title: 3wk_FG2

data_processing:
Base calling and quality scoring were performed in Illumina Novaseq 6000
The resulting high-quality reads were aligned to the mouse reference genome mm10 using bowtie2.
Duplicate reads were discarded with Picard (2.17.8)
Reads mapped to mitochondrial DNA together with low mapping quality reads were excluded from further analysis.
Peaks were called using MACS2 (v2.2.7.1), peaks from multiple samples were merged as concensus peak. pyDNase was used to retrieve cleavage event falling in the consensus peak. Differential accessibility analysis on the counts was performed using edgeR (v3.24.3)
Assembly: mm10

extract_protocol:
Cells were collected in cold PBS and cell membranes were disrupted in cold lysis buffer (10 mM Tris–HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). The nuclei were pelleted and resuspended in Tn5 enzyme and transposase buffer (Illumina Nextera® DNA library preparation kit, FC-121-1030).
The Nextera libraries were amplified using the Nextera® PCR master mix and KAPA biosystems HiFi hotstart readymix successively. AMPure XP beads (Beckman Coulter) were used to purify the transposed DNA and the amplified PCR products. All libraries were sequenced on a 100 cycle paired-end run on an Illumina NOVAseq instrument. The resulting ATACseq libraries were sequenced on Illumina NovaSeq 6000 at CMG of Indiana University School of Medicine and paired-end 50 bp reads were generated.

tag: cell line


title: SUDHL4_BTG1wt, repl2

status: Public on Jan 24 2023

type: SRA

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

country: USA

institute: Weill Cornell Medical College

library_source: transcriptomic

data_processing:
Genome_build: hg19
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
RNA-seq TPM were obtained using Rsubread and RefSeq gene annotation
RIP-seq reads were aligned to merged mm10-ERCC92 using STAR with default parameters
RIP-seq read counts were obtained using Rsubread and RefSeq gene annotation.  ERCC-normalized read counts were obtained using Rsubread and RefSeq gene annotation.  Read counts were normalized using RUVg method from RUVSeq package.  TPM were calculated using ERCC-normalized read counts.
Supplementary_files_format_and_content: Transcripts per million (TPM)

molecule: total RNA

organism: Homo sapiens

source_name: SUDHL4 cell line transfected with BTG1WT allele

extract_protocol:
Illumina TruSeq stranded mRNA kit
Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

tag: cell type

value: SUDHL4 cells

tag: transfection

value: BTG1WT allele


title: SUDHL4_V5-BTG1wt_RIPseq_IP, repl4

source_name: SUDHL4 cell line transfected with V5-BTG1WT allele

value: V5-BTG1WT allele

tag: rip antibody

value: RIPantibody


title: CD11b-positive B cells in the BM-2

city: Bunkyo-ku

first: Masashi

last: Kanayama

state: Tokyo

address: 1-5-45 Yushima

department: Department of Biodefense Research

country: Japan

institute: Medical Research Laboratory, Institute of Science Tokyo

data_processing:
Obtained raw reads were trimmed and quality-filtered using Trim Galore! (version 0.4.4) (Babraham Institute, UK), Trimmomatic (version 0.36) and cutadapt (version 1.16) software.
Trimmed reads were then mapped to the mouse GRCm38 genome using STAR (version 2.7.2b).
Reads on annotated genes were counted using featureCounts (version 1.6.1)
FPKM values were calculated from mapped reads by normalizing to total counts and transcripts.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0)
The list of differentially expressed genes detected by DESeq2 (basemean > 5 and fold-change < 0.25, or basemean > 5 and fold-change > 4) were used for GO enrichment analysis by the clusterProfiler package.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include sizeFactor-normalized count for each Sample (p<0.05)

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Total RNA was harvested using QIAGEN RNeasy micro kit.
Double-stranded cDNA libraries (RNA-seq libraries) were prepared using a SMART-seq HT kit (Clontech, USA) using a DNBSEQ MGIEasy Universal Library Conversion kit (MGI Tech, China) according to the manufacturers’ instructions.

tag: tissue

value: Bone marrow

value: Primary cell

value: B cell

tag: genotype

value: Wild type

tag: treatment

value: LPS injection


title: CD11b-positive B cells in the BM-3


title: SUDHL4_BTG1wt, repl3


title: murineGCB_cre_GFPMYCnegative, repl5

data_processing:
Genome_build: mm10
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
RNA-seq TPM were obtained using Rsubread and RefSeq gene annotation
RIP-seq reads were aligned to merged mm10-ERCC92 using STAR with default parameters
RIP-seq read counts were obtained using Rsubread and RefSeq gene annotation.  ERCC-normalized read counts were obtained using Rsubread and RefSeq gene annotation.  Read counts were normalized using RUVg method from RUVSeq package.  TPM were calculated using ERCC-normalized read counts.
Supplementary_files_format_and_content: Transcripts per million (TPM)

source_name: Germinal center B cells transfected with CD19-Cre control + GFP-Myc without expression of GFP-Myc

extract_protocol:
Takara SMART-Seq v4 Ultra Low Input RNA Kit
Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

value: Germinal center B cells

tag: sorting strategy

value: Live B220+ FAS+ GL7+ GFP-Myc- cells using BD Influx Cell Sorter


title: SUDHL4_BTG1q36h, repl3

source_name: SUDHL4 cell line transfected with BTG1Q36H allele

value: BTG1Q36H allele


title: murineGCB_Btg1q36h_het, repl3

source_name: Germinal center B cells transfected with heterozygous Btg1Q36H allele

value: heterozygous Btg1Q36H allele

value: Live B220+ FAS+ GL7+ cells using BD Influx Cell Sorter


title: MenSC-EVs_rep1

type: RNA

city: Xinxiang

first: JIE

last: LIAN

state: Henan

address: Jinsui Road

department: Henan Joint International Research Laboratory of Stem Cell Medicine

country: China

institute: Xinxiang Medical University

description:
MNP1
miRNAs expression of EVs isolated from conditioned medium of MenSCs culture over 48 hr.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: menstrual blood-derived stem cells, 48 hr, EVs, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: EVs were isolated from the cell-free conditioned medium of MenSCs culture over 48 hr by differential ultracentrifugation.

extract_protocol: RNA was prepared using the miRNeasy Serum/Plasma Kit (#217184, Qiagen) following the manufacturer's recommendations. RNA was quantified by Nanodrop 2000 spectrophotometer and quality was monitored with the Agilent Bioanalyzer 2100 (Agilent Technologies, USA).

treatment_protocol: Primary MenSCs were isolated from freshly drawn menstrual blood from healthy young female volunteers and cultured in DMEM medium supplemented with 10% FBS at 37℃ in a humidified 5% CO2 incubator. When MenSCs were cultured to 70-80% confluency, they were ready for further use. EVs were obtained from the cell-free conditioned medium of MenSCs (P3) culture over 48 h in DMEM with 10% EV-depleted FBS by differential ultracentrifugation.

