title: nm_ux_tn_E4_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ux_tn_E3_141204

status: Public on Apr 15 2016

type: SRA

city: La Jolla

first: Fred

middle: H

last: Gage

state: CA

address: 10010 N Torrey Pines Rd

country: USA

institute: The Salk Institute for Biological Studies

description:
sn_ne_counts.txt
sn_ne_tpm.txt

library_source: transcriptomic

data_processing:
sequencing reads were trimmed for low base-quality and aligned to mm10 using rsem-calculate-expression running bowtie version 1.0.0
expected counts (counts) and normalized transcripts per million (TPM) were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: sn_hc_counts.txt: tab-delimited file of counts (abundance measurements) from nuclei dissociated from a homecage mouse
Supplementary_files_format_and_content: sn_hc_tpm.txt: tab-delimited file of TPM values (normalized abundance) from nuclei dissociated from a homecage mouse
Supplementary_files_format_and_content: sn_ne_counts.txt: tab-delimited file of counts (abundance measurements) from FOS positive and FOS negative nuclei dissociated from a mouse exposed to a novel environment
Supplementary_files_format_and_content: sn_ne_tpm.txt:  tab-delimited file of TPM values (normalized abundance) from FOS positive and FOS negative nuclei dissociated from a mouse exposed to a novel environment
Supplementary_files_format_and_content: wc_counts.txt: tab-delimited file of counts (abundance measurements) from PTZ- and saline-treated whole cells
Supplementary_files_format_and_content: wc_tpm.txt: tab-delimited file of TPM values (normalized abundance) from PTZ- and saline-treated whole cells

molecule: total RNA

organism: Mus musculus

source_name: DGC_novel environment_single-nuclei

growth_protocol: All animal procedures were performed in accordance with the animal guidelines at the Salk Institute for Biological Studies.

extract_protocol:
dissociation protocol: Dounce
Smart-seq2
TSO concentration: 10uM
ERCC dilution: 1:2000

tag: sequencing method

value: single-nuclei RNA-seq

tag: strain

tag: treatment

value: novel environment

tag: facs sort

tag: cell type

value: dentate granule cell


title: Proliferating IMR90 shp53_1

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

data_processing:
Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (Bolger et al 2014). RNA-seq reads were then aligned to GRCh37.75(hg19) with STAR (Dobin et. al 2012) and genome-wide transcript counting was performed by HTSeq (Anders et al. 2015)  to generate a matrix of fragments per kilobase of exon per million fragments mapped (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing normalized count tables from each experiment

organism: Homo sapiens

source_name: IMR90 human fibrobasts

growth_protocol: IMR90 human fibroblasts were co-transduced with either pWZL- Hygro (empty vector control) or a pWZL- HRASV12- Hygro and indicated LMP vectors encoding validated GFP-linked shRNAs targeting BRD4 (Zuber et al., 2011), p65 (Chien et al., 2011), p53 (Lujambio et al., 2013), p53/Rb, or p21/p16 (Chicas et al., 2010). The infected population was selected using 2 μg/mL puromycin (Sigma) and 75 μg/mL hygromycin B (Roche) and cultured in DMEM 10% FBS. Quiescence was induced in cells transduced with PWZL-Hygro (empty vector) and LMP vectors by culturing for 4 days in 0.1% FBS.  For all samples RNA was extracted at Day 12 post-infection.RNA from independent triplicates was extracted.

extract_protocol:
Cells were lysed by adding RLT buffer directly to the culture dish. RNA was extracted using Rneasy Qiagen Kit.
RNA samples were used for Hi-Seq library construction with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. Samples are barcoded with TruSeq SBS Kit v3 (Illumina).

treatment_protocol: For JQ1 treatments, cells were treated with 100 nM of JQ1 or DMSO as vehicle for 48 hours (hr) prior to harvest. A working solution of JQ1 at 1 mM was prepared to use a final concentration of vehicle (DMSO) no higher than 1/10000

value: fetal lung fibroblasts

tag: cell line

tag: cell condition

value: proliferating

tag: viral transduction

value: cotransduced with pWZL-Hygro and shp53

value: no treatment


title: Quiescent IMR90 shp53_1

value: quiescent


title: Quiescent IMR90 shRen_3

value: cotransduced with pWZL-Hygro and shRen


title: nm_ux_tn_E5_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: Quiescent IMR90 shRen_1


title: Senescent IMR90 shRen_1

value: senescent

value: cotransduced with pWZL HRASV12 and shRen


title: nm_ux_ti_F8_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ux_tn_E2_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: Proliferating IMR90 shRen_3


title: Senescent IMR90 shRen_2


title: Proliferating IMR90 shRen_1


title: nm_ux_ti_F7_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ux_ti_F9_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: Proliferating IMR90 shRen_2


title: Proliferating IMR90 shp53_2


title: Quiescent IMR90 shRen_2


title: Senescent IMR90 shRen_3


title: nm_ux_ti_F12_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: WT_rep2_BS-seq

city: Beijing

first: Yongqiang

last: Li

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

library_source: genomic

data_processing:
Basecalling, trimming for low-quality reads and adaptor sequence were done by BGI (Shenzhen, China).
Bisulfite sequencing reads were mapped to the TAIR10 reference genome by using Bismark allowing two mismatches (Krueger and Andrews, 2011). Only reference genome cytosines covered with at least 5 reads were considered for analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bigWig files give methylation level for all Cs (three contexts) with depth >= 5. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: WT seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates under standard long-day conditions (16 h/light, 8 h/dark, 22°C).

extract_protocol:
Genomic DNA was extracted using CTAB.
The extracted DNA was sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.

tag: strain/background

tag: genotype/variation

value: WT

tag: age

value: 10 days

tag: tissue

value: seedling


title: nm_ux_ti_F10_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ux_ti_F11_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: mom1_BS-seq

source_name: mom1 seedlings


title: nm_ux_ti_E9_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: pial1/2_BS-seq

source_name: pial1/2 seedlings


title: nm_ux_ti_E12_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ux_ti_E11_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: pial2_RNA-seq

description:
pial2_RNAseq
Processed data file: col_rep2_pial2_gene_exp.diff.txt

data_processing:
Basecalling, trimming for low-quality reads and adaptor sequence were done by BGI (Shenzhen, China).
Sequenced clean reads were mapped to Arabidopsis thaliana (TAIR10) whole genome using TopHat v2.0.12 with parameters --bowtie1 --no-coverage-search --segment-length 20 -g 10 -p 10. Gene annotation and calculation of FPKM values were carried out using Cufflinks (v2.2.1) with the provision of a GTF annotation file (TAIR10). Gene expression differences were assessed by Cuffdiff use upper-quartile normalization, with false discovery rate correction for multiple testing.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: pial2 seedlings

extract_protocol:
Seedling materials were ground into powder in liquid nitrogen. Total RNA was harvested using TRIzol® Reagent (Invitrogen). Then, total RNA samples were treated with DNase I and the mRNA was enriched by using the oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: mom1_rep2_RNA-seq

description:
mom1_rep2_RNAseq
Processed data file: col_rep2_mom1_gene_exp.diff.txt


title: nm_ux_ti_E8_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: WT_rep2_RNA-seq

description:
col_rep2_RNAseq
Processed data files: col_rep2_mom1pial2_gene_exp.diff.txt, col_rep2_pial2_gene_exp.diff.txt, col_rep2_mom1_gene_exp.diff.txt


title: WT_rep1_BS-seq


title: nm_ux_ti_E7_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_tn_H6_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt

extract_protocol:
dissociation protocol: Dounce
Smart-seq2
TSO concentration: 1uM
ERCC dilution: 1:2000


title: nm_ui_tn_H5_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nrpe1_RNA-seq

description:
nrpe1_RNAseq
Processed data file: col_rep1_nrpe1_gene_exp.diff.txt

source_name: nrpe1 seedlings


title: pial1/2_RNA-seq

description:
pial1pial2_RNAseq
Processed data file: col_rep1_pial1pial2_gene_exp.diff.txt


title: nm_ui_tn_H4_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: WT_rep1_RNA-seq

description:
col_rep1_RNAseq
Processed data files: col_rep1_mom1_gene_exp.diff.txt, col_rep1_pial1pial2_gene_exp.diff.txt, col_rep1_nrpe1_gene_exp.diff.txt


title: nm_ux_ti_E10_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: mom1_rep1_RNA-seq

description:
mom1_rep1_RNAseq
Processed data file: col_rep1_mom1_gene_exp.diff.txt


title: nm_ui_tn_H2_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_tn_H1_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_tn_H3_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: Drosophila melanogaster Tailor KD S2 cell small RNA

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

data_processing:
3' adapter sequences were  trimmmed using the cutadapt utility
reads < 15nt in size were filtered
identical read sequences were collapsed using the fastq_collapser utility
Supplementary_files_format_and_content: read count table files (columns are read sequence and number of reads)

organism: Drosophila melanogaster

source_name: S2R+ cell

extract_protocol:
W1118 and tailor KO ovaries were dissected and flash frozen in liquid nitrogen. GFP dsRNA and CG1091 dsRNA soaked S2 cells were collected and washed with PBS. Total RNA was then extractedusing TRIzol according to manufacturer protocol.
For Illumina HiSeq Library: Libraries were created with the Illumina truseq small RNA cloning kit using a modified protocol. Small RNAs in the 19-28nt size range were first isolated from total RNA by PAGE purification before cloning. PAGE purification was also performed after ligation of RNAs to 3’ and 5’ linkers before processing in subsequent steps. All enzymatic reactions and oligos were used as indicated by manufacturer.

