title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D4_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D4_AD006_indexed

status: Public on Aug 23 2020

type: SRA

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

country: USA

institute: NCBI/NLM/NIH

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: AON

tag: Sex

value: male

tag: age

tag: strain


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D3_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D4_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D4_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D5_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D3_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D4_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D3_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D5_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_3_CEMBA180212_1C_4_D4_AD001_indexed


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title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G11_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G1_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G10_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G10_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F9_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F9_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G11_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G10_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F9_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F9_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G1_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F9_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G11_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F8_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F9_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F8_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F8_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F7_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G10_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F7_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F7_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F8_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F5_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F8_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F7_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F7_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F6_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F8_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F7_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F6_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F8_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F6_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F8_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F6_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F5_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F5_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F5_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F5_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F6_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F9_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F6_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F5_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F6_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F5_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G4_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G1_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F4_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F5_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F4_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F4_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F4_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_G10_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F4_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F3_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F3_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F3_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F3_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F4_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F3_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F4_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F3_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F4_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F2_AD010_indexed


title: spH2A.W_rep1 (ATAC-seq)

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

country: Germany

institute: Max Planck Insititue for Biology

description: Tn5 Transposase digested DNA fragments

data_processing:
Raw, unaligned BAM files were first sorted with samtools sort -n and then converted to fastq files with bedtools bamtofastq.
Adapter trimming was performed using TrimGalore version 0.6.2.
Reads were mapped to the S.pombe genome (ASM294v2.21) using Bowtie2 version 3.4.2.
Reads were filtered for a MAPQ score > 10 using SAMtools version 1.9 and subsequently filtered for duplicate reads using Picard tools MarkDuplicates version 2.18.
Biological replicates were subsequently merged for downstream analysis after confirming high correlation among replicates.
For data visualization, log2 ratio bigwig coverage files relative to input were generated using the deepTools version 3.1.2 utility bamCoverage with a bin size of 10 bp.
Genome_build: S.pombe - ASM294v2.21
Supplementary_files_format_and_content: *.bw: Normalized log2 ratio coverage of ATAC-seq coverage. Data is generated from merged replicates.

organism: Schizosaccharomyces pombe

source_name: yeast

extract_protocol:
The yeast cells were digested with zymolase to obtain spheroplasted cells,then incubated with Tn5 Transposase in TD buffer ( 10mM Tris-HCl pH 7.6, 5mM  MgCl2, 10% Dimethyl Formamide ) Use NEBNext High-Fidelity 2x PCR Master Mix and Nextera index kit (Illumina) to amplify and barcoded transposed DNA fragments.
NEBNext High-Fidelity 2x PCR Master Mix and Nextera index kit

tag: ecotype

tag: genotype

tag: treatment

value: Tn5 Transposase


title: WT_rep1 (ATAC-seq)

description: Tn5 Transposase digested DNA fragments

value: WT


title: spH2A.W_rep2 (ATAC-seq)

description: Tn5 Transposase digested DNA fragments


title: spH2A.W.4A_rep2 (ATAC-seq)

description: Tn5 Transposase digested DNA fragments


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F2_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F3_AD001_indexed


title: WT_rep2 (ATAC-seq)

description: Tn5 Transposase digested DNA fragments


title: spH2A.W.4A_rep1 (ATAC-seq)

description: Tn5 Transposase digested DNA fragments


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F3_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F2_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F2_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F6_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F2_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F1_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F2_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F2_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F1_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F1_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F11_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F11_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F11_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F1_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F10_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F1_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F10_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F10_AD004_indexed


title: Control2: L4 DRG uninjured

city: Athens

first: Oshri

last: Avraham

state: GA

address: 120 Cedar St

department: Cellular Biology

institute: University of Georgia

description: single cell

library_source: transcriptomic

data_processing:
A digital expression matrix was obtained using the 10X Genomics Cell Ranger pipeline.
Quantification and statistical analysis were done with Partek Flow package (https://www.partek.com/partek-flow/).
Genome_build: mus musculus mm10
Supplementary_files_format_and_content: csv files containing the UMI count matrix

molecule: total RNA

source_name: L4 DRG uninjured

extract_protocol:
Whole DRG’s were dissociated with enzyme mix (Papain, Collagenase) to a single cell suspension, washed in 1X PBS+0.2%BSA solution, passed through a 40-micron cell strainer and FACS sorted using live/dead staining. Sorted cells were loaded on the 10X Chromium system.
single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3′ Gel Bead and Library Kit (10x Genomics). polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform.  Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform (https://www.10xgenomics.com/single-cell/). libraries were then constructed using standard instrutions of the 10x plaform.

treatment_protocol: 3 days post sciatic nerve crush injury

tag: tissue

value: Dorsal root ganglion (L4)

value: 8-12 weeks


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F11_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F11_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F1_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F1_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F11_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F11_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F11_AD008_indexed


title: Injured2: L4 DRG injured

description: single cell

source_name: L4 DRG injured


title: OCM1-H3K18la_rep2

city: Shanghai

first: Peiwei

last: Chai

address: No.833 Zhizaoju Road

country: China

institute: Shanghai Jiao Tong University school of medcine

data_processing:
Mapping : bowtie -m 2 --maxIns 350, hg38
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig, (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

organism: Homo sapiens

growth_protocol: The cell line OCM1 were cultured in Dulbecco's modified Eagle medium (DMEM;Gibco,USA) supplemented with 10% certified heat-inactivated fetal bovine serum (FBS; Gibco, USA), penicillin (100 U/ml) and streptomycin (100μg/ml) at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Untreated

tag: cell type

value: Ocular melanoma cells/uveal region

tag: cell line

tag: chip antibody


title: OCM1-input_rep1

value: input


title: Control: L4 DRG uninjured

description: single cell


title: OCM1-input_rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E9_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F1_AD006_indexed


