title: WT5w2

city: Turku

first: Kati

last: Elima

address: Tykistökatu 6

department: MediCity

country: Finland

institute: University of Turku

data_processing:
Basecalls performed using the instrument manufacturer’s (Illumina HiSeq2000 ) Pipeline v1.5+ base calling software
Data filtering was as follows: the adaptor sequences were removed, the reads in which the precentage of unkonown bases is greater that 10% were removed, low quality reads were removed (the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality)
the reads were aligned against the mouse reference genome and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
gene expression level is calculated by using RPKM method
The strict algorithm used in identifying differentially expressed genes between two samples is described in Audic, S. and J. M. Claverie (1997). The significance of digital gene expression profiles. Genome Res 7(10): 986-95.
NOIseq method was used to screen differentially expressed genes between groups (Tarazano et al 2011 Genome Res 21: 2213)
Filtering of differentially expressed genes was done using the following thresholds: FDR ≤0.001 and the absolute value of log2Ratio ≥1 as the threshold
Supplementary_files_format_and_content: tab-delimited text files include RPKM values with annotations for each sample

source_name: liver tissue

extract_protocol:
RNA was extracted from 5 week old mouse liver tissue using the Nucleo-Spin RNA RNA Isolation Kit (Macherey-Nagel), and the quality of the isolated RNA was checked with the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols at BGI

tag: genotype/variation

value: wild-type

value: 5 week old

value: liver


title: Germinal-input-R2

status: Public on Jul 15 2016

type: SRA

city: Farmington

first: Jethro

last: Johnson

state: CT

address: 10 Discovery Drive

country: USA

institute: Jackson Laboratory for Genomic Medicine

library_source: genomic

data_processing:
fastq files were created with CASAVA 1.8.1
ChIP-seq reads were trimmed to a common length (40bp) and aligned to the mm10 genome assembly using BWA version 0.7.8 with the following configurations: -l 28 -k 2 -n 4
Aligned input samples were pooled and peaks were called  at a p value threshold of 0.005 using macs2 version 2.0.10 with default parameters.
An optimal peak set was generated for each cell type using the ENCODE Irreproducibility Discovery Rate (IDR) pipeline using a pooled consistency threshold of q < 0.005.
Genome_build: mm10
Supplementary_files_format_and_content: ENCODE narrowPeak

molecule: genomic DNA

organism: Mus musculus

source_name: Germinal Center B cells

extract_protocol:
Female mouse C57BL/6 B cell populations were sorted on BD FACSAriaII, BD Influx or Beckman Coulter MoFlo XDP cell sorters; collected cells were centrifuged and cross-linked with 1% formaldehyde and sonicated to shear the chromatin to ~500bp fragments; DNA was isolated with antibodies and purified by phenol-chloroform extraction
Libraries were prepared with Illumina's DNA Sample prep kit according to the manufacturer's instructions

tag: strain

tag: tissue

value: Spleen

tag: age

value: 7 weeks

tag: Sex

value: Female

tag: immunization

value: SRBC

tag: flow strategy

tag: chip antibody


title: KO5w5

library_source: transcriptomic

molecule: total RNA

value: Stab1 knock-out


title: WT5w3


title: Germinal-input-R1


title: KO5w4


title: KO5w3


title: KO5w2


title: KO5w1


title: Marginal-H3K4me3-R2

source_name: Marginal Zone B cells

value: 7-9 weeks


title: Bcell-b1a-R5

description: PolyA+ RNA

data_processing:
fastq files were created with CASAVA 1.8.1
Sequenced reads were mapped to mm10 using STAR version 2.3.0e with parameters  --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated
The number of reads mapping to protein coding gene annotations from Ensembl version 72 and de novo assembled lncRNA annotations from the current study was determined using featureCounts (Subread version 1.4.3).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited count matrix containing raw read counts for

source_name: B1A B cells

extract_protocol:
Female mouse C57BL/6 B cell populations were sorted on BD FACSAriaII, BD Influx or Beckman Coulter MoFlo XDP cell sorters; collected cells were centrifuged and ressuspended in Trizol and RNA was extracted with the Rneasy kit (Qiagen) according to the manufacturer's instructions
Libraries were prepared with Illumina's TruSeq stranded mRNA Sample Preparation kit according to the manufacturer's instructions

value: Peritoneal cavity


title: latecEC_15c

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

department: pRED

country: Switzerland

institute: Roche

description: processed data file: EC_Model_Cyno_counts.gct

data_processing:
Illumina CASAVA v1.8.2  software used for basecalling and fastq file generation
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Cynomolgus monkey genome version 5.0 (Ebeling et al. 2011, PMID: 21862625. Equivalent to MacFas_Jun2011)for monkey samples or to the human genome (GRCh38/hg38) for human samples, respectively, using bowtie2
Reads Counts were calculated using HTSeq. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted to generate read count values at the gene level for each sample
Genome_build: Cynomolgus monkey genome version 5.0 (Ebeling et al. 2011, PMID: 21862625. Equivalent to MacFas_Jun2011)and human genome (GRCh38/hg38)
Supplementary_files_format_and_content: tab-delimited gct files include read count values at the gene level for each sample, entrez-gene-ID, gene-symbol

organism: Macaca fascicularis

source_name: macaque endothelial cell

growth_protocol: Cynomolgus monkey IPSCs (cIPSCs) were established from fibroblasts derived from kidney fibroblasts from a female, 14 year old Cynomolgus monkey using Sendai virus particles (Invitrogen Cytotune) and the Yamanaka factors (Oct4, Sox2, Klf4, C-Myc). cIPSCs  were cultured on matrigel (BD Bioscience) coated plates supplemented with Y-27632 (Calbiochem). Human IPSCs (hIPSC) derived from neonatal foreskin fibroblasts were cultured on matrigel-coated plates in mTesR1 (StemCell Technologies) medium including supplements. Human primary cells (from Lonza: HUVEC, HSVEC; from Cascade Biologics: HPAEC) were grown until confluency in EGM-2 medium (Lonza).

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: TAGCTT

treatment_protocol: IPSCs were detached using Accutase (Stem Cell Technologies) and seeded on growth factor reduced matrigel (BD Bioscience) in the corresponding stem cell medium (mTesR1 for hIPSCs, MT medium for cIPSCs) supplemented with 10 µM Rock Inhibitor Y-27632. After 24 hours, cells were washed with PBS and covered with priming medium consisting of N2B27 supplemented with 25ng/ml BMP4 (Gibco) and 1 µM CP21 (Roche). After priming period (between 3-4 days), cells were washed and medium was switched to induction medium consisting of StemPro34-SFM complete (Gibco) supplemented with 200ng/ml VEGF (Peprotech) and 2µM Forskolin. Induction medium was changed every other day.  At day 6 of differentiation, ECs were dissociated with Accutase or 0.05% Trypsin-EDTA and MACS-separated using CD144 MicroBeads (Miltenyi Biotec) and an autoMACSpro separator (Miltenyi Biotec). Positive sorted cells were replated on human fibronectin (Sigma-Aldrich) coated dishes in EC expansion medium consisting of StemPro-34 SFM supplemented with 50ng/ml VEGF.

tag: cell type

value: IPSC-derived endothelial cell (EC)

tag: time

tag: treatment

value: N2B27-CP21-BMP4 (2d), Stempro-VEGF-FSK (3d), Stempro-VEGF (9d)

tag: macs-separation

value: CD144+, MACS-separated using CD144 MicroBeads (Miltenyi Biotec)


title: Marginal-H3K4me1-R3


title: Bcell-b1a-R4

description: PolyA+ RNA


title: latecEC_15b

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: ACTTGA


title: Marginal-H3K4me3-R1


title: Marginal-H3K4me1-R2


title: latecEC_15a

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: ATCACG


title: Bcell-b1a-R3

description: PolyA+ RNA


title: Marginal-input-R3


title: Bcell-b1a-R1

description: PolyA+ RNA


title: Bcell-b1a-R2

description: PolyA+ RNA


title: latecEC_11b

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: GATCAG

value: N2B27-CP21-BMP4 (2d), Stempro-VEGF-FSK (3d), Stempro-VEGF (5d)


title: latecEC_11c

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: CGTACG


title: WT5w1


title: Bcell-germinal-R15

description: PolyA+ RNA


title: earlycEC_6c

value: N2B27-CP21-BMP4 (2d), Stempro-VEGF-FSK (3d)


title: Marginal-input-R1


title: latecEC_11a

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: TTAGGC


title: Bcell-germinal-R14

description: PolyA+ RNA


title: Marginal-input-R2


title: earlycEC_6b


title: Marginal-H3K4me1-R1


title: earlycEC_6a


title: Bcell-germinal-R12

description: PolyA+ RNA


title: cMPG_5c

source_name: macaque mesodermal progenitor

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: ACTGAT

value: IPSC-derived mesodermal progenitor

value: N2B27-CP21-BMP4 (2d), Stempro-VEGF-FSK (2d)


title: Follicular-H3K4me1-R3

source_name: Follicular B cells


title: Follicular-H3K4me3-R2


title: Bcell-germinal-R11

description: PolyA+ RNA


title: cMPG_5b

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: GTTTCG


title: Follicular-H3K4me1-R2


title: Follicular-input-R3


title: Bcell-marginal-R13

description: PolyA+ RNA


title: cMPG_4c

value: N2B27-CP21-BMP4 (2d), Stempro-VEGF-FSK (1d)


title: Follicular-input-R2


title: Bcell-marginal-R12

description: PolyA+ RNA


title: cMPG_4a


title: Follicular-input-R1


title: Follicular-H3K4me3-R3


title: Bcell-germinal-R13

description: PolyA+ RNA


title: Mature-H3K4me3-R5

source_name: Mature B cells

value: Bone marrow


title: Bcell-follicular-R15

description: PolyA+ RNA


title: Mature-H3K4me3-R4


title: cMPG_3c

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: GAGTGG


title: Bcell-follicular-R14

description: PolyA+ RNA


title: cMPG_3b

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: GTGGCC


title: Mature-H3K4me1-R2


title: cMPG_5a

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: ATTCCT


title: Bcell-marginal-R15

description: PolyA+ RNA


title: Bcell-follicular-R12

description: PolyA+ RNA


title: Bcell-marginal-R14

description: PolyA+ RNA


title: Mature-H3K4me1-R1


title: Bcell-follicular-R13

description: PolyA+ RNA


title: Mature-input-R5


title: cIPSC_0b

source_name: macaque induced pluripotent stem cell

value: induced pluripotent stem cell (IPSC)

value: MT-MG


title: Follicular-H3K4me1-R1

value: Spleen


title: cIPSC_0c


title: cMPG_4b


title: Bcell-follicular-R11

description: PolyA+ RNA

value: Female


title: cIPSC_0a


title: Mature-input-R4


title: Mature-input-R2


title: Bcell-mature-R4

description: PolyA+ RNA


title: Bcell-marginal-R11

description: PolyA+ RNA


title: Bcell-mature-R1

description: PolyA+ RNA


title: Immature-H3K4me3-R5

source_name: Immature B cells


title: Mature-input-R1


title: Bcell-mature-R2

description: PolyA+ RNA


title: Immature-H3K4me1-R5


title: Immature-H3K4me3-R4


title: Bcell-immature-R5

description: PolyA+ RNA


title: Immature-H3K4me1-R1


title: Bcell-immature-R4

description: PolyA+ RNA


title: Immature-input-R4


title: Immature-input-R5


title: Bcell-mature-R3

description: PolyA+ RNA


title: Immature-input-R1


title: Bcell-immature-R1

description: PolyA+ RNA


title: Bcell-immature-R2

description: PolyA+ RNA


title: Pre-H3K4me3-R6

source_name: Pre B cells


title: Bcell-immature-R3

description: PolyA+ RNA


title: Bcell-pre-R5

description: PolyA+ RNA


title: total scnRNAs from PDD1 KO cells rescued with PDD1-MIM22 mutant (20264)

city: Vienna

first: Kensuke

last: Kataoka

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA

description:
Sample 7
small RNA seq

data_processing:
Following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed.
Genome_build: Tetra_therm_micronuc_V2 (https://www.ncbi.nlm.nih.gov/bioproject/51571)
Supplementary_files_format_and_content: Normalized numbers (RPKM) of sequenced 26-32-nt RNAs that map uniquely to the MIC super contig (SC)1: 2,000,001-2,300,000 or the SC114: 1-300,000 genome are shown as histograms with 100-bp bin.