value: Tailor mutant

value: S2R+ cell


title: Drosophila melanogaster GFP KD S2 cell small RNA


title: nrpe1_BS-seq


title: nm_ui_tn_G6_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: Drosophila melanogaster W1118 ovary small RNA

source_name: ovary

value: ovary


title: mom1pial2_RNA-seq

description:
mom1pial2_RNAseq
Processed data file: col_rep2_mom1pial2_gene_exp.diff.txt

source_name: mom1pial2 seedlings


title: nm_ui_tn_G5_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt

value: single-nuclei RNA-seq


title: Drosophila melanogaster Tailor KO ovary small RNA


title: nm_ui_tn_G2_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt

value: novel environment


title: nm_ui_ti_H8_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt

value: dentate granule cell


title: nm_ui_ti_H9_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_tn_G3_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_tn_G1_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_tn_G4_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_ti_H7_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_ti_H10_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_ti_G12_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_ti_H11_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_ti_G8_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_ti_G11_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_B4_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt

extract_protocol:
dissociation protocol: Dounce
Smart-seq2
TSO concentration: 10uM
ERCC dilution: 1:200


title: nm_ui_ti_H12_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_ti_G7_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_B6_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_ti_G9_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nm_ui_ti_G10_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_B3_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_B2_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_A6_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_B1_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_A5_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_A4_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_B8_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_B9_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_A2_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_A3_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_A1_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_tn_B5_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_B10_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_B12_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_B7_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_B11_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_A9_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_A8_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_A7_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_A10_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_D3_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt

extract_protocol:
dissociation protocol: Dounce
Smart-seq2
TSO concentration: 1uM
ERCC dilution: 1:200


title: nc_ux_ti_A11_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_D5_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_C5_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_D2_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_C2_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_C4_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_D1_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_ti_D9_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_C3_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_C1_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_C6_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_ti_D7_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_ti_D11_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_ti_D12_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_ti_C7_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_ti_D10_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_ti_C9_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_ti_C8_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ux_ti_A12_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_D6_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_ti_C11_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_tn_D4_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: Dn1HNP_C1E40K79_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt

extract_protocol:
dissociation protocol: Dounce
C1
TSO concentration: C1 standard protocol
ERCC dilution: 1:2000

value: home-cage


title: Dn1HNP_C1E40K89_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K81_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K94_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: nc_ui_ti_C10_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: Dn1HNP_C1E40K88_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K77_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K72_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K58_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K37_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K68_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K73_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K69_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K48_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: nc_ui_ti_C12_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: nc_ui_ti_D8_141204

description:
sn_ne_counts.txt
sn_ne_tpm.txt


title: Dn1HNP_C1E40K52_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K83_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K33_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K34_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dc1_HG_H5_507e

description:
wc_counts.txt
wc_tpm.txt

extract_protocol:
dissociation protocol: protease
Smart-seq2
TSO concentration: 10uM
ERCC dilution: 1:2000

value: whole-cell RNA-seq

value: PTZ

value: GFP+


title: Dc1_HG_H6_frz507a

description:
wc_counts.txt
wc_tpm.txt

value: Saline


title: Dn1HNP_C1E40K16_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K23_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K24_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K32_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dc1_HG_H4_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_H4_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_H3_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_H5_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_H3_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_H2_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dn1HNP_C1E40K36_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dn1HNP_C1E40K30_117

description:
sn_hc_counts.txt
sn_hc_tpm.txt


title: Dc1_HG_G6_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_H1_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_H1_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_G4_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_G5_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_G1_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_G2_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_G2_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_G3_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_G4_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_F6_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_H2_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_F5_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_F6_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_F4_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_F3_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_F2_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_F1_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_E5_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_E6_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_E6_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_F1_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_E4_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_E4_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_G5_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_G1_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_E1_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_E1_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_E3_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D6_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_F3_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D3_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D4_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D4_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D5_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D5_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D3_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D1_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_E5_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_C6_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_C4_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D2_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_C3_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_C6_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D2_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_C1_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_C5_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_E2_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_B6_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_C2_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_C1_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D6_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_B5_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_D1_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_B4_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_B5_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_B4_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_B3_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_C5_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_C3_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_B3_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_B1_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_B2_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_A6_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_A4_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_A6_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_A5_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_A5_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_B1_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_A4_507e

description:
wc_counts.txt
wc_tpm.txt


title: H3K27me3 juvenile endocrine (EA75)

city: Stanford

first: Seung

last: Kim

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

data_processing:
Reads were aligned to hg19 using Bowtie.
A custom script was used to calculate ChIP-Seq read counts 2 kb upstream and downstream of transcription start site of age-dependent genes. The TSS coordinates were downloaded from the UCSC genome browser using RefSeq reference transcriptome list.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include tag counts normalized to the sequencing depth. 'adult_*.txt' and 'juv_*.txt' files include different gene loci that were categorized as adult or juvenile genes, respectively.

source_name: pancreas, juvenile, H3K27me3 ChIP

extract_protocol:
Previously described ChIP-Seq methods were used (Rada-Iglesias et al. 2011 [PMID: 21160473]; Wapinski et al. 2013 [PMID: 24243019]).
Illumina HiSeq/TruSeq

value: endocrine

value: juvenile

tag: chip antibody

value: rabbit H3K27me3 (Diagenode, pAb-069-010)

value: pancreas


title: H3K27me3 adult endocrine (EA28)

source_name: pancreas, adult, H3K27me3 ChIP

value: adult


title: H3K27me3 adult endocrine (EA16)


title: Dc1_HG_A2_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_A3_frz507a

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_A2_507e

description:
wc_counts.txt
wc_tpm.txt


title: Dc1_HG_A3_507e

description:
wc_counts.txt
wc_tpm.txt


title: Input_Etoposide IMR90

description: ChIP-Seq

data_processing:
Raw reads were mapped to the reference human genome assembly GRCh37 (hg19) using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) allowing two-mismatches for only unique alignment; -v 2 -m 1 -best --strata. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net).
To identify ChIP-Seq enriched regions (or peaks), HOMER suite was used (http://homer.salk.edu/homer/). For H3K27ac and BRD4 ChIP-Seq, the parameter of findPeaks was set to find histone enriched regions (findPeaks.pl -style histone), and also used to identify H3K27ac-enriched super-enhancers with the default setting (findPeaks.pl -style super). Since H3K27ac and BRD4 enriched regions are broad in the genome, we avoided redundant detection from peak calling by merging multiple peaks into a single region when the distance between centers was less than 5000-bp (mergePeaks.pl -d 5000). From given extended regions, the ChIP-Seq signal of tag density was re-calculated by normalizing to a read depth of 10 million tags at a given size of the merged region (annotatePeaks.pl -size given). To create a density plot, +/- 5,000-bp of ChIP-Seq regions were used to count tags with 20-bp bins (annotatePeaks.pl -size 5000 -hist 25 -ghist).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: IMR90 human fibroblasts were transduced with pWZL- Hygro (empty vector control) or a pWZL- HRASV12- Hygro and cultured in DMEM 10% FBS.  The infected population was selected using 75 μg/mL hygromycin B (Roche). Quiescence was induced in cells transduced with PWZL-Hygro vector by culturing for 4 days in 0.1% FBS. Cells were processed at day 12 post-infection.

extract_protocol:
Five to 30 million IMR90 cells were crosslinked for 10 minutes using 1 % formaldehyde, followed by quenching with 0.125M glycine for 10 minutes. To prepare chromatin from crosslinked-senescent cells, aliquots of less than 1 million cells were kept in individual eppendorf tubes for sonication to maximize the chromatin fragmentation efficiency.
After purifying immunoprecipitated DNA, a TruSeq ChIP Sample Prep Kit (Illumina) was used to construct the ChIP-Seq library following  the manufacturer’s protocol except for amplifying the adaptor-ligated library for 15 cycles.
ChIP-Seq libraries were sequenced using an Illumina HiSeq 2000 platform with single end reads of 50 bases. Four libraries at equal molarity were pooled to aim for a sequencing depth of 20-40 million aligned reads per sample.

tag: antibody

value: Etoposide


title: H3K27ac ChIP-Seq_Etoposide IMR90

description: ChIP-Seq

value: H3K27ac (ab4729; Abcam)


title: Input_DMSO IMR90

description: ChIP-Seq

value: DMSO


title: Input_Proliferating IMR90 replicate

description: ChIP-Seq

value: proliferating


title: Input_Senescent IMR90 replicate

description: ChIP-Seq

value: senescent


title: BRD4 ChIP-Seq_Quiescent IMR90 replicate

description: ChIP-Seq

value: Brd4 (A301-985A; Bethyl)

value: quiescent


title: BRD4 ChIP-Seq_Senescent IMR90 replicate

description: ChIP-Seq


title: BRD4 ChIP-Seq_Proliferating IMR90 replicate

description: ChIP-Seq


title: H3K27ac ChIP-Seq_Senescent IMR90 replicate

description: ChIP-Seq


title: H3K27ac ChIP-Seq_Quiescent IMR90 replicate

description: ChIP-Seq


title: H3K27ac ChIP-Seq_Proliferating IMR90 replicate

description: ChIP-Seq


title: Input_Senescent IMR90

extract_protocol:
Five to 30 million IMR90 cells were crosslinked for 10 minutes using 1 % formaldehyde, followed by quenching with 0.125M glycine for 10 minutes. To prepare chromatin from crosslinked-senescent cells, aliquots of less than 1 million cells were kept in individual eppendorf tubes for sonication to maximize the chromatin fragmentation efficiency.
After purifying immunoprecipitated DNA, a TruSeq ChIP Sample Prep Kit (Illumina) was used to construct the ChIP-Seq library following  the manufacturer’s protocol except for amplifying the adaptor-ligated library for 15 cycles.
ChIP-Seq libraries were sequenced using an illumina HiSeq 2000 platform with single end reads of 50 bases. Four libraries at equal molarity were pooled to aim for a sequencing depth of 20-40 million aligned reads per sample.

value: fibrobasts

value: none (input)


title: H3K27Ac ChIP-Seq_Senescent IMR90


title: Input_Proliferating IMR90


title: BRD4 ChIP-Seq_Quiescent IMR90


title: BRD4 ChIP-Seq_Senescent IMR90


title: BRD4 ChIP-Seq_Proliferating IMR90


title: H3K27Ac ChIP-Seq_Proliferating IMR90


title: Input_Quiescent IMR90


title: H3K27me3 juvenile endocrine (EA46)


title: C57BL-6

city: Montreal

first: Krystel

last: Vincent

state: Quebec

address: 2950, chemin de la Polytechnique, Marcelle-Coutu Pavilion

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were masked for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: Thymocytes

extract_protocol:
Thymocytes were extracted by gently crushing freshly isolated thymi of 8-12 week old mice in between 2 microslides. Thymocyte suspension was submitted to standard Trizol RNA extraction protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Thymus

value: 8-12 weeks


title: H3K27ac ChIP-Seq_DMSO IMR90

description: ChIP-Seq


title: db/+

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description: mature microRNA

data_processing:
Illumina Casava1.3 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and aligned to mouse genome assembly mm10 using novoalign with parameter -h 60 -r Random -c 16
For each mature miRNA (defined in mirBase release 21), the reads located at its genomic location(s) were then counted and summarized as raw counts.
The total count of each mature miRNA was normalized by Trimmed Mean of M-values (TMM) using bioconductor edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited data files containing raw counts and TMM-normalized counts for each sample.

