title: SLX-9780.N701_N505

description: Young HSC WT


title: SLX-9780.N701_N508

status: Public on May 22 2017

type: SRA

city: Cambridge

first: Anthony

last: Green

state: Cambridgeshire

address: Hills Road

department: Department of heamatology

country: United Kingdom

institute: University of Cambridge

description: Young HSC WT

library_source: transcriptomic

data_processing:
Illumina basecalling
Reads mapped to Mouse GRC38-77 reference genome from ENSEMBL plus ERCC92 spike-in controls with tophat 2.0.13 and bowtie 2.2.3
Gene expression count matrix was calculated with htseq
Genome_build: GRC38 release 77
Supplementary_files_format_and_content: Tabular separated raw counts. First column is the genes, second column is the counts.

molecule: polyA RNA

organism: Mus musculus

source_name: Hematopoietic Stem Cell

growth_protocol: not applicable

extract_protocol:
hematopoietic stem cells were isolated from whole bone marrow using ESLAM markers foir FACS sorting
The libraries were constructed according to Picelli et al 2014 using Nextera Illumina Kit

treatment_protocol: not applicable

tag: tissue

value: whole bone marrow

tag: cell type

value: Hematopoietic Stem Cell

tag: age

value: 4 Months (young)

tag: genotype

value: Wild Type


title: SLX-9780.N702_N507

description: Young HSC WT


title: SLX-9780.N701_N503

description: Young HSC WT


title: SLX-9780.N702_N503

description: Young HSC WT


title: SLX-9780.N701_N517

description: Young HSC WT


title: SLX-9775.N712_N507

description: Young HSC WT


title: SLX-9780.N701_N507

description: Young HSC WT


title: SLX-9780.N701_N506

description: Young HSC WT


title: SLX-9775.N712_N502

description: Young HSC WT


title: SLX-9775.N711_N517

description: Young HSC WT


title: SLX-9775.N712_N503

description: Young HSC WT


title: SLX-9775.N712_N504

description: Young HSC WT


title: SLX-9775.N711_N506

description: Young HSC WT


title: SLX-9775.N712_N508

description: Young HSC WT


title: SLX-9780.N701_N502

description: Young HSC WT


title: SLX-9775.N711_N508

description: Young HSC WT


title: SLX-9775.N711_N502

description: Young HSC WT


title: SLX-9775.N712_N505

description: Young HSC WT


title: SLX-9775.N711_N504

description: Young HSC WT


title: SLX-9775.N710_N508

description: Young HSC WT


title: SLX-9775.N712_N506

description: Young HSC WT


title: SLX-9775.N710_N507

description: Young HSC WT


title: SLX-9775.N711_N505

description: Young HSC WT


title: SLX-9775.N711_N503

description: Young HSC WT


title: SLX-9775.N711_N507

description: Young HSC WT


title: SLX-9780.N701_N504

description: Young HSC WT


title: SLX-9775.N712_N517

description: Young HSC WT


title: SLX-9775.N710_N506

description: Young HSC WT


title: SLX-9775.N709_N504

description: Young HSC WT


title: SLX-9775.N710_N503

description: Young HSC WT


title: SLX-9775.N710_N505

description: Young HSC WT


title: SLX-9775.N710_N502

description: Young HSC WT


title: SLX-9775.N709_N517

description: Young HSC WT


title: SLX-9775.N710_N504

description: Young HSC WT


title: SLX-9775.N709_N505

description: Young HSC WT


title: SLX-9775.N709_N507

description: Young HSC WT


title: SLX-9775.N708_N504

description: Young HSC WT


title: SLX-9775.N708_N507

description: Young HSC WT


title: SLX-9775.N709_N503

description: Young HSC WT


title: SLX-9775.N708_N506

description: Young HSC WT


title: SLX-9775.N708_N505

description: Young HSC WT


title: SLX-9775.N710_N517

description: Young HSC WT


title: SLX-9775.N707_N507

description: Young HSC WT


title: SLX-9775.N708_N503

description: Young HSC WT


title: SLX-9775.N708_N502

description: Young HSC WT


title: SLX-9775.N709_N506

description: Young HSC WT


title: SLX-9775.N707_N508

description: Young HSC WT


title: SLX-9775.N707_N517

description: Young HSC WT


title: SLX-9775.N707_N504

description: Young HSC WT


title: SLX-9775.N707_N503

description: Young HSC WT


title: SLX-9775.N707_N502

description: Young HSC WT


title: SLX-9775.N707_N505

description: Young HSC WT


title: SLX-9775.N707_N506

description: Young HSC WT


title: SLX-9775.N709_N508

description: Young HSC WT


title: SLX-9775.N706_N517

description: Young HSC WT


title: SLX-9775.N709_N502

description: Young HSC WT


title: SLX-9775.N708_N508

description: Young HSC WT


title: SLX-9775.N708_N517

description: Young HSC WT


title: SLX-9775.N706_N504

description: Young HSC WT


title: SLX-9775.N706_N503

description: Young HSC WT


title: SLX-9775.N706_N507

description: Young HSC WT


title: SLX-9775.N706_N502

description: Young HSC WT


title: SLX-9775.N706_N505

description: Young HSC WT


title: SLX-9775.N706_N506

description: Young HSC WT


title: SLX-9775.N705_N517

description: Young HSC WT


title: SLX-9775.N705_N508

description: Young HSC WT


title: SLX-9775.N705_N507

description: Young HSC WT


title: SLX-9775.N705_N504

description: Young HSC WT


title: SLX-9775.N705_N503

description: Young HSC WT


title: SLX-9775.N705_N502

description: Young HSC WT


title: SLX-9775.N704_N508

description: Young HSC WT


title: SLX-9775.N704_N507

description: Young HSC WT


title: SLX-9775.N704_N506

description: Young HSC WT


title: SLX-9775.N704_N503

description: Young HSC WT


title: SLX-9775.N706_N508

description: Young HSC WT


title: SLX-9775.N704_N502

description: Young HSC WT


title: SLX-9775.N704_N505

description: Young HSC WT


title: SLX-9775.N704_N504

description: Young HSC WT


title: SLX-9775.N703_N506

description: Young HSC WT


title: SLX-9775.N703_N504

description: Young HSC WT


title: SLX-9775.N703_N507

description: Young HSC WT


title: SLX-9775.N703_N505

description: Young HSC WT


title: SLX-9775.N703_N517

description: Young HSC WT


title: SLX-9775.N703_N503

description: Young HSC WT


title: SLX-9775.N705_N505

description: Young HSC WT


title: SLX-9775.N702_N508

description: Young HSC WT


title: SLX-9775.N703_N502

description: Young HSC WT


title: SLX-9775.N702_N505

description: Young HSC WT


title: SLX-9775.N702_N507

description: Young HSC WT


title: SLX-9775.N702_N506

description: Young HSC WT


title: SLX-9775.N702_N503

description: Young HSC WT


title: SLX-9775.N702_N504

description: Young HSC WT


title: SLX-9775.N701_N517

description: Young HSC WT


title: SLX-9775.N702_N502

description: Young HSC WT


title: SLX-9775.N701_N507

description: Young HSC WT


title: SLX-9775.N704_N517

description: Young HSC WT


title: SLX-9775.N701_N506

description: Young HSC WT


title: SLX-9775.N701_N508

description: Young HSC WT


title: SLX-9775.N705_N506

description: Young HSC WT


title: SLX-9775.N701_N505

description: Young HSC WT


title: SLX-9775.N703_N508

description: Young HSC WT


title: SLX-9775.N701_N504

description: Young HSC WT


title: SLX-9775.N702_N517

description: Young HSC WT


title: SLX-9774.N712_N503

description: Young HSC JAK2 HOM

value: JAK2 V617F Homozygous


title: SLX-9774.N712_N504

description: Young HSC JAK2 HOM


title: SLX-9774.N712_N502

description: Young HSC JAK2 HOM


title: SLX-9775.N701_N503

description: Young HSC WT


title: SLX-9774.N712_N507

description: Young HSC JAK2 HOM


title: SLX-9774.N712_N505

description: Young HSC JAK2 HOM


title: SLX-9774.N712_N508

description: Young HSC JAK2 HOM


title: SLX-9774.N712_N506

description: Young HSC JAK2 HOM


title: SLX-9774.N711_N517

description: Young HSC JAK2 HOM


title: SLX-9774.N712_N517

description: Young HSC JAK2 HOM


title: SLX-9775.N701_N502

description: Young HSC WT


title: SLX-9774.N711_N506

description: Young HSC JAK2 HOM


title: SLX-9774.N711_N503

description: Young HSC JAK2 HOM


title: SLX-9774.N711_N507

description: Young HSC JAK2 HOM


title: SLX-9774.N711_N508

description: Young HSC JAK2 HOM


title: SLX-9774.N711_N504

description: Young HSC JAK2 HOM


title: SLX-9774.N710_N507

description: Young HSC JAK2 HOM


title: SLX-9774.N711_N502

description: Young HSC JAK2 HOM


title: SLX-9774.N710_N517

description: Young HSC JAK2 HOM


title: SLX-9774.N710_N505

description: Young HSC JAK2 HOM


title: SLX-9774.N710_N508

description: Young HSC JAK2 HOM


title: SLX-9774.N711_N505

description: Young HSC JAK2 HOM


title: SLX-9774.N710_N502

description: Young HSC JAK2 HOM


title: SLX-9774.N710_N506

description: Young HSC JAK2 HOM


title: SLX-9774.N710_N503

description: Young HSC JAK2 HOM


title: SLX-9774.N709_N508

description: Young HSC JAK2 HOM


title: SLX-9774.N710_N504

description: Young HSC JAK2 HOM


title: SLX-9774.N709_N517

description: Young HSC JAK2 HOM


title: morc-1_F5_ChIPseq_H3K9me3_Input

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

country: USA

institute: Johns Hopkins University

description:
DNA from fragmented chromatin
ChIPseq_1kb_region_FPKM.txt

library_source: genomic

data_processing:
Basecalling was performed using Illumina's default Real Time Analysis (RTA) basecalling and quality scoring software application.
Conversion from qseq files to fastq files and demultiplexing was performed using custom Awk and Python scripts
Reads were aligned to the C. elegans genome (WS190) using Bowtie 0.12.7.
Genome_build: WS190
RPKM values for non-overlapping 1kb genomic regions were calculated as the number of reads that perfectly aligned to
Supplementary_files_format_and_content: The processed data file is a text file containing matrix of 1kb genomic regions (rows) and all ChIP-seq experiments (columns). Values in matrix represent reads per million mapped reads per kb (RPKM). First column is the choromosome location, second column is the start position of the 1kb region, and the remaning columns are the RPKM values.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Whole animal, young adult

growth_protocol: P0 and subsequent generations (F1-F5) were grown at 25C, all previous generations had been grown at 20C. Worms were fed OP50 E. coli.

extract_protocol:
40 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-H3K36me3 (300-95289, WAKO) was added to 400 μl of the lysate (containing approximately 10 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein  A(for H3K9me3) or protein G (for H3K36me3) Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 80 μg of proteinase K) at 65 °C for 4 hours with continuous agitation  (IP input lysate was treated similarly to reverse crosslink). DNA was extracted by phenolchloroform and dissolved in TE buffer.
ChIP-seq libraries were made using NuGen Ovation Ultralow Library Systems v2 according to manufacturer’s instructions.

treatment_protocol: 500 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.3ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml Bioruptor Microtube  (Diagenode) and sonicated (Bioruptor Pico [Diagenode], interval: 0.5, three times of 3-minute sonication).

