title: P_Ctrl_2

value: Vehicle


title: P_Ctrl_3

status: Public on Jul 19 2022

type: SRA

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

country: Spain

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

library_source: transcriptomic

data_processing:
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to mm10 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and Log2 Fold Change values for differential expression of case vs control

molecule: total RNA

organism: Mus musculus

source_name: Macrophages

growth_protocol: Primary bone marrow derived macrophages (P-BMDMs) differentiated with complete 10% FCS and M-CSF were trypsinized and plated in 6-well plates (1million cells/well) in complete medium. Immortalized macrophages (I-BMDMs) were plated in complete medium (containing 10% FCS), similar to P-BMDMs

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: P-BMDM and I-BMDM were treated with thyroid hormone (10 nM) or vehicle.

tag: cell type

value: Immortal bone marrow derived macrophages

tag: treatment


title: P_Ctrl_1


title: T3_3

value: Bone marrow derived macrophages

value: thyroid hormone T3


title: T3_2


title: Ctrl_3


title: T3_1


title: SiHa, pv, 3

city: Linhai

first: Hui-Hui

last: Xu

state: Zhejiang province

country: China

institute: Taizhou Hospital

data_processing:
BGISEQ-500
Sequence reads were trimmed for adaptor sequence/low-quality sequence (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using BGISEQ-500 genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using BGISEQ-500 genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Homo sapiens

source_name: SiHa

growth_protocol: The human cervical carcinoma cell lines SiHa were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using BGI Kit following manufacturer's protocols.

treatment_protocol:
transfected with the recombinant pVITRO2-mcs vector (InvivoGen, NY, USA) containing HLA-G cDNA or empty vector by Lipofectamine 3000 reagent (InvitroGen, NY, USA) according to the manual instructions.
The transfectants were selected with 50 μg/ml hygromycin B (InvitroGen, NY, USA)

tag: cell line

value: SiHa

value: human cervical carcinoma cell

tag: genotype

value: control

value: pVITRO2-hygro-mcs vector transfection


title: Ctrl_2


title: HeLa, HLA-G, 5

source_name: HeLa

growth_protocol: The human cervical carcinoma cell lines HeLa were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

value: HeLa

value: HLA-G overexpression

value: pVITRO2-hygro-mcs_HLA-G transfection


title: Ctrl_1


title: HeLa, pv, 1


title: KRAS+P53-liver tumor-2

city: Hefei

first: yiqing

last: Shen

address: University of Science and Technology of China

data_processing:
Quality Control:  In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or  fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by  Cutadapt (V1.9.1) to be high quality clean data.
Mapping:  Firstly, reference genome sequences and gene model annotation files of relative species were downloaded  from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index  reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2  (v2.0.1).
Expression analysis  In the beginning transcripts in fasta format are converted from known gff annotation file and indexed  properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform  expression levels from the pair-end clean data.
Differential expression analysis  Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative  binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit  (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer  (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose  gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation  sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A)  mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit.  The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and  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 doublestranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptorligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size  of 300 bp) were recovered. Each sample was then amplified by PCR for 13 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 beads, validated using an Qsep100 (Bioptic， Taiwan， China), and quantified by Qubit3.0  Fluorometer (Invitrogen, Carlsbad, CA, USA).

tag: tissue

value: liver

tag: Sex

value: male

tag: disease state

value: liver cancer

tag: strain


title: KRAS+P53-liver tumor-3

institute: University of Science and Technology of China


title: WT-liver-1

value: healthy

value: WT


title: KRAS+PTEN-liver tumor-3


title: KRAS+P53-liver tumor-1


title: LS174T GNAS R201H CDX tumor Dox (-)

city: HOUSTON

first: John Paul

state: TX

address: 1515 Holcombe Blvd

department: Gastrointestinal Medical Oncology

country: USA

institute: The University of Texas MD Anderson Cancer Center

description: Sample 7

data_processing:
Raw BAM/FASTQ files were mapped to the human reference genome (hg38) using STAR (version 2.7.2b) RNASeq alignment tool. Biobambam (version 0.0.191) was used to mark duplicates and index raw files before alignment.
Xenome (version 1.0.1-r) was used to segregate mouse and human reads from raw RNAseq files of CDX models. Mouse reference genome (GRCm39) and gene annotation file (Gencode.vM26) were used for mapping and annotating mouse reads. Extracted human reads for each CDX sample were stored in FASTQ files and input to the downstream STAR (version 2.7.2b) RNASeq alignment tool.
HTSeq (version 0.11.0) was utilized to extract raw read counts from STAR-aligned RNAseq files of both cell lines and CDX models.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each Sample

source_name: CDX tumor

growth_protocol: All cell lines were grown in RPMI-1640 medium supplemented with 10% FBS, 2mM glutamine, and 1% Pen-Strep at standard culture conditions (37 °C, 5% CO2, 95% humidity). Cells were maintained at low passages, authenticated by STR analysis and tested to rule out mycoplasma contamination.

extract_protocol:
RNA was extracted using RNAqueous™ Total RNA Isolation Kit (Catalog number: AM1912). RNA concentraction ≥ 20 ng/µl for each sample was used for library construction.
Before library construction, quality control for each RNA samples was performed to guarantee the reliability of the data. RNA degradation and potential contamination were tested by Agarose Gel Electrophoresis. Agilent 2100 was used to check the RNA integrity and quantitation. After the QC procedures, mRNA from each smaple was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

value: Colorectal cancer cell line

value: CDX tumor

value: GNASR201H Dox(-)


title: LS174T GNAS R201H CDX tumor Dox (+)

description: Sample 8

value: GNASR201H Dox(+)


title: WT-liver-3


title: WT-liver-2


title: P53+PTEN-liver tumor-2

value: WT (P53+PTEN-)


title: P53+PTEN-liver tumor-3


title: KM12 GNAS KO CDX tumor

description: Sample 4

value: GNAS Knock-out


title: P53+PTEN-liver tumor-1


title: KRAS+PTEN-liver tumor-2


title: KRAS+PTEN-liver tumor-1


title: KM12 parental CDX tumor

description: Sample 3


title: 10x VDJ Knockout 2

city: Oxford

first: Alexander

last: Clarke

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

description:
Knockout 2
10x VDJ

library_source: transcriptomic single cell

data_processing:
cellranger-6.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Viable, dump-negative tdTomato+ B cells were flow sorted
Approximately 17,000 cells per sample were loaded onto the 10X Genomics Chromium Controller (Chip K). Gene expression and BCR sequencing libraries were prepared using the 10x Genomics Single Cell 5' Reagent Kits v2 (Dual Index) following manufacturer user guide (CG000330 Rev B)

value: Spleen

value: B cells

value: Tfam KO

value: Aicda-Cre x Tfam flox x Rosa26-Stop-tdTomato


title: 10x VDJ Wild type 1

description:
Wild type 1
10x VDJ

value: Wild type

value: Aicda-Cre x Rosa26-Stop-tdTomato


title: 10x VDJ Knockout 3

description:
Knockout 3
10x VDJ


title: 10x VDJ Knockout 1

description:
Knockout 1
10x VDJ


title: 10x VDJ Wild type 3

description:
Wild type 3
10x VDJ


title: 10x VDJ Wild type 2

description:
Wild type 2
10x VDJ


title: 10x 5' Gex Knockout 3

description:
Knockout 3
10x 5' Gex


title: 10x 5' Gex Wild type 3

description:
Wild type 3
10x 5' Gex


title: 10x 5' Gex Knockout 2

description:
Knockout 2
10x 5' Gex


title: 10x 5' Gex Knockout 1

description:
Knockout 1
10x 5' Gex


title: 10x 5' Gex Wild type 1

description:
Wild type 1
10x 5' Gex


title: 10x 5' Gex Wild type 2

description:
Wild type 2
10x 5' Gex


title: E8.5_Tet_TKO_4

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: TET TKO chimera cells at E8.5

data_processing:
FastQ files were processed using CellRanger Single Cell 3' pipeline version 3.1.0
Assembly: NOT PROVIDED
Supplementary files format and content: Tsv files contain barcodes of detected cells.
Supplementary files format and content: Tsv files contain IDs of detected genes.
Supplementary files format and content: Mtx files contain matrix of raw count values.

source_name: E8.5 embryo

extract_protocol:
10x Genomics Single Cell Gene Expression
Single embryos were dissociated into single-cells using 200μl of TriplE Express for 10 minutes at 37°C on a shaking incubator then quenched with 1ml of ice-cold 10% FCS in PBS. Cells were filtered using a 40μM Flowmi cell strainer, span down at 300g for 5 minutes then resuspended in 50μl of PBS containing 0.04% BSA. Cells were counted and viability assessed using trypan blue staining on a Countess II instrument (Invitrogen). >95% of cells were negative for trypan blue indicating high sample quality. embryos were pooled and dissociated as above then flow-sorted using the BD Influx High-Speed Cell Sorter (BD Biosciences) or a BD FACSAriaTM system (BD Biosciences) in a biosafety cabinet, collecting DAPI negative singlets into two 1.5ml tubes, one for tomato positive (knockout cells) and one for tomato negative (host cells). Cells were spun down at 300g for 5 minutes and resuspended in 50ul of PBS containing 0.04% BSA then counted as above. embryos were pooled and dissociated as above then flow-sorted using the BD Influx High-Speed Cell Sorter (BD Biosciences) or a BD FACSAriaTM system (BD Biosciences) in a biosafety cabinet, collecting DAPI negative singlets into two 1.5ml tubes, one for tomato positive (knockout cells) and one for tomato negative (host cells). Cells were spun down at 300g for 5 minutes and resuspended in 50ul of PBS containing 0.04% BSA then counted as above.
scRNA-seq was performed using 10x Genomics 3' v3 following manufacturers instructions and loading 16,000 cells. Sequencing was performed using an Illumina Novaseq using the recommended read lengths.

value: TET TKO

tag: background


title: E8.5_WT_tdTomato-_1

description: Wildtype host cells at E8.5

value: Wildtype


title: E8.5_WT_tdTomato-_2

description: Wildtype host cells at E8.5


title: E8.5_Tet_TKO_1

description: TET TKO chimera cells at E8.5


title: Lung immune cells, gene expression library

city: Bar Harbor

first: Guangwen

last: Ren

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description:
polyA RNA
GR20001

data_processing:
The raw data (FASTQ file) of each library were produced and demultiplexed using Illumina bcl2fastq 2.20.0.422.
For all libraries, R1 contains a 16bp cell barcode + 12bp UMI barcode and R2 contains the biological reads. If present, I1 contains the 8bp i7 index which is needed for 10X CellRanger pipelines.
An unfiltered digital gene expression matrix was generated for each gene expression library against the 10X Genomics mouse reference genome (mm10-3.0.0) build using CellRanger v3.1.0
A digital counts matrix was generated for each hashtag library using CITE-Seq-Count v1.4.3. This produces a matrix of counts with hashtag labels for rows and cell barcodes for columns.
Assembly: GRCm38.93
Supplementary files format and content: Transcriptomic and HashTag (HTO) counts matrices in Matrix Market sparse CSC matrix format. Rows correspond to genes in the order provided in features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

molecule: polyA RNA

source_name: Lung

extract_protocol:
Sorted lung CD45+ immune cells from WT or Ptgs2-cKO mice were labeled with cell hashing antibodies and 24,000 cells (12,000 cells from each hashtagged sample) were loaded into one lane of a 10X Chromium microfluidic chip. Cells capture, lysis and RNA extraction were performed using the 10X V3 Chromium technology following the manufacturer’s protocol.
Single cell capture, barcoding and library preparation were performed with the 10x Chromium system using version 3 chemistry, following the manufacturer’s protocol. cDNA was synthesized and amplified as per manufacturer’s protocol and amplified to construct an Illumina sequencing library. cDNA and libraries were checked for quality on an Agilent 4200 TapeStation, quantified by KAPA qPCR.

value: Lung

value: Immune cells

value: Female

tag: development stage

value: adult

value: WT and Ptgs2-cKO

tag: age

value: 10 weeks

tag: library type

value: RNA


title: E8.5_Tet_TKO_3

description: TET TKO chimera cells at E8.5


title: E8.5_Tet_TKO_2

description: TET TKO chimera cells at E8.5


title: WT_7

description: Wildtype E8.5 embryos

extract_protocol:
10x Genomics Single Cell Gene Expression
Single embryos were dissociated into single-cells using 200μl of TriplE Express for 10 minutes at 37°C on a shaking incubator then quenched with 1ml of ice-cold 10% FCS in PBS. Cells were filtered using a 40μM Flowmi cell strainer, span down at 300g for 5 minutes then resuspended in 50μl of PBS containing 0.04% BSA. Cells were counted and viability assessed using trypan blue staining on a Countess II instrument (Invitrogen). >95% of cells were negative for trypan blue indicating high sample quality.
scRNA-seq was performed using 10x Genomics 3' v3 following manufacturers instructions and loading 16,000 cells. Sequencing was performed using an Illumina Novaseq using the recommended read lengths.

