title: APH/FLAG Ab-IP

value: APH treated

value: FLAG Ab-IPed


title: Dnmt3a WT rep3

status: Public on Jan 19 2018

type: SRA

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

country: USA

institute: NIEHS

description:
Dnmt3a_WT.mapped_depth.bigWig
Dnmt3a_WT.pctMeth.bigWig

library_source: genomic

data_processing:
Raw sequenced reads were filtered to retain only read pairs with average base quality score of at least 20 for each read.  Sequenced reads were trimmed to remove the final base from the 3' end.
Reads were mapped against mm9 reference genome with Bismark v0.14.0 (parameters: -X 10000 --non_bs_mm -n 2 -l 50 -e 70 --chunkmbs 1024), using Bowtie v0.12.8 as the underlying alignment tool. PE150 reads unmapped at full length were trimmed to PE75 and re-submitted to Bismark with the previously described parameters.
All mapped hits from the same animal were concatenated, then duplicates removed with the Bismark deduplication script (deduplicate_bismark_alignment_output.pl).
Mapped reads were then processed as follows:  1. Separated by source strand (plus or minus).  2. Clipped positions with positional methylation bias (identified using bismark_methylation_extractor, --mbias_only option).  3.  Trimmed redundant mapped bases from overlapping mapped reads in a read pair to avoid bias in quantification of methylation status.
Data from replicate animals were combined with MergeSamFiles.jar from the Picard suite (v1.119).
The CpG context of genomic cytosines was considered confirmed if at least 95% of mapped bases at the N+1 position were 'G' with a total depth of at least 5; both the plus and minus strand data were required to pass these criteria. Assessment of cytosine context was performed after merging all animals in the study.
Percent methylation at each genomic cytosine was calculated as methylated cytosine bases / total cytosine bases; reciprocal CpG sites (i.e. plus and minus strand) were combined for these calculations. Sites for which the CpG context of the reference cystosine could not be confirmed were excluded.
Mapped reads were converted to aggregate coverage by BEDtools v2.24.0 genomeCoverageBed (to generate bedGraph files) and then UCSC command-line utilities bedGraphToBigWig (to generate bigWig files).
DMRs were identified via MOABS v1.3.2 using default parameters except ‘--minNominalDif=0.2’.
Genome_build: mm9
Supplementary_files_format_and_content: Aggregate coverage by mapped reads (merged for all 3 replicates, both strands); format = bigWig.
Supplementary_files_format_and_content: Percent methylation at single-base resolution; calculations are done with merged replicate animals & combined strand information. Format = bigWig.
Supplementary_files_format_and_content: Differentially methylated regions (DMRs) between null and WT. Format = BED.

molecule: genomic DNA

organism: Mus musculus

source_name: naïve splenic B cells

growth_protocol: Animals were housed in a specific pathogen-free environment at the National Institute of Environmental Health Sciences (NIEHS). All animal experiments were approved by the NIEHS Institutional Animal Care and Use Committee and were performed according to NIH guidelines for the care and use of laboratory animals.

extract_protocol:
Spleen was harvested, and B220+IgD++GL7- B cells were sorted to a purity of 98-99%. Using the Trizol reagent, genomic DNA was extracted from the organic phase and further purified by performing Phenol-chloroform extractions.
For each sample, 1500 ng intact genomic DNA and 1.5 ng unmethylated lambda DNA (Promega) were fragmented using a Covaris S220 Focused-ultrasonicator. Sequencing libraries were prepared using the NEXTflex Bisulfite-Seq Kit (BIOO Scientific) with a starting input of 1000 ng and using agarose gel size selection. Bisulfite conversion was performed using an EpiTect Bisulfite Kit (Qiagen). Bisulfite converted DNA product was PCR amplified for 10 cycles using KAPA HiFi Uracil+ Ready Mix (Kapa Biosystems). After library construction, all six libraries were equally multiplexed and sequenced using the Illumina NextSeq500 platform in paired-end format for 76 or 151 cycles at the NIEHS Epigenomics Core Laboratory.

tag: strain

value: B6;129 (mixed background of C57BL/6 and 129)

tag: genotype

tag: Sex

value: male

tag: age

value: 2-4 months

tag: tissue

value: spleen

tag: cell type

value: naive B cells

tag: markers

tag: stimulus


title: Dnmt3a WT rep1


title: DMSO/FLAG Ab-IP

status: Public on Jan 20 2018

city: Kyoto

first: Masamichi

last: Ishiai

state: Kyoto

address: Yoshidakonoe-cho, Sakyo-ku

department: Radiation Biology Center

country: Japan

institute: Kyoto University

data_processing:
Basecalls performed using Illumina CASAVA v1.8.
Adapter sequences were trimmed using cutadapt v1.1 with -n 2 option.
Reads with many (>80%) low-quality (score <20) bases were discarded. Low quality (score <20) bases were trimmed from both ends of the reads. Reads shorter than 20nt were discarded.
The filter-passed reads were aligned to the human genome hg19 using bowtie v0.12.7 with --maxins 600 --seedlen 20 --all options.
Peak calling was performed using MACS v1.4.2 with the threshold of p-value < 1e-5. The detected peaks were annotated using SnpEff v3.2.
Genome_build: hg19
Supplementary_files_format_and_content: wig files including fragment pileup were created using MACS v1.4.2 with a option -w.

organism: Homo sapiens

source_name: U2OS cells expressing FANCD2-3xFLAG

growth_protocol: U2OS cells were cultured in DMEM supplemented with 10% FCS in 5% CO2 at 37 degree.

extract_protocol:
Lysates were clarified from sonicated nuclei and FANCD2-DNA complexes were isolated with antibody.
After franmentation to 200 bp using covaris, DNA libraries were prepared using the NEBNext ChIP-Seq library prep reagent set for Illumina (NEB #E6200) and the NEBNext multiplex oligos for Illumina (NEB #E7335 and #E7500) according to the instructions. Adapter ligated DNA was PCR amplified for 15 cycles. Libraries were sequenced on the Illumina Genome Analyzer IIx following the manufacturer's protocols (75 bp paried-end run).

treatment_protocol: Cells are treated at 0.4 micro M (for APH), or untreated (for DMSO) for 24 hours.

tag: treatment

value: DMSO control

tag: antibody


title: Dnmt3a null rep3

description:
Dnmt3a_null.mapped_depth.bigWig
Dnmt3a_null.pctMeth.bigWig


title: Dnmt3a null rep1


title: APH/normal IgG-IP

value: normal mouse IgG-Iped


title: DMSO/normal IgG-IP

value: DMSO (solvent) control


title: Sample_53_AICDAhigh_DLBCL_ERRBS5

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
CPM were obtained using Rsubread
ERRBS reads were filtered from the adapter sequences using FAR software and aligned to genome using the bismark alignment software, retaining uniquely aligning reads with maximum of 2 directional mismatches
methylCall files were generated using methylKit
Genome_build: hg19

source_name: human DLBCL primary case

extract_protocol: DNA was extracted using Qiagen Puregene kit protocol; Libraries were prepared using RRBS and ERRBS as described in manuscript

value: ABC-DLBCL


title: Sample_55_AICDAhigh_DLBCL_ERRBS7


title: Sample_54_AICDAhigh_DLBCL_ERRBS6


title: Sample_58_AICDAhigh_DLBCL_ERRBS10

value: GCB-DLBCL


title: Sample_57_AICDAhigh_DLBCL_ERRBS9


title: Sample_51_AICDAhigh_DLBCL_ERRBS3


title: Sample_50_AICDAhigh_DLBCL_ERRBS2


title: Sample_52_AICDAhigh_DLBCL_ERRBS4


title: Sample_48_AICDAlow_DLBCL_ERRBS19


title: Sample_49_AICDAhigh_DLBCL_ERRBS1


title: Sample_46_AICDAlow_DLBCL_ERRBS17


title: Sample_47_AICDAlow_DLBCL_ERRBS18


title: Sample_45_AICDAlow_DLBCL_ERRBS16


title: Primary human melanocytes, Keap1 siRNA-treated

city: Seoul

first: Sang Ho

last: Oh

address: 50-1 Yonsei-ro

department: Dermatology

country: South Korea

institute: Yonsei University College of Medicine

description:
PHM_Keap1_siRNA
Gene expression data from primary human melanocytes treated with Keap1 siRNA.

library_source: transcriptomic

data_processing:
Reads were quality trimmed and filtered using the NGS QC toolkit v2.3 to remove reads containing low-quality bases.
After preprocessing, the RNA sequenced reads were mapped to the human genome using RSEM with bowtie2 v2.0.0-beta7.
FPKM (fragments per kilobase of exon per million fragments mapped) for RNA-Seq were calculated using RSEM.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Wig files were generated using RSEM.

molecule: total RNA

source_name: Primary human melanocytes, Keap1 siRNA

growth_protocol: Melanocytes were incubated (37°C, humidified 5% CO2) in MGM-4 growth media (Lonza, Walkerville, MD, USA), using cells from passages 3-8 for experimentation.

extract_protocol:
Total cellular RNA was isolated using an RNeasy Plus Mini Kit (QIAGEN, Valencia, USA).
An RNA sequencing library was prepared using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: To suppress Keap1, primary human melanocytes were transfected (TransIT-TKO reagent; Mirus Bio, Madison, WI, USA) as specified by the manufacturer with 10 nM of siRNA (Bioneer Corp, Daejeon, South Korea). An equivalent amount of scrambled siRNA was used as a negative control.

tag: gender

value: Male

value: 12 years

value: Foreskin

value: Melanocytes

tag: passages

value: Keap1 siRNA


title: Sample_43_AICDAlow_DLBCL_ERRBS14


title: Sample_44_AICDAlow_DLBCL_ERRBS15


title: Sample_41_AICDAlow_DLBCL_ERRBS12


title: Sample_42_AICDAlow_DLBCL_ERRBS13


title: Sample_40_AICDAlow_DLBCL_ERRBS11


title: Sample_39_AICDAlow_DLBCL_ERRBS10


title: Dnmt3a null rep2


title: Sample_37_AICDAlow_DLBCL_ERRBS8


title: Sample_56_AICDAhigh_DLBCL_ERRBS8


title: Sample_36_AICDAlow_DLBCL_ERRBS7

value: uncharacterized DLBCL


title: Sample_34_AICDAlow_DLBCL_ERRBS5


title: Sample_35_AICDAlow_DLBCL_ERRBS6


title: Sample_33_AICDAlow_DLBCL_ERRBS4


title: Sample_31_AICDAlow_DLBCL_ERRBS2


title: Sample_30_AICDAlow_DLBCL_ERRBS1


title: Sample_32_AICDAlow_DLBCL_ERRBS3


title: Sample_26_AICDAhigh_DLBCL_RNAseq7

extract_protocol: RNA was extracted using TruSeq kit protocol; Libraries were prepared as described in manuscript.