source_name: Aortic vascular smooth muscle cells

growth_protocol: Vascular smooth muscle cells from 10-12 weeks old type 2 diabetic db/db mice and control db/+ mice were isolated  from thoracic aortas of type 2 diabetic db/db mice and control db/+ mice.

extract_protocol:
Total RNA was extrated using miRNAeasy columns (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured in DMEM/F-12 medium supplemented with 10% Fetal bovine serum and antibiotics

value: db/+

tag: phenotype

value: Control mice

tag: genetic background

value: Lepr+/-

value: VSMC


title: db/db

description: mature microRNA

value: db/db

value: Type 2 diabetic mice

tag: stock number jackson labs


title: P0 GFP-

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
Bcl converion and demultiplexing using CASAVA 1.8.2. Adapter masked fastq files were generated.
Quality filter by FASTX Toolkit 0.0.13 (fastq_quality_filter: -Q33 -q 20 -p 80 was used as a parameter, fastq_quality_trimmer: -Q33 -t 20 -l 10 was used as a parameter). Fastq files were generated.
Read alignment using Tophat 2.0.9 using mm10 reference genome. BAM files were generated.
FPKM calculation using Cufflinks 2.2.1. Plain text (can be read by excel) files were generated. Both Tophat and Cufflinks used UCSC mm10 gtf file as guided annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing FPKM values for each sample and result of differential gene expression analysis

source_name: FACS-sorted GFP+ cells

growth_protocol: Dams and the weaned mice were maintained on an ad libitum feeding.

extract_protocol:
Total RNA was extracted with Rneasy Plus Mini Kit (QIAGEN) according to manufactureer's protocol. Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RIN was confirmed as greater 7 for each sample using Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies).
The cDNA libraries were prepared using the NEXTflex™ Rapid RNA Sequencing Kit and NEXTflex™ RNA-Seq Barcodes – 24 Kit (BioO Scientific) as per the manufacturer’s instructions. The final product was assessed for its size distribution using Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). Six libraries were pooled per HiSeq lane, followed by on-board cluster generation on a Rapid Run single-end flow cell and subsequent 50 cycles sequencing (v3 sequencing kit) according to the manufacturer's instructions (HiSeq 2500, Illumina).

treatment_protocol: The day on which a copulation plug was found was designated as embryonic day (E) 0, and the succeeding days of gestation were numbered in order. When embryos were E13, E15, or E17, embryos were harvested from dams euthanized with CO2 inhalation followed bypneumothorax. Postnatal day (P) 0 pups were sacrificed with decapitation. Olfactory bulbs were surgically dissected out from embryo/pup brains, and cells s were dissociated using Papain Dissociation System (Worthington Biochemical Corporation) according to manufacturer's protocol. GFP+ and GFP- cells were sorted out with BD FACSVantage SE.

value: olfactory bulb

tag: cell population

value: GFP-

value: Mixed 129 x C57BL/6J backgroud mice for homozygous or heterozygous NTS-IERS-tauGFP allel in neurotensin (NTS) allele is replaced with NTS-IRES-tauGFP.


title: E17 GFP-

tag: strain


title: Input_Quiescent IMR90 replicate

description: ChIP-Seq

tag: treatment


title: E15 GFP-


title: E13 GFP-


title: P0 GFP+

value: GFP+


title: E13 GFP+


title: E15 GFP+


title: P15 satellite cells/cytokine medium

city: Shanghai

first: Xin

last: Fu

address: 320 Yueyang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Raw reads were mapped to mm10 using Tophat v2.0.1 with default parameters.
Reads that have multiple hits on genome were filtered out using samtoolsrmdup (v. 0.1.19).
Gene expression was quantified as the number of reads per kilo-base per million of total mapped reads (RPKM) by GENCODE annotation (Gencode M2).
The number of reads that map to each gene was counted by Python package HTSeq (v. 0.5.4p2).
Genome_build: mm10
Supplementary_files_format_and_content: text file with RPKM values for all Samples. The columns are chromosome coordinates, gene symbols, and RPKM.

source_name: P15 satellite cells cultured in cytokine medium

growth_protocol: Satellite cells were cultured on collagen-coated dishes in F10 basal medium or T cell conditional medium or cytokine medium

extract_protocol:
RNA was extracted with Qiagen mini RNA extract kit.
cDNA library was constructed using TruSeq RNA-Seq Sample Prep Kits (Illumina) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: T cell conditional medium (F10 medium with 15% FBS:T cell medium=50:50, together with 2.5 ng/ml FGF). Cytokine cocktail medium (F10 medium containing 15% FBS, 5 ng/ml IL-1α, 5 ng/ml IL-13, 10 ng/ml IFN-γ, and 10 ng/ml TNF-α, and 2.5 ng/ml FGF)

tag: gender

value: Pooled male and female

value: 1-3 days

value: limb skeletal muscle


title: P2 satellite cells/cytokine medium

source_name: P2 satellite cells cultured in cytokine medium


title: H3K27Ac ChIP-Seq_Quiescent IMR90

tag: cell type

value: fibrobasts

value: H3K27ac (ab4729; Abcam)

value: quiescent


title: P15 satellite cells/T cell medium

source_name: P15 satellite cells cultured in T cell medium


title: P0 satellite cells/cytokine medium

source_name: P0 satellite cells cultured in cytokine medium


title: P1 satellite cells/T cell medium

source_name: P1 satellite cells cultured in T cell medium


title: Cumulus cells (2 month-old), strain: C57BL/6 3

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned on mouse genome (mm9) using tophat2 (version 2.1.0) with option "--no-coverage search".
Gene expression was estimated using cufflinks (version 2.1.0) with default options.
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.

source_name: Cumulus cells

growth_protocol: Minimum Essential Medium alpha (MEMα) with 75 μg/ml penicillin G, 50 μg/ml streptomycin sulfate, 0.23 mM pyruvate, 3 mg/ml bovine serum albumin (BSA; Sigma-Aldrich, St Louis, MO), and 10 μM of the phosphodiesterase inhibitor, milrinone (Sigma-Aldrich) was used as the basic culture medium.

extract_protocol:
Total RNA was extracted using a miRCURY RNA Isolation Kit
Libraries for the RNA-seq were prepared from total RNAs extracted from the MGCs of eCG-primed mice according to the manufacturer's protocol

value: 2 months


title: COC (3 week-old, PMSG-primed), strain: BDF1

source_name: COC

value: 3 weeks


title: Mural granulosa cells (2 month-old), strain: C57BL/6 1

source_name: Mural granulosa cells


title: Mural granulosa cells (2 month-old), strain: C57BL/6 2


title: COC (3 week-old, PMSG-primed), strain: DBA/2


title: P1 satellite cells/cytokine medium

source_name: P1 satellite cells cultured in cytokine medium


title: P0 satellite cells/T cell medium

source_name: P0 satellite cells cultured in T cell medium


title: Cumulus cells (2 month-old), strain: C57BL/6 1


title: Cumulus cells (10 month-old), strain: C57BL/6 3

value: 10 months


title: Cumulus cells (10 month-old), strain: C57BL/6 2


title: Cumulus cells (2 month-old), strain: C57BL/6 2


title: Cumulus cells (10 month-old), strain: C57BL/6 1


title: E17 GFP+


title: 56hpf_con3 (ESD-21_N1)

city: Illkirch

first: Julien

last: Vermot

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2.
Reads were mapped onto the zv9 assembly of  Danio rerio genome using Tophat2.0.10 and bowtie-2-2.1.0.
Quantification of gene expression has been performed using HTSeq-0.5.4p3.
Normalization was performed using DESeq_1.10.1.
Genome_build: zv9
Supplementary_files_format_and_content: tabulated text file containing normalized read counts.

organism: Danio rerio

source_name: heart

growth_protocol: Embryos were collected, staged and grown under standard conditions

extract_protocol:
Dissected hearts were lysed and the RNA extracted using a Nucleospin XS kit from Machinery Nagel, according to the manufacturers instructions
Amplified cDNA was prepared from 5 ng of total RNA using the Ovation RNA-seq system V2 (NuGEN Technologies, Inc.) following manufacturer's instructions. Briefly, total RNA were reverse-transcribed into first-strand cDNA using a combination of random and poly-T DNA/RNA chimeric SPIA primers. Priming sites created by a heating fragmentation of mRNA within the cDNA/mRNA complex were then used to synthesize the second strand cDNA using a DNA polymerase. The resulting double-stranded cDNA with a unique RNA/DNA heteroduplex at one end were purified using Agencourt RNAClean XP beads (Beckman Coulter Inc.) and used  as substrate in the linear amplification process, SPIA (single primer isothermal amplification). Amplified cDNA was purified using AMPure XP beads (Beckman Coulter Inc.) and 500 ng was fragmented by sonication using a Covaris E210 instrument (with duty cycle: 10X, intensity: 5 and cycle/burst: 200 for 180 seconds). The next steps of RNA-Seq Library preparation were performed on the Mondrian™ SP Workstation using Ovation® SP Ultralow Library Systems kit (NuGEN Technologies, Inc.) according to manufacturer's instructions. Briefly, 100 ng of amplified cDNA were blunted, phosphorylated and ligated to indexed adapter dimers. The libraries were then enriched by PCR amplification (2 min at 72 degrees Celsius; [30 sec at 94 degrees Celsius, 30 sec at 60 degrees Celsius, 1 min at 72 degrees Celsius] x 8 cycles; 5 min at 72 degrees Celsius) and surplus PCR primers were removed by purification using AMPure XP beads. DNA libraries were checked for quality using 2100 Bioanalyzer (Agilent) and quantified using Kapa Sybr Fast Light Cycler 480 qPCR Kit (Kapa Biosystems) according to manufacturer's recommendations. The libraries were loaded in the flow cell at 7pM concentration and sequenced in the Illumina Hiseq 2500 as single-end 50 base reads following Illumina’s instructions.