organism: Tetrahymena thermophila

source_name: Conjugating cells at 3 hpm

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30 °C. For conjugation, growing cells (~5-7 x 105/ml) of two different mating types were washed, pre-starved (~12-24 hr) and mixed in 10 mM Tris (pH 7.5) at 30 °C.

extract_protocol: RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24

value: PDD1 KO rescued with PDD1-MIM22 mutant

value: conjugating cells

value: 3 hpm


title: Bcell-pre-R4

description: PolyA+ RNA

value: 7-9 weeks


title: Pre-H3K4me1-R3


title: Pre-H3K4me3-R3


title: Bcell-mature-R5

description: PolyA+ RNA


title: total scnRNAs from PDD1 KO cells rescued with PDD1-MUT26 mutant (35264)

description:
Sample 5
small RNA seq

value: PDD1 KO rescued with PDD1-MUT26 mutant


title: Pre-H3K4me1-R1


title: Bcell-pre-R2

description: PolyA+ RNA


title: Pre-input-R6


title: total scnRNAs from PDD1 KO cells rescued with wild-type PDD1 (20265)

description:
Sample 4
small RNA seq

source_name: Conjugating cells at 10.5 hpm

value: PDD1 KO rescued with wild-type PDD1


title: cMPG_3a

extract_protocol:
at different treament time points cells were resuspended in QIAzol for cell lysis and the lysate was processed with miRNeasy Mini kit combined with DNase treatment on a solid support for RNA extraction (Qiagen Inc., USA). RNA quality with RIN values > 9.7 was determined by electrophoresis on Agilent RNA 6000 Nano Bioanalyzer microfluidic chips.
For RNA-sequencing library preparation, 500 ng total RNA was used as input. First, mRNA was enriched using Oligo-dT-containing capture beads using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina #RS-122-2101). Enriched mRNA was resuspended in TruSeq Fragmentation buffer and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of barcoded sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). 6 barcoded samples were pooled to fit onto 1 lane of an Illumina flow cell containing in total 8 lanes. Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing.
barcode: GGCTAC


title: total scnRNAs from PDD1 KO cells rescued with PDD1-MIM22 mutant (20267)

description:
Sample 8
small RNA seq


title: Pre-input-R3


title: Bcell-pro-R5

description: PolyA+ RNA

source_name: Pro B cells


title: Bcell-pre-R1

description: PolyA+ RNA


title: total scnRNAs from PDD1 KO cells @10.5 hpm (18293)

description:
Sample 2
small RNA seq

value: PDD1 KO


title: Pre-input-R1


title: total scnRNAs from PDD1 KO cells @3 hpm (11197)

description:
Sample 1
small RNA seq


title: total scnRNAs from PDD1 KO cells rescued with wild-type PDD1 (20262)

description:
Sample 3
small RNA seq


title: Bcell-pro-R3

description: PolyA+ RNA


title: Pro-H3K4me3-R5


title: Bcell-pro-R4

description: PolyA+ RNA


title: Pro-H3K4me3-R4


title: Pro-H3K4me1-R5


title: total scnRNAs from PDD1 KO cells rescued with PDD1-MUT26 mutant (35265)

description:
Sample 6
small RNA seq


title: Bcell-pro-R2

description: PolyA+ RNA


title: Bcell-pre-R3

description: PolyA+ RNA


title: Input for ChIP (Sample 11) from new MACs of PDD1 KO rescued with PDD1-MUT26 mutant

description: Sample 10

data_processing:
The first 36-nt sequences of the reads that map to the micronuclear genome were used in downstream analyses
The numbers of normalized sequence reads (RPMs) from the ChIP sample that mapped to each 100-bp bin were divided by the numbers of reads from the Input sample, and these normalized scores were mapped to a representative 100-kb MIC locus, the LMR, as previously described, (Schoeberl et al., 2012) and to a modeled IES consisting of the 5,606 predicted IESs that range from 1-5 kb in length along with their flanking sequences.
Genome_build: LMR locus: Described in Schoeberl et al. (2012) Genes Dev 26, 1729-42.
Genome_build: IESs: Listed in Schoeberl et al. (2012) Genes Dev 26, 1729-42.
Supplementary_files_format_and_content: histograms of mapped normalized sequence read numbers

source_name: New MACs @ 12 hpm

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30⁰C overnight. To induce conjugation, exponentially growing cells (~3-5x 105/ml) of two different mating types were starved in 10 mM Tris-HCl (pH 7.5) at 30°C for 8-14 h and mixed for conjugation (7x 105/ml) at 30°C.

extract_protocol: Chromatin immunoprecipitation was performed with the new MACs only when their purity was above 80%. Chromatin from the new MACs was sheared into 150-500 bp fragments (peak ~300 bp) in Sonication buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.1% SDS, 1x complete protease inhibitor cocktail, 1 mM PMSF) using a probe sonicator. For ChIP, 20 mg of Protein A Sepharose CL-4B beads (GE Healthcare) was washed with TE twice and with ChIP buffer (25 mM Tris-HCl pH 8.0, 167 mM NaCl, 5 mM EDTA, 0.05% SDS, 1% Triton X-100, 1x complete protease inhibitor cocktail, 1 mM PMSF) 3 times and was then pre-incubated with 90 µl of ChIP buffer containing 10 µl of 10 mg/ml BSA (NEB) (total ~200 µl suspension) at 4°C for 1 h. The fragmented chromatin from 2 million new MACs in Sonication buffer was diluted with an equal volume of 2x ChIP dilution buffer (334 mM NaCl, 2% Triton X-100, 1x complete protease inhibitor cocktail), adjusted to 1 ml with ChIP buffer and incubated with a 25 µl suspension of the beads at 4°C for 2 h for the pre-absorption. To couple an antibody to the beads, the 10 µl suspension of the beads pre-incubated with BSA was incubated with an antibody (20 µg anti-H3K9me3, 30 µg anti-H3K27me3 or 5 µg anti-Pdd1p) in 0.5 ml of ChIP buffer at 4°C for 2 h and was then washed with ChIP buffer 3 times. The pre-absorbed chromatin was incubated with the antibody-coupled beads at 4°C overnight. The beads were washed once with Low-salt wash buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) and twice each with High-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), LiCl wash buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% sodium deoxycholate, 1% NP-40) and TE. The immunoprecipitated chromatin was eluted with Elution buffer (0.1 M NaHCO3, 1% SDS). For cross-linking reversal, the NaCl concentration of the sample was adjusted to 200 mM, and the sample was incubated at 65°C for ~12 h. The DNA was extracted, and DNA libraries were generated from the immunoprecipitated DNA and 20 ng of the fragmented chromatin DNA without immunoprecipitation (Input) using the NEBNext DNA Library Prep Reagent Set for Illumina (NEB) and the KAPA Real-Time Library Amplification Kit (KAPA Biosystems). The libraries were sequenced using the HiSeq2000 platform (Illumina) with 50-nt single-end reads.

treatment_protocol: Nuclei from cells at 12 hpm were dissociated and stained with DAPI in TMSN buffer (0.25 M sucrose, 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 3 mM CaCl2, 0.016% NP-40, 1 mM PMSF, 1x complete proteinase inhibitor cocktail (Roche), 0.1 µg/ml DAPI) using a dounce homogenizer with 15 strokes. The nuclear fraction was collected by centrifugation at 4,500 g at 4°C for 5 min and then washed with TMSN buffer once and with TMSN(-) buffer (TMSN buffer without complete proteinase inhibitor cocktail) twice. The nuclei were fixed with 1.25 mg/ml Di(N-succinimidyl) glutarate (Sigma) in PBSN buffer (PBS with 0.016% NP-40) at room temperature for 30 min, collected by centrifugation at 9,000 g at 4°C for 5 min, and washed with PBSN buffer twice. The DSG-fixed nuclei were re-fixed with 1% paraformaldehyde (Sigma) in PBSN buffer at room temperature for 10 min. The paraformaldehyde was quenched with 0.25 M glycine at room temperature for 5 min. The nuclei were washed with PBSN buffer containing 0.1 µg/ml DAPI twice and then with PBSN(+) buffer (PBSN with 1x complete proteinase inhibitor cocktail and 0.1 µg/ml DAPI) once, and the nuclear pellet was stored at -80°C. The nuclei were resuspended in PBSN(+), and the new MACs were collected according to their size and DAPI intensity using a FACSAria III (BD Biosciences). The purity of the collected new MACs was assessed by immuno-DNA-FISH using a Cy3-labeled probe against Tlr1 and an anti-Pdd1p antibody (Abcam) for wild-type, JUB1 KO, WT-rescue and MIM22 cells or an anti-H3K4me3 (Abcam) antibody for PDD1 KO cells: Tlr1-negative nuclei were counted as parental (old) MACs; Tlr1-positive, and Pdd1p- or H3K4me3-positive nuclei were counted as new MACs; Tlr1-positive but Pdd1p- or H3K4me3-negative nuclei were counted as MICs. Contamination of the parental MACs was rare (<2%), and most of the contaminants in our new MAC preparations were MICs.

value: none (input)

value: new macronuclei (MACs)

value: 12 hpm


title: Pro-H3K4me1-R1


title: Bcell-pro-R1

description: PolyA+ RNA


title: Pdd1p ChIP from new MACs of PDD1 KO rescued with PDD1-MUT26 mutant

description: Sample 11

value: anti-Pdd1p (Abcam, catalog#:ab5338, lot#:GR44706-1)


title: 1g_BTN3_C25_IL3971-710-502_CGAGGCTG-CTCTCTAT BTN03 Mic-scRNA-Seq

city: Stanford

first: Stephen

last: Quake

state: CA

address: 450 Serra Mall

institute: Stanford Department of Bioengineering

description: polyA RNA Mic-scRNA-Seq

data_processing:
Aligned using STAR
Genes which overlapped with intergenic regions, introns, or multiples genes removed
Number of reads aligning to each gene counted
Genome_build: mm10
Supplementary_files_format_and_content: matrix, samples as rows and genes as columns. data is is log10(counts per million reads)

molecule: polyA RNA

source_name: striatum

extract_protocol:
Acute brain slices were cut from 5-7 weeks old male mouse and after papain treatment dissociated mechanically (SI Methods). Live cells were purified by either magnetic bead-activated cell sorting (MACS;Miltenyi Biotec) or by fluorescence-activated cell sorting (FACS). For cell type specific isolation genetically labeled MSN subtypes D1-, D2-MSN, and astrocytes were purified by FACS.
Single cells were captured on a microfluidic chip on the C1 system (Fluidigm) and whole-transcriptome amplified cDNA was prepared on chip using theSMARTer Ultra LowRNAkit for Illumina (Clontech). For smart-seq2 protocol, three MSN populations (D1-MSN tdTom+, D1-MSN GFP+ and tdTom+/GFP+ MSNs) sorted individually into 96 well plates with lysis buffer and spun down and frozen at -80°C and amplified using the protocol as described previously (Picelli et al., 2013). Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

tag: experiment

tag: major cell type

value: Astro

tag: protocol

value: Mic-scRNA-Seq


title: p19R2

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

description: biological replicate 2

data_processing:
The MiSeq generated FASTQ files were imported in CLC genomics workbench v6.5 discarding reads with poor quality (<Q30). Read duplicates were removed from each sample independently using the duplicate read removal plugin, Illumina adapter residues were then trimmed using the TruSeq adaptor sequence and finally filtered using the following criteria: low sequence quality <0.01, maximum of 2 ambiguous nucleotides, read length between 35 and 80 nucleotides.
FASTQ files were imported in CLC genomics workbench v8.0.1 discarding poor quality reads (<Q30). For each library, reads were trimmed and filtered using the following criteria: sequence quality <0.01, no ambiguous nucleotides, minimum read length >35 nucleotides, trimming against the Illumina adaptor sequence, and finally a hard trim of 10 nucleotides at the 5’ end and 2 nucleotides at the 3’ end. The filtered reads were mapped to the N. benthamiana transcriptome v5-primary transcript (Nakasuki et al. 2014) obtained from the N. benthamiana genome and transcriptome website (http://benthgenome.qut.edu.au/) with the following criteria: a mismatch, gap and insertion cost on the maximum settings (stringent mapping), mapped reads having more than 5 hits were removed reads should have 80% identity and 50% coverage to the reference transcriptome. The remaining unmapped reads were then re-mapped against the transcriptome v5-alternate transcripts following the same criteria. An additional annotation of the transcriptome was performed against the A. thaliana database using BLAST2GO Pro v3.0. Expression values were calculated using the RPKM (Reads per kilobase transcript per million reads) method (Mortazavi et al. 2008). Differentially expressed genes between the tobacco leaves infiltrated with A. tumefaciens GV3101 (pMP90, P103::MDP0000320772) and control were statistically determined using a Baggerley’s ‘on proportions’ weighted test (Baggerly et al. 2003), a false discovery rate corrected p-value (Benjamini-Hotchberg correction) was set at 0.01, a fold-change cut-off value set at 10-fold increase or decrease in expression, and a minimum mean RPKM difference between both groups set at 10.
Genome_build: N. benthamiana transcriptome v5-primary and alternate transcript (Nakasuki et al. 2014)
Supplementary_files_format_and_content: tab-delimited text files include, unique and toal hit reads, RPKM values for each Sample; Log2 transformed fold change for each contig.

