title: uty_nov30

data_processing:
NexteraPE-PE adapters were removed using Trimmomatic 0.36
Reads were aligned to mm9 reference genome using Bowtie2.2.6. Obtained bam files were converted to bigwig files for visualization.
PCR duplicates were removed with Picard MarkDuplicates 2.4.1 and reads mapping to mitochondiral DNA were removed.
Deeptools was used to shift reads coordinates to represent the real Tn5 binding site and to remove ENCODE's blacklisted regions (signal artefact regions).
MACS 2.0.10 was used for peak calling using q-value < 0.01 to define peaks
DESeq2 was used to identify DARs (differentially accessible regions) between b6 and uty.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file for each sample
Supplementary_files_format_and_content: Differentially accessible regions identified by DESeq2

source_name: cardiomyocyte-specific nuclei from cardiac left ventricles

extract_protocol:
Nuclei were extracted from frozen samples of left ventricles and labeled with an Alexa fluor 642-coupled antibody  raised against the pericentriolar 1 protein (PCM1) (SCBT, Dallas, TX), i.e. an antigen that accumulates specifically around nuclei from cardiomyocytes.  For each sample, 50,000 cardiomyocyte-specific nuclei were then obtained by cytofluorometry sorting.
The library was constructed as cited previously (doi: 10.1002/0471142727.mb2129s109),   using Nextera Tn5 Transposase from Illumina

value: cardiac left ventricles


title: zBr2dpf4_S2

status: Public on Sep 18 2020

type: SRA

city: Philadelphia

first: Bushra

last: Raj

state: PA

address: 421 Curie Boulevard

country: USA

institute: University of Pennsylvania

description:
zf2dpf_cc_filt.cluster.rds
zf2dpf_cc_filt_MarkRes6.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds

library_source: transcriptomic

data_processing:
Single-cell RNA Sequencing data (FASTQ files) were processed using Cell Ranger v2.0.2 to generate count matrices
Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 (release-86) genome assembly. File uploaded as Danio_rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates (marked as *b in raw files) and the processing was done using the combination of all data (processed data files have comb* prefix)
scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping
Genome_build: GRCz10
Supplementary_files_format_and_content: *barcodes.tsv files contain 10X Genomics cell barcodes, *genes.tsv files contain gene names, *matrix.mtx contain transcriptome count data, *web_summary.html contain summary statistics for transcript mapping, .rds files are the processed R objects, .txt files contain marker genes identified for each cluster in the dataset, URD*.rds files are the processed R objects for performing URD cell trajectory analysis. tree*.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus.
Supplementary_files_format_and_content: scGESTALT data:  Gest-zBr15dpf8 and Gest-zBr15dpf9 correspond to two samples from the same zebrafish (ZF1). Gest-zBr15dpf10 and Gest-zBr15dpf11 correspond to two samples from the same zebrafish (ZF2). Gest-zBr15dpf12 and Gest-zBr15dpf13 correspond to two samples from the same zebrafish (ZF3). Gest-zBr15dpf14 and Gest-zBr15dpf15 correspond to two samples from the same zebrafish (ZF4).
Supplementary_files_format_and_content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers (CellBarcode and CellUMI) that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences (HMID column) , the t-SNE cluster membership number (ClusterIdent column), and unique identifier (Readname). zfAllMerge-FILTEREDUSEME.xlsx contains the merged statistics of all samples, filtered to contain high confidence barcodes, the barcode sequence aligned to a reference unedited sequence (mergedRead column), mutations at each target site (target[X] columns) and the edited sequences at each target site (sequence[X] columns) were used for downstream analysis. Further details of columns can be found at https://github.com/shendurelab/Cas9FateMapping

molecule: total RNA

organism: Danio rerio

source_name: zebrafish brain

extract_protocol:
Libraries were prepared as described in manufacturer's protocol for v2 kits
Single-cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol  to generate single-cell cDNA libraries and prepared for sequencing

tag: tissue

value: brain

tag: developmental stage


title: Unstimulated - CD8+ - 41BB CAR - Donor 3

city: Memphis

first: Patrick

middle: Allen

last: Schreiner

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Children's Research Hospital

data_processing:
Read alignment was performed using STAR and BWA software
Gene level quantification was performed by HTSeq
Differentially expressed genes were identified using limma voom
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

organism: Homo sapiens

source_name: Osteosarcoma cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from whole blood of healthy donors by Lymphoprep gradient centrifugation, stimulated with CD3/CD28 antibodies, and transduced with retroviral vectors encoding EphA2 Delta-, CD28 zeta-, 41BB zeta-, and MyD88.CD40 (MC) zeta-CARs. The resulting CAR T cells were maintained in RPMI with 10% FBS, 10 ng/mL IL-7 and 5 ng/mL IL-15.

extract_protocol:
poly-A selected
stranded mRNA

treatment_protocol: CAR T cells were taken directly from culture or stimulated with LM7 tumor cells at a 2:1 T cell:tumor cell ratio for 24 hours before being sorted (FACS) into CD4+transgene+ and CD8+transgene+ populations.

tag: agent

tag: cell type

value: Unstimulated - CD8+ - 41BB CAR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A3_ad012

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: PIR

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A2_ad007


title: uty_nov5

city: Montreal

first: Christian

middle: F

last: Deschepper

state: QC

address: 110 Pine Ave West

department: Institut de recherches cliniques de Montréal (IRCM)

country: Canada

institute: Université de Montréal

growth_protocol: adult male mice were used at 40 days of age to harvest cardiac tissues


title: Unstimulated - CD8+ - 41BB CAR - Donor 2


title: zBr2dpf2_S4


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A2_ad002


title: zBr2dpf3_S1


title: uty_nov22


title: zBr2dpf1_S3


title: b6_y129_nov5


title: Unstimulated - CD4+ - 41BB CAR - Donor 3

value: Unstimulated - CD4+ - 41BB CAR


title: Unstimulated - CD8+ - 41BB CAR - Donor 1


title: b6_y129_nov22


title: b6_y129_nov30


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A2_ad010


title: zBr36hpf2_S7

description:
zf36hpf_cc_filt.cluster.rds
zf36hpf_cc_filt_MarkRes6.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds


title: Unstimulated - CD4+ - 41BB CAR - Donor 2


title: zBr36hpf1_S8


title: Mouse day 7 biorep 3

city: London

first: Teresa

last: Rayon

address: Midland Road

country: United Kingdom

institute: Francis Crick Institute

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_7_3

data_processing:
basecalling with bcl2fastq v2.20.0
alignment and quantification with BABS-RNASeq (https://github.com/crickbabs/BABS-RNASeq) and default parameters
Genome_build: GRCm38 Ensembl release-89
Supplementary_files_format_and_content: tab-delimited expression matrices from RSEM

molecule: polyA RNA

source_name: Neural progenitor cells day 7

growth_protocol: To obtain mouse neural progenitors of posterior identity, mouse ESCs were dissociated with 0.05% trypsin, feeders removed by differential binding to gelatin-coated plates, and 60,000-80,000 cells were plated per 35mm CELLBIND dish in N2B27 medium supplemented with 10ng/ml of bFGF (100-18B Peprotech) from days –3 to –1. On day -1, N2B27 was supplemented with 10ng/ml bFGF (100-18B Peprotech), 5µM CHIR99021 (Axon), 10uM SB431542 (LT S0400) and 2uM DMH1 (A12820 Adooq Bioscience). From day 0 onwards cells and cultured in N2B27 supplemented with 100nM RA (R2625 Sigma Aldrich) and 500nM SAG (566660 Calbiochem) for neural induction. Medium was changed daily. N2B27 medium contained a 1:1 ratio of DMEM/F12:Neurobasal medium (21331020 and 21103049 ThermoFisher Scientific) supplemented with 1xN2 (17502001 ThermoFisher Scientific), 1xB27 (17504001 ThermoFisher Scientific), 2mM L-glutamine (25030024 ThermoFisher Scientific), 40mg/ml BSA (A7979 Sigma Aldrich), Penicillin/Streptomycin (15140122 ThermoFisher Scientific)  and 0.1mM 2-mercaptoethanol (21985023 ThermoFisher Scientific).