tag: line

value: AB

value: heart

tag: developmental stage


title: 48hpf_con2 (ESD-14_N3)


title: 48hpf_con3 (ESD-15_N5)


title: 56hpf_con2 (ESD-20_N8)


title: 48hpf_con1 (ESD-13_N1)


title: 56hpf_con1 (ESD-19_N6)


title: Ba/F3-MPL DEL t24 rep2

status: Public on Apr 14 2016

city: Heidelberg

first: Javier

last: Perales-Paton

state: Baden-Württemberg

address: Im Neuenheimer Feld 267

department: Faculty of Medicine

country: Germany

institute: Heidelberg University

description:
Replica 2
RNAseq - human CALR 52bp del BaF3-MPL cells, 24 hours after IL3-widthdrawal

data_processing:
The mRNA reads were aligned on the mouse reference genome (mm10 assembly, UCSC) using the TopHat2 algorithm (v. 2.0.10), retrieving the best hit with the default parameters, but allowing a maximum of five multi-hits with the same alignment score.
The gene-level expression was quantified as the sum of all reads mapping on the exons for each gene towards the gene annotation for the mouse genome (mm10, UCSC) using HTSeq-count (v. 0.5.4p5)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text files with read counts per gene measurements by HTSeq-Count

molecule: polyA RNA

source_name: Ba/F3 cells

growth_protocol: Ba/F3 cell lines expressing type I cytokine receptors were maintained in RPMI 140 medium and supplemented with 10% FBS, 5% penicillin/streptomycin, 2 ng/mL murine IL3, and 2 mg/mL hygromycin.

extract_protocol:
NEBNext Ultra RNA Library Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Following IL-3 withdrawal, Ba/F3-MPL cells overexpressing either human CALR 52 bp deletion mutant, human wild-type CALR or Empty-vector were collected in order to extract the mRNA at different culture time points (0 and 24 hours).

tag: cell line

tag: first transformation

value: human MPL gene

tag: second transformation

value: human CALR 52bp deletion mutant gene

tag: culture time after il3-widthdrawal

value: 24 hours


title: Ba/F3-MPL WT t24 rep2

description:
Replica 2
RNAseq - human wild-type CALR BaF3-MPL cells, 24 hours after IL3-widthdrawal

value: human wild-type CALR gene


title: P2 satellite cells/T cell medium

source_name: P2 satellite cells cultured in T cell medium

tag: age

tag: tissue


title: Ba/F3-MPL EV t24 rep2

description:
Replica 2
RNAseq - empty-vector BaF3-MPL cells, 24 hours after IL3-widthdrawal

value: empty vector


title: Ba/F3-MPL DEL t24 rep1

description:
Replica 1
RNAseq - human CALR 52bp del BaF3-MPL cells, 24 hours after IL3-widthdrawal


title: Ba/F3-MPL EV t24 rep1

description:
Replica 1
RNAseq - empty-vector BaF3-MPL cells, 24 hours after IL3-widthdrawal


title: Ba/F3-MPL WT t24 rep1

description:
Replica 1
RNAseq - human wild-type CALR BaF3-MPL cells, 24 hours after IL3-widthdrawal


title: Ba/F3-MPL DEL t0 rep2

description:
Replica 2
RNAseq - human CALR 52bp del BaF3-MPL cells, 0 hours after IL3-widthdrawal

value: 0 hours


title: Ba/F3-MPL EV t0 rep1

description:
Replica 1
RNAseq - empty-vector BaF3-MPL cells, 0 hours after IL3-widthdrawal


title: Ba/F3-MPL WT t0 rep2

description:
Replica 2
RNAseq - human wild-type CALR BaF3-MPL cells, 0 hours after IL3-widthdrawal


title: Ba/F3-MPL EV t0 rep2

description:
Replica 2
RNAseq - empty-vector BaF3-MPL cells, 0 hours after IL3-widthdrawal


title: Ba/F3-MPL DEL t0 rep1

description:
Replica 1
RNAseq - human CALR 52bp del BaF3-MPL cells, 0 hours after IL3-widthdrawal


title: Ba/F3-MPL WT t0 rep1

description:
Replica 1
RNAseq - human wild-type CALR BaF3-MPL cells, 0 hours after IL3-widthdrawal


title: P0 satellite cells/F10 medium

source_name: P0 satellite cells cultured in F10 medium

value: Pooled male and female


title: wtATMIN + 24h DMSO, replicate 2

city: Vienna

first: Abdelghani

last: Mazouzi

address: Lazarettgasse Lazarettgasse 14, AKH BT 25.3, 7.105

country: Austria

institute: CeMM

description: expression profile of wt MEFs treated with DMSO, replicate 2

data_processing:
Alignments to genome version mm10 and the corresponding Ensgene annotation were performed with Bowtie2 (v2.4.0) and Tophat2 (v2.0.13), using a seed length of 15nt, a <4% error rate and discarding reads with >100 hits.
Read counts per gene were generated by RPKM_count.py (RSeQC, v2.6.1), only uniquely aligned reads were accepted
DESeq2 (v1.6.3) was used for normalization and differential expression analysis, with default settings except for a “local” dispersion fit and an adjusted pvalue cutoff of 0.001. For DESeq2 analysis, only genes covered by at least 1 read in at least 3 samples were taken into account.
Genome_build: mm10
Supplementary_files_format_and_content: One table with raw read counts per gene for each replicate, in text format.
Supplementary_files_format_and_content: Ten tables in text format, with results of pair-wise differential expression analyses including gene ids, expression levels (normalized read counts, rpkm, vst) per replicate and per group, log2-fold changes and multiple-test corrected p-values (padj).
Supplementary_files_format_and_content: Compared groups are indicated in the file names, separated by "-"; the second group is considered as control.

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEFs were cultured in complete DMEM (10% FCS, 1% Pen/Strep) treated with DMSO or APH

extract_protocol:
TRIzol (Life Technologies) from 107 cells per replicate
Illumina TruSeq RNA Sample Prep Kit v2
from 1µg RNA per library

value: wt MEFs

value: DMSO


title: wtATMIN + 24h APH, replicate 2

description: expression profile of wt MEFs treated with1µM APH for 24h, replicate 2

value: 1µM APH for 24h


title: ATMIN neg. + 24h DMSO, replicate 2

description: expression profile of ATMIN knock-out MEFs treated with DMSO, replicate 2

value: ATMIN knock-out MEFs


title: ATMIN neg. + 24h APH, replicate 1

description: expression profile of ATMIN knock-out MEFs treated with1µM APH for 24h, replicate 1


title: wtATMIN + 24h APH, replicate 1

description: expression profile of wt MEFs treated with1µM APH for 24h, replicate 1


title: ATM neg. + 24h APH, replicate 2

description: expression profile of ATM knock-out MEFs treated with1µM APH for 24h, replicate 2

value: ATM knock-out MEFs


title: wtATMIN + 24h DMSO, replicate 1

description: expression profile of wt MEFs treated with DMSO, replicate 1


title: ATM neg. + 24h APH, replicate 1

description: expression profile of ATM knock-out MEFs treated with1µM APH for 24h, replicate 1


title: ATMIN neg. + 24h DMSO, replicate 1

description: expression profile of ATMIN knock-out MEFs treated with DMSO, replicate 1


title: ATM neg. + 24h DMSO, replicate 2

description: expression profile of ATM knock-out MEFs treated with DMSO, replicate 2


title: wtATM + 24h APH, replicate 1


title: wtATM + 24h APH, replicate 2


title: ATMIN neg. + 24h APH, replicate 2

description: expression profile of ATMIN knock-out MEFs treated with1µM APH for 24h, replicate 2


title: ATMIN neg. + 4h APH, replicate 1

description: expression profile of ATMIN knock-out MEFs treated with1µM APH for 4h, replicate 1

value: 1µM APH for 4h


title: ATMIN neg. + 4h DMSO, replicate 2


title: wtATM + 24h DMSO, replicate 1


title: wtATM + 24h DMSO, replicate 2


title: ATMIN neg. + 4h DMSO, replicate 1


title: wtATMIN + 4h APH, replicate 1

description: expression profile of wt MEFs treated with1µM APH for 4h, replicate 1


title: wtATMIN + 4h DMSO, replicate 2


title: wtATMIN + 4h APH, replicate 2

description: expression profile of wt MEFs treated with1µM APH for 4h, replicate 2


title: wtATMIN + 4h DMSO, replicate 1


title: ATM neg. + 4h APH, replicate 1

description: expression profile of ATM knock-out MEFs treated with1µM APH for 4h, replicate 1


title: ATM neg. + 4h APH, replicate 2

description: expression profile of ATM knock-out MEFs treated with1µM APH for 4h, replicate 2


title: ATM neg. + 4h DMSO, replicate 2


title: ATM neg. + 24h DMSO, replicate 1

description: expression profile of ATM knock-out MEFs treated with DMSO, replicate 1


title: wtATM + 4h DMSO, replicate 1


title: wtATM + 4h DMSO, replicate 2

description: expression profile of wt MEFs treated with DMSO, replicate 2


title: ATMIN neg. + 4h APH, replicate 2

description: expression profile of ATMIN knock-out MEFs treated with1µM APH for 4h, replicate 2


title: wtATM + 4h APH, replicate 1


title: wtATM + 4h APH, replicate 2


title: ATM neg. + 4h DMSO, replicate 1


title: WT_SHAM1

city: Leiden

first: Else

last: Eising

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description:
Sample name: 9017236
RNA isolated 24h after sham surgery
Deep-SAGE sequencing

data_processing:
reads were trimmed to 17 bps to equalize the length of all reads, after which the Nlalll recognition site sequence (CATG) was added to the 3’ end of the reads, creating reads with a length of 21 bps.
The reads were aligned against the UCSC mm9 mouse genome using Bowtie short read aligner (version 0.12.9), allowing for a maximum of one mismatch and a maximum of one possible position in the genome (options: -k 1 -m 1 -n 1 --best --strata).
Mouse exon annotation information was retrieved from BIOMART (Ensembl build 64), and was used to calculate the number of reads per gene for each sample. Only reads aligned to known exons in the sense direction were used for downstream statistical and biological analyses. Analyses were performed at gene level, and reads were summed per gene also when aligned to different locations within a gene, e.g. as a consequence of alternative polyadenylation.
To account for differences in library size, the data was first normalized using the trimmed mean of M-values (TMM) method of the EdgeR Bioconductor package
Genome_build: UCSC mm9
Supplementary_files_format_and_content: Text file containing the count data file, listing the read counts per gene for each sample
Supplementary_files_format_and_content: Text file containing the TMM normalized count data file, listing the normalized read count per gene for each sample

source_name: Middle cortex

extract_protocol:
Frozen tissue of the mid-part of the cortex was crunched using a mortar and subsequently homogenized in lysis buffer using the Ultra-turrax T25 Polytron (Janke & Kunkel, Staufen, Germany) mechanical homogenizer. Total RNA was isolated using the Machery Nagel RNA isolation kit (Düren, Germany). Contaminating DNA was removed by on-column treatment with rDNase. Agilent 2100 Bioanalyzer total RNA nanochips (Agilent, Foster City, CA, USA) were used to determine RNA integrity. RNA samples included in this study had RIN (RNA integrity number) values between 8.9 and 10.
mRNA was hybridized to Oligo(dT) beads. On the beads, double-stranded cDNA was synthesized, which was digested with Nlalll and Mmel restriction enzymes to create a 17-base-pair (bp) cDNA sequence. The sequence was flanked by two GEX adapters and amplified by PCR for 15 cycles, during which a 6-bp barcode index was introduced that allowed discrimination of reads from up to 12 different samples after sequencing.