organism: Nicotiana benthamiana

source_name: Nicotiana benthamiana leaves infiltrated with Agrobacterium tumefaciens transformed with pBIN61(P19) only (control)

growth_protocol: The two Agrobacterium tumefaciens GV3101-pMP90 strains (p103::MDP0000320772 and pBIN61-P19) were grown in 50 mL of LB liquid medium supplemented with gentamycin (30 mg/L), rifampicin (10 mg/L), kanamycin (50 mg/L), and acetosyringone (30 mg/mL). The cultures in 100 mL Erlenmeyer flasks were agitated at 130 rpm/28°C for 48 h. After centrifugation (4000 rpm/10 min), cultures were re-suspended in 20 mM MES, 20 mM MgSO4 infiltration buffer supplemented with 150 mg/mL acetosyringone. After 2 hours, p103::MDP0000320772 and pBIN61-P19 A. tumefaciens cultures were adjusted to OD600=0.8 and 1, respectively. Three-weeks old N. benthamiana plants were used for the transient expression study. Plants were divided into two groups, p103::MDP0000320772/pBIN61-p19 and pBIN61-P19(control), each with 4 biological replicates constituted by a pool of 6 plants. For each plant, the four first leaves were infiltrated with 0.5mL infiltration buffer using a 1 mL needleless syringe. After 6 days, the leaves were collected and flash frozen in liquid nitrogen.

extract_protocol:
Total RNA from N. benthamiana leaves was extracted using the RNeasy plant mini kit (QIAGEN, Leusden, The Netherlands) coupled with on-column DNase I treatment, following the manufacturer’s guidelines.  Total RNA integrity (RIN>8) was assessed using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA purity was assessed using a Nanodrop ND1000 spectrophotometer (Thermo scientific, Villebon-sur-Yvette, France). Total RNA was quantified using a Qubit RNA assay kit (Life technologies, Carlsbad, CA, USA).
cDNA libraries were prepared from 10ng mRNA using the SMARTer Stranded RNA-Seq kit according to the manufacturer’s guidelines (ClonTech laboratories, Mountain View, CA, USA). Libraries were analyzed and quantified as described in Legay et al. 2015. The pooled libraries were sequenced on an Illumina MiSeq using 5 consecutive runs (Illumina MiSeq reagent V3-150 cycles) to generate 76 base-pairs paired-end reads.

value: leaves

tag: transformant


title: H3K27me3 ChIP from wild-type new MACs

description: Sample 7

value: wild-type

value: anti-H3K27me3 (Merck Millipore, catalog#:#07-449, lot#:JBC1873477)


title: p19R4

description: biological replicate 4


title: Pro-input-R5

extract_protocol:
Female mouse C57BL/6 B cell populations were sorted on BD FACSAriaII, BD Influx or Beckman Coulter MoFlo XDP cell sorters; collected cells were centrifuged and cross-linked with 1% formaldehyde and sonicated to shear the chromatin to ~500bp fragments; DNA was isolated with antibodies and purified by phenol-chloroform extraction
Libraries were prepared with Illumina's DNA Sample prep kit according to the manufacturer's instructions

value: Bone marrow

value: Female


title: Pro-input-R4


title: H3K9me3 ChIP from wild-type new MACs

description: Sample 6

value: anti-H3K9me3 (Merck Millipore, catalog#:07-442, lot#:2190636)


title: p19R3

description: biological replicate 3


title: 30min-JQ1-replicate2 (PRO-seq)

city: Nashville

first: Scott

middle: W

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

data_processing:
Library strategy: PRO-seq
Base-calling, filtering, and demultiplexing were performed using Illumina CASAVA 1.8.2 (HiSeq 2000) and bcl2fastq2 2.17 (NextSeq) with default settings.
Raw reads were processed to trim adaptor and low quality sequences using Trimmomatic (version 0.32) with parameters: -phred33 input.txt.gz output.txt.gz ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15.
For PRO-seq, reverse complements of the trimmed reads were generated using “fastx_reverse_complement” (version 0.0.13) with default settings, and the reverse complement sequences were aligned to the human genome hg19 using bowtie2 (version 2.2.4) with default settings. For ChIP-exo, pre-processed reads were aligned to hg19 using bowtie2 with default settings. For RNA-seq, pre-processed reads were aligned to hg19 using TopHat (version 2.0.10) with default settings.
H3K27ac peak calling was performed using MACS2 (version 2.0.10) with parameters: MACS2 callpeak -t H3K27ac.bam -c Input.bam --nomodel -f BAM -g hs -n -B.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage was normalized and calculated for each strand separately and reported in bedGraph format. The ChIP-exo peak file reports genome coordinates, peak length, read counts, and enrichment significance for each called H3K27ac peak. RNA-seq count files contain gene RefSeq IDs and their normalized read counts in reads per kilobase of transcript per million mapped reads (RPKM).

molecule: nuclear RNA

organism: Homo sapiens

source_name: t(8;21)-containing acute myeloid leukemia cell line

growth_protocol: RPMI 1640 supplemented with 10% FetalPlex and 2 mM L-Glutamine

extract_protocol:
Nuclei isolation by douncing in isotonic buffer with 0.1% Triton X-100
Nuclear run-on assays were performed with ATP, UTP, GTP, and biotin-11-CTP or with all 4 biotin-11-NTPs. Nuclei were lyzed with TRIzol, nuclear RNA was extracted and fragmented, and biotinylated RNA was purified with strepavidin magnetic beads, which was followed by 3' adaptor ligation, 5' repair, 5' adaptor ligation, reverse transcription, and PCR full-scale amplification.

treatment_protocol: 250 nM JQ1, 30 min

tag: cell line

value: Kasumi-1 cells

value: 250 nM JQ1, 30 min


title: p19R1

description: biological replicate 1


title: MYB93R4

description: biological replicate 4

source_name: Nicotiana benthamiana leaves infiltrated with Agrobacterium tumefaciens transformed with P103(35::MYB93) and pBIN61(P19)


title: 30min-JQ1-replicate1 (PRO-seq)


title: Pro-input-R1

value: 7-9 weeks


title: MYB93R3

description: biological replicate 3


title: 15min-JQ1-replicate2 (PRO-seq)

treatment_protocol: 250 nM JQ1, 15 min

value: 250 nM JQ1, 15 min


title: Pdd1p ChIP from JUB4KO new MACs

description: Sample 4

tag: genotype/variation

value: JUB4 KO


title: MYB93R2

description: biological replicate 2


title: Pdd1p ChIP from new MACs of PDD1 KO rescued with wild-type PDD1

description: Sample 9

value: PDD1 KO rescued with wild-type PDD1


title: 15min-JQ1-replicate1 (PRO-seq)


title: MYB93R1

description: biological replicate 1


title: Input for ChIP (Sample 2) from wild-type new MACs

description: Sample 1

value: none (input)

value: new macronuclei (MACs)


title: Pdd1p ChIP from wild-type new MACs

description: Sample 2

value: anti-Pdd1p (Abcam, catalog#:ab5338, lot#:GR44706-1)

value: 12 hpm


title: Input for ChIP (Sample 4) from JUB4 KO new MACs

description: Sample 3


title: hyphae

city: Danzhou

first: Hanqing

last: Cong

state: Hainan

address: Baodaoxincun

department: Tropical Crops Genetic Resources Institute

country: China

institute: Chinese Academy of Tropical Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
sRNA-seq reads were filtered to remove contaminant reads (reads shorter than 18 nt, reads with 5’ primer contaminants or poly A, or without a 3’ primer or insert tag)
sRNA tags were screened against GenBank and Rfam database version 10.1 (Gardner et al., 2009; Griffiths-Jones et al., 2005) to annotate and remove ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), and small nucleolar RNA (snoRNA) by using Basic Local Alignment Search Tool (BLAST).
All the sRNA reads were screened against the miRBase 21.0 using a BLASTn to identify the conserved milRNAs (Kozomara and Griffiths-Jones, 2014). Meanwhile, the prediction of novel milRNAs was carried out using Mireap program which could identify known miRNAs and novel candidates with canonical hairpin structure, and which was sufﬁciently supported by sequencing data (https://sourceforge.net/projects/mireap).
Expression analysis of two samples was performed using the DEGseq (2010) R package. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Reference genome is Fusarium oxysporum f. sp. melonis (Fom) genome, which was downloaded from the ‘Ensembl Genomes’ (http://fungi.ensembl.org/Fusarium_oxysporum_f_sp_melonis_26406/Info/Index) (Ma et al., 2014), all sRNA reads were mapped to this genome datausing Short Oligo Alignment Program (SOAP) (http://soap.genomics.org.cn) (Li et al., 2008) to map.
Supplementary_files_format_and_content: tab-delimited xls files include miRNA sequences information or DEGseq expression information for each Sample ...
Supplementary_files_format_and_content: fasta:fon_hyphae_sRNA.fa
Supplementary_files_format_and_content: fasta:fon_microconidia_sRNA.fa
Supplementary_files_format_and_content: sequences infromation:fon_hyphae_known_miRNA.xls
Supplementary_files_format_and_content: sequences infromation:fon_microconidia_known_miRNA.xls
Supplementary_files_format_and_content: fasta:fon_hyphae_miRNA_novel.fa
Supplementary_files_format_and_content: fasta:fon_microconidia_miRNA_novel.fa
Supplementary_files_format_and_content: DEGseq expression information:Known_miRNA_Diff_Exp.DEGseq.xls
Supplementary_files_format_and_content: DEGseq expression information:Novel_miRNA_Diff_Exp.DEGseq.xls

organism: Fusarium oxysporum f. sp. niveum

source_name: hyphae of Fusarium oxysporum

growth_protocol: Fusarium oxysporum f. sp. niveum (Fon) was isolated from infected watermelon grown in Hainan province, China.To collect the hyphae and microconidia, Fon were grown at 25 °C on potato dextrose medium at stationary and at 150 rpm on orbital shaker for 5 days, respectively. Fon hyphae were isolated by filtration through a sieve (100 mesh) and microconidia were collected first by filtration then centrifugation (5000 rpm, 10 min), then washed with sterilized distilled water and immediately frozen in liquid nitrogen, stored at -80°C.