title: Sample_27_AICDAhigh_DLBCL_RNAseq8


title: Sample_29_AICDAhigh_DLBCL_RNAseq10


title: Sample_28_AICDAhigh_DLBCL_RNAseq9


title: Sample_24_AICDAhigh_DLBCL_RNAseq5


title: Sample_23_AICDAhigh_DLBCL_RNAseq4


title: Sample_21_AICDAhigh_DLBCL_RNAseq2


title: Sample_25_AICDAhigh_DLBCL_RNAseq6


title: Sample_38_AICDAlow_DLBCL_ERRBS9


title: Sample_22_AICDAhigh_DLBCL_RNAseq3


title: Sample_20_AICDAhigh_DLBCL_RNAseq1


title: Sample_19_AICDAlow_DLBCL_RNAseq19


title: Control rep-1

status: Public on Jan 22 2018

city: Houston

first: Samuel

middle: Emerson

last: Harvey

state: TEXAS

address: One Baylor Plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

data_processing:
Paired-end RNA-seq reads for each sample were mapped to the human genome (GRCh37) and transcriptome (Gencode v24 backmapped to GRCh37) using STAR v2.5.3a using the following command: STAR --runThreadN 16 --alignEndsType EndToEnd –outSAMtype BAM SortedByCoordinate --readFilesCommand zcat
Gene expression quantification and differential gene expression was conducted for all replicates cuffdiff v2.2.1 using the following command: cuffdiff -p 8 –max-bundle-frags 1000000000 --library-type fr-firststrand -o output_dir gencode.v24lift37.annotation.gtf
Alternative splicing quantification and differential analysis was conducted for all replicates using rMATS v3.2.5 using the following command: python RNASeq-MATS.py -gtf gencode.v24lift37.annotation.gtf -o output_dir  -t paired -len 100 -analysis U -libType fr-firststrand
Genome_build: GRCh37
Supplementary_files_format_and_content: Unfiltered FPKM values and log2FC are provided in cuffdiff outputted tab-delimited gene_exp.diff file titled shNS_and_shhnRNPF.cuffdiff.gene_diff.txt.gz. Unfiltered alternative splicing output from rMATS for skipped exons (SE) using only junction counts are provided in the tab-delimited file shNS_and_shhnRNPF.rmats.se.junction_count_only.txt.gz

source_name: HMLE cells

growth_protocol: The maintenance of immortalized human mammary epithelial cells HMLE was conducted as previously described (Brown et al., 2011)

extract_protocol:
Total RNA was extracted using standard Trizol extraction procedures
Stranded paired-end polyA-purified RNA sequencing libraries were prepared using Illumina TruSeq protocols

treatment_protocol: Cell lines stably expressing the relevant shRNA were generated using lentiviral vectors using standard infection protocols

value: Immortalized breast epithelial cells

tag: cell line

value: HMLE

value: Non-specific shRNA treated


title: hnRNPF KD rep-2

value: hnRNPF shRNA treated


title: Sample_14_AICDAlow_DLBCL_RNAseq14


title: Sample_18_AICDAlow_DLBCL_RNAseq18


title: Sample_17_AICDAlow_DLBCL_RNAseq17


title: Sample_15_AICDAlow_DLBCL_RNAseq15


title: Sample_12_AICDAlow_DLBCL_RNAseq12


title: Sample_11_AICDAlow_DLBCL_RNAseq11


title: Sample_13_AICDAlow_DLBCL_RNAseq13


title: Sample_16_AICDAlow_DLBCL_RNAseq16


title: Sample_9_AICDAlow_DLBCL_RNAseq9


title: Sample_8_AICDAlow_DLBCL_RNAseq8


title: HEC-1-A shControl-input

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: no IP (input RNA)

data_processing:
For m6A-seq, reads were aligned to the reference genome (hg38) using Tophat (v2.0.14, ref) with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks, the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. edgeR was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median reads count of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c) and median reads count of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c).
Genome_build: hg38
Supplementary_files_format_and_content: m6A peaks bed

molecule: polyA RNA

source_name: HEC-1-A cell line

growth_protocol: Stable HEC-1-A was grown in McCoy’s 5A medium (Gibco, 16600) supplemented with 10% FBS (Gibco), 1% Penicillin-Streptomycin (Gibco, 15140), and 1ug/ml puromycin

extract_protocol:
Tissues were homogenized in Trizol reagent with a Tissure-Tearor. Total RNA were extracted using manufacturer’s instructions.Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols. Cell line total RNA was isolated from stable cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.
TruSeq Small RNA Sample Preparation Kit (Illumina)

treatment_protocol: we used CRISPR-Cas9 genome editing system from IDT to generate a METTL14+/- cell line in HEC-1-A, then transfected the METTL14+/- cell lines with a PiggyBac Transposon System (SBI) encoding FLAG-tagged wilytype METTL14 or Flag-tagged METTL14(R298P) to generate wt/mu METTL14 stable cell line; we used TRC Lentiviral Human shRNA systems encoding a control shRNA or shRNA targeting METTL3 to generate shControl or shMETTL3 stable HEC-1-A cell line

value: HEC-1-A knockdown control stable cell line

value: no IP (input RNA)


title: Sample_7_AICDAlow_DLBCL_RNAseq7


title: Sample_6_AICDAlow_DLBCL_RNAseq6


title: Sample_5_AICDAlow_DLBCL_RNAseq5


title: Sample_3_AICDAlow_DLBCL_RNAseq3


title: Sample_2_AICDAlow_DLBCL_RNAseq2


title: Sample_4_AICDAlow_DLBCL_RNAseq4


title: ChrX_male_APH_ExpC

city: Heidelberg

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

country: Germany

institute: German Cancer Research Center

description:
HTGTS
ChrX_Male_APH.tlx

data_processing:
Library strategy: LAM-HTGTS
HTGTS Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
HTGTS reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
Best-path searching algorithm was used to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
The bait alignment must extend 10 nucleotides past the primer to avoid possible mispriming events and other artifacts
Potential duplicates were removed by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Reads with greater than 30bp gap between bait and prey sequences were filtered out.
Additional stringency was applied to post-filtered HTGTS junctions: reads with shorter than 50bp bait sequences were eliminated from downstream analysis due to potential artifacts; only one unique junctions at each location were preserved for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: HTGTS: tab delimited text files (translocation junctions) contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); cigar for bait sequence (B_Cigar); cigar for prey sequence (Cigar); the entire stitched paired end read sequence (Seq); 10 bp sequence around the junction, 5bp from bait and 5bp from prey (J_seq); barcode used for demultiplex (Barcode); number of unaligned sequences (unaligned);  pass (0) or fail (1) the “Bait only” filter (baitonly); pass (0) or fail (1) the “Uncut” filter (uncut); number of nucleotides not aligned to the bait (misprimed); pass (0) or fail (1) the “Frequent cutter” filter (freqcut); number of nucleotides between bait and prey sequences (largegap); pass (0) or fail (1) the “Map quality” filter (mapqual); pass (0) or fail (1) the “Breaksite” filter (breaksite); pass (0) or fail (1) the “Sequential” filter (sequential); pass (0) or fail (1) the “Repeat sequence” filter (repeatseq); number of duplicates in this library (duplicate); and the experiment associated with the read (note).

source_name: Neural stem/progenitor cells

growth_protocol: NSPCs were isolated and cultured as described in Wei et al. 2017 and Wei et al., 2016

extract_protocol:
Genomic DNA was extracted overnight at 55 degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH 8.0, 0.2 mg/mL proteinase K, prior to DNA fragmentation
HTGTS: LAM-PCR-mediated HTGTS (Frock et al., 2015 and Hu et al., 2016; see manuscript for details)

treatment_protocol: See details in Wei et al.; treatment of samples is indicated in "characteristics: treatment" column

value: APH

tag: bait dsb


title: ChrX_male_DMSO_ExpB

description:
HTGTS
ChrX_Male_DMSO.tlx

value: DMSO


title: ChrX_male_DMSO_ExpA

description:
HTGTS
ChrX_Male_DMSO.tlx


title: ChrX_male_APH_ExpB

description:
HTGTS
ChrX_Male_APH.tlx


title: ChrX_female_APH_ExpC

description:
HTGTS
ChrX_Female_APH.tlx


title: ChrX_male_APH_ExpA

description:
HTGTS
ChrX_Male_APH.tlx


title: ChrX_female_DMSO_ExpB

description:
HTGTS
ChrX_Female_DMSO.tlx


title: ChrX_female_DMSO_ExpA

description:
HTGTS
ChrX_Female_DMSO.tlx


title: Chr19_DMSO_ExpB

description:
HTGTS
Chr19_DMSO.tlx


title: ChrX_female_DMSO_ExpC

description:
HTGTS
ChrX_Female_DMSO.tlx


title: Sample_10_AICDAlow_DLBCL_RNAseq10


title: Chr19_DMSO_ExpA

description:
HTGTS
Chr19_DMSO.tlx


title: Chr19_DMSO_ExpC

description:
HTGTS
Chr19_DMSO.tlx


title: Sample_1_AICDAlow_DLBCL_RNAseq1


title: Chr18_DMSO_ExpC

description:
HTGTS
Chr18_DMSO.tlx


title: Chr18_DMSO_ExpA

description:
HTGTS
Chr18_DMSO.tlx


title: Chr18_DMSO_ExpB

description:
HTGTS
Chr18_DMSO.tlx


title: Chr19_APH_ExpA

description:
HTGTS
Chr19_APH.tlx


title: Chr18_APH_ExpC

description:
HTGTS
Chr18_APH.tlx


title: Chr17_DMSO_ExpE

description:
HTGTS
Chr17_DMSO.tlx


title: Chr17_DMSO_ExpD

description:
HTGTS
Chr17_DMSO.tlx


title: ChrX_female_APH_ExpB

description:
HTGTS
ChrX_Female_APH.tlx


title: Chr18_APH_ExpA

description:
HTGTS
Chr18_APH.tlx


title: Chr17_DMSO_ExpC

description:
HTGTS
Chr17_DMSO.tlx


title: ChrX_female_APH_ExpA

description:
HTGTS
ChrX_Female_APH.tlx


title: ChrX_male_DMSO_ExpC

description:
HTGTS
ChrX_Male_DMSO.tlx


title: Chr17_DMSO_ExpF

description:
HTGTS
Chr17_DMSO.tlx


title: Chr17_DMSO_ExpB

description:
HTGTS
Chr17_DMSO.tlx


title: Chr17_APH_ExpF

description:
HTGTS
Chr17_APH.tlx


title: Chr17_APH_ExpB

description:
HTGTS
Chr17_APH.tlx


title: Chr17_APH_ExpD

description:
HTGTS
Chr17_APH.tlx


title: Chr17_APH_ExpC

description:
HTGTS
Chr17_APH.tlx


title: Chr14_APH_ExpC

description:
HTGTS
Chr14_APH.tlx


title: Chr14_DMSO_ExpB

description:
HTGTS
Chr14_DMSO.tlx


title: Chr17_APH_ExpA

description:
HTGTS
Chr17_APH.tlx


title: Chr17_DMSO_ExpA

description:
HTGTS
Chr17_DMSO.tlx


title: Chr17_APH_ExpE

description:
HTGTS
Chr17_APH.tlx


title: Chr14_APH_ExpB

description:
HTGTS
Chr14_APH.tlx


title: Chr14_DMSO_ExpA

description:
HTGTS
Chr14_DMSO.tlx


title: Chr14_DMSO_ExpC

description:
HTGTS
Chr14_DMSO.tlx


title: Chr18_APH_ExpB

description:
HTGTS
Chr18_APH.tlx


title: Chr14_APH_ExpA

description:
HTGTS
Chr14_APH.tlx


title: Chr13_DMSO_ExpB

description:
HTGTS
Chr13_DMSO.tlx


title: Chr13_DMSO_ExpD

description:
HTGTS
Chr13_DMSO.tlx


title: Chr13_DMSO_ExpC

description:
HTGTS
Chr13_DMSO.tlx


title: Chr13_DMSO_ExpA

description:
HTGTS
Chr13_DMSO.tlx


title: Chr13_DMSO_ExpE

description:
HTGTS
Chr13_DMSO.tlx


title: Chr13_APH_ExpC

description:
HTGTS
Chr13_APH.tlx


title: Chr13_APH_ExpB

description:
HTGTS
Chr13_APH.tlx


title: Chr11_DMSO_ExpC

description:
HTGTS
Chr11_DMSO.tlx


title: Chr11_APH_ExpC

description:
HTGTS
Chr11_APH.tlx


title: Chr10_APH_ExpC

description:
HTGTS
Chr10_APH.tlx


title: Chr10_APH_ExpB

description:
HTGTS
Chr10_APH.tlx


title: Chr10_DMSO_ExpA

description:
HTGTS
Chr10_DMSO.tlx


title: Chr10_DMSO_ExpC

description:
HTGTS
Chr10_DMSO.tlx


title: Chr11_APH_ExpB

description:
HTGTS
Chr11_APH.tlx


title: Chr11_APH_ExpA

description:
HTGTS
Chr11_APH.tlx


title: Chr10_DMSO_ExpB

description:
HTGTS
Chr10_DMSO.tlx


title: Chr9_DMSO_ExpA

description:
HTGTS
Chr9_DMSO.tlx


title: Chr10_APH_ExpA

description:
HTGTS
Chr10_APH.tlx


title: Chr9_APH_ExpB

description:
HTGTS
Chr9_APH.tlx


title: Chr9_APH_ExpC

description:
HTGTS
Chr9_APH.tlx


title: Chr13_APH_ExpE

description:
HTGTS
Chr13_APH.tlx


title: Chr9_DMSO_ExpB

description:
HTGTS
Chr9_DMSO.tlx


title: Chr13_APH_ExpD

description:
HTGTS
Chr13_APH.tlx


title: Chr8_DMSO_ExpC

description:
HTGTS
Chr8_DMSO.tlx


title: Chr9_APH_ExpA

description:
HTGTS
Chr9_APH.tlx


title: Chr8_DMSO_ExpB

description:
HTGTS
Chr8_DMSO.tlx


title: Chr13_APH_ExpA

description:
HTGTS
Chr13_APH.tlx


title: Chr11_DMSO_ExpB

description:
HTGTS
Chr11_DMSO.tlx


title: Chr11_DMSO_ExpA

description:
HTGTS
Chr11_DMSO.tlx


title: Chr8_DMSO_ExpA

description:
HTGTS
Chr8_DMSO.tlx


title: Chr8_APH_ExpC

description:
HTGTS
Chr8_APH.tlx


title: Chr9_DMSO_ExpC

description:
HTGTS
Chr9_DMSO.tlx


title: TAB-seq_ventral_DG_enriched_environment_rep4

city: San Diego

first: Eran

last: Mukamel

state: United States

address: 9500 Gilman Dr.