title: OCM1-H3K18la_rep1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E9_AD010_indexed


title: OCM1-Oxamate

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Hg38
Supplementary_files_format_and_content:  xls files include RPKM values for each Sample

extract_protocol:
OCM1 cells samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: treated with glycolysis inhibitors

value: oxamate


title: OCM1-2dg


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E9_AD012_indexed


title: Injured: L4 DRG injured

description: single cell


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E9_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F10_AD006_indexed


title: OCM1-Control

value: control


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E9_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E9_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F10_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F10_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E8_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E9_AD002_indexed


title: D7 riboprofiling FP rep2

city: Singapore

first: Yue

last: Wan

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Library strategy: Ribosomal Profiling
Raw sequencing reads from ic-SHAPE library were first trimmed to remove adaptors using cutadapt (version 1.12), collapsed to remove PCR duplicates and trimmed to remove the leading 15-nt containing both the unique molecular identifiers and index sequences.
The processed reads were then mapped to an in-house reference transcriptome using bowtie (version: 0.12.8)
The RTstop counts were then compuated as the coverage of 5' end of each read using genomecov from bedtools (verison 2.25.0).
Genome_build: GRCh38 based transcriptome
Supplementary_files_format_and_content: Tab-delimited text files include Rtstop counts for each position if available.

source_name: early neurons

growth_protocol: HEK293T cells were obtained from neighbouring labs, and cultured in DMEM with 10% FBS and 1% Pen-Strep.  Human ESCs, neural stem cell induction and neuronal differentiation were performed as previously described. Briefly, human embryonic stem cells (H9) were cultured in mTeSRTM1 (#05851, stem cell technologies) medium, in the presence of 1X Supplement (#05852, stem cell technologies). hESC H9 cells were used as Day 0 sample in this manuscript. Yeast cells (S288C) were grown to log phase in YPD media at 30°C.

extract_protocol:
RNA was extracted by trizol, and mRNA was purifiied by Poly(A)Purist™ MAG Kit
RNA secondary structure libraries were performed by published icSHAPE method. Ribosome profiling was performed by following illumina TruSeq Ribo Profile (mammalian) Library Prep kit (RPHMR12126). RNA sequence library was performed by following NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760L).
RNA structure, RNA expression, RNA decay and translation efficiency libraries were performed for the same 4 time point. Then all the different data can be used to do correlation analysis with high confidence.

treatment_protocol: To determine the half-life of cellular RNAs, we stopped transcription by treating cells with 5mM Actinomycin D (A1410, Sigma) for 0, 1, 2, 4 and 8 hours.

value: early neurons

tag: batch

tag: development stage

tag: library type

value: Ribosomal Profiling

value: Footprint


title: D14 riboprofiling mRNA rep2

source_name: neurons

value: neurons

value: mRNA


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E8_AD010_indexed


title: D8 riboprofiling mRNA rep2

source_name: neuronal precursor cells

value: neuronal precursor cells


title: D8 riboprofiling FP rep2


title: D7 riboprofiling mRNA rep2

source_name: hESCs

value: hESCs


title: D0 riboprofiling mRNA rep2


title: D0 riboprofiling FP rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E7_AD012_indexed

value: AON


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E8_AD006_indexed

value: male


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E7_AD007_indexed


title: D14 riboprofiling mRNA rep1


title: D8 riboprofiling mRNA rep1


title: D14 riboprofiling FP rep1


title: D7 riboprofiling FP rep1


title: D14 riboprofiling FP rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E9_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E8_AD008_indexed


title: D7 riboprofiling mRNA rep1


title: D0 riboprofiling mRNA rep1


title: 535-59

type: genomic

city: Durham

first: Elaine

last: Guevara

state: North Carolina

address: 130 Science Drive

department: Evolutionary Anthropology

institute: Duke University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: samples were scanned using an Illumina BeadArrayTM reader

data_processing:
.idat files were quality filtered and converted to beta values using the Chimp Analysis Methylation Pipeline R package
beta values

label: Cy5 and Cy3

organism: Pan troglodytes

source_name: normal blood sample

label_protocol: Standard Illumina Protocol

extract_protocol: silica colum

value: Female

value: blood


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E7_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E7_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E6_AD010_indexed


title: 3140-39


title: D14 icShape DMSO batch2 rep2

data_processing:
Library strategy: icSHAPE
Raw sequencing reads from ic-SHAPE library were first trimmed to remove adaptors using cutadapt (version 1.12), collapsed to remove PCR duplicates and trimmed to remove the leading 15-nt containing both the unique molecular identifiers and index sequences.
The processed reads were then mapped to an in-house reference transcriptome using bowtie (version: 0.12.8)
The RTstop counts were then compuated as the coverage of 5' end of each read using genomecov from bedtools (verison 2.25.0).
Genome_build: GRCh38 based transcriptome
Supplementary_files_format_and_content: Tab-delimited text files include Rtstop counts for each position if available.

value: icSHAPE

value: DMSO


title: D14 icShape DMSO batch2 rep1


title: D14 icShape NAIN3 batch2 rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E8_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E8_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E7_AD001_indexed


title: D8 riboprofiling FP rep1


title: 931-35


title: D8 icShape NAIN3 batch2 rep2


title: D8 icShape NAIN3 batch2 rep1


title: 4647-11

value: Male


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E7_AD002_indexed


title: D8 icShape DMSO batch2 rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E8_AD004_indexed


title: D7 icShape NAIN3 batch2 rep2


title: D7 icShape NAIN3 batch2 rep1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E7_AD008_indexed


title: 4510-12


title: D0 riboprofiling FP rep1


title: D7 icShape DMSO batch2 rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E7_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E8_AD002_indexed


title: D14 icShape NAIN3 batch2 rep1


title: 4721-10


title: D7 icShape DMSO batch2 rep1


title: D0 icShape NAIN3 batch2 rep2


title: D0 icShape NAIN3 batch2 rep1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E6_AD008_indexed