treatment_protocol: Mice were anesthetized using 1.5% isoflurane in pressurized air (20% O2 and 80% N2) and placed onto a stereotactic frame (David Kopf Instruments, Tujunga, CA, USA). Core body temperature was maintained at 37°C with a heating pad. After exposure of the skull two burr holes were prepared at the following coordinates over the right hemisphere for: (i) CSD induction on the occipital cortex (3.5 mm posterior, 2 mm lateral) and (ii) CSD recording from the frontal cortex (1.5 mm anterior from bregma; 2 mm lateral). At the recording site in the frontal cortex a sharp glass capillary electrode (FHC Inc., Bowdoin, ME, USA) filled with 150 mM NaCl was advanced to a depth of 200–300 μm. Data were sampled (200 Hz), amplified (10X) and low-pass filtered at 4 Hz and analyzed off-line using LabChart (AD Instruments, Colorado Springs, CO, USA). A reversible DC deflection that was > 5 mV in amplitude was considered a CSD event. Seven CSDs were induced by brief application (30 sec) of a cotton pellet (Interguide Dental Supply, Burlingame, CA, USA) soaked in 300 mM KCl on the dura overlaying the occipital cortex. Between each KCl application the stimulation area was rinsed thoroughly with saline. The inter-application interval was 5 min; each application induced a single CSD, both in WT and mutant mice. In Sham-treated animals 300 mM NaCl was applied seven times instead of KCl; NaCl application does not induce CSDs, neither in WT nor in mutant mice. Mice received a subcutaneous injection of 5 mg/kg carprofen for post-operative analgesia after the last CSD or after the last NaCl application. Five min after the 7th CSD induction or 7th NaCl application, the skin overlaying the skull was sutured and the mice were returned to their home cages to recover from surgery under a heating lamp (37°C). Twenty-four hours after the end of the CSD or Sham procedure, animals were sacrificed by cervical dislocation and the middle part of the cortex – through which the CSD waves ran –  from the right hemisphere that was located between the cortical thirds parts that contained either the stimulation (occipital cortex) or the recording (frontal cortex) burr holes was isolated (Fig. 1). After visual inspection to confirm that the cortical tissue did not show obvious damage caused by the surgery or CSD/Sham procedure, it was snap-frozen in liquid N2 within 15 min from the moment of sacrifice, and stored at -80°C until RNA isolation.

tag: genotype/variation

value: wild-type

tag: protocol

value: sham surgery

value: 2-4 months

value: Middle cortex


title: WT_CSD5

description:
Sample name: 9017231
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: WT_CSD4

description:
Sample name: 7126200
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: WT_CSD6

description:
Sample name: 9017230
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: WT_SHAM4

description:
Sample name: 9015691
RNA isolated 24h after sham surgery
Deep-SAGE sequencing


title: WT_SHAM2

description:
Sample name: 9014016
RNA isolated 24h after sham surgery
Deep-SAGE sequencing


title: WT_SHAM6

description:
Sample name: 7124155
RNA isolated 24h after sham surgery
Deep-SAGE sequencing


title: WT_SHAM3

description:
Sample name: 9015694
RNA isolated 24h after sham surgery
Deep-SAGE sequencing


title: WT_CSD1

description:
Sample name: 7126199
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: WT_CSD2

description:
Sample name: 9015695
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: RQ_SHAM4

description:
Sample name: 9016467
RNA isolated 24h after sham surgery
Deep-SAGE sequencing

value: Homozygous R192Q CACNA1A Knock-in


title: RQ_SHAM5

description:
Sample name: 9016466
RNA isolated 24h after sham surgery
Deep-SAGE sequencing


title: RQ_SHAM3

description:
Sample name: 9014731
RNA isolated 24h after sham surgery
Deep-SAGE sequencing


title: RQ_SHAM6

description:
Sample name: 9013752
RNA isolated 24h after sham surgery
Deep-SAGE sequencing


title: WT_CSD3

description:
Sample name: 7126202
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: WT_SHAM5

description:
Sample name: 9016499
RNA isolated 24h after sham surgery
Deep-SAGE sequencing


title: Pooled RNA from Gnasxlm+/p- 4 and Gnasxlm+/p- 5 hypothalamic isolates

city: Liverpool

first: Andrew

last: Holmes

address: Institute of Integrative Biology

department: Institute of Integrative Biology

country: United Kingdom

institute: University of Liverpool

data_processing:
fastq files were mapped to the mm10 build of the Mus musculus genome using TopHat 2.0.4 while incorporating a repeatmask file obtained from RepeatMasker.
Mapped reads were processed using Cufflinks 2.0.2 to the GTF transcript annotation file provided by Illumina iGenomes
Genome_build: mm10
Supplementary_files_format_and_content: .diff files show differences between wildtype and knockout samples. Cds = coding sequences, cds_exp = expressed coding sequences, gene_exp = gene expression, isoform_exp = isoform expression, tss_group_exp = Transcription start site

extract_protocol:
RNA was extracted from 40 mg hypothalamic tissue samples using the Stratagene RNA extraction kit following the protocol for tissue extraction. This included homogenization of tissue samples with 600 µL lysis buffer containing 4.2 µL β-Mercaptoethanol. Homogenate was added, 700 μL at a time, to a prefilter spin-cup in a 2 mL receptacle tube and centrifuged for 5 minutes. The filtrate was added to an equal volume of 70% EtOH and mixed thoroughly. From the filtrate/EtOH mixture, 700 µL was transferred to an RNA-binding spin-cup and centrifuged for 1 minute, the filtrate was discarded and the rest of the mixture added to the spin-cup and centrifuged for 1 minute.
6 wildtype and 6 Gnasxlm+/p- RNA isolates were used, which were pooled in pairs in equal concentrations prior to rRNA removal using the RiboMinus kit (Life Technologies).For each pooled sample, 50ng of RNA was used for library preparation using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre)

tag: strain background

value: Gnasxlm+/p-

value: brain; hypothalamus


title: Pooled RNA from Gnasxlm+/p- 3 and Gnasxlm+/p- 6 hypothalamic isolates


title: RQ_CSD5

description:
Sample name: 7129441
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: RQ_CSD6

description:
Sample name: 7124791
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: RQ_SHAM1

description:
Sample name: 9015363
RNA isolated 24h after sham surgery
Deep-SAGE sequencing


title: RQ_CSD4

description:
Sample name: 9015364
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: Pooled RNA from wildtype 4 and wildtype 5 hypothalamic isolates

value: wild type


title: RQ_CSD3

description:
Sample name: 7122832
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: Pooled RNA from Gnasxlm+/p- 1 and Gnasxlm+/p- 2 hypothalamic isolates


title: RQ_CSD2

description:
Sample name: 9016477
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: RQ_CSD1

description:
Sample name: 9013751
RNA isolated 24h after the induction of cortical spreading depression
Deep-SAGE sequencing


title: Pooled RNA from wildtype 1 and wildtype 2 hypothalamic isolates


title: Pooled RNA from wildtype 3 and wildtype 6 hypothalamic isolates


title: P18 brain oligodendrocytes_RNASeq_n3

city: New York

first: Sarah

last: Moyon

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: CUNY ASRC

description: Sample name: plp18n3

data_processing:
250 ng of total RNA per sample were used for library construction by the TruSeq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2000 instrument for the FACS samples according to the manufacturer's instructions for 50 bp paired end read runs.
High-quality reads were aligned to the mouse reference genome (mm10), RefSeq exons, splicing junctions, and contamination databases (ribosome and mitochondria sequences) using the Burrows-Wheeler Aligner (BWA) algorithm. The read count for each RefSeq transcript was extracted using uniquely aligned reads to exon and splice-junction regions for each transcript.
The raw read counts were inputted into DESeq2 v1.2.5 (Anders and Huber, 2010) for calculation of normalized signal for each transcript and to ascertain differential gene expression with associated q-values.
Differentially expressed genes were selected at a q-value < 0.01. An additional filter for fold change > 2 was used for the OPC–OL comparison, given the large differences between the two sample groups.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized signal for each transcript, for each sample, using DESeq2 v.1.2.5

source_name: Brain

extract_protocol:
Total RNAs were obtained from FAC-sorted P2 oligodendrocyte progenitor cells or P18 oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: Post-natal day 18

value: brain

value: Primary FAC-sorted Plp1-GFP+ cells


title: P18 brain oligodendrocytes_RNASeq_n2

description: Sample name: plp18n2


title: P2 brain oligodendrocyte progenitor cells_RNASeq_n3

description: Sample name: pdgfrap2n3

value: Post-natal day 2

value: Primary FAC-sorted Pdgfra::GFP+ cells


title: P2 brain oligodendrocyte progenitor cells_RNASeq_n2

description: Sample name: pdgfrap2n2


title: P2 brain oligodendrocyte progenitor cells_RNASeq_n1

description: Sample name: pdgfrap2n1


title: P18 brain oligodendrocytes_ERRBS_n2

description: Sample name: plp18n2

data_processing:
ERRBS libraries for DNA methylation analysis were prepared from 50 ng input DNA per biological replicate following a modification (Akalin et al., 2012a) of a published protocol (Gu et al., 2011) and sequenced using the Illumina HiSeq 2000 instrument according to the manufacturer's instructions for 50 bp single end read runs.
The raw sequencing reads were aligned as previously reported (Akalin et al., 2012a).
DNA methylation levels were calculated as the ratio of cytosine reads over the total number of sequenced reads for each individual CpG site.
Determination of differential methylation was first performed at the single base level, using only CpG dinucleotides with at least 10 sequencing reads and covered in all the samples. The methylKit R package (Akalin et al., 2012b) was used to determine methylation differences between OPC and OL samples, and to test for significance of difference by logistic regression. Determination of differential methylation was first performed at the single base level, using only CpG dinucleotides with at least 10 sequencing reads and covered in all the samples. The methylKit R package (Akalin et al., 2012b) was used to determine methylation differences between OPC and OL samples, and to test for significance of difference by logistic regression.
Regional methylation analysis – with a minimum of 2 CpGs per region – was then performed using the eDMR algorithm (Li et al., 2013), which is based on a bimodal normal distribution model and weighted cost function for regional methylation analysis optimization. The dependence adjustment of the Stouffer-Liptak test was used to combine p-values within a region (Kechris et al., 2010; Pedersen et al., 2012), and a false discovery rate correction was applied to correct for multiple hypothesis testing (Benjamini and Hochberg, 1995).
Differentially methylated regions were selected at a q-value < 0.05 and with a minimum mean difference of 10% per region.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each CpGs, for each sample, using methylKit R package (Akalin et al., 2012b)

extract_protocol:
Genomic DNAs were obtained from FAC-sorted P2 oligodendrocyte progenitor cells or P18 oligodendrocytes, isolated from mouse brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), in accordance with the manufacturer’s protocol, to isolate DNA and RNA simultaneously from the same cell pellet. DNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop (Thermo Scientific), and DNA quality checked by agarose gel electrophoresis for a single high molecular weight band.
ERRBS libraries for DNA methylation analysis were prepared from 50 ng input DNA per biological replicate following a modification (Akalin et al., 2012a) of a published protocol (Gu et al., 2011) .