tag: strain background


title: WT_6

description: Wildtype E8.5 embryos


title: WT_4

description: Wildtype E8.5 embryos


title: TGF6_3

status: Public on Jul 20 2022

city: Athens

first: Jingwen

last: Song

state: Ohio

address: 172 Water Tower Drive, 101 Konner Bldg.25, The Rideges

department: biological Sciences

institute: Ohio university

data_processing:
Preparation of clean sequence reads  Constructed sequencing libraries were subject to sequencing with Illumina NovaseqTM 6000 platform (paired-end, 150 bp). Prior to assembly, reads containing sequencing adaptors, reads containing sequencing primers, and sequences with q quality score lower than 20 were removed.
Alignment of reads  The cleaned sequencing reads were aligned to reference genome [https://www.ncbi.nlm.nih.gov/genome/guide/human/] using HISAT2 package. Multiple alignments were allowed for each read sequence (up to 20 by default), with a maximum of two mismatches allowed. HISAT2 also built a database of potential splice junctions.
Transcript abundance estimation and differential expression analysis  Aligned reads of individual samples were assembled using StringTie. Transcriptomes from all samples were then merged to reconstruct a comprehensive transcriptome using a proprietary Perl script of LC Sciences (Houston, Texas, U.S.A.). Following transcriptome reconstruction, FPKM reads were evaluated by StringTie, and differential expressed genes were evaluated by edgeR. The differentially expressed mRNAs and genes were selected with log2 (fold change) ≥1 or log2 (fold change) ≤-1, and with p values < 0.05.

source_name: lung

growth_protocol: Human non-small lung cancer cell line A549 cells were purchased from ATCC. A549 cells were cultured in standard Dulbecco’s Modified Eagle Medium (DMEM contains 25mM glucose) supplemented with 10% fetal bovine serum, 1% penicillin, and 50ug/ml streptomycin in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol:
The total RNA was extracted using GeneJET RNA Purification Kit (Thermo Scientific™) following manufacture’s instruction.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer.

treatment_protocol: A549 cells which grown on 100mm plates (1*10^6 cells) were individually treated with 0.5mM ATP, 10ng/ml TGF-β for 2h and 6h.

value: human non-small lung cancer cell line A549

value: 10ng/ml TGF-β 6h treatment


title: WT_1

description: Wildtype E8.5 embryos


title: WT_2

description: Wildtype E8.5 embryos


title: WT_3

description: Wildtype E8.5 embryos


title: Dnmt3b_KO_2

description: Dnmt3b null E8.5 embryos

value: Dnmt3b null


title: Dnmt3a_KO_2

description: Dnmt3a null E8.5 embryos

value: Dnmt3a null


title: Qiagen_S1

city: Tartu

first: Kaspar

last: Valgepea

state: Tartu

address: Nooruse 1, room 520

department: Institute of Technology

country: Estonia

institute: University of Tartu

data_processing:
The quality of NextSeq raw reads was verified using MultiQC (Ewels et al., 2016) and adapter sequences were trimmed using the Cutadapt package (version 2.10; Martin 2011)
Sequencing reads were aligned and mapped to the genome of C. autoethanogenum DSM 10061 (NC_022592.1) using the Rsubread package (version 2.4.2; Liao et al., 2019).
Genomic features were assigned using the featureCounts functions within Rsubread
Raw library sizes were normalized and transcript abundances in reads per kilobase of transcript per million mapped reads (RPKM) were estimated from feature counts and gene lengths using edgeR (version 3.32.1; Robison et al., 2010).
Assembly: NC_022592.1
Supplementary files format and content: RPKM value tab-delimited text files

organism: Clostridium autoethanogenum

source_name: bacteria cell

growth_protocol: Clostridium autoethanogenum was grown on syngas or CO in chemically defined medium anaerobically at 37C and a pH of 5 in chemostats at dilution rate ~1 and 2.0 day-1

extract_protocol:
Frozen pellets were thawed and total RNA was extracted using cellular lysis in RNase-free acid-washed glass beads (Merck) and RNeasy mini kit (Qiagen) with off-column DNase treatment followed by enrichment and purification using RNA Clean & ConcentratorTM (Zymo Research).
Ribosomal RNA were removed as follows: samples referred to as “NuGEN” were processed with Prokaryotic AnyDeplete™ (0363; NuGEN), “Qiagen” samples with QIAseq® FastSelect™ Kit (335925; Qiagen), and “Zymo” samples with Zymo-Seq RiboFree™ Total RNA Library Kit (R3000; Zymo Research)
Stranded mRNA libraries were prepared for NuGEN samples with Universal Prokaryotic RNA-Seq, Prokaryotic AnyDeplete™ (0363; NuGEN); for Qiagen samples with QIAseq® Stranded RNA Lib Kit (180743; Qiagen); for Zymo with Zymo-Seq RiboFree™ Total RNA Library Kit (R3000; Zymo Research). Constructed mRNA libraries were prepared for sequencing using the MiSeq v3 150 cycles sequencing kit (MS-102-3001; Illumina).

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

tag: physiological state

value: CO chemostat at 1 day-1


title: Dnmt3a_KO_1

description: Dnmt3a null E8.5 embryos


title: Dnmt3b_KO_11

description: Dnmt3b null E8.5 embryos


title: Lung immune cells, hashtag library

description:
Hashtag-derived oligonucleotide (HTO)
GR20002-HTO

value: HTO


title: Dnmt3b_KO_12

description: Dnmt3b null E8.5 embryos


title: Dnmt3a_KO_13

description: Dnmt3a null E8.5 embryos


title: E7.5_WT_tdTomato-_1

description: Wildtype host cells at E7.5

source_name: E7.5 embryo


title: E7.5_Tet_TKO

description: TET TKO chimera cells at E7.5


title: Dnmt1_KO_2

description: Dnmt1 null E8.5 embryos

value: Dnmt1 null


title: Dnmt1_KO_3

description: Dnmt1 null E8.5 embryos


title: NuGEN_S1


title: Dnmt1_KO_1

description: Dnmt1 null E8.5 embryos


title: Dnmt3b_KO_1

description: Dnmt3b null E8.5 embryos


title: E8.5_plate8_H09_BSseq

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina Novaseq platform using the default RTA analysis software.
BS-seq libraries were aligned to the bisuflite converted GRCm38 mouse genome using Bismark (v0.22.1) in single-end non-directional mode. Following the removal of PCR duplicates, we retained a mean of 1.6 million reads per cell. Methylation calling and separation of endogenous methylation (from A-C-G and T-C-G trinucleotides) and chromatin accessibility (G-C-A, G-C-C and G-C-T trinucleotides) was performed with Bismark using the --NOMe option of the coverage2cytosine script.
Following our previous approach, individual CpG or GpC sites in each cell were modelled using a binomial distribution where the number of successes is the number of reads that support methylation and the number of trials is the total number of reads. A CpG methylation or GpC accessibility rate for each site and cell was calculated by maximum likelihood. The rates were subsequently rounded to the nearest integer (0 or 1).
Assembly: GRCm38
Supplementary files format and content: Accessibiliy file  <chromosome><position><methylated_reads><nonmethylated_reads><binary_accessibility_status>
Supplementary files format and content: Methylation file  <chromosome><position><methylated_reads><nonmethylated_reads><binary_methylation_status>

molecule: genomic DNA

source_name: Early embryo

extract_protocol: Single-cells were sorted using flow cytometry into 96 well PCR plates containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL (Sigma)). Samples were incubated for 15 minutes at 37°C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at -80°C prior to processing. Poly-A RNA was captured on oligo-dT conjugated to magnetic beads and amplified cDNA was prepared according to the G&T-seq and Smartseq2 protocols. The lysate containing gDNA was purified on AMPureXP beads before bisulfite-seq libraries were prepared according to the scBS-seq protocol.

value: E8.5 embryo


title: E8.5_plate8_H05_BSseq


title: E8.5_plate8_H07_BSseq


title: WT_5

description: Wildtype E8.5 embryos


title: Dnmt3a_KO_14

description: Dnmt3a null E8.5 embryos


title: E8.5_plate8_H12_BSseq


title: E8.5_plate8_H10_BSseq


title: E8.5_plate8_H08_BSseq


title: E8.5_plate8_H02_BSseq


title: E8.5_plate8_H06_BSseq


title: Fibro-iPSC.2

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 26, based on Ensembl version 88
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

source_name: adult dermal fibroblasts

growth_protocol: hiPSCs were grown in mTeSR1 medium (STEMCELL) on Matrigel or in DEF-CS™ 500 Basal Medium with Additives (Takara Bio) on coated (COAT-1, Takara Bio) cell culture vessels

extract_protocol:
Total RNA extraction was done using TRIzol (Invitrogen) and further purification with the RNeasy Micro Kit (QIAGEN) from 3 x 10^6 Fibro-iPSC.2 and Fibro-iPSC.2_IFN cells, and from 5 x 10^6 cells for all other samples.
cDNA library preparation was done using 1000 ng RNA for hiPSC22_IFN and 4000 ng RNA for all other samples, using the KAPA Hyperprep RNAseq stranded kit (KAPA) with polyA capture. 9 and 7 PCR cycles for hiPSC22_IFN and all other iPSC samples, respectively, were used for library amplification. All libraries were diluted to 10 nM and normalized by qPCR using the KAPA library quantification kit (KAPA). Libraries were pooled to equimolar concentration. Sequencing was performed with the Illumina Nextseq500 using the Nextseq High Output 150 cycles (2x80bp for hiPSC22 and hiPSC22_IFN, and 2x75bp for all other iPSCs) using 2 pM of the pooled libraries.

treatment_protocol: For treated hiPSCs: 40 ng/mL recombinant human IFN-γ (Gibco) for 72 hours

value: human induced pluripotent stem cells (hiPSCs)