value: EVs from conditioned medium of MenSCs culture

tag: Sex

value: female

tag: diagnosis

value: healthy


title: SUDHL4_V5-BTG1q36h_RIPseq_IP, repl1

source_name: SUDHL4 cell line transfected with V5-BTG1Q36H allele

value: SUDHL4 cells

value: V5-BTG1Q36H allele


title: murineGCB_cre, repl3

source_name: Germinal center B cells transfected with CD19-Cre control

value: CD19-Cre control


title: SUDHL4_V5-BTG1q36h_RIPseq_input, repl2


title: 3wk_veh3

city: Indianapolis

first: Kenneth

last: White

state: IN

address: 635 Barnhill Drive

institute: Indiana University School of Medicine

library_source: genomic

molecule: genomic DNA

source_name: MPC2 cells

growth_protocol: Murine progenitor cells clone 2 (MPC2), a conditionally immortalized mesenchymal stem cell line, were cultured in MEM-alpha (Invitrogen, Thermo-Fisher Scientific) supplemented with 10% fetal bovine serum (FBS; Hyclone), 25 mM L-glutamine, and 25 mM penicillin-streptomycin (Sigma-Aldrich, St. Louis, MO, USA) at 33°C and 5% CO2 to proliferate. Cells were plated at a density of 1.0x10^5 cells per well in 6- or 12-well plates and incubated overnight before being transferred to a 37°C incubator for osteogenic differentiation and cultured in maintenance media supplemented with mineralization conditions of 4 mM beta-glycerophosphate and 50 ug/mL ascorbic acid. Cells were differentiated for 3 weeks with osteogenic media changes every 2-3 days.

treatment_protocol: Both cell types were treated for 48 hours with either vehicle (DMSO) or 50 uM of the HIF-PHI FG-4592 (Roxadustat)

value: Osteocyte

value: vehicle (DMSO)


title: murineGCB_Btg1q36h_het, repl2


title: undiff FG1

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.2a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v1.6.2) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 2 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.24.3).
Assembly: mm10
Supplementary files format and content: raw count

extract_protocol:
Total RNA was extracted (with a DNase step) using the same methods as described in “RNA preparation” section of methods. Total RNA was evaluated for its quantity and quality using Agilent Bioanalyzer 2100. For RNA quality, a RIN number of 7 or higher is desired. The RIN number for all of the samples was 10. 100 ng of total RNA was used.
cDNA library preparation includes mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporate). Each resulting indexed library was quantified and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity. The pooled libraries were denatured and neutralized before loading to NovaSeq 6000 sequencer at 300pM final concentration for 100b paired-end sequencing (Illumina, Inc.). Approximately 30-40M reads per library were generated. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

value: MSC

value: 50 uM FG-4592 (Roxadustat)


title: CD11b-positive B cells in the BM-1

value: Bone marrow

value: Primary cell

value: B cell

value: Wild type


title: SUDHL4_V5-BTG1wt_RIPseq_IP, repl3

value: V5-BTG1WT allele

value: RIPantibody


title: undiff veh1


title: 3wk_veh2


title: murineGCB_cre, repl4

value: Germinal center B cells

value: Live B220+ FAS+ GL7+ cells using BD Influx Cell Sorter


title: murineGCB_cre, repl2


title: 3wk FG3


title: SUDHL4_V5-BTG1q36h_RIPseq_input, repl1


title: SUDHL4_V5-BTG1q36h_RIPseq_IP, repl2


title: MenSC-EVs_rep2

description:
MNP6
miRNAs expression of EVs isolated from conditioned medium of MenSCs culture over 48 hr.

source_name: menstrual blood-derived stem cells, 48 hr, EVs, replicate 2

value: EVs from conditioned medium of MenSCs culture

value: female


title: CD11b-negative B cells in the BM-2

value: LPS injection


title: undiff_FG2


title: Naïve peritoneal macrophage-3

source_name: Peritoneal cavity

value: Peritoneal cavity

value: Macrophage

value: Naive (No treatment)


title: 3wk_FG1

value: Osteocyte


title: SUDHL4_V5-BTG1wt_RIPseq_IP, repl1

value: SUDHL4 cells


title: SUDHL4_V5-BTG1wt_RIPseq_input, repl4


title: SUDHL4_V5-BTG1wt_RIPseq_IP, repl2


title: undiff_veh2

value: MSC

value: vehicle (DMSO)


title: SUDHL4_V5-BTG1wt_RIPseq_input, repl3


title: CD11b-negative B cells in the BM-1

value: Bone marrow

value: Primary cell


title: LuCaP81 castrated Enzalutamide

status: Public on Jan 23 2023

first: Michael

middle: M

last: Shen

address: 1130 St. Nicholas Avenue

institute: Columbia University Irving Medical Center

data_processing:
RNA-seq pipeline description: Columbia Genome Center standard pipeline
Libraries were sequenced using Illumina HiSeq 2000 at Columbia Genome Center. We multiplexed samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.
We used RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming. We mapped the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks (version 2.0.2) with default settings.
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: counts

source_name: Prostate PDX

growth_protocol: Xenograft tissue fragments from LuCaP xenograft lines were grafted subcutaneously in male CIEA NOG mice 8-10 weeks of age (Taconic).

extract_protocol:
100mg of tissue was homogenized in TRIzol Reagent (Invitrogen) using a Polytron PT1300D homogenizer at speed 15. RNA extraction was performed using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Invitrogen).
Libraries were prepared by the Columbia Genome Center. Poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). Libraries were prepared using the Illumina TruSeq RNA prep kit.

treatment_protocol: When tumors reached 7-8mm in diameter, mice were treated with one of 13 perturbagens as previously described (Aytes et al., 2014) or PBS vehicle daily for 5 consecutive days. In parallel, a separate set of host animals with tumors 7-8mm in diameter were castrated.  Starting at 3 days after castration, animals were treated with one of 13 perturbagens or PBS vehicle daily for 5 consecutive days.

tag: xenograft line

value: LuCaP 81

tag: host

value: Castrated

value: Enzalutamide


title: LuCaP81 castrated BAY-11-7082


title: Naïve peritoneal macrophage-1

value: Wild type


title: LuCaP81 castrated LY294002


title: undiff_FG3

value: 50 uM FG-4592 (Roxadustat)


title: CD11b-negative B cells in the BM-3

value: B cell


title: LuCaP81 castrated PD325901


title: LuCaP81 castrated Dasatinib

value: Dasatinib


title: LuCaP81 castrated PBS (vehicle)

value: PBS (vehicle)


title: undiff_FG1


title: undiff_veh3


title: LuCaP81 castrated MK2206


title: LuCaP81 PD325901

value: Intact


title: LuCaP81 castrated Testosterone

value: Testosterone


title: LuCaP81 castrated Rapamycin

value: Rapamycin


title: SUDHL4_V5-BTG1wt_RIPseq_input, repl2

value: V5-BTG1WT allele


title: Pac1-r KO PACAP 30 min treatment, 1

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Dye-swap (Cy3/Cy5) of Cont vs PACAP 30min KO mouse palm skin

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

source_name: saline solution-treated palm skin Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: All experimental procedures involving animals were approved by the Institutional Animal Care and Use Committee of Hoshi University. The Adcyap1r1 -/- mice (PAC1R KO) and the C57BL/6 (WT) were bred and maintained under specific pathogen-free conditions in the animal facility of Hoshi University. Animals were housed with a 12-h/12-h light/dark cycle and were given free access to water and standard rodent chow. Nine- to ten-weeks old mice were used for the experiments.