extract_protocol:
Qiagen RNeasy Plus Micro Kit
KAPA mRNA

value: ES-derived neural progenitor cells

tag: starting conditions

value: differentiation from neuromesodermal progenitors

tag: cell line

tag: treatment

value: RA and SAG

tag: time

value: day 7


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A2_ad006


title: Mouse day 7 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_7_2


title: Unstimulated - CD4+ - 41BB CAR - Donor 1


title: zBr24hpf3_S2

description:
zf24hpf_cc_filt.cluster.rds
zf24hpf_cc_filt_MarkRes5.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A2_ad008


title: Unstimulated - CD8+ - CD28 CAR - Donor 3

value: Unstimulated - CD8+ - CD28 CAR


title: Mouse day 7 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_7_1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A2_ad001


title: Unstimulated - CD8+ - CD28 CAR - Donor 2


title: zBr24hpf1_S3


title: zBr24hpf2_S4


title: Mouse day 6 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_6_3

source_name: Neural progenitor cells day 6

value: day 6


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A2_ad012


title: Mouse day 6 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_6_2


title: Unstimulated - CD8+ - CD28 CAR - Donor 1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A2_ad004


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A12_ad002


title: zBr20hpf2_S2

description:
zf20hpf_cc_filt.cluster.rds
zf20hpf_cc_filt_MarkRes4.5.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds


title: Unstimulated - CD4+ - CD28 CAR - Donor 3

value: Unstimulated - CD4+ - CD28 CAR


title: zBr20hpf3_S1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A12_ad012


title: Unstimulated - CD4+ - CD28 CAR - Donor 2


title: Mouse day 5 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_5_3

source_name: Neural progenitor cells day 5

value: day 5


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A12_ad004


title: Mouse day 6 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_6_1


title: zBr18hpf2_18S_S4

description:
zf18s_cc_filt.cluster.rds
zf18s_filt_MarkRes5.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds

value: 18hpf, 18somites


title: Unstimulated - CD4+ - CD28 CAR - Donor 1


title: Mouse day 5 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_5_2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A12_ad010


title: Unstimulated - CD8+ - 4H5D CAR - Donor 3

value: Unstimulated - CD8+ - 4H5D CAR


title: Mouse day 5 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_5_1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A12_ad008


title: zBr18hpf1_18S_S3


title: Mouse day 4 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_4_3

source_name: Neural progenitor cells day 4

value: day 4


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A12_ad006


title: Unstimulated - CD8+ - 4H5D CAR - Donor 2


title: Mouse day 4 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_4_2


title: Unstimulated - CD8+ - 4H5D CAR - Donor 1


title: Mouse day 4 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_4_1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A11_ad001


title: zBr14hpf2_10S_S6

description:
zf10s_cc_filt.cluster.rds
zf10s_filt_MarkRes4.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds

value: 14hpf, 10somites


title: zBr16hpf1_14S_S1

description:
zf14s_cc_filt.cluster.rds
zf14s_cc_filt_MarkRes5.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds

value: brain

value: 16hpf, 14somites


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A11_ad002

value: PIR


title: zBr14hpf1_10S_S5


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A11_ad006

value: male


title: Unstimulated - CD4+ - 4H5D CAR - Donor 2

value: Unstimulated - CD4+ - 4H5D CAR


title: Unstimulated - CD4+ - 4H5D CAR - Donor 1


title: zBr20hpf1_S1


title: Mouse day 3.5 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_3-5_2

source_name: Neural progenitor cells day 3.5

value: ES-derived neural progenitor cells

value: day 3.5


title: zBr12hpf2_S2

description:
zf6s_cc_filt.cluster.rds
zf6s_filt_MarkRes4.5.txt
URD_retinanewnokND.rds
URD_hypoND.rds
tree-hypoND_knn-100_sigma-8_40F-80B_NO-_ks_0001.rds
tree-retinanewnokND_knn-140_sigma-14_40F-80B_NO-15d-29-15d-39-15d-43-15d-62_pref_01.rds

value: 12hpf, 6somites


title: Mouse day 3.5 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_3-5_3

value: differentiation from neuromesodermal progenitors

value: RA and SAG


title: Mouse day 3.5 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_3-5_1


title: zBr12hpf1_S1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A11_ad008


title: H1 Wnt3a-treated 48 hour

first: Theresa

last: Gaasterland

address: 9600 Gilman Drive MS 0202

department: Scripps Institution of Oceanography

institute: University of California San Diego

data_processing:
alignment to reference hg19 human genome (hg19; mapped with bowtie v0.12.7, up to 3 mismatches, 1 match site allowed)
sam output files converted to bam format (samtools view, sort, index commands; samtools 0.1.12a)
generated readcounts per sample, normalized by millions-of-reads-per-sample (cuffdiff v1.3.0)
extracted normalized readcounts for each sample into one table (boutique scripts)
set aside ncRNA, miRNA, rRNA genes, zero signal, low signal (boutique scripts)
Genome_build: calculated log2 ratios for pairwise comparisons: each of 3h, 6h, 12h, 24h, 48h compared to 0h within treatment
Supplementary_files_format_and_content: identified differential patterns across time points

source_name: H1/WA01/NIH stem cell registry number 0043 human embryonic stem cells

growth_protocol: cells grown in Essential 8 (E8) media

extract_protocol:
Total RNA from cells was isolated using TRIzol (Life Technologies) and purified using DirectZOL RNA miniprep kit; RNA was transferred to NovoGene for library preparation and deep sequencing.
Minibead NEB Next Ultra RNA prep kit for Illumina
paired read, 150bp; 250-350 bp insert cDNA library

treatment_protocol: continuous treatment for 3, 6, 12, 24, 48 hours with one of Wnt3a protein (5 nM), CHIR98014 (250 nM), or FZD7-specific WNT mimetic (5 nM)

value: embryonic stem cell

value: Wnt3a protein (5 nM)