value: no treatment

tag: culture medium

value: mTeSR1 medium (STEMCELL) on Matrigel

tag: reprogramming method

value: lentivirus


title: E8.5_plate8_G06_BSseq


title: E8.5_plate8_G08_BSseq


title: E8.5_plate8_H11_BSseq


title: E8.5_plate8_G10_BSseq


title: E8.5_plate8_G07_BSseq


title: E8.5_plate8_H03_BSseq


title: E8.5_plate8_G09_BSseq


title: E8.5_plate8_H01_BSseq


title: E8.5_plate8_G03_BSseq


title: E8.5_plate8_G04_BSseq


title: E8.5_plate8_G02_BSseq


title: E8.5_plate8_F12_BSseq


title: E8.5_plate8_F09_BSseq


title: E8.5_plate8_F10_BSseq


title: E8.5_plate8_G11_BSseq


title: E8.5_plate8_F05_BSseq


title: E8.5_plate8_G12_BSseq


title: E8.5_plate8_F07_BSseq


title: E8.5_plate8_F06_BSseq


title: E8.5_plate8_F04_BSseq


title: E8.5_plate8_E11_BSseq


title: E8.5_plate8_E12_BSseq


title: E8.5_plate8_F01_BSseq


title: E8.5_plate8_F03_BSseq


title: E8.5_plate8_F02_BSseq


title: E8.5_plate8_G01_BSseq


title: E8.5_plate8_H04_BSseq


title: E8.5_plate8_E08_BSseq


title: E8.5_plate8_E09_BSseq


title: E8.5_plate8_E06_BSseq


title: E8.5_plate8_E03_BSseq


title: E8.5_plate8_E04_BSseq


title: E8.5_plate8_F11_BSseq


title: E8.5_plate8_E05_BSseq


title: E8.5_plate8_E02_BSseq


title: E8.5_plate8_G05_BSseq


title: E8.5_plate8_E01_BSseq


title: E8.5_plate8_D12_BSseq


title: E8.5_plate8_F08_BSseq


title: E8.5_plate8_D11_BSseq


title: E8.5_plate8_D06_BSseq


title: E8.5_plate8_D10_BSseq


title: E8.5_plate8_D04_BSseq


title: E8.5_plate8_D08_BSseq


title: E8.5_plate8_E07_BSseq


title: E8.5_plate8_D07_BSseq


title: E8.5_plate8_E10_BSseq


title: E8.5_plate8_D03_BSseq


title: E8.5_plate8_D09_BSseq


title: E8.5_plate8_C12_BSseq


title: E8.5_plate8_C11_BSseq


title: E8.5_plate8_C09_BSseq


title: E8.5_plate8_D02_BSseq


title: E8.5_plate8_D01_BSseq


title: E8.5_plate8_C08_BSseq


title: E8.5_plate8_C07_BSseq


title: E8.5_plate8_C01_BSseq


title: E8.5_plate8_C03_BSseq


title: E8.5_plate8_B11_BSseq


title: E8.5_plate8_B12_BSseq


title: E8.5_plate8_C05_BSseq


title: E8.5_plate8_B09_BSseq


title: E8.5_plate8_C04_BSseq


title: E8.5_plate8_B10_BSseq


title: E8.5_plate8_C10_BSseq


title: E8.5_plate8_B08_BSseq


title: E8.5_plate8_D05_BSseq


title: E8.5_plate8_A11_BSseq


title: E8.5_plate8_B07_BSseq


title: E8.5_plate8_B06_BSseq


title: E8.5_plate8_B02_BSseq


title: E8.5_plate8_A12_BSseq


title: E8.5_plate8_A08_BSseq


title: E8.5_plate8_A05_BSseq


title: E8.5_plate8_A10_BSseq


title: E8.5_plate8_B03_BSseq


title: E8.5_plate8_C06_BSseq


title: E8.5_plate8_C02_BSseq


title: E8.5_plate8_A09_BSseq


title: E8.5_plate8_B04_BSseq


title: E8.5_plate8_A06_BSseq


title: E8.5_plate8_B05_BSseq


title: E8.5_plate8_A03_BSseq


title: E8.5_plate8_A07_BSseq


title: E8.5_plate7_H12_BSseq


title: E8.5_plate7_H11_BSseq


title: E8.5_plate7_H10_BSseq


title: E8.5_plate8_A01_BSseq


title: E8.5_plate8_A04_BSseq


title: E8.5_plate7_H09_BSseq


title: E8.5_plate7_H08_BSseq


title: E8.5_plate7_H07_BSseq


title: E8.5_plate7_H01_BSseq


title: E8.5_plate7_H05_BSseq


title: E8.5_plate7_H04_BSseq


title: E8.5_plate7_H02_BSseq


title: E8.5_plate7_H06_BSseq


title: E8.5_plate7_G12_BSseq


title: E8.5_plate7_G11_BSseq


title: E8.5_plate7_G07_BSseq


title: E8.5_plate7_G10_BSseq


title: E8.5_plate8_A02_BSseq


title: E8.5_plate7_G06_BSseq


title: E8.5_plate7_G05_BSseq


title: E8.5_plate7_G04_BSseq


title: E8.5_plate7_G03_BSseq


title: E8.5_plate7_G08_BSseq


title: E8.5_plate7_G02_BSseq


title: E8.5_plate7_G01_BSseq


title: E8.5_plate7_F11_BSseq


title: E8.5_plate7_F08_BSseq


title: E8.5_plate7_F10_BSseq


title: E8.5_plate8_B01_BSseq


title: E8.5_plate7_F12_BSseq


title: E8.5_plate7_H03_BSseq


title: E8.5_plate7_F03_BSseq


title: E8.5_plate7_F05_BSseq


title: E8.5_plate7_F09_BSseq


title: E8.5_plate7_G09_BSseq


title: E8.5_plate7_E12_BSseq


title: E8.5_plate7_F07_BSseq


title: E8.5_plate7_F02_BSseq


title: E8.5_plate7_F01_BSseq


title: E8.5_plate7_E11_BSseq


title: E8.5_plate7_E09_BSseq


title: E8.5_plate7_E06_BSseq


title: E8.5_plate7_E04_BSseq


title: E8.5_plate7_E08_BSseq


title: E8.5_plate7_E05_BSseq


title: E8.5_plate7_E02_BSseq


title: E8.5_plate7_E07_BSseq


title: E8.5_plate7_E01_BSseq


title: E8.5_plate7_E03_BSseq


title: E8.5_plate7_D12_BSseq


title: E8.5_plate7_F04_BSseq


title: E8.5_plate7_D07_BSseq


title: E8.5_plate7_D11_BSseq


title: E8.5_plate7_D06_BSseq


title: E8.5_plate7_F06_BSseq


title: E8.5_plate7_D09_BSseq


title: E8.5_plate7_D04_BSseq


title: E8.5_plate7_D03_BSseq


title: E8.5_plate7_C09_BSseq


title: E8.5_plate7_C11_BSseq


title: E8.5_plate7_D08_BSseq


title: E8.5_plate7_D05_BSseq


title: E8.5_plate7_D10_BSseq


title: E8.5_plate7_C07_BSseq


title: E8.5_plate7_D01_BSseq


title: E8.5_plate7_C12_BSseq


title: E8.5_plate7_C04_BSseq


title: E8.5_plate7_E10_BSseq


title: E8.5_plate7_C08_BSseq


title: E8.5_plate7_C10_BSseq


title: E8.5_plate7_B12_BSseq


title: E8.5_plate7_B11_BSseq


title: E8.5_plate7_C06_BSseq


title: E8.5_plate7_C05_BSseq


title: E8.5_plate7_B06_BSseq


title: E8.5_plate7_B08_BSseq


title: E8.5_plate7_C02_BSseq


title: E8.5_plate7_B05_BSseq


title: E8.5_plate7_B03_BSseq


title: E8.5_plate7_C03_BSseq


title: E8.5_plate7_C01_BSseq


title: E8.5_plate7_A12_BSseq


title: E8.5_plate7_B01_BSseq


title: E8.5_plate7_B10_BSseq


title: E8.5_plate7_D02_BSseq


title: E8.5_plate7_B04_BSseq


title: E8.5_plate7_B09_BSseq


title: E8.5_plate7_A09_BSseq


title: E8.5_plate7_A10_BSseq


title: E8.5_plate7_A06_BSseq


title: E8.5_plate7_A05_BSseq


title: E8.5_plate7_A01_BSseq


title: E8.5_plate6_H11_BSseq


title: E8.5_plate7_B07_BSseq


title: E8.5_plate7_A02_BSseq


title: E8.5_plate6_H10_BSseq


title: E8.5_plate7_A04_BSseq


title: E8.5_plate7_A03_BSseq


title: E8.5_plate6_H12_BSseq


title: E8.5_plate7_B02_BSseq


title: E8.5_plate6_H06_BSseq


title: E8.5_plate7_A11_BSseq


title: E8.5_plate6_H02_BSseq


title: E8.5_plate6_H08_BSseq


title: E8.5_plate6_H07_BSseq


title: E8.5_plate7_A07_BSseq


title: E8.5_plate6_G10_BSseq


title: E8.5_plate6_H04_BSseq


title: E8.5_plate6_G08_BSseq


title: E8.5_plate7_A08_BSseq


title: E8.5_plate6_H05_BSseq


title: E8.5_plate6_H03_BSseq


title: E8.5_plate6_G05_BSseq


title: E8.5_plate6_H01_BSseq


title: E8.5_plate6_G12_BSseq


title: E8.5_plate6_H09_BSseq


title: E8.5_plate6_G06_BSseq


title: E8.5_plate6_G09_BSseq


title: E8.5_plate6_G04_BSseq


title: E8.5_plate6_G11_BSseq


title: E8.5_plate6_G07_BSseq


title: E8.5_plate6_F12_BSseq


title: E8.5_plate6_G01_BSseq


title: E8.5_plate6_F10_BSseq


title: E8.5_plate6_F09_BSseq


title: E8.5_plate6_F08_BSseq


title: E8.5_plate6_G03_BSseq


title: E8.5_plate6_G02_BSseq


title: E8.5_plate6_F07_BSseq


title: E8.5_plate6_F11_BSseq


title: E8.5_plate6_F06_BSseq


title: E8.5_plate6_F01_BSseq


title: E8.5_plate6_E10_BSseq


title: E8.5_plate6_F03_BSseq


title: E8.5_plate6_E11_BSseq


title: E8.5_plate6_F02_BSseq


title: E8.5_plate6_E12_BSseq


title: E8.5_plate6_F05_BSseq


title: E8.5_plate6_E07_BSseq


title: E8.5_plate6_E08_BSseq


title: E8.5_plate6_E04_BSseq


title: E8.5_plate6_E06_BSseq


title: E8.5_plate6_E03_BSseq


title: E8.5_plate6_D11_BSseq


title: E8.5_plate6_D12_BSseq


title: E8.5_plate6_D10_BSseq


title: E8.5_plate6_E01_BSseq


title: E8.5_plate6_E05_BSseq


title: E8.5_plate6_D09_BSseq


title: E8.5_plate6_D07_BSseq


title: E8.5_plate6_D08_BSseq


title: E8.5_plate6_E02_BSseq


title: E8.5_plate6_D06_BSseq


title: E8.5_plate6_D05_BSseq


title: E8.5_plate6_D02_BSseq


title: E8.5_plate6_D01_BSseq


title: E8.5_plate6_C12_BSseq


title: E8.5_plate6_D03_BSseq


title: E8.5_plate6_F04_BSseq


title: E8.5_plate6_E09_BSseq


title: E8.5_plate6_C11_BSseq


title: E8.5_plate6_C10_BSseq


title: E8.5_plate6_C07_BSseq


title: E8.5_plate6_C08_BSseq


title: E8.5_plate6_C05_BSseq


title: E8.5_plate6_C03_BSseq


title: E8.5_plate6_C06_BSseq


title: E8.5_plate6_C04_BSseq


title: E8.5_plate6_C02_BSseq


title: E8.5_plate6_B11_BSseq


title: E8.5_plate6_B12_BSseq


title: E8.5_plate6_B09_BSseq


title: E8.5_plate6_B08_BSseq


title: E8.5_plate6_B10_BSseq


title: E8.5_plate6_D04_BSseq


title: E8.5_plate6_B07_BSseq


title: E8.5_plate6_C01_BSseq


title: E8.5_plate6_B06_BSseq


title: E8.5_plate6_B05_BSseq


title: E8.5_plate6_B03_BSseq


title: E8.5_plate6_B02_BSseq


title: E8.5_plate6_B01_BSseq


title: E8.5_plate6_C09_BSseq


title: E8.5_plate6_A08_BSseq


title: E8.5_plate6_A10_BSseq


title: E8.5_plate6_A09_BSseq


title: E8.5_plate6_A11_BSseq


title: E8.5_plate6_A07_BSseq


title: E8.5_plate6_A12_BSseq


title: E8.5_plate6_A02_BSseq


title: E8.5_plate5_H12_BSseq


title: E8.5_plate5_H08_BSseq


title: E8.5_plate6_A03_BSseq


title: E8.5_plate6_A05_BSseq


title: E8.5_plate6_A06_BSseq


title: E8.5_plate5_H07_BSseq


title: E8.5_plate5_H11_BSseq


title: E8.5_plate5_H06_BSseq


title: E8.5_plate5_H09_BSseq


title: E8.5_plate5_H05_BSseq


title: E8.5_plate5_H03_BSseq


title: E8.5_plate5_H04_BSseq


title: E8.5_plate5_G10_BSseq


title: E8.5_plate5_G09_BSseq


title: E8.5_plate5_G04_BSseq


title: E8.5_plate5_H01_BSseq


title: E8.5_plate5_G12_BSseq


title: E8.5_plate6_A01_BSseq


title: E8.5_plate5_H10_BSseq


title: E8.5_plate6_A04_BSseq


title: E8.5_plate5_G08_BSseq


title: E8.5_plate5_G06_BSseq


title: E8.5_plate5_G07_BSseq


title: E8.5_plate6_B04_BSseq


title: E8.5_plate5_G02_BSseq


title: E8.5_plate5_G01_BSseq


title: E8.5_plate5_H02_BSseq


title: E8.5_plate5_G03_BSseq


title: E8.5_plate5_F12_BSseq


title: E8.5_plate5_F10_BSseq


title: E8.5_plate5_F06_BSseq


title: E8.5_plate5_F11_BSseq


title: E8.5_plate5_F04_BSseq


title: E8.5_plate5_F03_BSseq


title: E8.5_plate5_F08_BSseq


title: E8.5_plate5_G11_BSseq


title: E8.5_plate5_F05_BSseq


title: E8.5_plate5_G05_BSseq


title: E8.5_plate5_F01_BSseq


title: E8.5_plate5_E12_BSseq


title: E8.5_plate5_E10_BSseq


title: E8.5_plate5_F09_BSseq


title: E8.5_plate5_E05_BSseq


title: E8.5_plate5_E09_BSseq


title: E8.5_plate5_E02_BSseq


title: E8.5_plate5_E07_BSseq


title: E8.5_plate5_D12_BSseq


title: E8.5_plate5_D11_BSseq


title: E8.5_plate5_E08_BSseq


title: E8.5_plate5_D10_BSseq


title: E8.5_plate5_E06_BSseq


title: E8.5_plate5_E01_BSseq


title: E8.5_plate5_E04_BSseq


title: E8.5_plate5_E03_BSseq


title: E8.5_plate5_D08_BSseq


title: E8.5_plate5_F07_BSseq


title: E8.5_plate5_F02_BSseq


title: E8.5_plate5_D05_BSseq


title: E8.5_plate5_D02_BSseq


title: E8.5_plate5_C12_BSseq


title: E8.5_plate5_D01_BSseq


title: E8.5_plate5_D04_BSseq


title: E8.5_plate5_E11_BSseq


title: E8.5_plate5_C09_BSseq


title: E8.5_plate5_D03_BSseq


title: E8.5_plate5_D09_BSseq


title: E8.5_plate5_D06_BSseq


title: E8.5_plate5_C10_BSseq


title: E8.5_plate5_C07_BSseq


title: E8.5_plate5_D07_BSseq