tag: strain

tag: replicate

tag: generation

tag: barcode

value: GCACTA

tag: antibody


title: met-1morc-1_F5_rep1_ChIPseq_H3K9me3_Input

value: GTCGTA


title: SLX-9774.N709_N504

description: Young HSC JAK2 HOM


title: SLX-9774.N709_N505

description: Young HSC JAK2 HOM


title: SLX-9774.N708_N508

description: Young HSC JAK2 HOM


title: SLX-9774.N709_N503

description: Young HSC JAK2 HOM


title: SLX-9774.N709_N502

description: Young HSC JAK2 HOM


title: SLX-9774.N709_N506

description: Young HSC JAK2 HOM


title: SLX-9774.N709_N507

description: Young HSC JAK2 HOM


title: WT_F5_ChIPseq_H3K9me3_Input

value: TGGTGA


title: SLX-9774.N708_N517

description: Young HSC JAK2 HOM


title: met-1_F5_rep2_ChIPseq_H3K9me3_Input

value: GTGCTT


title: met-1morc-1_F5_rep2_ChIPseq_H3K9me3_Input


title: SLX-9774.N708_N507

description: Young HSC JAK2 HOM


title: met-1_F5_rep1_ChIPseq_H3K9me3_Input


title: SLX-9774.N708_N505

description: Young HSC JAK2 HOM


title: SLX-9774.N708_N502

description: Young HSC JAK2 HOM


title: SLX-9774.N708_N504

description: Young HSC JAK2 HOM


title: met-1morc-1_F5_rep1_ChIPseq_H3K9me3

description:
DNA from immunoprecipitated chromatin
ChIPseq_1kb_region_FPKM.txt

value: TTGGCA

value: Anti-Histone H3 (tri methyl K9)


title: morc-1_F5_ChIPseq_H3K9me3

value: GAGTCA


title: SLX-9774.N707_N508

description: Young HSC JAK2 HOM


title: met-1morc-1_F5_rep2_ChIPseq_H3K9me3


title: met-1_F5_rep2_ChIPseq_H3K9me3

value: TCAGAG


title: met-1_F5_rep1_ChIPseq_H3K9me3


title: SLX-9774.N708_N503

description: Young HSC JAK2 HOM


title: SLX-9774.N707_N507

description: Young HSC JAK2 HOM


title: SLX-9774.N707_N517

description: Young HSC JAK2 HOM


title: WT_F5_ChIPseq_H3K9me3

value: GGAGAA


title: SLX-9774.N707_N506

description: Young HSC JAK2 HOM


title: SLX-9774.N708_N506

description: Young HSC JAK2 HOM


title: met-1_hrde-1_late_rep2_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: met-1_hrde-1_F4_rep2_ChIPseq_H3K36me3_cCS107p
processed data file: ChIPseq_1kb_region_RPKM.txt

data_processing:
Basecalling was performed using Illumina's default Real Time Analysis (RTA) basecalling and quality scoring software application.
Conversion from qseq files to fastq files and demultiplexing was performed using custom Awk and Python scripts
alignment: Reads were aligned to the C. elegans genome (WS190) using Bowtie 0.12.7.
RPKM values for non-overlapping 1kb genomic regions were calculated as the number of reads that perfectly aligned to either strand normalized to the sequencing depth of the library in millions.
genome build: C. elegans genome (WS190)
processed data files format and content: The processed data file is a text file containing matrix of 1kb genomic regions (rows) and all ChIP-seq experiments (columns). Values in matrix represent reads per million mapped reads per kb (RPKM). First column is the choromosome location, second column is the start position of the 1kb region, and the remaning columns are the RPKM values.

extract_protocol:
50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-H3K36me3 (300-95289, WAKO) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein  A(for H3K9me3) or protein G (for H3K36me3) Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 80 μg of proteinase K) at 65 °C for 4 hours with continuous agitation  (IP input lysate was treated similarly to reverse crosslink). DNA was extracted by phenolchloroform and dissolved in TE buffer.
ChIP-seq libraries were made using NuGen Ovation Ultralow Library Systems v2 according to manufacturer’s instructions.

treatment_protocol: 500 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication).

value: Anti-Histone H3 (tri methyl K36)


title: met-1_hrde-1_late_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: met-1_hrde-1_F4_rep1_ChIPseq_H3K36me3_cCS83p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: SLX-9774.N706_N508

description: Young HSC JAK2 HOM


title: SLX-9774.N707_N503

description: Young HSC JAK2 HOM


title: SLX-9774.N707_N504

description: Young HSC JAK2 HOM


title: met-1_hrde-1_early_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: met-1_hrde-1_F1_rep2_ChIPseq_H3K36me3_cCS106p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: CACAGT


title: met-1_morc-1_late_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: met-1_morc-1_F4_rep1_ChIPseq_H3K36me3_cCS81p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: met-1_morc-1_late_rep2_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: met-1_morc-1_F4_rep2_ChIPseq_H3K36me3_cCS105p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: SLX-9774.N707_N505

description: Young HSC JAK2 HOM


title: met-1_late_rep2_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: met-1_F4_rep2_ChIPseq_H3K36me3_cCS103p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: met-1_morc-1_early_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: met-1_morc-1_F1_rep2_ChIPseq_H3K36me3_cCS104p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: CGTAGA


title: SLX-9774.N706_N517

description: Young HSC JAK2 HOM

value: whole bone marrow


title: met-1_late_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: met-1_F4_rep1_ChIPseq_H3K36me3_cCS79p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: SLX-9774.N706_N507

description: Young HSC JAK2 HOM

value: Hematopoietic Stem Cell


title: SLX-9774.N706_N504

description: Young HSC JAK2 HOM

value: 4 Months (young)


title: SLX-9774.N706_N505

description: Young HSC JAK2 HOM


title: SLX-9774.N707_N502

description: Young HSC JAK2 HOM


title: SLX-9774.N706_N503

description: Young HSC JAK2 HOM


title: met-1_early_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: met-1_F1_rep2_ChIPseq_H3K36me3_cCS102p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: AGCATG


title: hrde-1_late_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: hrde-1_F4_rep1_ChIPseq_H3K36me3_cCS77p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: hrde-1_late_rep2_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: hrde-1_F4_rep2_ChIPseq_H3K36me3_cCS101p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: hrde-1_early_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: hrde-1_F1_rep2_ChIPseq_H3K36me3_cCS100p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: AAGAGG


title: morc-1_late_rep2_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: morc-1_F5_rep2_ChIPseq_H3K36me3_cCS47p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: SLX-9774.N706_N502

description: Young HSC JAK2 HOM

value: JAK2 V617F Homozygous


title: morc-1_early_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: morc-1_F1_rep2_ChIPseq_H3K36me3_cCS98p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: AAGCCT


title: SLX-9774.N705_N507

description: Young HSC JAK2 HOM


title: SLX-9774.N705_N517

description: Young HSC JAK2 HOM


title: SLX-9774.N706_N506

description: Young HSC JAK2 HOM


title: WT_late_rep3_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: WT_F5_rep1_ChIPseq_H3K36me3_cCS35p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: AGTGAG


title: SLX-9774.N705_N505

description: Young HSC JAK2 HOM


title: SLX-9774.N705_N506

description: Young HSC JAK2 HOM


title: WT_late_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: WT_F4_rep1_ChIPseq_H3K36me3_cCS73p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: WT_late_rep2_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: WT_F4_rep2_ChIPseq_H3K36me3_cCS97p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: GTGCTT


title: met-1_hrde-1_late_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: met-1_hrde-1_F4_rep2_ChIPseq_input_cCS95p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: GCACTA


title: WT_early_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: WT_F1_rep2_ChIPseq_H3K36me3_cCS96p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: ACCTCA


title: SLX-9774.N704_N517

description: Young HSC JAK2 HOM


title: SLX-9774.N705_N502

description: Young HSC JAK2 HOM


title: met-1_hrde-1_early_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: met-1_hrde-1_F1_rep2_ChIPseq_input_cCS94p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: SLX-9774.N705_N504

description: Young HSC JAK2 HOM


title: met-1_morc-1_late_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: met-1_morc-1_F4_rep2_ChIPseq_input_cCS93p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: TGGTGA


title: met-1_morc-1_early_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: met-1_morc-1_F1_rep2_ChIPseq_input_cCS92p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: AACCAG


title: SLX-9774.N705_N503

description: Young HSC JAK2 HOM


title: met-1_late_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: met-1_F4_rep2_ChIPseq_input_cCS91p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: TTGGCA


title: SLX-9774.N705_N508

description: Young HSC JAK2 HOM


title: morc-1_late_rep1_ChIPseq_H3K36me3

description:
DNA from immunoprecipitated chromatin
Sample name: morc-1_F4_rep2ChIPseq_H3K36me3_cCS99p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: GTCGTA

value: Anti-Histone H3 (tri methyl K36)


title: SLX-9774.N704_N506

description: Young HSC JAK2 HOM


title: SLX-9774.N704_N508

description: Young HSC JAK2 HOM


title: SLX-9774.N704_N507

description: Young HSC JAK2 HOM


title: SLX-9774.N704_N504

description: Young HSC JAK2 HOM


title: met-1_early_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: met-1_F1_rep2_ChIPseq_input_cCS90p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: CACAGT


title: hrde-1_early_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: hrde-1_F1_rep2_ChIPseq_input_cCS88p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: CGTAGA


title: morc-1_late_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: morc-1_F4_rep2_ChIPseq_input_cCS87p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: GAGTCA


title: SLX-9774.N704_N502

description: Young HSC JAK2 HOM

value: whole bone marrow

value: Hematopoietic Stem Cell

value: 4 Months (young)


title: morc-1_early_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: morc-1_F1_rep2_ChIPseq_input_cCS20p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: SLX-9774.N704_N503

description: Young HSC JAK2 HOM

value: JAK2 V617F Homozygous


title: SLX-9774.N703_N517

description: Young HSC JAK2 HOM


title: SLX-9774.N703_N508

description: Young HSC JAK2 HOM


title: SLX-9774.N703_N507

description: Young HSC JAK2 HOM


title: WT_early_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: WT_F1_rep2_ChIPseq_input_cCS18p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: SLX-9774.N703_N505

description: Young HSC JAK2 HOM


title: hrde-1_late_rep2_ChIPseq_H3K9me3

description:
DNA from immunoprecipitated chromatin
Sample name: hrde-1_F5_rep2_ChIPseq_H3K9me3_cCS29p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: Anti-Histone H3 (tri methyl K9)


title: SLX-9774.N703_N506

description: Young HSC JAK2 HOM


title: SLX-9774.N703_N504

description: Young HSC JAK2 HOM


title: hrde-1_early_rep1_ChIPseq_H3K9me3

description:
DNA from immunoprecipitated chromatin
Sample name: hrde-1_F1_rep1_ChIPseq_H3K9me3_cCS16p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: morc-1_late_rep2_ChIPseq_H3K9me3

description:
DNA from immunoprecipitated chromatin
Sample name: morc-1_F5_rep3_ChIPseq_H3K9me3_cCS44p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: SLX-9774.N703_N503

description: Young HSC JAK2 HOM


title: SLX-9774.N702_N517

description: Young HSC JAK2 HOM


title: SLX-9774.N703_N502

description: Young HSC JAK2 HOM


title: hrde-1_late_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: hrde-1_F4_rep2_ChIPseq_input_cCS89p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: TCAGAG