extract_protocol:
Fon hyphae were isolated by filtration through a sieve (100 mesh) and microconidia were collected first by filtration then centrifugation (5000 rpm, 10 min), after washed with sterilized distilled water and immediately frozen in liquid nitrogen, stored at -80°C. Total RNA was extracted with Axyprep™ multisource total RNA miniprep kit. sRNA fraction between 18~30 nucleotides (nt) were extracted using 15% polyacrylamide / 8 M urea denaturing gel electrophoresis (PAGE) with radioactively labeled RNA as size markers. After ligated to 5’ and 3’ adapters sequentially using truncated rhythmT4 RNA ligase (Invitrogen, Carlsbad, CA), the sRNAs were reverse converted to cDNA using Superscript III reverse transcriptase (Invitrogen, Carlsbad, CA). PCR ampliﬁcation was performed to enrich the adapter-modiﬁed cDNA libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: propagule

value: hyphae

value: 5 days


title: Input for ChIP (Sample 9)  from new MACs of PDD1 KO rescued with wild-type PDD1

description: Sample 8


title: microconidia

source_name: microconidia of Fusarium oxysporum

value: microconidia


title: 0min-JQ1-replicate2 (PRO-seq)

treatment_protocol: untreated

value: untreated


title: 0min-JQ1-replicate1 (PRO-seq)


title: Nie1-2 (9996)

status: Public on Jul 14 2016

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Base calling was done by RTA version 1.17.20 and 1.18.61. Base call files (bcl) were converted by fastq by CASAVA version 1.8.2.
Sequenced reads were trimmed for adaptor sequence.  Read mapping and counting were performed by the rmake pipeline version 1.0c (http://physiology.med.cornell.edu/faculty/mason/lab/r-make/; Sheng Li, Nat Biot 2014).
Reads were mapped to TAIR10 genome assemly and TAIR10 gene models using the STAR aligner version 2.4.2a with parameters "--runThreadN 11 --outFilterMultimapNmax 1 --readFilesCommand zcat --outSAMunmapped Within --outStd SAM".  STAR index were generated from TAIR10 genome sequences and TAIR10 gene model GTF file and paramter "--ajdbOverhang 99".  Only read1 of the PE reads from HiSeq 4000 were mapped.
Read counts on genes for individual accessions were quantified by the count program in rmake.
To generate the gene by accession expression matrix (supplementary file), raw read counts were first quantile-normalized, then normalized by the RUVg functon in the R package RUVseq version 1.5.0, using a set of 21 reference genes from Wang et al. (Scientific Reports 2014; doi:10.1038/srep06781) with parameter k=4.
Genome_build: TAIR10
Supplementary_files_format_and_content: one tab-delimited text files of raw read counts for each sample

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Plants were grown in long-day growth chamber at 22 degree celsius.

extract_protocol:
Total RNA was extracted from frozen leave tissue from 10 rosettes just before bolting, using the RNeasy Mini Kit according to protocol (QIAGEN).
The mRNA libraries were constructed using the TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) using 1 - 4 µg total RNA, according to manufacturer's instructions with modifications to confer strand specificity. The mRNA was purified using the RNA Purifications Beads as per Illumina protocol instructions. The mRNA was incubated in the Elute, Prime, Fragment Mix at 94˚C for 8 min. After first strand synthesis (as per Illumina protocol instructions), the product was purified using RNAClean XP beads (Beckman, Brea, CA) as per manufacturer's instructions and eluted in 18 µL nuclease free water. Second strand synthesis was performed by adding the RNAClean XP purified product to 2.5 µL 10x NEB Buffer 2 (New England Biolabs, Ipswich, MA), 2 µL dUTP mix (10mM dATPs, 10mM dGTPs, 10mM dCTPs, and 20mM dUTPs), 0.5 µL RNAse H (2 U/µL), 1 µL DNA Polymerase I (E. coli) (New England Biolabs), and 1 µL DTT (100 mM). The 25 µL mixture was incubated at 16˚C for 2.5 hours. The addition of a 3’ A base and Adapter ligation was performed per Ilumina protocol instructions. The purified ligation products were incubated with 2 µL Uracil DNA Glycosylase (Fermentas) before PCR amplification (also done per Illumina protocol specifications 12 cycles). The reaction products were purified using AMPure XP beads according to manufacturer’s specifications. RNA-seq libraries were sequenced using the Illumina HiSeq 2500 (Illumina) with SE 1X100 Single index read or on HiSeq 4000 with 2X150 PE reads.

tag: cultivar

tag: ecotype id

tag: developmental stage

value: before bolting

tag: light condition

value: long day

tag: tissue

value: leaf


title: Star-8 (9998)


title: TueSB30-3 (9999)


title: Rue3.1-31 (9997)


title: Vash-1 (9991)


title: Nemrut-1 (9993)


title: HKT2.4 (9995)


title: Lag2.2 (9990)


title: Dog-4 (9992)


title: Input for ChIP (Samples 6 & 7) from wild-type new MACs

description: Sample 5

value: wild-type

tag: chip antibody


title: Lecho-1 (9987)


title: Slavi-1 (9985)


title: Ciste-1 (9983)


title: Angit-1 (9981)


title: Voeran-1 (9979)


title: Rovero-1 (9976)


title: Ciste-2 (9984)


title: Bozen-1.2 (9972)


title: Mitterberg-1-181 (9973)


title: Altenb-2 (9970)


title: Monte-1 (9966)


title: Moran-1 (9967)


title: Apost-1 (9982)


title: Timpo-1 (9968)


title: Valsi-1 (9969)


title: Bak-7 (9989)


title: Bak-2 (9988)


title: Lago-1 (9963)


title: Mammo-1 (9964)


title: Shigu-2 (9959)


title: Kidr-1 (9960)


title: Krazo-2 (9961)


title: Shigu-1 (9958)


title: Borsk-2 (9957)


title: Kly-1 (9951)


title: Vie-0 (9950)


title: Koz-2 (9953)


title: Ale-Stenar-56-14 (997)


title: Qui-0 (9949)


title: Mer-6 (9946)


title: Angel-1 (9980)


title: Ped-0 (9947)


title: Leo-1 (9945)


title: Don-0 (9944)


title: Agu-1 (9942)


title: Fei-0 (9941)


title: Mammo-2 (9965)


title: Toufl-1 (9940)


title: Leb-3 (9954)


title: CATS-6 (9937)


title: Galdo-1 (9962)


title: Cdm-0 (9943)


title: MOU2-25 (9931)


title: LCL-16 (9936)


title: QUI-8 (9934)


title: ARR-17 (9927)


title: DIR-9 (9920)


title: LEC-25 (9930)


title: SAUL-24 (9918)


title: PLY-20 (9924)


title: BEZ-9 (9928)


title: Kly-4 (9952)


title: WAV-8 (9938)


title: ISS-20 (9929)


title: GEN-8 (9909)


title: ESP-1-11 (9908)


title: ARGE-1-15 (9911)


title: CON-7 (9913)


title: ENC-2-1 (9907)


title: Ven-0 (9905)


title: Vas-0 (9904)


title: Val-0 (9903)


title: Usa-0 (9902)


title: Mah-6 (9906)


title: Urd-1 (9901)


title: VED-10 (9933)


title: FOR-23 (9921)


title: Tau-0 (9899)


title: Som-0 (9898)


title: Smt-1 (9897)


title: Tri-0 (9900)


title: Sfb-6 (9895)


title: Sam-0 (9892)


title: Sal-0 (9891)


title: MAR-4-16 (9915)


title: Sca-0 (9893)


title: Sen-0 (9894)


title: Rib-1 (9890)


title: Pva-1 (9888)


title: Pie-0 (9881)


title: Piq-0 (9883)


title: Pib-1 (9880)


title: Pdl-0 (9877)


title: Per-0 (9879)


title: Pil-0 (9882)


title: Pad-0 (9876)


title: Ovi-1 (9875)


title: Prd-0 (9885)


title: Pee-0 (9878)


title: Ndc-0 (9873)


title: Nac-0 (9871)


title: Oja-0 (9874)


title: Nag-0 (9872)


title: Mie-1 (9867)


title: Mdd-0 (9866)


title: Mat-0 (9864)


title: Pru-0 (9886)


title: Moe-0 (9868)


title: Lro-0 (9859)


title: Mac-0 (9861)


title: Mad-0 (9862)


title: Lch-0 (9856)


title: Lum-0 (9860)


title: Lam-0 (9855)


title: Loz-0 (9858)


title: Laf-1 (9854)


title: Hue-3 (9851)


title: Moz-0 (9870)


title: Hec-0 (9850)


title: Ezc-2 (9846)


title: Gud-3 (9849)


title: Glo-1 (9848)


title: Evs-0 (9845)


title: Ees-0 (9841)


title: Coy-0 (9839)


title: Cot-0 (9838)


title: Elp-0 (9843)


title: Ini-0 (9852)


title: Dar-0 (9840)


title: Cod-0 (9836)


title: Cir-0 (9835)


title: Esn-2 (9844)


title: Cho-0 (9834)


title: Cat-0 (9832)


title: Bur-0 (9829)


title: Bus-0 (9830)


title: Lac-0 (9853)


title: Bra-0 (9828)


title: Bos-0 (9827)


title: Bor-0 (9826)


title: Cas-0 (9831)


title: Aru-0 (9821)


title: Bae-0 (9823)


title: Bes-5 (9824)


title: Ace-0 (9817)


title: Amu-0 (9819)


title: Cha-0 (9833)


title: Pra-6 (9948)


title: Ha-HBT3-11 (9815)


title: Tu-WH (9816)

value: Tu-WH


title: Aitba-2 (9939)


title: Fell1-10 (9814)


title: Tu-W1 (9812)


title: BI-4 (9813)


title: Tu-KB-6 (9809)


title: Tu-NK-12 (9811)


title: Schl-7 (9807)


title: Tu-B2-3 (9808)


title: Boa-0 (9825)


title: Obe1-15 (9804)


title: Ha-SP-2 (9801)


title: Kus3-1 (9802)


title: Pfn-10 (9805)


title: Muh-2 (9803)


title: Hart-2 (9799)


title: Ha-HBT2-10 (9797)


title: Ha-S-B (9800)

value: Ha-S-B


title: Ha-P2-1 (9798)


title: Wank-2 (9795)


title: Lu4-2 (9792)


title: Obh-13 (9789)


title: Tu-B1-2 (9794)


title: Ha-P-13 (9786)


title: KBG1-14 (9788)


title: Ha-HBT1-2 (9785)


title: Bach2-1 (9796)


title: Tu-PK-7 (9783)


title: Haes-1 (9791)


title: Gn2-3 (9790)


title: Erg2-6 (9784)


title: Ru-N2 (9793)


title: Kus2-2 (9781)


title: Ru-2 (9806)


title: Fell2-4 (9780)


title: Bach-7 (9778)


title: Bai-10 (9779)


title: Gn-1 (9777)


title: Lu3-30 (9782)


title: Fell3-7 (9776)


title: Berg-1 (9775)


title: Alt-1 (9774)


title: KBG2-13 (9770)


title: HE-1 (9769)


title: Pfn-N2.2-6 (9771)


title: Hof-1 (9772)


title: Ru4-16 (9768)


title: Etna-2 (9762)


title: Staro-2 (9756)


title: Staro-1 (9757)


title: Anz-0 (9759)


title: Zagub-1 (9748)


title: Zabar-1 (9747)


title: Vajug-1 (9755)


title: Sredn-1 (9754)


title: Iasi-1 (9744)


title: Toc-1 (9739)


title: Teiu-1 (9742)


title: Ulies-1 (9737)


title: Orast-1 (9741)


title: Bran-1 (9738)


title: Bela-4 (9735)


title: Teiu-2 (9736)


title: Bela-2 (9733)


title: Halca-1 (9732)


title: Stiav-3 (9731)


title: Stiav-1 (9728)


title: Stiav-2 (9729)


title: Bela-1 (9730)


title: Slavi-2 (9723)


title: Knjas-1 (9749)


title: Malii-1 (9746)


title: Epidauros-1 (9725)


title: Furni-1 (9743)


title: Schip-1 (9721)


title: Sij 1/96 (9745)


title: Kardz-2 (9717)


title: Koren-1 (9719)


title: Bela-3 (9734)


title: Olympia-2 (9727)


title: Dolna-1 (9712)


title: Stara-1 (9713)


title: Zerev-1 (9709)


title: Choto-1 (9705)


title: Podvi-1 (9707)


title: Dospa-1 (9706)


title: Dolna-1 (9711)


title: Melni-1 (9703)


title: Zerev-1 (9710)


title: Faneronemi-3 (9726)


title: Kolar-2 (9702)


title: Grivo-1 (9714)


title: Melni-2 (9704)


title: Ivano-1 (9701)


title: Kolar-1 (9699)


title: Goced-1 (9698)


title: Kardz-1 (9708)


title: Malak-1 (9720)


title: Groch-1 (9722)


title: Castelfed-3-209 (9693)


title: Castelfed-3-206 (9690)


title: Castelfed-4-214 (9696)


title: Castelfed-1-199 (9683)


title: Castelfed-2-200 (9684)


title: Castelfed-1-196 (9680)


title: Mitterberg-4-194 (9678)


title: Castelfed-1-195 (9679)


title: Castelfed-1-198 (9682)


title: Mitterberg-3-189 (9673)


title: Mitterberg-2-185 (9669)


title: Mitterberg-1-180 (9665)


title: Mitterberg-1-182 (9666)


title: Teano-1 (9663)


title: Pigna-1 (9659)


title: Sarno-1 (9660)


title: Dolen-1 (9697)


title: Nicas-1 (9658)


