title: MDAMB231_RNA-seq_sgB_nuc_rep2

description: RNA-seq

data_processing:
The human genome indexes were built with gene annotations (gencode v33) and the human GRCh38 reference genome sequences by using STAR (version 2.7.2b) and RSEM (version 1.2.31) software.
Then raw reads from RNA-seq were quality controlled through FastQC (version 0.11.5, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and mapped to the reference genome with built index by use of STAR.
After alignments, RSEM was used to estimate the read counts of genes. To analyze the differentially expressed genes, we kept the genes with read counts >= 5 in at least 50% samples, corrected with removing batch effects (sva R package for the whole cell and RUVSeq for cell nucleus and cytoplasm) and passed them to DESeq2 (version 1.32.0) using shrinkage estimators for dispersion and fold change.
The gene enrichment and GSEA analyses were performed by clusterProfiler R package.
Genome_build: hg38
Supplementary_files_format_and_content: gene counts and results from DESeq2

molecule: nuclear RNA

growth_protocol: MDA-MB-231 cas9 cells were transduced with sgRNAs by lentiviral transduction using an MOI of 4. 24 hours later, 2ug/ml puromycin was added and the cells were selected for 4 days before RNA collection.

extract_protocol:
Trizol (Qiagen) was used to purify RNA using manufacturers protocols.
Whole cell RNA was polyA selected whereas nuclear and cytoplasmic RNAs were rRNA depleted. Following this, RNAseq libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Illumina Platforms) (Kapa Biosystems), using 12 cycles of PCR amplification. Libraries were purified using AxyPrep Mag PCR Clean-up kit (Thermo Fisher Scientific). Each library was quantified using a Qubit fluorometer (Life Technologies) and the size distribution assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

treatment_protocol: For nuclear/cytoplasmic isolation, cells were trypsinized and washed once with PBS. Then, hypotonic buffer (10mM Tris pH 7.4, 1.5mM MgCl2, 10mM KCl, 1% NP-40) was added to 1x106 cells and incubated on ice for 10 minutes. The nuclei were spun down at 5000xg at 4°C for 10 minutes and the supernatant containing the cytoplasmic fraction was collected. The nuclear pellet was washed once with hypotonic buffer, spun down, and resuspended in hypotonic buffer. RNA from the cytoplasmic and nuclear fractions were isolated with Trizol (Qiagen) using manufacturers protocols.


title: MDAMB231_RNA-seq_sgB_nuc_rep1

status: Public on Mar 25 2023

type: SRA

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

country: USA

institute: Beckman Research Institute of City of Hope

description: RNA-seq

library_source: transcriptomic

organism: Homo sapiens

tag: cell line

tag: treatment


title: MDAMB231_RNA-seq_sgB_cyto_rep2

description: RNA-seq

molecule: cytoplasmic RNA


title: MDAMB231_RNA-seq_sgB_cyto_rep1

description: RNA-seq


title: MDAMB231_RNA-seq_sgNS_nuc_rep1

description: RNA-seq

value: sgNS


title: MDAMB231_RNA-seq_sgNS_cyto_rep1

description: RNA-seq


title: MDAMB231_RNA-seq_sgNS_cyto_rep2

description: RNA-seq


title: MDAMB231_RNA-seq_sgB_rep1

description: RNA-seq

molecule: polyA RNA


title: MDAMB231_RNA-seq_sgA_rep2

description: RNA-seq


title: MDAMB231_RNA-seq_sgA_rep1

description: RNA-seq


title: MDAMB231_RNA-seq_sgNS_nuc_rep2

description: RNA-seq


title: MDAMB231_RNA-seq_sgNS_rep2

description: RNA-seq


title: MDAMB231_RNA-seq_sgB_rep2

description: RNA-seq


title: KOPTK1_NOTCH1-On2_RNA-seq

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

data_processing:
The sequence reads were aligned to the reference human genome  hg19 (GRCh37-lite; http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/README.GRCh37-lite) using BWA-0.5.7 aln.
RNA-seq pair-end reads were aligned to an extended reference transcriptome that consists of the reference genome and annotated exon–exon junctions using BWA-0.5.7 aln. To generate the custom reference transcriptome (built from NCBI GRCh37-lite reference and Ensembl v75 annotations) and ‘reposition’ reads that spanned exon-exon junctions we used JAGuaR v 2.0.3.
For RPKM normalization, we used the total number of reads aligned into coding exons normalized by total exon length
Genome_build: hg19a
Supplementary_files_format_and_content: RPKM_and_read_counts.xlsx

molecule: total RNA

growth_protocol: T-ALL cell lines were cultured in RPMI 1640 medium containing 10% FBS, 2mM L-glutamine, 1Mm sodium pyruvate, and penicillin/streptomycin.

extract_protocol:
RNA was isolated from live cells with TRIzol reagent followed by purification over PureLink RNA mini kit columns (Invitrogen).
RNA-seq was performed using a poly A library construction protocol with strand specific cDNA synthesis and 8 cycles of PCR. Purification of polyA+ mRNA and mRNA(-) was done by Flow-through total RNA using MultiMACS 96 Separation Unit. For library Construction, 96-well Plate-based Strand-specific cDNA Synthesis using Maxima H Minus Strand Specific 96-well was used for Illumina HiSeq 2500 Sequencing.

treatment_protocol:
NOTCH1-samples: KOPTK1 cells were treated with 1μM Compound E (GSI) or vehicle (DMSO) for 3 days and sorted for viability by FACS prior to sequencing.
RUNX1-samples: KOPTK1 cells were transduced with GFP-tagged shRUNX1-58 lentiviruses or non-silencing control and sorted by FACS on day 5 post-transduction prior to sequencing.

tag: cell type

value: T-ALL cell

tag: time

value: sorted by FACS on day 3 post-treatment

tag: anatomic site

value: Pleural Effusion

tag: anatomic sub-site

value: T-cell Lymphoblastic Leukemia


title: MDAMB231_RNA-seq_sgNS_rep1

description: RNA-seq


title: KOPTK1_NOTCH1-Off2_RNA-seq


title: KOPTK1_RUNX1-On_RNA-seq

value: sorted by FACS on day 5 post-transduction


title: KOPTK1_NOTCH1-Off_RNA-seq


title: KOPTK1_RUNX1-Off2_RNA-seq


title: KOPTK1_NOTCH1-On_RNA-seq


title: KOPTK1_RUNX1-On_inputDNA

library_source: genomic

data_processing:
The sequence reads were aligned to the reference human genome  hg19 (GRCh37-lite; http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/README.GRCh37-lite) using BWA-0.5.7 aln.
In all the downstream analyses, duplicate reads are removed and mapQ >= 5 is used.
FindER.1.0.0b is used with IP-signal data and DNA input control data to call the peaks at FDR <=0.01 with minimum peak size 300bp and maximum peaks within gap between peaks is 100bp are merged together.
Genome_build: hg19 (GRCh37-lite) http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/README.GRCh37-lite
Supplementary_files_format_and_content: bigwig files were generated using UCSC utilities.

molecule: genomic DNA

extract_protocol:
ChIP-seq libraries were constructed using a validated antibodies listed here: http://www.epigenomes.ca/data/CEMT/metadata/antibody_qc.html
A customized version of paired-end sample Prep Kit from Illumina V.1.1 was used for sample preparation. Libraries were indexed, pooled and sequenced using paired-end 75nt sequencing chemistry on an Illumina HiSeq 2500 platform following the manufacturer’s protocols (Illumina, Hayward, CA). The resulting sequence reads were split by index and aligned to the reference human genome (GRCh37-lite; http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/README.GRCh37-lite) using BWA-0.5.7 aln.

value: non-silencing control

tag: chip antibody


title: KOPTK1_RUNX1-On_H3K9me3


title: KOPTK1_RUNX1-On_H3K4me3

value: anti-H3K4me3 antibody (9751S), lot# 7)


title: KOPTK1_RUNX1-On_H3K4me1


title: KOPTK1_RUNX1-On_H3K27me3


title: KOPTK1_RUNX1-Off_H3K9me3

value: GFP-tagged shRUNX1-58 lentiviruses


title: KOPTK1_RUNX1-Off_inputDNA


title: KOPTK1_RUNX1-On_H3K27ac

value: anti-H3K27ac antibody (ab4729, lot# GR55451-1)


title: KOPTK1_RUNX1-On_H3K36me3

value: anti-H3K36me3 antibody (ab-9050, lot# GR56602-1)


title: KOPTK1_RUNX1-Off_H3K27ac


title: KOPTK1_RUNX1-Off_H3K27me3


title: KOPTK1_RUNX1-Off_H3K4me3


title: KOPTK1_RUNX1-Off_H3K36me3


title: KOPTK1_RUNX1-Off2_inputDNA

value: GFP-tagged shRUNX1-59 lentiviruses


title: KOPTK1_RUNX1-Off2_H3K4me1


title: KOPTK1_RUNX1-Off2_H3K36me3


title: KOPTK1_RUNX1-Off2_H3K4me3


title: KOPTK1_RUNX1-Off_RNA-seq


title: KOPTK1_RUNX1-Off2_H3K9me3


title: KOPTK1_RUNX1-Off2_H3K27ac


title: KOPTK1_RUNX1-Off2_H3K27me3


title: KOPTK1_NOTCH1-On_inputDNA

value: DMSO control


title: KOPTK1_NOTCH1-On_H3K4me3


title: KOPTK1_NOTCH1-On_H3K4me1


title: KOPTK1_NOTCH1-On_H3K9me3


title: KOPTK1_NOTCH1-Off_inputDNA

value: GSI inhibition


title: KOPTK1_NOTCH1-On_H3K27me3


title: KOPTK1_NOTCH1-On_H3K36me3


title: KOPTK1_NOTCH1-Off_H3K9me3


title: KOPTK1_NOTCH1-Off_H3K4me1


title: KOPTK1_NOTCH1-Off_H3K4me3


title: KOPTK1_RUNX1-Off_H3K4me1


title: KOPTK1_NOTCH1-Off_H3K36me3


title: Pool-C-control

city: Hradec Králové

first: Tereza

last: Stverakova

address: Sokolská 581

department: Department of Clinical Biochemistry and Diagnostics

country: Czech Republic

institute: Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Czech Republic

data_processing:
The acquired data were evaluated with miRge3.0 formicroRNA expression using database miRbase and the integrated DESeq2 module for differential expression. FastQC v0.11.9 and MultiQCv1.13 were used for quality control of the sequencing reads. The output sequencing data were further evaluated using the DEApp web interface.
Assembly: hsa22
Supplementary files format and content: Comma separated file containing baseMean, log2FoldChange, lfcSE, pvalue and padj values.

source_name: FFPE healthy

extract_protocol:
Three to five 4-5 µm thin slices of formalin-fixed, paraffin-embedded tissue samples were deparaffinized using xylene and 96% ethanol. Total RNA was extracted using a commercial kit according to the manufacturer´s protocol: FFPE RNA/DNA Purification Plus Kit (Norgen Biotek, Thorold, Canada). The extracted RNA was eluted in 30 µl of RNase-free water.
Two pools of extracted RNA from malignant and non-malignant samples were prepared for sequencing analysis. The RealSeq®-Biofluids, Plasma/Serum miRNA Library Kit for Illumina® sequencing (RealSeq Biosciences, Santa Cruz, CA, USA) was used for library preparation. The whole procedure was carried out according to the manufacturer's protocol. The input amount of RNA was 150-170 ng.