title: SLX-9774.N704_N505

description: Young HSC JAK2 HOM


title: SLX-9774.N702_N508

description: Young HSC JAK2 HOM


title: morc-1_early_rep1_ChIPseq_H3K9me3

description:
DNA from immunoprecipitated chromatin
Sample name: morc-1_F1_rep2_ChIPseq_H3K9me3_cCS26p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: GGAGAA


title: WT_late_rep1_ChIPseq_H3K9me3

description:
DNA from immunoprecipitated chromatin
Sample name: WT_F4_rep1_ChIPseq_H3K9me3_cCS13p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: WT_early_rep1_ChIPseq_H3K9me3

description:
DNA from immunoprecipitated chromatin
Sample name: WT_F1_rep2_ChIPseq_H3K9me3_cCS24p
processed data file: ChIPseq_1kb_region_RPKM.txt


title: SLX-9774.N702_N506

description: Young HSC JAK2 HOM


title: hrde-1_late_rep2_mRNAseq

description:
polyA mRNA
Sample name: hrde-1_F4_rep2_mRNAseq_cRS60p
processed data file: mRNA_normalized_counts.txt

data_processing:
Basecalling was performed using Illumina's default Real Time Analysis (RTA) basecalling and quality scoring software application.
Conversion from qseq files to fastq files and demultiplexing was performed using custom Awk and Python scripts
trimming and filtering: Reads were adapter-trimmed and quality filtered (Q30) using Trimmomatic v.0.35.
alignment: Reads were aligned to the C. elegans genome and transcriptome (WS230) using TopHat2.
Gene expression RPKM values were obtained using CuffDiff2.
genome build:  C. elegans genome (WS230)
processed data files format and content: Processed data file contains a matrix of genes (rows) and normalized read counts in each library (columns). Read counts are normalized to total library size.

molecule: total RNA

extract_protocol:
RNA extraction from gravid hermaphrodites was performed as previous described (Billi et al., 2012a). In brief, worms were collected in TriReagent (Ambion) and subjected to three freeze-thaw cycles.  After phase-separating using 1-bromo-3-chloropropane (BCP), RNA was precipitated in isopropanol at -80°C for one hour. RNA was pelleted by centrifugation at 15,000g for 30 minutes at 4°C. After 2 washes in 70% ethanol and 1 wash in 75% ethanol, the pellet was resuspended in water.
mRNA libraries were constructed using Illumina TruSeq Stranded mRNA Library Prep Kit for NeoPrep and an Illumina NeoPrep Library Prep machine according to manufacturer’s instructions.

value: ACTTGA


title: SLX-9774.N702_N504

description: Young HSC JAK2 HOM


title: SLX-9774.N702_N505

description: Young HSC JAK2 HOM


title: hrde-1_early_rep1_mRNAseq

description:
polyA mRNA
Sample name: hrde-1_F1_rep1_mRNAseq_cRS53p
processed data file: mRNA_normalized_counts.txt

value: ACAGTG


title: hrde-1_early_rep2_mRNAseq

description:
polyA mRNA
Sample name: hrde-1_F1_rep2_mRNAseq_cRS59p
processed data file: mRNA_normalized_counts.txt

value: GTGGCC


title: SLX-9774.N702_N503

description: Young HSC JAK2 HOM


title: SLX-9774.N702_N502

description: Young HSC JAK2 HOM


title: hrde-1_late_rep1_ChIPseq_H3K9me3

description:
DNA from immunoprecipitated chromatin
Sample name: hrde-1_F4_rep1_ChIPseq_H3K9me3_cCS17p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: AACCAG


title: morc-1_late_rep2_mRNAseq

description:
polyA mRNA
Sample name: morc-1_F4_rep2_mRNAseq_cRS58p
processed data file: mRNA_normalized_counts.txt

value: TAGCTT


title: morc-1_late_rep1_mRNAseq

description:
polyA mRNA
Sample name: morc-1_F4_rep1_mRNAseq_cRS52p
processed data file: mRNA_normalized_counts.txt

value: AGTTCC


title: morc-1_early_rep2_mRNAseq

description:
polyA mRNA
Sample name: morc-1_F1_rep2_mRNAseq_cRS57p
processed data file: mRNA_normalized_counts.txt

value: ATCACG


title: morc-1_late_rep1_ChIPseq_H3K9me3

description:
DNA from immunoprecipitated chromatin
Sample name: morc-1_F4_rep1_ChIPseq_H3K9me3_cCS15p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: CACAGT


title: SLX-9774.N701_N517

description: Young HSC JAK2 HOM


title: WT_early_rep2_mRNAseq

description:
polyA mRNA
Sample name: WT_F1_rep2_mRNAseq_cRS55p
processed data file: mRNA_normalized_counts.txt

value: GTGAAA


title: SLX-9774.N701_N505

description: Young HSC JAK2 HOM


title: hrde-1_late_rep1_sRNAseq

description:
small RNA
Sample name: hrde-1_F4_rep1_sRNAseq_cRS46p
processed data file: sRNA_normalized_counts.txt

data_processing:
Basecalling was performed using Illumina's default Real Time Analysis (RTA) basecalling and quality scoring software application.
Conversion from qseq files to fastq files and demultiplexing was performed using custom Awk and Python scripts
trimming and filtering: Small RNAs were parsed from adapter sequences (CASHX v.2.3), and reads 18-32 nt long and passing a Q30 threshold were retained.
alignment: Reads were aligned to the C. elegans genome (WS230) using CASHX v.2.3.
Total 22G RNAs read counts for all genes and for mutator-class siRNA targets were quantified using DESeq2.
genome build:  C. elegans genome (WS230)
processed data files format and content: Processed data file contains a matrix of genes (rows) and normalized 22G RNA counts in each library (columns). 22G RNA counts are normalized to total library size.

extract_protocol:
RNA extraction from gravid hermaphrodites was performed as previous described (Billi et al., 2012a). In brief, worms were collected in TriReagent (Ambion) and subjected to three freeze-thaw cycles.  After phase-separating using 1-bromo-3-chloropropane (BCP), RNA was precipitated in isopropanol at -80°C for one hour. RNA was pelleted by centrifugation at 15,000g for 30 minutes at 4°C. After 2 washes in 70% ethanol and 1 wash in 75% ethanol, the pellet was resuspended in water.
Phosphate independent small RNA libraries were constructed as described in (Phillips et al., 2014) using RNA 5’ polyphosphatase (Illumina) and the Illumina TruSeq Small RNAi Library Prep Kit.

value: CATGGC


title: SLX-9774.N701_N508

description: Young HSC JAK2 HOM

value: whole bone marrow


title: morc-1_early_rep1_mRNAseq

description:
polyA mRNA
Sample name: morc-1_F1_rep1_mRNAseq_cRS51p
processed data file: mRNA_normalized_counts.txt

value: CTTGTA


title: SLX-9774.N701_N504

description: Young HSC JAK2 HOM

value: Hematopoietic Stem Cell

value: 4 Months (young)


title: SLX-9774.N701_N506

description: Young HSC JAK2 HOM

value: JAK2 V617F Homozygous


title: SLX-9774.N701_N503

description: Young HSC JAK2 HOM


title: WT_late_rep1_mRNAseq

description:
polyA mRNA
Sample name: WT_F4_rep1_mRNAseq_cRS50p
processed data file: mRNA_normalized_counts.txt

value: AGTCAA


title: SLX-9774.N701_N502

description: Young HSC JAK2 HOM


title: hrde-1_late_rep2_sRNAseq

description:
small RNA
Sample name: hrde-1_F4_rep2_sRNAseq_cRS48p
processed data file: sRNA_normalized_counts.txt

value: CCAACA


title: SLX-9773.N712_N508

description: Old HSC WT

value: 18 Months (Old)

value: Wild Type


title: hrde-1_late_rep1_mRNAseq

description:
polyA mRNA
Sample name: hrde-1_F4_rep1_mRNAseq_cRS54p
processed data file: mRNA_normalized_counts.txt

value: ATGTCA


title: hrde-1_early_rep2_sRNAseq

description:
small RNA
Sample name: hrde-1_F1_rep2_sRNAseq_cRS47p
processed data file: sRNA_normalized_counts.txt

value: CATTTT


title: hrde-1_early_rep1_sRNAseq

description:
small RNA
Sample name: hrde-1_F1_rep1_sRNAseq_cRS45p
processed data file: sRNA_normalized_counts.txt

value: CAGGCG


title: SLX-9773.N712_N507

description: Old HSC WT


title: morc-1_late_rep3_sRNAseq

description:
small RNA
Sample name: morc-1_F5_rep3_sRNAseq_cRS44p
processed data file: sRNA_normalized_counts.txt

value: CACTCA


title: SLX-9774.N702_N507

description: Young HSC JAK2 HOM


title: WT_late_rep2_mRNAseq

description:
polyA mRNA
Sample name: WT_F4_rep2_mRNAseq_cRS56p
processed data file: mRNA_normalized_counts.txt

value: GTTTCG


title: SLX-9773.N712_N504

description: Old HSC WT


title: SLX-9773.N712_N506

description: Old HSC WT


title: morc-1_late_rep1_sRNAseq

description:
small RNA
Sample name: morc-1_F4_rep1_sRNAseq_cRS36p
processed data file: sRNA_normalized_counts.txt

value: ACTTGA


title: WT_late_rep1_ChIPseq_input

description:
DNA from fragmented chromatin
Sample name: WT_F4_rep2_ChIPseq_input_cCS85p
processed data file: ChIPseq_1kb_region_RPKM.txt

value: GGAGAA


title: WT_early_rep1_mRNAseq

description:
polyA mRNA
Sample name: WT_F1_rep1_mRNAseq_cRS49p
processed data file: mRNA_normalized_counts.txt

value: GCCAAT


title: morc-1_late_rep2_sRNAseq

description:
small RNA
Sample name: morc-1_F4_rep2_sRNAseq_cRS40p
processed data file: sRNA_normalized_counts.txt

value: CAAAAG


title: SLX-9774.N701_N507

description: Young HSC JAK2 HOM

value: whole bone marrow


title: SLX-9773.N712_N503

description: Old HSC WT

value: Hematopoietic Stem Cell


title: morc-1_early_rep3_sRNAseq

description:
small RNA
Sample name: morc-1_F1_rep3_sRNAseq_cRS43p
processed data file: sRNA_normalized_counts.txt

value: CACGAT


title: SLX-9773.N712_N502

description: Old HSC WT


title: morc-1_early_rep2_sRNAseq

description:
small RNA
Sample name: morc-1_F1_rep2_sRNAseq_cRS39p
processed data file: sRNA_normalized_counts.txt

value: ATTCCT


title: morc-1_early_rep1_sRNAseq

description:
small RNA
Sample name: morc-1_F1_rep1_sRNAseq_cRS35p
processed data file: sRNA_normalized_counts.txt

value: CAGATC


title: SLX-9773.N712_N517

description: Old HSC WT


title: SLX-9773.N711_N507

description: Old HSC WT


title: SLX-9773.N711_N508

description: Old HSC WT


title: WT_late_rep3_sRNAseq

description:
small RNA
Sample name: WT_F5_rep3_sRNAseq_cRS42p
processed data file: sRNA_normalized_counts.txt

value: CACCGG


title: WT_late_rep1_sRNAseq

description:
small RNA
Sample name: WT_F4_rep1_sRNAseq_cRS34p
processed data file: sRNA_normalized_counts.txt


title: WT_early_rep1_sRNAseq

description:
small RNA
Sample name: WT_F1_rep1_sRNAseq_cRS33p
processed data file: sRNA_normalized_counts.txt

value: ACAGTG


title: WT_526

city: Smithville

first: Kei-ichi

last: Takata

state: TX

address: 1808 Park Road 1C

department: Department of Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.7) and Bowtie2 (version 2.0.6).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on March 6, 2013) was enumerated using htseq-count from HTSeq package (version 0.5.3p9).
Genes with less than 10 fragments in all the samples were removed, and then the effective cpm (count per million effective fragments) value for each gene was calculated by R/Bioconductor package edgeR (version 3.0.8).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is gene symbol. The other columns are cpm values (estimated by edgeR) for all the samples.

