in either capsule-inducing (DMEM, 37 °C, 5% CO2) or capsule non-inducing (DMEM, 30 °C, room air) conditions prior to isolation of total RNA.

tag: replicate

tag: induction date

tag: library date

tag: sample id


title: 00000-37C.CO2.1440m-3-08.30.13-09.30.13-416

description: wildtype in 37°C + CO2 for 1440mins


title: 00000-37C.CO2.1440m-2-08.30.13-09.30.13-415

description: wildtype in 37°C + CO2 for 1440mins


title: 00000-37C.CO2.90m-2-09.13.13-10.08.13-418

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.480m-3-08.30.13-09.30.13-413

description: wildtype in 37°C + CO2 for 480mins


title: 00000-37C.CO2.480m-2-08.30.13-09.30.13-412

description: wildtype in 37°C + CO2 for 480mins


title: 00000-37C.CO2.480m-1-08.30.13-09.30.13-411

description: wildtype in 37°C + CO2 for 480mins


title: 00000-37C.CO2.180m-1-08.30.13-09.30.13-408

description: wildtype in 37°C + CO2 for 180mins


title: 00000-37C.CO2.1440m-1-08.30.13-09.30.13-414

description: wildtype in 37°C + CO2 for 1440mins


title: 00000-37C.CO2.180m-3-08.30.13-09.30.13-410

description: wildtype in 37°C + CO2 for 180mins


title: 00000-37C.CO2.90m-1-09.13.13-10.08.13-417

description: wildtype in 37°C + CO2 for 90mins


title: 05420-37C.CO2.90m-3-09.13.13-10.08.13-422


title: 00000-37C.CO2.90m-3-09.13.13-10.08.13-419

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-08.30.13-09.30.13-407

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-08.30.13-09.30.13-406

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-08.30.13-09.30.13-405

description: wildtype in 37°C + CO2 for 90mins


title: USV101 tagged capsule non-inducing ip

description: ChIP-seq IP: USV101 tagged capsule non-inducing


title: 00000-30C.0m-3-08.30.13-09.30.13-404

description: wildtype in 30°C


title: 00000-30C.0m-2-08.30.13-09.30.13-403

description: wildtype in 30°C


title: 00000-30C.0m-1-08.30.13-09.30.13-402

description: wildtype in 30°C


title: 00000-37C.CO2.180m-2-08.30.13-09.30.13-409

description: wildtype in 37°C + CO2 for 180mins


title: 01438-37C.CO2.90m-3-03.29.13-04.17.13-401

description: SWI6(CNAG_01438)Δ in 37°C + CO2 for 90mins


title: 02566-37C.CO2.90m-2-03.29.13-04.17.13-397

description: FKH2(CNAG_02566)Δ in 37°C + CO2 for 90mins


title: 02566-37C.CO2.90m-1-03.29.13-04.17.13-396


title: 01438-37C.CO2.90m-1-03.29.13-04.17.13-399


title: 03378-37C.CO2.90m-3-03.29.13-04.17.13-395

description: CLR2(CNAG_03378)Δ in 37°C + CO2 for 90mins


title: 03378-37C.CO2.90m-1-03.29.13-04.17.13-393


title: 03378-37C.CO2.90m-2-03.29.13-04.17.13-394


title: 02566-37C.CO2.90m-3-03.29.13-04.17.13-398


title: 01438-37C.CO2.90m-2-03.29.13-04.17.13-400


title: 00000-37C.CO2.90m-2-03.29.13-04.17.13-391

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-04.12.13-04.17.13-380

description: wildtype in 37°C + CO2 for 90mins


title: 07464-37C.CO2.90m-2-02.15.13-03.13.13-376

description: MBS1(CNAG_07464)Δ in 37°C + CO2 for 90mins


title: 07464-37C.CO2.90m-3-02.15.13-03.13.13-377


title: 00000-37C.CO2.90m-1-03.29.13-04.17.13-390

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-04.12.13-04.17.13-378

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-04.12.13-04.17.13-379

description: wildtype in 37°C + CO2 for 90mins


title: 07464-37C.CO2.90m-1-02.15.13-03.13.13-375


title: 03894-37C.CO2.90m-1-02.15.13-03.13.13-372

description: PDR802(CNAG_03894)Δ in 37°C + CO2 for 90mins


title: 05861-37C.CO2.90m-2-02.15.13-03.13.13-370

description: FKH101(CNAG_05861)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-03.29.13-04.17.13-392