title: D0 icShape DMSO batch2 rep2


title: 2369-42


title: 2053-46


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E6_AD012_indexed


title: D0 icShape DMSO batch2 rep1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E6_AD006_indexed


title: D14 icShape NAIN3 batch1 rep2


title: 2366-39


title: D14 icShape NAIN3 batch1 rep1


title: D14 icShape DMSO batch1 rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_F10_AD001_indexed


title: 1202-33


title: D14 icShape DMSO batch1 rep1


title: D8 icShape NAIN3 batch1 rep2


title: D8 icShape NAIN3 batch1 rep1


title: 726-45


title: D8 icShape DMSO batch1 rep1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E6_AD004_indexed


title: 725-45


title: D8 icShape DMSO batch1 rep2


title: 348-43


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E5_AD006_indexed


title: D7 icShape DMSO batch1 rep2


title: D7 icShape NAIN3 batch1 rep2


title: D7 icShape NAIN3 batch1 rep1


title: D0 icShape NAIN3 batch1 rep2


title: D0 icShape NAIN3 batch1 rep1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E5_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E5_AD004_indexed


title: D0 icShape DMSO batch1 rep1


title: 724*2-45


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E6_AD007_indexed


title: D0 icShape DMSO batch1 rep2


title: 716-37


title: 1040-42


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E5_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E6_AD001_indexed


title: 6487-12


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E5_AD010_indexed


title: 6427-14


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E5_AD012_indexed


title: 6377-15


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E5_AD001_indexed


title: spH2A.W2f_rep2 (RNA-seq)

description: spH2A.W 2%formamide

data_processing:
bamtofastq (bedtools v2.26):  bam-files transformed to fastq for kallisto
kallisto v 0.43.1 for counts and tpms:  Alignment to the Schizosaccharomyces pombe with kallisto calculating counts and tpms
R v3.3.1, library( "DESeq2" ) for DEGs:  Differentially expressed genes (DEGs) were classified as having an adjusted p-value < 0.1 and Fold Change >1 and <-1, used counts found with kallisto
R v3.5.1,library(ggplot2), library("dplyr"):  DEGs groups treated vs untreated were plotted
Genome_build: S.pombe - ASM294v2.21
Supplementary_files_format_and_content: kallisto output files with counts and tpms

growth_protocol: yeast cells were grown in YES media at 32°C and harvested 0.6-0.8 x 107 for RNA extraction

extract_protocol:
Total RNA were isolated using RNeasy Plus Mini kit (QIAGEN Cat# 74136) and 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2% v/v formamide added to cell culture for 4 hours


title: spH2A.W2f_rep3 (RNA-seq)

description: spH2A.W 2%formamide


title: 6208-16


title: D7 icShape DMSO batch1 rep1


title: spH2A.W2f_rep1 (RNA-seq)

description: spH2A.W 2%formamide


title: 6182-57


title: 931-44


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E5_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E4_AD012_indexed


title: WT2f_rep3 (RNA-seq)

description: wild type 2%formamide

value: WT


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E4_AD006_indexed


title: 6182-43


title: WT2f_rep2 (RNA-seq)

description: wild type 2%formamide


title: 6176-17


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E4_AD008_indexed


title: 6104-17


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E4_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E4_AD010_indexed


title: WT2f_rep1 (RNA-seq)

description: wild type 2%formamide


title: spH2A.W_rep2 (RNA-seq)


title: 6396-13


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E3_AD006_indexed


title: 6046-18


title: 6174-17


title: spH2A.W_rep1 (RNA-seq)


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E3_AD010_indexed


title: 6035-18


title: WT_rep3 (RNA-seq)

description: wild type


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E4_AD001_indexed


title: WT_rep2 (RNA-seq)

description: wild type


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E6_AD002_indexed


title: 6007-18


title: spH2A.W.4A_H3_rep2 (ChIP-seq)

description: anti-H3_rep2 IP from Input_rep2

data_processing:
bamtofastq (bedtools v2.26)
adapter trimming with cutadapt v1.3
Mapping to Schizosaccharomyces pombe with bowtie2 v 2.2.9
samtools to convert bowtie2 results from sam to bam format
calculation of coverage normalized to input with log2 ratio and 10 bp length with deeptools v2.2.4 bamcompare function
Visualization with IGV v2.4.1
Genome_build: S.pombe - ASM294v2.21
Supplementary_files_format_and_content: *.bw: Normalized to input log2 ratio coverage with 10 bp of length

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with indicated antibody.
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs)

value: anti-H3 (Abcam, ab1791)


title: 5957-1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E4_AD002_indexed


title: 5951-19


title: 5957-19


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E4_AD007_indexed


title: spH2A.W_rep3 (RNA-seq)

value: control


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E3_AD007_indexed


title: 5951-1


title: spH2A.W.4A_H3K9me2_rep2 (ChIP-seq)

description: anti-H3K9me2_rep2 IP from Input_rep2

value: anti-H3K9me2 (Abcam, ab1220)


title: 5883-20


title: WT_rep1 (RNA-seq)

description: wild type


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E3_AD008_indexed


title: spH2A.W.4A_H3K9me2_rep1 (ChIP-seq)

description: anti-H3K9me2_rep1 IP from Input_rep1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E2_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E3_AD004_indexed


title: spH2A.W.4A_H2A.Z_rep2 (ChIP-seq)

description: anti-H2A.Z_rep2 IP from Input_rep2

value: anti-H2A.Z (Active Motif, 39640)