source_name: testis

extract_protocol:
Four biological replicates were prepared for Poln+/+ and PolnΔEx2/ΔEx2 mice. RNA was purified from testis of 68-day old male mice with RNeasy kit (QIAGEN) with on-column DNase treatment.
The libraries were prepared using the Illumina TruSeq stranded total RNA kit according to the manufacturer’s protocol, except that the PCR amplification cycle was reduced to 10. The libraries were sequenced on HiSeq 2000 (Illumina), generating 53-73 million pairs of 75 bp reads per sample. Each pair of reads represents a cDNA fragment from the library.

value: testis

tag: genotype/variation

value: wild type


title: SLX-9773.N711_N502

description: Old HSC WT

value: 18 Months (Old)

value: Wild Type


title: SLX-9773.N711_N506

description: Old HSC WT


title: WT_496


title: SLX-9773.N710_N517

description: Old HSC WT


title: SLX-9773.N710_N507

description: Old HSC WT


title: SLX-9773.N710_N505

description: Old HSC WT


title: WT_529


title: WT_499


title: WT_early_rep3_sRNAseq

description:
small RNA
Sample name: WT_F1_rep3_sRNAseq_cRS41p
processed data file: sRNA_normalized_counts.txt

value: CAACTA


title: SLX-9773.N710_N504

description: Old HSC WT


title: SLX-9773.N711_N505

description: Old HSC WT


title: SLX-9773.N712_N505

description: Old HSC WT


title: SLX-9773.N711_N504

description: Old HSC WT


title: SLX-9773.N711_N503

description: Old HSC WT


title: poln_497

value: poln


title: SLX-9773.N710_N508

description: Old HSC WT


title: WT_early_rep2_sRNAseq

description:
small RNA
Sample name: WT_F1_rep2_sRNAseq_cRS37p
processed data file: sRNA_normalized_counts.txt

value: ACTGAT


title: Cardiomyocite Mutant 4

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
FPKM
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: mouse cardiomyociites

extract_protocol: One hundred and fifty nanograms from (number of samples) RNA samples was used to generate libraries following Illumina TruSeq Stranded mRNA kit as per protocol. cDNA libraries generated from these samples were size indexed and validated using Agilent Bioanalyzer and concentration validated by qPCR.  4 different libraries were normalized to 10nM and pooled together. 8pM of pooled libraries were loaded onto Illumina cBot for cluster generation. Clustered flow cell was then sequenced Pair-end 100 cycles using Illumina HighSeq 2000.

value: Raf1 L613V/+ knock-in


title: poln_523


title: SLX-9773.N710_N503

description: Old HSC WT


title: SLX-9773.N710_N506

description: Old HSC WT


title: poln_521


title: SLX-9773.N711_N517

description: Old HSC WT


title: poln_498


title: Cardiomyocite Mutant 1


title: WT_late_rep2_sRNAseq

description:
small RNA
Sample name: WT_F4_rep2_sRNAseq_cRS38p
processed data file: sRNA_normalized_counts.txt

value: ATGAGC


title: Cardiomyocite Control 3

value: control


title: SLX-9773.N709_N505

description: Old HSC WT

value: whole bone marrow


title: SLX-9773.N709_N506

description: Old HSC WT

value: Hematopoietic Stem Cell


title: SLX-9773.N710_N502

description: Old HSC WT


title: SLX-9773.N709_N517

description: Old HSC WT


title: Cardiomyocite Mutant 3


title: SLX-9773.N709_N504

description: Old HSC WT


title: Cardiomyocite Mutant 2


title: Cardiomyocite Control 2


title: SLX-9773.N709_N508

description: Old HSC WT


title: Cardiomyocite Control 1


title: Wild-type LSK cells rep 1

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

data_processing:
Reads were mapped to mouse genome mm9 using Subread. Only uniquely mapped reads were retained. Mapped reads were assigned to mouse RefSeq genes using featureCounts. NCBI RefSeq mouse annotation build 37.2 was used. Genes were removed from analysis if they failed to achieve a RPKM (reads per kilo exonic bases per million mapped reads) value of 0.5 or greater in at least two libraries.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. A false discovery rate cutoff of 0.1 was applied when calling differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file including normalized log2-RPKM expression values of genes.

source_name: Bone marrow

extract_protocol:
RNA was extracted from sorted LSK cells using the RNeasy Kit (Qiagen, Valencia CA).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

value: Bone marrow

value: LSK (Lin-Sca+Kit+)

value: Wild-type


title: SLX-9773.N708_N517

description: Old HSC WT


title: Cardiomyocite Control 4


title: SLX-9773.N709_N507

description: Old HSC WT


title: Wild-type LSK cells rep 2


title: SLX-9773.N708_N508

description: Old HSC WT


title: SLX-9773.N709_N503

description: Old HSC WT


title: Hhex-deleted LSK cells rep 1

value: Hhex deletion


title: SLX-9773.N709_N502

description: Old HSC WT


title: Hhex-deleted LSK cells rep 2


title: SLX-9773.N708_N507

description: Old HSC WT


title: SLX-9773.N708_N505

description: Old HSC WT


title: SLX-9773.N708_N504

description: Old HSC WT


title: SLX-9773.N708_N506

description: Old HSC WT


title: SLX-9773.N708_N503

description: Old HSC WT


title: SLX-9773.N707_N508

description: Old HSC WT


title: SLX-9773.N708_N502

description: Old HSC WT


title: SLX-9773.N707_N507

description: Old HSC WT


title: SLX-9773.N707_N505

description: Old HSC WT


title: SLX-9773.N707_N506

description: Old HSC WT


title: SLX-9773.N707_N503

description: Old HSC WT


title: SLX-9773.N706_N517

description: Old HSC WT


title: SLX-9773.N707_N504

description: Old HSC WT


title: SLX-9773.N707_N502

description: Old HSC WT


title: SLX-9773.N706_N506

description: Old HSC WT


title: SLX-9773.N706_N505

description: Old HSC WT


title: SLX-9773.N706_N504

description: Old HSC WT


title: SLX-9773.N706_N503

description: Old HSC WT


title: SLX-9773.N705_N517

description: Old HSC WT


title: SLX-9773.N705_N504

description: Old HSC WT


title: SLX-9773.N705_N505

description: Old HSC WT


title: SLX-9773.N706_N502

description: Old HSC WT


title: SLX-9773.N705_N503

description: Old HSC WT


title: SLX-9773.N707_N517

description: Old HSC WT


title: SLX-9773.N704_N517

description: Old HSC WT


title: SLX-9773.N704_N507

description: Old HSC WT


title: SLX-9773.N704_N508

description: Old HSC WT


title: SLX-9773.N705_N502

description: Old HSC WT


title: SLX-9773.N704_N506

description: Old HSC WT


title: SLX-9773.N706_N508

description: Old HSC WT


title: SLX-9773.N703_N517

description: Old HSC WT


title: SLX-9773.N704_N502

description: Old HSC WT


title: SLX-9773.N704_N503

description: Old HSC WT


title: SLX-9773.N706_N507

description: Old HSC WT


title: SLX-9773.N704_N505

description: Old HSC WT


title: SLX-9773.N704_N504

description: Old HSC WT


title: SLX-9773.N703_N508

description: Old HSC WT


title: SLX-9773.N703_N507

description: Old HSC WT


title: SLX-9773.N705_N506

description: Old HSC WT


title: SLX-9773.N703_N503

description: Old HSC WT


title: SLX-9773.N705_N507

description: Old HSC WT


title: SLX-9773.N703_N504

description: Old HSC WT


title: SLX-9773.N703_N502

description: Old HSC WT


title: SLX-9773.N702_N508

description: Old HSC WT


title: SLX-9773.N702_N517

description: Old HSC WT


title: SLX-9773.N702_N507

description: Old HSC WT


title: SLX-9773.N702_N503

description: Old HSC WT


title: SLX-9773.N702_N505

description: Old HSC WT


title: SLX-9773.N702_N506

description: Old HSC WT


title: SLX-9773.N701_N517

description: Old HSC WT


title: SLX-9773.N702_N504

description: Old HSC WT


title: SLX-9773.N701_N507

description: Old HSC WT


title: SLX-9773.N701_N505

description: Old HSC WT


title: SLX-9773.N702_N502

description: Old HSC WT


title: SLX-9773.N701_N508

description: Old HSC WT


title: SLX-9773.N701_N502

description: Old HSC WT


title: SLX-9773.N701_N504

description: Old HSC WT


title: SLX-9772.N712_N504

description: Old HSC JAK2 HOM

value: JAK2 V617F Homozygous


title: SLX-9772.N712_N506

description: Old HSC JAK2 HOM


title: SLX-9772.N712_N505

description: Old HSC JAK2 HOM


title: SLX-9773.N703_N506

description: Old HSC WT


title: SLX-9773.N701_N503

description: Old HSC WT


title: SLX-9772.N712_N508

description: Old HSC JAK2 HOM


title: SLX-9772.N712_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N712_N503

description: Old HSC JAK2 HOM


title: SLX-9773.N703_N505

description: Old HSC WT


title: SLX-9772.N711_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N712_N502

description: Old HSC JAK2 HOM


title: SLX-9772.N711_N508

description: Old HSC JAK2 HOM


title: SLX-9772.N711_N507

description: Old HSC JAK2 HOM


title: SLX-9772.N711_N505

description: Old HSC JAK2 HOM


title: SLX-9772.N711_N503

description: Old HSC JAK2 HOM


title: SLX-9773.N701_N506

description: Old HSC WT


title: SLX-9772.N710_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N711_N502

description: Old HSC JAK2 HOM


title: SLX-9772.N710_N507

description: Old HSC JAK2 HOM


title: SLX-9772.N710_N506

description: Old HSC JAK2 HOM


title: SLX-9772.N710_N504

description: Old HSC JAK2 HOM


title: SLX-9772.N710_N503

description: Old HSC JAK2 HOM


title: SLX-9772.N710_N505

description: Old HSC JAK2 HOM


title: SLX-9772.N709_N508

description: Old HSC JAK2 HOM


title: SLX-9772.N709_N506

description: Old HSC JAK2 HOM


title: SLX-9772.N709_N505

description: Old HSC JAK2 HOM


title: SLX-9772.N712_N507

description: Old HSC JAK2 HOM


title: SLX-9772.N709_N507

description: Old HSC JAK2 HOM


title: SLX-9772.N709_N503

description: Old HSC JAK2 HOM


title: SLX-9772.N710_N502

description: Old HSC JAK2 HOM


title: SLX-9772.N709_N502

description: Old HSC JAK2 HOM


title: SLX-9772.N711_N504

description: Old HSC JAK2 HOM


title: SLX-9772.N708_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N711_N506