tag: treatment time

value: 48 hour


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A11_ad010


title: zBr16hpf2_14S_S2


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A11_ad007


title: Mouse day 3 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_3_2

source_name: Neural progenitor cells day 3

value: day 3


title: Unstimulated - CD4+ - 4H5D CAR - Donor 3


title: H1 Wnt3a-treated 6 hour

value: H1/WA01/NIH stem cell registry number 0043

value: 6 hour


title: scRNA-Seq of gbm cell lines of human and mouse

city: Zhejiang

first: Chong

last: Liu

address: NO.866 of Yuhang Tong Road

country: China

institute: Medical College of Zhejiang University

data_processing:
Sequenced reads were aligned to reference genome by cellranger.
The matrix was separated according to the cell type judgment result obtained by the cellranger.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
To select high quality cells for further analysis: 1) Removed genes detected in < 3 cells. 2) Filted cells with unique molecular identified (UMI) ≤ 150 or ≥ 4500 (UMI ≤ 200 or ≥ 6,500 were removed in mouse cell line sample; UMI ≤ 200 or ≥ 7,000 were removed in human cell line sample). 3) Removed cells that have ≥ 20% mitochondrial counts (cells that have ≥ 15% mitochondrial counts were filtered in cell line sample). Normalization was performed using the function “LogNormalize” of the R package Seurat.
Genome_build: mm10, hg19, GRCh38

organism:
Homo sapiens
Mus musculus

source_name: Brain

growth_protocol: The mouse and human GBM cell lines were maintained in human GBM complete media, which contained Neurobasal (Gibco, #21103-049); Glutamine (Gibco, #21051-024), 1x; Pen/Strep (HyClone, #SV30010), 1x; Na Pyruvate (Gibco, #11360-070), 1x; Gentamycin (Sigma, #46305), 50 µg/mL; Trace Elements B (Cellgro, #99-175-CI), 1x; d-Biotin (Sigma, #B4639), 10 ng/mL; SATO 10 µl/mL; Transferrin (Sigma, #T-1147), 100 µg/mL; BSA (Sigma, #A-4161), 100 µg/mL; Putrescine (Sigma, #P-5780), 16 µg/mL; Progesterone (Sigma, #P8783), 60 ng/mL; Sodium selenite (Sigma, #S5261), 40 ng/mL; Insulin (Sigma, 3I6634), 5 µl/mL; B-27(without Vitamin) (Gibco, #12587-010), 20 µl/mL supplemented with growth factors as indicated. The concentration of growth factors was used as following: EGF (50 ng/ml) /FGF (20 ng/ml) or PDGFAA (20 ng/ml). 1/2 media with fresh growth factors were regularly replaced every 4-5 days.

extract_protocol:
Primary tumor tissue or cell line were resuspended to single cell suspension for further experiment.
scRNA libraries were prepared for sequencing using standard Illumina protocols

value: brain tumor

tag: genotype


title: H1 Wnt3a-treated 24 hour

value: 24 hour


title: Mouse day 3 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_3_1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A10_ad004


title: 062_DIOLs_d25_rep2

city: Fukuoka

first: Nobuhiko

last: Hamazaki

state: Fukuoka

address: Maidashi 3-1-1, Higashi-ku,

department: Department of Developmental Stem Cell Biology

country: Japan

institute: Kyushu University

data_processing:
Fastq files from sequencing experiments were mapped to the mouse mm10 genome using default parameters for STAR (v2.6.0, Dobin et al., 2013)
Mapped reads were counted by featureCount (v1.6.0, Liao et al., 2014, -O -s 2).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including TPM values for each Sample.

growth_protocol: ESC lines were cultured in 2i plus LIF without feeders (Ying et al., 2008). PGCLC induction was performed as described (Hayashi and Saitou, 2013). PGCLCs were purified by FACSAria II or Fusion (BD Bioscience) and aggregated with E12.5 female gonadal somatic cells in a low-binding U-bottom 96-well plate (NUNC) for 2 days of culture in GK15 supplemented with 1 μM retinoic acid. To strictly remove residual PGCs from dissociated gonadal cells, both SSEA1 and CD31 antibodies (Miltenyi Biotech) were used according to the manufacturer’s instructions. 5,000 PGCLCs were cultured with 75,000 gonadal somatic cells to produce one reconstituted ovary. IVD culture was performed as described (Hikabe et al., 2016). rOvaries (5,000 PGCLCs and 75,000 gonadal somatic cells) were placed on Transwell-COL membranes soaked in αMEM-based IVDi medium: αMEM supplemented with 2% FCS, 150 μM ascorbic acid (Sigma), 1× Glutamax, 1× penicillin/streptomycin and 55 μM 2-mercaptoethanol (Life Technologies). At 4 days of culture, the culture medium was changed to StemPro-34-based IVDi medium: StemPro-34 SFM (Life Technologies) supplemented with 10% FCS, 150 μM ascorbic acid, 1× Glutamax, 1× penicillin/streptomycin, and 55 μM 2-mercaptoethanol. From 7 days to 10 days of culture, 500 nM ICI182780 was added to the StemPro-34-based IVDi medium. IVG culture was performed as described (Hikabe et al., 2016). Briefly, the isolated secondary follicles on the Transwell-COL membranes were soaked in IVG medium: αMEM supplemented with 5% FCS, 2% polyvinylpyrrolidone (Sigma), 150 μM ascorbic acid, 1× Glutamax, 1× penicillin/streptomycin, 100 μM 2-mercaptoethanol, 55 μg ml−1 sodium pyruvate (Nacalai Tesque), 0.1 IU ml−1 follicle-stimulating hormone (Follistim; MSD), 15 ng ml−1 BMP15 and 15 ng ml−1 GDF9 (R&D Systems). At 2 days of culture, BMP15 and GDF9 were withdrawn from the medium and then follicles were incubated in 0.1% TypeIV Collagenase (MP Biomedicals). After washing with αMEM supplemented with 5% FCS several times, the follicles were cultured in IVG-αMEM without BMP15 and GDF9. At 11 days of culture, cumulus-oocyte complexes grown on the membrane were picked up by a fine glass capillary. Cumulus–oocyte complexes were transferred to IVM medium: αMEM supplemented with 5% FCS, 25 μg ml−1 sodium pyruvate, 1× penicillin/streptomycin, 0.1 IU ml−1 follicular-stimulating hormone, 4 ng ml−1 EGF, and 1.2 IU ml−1 hCG (gonadotropin; ASKA). At 16 h of culture, swollen cumulus cells were stripped from the oocytes by treating with hyaluronidase (Sigma), and then MII oocytes were determined by 1st polar body extrusion. For direct induction of ngDIOs, 5x10^4 ESCs were transferred into a low-cell-binding U-bottom 96-well plate (NUNC) in S10 medium (StemPro-34 SFM (Life Technologies) supplemented with 10% FCS, 150 μM ascorbic acid, 1× Glutamax, 1× penicillin/streptomycin and 55 μM 2-mercaptoethanol) with 150 ng/ml SCF, 0.5 µM of Shield1 (Clontech), and 10 nM Y-27632 (Wako). For the extended culture, we transferred the aggregates onto Transwell-COL membranes using mouth pipet on day 2,  and cultured under normoxic conditions (20% O2 and 5% CO2 at 37 °C) for 2-4 weeks. For induction of GV and MII DIO, 5x10^4 ESCs were aggregated with 30,000-75,000 E12.5 female gonadal somatic cells in S10 medium with 0.5 µM of Shield1 and cultured for 2 days and transferred onto Transwell-COL membranes (Corning) soaked in S10 medium with 0.5 µM of Shield1 and cultured for 28 days. At 21-28 days of culture, individual follicles were manually isolated using sharpened tungsten needles. The Isolated follicles were further differentiated by IVG for 7-11 days and IVM culture and fertilized by IVF as previously described (Hayashi et al., 2017; Hikabe et al., 2016).