tag: tissue

value: FFPE healthy

value: non-malignant


title: Pool-B-tumor

source_name: FFPE tumor

value: FFPE tumor

value: malignant


title: Pool-A-tumor


title: Pool-D-control


title: KOPTK1_NOTCH1-Off_H3K27me3

value: T-ALL cell


title: Ctl

city: San Francisco

first: Jeremy

middle: Michael

last: Shea

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California, San Francisco

data_processing:
Library strategy: hMeDIP-Seq
FASTQ reads were aligned to the mouse genome (mm10) using Bowtie2 with default parameters.
MACS2 callpeak was used to find peaks between the conditions using the BAM output.
Bedgraph files were outputted from MACS2 for each condition.
Assembly: mm10
Supplementary files format and content: Bedgraph files of combined samples from each condition

organism: Mus musculus

source_name: Hippocampal neurons

growth_protocol: Tet2 was deleted from CamkII cells in 4 month old mice by tamoxifen injection.

extract_protocol:
Nuclei were isolated from hippocampi followed by FACS isolation of neuronal nuclei. DNA was extracted from neuronal nuclei.
Equal amounts of DNA were sonicated to 300-500bp followed by end cleanup and NEB-Next adapter ligation. DNA was treated with USER enzyme followed by DNA cleanup. DNA was denatured, and subjected to immunoprecipitation with a 5-hydroxymethylcytosine antibody (ActiveMotif) followed by extensive washing. Captured DNA was amplified by PCR and purified.

treatment_protocol: Mice were maintained for 60 days after injection and then euthanized for neuronal isolation

tag: strain

tag: brain region

value: hippocampus

value: Neurons

tag: sample name

value: Ctl

tag: genotype


title: KOPTK1_NOTCH1-On_H3K27ac

value: sorted by FACS on day 3 post-treatment

value: Pleural Effusion


title: Tet10

value: cKO


title: Tet9

value: WT


title: Tet5


title: Tet4


title: KOPTK1_NOTCH1-Off_H3K27ac

value: anti-H3K27ac antibody (ab4729, lot# GR55451-1)


title: Tet3


title: Tet1


title: CUTLL1_RUNX1-On_inputDNA

description: Anatomic site: Pleural effusion

data_processing:
The sequence reads were split by index and aligned to the reference human genome (GRCh37-lite; http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/README.GRCh37-lite) using BWA-0.5.7 aln.
In all the downstream analyses, duplicate reads are removed and mapQ >= 5 is used.
FindER.1.0.0b is used with IP-signal data and DNA input control data to call the peaks at FDR <=0.01 with minimum peak size 300bp and maximum peaks within gap between peaks is 100bp are merged together.
Genome_build: hg19 (GRCh37-lite) http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/README.GRCh37-lite
Supplementary_files_format_and_content: bigwig and bed files

source_name: CUTLL1, non-silencing control, day 3, input

extract_protocol:
ChIP-seq libraries were constructed using a validated anti-H3K27ac antibody (Abcam ab4729).
A customized version of paired-end sample Prep Kit from Illumina V.1.1 was used for sample preparation. Libraries were indexed, pooled and sequenced using paired-end 75nt V3 (or V4?) sequencing chemistry on an Illumina HiSeq 2500 platform following the manufacturer’s protocols (Illumina, Hayward, CA).

treatment_protocol:
CUTLL1 cells were transduced with GFP-tagged shRUNX1-90 lentiviruses or non-silencing control and sorted by FACS on day 3 post-transduction prior to ChIP-seq analysis.
KOPT-K1 cells were transduced with GFP-tagged shRUNX1-58 lentiviruses or non-silencing control and sorted by FACS on day 5 post-transduction prior to ChIP-seq analysis.

value: non-silencing control

value: sorted by FACS on day 3


title: KOPTK1_RUNX1-Off_MiSeq_rep2

source_name: KOPT-K1, shRUNX1, day 7

growth_protocol: KOPT-K1, HPBALL, and RPMI 8402 cell lines were grown in RPMI 1640 media supplemented with 10% FBS, penicillin/streptomycin solution, and 2mM L-glutamine.

extract_protocol:
RNA was isolated from live cells with TRIzol reagent followed by purification over PureLink RNA mini kit columns (Invitrogen).
RNA-seq was performed using a Poly-A library construction protocol with strand specific cDNA synthesis and 8 cycles of PCR. Purification of polyA+ mRNA and mRNA(-) was done by Flow-through total RNA using MultiMACS 96 Separation Unit. For library construction, 96-well Plate-based Strand-specific cDNA Synthesis using Maxima H Minus Strand Specific 96-well was used for Illumina MiSeq Sequencing.

treatment_protocol: Cell lines (KOPT-K1, HPBALL, RPMI 8402) were transduced with shRUNX1 lentiviruses carrying a puromycin resistance marker and selected for 4 days beginning at 3 days post-transduction. Cells were then harvested for RNA-seq analysis (day 7 post-transduction). Each transduction was performed in duplicate.

value: GFP-tagged shRUNX1-58 lentiviruses

value: day 7 post-transduction

value: T-cell Lymphoblastic Leukemia


title: HPBALL_RUNX1-Off_MiSeq_rep2

source_name: HPBALL, shRUNX1, day 7

value: HPBALL

value: Peripheral Blood


title: RPMI_RUNX1-On_MiSeq_rep1

source_name: RPMI 8402, non-silencing control, day 7

value: RPMI 8402


title: HPBALL_RUNX1-Off_MiSeq_rep1

value: T-ALL cell


title: RPMI_RUNX1-Off_MiSeq_rep2

source_name: RPMI 8402, shRUNX1, day 7


title: CUTLL1_RUNX1-Off_inputDNA

description: Anatomic site: Pleural effusion

source_name: CUTLL1, shRUNX1, day 3, input

value: GFP-tagged shRUNX1-90 lentiviruses

value: sorted by FACS on day 3 post-transduction


title: CUTLL1_RUNX1-On_H3K27ac

description: Anatomic site: Pleural effusion

source_name: CUTLL1, non-silencing control, day 3, H3K27ac ChIP

value: anti-H3K27ac antibody (Abcam ab4729, lot# GR24399-4)


title: RPMI_RUNX1-On_MiSeq_rep2


title: RPMI_RUNX1-Off_MiSeq_rep1


title: CUTLL1_RUNX1-Off_H3K27ac

description: Anatomic site: Pleural effusion

source_name: CUTLL1, shRUNX1, day 3, H3K27ac ChIP


title: KOPTK1_RUNX1-On_MiSeq_rep2

source_name: KOPT-K1, non-silencing control, day 7


title: KOPTK1_RUNX1-Off_MiSeq_rep1


title: KOPTK1_RUNX1-On_MiSeq_rep1


title: HPBALL_RUNX1-On_MiSeq_rep1

source_name: HPBALL, non-silencing control, day 7


title: HPBALL_RUNX1-On_MiSeq_rep2


title: Tet6

value: hippocampus

value: Neurons


title: Patient2, PBMC, 9months

city: wuhan

first: Yinqiang

last: Zhang

address: Jiefang avenue no.1277

country: China

institute: Huazhong university of science and technology

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
After harvested, tissues were washed in ice-cold RPMI1640 and dissociated using Multi-tissue dissociation kit 2from Miltenyi Biotec as instructions. DNase treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Miltenyi 130-094-183) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albuminat.
Single-cell RNA-seq libraries were prepared using SeekOne® DD Single Cell 5’ library preparation kit (SeekGene Catalog No.). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then loaded to the sample well in SeekOne® DD Chip S5. Subsequently Gel Beads and Partitioning Oil were dispensed into corresponding wells separately in chip. After emulsion droplet generation reverse transcription were performed at 53°Cfor 45 minutes and inactivated at 85°C for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Bar code and Unique Molecular Index. The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on illumina NovaSeq 6000 with PE150 read length.

value: PBMC

value: allogeneic CAR-T cells


title: Patient1, PBMC, 12months

value: WT

value: autologous CAR-T cells


title: sc15, scRNAseq

city: Beijing

first: Xiaolong

last: Fan

address: No.19, Xinjiekouwai St, Haidian District

institute: Beijing Normal University

description: 10x Genomics

data_processing:
The Read10X function in Seurat (version 3.1.0) (https://satijalab.org/seurat/vignettes.html) generated the reads in the output of the cellranger pipeline from 10X, which returns a unique molecular identified (UMI) count matrix. Cells in the UMI count matrix with fewer than 200 transcripts, and genes with fewer than three cells were removed. The matrix was then analyzed with default parameters in Seurat. The workflow included the following steps: data pre-processing and normalization, feature selection (nfeatures = 500), data scaling, linear dimensional reduction, determination of the dimensionality for principal components with p values < e-10, and t-SNE-based cell clustering and identification of cluster markers
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: glioma

extract_protocol:
Fresh tumor samples were collected at the time of resection from the operating room. Following washing with phosphate-buffered saline (PBS), the samples were minced with a surgical scissors, then enzymatically dissociated using trypsin-EDTA solution. Following filtrating through a cell strainer and red blood cell lysis.
The cell suspension was loaded into Chromium microfluidic chips with 30 chemistry and barcoded with a 10X Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed. Sequencing was performed according to 10X Genomics recommended single cell RNA-seq protocol on the Illumina NovaSeq 6000 with a paired-end 150 bp reading strategy.

tag: Sex

value: Male

tag: who grade

value: WHO II

tag: histomorphology

value: OA

tag: age

tag: idh status

value: IDH mutant

value: glioma


title: sc14, scRNAseq

description: 10x Genomics

value: Female

value: WHO III


title: sc16, scRNAseq

description: 10x Genomics

value: AO


title: sc12, scRNAseq

description: 10x Genomics

value: A


title: sc13, scRNAseq

description: 10x Genomics


title: sc11, scRNAseq

description: 10x Genomics


title: sc10, scRNAseq

description: 10x Genomics


title: sc9, scRNAseq

description: 10x Genomics

value: O


title: sc7, scRNAseq

description: 10x Genomics


title: sc3, scRNAseq

description: 10x Genomics

value: AA


title: sc4, scRNAseq

description: 10x Genomics


title: sc2, scRNAseq

description: 10x Genomics


title: sc5, scRNAseq

description: 10x Genomics


title: sc6, scRNAseq

description: 10x Genomics


title: sc8, scRNAseq

description: 10x Genomics


title: sc1, scRNAseq

description: 10x Genomics


title: 12-day-old seedlings, run 8, snRNA-seq

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
10x Genomics
seedling_12d_230221.rds

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software v6.1.2. Data filtering was performed with Seurat v4.1.0
Assembly: TAIR10
Supplementary files format and content: Seurat object

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Arabidopsis accession Col-0 seeds were surface sterilized and imbibed for 3d at 4oC in complete darkness and grown in long day conditions for 12 days

extract_protocol:
Tissue was chopped in 500-1,000 µL of cold NPB (NPB; 20mM MOPS (pH 7), 40mM NaCl, 90mM KCl, 2mM EDTA, 0.5mM EGTA, 0.5mM spermidine, 0.2mM spermine, 1:100 protease inhibitor cocktail, 2% BSA, and 1:1000 SUPERase IN) with a razor blade on ice for 5 min to release nuclei and incubated in 10 mL NPB. The crude nuclei extract was sequentially filtered through 70 µm and 30 µm cell strainers. BSA, Triton X-100, and NP40 were added to final concentrations of 2%, 0.05%, and 0.05%, respectively, and the extract was incubated at 4ºC for 10 min with rotation. Nuclei were pelleted by centrifugation at 700 x g for 5 min with a swing-rotor centrifuge, The pellet was resuspended in 10 mL of NPBd (NPB, 0.05% Triton X-100, 0.05% NP40, 2% BSA) by pipetting and incubated for 10 min, followed by centrifugation at 700 x g for 5 min, with additional washes until the pellet became translucent. The pellet was then resuspended in 1 mL NPB and centrifuged at 50 x g for 3 min in a fixed-rotor centrifuge to pellet non-nuclei debris (including pollen grains from flower tissues), and the supernatant was taken. This step was repeated until the supernatant cleared or a significant size of pellet was not observed. For root-containing tissues (seedlings), the nuclei suspension was filtered through Flowmi strainers (40 µm) to remove additional sources of debris. Finally, nuclei were pelleted by centrifugation at 700 x g for 10 min with a swing-rotor centrifuge and resuspended in an appropriate volume of NPB. Nuclei were counted manually with a hemocytometer.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.1, 10x Genomics)

value: Seedling


title: 1.25do seeds, Curio slide-seq

description:
Slide-seq (Curio Biosciences Seeker Tile)
221121_curio_seed_seurat.rds
This Spatial Transcriptomics workflow does not include an imaging step, so there is not an associated image.