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E3_AD001_indexed


title: spH2A.W.4A_H2A.Z_rep1 (ChIP-seq)

description: anti-H2A.Z_rep1 IP from Input_rep1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E1_AD004_indexed


title: 5867-2


title: 5867-20


title: spH2A.W.4A_Input_rep2 (ChIP-seq)

description: Sonicated chromatin input DNA


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E2_AD012_indexed


title: 5867-1


title: spH2A.W.4A_Input_rep1 (ChIP-seq)

description: Sonicated chromatin input DNA


title: 5803-20


title: spH2A.W.4A_H3_rep1 (ChIP-seq)

description: anti-H3_rep1 IP from Input_rep1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E2_AD006_indexed


title: spH2A.W_H3_rep2 (ChIP-seq)

description: anti-H3_rep2 IP from Input_rep2


title: 5803-1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E1_AD008_indexed


title: 5883-2


title: 5787-29


title: spH2A.W_H3_rep1 (ChIP-seq)

description: anti-H3_rep1 IP from Input_rep1


title: spH2A.W_H3K9me2_rep2 (ChIP-seq)

description: anti-H3K9me2_rep2 IP from Input_rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E1_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E2_AD010_indexed


title: 5769-20


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E3_AD002_indexed


title: spH2A.W_H3K9me2_rep1 (ChIP-seq)

description: anti-H3K9me2_rep1 IP from Input_rep1


title: 5753-21


title: spH2A.W_H2A.Z_rep1 (ChIP-seq)

description:
anti-H2A.Z_rep1 IP from Input_rep1
W6_H2A.Z_to_H3.log2r.bw generated by normalizing wt6_h2az.85550_sorted.aligned.bam to wt6_h3.85552_sorted.aligned.bam


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E2_AD007_indexed


title: 5769-3


title: spH2A.W_H2A.Z_rep2 (ChIP-seq)

description:
anti-H2A.Z_rep2 IP from Input_rep2
W6_H2A.Z_to_H3.log2r.bw generated by normalizing wt6_h2az.85550_sorted.aligned.bam to wt6_h3.85552_sorted.aligned.bam


title: 5717-3


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E1_AD002_indexed


title: spH2A.W_H2A_rep1 (ChIP-seq)

description:
anti-H2A_rep1 IP from Input_rep1
W6_H2A_to_H3.log2r.bw generated by normalizing wt6_h2a.85549_sorted.aligned.bam to wt6_h3.85552_sorted.aligned.bam

value: anti-H2A (Active Motif, 39235)


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E10_AD001_indexed


title: 5687-4


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E1_AD006_indexed


title: spH2A.W_Input_rep2 (ChIP-seq)

description: Sonicated chromatin input DNA


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E2_AD002_indexed


title: spH2A.W_Input_rep1 (ChIP-seq)

description: Sonicated chromatin input DNA


title: 5687-22


title: 5679-4


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E2_AD004_indexed


title: 5679-22


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E11_AD006_indexed


title: WT_H3_rep1 (ChIP-seq)

description: anti-H3_rep1 IP from Input_rep1


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E11_AD012_indexed


title: WT_H3K9me2_rep2 (ChIP-seq)

description: anti-H3K9me2_rep2 IP from Input_rep2


title: 5676-22


title: 5717-20


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E11_AD010_indexed


title: 5659*2-22


title: spH2A.W_H2A_rep2 (ChIP-seq)

description:
anti-H2A_rep2 IP from Input_rep2
W6_H2A_to_H3.log2r.bw generated by normalizing wt6_h2a.85549_sorted.aligned.bam to wt6_h3.85552_sorted.aligned.bam


title: 5658-22


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E11_AD001_indexed


title: WT_H3K9me2_rep1 (ChIP-seq)

description: anti-H3K9me2_rep1 IP from Input_rep1


title: WT_H2A.Z_rep2 (ChIP-seq)

description:
anti-H2A.Z_rep2 IP from Input_rep2
WT_H2A.Z_to_H3.log2r.bw generated by normalizing wt_h2az.85545_sorted.aligned.bam to wt_h3.85547_sorted.aligned.bam


title: 5630-22


title: WT_H2A.Z_rep1 (ChIP-seq)

description:
anti-H2A.Z_rep1 IP from Input_rep1
WT_H2A.Z_to_H3.log2r.bw generated by normalizing wt_h2az.85545_sorted.aligned.bam to wt_h3.85547_sorted.aligned.bam


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E11_AD002_indexed


title: WT_H2A_rep2 (ChIP-seq)

description:
anti-H2A_rep2 IP from Input_rep2
WT_H2A_to_H3.log2r.bw generated by normalizing wt_h2a.85544_sorted.aligned.bam to wt_h3.85547_sorted.aligned.bam


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E11_AD008_indexed


title: WT_H2A_rep1 (ChIP-seq)

description:
anti-H2A_rep1 IP from Input_rep1
WT_H2A_to_H3.log2r.bw generated by normalizing wt_h2a.85544_sorted.aligned.bam to wt_h3.85547_sorted.aligned.bam


title: 5563-23


title: WT_H3_rep2 (ChIP-seq)

description: anti-H3_rep2 IP from Input_rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E10_AD007_indexed


title: WT_Input_rep2 (ChIP-seq)

description: Sonicated chromatin input DNA


title: 5556-23


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E10_AD006_indexed


title: 5555-5


title: WT_Input_rep1 (ChIP-seq)

description: Sonicated chromatin input DNA


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E10_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E11_AD004_indexed


title: 5630-4


title: AD52_Hip_rep8

type: RNA

city: Toon

first: Junichi

last: Iga

state: Ehime

address: Shitsukawa 454

department: Neuropsychiatry

country: Japan

institute: Ehime University

description: Hippocampal gene expression at 52 week

hyb_protocol: Hybridization, washing and scanning steps with SurePrint G3 Mouse 8x60K ver.2.0 were conducted using Gene Expression Hybridization Kit (Agilent), Gene Expression Wash Pack (Agilent, #5188-5327) and Agilent Microarray Scanner (G2505C).