extract_protocol:
For direct induction of DIOs, 5x10^4 ESCs were transferred into a low-cell-binding U-bottom 96-well plate (NUNC) in S10 medium (StemPro-34 SFM (Life Technologies) supplemented with 10% FCS, 150 μM ascorbic acid, 1× Glutamax, 1× penicillin/streptomycin and 55 μM 2-mercaptoethanol) with 150 ng/ml SCF, 0.5 µM of Shield1 (Clontech), and 10 nM Y-27632 (Wako). For the extended culture, we transferred the aggregates onto Transwell-COL membranes using a mouth pipet on day 2, and cultured them under normoxic conditions (20% O2 and 5% CO2 at 37 °C) for 2-4 weeks. For induction of fgDIOs and MII DIOs, 5x10^4 ESCs were aggregated with 30,000-75,000 E12.5 female gonadal somatic cells in S10 medium with 0.5 µM of Shield1 and cultured for 2 days, then transferred onto Transwell-COL membranes (Corning) soaked in S10 medium with 0.5 µM of Shield1 and cultured for 28 days. At 21-28 days of culture, individual follicles were manually isolated using sharpened tungsten needles. The isolated follicles were further differentiated by IVG for 7-11 days and IVM culture and fertilized by IVF as previously described  (Hikabe et al., 2016, Nature, Hayashi et al., 2017., Nat. Protcol)
Ovaries (in vivo) and rOvaries (in vitro) at each developmental stage were treated with CTK solution (0.1 mg/ml collagenase IV, 0.25% trypsin, 20% KSR and 1 mM CaCl2 in PBS) for 30 minutes at 37°C, then transferred into Accutase (Nacalai) and incubated at 37°C for 15 minutes. The IVD day11 or day13 SC+oocytes were isolated by FACS-sorting. For FACS preparation, the cells were dissociated by gentle pipetting and filtered by using a 70 μm-pored nylon mesh to remove cell clumps. Collected samples were transferred into a 1.5 ml DNA LoBind tube (Eppendorf). Directional RNA-seq libraries were prepared as described previously (Hamazaki et al., 2015). Briefly, polyA-tailed RNA were extracted by Dynabeads mRNA Purification Kit.
Extracted polyA+RNA were converted to cDNA libraries by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: directly induced oocytes (DIOs)


title: Mouse day 2.5 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_2-5_3

source_name: Neural progenitor cells day 2.5

value: day 2.5


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A11_ad012

value: PIR

value: male


title: H1 Wnt3a-treated 3 hour

value: 3 hour


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A10_ad010


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A10_ad001


title: H1 Wnt3a-treated 0 hour

value: 0 hour


title: 061_DIOLs_d25_rep1


title: H1 FZD7-specific WNT mimetic-treated 48 hour

value: FZD7-specific WNT mimetic (5 nM)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A10_ad006


title: 059_DIOLs_d15_rep1


title: Mouse day 2.5 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_2-5_2

value: ES-derived neural progenitor cells

value: differentiation from neuromesodermal progenitors


title: 060_DIOLs_d15_rep2


title: GSC11_siSc

type: RNA

city: Pamplona

first: Marta

middle: Maria

last: Alonso Roldán

state: Navarra

address: CIMA building , Pio XII 55

department: Dpt of Pediatrics

country: Spain

institute: University Hospital of Navarra

description: Control

data_processing:
Quantitative miRNA expression data were normalized and quantified using ABI7700 sequence detection system.
ΔCt = (Ct(miRNA) - Average Ct (Housekeepings)), where housekeeping genes are hsa-SNORD48 (P17), hsa-SNORD47 (P18), hsa-SNORD44 (P19) and hsa-U6 (P20). Fold Change= 2^-ΔCt_GSC11_siSox2/2^-ΔCt_GSC11_siSc

source_name: Glioma stem-like cell GSC11

growth_protocol: GSC11 cell line were cultured and maintained in serum-free medium containing Dulbecco's modified Eagle's medium/nutrient mixture F12 (1:1, vol/vol) supplemented with 10% of Penicillin/Streptomycin, B27 10x, and 20 ng/ml of both EGF and FGF growth factors. GSC11 cells were grown at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA from scrambled and SOX2-knock down GSC-11 cells was reverse transcribed into cDNA using Taqman miRNA Reverse Transcription Kit and loaded into the miRNA array panel

treatment_protocol: GSC11 cells were transfected with a specific siRNA against SOX2 or a non-targeting control siRNA (si-Scramble) using Lipofectamine 2000. The cells were then cultured for 72 h after transfection and subjected to the miRNA array.

value: Glioma stem-like cell

tag: genotype/variation

value: non-targeting control siRNA (si-Scramble) expression


title: GSC11_siSOX2

description: Test

value: down-modulated SOX2 expression


title: Mouse day 2 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_2_3

source_name: Neural progenitor cells day 2

value: RA and SAG

value: day 2


title: H1 FZD7-specific WNT mimetic-treated 24 hour

value: H1/WA01/NIH stem cell registry number 0043

value: embryonic stem cell


title: Mouse day 3 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_3_3

value: day 3


title: H1 Wnt3a-treated 12 hour

value: Wnt3a protein (5 nM)

value: 12 hour


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A10_ad007

value: PIR


title: H1 FZD7-specific WNT mimetic-treated 12 hour


title: 058_DIOLs_d10_rep2

value: directly induced oocytes (DIOs)


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A10_ad002

value: male


title: Mouse day 2 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_2_2


title: H1 FZD7-specific WNT mimetic-treated 6 hour

value: 6 hour


title: Mouse day 2 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_2_1


title: 057_DIOLs_d10_rep1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A10_ad008


title: H1 FZD7-specific WNT mimetic-treated 3 hour

value: FZD7-specific WNT mimetic (5 nM)