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Seeker Bioinformatics Pipeline v0.1.0. Data filtering was performed with Seurat v4.1.0
Assembly: TAIR10
Supplementary files format and content: Seurat object
Library strategy: Spatial transcriptomics

source_name: Germinating seeds

growth_protocol: Arabidopsis accession Col-0 seeds were surface sterilized and imbibed for 3d at 4oC in complete darkness and exposed to long day conditions for 32 hours

extract_protocol:
Germinating seeds (1.25d) were submerged in OCT in a cryomold (Sakura), and flash frozen in a liquid N2 cooled isopentane bath. Tissue blocks were acclimated to -18oC in a pre-cooled cryostat chamber (Leica) for 1 h. Tissue blocks were trimmed until the tissue was entered, after which 10 µm sections were visually inspected until the region of interest was exposed. Following sectioning, the frozen section was arranged onto the center of the Curio Seeker Tile (Curio Bioscience) and gently melted and stored at -80oC until further processing according to the manufacturer’s specifications.
Library construction was performed according to the manufacturer's specification (Seeker Tile Kit, Curio Bioscience)

value: Germinating seeds


title: 3-day-old seedlings, run 2, snRNA-seq

description:
10x Genomics
seedling_3d_230221.rds

growth_protocol: Arabidopsis accession Col-0 seeds were surface sterilized and imbibed for 3d at 4oC in complete darkness and grown in long day conditions for 3 days


title: 6-day-old seedlings, run 4, snRNA-seq

description:
10x Genomics
seedling_6d_230221.rds

growth_protocol: Arabidopsis accession Col-0 seeds were surface sterilized and imbibed for 3d at 4oC in complete darkness and grown in long day conditions for 6 days


title: 12-day-old seedlings, run 5, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 3-day-old seedlings, run 3, snRNA-seq

description:
10x Genomics
seedling_3d_230221.rds


title: 6-day-old seedlings, run 5, snRNA-seq

description:
10x Genomics
seedling_6d_230221.rds


title: 6-day-old seedlings, run 1, snRNA-seq

description:
10x Genomics
seedling_6d_230221.rds


title: 6-day-old seedlings, run 3, snRNA-seq

description:
10x Genomics
seedling_6d_230221.rds


title: 6-day-old seedlings, run 6, snRNA-seq

description:
10x Genomics
seedling_6d_230221.rds


title: 3-day-old seedlings, run 1, snRNA-seq

description:
10x Genomics
seedling_3d_230221.rds


title: 3-day-old seedlings, run 4, snRNA-seq

description:
10x Genomics
seedling_3d_230221.rds


title: 12-day-old seedlings, run 4, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 6, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 6-day-old seedlings, run 2, snRNA-seq

description:
10x Genomics
seedling_6d_230221.rds


title: 12-day-old seedlings, run 7, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 9, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 3, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 2, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: Human Islet 4 [ATAC-Seq]

city: St. Louis

first: Jeffrey

middle: Robert

last: Millman

state: MO

address: 660 South Euclid

institute: Washington University in St. Louis

description: Mapped to Human Genome

library_source: genomic single cell

data_processing:
Data was generated and processed by McDonnell Genome Institute (MGI) at Washington University
Multiomic sequencing files were processed using cellranger-arc-2.0.0
Supplementary files format and content: Processed files are in atac_fragment files, matrix files, and per_barcode_metrics file

source_name: Human islets

growth_protocol: Stem cells were cultured, grown, and differentiated into SC-islets as described (Hogrebe et al., Nature Protocols 2021)

extract_protocol:
Transplanted cells were extracted use Miltenyi Mouse Cell Depletion Kit
Library construction for single cell was constructed using 10X Chromium Protocol.

treatment_protocol: Transplant was performed by kidney capsul transplantation in NSG mice. Differentiated cells were treated with shRNA containing lentivirus for knockdown. For CRISPR activation, stem cells were treated with guideRNA containing virus, puromycin treated and differentiated.

value: Primary

tag: Stage

tag: kit used

value: 10x Single Cell Multiome ATAC + Gene Expression v1 kit


title: Human Islet 4 [RNA-Seq]

description: Mapped to Human Genome

tag: cell type


title: Human Islet 3 [ATAC-Seq]

description: Mapped to Human Genome


title: Human Islet 3 [RNA-Seq]

description: Mapped to Human Genome


title: 12-day-old seedlings, run 21, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 20, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 18, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 17, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 19, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: Caco-2, polysorbate 80, 0.05%, Rep3

city: Davos-Wolfgang

first: Ismail

last: Ogulur

address: Herman-Burchard-Strasse 9

country: Switzerland

institute: Swiss Institute of Allergy and Asthma Research (SIAF)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (parameters- Minimum length (R1): 20  Quality cutoff: 20)
Trimmed sequence reads were mapped to the reference genome GRCh38/hg38 by STAR aligner version 2.7.9a. (parameters- Gene model: gencode.v38.annotation.gtf   Length of the genomic sequence around annotated junctions: 100)
Read counts assesed by featureCounts (parameter- Minimum mapping quality per read: 10)
Differentially expressed genes were assessed by DESeq2 version 1.32.0
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts each sample

extract_protocol:
RNeasy Plus Micro Kit
PolyA, TruSeq RNA Kit

tag: cell line

tag: treatment

value: polysorbate 80


title: Caco-2, polysorbate 80, 0.05%, Rep4


title: Caco-2, polysorbate 80, 0.05%, Rep1


title: 12-day-old seedlings, run 13, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 11, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: Caco-2, polysorbate 20, 0.05%, Rep4

value: polysorbate 20


title: Caco-2, polysorbate 20, 0.05%, Rep5


title: Caco-2, polysorbate 20, 0.05%, Rep1


title: Caco-2,Unexposed Control, Rep5


title: Caco-2, polysorbate 20, 0.05%, Rep3


title: Caco-2, polysorbate 80, 0.05%, Rep2


title: 12-day-old seedlings, run 15, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 14, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 12, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: Caco-2, polysorbate 20, 0.05%, Rep2


title: 12-day-old seedlings, run 22, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 1, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: Caco-2, polysorbate 80, 0.05%, Rep5


title: Caco-2,Unexposed Control, Rep3


title: 40-day-old apical stem, run 3, CellPlex snRNA-seq

description:
10x Genomics
stem_230221.rds

source_name: Stem

growth_protocol: Arabidopsis accession Col-0 plants were grown in soil for 40d under long day conditions

extract_protocol:
Tissue was chopped in 500-1,000 µL of cold NPB (NPB; 20mM MOPS (pH 7), 40mM NaCl, 90mM KCl, 2mM EDTA, 0.5mM EGTA, 0.5mM spermidine, 0.2mM spermine, 1:100 protease inhibitor cocktail, 2% BSA, and 1:1000 SUPERase IN) with a razor blade on ice for 5 min to release nuclei and incubated in 10 mL NPB. The crude nuclei extract was sequentially filtered through 70 µm and 30 µm cell strainers. BSA, Triton X-100, and NP40 were added to final concentrations of 2%, 0.05%, and 0.05%, respectively, and the extract was incubated at 4ºC for 10 min with rotation. Nuclei were pelleted by centrifugation at 700 x g for 5 min with a swing-rotor centrifuge, The pellet was resuspended in 10 mL of NPBd (NPB, 0.05% Triton X-100, 0.05% NP40, 2% BSA) by pipetting and incubated for 10 min, followed by centrifugation at 700 x g for 5 min, with additional washes until the pellet became translucent. The pellet was then resuspended in 1 mL NPB and centrifuged at 50 x g for 3 min in a fixed-rotor centrifuge to pellet non-nuclei debris (including pollen grains from flower tissues), and the supernatant was taken. This step was repeated until the supernatant cleared or a significant size of pellet was not observed. Finally, nuclei were pelleted by centrifugation at 700 x g for 10 min with a swing-rotor centrifuge and resuspended in an appropriate volume of NPB. Nuclei were counted manually with a hemocytometer.
Library construction was performed according to the manufacturer's specification with sample multiplexing using the 3' CellPlex Kit (Chromium Next GEM Single Cell 3' HT Kit v3.1, 3' CellPlex Kit Set A, 10x Genomics)

value: Stem


title: 12-day-old seedlings, run 10, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: 12-day-old seedlings, run 16, snRNA-seq

description:
10x Genomics
seedling_12d_230221.rds


title: SC-Islet Stage6 month 12 [RNA-Seq]

description:
Mapped to Human Genome
month12.per_barcode_metrics.csv
month12

source_name: Stem Cell Derived Islets

extract_protocol:
Transplanted cells were extracted use Miltenyi Mouse Cell Depletion Kit
Library construction for single cell was constructed using 10X Chromium Protocol.
Single Nuclei Mulitome Gene Expression and ATAC sequencing

value: ES-Derived Islet

value: In vitro


title: Caco-2,Unexposed Control, Rep4


title: Caco-2,Unexposed Control, Rep1


title: Caco-2,Unexposed Control, Rep2


title: 40-day-old apical stem, run 2, CellPlex snRNA-seq

description:
10x Genomics
stem_230221.rds


title: 40-day-old apical stem, run 3, snRNA-seq

description:
10x Genomics
stem_230221.rds

extract_protocol:
Tissue was chopped in 500-1,000 µL of cold NPB (NPB; 20mM MOPS (pH 7), 40mM NaCl, 90mM KCl, 2mM EDTA, 0.5mM EGTA, 0.5mM spermidine, 0.2mM spermine, 1:100 protease inhibitor cocktail, 2% BSA, and 1:1000 SUPERase IN) with a razor blade on ice for 5 min to release nuclei and incubated in 10 mL NPB. The crude nuclei extract was sequentially filtered through 70 µm and 30 µm cell strainers. BSA, Triton X-100, and NP40 were added to final concentrations of 2%, 0.05%, and 0.05%, respectively, and the extract was incubated at 4ºC for 10 min with rotation. Nuclei were pelleted by centrifugation at 700 x g for 5 min with a swing-rotor centrifuge, The pellet was resuspended in 10 mL of NPBd (NPB, 0.05% Triton X-100, 0.05% NP40, 2% BSA) by pipetting and incubated for 10 min, followed by centrifugation at 700 x g for 5 min, with additional washes until the pellet became translucent. The pellet was then resuspended in 1 mL NPB and centrifuged at 50 x g for 3 min in a fixed-rotor centrifuge to pellet non-nuclei debris (including pollen grains from flower tissues), and the supernatant was taken. This step was repeated until the supernatant cleared or a significant size of pellet was not observed. Finally, nuclei were pelleted by centrifugation at 700 x g for 10 min with a swing-rotor centrifuge and resuspended in an appropriate volume of NPB. Nuclei were counted manually with a hemocytometer.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.1, 10x Genomics)


title: 40-day-old apical stem, run 2, snRNA-seq

description:
10x Genomics
stem_230221.rds


title: SC-Islet Stage6 month 6 [ATAC-Seq]

description:
Mapped to Human Genome
month6.per_barcode_metrics.csv
month6


title: 40-day-old apical stem, run 1, CellPlex snRNA-seq

description:
10x Genomics
stem_230221.rds


title: SC-Islet Stage6 month 12 [ATAC-Seq]


title: 40-day-old basal stem, run 2, snRNA-seq

description:
10x Genomics
stem_230221.rds


title: 40-day-old apical stem, run 1, snRNA-seq

description:
10x Genomics
stem_230221.rds


title: 40-day-old basal stem and brached stem, run 2, CellPlex snRNA-seq

description:
10x Genomics
stem_230221.rds


title: 40-day-old basal stem, run 1, snRNA-seq

description:
10x Genomics
stem_230221.rds


title: SC-Islet ARID1B knockdown [ATAC-Seq]