description: Old HSC JAK2 HOM


title: SLX-9772.N709_N504

description: Old HSC JAK2 HOM


title: SLX-9772.N709_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N708_N508

description: Old HSC JAK2 HOM


title: SLX-9772.N708_N506

description: Old HSC JAK2 HOM


title: SLX-9772.N708_N504

description: Old HSC JAK2 HOM


title: SLX-9772.N710_N508

description: Old HSC JAK2 HOM


title: SLX-9772.N708_N505

description: Old HSC JAK2 HOM


title: SLX-9772.N708_N503

description: Old HSC JAK2 HOM


title: SLX-9772.N708_N507

description: Old HSC JAK2 HOM


title: SLX-9772.N708_N502

description: Old HSC JAK2 HOM


title: SLX-9772.N707_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N707_N508

description: Old HSC JAK2 HOM


title: SLX-9772.N707_N506

description: Old HSC JAK2 HOM


title: SLX-9772.N707_N505

description: Old HSC JAK2 HOM


title: SLX-9772.N707_N504

description: Old HSC JAK2 HOM


title: SLX-9772.N707_N503

description: Old HSC JAK2 HOM


title: SLX-9772.N707_N507

description: Old HSC JAK2 HOM


title: SLX-9772.N707_N502

description: Old HSC JAK2 HOM


title: SLX-9772.N706_N506

description: Old HSC JAK2 HOM


title: SLX-9772.N706_N507

description: Old HSC JAK2 HOM


title: SLX-9772.N706_N508

description: Old HSC JAK2 HOM


title: SLX-9772.N706_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N706_N504

description: Old HSC JAK2 HOM


title: SLX-9772.N706_N502

description: Old HSC JAK2 HOM


title: SLX-9772.N706_N505

description: Old HSC JAK2 HOM


title: SLX-9772.N705_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N705_N507

description: Old HSC JAK2 HOM


title: SLX-9772.N706_N503

description: Old HSC JAK2 HOM


title: SLX-9772.N705_N508

description: Old HSC JAK2 HOM


title: SLX-9772.N705_N506

description: Old HSC JAK2 HOM


title: SLX-9772.N705_N505

description: Old HSC JAK2 HOM


title: SLX-9772.N705_N504

description: Old HSC JAK2 HOM


title: SLX-9772.N705_N502

description: Old HSC JAK2 HOM


title: SLX-9772.N704_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N704_N505

description: Old HSC JAK2 HOM


title: ∆moago1_b

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Mycelial tissues from targeted deletion mutant of M. oryzae Argonaute MGG_14873.6, replicate 2

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: Magnaporthe oryzae genome assembly 8 from Broad Institute
Supplementary_files_format_and_content: tag count file

organism: Pyricularia oryzae

source_name: Mycelium

extract_protocol:
Mycelial tissues were collected and flash frozen in liquid nitrogen. Total RNA was extracted by TRIzol Reagent (Ambion by Life Technologies) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-930-1012). RNA-seq libraries were constructed using the Illumina TruSeq RNA sample preparation kit (RS-930-2001).

value: Mycelium grown in complete media for 5 days


title: ∆moago2_a

description: Mycelial tissues from targeted deletion mutant of M. oryzae Argonaute MGG_13617.6, replicate 1


title: ∆moago2_b

description: Mycelial tissues from targeted deletion mutant of M. oryzae Argonaute MGG_13617.6, , replicate 2


title: SLX-9772.N704_N508

description: Old HSC JAK2 HOM


title: SLX-9772.N704_N507

description: Old HSC JAK2 HOM


title: ∆mordrp1_a

description: Mycelial tissues from targeted deletion mutant of M. oryzae RdRP MGG_02748.6, replicate 1


title: SLX-9772.N704_N502

description: Old HSC JAK2 HOM


title: ∆moago1_a

description: Mycelial tissues from targeted deletion mutant of M. oryzae Argonaute MGG_14873.6, replicate 1


title: ∆mordrp3_b

description: Mycelial tissues from targeted deletion mutant of M. oryzae RdRP MGG_06205.6, replicate 2


title: ∆modcl2/1_b

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein2 (MGG_12357.6) and Dicer-like protein1 (MGG_01541.6), replicate 2


title: ∆modcl2/1_a

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein2 (MGG_12357.6) and Dicer-like protein1 (MGG_01541.6), replicate 1


title: ∆mordrp3_a

description: Mycelial tissues from targeted deletion mutant of M. oryzae RdRP MGG_06205.6, replicate 1


title: SLX-9772.N705_N503

description: Old HSC JAK2 HOM


title: SLX-9773.N705_N508

description: Old HSC WT


title: SLX-9772.N703_N505

description: Old HSC JAK2 HOM


title: SLX-9772.N704_N504

description: Old HSC JAK2 HOM


title: ∆mordrp1_b

description: Mycelial tissues from targeted deletion mutant of M. oryzae RdRP MGG_02748.6, replicate 2


title: ∆modcl1/2_a

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein1 (MGG_01541.6) and Dicer-like protein2 (MGG_12357.6), replicate 1


title: SLX-9772.N704_N506

description: Old HSC JAK2 HOM


title: ∆mordrp2_b

description: Mycelial tissues from targeted deletion mutant of M. oryzae RdRP MGG_13453.6, replicate 2


title: SLX-9772.N704_N503

description: Old HSC JAK2 HOM


title: SLX-9772.N703_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N703_N503

description: Old HSC JAK2 HOM


title: SLX-9772.N703_N504

description: Old HSC JAK2 HOM


title: SLX-9772.N703_N507

description: Old HSC JAK2 HOM


title: SLX-9772.N703_N508

description: Old HSC JAK2 HOM


title: ∆modcl2_b

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein2 (MGG_12357.6), replicate 2


title: ∆mordrp2_a

description: Mycelial tissues from targeted deletion mutant of M. oryzae RdRP MGG_13453.6, replicate 1


title: ∆modcl2_a

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein2 (MGG_12357.6), replicate 1


title: SLX-9772.N703_N502

description: Old HSC JAK2 HOM


title: SLX-9772.N703_N506

description: Old HSC JAK2 HOM


title: ∆modcl1/2_b

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein1 (MGG_01541.6) and Dicer-like protein2 (MGG_12357.6), replicate 2


title: ∆modcl1_b

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein1 (MGG_01541.6), replicate 2


title: SLX-9772.N702_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N702_N507

description: Old HSC JAK2 HOM


title: SLX-9772.N702_N508

description: Old HSC JAK2 HOM


title: Wt7015_a

description: Mycelial tissues from wild type, Magnaporthe oryzae strain 70-15, replicate 1


title: Wt7015_b

description: Mycelial tissues from wild type, Magnaporthe oryzae strain 70-15, replicate 2


title: ∆moago3

description: Mycelial tissues from targeted deletion mutant of M. oryzae Argonaute MGG_01294.6


title: Wt7015_I


title: SLX-9772.N701_N508

description: Old HSC JAK2 HOM


title: SLX-9772.N702_N505

description: Old HSC JAK2 HOM


title: SLX-9772.N702_N506

description: Old HSC JAK2 HOM


title: SLX-9772.N702_N502

description: Old HSC JAK2 HOM


title: ∆moago2

description: Mycelial tissues from targeted deletion mutant of M. oryzae Argonaute MGG_13617.6


title: ∆mordrp3

description: Mycelial tissues from targeted deletion mutant of M. oryzae RdRP MGG_06205.6


title: SLX-9772.N701_N507

description: Old HSC JAK2 HOM


title: ∆mordrp2

description: Mycelial tissues from targeted deletion mutant of M. oryzae RdRP MGG_13453.6


title: ∆moago1

description: Mycelial tissues from targeted deletion mutant of M. oryzae Argonaute MGG_14873.6


title: SLX-9772.N701_N517

description: Old HSC JAK2 HOM


title: SLX-9772.N701_N504

description: Old HSC JAK2 HOM


title: SLX-9772.N702_N504

description: Old HSC JAK2 HOM


title: SLX-9772.N701_N503

description: Old HSC JAK2 HOM


title: High BC 3

city: Tartu

first: Kaspar

last: Valgepea

state: Tartumaa

address: Nooruse 1

department: Institute of Technology

country: Estonia

institute: University of Tartu

description: processed data file: Compiled RPKMs.txt, Expression changes.txt

data_processing:
Basecalling was done using Illumina CASAVA 1.8.2 software.
Sequencing reads were aligned to the genome using Rsubread (Liao et al., 2013) and ribosomal RNA genes were moved prior further analysis. Reads for carbon monoxide dehydrogenase genes with initial IDs of CAETHG_1620 and 1621 (Brown et al., 2014) were manually mapped with IDs CAETGH_RS07861 and RS07862, respectively.
Transcript abundances (RPKMs) were estimated using the RPKM function of edgeR (Robinson et al., 2009) using normalisation across all samples.
Significant transcript expression changes between High and Low BC samples were determined using limma (Ritchie et al., 2015), only for transcripts with >10 reads per million mapped reads in at least two samples, by a -value<0.05 after false discovery rate correction (Benjamini and Hochberg, 1995).
Genome_build: NC_022592.1
Supplementary_files_format_and_content: Tab-delimited text file "Compiled RPKMs.txt" includes RPKM values for each sample identified by sample title.
Supplementary_files_format_and_content: Tab-delimited text file "Expression changes.txt" includes log2 fold change with q-values for the signficantly differently expressed transcripts comparing High to Low BC samples.

organism: Clostridium autoethanogenum

source_name: bacterial cell

growth_protocol: Clostridium autoethanogenum was grown on syngas in chemically defined medium anaerobically at 37C and a pH of 5 in chemostats at dilution rate ~1 1/day.

extract_protocol:
Frozen pellets were thawed and total RNA extracted using two cycles of cellular lysis in RNase-free zirconia beads (Ambion). RNA was purified using the RNeasy mini kit (Qiagen) with off-column DNase treatment followed by enrichment and purification using RNA Clean & ConcentratorTM (Zymo Research). Next, ribosomal RNA was removed using the Ribo-Zero rRNA removal kit (Illumina).
mRNA libraries were prepared using standard TruSeq library preparation protocols (Illumina).

treatment_protocol: Culture was pelleted by rapid centrifugation (5,000 × g for 3 min at 4C) followed by resuspension in 5 mL of RNAlater (Qiagen). Samples were stored at 4C overnight, centrifuged (4000 × g for 10 min at 4C) and the pellets stored at -80C.