data_processing: The 75th percentile shift normalization and baseline transformation(baseline to median of all samples (all bloods or all hippocampi)) were performed using Agilent GeneSpring GX ver 14.9.

source_name: AD52 Hip rep8

label_protocol: RNA (50ng) was used for microarray analysis. The Low Input Quick Amp Labeling Kit (Agilent) was used to generate amplified and biotinylated sense-strand DNA targets.

growth_protocol: The 3xTg-AD male mice (n=8 at 12 w.o.a; n=8 at 52 w.o.a) and age-matched B6129SF2 WT male mice (n=8 at 12 w.o.a; n=8 at 52 w.o.a) were bred at Ehime University from parents originally purchased from Jackson Laboratory (Bar Harbor, ME, USA, 3xTG-AD, MMRRC #34830; B6129SF1/J, JAX #101043) in a specific pathogen-free facility under climate-controlled conditions at room temperature (22 +/- 2 ℃) with 50% humidity and a 12-h light/dark cycle. Mice were provided with water and standard diet (MF, Oriental Yeast Co. Ltd.) at libitum.

extract_protocol: Total RNA was extracted from frozen hippocampi using RNeasy Mini Kit (QIAGEN, #74104) and from blood using RNeasy Protect Animal Blood Kit (QIAGEN, #73224) according to the manufacturer instructions.

treatment_protocol: Mice at 12 or 52 w.o.a. were anesthetized and killed by decapitation. Hippocampi were immediately stored, and bloods were collected in RNeasy Protect Animal Blood Tube (QIAGEN, #73224) and stored at -80℃ for RNA processing.

value: hippocampus

value: 52 weeks


title: AD52_Hip_rep7

description: Hippocampal gene expression at 52 week

scan_protocol: Hybridization, washing and scanning steps with SurePrint G3 Mouse 8x60K ver.2.0 were conducted using Gene Expression Hybridization Kit (Agilent), Gene Expression Wash Pack (Agilent, #5188-5327) and Agilent Microarray Scanner (G2505C).

source_name: AD52 Hip rep7


title: 5555-23


title: AD52_Hip_rep6

description: Hippocampal gene expression at 52 week

source_name: AD52 Hip rep6


title: AD52_Hip_rep5

description: Hippocampal gene expression at 52 week

source_name: AD52 Hip rep5


title: AD52_Hip_rep4

description: Hippocampal gene expression at 52 week

source_name: AD52 Hip rep4


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E11_AD007_indexed


title: 5465-24


title: D14 RNAdecay 8h rep2

data_processing:
Library strategy: RNAdecay
Raw sequencing reads from ic-SHAPE library were first trimmed to remove adaptors using cutadapt (version 1.12), collapsed to remove PCR duplicates and trimmed to remove the leading 15-nt containing both the unique molecular identifiers and index sequences.
The processed reads were then mapped to an in-house reference transcriptome using bowtie (version: 0.12.8)
The RTstop counts were then compuated as the coverage of 5' end of each read using genomecov from bedtools (verison 2.25.0).
Genome_build: GRCh38 based transcriptome
Supplementary_files_format_and_content: Tab-delimited text files include Rtstop counts for each position if available.

value: neurons

value: RNAdecay

value: Actinmycin D


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E10_AD010_indexed

value: AON

value: male


title: 5461-24

value: Female

value: blood


title: AD52_Hip_rep2

description: Hippocampal gene expression at 52 week

source_name: AD52 Hip rep2


title: 535-48


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E3_AD012_indexed


title: D8 RNAdecay 8h rep2

value: early neurons


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E10_AD008_indexed


title: D8 RNAdecay 8h rep1


title: 535-39


title: D7 RNAdecay 8h rep2

value: neuronal precursor cells


title: 39_319_CD4CD8_GFPpos

city: Atlanta

first: Gregory

middle: K

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: 616_Michelle_CD4-CD4CD8_DESeq2_NormCounts.txt

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the human (GRCh38) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: CD4 positive T Cells

extract_protocol:
Sorted populations were stored in 350l of RLT buffer with 1% of 2-Mercaptoethanol (BME) at -80°C, purified using Qiagen RNeasy Micro columns, and RNA quality was assessed using an Agilent Bioanalyzer.
Ten nanograms of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Illumina NexteraXT DNA Library Preparation kit.