title: Cxxc1.KO.mRNA-seq

city: Guangzhou

first: Lai

last: Wei

address: 54 S. Xianlie Road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v1.0.1
RNA-seq data analysis using Partek Genomic Suite 6.6
Genome_build: mm9
Supplementary_files_format_and_content: RNA-Seq's raw counts of sequencing reads

source_name: thymus

extract_protocol:
Total RNA was extracted from WT and Cxxc1-deficient DP thymocytes with TRIzol reagent.
mRNA-seq libraries were prepared using NEBNext® mRNA Library Prep Master Mix Set for Illumina according to the manufacture’s protocol (NEB, USA) .

value: DP thymocytes

tag: genotype


title: P2 brain oligodendrocyte progenitor cells_ERRBS_n3

description: Sample name: pdgfrap2n3

tag: strain


title: Cxxc1.KO.H3K4me3.ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome
SICER version 1.1 was used to identify significant peaks (FDR = 10-5) with both Input DNA and ChIP DNA
Output of the peak files was converted to browser-extensible data (BED) files and viewed with UCSC genome browser.
MEME-ChIP was used to perform the consensus binding motif analysis for Cxxc1.
Genome_build: mm9

extract_protocol: ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems, USA) according to the manufacture’s protocol.

tag: chip antibody


title: Input.WT.ChIP-seq


title: RQ_SHAM2

description:
Sample name: 9014730
RNA isolated 24h after sham surgery
Deep-SAGE sequencing


title: P18 brain oligodendrocytes_RNASeq_n1

description: Sample name: plp18n1


title: P18 brain oligodendrocytes_ERRBS_n3

description: Sample name: plp18n3


title: Cxxc1.WT.H3K4me3.ChIP-seq


title: P2 brain oligodendrocyte progenitor cells_ERRBS_n2

description: Sample name: pdgfrap2n2


title: Cxxc1.WT.ChIP-seq


title: input SFN treated

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

data_processing:
Library strategy: ChIP tagmentation sequencing
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Alignment (BWA) Tool with the default configurations
Uniquely mapped reads were filtered to uniue reads to avoid PCR artifact
The MPILEUP function in the Samtools (Li et al., 2009) was used to pile up reads overlapping SNP positions.
A binomial test was used to evaluate if there is a difference in the counts of reads of tested alleles
Genome_build: hg19

growth_protocol: human GM12763 were grown as recommended by Coriell

extract_protocol: Lysates were clarified from sonicated nuclei and NRF2-DNA complexes were isolated with antibody (Abcam, Clone ID EP1808Y).  Libraries were prepared according to Illumina's Nextera XT Library Preparation Kit. Briefly, PCR amplifed ChIPed DNA was tagmentated using Tn5-based transposition for library construction.  DNA was further PCR amplified with Illumina primers for 11 cycles and library fragments ranged from 200-375 bp on a bioanalyzer. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina MiSeq following the manufacturer's protocols.

treatment_protocol: human GM12763 were treated at a density of 900,000 cells/ml with 10 μM D,L-sulforaphane (Calbiochem) for 5 hours

value: lymphoblastoid cell line


title: NRF2 ChIP SFN treated rep3

value: rabbit monoclonal anti-NRF2 (Abcam, Clone ID EP1808Y)


title: Cxxc1.KO.ChIP-seq


title: CAC1_rep1_RTT106_OF_sample

first: Iestyn

last: Whitehouse

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute

data_processing:
Data were aligned to the *UCSC (sacCer3, April 2011)* build of the S. cerevisiae genome: using BOWTIE2
Position of 5' end of reads with Q30 or greater are reported in SGR files.
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab-delimited text. Chromosome, Position (base-pair), Value

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 30 °C in YEP medium supplemented with 2% glucose. At optical density (OD600) 0.3, doxycycline was added to final concentrations of 40 mg l−1, and the culture shaken at 30 °C for 2.5 h. Fifty-millilitre cultures were used for labeling experiments, and 200-ml cultures for purification and library generation.

extract_protocol:
Genomic DNA was purified and heat-denatured: DNA was bound to Source 15Q resin in batch at 50mM NaOH, pH12, and eluted in NaCl, using 50mM steps (at pH 12). Fractions from 600-750 mM NaCl were collected, concentrated by precipitation. Double-stranded sequencing adaptors with N6 random overhangs ligated to each end; after second-strand synthesis using Taq, material from 200-1000bp was gel-purified and amplified by PCR. Products from 200-800 bp were gel-purified from two successive 2.5% agarose gels or using Ampure XP beads for size-selection.
See extract protocol
Okazaki-fragment (OF) sequencing

value: cac1_null_rtt106_null [yIW514]

tag: cell cycle stage

value: Asynchronous culture


title: RTT106_rep1_OF_sample

value: rtt106_null [yIW401]


title: P5 mouse Olig1cre/+;Dnmt1flox/flox;Pdgfra-GFP OPC_n2

description: Sample name: Dnmt1.cKOOPC_n2

data_processing:
RNA libraries were sequenced using the Illumina HiSeq 2500 instrument for the FACS samples according to the manufacturer's instructions for 100 bp paired-end read runs.
High-quality reads were aligned to the mouse reference genome (mm10), RefSeq exons, splicing junctions, and contamination databases (ribosome and mitochondria sequences) using the Burrows-Wheeler Aligner (BWA) algorithm. The read count for each RefSeq transcript was extracted using uniquely aligned reads to exon and splice-junction regions for each transcript.
The raw read counts were inputted into DESeq2 v1.2.5 (Anders and Huber, 2010) for calculation of normalized signal for each transcript and to ascertain differential gene expression with associated q-values.
Differentially expressed genes were selected at a p-value < 0.05.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include normalized signal for each transcript, for each sample, using DESeq2 v.1.2.5.

source_name: P5 brain oligodendrocyte progenitor cells, Dnmt1 cKO

extract_protocol:
Total RNAs were obtained from FAC-sorted P5 oligodendrocyte progenitor cells, isolated from mouse Olig1+/+;Dnmt1flox/flox;Pdgfra-GFP or Olig1cre/+;Dnmt1flox/flox;Pdgfra-GFP brains. We used AllPrep DNA/RNA Mini Kit (Qiagen), with on-column DNase treatment during the RNA isolation, in accordance with the manufacturer's protocol, to isolate DNA and RNA simultaneously from the same cell pellet. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).
50 ng of total RNA per sample were used for library construction by the TruSeq RNA Sample Prep Kit (Illumina).

value: Post-natal day 5

tag: cell type

tag: strain/background


title: NRF2 ChIP SFN treated rep2


title: NRF2 ChIP SFN treated rep1


title: Cxxc1.WT.mRNA-seq


title: P5 mouse Olig1cre/+;Dnmt1flox/flox;Pdgfra-GFP OPC_n1

description: Sample name: Dnmt1.cKOOPC_n1

tag: developmental stage


title: ISW1_rep1_CHD1_OF_sample

value: isw1_null_chd1_null [yIW411]


title: CAC1_rep1_OF_sample

value: cac1_null [yIW397]


title: P5 mouse Olig1+/+;Dnmt1flox/flox;Pdgfra-GFP OPC_n2

description: Sample name: ControlOPC_n2

source_name: P5 brain oligodendrocyte progenitor cells, control

value: Olig1+/+;Dnmt1flox/flox;Pdgfra-GFP+ OPC


title: IAA26-P108H-GFP 2 Lane 1

city: College Park

first: James

middle: N

last: Culver

state: MD

address: 4291 Fieldhouse Dr.

department: Plant Science and Landscape Architecture

institute: University of Maryland, College Park

data_processing:
llumina Casava software used for basecalling.
Raw reads were mapped to the Arabidopsis thaliana Col-0 genome reference TAIR10 using the CLC Genomics Workbench v 7.5.1 RNA-seq analysis tool and default parameters. (Mismatch cost 2, Insertion cost 3, Deletion Cost 3, Length fraction 0.8, Similarity fraction 0.8, Max hits for a read 10)
Genome_build: Col-0 TAIR10
Supplementary_files_format_and_content: tab-delimited text files include Gene ID, Chromosome, Region, RPKM value, Total gene reads, and Total exon reads.

source_name: Leaves

growth_protocol: All plants were maintained in growth chambers for a 12-h photoperiod at 24°C.

extract_protocol:
Total RNA was isolated from seven-week-old pIAA26::IAA26-P108H-GFP transgenic plants and non-transformed control plants using the RNeasy kit (Qiagen).  Four fully expanded leaves were collected from each test plant and total RNA from four to six individual test plants was pooled for each of the three biological replicates.
RNA libraries were prepared by the by the UM-IBBR Sequencing Core at University of Maryland, College Park (http://ibbr.umd.edu/facilities/sequencing) using the Illuminia TrueSeq RNA library kit according to the manufacturer's instructions.

tag: ecotype

value: Shahdara

tag: developmetal stage

value: 7-week-old plants

value: auxin resistant pIAA26::IAA26-P108H-GFP transgenic

value: leaf


title: IAA26-P108H-GFP 2 Lane 2


title: IAA26-P108H-GFP 3 Lane 1


title: P5 mouse Olig1+/+;Dnmt1flox/flox;Pdgfra-GFP OPC_n1

description: Sample name: ControlOPC_n1

value: brain


title: IAA26-P108H-GFP 3 Lane 2


title: IAA26-P108H-GFP 1 Lane 2


title: IAA26-P108H-GFP 1 Lane 1


title: ISW1_rep1_OF_sample

value: isw1_null [yIW394]


title: SF1_ChIPseq

city: Houston

first: Francesco

middle: J

last: DeMayo

state: Texas

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
50-nt sequence reads identified by the Sequencing Service (using Ilumina's Hi-seq)
reads mapped to the genome using the BWA algorithm with default settings
tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp
density of fragments, in 32-nt bins divided genome, defined in BAR files
peaks were defined using MACS
Genome_build: Build 37.1 mm9

source_name: whole uterus

growth_protocol: standard chow

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input  DNAs by the standard consecutive enzymatic steps of end-polishing,  dA-addition, and adaptor ligation (performed on the Apollo 324  system). After a final PCR amplification step, the resulting DNA  libraries were quantified and sequenced on HiSeq 2500 (50 nt reads,  single end).