tag: physiological state

value: High biomass concentration (1.4 gDCW/L) chemostat biological replicate 3


title: High BC 1

value: High biomass concentration (1.4 gDCW/L) chemostat biological replicate 1


title: SLX-9772.N701_N505

description: Old HSC JAK2 HOM

value: 18 Months (Old)


title: SLX-9772.N702_N503

description: Old HSC JAK2 HOM


title: ∆modcl2

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein2 (MGG_12357.6)


title: ∆modcl1

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein1 (MGG_01541.6)


title: ∆mordrp1

description: Mycelial tissues from targeted deletion mutant of M. oryzae RdRP MGG_02748.6


title: SLX-9772.N701_N502

description: Old HSC JAK2 HOM


title: High BC 2

value: High biomass concentration (1.4 gDCW/L) chemostat biological replicate 2


title: 35159_OMP_IGF1R18

city: Köln

first: Eva

last: Tsaousidou

address: Gleueler Str. 50

department: Neuronal Control of Metabolism

country: Germany

institute: Max-Planck-Institute for Metabolism Research

data_processing:
Raw sequence reads were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore! (v0.3.7, parameters: --paired --length 25). Trimmed sequences were aligned using Tophat2 (Kim et al., 2013) (v2.0.14, parameters: --no-mixed --library-type=fr-firststrand -g 2 -r 500 --mate-std-dev 525) against the mouse reference genome (build GRCm38), supplying GENCODE annotation (Harrow et al., 2012) (release M2, main annotation) for improved mapping. Multi-mapped reads were filtered using samtools (Li et al., 2009) (v1.2, parameters: view -F 0x100 -b –h).
Read counts were obtained using SeqMonk RNA-seq quantification pipeline
Data visualisation and analysis was performed using SeqMonk, custom RStudio and the following Bioconductor packages: Deseq2 (Love et al., 2014), topGO and org.Mm.eg.db. To account for tissue specific expression, we defined all genes with an FPKM of > 2 in at least half of all samples as ‘expressed’.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each sample; results for differential gene expression analysis

source_name: Olfactory epithelium

extract_protocol:
Olfactory epithelium was dissected and RNA was isolated using RNEasy Qiagen columns. RNA-seq library preparation and measurement was performed by the Cologne Center for Genomics, Cologne, Germany.
Stranded TruSeq RNA-seq library preparation was principally conducted as previously described (Sultan et al., 2012) with 2 μg of extracted RNA and poly-A enrichment. Barcoded libraries were sequenced with 100 bp paired-end reads on an Illumina HiSeq2500.

value: OMPflfl (Ctrl)

value: 40 weeks


title: Medium BC 3

description: Compiled RPKMs.txt

value: Medium biomass concentration (1.1 gDCW/L) chemostat biological replicate 3


title: 35158_OMP_IGF1R17


title: Medium BC 2

description: Compiled RPKMs.txt

value: Medium biomass concentration (1.1 gDCW/L) chemostat biological replicate 2


title: 35157_OMP_IGF1R12


title: ∆modcl2/1

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein2 (MGG_12357.6) and Dicer-like protein1 (MGG_01541.6)


title: ∆modcl1/2

description: Mycelial tissues from targeted deletion mutant of M. oryzae Dicer-like protein1 (MGG_01541.6) and Dicer-like protein2 (MGG_12357.6)


title: Wt7015

description: Mycelial tissues from wild type, Magnaporthe oryzae strain 70-15


title: 35141_IGF1R_flfl3

value: OMPIGF1 (KO)


title: Medium-Low BC 1

description: Compiled RPKMs.txt

value: Medium-Low biomass concentration (0.7 gDCW/L) chemostat biological replicate 1


title: 35140_IGF1R_flfl13


title: Low BC 3

value: Low biomass concentration (0.5 gDCW/L) chemostat biological replicate 3


title: Medium BC 1

description: Compiled RPKMs.txt

value: Medium biomass concentration (1.1 gDCW/L) chemostat biological replicate 1


title: Low BC 2

value: Low biomass concentration (0.5 gDCW/L) chemostat biological replicate 2


title: SLX-9772.N701_N506

description: Old HSC JAK2 HOM

value: whole bone marrow

value: Hematopoietic Stem Cell


title: Low BC 1

value: Low biomass concentration (0.5 gDCW/L) chemostat biological replicate 1


title: Medium-Low BC 2

description: Compiled RPKMs.txt

value: Medium-Low biomass concentration (0.7 gDCW/L) chemostat biological replicate 2


title: 35139_IGF1R_flfl2


title: Input K562 NHS

status: Public on May 21 2017

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

data_processing:
The sequenced ChIP-reads were trimmed, clipped and filtered to 36 nucleotide with fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). A minimum requirement for accepted reads was set to 99% probability for correct identification of at least 0.8 fraction of bases.
The reads were aligned to hg19 using Bowtie (Langmead et al., 2009). Please note that in the processed data files (bigWig) 36 nt from single end were aligned to hg19 for enabling direct comparison with our previous data (GSE43579; Vihervaara et al., PNAS, 2013). The raw data files (fastq) are provided as paired end sequencing data (PE100).
Genome_build: hg19

organism: Homo sapiens

source_name: K562 cells

growth_protocol: Human K562 erythroleukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium (Sigma), containing 10% fetal calf serum, 2 mM L-glutamate, 100 μg/ml streptomycin, and 100 U/ml penicillin. The cells were cultured according to standard procedures and maintained under 5x 10^5 cells/mL confluency.

extract_protocol:
After tretments, the cells were cross-linked with 1% fromaldehyde, quenched with glycine, washed twice with PBS and flash-frozen. The ChIP-experiments were conducted as described for GSE43579 (Vihervaara et al., Transcriptional response to stress in the dynamic chromatin environment of cycling and mitotic celss, 2013, PNAS, 110: 36, E3388-3397).
The libraries were generated with Nextera DNA Sample Preparation kit (Illumina). Paired-end sequencing (HiSeq PE100) was performed with Illumina.

treatment_protocol: To avoid provoking transcriptional changes by freshly added media, the cells were expanded 24 h prior to the treatments to confluence of 2x10^5 cells/ml. For treatments, 1x10^7 cells were concentrated in 10 mL media and placed into 37°C incubator (NHS) or submerged into 42°C water bath for 30 min (HS30).

tag: cell line

tag: treatment

value: Non-treated (NHS)

value: no antibody, fragmented total chromatin


title: day 7 wheat straw rep2

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

country: France

institute: INRAE - Aix Marseille University

data_processing:
QCed reads from each library were aligned to the genome Pycnoporus coccineus BRFM 310 v1.0 using TopHat (Kim et al., 2013) with only unique mapping allowed.
R was used for data manipulations (R Core Team, 2013). Raw read counts obtained from HTSeq were used for the calculation using DESeq2 (Love et al. 2014).
Genome_build: Pycnoporus coccineus BRFM 310 v1.0 http://genome.jgi.doe.gov/Pycco1/Pycco1.home.html
Supplementary_files_format_and_content: raw_counts

organism: Trametes coccinea

source_name: mycelium

growth_protocol: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 7 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted wheat straw (15 g.l-1 )

extract_protocol:
Total RNA was extracted from mycelia  harvested by filtering through Miracloth, squeeze dried, snap frozen in liquid nitrogen and stored at -80°C until use. Frozen fungal pellets were ground using the SamplePrep 6770 FreezerMill (Spex). RNA extraction was done from one hundred milligram of ground mycelium in 1 mL TRIZOL (Ambion). RNAs were precipitated with isopropanol, treated with DNAse I (QIAGEN) and resuspended in 25 µL RNAse Free water. RNA purity and integrity were analyzed on NanoDrop Spectrophotometer and Agilent 2100 BioAnalyzer.
cDNA libraries were prepared using the TruSeq RNA-Seq Sample Prep Kit V2 (Illumina Inc., San Diego, CA), and submitted to sequencing using Illumina 2x75 bp technology (Beckman Coulter Genomics).

value: CIRM-BRFM 310

tag: lignocellulosic substrates

value: wheat straw

tag: time point

value: day 7


title: day 7 wheat straw rep3


title: H4ac K562 HS30

value: Heat shocked (HS30)

value: Upstate 06-866

value: Recognizes H4 acetylation at lysines 5, 8, 12 and 16.


title: H4ac K562 NHS


title: Low BC 4

value: Low biomass concentration (0.5 gDCW/L) chemostat biological replicate 4


title: day 7 wheat straw rep1


title: day 7 aspen rep1

growth_protocol: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 7 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), 1 mm Wiley-milled aspen (15 g.l-1 )

value: aspen


title: day 7 aspen rep2


title: 35156_OMP_IGF1R11

value: OMPflfl (Ctrl)

value: 40 weeks


title: day 7 pine rep3

growth_protocol: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 7 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted pine wood fragments < 2 mm (15 g.l-1)

value: pine


title: day 7 pine rep1


title: day 7 pine rep2


title: day 7 aspen rep3


title: day 7 maltose rep3

growth_protocol: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 7 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (20 g.l-1)

value: maltose


title: day 3 wheat straw rep2

growth_protocol: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted wheat straw (15 g.l-1 )

value: day 3


title: day 3 wheat straw rep3


title: day 7 maltose rep1


title: day 3 wheat straw rep1


title: 35138_IGF1R_flfl1

value: OMPIGF1 (KO)


title: day 3 aspen rep1

growth_protocol: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), 1 mm Wiley-milled aspen (15 g.l-1 )


title: day 3 aspen rep2


title: day 3 pine rep2

growth_protocol: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted pine wood fragments < 2 mm (15 g.l-1)


title: day 3 pine rep1


title: day 3 pine rep3


title: day 3 maltose rep3

growth_protocol: Liquid cultures of P. coccineus CIRM-BRFM 310 were grown for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (20 g.l-1)


title: day 7 maltose rep2


title: PRO-seq K562 NHS, replicate 1

description:
Nascent RNA
Normalized_PRO-seq_K562_combined_replicates_NHS_plusStrand.bigWig
Normalized_PRO-seq_K562_combined_replicates_NHS_minusStrand.bigWig

data_processing:
Library strategy: PRO-seq
Adapters were removed using cutadapt (Marcel, 2011)
The reads were trimmed and filtered to 15-36 bp and complement of reads were generated using fastx (http://hannonlab.cshl.edu/fastx_toolkit/).
The reads were aligned to hg19 using Bowtie (Langmead et al., 2009) selecting only uniquely mapping reads with up to two mismatches.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized and replicate-combined bigWig files. Since PRO-seq is strand-specific, the plus strand and minus strands are given in separate bigWig files.

growth_protocol: Human K562 erythroleukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium (Sigma), containing 10% fetal calf serum, 2 mM L-glutamate, 100 μg/ml streptomycin, and 100 U/ml penicillin. The cells were grown below 5x10^5 cells/mL confluency.

extract_protocol:
After tretments, the cells were harvested by centrifugation, and washed twice with PBS. Nuclei were isolated and run-on reactions were performed with biotinylated nucleotides as described by Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013 Feb 22;339(6122):950-3.
The libraries were generated using TruSeq small-RNA adaptors, amplified 11 cycles, gel-purified and size-selected to 140-350 bp fragments. The libraries were sequenced using HiSeq 2000 (Illumina).


title: PRO-seq K562 NHS, replicate 2


title: PRO-seq K562 HS30, replicate 1

description:
Nascent RNA
Normalized_PRO-seq_K562_combined_replicates_HS30_plusStrand.bigWig
Normalized_PRO-seq_K562_combined_replicates_HS30_minusStrand.bigWig

value: 30min at 42°C (HS30)


title: YH_rep3

status: Public on May 20 2017

city: Chuzhou

first: jingen

last: Xu

state: Anhui

address: No. 9 Donghua Road

department: College of Animal Science

country: China

institute: Anhui Science and Technology University

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the Sscrofa10.2.69 genome assembly using Tophat version 2.0.9 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generated and normalized using Cufflink version 2.2.1.Linux_x86_64; the normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed using edgeR function package in R program version 2.10.0
Genome_build: Sscrofa10.2.69
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each sample

organism: Sus scrofa

source_name: YH, longissimus dorsi muscle

growth_protocol: Wei pigs were reared commercial pig feed and water ad libitum until they were slaughtered at weight of 90 kg.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat#A63987, Beckman Coulter, Inc. CA, US) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA-seq libraries were prepared using TruSeq RNA Sample Pre Kit v2 –Set A/ B (Illumina).

treatment_protocol: Yorkshire pigs were reared under similar conditions with Wei pigs.

tag: breed

value: Wei

value: Skeletal muscle


title: day 3 maltose rep2

value: CIRM-BRFM 310


title: YH_rep2


title: LWH_rep2

source_name: LWH, longissimus dorsi muscle

value: Yorkshire


title: FMC_Ar_H2O2_3

city: Gainesville

first: Robert

middle: A

last: Burne

state: Florida

address: 1395 Center Drive

department: Oral BIology

institute: University of Florida

description:
enriched mRNA
repeat 3 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count
diifferential expression data generated at http://vicbioinformatics.com/degust/index.html, using EdgeR
Genome_build: NC_004350.2
Supplementary_files_format_and_content: excel file with raw counts. The files contain four columns of count data (one for each raw data file associated with the sample) and a column of summed reads.  Each sample is associated with 4 raw data files that were created when the sequencing results of each library was split into four parts due to file size.

organism: Streptococcus mutans

source_name: Bacterial batch culture

growth_protocol: Bacterial cells were grown in FMC medium with and without 1.5% arginine. Bacterial cultures were incubated aerobically without agitation in the presence of 5% CO2 at 37°C until they reached mid-exponential phase (OD600 ≈ 0.6).