tag: subjectid

tag: culture

tag: egfp

value: GFPpos


title: AD12_Hip_rep8

description: Hippocampal gene expression at 12 week

source_name: AD12 Hip rep8

value: 12 weeks


title: 5315-24


title: D7 RNAdecay 8h rep1


title: AD12_Hip_rep7

description: Hippocampal gene expression at 12 week

source_name: AD12 Hip rep7


title: 38_319_CD4CD8_GFPneg

value: GFPneg


title: 5295-26

value: Male


title: 5293-26


title: 37_319_CD4_GFPpos


title: D0 RNAdecay 8h rep2

value: hESCs


title: AD52_Hip_rep1

description: Hippocampal gene expression at 52 week

source_name: AD52 Hip rep1


title: D0 RNAdecay 8h rep1


title: AD52_Hip_rep3

description: Hippocampal gene expression at 52 week

source_name: AD52 Hip rep3


title: 5250-7


title: D14 RNAdecay 8h rep1


title: 36_319_CD4_GFPneg


title: AD12_Hip_rep5

description: Hippocampal gene expression at 12 week

source_name: AD12 Hip rep5


title: D14 RNAdecay 4h rep2


title: 524*2-45


title: 34_318_CD4CD8_GFPpos

value: female


title: D14 RNAdecay 4h rep1


title: 33_318_CD4CD8_GFPneg


title: 5229-26


title: D8 RNAdecay 4h rep2

source_name: early neurons


title: 32_318_CD4_GFPpos


title: 5188-9


title: D8 RNAdecay 4h rep1


title: 31_318_CD4_GFPneg


title: D7 RNAdecay 4h rep2


title: 5188-27


title: 510-40


title: 5184-8


title: 28_543_CD4CD8_GFPneg


title: D7 RNAdecay 4h rep1


title: AD12_Hip_rep4

description: Hippocampal gene expression at 12 week

source_name: AD12 Hip rep4

value: hippocampus


title: D0 RNAdecay 4h rep2


title: 5074-8


title: AD12_Hip_rep2

description: Hippocampal gene expression at 12 week

source_name: AD12 Hip rep2


title: AD12_Hip_rep3

description: Hippocampal gene expression at 12 week

source_name: AD12 Hip rep3


title: AD12_Hip_rep1

description: Hippocampal gene expression at 12 week

source_name: AD12 Hip rep1


title: AD12_Hip_rep6

description: Hippocampal gene expression at 12 week

source_name: AD12 Hip rep6


title: C52_Hip_rep8

description: Hippocampal gene expression at 52 week

source_name: C52 Hip rep8

value: B6129SF2 WT

value: 52 weeks


title: 27_543_CD4_GFPpos


title: 26_543_CD4_GFPneg


title: D0 RNAdecay 4h rep1

source_name: hESCs

value: RNAdecay


title: C52_Hip_rep7

description: Hippocampal gene expression at 52 week

source_name: C52 Hip rep7


title: 5073-9

source_name: normal blood sample


title: C52_Hip_rep6

description: Hippocampal gene expression at 52 week

source_name: C52 Hip rep6


title: 24_540_CD4CD8_GFPpos

source_name: CD4 positive T Cells


title: D14 RNAdecay 2h rep2

source_name: neurons

value: neurons

value: Actinmycin D


title: C52_Hip_rep5

description: Hippocampal gene expression at 52 week

source_name: C52 Hip rep5


title: 5073-28


title: 29_543_CD4CD8_GFPpos


title: C52_Hip_rep4

description: Hippocampal gene expression at 52 week

source_name: C52 Hip rep4


title: D14 RNAdecay 2h rep1


title: 23_540_CD4CD8_GFPneg

value: male


title: 5066-9

value: Female


title: C52_Hip_rep2

description: Hippocampal gene expression at 52 week

source_name: C52 Hip rep2


title: D8 RNAdecay 2h rep2


title: 5066-27

value: blood


title: C52_Hip_rep1

description: Hippocampal gene expression at 52 week

source_name: C52 Hip rep1


title: 22_540_CD4_GFPpos


title: D7 RNAdecay 2h rep2

source_name: neuronal precursor cells


title: 21_540_CD4_GFPneg


title: D8 RNAdecay 2h rep1

source_name: early neurons

value: early neurons


title: C12_Hip_rep7

description: Hippocampal gene expression at 12 week

source_name: C12 Hip rep7


title: 5062-10


title: D7 RNAdecay 2h rep1

value: neuronal precursor cells


title: C12_Hip_rep6

description: Hippocampal gene expression at 12 week

source_name: C12 Hip rep6


title: C12_Hip_rep8

description: Hippocampal gene expression at 12 week

source_name: C12 Hip rep8


title: C52_Hip_rep3

description: Hippocampal gene expression at 52 week

source_name: C52 Hip rep3


title: 4746-20


title: 4721-29


title: D0 RNAdecay 2h rep2


title: D0 RNAdecay 2h rep1


title: 16_796_CD4_GFPneg


title: 5062-28


title: 4703-29


title: 14_312_CD4CD8_GFPpos

value: GFPpos


title: D14 RNAdecay 1h rep1


title: 13_312_CD4CD8_GFPneg


title: 4654-29


title: C12_Hip_rep4

description: Hippocampal gene expression at 12 week

source_name: C12 Hip rep4

value: 12 weeks


title: C12_Hip_rep5

description: Hippocampal gene expression at 12 week

source_name: C12 Hip rep5


title: C12_Hip_rep2

description: Hippocampal gene expression at 12 week

source_name: C12 Hip rep2


title: C12_Hip_rep3

description: Hippocampal gene expression at 12 week

source_name: C12 Hip rep3


title: 19_796_CD4CD8_GFPpos


title: 18_796_CD4CD8_GFPneg

value: GFPneg


title: D8 RNAdecay 1h rep1


title: D8 RNAdecay 1h rep2


title: 17_796_CD4_GFPpos


title: 4716-29

source_name: normal blood sample

value: Male


title: D7 RNAdecay 1h rep1


title: 9_914_CD4CD8_GFPpos

source_name: CD4 positive T Cells


title: D0 RNAdecay 1h rep2

source_name: hESCs

value: hESCs


title: 11_312_CD4_GFPneg

value: female


title: D14 RNAdecay 1h rep2

source_name: neurons


title: 4648-20


title: 4647-30


title: 8_914_CD4CD8_GFPneg


title: 4510-30


title: 7_914_CD4_GFPpos


title: AD52_bld_rep7

description: Blood gene expression at 52 week

source_name: AD52 bld rep7


title: 6_914_CD4_GFPneg


title: C12_Hip_rep1

description: Hippocampal gene expression at 12 week

source_name: C12 Hip rep1

value: hippocampus


title: AD52_bld_rep5

description: Blood gene expression at 52 week

source_name: AD52 bld rep5


title: D14 RNAdecay 0h rep2


title: AD52_bld_rep6

description: Blood gene expression at 52 week

source_name: AD52 bld rep6


title: 4_890_CD4CD8_GFPpos


title: D0 RNAdecay 1h rep1


title: AD52_bld_rep8

description: Blood gene expression at 52 week

source_name: AD52 bld rep8


title: 4345-31


title: 4345-13


title: 4510-18


title: D7 RNAdecay 1h rep2

source_name: neuronal precursor cells