title: E8.5_plate5_C11_BSseq


title: E8.5_plate5_C03_BSseq


title: E8.5_plate5_B11_BSseq


title: E8.5_plate5_C01_BSseq


title: E8.5_plate5_B12_BSseq


title: E8.5_plate5_B08_BSseq


title: E8.5_plate5_B10_BSseq


title: E8.5_plate5_C02_BSseq


title: E8.5_plate5_B07_BSseq


title: E8.5_plate5_C04_BSseq


title: E8.5_plate5_B09_BSseq


title: E8.5_plate5_C08_BSseq


title: E8.5_plate5_B06_BSseq


title: E8.5_plate5_B05_BSseq


title: E8.5_plate5_B04_BSseq


title: E8.5_plate5_C06_BSseq


title: E8.5_plate5_B01_BSseq


title: E8.5_plate5_B02_BSseq


title: E8.5_plate5_B03_BSseq


title: E8.5_plate5_A12_BSseq


title: E8.5_plate5_A10_BSseq


title: E8.5_plate5_C05_BSseq


title: E8.5_plate5_A08_BSseq


title: E8.5_plate5_A05_BSseq


title: E8.5_plate5_A09_BSseq


title: E8.5_plate5_A07_BSseq


title: E8.5_plate5_A01_BSseq


title: E8.5_plate5_A04_BSseq


title: E8.5_plate4_H11_BSseq


title: E8.5_plate5_A03_BSseq


title: E8.5_plate4_H07_BSseq


title: E8.5_plate4_H12_BSseq


title: E8.5_plate5_A02_BSseq


title: E8.5_plate4_H09_BSseq


title: E8.5_plate4_H05_BSseq


title: E8.5_plate4_H08_BSseq


title: E8.5_plate4_H06_BSseq


title: E8.5_plate5_A06_BSseq


title: E8.5_plate5_A11_BSseq


title: E8.5_plate4_G12_BSseq


title: E8.5_plate4_H10_BSseq


title: E8.5_plate4_H02_BSseq


title: E8.5_plate4_G10_BSseq


title: E8.5_plate4_G09_BSseq


title: E8.5_plate4_H04_BSseq


title: E8.5_plate4_G05_BSseq


title: E8.5_plate4_H01_BSseq


title: E8.5_plate4_G04_BSseq


title: E8.5_plate4_G11_BSseq


title: E8.5_plate4_G08_BSseq


title: E8.5_plate4_G07_BSseq


title: E8.5_plate4_G01_BSseq


title: E8.5_plate4_G03_BSseq


title: E8.5_plate4_F12_BSseq


title: E8.5_plate4_G06_BSseq


title: E8.5_plate4_F11_BSseq


title: E8.5_plate4_F05_BSseq


title: E8.5_plate4_F09_BSseq


title: E8.5_plate4_F01_BSseq


title: E8.5_plate4_F08_BSseq


title: E8.5_plate4_F04_BSseq


title: E8.5_plate4_F03_BSseq


title: E8.5_plate4_F06_BSseq


title: E8.5_plate4_F10_BSseq


title: E8.5_plate4_F07_BSseq


title: E8.5_plate4_E11_BSseq


title: E8.5_plate4_G02_BSseq


title: E8.5_plate4_H03_BSseq


title: E8.5_plate4_E12_BSseq


title: E8.5_plate4_E10_BSseq


title: E8.5_plate4_E07_BSseq


title: E8.5_plate4_E05_BSseq


title: E8.5_plate4_E02_BSseq


title: E8.5_plate4_E01_BSseq


title: E8.5_plate4_D12_BSseq


title: E8.5_plate4_E08_BSseq


title: E8.5_plate4_D09_BSseq


title: E8.5_plate4_E06_BSseq


title: E8.5_plate4_D06_BSseq


title: E8.5_plate4_E04_BSseq


title: E8.5_plate4_E09_BSseq


title: E8.5_plate4_D07_BSseq


title: E8.5_plate4_D03_BSseq


title: E8.5_plate4_D10_BSseq


title: E8.5_plate4_C12_BSseq


title: E8.5_plate4_D02_BSseq


title: E8.5_plate4_F02_BSseq


title: E8.5_plate4_D08_BSseq


title: E8.5_plate4_E03_BSseq


title: E8.5_plate4_D05_BSseq


title: E8.5_plate4_D04_BSseq


title: E8.5_plate4_C04_BSseq


title: E8.5_plate4_C03_BSseq


title: E8.5_plate4_D11_BSseq


title: E8.5_plate4_D01_BSseq


title: E8.5_plate4_C02_BSseq


title: E8.5_plate4_C11_BSseq


title: E8.5_plate4_B10_BSseq


title: E8.5_plate4_B07_BSseq


title: E8.5_plate4_C10_BSseq


title: E8.5_plate4_C09_BSseq


title: E8.5_plate4_C08_BSseq


title: E8.5_plate4_B05_BSseq


title: E8.5_plate4_C07_BSseq


title: E8.5_plate4_B04_BSseq


title: E8.5_plate4_B03_BSseq


title: E8.5_plate4_C06_BSseq


title: E8.5_plate4_A10_BSseq


title: E8.5_plate4_C05_BSseq


title: E8.5_plate4_A08_BSseq


title: E8.5_plate4_B12_BSseq


title: E8.5_plate4_C01_BSseq


title: E8.5_plate4_A07_BSseq


title: E8.5_plate4_B08_BSseq


title: E8.5_plate4_B09_BSseq


title: E8.5_plate4_B06_BSseq


title: E8.5_plate4_A04_BSseq


title: E8.5_plate4_A06_BSseq


title: E8.5_plate3_H12_BSseq


title: E8.5_plate4_A02_BSseq


title: E8.5_plate4_B01_BSseq


title: E8.5_plate4_B02_BSseq


title: E8.5_plate4_A12_BSseq


title: E8.5_plate4_A11_BSseq


title: E8.5_plate4_A09_BSseq


title: E8.5_plate3_H08_BSseq


title: E8.5_plate3_H04_BSseq


title: E8.5_plate3_H03_BSseq


title: E8.5_plate3_H02_BSseq


title: E8.5_plate4_B11_BSseq


title: E8.5_plate4_A05_BSseq


title: E8.5_plate4_A03_BSseq


title: E8.5_plate4_A01_BSseq


title: E8.5_plate3_H01_BSseq


title: E8.5_plate3_G12_BSseq


title: E8.5_plate3_G08_BSseq


title: E8.5_plate3_G09_BSseq


title: E8.5_plate3_H10_BSseq


title: E8.5_plate3_H11_BSseq


title: E8.5_plate3_H07_BSseq


title: E8.5_plate3_G04_BSseq


title: E8.5_plate3_H05_BSseq


title: E8.5_plate3_H09_BSseq


title: E8.5_plate3_G05_BSseq


title: E8.5_plate3_H06_BSseq


title: E8.5_plate3_F11_BSseq


title: E8.5_plate3_F12_BSseq


title: E8.5_plate3_G11_BSseq


title: E8.5_plate3_F09_BSseq


title: E8.5_plate3_G06_BSseq


title: E8.5_plate3_F08_BSseq


title: E8.5_plate3_G01_BSseq


title: E8.5_plate3_G02_BSseq


title: E8.5_plate3_F10_BSseq


title: E8.5_plate3_G07_BSseq


title: E8.5_plate3_F07_BSseq


title: E8.5_plate3_F05_BSseq


title: E8.5_plate3_F04_BSseq


title: E8.5_plate3_F06_BSseq


title: E8.5_plate3_G10_BSseq


title: E8.5_plate3_E12_BSseq


title: E8.5_plate3_F02_BSseq


title: E8.5_plate3_E08_BSseq


title: E8.5_plate3_E11_BSseq


title: E8.5_plate3_F01_BSseq


title: E8.5_plate3_G03_BSseq


title: E8.5_plate3_F03_BSseq


title: E8.5_plate3_E09_BSseq


title: E8.5_plate3_E04_BSseq


title: E8.5_plate3_E10_BSseq


title: E8.5_plate3_E06_BSseq


title: E8.5_plate3_E05_BSseq


title: E8.5_plate3_E01_BSseq


title: E8.5_plate3_E02_BSseq


title: E8.5_plate3_D04_BSseq


title: E8.5_plate3_D10_BSseq


title: E8.5_plate3_D03_BSseq


title: E8.5_plate3_D08_BSseq


title: E8.5_plate3_E07_BSseq


title: E8.5_plate3_D09_BSseq


title: E8.5_plate3_D01_BSseq


title: E8.5_plate3_C08_BSseq


title: E8.5_plate3_D07_BSseq


title: E8.5_plate3_D12_BSseq


title: E8.5_plate3_C09_BSseq


title: E8.5_plate3_D06_BSseq


title: E8.5_plate3_D02_BSseq


title: E8.5_plate3_C05_BSseq


title: E8.5_plate3_C01_BSseq


title: E8.5_plate3_C04_BSseq


title: E8.5_plate3_C12_BSseq


title: E8.5_plate3_B09_BSseq


title: E8.5_plate3_C10_BSseq


title: E8.5_plate3_E03_BSseq


title: E8.5_plate3_D05_BSseq


title: E8.5_plate3_B08_BSseq


title: E8.5_plate3_C02_BSseq


title: E8.5_plate3_C07_BSseq


title: E8.5_plate3_C03_BSseq


title: E8.5_plate3_C11_BSseq


title: E8.5_plate3_B05_BSseq


title: E8.5_plate3_B12_BSseq


title: E8.5_plate3_A12_BSseq


title: E8.5_plate3_D11_BSseq


title: E8.5_plate3_B10_BSseq


title: E8.5_plate3_B11_BSseq


title: E8.5_plate3_B07_BSseq


title: E8.5_plate3_C06_BSseq


title: E8.5_plate3_B04_BSseq


title: E8.5_plate3_B06_BSseq


title: GLH-4 CLIP in glh-1 rep2

city: Worcester

first: Siyuan

last: Dai

state: MA

address: 368 Plantation St.

department: RTI

institute: UMass Chan Medical School

data_processing:
cutadapt, trim 3' linkers
STAR, mapping to C. elegans genome and transcriptome
samtools and bedtools, convert aligned sam files to bam files
deeptools, convert to bigwig files and plot the metagene analysis along the composite target space.
Assembly: WS262, WBcel235
Supplementary files format and content: bigwig

organism: Caenorhabditis elegans

source_name: C. elegans yound adults

growth_protocol: C. elegans were grown on NGM plates with OP50 E. coli

extract_protocol:
Independent synchronized populations of young adult animals were exposed to UV light and then subjected to extraction, partial RNase digestion (Thermo Scientific), and FLAG protein immunoprecipitation (Sigma Aldrich). Electrophoresis on a denaturing poly-acrylamide gel was then used to separate the proteins in the IP complex, followed by excision of a gel-slice corresponding in size to the GLH protein.
Purified RNA fragments were ligated with 3' and 5' linkers. cDNA were generated by reverse transcribed and further amplified by PCR. A size selection procedure on native PAGE were carried out.
CLIP-seq

treatment_protocol: glh-1 DQAD worms were grown on auxin plates then removed from auxin. Worms were crosslinked by UV.

value: flag::glh-4 glh-1

value: UV crosslink


title: E8.5_plate3_A03_BSseq


title: GLH-4 CLIP in glh-1 rep1


title: E8.5_plate3_B03_BSseq


title: GLH-4 CLIP rep2


title: E8.5_plate3_A01_BSseq


title: E8.5_plate3_A11_BSseq


title: GLH-1 DQAD 4h

value: cultured with 500mM IAA and remove from auxin, UV crosslink


title: E8.5_plate2_H12_BSseq


title: E8.5_plate3_A07_BSseq


title: E8.5_plate3_A09_BSseq


title: E8.5_plate3_B01_BSseq


title: E8.5_plate2_H10_BSseq


title: GLH-1 DQAD 0h

value: cultured with 500mM IAA and remove from auxin, UV crosslink  UV crosslink


title: E8.5_plate3_A05_BSseq


title: E8.5_plate3_A10_BSseq


title: E8.5_plate3_A02_BSseq


title: E8.5_plate3_B02_BSseq


title: E8.5_plate2_H09_BSseq


title: E8.5_plate2_H08_BSseq


title: GLH-4 CLIP rep1


title: E8.5_plate2_H07_BSseq


title: E8.5_plate3_A04_BSseq


title: E8.5_plate2_H11_BSseq


title: E8.5_plate2_H06_BSseq


title: GLH-1 CLIP in prg-1 rep2

value: flag::glh-1 prg-1


title: E8.5_plate2_H04_BSseq


title: E8.5_plate3_A08_BSseq


title: GLH-1 DQAD 2h

value: culture with 500mM IAA and remove from auxin,  UV crosslink


title: GLH-1 CLIP in prg-1 rep1


title: E8.5_plate3_A06_BSseq


title: GLH-1 K391A CLIP rep1


title: GLH-1 CLIP in rde-3 rep2

value: flag::glh-1; rde-3


title: E8.5_plate2_H02_BSseq


title: GLH-1 CLIP rep1


title: GLH-1 K391A CLIP rep2


title: E8.5_plate2_H05_BSseq


title: GLH-1 CLIP in rde-3 rep1


title: E8.5_plate2_G12_BSseq


title: E8.5_plate2_H01_BSseq


title: E8.5_plate2_G10_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C370]

type: genomic

city: Granada

first: Guillermo

last: Barturen

state: Andalucia

address: Faculty of Science. Fuente nueva s/n

department: Department of Genetics

institute: University of Granada

hyb_protocol: DNA methylation information was profiled with the Illumina's Infinium MethylationEPIC BeadChip, after sample normalization to 500ng and bisulfite conversion with EZ-96 DNA Methylation Kit, as recommended by the manufacturer.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Samples and probes were quality controlled by gender prediction agreement (outliers > 5 standard deviations), signal from noise detection p-value < 0.1 and minimum number of beads (>3) that passed the detection p-value. Additionally, sexual chromosomes, cross-reactive probes and probes with overlapping SNPs from dbSNP (v.147)  were discarded. Beta normalized values (Functional normalization implemented in minfi R package)
The B.Methylation.txt contains Average Beta values

label: Cy5 and Cy3

source_name: Validation_MILD_whole Blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from whole blood samples by means of the QIAamp DNA Blood Mini kit and the automatic platform QIAcube Connect. Afterwards, DNA quality was validated and normalized using the NanoDrop 2000c and the Qubit4.