title: Giffo-1 (9653)


title: Liri-1 (9654)


title: Marti-1 (9656)


title: Marce-1 (9655)


title: Corig-1 (9650)


title: Filet-1 (9651)


title: Basen-1 (9647)


title: Cimin-1 (9661)


title: Aiell-1 (9646)


title: Gradi-1 (9645)


title: Castelfed-1-197 (9681)


title: Bisig-1 (9648)


title: Bivio-1 (9649)


title: Rakit-3 (9642)


title: Zupan-1 (9644)


title: Rakit-1 (9640)


title: Mitterberg-2-184 (9668)


title: Panke-1 (9639)


title: Noveg-3 (9638)


title: Stilo-1 (9662)


title: Noveg-1 (9636)


title: Noveg-2 (9637)


title: Lebja-4 (9633)


title: Masl-1 (9634)


title: K-oze-3 (9630)


title: Lebja-1 (9631)


title: K-oze-1 (9629)


title: Kolyv-6 (9628)


title: Fondi-1 (9652)


title: Kolyv-5 (9627)


title: Bijisk-4 (9622)


title: Chaba-1 (9623)


title: Basta-3 (9621)


title: Lebja-2 (9632)


title: Chaba-2 (9624)


title: Kolyv-3 (9626)


title: Basta-2 (9620)


title: Basta-1 (9619)


title: Parti-1 (9615)


title: Karag-1 (9617)


title: Lesno-2 (9612)


title: Balan-1 (9613)


title: Krazo-1 (9616)


title: Adam-1 (9609)


title: Karag-2 (9608)


title: Panik-1 (9607)


title: Lesno-1 (9611)


title: Lesno-4 (9610)


title: IP-Vpa-1 (9602)


title: IP-Voz-0 (9601)


title: Aitba-1 (9606)


title: IP-Vig-1 (9597)


title: IP-Vin-0 (9599)


title: IP-Vdm-0 (9594)


title: IP-Vis-0 (9600)


title: IP-Ver-5 (9596)


title: IP-Vaz-0 (9593)


title: IP-Vdt-0 (9595)


title: IP-Vae-2 (9592)


title: IP-Vad-0 (9591)


title: IP-Trs-0 (9590)


title: IP-Ses-0 (9582)


title: IP-Svi-0 (9585)


title: IP-Tam-0 (9586)


title: IP-Sdv-3 (9581)


title: IP-Tol-7 (9588)


title: IP-San-10 (9579)


title: IP-Scm-0 (9580)


title: IP-Sne-0 (9583)


title: IP-Pob-0 (9570)


title: IP-Ren-6 (9575)


title: IP-Rel-0 (9574)


title: IP-Pds-1 (9569)


title: IP-Rev-0 (9576)


title: IP-Rds-0 (9573)


title: IP-Sac-0 (9578)


title: IP-Pue-0 (9572)


title: IP-Oso-0 (9566)


title: IP-Pal-0 (9567)


title: IP-Nav-0 (9563)


title: IP-Pan-0 (9568)


title: IP-Nog-17 (9564)


title: IP-Mur-0 (9562)


title: IP-Tdc-0 (9587)


title: IP-Stp-0 (9584)


title: IP-Ria-0 (9577)


title: IP-Moc-11 (9558)


title: IP-Moa-0 (9557)


title: IP-Men-2 (9556)


title: IP-Lab-7 (9552)


title: IP-Lso-0 (9554)


title: IP-Jim-1 (9551)


title: IP-Mot-0 (9560)


title: IP-Iso-4 (9550)


title: IP-Hor-0 (9547)


title: IP-Hum-2 (9549)


title: IP-Gra-0 (9543)


title: IP-Orb-10 (9565)


title: IP-Her-12 (9545)


title: IP-Fun-0 (9542)


title: IP-Hom-4 (9546)


title: IP-Hoy-0 (9548)


title: IP-Gua-1 (9544)


title: IP-Mon-5 (9559)


title: IP-Cum-1 (9537)


title: IP-Mun-0 (9561)


title: IP-Coc-1 (9535)


title: IP-Cem-0 (9533)


title: IP-Cmo-3 (9534)


title: IP-Cdo-0 (9532)


title: IP-Cur-4 (9538)


title: IP-Ldd-0 (9553)


title: IP-Vim-0 (9598)


title: IP-Cdc-3 (9531)


title: IP-Car-1 (9530)


title: IP-Cap-1 (9529)


title: IP-Bis-0 (9525)


title: IP-Cad-0 (9527)


title: IP-Cab-3 (9526)


title: IP-Ben-0 (9523)


title: IP-Ber-0 (9524)


title: IP-Bea-0 (9522)


title: IP-Elb-0 (9540)


title: IP-All-0 (9517)


title: IP-Ali-1 (9516)


title: IP-Fue-2 (9541)


title: IP-Adm-0 (9514)


title: IP-Adc-5 (9513)


title: IP-Vid-1 (9512)


title: IP-Ala-0 (9515)


title: IP-Rei-0 (9510)


title: IP-Reg-0 (9509)


title: IP-Mos-1 (9508)


title: IP-Alm-0 (9518)


title: Spro 2 (9451)

value: Spro 2


title: 11C1 (9503)


title: IP-Alo-0 (9506)


title: Lan 1 (9421)

value: Lan 1


title: Kia 1 (9409)

value: Kia 1


title: IP-Coa-0 (9507)


title: HolA-1 2 (9405)

value: HolA-1 2


title: Nyl 13 (9433)

value: Nyl 13


title: HolA-1 1 (9404)

value: HolA-1 1


title: Gron 12 (9386)

value: Gron 12


title: IP-Ara-4 (9520)


title: Adal 1 (9321)

value: Adal 1


title: Gron 14 (9388)

value: Gron 14


title: IP-Ang-0 (9519)


title: CHA-41 (932)


title: Kal 1 (9408)

value: Kal 1


title: Gol-2 (9314)


title: Ullapool-8 (9312)


title: LIN S-5 (915)

value: LIN S-5


title: Yeg-7 (9133)

value: before bolting


title: Yeg-5 (9131)

value: long day


title: Yeg-8 (9134)

value: leaf


title: Yeg-4 (9130)


title: Yeg-2 (9128)


title: IP-Bar-1 (9521)


title: Edinburgh-1 (9298)


title: IP-Vav-0 (9511)


title: Bak-5 (9121)


title: Lag2-4 (9111)


title: Lag2-6 (9113)


title: Lag2-10 (9115)


title: Geg-14 (9125)


title: Lag1-8 (9106)


title: Lag2-7 (9114)


title: Lag1-7 (9105)


title: Istisu-5 (9095)


title: Lag1-6 (9104)


title: Lag1-4 (9102)


title: Nar-3 (9089)


title: Nar-5 (9091)


title: Lerik2-7 (9085)


title: Istisu-9 (9099)


title: Lerik2-6 (9084)


title: Lag1-5 (9103)


title: Lerik2-1 (9079)


title: Lerik1-7 (9078)


title: MIC-31 (870)


title: Lerik1-4 (9075)


title: 328ME059 (8584)


title: LP3413.41 (8472)


title: Xan-3 (9067)


title: Uod-2 (8428)


title: Wil-1 (8419)


title: Kas-2 (8424)


title: Sr:5 (8386)


title: Sap-0 (8378)


title: Rd-0 (8366)


title: Pa-1 (8353)


title: Pla-0 (8357)


title: Ost-0 (8351)


title: Lag1-2 (9100)


title: Rak-2 (8365)


title: Ge-0 (8297)


title: Lisse (8430)

value: Lisse


title: Lu-1 (8334)


title: Lerik2-3 (9081)


title: DraII-1 (8284)


title: Lip-0 (8325)


title: Na-1 (8343)


title: Mir-0 (8337)


title: En-1 (8290)


title: Cen-0 (8275)


title: Ba5-1 (8259)


title: Bla-1 (8264)


title: San-2 (8247)


title: PHW-34 (8244)


title: Kent (8238)

value: Kent


title: NC-6 (8246)


title: Koln (8239)

value: Koln


title: Gul1-2 (8234)


title: Dem-4 (8233)


title: HSm (8236)

value: HSm


title: Bro1-6 (8231)


title: RMX3.22 (8132)


title: PT2.21 (8077)


title: PNA3.10 (7917)


title: KYC-33 (801)


title: RRS-10 (7515)


title: Zal-1 (768)


title: Lp2-6 (7521)


title: Kar-1 (763)


title: Ber (7458)

value: Ber


title: WAR (7477)

value: WAR


title: Boo2-1 (8266)


title: Jl-3 (7424)


title: Zu-1 (7418)


title: KNO1.37 (7717)


title: Var2-6 (7517)


title: Ko-2 (7427)


title: Wc-1 (7404)


title: Wil-2 (7413)


title: Ws-0 (7396)


title: H55 (7461)


title: Tul-0 (7377)


title: Ven-1 (7384)


title: Tsu-0 (7373)


title: Tscha-1 (7372)


title: Tiv-1 (7355)


title: Tha-1 (7353)


title: Tac-0 (7350)


title: Ste-0 (7346)


title: Sf-2 (7328)


title: Ting-1 (7354)


title: Sf-1 (7327)


title: Rsch-4 (7322)


title: Sapporo-0 (7330)


title: Oy-0 (7288)


title: LI-SET-019 (728)


title: Rhen-1 (7316)


title: Or-0 (7282)


title: Petergof (7296)

value: Petergof


title: Nz-1 (7263)


title: Li-7 (7231)


title: Mnz-0 (7244)


title: Le-0 (7218)


title: Rou-0 (7320)


title: Kb-0 (7202)


title: Hh-0 (7169)


title: Me-0 (7250)


title: Mv-0 (7248)


title: Hi-0 (7167)


title: Hn-0 (7165)


title: Gd-1 (7161)


title: Edi-0 (7111)


title: Dr-0 (7106)


title: Dra-0 (7103)


title: Po-0 (7308)


title: Ct-1 (7067)


title: Bur-0 (7058)


title: Bch-1 (7028)


title: Kn-0 (7186)


title: Do-0 (7102)


title: Bd-0 (7013)


title: Alst-1 (6989)


title: Wei-0 (6979)


title: Ang-0 (6992)


title: Ull2-5 (6974)


title: Uod-7 (6976)


title: Ts-5 (6971)


title: Hau-0 (7164)


title: En-2 (7119)


title: Sq-1 (6966)


title: NFA-10 (6943)


title: Durh-1 (7107)


title: Mt-0 (6939)


title: Hod (8235)

value: Hod


title: Pu2-8 (6957)


title: LL-0 (6933)


title: Ull2-3 (6973)


title: Da-0 (7094)


title: Mrk-0 (6937)


title: HR-10 (6923)


title: Fab-2 (6917)


title: Cvi-0 (6911)


title: CIBC-5 (6908)


title: Buckhorn Pass (7033)

value: Buckhorn Pass


title: NFA-8 (6944)


title: Ts-1 (6970)


title: CIBC-17 (6907)


title: Bil-5 (6900)


title: Ren-11 (6960)


title: C24 (6906)


title: Kz-13 (6830)


title: ANH-1 (6680)


title: LI-EF-018 (687)


title: Bg-2 (6709)


title: UduI 3-36 (6390)

value: UduI 3-36


title: ZdrI 1-23 (6424)

value: ZdrI 1-23


title: CSHL-5 (6744)


title: TV-38 (6284)


title: LI-OF-065 (630)


title: TV-22 (6268)


title: TV-7 (6255)


title: TOM 07 (6241)

value: TOM 07


title: TFA 08 (6218)

value: TFA 08


title: TOM 06 (6240)

value: TOM 06


title: TGR 01 (6220)

value: TGR 01

value: before bolting


title: TDr-16 (6201)

value: long day

value: leaf


title: TAL 03 (6177)

value: TAL 03


title: TDr-13 (6198)


title: TDr-9 (6195)


title: TDr-8 (6194)


title: ZdrI 2-9 (6434)

value: ZdrI 2-9


title: TAD 06 (6174)

value: TAD 06


title: TAD 01 (6169)

value: TAD 01


title: ZdrI 2-21 (6445)

value: ZdrI 2-21


title: TAA 17 (6166)

value: TAA 17


title: UduI 1-11 (6296)

value: UduI 1-11


title: T960 (6148)


title: TAA 04 (6154)

value: TAA 04


title: TAD 03 (6171)

value: TAD 03


title: T930 (6145)