value: 3 hour


title: Mouse day 1.5 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_1-5_3

source_name: Neural progenitor cells day 1.5

value: ES-derived neural progenitor cells

value: differentiation from neuromesodermal progenitors

value: day 1.5


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A1_ad006


title: 056_MII_DIOL_rep2


title: H1 FZD7-specific WNT mimetic-treated 0 hour

value: 0 hour


title: 055_MII_DIOL_rep1


title: Mouse day 2.5 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_2-5_1

value: RA and SAG

value: day 2.5


title: 054_IVD_d13_KO_Sohlh1_rep2

extract_protocol:
IVD culture was performed as described previously (Hikabe et al., 2016, Nature). rOvaries (5,000 PGCLCs and 75,000 gonadal somatic cells) were placed on Transwell-COL membranes soaked in αMEM-based IVDi medium: αMEM supplemented with 2% FCS, 150 μM ascorbic acid (Sigma), 1× Glutamax, 1× penicillin/streptomycin and 55 μM 2-mercaptoethanol (Life Technologies). At 4 days of culture, the culture medium was changed to StemPro-34-based IVDi medium: StemPro-34 SFM (Life Technologies) supplemented with 10% FCS, 150 μM ascorbic acid, 1× Glutamax, 1× penicillin/streptomycin, and 55 μM 2-mercaptoethanol. From 7 days to 10 days of culture, 500 nM ICI182780 was added to the StemPro-34-based IVDi medium.Ovaries (in vivo) and rOvaries (in vitro) at each developmental stage were treated with CTK solution (0.1 mg/ml collagenase IV, 0.25% trypsin, 20% KSR and 1 mM CaCl2 in PBS) for 30 minutes at 37°C, then transferred into Accutase (Nacalai Tesque) and incubated at 37°C for 15 minutes. The IVD day11 or day13 SC+oocytes were isolated by FACS-sorting. For FACS preparation, the cells were dissociated by gentle pipetting and filtered by using a 70 μm-pored nylon mesh to remove cell clumps.
Ovaries (in vivo) and rOvaries (in vitro) at each developmental stage were treated with CTK solution (0.1 mg/ml collagenase IV, 0.25% trypsin, 20% KSR and 1 mM CaCl2 in PBS) for 30 minutes at 37°C, then transferred into Accutase (Nacalai) and incubated at 37°C for 15 minutes. The IVD day11 or day13 SC+oocytes were isolated by FACS-sorting. For FACS preparation, the cells were dissociated by gentle pipetting and filtered by using a 70 μm-pored nylon mesh to remove cell clumps. Collected samples were transferred into a 1.5 ml DNA LoBind tube (Eppendorf). Directional RNA-seq libraries were prepared as described previously (Hamazaki et al., 2015). Briefly, polyA-tailed RNA were extracted by Dynabeads mRNA Purification Kit.
Extracted polyA+RNA were converted to cDNA libraries by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: Blimp1-Venus and Stella-CFP

value: in vitro oocytes


title: Mouse day 1.5 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_1-5_2


title: H1 CHIR98014-treated 48 hour

value: H1/WA01/NIH stem cell registry number 0043

value: embryonic stem cell

value: 48 hour


title: Mouse day 1.5 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_1-5_1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A1_ad008

value: PIR


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A1_ad001


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A1_ad004


title: H1 CHIR98014-treated 24 hour

value: 24 hour


title: 053_IVD_d13_KO_Sohlh1_rep1


title: Mouse day 1 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_1_2

source_name: Neural progenitor cells day 1

value: day 1


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A1_ad007

value: male


title: H1 CHIR98014-treated 12 hour

value: 12 hour


title: Mouse day 1 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_1_3


title: 052_DIOLs_d5_rep2

value: directly induced oocytes (DIOs)


title: Mouse day 1 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_1_1

value: ES-derived neural progenitor cells


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A1_ad002


title: H1 CHIR98014-treated 6 hour

value: 6 hour


title: 050_DIOLs.S_d14_rep2.gz


title: 051_DIOLs_d5_rep1


title: H1 CHIR98014-treated 3 hour

value: 3 hour


title: Mouse day 0.5 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_0-5_2

source_name: Neural progenitor cells day 0.5

value: differentiation from neuromesodermal progenitors

value: day 0.5


title: H1 CHIR98014-treated 0 hour

value: 0 hour


title: CEMBA181008_5G_1_CEMBA181008_5G_2_A1_ad010


title: 048_IVD_d11_KO_Figla_rep2

value: Blimp1-Venus and Stella-CFP


title: Mouse day 0.5 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_0-5_1

value: RA and SAG


title: 049_DIOLs.S_d14_rep1


title: Regenerative cardiac cells - mRNA_9dpa_rep2

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

description:
9 day postamputation (9 dpa)
mRNA_9dpa_rep2

data_processing:
All ChIP-Seq data sets were trimmed and aligned to zebrafish genome build danRer10 genome using Bowtie2. Reads from RNA-seq experiments were aligned to zebrafish genome build danRer10 using STAR
Duplicate reads were removed with SAM tools.
MACS2 was used to identify regions of ChIP-seq peaks. The mRNA expression of a gene was quantified by FPKM based on RefSeq gene annotation using Cuffdiff.
The top 10000 peaks were used for known motif enrichment analysis, which were performed using HOMER (v4.9).
Super enhancers (SEs) were identified using ROSE.
Genome_build: danRer10
Supplementary_files_format_and_content: Bigwig(bw) files were generated using deepTools

source_name: Regenerative cardiac cells

growth_protocol: Zebrafish TAB lines (hybrid from AB and Tubingen lines) were maintained under an ambient temperature of 27uC with a timercontrolled light period 14 h light and 10 h dark. All experiments were performed in accordance with Animal Care and Use Committee guidelines of Shanghai Ocean University.

extract_protocol:
For each sample, fixed tissues were lysed to prepare nuclear extracts. After chromatin shearing by sonication, lysates were incubated overnight at 4°C with protein A Dynabeads (Invitrogen) coupled with 3-5 μg of antibody specific for H3K9Ac or H3K9Me3.
ChIP-seq libraries were generated by ThruPLEX-FD Prep Kit (Product No.R40012, Rubicon, Ann Arbor, USA), and sequenced by Illumina Hiseq 2500 using the paired-end module and with 150 bp reads on each end. the mRNA-seq library preparation from 1 μg of total RNA was performed with TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's instructions, and 2 x 150 paired-end sequencing performed on Illumina Hiseq 2500.

treatment_protocol: After resection of the ventricular apex, the heart tissues were dissected at the day indicated (0d, 6d, 9d).

value: Heart

value: Regenerative cardiac cells


title: Regenerative cardiac cells - mRNA_9dpa_rep1

description:
9 day postamputation (9 dpa)
mRNA_9dpa_rep1


title: 047_IVD_d11_KO_Figla_rep1

value: in vitro oocytes


title: Mouse day 0 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_0_3

source_name: Neural progenitor cells day 0

value: control

value: day 0


title: Regenerative cardiac cells - mRNA_6dpa_rep2

description:
6 day postamputation (6 dpa)
mRNA_6dpa_rep2


title: 046_DIOLs.S_day7_rep2


title: 045_DIOLs.S_day7_rep1


title: Regenerative cardiac cells - mRNA_6dpa_rep1

description:
6 day postamputation (6 dpa)
mRNA_6dpa_rep1


title: 044_DIOLs.S_day5_rep2


title: Regenerative cardiac cells - mRNA_0dpa_rep2

description:
0 day postamputation (0 dpa)
mRNA_0dpa_rep2


title: Regenerative cardiac cells - mRNA_0dpa_rep1

description:
0 day postamputation (0 dpa)
mRNA_0dpa_rep1


title: Mouse day 0 biorep 1

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_0_1


title: Regenerative cardiac cells - H3K9me3_9dpa

description:
9 day postamputation (9 dpa)
H3K9me3_9dpa

tag: chip antibody

value: H3K9me3 (CST, D4W1U)


title: 043_DIOLs.S_day5_rep1


title: 042_DIOLs.S_day3_rep2


title: Root-tip protoplast cells, WT, scRNA-seq, replicate 3

city: Zwijnaarde

first: Kevin

last: Verstaen

address: Technologiepark-Zwijnaarde 71

department: VIB Single Cell Core

country: Belgium

institute: VIB

description: Root tips of 6-d-old-seedlings Arabidopsis thailiana Col-0, replicate 1

data_processing:
Demultiplexing; Cell Ranger mkfastq; version 2.0.2
Read alignment + counting; Cell Ranger count; version 2.0.2
Genome_build: TAIR 10; Ensembl Plants, release 40
Supplementary_files_format_and_content: h5 file containing filtered count matrix  (output Cell Ranger count)

organism: Arabidopsis thaliana

source_name: root tip

growth_protocol: All seeds were surface sterilized, sown on solid 1⁄2 MS plates without sucrose, and stratified for 24h at 4°C two days before they were grown at 22°C in continuous light conditions.