title: AD52_bld_rep4

description: Blood gene expression at 52 week

source_name: AD52 bld rep4


title: D8 RNAdecay 0h rep2

source_name: early neurons


title: 3_890_CD4CD8_GFPneg


title: D14 RNAdecay 0h rep1


title: 4152-32


title: 2_890_CD4_GFPpos


title: D8 RNAdecay 0h rep1


title: 1_890_CD4_GFPneg


title: AD52_bld_rep3

description: Blood gene expression at 52 week

source_name: AD52 bld rep3


title: 4648-2


title: AD12_bld_rep8

description: Blood gene expression at 12 week

source_name: AD12 bld rep8


title: AD12_bld_rep6

description: Blood gene expression at 12 week

source_name: AD12 bld rep6


title: 4305-32


title: 4141-15


title: 4047-33


title: D7 RNAdecay 0h rep1


title: AD12_bld_rep7

description: Blood gene expression at 12 week

source_name: AD12 bld rep7


title: 12_312_CD4_GFPpos


title: 3915-24


title: D0 RNAdecay 0h rep1


title: Ssrp1 KO rep2

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to mm10 genome using Hisat2.
Raw count were generated by featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw count values for each Sample.

source_name: Embryonic stem cell

growth_protocol: Mouse E14 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin(Sigma),in medium(Hyclone) that supplement with 15% FBS（Hyclone）,10ng/ml mLIF (GeneScript)，1% Penicillin-Streptomycin (Solarbio)，1% GlutaMAX(Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Total RNA was extracted with RNAiso Plus (Takara) and was subjected to DNaseI (Thermo Scientific) for 30min
1 μg total RNA with RIN value above 9 was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The rRNA was depleted from total RNA using mouse Ribo-Zero rRNA removal Kit (Illumina). The rRNA-depleted RNA was then fragmented and reverse-transcribed. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase with random primers and Actinomycin D. The second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The double stranded cDNA were ligated with adapters, amplified by PCR and purified. libraries with different indices were multiplexed and loaded on an Illumina instrument according to manufacturer’s instructions (Illumina) and pair-end sequenced for 10G data.

treatment_protocol: We used Cas9-gRNA to knockout Ssrp1 in embryonic stem cells. Wild-type (WT) ESC and Ssrp1 knockout cell lines were cultured under serum conditions. The shRNA of Usp7 was cloned into pSuper puro vector. WT ESCs were transfected with 1000ng pSuper puro vector. After transfection for 24h, the cells were treated with 1ug/ml puromycine for 3days and the medium were changed every 24h.

value: E14 embryonic stem cells (ESCs)

value: Ssrp1 KO


title: Ssrp1 KO rep1


title: D0 RNAdecay 0h rep2

value: RNAdecay


title: 3915-34

source_name: normal blood sample


title: Ssrp1 Control rep1

value: wild type


title: Ssrp1 Control rep2


title: D14 RNASeq rep2

data_processing:
Raw sequencing reads from ic-SHAPE library were first trimmed to remove adaptors using cutadapt (version 1.12), collapsed to remove PCR duplicates and trimmed to remove the leading 15-nt containing both the unique molecular identifiers and index sequences.
The processed reads were then mapped to an in-house reference transcriptome using bowtie (version: 0.12.8)
The RTstop counts were then compuated as the coverage of 5' end of each read using genomecov from bedtools (verison 2.25.0).
Genome_build: GRCh38 based transcriptome
Supplementary_files_format_and_content: Tab-delimited text files include Rtstop counts for each position if available.

value: neurons

value: RNAseq


title: AD12_bld_rep4

description: Blood gene expression at 12 week

source_name: AD12 bld rep4


title: AD12_bld_rep5

description: Blood gene expression at 12 week

source_name: AD12 bld rep5


title: AD12_bld_rep3

description: Blood gene expression at 12 week

source_name: AD12 bld rep3


title: 3867-34

value: Female


title: D14 RNASeq rep1

source_name: neurons


title: abcam 2 Ssrp1

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to mm10 genome using Bowtie2.
Bigwig file was generated by bamCompare from Deeptools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files, ChIP-seq normalized signal

growth_protocol: Mouse E14 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin(Sigma),in medium(Hyclone) that supplement with 15% FBS（Hyclone）,10ng/ml mLIF (GenScript)，1% Penicillin-Streptomycin (Solarbio)，1% GlutaMAX(Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Cells were lysed and chromatin was extracted. Anti-Ssrp1 antibody was used to immunoprecipiate Ssrp1 in mESCs. And Anti-Usp7 antibody was used to immunoprecipiate Usp7 in WT and Ssrp1 KO mESCs. Proteins on chromatin associated with Ssrp1 was digested and chromatin was decrosslinked at 65 degree overnight. DNA was extracted in phenol-chloroform.
For ChIP-seq, 5ng of Ssrp1-assocated chromatin DNA was used in ChIP-seq library preparation.  Libraries were prepared according to Illumina protocols and library fragments of ~250 bp were used for sequencing.

treatment_protocol: Mouse E14 embryonic stem cells

value: Wildytpe

value: Anti-Ssrp1 (abcam ab137034)


title: abcam 2 Input


title: D7 RNAdecay 0h rep2

value: neuronal precursor cells

value: Actinmycin D


title: 3521-37

value: blood


title: 3459-38


title: D8 RNASeq rep2

value: early neurons


title: abcam 1 Input


title: D8 RNASeq rep1


title: 3915-16


title: C52_bld_rep8

description: Blood gene expression at 52 week

source_name: C52 bld rep8

value: B6129SF2 WT

value: 52 weeks


title: D7 RNASeq rep2


title: AD12_bld_rep1

description: Blood gene expression at 12 week

source_name: AD12 bld rep1

value: 12 weeks


title: AD52_bld_rep2

description: Blood gene expression at 52 week

source_name: AD52 bld rep2


title: 3106-40


title: C52_bld_rep7

description: Blood gene expression at 52 week

source_name: C52 bld rep7


title: Wildtype Usp7

value: Anti-Usp7 (Bethyl A300-033A)