tag: subject status

value: SARS-CoV-2 positive individual

tag: gender

value: M

tag: cohort

value: Validation

value: MILD

tag: tissue/cell type

value: Whole Blood


title: GLH-1 CLIP rep2

tag: treatment


title: E8.5_plate2_G09_BSseq

tag: tissue

value: E8.5 embryo


title: Whole blood DNA methylation_Validation_MILD [INVN02020C375]

value: F


title: E8.5_plate2_G11_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C374]


title: E8.5_plate2_G08_BSseq


title: E8.5_plate2_G07_BSseq


title: E8.5_plate2_G06_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C367]


title: E8.5_plate2_H03_BSseq


title: E8.5_plate2_G05_BSseq


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C364]

source_name: Validation_SEVERE_whole Blood

value: SEVERE


title: E8.5_plate2_G04_BSseq


title: E8.5_plate2_G03_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C368]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C275]


title: E8.5_plate2_G02_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C373]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C273]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C369]


title: E8.5_plate2_G01_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C274]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C365]


title: E8.5_plate2_F12_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C268]


title: E8.5_plate2_F10_BSseq


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C270]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C366]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C269]


title: E8.5_plate2_F09_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C262]


title: E8.5_plate2_F07_BSseq


title: E8.5_plate2_F06_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C258]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C259]


title: E8.5_plate2_F05_BSseq


title: E8.5_plate2_F04_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C257]


title: E8.5_plate2_F03_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C271]


title: E8.5_plate2_F11_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C266]


title: E8.5_plate2_F02_BSseq


title: E8.5_plate2_F08_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C256]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C254]


title: E8.5_plate2_F01_BSseq


title: E8.5_plate2_E12_BSseq


title: positive, engram

city: New York

first: Xiaonan

last: Guan

state: NY

address: 1150 St Nicholas Ave, 403

institute: Russ Berrie Medical Science Pavillion

data_processing:
Raw reads were trimmed using cutadapt and then mapped to mouse genome (mm10) using Bismark
Mcomp module from MOABS was used to call the differently methylated cytosines (DMCs) and regions (DMRs).
Only Cytosines covered with at least five reads were used for further analysis. Differences in DNA methylation levels greater than 0.2 and P value from Fisher Exact Test greater than 0.5 were considered as DMCs. The differently methylated regions at least included two DMCs, and the max distance between two DMCs was 300 bp.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Hippocampal tissue

extract_protocol:
Five-week old male mice labeled with ChR2-YFP transgene1 after conditioning were euthanized by isoflurane. Mouse brains were rapidly extracted, and the hippocampal regions were isolated by microdissection. Eight mice were pooled by each experimental condition. Single cell suspension was prepared according to the guideline of Adult Brain Dissociation Kit (Miltenyi Botec, Cat No: 13-107-677). Briefly, the hippocampal samples were incubated with digestion enzymes in the C Tube placed on the gentleMACS Octo Dissociator with Heaters with gentleMACS Program: 37C_ABDK_01. After termination of the program, the samples were applied through a MACS SmartStrainer (70 μm). Then a debris removal step and a red blood cell removal step were applied to obtain single cell suspension.
Followed EpiNext™ High-Sensitivity Bisulfite-Seq Kit

value: Hippocampal tissue

tag: cell type

value: vCA1 cells

value: Appetitive stimulation (male mice engaged in social interaction with female mice)


title: negative, engram

value: Aversive stimulation (electrical shock)


title: Whole blood DNA methylation_Validation_MILD [INVN02020C234]

tag: disease state


title: E8.5_plate2_E11_BSseq

tag: strain


title: Whole blood DNA methylation_Validation_MILD [INVN02020C233]


title: neutral, engram

value: In the same cage without aversive or appetitive stimulation


title: E8.5_plate2_E10_BSseq


title: Ago2_RS_1_ChIPinput

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

data_processing:
Datasets were quality filtered with the fastq_quality_filter tool from FASTX-Toolkit using parameters –q 20 –p 80 (Hannon, 2010) and quality was assessed using FastQC (Andrews, 2010). ChIP-seq data was aligned to the mouse genome build mm10 using Bowtie2 (Langmead and Salzberg, 2012). Peaks were called with MACS2 at q=0.2 for round spermatid, spermatogonia, and mESC datasets, and q= 0.05 for pachytene spermatocyte datasets (Zhang et al., 2008).
genome build: mm10
bigWig file representing ChIP minus input signal

source_name: round spermatids

extract_protocol:
Cells were cross-linked for ChIP-seq with 1% formaldehyde at room temperature for 10 minutes. The formaldehyde was quenched with 2.5M glycine at room temperature for 10 minutes. Fixed cells were spun down at 6000xg for 3 minutes at 4°C. Cells were washed with cold PBS twice and resuspended in 100ul ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tri-HCl at pH 8.1) before being snap frozen in liquid nitrogen. Immunoprecipitation was carried out as previously described (Lesch et al 2016)
DNA integrity and fragment size were confirmed on a BioAnalyzer.  Approximately 5-10ng of DNA was end-repaired, A-tailed, adapter-ligated, and PCR enriched (8-10 cycles) using the KAPA Hyper Library Preparation kit (KAPA Biosystems, #KK8504).

tag: ip antibody

tag: condition

value: wild type


title: Whole blood DNA methylation_Validation_MILD [INVN02020C255]

tag: age


title: Ago2_RS_1_ChIP

value: Millipore, 04-642


title: Whole blood DNA methylation_Validation_MILD [INVN02020C231]


title: E8.5_plate2_E09_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C232]


title: Ago2_spermatogonia_1_ChIP

source_name: spermatogonia (ckit+)


title: Ago2_spermatogonia_1_ChIPinput


title: Ago2_mESCs_millipore_ChIPinput

source_name: mESCs


title: E8.5_plate2_E08_BSseq


title: Ago2_mESCs_millipore_ChIP


title: LLC Subcutaneous 3

type: RNA

city: Kyoto

first: Ryo

last: Miyata

state: Kyoto

address: 54 Kawaharacho, Shogoin, Sakyoku

department: Thoracic Surgety

country: Japan

institute: Kyoto University Graduate School of Medicine

description: GFP-laveled 3LL (murine lung cancer cell line)

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Hybridized arrays were washed and stained on the Agilent Technologies GeneChip Fluidics Station 450 and scanned on the Agilent Technologies Scanner GCS3000.

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label: biotin

source_name: 3LL-GFP_subcutaneous_RIN 7.80

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

extract_protocol: Total RNA extraction using Qiagen's RNeasy Plus Mini Kit was performed according to the manufacturer's instructions. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

value: C57/BL6 mice

value: lung

value: Lewis Lung Carcinoma (LLC)

value: cell line, subcutaneous transplantation, GFP+ cell isolation at 7 days post-transplantation


title: LLC Subcutaneous 1

source_name: 3LL-GFP_subcutaneous_RIN 8.60


title: LLC Lung 1

source_name: 3LL-GFP_lung_RIN 8.30

value: cell line, intrapulmonary transplantation, GFP+ cell isolation at 7 days post-transplantation


title: E8.5_plate2_E07_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C222]

value: SARS-CoV-2 positive individual

value: Validation

value: MILD


title: LLC Subcutaneous 2

source_name: 3LL-GFP_subcutaneous_RIN 7.50


title: LLC Dish 2

source_name: 3LL-GFP_dish_RIN 8.60

value: cell line, culture, 7 days


title: LLC Lung 2

source_name: 3LL-GFP_lung_RIN 7.90


title: LLC Dish 1

source_name: 3LL-GFP_dish_RIN 8.50


title: LLC Lung 3


title: E8.5_plate2_E06_BSseq

value: E8.5 embryo


title: E8.5_plate2_E04_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C179]

value: M

value: Whole Blood


title: Whole blood DNA methylation_Validation_MILD [INVN02020C226]

value: F


title: E8.5_plate2_E03_BSseq


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C210]

value: SEVERE


title: ATAC: ATRX KO, Etoposide treated, replicate 2

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

data_processing:
ATAC-Seq raw reads were aligned using bowtie against the hg19 version of the human genome, followed by HOMER to generate bigwig files
Assembly: hg19
Supplementary files format and content: ATAC-seq signal in bigwig format

source_name: U87T cell line

extract_protocol:
Cells were harvested and ATAC-seq was performed in two biological replicates according to the Omni-ATAC-seq protocol. DNA was purified using a MinElute PCR purification kit (Qiagen) and eluted in 10 l Elution Buffer for library amplification
PCR amplification of tagmented DNA was done using the NEBNext HiFi PCR mastermix (New England Bioloabs) with a universal forward and sample-specific reverse oligo for sample barcoding

treatment_protocol: WT, DAXX_KO and ATRX_KO U87-T cells were treated with DMSO or 50 uM etoposide for 24 h.

tag: cell line

value: U87T cell line

tag: genotype

value: Etoposide

tag: replicate


title: ATAC: ATRX KO, untreated, replicate 1

value: DMSO


title: ATAC: DAXX KO, untreated, replicate 1


title: ATAC: DAXX KO, Etoposide treated, replicate 2


title: ATAC: DAXX KO, Etoposide treated, replicate 1


title: E8.5_plate2_E05_BSseq

source_name: Early embryo


title: Whole blood DNA methylation_Validation_MILD [INVN02020C178]


title: Ago2_mESCs_abcam_ChIPinput

value: wild type


title: E8.5_plate2_E01_BSseq


title: ATAC: DAXX/ATRX WT, Etoposide treated, replicate 1

value: WT


title: ATAC: DAXX/ATRX WT, Etoposide treated, replicate 2


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C176]


title: ATAC: DAXX/ATRX WT, untreated, replicate 2


title: ATAC: DAXX/ATRX WT, untreated, replicate 1


title: ATAC: ATRX KO, untreated, replicate 2


title: E8.5_plate2_D12_BSseq


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C177]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C175]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C218]


title: Ago2_mESCs_abcam_ChIP

value: Abcam, ab32381


title: ATAC: ATRX KO, Etoposide treated, replicate 1


title: E8.5_plate2_D11_BSseq


title: ATAC: DAXX KO, untreated, replicate 2


title: E8.5_plate2_D10_BSseq


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C171]


title: E8.5_plate2_E02_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C174]


title: MDS-RS-14-NT

city: Houston

first: Simona

last: Colla

institute: University of Texas MD Anderson Cancer Center

data_processing:
Raw-sequencing data from the Illumina platform were converted to fastq files and aligned to the reference genome (hg19), using the STAR algorithm in single-pass mode with default parameters.
HTSeq-count was then utilized to generate the raw counts for each gene.
Raw counts were then analyzed by DESeq2 for data processing, normalization, and differential expression analysis, according to standard procedures.
Differential analysis by DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes differential analysis results (by DeSeq2) and TPM values for each sample

source_name: primary BM cells from SF3B1-mutant MDS-RS samples

growth_protocol: MACS-purified CD34+ cells were subjected to a 3-phase in vitro culture as described previously (Huang et al., 2020a). Cells were maintained in phase 1 from the day of collection until day 8, at which time the cells underwent ribonucleoprotein-based gene editing and were transitioned to phase 2 medium. On day 13 of culture, the cells were transitioned to phase 3 medium. Samples for Western blot and cytospin analyses, and sample for flow cytometry were harvested on day 13 or 15 of culture, respectively.

extract_protocol:
RNA was harvested using AllPrep DNA/RNA kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions.