extract_protocol:
Root tips of 6-d-old seedlings were cut and incubated in protoplasting Solution B [1.5% (wt/vol) cellulysin and 0.1% (wt/vol) pectolyase in Solution A (600 mM mannitol, 2 mMMgCl2, 0.1% [wt/vol] BSA, 2 mMCaCl2, 2 mMMes, 10mMKCl, pH 5.5)] for approximately 1 h at room temperature. Conditions were optimized to ensure the inner vascular cell types were dissociated well (even if this was to some extent at the expense of the outer cell files) by microscopic analysis of the protoplasting at regular intervals. Cells were filtered through a 70 μm cell strainer and spun down at 200 × g for 6 min; resuspended in Solution A, filtered through a 40 μm cell strainer and stained for live/dead using 4′,6- diamidino-2-phenylindole (DAPI) at 14 μM final concentration. Cells were sorted on a BD Aria II, and protoplasts not containing the DAPI signal were selected for further analysis.
Sorted cells were centrifuged at 4°C at 400g and resuspended in PBS+0,04%BSA to yield an estimated concentration of 1000 cells/μl. Cellular suspensions were loaded on a GemCode Single Cell 3’ Gel Bead and Library Kit (V2 chemistry, 10X Genomics) according to the manufacturer’s instructions.

tag: ecotype

value: wild type

value: root tip

value: protoplast cells


title: Mouse day 0.5 biorep 3

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_0-5_3

value: ES-derived neural progenitor cells


title: 041_DIOLs.S_day3_rep1

value: directly induced oocytes (DIOs)


title: Regenerative cardiac cells - H3K9me3_6dpa

description:
6 day postamputation (6 dpa)
H3K9me3_6dpa

tag: tissue


title: Regenerative cardiac cells - H3K9me3_0dpa

description:
0 day postamputation (0 dpa)
H3K9me3_0dpa


title: Root-tip protoplast cells, WT, scRNA-seq, replicate 1


title: 040_DIOLs.S_day1_rep2


title: 039_DIOLs.S_day1_rep1


title: Mouse day 0 biorep 2

description:
expression_matrix.mouse.abundance.tsv
expression_matrix.mouse.counts.tsv
m_0_2


title: Injury_Myf6KO_RNASeq_Rep2

city: Ottawa

first: Theodore

last: Perkins

state: Ontario

address: 501 Smyth Rd.

department: Regenerative Medicine Program

institute: Ottawa Hospital Research Institute

description:
293R
Injury_WT_vs_Myf6KO_DiffExpr.tsv

data_processing:
ChIP-seq and control reads mapped to mm10 genome using bowtie v 1.1.0 with parameters: -l 32 --strata --best -y --chunkmbs 3072 -a -n 2 -m 1 -p 4
Fragment length for Myf6 was estimated using the MaSC programming (with result 127)
Peaks were called comparing the Myf6 reads against the control using MACS version 2.1.0.20140616 with parameters --gsize=mm --keep-dup=1 --qval=0.05 --nomodel --extsize=127
RNA-seq reads were mapped to mm10 gene definitions GENCODE M12 (GRCm38.p5) using hisat 2.1.0 with parameters -p 1 --dta
Mapped RNA-seq sam file was sorted, indexed and converted to BAM using samtools
Read counts per gene were obtained using featureCounts with mm10 gene definitions GENCODE M12 (GRCm38.p5)
Differential expression was assessed using DESeq2 (WT vs KO, for both uninjured and injured conditions) using parameters
Genome_build: mm10
Supplementary_files_format_and_content: Myf6 peak calls and two differential expression analyses

source_name: Hind limb skeletal muscle RNA

extract_protocol:
RNA was extracted by Trizol method
RNA-Seq libraries were constructed from total RNA with the TruSeq RNA v2 kit (Illumina).

value: Hind limb skeletal muscle

value: Myf6 KO

tag: protocol

value: Injury


title: Injury_Myf6KO_RNASeq_Rep3

description:
294R
Injury_WT_vs_Myf6KO_DiffExpr.tsv


title: olfactory bulb_adult mice_DN_rep3

city: Zhengzhou

first: Ao

last: Shen

address: No. 1 Jianshe East Road

institute: First Affiliated Hospital of Zhengzhou University

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: Olfactory bulb

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: All mice were raised in Pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Mice were deeply anesthetized with pentobarbital sodium and then olfactory bulbs were rapidly dissected from the fresh brains.

value: 8 weeks old

value: male

value: Olfactory bulb

tag: disease state

value: DN (diabetic nephropathy; type II diabetic kidney disease)


title: Regenerative cardiac cells - H3K9ac_0dpa

description:
0 day postamputation (0 dpa)
H3K9ac_0dpa

value: Heart

value: H3K9ac (Abcam, ab4441)


title: Root-tip protoplast cells, WT, scRNA-seq, replicate 2

tag: cell type


title: Tet/Tet neurons

city: Hyderabad

first: Kommu

middle: Naga

last: Mohan

state: Telangana

address: shameerpet, Jawaharnagar

department: Biological Sciences

country: India

institute: Birla Institute of Technology, Pilan- Hyderabad Campus

data_processing:
Sequence reads from bisulfite-treated Classic RRBS libraries were identified using standard Illumina base calling software and then raw FASTQ files were adapter, filled-in nucleotides and quality trimmed using TrimGalore 0.6.4.
FastQC 0.11.8 was used to assess the effect of trimming and overall quality distributions of the data
Alignment to the mm10 reference genome was performed using Bismark 0.19.0.
Methylated and unmethylated read totals for each CpG site were called using MethylDackel 0.3.0. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Fisher’s exact test was performed for each CpG site that has at least five reads coverage, 10% difference in methylation value between groups and a p-value (unadjusted) of < 0.05. in order to identify significantly differentially methylated cytosines.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files, UCSC browser tracks

source_name: Differentiated neurons derived from ESCs

growth_protocol: R1 and  Tet/Tet ESCs were cultured in ES media composed of Knock out DMEM F12, supplemented with FBS, NEAA, Glutamax, β-Mercaptoethanol, Penicillin /Streptomycin and LIF. Tet/Tet cells were grown in presence of Puromycin (1ug/ml) and Neomycin (150ug/ml). On reaching confluency (i.e 1 × 106 cells), 1/6th of the cells were seeded for embryoid-body(EB) formation. The culture media is ES medium without LIF. After 2 days, these EBs are induced to form neurons for 10-15 days in Ndiff227 media.