description:
Mapped to Human Genome
shARID1B.per_barcode_metrics.csv
shARID1B


title: SC-Islet GFP Control [ATAC-Seq]

description:
Mapped to Human Genome
shGFPCtrl.per_barcode_metrics.csv
shGFPCtrl


title: 40-day-old basal stem and brached stem, run 1, CellPlex snRNA-seq

description:
10x Genomics
stem_230221.rds


title: 40-day-old branched stem, run 2, snRNA-seq

description:
10x Genomics
stem_230221.rds


title: SC-Islet ARID1B knockdown [RNA-Seq]


title: CRISPRA SC-Islet CTCF Doxycycline [RNA-Seq]

description:
Mapped to Human Genome
CTCFDox.per_barcode_metrics.csv
CTCFDox


title: CRISPRA SC-Islet CTCF Untreated Control [RNA-Seq]

description:
Mapped to Human Genome
CTCFCtrl.per_barcode_metrics.csv
CTCFCtrl


title: CRISPRA SC-Islet CTCF Doxycycline [ATAC-Seq]


title: 40-day-old branched stem, run 1, snRNA-seq

description:
10x Genomics
stem_230221.rds


title: CRISPRA SC-Islet CTCF Untreated Control [ATAC-Seq]


title: 1.25-day-old seeds, run 6, snRNA-seq

description:
10x Genomics
seed_125d_230221.rds

extract_protocol:
Tissue was chopped in 500-1,000 µL of cold NPB (NPB; 20mM MOPS (pH 7), 40mM NaCl, 90mM KCl, 2mM EDTA, 0.5mM EGTA, 0.5mM spermidine, 0.2mM spermine, 1:100 protease inhibitor cocktail, 2% BSA, and 1:1000 SUPERase IN) with a razor blade on ice for 5 min to release nuclei and incubated in 10 mL NPB. For the 0d and 1.25d seed samples, the nuclei were extracted in 5 mL NPB with a Dounce homogenizer with 20 strokes of the loose pestle followed by 20 strokes of the tight pestle. The crude nuclei extract was sequentially filtered through 70 µm and 30 µm cell strainers. BSA, Triton X-100, and NP40 were added to final concentrations of 2%, 0.05%, and 0.05%, respectively, and the extract was incubated at 4ºC for 10 min with rotation. Nuclei were pelleted by centrifugation at 700 x g for 5 min with a swing-rotor centrifuge, The pellet was resuspended in 10 mL of NPBd (NPB, 0.05% Triton X-100, 0.05% NP40, 2% BSA) by pipetting and incubated for 10 min, followed by centrifugation at 700 x g for 5 min, with additional washes until the pellet became translucent. The pellet was then resuspended in 1 mL NPB and centrifuged at 50 x g for 3 min in a fixed-rotor centrifuge to pellet non-nuclei debris (including pollen grains from flower tissues), and the supernatant was taken. This step was repeated until the supernatant cleared or a significant size of pellet was not observed. Finally, nuclei were pelleted by centrifugation at 700 x g for 10 min with a swing-rotor centrifuge and resuspended in an appropriate volume of NPB. Nuclei were counted manually with a hemocytometer.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.1, 10x Genomics)


title: 1.25-day-old seeds, run 4, snRNA-seq

description:
10x Genomics
seed_125d_230221.rds


title: 1.25-day-old seeds, run 5, snRNA-seq

description:
10x Genomics
seed_125d_230221.rds


title: Transplanted SC-Islet 3 [RNA-Seq]

description:
Mapped to Human Genome
txpscislet3.per_barcode_metrics.csv
txpscislet3

value: In vivo


title: 1.25-day-old seeds, run 3, snRNA-seq

description:
10x Genomics
seed_125d_230221.rds


title: SC-Islet Stage6 month 6 [RNA-Seq]


title: SC-Islet GFP Control [RNA-Seq]


title: 40-day-old branched stem, run 3, snRNA-seq

description:
10x Genomics
stem_230221.rds


title: Transplanted SC-Islet 1 [RNA-Seq]

description:
Mapped to Human Genome
txpscislet1.per_barcode_metrics.csv
txpscislet1


title: Transplanted SC-Islet 3 [ATAC-Seq]


title: Transplanted SC-Islet 2 [ATAC-Seq]

description:
Mapped to Human Genome
txpscislet2.per_barcode_metrics.csv
txpscislet2


title: Transplanted SC-Islet 1 [ATAC-Seq]


title: Human Islet 2 [RNA-Seq]

description:
Mapped to Human Genome
humanislet2.per_barcode_metrics.csv
humanislet2


title: 1.25-day-old seeds, run 1, snRNA-seq

description:
10x Genomics
seed_125d_230221.rds


title: Human Islet 1 [RNA-Seq]

description:
Mapped to Human Genome
humanislet1.per_barcode_metrics.csv
humanislet1


title: 44-day-old silique, run 6, snRNA-seq

description:
10x Genomics
silique_230221.rds

source_name: Silique

value: Silique


title: 44-day-old silique, run 5, snRNA-seq

description:
10x Genomics
silique_230221.rds


title: 44-day-old silique, run 4, snRNA-seq

description:
10x Genomics
silique_230221.rds


title: 44-day-old silique, run 3, snRNA-seq

description:
10x Genomics
silique_230221.rds


title: Human Islet 1 [ATAC-Seq]


title: SC-Islet Stage6 week 4 [RNA-Seq]

description:
Mapped to Human Genome
week4.per_barcode_metrics.csv
week4


title: 44-day-old silique, run 2, snRNA-seq

description:
10x Genomics
silique_230221.rds


title: 44-day-old silique, run 8, snRNA-seq

description:
10x Genomics
silique_230221.rds


title: Human Islet 2 [ATAC-Seq]


title: Transplanted SC-Islet 2 [RNA-Seq]


title: 21-day-old rosette, run 8, snRNA-seq

description:
10x Genomics
rosette_21d_230221.rds

source_name: Rosette

growth_protocol: Arabidopsis accession Col-0 plants were grown in soil for 21d under long day conditions

value: Rosette


title: 21-day-old rosette, run 7, snRNA-seq

description:
10x Genomics
rosette_21d_230221.rds


title: SC-Islet Stage6 week 2 [RNA-Seq]

description:
Mapped to Human Genome
week2.per_barcode_metrics.csv
week2


title: SC-Islet Stage6 week 3 [RNA-Seq]

description:
Mapped to Human Genome
week3.per_barcode_metrics.csv
week3


title: 21-day-old rosette, run 6, snRNA-seq

description:
10x Genomics
rosette_21d_230221.rds


title: 1.25-day-old seeds, run 2, snRNA-seq

description:
10x Genomics
seed_125d_230221.rds


title: SC-Islet Stage6 week 3 [ATAC-Seq]


title: SC-Islet Stage6 week 2 [ATAC-Seq]


title: SC-Islet 2 [RNA-Seq]

description:
Mapped to Human Genome
scislet2.per_barcode_metrics.csv
scislet2


title: 21-day-old rosette, run 4, snRNA-seq

description:
10x Genomics
rosette_21d_230221.rds


title: SC-Islet 2 [ATAC-Seq]


title: 44-day-old silique, run 7, snRNA-seq

description:
10x Genomics
silique_230221.rds


title: 21-day-old rosette, run 5, snRNA-seq

description:
10x Genomics
rosette_21d_230221.rds


title: 21-day-old rosette, run 3, snRNA-seq

description:
10x Genomics
rosette_21d_230221.rds


title: SC-Islet Stage6 week 4 [ATAC-Seq]


title: SC-Islet 1 [ATAC-Seq]

description:
Mapped to Human Genome
scislet1.per_barcode_metrics.csv
scislet1


title: 21-day-old rosette, run 2, snRNA-seq

description:
10x Genomics
rosette_21d_230221.rds


title: 21-day-old rosette, run 1, snRNA-seq

description:
10x Genomics
rosette_21d_230221.rds


title: 30-day-old rosette, run 6, snRNA-seq

description:
10x Genomics
rosette_30d_230221.rds

growth_protocol: Arabidopsis accession Col-0 plants were grown in soil for 30d under long day conditions


title: 30-day-old rosette, run 5, snRNA-seq

description:
10x Genomics
rosette_30d_230221.rds


title: 44-day-old silique, run 1, snRNA-seq

description:
10x Genomics
silique_230221.rds


title: 5KO

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Cerebral cortex

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

value: Cerebral cortex

value: microglia

value: Bach1 cKO

value: untreated


title: 30-day-old rosette, run 4, snRNA-seq

description:
10x Genomics
rosette_30d_230221.rds


title: 30-day-old rosette, run 3, snRNA-seq

description:
10x Genomics
rosette_30d_230221.rds


title: 6WT

value: Bach1 fl/fl


title: 30-day-old rosette, run 2, snRNA-seq

description:
10x Genomics
rosette_30d_230221.rds


title: 1WT


title: 2KO


title: SC-Islet 1 [RNA-Seq]


title: Liver_Normal_diet_9w_rep5

type: RNA

city: Takatsuki

first: Tatsuya

last: Ishigure

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: Japan Tobacco Inc.

description: Gene expression after 9w dietary intervention

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Liver, Normal diet, 9w, replicate 5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoPad DS-11 spectrophotometer.

extract_protocol: Total RNA was extracted from frozen liver tissue by using the Mixermill (Retsch) and RNeasy Mini Kit (QIAGEN) according to manufacter’s instructions. RNA was quantified using a NanoPad DS-11 spectrophotometer (DeNovix) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Liver

tag: diet

value: Normal

tag: period


title: Liver_Normal_diet_9w_rep4

source_name: Liver, Normal diet, 9w, replicate 4

tag: tissue


title: 5WT.

source_name: Brain

extract_protocol:
Total RNA was harvested by Trizol reagent total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

value: Brain

value: endothelial cell

value: WT

tag: developmental stage


title: Liver_Normal_diet_9w_rep3

source_name: Liver, Normal diet, 9w, replicate 3


title: Flowers, run 6, snRNA-seq

description:
10x Genomics
flower_230221.rds

source_name: Whole flowers

growth_protocol: Arabidopsis accession Col-0 plants were grown in soil for 37d under long day conditions

value: Whole flowers


title: 3WT.