extract_protocol: kit: QIAGEN, Rneasy Micro

treatment_protocol: Adult C57BL/6 mice (Tokyo Laboratory Animals Science Co., Ltd., Tokyo, Japan) and the PAC1R KO mice were anaesthetized with three types of mixed anesthetic agents (5 mL kg-1, i.p.). 5 µL of vehicle (saline containing 0.1% BSA) containing 10-7 mol/L of PACAP and 5 µL of vehicle alone were intradermal injected into the center of the footpad with a 26G needle attached to a 10 µL glass syringe (HAMILTON, Reno, NV, USA)

tag: strain

value: Pac1-r KO

value: Palm skin

source_name: PACAP-treated palm skin Cy5


title: Pac1-r KO PACAP 60 min treatment, 2

description: Dye-swap (Cy3/Cy5) of Cont vs PACAP 60min KO mouse palm skin

source_name: PACAP-treated palm skin Cy3

source_name: saline solution-treated palm skin Cy5


title: LuCaP81 castrated Sorafenib

value: Sorafenib


title: Wild type PACAP 30 min treatment, 1

description: Dye-swap (Cy3/Cy5) of Cont vs PACAP 30min WT mouse palm skin


title: Wild type PACAP 30 min treatment, 2


title: Pac1-r KO PACAP 60 min treatment, 1


title: undiff_veh1

value: MSC

value: vehicle (DMSO)


title: murineGCB_cre, repl1

value: Germinal center B cells

value: CD19-Cre control

value: Live B220+ FAS+ GL7+ cells using BD Influx Cell Sorter


title: LuCaP81 Dasatinib

value: LuCaP 81


title: LuCaP81 Imatinib

value: Imatinib


title: Naïve peritoneal macrophage-2

value: Peritoneal cavity

value: Primary cell

value: Macrophage

value: Wild type

value: Naive (No treatment)


title: LuCaP81 Enzalutamide

value: Intact

value: Enzalutamide


title: LuCaP81 Sorafenib


title: LuCaP81 PBS (vehicle)

value: PBS (vehicle)


title: LuCaP81 castrated Imatinib

value: Castrated


title: LuCaP81 Calcitriol

value: Calcitriol


title: LuCaP81 castrated WP1066


title: LuCaP78 castrated PD325901

value: LuCaP 78


title: LuCaP78 castrated BAY-11-7082


title: LuCaP81 castrated Docetaxel

value: Docetaxel


title: LuCaP78 castrated MK2206


title: Wild type PACAP 60 min treatment, 1

description: Dye-swap (Cy3/Cy5) of Cont vs PACAP 60min WT mouse palm skin

value: Palm skin


title: LuCaP81 WP1066


title: SUDHL4_V5-BTG1wt_RIPseq_input, repl1

value: SUDHL4 cells

value: V5-BTG1WT allele


title: LuCaP81 BAY-11-7082

value: LuCaP 81


title: LuCaP78 castrated PBS (vehicle)


title: Pac1-r KO PACAP 30 min treatment, 2

value: Pac1-r KO


title: LuCaP78 WP1066


title: Wild type PACAP 60 min treatment, 2


title: LuCaP81 Docetaxel


title: LuCaP81 LY294002


title: LuCaP81 castrated Calcitriol


title: LuCaP81 Testosterone

value: Testosterone


title: LuCaP78 castrated Imatinib

value: Imatinib


title: LuCaP78 castrated Enzalutamide


title: LuCaP78 castrated Docetaxel


title: LuCaP81 Rapamycin

value: Rapamycin


title: LuCaP78 castrated Testosterone


title: LuCaP78 castrated Dasatinib

value: Dasatinib


title: LuCaP78 PD325901


title: LuCaP78 castrated Calcitriol


title: LuCaP78 Enzalutamide


title: LuCaP78 castrated LY294002


title: LuCaP78 Sorafenib

value: Sorafenib


title: LuCaP81 MK2206

value: Intact


title: LuCaP78 castrated WP1066


title: LuCaP78 castrated Sorafenib


title: LuCaP78 MK2206


title: LuCaP78 PBS (vehicle)


title: LuCaP78 Dasatinib


title: LuCaP78 castrated Rapamycin


title: LuCaP78 LY294002


title: LuCaP78 Docetaxel


title: LuCaP78 Imatinib


title: LuCaP78 BAY-11-7082


title: LuCaP78 Calcitriol


title: LuCaP77 castrated LY294002

value: LuCaP 77


title: LuCaP78 Rapamycin


title: LuCaP77 castrated MK2206


title: LuCaP77 castrated PBS (vehicle)

value: PBS (vehicle)


title: LuCaP78 Testosterone


title: LuCaP77 WP1066


title: LuCaP77 castrated Docetaxel

value: Castrated


title: LuCaP77 Imatinib


title: LuCaP77 Dasatinib


title: LuCaP77 MK2206


title: LuCaP77 LY294002


title: LuCaP77 Sorafenib


title: LuCaP77 Rapamycin


title: LuCaP77 Calcitriol

value: Calcitriol


title: LuCaP77 PD325901


title: LuCaP147 castrated BAY-11-7082

value: LuCaP 147


title: LuCaP77 Testosterone


title: LuCaP147 castrated WP1066


title: LuCaP147 castrated LY294002


title: LuCaP147 castrated Dasatinib


title: LuCaP147 castrated Imatinib


title: LuCaP147 castrated PD325901


title: LuCaP147 castrated Sorafenib


title: LuCaP147 castrated Enzalutamide

value: Enzalutamide


title: LuCaP147 castrated MK2206


title: LuCaP147 castrated Docetaxel

value: Docetaxel


title: LuCaP77 castrated Enzalutamide


title: LuCaP147 castrated PBS (vehicle)


title: LuCaP147 castrated Rapamycin


title: LuCaP147 castrated Calcitriol


title: LuCaP77 Enzalutamide


title: LuCaP147 PD325901


title: LuCaP147 Dasatinib


title: LuCaP147 Imatinib


title: LuCaP147 BAY-11-7082


title: LuCaP147 Enzalutamide


title: LuCaP147 Sorafenib


title: LuCaP147 WP1066


title: LuCaP147 Calcitriol


title: LuCaP147 MK2206


title: LuCaP147 PBS (vehicle)


title: LuCaP73 castrated Dasatinib

value: LuCaP 73


title: LuCaP73 castrated LY294002


title: LuCaP73 castrated Enzalutamide


title: LuCaP73 castrated Imatinib


title: LuCaP147 Rapamycin


title: LuCaP147 Docetaxel


title: LuCaP73 castrated BAY-11-7082


title: LuCaP73 castrated WP1066


title: LuCaP73 castrated Calcitriol


title: LuCaP147 castrated Testosterone


title: LuCaP73 castrated Sorafenib


title: LuCaP73 castrated Rapamycin


title: LuCaP73 castrated PBS (vehicle)


title: LuCaP73 castrated Testosterone


title: LuCaP147 LY294002


title: LuCaP73 castrated PD325901


title: LuCaP73 PD325901


title: LuCaP73 castrated Docetaxel


title: LuCaP147 Testosterone


title: LuCaP73 Imatinib


title: LuCaP73 Enzalutamide


title: LuCaP73 MK2206


title: LuCaP73 WP1066


title: LuCaP73 Dasatinib


title: LuCaP73 castrated MK2206


title: LuCaP73 Docetaxel


title: LuCaP73 LY294002


title: LuCaP73 PBS (vehicle)