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen). To remove 16S and 23S rRNAs, 6 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from the enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.  Single-ended short reads were obtained from a set of bar-coded cDNA libraries

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

tag: parental strain

tag: media

value: FMC 0.5 mM H2O2

tag: arginine

value: Present


title: FMC_H2O2_3

description:
enriched mRNA
repeat 3 of 3

value: Absent


title: PRO-seq K562 HS30, replicate 2


title: LWH_rep1

tag: tissue


title: FMC_Ar_pH5.5_1

description:
enriched mRNA
repeat 1 of 3


title: CNTRENE CL100LM unexposed

city: Springfield

first: Paul

last: Schweiger

address: 901 S. National Ave

department: Biology

institute: Missouri State University

data_processing:
Bases were called using Illumina 1.9
FastQC 0.11.2
Transcript abundance quantified with kallisto v0.43.1 with tpm normalization
Genome_build: MG1655
Supplementary_files_format_and_content: h5, and tsv files were generated in kallisto v0.43.1

organism: Escherichia coli K-12

source_name: CNTRENE CL100LM unexposed

growth_protocol: Escherichia coli were grown in M9 medium with 1mM thiamine and 2% glucose at 37C and 200 rpm until they reached mid-log phase

extract_protocol:
Qiagen RNeasy Plus Mini Kit
Libraries were prepared by removing ribosomal rRNA using the bacterial Ribo-Zero rRNA Removal Kit (Illumina, San Diego, Ca, USA) according to the manufacturer’s instructions and the SMARTer Stranded RNA-Seq kit (Clontech, Mountain View, Ca, USA) was used to prepare cDNA from RNA samples according to the manufacturer’s instructions.

treatment_protocol: 1.05 ug/ml of CNTRENE CL100LM were added to exposed cells

tag: agent


title: FMC_Ar_H2O2_2

description:
enriched mRNA
repeat 2 of 3


title: FMC_Ar_pH5.5_3

description:
enriched mRNA
repeat 3 of 3


title: CNTRENE CL100LM exposed

source_name: CNTRENE CL100LM exposed

tag: strain

value: 1.05 ug/ml of CNTRENE CL100LM


title: FMC_H2O2_2

description:
enriched mRNA
repeat 2 of 3


title: FMC_pH5.5_2

description:
enriched mRNA
repeat 2 of 3


title: FMC_pH5.5_3

description:
enriched mRNA
repeat 3 of 3


title: FMC_pH5.5_1

description:
enriched mRNA
repeat 1 of 3


title: FMC_Ar_pH7_3

description:
enriched mRNA
repeat 3 of 3


title: FMC_Ar_pH7_2

description:
enriched mRNA
repeat 2 of 3


title: FMC_Ar_pH7_1

description:
enriched mRNA
repeat 1 of 3


title: YH_rep1


title: FMC_pH7_1

description:
enriched mRNA
repeat 1 of 3


title: FMC_pH7_2

description:
enriched mRNA
repeat 2 of 3


title: FMC_Ar_H2O2_1

description:
enriched mRNA
repeat 1 of 3


title: FMC_H2O2_1

description:
enriched mRNA
repeat 1 of 3


title: Cerebral Cortex from WT mice

status: Public on May 19 2017

city: Padova

first: Francesca

last: D'Avanzo

state: PD

address: c/o Pediatric Research Institute, Corso Stati Uniti, 4

department: Women’s and Children’s Health

country: Italy

institute: University of Padova

data_processing:
Sequenced reads were trimmed for low-quality sequence, then mapped to mouse genome (mm9) using PASS software v2.10 (http://pass.cribi.unipd.it) with parameters best-hit, two maximum mismatch and no GAP.
The number of reads aligned on each gene for each sample was determined using a self-written script; only reads aligned to a single gene and only genes with a coverage higher than 50% of their length were considered.
Differentially expressed genes (DEGs) were identified for the comparison CxH vs CxWT, MH vs MWT, CxH vs MH and CxWT vs MWT, using DEGseq R package (https://bioconductor.org/packages/release/bioc/html/DEGseq.html) with LRT (Likelihood Ratio Test) as statistical method.
Genome_build: mm9
Supplementary_files_format_and_content: A unique tab-delimited text file of raw counts values obtained from each sample. Rows represent genes expressed as Entrez ID and MGI ID relative to mm9 mouse genome build; CxH, CxWT, MH and MWT represent raw counts of sequencing reads for each sample.

source_name: Cerebral Cortex

extract_protocol:
Brains were removed, cerebral cortexes (Cx) and midbrain/diencephalon/hippocampus (M) areas were isolated, placed overnight at 4°C in RNA later Tissue Collection - RNA Stabilization Solution (Thermo Fisher Scientific) and stored at -80°C until RNA extraction. Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific)  and quantified through NanoDrop 1000 Spectrometer (Thermo Fisher Scientific). Total RNA integrity was assessed through Agilent Bioanalyzer 2100 and RNA 6000 Nano Kit (Agilent Biotechnologies). mRNA was purified by using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific) according to the supplied protocol; mRNA enrichment was assessed by using the 2100 Bioanalyzer and RNA 6000 Pico kit (Agilent Biotechnologies).
RNA libraries were prepared for sequencing using standard SOLiD Whole Transcriptome Analysis kit

value: Cerebral Cortex

tag: age

value: 9 months

tag: genotype

value: wild type


title: Midbrain/diencephalon/hippocampus from Ids-KO mice

source_name: Midbrain/diencephalon/hippocampus

value: Midbrain/diencephalon/hippocampus

value: Ids-/-


title: Cerebral Cortex from Ids-KO mice


title: WT [re-analysis]

city: West Lafayette

first: Elizabeth

middle: J

last: Tran

state: IN

address: 175 S. University Street

department: Biochemistry

institute: Purdue University

description: wt rep1, wt rep2

data_processing:
Color space reads were mapped to the yeast reference genome (sacCer3) using the SHort Read Mapping Program 2 (SHRiMP2, ver. 2.2.3) with the option --single-best-mapping
The aligned reads were imported into R. Only the first mapped read in a proper pair (flags = 83, 99) with a mapping quality mapq ≥ 40 was retained.
The gene annotation for S. cerevisiae was retrieved from SGD (R64-2-1). The reads were counted against the genomic features using GenomicAlignments from Bioconductor to determine the number of reads for sense RNA transcripts. The mode of “IntersectionNotEmpty” was used for the summarizeOverlaps function.
rDNA and genes with a low number (<10) of overlapping reads across all samples were removed from the count matrix. edgeR was used to determine differential gene expression.
Genome_build: sacCer3 from UCSC
Supplementary_files_format_and_content: Tab-delimited ".txt" files report transcript counts over all genes and normalized abudnace measurement (edgeR). ".bedgraph" files were generated using R with dataValue representing the sum of normalized genome coverage from the two replicates of each strain.

organism: Saccharomyces cerevisiae BY4741

source_name: wild type (reference) strain

growth_protocol: Cultures were grown at 30°C in YP+2% Glucose (rich media) to mid-log phase. Cells were harvested by centrifugation and flash frozen in liquid nitrogen.

extract_protocol:
RNA was extracted using a standard hot acid phenol protocol. Total RNA was depleted for ribosomal RNA using the Ribominus Transcriptome Isolation Kit (yeast and bacteria) from Life Technologies. Ribosomal RNA depeletion was conducted twice and resulting RNA integrity was verified using a bioanalyzer.
Libraries were prepared using Life Technologies SOLiD Total RNA-seq kit (4452437) according to manufacturer's instructions.
RNA-Seq, strand-specific, paired-end

tag: strain information

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0


title: FMC_Ar_pH5.5_2

description:
enriched mRNA
repeat 2 of 3


title: Midbrain/diencephalon/hippocampus from WT mice


title: Zmym3 KO c-KIT+ pre-meiotic cellsreplicate 2

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
The sequencing reads were mapped to the mouse genome (UCSC mm9) by TopHat (v2.0.6).
The expression level of mRNAs was represented by FPKM calculated by Cufflinks (v2.0.2).
The differentially expressed genes were identified with Cuffdiff.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: The expression level of mRNAs.

source_name: testes

extract_protocol:
Total RNA from mouse testis cells and mSSCs was extracted using Trizol. The RNA libraries were constructed by Illumina library preparation protocols. High-throughput sequencing was performed on HiSeq4000/HiSeq X 10.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Zmym3 WT and KO SSC were cultured on laminin-coated dishes.  c-KIT+ cells were induced from both WT and KO SSCs by 100 nM RA 36 h after RA treatment. For collecting the spermatocytes, the testes were firstly digested into single cells. The cells were firstly FACS sorted to collect tetraploid cells which were further sorted into two populations based on their forward scatter (FSC) and side scatter (SSC) features. The population of larger sizes consisted mainly of pachytene spermatocytes of about 80% purity based on the co-immunostaining of SYCP3 and rH2AX were collected.

tag: gender

value: male

tag: development stage

value: knockout type


title: Zmym3 WT SSC replicate 1


title: Zmym3 WT SSC replicate 2


title: Zmym3 KO SSC replicate 2


title: Zmym3 KO c-KIT+ pre-meiotic cellsreplicate 1


title: Zmym3 WT c-KIT+ pre-meiotic cells replicate 1


title: Zmym3 KO SSC replicate 1


title: Zmym3 WT c-KIT+ pre-meiotic cells replicate 2


title: 717-MES_input

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

data_processing:
Peaks were called using the RSEG algorithm using the following arguments (rseg-diff -d k41.hg19.bed  -m 2 -v -i 20 -c human.hg19.size.bed -o )
Genome_build: hg19
Supplementary_files_format_and_content: bed files: rseg-diff ouput files.

source_name: Neuroblatoma TIC line

extract_protocol: Cultured cells were fixed with 1% formaldehyde. Nuclei were isolated and the DNA was sheared to 200 to 300 bp fragments. Histon-bound DNA was precipitated using antibodies H3K27Ac (#4729, Abcam) and H3K4me3 (#04-745, Millipore).  De-crosslinked DNA was purified using Qiagen PCR purification kit (Qiagen) and quantified with Quant-IT Picogreen (Invitrogen). The DNA was used to generate sequencing libraries according to the manufactures procedure (Life Technologies): The DNA was end-polished, dA-tailed and adaptors with barcodes were ligated. The fragments were amplified (8 cycles) and quantified with a Bioanalyzer (Agilent). The libraries were prepped with the 5500W Flowchip v2 kit  (Life Technologies) and sequenced on the SOLiD Wildfire (Illumina) resulting in 50 bp reads. Alternatively, the libraries were sequenced using the HiSeq PE cluster kit v4 (Illumina) with the HiSeq2500 (Illumina) resulting in 125 bp reads.