title: Liver_Normal_diet_9w_rep2

source_name: Liver, Normal diet, 9w, replicate 2


title: Liver_CDAA_diet_9w_rep5

source_name: Liver, CDAA diet, 9w, replicate 5

value: CDAA


title: Liver_Normal_diet_9w_rep1

source_name: Liver, Normal diet, 9w, replicate 1


title: Liver_CDAA_diet_9w_rep4

source_name: Liver, CDAA diet, 9w, replicate 4


title: 2ECKO

value: STINGECKO


title: Flowers, run 5, snRNA-seq

description:
10x Genomics
flower_230221.rds


title: Flowers, run 4, snRNA-seq

description:
10x Genomics
flower_230221.rds


title: Liver_Normal_diet_4w_rep4

description: Gene expression after 4w dietary intervention

source_name: Liver, Normal diet, 4w, replicate 4


title: Liver_CDAA_diet_9w_rep1

source_name: Liver, CDAA diet, 9w, replicate 1


title: 30-day-old rosette, run 1, snRNA-seq

description:
10x Genomics
rosette_30d_230221.rds


title: Liver_CDAA_diet_9w_rep3

source_name: Liver, CDAA diet, 9w, replicate 3


title: Liver_Normal_diet_4w_rep5

source_name: Liver, Normal diet, 4w, replicate 5


title: Flowers, run 3, snRNA-seq

description:
10x Genomics
flower_230221.rds


title: Liver_CDAA_diet_9w_rep2

source_name: Liver, CDAA diet, 9w, replicate 2


title: 1ECKO


title: Liver_Normal_diet_4w_rep1

source_name: Liver, Normal diet, 4w, replicate 1


title: Liver_CDAA_diet_4w_rep4

source_name: Liver, CDAA diet, 4w, replicate 4


title: Kit-W/sh-T Sample 6 [KOC6_S11]

city: Ribeirao Preto

first: Juliana

middle: Yumi

last: Sakita

state: Sao Paulo

address: Av. do Café, s/ nº

department: Genetics

country: Brazil

institute: Ribeirao Preto Medical School - University of Sao Paulo

description: Tabcontagemtumoralografico.txt

data_processing:
Checking of the Fastq read data quality, alignment of reads to the mouse genome (NCBI37.p3/mm9) and read counts were carried out using the Qiagen software GeneGlobe Data Analysis Center. Data normalization, gene identification, differentially expressed genes (p < 0.05) between Kit-B6 and Kit-W/SH mouse groups were done using the R package DESeq2.
Assembly: mm9
Supplementary files format and content: Processed data file is a tab-delimited file containing unnormalized gene counts

source_name: Colon

extract_protocol:
Following tumorsharvesting and freezing steps, RNA extraction was performed with Qiagen RNeasy (#74106) and Qiagen RNase-free DNase kits (#79254).
QIAseq Targeted RNAseq Mouse Immuno-Oncology panel (#333005) and QIAseq Targeted RNA 96-Index I (#333117) were used to generate cDNA libraries.

value: Colon

value: Cancer cell

value: Kit "sash" mutation

value: Saline


title: Liver_Normal_diet_4w_rep2

source_name: Liver, Normal diet, 4w, replicate 2


title: Kit-W/sh-T Sample 5 [KOC5_S10]

description: Tabcontagemtumoralografico.txt


title: Liver_CDAA_diet_4w_rep1

source_name: Liver, CDAA diet, 4w, replicate 1


title: Liver_CDAA_diet_4w_rep3

source_name: Liver, CDAA diet, 4w, replicate 3


title: Liver_CDAA_diet_4w_rep5

source_name: Liver, CDAA diet, 4w, replicate 5


title: Kit-W/sh-T Sample 4 [KOC4_S9]

description: Tabcontagemtumoralografico.txt


title: Liver_Normal_diet_4w_rep3

source_name: Liver, Normal diet, 4w, replicate 3


title: Liver_CDAA_diet_4w_rep2

source_name: Liver, CDAA diet, 4w, replicate 2


title: Liver_Normal_diet_2w_rep5

description: Gene expression after 2w dietary intervention

source_name: Liver, Normal diet, 2w, replicate 5


title: Liver_Normal_diet_2w_rep4

source_name: Liver, Normal diet, 2w, replicate 4


title: Kit-W/sh-T Sample 2 [KOC2_S7]

description: Tabcontagemtumoralografico.txt


title: Liver_Normal_diet_2w_rep3

source_name: Liver, Normal diet, 2w, replicate 3


title: Kit-W/sh-T Sample 3 [KOC3_S8]

description: Tabcontagemtumoralografico.txt


title: Kit-W/sh-T Sample 1 [KOC1_S6]

description: Tabcontagemtumoralografico.txt


title: 0-day-old imbibed seeds, run 3, snRNA-seq

description:
10x Genomics
seed_0d_230221.rds

source_name: Imbibed seeds

growth_protocol: Arabidopsis accession Col-0 seeds were surface sterilized and imbibed for 3d at 4oC in complete darkness

value: Imbibed seeds

value: 0-days-old (3d cold treatment)


title: Flowers, run 2, snRNA-seq

description:
10x Genomics
flower_230221.rds

source_name: Whole flowers


title: Liver_Normal_diet_2w_rep2

source_name: Liver, Normal diet, 2w, replicate 2


title: Liver_Normal_diet_2w_rep1

source_name: Liver, Normal diet, 2w, replicate 1


title: Flowers, run 1, snRNA-seq

description:
10x Genomics
flower_230221.rds


title: Liver_CDAA_diet_2w_rep3

source_name: Liver, CDAA diet, 2w, replicate 3


title: 0-day-old imbibed seeds, run 4, snRNA-seq

description:
10x Genomics
seed_0d_230221.rds


title: Kit-B6-T Sample 5 [WTC5_S5]

description: Tabcontagemtumoralografico.txt

value: wild type


title: Kit-B6-T Sample 4 [WTC4_S4]

description: Tabcontagemtumoralografico.txt


title: Liver_CDAA_diet_2w_rep2

source_name: Liver, CDAA diet, 2w, replicate 2


title: Liver_CDAA_diet_2w_rep5

source_name: Liver, CDAA diet, 2w, replicate 5


title: Kit-B6-T Sample 3 [WTC3_S3]

description: Tabcontagemtumoralografico.txt

source_name: Colon


title: Liver_CDAA_diet_2w_rep1

source_name: Liver, CDAA diet, 2w, replicate 1


title: Liver_Normal_diet_1w_rep5

description: Gene expression after 1w dietary intervention

source_name: Liver, Normal diet, 1w, replicate 5


title: 0-day-old imbibed seeds, run 2, snRNA-seq

description:
10x Genomics
seed_0d_230221.rds


title: Kit-B6-T Sample 2 [WTC2_S2]

description: Tabcontagemtumoralografico.txt


title: 0-day-old imbibed seeds, run 1, snRNA-seq

description:
10x Genomics
seed_0d_230221.rds


title: Kit-B6-T Sample 1 [WTC1_S1]

description: Tabcontagemtumoralografico.txt


title: Liver_Normal_diet_1w_rep4

source_name: Liver, Normal diet, 1w, replicate 4


title: Liver_Normal_diet_1w_rep2

source_name: Liver, Normal diet, 1w, replicate 2


title: Liver_CDAA_diet_1w_rep5

source_name: Liver, CDAA diet, 1w, replicate 5


title: Liver_CDAA_diet_2w_rep4

source_name: Liver, CDAA diet, 2w, replicate 4


title: S.islandicus.REY15A.cbp1.ChIP-seq.input.replicate2

status: Public on Mar 24 2023

city: London

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

country: United Kingdom

institute: University College London

data_processing:
Paired-end reads were mapped using Bowtie v1.1.2 [30] with parameters -v 2 -m 1 --fr over the first 50 nt allowing only for uniquely mapped  read pairs to be included
We sampled from the alignments to obtain a defined fragment size distribution (normal distribution, mean 120 bp, sd 18 bp) using a custom R script (https://github.com/fblombach/ChIP-seq/blob/master/read_sampling.R)
Coverage normalized to input ("normRatio") was calculated using deeptools bamCompare with SES scaling (10,000 bins, 200 bp bin width)
Assembly: NC_017276.1
Supplementary files format and content: bigwig files with occupancy normalised against the chromatin input samples, scaled by the Signal Extraction Scaling method

organism: Saccharolobus islandicus REY15A

source_name: microbial cells

growth_protocol: Strains were grown in Brock medium supplemented with 0.2% sucrose, 0.2% tryptone, and 20 µg/ml uracil at 75 °C in Erlenmeyer shake flasks at 150 rpm

extract_protocol:
Qiagen QIAquick PCR purification
NEBNext Ultra II DNA library prep kit for Illumina

value: cbp1, pyrEF, lacS

tag: chip antibody

value: none (input)

value: microbial cells


title: S.islandicus.REY15A.cbp1.ChIP-seq.Rpo47.replicate1


title: SAMPLE 2_CaOV3 sprinkled with exosomes

city: Suita

first: MASAKI

last: KOBAYASHI

address: 2-2 Yamadaoka

department: Department of Obstetrics and Gynecology

institute: Osaka University Graduate School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ovarian cancer cells_exosomes

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

growth_protocol: CaOV3 and OVCAR3 were cultured in DMEM supplemented with 10% FBS and 100 U/mL penicillin/streptomycin and incubated in 95% air/5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using TRIzol reagent (#15596–018; Life Technologies, Carlsbad, CA:). RNA isolated from cells and exosomes was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc. Santa Clara, CA)

treatment_protocol: SAMPLE 2 and 4 were sprinkled with exosomes isolated from the supernatant fluids of fibroblast cultures. (SAMPLE 1 and 3 were controls and not sprinkled with them.) In 24 hours after the sprinkle, total RNA was extracted.

value: ovarian cancer cells


title: S.islandicus.REY15A.E234.ChIP-seq.input.replicate1

value: E234 (pyrEF, lacS)


title: S.islandicus.REY15A.cbp1.ChIP-seq.Rpo47.replicate2


title: S.islandicus.REY15A.E234.ChIP-seq.Rpo47.replicate1


title: S.islandicus.REY15A.E234.ChIP-seq.input.replicate2


title: S.islandicus.REY15A.cbp1.ChIP-seq.input.replicate1


title: S.islandicus.REY15A.E234.ChIP-seq.Rpo47.replicate2


title: SAMPLE 3_OVCAR3 not sprinkled with exosomes

source_name: ovarian cancer cells_control


title: S.islandicus.REY15A.cbp1.ChIP-seq.Cbp1.replicate1


title: S.islandicus.REY15A.E234.ChIP-seq.Cbp1.replicate2


title: S.islandicus.REY15A.cbp1.ChIP-seq.Cbp1.replicate2


title: Liver_CDAA_diet_1w_rep2

source_name: Liver, CDAA diet, 1w, replicate 2

value: Liver


title: S.islandicus.REY15A.E234.ChIP-seq.Cbp1.replicate1


title: SAMPLE 4_OVCAR3 sprinkled with exosomes

value: exosomes isolated from the supernatant fluids of fibroblast cultures


title: Liver_CDAA_diet_1w_rep3

source_name: Liver, CDAA diet, 1w, replicate 3


title: Embryo_11 Endoderm [DNA_batch21_sc95]

first: Fan

last: Guo

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

data_processing:
Processing of the scChaRM-seq DNA data:Trim Galore (v0.4.4) was used to remove random primer sequences, low-quality bases and adaptor sequences from the single-cell bisulfite data. Only reads longer than 50 bp after trimming were retained for alignment. Then, clean reads were mapped to the monkey reference genome mf5 by Bismark (v0.7.6) in paired-end mode, and unmapped reads were re-aligned to the reference genome in single-end mode. Duplicate reads from PCR were removed by the SAMtools (v0.1.18) command “samtools rmdup”, and only nonduplicate reads were used to perform the downstream analysis. The GCH (G=A, T or C) and WCG (W=A or T) sites (≥1× sequencing depth) in each single cell were summed. Then, the chromatin accessibility and DNA methylation level were calculated as the average GCH or WCG level, respectively.
Genome_build: mf5
Supplementary_files_format_and_content: bedgraph files；RNAid_DNAid_celltype.csv
Assembly: mf5
Supplementary files format and content: bedgraph files;csv files

organism: Macaca fascicularis

source_name: in vitro

growth_protocol: The creation of cynomolgus monkey embryos including oocyte retrieval, intracytoplasmic sperm injection, and pre-implantation embryo culture were performed as described by Yamasaki et al (Nakamura et al., 2016). Briefly, female cynomolgus monkeys 7-10 years old with a successful reproductive history were used for mature oocyte collection by super-ovulation with follicle-stimulation hormone. The day collected oocytes were artificially fertilized by sperm injection was designated as embryonic day (E) 0. When the embryos developed to E6-E7, embryos with an  expanded blastocoel (>75% volume of the embryo) were selected for further culture .