title: LuCaP73 Sorafenib


title: LuCaP73 Testosterone


title: LuCaP73 Calcitriol


title: visceral adipose tissue, 912, A

city: Jerusalem

first: Naomi

last: Habib

address: Safra Campus

department: Center for brain sciences

country: Israel

institute: Hebrew University of Jerusalem

description:
Adipose_Macrophages_RNAcounts.mtx.gz
Adipose_Macrophages_features.tsv.gz
Adipose_Macrophages_barcodes.tsv.gz

data_processing:
Basecalling was performed using Illumina NextSeq 500 and HiSeq2500 platforms
De-multiplexing of the samples and fastq files generation were done using 10x Cellranger v5.0 mkfastq command
Alignment to the genome, filtering, barcode counting and UMI counting were done using 10x Cellranger v5.0 count command
Seurat package for assembling processed data
Assembly: mm10
Supplementary files format and content: RNA counts per gene and per cell

molecule: nuclear RNA

source_name: visceral adipose tissue

extract_protocol:
Hippocampal nuclei extractoin was done by Dounce homogenization of the tissue in hypotonic lysis buffer with 0.1% NP-40. The nuceli were washed in PBS+0.2%BSA and filterd through 30micron filter.   Visceral adipose nuclei were extracted using salt-Tris (ST)-based buffers. Frozen visceral adipose tissue was placed into a gentleMACSTM C tube (Miltenyi, 130-096-334) with 1 mL TST buffer and homogenized using the gentleMACSTM Octo dissociator (Miltenyi). The sample was removed and with a further 1 mL of TST, was transferred to a 15 mL conical tube on ice for 10 min. Next, the sample was filtered through a 40 μm FalconTM cell strainer (Thermo Fisher, 08-771-1), to which 3 mL of 1x ST buffer was also added through the filter. The resulting 5 mL sample was then centrifuged at 500 g for 5 min at 4°C in a swinging bucket centrifuge, following which the supernatant was removed and the pellet re-suspended in 1x ST buffer (volume determined by pellet size). The nuclei-containing solution was transferred to a 5 mL polystyrene tube through a 35 μm cell strainer cap.  Next, the nuclei were loaded on 10x Chromium Next GEM Chip G Single Cell Kit (PN-1000127) for the single nuclei-bead emultion (GEM) generation.
Nuclei barcoding and RNA-seq libraries were prepared according to 10x Chromium Next GEM Single Cell 3' Reagent kit (PN-1000121).
single nulei RNA-seq

treatment_protocol: To induce obesity, at 6-9 weeks of age, both transgenic 5xFAD and WT mice were switched to a high-fat diet (HFD) for a total of 24-28 weeks. Non-obese controls were kept on regular chow (control diet, CD).

value: visceral adipose tissue

tag: diet

value: HFD


title: LuCaP73 Rapamycin


title: visceral adipose tissue, 976, A

value: CD


title: visceral adipose tissue, 699, A


title: LuCaP73 BAY-11-7082


title: visceral adipose tissue, 650, A


title: visceral adipose tissue, 660, A


title: visceral adipose tissue, 657, A


title: visceral adipose tissue, 907, A


title: visceral adipose tissue, 703, A


title: visceral adipose tissue, 638, A


title: visceral adipose tissue, 641, A


title: visceral adipose tissue, 640, A


title: visceral adipose tissue, 647, A


title: visceral adipose tissue, 637, A


title: visceral adipose tissue, 634, A


title: visceral adipose tissue, 697, A


title: visceral adipose tissue, 909, A


title: visceral adipose tissue, 639, A


title: visceral adipose tissue, 651, A


title: visceral adipose tissue, 698, A


title: visceral adipose tissue, 897, A


title: visceral adipose tissue, 636, A


title: visceral adipose tissue, 910, A


title: K562, LP1, pool_2, mapping

city: Saint Louis

first: Barak

last: Cohen

state: MO

address: 4515 Mckinley Ave

institute: Washington University in St. Louis

data_processing:
We first filtered for reads that contained barcodes in the correct sequence context. Barcodes were associated with their corresponding integration site sequence, which was then aligned to the reference genome with BWA (v0.7.17) using default parameters. We only kept barcodes where the reads for one location represented at least 80% of all the locations for that barcode.
Assembly: hg38
Supplementary files format and content: Bed containing location of each barcode. The start and end positions are the same and indicate the base immediately 3' of the landing pad. The column after the barcode indicate the number of reads supporting each barcode. The same location is often mapped to multiple barcodes (usually similar barcodes) due to errors in barcode PCR/sequencing, but undergoes further filtering later.
Library strategy: barcode sequencing

growth_protocol: K562 cells were grown in IMDM (Isocove's Modified Dulbecco's Medium) supplemented with 10% fetal bovine serum (FBS), 1% non-essential amino acids (NEAA) and 1% penicillin/streptomycin (pen/strep).

extract_protocol:
Genomic DNA was extracted using TRIzol according to manufacturer's instructions.
Barcodes along with the integrated location were amplified from DNA using custom primers. Sequencing adapters were added to the amplified barcodes for Illumina sequencing.

value: chronic myelogenous leukemia

tag: clonal cell-line

value: Stable cell lines containing reporter genes integrated at multiple locations


title: K562, Pool4, Rep1

description: pool4_SL4-combined_cells_umis_tripbc_intranscriptome_denoise_10_5_2_10.tsv

data_processing:
Reads were processed with a custom pipeline described in the paper
Assembly: hg38
Supplementary files format and content: The processed data files have four columns for each RNA molecule: cell-barcode, umi,  location barcode and number of reads supporting the RNA molecule.
Library strategy: barcode sequencing

molecule: polyA RNA

extract_protocol:
K562 clonal cells containing reporter genes integrated in different locations were pooled and used for 10x scRNA-seq.
We captured mRNA from reporter genes integrated at different locations using the 10X scRNA-seq platform as described in the paper


title: K562, Pool4, Rep2


title: K562, LP3, mapping


title: K562, Pool3, Rep2

description: pool3_LP1_combined_cells_umis_tripbc_denoise.tsv


title: K562, Pool2, Rep2 capture sequence

description: pool2_LP1_combined_cells_umis_tripbc_denoise.tsv

tag: rna capture

value: cs


title: K562, Pool3, Rep1


title: K562, Pool2, Rep1 polyA

value: pa


title: T-cells, TC1, NANA

data_processing:
Basecalling was performed using Illumina NextSeq 500
De-multiplexing of the samples and fastq files generation were done using Illumina's  bcl2fastq tool
Alignment to the genome was done with STAR
Gene counts were obtained with HTseq
Differential analysis was done using DESeq2 R package
Assembly: hg38
Supplementary files format and content: raw counts

source_name: T-cells

extract_protocol:
RNA was extracted with Qiagen RNeasy kit (74104)
Poly-A mRNA was isolated with NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and used as an input for libaray preparation with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760). Quantification of the libraries was done by Qubit HS  DNA assay and TapeStation.