treatment_protocol: Ovariectomized mice at 6 weeks of age and rested for 2 weeks to deplete endogenous hormones

value: 8 weeks

tag: estrous cycle

value: ovariectomized

tag: antibody

tag: antibody vendor

value: Millipore, cat # 07-618


title: Control 3 Lane 2

value: control

tag: tissue


title: CAC1_RTT106_OF_sample

data_processing:
Data were aligned to the May 2008 build of the S. cerevisiae genome: using BOWTIE2
Position of 5' end of reads with Q30 or greater are reported in SGR files.
Genome_build: UCSC SacCer2 (June 2008)

extract_protocol:
Genomic DNA was purified and heat-denatured: DNA was bound to Source 15Q resin in batch at 50mM NaOH, pH12, and eluted in NaCl, using 50mM steps (at pH 12). Fractions from 600-750 mM NaCl were collected, concentrated by precipitation. Double-stranded sequencing adaptors with N6 random overhangs ligated to each end; after second-strand synthesis using Taq, material from 200-1000bp was gel-purified and amplified by PCR. Products from 200-800 bp were gel-purified from two successive 2.5% agarose gels or using Ampure XP beads for size-selection.
See extract protocol

tag: strain/genotype

value: cac1_null_rtt106_null [yIW514]


title: Control 3 Lane 1

tag: genotype/variation


title: CAC1_OF_sample

value: Asynchronous culture


title: CHD1_rep1_OF_sample

value: chd1_null [yIW395]


title: Control 2 Lane 1


title: ISW1_CHD1_OF_sample


title: Control 1 Lane 2


title: Control 1 Lane 1


title: ISW1_OF_sample


title: FC/FC3_T30_pool-2

status: Public on Apr 13 2016

city: South Mimms

first: Theo

last: Kantidakis

address: Blanche Lane

department: Clare Hall Laboratories

institute: Francis Crick Institute

description:
NGS-6789
processed data file: mm10_Calls.txt
24 hours exposure to tamoxifen, harvested at day 30

data_processing:
Base Calling and alignment performed using the Torrent Suite 4.2.1
Mpileups generated by samtools 0.1.16
Variant Calling with Varscan 2.3.6 default parameters
Calls combined and manually reviewed and filtered
Genome_build: hg19 and mm10 as appropriate
Supplementary_files_format_and_content: [hg19_Calls.txt, mm10_Calls.txt] Tab delimited text file, binary presence/absence calls

extract_protocol:
gDNA was extracted using Qiagen's QIAamp DNA kit. RNAse treatment was performed.
DNA libraries were prepared according to manufacturer's (Thermo Fischer Scientific) instructions.

value: Immortalized Mouse Embryonic Fibroblast (MEF) cells in which both Mll2 alleles had been targeted by loxP (F/F cells)

tag: treatment

value: 24 hours exposure to tamoxifen

tag: resulting cell type

value: MLL2 FC/FC MEF cells

tag: harvest time

value: day 30


title: F/F3_T30_pool-2

description:
NGS-6787
processed data file: mm10_Calls.txt
Harvested at day 30

value: MLL2 F/F cells


title: Input

tag: age

tag: strain


title: FC/FC3_T30_pool-1

description:
NGS-6788
processed data file: mm10_Calls.txt
24 hours exposure to tamoxifen, harvested at day 30


title: F/F3_T30_pool-1

description:
NGS-6786
processed data file: mm10_Calls.txt
Harvested at day 30


title: FC/FC3_T0_pool-2

description:
NGS-6785
processed data file: mm10_Calls.txt
24 hours exposure to tamoxifen, harvested at day 1

value: day 1


title: FC/FC3_T0_pool-1

description:
NGS-6784
processed data file: mm10_Calls.txt
24 hours exposure to tamoxifen, harvested at day 1


title: F/F3_T0_pool-1

description:
NGS-6782
processed data file: mm10_Calls.txt
Harvested at day 1


title: FC/FC2_T30_pool-1

description:
NGS-6780
processed data file: mm10_Calls.txt
24 hours exposure to tamoxifen, harvested at day 30


title: F/F2_T30_pool-2

description:
NGS-6779
processed data file: mm10_Calls.txt
Harvested at day 30


title: F/F3_T0_pool-2

description:
NGS-6783
processed data file: mm10_Calls.txt
Harvested at day 1


title: F/F2_T30_pool-1

description:
NGS-6778
processed data file: mm10_Calls.txt
Harvested at day 30


title: FC/FC2_T30_pool-2

description:
NGS-6781
processed data file: mm10_Calls.txt
24 hours exposure to tamoxifen, harvested at day 30


title: FC/FC2_T0_pool-2

description:
NGS-6777
processed data file: mm10_Calls.txt
24 hours exposure to tamoxifen, harvested at day 1


title: Control 2 Lane 2

value: Shahdara

value: 7-week-old plants


title: F/F2_T0_pool-1

description:
NGS-6774
processed data file: mm10_Calls.txt
Harvested at day 1


title: DSET_pool-2

description:
NGS-6773
processed data file: hg19_Calls.txt

value: HCT116 cells, MLL2 DSET (Guo et al, 2013)


title: F/F2_T0_pool-2

description:
NGS-6775
processed data file: mm10_Calls.txt
Harvested at day 1


title: CHD1_OF_sample

tag: cell cycle stage


title: DSET_pool-1

description:
NGS-6772
processed data file: hg19_Calls.txt

tag: cell type


title: KO19_pool-1

description:
NGS-6768
processed data file: hg19_Calls.txt

value: HCT116 cells, MLL2 KO, clone 19 (Guo et al, 2012)


title: KO34_pool-2

description:
NGS-6771
processed data file: hg19_Calls.txt

value: HCT116 cells, MLL2 KO, clone 34 (Guo et al, 2012)


title: KO34_pool-1

description:
NGS-6770
processed data file: hg19_Calls.txt


title: Parental_pool-1

description:
NGS-6766
processed data file: hg19_Calls.txt

value: HCT116 cells parental (Guo et al, 2012)


title: nEA-HFSCs_IgG_ctrl

first: Jayhun

last: Lee

state: TX

address: 6431 Fannin St. MSE R222

department: Microbiology and Molecular Genetics

institute: The University of Texas Health Science Center at Houston

data_processing:
FASTX barcode splitter to split multiplexed samples
Trimmomatic tool (v0.22) to clip out adapter sequences
FASTQ quality filter to filter out low quality reads
Bowtie2 to align reads to mm9 genome assembly
BamTools to filter aligned reads
MACS and HOMER used for peak calling
Combining and merging of all MACS peaks from all samples into a customized non-overlapping genomic annotation
Quantification of reads using HOMER or Cuffdiff on pre-annotated genomic location as well as on a customized non-overlapping annotation
Genome_build: mm9
Supplementary_files_format_and_content: Reads aligned with Bowtie2 were filtered with BamTools to generate bam files

source_name: Mouse skin

extract_protocol:
15-20 mice of CD1 x FVB wild-type strain between PD22-25 (early anagen, anagen I-IIIa) and PD38-44 (late catagen, catagen VII-VIII) were used. ~3-4 million bulge and non-bulge cell nuclei were isolated and treated with microccoccal nuclease (MNase) (50U, Affymetrix) (~12min, room temperature) to generate mono-nucleosomal fragments. Isolated chromatin was processed further for immunoprecipitation. Eluted ChIP DNA were used for sequencing library generation.
ChIP DNA was quantified using Quant-iT dsDNA HS reagent (Invitrogen). Nanograms of ChIP DNA for each sample were processed using following steps: 1) end-repair using End-It DNA End-Repair Kit (Epicentre Biotechnologies), 2) addition of single A-base using Klenow Fragment (3’->5’ exo-) (New England Biolabs) and dATP (Invitrogen), 3) ligation of barcoded adapters to A-overhang (Enzymatics), 4) gel purification using SYBR gold (Invitrogen) and low Tm agarose gel, 5) PCR enrichment (13-14 cycles) using Phusion Polymerase (New England Biolabs), 6) PCR purify using AMPure kit (Agencourt), 7) native acrylamide gel purification, 8) PCIAA (Phenol-Chloroform-Isoamylalchol) extraction, and 9) ethanol precipitation. Purified DNA samples were measured in their quality and quantity using bioanalyzer before sequencing at the Cornell University Institute for Biotechnology.

value: CD1 x FVB

tag: gender

value: Male

tag: sorting markers

value: CD34- / α6-integrin+

tag: chip antibody

value: IgG (Cell Signaling)


title: LC-HFSCs_IgG_ctrl

value: CD34+ / α6-integrin+


title: LC-HFSCs_H3K27me3

value: H3K27me3 (Millipore)


title: nEA-HFSCs_H3K9me3

value: H3K9me3 (Millipore and Abcam)


title: LC-HFSCs_H3K9me3


title: EA-HFSCs_IgG_ctrl


title: LC-HFSCs_H3K4me3

value: H3K4me3 (ActiveMotif)


title: FC/FC2_T0_pool-1

description:
NGS-6776
processed data file: mm10_Calls.txt
24 hours exposure to tamoxifen, harvested at day 1

value: Immortalized Mouse Embryonic Fibroblast (MEF) cells in which both Mll2 alleles had been targeted by loxP (F/F cells)

value: 24 hours exposure to tamoxifen

value: MLL2 FC/FC MEF cells


title: EA-HFSCs_H3K27me3


title: EA-HFSCs_H3K9me3


title: H3K4Me3.F/F_NGS-6295

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the mm10 version of the mouse genome assembly using BWA v0.7.10 with default settings.
Mapped reads were extended 3' to a size of 200bp in a strand-specific manner.
Reads Per Kilobase Million (RPKM) scores were calculated for each sample across all Refseq transcripts +/- 500bp.
Peaks were called against a control using MACS v1.4.2 with the following settings: --gsize (mm), --mfold (8,30), --pvalue (0.00001). H3K4Me1, H3K4Me2, H3K4Me3 and gH2AX peaks were called against an H3 control, while RNAPII peaks were called against an IgG control.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM scores calculated for each sample across all Refseq transcripts +/- 500bp (tab-delimited text file).  ChIP-seq peaks called by MACS (bed file).