extract_protocol:
The single-cell isolation procedures were performed according to the protocol previously described (Ma et al., 2019a). In brief, the pIVC cynomolgus embryos were  dissected by removing the extraembryonic tissues, then the inner embryonic bodies were digested with 500 μL of 1 × TrypLE for 15 min at 37°C and dissociated into single cells by mouth pipetting. Advanced DMEM/F12 containing 10% FBS was added to terminate the enzymatic reaction and the cells were centrifuged at 300 g for 5 min at room temperature, followed by the resuspension with 100 μL pre-cold 0.1% BSA/PBS.
Single cells were individually picked into ice-cold lysis buffer under stereoscopic microscope. single cells were picked of each stage and then the subjected to construct scChaRM-seq library. The method of library construction was described in our recently published method (Yan et al., 2021). In brief, in vitro CpG methylation was performed by M.CviPI (New England Biolabs, NEB) supplemented with S-adenosyl-methionine (SAM;NEB) and terminated by adding RLT buffer (QIAGEN). Then the genome DNA and mRNA were separated by capturing mRNA with oligo(dT) primers conjugated beads (Invitrogen), the supernatant containing genomic DNA was transferred into another PCR tube to bisulfite conversion (Zymo Research) and DNA library construction using previously descried TAILS method (Gu et al., 2019). The captured mRNA was subjected correspondingly to cDNA synthesis, PCR amplification and library construction (Gu et al., 2019).

value: in vitro

value: Embryo

value: WT

tag: time


title: Embryo_11 Endoderm [DNA_batch21_sc94]

tag: genotype


title: Liver_Normal_diet_1w_rep1

source_name: Liver, Normal diet, 1w, replicate 1

value: Normal


title: Liver_CDAA_diet_1w_rep1

source_name: Liver, CDAA diet, 1w, replicate 1

value: CDAA


title: SAMPLE 1_CaOV3 not sprinkled with exosomes


title: Liver_Normal_diet_1w_rep3

source_name: Liver, Normal diet, 1w, replicate 3


title: Liver_CDAA_diet_1w_rep4

source_name: Liver, CDAA diet, 1w, replicate 4


title: Embryo_3 EVT [DNA_batch21_sc93]


title: Embryo_4 STB [DNA_batch21_sc92]


title: Embryo_3 EVT [DNA_batch21_sc91]


title: Embryo_3 EVT [DNA_batch21_sc90]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch21_sc89]


title: Embryo_7 Mesoderm [DNA_batch21_sc74]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc9]


title: Embryo_7 Mesoderm [DNA_batch21_sc76]


title: Embryo_7 Mesoderm [DNA_batch21_sc82]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc8]


title: Embryo_7 Mesoderm [DNA_batch21_sc83]


title: Embryo_7 Mesoderm [DNA_batch21_sc79]


title: Embryo_11 Endoderm [DNA_batch21_sc80]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch21_sc86]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch21_sc84]


title: Embryo_2 CTB [DNA_batch21_sc81]


title: Embryo_3 EVT [DNA_batch21_sc78]


title: Embryo_5 EPI [DNA_batch21_sc87]


title: Embryo_3 EVT [DNA_batch21_sc85]


title: Embryo_5 EPI [DNA_batch21_sc77]


title: Embryo_3 EVT [DNA_batch21_sc88]


title: Embryo_7 Mesoderm [DNA_batch21_sc72]


title: Embryo_7 Mesoderm [DNA_batch21_sc73]


title: Embryo_7 Mesoderm [DNA_batch21_sc71]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc7]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc70]


title: Embryo_7 Mesoderm [DNA_batch21_sc69]


title: Embryo_7 Mesoderm [DNA_batch21_sc66]


title: Embryo_7 Mesoderm [DNA_batch21_sc67]


title: Embryo_8 Neural ectoderm [DNA_batch21_sc68]


title: Embryo_8 Neural ectoderm [DNA_batch21_sc64]


title: Embryo_8 Neural ectoderm [DNA_batch21_sc65]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc63]


title: Embryo_12 Blood cells [DNA_batch21_sc60]


title: Embryo_7 Mesoderm [DNA_batch21_sc62]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc61]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc6]


title: Embryo_7 Mesoderm [DNA_batch21_sc56]


title: Embryo_7 Mesoderm [DNA_batch21_sc57]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc52]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc51]


title: Embryo_8 Neural ectoderm [DNA_batch21_sc59]


title: Embryo_7 Mesoderm [DNA_batch21_sc50]


title: Embryo_8 Neural ectoderm [DNA_batch21_sc54]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc58]


title: Embryo_7 Mesoderm [DNA_batch21_sc47]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc49]


title: Embryo_8 Neural ectoderm [DNA_batch21_sc44]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc5]


title: Embryo_8 Neural ectoderm [DNA_batch21_sc43]


title: Embryo_3 EVT [DNA_batch21_sc48]


title: Embryo_7 Mesoderm [DNA_batch21_sc45]


title: Embryo_8 Neural ectoderm [DNA_batch21_sc46]


title: Embryo_5 EPI [DNA_batch21_sc40]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc4]


title: Embryo_3 EVT [DNA_batch21_sc39]


title: Embryo_8 Neural ectoderm [DNA_batch21_sc53]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc38]


title: Embryo_4 STB [DNA_batch21_sc42]


title: Embryo_3 EVT [DNA_batch21_sc37]


title: Embryo_2 CTB [DNA_batch21_sc41]


title: Embryo_7 Mesoderm [DNA_batch21_sc55]


title: Embryo_4 STB [DNA_batch21_sc35]


title: Embryo_3 EVT [DNA_batch21_sc33]


title: Embryo_12 Blood cells [DNA_batch21_sc34]


title: Embryo_4 STB [DNA_batch21_sc32]


title: Embryo_3 EVT [DNA_batch21_sc30]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc31]


title: Embryo_2 CTB [DNA_batch21_sc27]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc3]


title: Embryo_3 EVT [DNA_batch21_sc28]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc26]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc24]


title: Embryo_3 EVT [DNA_batch21_sc25]


title: Embryo_3 EVT [DNA_batch21_sc22]


title: Embryo_3 EVT [DNA_batch21_sc23]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc20]


title: Embryo_5 EPI [DNA_batch21_sc2]


title: Embryo_2 CTB [DNA_batch21_sc21]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc19]


title: Embryo_3 EVT [DNA_batch21_sc17]


title: Embryo_3 EVT [DNA_batch21_sc15]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch21_sc12]


title: Embryo_1 EXMC [DNA_batch21_sc10]


title: Embryo_4 STB [DNA_batch21_sc16]


title: Embryo_3 EVT [DNA_batch21_sc18]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc14]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc36]


title: Embryo_5 EPI [DNA_batch21_sc11]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc13]


title: Embryo_6 Non-neural ectoderm [DNA_batch21_sc1]


title: Embryo_2 CTB [DNA_batch20_sc9]


title: Embryo_4 STB [DNA_batch20_sc8]


title: Embryo_3 EVT [DNA_batch20_sc51]


title: Embryo_1 EXMC [DNA_batch21_sc29]


title: Embryo_11 Endoderm [DNA_batch20_sc47]


title: Embryo_2 CTB [DNA_batch20_sc48]


title: Embryo_3 EVT [DNA_batch20_sc7]


title: Embryo_2 CTB [DNA_batch20_sc5]


title: Embryo_5 EPI [DNA_batch20_sc50]


title: Embryo_8 Neural ectoderm [DNA_batch20_sc44]


title: Embryo_2 CTB [DNA_batch20_sc49]


title: Embryo_3 EVT [DNA_batch20_sc46]


title: Embryo_8 Neural ectoderm [DNA_batch20_sc42]


title: Embryo_7 Mesoderm [DNA_batch20_sc43]


title: Embryo_7 Mesoderm [DNA_batch20_sc41]


title: Embryo_5 EPI [DNA_batch20_sc4]


title: Embryo_6 Non-neural ectoderm [DNA_batch20_sc40]


title: Embryo_7 Mesoderm [DNA_batch20_sc38]


title: Embryo_7 Mesoderm [DNA_batch20_sc35]


title: Embryo_6 Non-neural ectoderm [DNA_batch20_sc37]


title: Embryo_7 Mesoderm [DNA_batch20_sc36]


title: Embryo_7 Mesoderm [DNA_batch20_sc33]


title: Embryo_7 Mesoderm [DNA_batch20_sc34]


title: Embryo_8 Neural ectoderm [DNA_batch20_sc32]


title: Embryo_5 EPI [DNA_batch20_sc45]


title: Embryo_2 CTB [DNA_batch20_sc3]


title: Embryo_1 EXMC [DNA_batch20_sc30]


title: Embryo_7 Mesoderm [DNA_batch20_sc31]


title: Embryo_6 Non-neural ectoderm [DNA_batch20_sc39]


title: Embryo_12 Blood cells [DNA_batch20_sc2]


title: Embryo_3 EVT [DNA_batch20_sc26]


title: Embryo_3 EVT [DNA_batch20_sc29]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch20_sc28]


title: Embryo_5 EPI [DNA_batch20_sc27]


title: Embryo_11 Endoderm [DNA_batch20_sc14]


title: Embryo_7 Mesoderm [DNA_batch20_sc12]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch20_sc11]


title: Embryo_3 EVT [DNA_batch20_sc10]


title: Embryo_11 Endoderm [DNA_batch20_sc25]


title: Embryo_5 EPI [DNA_batch20_sc22]


title: Embryo_3 EVT [DNA_batch19_sc95]


title: Embryo_5 EPI [DNA_batch20_sc23]


title: Embryo_2 CTB [DNA_batch20_sc21]


title: Embryo_7 Mesoderm [DNA_batch20_sc19]


title: Embryo_11 Endoderm [DNA_batch20_sc20]


title: Embryo_3 EVT [DNA_batch19_sc93]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch20_sc18]


title: Embryo_11 Endoderm [DNA_batch20_sc15]


title: Embryo_7 Mesoderm [DNA_batch20_sc17]


title: Embryo_12 Blood cells [DNA_batch19_sc94]


title: Embryo_11 Endoderm [DNA_batch20_sc13]


title: Embryo_5 EPI [DNA_batch20_sc1]


title: Embryo_3 EVT [DNA_batch19_sc92]


title: Embryo_3 EVT [DNA_batch19_sc96]


title: Embryo_6 Non-neural ectoderm [DNA_batch20_sc16]


title: Embryo_2 CTB [DNA_batch19_sc89]


title: Embryo_4 STB [DNA_batch19_sc9]


title: Embryo_3 EVT [DNA_batch19_sc87]


title: Embryo_3 EVT [DNA_batch19_sc91]


title: Embryo_3 EVT [DNA_batch19_sc88]


title: Embryo_2 CTB [DNA_batch19_sc86]


title: Embryo_3 EVT [DNA_batch19_sc90]


title: Embryo_4 STB [DNA_batch19_sc81]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc8]


title: Embryo_3 EVT [DNA_batch19_sc78]


title: Embryo_4 STB [DNA_batch19_sc77]


title: Embryo_4 STB [DNA_batch19_sc83]


title: Embryo_3 EVT [DNA_batch19_sc84]


title: Embryo_3 EVT [DNA_batch19_sc75]


title: Embryo_4 STB [DNA_batch19_sc73]


title: Embryo_2 CTB [DNA_batch19_sc82]


title: Embryo_3 EVT [DNA_batch19_sc80]


title: Embryo_3 EVT [DNA_batch19_sc70]


title: Embryo_3 EVT [DNA_batch19_sc69]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc7]


title: Embryo_3 EVT [DNA_batch19_sc79]


title: Embryo_2 CTB [DNA_batch19_sc67]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc66]


title: Embryo_12 Blood cells [DNA_batch19_sc65]


title: Embryo_7 Mesoderm [DNA_batch19_sc64]


title: Embryo_4 STB [DNA_batch19_sc68]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch19_sc63]


title: Embryo_12 Blood cells [DNA_batch19_sc85]


title: Embryo_7 Mesoderm [DNA_batch19_sc62]


title: Embryo_7 Mesoderm [DNA_batch19_sc60]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc61]


title: Embryo_7 Mesoderm [DNA_batch19_sc59]


title: Embryo_3 EVT [DNA_batch19_sc76]