treatment_protocol: The cells were treated with 12.5mg/ml NANA for 24hr

tag: individual

value: T-cells

value: NANA treatment


title: K562, Pool2, Rep1 capture sequence

tag: cell line


title: T-cells, TC1

tag: cell type

value: Control


title: T-cells, SR1


title: K562, transcriptome, rep1

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were processed using CellRanger 6.0.1.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
K562 clonal cells containing reporter genes integrated in different locations were pooled and used for 10x scRNA-seq.
We performed 10x scRNA-seq with the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 kit according to manufacturer's instructions.


title: T-cells, SP1, NANA


title: K562, LP1, pool_1, mapping


title: T-cells, SR1, NANA


title: K562, Pool2, Rep2 polyA


title: T-cells, AK1, NANA


title: K562, Pool1, Rep2

description: pool1_LP3_combined_cells_umis_tripbc_denoise.tsv


title: K562, Pool1, Rep1


title: K562, transcriptome, rep2

description: 10x Genomics

value: K562 clonal cells containing reporter genes integrated in different locations


title: T-cells, SP1


title: C388_H7_Mouse_EB_6D_B77

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

data_processing:
Following quality controls (performed with FastQC v0.11.2 ( https://www.bioinformatics.babraham.ac.uk/projects/fastqc), sequencing reads were processed with Trim Galore! v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to perform quality and adapter trimming (parameters: --stringency 3 –q 20). Trimmed reads were next aligned to the mouse reference genome (mm10/GRCm38.p6) using STAR v2.7.1a 51 with options: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04. Gene expression levels were quantified with featureCounts v1.6.1 38 (options: -t exon -g gene_name) using the GENCODE Release M23 annotation. Multi-mapped reads were excluded from quantification.
Assembly: mm10/GRCm38
Supplementary files format and content: Tab-delimited text file of raw read counts matrix per gene/cell.

source_name: Embryoid Bodies (EB)

growth_protocol: E14 mouse WT and mutant (Dnmt3a -/-   and Dnmt3b -/-) ESCs were cultured in high-glucose DMEM (Euroclone) supplemented with 15% FBS (Millipore Corp., Billerica, MA, USA), 0.1 mmol/l nonessential amino acids (Invitrogen), 1 mmol/l sodium pyruvate (Invitrogen), 0.1 mmol/l β-mercaptoethanol, 1500 U/ml Leukemia Inhibitory Factor (LIF; Millipore), 25 U/ml penicillin, and 25 μg/ml streptomycin. To induce formation of EBs, Wild type and mutant ESCs were transferred using trypsin to low-attachment plates (CORNING) in Alpha-MEM (BE02-002F LONZA) supplemented with 10% KOSR (10828-028 GIBCO), 5% FBS (Millipore), 1% nonessential amino acids (Invitrogen), 1% sodium pyruvate (Invitrogen), 0.1 mmol/l β-mercaptoethanol, 25 U/ml penicillin and 25 μg/ml streptomycin. Medium was changed every 3 days.

extract_protocol: Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).

value: Embryoid Bodies (EB)