extract_protocol:
Cells were cross-linked with  1% formaldehyde. Nuclei were extracted in low salt conditions and burst in high salt before shearing the DNA to reduce the size to ~400 bp and performing ChIP with the appropriate antibodies.
DNA libraries were prepared according to Illumina's standard instructions.

value: Immortalised Mouse Embryonic Fibroblast (MEF) cells in which both Mll2 alleles had been targeted by loxP (F/F cells)

value: H3K4Me3 - Abcam, ab8580


title: EA-HFSCs_H3K4me3


title: WT_OF_sample

value: WT [yIW347]

value: Asynchronous culture


title: H3K4Me3.F/F_NGS-6287


title: H3K4Me3.FC/FC_NGS-6299


title: Parental_pool-2

description:
NGS-6767
processed data file: hg19_Calls.txt


title: H3K4Me3.FC/FC_NGS-6291


title: H3K4Me2.F/F_NGS-6294

value: H3K4Me2 - Abcam, ab32356


title: H3K4Me3.FC/FC_NGS-6283


title: KO19_pool-2

description:
NGS-6769
processed data file: hg19_Calls.txt

value: HCT116 cells, MLL2 KO, clone 19 (Guo et al, 2012)


title: H3K4Me3.F/F_NGS-6279


title: H3K4Me2.FC/FC_NGS-6290


title: nEA-HFSCs_H3K4me3

value: CD1 x FVB


title: nEA-HFSCs_H3K27me3

value: Male


title: H3K4Me1.F/F_NGS-6293

value: H3K4Me1 - Abcam, ab8895


title: H3K4Me2.F/F_NGS-6278


title: H3K4Me2.FC/FC_NGS-6298


title: H3K4Me2.FC/FC_NGS-6282

value: H3K4Me2 - Abcam, ab8895


title: H3K4Me1.F/F_NGS-6285


title: H3K4Me1.FC/FC_NGS-6281


title: H3K4Me1.FC/FC_NGS-6297


title: GRO.FC/FC_NGS-4883

data_processing:
library strategy: Gro-Seq
Basecalls performed using CASAVA version 1.4
Reads were aligned to the mm10 version of the mouse genome assembly using BWA v0.7.10 with default settings.
Mapped reads were extended 3' to a size of 200bp in a strand-specific manner.  GRO-seq read strand information was reversed.
Reads Per Kilobase Million (RPKM) scores were calculated for each sample across all Refseq transcripts +/- 500bp.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM scores calculated for each sample across all Refseq transcripts +/- 500bp (tab-delimited text file).

extract_protocol:
Transcription competent nuclei were prepared using the Nuclei Isolation Kit (Sigma) according to manufacturers' recommendations and Run-On was performed as previously described (Core et al., 2008)
Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols


title: GRO.FC/FC_NGS-4884


title: H3K4Me1.F/F_NGS-6277


title: GRO.F/F_NGS-4885

value: MLL2 F/F cells


title: GRO.F/F_NGS-4882


title: H3K4Me2.F/F_NGS-6286


title: H2AX.F/F_NGS-3401

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the mm10 version of the mouse genome assembly using BWA v0.7.10 with default settings.
Mapped reads were extended 3' to a size of 200bp in a strand-specific manner.
Reads Per Kilobase Million (RPKM) scores were calculated for each sample across all Refseq transcripts +/- 500bp.
Peaks were called against a control using MACS v1.4.2 with the following settings: --gsize (mm), --mfold (8,30), --pvalue (0.00001). gH2AX peaks were called against an H3 control, while RNAPII peaks were called against an IgG control.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM scores calculated for each sample across all Refseq transcripts +/- 500bp (tab-delimited text file).  ChIP-seq peaks called by MACS (bed file).

value: anti-H2AX (Abcam, catalog# ab11175)


title: RNAPolII.F/F_NGS-3404

value: monoclonal anti-RNAPII clone 4H8 (Francis Crick Institute)


title: RNAPolII.F/F_NGS-6271


title: H2AX.F/F_NGS-6270


title: H2AX.FC/FC_NGS-6275


title: H2AX.F/F_NGS-3389


title: H2AX.FC/FC_NGS-3407


title: H2AX.FC/FC_NGS-3395


title: 27217 (RR 2 Gy 14 d) rep2

city: Bellaterra

first: Mireia

last: Borràs-Fresneda

address: s/n

country: Spain

institute: Universitat Autònoma de Barcelona

description: irradiated 14 d

data_processing:
Illumina Casava 1.8 software used for basecalling
Sequenced reads were trimmed in order to improve the percentage of mapped reads. Then, reads were aligned to the hg19 using TopHat2 splice-junction mapper (version 2.1.0)
Mapped reads were categorised with htseq-count (HTseq version 0.6.1). Deffault settings were applied with the exception of the overlap resolution mode, where the intersection-noempty mode was used
Normalisation was performed using the default method for edgeR (version 3.10.2), then a matrix was designed and the dispersion values were estimated using Cox-Reid profile-adjusted likelihood method
The generalised linear model likelihood ratio test was used to determine differential expression also with edgeR package. Fold-changes were reported as the log (base 2) of normalized count abundance of the irradiated samples divided by count abundance for the sham-irradiated samples. P values for each gene were then corrected for multiple comparisons using Benjamini & Hochberg false discovery rate
Genome_build: hg19
Supplementary_files_format_and_content: csv files that include reads counts for each sample and different expression results for irradiated versus sham-irradiated samples

source_name: lymphocytes

extract_protocol:
Total RNA was extracted using the SPLIT RNA Extraction kit. RNA concentration and purity for each sample were verified as well as RNA integrity
Libraries were prepared according the Lexogen Quantseq 3’ mRNA-Seq Library Prep kit for Illumina following the manufacturer's instructions

value: lymphoblastoid cell line

tag: cell line

value: radioresistant (RR)

value: irradiated

tag: time point


title: RNAPolII.FC/FC_NGS-6276

value: Immortalized Mouse Embryonic Fibroblast (MEF) cells in which both Mll2 alleles had been targeted by loxP (F/F cells)

value: 24 hours exposure to tamoxifen

value: MLL2 FC/FC MEF cells


title: 27216 (RS 2 Gy 14 d) rep2

description: irradiated 14 d

value: radiosensitive (RS)


title: 27215 (RR 0 Gy 14 d) rep2

description: sham-irradiated 14 d

value: sham-irradiated


title: RNAPolII.FC/FC_NGS-3398


title: IgG.F/F_NGS-3399

value: anti-IgG (Sigma, catalog# M8642)


title: IgG.F/F_NGS-6267


title: IgG.F/F_NGS-3387


title: 27212 (RS 2 Gy 24 h) rep2

description: irradiated 24 h


title: H3K4Me1.FC/FC_NGS-6289

value: Immortalised Mouse Embryonic Fibroblast (MEF) cells in which both Mll2 alleles had been targeted by loxP (F/F cells)


title: RNAPolII.F/F_NGS-3392


title: 27213 (RR 2 Gy 24 h) rep2

description: irradiated 24 h


title: 27211 (RR 2 Gy 4 h) rep2

description: irradiated 4h


title: IgG.FC/FC_NGS-6272


title: 27209 (RR 0 Gy 4 h) rep2

description: sham-irradiated 4 h

value: 4 h


title: IgG.FC/FC_NGS-3405


title: RNAPolII.FC/FC_NGS-3410


title: 27214 (RS 0 Gy 14 d) rep2

description: sham-irradiated 14 d


title: H3.F/F_NGS-6296

value: anti-H3 (Abcam, catalog# ab1791)


title: H3.F/F_NGS-3403


title: H3.F/F_NGS-3391


title: H3.F/F_NGS-6280


title: H3.FC/FC_NGS-6300


title: 27203 (RR 2 Gy 24 h) rep1

description:
irradiated 24 h
Differential_expression_RR_14d.csv


title: 27205 (RR 0 Gy 14 d) rep1

description: sham-irradiated 14 d


title: RTT106_OF_sample

value: rtt106_null [yIW401]

value: Asynchronous culture


title: SX7

city: Beibei

first: Zhi-Liang

last: Zheng

state: Chongqing

address: 15 Ganjuchun

department: Citrus Research Institute

institute: Southwest University

description: Rep. 3

data_processing:
Basecalls performed by BGI company.
Raw data were preprocessed by removing adaptor sequences and/or low quality reads, resulting in clean reads data.
These clean reads data were then mapped to the sweet orange reference sequences (version 2.0) published in 2013
Genome_build: Sweet orange version 2.0. http://citrus.hzau.edu.cn/orange/  Publication of reference genome: http://www.ncbi.nlm.nih.gov/pubmed/23179022
Supplementary_files_format_and_content: excel files were generated with geneID and raw count.

organism: Citrus sinensis

source_name: Fruit tissue

growth_protocol: Field grown trees

extract_protocol:
Fruits were harvested, and total RNA was extracted using the ethanol- and LiCl-based protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fruit

tag: fruit stage

value: 142 DPA

tag: cultivar

value: Xinhui

tag: fruit acidity

value: Acidic


title: H3.FC/FC_NGS-6292


title: 27204 (RS 0 Gy 14 d) rep1

description: sham-irradiated 14 d

value: lymphoblastoid cell line


title: 27208 (RS 0 Gy 4 h) rep2

description: sham-irradiated 4 h


title: 27210 (RS 2 Gy 4 h) rep2

description: irradiated 4 h

value: irradiated


title: IgG.FC/FC_NGS-3393

value: Immortalized Mouse Embryonic Fibroblast (MEF) cells in which both Mll2 alleles had been targeted by loxP (F/F cells)


title: 27202 (RS 2 Gy 24 h) rep1

description:
irradiated 24 h
Differential_expression_RS_14d.csv


title: H3.FC/FC_NGS-6284

value: 24 hours exposure to tamoxifen


title: 27200 (RS 2 Gy 4 h) rep1

description:
irradiated 4 h
Differential_expression_RS_24h.csv


title: SX5

description: Rep. 2

tag: tissue


title: SX4

description: Rep. 1


title: H3.FC/FC_NGS-3409

value: MLL2 FC/FC MEF cells


title: 27201 (RR 2 Gy 4 h) rep1

description:
irradiated 4h
Differential_expression_RR_24h.csv

value: radioresistant (RR)