title: T860 (6138)


title: TAA 14 (6163)

value: TAA 14


title: T880 (6140)


title: T850 (6137)


title: T530 (6111)


title: T800 (6133)


title: T480 (6108)


title: TFA 07 (6217)

value: TFA 07


title: T470 (6107)


title: TDr-18 (6203)


title: T460 (6106)


title: T1090 (6099)


title: Sr:3 (6086)


title: Fly2-2 (6024)


title: Gro-3 (6025)


title: Eds-9 (6017)


title: Hov3-5 (6038)


title: T1070 (6097)


title: Lis-3 (6041)


title: Nyl-2 (6064)


title: Eden-1 (6009)


title: DraIV 6-22 (5993)

value: DraIV 6-22


title: DraIV 3-7 (5921)

value: DraIV 3-7


title: DraIV 6-13 (5984)

value: DraIV 6-13


title: DraIV 5-12 (5950)

value: DraIV 5-12

value: before bolting


title: DraIV 1-11 (5893)

value: DraIV 1-11

value: long day

value: leaf


title: Fja1-5 (6020)


title: DraIV 1-8 (5890)

value: DraIV 1-8


title: Duk (6008)

value: Duk


title: DraIV 2-9 (5907)

value: DraIV 2-9


title: Bor-1 (5837)


title: App1-14 (5831)


title: UKID116 (5822)


title: UKID107 (5811)


title: DraII-6 (5874)


title: UKID96 (5800)


title: Dra-3 (5860)


title: UKID93 (5798)


title: Ty-1 (5784)


title: UKID114 (5818)


title: UKID74 (5779)


title: Sna-1 (5778)


title: For-2 (5741)


title: UKNW06-003 (5353)


title: UKID11 (5718)


title: UKSE06-541 (5279)


title: UKSE06-252 (5104)


title: UKNW06-403 (5577)


title: UKSE06-432 (5210)


title: UKSE06-470 (5236)


title: UKNW06-102 (5395)


title: UKNW06-354 (5535)


title: UKSW06-207 (4807)


title: UKSE06-118 (5023)


title: Cal-2 (5720)


title: UKSW06-285 (4884)


title: UKSE06-325 (5151)


title: Cnt-1 (5726)


title: Bra-1 (5717)


title: UKSW06-179 (4779)


title: UKNW06-481 (5644)


title: UKSE06-639 (5349)


title: UKNW06-233 (5486)


title: UKSE06-533 (5276)


title: BRR60 (506)


title: UKSW06-341 (4939)


title: UKSW06-360 (4958)


title: UKSW06-226 (4826)


title: UKID63 (5768)


title: Set-1 (5772)


title: Kil-0 (5748)


title: UKSW06-333 (4931)


title: Borky1 (428)


title: Zdarec3 (403)


title: Doubravnik7 (410)


title: TOU-A1-89 (351)


title: Draha2 (424)


title: TOU-A1-88 (350)


title: PYL-6 (265)


title: Pent-46 (2212)


title: MNF-Pin-40 (2017)


title: MNF-Riv-21 (1890)


title: Paw-26 (2171)


title: Map-8 (2031)


title: SLSP-31 (2276)


title: KBS-Mac-74 (1741)


title: MNF-Pot-75 (1872)


title: Mdn-1 (1829)


title: MAR2-3 (159)


title: Pent-23 (2202)


title: Rod-17-319 (1435)


title: Haz-10 (1684)


title: Ste-40 (2317)


title: MNF-Pin-39 (2016)


title: Angso-74-430 (1317)


title: MNF-Che-2 (1925)


title: Yng-4 (2370)


title: Tnz-1 (10024)


title: Brosarp-34-145 (1066)


title: LDV-46 (139)


title: SLSP-35 (2278)


title: Uk-3 (10022)


title: Aledal-6-49 (1158)


title: LDV-18 (108)


title: Strand-1 (10023)


title: Bg-5 (10026)


title: Hl-0 (10021)


title: Sha (10015)

value: Sha


title: Petro-1 (10017)


title: Jl-2 (10020)


title: Ale-Stenar-64-24 (1002)


title: Istisu-1 (10012)


title: Sij-1 (10008)


title: Del-10 (10016)


title: Sij-4 (10010)


title: Lerik1-3 (10013)


title: MNF-Jac-12 (1954)


title: Yeg-1 (10011)


title: Dobra-1 (10018)


title: Kastel-1 (10006)


title: TueV-13 (10001)


title: Tuescha-9 (10000)


title: BXH19/TyJ FAIRE Replicate 1

city: Duarte

first: Juan

last: Du

address: 1500 E. Duarte Rd

institute: Beckman Research Institute, City of Hope

description:
BXH19.bw
BXH19-peaks.npf

data_processing:
FAIRE was performed on flash frozen liver tissues from two biological replicates in each strain as previously described (Giresi et al., 2007). Isolated FAIRE DNAs from each sample were barcoded and sequenced on the Illumina HiSeq 2500 to produce 100x100bp paired-end reads. Sequenced reads were mapped to mouse reference genome (version mm9) using Bowtie (Langmead et al. 2009) and only reads that can be mapped to single location in the genome were retained.
Peak calling was performed with F-seq using default parameters and 400bp feature length (Boyle et al. 2008). To find reproducible peaks across replicates, we utilized the Irreproducible Discovery Rate (IDR) framework (Li et al. 2011).
To identify variable chromatin site among different strains, we first counted the FAIRE-seq reads from each FAIRE-seq library overlapping with union set of accessible chromatin sites. We normalized the read counts using quantile normalization (Hicks and Irizarry 2015). We then used DEseq (Anders and Huber 2010) to identify variable chromatin sites among the seven strains. We ranked the accessible chromatin sites by adjusted p-values from DEseq. The top 5% with smallest adjusted p-values was considered as most variable chromatin sites, while the bottom 5% with biggest adjusted p-values was considered as least variable (common) chromatin site among the seven strains.
Genome_build: mm9
Supplementary_files_format_and_content: Peak file: narrowPeaks
Supplementary_files_format_and_content: Variable/common chromatin file: bed format
Supplementary_files_format_and_content: Processed FAIRE-seq data: BigWig format

source_name: Liver

growth_protocol: Livers were harvested from humanely euthanized mice

extract_protocol:
Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al., 2007)
Libraries were prepard according to Illumina instructions for DNA samples

treatment_protocol: Mice were fed a high-fat, high-sucrose diet (Research Diets D12266B)

tag: strain

tag: diet

value: high-fat, high-sucrose


title: BXH2/TyJ FAIRE Replicate 1

description:
BXH2.bw
BXH2-peaks.npf


title: BXH2/TyJ FAIRE Replicate 2

description:
BXH2.bw
BXH2-peaks.npf


title: BXH19/TyJ FAIRE Replicate 2

description:
BXH19.bw
BXH19-peaks.npf


title: KZ10 (10019)


title: Xan-1 (10014)


title: fl_rep3

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 41bpX18bp pair-end sequencing. Second mate was used for sample demultiplexing, at which point individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All. Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file that includes raw count data for each sample

source_name: Eμ-Myc Cre-ERT2+;miR-17~92 fl/fl

growth_protocol: Eµ-Myc cells were cultured on a layer of irradiated Ink4a-null MEF feeder cells in DMEM and IMDM medium (50:50 mix) supplemented with 10% fetal bovine serum (FBS), 20000U/ml penicillin, 7mM streptomycin, 2mM glutamine, and β-mercaptoethanol. Cells were seeded at a density of 1 x 105 cells/mL in 3.5 cm dishes, and grown for 48 hours prior to RNA collection.

extract_protocol:
RNA was extacted using Trizol following manufacturer's protocol.
For cDNA synthesis, custom oligo-dT primers were used with a barcode and adapter-linker sequence (CCTACACGACGCTCTTCCGATCT—XXXXXXXX-T15). After first strand synthesis, samples were pooled together based on Actb qPCR values, and RNA-DNA hybrids degraded using consecutive acid-alkali treatment. A second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (NEB) followed by SPRI clean-up. The mixture was then PCR enriched for 12 cycles and SPRI purified to yield final strand specific RNA-seq libraries as previously described (Jha et al., 2015)
3' RNA-Seq

treatment_protocol: Deletion of miR-17~92 was achieved by culturing Eµ-Myc Cre-ERT2+;miR-17~92fl/fl cells with 250 nM 4-OHT for four days, followed by subcloning 4-OHT-treated cells to isolate cells deficient for miR-17~92. Cells were then grown in parallel for 48 hours prior to collection of total RNA.

tag: genotype

value: floxed

tag: cell type

value: lymphoma cells


title: Sij-2 (10009)


title: TueWal-2 (10002)


title: del_rep3


title: del_rep2


title: fl_rep1


title: fl_rep2


title: del_rep1


title: CBA/J FAIRE Replicate 1

description:
CBA-peaks.npf
CBA.bw

data_processing:
FAIRE was performed on flash frozen liver tissues from two biological replicates in each strain as previously described (Giresi et al., 2007). Isolated FAIRE DNAs from each sample were barcoded and sequenced on the Illumina HiSeq 2500 to produce 100x100bp paired-end reads. We generated pseudo-genome for each non-reference strains by introducing SNPs from relevant strain into the reference mouse genome (mm9). Then we mapped FAIRE-seq reads from each replicate to the appropriate pseudo-genome using bowtie1 (Langmead et al., 2009) and only reads that could be mapped to single location in the genome were retained.
Peak calling was performed with F-seq using default parameters and 400bp feature length (Boyle et al., 2008). To find reproducible peaks across replicates, we utilized the Irreproducible Discovery Rate (IDR) framework (Li et al., 2011).
To identify variable chromatin site among different strains, we first counted the FAIRE-seq reads from each FAIRE-seq library overlapping with union set of accessible chromatin sites. We normalized the read counts using quantile normalization (Hicks and Irizarry, 2015). We then used DEseq (Anders and Huber, 2010) to identify variable chromatin sites among the seven strains. We ranked the accessible chromatin sites by adjusted p-values from DEseq. The top 5% with smallest adjusted p-values was considered as most variable chromatin sites, while the bottom 5% with biggest adjusted p-values was considered as least variable (common) chromatin site among the seven strains.
Genome_build: mm9
Supplementary_files_format_and_content: Peak file: narrowPeaks
Supplementary_files_format_and_content: Variable/common chromatin file: bed format

value: CBA/J

value: liver


title: AKR/J FAIRE Replicate 2

description:
AKR-peaks.npf
AKR.bw

value: AKR/J


title: C3H/HeJ FAIRE Replicate 2

description:
C3HHeJ-peaks.npf
C3HHeJ.bw


title: DBA/2J FAIRE Replicate 1

description:
DBA-peaks.npf
DBA.bw


title: C57BL/6J FAIRE Replicate 1

description:
BL6-peaks.npf
BL6.bw


title: BALB/cJ FAIRE Replicate 1

description:
BALB-peaks.npf
BALB.bw

value: BALB/cJ


title: AKR/J FAIRE Replicate 1

description:
AKR-peaks.npf
AKR.bw


title: BALB/cJ FAIRE Replicate 2

description:
BALB-peaks.npf
BALB.bw


title: C57BL/6J FAIRE Replicate 2

description:
BL6-peaks.npf
BL6.bw


title: CBA/J FAIRE Replicate 2

description:
CBA-peaks.npf
CBA.bw


title: A/J FAIRE Replicate 1

description:
AJ-peaks.npf
AJ.bw

value: A/J


title: DBA/2J FAIRE Replicate 2

description:
DBA-peaks.npf
DBA.bw


title: Wiz_ChIP-seq_2

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

data_processing:
For ChIP-seq, sequenced reads were provided by the sequencing service provider (Active Motif) in a .fastq.gz format. Reads were mapped to the mouse mm10 genome, using the Bowtie2 program using default settings.
For ChIP-seq, peak calling was done using MACS2 (Version  2.1.0) by first filtering out duplicate reads then using default parameters and the following options -s 75 --bw 200 -m 10 30 –p 0.0000001. Peaks were considered significant if they had a p value of equal or less than 1E-20
For RNA-seq, sequenced reads were provided by the sequencing service provider (Australian Genome Research Facility) in a .fastq.gz format. Reads were mapped to the mouse mm10 genome using the program Tophat (version 2.0.11) with the following parameters: -I 100000 --library-type=fr-unstranded --read-edit-dist 3 --no-coverage-search --read-mismatches 3
For RNA-seq, read counts for gene exons were extracted using the program htseq-count (version 0.6.1) with the options -s no -m intersection-strict. Normalization and differnetial gene expression was assessed using the R-package DEseq, with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: For processed ChIP-seq data, Bigwig format files showing the mapped read density across the genome. For processed RNA-seq data, tab-delimited text files include raw read counts for each of the samples

extract_protocol:
Cerebellum were removed and pooled from 2 mice and flash frozen on dry ice. Cerebellum were sent to Active Motif (CA, USA) who then carried out ChIP and library construction as well as Input DNA library construction (Cat No. 25001 and 25046).
ChIP libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: Cerebellum pooled

tag: age

value: 56 days post partum

value: Wiz +/+

value: Anti-Wiz NBP180586, Novus Biologicals, USA


title: Input_ChIP-seq (2)

value: input


title: Wiz_ChIP-seq_1


title: Star-8 (9998)

data_processing:
Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions

source_name: leaf

extract_protocol:
DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations.
Approximately one to three micrograms of genomic DNA was sonicated to ~100 bp using the Covaris S2 System using the following parameters: cycle number = 6, duty cycle = 20%, intensity = 5, cycles/burst = 200 and time = 60 seconds. Sonicated DNA was purified using Qiagen DNeasy minielute columns (Qiagen). Each sequencing library was constructed similar to genomic DNA libraries except the ligation was performed with methylated adapters provided by Illumina. Ligation products were purified with AMPure XP beads (Beckman) at a ratio of 1.8X of beads to sample. Up to 450 ng of ligated DNA was bisulfite treated using the MethylCode Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines and then PCR amplified using Pfu Cx Turbo (Agilent, Santa Clara, CA) using the following PCR conditions (2 minutes at 95C, 4 cycles of 15 seconds at 98C, 30 seconds at 60C, 4 minutes at 72C and 10 minutes at 72C).