tag: Stage

tag: genotype ext

tag: batch


title: C388_H6_Mouse_EB_6D_B77

tag: genotype


title: C388_G3_Mouse_EB_6D_B77


title: C388_G2_Mouse_EB_6D_B77


title: C388_G10_Mouse_EB_6D_B77


title: C388_H1_Mouse_EB_6D_B77


title: C388_G4_Mouse_EB_6D_B77


title: C388_F12_Mouse_EB_6D_B77


title: C388_F7_Mouse_EB_6D_B77


title: C388_G6_Mouse_EB_6D_B77


title: C388_F10_Mouse_EB_6D_B77


title: C388_G5_Mouse_EB_6D_B77


title: C388_G9_Mouse_EB_6D_B77


title: C388_F5_Mouse_EB_6D_B77


title: C388_F1_Mouse_EB_6D_B77


title: C388_F11_Mouse_EB_6D_B77


title: C388_F8_Mouse_EB_6D_B77


title: C388_G1_Mouse_EB_6D_B77


title: T-cells, AK1

tag: treatment


title: C388_E6_Mouse_EB_6D_B77


title: C388_E4_Mouse_EB_6D_B77


title: C388_E3_Mouse_EB_6D_B77


title: C388_E1_Mouse_EB_6D_B77


title: C388_G7_Mouse_EB_6D_B77


title: C388_D9_Mouse_EB_6D_B77


title: C388_G8_Mouse_EB_6D_B77


title: C388_E10_Mouse_EB_6D_B77


title: C388_F4_Mouse_EB_6D_B77


title: C388_E9_Mouse_EB_6D_B77


title: C388_F3_Mouse_EB_6D_B77


title: C388_E5_Mouse_EB_6D_B77


title: C388_G12_Mouse_EB_6D_B77


title: C388_E12_Mouse_EB_6D_B77


title: C388_E7_Mouse_EB_6D_B77


title: C388_D4_Mouse_EB_6D_B77


title: C388_F9_Mouse_EB_6D_B77


title: C388_D8_Mouse_EB_6D_B77


title: C388_D3_Mouse_EB_6D_B77


title: C388_D5_Mouse_EB_6D_B77


title: C388_D7_Mouse_EB_6D_B77


title: C388_D11_Mouse_EB_6D_B77


title: C388_D12_Mouse_EB_6D_B77


title: C388_E11_Mouse_EB_6D_B77


title: C388_D10_Mouse_EB_6D_B77


title: C388_D2_Mouse_EB_6D_B77


title: C388_D1_Mouse_EB_6D_B77


title: C388_C7_Mouse_EB_6D_B77


title: C388_C9_Mouse_EB_6D_B77


title: C388_C8_Mouse_EB_6D_B77


title: C388_D6_Mouse_EB_6D_B77


title: C388_C2_Mouse_EB_6D_B77


title: C388_C11_Mouse_EB_6D_B77


title: C388_C6_Mouse_EB_6D_B77


title: C388_B6_Mouse_EB_6D_B77


title: C388_B5_Mouse_EB_6D_B77


title: C388_C3_Mouse_EB_6D_B77


title: C388_C5_Mouse_EB_6D_B77


title: C388_B11_Mouse_EB_6D_B77


title: C388_A8_Mouse_EB_6D_B77


title: C388_B10_Mouse_EB_6D_B77


title: C388_A9_Mouse_EB_6D_B77


title: C388_A11_Mouse_EB_6D_B77


title: C380_H6_Mouse_EB_3D_B77


title: C388_B7_Mouse_EB_6D_B77


title: C388_B1_Mouse_EB_6D_B77


title: C380_G9_Mouse_EB_3D_B77


title: C388_B9_Mouse_EB_6D_B77


title: C388_B4_Mouse_EB_6D_B77


title: C380_G8_Mouse_EB_3D_B77


title: C380_G5_Mouse_EB_3D_B77


title: C380_G2_Mouse_EB_3D_B77


title: C388_B8_Mouse_EB_6D_B77


title: C380_H11_Mouse_EB_3D_B77


title: C388_B3_Mouse_EB_6D_B77


title: C380_H8_Mouse_EB_3D_B77


title: C380_H9_Mouse_EB_3D_B77


title: C388_B12_Mouse_EB_6D_B77


title: C380_G7_Mouse_EB_3D_B77


title: C380_G6_Mouse_EB_3D_B77


title: C380_G12_Mouse_EB_3D_B77


title: C380_F10_Mouse_EB_3D_B77


title: C380_F1_Mouse_EB_3D_B77


title: C380_G1_Mouse_EB_3D_B77


title: C380_F11_Mouse_EB_3D_B77


title: C380_H7_Mouse_EB_3D_B77


title: C380_E9_Mouse_EB_3D_B77


title: C380_F6_Mouse_EB_3D_B77


title: C380_F7_Mouse_EB_3D_B77


title: C380_E8_Mouse_EB_3D_B77


title: C380_G10_Mouse_EB_3D_B77


title: C380_G4_Mouse_EB_3D_B77


title: C380_E5_Mouse_EB_3D_B77


title: C380_F9_Mouse_EB_3D_B77


title: C380_E4_Mouse_EB_3D_B77


title: C388_A2_Mouse_EB_6D_B77


title: C380_F4_Mouse_EB_3D_B77


title: C380_E1_Mouse_EB_3D_B77


title: C380_F3_Mouse_EB_3D_B77


title: C380_G3_Mouse_EB_3D_B77


title: C380_F5_Mouse_EB_3D_B77


title: C380_D6_Mouse_EB_3D_B77


title: C380_H5_Mouse_EB_3D_B77


title: C380_E3_Mouse_EB_3D_B77


title: C380_D4_Mouse_EB_3D_B77


title: C380_E2_Mouse_EB_3D_B77


title: C380_F8_Mouse_EB_3D_B77


title: C380_F2_Mouse_EB_3D_B77


title: C380_E7_Mouse_EB_3D_B77


title: C380_E6_Mouse_EB_3D_B77


title: C380_E11_Mouse_EB_3D_B77


title: C380_C8_Mouse_EB_3D_B77


title: C380_D8_Mouse_EB_3D_B77


title: C380_D3_Mouse_EB_3D_B77


title: C380_D12_Mouse_EB_3D_B77


title: C380_D2_Mouse_EB_3D_B77


title: C380_C1_Mouse_EB_3D_B77


title: C380_C9_Mouse_EB_3D_B77


title: C380_D5_Mouse_EB_3D_B77


title: C380_C11_Mouse_EB_3D_B77


title: C380_B9_Mouse_EB_3D_B77


title: C380_B6_Mouse_EB_3D_B77


title: C380_D11_Mouse_EB_3D_B77


title: C380_D1_Mouse_EB_3D_B77


title: C380_C6_Mouse_EB_3D_B77


title: C380_B5_Mouse_EB_3D_B77


title: C380_C3_Mouse_EB_3D_B77


title: C380_C5_Mouse_EB_3D_B77


title: C380_C10_Mouse_EB_3D_B77


title: C380_B7_Mouse_EB_3D_B77


title: C380_C4_Mouse_EB_3D_B77


title: C380_E10_Mouse_EB_3D_B77


title: C380_C7_Mouse_EB_3D_B77


title: C380_B3_Mouse_EB_3D_B77


title: C388_C12_Mouse_EB_6D_B77


title: C380_B1_Mouse_EB_3D_B77


title: C380_D9_Mouse_EB_3D_B77


title: C380_E12_Mouse_EB_3D_B77


title: C380_C2_Mouse_EB_3D_B77


title: C380_B8_Mouse_EB_3D_B77


title: C380_B2_Mouse_EB_3D_B77


title: C380_D7_Mouse_EB_3D_B77


title: C380_B10_Mouse_EB_3D_B77


title: C380_A2_Mouse_EB_3D_B77


title: C378_F3_Mouse_EB_8D_B77


title: C380_A8_Mouse_EB_3D_B77


title: C378_F2_Mouse_EB_8D_B77


title: C380_A10_Mouse_EB_3D_B77


title: C380_A9_Mouse_EB_3D_B77


title: C378_E4_Mouse_EB_8D_B77


title: C378_G2_Mouse_EB_8D_B77


title: C378_E8_Mouse_EB_8D_B77


title: C378_E2_Mouse_EB_8D_B77


title: C380_B4_Mouse_EB_3D_B77


title: C380_A7_Mouse_EB_3D_B77


title: C378_F1_Mouse_EB_8D_B77