title: Embryo_3 EVT [DNA_batch19_sc72]


title: Embryo_2 CTB [DNA_batch19_sc74]


title: Embryo_7 Mesoderm [DNA_batch19_sc58]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc57]


title: Embryo_7 Mesoderm [DNA_batch19_sc55]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc54]


title: Embryo_7 Mesoderm [DNA_batch19_sc53]


title: Embryo_4 STB [DNA_batch19_sc52]


title: Embryo_7 Mesoderm [DNA_batch19_sc50]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc5]


title: Embryo_7 Mesoderm [DNA_batch19_sc46]


title: Embryo_5 EPI [DNA_batch19_sc47]


title: Embryo_7 Mesoderm [DNA_batch19_sc48]


title: Embryo_7 Mesoderm [DNA_batch19_sc45]


title: Embryo_7 Mesoderm [DNA_batch19_sc49]


title: Embryo_7 Mesoderm [DNA_batch19_sc42]


title: Embryo_5 EPI [DNA_batch19_sc43]


title: Embryo_5 EPI [DNA_batch19_sc39]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc4]


title: Embryo_5 EPI [DNA_batch19_sc41]


title: Embryo_11 Endoderm [DNA_batch19_sc36]


title: Embryo_7 Mesoderm [DNA_batch19_sc35]


title: Embryo_3 EVT [DNA_batch19_sc34]


title: Embryo_5 EPI [DNA_batch19_sc38]


title: Embryo_7 Mesoderm [DNA_batch19_sc51]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch19_sc30]


title: Embryo_3 EVT [DNA_batch19_sc31]


title: Embryo_10 PS and derivative [DNA_batch19_sc33]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc6]


title: Embryo_2 CTB [DNA_batch19_sc32]


title: Embryo_7 Mesoderm [DNA_batch19_sc29]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc3]


title: Embryo_2 CTB [DNA_batch19_sc27]


title: Embryo_7 Mesoderm [DNA_batch19_sc28]


title: Embryo_7 Mesoderm [DNA_batch19_sc44]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc23]


title: Embryo_5 EPI [DNA_batch19_sc24]


title: Embryo_5 EPI [DNA_batch19_sc21]


title: Embryo_3 EVT [DNA_batch19_sc20]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch19_sc37]


title: Embryo_4 STB [DNA_batch19_sc2]


title: Embryo_2 CTB [DNA_batch19_sc19]


title: Embryo_5 EPI [DNA_batch19_sc18]


title: Embryo_5 EPI [DNA_batch19_sc17]


title: Embryo_2 CTB [DNA_batch19_sc14]


title: Embryo_4 STB [DNA_batch19_sc15]


title: Embryo_4 STB [DNA_batch19_sc12]


title: Embryo_3 EVT [DNA_batch19_sc13]


title: Embryo_6 Non-neural ectoderm [DNA_batch19_sc10]


title: Embryo_3 EVT [DNA_batch19_sc26]


title: Embryo_2 CTB [DNA_batch19_sc25]


title: Embryo_2 CTB [DNA_batch18_sc94]


title: Embryo_1 EXMC [DNA_batch19_sc1]


title: Embryo_3 EVT [DNA_batch19_sc11]


title: Embryo_3 EVT [DNA_batch18_sc90]


title: Embryo_3 EVT [DNA_batch18_sc91]


title: Embryo_4 STB [DNA_batch18_sc93]


title: Embryo_3 EVT [DNA_batch18_sc92]


title: Embryo_3 EVT [DNA_batch18_sc89]


title: Embryo_2 CTB [DNA_batch18_sc88]


title: Embryo_2 CTB [DNA_batch19_sc22]


title: Embryo_1 EXMC [DNA_batch18_sc9]


title: Embryo_3 EVT [DNA_batch18_sc86]


title: Embryo_2 CTB [DNA_batch19_sc16]


title: Embryo_3 EVT [DNA_batch18_sc87]


title: Embryo_3 EVT [DNA_batch18_sc81]


title: Embryo_4 STB [DNA_batch18_sc83]


title: Embryo_3 EVT [DNA_batch18_sc84]


title: Embryo_3 EVT [DNA_batch18_sc85]


title: Embryo_3 EVT [DNA_batch18_sc82]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch19_sc56]


title: Embryo_3 EVT [DNA_batch18_sc80]


title: Embryo_10 PS and derivative [DNA_batch18_sc8]


title: Embryo_3 EVT [DNA_batch18_sc79]


title: Embryo_3 EVT [DNA_batch18_sc75]


title: Embryo_3 EVT [DNA_batch18_sc76]


title: Embryo_3 EVT [DNA_batch18_sc73]


title: Embryo_3 EVT [DNA_batch18_sc74]


title: Embryo_3 EVT [DNA_batch18_sc72]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch18_sc71]


title: Embryo_1 EXMC [DNA_batch18_sc7]


title: Embryo_4 STB [DNA_batch18_sc70]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch18_sc66]


title: Embryo_4 STB [DNA_batch18_sc68]


title: Embryo_4 STB [DNA_batch18_sc67]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch18_sc65]


title: Embryo_3 EVT [DNA_batch18_sc69]


title: Embryo_4 STB [DNA_batch18_sc64]


title: Embryo_4 STB [DNA_batch18_sc60]


title: Embryo_3 EVT [DNA_batch18_sc61]


title: Embryo_7 Mesoderm [DNA_batch18_sc59]


title: Embryo_7 Mesoderm [DNA_batch18_sc58]


title: Embryo_7 Mesoderm [DNA_batch18_sc57]


title: Embryo_10 PS and derivative [DNA_batch18_sc6]


title: Embryo_6 Non-neural ectoderm [DNA_batch18_sc53]


title: Embryo_6 Non-neural ectoderm [DNA_batch18_sc55]


title: Embryo_3 EVT [DNA_batch18_sc78]


title: Embryo_3 EVT [DNA_batch18_sc56]


title: Embryo_7 Mesoderm [DNA_batch18_sc54]


title: Embryo_7 Mesoderm [DNA_batch18_sc51]


title: Embryo_8 Neural ectoderm [DNA_batch18_sc50]


title: Embryo_3 EVT [DNA_batch18_sc63]


title: Embryo_6 Non-neural ectoderm [DNA_batch18_sc46]


title: Embryo_7 Mesoderm [DNA_batch18_sc49]


title: Embryo_3 EVT [DNA_batch18_sc62]


title: Embryo_7 Mesoderm [DNA_batch18_sc44]


title: Embryo_12 Blood cells [DNA_batch18_sc43]


title: Embryo_5 EPI [DNA_batch18_sc40]


title: Embryo_7 Mesoderm [DNA_batch18_sc41]


title: Embryo_10 PS and derivative [DNA_batch18_sc4]


title: Embryo_11 Endoderm [DNA_batch18_sc38]


title: Embryo_7 Mesoderm [DNA_batch18_sc47]


title: Embryo_6 Non-neural ectoderm [DNA_batch18_sc52]


title: Embryo_10 PS and derivative [DNA_batch18_sc36]


title: Embryo_1 EXMC [DNA_batch18_sc35]


title: Embryo_4 STB [DNA_batch18_sc33]


title: Embryo_1 EXMC [DNA_batch18_sc34]


title: Embryo_10 PS and derivative [DNA_batch18_sc3]


title: Embryo_4 STB [DNA_batch18_sc32]


title: Embryo_10 PS and derivative [DNA_batch18_sc27]


title: Embryo_10 PS and derivative [DNA_batch18_sc31]


title: Embryo_4 STB [DNA_batch18_sc28]


title: Embryo_5 EPI [DNA_batch18_sc42]


title: Embryo_11 Endoderm [DNA_batch18_sc39]


title: Embryo_3 EVT [DNA_batch18_sc29]


title: Embryo_10 PS and derivative [DNA_batch18_sc26]


title: Embryo_8 Neural ectoderm [DNA_batch18_sc45]


title: Embryo_10 PS and derivative [DNA_batch18_sc24]


title: Embryo_1 EXMC [DNA_batch18_sc18]


title: Embryo_10 PS and derivative [DNA_batch18_sc17]


title: Embryo_10 PS and derivative [DNA_batch18_sc22]


title: Embryo_1 EXMC [DNA_batch18_sc30]


title: Embryo_3 EVT [DNA_batch19_sc71]


title: Embryo_10 PS and derivative [DNA_batch18_sc14]


title: Embryo_5 EPI [DNA_batch18_sc16]


title: Embryo_3 EVT [DNA_batch18_sc21]


title: Embryo_10 PS and derivative [DNA_batch18_sc15]


title: Embryo_10 PS and derivative [DNA_batch18_sc13]


title: Embryo_1 EXMC [DNA_batch18_sc10]


title: Embryo_1 EXMC [DNA_batch18_sc20]


title: Embryo_1 EXMC [DNA_batch18_sc2]


title: Embryo_2 CTB [DNA_batch18_sc12]


title: Embryo_1 EXMC [DNA_batch18_sc19]


title: Embryo_1 EXMC [DNA_batch18_sc37]


title: Embryo_1 EXMC [DNA_batch18_sc11]


title: Embryo_1 EXMC [DNA_batch18_sc1]


title: Embryo_7 Mesoderm [DNA_batch17_sc96]


title: Embryo_5 EPI [DNA_batch17_sc94]


title: Embryo_3 EVT [DNA_batch17_sc93]


title: Embryo_2 CTB [DNA_batch17_sc92]


title: Embryo_11 Endoderm [DNA_batch17_sc86]


title: Embryo_4 STB [DNA_batch17_sc9]


title: Embryo_11 Endoderm [DNA_batch17_sc90]


title: Embryo_3 EVT [DNA_batch17_sc87]


title: Embryo_7 Mesoderm [DNA_batch17_sc88]


title: Embryo_7 Mesoderm [DNA_batch17_sc89]


title: Embryo_2 CTB [DNA_batch17_sc91]


title: Embryo_4 STB [DNA_batch17_sc85]


title: Embryo_5 EPI [DNA_batch17_sc8]


title: Embryo_5 EPI [DNA_batch17_sc84]


title: Embryo_5 EPI [DNA_batch17_sc83]


title: Embryo_11 Endoderm [DNA_batch17_sc80]


title: Embryo_3 EVT [DNA_batch17_sc81]


title: Embryo_7 Mesoderm [DNA_batch17_sc82]


title: Embryo_3 EVT [DNA_batch17_sc79]


title: Embryo_3 EVT [DNA_batch17_sc78]


title: Embryo_3 EVT [DNA_batch17_sc77]


title: Embryo_3 EVT [DNA_batch17_sc76]


title: Embryo_3 EVT [DNA_batch17_sc73]


title: Embryo_5 EPI [DNA_batch17_sc75]


title: Embryo_11 Endoderm [DNA_batch17_sc71]


title: Embryo_5 EPI [DNA_batch17_sc74]


title: Embryo_3 EVT [DNA_batch17_sc70]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch17_sc68]


title: Embryo_5 EPI [DNA_batch17_sc69]


title: Embryo_3 EVT [DNA_batch17_sc67]


title: Embryo_11 Endoderm [DNA_batch17_sc7]


title: Embryo_3 EVT [DNA_batch17_sc62]


title: Embryo_7 Mesoderm [DNA_batch17_sc65]


title: Embryo_7 Mesoderm [DNA_batch17_sc63]


title: Embryo_8 Neural ectoderm [DNA_batch17_sc61]


title: Embryo_4 STB [DNA_batch17_sc6]


title: Embryo_2 CTB [DNA_batch17_sc58]


title: Embryo_3 EVT [DNA_batch17_sc56]


title: Embryo_5 EPI [DNA_batch17_sc54]


title: Embryo_5 EPI [DNA_batch17_sc64]


title: Embryo_5 EPI [DNA_batch17_sc55]


title: Embryo_2 CTB [DNA_batch17_sc66]


title: Embryo_7 Mesoderm [DNA_batch17_sc53]