description: wildtype in 37°C + CO2 for 90mins


title: 05861-37C.CO2.90m-3-02.15.13-03.13.13-371


title: 05861-37C.CO2.90m-1-02.15.13-03.13.13-369


title: 00000-37C.CO2.90m-3-02.15.13-03.13.13-368

description: wildtype in 37°C + CO2 for 90mins


title: 03894-37C.CO2.90m-2-02.15.13-03.13.13-373


title: 04353-37C.CO2.90m-1-02.19.13-03.13.13-363

description: CLR1(CNAG_04353)Δ in 37°C + CO2 for 90mins


title: 04353-37C.CO2.90m-2-02.19.13-03.13.13-364


title: 00000-37C.CO2.90m-2-02.15.13-03.13.13-367

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-02.15.13-03.13.13-366

description: wildtype in 37°C + CO2 for 90mins


title: 07435-37C.CO2.90m-2-02.19.13-03.13.13-361

description: HAP2(CNAG_07435)Δ in 37°C + CO2 for 90mins


title: 07435-37C.CO2.90m-3-02.19.13-03.13.13-362


title: 06352-37C.CO2.90m-3-02.19.13-03.13.13-359

description: BIK1(CNAG_06352)Δ in 37°C + CO2 for 90mins


title: 06352-37C.CO2.90m-2-02.19.13-03.13.13-358


title: 07435-37C.CO2.90m-1-02.19.13-03.13.13-360


title: 03894-37C.CO2.90m-3-02.15.13-03.13.13-374


title: 00000-37C.CO2.90m-2-02.19.13-03.13.13-355

description: wildtype in 37°C + CO2 for 90mins


title: 04353-37C.CO2.90m-3-02.19.13-03.13.13-365


title: 07680-37C.CO2.90m-3-09.25.12-10.16.12-347

description: HAP5(CNAG_07680)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-02.19.13-03.13.13-354

description: wildtype in 37°C + CO2 for 90mins


title: 07680-37C.CO2.90m-2-09.25.12-10.16.12-346


title: 00000-37C.CO2.90m-1-09.25.12-10.16.12-342

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-09.21.12-10.16.12-333

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-09.25.12-10.16.12-343

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-09.25.12-10.16.12-344

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-09.21.12-10.16.12-332

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-09.21.12-10.16.12-331

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-09.13.12-09.20.12-324

description: wildtype in 37°C + CO2 for 90mins


title: 00440-37C.CO2.90m-1-08.31.12-09.06.12-307

description: SSN801(CNAG_00440)Δ in 37°C + CO2 for 90mins


title: 00440-37C.CO2.90m-2-08.31.12-09.06.12-308


title: 00000-37C.CO2.90m-3-09.11.12-09.20.12-312

description: wildtype in 37°C + CO2 for 90mins


title: 05431-37C.CO2.90m-2-08.31.12-09.06.12-305

description: RIM101(CNAG_05431)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-09.11.12-09.20.12-310

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-09.13.12-09.20.12-322

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-09.13.12-09.20.12-323

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-08.31.12-09.06.12-303

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-09.11.12-09.20.12-311

description: wildtype in 37°C + CO2 for 90mins


title: 07797-37C.CO2.90m-3-08.17.12-09.06.12-294

description: CLR6(CNAG_07797)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-08.31.12-09.06.12-302

description: wildtype in 37°C + CO2 for 90mins


title: 07797-37C.CO2.90m-2-08.17.12-09.06.12-293


title: 05431-37C.CO2.90m-1-08.31.12-09.06.12-304


title: 00000-37C.CO2.90m-1-08.31.12-09.06.12-301

description: wildtype in 37°C + CO2 for 90mins


title: 00440-37C.CO2.90m-3-08.31.12-09.06.12-309


title: 07680-37C.CO2.90m-1-09.25.12-10.16.12-345


title: 06352-37C.CO2.90m-1-02.19.13-03.13.13-357


title: 07797-37C.CO2.90m-1-08.17.12-09.06.12-292


title: 00000-37C.CO2.90m-3-02.19.13-03.13.13-356

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-08.17.12-09.06.12-291

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-08.10.12-08.20.12-277

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-08.10.12-08.20.12-278

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-08.10.12-08.20.12-279

description: wildtype in 37°C + CO2 for 90mins


title: 02153-37C.CO2.90m-3-07.31.12-08.20.12-273

description: TUP1(CNAG_02153)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-08.17.12-09.06.12-290

description: wildtype in 37°C + CO2 for 90mins


title: 02153-37C.CO2.90m-2-07.31.12-08.20.12-272


title: 05431-37C.CO2.90m-3-08.31.12-09.06.12-306


title: 03202-37C.CO2.90m-1-07.31.12-08.20.12-268

description: CAC1(CNAG_03202)Δ in 37°C + CO2 for 90mins


title: 03202-37C.CO2.90m-2-07.31.12-08.20.12-269


title: 00000-37C.CO2.90m-2-07.31.12-08.20.12-266

description: wildtype in 37°C + CO2 for 90mins


title: 03279-37C.CO2.90m-2-06.29.12-07.28.12-263

description: CCD4(CNAG_03279)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-07.31.12-08.20.12-265