value: myelodysplastic syndromes with ringed sideroblasts (MDS-RS)

value: CD34+ cells subjected to a 3-phase in vitro culture

value: SF3B1 mutant

tag: gene editing

value: NT

tag: time

value: Day 13


title: Whole blood DNA methylation_Validation_MILD [INVN02020C173]

tag: subject status

value: SARS-CoV-2 positive individual

value: Validation

value: MILD


title: MDS-RS-13-EIF2AK1

value: primary BM cells from SF3B1-mutant MDS-RS samples


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C170]

tag: gender

value: F

value: Whole Blood


title: MDS-RS-14-EIF2AK1


title: E8.5_plate2_D08_BSseq

value: E8.5 embryo


title: E8.5_plate2_D09_BSseq


title: E8.5_plate2_D07_BSseq


title: MDS-RS-13-NT


title: Whole blood DNA methylation_Validation_MILD [INVN02020C169]

value: M

tag: cohort


title: input, DAXX KO cells

description: input, DAXX KO cells

data_processing:
The data was aligned using bowtie against hg19 version of the human genome and HOMER was used to generate bigwig files and call significant peaks vs input using –style factor option
DESeq2 was used for differentail expression analysis
Supplementary_files_format_and_content: Prosessed files contains the CHIP-seq signal in bigwig format

source_name: U87 glioblastoma cells

extract_protocol:
Etoposide (10 uM) treated cells were harvested after 24 hours of treatment, fixed with formaldehyde for 10 min followed by quenching with glycine. 25 million cells per sample were sonicated using Covaris sonicator to obtain fragments of size between 100-500 bp. Chromatin was incubated with 10 mg of p53 antibody (Santa Cruz sc-126X) overnight followed by pull-down using protein- G Dynabeads (life technologies). Beads were washed, eluted and reverse cross-linked overnight. IP DNA was purified using Sigma PCR purification kit.
Libraries were prepared using Illumina protocol and sequencing 75bp single end on Illumina Nextseq500 on high-output mode

value: U87 glioblastoma cells

tag: ChIP

value: input

tag: daxx status

value: KO


title: E8.5_plate2_D06_BSseq

tag: tissue


title: MDS-RS-3-bis-EIF2AK1

tag: cell type


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C167]

tag: disease state

value: SEVERE

tag: tissue/cell type


title: E8.5_plate2_D05_BSseq

tag: strain


title: IgG, DAXX KO cells

description: IgG, DAXX KO cells

value: IgG


title: input, DAXX WT cells

description: input, DAXX WT cells

value: WT


title: MDS-RS-3-bis-NT

value: myelodysplastic syndromes with ringed sideroblasts (MDS-RS)

value: CD34+ cells subjected to a 3-phase in vitro culture

value: SF3B1 mutant


title: E8.5_plate2_D04_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C166]

source_name: Validation_MILD_whole Blood

value: SARS-CoV-2 positive individual


title: E8.5_plate2_D03_BSseq


title: p53, DAXX KO cells

description: p53, DAXX KO cells


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C172]

source_name: Validation_SEVERE_whole Blood

value: Validation


title: p53, DAXX WT cells

description: p53, DAXX WT cells


title: Whole blood DNA methylation_Validation_MILD [INVN02020C165]

value: MILD


title: E8.5_plate2_D02_BSseq


description:
ATRX.KO.trt.3
ATRX KO cells, Etoposide treated, replicate 3

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

extract_protocol:
Total RNA was extracted using Trizol following manufacturer’s instructions. RNA was treated with Turbo DNA-free kit (life technologies) and quality checked with TapeStation (Agilent).
Sequencing library preparation was then completed using the QuantSeq 3’-mRNA kit (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions

value: ATRX KO

tag: treatment

value: etoposide


description:
ATRX.KO.trt.1
ATRX KO cells, Etoposide treated, replicate 1


description:
ATRX.KO.trt.2
ATRX KO cells, Etoposide treated, replicate 2


title: ATRX KO cells, untreated, replicate 3

description:
ATRX.KO.ctr.3
ATRX KO cells, untreated, replicate 3

value: control


title: E8.5_plate2_D01_BSseq

value: E8.5 embryo


description:
ATRX.WT.trt.3
ATRX WT cells, Etoposide treated, replicate 3


title: Whole blood DNA methylation_Validation_MILD [INVN02020C163]

tag: age

value: M

value: Whole Blood


title: Whole blood DNA methylation_Validation_MILD [INVN02020C162]

value: F


title: E8.5_plate2_C12_BSseq


title: ATRX KO cells, untreated, replicate 1

description:
ATRX.KO.ctr.1
ATRX KO cells, untreated, replicate 1

tag: cell line

value: U87 glioblastoma cells


title: ATRX KO cells, untreated, replicate 2

description:
ATRX.KO.ctr.2
ATRX KO cells, untreated, replicate 2

tag: genotype


title: Whole blood DNA methylation_Validation_MILD [INVN02020C161]


title: E8.5_plate2_C11_BSseq


title: IgG, DAXX WT cells

description: IgG, DAXX WT cells


title: E8.5_plate2_C09_BSseq


title: ATRX WT cells, untreated, replicate 3

description:
ATRX.WT.ctr.3
ATRX WT cells, untreated, replicate 3

tag: replicate


title: Whole blood DNA methylation_Validation_MILD [INVN02020C159]


description:
ATRX.WT.trt.1
ATRX WT cells, Etoposide treated, replicate 1


title: E8.5_plate2_C10_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C158]


description:
DAXX.KO.trt.2
DAXX KO cells, Etoposide treated, replicate 2


description:
DAXX.KO.trt.3
DAXX KO cells, Etoposide treated, replicate 3


title: E8.5_plate2_C08_BSseq


title: ATRX WT cells, untreated, replicate 1

description:
ATRX.WT.ctr.1
ATRX WT cells, untreated, replicate 1


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C164]

value: SEVERE


title: Whole blood DNA methylation_Validation_MILD [INVN02020C156]


description:
DAXX.KO.trt.1
DAXX KO cells, Etoposide treated, replicate 1


description:
ATRX.WT.trt.2
ATRX WT cells, Etoposide treated, replicate 2


title: E8.5_plate2_C07_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C157]


title: ATRX WT cells, untreated, replicate 2

description:
ATRX.WT.ctr.2
ATRX WT cells, untreated, replicate 2


title: E8.5_plate2_C06_BSseq


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C155]


title: DAXX KO cells, untreated, replicate 2

description:
DAXX.KO.ctr.2
DAXX KO cells, untreated, replicate 2


title: DAXX KO cells, untreated, replicate 1

description:
DAXX.KO.ctr.1
DAXX KO cells, untreated, replicate 1


title: DAXX KO cells, untreated, replicate 3

description:
DAXX.KO.ctr.3
DAXX KO cells, untreated, replicate 3


description:
DAXX.WT.trt.3
DAXX WT cells, Etoposide treated, replicate 3


title: E8.5_plate2_C05_BSseq


title: DAXX WT cells, untreated, replicate 2

description:
DAXX.WT.ctr.2
DAXX WT cells, untreated, replicate 2


description:
DAXX.WT.trt.1
DAXX WT cells, Etoposide treated, replicate 1


title: E8.5_plate2_C04_BSseq


title: DAXX WT cells, untreated, replicate 3

description:
DAXX.WT.ctr.3
DAXX WT cells, untreated, replicate 3


title: Whole blood DNA methylation_Validation_MILD [INVN02020C154]


title: Whole blood DNA methylation_Validation_MILD [INVN02020C153]


title: DAXX WT cells, untreated, replicate 1

description:
DAXX.WT.ctr.1
DAXX WT cells, untreated, replicate 1


title: Whole blood DNA methylation_Validation_MILD [INVN02020C152]


title: E8.5_plate2_C03_BSseq


title: cord 545 3DA

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
Sequencing was conducted on an Illumina NextSeq 500 system with 41 base pair paired-end reads
Base calling was performed by Real Time Analysis (RTA) v2.11.3 using NextSeq 500 Control Software v4.0.2
Sequencing reads were mapped to hg38 genome using STAR aligner (version 2.7.8a)
Gene based counting was performed using the STAR aligner (version 2.7.8a) .
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.30.1 )
Genome_build: hg38
Supplementary_files_format_and_content: comma-delimited text file include raw counts for each Sample generated by STAR aligner.

growth_protocol: CD34+ cord blood cells were grown is Stemspan SFEM medium, supplemented with 100 ng/ml SCF, TPO and Flt3L and 10 mM 3DA or DMSO

extract_protocol:
RNA was isolated using the Nucleospin RNA XS (Macherey-Nagel)
RNA-seq libraries were prepared for sequencing using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) followed by Nextera XT (Illumina) library preparation. Libraries were sequenced on the Illumina NextSeq 500 following the manufacturer's protocols.

treatment_protocol: Every 3 days medium was refreshed and new compounds were added. At day 9 the cells were sorted for CD34+CD38-

tag: days of culture


title: E8.5_plate2_C02_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C151]


title: E8.5_plate2_C01_BSseq


title: cord 535 3DA


description:
DAXX.WT.trt.2
DAXX WT cells, Etoposide treated, replicate 2


title: Whole blood DNA methylation_Validation_MILD [INVN02020C150]


title: cord 522 DMSO

value: DMSO


title: E8.5_plate2_B12_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C148]


title: cord 338 DMSO


title: cord 522 3DA


title: Whole blood DNA methylation_Validation_MILD [INVN02020C147]


title: cord 338 3DA


title: E8.5_plate2_B09_BSseq


title: GH4:318GCecum

city: Matsudo

first: Akihito

last: Yausoka

state: Chiba

address: Iwase 550

department: Human nutrition

institute: Seitoku University

description:
Caecum_Amyg, Caecum_Hypo, Caecum_Liver
16S rRNA gene amplicion

data_processing:
mRNA-seq:
The Fastq data were checked by Fastqc quality check program and trimmed using the fastx-clipper and cutadapt program to remove adaptor sequence (>1%) and low-quality reads (quality < 30, length < 20 base). Cleaned reads were mapped against Mus musculus reference genome GRCm 38 (mm10, https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/) using tophat program (tophat-program: –ribrary-type FR second Strand -g20 -N2). The rate of mapped reads to the obtained reads was 96.5 % on average. The resulting BAM data were used to obtain the reads on the exons of known protein coding genes (mm10) on the featureCounts program (https://sourceforge.net/projects/subread/files/subread-2.0.0/). The reads per kilobase of exon model per million mapped reads (RPKM) for each tissue were filtered (RPKM < 0.3). The rate of filtered reads to the obtained reads was 56.8 % on average. Differentially expressed genes (DEGs) were predicted using the DESeq2 package on R statistical software (p < 0.01) (https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Cluster dendrograms were drawn by hclust package (https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust).
16S DNA-seq:
The processing of sequencing data, including quality filtering, chimera check, operational taxonomic unit (OTU) definition, and taxonomy assignment was carried out using the Quantitative Insights Into Microbial Ecology (QIIME software package version 1.8.0.), EA-Utils (ver. 1.1.2–537), the gold database (http://drive5.com/otupipe/gold.tz) and USEARCH (ver. 5.2.32, https://www.drive5.com/usearch/). Principal coordinate analysis, alpha diversity (Shannon index) analysis, and beta diversity analysis were conducted using vegan (Package vegan version 2.3-4) on R (2015, version 3.1.3) (Oksanen J et al., 2016).
Assembly: mm10; Quantitative Insights Into Microbial Ecology (QIIME software package version 1.8.0.)

source_name: Gut microbiome

growth_protocol: Five-week-old (postnatal day 35, PD35) male C57BL/6N mice were procured from Charles River (Hino, Japan). The animals were shipped in cardboard cages (5 mice / 1 cage), housed in air conditioned rooms (22 ± 2 °C, and 50 ± 5% humidity), and subjected to a cyclic 12 h light (8 a.m.–8 p.m.) and dark (8 p.m.–8 a.m.) environment. The light intensity was 100 lx at the front of the cages and 40 lx behind the cages. Five mice were acclimatized in a cage (24 cm length × 17.2 cm width × 12.9 cm depth, 413 cm2 floor area) with free access to the chow diet (MF, Oriental yeast, Tokyo, Japan) and water until PD40 (Fig. 1).

extract_protocol:
mRNA-seq: Total RNA was isolated from amygdala, hypothalamus or liver using TRI Reagent (MRC molecular research center, OH, USA). Total RNA from the liver was further purified using SimplyRNA tissue kit on Maxwell RNA extraction system (Promega). RNA quality was accessed using RNA 6000 Nano Series II Kit on Agilent 2100 Bioanalyzer (Agilent141 Technologies, Santa Clara, CA, USA). RNA integrity number for each tissue RNA was higher than 8.5.
mRNA-seq: 200ng of Total RNA was constructed in a library using Smarter Stranded Total RNA Sample Prep Kit HI Mammalian (Clontech Laboratory, Inc.). The library was quantified using High Sensitivity DNA kit on Agilent 2100 Bioanalyzer and subjected to 50 bp single end sequencing analysis (55.7 million / sample on average) on a Hiseq system (Illumina).
16S DNA-seq: DNA was extracted from the cecal samples using the bead-beating method described by Odamaki et al (Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao JZ et al. (2016). Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. BMC Microbiol. 16, 90.).
16S DNA-seq:  The 16S rRNA V3–V4 region was amplified using Tru357F (5’-CGCTCTTCCGATCTCTG TACGGRAGGCAGCAG-3’) and Tru806R (5’-CGCTCTTCCGATCTGAC GGACTACHVGGGTWTCTAAT-3’) primers and sequenced on Illumina MiSeq.