title: 3440-38


title: D0 RNASeq rep2

source_name: hESCs

value: hESCs


title: 2525-42


title: abcam 1 Ssrp1

value: E14 embryonic stem cells (ESCs)


title: D0 RNASeq rep1


title: AD52_bld_rep1

description: Blood gene expression at 52 week

source_name: AD52 bld rep1


title: 2159-26


title: 150-52


title: Ssrp1 KO Usp7

value: Ssrp1 KO


title: Twist1-OE Input DNA rep2

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

data_processing:
Adaptors from raw sequencing data were removed using Trimmomatic {Bolger, 2014} and aligned to the mm10 mouse genome (GENCODE GRCm38.p5; Frankish, 2018) using BWA aligner
duplicates/unpaired sequences were removed using the MarkDuplicates program from picardtools(http://broadinstitute.github.io/picard/).
MACS2 (https://github.com/taoliu/MACS) (Zhang et al., 2008) were used for ChIP-seq peak calling for both Twist1-/-; Flag-Twist1 O/E and Twist1-/- IP samples against genomic input.
Peak coordinates from the two replicates were merged, using the most extreme start and end positions of the two replicates.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak

source_name: Embryoid Bodies

growth_protocol: The ESCs were cultured in complete mESC medium (high glucose DMEM (Gibco), 12.5 % (v/v) heat-inactivated FBS (Fisher Biotec Australia), 10 mM β-mercaptoethanol, 0.09 % (v/v), 1X non-essential amino acids (100X Thermo Fisher Scientific), 1 % (v/v) nucleosides (100X, Merck) and 10 mil U/mL ESGRO® mouse leukaemia inhibitory factor (Merck)). ESCs were passaged every 2–3 days.

extract_protocol:
Cells were crosslinked for 10 minutes with 1% Formaldehyde solution at room temperature and quenched with 0.25M Glycine for 2 minutes.  Cells were then lysed in lysis buffers to remove cytoplasmic materials. To fragment chromatin, the cells were sonicated on the Bioruptor Plus (Diagenode) using the following program: 30 seconds on, 30 seconds off for 40 minutes on High power. To separate cell debris from chromatin, the supernatant was collected after centrifuging at 14,000 g and then incubated with antibody-conjugated Dynabeads overnight at 4 °C.
Libraries were prepared using TruSeq ChIP Sample Prep Kit (Illumina)  following manufacturer instruction

treatment_protocol: Embryoid bodies (EB) were differentiated in EB-medium consisting of Dulbecco’s Modified Eagle’s Medium supplemented with 15% Fetal Calf Serum, 1% Non-essential amino-acid supplement and 0.1 µM 2-Mercaptoethanol. Single ES cells were seeded onto aggrewells in a 24 well plate (Stem Cell Technologies, Cat. No. 34411) at 1.5 × 10^6 cells per well in EB-medium. Cell aggregates were transferred to non-tissue culture treated 10 cm plates and EB-medium 24 hrs later, and placed on an orbital-shaker under slight rotation at 37 °C, 5% CO2, to prevent single EBs from attaching to each other or surfaces.  Media was refreshed every 48 hrs.

value: ESC-derived embroid body

value: Embryoid Bodies


title: Usp7_KD rep2

source_name: E14 embryonic stem cells

extract_protocol:
Total RNA was extracted with RNAiso Plus (Takara) and was subjected to DNase Ｉ(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: E14 embryonic stem cells


title: Ssrp1 KO Input


title: C52_bld_rep5

description: Blood gene expression at 52 week

source_name: C52 bld rep5


title: C52_bld_rep6

description: Blood gene expression at 52 week

source_name: C52 bld rep6


title: D7 RNASeq rep1

source_name: neuronal precursor cells

value: RNAseq


title: Twist1-OE Input DNA rep1


title: C52_bld_rep4

description: Blood gene expression at 52 week

source_name: C52 bld rep4


title: Wildtype Input

source_name: Embryonic stem cell

value: Wildytpe


title: C52_bld_rep1

description: Blood gene expression at 52 week

source_name: C52 bld rep1


title: Twist1-KO Input DNA


title: C52_bld_rep3

description: Blood gene expression at 52 week

source_name: C52 bld rep3


title: Usp7_KD rep1


title: Usp7_Control rep2

value: control


title: 1215-40

source_name: normal blood sample

value: Male


title: Usp7_Control rep1


title: 2159-45

value: Female


title: 1202-41

value: blood


title: Twist1-OE_ChIPseq_4

value: TWIST1 (abcam, ab50887 lot 122116)


title: Twist1-OE_ChIPseq_3


title: Ssrp1_KO rep2


title: C52_bld_rep2

description: Blood gene expression at 52 week

source_name: C52 bld rep2

value: B6129SF2 WT


title: Twist1-OE_ChIPseq_2


title: C12_bld_rep7

description: Blood gene expression at 12 week

source_name: C12 bld rep7


title: C12_bld_rep6

description: Blood gene expression at 12 week

source_name: C12 bld rep6


title: Ssrp1_KO rep1


title: 142*2-54


title: C12_bld_rep8

description: Blood gene expression at 12 week

source_name: C12 bld rep8


title: AD12_bld_rep2

description: Blood gene expression at 12 week

source_name: AD12 bld rep2


title: Twist1-OE_ChIPseq_1


title: Ssrp1_Control rep1


title: Twist1-KO_ChIPseq_3


title: Ssrp1_Control rep2


title: C12_bld_rep5

description: Blood gene expression at 12 week

source_name: C12 bld rep5


title: Twist1-KO_ChIPseq_2


title: C12_bld_rep3

description: Blood gene expression at 12 week

source_name: C12 bld rep3