value: leaf


title: Rue3.1-31 (9997)


title: Nie1-2 (9996)


title: Dog-4 (9992)


title: Lecho-1 (9987)


title: Jablo-1 (9986)


title: C3H/HeJ FAIRE Replicate 1

description:
C3HHeJ-peaks.npf
C3HHeJ.bw


title: Bak-7 (9989)


title: Ciste-1 (9983)


title: Vash-1 (9991)


title: Lag2-2 (9990)


title: Rovero-1 (9976)


title: Angit-1 (9981)


title: Mitterberg-1-181 (9973)


title: Valsi-1 (9969)


title: Krazo-2 (9961)


title: Slavi-1 (9985)


title: Monte-1 (9966)


title: Lago-1 (9963)


title: Mammo-2 (9965)


title: Bozen-1.2 (9972)


title: Mammo-1 (9964)


title: Shigu-1 (9958)


title: Galdo-1 (9962)


title: Stepn-1 (9956)


title: Leb-3 (9954)


title: Borsk-2 (9957)


title: Kly-1 (9951)


title: Koz-2 (9953)


title: Angel-1 (9980)


title: Vie-0 (9950)


title: Qui-0 (9949)


title: Ale-Stenar-56-14 (997)


title: Agu-1 (9942)


title: Leo-1 (9945)


title: Fei-0 (9941)


title: Don-0 (9944)


title: Mer-6 (9946)


title: Ped-0 (9947)


title: WAV-8 (9938)


title: Pra-6 (9948)


title: Toufl-1 (9940)


title: CATS-6 (9937)


title: LCL-16 (9936)


title: VED-10 (9933)


title: A/J FAIRE Replicate 2

description:
AJ-peaks.npf
AJ.bw


title: BAU-15 (9935)


title: NOZ-6 (9932)


title: MOU2-25 (9931)


title: BEZ-9 (9928)


title: TRE-1 (9926)


title: FOR-23 (9921)


title: PLO-1 (9923)


title: BRE-14 (9919)


title: PLY-20 (9924)


title: DIR-9 (9920)


title: RAD-21 (9917)


title: MIL-2 (9922)


title: MOL-1 (9916)


title: MAR-4-16 (9915)


title: Aitba-2 (9939)


title: CON-7 (9913)


title: IST-29 (9914)


title: ISS-20 (9929)


title: Mah-6 (9906)


title: Vas-0 (9904)


title: Tri-0 (9900)


title: BRI-2 (9910)


title: ESP-1-11 (9908)


title: Usa-0 (9902)


title: Ven-0 (9905)


title: Tau-0 (9899)


title: Urd-1 (9901)


title: Smt-1 (9897)


title: Val-0 (9903)


title: Som-0 (9898)


title: Sen-0 (9894)


title: Sfb-6 (9895)


title: Sca-0 (9893)


title: Sam-0 (9892)


title: Rib-1 (9890)


title: Piq-0 (9883)


title: Sal-0 (9891)


title: Pru-0 (9886)


title: Pil-0 (9882)


title: Pva-1 (9888)


title: Prd-0 (9885)


title: Pib-1 (9880)


title: Pee-0 (9878)


title: Pdl-0 (9877)


title: Pad-0 (9876)


title: Ovi-1 (9875)


title: Per-0 (9879)


title: Oja-0 (9874)


title: Ndc-0 (9873)


title: Mie-1 (9867)


title: Moe-0 (9868)


title: Moz-0 (9870)


title: Moj-0 (9869)


title: Mdd-0 (9866)


title: Mac-0 (9861)


title: Leg-0 (9857)


title: Loz-0 (9858)


title: Lch-0 (9856)


title: Pie-0 (9881)


title: Mat-0 (9864)


title: Hue-3 (9851)


title: Ini-0 (9852)


title: Laf-1 (9854)


title: Lac-0 (9853)


title: Lam-0 (9855)


title: Hec-0 (9850)


title: Nac-0 (9871)


title: Glo-1 (9848)


title: Fel-2 (9847)


title: Ezc-2 (9846)


title: Esn-2 (9844)


title: Gud-3 (9849)


title: Nag-0 (9872)


title: Lro-0 (9859)


title: Elp-0 (9843)


title: Evs-0 (9845)


title: Lum-0 (9860)


title: Mad-0 (9862)


title: Ees-0 (9841)


title: Coy-0 (9839)


title: Cot-0 (9838)


title: Cod-0 (9836)


title: Con-0 (9837)


title: IP-Bur-0 (9829)


title: IP-Bus-0 (9830)


title: Cas-0 (9831)


title: Bor-0 (9826)


title: Amu-0 (9819)


title: Are-0 (9820)


title: Boa-0 (9825)


title: Ace-0 (9817)


title: Aul-0 (9822)


title: Aru-0 (9821)


title: Dar-0 (9840)


title: Cat-0 (9832)


title: Bae-0 (9823)


title: Cir-0 (9835)


title: Bos-0 (9827)


title: IP-Cha-0 (9833)


title: Tu-WH (9816)

value: Tu-WH


title: Fell1-10 (9814)


title: Ha-HBT3-11 (9815)


title: BI-4 (9813)


title: Tu-KB-6 (9809)


title: Ru-2 (9806)


title: Cho-0 (9834)


title: Tu-W1 (9812)


title: Tu-NK-12 (9811)


title: Bes-5 (9824)


title: Tu-B2-3 (9808)


title: Ha-S-B (9800)

value: Ha-S-B


title: Hart-2 (9799)


title: Obe1-15 (9804)


title: Kus3-1 (9802)


title: Tu-KS-7 (9810)


title: Schl-7 (9807)


title: Pfn-10 (9805)


title: Bach2-1 (9796)


title: Ha-HBT2-10 (9797)


title: Ru-N2 (9793)


title: HI-4 (9787)


title: Ha-P-13 (9786)


title: Ha-P2-1 (9798)


title: Tu-PK-7 (9783)


title: Wank-2 (9795)


title: Ha-SP-2 (9801)


title: Muh-2 (9803)


title: Obh-13 (9789)


title: Gn2-3 (9790)


title: Tu-B1-2 (9794)


title: Lu4-2 (9792)


title: Hof-1 (9772)


title: Erg2-6 (9784)


title: Pfn-N2.2-6 (9771)


title: Kus2-2 (9781)


title: HE-1 (9769)


title: Gn-1 (9777)


title: Alt-1 (9774)


title: Bai-10 (9779)


title: Fell2-4 (9780)


title: Haes-1 (9791)


title: Bik-1 (9761)


title: Zabar-1 (9747)


title: Ha-HBT1-2 (9785)


title: Knjas-1 (9749)


title: Sredn-1 (9754)


title: KBG1-14 (9788)


title: Bach-7 (9778)


title: Lu3-30 (9782)


title: Berg-1 (9775)


title: Staro-2 (9756)


title: Malii-1 (9746)


title: Fell3-7 (9776)


title: KBG2-13 (9770)


title: Vajug-1 (9755)


title: Bela-2 (9733)


title: Furni-1 (9743)


title: Orast-1 (9741)


title: Bran-1 (9738)


title: Teiu-2 (9736)


title: Iasi-1 (9744)


title: Olympia-2 (9727)


title: Slavi-2 (9723)


title: Stiav-2 (9729)


title: Halca-1 (9732)


title: Stiav-1 (9728)


title: Toc-1 (9739)


title: Ulies-1 (9737)


title: Groch-1 (9722)


title: Bela-3 (9734)


title: Sij 1/96 (9745)


title: Faneronemi-3 (9726)


title: Stara-1 (9713)


title: Zerev-1-35 (9710)


title: Bela-1 (9730)


title: Schip-1 (9721)


title: Smolj-1 (9718)


title: Kardz-2 (9717)


title: Leska-1-44 (9716)


title: Podvi-1 (9707)


title: Ru4-16 (9768)


title: Zerev-1-34 (9709)


title: Kardz-1 (9708)


title: Goced-1 (9698)


title: Castelfed-4-210 (9694)


title: Dolen-1 (9697)


title: Koren-1 (9719)


title: Choto-1 (9705)


title: Kolar-2 (9702)


title: Melni-2 (9704)


title: Melni-1 (9703)


title: Mitterberg-4-192 (9676)


title: Castelfed-4-214 (9696)


title: Mitterberg-2-184 (9668)


title: Dospa-1 (9706)


title: Castelfed-2-200 (9684)


title: Grivo-1 (9714)


title: Cimin-1 (9661)


title: Nicas-1 (9658)


title: Kolar-1 (9699)


title: Dolna-1-10 (9700)


title: Ivano-1 (9701)


title: Marti-1 (9656)


title: Castelfed-1-195 (9679)


title: Mitterberg-4-194 (9678)


title: Liri-1 (9654)


title: Castelfed-3-206 (9690)


title: Giffo-1 (9653)


title: Mitterberg-3-187 (9671)


title: Pigna-1 (9659)


title: Marce-1 (9655)


title: Sarno-1 (9660)


title: Melic-1 (9657)


title: Castelfed-3-209 (9693)


title: Fondi-1 (9652)


title: Corig-1 (9650)


title: Rakit-2 (9641)


title: Basen-1 (9647)


title: Filet-1 (9651)


title: Stilo-1 (9662)


title: Zupan-1 (9644)


title: Noveg-2 (9637)


title: Bisig-1 (9648)


title: Noveg-3 (9638)


title: Sever-1 (9643)


title: Gradi-1 (9645)


title: Aiell-1 (9646)


title: Noveg-1 (9636)


title: Rakit-1 (9640)


title: Nosov-1 (9635)


title: Lebja-4 (9633)


title: Lebja-2 (9632)


title: Kolyv-6 (9628)


title: K-oze-1 (9629)


title: Lebja-1 (9631)


title: Kolyv-2 (9625)


title: Chaba-1 (9623)


title: Kolyv-5 (9627)


title: Basta-2 (9620)


title: Kolyv-3 (9626)


title: Bivio-1 (9649)


title: Karag-1 (9617)


title: Parti-1 (9615)


title: Panke-1 (9639)


title: Basta-1 (9619)


title: Balan-1 (9613)


title: Krazo-1 (9616)


title: Lesno-4 (9610)


title: Basta-3 (9621)


title: Adam-1 (9609)


title: Lesno-2 (9612)


title: Masl-1 (9634)


title: Karag-2 (9608)


title: Lesno-1 (9611)


title: IP-Vig-1 (9597)


title: IP-Vis-0 (9600)


title: IP-Voz-0 (9601)


title: IP-Vin-0 (9599)


title: IP-Svi-0 (9585)


title: IP-Tol-7 (9588)