extract_protocol:
Cell pellets from trypsinized R1 and Tet/Tet ESCs were resuspended in 1X PBS and centrifuged at 1,000 rpm for five min at room temperature in a swing-out rotor. The pellets were washed once again with 1X PBS, resuspended in a lysis buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA, 50 mM NaCl, 0.5% SDS) and treated with Proteinase K (50µg/ml) at 50℃ for two hours. The cell lysates were extracted with phenol: chloroform (1:1 ratio), centrifuged at 12,000 rpm for 10 min at room temperature and the supernatants were extracted with chloroform and centrifuged in the same manner. DNAs in the supernatants were precipitated using sodium acetate (final concentration = 0.3 M, pH 5.2) and an equal volume of isopropanol for five minutes by gentle inversions. The precipitated DNAs were spooled using sterile glass rods, washed with 70% ethanol, dried at room temperature for 15-30 minutes and dissolved in 1X TE buffer (10mM Tris-Cl, 1mM EDTA, pH 8.0). In case of neurons, confluent dishes of neurons were scraped with lysis buffer(RLT buffer with BME) and further QIAGEN All Prep Kit(Cat No. 80204) procedure was followed for the DNA extraction. The extracted DNAs were then quantified using NanoDrop.
200 ng of starting input genomic DNA was digested with 30 units of MspI (NEB) and then purified with Zymo Research DNA Clean & Concentrator™-5 (Cat#: D4003). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor-ligated fragments ≥50 bp in size were recovered using the DNA Clean & Concentrator™-5 (Cat#: D4003). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (Cat#: D5030). Preparative-scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator™-5 (Cat#: D4003) for sequencing on an Illumina HiSeq.

value: Dnmt1 Tet/Tet

value: Tet/Tet


title: R1 neurons

value: Differentiated neurons derived from ESCs

value: Wild type


title: Injury_RNASeq_Rep2

description:
511R
Injury_WT_vs_Myf6KO_DiffExpr.tsv

value: WT


title: olfactory bulb_adult mice_DN_rep1


title: Injury_RNASeq_Rep3

description:
512R
Injury_WT_vs_Myf6KO_DiffExpr.tsv


title: Tet/Tet ESC

source_name: ESCs

value: ESCs


title: MT_HF3

city: Suita

first: Hajime

last: Watanabe

address: Yamadaoka 2-1

institute: Osaka University

data_processing:
Processing of raw reads was done by Novogene as part of the service. According to their QC, all samples had quality score Q30 >90%. Delivered data were clean reads of 150 bp in lengh (trimmed of adapters), roughly 20,000,000 paired reads (10,000,000 pairs) per sample.
Mapping, expression profile comparison, clustering and functional test were all performed using the CLC Genomics Workbench software.
Genome_build: For mapping, we used the 2010 D. magna genome assembly v2.4 (GenBank accession LRGB00000000) together with the 2014 D. magna evg7f9b gene set as reference (http://arthropods.eugenes.org/EvidentialGene/daphnia/daphnia_magna/Genes/earlyaccess/). This gene set contains 29121 gene loci together with 17228 “culled” transcripts which may as well contain some valid loci. Among these genes, some are split-mapped, meaning that they consist of two fragments that mapped to distant positions in the genome assembly. Because these split-mapped genes disturb the visualization of gene distribution on the genome by the CLC Genomics Workbench software, we edited the gene set and treated the split fragments as two different genes. As a result, there are total 47,109 genes in the full set of our analysis. Also, although the original ID of each gene is in the format [Dapma7bEVm][6 digits], we added 7 characters indicating the scaffold/contig the gene is mapped to and 7 characters indicating its split attribute to make new unique IDs as can be seen in the processed data files.
Supplementary_files_format_and_content: Expression_data.xlsx is a microsoft excel spreadsheet containing various information of all 47,109 genes. This sheet includes:1) Feature and Gene IDs, 2) annotation (gene name, GO terms) 2) expression values (total gene reads), normalized expression values (RPM) of each gene across all 9 samples
Supplementary_files_format_and_content: Differential_expression_genes_data.xlsx is a microsoft excel spreadsheet containing 2 sheets listed 220 DEGs of WT and MT under nutrient rich (HF) and 2770 DEGs of WT and MT under starved (LF) conditions. DEGs were filtered based on false discovery rate (FDR) p-value cutoff FDR p < 0.05 and fold change cutoff FC ≥ |1.5|. These sheets includes: 1) Gene ID and annotations (Gene name and GO biological process), 2) Fold change and FDR p-value.

organism: Daphnia magna

source_name: whole body

growth_protocol: For maintenance of the NIES (wild type) strain, 80 individuals were cultured in the 5 L ADaM (artificial daphnia medium) and daily fed 0.16 ml of 7x10^9 cells/ml Chlorella (Chlorella vulgaris) algae. Mutant line was maintained similarly by culturing 40 individuals in 2.5 L ADaM and daily feeding with 0.08 ml of 7x10^9 cells/ml Chlorella algae. These cultures were performed at 22-24◦C and under a light/dark photoperiod of 16/8 h.

extract_protocol:
For RNA-seq sampling, 5 daphniids were cultured individually in each condition until producing 2nd clutch (day 12). Eggs were removed before homogenization for RNA extraction by using Sepasol-RNAI solution (Nacalai Tesque, Kyoto, Japan) and purified by phenol-chloroform. Each treatment was repeated 3 times for triplicates of sampling. According to QC report from Novogene service, all samples passed agarose gel electrophoresis test and Agilent 2100 analysis test.
All libraries were constructed following Novogene's protocol (jp.novogene.com). According to their service description, mRNA was first enriched using oligo(dT) beads, fragmented, followed by cDNA synthesis using random hexamers. After terminal repair, A overhang and sequencing adaptor were added. Finally, cDNA library were completed through size selection and PCR enrichment and then sequenced by Illumina sequencer.