title: C378_D8_Mouse_EB_8D_B77


title: C378_E5_Mouse_EB_8D_B77


title: C378_E10_Mouse_EB_8D_B77


title: C378_G4_Mouse_EB_8D_B77


title: C380_A3_Mouse_EB_3D_B77


title: C388_C10_Mouse_EB_6D_B77


title: C380_B11_Mouse_EB_3D_B77


title: C378_D5_Mouse_EB_8D_B77


title: C378_D11_Mouse_EB_8D_B77


title: C378_E1_Mouse_EB_8D_B77


title: C378_D3_Mouse_EB_8D_B77


title: C378_D9_Mouse_EB_8D_B77


title: C378_E11_Mouse_EB_8D_B77


title: C378_D2_Mouse_EB_8D_B77


title: C378_E12_Mouse_EB_8D_B77


title: C378_C8_Mouse_EB_8D_B77


title: C378_D4_Mouse_EB_8D_B77


title: C378_D10_Mouse_EB_8D_B77


title: C378_C9_Mouse_EB_8D_B77


title: C378_C7_Mouse_EB_8D_B77


title: C378_C11_Mouse_EB_8D_B77


title: C378_C6_Mouse_EB_8D_B77


title: C378_C4_Mouse_EB_8D_B77


title: C378_C1_Mouse_EB_8D_B77


title: C378_C10_Mouse_EB_8D_B77


title: C378_B8_Mouse_EB_8D_B77


title: C378_B7_Mouse_EB_8D_B77


title: C378_B5_Mouse_EB_8D_B77


title: C378_B1_Mouse_EB_8D_B77


title: C303_H6_Ebs_3A38_6D


title: C303_H3_Ebs_3A38_6D


title: C303_H5_Ebs_3A38_6D


title: C303_G9_Ebs_3A38_6D


title: C303_G5_Ebs_3A38_6D


title: C303_G2_Ebs_3A38_6D


title: C378_C12_Mouse_EB_8D_B77


title: C303_G3_Ebs_3A38_6D


title: C303_G11_Ebs_3A38_6D


title: C303_H7_Ebs_3A38_6D


title: C303_G10_Ebs_3A38_6D


title: C378_B10_Mouse_EB_8D_B77


title: C303_H8_Ebs_3A38_6D


title: C303_H1_Ebs_3A38_6D


title: C303_H10_Ebs_3A38_6D


title: C303_H9_Ebs_3A38_6D


title: C378_C3_Mouse_EB_8D_B77


title: C303_F9_Ebs_3A38_6D


title: C303_F11_Ebs_3A38_6D


title: C303_E9_Ebs_3A38_6D


title: C378_A9_Mouse_EB_8D_B77


title: C378_B11_Mouse_EB_8D_B77


title: C303_E6_Ebs_3A38_6D


title: C303_E11_Ebs_3A38_6D


title: C303_E12_Ebs_3A38_6D


title: C303_F5_Ebs_3A38_6D


title: C303_F8_Ebs_3A38_6D


title: C303_F6_Ebs_3A38_6D


title: C303_G4_Ebs_3A38_6D


title: C303_F7_Ebs_3A38_6D


title: C303_F1_Ebs_3A38_6D


title: C303_D3_Ebs_3A38_6D


title: C303_H11_Ebs_3A38_6D


title: C303_D2_Ebs_3A38_6D


title: C303_F2_Ebs_3A38_6D


title: C303_D1_Ebs_3A38_6D


title: C303_E4_Ebs_3A38_6D


title: C303_D10_Ebs_3A38_6D


title: C303_F3_Ebs_3A38_6D


title: C378_B2_Mouse_EB_8D_B77


title: C303_F10_Ebs_3A38_6D


title: C303_F4_Ebs_3A38_6D


title: C303_H2_Ebs_3A38_6D


title: C303_E3_Ebs_3A38_6D


title: C303_D9_Ebs_3A38_6D


title: C303_C6_Ebs_3A38_6D


title: C303_D8_Ebs_3A38_6D


title: C303_E7_Ebs_3A38_6D


title: C303_D4_Ebs_3A38_6D


title: C303_C5_Ebs_3A38_6D


title: C303_E10_Ebs_3A38_6D


title: C303_D7_Ebs_3A38_6D


title: C303_C7_Ebs_3A38_6D


title: C303_D6_Ebs_3A38_6D


title: C303_C11_Ebs_3A38_6D


title: C303_B6_Ebs_3A38_6D


title: C303_B9_Ebs_3A38_6D


title: C303_C3_Ebs_3A38_6D


title: C303_C10_Ebs_3A38_6D


title: C303_C4_Ebs_3A38_6D


title: C303_C8_Ebs_3A38_6D


title: C303_A7_Ebs_3A38_6D


title: C303_B1_Ebs_3A38_6D


title: C303_A8_Ebs_3A38_6D


title: C303_A5_Ebs_3A38_6D


title: C303_B3_Ebs_3A38_6D


title: C303_C12_Ebs_3A38_6D


title: C303_A10_Ebs_3A38_6D


title: C303_B2_Ebs_3A38_6D


title: C303_B7_Ebs_3A38_6D


title: C303_A9_Ebs_3A38_6D


title: C303_A2_Ebs_3A38_6D


title: C303_B4_Ebs_3A38_6D


title: C303_B5_Ebs_3A38_6D


title: C303_A4_Ebs_3A38_6D


title: C303_A3_Ebs_3A38_6D


title: C307_H5_Ebs_3A38_8D


title: C307_G6_Ebs_3A38_8D


title: C307_H2_Ebs_3A38_8D


title: C307_G8_Ebs_3A38_8D


title: C307_H9_Ebs_3A38_8D


title: C307_H7_Ebs_3A38_8D


title: C303_B10_Ebs_3A38_6D


title: C378_B6_Mouse_EB_8D_B77


title: C307_G3_Ebs_3A38_8D


title: C303_A12_Ebs_3A38_6D


title: C307_G2_Ebs_3A38_8D


title: C307_F8_Ebs_3A38_8D


title: C307_F9_Ebs_3A38_8D


title: C307_F7_Ebs_3A38_8D


title: C307_F4_Ebs_3A38_8D


title: C307_F5_Ebs_3A38_8D


title: C307_F6_Ebs_3A38_8D


title: C307_G12_Ebs_3A38_8D


title: C307_G7_Ebs_3A38_8D


title: C307_F1_Ebs_3A38_8D


title: C307_G9_Ebs_3A38_8D


title: C307_H6_Ebs_3A38_8D


title: C307_F10_Ebs_3A38_8D


title: C307_E9_Ebs_3A38_8D


title: C307_E7_Ebs_3A38_8D


title: C307_G5_Ebs_3A38_8D


title: C307_G10_Ebs_3A38_8D


title: C307_F2_Ebs_3A38_8D


title: C307_E5_Ebs_3A38_8D


title: C307_G4_Ebs_3A38_8D


title: C307_F11_Ebs_3A38_8D


title: C307_E6_Ebs_3A38_8D


title: C307_E1_Ebs_3A38_8D


title: C307_D9_Ebs_3A38_8D


title: C307_F3_Ebs_3A38_8D


title: C307_D2_Ebs_3A38_8D


title: C307_D7_Ebs_3A38_8D


title: C307_E2_Ebs_3A38_8D


title: C307_D8_Ebs_3A38_8D


title: C307_C8_Ebs_3A38_8D


title: C307_D3_Ebs_3A38_8D


title: C307_E11_Ebs_3A38_8D


title: C307_D5_Ebs_3A38_8D


title: C307_D4_Ebs_3A38_8D


title: C307_E10_Ebs_3A38_8D


title: C307_D6_Ebs_3A38_8D


title: C307_E12_Ebs_3A38_8D


title: C307_C7_Ebs_3A38_8D


title: C307_D11_Ebs_3A38_8D


title: C307_C9_Ebs_3A38_8D


title: C307_E4_Ebs_3A38_8D


title: C307_C6_Ebs_3A38_8D


title: C307_D12_Ebs_3A38_8D


title: C307_C4_Ebs_3A38_8D


title: C307_C3_Ebs_3A38_8D


title: C307_E3_Ebs_3A38_8D


title: C307_C2_Ebs_3A38_8D


title: C307_C5_Ebs_3A38_8D


title: C307_B5_Ebs_3A38_8D


title: C307_B1_Ebs_3A38_8D


title: C291_H9_Ebs_3A38_3D


title: C307_B4_Ebs_3A38_8D


title: C307_B12_Ebs_3A38_8D


title: C291_H8_Ebs_3A38_3D


title: C307_D10_Ebs_3A38_8D


title: C307_C12_Ebs_3A38_8D


title: C307_B7_Ebs_3A38_8D


title: C291_G9_Ebs_3A38_3D