department: Cognitive Science

institute: University of California-San Diego

data_processing:
Library strategy: TAB-Seq
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, and TAB-seq datasets were performed as described in Zhang et al., 2017 (in submission)
TAB-seq: Adapters were trimmed using Trim Galore v0.4.0
TAB-seq: TAB-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/ and Lister et al., 2013) for alignment and hmC calling
Genome_build: mm10
Supplementary_files_format_and_content: tab delimed text files of gene expression counts estimated using STAR version STAR_2.5.1b_modified
Supplementary_files_format_and_content: tab delimited text files of gene expression levels estimated using RSEM v1.2.30
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
Supplementary_files_format_and_content: tab delimited text files of hydroxymethylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for hydroxymethylated cytosines)

source_name: whole tissue from ventral dentate gyrus in mouse

growth_protocol: All procedures were performed in accordance with the guidelines established by the Canadian Council on Animal Care (CCAC) with protocols approved by the McGill University Facility Animal Care Committee (FACC). Male C57/Bl/6 mice were bred at the Douglas Institute to avoid transportation stress. Mice were weaned on postnatal day 22, and siblings were assigned to either standard or enriched housing conditions. Standard housed animals were raised three male mice from different mothers in a 30 x 18 cm cage. The enriched group contained 12 male mice, housed in a larger rectangular plexiglass cage (78 x 86 cm) with a plexiglass top, which contained a variety of toys such as running wheels, a bridge, and novel objects. Toys were changed weekly. For both conditions, food and water were ad libitum, and bedding was changed biweekly, cleaning the cages with a Peroxyguard solution. Animals remained in the respective housing conditions for eight weeks. Mice were sacrificed on age day 80 (post sexual maturation) between 10:30 am to 12 pm.

extract_protocol:
Tissue collection consisted of rapid removal of the brain, followed by flash freezing and storage at -80C. Frozen brains were sliced coronally at 200 µm thickness until reaching bregma -2.30. The brains were then removed from mounting position, rotated, and remounted to the mounting position for horizontal slicing ventral dentate tissue. Horizontal sections were sliced from interaural 3.24 mm to 0.92 mm26. A 300 µm diameter puncher was used to punch dorsal and ventral dentate gyrus region separately. RNA and DNA extraction were performed from the same sample using Qiagen Allprep DNA/RNA Mini kit (Qiagen, Cat# 80204.).  We performed on-column DNase I treatment during RNA extraction and on-column RNaseA treatment during DNA extraction. RNA was examined by Bioanalyzer 2100 (Agilent technologies, Santa clara, USA).
TAB-seq: DNA from the same samples was separated for TAB-seq and MethylC-seq library preparation. Protection and oxidation portions of library preparation were performed in-house using the Wisegene kit as described in Yu et al6. Three spike-in control DNAs, lambda DNA (Cat# D1501, Promega), 5mC (Cat# S001, Wisegene) and 5hmC (Cat# S002, Wisegene) were added to each sample (2.5 µg of total DNA) before DNA shearing, in order to evaluate the bisulfite conversion efficiency, the protection rate of 5 hmC, and the oxidation rate of TET. Bisulfite conversion was then performed at the Genome Quebec Innovation Centre on the processed TAB-seq sample, as well as 1 µg of DNA for the MethylC-seq library. Methylated and unmethylated DNA sets (Cat# D5017, pUC19 DNA set, Zymo research) were added as spike-in controls (2 ng spike-in control in 1 ug DNA) to evaluate bisulfite conversion efficiency. The whole genome bisulfite sequencing (WGBS) libraries were prepared using NimbleGen SeqCap Epi Enrichment System (Cat# 07145519001, Roche NimbleGen, Inc.). Library amplification was done using KAPA HiFi Hotstart Uracil + DNA polymerase (Cat# KK2802, Kapa Biosystems).

tag: housing condition

value: enriched environment

value: brain (dentate gyrus of the hippocampus)

value: 80 days

value: male


title: TAB-seq_ventral_DG_enriched_environment_rep3


title: TAB-seq_ventral_DG_enriched_environment_rep5


title: TAB-seq_ventral_DG_enriched_environment_rep1


title: Chr8_APH_ExpB

description:
HTGTS
Chr8_APH.tlx


title: Chr7_DMSO_ExpC

description:
HTGTS
Chr7_DMSO.tlx


title: Chr8_APH_ExpA

description:
HTGTS
Chr8_APH.tlx


title: Chr7_DMSO_ExpB

description:
HTGTS
Chr7_DMSO.tlx


title: TAB-seq_dorsal_DG_enriched_environment_rep3

source_name: whole tissue from dorsal dentate gyrus in mouse


title: TAB-seq_dorsal_DG_enriched_environment_rep5


title: TAB-seq_dorsal_DG_enriched_environment_rep4


title: TAB-seq_dorsal_DG_enriched_environment_rep2


title: Chr7_DMSO_ExpA

description:
HTGTS
Chr7_DMSO.tlx


title: Chr7_APH_ExpB

description:
HTGTS
Chr7_APH.tlx


title: TAB-seq_ventral_DG_standard_housing_rep5

value: standard housing


title: TAB-seq_dorsal_DG_enriched_environment_rep1


title: Chr7_APH_ExpC

description:
HTGTS
Chr7_APH.tlx


title: TAB-seq_ventral_DG_standard_housing_rep4


title: TAB-seq_ventral_DG_enriched_environment_rep2


title: TAB-seq_ventral_DG_standard_housing_rep2


title: Chr7_APH_ExpA

description:
HTGTS
Chr7_APH.tlx


title: TAB-seq_ventral_DG_standard_housing_rep3


title: TAB-seq_ventral_DG_standard_housing_rep1


title: TAB-seq_dorsal_DG_standard_housing_rep5


title: TAB-seq_dorsal_DG_standard_housing_rep4


title: Chr6_APH_ExpA

description:
HTGTS
Chr6_APH.tlx


title: Chr6_DMSO_ExpB

description:
HTGTS
Chr6_DMSO.tlx


title: Chr6_DMSO_ExpC

description:
HTGTS
Chr6_DMSO.tlx


title: Chr5_DMSO_ExpC

description:
HTGTS
Chr5_DMSO.tlx


title: Chr6_DMSO_ExpA

description:
HTGTS
Chr6_DMSO.tlx


title: Chr6_APH_ExpC

description:
HTGTS
Chr6_APH.tlx


title: Chr5_DMSO_ExpB

description:
HTGTS
Chr5_DMSO.tlx


title: TAB-seq_dorsal_DG_standard_housing_rep2


title: Chr5_DMSO_ExpA

description:
HTGTS
Chr5_DMSO.tlx


title: MethylC-seq_ventral_DG_enriched_environment_rep5

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, and TAB-seq datasets were performed as described in Zhang et al., 2017 (in submission)
MethylC-seq: Adapters were trimmed using Trim Galore v0.4.0
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/ and Lister et al., 2013) for alignment and mC calling
MethylC-seq: DMRs were identified using DSS v2.10.0 (smoothing=True)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimed text files of gene expression counts estimated using STAR version STAR_2.5.1b_modified
Supplementary_files_format_and_content: tab delimited text files of gene expression levels estimated using RSEM v1.2.30
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
Supplementary_files_format_and_content: tab delimited text files of hydroxymethylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for hydroxymethylated cytosines)

extract_protocol:
Tissue collection consisted of rapid removal of the brain, followed by flash freezing and storage at -80C. Frozen brains were sliced coronally at 200 µm thickness until reaching bregma -2.30. The brains were then removed from mounting position, rotated, and remounted to the mounting position for horizontal slicing ventral dentate tissue. Horizontal sections were sliced from interaural 3.24 mm to 0.92 mm26. A 300 µm diameter puncher was used to punch dorsal and ventral dentate gyrus region separately. RNA and DNA extraction were performed from the same sample using Qiagen Allprep DNA/RNA Mini kit (Qiagen, Cat# 80204.).  We performed on-column DNase I treatment during RNA extraction and on-column RNaseA treatment during DNA extraction. RNA was examined by Bioanalyzer 2100 (Agilent technologies, Santa clara, USA).
Bisulfite-Seq (MethylC-seq): DNA from the same samples was separated for TAB-seq and MethylC-seq library preparation. Protection and oxidation portions of library preparation were performed in-house using the Wisegene kit as described in Yu et al6. Three spike-in control DNAs, lambda DNA (Cat# D1501, Promega), 5mC (Cat# S001, Wisegene) and 5hmC (Cat# S002, Wisegene) were added to each sample (2.5 µg of total DNA) before DNA shearing, in order to evaluate the bisulfite conversion efficiency, the protection rate of 5 hmC, and the oxidation rate of TET. Bisulfite conversion was then performed at the Genome Quebec Innovation Centre on the processed TAB-seq sample, as well as 1 µg of DNA for the MethylC-seq library. Methylated and unmethylated DNA sets (Cat# D5017, pUC19 DNA set, Zymo research) were added as spike-in controls (2 ng spike-in control in 1 ug DNA) to evaluate bisulfite conversion efficiency. The whole genome bisulfite sequencing (WGBS) libraries were prepared using NimbleGen SeqCap Epi Enrichment System (Cat# 07145519001, Roche NimbleGen, Inc.). Library amplification was done using KAPA HiFi Hotstart Uracil + DNA polymerase (Cat# KK2802, Kapa Biosystems).