title: Embryo_2 CTB [DNA_batch17_sc51]


title: Embryo_11 Endoderm [DNA_batch17_sc60]


title: Embryo_1 EXMC [DNA_batch17_sc52]


title: Embryo_3 EVT [DNA_batch17_sc57]


title: Embryo_5 EPI [DNA_batch17_sc5]


title: Embryo_3 EVT [DNA_batch17_sc59]


title: Embryo_3 EVT [DNA_batch17_sc50]


title: Embryo_3 EVT [DNA_batch17_sc49]


title: Embryo_1 EXMC [DNA_batch17_sc47]


title: Embryo_7 Mesoderm [DNA_batch17_sc46]


title: Embryo_3 EVT [DNA_batch17_sc48]


title: Embryo_11 Endoderm [DNA_batch17_sc45]


title: Embryo_3 EVT [DNA_batch17_sc43]


title: Embryo_2 CTB [DNA_batch18_sc77]


title: Embryo_2 CTB [DNA_batch17_sc41]


title: Embryo_11 Endoderm [DNA_batch17_sc40]


title: Embryo_7 Mesoderm [DNA_batch17_sc39]


title: Embryo_2 CTB [DNA_batch17_sc38]


title: Embryo_3 EVT [DNA_batch17_sc35]


title: Embryo_3 EVT [DNA_batch17_sc37]


title: Embryo_3 EVT [DNA_batch17_sc36]


title: Embryo_2 CTB [DNA_batch17_sc3]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch17_sc33]


title: Embryo_7 Mesoderm [DNA_batch17_sc31]


title: Embryo_7 Mesoderm [DNA_batch17_sc30]


title: Embryo_11 Endoderm [DNA_batch17_sc32]


title: Embryo_11 Endoderm [DNA_batch17_sc29]


title: Embryo_3 EVT [DNA_batch17_sc28]


title: Embryo_11 Endoderm [DNA_batch17_sc34]


title: Embryo_3 EVT [DNA_batch17_sc25]


title: Embryo_3 EVT [DNA_batch17_sc27]


title: Embryo_11 Endoderm [DNA_batch17_sc44]


title: Embryo_7 Mesoderm [DNA_batch17_sc26]


title: Embryo_3 EVT [DNA_batch17_sc22]


title: Embryo_3 EVT [DNA_batch17_sc23]


title: Embryo_3 EVT [DNA_batch17_sc21]


title: Embryo_3 EVT [DNA_batch17_sc24]


title: Embryo_3 EVT [DNA_batch17_sc42]


title: Embryo_11 Endoderm [DNA_batch17_sc20]


title: Embryo_2 CTB [DNA_batch17_sc4]


title: Embryo_4 STB [DNA_batch17_sc19]


title: Embryo_4 STB [DNA_batch17_sc18]


title: Embryo_3 EVT [DNA_batch17_sc17]


title: Embryo_2 CTB [DNA_batch17_sc13]


title: Embryo_2 CTB [DNA_batch17_sc12]


title: Embryo_2 CTB [DNA_batch17_sc15]


title: Embryo_3 EVT [DNA_batch16_sc92]


title: Embryo_2 CTB [DNA_batch16_sc91]


title: Embryo_3 EVT [DNA_batch16_sc90]


title: Embryo_6 Non-neural ectoderm [DNA_batch17_sc11]


title: Embryo_3 EVT [DNA_batch16_sc88]


title: Embryo_4 STB [DNA_batch16_sc86]


title: Embryo_1 EXMC [DNA_batch17_sc10]


title: Embryo_3 EVT [DNA_batch16_sc95]


title: Embryo_3 EVT [DNA_batch16_sc89]


title: Embryo_4 STB [DNA_batch18_sc23]


title: Embryo_2 CTB [DNA_batch16_sc9]


title: Embryo_5 EPI [DNA_batch17_sc2]


title: Embryo_3 EVT [DNA_batch16_sc83]


title: Embryo_5 EPI [DNA_batch16_sc85]


title: Embryo_3 EVT [DNA_batch16_sc93]


title: Embryo_5 EPI [DNA_batch17_sc16]


title: Embryo_7 Mesoderm [DNA_batch16_sc81]


title: Embryo_7 Mesoderm [DNA_batch16_sc80]


title: Embryo_3 EVT [DNA_batch16_sc76]


title: Embryo_3 EVT [DNA_batch16_sc94]


title: Embryo_3 EVT [DNA_batch16_sc74]


title: Embryo_4 STB [DNA_batch16_sc8]


title: Embryo_4 STB [DNA_batch16_sc87]


title: Embryo_11 Endoderm [DNA_batch16_sc77]


title: Embryo_7 Mesoderm [DNA_batch16_sc73]


title: Embryo_3 EVT [DNA_batch16_sc75]


title: Embryo_3 EVT [DNA_batch16_sc71]


title: Embryo_5 EPI [DNA_batch16_sc82]


title: Embryo_5 EPI [DNA_batch17_sc1]


title: Embryo_7 Mesoderm [DNA_batch16_sc68]


title: Embryo_4 STB [DNA_batch16_sc67]


title: Embryo_1 EXMC [DNA_batch16_sc7]


title: Embryo_2 CTB [DNA_batch16_sc70]


title: Embryo_4 STB [DNA_batch16_sc69]


title: Embryo_12 Blood cells [DNA_batch16_sc78]


title: Embryo_3 EVT [DNA_batch16_sc66]


title: Embryo_4 STB [DNA_batch16_sc64]


title: Embryo_5 EPI [DNA_batch16_sc65]


title: Embryo_4 STB [DNA_batch16_sc63]


title: Embryo_4 STB [DNA_batch16_sc6]


title: Embryo_2 CTB [DNA_batch16_sc59]


title: Embryo_3 EVT [DNA_batch16_sc60]


title: Embryo_3 EVT [DNA_batch16_sc62]


title: Embryo_3 EVT [DNA_batch16_sc61]


title: Embryo_3 EVT [DNA_batch16_sc57]


title: Embryo_3 EVT [DNA_batch16_sc58]


title: Embryo_2 CTB [DNA_batch17_sc14]


title: Embryo_4 STB [DNA_batch16_sc55]


title: Embryo_4 STB [DNA_batch16_sc56]


title: Embryo_3 EVT [DNA_batch16_sc53]


title: Embryo_3 EVT [DNA_batch16_sc54]


title: Embryo_2 CTB [DNA_batch16_sc51]


title: Embryo_3 EVT [DNA_batch16_sc50]


title: Embryo_3 EVT [DNA_batch16_sc49]


title: Embryo_4 STB [DNA_batch16_sc5]


title: Embryo_4 STB [DNA_batch16_sc47]


title: Embryo_3 EVT [DNA_batch16_sc46]


title: Embryo_3 EVT [DNA_batch16_sc52]


title: Embryo_3 EVT [DNA_batch16_sc43]


title: Embryo_2 CTB [DNA_batch16_sc44]


title: Embryo_2 CTB [DNA_batch16_sc42]


title: Embryo_3 EVT [DNA_batch16_sc40]


title: Embryo_6 Non-neural ectoderm [DNA_batch16_sc4]


title: Embryo_3 EVT [DNA_batch16_sc41]


title: Embryo_3 EVT [DNA_batch16_sc39]


title: Embryo_3 EVT [DNA_batch16_sc45]


title: Embryo_3 EVT [DNA_batch16_sc37]


title: Embryo_3 EVT [DNA_batch16_sc34]


title: Embryo_2 CTB [DNA_batch16_sc35]


title: Embryo_2 CTB [DNA_batch16_sc31]


title: Embryo_3 EVT [DNA_batch16_sc33]


title: Embryo_3 EVT [DNA_batch16_sc32]


title: Embryo_3 EVT [DNA_batch16_sc30]


title: Embryo_3 EVT [DNA_batch16_sc3]


title: Embryo_2 CTB [DNA_batch16_sc29]


title: Embryo_3 EVT [DNA_batch16_sc27]


title: Embryo_3 EVT [DNA_batch16_sc48]


title: Embryo_3 EVT [DNA_batch16_sc26]


title: Embryo_3 EVT [DNA_batch16_sc28]


title: Embryo_3 EVT [DNA_batch16_sc25]


title: Embryo_3 EVT [DNA_batch16_sc24]


title: Embryo_3 EVT [DNA_batch16_sc22]


title: Embryo_2 CTB [DNA_batch16_sc23]


title: Embryo_3 EVT [DNA_batch16_sc21]


title: Embryo_4 STB [DNA_batch16_sc2]


title: Embryo_2 CTB [DNA_batch16_sc20]


title: Embryo_3 EVT [DNA_batch16_sc19]


title: Embryo_3 EVT [DNA_batch16_sc18]


title: Embryo_3 EVT [DNA_batch16_sc17]


title: Embryo_3 EVT [DNA_batch16_sc36]


title: Embryo_3 EVT [DNA_batch16_sc16]


title: Embryo_2 CTB [DNA_batch16_sc38]


title: Embryo_3 EVT [DNA_batch16_sc15]


title: Embryo_3 EVT [DNA_batch16_sc13]


title: Embryo_3 EVT [DNA_batch16_sc11]


title: Embryo_2 CTB [DNA_batch16_sc12]


title: Embryo_3 EVT [DNA_batch16_sc14]


title: Embryo_3 EVT [DNA_batch16_sc1]


title: Embryo_3 EVT [DNA_batch15_sc95]


title: Embryo_2 CTB [DNA_batch15_sc91]


title: Embryo_3 EVT [DNA_batch15_sc93]


title: Embryo_3 EVT [DNA_batch15_sc92]


title: Embryo_3 EVT [DNA_batch15_sc90]


title: Embryo_12 Blood cells [DNA_batch15_sc9]


title: Embryo_3 EVT [DNA_batch15_sc88]


title: Embryo_2 CTB [DNA_batch15_sc89]


title: Embryo_3 EVT [DNA_batch15_sc84]


title: Embryo_2 CTB [DNA_batch15_sc83]


title: Embryo_2 CTB [DNA_batch15_sc85]


title: Embryo_3 EVT [DNA_batch15_sc86]


title: Embryo_4 STB [DNA_batch15_sc82]


title: Embryo_3 EVT [DNA_batch15_sc81]


title: Embryo_3 EVT [DNA_batch15_sc79]


title: Embryo_7 Mesoderm [DNA_batch15_sc8]


title: Embryo_2 CTB [DNA_batch15_sc80]


title: Embryo_3 EVT [DNA_batch15_sc77]


title: Embryo_2 CTB [DNA_batch15_sc75]


title: Embryo_3 EVT [DNA_batch15_sc76]


title: Embryo_3 EVT [DNA_batch15_sc94]


title: Embryo_3 EVT [DNA_batch16_sc10]


title: Embryo_3 EVT [DNA_batch15_sc72]


title: Embryo_7 Mesoderm [DNA_batch15_sc70]


title: Embryo_12 Blood cells [DNA_batch15_sc71]


title: Embryo_3 EVT [DNA_batch15_sc69]


title: Embryo_3 EVT [DNA_batch15_sc87]


title: Embryo_6 Non-neural ectoderm [DNA_batch15_sc64]


title: Embryo_3 EVT [DNA_batch15_sc63]


title: Embryo_7 Mesoderm [DNA_batch15_sc65]


title: Embryo_8 Neural ectoderm [DNA_batch15_sc68]


title: Embryo_8 Neural ectoderm [DNA_batch15_sc62]


title: Embryo_7 Mesoderm [DNA_batch15_sc67]


title: Embryo_9 Extraembryonic Mesoderm [DNA_batch15_sc66]


title: Embryo_3 EVT [DNA_batch15_sc78]


title: Embryo_3 EVT [DNA_batch15_sc74]


title: Embryo_3 EVT [DNA_batch15_sc73]


title: Embryo_6 Non-neural ectoderm [DNA_batch15_sc7]