treatment_protocol: Subsequently, mice were shifted to the single-housing (SH) condition (one mouse in one cage of 18 cm length × 11 cm width × 11 cm depth, 198 cm2 floor area) or in the group-housing (GH) condition (same as the acclimatization) with free access to the chow diet and water until PD44. Mice and cecal samples in the different conditions were handled separately under sterile conditions. Cecal content was collected on the PD44, and the mice were euthanized by cervical dislocation. The amygdala, hypothalamus, and liver were collected and stored at −80 °C.

value: Grouip housing

value: Caecal content

tag: library construction


title: E8.5_plate2_B10_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C149]

tag: subject status


title: Whole blood DNA methylation_Validation_MILD [INVN02020C146]

tag: gender


title: GH1:317GCecum

value: The 16S rRNA V3–V4 region was amplified using Tru357F (5’-CGCTCTTCCGATCTCTG TACGGRAGGCAGCAG-3’) and Tru806R (5’-CGCTCTTCCGATCTGAC GGACTACHVGGGTWTCTAAT-3’) primers and sequenced on Illumina MiSeq.


title: GH2:327GCecum


title: Whole blood DNA methylation_Validation_MILD [INVN02020C144]

tag: cohort


title: LLC Dish 3

description: GFP-laveled 3LL (murine lung cancer cell line)

source_name: 3LL-GFP_dish_RIN 8.40

value: C57/BL6 mice

value: lung

value: Lewis Lung Carcinoma (LLC)

tag: condition

value: cell line, culture, 7 days


title: E8.5_plate2_B07_BSseq


title: cord 545 DMSO


title: GH3:328GCecum


title: SH2:334SCecum

value: Single housing


title: E8.5_plate2_B11_BSseq


title: E8.5_plate2_B08_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C143]

value: SARS-CoV-2 positive individual

value: Validation

value: MILD


title: SH1:330SCecum


title: SH4:320SCecum


title: cord 535 DMSO


title: Whole blood DNA methylation_Validation_MILD [INVN02020C142]

value: M


title: Tet-tko-chimera_embryo05_H12_RNAseq

data_processing:
Libraries were sequenced on the Illumina Nextseq500 platform using the default RTA analysis software.
RNA-seq libraries were aligned to the GRCm38 mouse genome build using HISAT2 (v2.1.0) using options --dta --no-softclipping --no-mixed --no-discordant, yielding a mean of 611,000 aligned reads per cell.
Subsequently, gene expression counts were quantified from the mapped reads using featureCounts with the Ensembl gene annotation (version 87). Only protein-coding genes matching canonical chromosomes were considered. The read counts were log-transformed and size-factor adjusted.
Assembly: GRCm38
Supplementary files format and content: A table of genes (rows) x cells (columns). The first column is the ensembl gene ID

extract_protocol: Single-cells were sorted  using flow cytometry (E6.5, E7.5) into 96 well PCR plates containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL (Sigma)). Samples were incubated for 15 minutes at 37°C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at -80°C prior to processing. Poly-A RNA was captured on oligo-dT conjugated to magnetic beads and amplified cDNA was prepared according to the G&T-seq and Smartseq2 protocols. The lysate containing gDNA was purified on AMPureXP beads before bisulfite-seq libraries were prepared according to the scBS-seq protocol.

value: E7.5 embryo


title: E8.5_plate2_B06_BSseq

value: E8.5 embryo


title: Whole blood DNA methylation_Validation_MILD [INVN02020C141]

value: Whole Blood


title: Tet-tko-chimera_embryo05_H09_RNAseq


title: Tet-tko-chimera_embryo05_H11_RNAseq


title: Tet-tko-chimera_embryo05_H10_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C139]


title: Tet-tko-chimera_embryo05_H08_RNAseq


title: Tet-tko-chimera_embryo05_H05_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C140]


title: Tet-tko-chimera_embryo05_H06_RNAseq


title: E8.5_plate2_B04_BSseq


title: E8.5_plate2_B03_BSseq


title: E8.5_plate2_B05_BSseq


title: Tet-tko-chimera_embryo05_H03_RNAseq


title: E8.5_plate2_B02_BSseq


title: Tet-tko-chimera_embryo05_H02_RNAseq


title: E8.5_plate2_B01_BSseq


title: Tet-tko-chimera_embryo05_G11_RNAseq


title: SH3:324SCecum


title: Tet-tko-chimera_embryo05_G12_RNAseq


title: E8.5_plate2_A12_BSseq


title: Tet-tko-chimera_embryo05_G10_RNAseq


title: E8.5_plate2_A11_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C133]

value: F


title: Whole blood DNA methylation_Validation_MILD [INVN02020C131]


title: Tet-tko-chimera_embryo05_G08_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C138]


title: E8.5_plate2_A10_BSseq


title: Tet-tko-chimera_embryo05_H04_RNAseq


title: Tet-tko-chimera_embryo05_H07_RNAseq


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C116]

value: SEVERE


title: Whole blood DNA methylation_Validation_NEGATIVE [INVN02020C135]

source_name: Validation_NEGATIVE_whole Blood

value: SARS-CoV-2 negative individual

value: NEGATIVE


title: Tet-tko-chimera_embryo05_G05_RNAseq


title: E8.5_plate2_A09_BSseq


title: Tet-tko-chimera_embryo05_H01_RNAseq


title: E8.5_plate2_A08_BSseq


title: Tet-tko-chimera_embryo05_G04_RNAseq


title: Tet-tko-chimera_embryo05_G03_RNAseq


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020C115]


title: Tet-tko-chimera_embryo05_G06_RNAseq


title: Whole blood DNA methylation_Validation_NEGATIVE [INVN02020C137]


title: E8.5_plate2_A07_BSseq


title: Tet-tko-chimera_embryo05_G02_RNAseq


title: E8.5_plate2_A06_BSseq


title: Tet-tko-chimera_embryo05_G01_RNAseq


title: Tet-tko-chimera_embryo05_F12_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B767]


title: Tet-tko-chimera_embryo05_G07_RNAseq


title: Tet-tko-chimera_embryo05_F11_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020C114]


title: E8.5_plate2_A03_BSseq


title: E8.5_plate2_A05_BSseq


title: Tet-tko-chimera_embryo05_F09_RNAseq


title: Tet-tko-chimera_embryo05_F05_RNAseq


title: Tet-tko-chimera_embryo05_F06_RNAseq


title: Tet-tko-chimera_embryo05_F08_RNAseq


title: E8.5_plate2_A02_BSseq


title: Tet-tko-chimera_embryo05_F07_RNAseq


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020B713]


title: Whole blood DNA methylation_Validation_MILD [INVN02020B714]


title: Whole blood DNA methylation_Validation_MILD [INVN02020B122]


title: E8.5_plate2_A04_BSseq


title: Whole blood DNA methylation_Validation_SEVERE [INVN02020B712]


title: Tet-tko-chimera_embryo05_F04_RNAseq


title: E8.5_plate2_A01_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B107]


title: Tet-tko-chimera_embryo05_F02_RNAseq


title: Tet-tko-chimera_embryo05_E12_RNAseq


title: Tet-tko-chimera_embryo05_F10_RNAseq


title: Tet-tko-chimera_embryo05_E11_RNAseq


title: E8.5_plate1_H12_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B106]


title: Tet-tko-chimera_embryo05_E09_RNAseq


title: Tet-tko-chimera_embryo05_E08_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B104]


title: Tet-tko-chimera_embryo05_E03_RNAseq


title: Tet-tko-chimera_embryo05_E05_RNAseq


title: Tet-tko-chimera_embryo05_F03_RNAseq


title: Tet-tko-chimera_embryo05_E10_RNAseq


title: E8.5_plate1_H07_BSseq


title: Tet-tko-chimera_embryo05_E04_RNAseq


title: Tet-tko-chimera_embryo05_D11_RNAseq


title: Tet-tko-chimera_embryo05_E06_RNAseq


title: E8.5_plate1_H08_BSseq


title: Tet-tko-chimera_embryo05_G09_RNAseq


title: E8.5_plate1_H10_BSseq


title: E8.5_plate1_H11_BSseq


title: E8.5_plate1_H09_BSseq


title: Tet-tko-chimera_embryo05_E02_RNAseq


title: E8.5_plate1_H06_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B105]


title: Whole blood DNA methylation_Validation_MILD [INVN02020B103]


title: Whole blood DNA methylation_Validation_MILD [INVN02020B100]


title: Tet-tko-chimera_embryo05_D10_RNAseq


title: Tet-tko-chimera_embryo05_D12_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B101]


title: E8.5_plate1_H05_BSseq


title: Tet-tko-chimera_embryo05_D09_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B098]


title: Whole blood DNA methylation_Validation_MILD [INVN02020B102]


title: Tet-tko-chimera_embryo05_D06_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B099]


title: Tet-tko-chimera_embryo05_D05_RNAseq


title: E8.5_plate1_H04_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B096]


title: Whole blood DNA methylation_Validation_MILD [INVN02020B097]


title: Tet-tko-chimera_embryo05_D02_RNAseq


title: E8.5_plate1_H01_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B095]


title: Tet-tko-chimera_embryo05_F01_RNAseq


title: Tet-tko-chimera_embryo05_D04_RNAseq


title: Tet-tko-chimera_embryo05_C12_RNAseq


title: Tet-tko-chimera_embryo05_D01_RNAseq


title: Whole blood DNA methylation_Validation_NEGATIVE [INVN02020B093]


title: E8.5_plate1_G12_BSseq


title: E8.5_plate1_G11_BSseq


title: Tet-tko-chimera_embryo05_C11_RNAseq


title: E8.5_plate1_H03_BSseq


title: Tet-tko-chimera_embryo05_C10_RNAseq


title: Tet-tko-chimera_embryo05_C09_RNAseq


title: Tet-tko-chimera_embryo05_C08_RNAseq


title: Tet-tko-chimera_embryo05_E01_RNAseq


title: Tet-tko-chimera_embryo05_D08_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B090]


title: Tet-tko-chimera_embryo05_C07_RNAseq


title: Tet-tko-chimera_embryo05_D07_RNAseq


title: E8.5_plate1_G10_BSseq


title: Whole blood DNA methylation_Validation_NEGATIVE [INVN02020B087]


title: Tet-tko-chimera_embryo05_D03_RNAseq


title: Tet-tko-chimera_embryo05_C04_RNAseq


title: E8.5_plate1_G08_BSseq


title: Tet-tko-chimera_embryo05_C05_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B081]


title: E8.5_plate1_G07_BSseq


title: Tet-tko-chimera_embryo05_C02_RNAseq


title: Whole blood DNA methylation_Validation_NEGATIVE [INVN02020B070]


title: Tet-tko-chimera_embryo05_C01_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B067]


title: E8.5_plate1_G06_BSseq


title: Tet-tko-chimera_embryo05_B10_RNAseq


title: Tet-tko-chimera_embryo05_B11_RNAseq


title: E8.5_plate1_G04_BSseq


title: Tet-tko-chimera_embryo05_B08_RNAseq


title: E8.5_plate1_G05_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B063]


title: Whole blood DNA methylation_Validation_NEGATIVE [INVN02020B064]


title: Tet-tko-chimera_embryo05_E07_RNAseq


title: Whole blood DNA methylation_Validation_NEGATIVE [INVN02020B059]


title: Whole blood DNA methylation_Validation_MILD [INVN02020B085]


title: Tet-tko-chimera_embryo05_B06_RNAseq


title: E8.5_plate1_G09_BSseq


title: Tet-tko-chimera_embryo05_B05_RNAseq


title: E8.5_plate1_G03_BSseq


title: Tet-tko-chimera_embryo05_C03_RNAseq


title: Tet-tko-chimera_embryo05_B12_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B054]


title: Tet-tko-chimera_embryo05_B03_RNAseq


title: Tet-tko-chimera_embryo05_B09_RNAseq


title: Tet-tko-chimera_embryo05_B07_RNAseq


title: E8.5_plate1_G01_BSseq


title: Tet-tko-chimera_embryo05_A12_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B051]


title: Whole blood DNA methylation_Validation_MILD [INVN02020B048]


title: Tet-tko-chimera_embryo05_B01_RNAseq


title: Tet-tko-chimera_embryo05_A10_RNAseq


title: E8.5_plate1_F12_BSseq


title: Tet-tko-chimera_embryo05_A11_RNAseq


title: E8.5_plate1_F11_BSseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B044]


title: Tet-tko-chimera_embryo05_A08_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B043]


title: Tet-tko-chimera_embryo05_B04_RNAseq


title: Tet-tko-chimera_embryo05_A06_RNAseq


title: Tet-tko-chimera_embryo05_A05_RNAseq


title: E8.5_plate1_F09_BSseq


title: Tet-tko-chimera_embryo05_A07_RNAseq


title: E8.5_plate1_G02_BSseq


title: Tet-tko-chimera_embryo05_A04_RNAseq


title: Whole blood DNA methylation_Validation_MILD [INVN02020B042]