title: MethylC-seq_ventral_DG_enriched_environment_rep4


title: Chr5_APH_ExpA

description:
HTGTS
Chr5_APH.tlx


title: Chr5_APH_ExpC

description:
HTGTS
Chr5_APH.tlx


title: Chr5_APH_ExpB

description:
HTGTS
Chr5_APH.tlx


title: MethylC-seq_ventral_DG_enriched_environment_rep3


title: MethylC-seq_dorsal_DG_enriched_environment_rep5


title: Chr4_DMSO_ExpC

description:
HTGTS
Chr4_DMSO.tlx


title: Chr6_APH_ExpB

description:
HTGTS
Chr6_APH.tlx


title: MethylC-seq_ventral_DG_enriched_environment_rep2


title: MethylC-seq_dorsal_DG_enriched_environment_rep4


title: MethylC-seq_dorsal_DG_enriched_environment_rep3


title: MethylC-seq_ventral_DG_enriched_environment_rep1


title: Chr4_DMSO_ExpB

description:
HTGTS
Chr4_DMSO.tlx


title: Chr4_DMSO_ExpA

description:
HTGTS
Chr4_DMSO.tlx


title: Chr4_APH_ExpC

description:
HTGTS
Chr4_APH.tlx


title: TAB-seq_dorsal_DG_standard_housing_rep1


title: Chr4_APH_ExpB

description:
HTGTS
Chr4_APH.tlx


title: MethylC-seq_dorsal_DG_enriched_environment_rep2


title: Chr4_APH_ExpA

description:
HTGTS
Chr4_APH.tlx


title: Chr3_DMSO_ExpC

description:
HTGTS
Chr3_DMSO.tlx


title: Chr3_DMSO_ExpB

description:
HTGTS
Chr3_DMSO.tlx


title: MethylC-seq_dorsal_DG_enriched_environment_rep1


title: MethylC-seq_ventral_DG_standard_housing_rep5


title: MethylC-seq_ventral_DG_standard_housing_rep4


title: Chr19_APH_ExpB

description:
HTGTS
Chr19_APH.tlx


title: Chr3_APH_ExpC

description:
HTGTS
Chr3_APH.tlx


title: MethylC-seq_ventral_DG_standard_housing_rep2


title: Chr3_APH_ExpB

description:
HTGTS
Chr3_APH.tlx


title: MethylC-seq_ventral_DG_standard_housing_rep1


title: MethylC-seq_dorsal_DG_standard_housing_rep5


title: Chr2_DMSO_ExpC

description:
HTGTS
Chr2_DMSO.tlx


title: Chr3_APH_ExpA

description:
HTGTS
Chr3_APH.tlx


title: Chr2_DMSO_ExpA

description:
HTGTS
Chr2_DMSO.tlx


title: TAB-seq_dorsal_DG_standard_housing_rep3


title: Chr2_DMSO_ExpB

description:
HTGTS
Chr2_DMSO.tlx


title: MethylC-seq_dorsal_DG_standard_housing_rep3


title: Chr2_APH_ExpB

description:
HTGTS
Chr2_APH.tlx


title: Chr2_APH_ExpA

description:
HTGTS
Chr2_APH.tlx


title: MethylC-seq_dorsal_DG_standard_housing_rep4


title: MethylC-seq_dorsal_DG_standard_housing_rep2


title: Chr1_DMSO_ExpC

description:
HTGTS
Chr1_DMSO.tlx


title: MethylC-seq_ventral_DG_standard_housing_rep3


title: MethylC-seq_dorsal_DG_standard_housing_rep1


title: RNA-seq_ventral_DG_enriched_environment_rep5

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, and TAB-seq datasets were performed as described in Zhang et al., 2017 (in submission)
RNA-seq: Adapters were trimmed using Trim Galore v0.4.0
RNA-seq: Trimmed reads were aligned to the mm10 genome using STAR version STAR_2.5.1b_modified guided by all genes from Gencode vM7 (level 3).
RNA-seq: Gene counts were estimated using quantmode in STAR version STAR_2.5.1b_modified
RNA-seq: Gene expression levels in TPMs were estimated using RSEM v1.2.30
Genome_build: mm10
Supplementary_files_format_and_content: tab delimed text files of gene expression counts estimated using STAR version STAR_2.5.1b_modified
Supplementary_files_format_and_content: tab delimited text files of gene expression levels estimated using RSEM v1.2.30
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
Supplementary_files_format_and_content: tab delimited text files of hydroxymethylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for hydroxymethylated cytosines)

extract_protocol:
Tissue collection consisted of rapid removal of the brain, followed by flash freezing and storage at -80C. Frozen brains were sliced coronally at 200 µm thickness until reaching bregma -2.30. The brains were then removed from mounting position, rotated, and remounted to the mounting position for horizontal slicing ventral dentate tissue. Horizontal sections were sliced from interaural 3.24 mm to 0.92 mm26. A 300 µm diameter puncher was used to punch dorsal and ventral dentate gyrus region separately. RNA and DNA extraction were performed from the same sample using Qiagen Allprep DNA/RNA Mini kit (Qiagen, Cat# 80204.).  We performed on-column DNase I treatment during RNA extraction and on-column RNaseA treatment during DNA extraction. RNA was examined by Bioanalyzer 2100 (Agilent technologies, Santa clara, USA).
RNA-seq: The RNA libraries were prepared in McGill University and Genome Quebec Innovation Centre using Illumina TruSeq Stranded total RNA LT set (Cat# RS-122-2301, Illumina Canada Ulc.). Paired-end, 100bp read-length RNA-seq was collected using HiSeq 2000 at a depth of 30 M sequencing.


title: Chr3_DMSO_ExpA

description:
HTGTS
Chr3_DMSO.tlx


title: Chr1_APH_ExpC

description:
HTGTS
Chr1_APH.tlx


title: Chr1_DMSO_ExpA

description:
HTGTS
Chr1_DMSO.tlx


title: Chr1_DMSO_ExpB

description:
HTGTS
Chr1_DMSO.tlx


title: Chr1_APH_ExpB

description:
HTGTS
Chr1_APH.tlx


title: Chr1_APH_ExpA

description:
HTGTS
Chr1_APH.tlx


title: RNA-seq_ventral_DG_enriched_environment_rep2


title: RNA-seq_ventral_DG_enriched_environment_rep1


title: RNA-seq_dorsal_DG_enriched_environment_rep4


title: Chr2_APH_ExpC

description:
HTGTS
Chr2_APH.tlx


title: RNA-seq_dorsal_DG_enriched_environment_rep3


title: RNA-seq_dorsal_DG_enriched_environment_rep1


title: RNA-seq_ventral_DG_standard_housing_rep5


title: RNA-seq_ventral_DG_standard_housing_rep3


title: RNA-seq_ventral_DG_standard_housing_rep1


title: RNA-seq_ventral_DG_standard_housing_rep2


title: RNA-seq_dorsal_DG_standard_housing_rep5


title: RNA-seq_dorsal_DG_standard_housing_rep2


title: RNA-seq_dorsal_DG_standard_housing_rep3


title: RNA-seq_dorsal_DG_standard_housing_rep4


title: RNA-seq_dorsal_DG_standard_housing_rep1


title: Chr19_APH_ExpC

description:
HTGTS
Chr19_APH.tlx


title: RNA-seq_ventral_DG_enriched_environment_rep3


title: fkh1Δ dbf4-gst HU-60'

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

description: Mutant fkh1Δ Dbf4 protein have been fused with gst motif 60' after release in S-Phase in presence of HU(200mM)

data_processing:
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files correspond to signal  ratio smoothed with a 1000 bp window and a 1 bp step

organism: Saccharomyces cerevisiae

source_name: Genomic DNA from Saccharomyces cerevisiae

growth_protocol: Cells were grown on YPD at 25°C

extract_protocol:
Standard protocol for preparation of yeast genomic DNA
Libraries were constructed using standard Illumina kits (TruSeq SBS Kit v3) and protocols. Sequencer: HiSeq4000. Reads lenght: 51.

treatment_protocol: Samples were released from alpha-factor arrest in the presence of 200 mM HU (hydroxyurea).

tag: genotype/variation

value: fkh1delta dbf4-gst HU-60'


title: Sample_19_VavPBcl2plusAicda_4_RNAseq

description: Sample 19

data_processing:
Illumina Casava1.8 software used for basecalling.
ERRBS reads were aligned to the mouse genome using the Bismark alignment software with a maximum of 2 mismatches and only those reads that mapped to a unique location were retained. Bisulfite-converted reads were aligned to in silico bisulfate converted MspI fragments using ELAND aligner. In order to assign a methylation score for a base position, read bases that aligned to a position were required to have at least 20 phred quality score and 10x coverage. Only CpG dinucleotides that satisfied these coverage and quality criteria were used in the subsequent analysis. Percent methylation for individual Cs in the genome were calculated as the ratio of the number of alignments with C (methylated), over the number of alignments with either C (methylated) or T (unmethylated). methylCall files were generated using methylKit.
RNA-seq reads were aligned to mm10 using STAR with default parameters. CPM were obtained using Rsubread and mm10 RefSeq gene annotation.
Exome samples were aligned to the Mus musculus GRCm38 using STAR. A pileup of sorted bam files was prepared for each gene with quality score > 20 using samtools. From each pileup, a list of single nucleotide polymorphisms was generated at each base with minimum coverage of 10 reads using VarScan 2.3.4. We quantified mutation burden as the number of mutated bases (e.g. nonsynonymous or indels), normalized to the total number of sequenced nucleotides in kilobases, excluding nucleotides that mapped to bases with less than 10 reads of coverage.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: methylCall files are tab-delimited; columns indicate cytosine position (cpg ID, chr, base, strand), as well as coverage (in reads), and frequency of C (methylated) and frequency of T (unmethylated) bases.
Supplementary_files_format_and_content: CPM files are tab-delimited; values indicate read counts per million aligned reads per RefSeq gene ID.
Supplementary_files_format_and_content: mutationBurden files are tab-delimited; columns indicate mutation burden (mutation event/1e03 nt) for nonsynonymous and indel mutations, respectively. Only bases with minimum 10X coverage were assessed.

source_name: VavP-Bcl2 murine B cell tumor overexpressing Aicda

growth_protocol: Not applicable.

value: VavP-Bcl2+Aicda B cell tumor


title: Sample_21_VavPBcl2plusAicda_6_RNAseq

description: Sample 21


title: Aicda-/- Replicate 1

city: Madrid

first: Ángel

middle: F

last: Álvarez-Prado

address: Melchor Fernández Almagro, 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares

data_processing:
Alignment with Novoalign 2.08.01; command line options: -o SAM -F ILM1.8 -H -r None -q 2
Generation of sorted bamfile with samtools 0.1.19
Analysis of mutations by a custom Perl script
Identification of AID targets was done by comparing the mutational load of Ung-/-Msh2-/- B cells with that of the negative control Aicda-/- (FDR ≤0.05; Fisher test + FDR Benjamini-Hochberg correction; done by R stats package v3.1.1). Only those targets identified in the two replicates were kept (291 targets).
Supplementary_files_format_and_content: Tab delimited text file including gene name, coordinates, ENSEMBL ID and total mutation frequency of the 291 AID targets identified in this study for the 9 samples analyzed.

source_name: Peyer's patches germinal center B cells

extract_protocol: Genomic DNA was isolated by standard liquid-liquid  phenol-chloroform  and chloroform double extraction followed by precipitation with ethanol. It  was quantified in an Invitrogen Qubit Fluorometer and fragmented in a   Covaris sonicator to an average fragment size of ~200nts. Fragments were purified using Agencourt AMPure XP beads. Quality was assessed with the 2100 Bioanalyzer (Agilent). Then, fragment ends were repaired, adapters were ligated and the resulting library was amplified and hybridized with our custom  SureSelectXT library of RNA probes. DNA-RNA hybrids were then captured by  magnetic bead selection. After indexing, libraries were single-end sequenced in  and Illumina HiSeq 2500 platform.