tag: cell type

value: Neuroblatoma TIC line

tag: growth medium

value: neural stem cell medium

tag: chip antibody


title: 700-MES_H3K4me3

value: H3K4me3 (#04-745, Millipore)


title: FMC_pH7_3

description:
enriched mRNA
repeat 3 of 3


title: 717-MES_H3K27ac


title: 717-MES_H3K4me3


title: 700-MES_input


title: LWH_rep3

value: Skeletal muscle


title: SK-N-BE(2C)-PRRX1-on_H3K27ac

source_name: Neuroblatoma cell line

value: Neuroblatoma cell line

value: DMEM 10% FCS


title: SK-N-BE(2C)-PRRX1-off_H3K27ac


title: SK-N-BE(2C)-PRRX1-on_input


title: SK-N-BE(2C)-PRRX1-off_input


title: 700-MES_H3K27ac


title: dpdr-1_no-carbon_4h_2

city: Freising

first: Nils

last: Thieme

state: Bavaria

address: Hans-Carl-von-Carlowitz-Platz 2

department: Holzforschung München

institute: Technische Universität München

data_processing:
Basecalls performed using casava 1.8.2 and 1.8.4 and quality filtered using bbduk and fastxtoolkit
reads were mapped with Tophat v2.0.4 and Bowtie2.0.0 to Neurospora crassa OR74A Broad v12 genome and provided with Neurospora crassa OR74A Broad v12 transcripts.gtf
fragments per kilobase of transcript per million mapped reads (FPKMS) were calculated with Cufflinks v2.0.2 with parameters --max-bundle-frags=10000000 --compatible-hits-norm -u -g (providing Neurospora crassa OR74A Broad v12 transcripts.gtf)
rawcounts with htseq 0.6.0 with parameters  --stranded=no -m intersection-strict
Genome_build: Neurospora crassa OR74A Broad v12 assembly
Supplementary_files_format_and_content: Rawcounts and normalized counts in FPKMs

organism: Neurospora crassa

growth_protocol: Conidia obtained from 10-day-old pregrown cultures was used to inoculate 3 ml of 1x Vogel’s salts plus 2% (w/v) sucrose at 1x106 cells/mL in 24 deep well plates. The bottoms of the wells for each plate were initially scratched with a sharp needle to allow adherence and formation of mycelial mat. After 16 hours of growth, mycelia were washed three times in 1 x Vogel’s salts without added carbon and transferred to 1 x Vogel’s salts with their respective new carbon source (either 2% sucrose, 1% pectin, 2 mM L-rhamnose or no carbon source).

extract_protocol:
After 4 hours of induction, mycelia were harvested over Whatman #1 filter paper and subsequently flash frozen in liquid nitrogen for storage at -80˚C. RNA was  prepared using the TRIzol reagent (Invitrogen).
Stranded cDNA libraries were generated using the Illumina Truseq Stranded RNA LT kit. mRNA was purified from 1 ug of total RNA using magnetic beads containing poly-T oligos. The purified mRNA was fragmented and reverse transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with an end-pair, A-tailing, adapter ligation, and 10 cycles of PCR. The prepared library was then quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. The quantified library was then then multiplexed with other libraries, and the pool of libraries was then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate a clustered flowcell for sequencing. Sequencing of the flowcell was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit, v3, following a 2x100 indexed run recipe.

value: 10 dpi

value: hyphal biomass

tag: treatment

value: induced for 4 hrs on no carbon source


title: dpdr-1_no-carbon_4h_3


title: dpdr-1_no-carbon_4h_1


title: dpdr-1_rhamnose_4h_2

value: induced for 4 hrs on 2 mM L-rhamnose


title: dpdr-1_rhamnose_4h_1


title: dpdr-1_pectin_4h_2

value: induced for 4 hrs on 1% pectin


title: dpdr-1_pectin_4h_1


title: WT_no-carbon_4h_3


title: WT_no-carbon_4h_2


title: WT_pectin_4h_2


title: WT_rhamnose_4h_2


title: WT_pectin_4h_1


title: WT_no-carbon_4h_1


title: WT_rhamnose_4h_3


title: WT_sucrose_4h_3

value: induced for 4 hrs on 2% sucrose


title: WT_sucrose_4h_2


title: Uninjured_3

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the transcriptome file with bwa v .0.5.9 with default parameters, converted to .bam format by samtools 0.1.19
Reads aligning to each transcript were counted with samtools v.0.1.19 idxstats,
Genome_build: transcripts as of March 2013, plus ERCC spike in probes and mitochondrial sequences.  File name included in submission is "mouse_refgu_ERCCRefseq.fa"
Supplementary_files_format_and_content: the total number of mapped reads and the length of each transcript was used to convert the read counts for each transcript in each sample to RPKM

source_name: Uninjured, TA muscle

extract_protocol:
Total RNA from each muscle sample was isolated by TRIzol Reagent (Thermo Scientific 15596026) according to manufacturer’s instructions and purified by Qiagen RNeasy columns.
one microgram of total RNA was used to make Illumina-compatible sequencing libraries, and the libraries were sequenced using 50 bp single reads on an Illumina HiSeq 1000

treatment_protocol: For cardiotoxin (CTX) injection, CTX from Naja mossambica mossambica (Sigma C9759) was dissolved in normal saline (0.9% w/v of NaCl) to make a 10 μM working solution, and was aliquoted and stored at -20°C. After anesthesia of the mouse with isoflurane (1.5%-2% in oxygen), the anterior aspect of the adult mouse hindlimb (8- to 10-week-old C57BL/6) was sterilized with 70% ethanol, shaved to expose the skin, and approximately 50 μL of CTX solution was injected into the midbelly of the tibialis anterior (TA) muscle using a 0.3ml U100 BD insulin syringe.

value: untreated

tag: Sex

value: female

value: tibialis anterior (TA) muscle


title: dbp2∆ [re-analysis]

description: dbp2∆ rep1, dbp2∆ rep2

source_name: dbp2Δ strain

value: MATa dbp2::KanMx ura3Δ0 leu2Δ0 his3Δ0 TRP1 met- lysΔ


title: WT_sucrose_4h_1


title: d_3_1

source_name: Cardiotoxin injury, TA muscle

value: 10 uM Naja mossambica mossambica (Sigma C9759) cardiotoxin


title: Uninjured_1


title: d_3_2


title: d_3_3


title: Uninjured_2


title: nuclear RNA seq

city: Shanghai

first: Hong

last: Cheng

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences

description: cytopasmic and nuclear RNA seq-RPM.xls

data_processing:
For iCLIP-seq,the reads containing parts of the 3’ Solexa primer were trimmed from the 3’ end using fastx-toolkit.  These iCLIP reads after random barcode evaluation and barcode removed, were mapped to the human genome (hg19) using bowtie2, allowing 0-2 mismatches.  Only uniquely mapped reads were used for further analysis.  The first nucleotide in the genome upstream of a mapping cDNA tag was defined as ‘cross-link nucleotide’.  The clustered binding sites were identified though the strategy described in (König J, et al.Nat Struct Mol Biol. 2010,17(7):909-15. ).  We performed the evaluation of cluster binding site with the recommended default parameters (FDR < 0.05 and cluster sites within a window of 10 nts).  Only the cluster binding sites and the cluster cDNA tag were used in further analyses.
RNA-seq reads were cleaned and mapped the human genome (hg19 version) TopHat2.0. Reads mapping to multiple independent genomic locations were assigned to the most abundant biotype of the locations. Genome annotations from RefSeq and ENSEMBL were downloaded from the UCSC genome browser website, and supplemented with published datasets.
Genome_build: hg19
Supplementary_files_format_and_content: bed or xlsl

source_name: uterine cervix

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Biochrom)

extract_protocol:
HeLa cells were irradiated with UV light at 300 mJ/cm2.  After cell lysis, RNAs were partially fragmented using 0.5 U/ml of RNase I, followed by immunoprecipitaions with or without (no antibody control) 10 μg of the ALYREF antibody immobilized on protein A Dynabeads (Life Technologies).  After extensive washing, immunoprecipitated RNAs were ligated at the 3’ ends to a RNA adapter and radioactively labeled by T4 polynucleotide kinase (Fermentas).  The protein-RNA complexes were then transferred to a nitrocellulose membrane.  Then, fragmented RNAs were purified from nitrocellulose membrane by PK treatment and phenol / chloroform extranction.
For iCLIP cDNA library preparation, fragmented RNAs, which were ligated with a RNA adapter (3' linker)  at the 3’ ends , reverse-transcribed with a primer containing a barcode (iCLIP RT primer).  The resulting cDNAs were purified by PAGE, circularized by single-stranded DNA ligase (Epicentre), linearized by restriction enzyme cleavage, and amplified and add P5/P3 adaptors by PCRs with (P3 and P5 solexa primer).
iCLIP-seq

treatment_protocol: Ctrl or indicated siRNAs were transfected with RNAimax (invitrogen)

tag: cell line

value: HeLa cell

value: uterine cervix


title: cytoplasmic RNA seq

description: cytopasmic and nuclear RNA seq-RPM.xls


title: iCLIP in CstF64 kd cells-rep2


title: iCLIP in Cntl cells-rep2


title: dpdr-1_pectin_4h_3


title: WT_rhamnose_4h_1


title: iCLIP in PABPN1 KD cells


title: iCLIP in CBP80 KD cells


title: iCLIP in CstF64 kd cells-rep1


title: wild-type Col RNA-seq

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: high-throughput profiling of transcriptome in WT (wild type)

data_processing:
The RNA-seq reads with strand direction were aligned to the Arabidopsis TAIR10 genome using tophat-2.0.11(Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads with no more than two mismatches were retained for subsequent analysis. The expression levels for gene models from TAIR10 were measured and normalized as reads per kilobase of exon model per million mapped reads (RPKM)(Mortazavi et al., 2008).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated using wig2bw program

organism: Arabidopsis thaliana

source_name: 12DAG seedlings

growth_protocol: The wild-type Col, atprmt5 mutants, m90 and s215 were grown on Murashige and Skoog plates with 3% Suc for 12 days

extract_protocol:
The seedlings were ground into a fine power in liquid nitrogen and processed using Trizol reagent (Invitrogen).
Strand-specific RNA-Seq libraries generated from Col, atprmt5, m90, s215 were constructed mRNA-Seq library by SMART method (Levin et al., 2010)

treatment_protocol: The seedlings grown at 23°C under 16 h of light followed by 8 h of darkness

tag: ecotype

value: Columbia

tag: genotype/variation

value: wild-type


title: iCLIP in Cntl cells


title: atprmt5 RNA-seq

description: high-throughput profiling of transcriptome in prmt5 (mutant)


title: m90 RNA-seq

description: high-throughput profiling of transcriptome in m90 (mutant)


title: ALYREF-rep3


title: iCLIP in Cntl cells-rep1


title: s215 RNA-Seq

description: high-throughput profiling of transcriptome in s215 (mutant)


title: no antibody-rep3


title: no antibody-rep2


title: ALYREF-rep1