title: E8.5_plate1_F08_BSseq


title: Whole blood DNA methylation_Discovery_MILD [997]

source_name: Discovery_MILD_whole Blood

value: Discovery


title: Tet-tko-chimera_embryo05_A02_RNAseq


title: Tet-tko-chimera_embryo05_A01_RNAseq


title: E8.5_plate1_F07_BSseq


title: Tet-tko-chimera_embryo05_A09_RNAseq


title: Tet-tko-chimera_embryo04_H12_RNAseq


title: E8.5_plate1_F10_BSseq


title: Tet-tko-chimera_embryo04_H09_RNAseq


title: Tet-tko-chimera_embryo04_H08_RNAseq


title: Tet-tko-chimera_embryo04_H11_RNAseq


title: Tet-tko-chimera_embryo04_H07_RNAseq


title: Tet-tko-chimera_embryo04_H10_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [99655]


title: E8.5_plate1_F05_BSseq


title: Whole blood DNA methylation_Discovery_MILD [99378]


title: Whole blood DNA methylation_Discovery_MILD [96882]


title: E8.5_plate1_F04_BSseq


title: Whole blood DNA methylation_Discovery_MILD [95772]


title: Tet-tko-chimera_embryo04_H05_RNAseq


title: E8.5_plate1_F06_BSseq


title: Tet-tko-chimera_embryo05_A03_RNAseq


title: E8.5_plate1_F02_BSseq


title: Whole blood DNA methylation_Validation_NEGATIVE [96013]


title: E8.5_plate1_F03_BSseq


title: Tet-tko-chimera_embryo04_H06_RNAseq


title: Tet-tko-chimera_embryo04_H04_RNAseq


title: Tet-tko-chimera_embryo04_H03_RNAseq


title: Whole blood DNA methylation_Validation_NEGATIVE [95498]


title: Tet-tko-chimera_embryo04_H01_RNAseq


title: Tet-tko-chimera_embryo04_H02_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [92266]


title: Tet-tko-chimera_embryo04_G12_RNAseq


title: Tet-tko-chimera_embryo04_G11_RNAseq


title: E8.5_plate1_F01_BSseq


title: E8.5_plate1_E12_BSseq


title: Whole blood DNA methylation_Discovery_MILD [92201]


title: Tet-tko-chimera_embryo04_G10_RNAseq


title: Whole blood DNA methylation_Validation_NEGATIVE [89670]


title: Tet-tko-chimera_embryo04_G09_RNAseq


title: Tet-tko-chimera_embryo04_G07_RNAseq


title: Tet-tko-chimera_embryo04_G06_RNAseq


title: E8.5_plate1_E11_BSseq


title: E8.5_plate1_E09_BSseq


title: E8.5_plate1_E10_BSseq


title: Tet-tko-chimera_embryo04_G05_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [88190]


title: E8.5_plate1_E07_BSseq


title: Tet-tko-chimera_embryo04_G02_RNAseq


title: E8.5_plate1_E08_BSseq


title: Tet-tko-chimera_embryo04_G01_RNAseq


title: Tet-tko-chimera_embryo05_B02_RNAseq


title: Tet-tko-chimera_embryo04_G03_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [88185]


title: Whole blood DNA methylation_Discovery_MILD [87629]


title: Whole blood DNA methylation_Discovery_MILD [8736]


title: Tet-tko-chimera_embryo04_G08_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [81847]


title: E8.5_plate1_E06_BSseq


title: Tet-tko-chimera_embryo04_F09_RNAseq


title: Tet-tko-chimera_embryo04_F12_RNAseq


title: Whole blood DNA methylation_Validation_NEGATIVE [81810]


title: E8.5_plate1_E04_BSseq


title: Tet-tko-chimera_embryo04_G04_RNAseq


title: Tet-tko-chimera_embryo04_F08_RNAseq


title: Tet-tko-chimera_embryo04_F10_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [79348]


title: Tet-tko-chimera_embryo04_F05_RNAseq


title: E8.5_plate1_E03_BSseq


title: E8.5_plate1_E02_BSseq


title: Tet-tko-chimera_embryo04_F06_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [79235]


title: Tet-tko-chimera_embryo04_F03_RNAseq


title: Tet-tko-chimera_embryo04_F07_RNAseq


title: E8.5_plate1_E01_BSseq


title: Tet-tko-chimera_embryo04_F04_RNAseq


title: Tet-tko-chimera_embryo04_F11_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [79111]


title: E8.5_plate1_D12_BSseq


title: Whole blood DNA methylation_Discovery_SEVERE [79139]

source_name: Discovery_SEVERE_whole Blood


title: Tet-tko-chimera_embryo04_E12_RNAseq


title: Tet-tko-chimera_embryo04_F01_RNAseq


title: E8.5_plate1_D11_BSseq


title: Tet-tko-chimera_embryo04_E11_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [77953]


title: Whole blood DNA methylation_Discovery_MILD [7718]


title: Tet-tko-chimera_embryo04_E10_RNAseq


title: Tet-tko-chimera_embryo04_E09_RNAseq


title: Tet-tko-chimera_embryo04_E08_RNAseq


title: Tet-tko-chimera_embryo04_E07_RNAseq


title: E8.5_plate1_D09_BSseq


title: Tet-tko-chimera_embryo04_E06_RNAseq


title: Whole blood DNA methylation_Discovery_SEVERE [76626]


title: E8.5_plate1_D07_BSseq


title: Tet-tko-chimera_embryo04_E05_RNAseq


title: Tet-tko-chimera_embryo04_E04_RNAseq


title: Tet-tko-chimera_embryo04_E03_RNAseq


title: E8.5_plate1_D08_BSseq


title: Whole blood DNA methylation_Discovery_NEGATIVE [73290]

source_name: Discovery_NEGATIVE_whole Blood


title: Whole blood DNA methylation_Validation_NEGATIVE [73139]


title: Tet-tko-chimera_embryo04_E02_RNAseq


title: Tet-tko-chimera_embryo04_D12_RNAseq


title: Tet-tko-chimera_embryo04_E01_RNAseq


title: E8.5_plate1_D06_BSseq


title: E8.5_plate1_D05_BSseq


title: Whole blood DNA methylation_Discovery_MILD [73001]


title: Tet-tko-chimera_embryo04_D11_RNAseq


title: E8.5_plate1_D10_BSseq


title: Tet-tko-chimera_embryo04_D10_RNAseq


title: Tet-tko-chimera_embryo04_F02_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [72838]


title: Tet-tko-chimera_embryo04_D09_RNAseq


title: E8.5_plate1_D04_BSseq


title: Tet-tko-chimera_embryo04_D08_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [76711]


title: E8.5_plate1_D03_BSseq


title: Whole blood DNA methylation_Discovery_MILD [72071]


title: Tet-tko-chimera_embryo04_D07_RNAseq


title: E8.5_plate1_D02_BSseq


title: Tet-tko-chimera_embryo04_D06_RNAseq


title: Tet-tko-chimera_embryo04_D05_RNAseq


title: Tet-tko-chimera_embryo04_D04_RNAseq


title: Tet-tko-chimera_embryo04_D03_RNAseq


title: E8.5_plate1_D01_BSseq


title: Whole blood DNA methylation_Discovery_SEVERE [70232]


title: Whole blood DNA methylation_Discovery_MILD [70884]


title: E8.5_plate1_C12_BSseq


title: Tet-tko-chimera_embryo04_D02_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [69977]


title: Tet-tko-chimera_embryo04_D01_RNAseq


title: Tet-tko-chimera_embryo04_C11_RNAseq


title: E8.5_plate1_C11_BSseq


title: Whole blood DNA methylation_Discovery_MILD [69445]


title: Whole blood DNA methylation_Discovery_SEVERE [67461]


title: Tet-tko-chimera_embryo04_C10_RNAseq


title: Tet-tko-chimera_embryo04_C12_RNAseq


title: Tet-tko-chimera_embryo04_C09_RNAseq


title: E8.5_plate1_C10_BSseq


title: Whole blood DNA methylation_Discovery_MILD [64988]


title: Tet-tko-chimera_embryo04_C07_RNAseq


title: E8.5_plate1_C09_BSseq


title: Tet-tko-chimera_embryo04_C06_RNAseq


title: E8.5_plate1_C08_BSseq


title: Whole blood DNA methylation_Discovery_SEVERE [64559]


title: E8.5_plate1_C07_BSseq


title: Tet-tko-chimera_embryo04_C02_RNAseq


title: Tet-tko-chimera_embryo04_C03_RNAseq


title: E8.5_plate1_C06_BSseq


title: Whole blood DNA methylation_Discovery_SEVERE [643240]


title: Tet-tko-chimera_embryo04_C04_RNAseq


title: E8.5_plate1_C05_BSseq


title: Tet-tko-chimera_embryo04_B11_RNAseq


title: Tet-tko-chimera_embryo04_C08_RNAseq


title: Tet-tko-chimera_embryo04_B12_RNAseq


title: Tet-tko-chimera_embryo04_C01_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [642947]


title: Tet-tko-chimera_embryo04_B08_RNAseq


title: E8.5_plate1_C03_BSseq


title: Whole blood DNA methylation_Discovery_SEVERE [642940]


title: Tet-tko-chimera_embryo04_C05_RNAseq


title: Tet-tko-chimera_embryo04_B09_RNAseq


title: Tet-tko-chimera_embryo04_B07_RNAseq


title: Whole blood DNA methylation_Discovery_SEVERE [642885]


title: E8.5_plate1_C04_BSseq


title: Tet-tko-chimera_embryo04_B10_RNAseq


title: Tet-tko-chimera_embryo04_B04_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [642883]


title: Tet-tko-chimera_embryo04_B06_RNAseq


title: Tet-tko-chimera_embryo04_B05_RNAseq


title: E8.5_plate1_C02_BSseq


title: E8.5_plate1_C01_BSseq


title: Tet-tko-chimera_embryo04_B02_RNAseq


title: E8.5_plate1_H02_BSseq


title: E8.5_plate1_B12_BSseq


title: Whole blood DNA methylation_Discovery_SEVERE [642882]


title: Whole blood DNA methylation_Discovery_SEVERE [643081]


title: Tet-tko-chimera_embryo04_B03_RNAseq


title: Whole blood DNA methylation_Discovery_SEVERE [642781]


title: Tet-tko-chimera_embryo04_B01_RNAseq


title: E8.5_plate1_B11_BSseq


title: Whole blood DNA methylation_Discovery_SEVERE [642780]


title: Tet-tko-chimera_embryo04_A10_RNAseq


title: Tet-tko-chimera_embryo04_A11_RNAseq


title: Tet-tko-chimera_embryo04_A12_RNAseq


title: Tet-tko-chimera_embryo04_A08_RNAseq


title: E8.5_plate1_B10_BSseq


title: Tet-tko-chimera_embryo04_A07_RNAseq


title: Whole blood DNA methylation_Discovery_SEVERE [642741]


title: Whole blood DNA methylation_Discovery_SEVERE [642740]


title: Tet-tko-chimera_embryo04_A04_RNAseq


title: E8.5_plate1_B09_BSseq


title: E8.5_plate1_B08_BSseq


title: Tet-tko-chimera_embryo04_A05_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [642731]


title: Whole blood DNA methylation_Discovery_SEVERE [642730]


title: E8.5_plate1_B07_BSseq


title: Tet-tko-chimera_embryo04_A03_RNAseq


title: Tet-tko-chimera_embryo04_A02_RNAseq


title: Tet-tko-chimera_embryo04_A01_RNAseq


title: Tet-tko-chimera_embryo02_H11_RNAseq


title: E8.5_plate1_B05_BSseq


title: E8.5_plate1_B06_BSseq


title: Tet-tko-chimera_embryo02_H12_RNAseq


title: Whole blood DNA methylation_Discovery_SEVERE [642552]


title: Whole blood DNA methylation_Discovery_SEVERE [642706]


title: Tet-tko-chimera_embryo04_A09_RNAseq


title: Whole blood DNA methylation_Discovery_SEVERE [642435]


title: Tet-tko-chimera_embryo02_H09_RNAseq


title: E8.5_plate1_B04_BSseq


title: Tet-tko-chimera_embryo02_H08_RNAseq


title: Tet-tko-chimera_embryo02_H07_RNAseq


title: Tet-tko-chimera_embryo02_H06_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [64142]


title: Whole blood DNA methylation_Discovery_MILD [639958]


title: Tet-tko-chimera_embryo02_H04_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [641493]


title: Tet-tko-chimera_embryo02_H03_RNAseq


title: Tet-tko-chimera_embryo02_H05_RNAseq


title: E8.5_plate1_B02_BSseq


title: E8.5_plate1_A12_BSseq


title: Tet-tko-chimera_embryo02_H02_RNAseq


title: Whole blood DNA methylation_Discovery_MILD [638383]


title: Tet-tko-chimera_embryo02_H10_RNAseq