tag: sorted cells

value: Aicda-/-

tag: immunophenotype

tag: #of mice


title: Sample_22_VavPBcl2plusAicda_7_RNAseq

description: Sample 22


title: Sample_18_VavPBcl2plusAicda_3_RNAseq

description: Sample 18


title: Ung-/- Msh2+/- Replicate 2


title: RNA-seq_dorsal_DG_enriched_environment_rep5

tag: strain

tag: Sex


title: RNA-seq_ventral_DG_standard_housing_rep4

tag: tissue

tag: age


title: Ung+/- Msh2-/- Replicate 2


title: fkh1Δ dbf4-fkh* HU-60'

description: Mutant fkh1Δ Dbf4 protein have been fused with fkh1 protein mutated for the DNA binding site, 60' after release in S-Phase in presence of HU(200mM)

value: fkh1delta dbf4-fkh* HU-60'


title: Sample_17_VavPBcl2plusAicda_1_RNAseq

description: Sample 17


title: Sample_16_VavPBcl2_6_RNAseq

description: Sample 16

source_name: VavP-Bcl2 murine B cell tumor

value: VavP-Bcl2 B cell tumor


title: RNA-seq_ventral_DG_enriched_environment_rep4


title: Ung+/- Msh2+/- Replicate 2


title: Ung-/- Msh2-/- Replicate 1


title: fkh1Δ HU-60'

description: Mutant fkh1Δ 60' after release in S-Phase in presence of HU(200mM)

value: fkh1delta HU-60'


title: Ung-/- Msh2+/- Replicate 1


title: Sample_15_VavPBcl2_5_RNAseq

description: Sample 15


title: Sample_20_VavPBcl2plusAicda_5_RNAseq

description: Sample 20


title: Ung+/- Msh2-/- Replicate 1


title: Ung-/- Msh2-/- Replicate 2


title: fkh1Δ dbf4-fkh HU-60'

description: Mutant fkh1Δ Dbf4 protein have been fused with fkh1 protein 60' after release in S-Phase in presence of HU(200mM)

value: fkh1delta dbf4-fkh HU-60'


title: Sample_30_VavPBcl2plusAicda_Repl4_exome

description: Sample 30

data_processing:
Library strategy: Exome-seq
Illumina Casava1.8 software used for basecalling.
ERRBS reads were aligned to the mouse genome using the Bismark alignment software with a maximum of 2 mismatches and only those reads that mapped to a unique location were retained. Bisulfite-converted reads were aligned to in silico bisulfate converted MspI fragments using ELAND aligner. In order to assign a methylation score for a base position, read bases that aligned to a position were required to have at least 20 phred quality score and 10x coverage. Only CpG dinucleotides that satisfied these coverage and quality criteria were used in the subsequent analysis. Percent methylation for individual Cs in the genome were calculated as the ratio of the number of alignments with C (methylated), over the number of alignments with either C (methylated) or T (unmethylated). methylCall files were generated using methylKit.
RNA-seq reads were aligned to mm10 using STAR with default parameters. CPM were obtained using Rsubread and mm10 RefSeq gene annotation.
Exome samples were aligned to the Mus musculus GRCm38 using STAR. A pileup of sorted bam files was prepared for each gene with quality score > 20 using samtools. From each pileup, a list of single nucleotide polymorphisms was generated at each base with minimum coverage of 10 reads using VarScan 2.3.4. We quantified mutation burden as the number of mutated bases (e.g. nonsynonymous or indels), normalized to the total number of sequenced nucleotides in kilobases, excluding nucleotides that mapped to bases with less than 10 reads of coverage.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: methylCall files are tab-delimited; columns indicate cytosine position (cpg ID, chr, base, strand), as well as coverage (in reads), and frequency of C (methylated) and frequency of T (unmethylated) bases.
Supplementary_files_format_and_content: CPM files are tab-delimited; values indicate read counts per million aligned reads per RefSeq gene ID.
Supplementary_files_format_and_content: mutationBurden files are tab-delimited; columns indicate mutation burden (mutation event/1e03 nt) for nonsynonymous and indel mutations, respectively. Only bases with minimum 10X coverage were assessed.

extract_protocol: DNA for exome sequencing was extracted using SeqCap EZ design mouse exome capture kit protocol; Libraries were prepared as described in manuscript.


title: wt HU-60'

description: Wild type 60' after release in S-Phase in presence of HU(200mM)

value: Wild type


title: Ung+/- Msh2+/- Replicate 1


title: Sample_29_VavPBcl2plusAicda_Repl3_exome

description: Sample 29


title: Sample_28_VavPBcl2plusAicda_Repl2_exome

description: Sample 28


title: Sample_27_VavPBcl2plusAicda_Repl1_exome

description: Sample 27


title: Sample_14_VavPBcl2_4_RNAseq

description: Sample 14


title: Sample_13_VavPBcl2_2_RNAseq

description: Sample 13


title: wt G1

description: Wild type in G1 phase of the cell cycle


title: Sample_26_VavPBcl2_Repl4_exome

description: Sample 26


title: Sample_12_VavPBcl2_1_RNAseq

description: Sample 12


title: Sample_23_VavPBcl2_Repl1_exome

description: Sample 23


title: Sample_11_VavPBcl2plusAicda_6_ERRBS

description:
Sample 11
ERRBS

extract_protocol: DNA for ERRBS was extracted using Qiagen Puregene kit protocol; Libraries were prepared as described in manuscript.


title: Sample_24_VavPBcl2_Repl2_exome

description: Sample 24


title: Sample_25_VavPBcl2_Repl3_exome

description: Sample 25


title: Sample_9_VavPBcl2plusAicda_4_ERRBS

description:
Sample 9
ERRBS


title: Foxa2 Zmpste24 KO replicate 2

city: Charlottesville

first: Irina

last: Bochkis

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of Virginia

description: chromatin immunoprecipitation

data_processing:
The reads were aligned to mouse genome (mm10; NCBI Build 38) using BWA (Li and Durbin, 2009). Duplicate reads were removed from the analysis. Reads (phred score > 20) that aligned uniquely were used for subsequent analysis.
Reads from two biological replicates were merged for these conditions (Lamin B1 young, Lamin B1 old, H3K9me3 young, H3K9me3 old, H3K9me32 young, H3K9me2 old). Reads from three biological replicates were merged for Foxa2 binding (Foxa2 WT and Foxa2 in Zmpste24 KO livers). Epic peak caller (https://github.com/daler/epic), a more efficient implementation of SICER domain-calling algorithm (Xu et al. 2014), was used to determine Lamin B1 associated domains (mm10 as species, window size of 10kb, gap size of 3). PeakSeq (Rozowsky et al., 2009) was used to identify bound peaks against input controls (Foxa2: FDR 5%, q-value=0.12).
Genome_build: mm10
Supplementary_files_format_and_content: bed files with peak calls from Epic caller (Lamin B1 and H3K9me3) and PeakSeq (Foxa2) with the following columns: chromosome, begin coordinate, end coordinate,

source_name: Liver

extract_protocol:
Snap-frozen mouse liver (100 mg) from wild type mice was used to prepare chromatin. Foxa2-specific rabbit antiserum (Seven Hills Bioreagents, WRAB-1200), rabbit antibody to Di Methyl-Histone H3 Lys9 (Cell Signaling, D85B4), goat antibody to lamin B1 (Santa Cruz Biotechnology, sc-6216) and rabbit anti-histone H3 (trimethyl K9) antibody (ab8898) were used for immunoprecipitation.
Libraries were prepared according to Illumina's instructions. Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). Broad custom adapters were then ligated to the ends of the modified DNA.  After adapter ligation DNA was PCR amplified with Broad custom primers for 16 cycles and library fragments of ~280 bp (~150-bp  insert plus ~130-bp adaptor and PCR primer sequences) were  isolated using Pippin Prep agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina Hiseq 2500 following the manufacturer's protocols.

value: Liver

value: 12 weeks


title: Foxa2 Zmpste24 KO replicate 3

description: chromatin immunoprecipitation


title: H3K9me2 old replicate 2

description: chromatin immunoprecipitation

value: 21 months


title: Foxa2 WT replicate 3

description: chromatin immunoprecipitation


title: Foxa2 WT replicate 1

description: chromatin immunoprecipitation


title: H3K9me2 young replicate 1

description: chromatin immunoprecipitation

value: 3 months


title: H3K9me2 old replicate 1

description: chromatin immunoprecipitation


title: Foxa2 Zmpste24 KO replicate 1

description: chromatin immunoprecipitation


title: Sample_5_VavPBcl2_5_ERRBS

description:
Sample 5
ERRBS


title: H3K9me2 young replicate 2

description: chromatin immunoprecipitation


title: Sample_8_VavPBcl2plusAicda_3_ERRBS

description:
Sample 8
ERRBS


title: Sample_6_VavPBcl2plusAicda_1_ERRBS

description:
Sample 6
ERRBS


title: Sample_7_VavPBcl2plusAicda_2_ERRBS

description:
Sample 7
ERRBS


title: H3K9me3 old replicate 2

description: chromatin immunoprecipitation


title: Sample_4_VavPBcl2_4_ERRBS

description:
Sample 4
ERRBS


title: H3K9me3 old replicate 1

description: chromatin immunoprecipitation


title: H3K9me3 young replicate 2

description: chromatin immunoprecipitation


title: Lamin B1 old replicate 2

description: chromatin immunoprecipitation


title: Sample_10_VavPBcl2plusAicda_5_ERRBS

description:
Sample 10
ERRBS


title: Sample_2_VavPBcl2_2_ERRBS

description:
Sample 2
ERRBS


title: Sample_3_VavPBcl2_3_ERRBS

description:
Sample 3
ERRBS


title: Sample_1_VavPBcl2_1_ERRBS

description:
Sample 1
ERRBS


title: Lamin B1 young replicate 1

description: chromatin immunoprecipitation


title: Foxa2 WT replicate 2

description: chromatin immunoprecipitation


title: Lamin B1 old replicate 1

description: chromatin immunoprecipitation


title: Lamin B1 young replicate 2

description: chromatin immunoprecipitation


title: 12+6h BPDL_1

city: PULLMAN

first: Amanda

middle: Jo

last: Brinkworth

state: WA

address: 1770 NE Stadium Way

department: School of Molecular Biosciences

institute: Washington State University

description:
Sample name: O
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA

data_processing:
Quality control:Sequenced reads were filtered to remove adapters and polyclonal sequences with Torrent Suite Software version 5.0.5.
Merging: Merged multiple fastq files from multiple sequencing chips of same cDNA libraries
Filtering: .fastq files have already been filtered by Torrent Suite to remove adapters and polyclonal sequences; Excluded reads with less than 30 nt with CLC Genomics Workbench
Alignment: Aligned to Chlamydia trachomatis 434/Bu core genome (AM884176) and plasmid (NZ_CP009926) using CLC parameters (Mismatch=2, Insertion=3, Deletion=3, Length=0.8, Similarity=0.8, Global=No, Strand=both, Max hits=10, Expression value=Unique counts, EM estimation=Yes)
Normalization: Quantile with CLC
Statistical Analysis: EdgeR with CLC
Genome_build: AM884176 + NZ_CP009926
Supplementary_files_format_and_content: Excel file with raw unique counts,  normalized expression values (NEV) and statisical analysis

organism: Chlamydia trachomatis

source_name: HeLa cells infected with C. trachomatis L2/434/Bu

growth_protocol: Seed Hela cels in T75 cm2 flasks for ~24h. At 75% confluency, Chlamydia trachomatis (multiplicity of infection=2) was added in fresh complete media and and allowed to infect (without centrifugation) for 30 minutes at 37C. Monolayers were washed to remove unattached bacteria, and infection proceeded for 12h.

extract_protocol:
RNA was collected after 0h treatment (samples A-E), 3h treatment (samples F-N), or 6h treatment (samples O-T) in Trizol and processed according to the Ribopure bacteria kit (Ambion). DNased RNA was applied to the MegaClear column (Ambion) to remove small RNAs, followed by two rounds of eukaryotic mRNA and rRNA depletion with the MicrobEnrich kit (Ambion), and 1-2 rounds of prokaryotic rRNA depletion with MicrobExpresss kit (Ambion). RNA was ethanol precipitated, and tested for integrity by RNA fragment analysis.
RNA was fragmented using RNAse III and cDNA was prepared as per the Ion Total RNA-seq Kit V2, and sequenced on an Ion Proton chip

treatment_protocol: At 12h p.i., complete growth media (DMEM,2.5 mM L-glutamine,10% FBS) containing 100 micromolar 2,2-Bipyridyl or ethanol vehicle was added to infected cells.

tag: host cell line

value: HeLa

value: BPDL

tag: total hours post-infection

tag: hours of treatment


title: RIBOseq with doxycycline [ON10]

city: ORSAY

first: Pierre

last: Bertin

address: Batiment 400, Université Paris Sud

institute: Institut de Biologie Intégrative de la Cellule

description:
ON10
Processed data file: plusVSminus_complete_RIBOseq.tsv

data_processing:
Library strategy: Ribo-Seq
Quality assessment with FastQC.
Low quality reads (< 30) and read’s adapters were trimmed using Cutadapt version 1.9.1 (selected kmer sizes were between 24 and 35 nucleotides).
RNA filtering was conducted mapping all reads on hg38 rRNA genes. Unmapped reads with bowtie 1.1.2 were conserved.
Filtered reads were mapped using Tophat2.1.1 and bowtie 1.1.2 on the hg38 genome allowing 2 mismatches.
Uniquely mapped reads were counted using featureCounts v1.5.0-p2 and normalised using SARTools package to apply DESeq2 method.
Genome_build: hg38 ENSEMBL
Supplementary_files_format_and_content: Tabular file from DESeq2 differential expression containing the log2foldchanges and the p-adjusted value for each gene and each replicates.
Supplementary_files_format_and_content: Columns content: Id (GeneID ENSEMBL), Name (Gene symbol ENSEMBL), baseMean (Mean of normalized counts over the samples and replicates), log2FoldChange (from DESeq2), p-adjusted (Pvalue adjusted by DESeq2 with Benjamini-Hotchberg method), minusDoxy (mean of normalized counts over replicates), plusDoxy (mean of normalized counts over replicates).