treatment_protocol: Prior to culturing under starved condition, in order to control for maternal effects, 40 Daphnia of each line were cultured in 2.5 liters ADaM medium and daily fed with 1.5 ´109 cells ml-1 Chlorella algae for at least 3 generations. Neonates from the third clutch were randomly assigned, transferred individually to a 50 ml conical tube containing 40 ml ADaM medium, and subjected to nutrient rich or starved treatments. Under the nutrient rich condition, 5.12´107 cells were given to each daphniid daily. For starvation, daphniids were fed with the 8-fold lower amounts of the algae. During culture, the medium was changed every day in order to avoid carbon (detrital) accumulation that could differentially affect resource availability

value: DNMT3.1 mutant

value: female

tag: condition

value: nutrient rich

value: post natal day 12, releasing 2nd clutch


title: R1 ESC


title: MT_HF1

tag: Sex


title: MT_HF2

tag: age


title: Injury_RNASeq_Rep1

description:
510R
Injury_WT_vs_Myf6KO_DiffExpr.tsv

value: Hind limb skeletal muscle

value: Injury


title: olfactory bulb_adult mice_NG_rep2

value: 8 weeks old

value: male

value: NG (DM; type II diabetes mellitus)


title: Regenerative cardiac cells - H3K9ac_9dpa

description:
9 day postamputation (9 dpa)
H3K9ac_9dpa

value: Heart

value: Regenerative cardiac cells


title: Myf6KO_RNASeq_Rep3

description:
294L
WT_vs_Myf6KO_DiffExpr.tsv

value: Myf6 KO

value: without injury


title: fgDIOLs_rep1

data_processing:
Reads were mapped with BMap
The alignments exported from BMap were summarized into a binary file in graph format using in-house program MPTC.
The methylation levels and coverage were exported from the file in graph format using in-hose program MethExport
Genome_build: Mus musculus (mm10) and Enterobacteria phage lambda
Supplementary_files_format_and_content: bedGraph

source_name: fully-grown DIOLs

growth_protocol: For induction of fgDIOLs, 5x10^4 ESCs were aggregated with 30,000-75,000 E12.5 female gonadal somatic cells in S10 medium with 0.5 µM of Shield1 and cultured for 2 days and transferred onto Transwell-COL membranes (Corning) soaked in S10 medium with 0.5 µM of Shield1 and cultured for 28 days. At 21-28 days of culture, individual follicles were manually isolated using sharpened tungsten needles. The Isolated follicles were further differentiated by IVG for 7-11 days.

extract_protocol:
Genomic DNA was purified with QIAamp DNA Micro Kit
Genomic DNA was spiked with unmethylated lambda DNA (Promega), treated with Methyl Easy Gold Kit from Zymo Research, and adaptor tagged with tPBAT protocol described in Miura F et al (2019), NAR, 47, e85

tag: strain

value: Fully-grown directly induced oocyte-like cells


title: MT_LF3

value: starved


title: Myf6KO_RNASeq_Rep2

description:
293L
WT_vs_Myf6KO_DiffExpr.tsv


title: Regenerative cardiac cells - H3K9ac_6dpa

description:
6 day postamputation (6 dpa)
H3K9ac_6dpa

value: H3K9ac (Abcam, ab4441)


title: fgDIOLs_rep2


title: olfactory bulb_adult mice_DN_rep2

value: Olfactory bulb

value: DN (diabetic nephropathy; type II diabetic kidney disease)


title: ngDIOLs_day5_rep2

source_name: non-growing DIOLs

growth_protocol: For direct induction of non-growing DIOLs, 5x10^4 ESCs were transferred into a low-cell-binding U-bottom 96-well plate (NUNC) in S10 medium (StemPro-34 SFM (Life Technologies) supplemented with 10% FCS, 150 μM ascorbic acid, 1× Glutamax, 1× penicillin/streptomycin and 55 μM 2-mercaptoethanol), 0.5 µM of Shield1 (Clontech), and 10 nM Y-27632 (Wako).

value: Non-growing directly induced oocyte-like cells


title: MT_LF1

value: DNMT3.1 mutant

value: female


title: Injury_Myf6KO_RNASeq_Rep1

description:
292R
Injury_WT_vs_Myf6KO_DiffExpr.tsv

value: Hind limb skeletal muscle


title: olfactory bulb_adult mice_NG_rep3


title: ngDIOLs_day5_rep1


title: WT_RNASeq_Rep3

description:
512L
WT_vs_Myf6KO_DiffExpr.tsv

value: WT


title: WT_LF3

value: NIES (wild type)

value: post natal day 12, releasing 2nd clutch


title: WT_LF2


title: WT_RNASeq_Rep1

description:
510L
WT_vs_Myf6KO_DiffExpr.tsv


title: olfactory bulb_adult mice_NG_rep1

value: 8 weeks old

value: male

value: NG (DM; type II diabetes mellitus)


title: PPT8-ESCs_rep1

growth_protocol: PPT8-ESCs were maintained in 2i plus LIF medium (Ying et al., 2008, Nature) without Shield1 addition.

value: Embryonic stem cells


title: WT_LF1


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H9_ad006

status: Public on Sep 17 2020

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

value: DG


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H9_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H9_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H9_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H8_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H8_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H8_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H9_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H7_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H8_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H8_ad007


title: MT_LF2


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H7_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H8_ad002


title: Myf6KO_RNASeq_Rep1

description:
292L
WT_vs_Myf6KO_DiffExpr.tsv

value: Myf6 KO

value: without injury


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H7_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H7_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H7_ad002


title: WT_RNASeq_Rep2

description:
511L
WT_vs_Myf6KO_DiffExpr.tsv


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H6_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H6_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H6_ad004


title: PPT8-ESCs_rep2


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H9_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H6_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H5_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H5_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H5_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H4_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H4_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H4_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H4_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H5_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H4_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H4_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H3_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H3_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H3_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H3_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H3_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H4_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H3_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H6_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H2_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H2_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H2_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H5_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H12_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H2_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H11_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H12_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H12_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H11_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H10_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H11_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H10_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H11_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H3_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H10_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H10_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H1_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H10_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H10_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H1_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H1_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H2_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G9_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G9_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H11_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H1_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G9_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G9_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H11_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G9_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G9_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G9_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H11_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G8_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G8_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H6_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G8_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G8_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_H10_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G8_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G7_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G8_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G7_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G7_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G7_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G6_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G7_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G7_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G7_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G6_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G6_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G6_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G5_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G9_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G6_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G5_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G5_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G5_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G5_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G5_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G5_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G4_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G4_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G5_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G4_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G4_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G4_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G4_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G3_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G4_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G3_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G3_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G3_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G4_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G3_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G3_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G2_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G2_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G2_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G2_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G2_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G12_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G2_ad001


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G11_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G2_ad002


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G11_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G11_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G11_ad004


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G11_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G11_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G10_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G10_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G10_ad008


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G10_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G1_ad012


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G1_ad007


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G1_ad010


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G10_ad006


title: CEMBA190627_10F_3_CEMBA190627_10F_4_G10_ad004


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_H6_ad006


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_H2_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H5_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H2_ad006


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_H11_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H3_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H11_ad007


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_H10_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H11_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H10_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H10_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H11_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H10_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H10_ad012


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_H1_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H1_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H1_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H1_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H1_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H1_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H1_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H2_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H11_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H1_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G9_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_H11_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G9_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G9_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G9_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G9_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G9_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G9_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G8_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G8_ad008


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_G7_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G6_ad010


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_G6_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G6_ad004


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G5_ad012


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_G5_ad007


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_G7_ad007


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_G5_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G7_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G4_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G4_ad012


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_G4_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G3_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G3_ad007


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_G6_ad006


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_G2_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G11_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G11_ad008


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G2_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G4_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G11_ad006


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title: CEMBA190627_10F_1_CEMBA190627_10F_2_G10_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G1_ad010


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G3_ad002


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G1_ad012


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G10_ad001


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G1_ad007


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G1_ad006


title: CEMBA190627_10F_1_CEMBA190627_10F_2_G1_ad002