title: IP-Sdv-3 (9581)


title: IP-Tdc-0 (9587)


title: IP-Vdm-0 (9594)


title: IP-Sac-0 (9578)


title: IP-Trs-0 (9590)


title: IP-Vad-0 (9591)


title: IP-Tor-1 (9589)


title: IP-Vim-0 (9598)


title: IP-Ver-5 (9596)


title: IP-Vdt-0 (9595)


title: Aitba-1 (9606)


title: IP-Vaz-0 (9593)


title: IP-Tam-0 (9586)


title: IP-Rev-0 (9576)


title: IP-Stp-0 (9584)


title: IP-Rel-0 (9574)


title: IP-Ses-0 (9582)


title: Panik-1 (9607)


title: IP-Vae-2 (9592)


title: IP-Sne-0 (9583)


title: IP-Ria-0 (9577)


title: IP-San-10 (9579)


title: IP-Rds-0 (9573)


title: IP-Pob-0 (9570)


title: IP-Scm-0 (9580)


title: IP-Pds-1 (9569)


title: IP-Pue-0 (9572)


title: IP-Pan-0 (9568)


title: IP-Nog-17 (9564)


title: IP-Nav-0 (9563)


title: IP-Pal-0 (9567)


title: IP-Oso-0 (9566)


title: IP-Mur-0 (9562)


title: IP-Orb-10 (9565)


title: IP-Men-2 (9556)


title: IP-Lso-0 (9554)


title: IP-Jim-1 (9551)


title: IP-Moa-0 (9557)


title: IP-Lab-7 (9552)


title: IP-Moc-11 (9558)


title: IP-Mon-5 (9559)


title: IP-Iso-4 (9550)


title: IP-Mot-0 (9560)


title: IP-Hoy-0 (9548)


title: IP-Hum-2 (9549)


title: IP-Hom-4 (9546)


title: IP-Her-12 (9545)


title: IP-Hor-0 (9547)


title: IP-Ldd-0 (9553)


title: IP-Gua-1 (9544)


title: IP-Elb-0 (9540)


title: IP-Cur-4 (9538)


title: IP-Gra-0 (9543)


title: IP-Fun-0 (9542)


title: IP-Ren-6 (9575)


title: IP-Mun-0 (9561)


title: IP-Cdc-3 (9531)


title: IP-Coc-1 (9535)


title: IP-Cum-1 (9537)


title: IP-Cab-3 (9526)


title: IP-Bis-0 (9525)


title: IP-Cap-1 (9529)


title: IP-Ara-4 (9520)


title: IP-Cad-0 (9527)


title: IP-Ber-0 (9524)


title: IP-Car-1 (9530)


title: IP-Cmo-3 (9534)


title: IP-Cem-0 (9533)


title: IP-Bea-0 (9522)


title: IP-Bar-1 (9521)


title: IP-Ben-0 (9523)


title: IP-Ang-0 (9519)


title: IP-Cdo-0 (9532)


title: IP-Vid-1 (9512)


title: IP-Adc-5 (9513)


title: IP-Ali-1 (9516)


title: IP-All-0 (9517)


title: IP-Ala-0 (9515)


title: IP-Alm-0 (9518)


title: IP-Fue-2 (9541)


title: IP-Vav-0 (9511)


title: IP-Adm-0 (9514)


title: IP-Rei-0 (9510)


title: IP-Mos-1 (9508)


title: Spro 2 (9451)

value: Spro 2


title: IP-Reg-0 (9509)


title: IP-Coa-0 (9507)


title: IP-Alo-0 (9506)


title: Nyl 13 (9433)

value: Nyl 13


title: 11C1 (9503)


title: Kal 1 (9408)

value: Kal 1


title: Spro 1 (9450)

value: Spro 1


title: Kia 1 (9409)

value: Kia 1


title: HolA-1 1 (9404)

value: HolA-1 1


title: Adal 1 (9321)

value: Adal 1


title: HolA-2 2 (9407)

value: HolA-2 2


title: Lan 1 (9421)

value: Lan 1


title: Gron 12 (9386)

value: Gron 12


title: Gron 14 (9388)

value: Gron 14


title: HolA-1 2 (9405)

value: HolA-1 2


title: Ullapool-8 (9312)


title: Yeg-5 (9131)


title: Yeg-8 (9134)


title: Gol-2 (9314)


title: Edi-1 (9298)


title: Geg-14 (9125)


title: Lag2-7 (9114)


title: Lag1-7 (9105)


title: Lag2-6 (9113)


title: CHA-41 (932)


title: Nar-5 (9091)


title: Lerik1-4 (9075)


title: Lag1-6 (9104)


title: Lag2-4 (9111)


title: Istisu-5 (9095)


title: Lerik2-3 (9081)


title: Lag1-8 (9106)


title: Xan-5 (9069)


title: Xan-6 (9070)


title: 328ME059 (8584)


title: Nar-3 (9089)


title: Lerik2-6 (9084)


title: MIC-31 (870)


title: wtfrt_1

city: Bangalore

first: Aalap

last: Mogre

state: Karnataka

address: NCBS, GKVK, Bellary Road

country: India

institute: National Centre for Biological Sciences

description: Replicate 1

data_processing:
Adapters from FASTX filtered reads were trimmed using Cutadapt.
Trimmed reads were aligned to the E. coli reference genome (NC_000913.3) using BWA, -q 30 flag was used for quality trimming.
Number of reads mapping to each gene were obtained from samfiles using custom Python scripts (only reads with mapping quality > 20 were considered).
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab delimited text files with gene names and the number of reads mapping to each gene.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: wtfrt_exponentially growing cells

growth_protocol: For RNA extraction, cells were grown in Luria-Bertani broth and harvested at the point of maximal growth rate after addition of stop solution to stabilise cellular RNA and stop transcription. Two biological replicates were harvested for each strain.

extract_protocol:
RNA was extracted using hot phenol-chloroform. DNase treated RNA was depleted of ribosomal RNA using the Ambion Microbe Express Kit (AM1905). RNA was checked for quality using Bioanalyzer (Agilent).
DNase treated RNA was depleted of ribosomal RNA using the Ambion Microbe Express Kit (AM1905). RNA was checked for quality using Bioanalyzer (Agilent). Checked RNA was used for library preparation and sequencing. Briefly, 100 ng of qubit quantified RNA was used for library preparation using the NEXTflex Rapid Directional RNA-Seq kit (5138-08 Bioo Scientific). The library was quantified using qubit and its quality was checked using Agilent Bioanalyzer before proceeding for sequencing on the Illumina NextSeq 500 sequencer.

treatment_protocol: No treatment; only the growth of strains in Luria-Bertani broth.

tag: mutation(s)

value: none; wild type

tag: growth phase

value: Exponentially growing cells

tag: molecule subtype

value: rRNA depleted RNA


title: fusA_rpoD_2

description: Replicate 2

source_name: fusA_rpoD_exponentially growing cells

value: FusAA608E - RpoDL261Q


title: fusA_topA_2

description: Replicate 2

source_name: fusA_topA_exponentially growing cells

value: FusAA608E - TopAS180L


title: rpoD_1

description: Replicate 1

source_name: rpoD_exponentially growing cells


title: fusA_topA_1

description: Replicate 1


title: rpoD_2

description: Replicate 2


title: Lag2-10 (9115)

value: leaf


title: Lag1-5 (9103)


title: RMXF413.15 (9045)


title: LP3413.41 (8472)


title: Uod-2 (8428)


title: Kas-2 (8424)


title: fusA_rpoD_1

description: Replicate 1


title: fusA_cyaA_2

description: Replicate 2

source_name: fusA_cyaA_exponentially growing cells

value: FusAA608E - CyaAN600Y


title: Istisu-9 (9099)


title: Wil-1 (8419)


title: wtfrt_2

description: Replicate 2


title: fusA_cyaA_1

description: Replicate 1


title: Sap-0 (8378)


title: fusA_cpxA_1

description: Replicate 1

source_name: fusA_cpxA_exponentially growing cells

value: FusAA608E - CpxAF218Y


title: Sr:5 (8386)


title: Pla-0 (8357)


title: Lis-1 (8326)


title: Mir-0 (8337)


title: fusA_2

description: Replicate 2

source_name: fusA_exponentially growing cells


title: cyaA_1

description: Replicate 1

source_name: cyaA_exponentially growing cells


title: cpxA_2

description: Replicate 2

source_name: cpxA_exponentially growing cells


title: fusA_1

description: Replicate 1


title: cpxA_1

description: Replicate 1


title: cyaA_2

description: Replicate 2


title: Pa-1 (8353)


title: Cen-0 (8275)


title: Boo2-1 (8266)


title: DraIII-1 (8285)


title: Per-1 (8354)


title: NC-6 (8246)


title: San-2 (8247)


title: PHW-34 (8244)


title: Ba5-1 (8259)


title: fusA_cpxA_2

description: Replicate 2


title: Rak-2 (8365)


title: Dem-4 (8233)


title: PHW-3 (8239)


title: HSm (8236)

value: HSm


title: Na-1 (8343)


title: En-1 (8290)


title: Bro1-6 (8231)


title: Zal-1 (768)


title: PNA3.10 (7917)


title: PNA3.40 (7947)


title: Lp2-6 (7521)


title: Kar-1 (763)


title: RRS-7 (7514)


title: Jl-3 (7424)


title: RRS-10 (7515)


title: Wu-0 (7415)


title: Zu-1 (7418)


title: Wil-2 (7413)


title: WAR (7477)

value: WAR


title: RMX3.22 (8132)


title: Wc-1 (7404)


title: Ws-0.2 (7396)


title: Ven-1 (7384)


title: Tul-0 (7377)


title: Tiv-1 (7355)


title: Ting-1 (7354)


title: Tac-0 (7350)


title: Tha-1 (7353)


title: PT2.21 (8077)


title: Tsu-0 (7373)


title: Sten-0 (7346)


title: Sapporo-0 (7330)


title: Su-0 (7342)


title: Si-0 (7337)


title: H55 (7461)


title: Ko-2 (7427)


title: Ber (7458)

value: Ber


title: Pn-0 (7307)


title: Rhen-1 (7316)


title: Rsch-4 (7322)


title: Rou-0 (7320)


title: Sf-1 (7327)


title: Po-0 (7308)


title: Oy-0 (7288)


title: Pt-0 (7305)


title: Or-0 (7282)


title: Nz-1 (7263)


title: LI-SET-019 (728)


title: Le-0 (7218)


title: No-0 (7273)


title: Mnz-0 (7244)


title: Litva (7236)

value: Litva


title: Kb-0 (7202)


title: Hh-0 (7169)


title: Me-0 (7250)


title: Hi-0 (7167)


title: Kn-0 (7186)


title: Hn-0 (7165)


title: Hau-0 (7164)


title: Gr-5 (7158)


title: Gd-1 (7161)


title: Fi-0 (7138)


title: Et-0 (7130)


title: Er-0 (7125)


title: En-2 (7119)


title: Do-0 (7102)


title: Pi-0 (7298)


title: Dra-0 (7103)


title: Durh-1 (7107)


title: Di-G (7096)

value: Di-G


title: Dr-0 (7106)


title: Mc-0 (7252)


title: Ct-1 (7067)


title: Sf-2 (7328)


title: Bch-1 (7028)


title: Bur-0 (7058)


title: Alst-1 (6989)


title: Da-0 (7094)


title: Boot-1 (7026)


title: Wei-0 (6979)


title: Ull2-5 (6974)


title: Ang-0 (6992)


title: Ak-1 (6987)


title: Ann-1 (6994)


title: Ts-5 (6971)


title: Ts-1 (6970)


title: Rennes-1 (6959)


title: NFA-10 (6943)


title: Pu2-7 (6956)


title: NFA-8 (6944)


title: Fab-2 (6917)


title: Cerv-1 (7068)


title: Got-7 (6921)


title: HR-10 (6923)


title: C24 (6906)


title: CIBC-17 (6907)


title: Ei-2 (6915)


title: Bil-5 (6900)


title: Bd-0 (7013)


title: Ag-0 (6897)


title: CSHL-5 (6744)


title: TV-7 (6255)


title: TV-38 (6284)


title: Bg-2 (6709)


title: ZdrI 2-21 (6445)

value: ZdrI 2-21


title: UduI 3-36 (6390)

value: UduI 3-36


title: Je-0 (7181)


title: ANH-1 (6680)