source_name: HELA cells (sh FBL integrated)

growth_protocol: Cells were grown into MEM medium 1X (21090-055) of Gibco by Life Technologies. Supplemented with FBS, non-essential amino acids, antibiotic – anti-mycotic and L-glutamine.

extract_protocol:
For each experiment, 150 million cells were treated with 100 µg/mL cycloheximide, harvested by trypsinization and centrifugation, and resuspended in lysis buffer.
Illumina TruSeq Small RNA RS-200-0012.

treatment_protocol: Samples were treated for 5 days with doxycycline (for +doxy samples) at a concentration of 1µg/mL.

value: HeLa (sh FBL integrated)

tag: antibiotic treatment

value: + doxycycline


title: RIBOseq without doxycycline [ON9]

description:
ON9
Processed data file: plusVSminus_complete_RIBOseq.tsv

value: - doxycycline


title: 12+6h BPDL_2

description:
Sample name: P
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA

tag: treatment


title: 12+6h BPDL_3

description:
Sample name: Q
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 12+3h BPDL_5

description:
Sample name: J
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 12+3h BPDL_3

description:
Sample name: H
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 18h (12+6h Mock)_2

description:
Sample name: S
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA

value: Mock


title: RIBOseq without doxycycline [ON7]

description:
ON7
Processed data file: plusVSminus_complete_RIBOseq.tsv


title: 18h (12+6h Mock)_1

description:
Sample name: R
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 12+3h BPDL_2

description:
Sample name: G
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 15h (12+3h Mock)_4

description:
Sample name: N
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: RIBOseq without doxycycline [ON11]

description:
ON11
Processed data file: plusVSminus_complete_RIBOseq.tsv


title: 15h (12+3h Mock)_3

description:
Sample name: M
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 12+3h BPDL_1

description:
Sample name: F
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 12+3h BPDL_4

description:
Sample name: I
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 15h (12+3h Mock)_2

description:
Sample name: L
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: RNAseq with doxycycline [ON6]

description:
ON6
Processed data file: plusVSminus_complete_RNAseq.tsv

data_processing:
Quality assessment with FastQC.
Low quality reads (< 30) were trimmed using Cutadapt version 1.9.1.
RNA filtering was conducted mapping all reads on hg38 rRNA genes. Unmapped reads with bowtie 1.1.2 were conserved.
Reads were mapped using Tophat2.1.1 and Bowtie1.1.2 on the hg38 genome allowing 2 mismatches.
Uniquely mapped reads were used to conduct differential expression analysis through SARTools package and DESeq2 method.
Genome_build: hg38 ENSEMBL
Supplementary_files_format_and_content: Tabular file from DESeq2 differential expression containing the log2foldchanges and the p-adjusted value for each gene and each replicates.
Supplementary_files_format_and_content: Columns content: Id (GeneID ENSEMBL), Name (Gene symbol ENSEMBL), baseMean (Mean of normalized counts over the samples and replicates), log2FoldChange (from DESeq2), p-adjusted (Pvalue adjusted by DESeq2 with Benjamini-Hotchberg method), minusDoxy (mean of normalized counts over replicates), plusDoxy (mean of normalized counts over replicates).

extract_protocol:
QIAGEN® RNeasy® mini kit (50) (ref: 74104).
Standard RNA-seq sequencing at Genewiz company (TruSeq RNA sample preparation v2).


title: 15h (12+3h Mock)_1

description:
Sample name: K
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 12h Untreated_5

description:
Sample name: E
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA

value: Untreated


title: RNAseq with doxycycline [ON4]

description:
ON4
Processed data file: plusVSminus_complete_RNAseq.tsv


title: 12h Untreated_4

description:
Sample name: D
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 12h Untreated_3

description:
Sample name: C
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: H3K9me3 young replicate 1

description: chromatin immunoprecipitation


title: 18h (12+6h Mock)_3

description:
Sample name: T
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: RIBOseq with doxycycline [ON12]

description:
ON12
Processed data file: plusVSminus_complete_RIBOseq.tsv


title: RNAseq without doxycycline [ON3]

description:
ON3
Processed data file: plusVSminus_complete_RNAseq.tsv


title: RIBOseq with doxycycline [ON8]

description:
ON8
Processed data file: plusVSminus_complete_RIBOseq.tsv


title: RNAseq without doxycycline [ON1]

description:
ON1
Processed data file: plusVSminus_complete_RNAseq.tsv


title: 12h Untreated_1

description:
Sample name: A
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: 12h Untreated_2

description:
Sample name: B
depleted for euk mRNA, euk rRNA, prok rRNA, small RNA


title: RNAseq without doxycycline [ON5]

description:
ON5
Processed data file: plusVSminus_complete_RNAseq.tsv


title: 9h (6+3h Mock)_2

description: depleted for euk mRNA, euk rRNA, prok rRNA, small RNA

data_processing:
Quality control:Sequenced reads were filtered to remove adapters and polyclonal sequences with Torrent Suite Software version 5.0.5.
Merging: Merged multiple fastq files from multiple sequencing chips of same cDNA libraries
Filtering: .fastq files have already been filtered by Torrent Suite to remove adapters and polyclonal sequences; Excluded reads with less than 30 nt with CLC Genomics Workbench
Alignment: Aligned to Chlamydia trachomatis 434/Bu core genome (AM884176) and plasmid (NZ_CP009926) using CLC parameters (Mismatch=2, Insertion=3, Deletion=3, Length=0.8, Similarity=0.8, Global=No, Strand=both, Max hits=10, Expression value=Unique counts, EM estimation=Yes)
Normalization: Quantile with CLC
Statistical Analysis: EdgeR with CLC
Genome_build: AM884176 + NZ_CP009926
Supplementary_files_format_and_content: Excel file with Normalized expression value (NEV),  and raw unique reads and statistical analysis.

growth_protocol: Seed Hela cels in T75 cm2 flasks for ~24h. At 75% confluency, Chlamydia trachomatis (multiplicity of infection=2) was added in fresh complete media and and allowed to infect (without centrifugation) for 30 minutes at 37C. Monolayers were washed to remove unattached bacteria, and infection proceeded for 6h.

extract_protocol:
RNA was collected after 3h treatment  in Trizol and processed according to the Ribopure bacteria kit (Ambion). DNased RNA was applied to the MegaClear column (Ambion) to remove small RNAs, followed by two rounds of eukaryotic mRNA and rRNA depletion with the MicrobEnrich kit (Ambion), and 1-2 rounds of prokaryotic rRNA depletion with MicrobExpresss kit (Ambion). RNA was ethanol precipitated, and tested for integrity by RNA fragment analysis.
RNA was fragmented using RNAse III and cDNA was prepared as per the Ion Total RNA-seq Kit V2, and sequenced on an Ion Proton chip

treatment_protocol: At 6h p.i., complete growth media (DMEM,2.5 mM L-glutamine,10% FBS) containing 100 micromolar 2,2-Bipyridyl or 2 microliters ethanol vehicle was added to infected cells.

value: MOCK


title: RNAseq with doxycycline [ON2]

description:
ON2
Processed data file: plusVSminus_complete_RNAseq.tsv


title: 9h (6+3h Mock)_3


title: 9h (6+3h Mock)_4


title: 9h (6+3h Mock)_1


title: 6+3h BPDL_3


title: F6 wt G1

source_name: Genomic DNA

extract_protocol:
Standard protocol for preparation of yeast genomic DNA
NeoPrep Illumina system for automatic NGS library preparation using TruSeq Nano DNA Library Prep Kit for NeoPrep (Illumia)_Sequencer:HiSeq 4000 (1x51 nt)

value: Wild type in G1 phase of the cell cycle


title: F7 wt HU-60'

value: Wild type 60' after release in S-Phase in presence of HU(200mM)


title: sox10:Gal4, fli1a:GFP+ sox10:DsRed+

status: Public on Jan 18 2018

city: Los Angeles

first: Gage

middle: DeKoeyer

last: Crump

state: CA

address: 1425 San Pablo St BCC403

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

data_processing:
Raw sequencing data in Fastq format were imported into Partek Flow® for alignment and quantification.
In pre-alignment QC, the reads from all samples were generally of high quality, with the average quality score for each sample exceeding 33.
The reads were then trimmed at both ends based on the Phred quality score, with a minimum end quality level of 20 and a minimum acceptable read length of 25.
Trimmed reads were aligned to the Danio rerio GRCz10 genome assembly (Emsembl_v80) using the TopHat 2 algorithm.
Aligned reads were quantified with the Partek E/M algorithm using default parameters to generate TPM values.
Genome_build: GRCz10
Supplementary_files_format_and_content: The csv text files have the TPM values for each gene in each sample.

organism: Danio rerio

source_name: pharyngeal arch cells

growth_protocol: Embryos were maintained at 28.5 degrees C until 27 hours post fertilization, and then transferred to 22 degrees C to slow their development. Embryos were dissociated and sorted once they achieved morphological criteria corresponding to the standard ~36 hpf stage

extract_protocol:
GFP/DsRed double-positive cells populations were collected into RLT lysis buffer (Qiagen), and total RNA was immediately extracted using the RNeasy Micro kit (Qiagen) according to the manufacturer’s instructions. The purified RNA was evaluated for quality and quantity  on a BioAnalyzer Pico RNA chip (Agilent, Santa Clara, CA) and then reverse transcribed into cDNA using the SMARTer kit (Clontech, Mountain View, CA). cDNA amplification was adjusted based on the RNA input quantity, and the size and amount of generated cDNA was measured by BioAnalyzer.
The samples were sonicated on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommendations. DNA libraries were assembled using the Kapa Hyper prep kit (Kapa Biosystems, Wilmington, MA) with NextFlex adapters (Bioo Scientific, Austin, TX). Libraries were assessed by Bioanalyzer and quantified using qPCR (Kapa Library Quantification kit). Sequencing was performed on a NextSeq 500 (75-bp paired end reads) (Illumina, San Diego, CA). Library construction and sequencing were performed at the USC Molecular Genomics Core at the USC Norris Comprehensive Cancer Center.

tag: Stage

value: 36 hpf

tag: identification

value: fin biopsies taken at 24 hpf genotyped for Gal4 and the UAS allele


title: 6+3h BPDL_2


title: nr2f2; nr2f5 mutant 1, fli1a:GFP+ sox10:DsRed+

value: nr2f2; nr2f5 mutant

value: ocular coloboma


title: 6+3h BPDL_4


title: F5 fkh1[delta] dbf4-fkh HU-60'

value: Mutant fkh1[delta] Dbf4 protein have been fused with fkh protein 60' after release in S-Phase in presence of HU(200mM)


title: 6+3h BPDL_1


title: F1 wt G1


title: F3 fkh1[delta] dbf4-GST HU-60'

value: Mutant fkh1[delta] Dbf4 protein have been fused with the tag GST 60' after release in S-Phase in presence of HU(200mM)


title: F8 fkh1[delta] HU-60'

value: Mutant fkh1[delta] 60' after release in S-Phase in presence of HU(200mM)


title: nr2f2; nr2f5 mutant 2, fli1a:GFP+ sox10:DsRed+


title: F2 wt HU-60'


title: trap-C0488

city: Billerica

first: Chunxiao

last: Xu

state: MA

address: 45A Middlesex Tpke

institute: EMD Serono Research and Development Institute

data_processing:
Align with RSEM (v1.2.31) using Bowtie2 (v 2.3.1) against mm10 using the ensGene gene annotations from UCSC
Merge RSEM output files (counts and TPMs) into matrices
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated values for raw counts and TPMs.  Row names are ENSG identifiers.  Column names are sample names, including the treatment arm

source_name: EMT-6 tumor grown orthotopically in a Balb/C mouse

extract_protocol:
Tumor samples were snap-frozen and sent to GeneWiz for RNA extraction, library preparation, and sequencing.
Ribosomal depletion followed by random priming

treatment_protocol: Treatment on days 0, 1, 2

value: Balb/C

value: Anti-PDL1/TGFβ Trap  (492ug, IV)


title: trap-C0487

growth_protocol: EMT-6 tumor grown orthotopically in a Balb/C mouse


title: sox10:Gal4; UAS:Nr2f5, fli1a:GFP+ sox10:DsRed+

value: sox10:Gal4; UAS:Nr2f5


title: trap-C0486


title: trap-C0485


title: trap-C0484


title: trap-C0483


title: trap-C0481


title: trap-C0482


title: trap-C0480


title: pdl1-C0478

value: Anti-PDL1 (400ug, IV)


title: trap-C0479


title: pdl1-C0477


title: pdl1-C0474


title: pdl1-C0473


title: pdl1-C0475


title: pdl1-C0469


title: trap-control-C0468

value: Anti-PDL1 (mut) /TGFβ  Trap control (492ug, IV)


title: pdl1-C0471


title: trap-control-C0463


title: trap-control-C0461


title: trap-control-C0464


title: trap-control-C0462


title: trap-control-C0467


title: trap-control-C0465


title: ATAC-seq from K562_E669Q cells CPT0H

city: Bethesda

first: Junko

last: Murai

address: 37 Convent Dr.