description: wildtype in 37°C + CO2 for 90mins


title: 03279-37C.CO2.90m-3-06.29.12-07.28.12-264


title: 00000-37C.CO2.90m-1-08.17.12-09.06.12-289

description: wildtype in 37°C + CO2 for 90mins


title: 02774-37C.CO2.90m-1-06.29.12-07.28.12-259

description: MAL13(CNAG_02774)Δ in 37°C + CO2 for 90mins


title: 02774-37C.CO2.90m-3-06.29.12-07.28.12-261


title: 02774-37C.CO2.90m-2-06.29.12-07.28.12-260


title: 00000-37C.CO2.90m-1-06.29.12-07.28.12-253

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-06.29.12-07.28.12-255

description: wildtype in 37°C + CO2 for 90mins


title: 02215-37C.CO2.90m-3-06.29.12-07.28.12-258

description: HAP3(CNAG_02215)Δ in 37°C + CO2 for 90mins


title: 06252-37C.CO2.90m-3-07.06.12-07.28.12-249

description: CCD6(CNAG_06252)Δ in 37°C + CO2 for 90mins


title: 07506-37C.CO2.90m-3-07.06.12-07.28.12-252

description: FAP1(CNAG_07506)Δ in 37°C + CO2 for 90mins


title: 03279-37C.CO2.90m-1-06.29.12-07.28.12-262


title: 07506-37C.CO2.90m-2-07.06.12-07.28.12-251


title: 00000-37C.CO2.90m-2-06.29.12-07.28.12-254

description: wildtype in 37°C + CO2 for 90mins


title: 02153-37C.CO2.90m-1-07.31.12-08.20.12-271


title: 02215-37C.CO2.90m-2-06.29.12-07.28.12-257


title: 00000-37C.CO2.90m-3-07.31.12-08.20.12-267

description: wildtype in 37°C + CO2 for 90mins


title: 05067-37C.CO2.90m-2-07.06.12-07.28.12-245

description: CLR5(CNAG_05067)Δ in 37°C + CO2 for 90mins


title: 06252-37C.CO2.90m-1-07.06.12-07.28.12-247


title: 05067-37C.CO2.90m-3-07.06.12-07.28.12-246


title: 05067-37C.CO2.90m-1-07.06.12-07.28.12-244


title: 00000-37C.CO2.90m-1-07.06.12-07.28.12-241

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-07.06.12-07.28.12-243

description: wildtype in 37°C + CO2 for 90mins


title: 03849-37C.CO2.90m-2-04.10.12-05.01.12-239

description: ASG1(CNAG_03849)Δ in 37°C + CO2 for 90mins


title: 03849-37C.CO2.90m-3-04.10.12-05.01.12-240


title: 03849-37C.CO2.90m-1-04.10.12-05.01.12-238


title: 03202-37C.CO2.90m-3-07.31.12-08.20.12-270


title: 06252-37C.CO2.90m-2-07.06.12-07.28.12-248


title: 00732-37C.CO2.90m-3-04.06.12-07.02.12-237

description: CCD3(CNAG_00732)Δ in 37°C + CO2 for 90mins


title: 00732-37C.CO2.90m-1-04.06.12-07.02.12-235


title: 00031-37C.CO2.90m-3-04.06.12-07.02.12-234

description: MLR1(CNAG_00031)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-07.06.12-07.28.12-242

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-04.06.12-07.02.12-231

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-04.06.12-07.02.12-229

description: wildtype in 37°C + CO2 for 90mins


title: 00031-37C.CO2.90m-2-04.06.12-07.02.12-233


title: 05420-37C.CO2.90m-3-04.10.12-05.01.12-222

description: USV101(CNAG_05420)Δ in 37°C + CO2 for 90mins


title: 05420-37C.CO2.90m-2-04.10.12-05.01.12-221


title: 05420-37C.CO2.90m-1-04.10.12-05.01.12-220


title: 00000-37C.CO2.90m-2-04.06.12-07.02.12-230

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-04.10.12-05.01.12-219

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-04.10.12-05.01.12-218

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-04.10.12-05.01.12-217

description: wildtype in 37°C + CO2 for 90mins


title: 03018-37C.CO2.90m-2-04.13.12-05.01.12-215

description: ASG101(CNAG_03018)Δ in 37°C + CO2 for 90mins


title: 01523-37C.CO2.90m-2-04.13.12-05.01.12-212

description: HOG1(CNAG_01523)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-04.13.12-05.01.12-209