institute: NCI

description: ATAC-seq DNA with DSMO treatment rom from K562-E669Q cells

data_processing:
BAM files are converted to BED files by Genomatix
Genome_build: hg19
Supplementary_files_format_and_content: BED

source_name: Lymphoblast

growth_protocol: Cancer cells were grown in RPMI1640 medium, 10% FBS

extract_protocol:
Fifty thousand K562-Vector, K562-WT, K562-E669Q cells were treated with DMSO or CPT (1000 nM) for 4 hours. To prepare nuclei, cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately following the nuclei preparation, the pellet was re-suspended in the transposase reaction mix [25 μl 2x TD buffer, 2.5 μl Transposase (Illumina) and 22.5 μl of nuclease free water], and incubated for 30 minutes at 37 °C. Directly following transposition, the sample was purified using a DNA Clean and Concentrator-5 (ZYMO RESEARCH) and eluted with 25 μl of DNA elution buffer. Following purification, we amplified library fragments using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermo-cycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. We amplified the full libraries for 5 cycles, after 5 cycles we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Syber Green at a final concentration of 0.6x. We ran this reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. Libraries were amplified for a total of 10–12 cycles and purified using a PCRClean DX yielding a final library concentration of ~30 nM in 20 μl.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).
Illumina paired-end sequencing

treatment_protocol: Cells were treated with DMSO for 4 hours, or 1000 nM camptothecin for 4 hours.

tag: cell line

tag: cell type

value: Cultured cancer cell line


title: ATAC-seq from K562_E669Q cells CPT4H

description: ATAC-seq DNA with camptothecin 1000 nM treatment for 4 hours from K562-E669Q cells


title: ATAC-seq from K562_WT cells CPT4H

description: ATAC-seq DNA with camptothecin 1000 nM treatment for 4 hours from K562-SLFN11 cells


title: trap-control-C0460


title: ATAC-seq from K562_WT cells CPT0H

description: ATAC-seq DNA with DSMO treatment from K562-SLFN11cells


title: trap-control-C0459


title: pdl1-C0476


title: control-C0458

value: Inactive Anti-PD-L1 Isotype Control (400ug, IV)


title: pdl1-C0472


title: ATAC-seq from K562_Vector cells CPT4H

description: ATAC-seq DNA with camptothecin 1000 nM treatment for 4 hours from K562-Vector cells


title: pdl1-C0470


title: ATAC-seq from K562_Vector cells CPT0H

description: ATAC-seq DNA with DSMO treatment from K562-Vector cells


title: control-C0455


title: control-C0456


title: control-C0457


title: control-C0453


title: trap-control-C0466


title: control-C0454


title: control-C0451


title: control-C0450


title: Control Reads (random shear) from CCRF-CEM SLFN11-KO (NS-Seq)

description:
Genomic DNA
Random shear /sequenced DNA used as control for peak calling

data_processing:
For peak calling, the SICER program and MACS2 program were used. Nascent strand reads were called by comparison to genomic reads of corresponding cell line. SICER algorithm was used with the following parameters: Window size 200 bp, Fragment size 150 bp, Gap size 600 bp, and FDR 0.01. MACS2 broad peak algorithm was also used for peak findings and quantification of signal value with the following parameters: q-value 0.01, Bandwidth 300, mfold 5-50 and Redundancy/duplicate threshold ‘auto’.
Illumina single read 105bp or 125bp sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks

source_name: Leukemic lymphoblasts

extract_protocol:
DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).
Illumina paired-end sequencing

treatment_protocol: Cells were treated with DMSO, 100 nM camptothecin, or 100 nM camptothecin with 2 uM VE-821 for 4 hours.

value: CCRF-CEM SLFN11-knockout


title: Control Reads (random shear) from CCRF-CEM parental cells (NS-Seq)

value: CCRF-CEM


title: Nascent strands reads from CCRF-CEM SLFN11-KO cells CPT

description:
Nascent DNA
Nascent strand DNA with camptothecin 100 nM treatment for 4 hours


title: control-C0449


title: Nascent strands reads from CCRF-CEM SLFN11-KO cells CPTATRi

description:
Nascent DNA
Nascent strand DNA with camptothecin 100 nM and VE-821 (ATR inhibitor) 2 uM treatment for 4 hours


title: UCK KO Rep1

city: Edmonton

first: Qiumin

last: Tan

state: Alberta

address: 6-16 Medical Sciences Building

department: Cell Biology

country: Canada

institute: University of Alberta

data_processing:
Illumina HiSeq 2500 software used for basecalling
Raw reads were first groomed by removing 13bp from the 5'-ends with random base concentration, then mapped to UCSC mm10 using TopHat v2.0.9
Expression level for each gene was estimated using Python program HTSeq (Anders et al., Bioinformatics 2014). Specifically htseq-count function of HTSeq accumulated the number of aligned reads that falls under the exons of the gene (union of all the exons of the gene). This read counts obtained are analogous to the expression level of the gene.
Using the obtained read counts, differential gene analyses were carried out using the DESeq2 package in the R environment.
Genome_build: mm10
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

source_name: hematopoietic stem and progenitor cells (HSPCs)

growth_protocol: standard animal house conditions

extract_protocol:
To isolate bone marrow HSPCs, single-cell suspensions were prepared as described above and red blood cells were lysed. Cells were incubated with c-Kit-biotin (1:50) for 30 min at 4 ºC. Cells were then washed twice with HBSS with 2% FBS, and incubated with anti-biotin microbeads (Miltenyi) and positively selected using a MACS stand and a MS column (Miltenyi) following the manufacturer’s protocol. Positively selected cells were then stained with a lineage marker cocktail in FITC (CD4, CD8a, CD11b, B220, Gr-1, Ter119), streptavidin PE, and Sca-1 PE-Cy7. HSPCs were defined as Lin- cKit+ Sca-1+, and sorted using the Sony SH800 cell sorter, and collected directly into TRIzol (Thermo Fisher Scientific).
Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.

value: Bone marrow

tag: genotype

value: UBC-cre/ERT2; Cicflox/flox + tamoxifen


title: UCK control Rep1

value: hematopoietic stem and progenitor cells (HSPCs)

value: Cicflox/flox + tamoxifen


title: UCK KO Rep2


title: Nascent strands reads from CCRF-CEM SLFN11-KO cells control

description:
Nascent DNA
Nascent strand DNA with DSMO treatment


title: UCK control Rep3


title: Nascent strands reads from CCRF-CEM parental cells CPTATRi


title: UCK KO Rep3


title: UCK control Rep2


title: RNA-seq_dorsal_DG_enriched_environment_rep2

tag: housing condition

value: enriched environment

value: brain (dentate gyrus of the hippocampus)

value: 80 days

value: male


title: Nascent strands reads from CCRF-CEM parental cells CPT


title: SSCi-D32-3

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
Fastq files were generated from reads passing chastity filter.
Transcript level quantitation was performed using Kallisto v0.42.5 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl v88 ftp site.
Gene level quantification was generated by summarization of the transcript level quantitation using tximport v0.99.9 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR v3.13.9.
Differential expression (DE) analysis of the organoid data was performed for each time-wise culturing condition using limma (3.32.2) with voom and eBayes functions. Genes having a mean of 10 counts-per-million (CPM) expression in at least one group were used in the analysis and those showing Benjamini-Hochberg false discovery rate (FDR) of < 1% and minimum fold change of 5 were considered in significant DE category.
Genome_build: GRCm38.p5 using Ensembl v88 annotation
Supplementary_files_format_and_content: Tab delimited text files containing transcript level counts, gene level counts, normalized gene level counts-per-million, or differential expression results.

source_name: ESC derived Retina organoids in static suspension culture, intact (SSCi) at day 32 of differentiation

growth_protocol: Mouse wild-type (WT) embryonic stem cells (ESCs) were isolated from the inner cell mass (ICM) of 3.5-day blastocyst of Nrl-GFP transgenic mice (Akimoto et al., 2006). A second WT ESC clone (R1) (Nagy et al., 1993) was obtained from A. Nagy, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada. ESCs were maintained on feeders of mouse embryonic fibroblasts (MEFs) in the presence of leukemia inhibitory factor (LIF) (Millipore) at 37°C, 5% CO2 (Ying et al., 2008). ESC clones were characterized by morphology, proliferation rate and expression of pluripotency markers (Chen, 2016). Maintenance medium of ESC culture consists of Knockout DMEM (Life Technologies) supplemented with 1x MEM non-essential amino acids (Sigma), 1x GlutaMAX (Life Technologies), 1x Penicillin-Streptomycin (PS) (Life Technologies), 1x 2-Mercaptoethanol (2-ME) (Life Technologies), 2000 U/ml LIF (Millipore), and 15% ES cell-qualified fetal bovine serum (FBS) (Life Technologies). Cells were passaged using TrypLE Express (Life Technologies) every three days.

extract_protocol:
TriPure isolation reagent (Roche, Basel, Switzerland)
TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego CA)

treatment_protocol: ESCs were differentiated into retinal organoids using modified HIPRO protocol, as described (Chen, 2016). After dissociation and removal of feeder cells, 3000 ESCs were plated in each well of PrimeSurface low adhesion U- shaped 96-well plate (Wako) with retinal differentiation medium constituted by GMEM (Life Technologies), 1x MEM non-essential amino acids (Sigma), 1x sodium pyruvate (Sigma), 1x 2-mercaptoethanol (2-ME) (Life Technologies) and 1.5%(v/v) knockout serum replacement (KSR) (Life Technologies). At differentiation day (D)1, 120 ul >9.5 mg/ml Matrigel (Corning) was diluted in 900 ul retinal differentiation medium. 20 ul of the diluted Matrigel was added to each well. Retinal organoids were transferred at D7 to a 100 mm Poly(2-hydroxyethyl methacrylate) (Sigma)-coated petri dish with 10 ml retinal maturation medium (DMEM/F12 with GlutaMAX (Life Technologies) with 1x 2-ME (Life Technologies) and 1x PS (Life Technologies). At D10, optic cups of retinal organoids were dissected from intact retinal organoids using a moria nickel-plated pin holder (Fine Science Tools) with 0.25 mm-diameter tungsten needles (Fine Science Tools). Dissected NR in static suspension culture (SSCd) or rotating-wall bioreactors (RWB) were supplied with DMEM/F12 with GlutaMAX (Life Technologies), 1x 2-ME (Life Technologies), 1x PS (Life Technologies), 1x N2 supplement (Life Technologies), 1 mM taurine (Sigma), 500 nM 9-cis retinal (Sigma) and 100 ng/ml insulin-like growth factor 1 (IGF1) (Life Technologies). From D18 and onwards, 1x MEM non-essential amino acid (Sigma), 1x B27 without Vitamin A (Life Technologies) and 2%(v/v) FBS (Atlanta Biologicals) were added to the culture. Intact organoids in static suspension culture (SSCi) were maintained in the same media, except 1x MEM non-essential amino acid (Sigma), 1x B27 without Vitamin A (Life Technologies) and 2% (v/v) FBS (Atlanta Biologicals) were added from D26 and onwards. Half-media exchanges were carried out every two days for all three conditions. The cultures were incubated in 5% O2 from D0 to D10 and with 20% O2 from D10 onwards.

value: ESC derived Retina organoids

tag: growth culture


title: SSCi-D32-2

value: static suspension culture, intact (SSCi)


title: SSCi-D32-1


title: SSCi-D25-2

source_name: ESC derived Retina organoids in static suspension culture, intact (SSCi) at day 25 of differentiation


title: Nascent strands reads from CCRF-CEM parental cells Control


title: control-C0452

value: Balb/C


title: SSCi-D25-1


title: SSCi-D18-2

source_name: ESC derived Retina organoids in static suspension culture, intact (SSCi) at day 18 of differentiation


title: SSCd-D28-3

source_name: ESC derived Retina organoids in static suspension culture, dissected (SSCd) at day 28 of differentiation


title: SSCd-D28-1

value: static suspension culture, dissected (SSCd)


title: SSCd-D22-3

source_name: ESC derived Retina organoids in static suspension culture, dissected (SSCd) at day 22 of differentiation


title: Control Reads (random shear) from CCRF-CEM parental cells (ATAC-Seq)

extract_protocol:
Five thousand CCRF-CEM parental and SLFN11-del cells were treated with DMSO, CPT (100 nM) or hydroxyurea (0.5 mM) for 2 and 4 hours. To prepare nuclei, cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately following the nuclei preparation, the pellet was re-suspended in the transposase reaction mix [25 μl 2x TD buffer, 2.5 μl Transposase (Illumina) and 22.5 μl of nuclease free water], and incubated for 30 minutes at 37 °C. Directly following transposition, the sample was purified using a DNA Clean and Concentrator-5 (ZYMO RESEARCH) and eluted with 25 μl of DNA elution buffer. Following purification, we amplified library fragments using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermo-cycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. We amplified the full libraries for 5 cycles, after 5 cycles we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Syber Green at a final concentration of 0.6x. We ran this reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. Libraries were amplified for a total of 10–12 cycles and purified using a PCRClean DX yielding a final library concentration of ~30 nM in 20 μl.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).
Illumina paired-end sequencing

treatment_protocol: Cells were treated with DMSO for 4 hours, or 100 nM camptothecin, or 0.5 mM hydroxyures for 2 and 4 hours.


title: ATAC-seq from CCRF-CEM SLFN11-KO cells CPT2H

description:
PCR amplified DNA
ATAC-seq DNA with camptothecin 100 nM treatment for 2 hours


title: ATAC-seq from CCRF-CEM SLFN11-KO cells CPT4H

description:
PCR amplified DNA
ATAC-seq DNA with camptothecin 100 nM treatment for 4 hours


title: SSCd-D22-2


title: ATAC-seq from CCRF-CEM SLFN11-KO cells CPT0H

description:
PCR amplified DNA
ATAC-seq DNA with DSMO treatment


title: ATAC-seq from CCRF-CEM parental cells CPT4H


title: SSCd-D22-1


title: Control Reads (random shear) from CCRF-CEM SLFN11-KO (ATAC-Seq)


title: RWB-D25-1

source_name: ESC derived Retina organoids in rotating-walled bioreactor (RWB) at day 25 of differentiation

value: rotating-walled bioreactor (RWB)


title: SSCd-D28-2


title: RWB-D22-3

source_name: ESC derived Retina organoids in rotating-walled bioreactor (RWB) at day 22 of differentiation


title: RWB-D25-3


title: ATAC-seq from CCRF-CEM parental cells CPT0H

value: Cultured cancer cell line


title: SSCd-D18-1

source_name: ESC derived Retina organoids in static suspension culture, dissected (SSCd) at day 18 of differentiation


title: SSCi-D18-1


title: ATAC-seq from CCRF-CEM parental cells CPT2H


title: D3 day21 rep3

city: Warsaw

first: Joanna

middle: Maria

last: Bem

address: Miecznikowa 1

department: Department of Cytology

country: Poland

institute: University of Warsaw

data_processing:
Basecalls performed using CASAVA.
The quality assessment of raw reads was performed with the FastQC tool. First, only adapters-containing reads were selected for further analyses. Later, adapters and low-quality reads were discarded. miRNA reads were aligned to mm10 using Bowtie1 and Partek Flow Software.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tab-delimited text file with TMM values for each sample and each miRNA.

source_name: Embryonic Stem Cells

growth_protocol: ESCs were cultured without feeder layer in medium composed of KnockOut DMEM, Gibco supplemented with 15% heat-inactivated FBS Performance Plus, Gibco with the addition of nonessential amino acids, L-glutamine, β-mercaptoethanol, penicillin, streptomycin and LIF. Embryoid bodies were generated using hanging drop technique and collected on day 7 of differentiation, embryoid body outgrowths were collected on day 21 of differentiation.

extract_protocol:
RNA was extracted at AROS Applied Biotechnology A/S Science Park Skejby (Denmark) with QIAsymphony RNA extraction kit from QIAGEN using the Biorobot QIAsymphony SP from QIAGEN (miRNA CT 400 program).
miRNA was quantified, with the use of Qubit fluorometer and c.a. 150 bp long barcoded libraries were created and the quality of libraries was validated with the use of Bioanalyzer 2100 DNA High Sensitivity kit (Agilent). Libraries’ concentrations were measured with KAPA Library Quantification Kit during qPCR.

treatment_protocol: Embryoid bodies and embryoid body outgrowths were cultured in KO-DMEM containing all necessary supplements, lacking LIF and supplemented with RA, ITS and N2.

value: Embryonic Stem Cells

tag: differenatiation stage

value: ESCs differentiating in Embryoid Body Outgrowths (day 21)


title: D3 day21 rep1


title: RWB-D22-1


title: RWB-D18-1

source_name: ESC derived Retina organoids in rotating-walled bioreactor (RWB) at day 18 of differentiation


title: RWB-D22-2


title: RWB-D18-2


title: SSCd-D18-3


title: D3 day21 rep2


title: NONO_LivNucRNA_ZT22

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the mm10 genome was performed using the STAR aligner version 2.4.0k using the --outFilterIntronMotifs RemoveNoncanonical parameter
Nuclear RNA-Seq and total RNA-Seq normalized gene expression (fpkm) was quantified across all gene exons and introns separately, using the top-expressed isoform as a proxy for gene expression
Genome_build: mm10
Supplementary_files_format_and_content: fpkm normalized table exon reads (text table)
Supplementary_files_format_and_content: fpkm normalized table intron reads (text table)

source_name: Liver

growth_protocol: Animals were maintained in a 12h:12h light:dark conditions. Mice were entrained to be fed only during the dark phase for one week prior to the tissue collection,

extract_protocol:
One portion of the liver was snap frozen to isolate total RNA, the rest of the tissue was homogenized to isolate liver nuclei and extract nuclear RNA. mRNA from either total liver tissue or liver nuclei was purified using Trizol reagent (Invitrogen)
Libraries were prepared using Illumina’s TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold according to manufacturer’s instructions

tag: time point

tag: strain

value: liver nuclei

value: 14 weeks

value: nono-/-


title: RWB-D25-2

tag: tissue


title: NONO_LivNucRNA_ZT20

tag: age


title: NONO_LivNucRNA_ZT10


title: SSCd-D18-2


title: NONO_LivNucRNA_ZT12


title: NONO_LivNucRNA_ZT4


title: NONO_LivNucRNA_ZT0


title: NONO_LivNucRNA_ZT2


title: NONO_LivNucRNA_ZT16


title: WT_LivNucRNA_ZT20

value: wild type


title: WT_LivNucRNA_ZT22


title: D3 ES rep2

value: undifferentiated ESCs (day 0)


title: WT_LivNucRNA_ZT18


title: NONO_LivNucRNA_ZT14


title: D3 day7 rep3

value: ESCs differentiating in Embryoid Bodies (day 7)


title: D3 day7 rep2


title: D3 ES rep3


title: NONO_LivNucRNA_ZT18


title: B8 day21 rep1


title: NONO_LivNucRNA_ZT8


title: B8 day21 rep3


title: D3 ES rep1


title: NONO_LivNucRNA_ZT6


title: B8 day7 rep3


title: B8 day21 rep2


title: WT_LivNucRNA_ZT16


title: B8 day7 rep2


title: B8 ES rep3


title: NONO_LivTotRNA_ZT18

value: total liver


title: NONO_LivTotRNA_ZT16


title: WT_LivNucRNA_ZT8


title: NONO_LivTotRNA_ZT22


title: WT_LivNucRNA_ZT12


title: NONO_LivTotRNA_ZT12


title: B8 ES rep1


title: B8 ES rep2


title: NONO_LivTotRNA_ZT6


title: NONO_LivTotRNA_ZT8


title: WT_LivNucRNA_ZT6


title: WT_LivNucRNA_ZT14


title: WT_LivNucRNA_ZT0


title: NONO_LivTotRNA_ZT14


title: B8 day7 rep1


title: WT_LivNucRNA_ZT4


title: WT_LivNucRNA_ZT2


title: NONO_LivTotRNA_ZT0


title: WT_LivNucRNA_ZT10


title: NONO_LivTotRNA_ZT20


title: FVB/NJ hippocampus rep 2

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

description: Library size selection for miRNA

data_processing:
Illumina Casava1.7 software for basecalling.
Adapter sequenced were trimmed from the reads, and they were mapped to mm10 mouse genome using bowtie v1.1.1 with parameters -q -v 3 -m 1 --best --strata, to allow SNPs between strains and miRNA editing.
Expressed miRNA-to-genome mismatch positions were called using FreeBayes FreeBayes v0.9.21 with parameters -F 0.01 -C 3 --pooled-continuous --min-base-quality 20 --min-coverage 10.
Alternatively, adapter sequences were removed and reads mapped directly to known miRNA (miRBase v21) and mouse genome mm10 using miRDeep2 v0.0.7, miraligner, and sRNAbench (sRNAtoolBox v1.0), to obtain miRNA and isomiR counts and to predict novel miRNAs.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: VCF file for miRNA-to-genome mismatch positions

growth_protocol: Mice were obtained from the Jackson Laboratory and singly housed for one week.

extract_protocol:
Samples were directly frozen in liquid nitrogen and stored in -80oC, and total RNA extracted with TriReagent.
miRNA libraries were prepared using Illumina TruSeq Small RNA Library Preparation kit and enriched for miRNA inserts by size selection using Covaris S-2. Library barcode is denoted as part of file name (6-letter index). Part of Hpc samples were resequenced (.2 extension in name).

treatment_protocol: Mice were killed by cervical dislobation. The brain was removed and dissections performed on a Petri dish filled with ice. Frontal cortex included 2 mm of the anterior part of the cortex. Hippocampus was dissected as a whole.

value: FVB/NJ

value: Wild type

value: 8 weeks

value: Hippocampus


title: FVB/NJ hippocampus rep 1

description: Library size selection for miRNA


title: DBA/2J hippocampus rep 3

description: Library size selection for miRNA


title: FVB/NJ hippocampus rep 3

description: Library size selection for miRNA


title: WT_LivTotRNA_ZT22


title: NONO_LivTotRNA_ZT4


title: NONO_LivTotRNA_ZT10


title: DBA/2J hippocampus rep 2

description: Library size selection for miRNA


title: NONO_LivTotRNA_ZT2


title: DBA/2J hippocampus rep 1

description: Library size selection for miRNA


title: WT_LivTotRNA_ZT16


title: C3H/HeJ hippocampus rep 3

description: Library size selection for miRNA


title: WT_LivTotRNA_ZT14


title: WT_LivTotRNA_ZT8


title: WT_LivTotRNA_ZT18


title: WT_LivTotRNA_ZT10


title: WT_LivTotRNA_ZT20