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-04.13.12-05.01.12-210

description: wildtype in 37°C + CO2 for 90mins


title: 01523-37C.CO2.90m-1-04.13.12-05.01.12-211


title: 00000-37C.CO2.90m-1-04.13.12-05.01.12-208

description: wildtype in 37°C + CO2 for 90mins


title: 00732-37C.CO2.90m-2-04.06.12-07.02.12-236


title: 00000-37C.CO2.90m-3-02.08.12-05.01.12-201

description: wildtype in 37°C + CO2 for 90mins


title: 00440-37C.CO2.90m-1-12.07.11-03.26.12-198

description: SSN801(CNAG_00440)Δ in 37°C + CO2 for 90mins


title: 05431-37C.CO2.90m-2-12.07.11-03.26.12-196

description: RIM101(CNAG_05431)Δ in 37°C + CO2 for 90mins


title: 05431-37C.CO2.90m-1-12.07.11-03.26.12-195


title: 00000-37C.CO2.90m-3-12.07.11-03.26.12-194

description: wildtype in 37°C + CO2 for 90mins


title: 05431-37C.CO2.90m-3-12.07.11-03.26.12-197


title: 05222-37C.CO2.90m-3-12.06.11-03.26.12-192

description: NRG1(CNAG_05222)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-2-12.07.11-03.26.12-193

description: wildtype in 37°C + CO2 for 90mins


title: 05222-37C.CO2.90m-1-12.06.11-03.26.12-190


title: 05222-37C.CO2.90m-2-12.06.11-03.26.12-191


title: 01551-37C.CO2.90m-3-12.06.11-03.26.12-189

description: GAT201(CNAG_01551)Δ in 37°C + CO2 for 90mins


title: 03018-37C.CO2.90m-3-04.13.12-05.01.12-216


title: 01551-37C.CO2.90m-2-12.06.11-03.26.12-188


title: 00000-37C.CO2.90m-3-12.06.11-03.26.12-186

description: wildtype in 37°C + CO2 for 90mins


title: 00871-37C.CO2.90m-3-12.08.11-03.19.12-183

description: CLR3(CNAG_00871)Δ in 37°C + CO2 for 90mins


title: 01551-37C.CO2.90m-1-12.06.11-03.26.12-187


title: 00000-37C.CO2.90m-2-12.06.11-03.26.12-185

description: wildtype in 37°C + CO2 for 90mins


title: 06276-37C.CO2.90m-3-12.08.11-03.19.12-180

description: CEP3(CNAG_06276)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-12.06.11-03.26.12-184

description: wildtype in 37°C + CO2 for 90mins


title: 00871-37C.CO2.90m-2-12.08.11-03.19.12-182


title: 00871-37C.CO2.90m-1-12.08.11-03.19.12-181


title: 00440-37C.CO2.90m-2-12.07.11-03.26.12-199


title: 06276-37C.CO2.90m-2-12.08.11-03.19.12-179


title: 06276-37C.CO2.90m-1-12.08.11-03.19.12-178


title: 00000-37C.CO2.90m-2-12.08.11-03.19.12-176

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-12.08.11-03.19.12-177

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-12.08.11-03.19.12-175

description: wildtype in 37°C + CO2 for 90mins


title: 04093-37C.CO2.90m-3-12.09.11-03.19.12-174

description: YRM103(CNAG_04093)Δ in 37°C + CO2 for 90mins


title: 04093-37C.CO2.90m-2-12.09.11-03.19.12-173


title: 04093-37C.CO2.90m-1-12.09.11-03.19.12-172


title: 04908-37C.CO2.90m-1-12.09.11-03.19.12-169

description: CLR4(CNAG_04908)Δ in 37°C + CO2 for 90mins


title: 04908-37C.CO2.90m-2-12.09.11-03.19.12-170


title: 04908-37C.CO2.90m-3-12.09.11-03.19.12-171


title: 00000-37C.CO2.90m-1-12.09.11-03.19.12-166

description: wildtype in 37°C + CO2 for 90mins


title: 00570-37C.CO2.90m-3-12.12.11-03.12.12-165

description: PKR1(CNAG_00570)Δ in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-12.09.11-03.19.12-168

description: wildtype in 37°C + CO2 for 90mins


title: 00570-37C.CO2.90m-2-12.12.11-03.12.12-164


title: 00570-37C.CO2.90m-1-12.12.11-03.12.12-163


title: 00000-37C.CO2.90m-2-12.12.11-03.12.12-161

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-1-12.12.11-03.12.12-160

description: wildtype in 37°C + CO2 for 90mins


title: 00000-37C.CO2.90m-3-12.12.11-03.12.12-162

description: wildtype in 37°C + CO2 for 90mins


title: 00883-37C.CO2.90m-3-12.14.11-02.13.12-150

description: ECM2201(CNAG_00883)Δ in 37°C + CO2 for 90mins