title: C291_G6_Ebs_3A38_3D


title: C291_G5_Ebs_3A38_3D


title: C307_C1_Ebs_3A38_8D


title: C307_B6_Ebs_3A38_8D


title: C291_H7_Ebs_3A38_3D


title: C291_G3_Ebs_3A38_3D


title: C307_B10_Ebs_3A38_8D


title: C307_C11_Ebs_3A38_8D


title: C307_C10_Ebs_3A38_8D


title: C291_F9_Ebs_3A38_3D


title: C307_B2_Ebs_3A38_8D


title: C291_G12_Ebs_3A38_3D


title: C291_G7_Ebs_3A38_3D


title: C291_H6_Ebs_3A38_3D


title: C291_F7_Ebs_3A38_3D


title: C307_B3_Ebs_3A38_8D


title: C307_B11_Ebs_3A38_8D


title: C307_B8_Ebs_3A38_8D


title: C307_B9_Ebs_3A38_8D


title: C291_H5_Ebs_3A38_3D


title: C291_F2_Ebs_3A38_3D


title: C291_F11_Ebs_3A38_3D


title: C291_G8_Ebs_3A38_3D


title: C291_G11_Ebs_3A38_3D


title: C291_E6_Ebs_3A38_3D


title: C291_G2_Ebs_3A38_3D


title: C291_E5_Ebs_3A38_3D


title: C291_F6_Ebs_3A38_3D


title: C291_F3_Ebs_3A38_3D


title: C291_F4_Ebs_3A38_3D


title: C291_E4_Ebs_3A38_3D


title: C291_G1_Ebs_3A38_3D


title: C291_D9_Ebs_3A38_3D


title: C291_F1_Ebs_3A38_3D


title: C291_E11_Ebs_3A38_3D


title: C291_E8_Ebs_3A38_3D


title: C291_E7_Ebs_3A38_3D


title: C291_F12_Ebs_3A38_3D


title: C291_F8_Ebs_3A38_3D


title: C291_D4_Ebs_3A38_3D


title: C291_F5_Ebs_3A38_3D


title: C291_D5_Ebs_3A38_3D


title: C291_E12_Ebs_3A38_3D


title: C291_E1_Ebs_3A38_3D


title: C291_D8_Ebs_3A38_3D


title: C291_D7_Ebs_3A38_3D


title: C291_D6_Ebs_3A38_3D


title: C291_E9_Ebs_3A38_3D


title: C291_D1_Ebs_3A38_3D


title: C291_D2_Ebs_3A38_3D


title: C291_D12_Ebs_3A38_3D


title: C291_E2_Ebs_3A38_3D


title: C291_D11_Ebs_3A38_3D


title: C291_C9_Ebs_3A38_3D


title: C291_C6_Ebs_3A38_3D


title: C291_C3_Ebs_3A38_3D


title: C291_C4_Ebs_3A38_3D


title: C291_E3_Ebs_3A38_3D


title: C291_C7_Ebs_3A38_3D


title: C291_C5_Ebs_3A38_3D


title: C291_D3_Ebs_3A38_3D


title: C291_B8_Ebs_3A38_3D


title: C291_C11_Ebs_3A38_3D


title: C291_B9_Ebs_3A38_3D


title: C291_B7_Ebs_3A38_3D


title: C291_B6_Ebs_3A38_3D


title: C291_B5_Ebs_3A38_3D


title: C291_C12_Ebs_3A38_3D


title: C291_B11_Ebs_3A38_3D


title: C291_C2_Ebs_3A38_3D


title: C291_A3_Ebs_3A38_3D


title: C291_A7_Ebs_3A38_3D


title: C291_A9_Ebs_3A38_3D


title: C291_B4_Ebs_3A38_3D


title: C291_B2_Ebs_3A38_3D


title: C291_B12_Ebs_3A38_3D


title: C288_H7_Mouse_EB_3D_3A2


title: C288_G9_Mouse_EB_3D_3A2


title: C288_H2_Mouse_EB_3D_3A2


title: C288_H1_Mouse_EB_3D_3A2


title: C291_A11_Ebs_3A38_3D


title: C288_G8_Mouse_EB_3D_3A2


title: C288_H8_Mouse_EB_3D_3A2


title: C288_H6_Mouse_EB_3D_3A2


title: C288_G7_Mouse_EB_3D_3A2


title: C288_G6_Mouse_EB_3D_3A2


title: C288_G3_Mouse_EB_3D_3A2


title: C288_G12_Mouse_EB_3D_3A2


title: C288_G10_Mouse_EB_3D_3A2


title: C288_F7_Mouse_EB_3D_3A2


title: C288_F8_Mouse_EB_3D_3A2


title: C288_G1_Mouse_EB_3D_3A2


title: C288_H5_Mouse_EB_3D_3A2


title: C288_G4_Mouse_EB_3D_3A2


title: C288_G5_Mouse_EB_3D_3A2


title: C288_F9_Mouse_EB_3D_3A2


title: C288_F6_Mouse_EB_3D_3A2


title: C288_F5_Mouse_EB_3D_3A2


title: C288_F12_Mouse_EB_3D_3A2


title: C288_F2_Mouse_EB_3D_3A2


title: C288_F3_Mouse_EB_3D_3A2


title: C288_E8_Mouse_EB_3D_3A2


title: C288_E5_Mouse_EB_3D_3A2


title: C288_E2_Mouse_EB_3D_3A2


title: C288_E1_Mouse_EB_3D_3A2


title: C288_E9_Mouse_EB_3D_3A2


title: C288_F1_Mouse_EB_3D_3A2


title: C288_E11_Mouse_EB_3D_3A2


title: C288_D9_Mouse_EB_3D_3A2


title: C288_D7_Mouse_EB_3D_3A2


title: C288_D6_Mouse_EB_3D_3A2


title: C288_E12_Mouse_EB_3D_3A2


title: C288_C8_Mouse_EB_3D_3A2


title: C288_C5_Mouse_EB_3D_3A2


title: C288_F4_Mouse_EB_3D_3A2


title: C288_E3_Mouse_EB_3D_3A2


title: C288_D12_Mouse_EB_3D_3A2


title: C288_C7_Mouse_EB_3D_3A2


title: C288_C4_Mouse_EB_3D_3A2


title: C288_D2_Mouse_EB_3D_3A2


title: C288_C12_Mouse_EB_3D_3A2


title: C288_E10_Mouse_EB_3D_3A2


title: C288_C11_Mouse_EB_3D_3A2


title: C288_D11_Mouse_EB_3D_3A2


title: C288_D10_Mouse_EB_3D_3A2


title: C288_B7_Mouse_EB_3D_3A2


title: C288_B8_Mouse_EB_3D_3A2


title: C288_B6_Mouse_EB_3D_3A2


title: C288_B3_Mouse_EB_3D_3A2


title: C288_B11_Mouse_EB_3D_3A2


title: C288_B10_Mouse_EB_3D_3A2


title: C288_A11_Mouse_EB_3D_3A2


title: C300_H8_Mouse_EB_6D_3A2


title: C288_D8_Mouse_EB_3D_3A2


title: C288_E7_Mouse_EB_3D_3A2


title: C288_A3_Mouse_EB_3D_3A2


title: C288_D4_Mouse_EB_3D_3A2


title: C288_C9_Mouse_EB_3D_3A2


title: C300_H4_Mouse_EB_6D_3A2


title: C300_H2_Mouse_EB_6D_3A2


title: C300_G9_Mouse_EB_6D_3A2


title: C300_G8_Mouse_EB_6D_3A2


title: C288_B12_Mouse_EB_3D_3A2


title: C288_C3_Mouse_EB_3D_3A2


title: C300_G5_Mouse_EB_6D_3A2


title: C300_G4_Mouse_EB_6D_3A2


title: C288_B9_Mouse_EB_3D_3A2


title: C288_D1_Mouse_EB_3D_3A2


title: C300_H5_Mouse_EB_6D_3A2


title: C288_C2_Mouse_EB_3D_3A2


title: C300_G1_Mouse_EB_6D_3A2


title: C300_G12_Mouse_EB_6D_3A2


title: C300_G2_Mouse_EB_6D_3A2


title: C300_G11_Mouse_EB_6D_3A2


title: C288_C10_Mouse_EB_3D_3A2


title: C300_F9_Mouse_EB_6D_3A2


title: C300_F6_Mouse_EB_6D_3A2


title: C300_F4_Mouse_EB_6D_3A2


title: C300_F2_Mouse_EB_6D_3A2


title: C300_F3_Mouse_EB_6D_3A2


title: C300_F1_Mouse_EB_6D_3A2


title: C300_F12_Mouse_EB_6D_3A2


title: C300_E9_Mouse_EB_6D_3A2


title: C300_G10_Mouse_EB_6D_3A2


title: C300_H7_Mouse_EB_6D_3A2


title: C300_E6_Mouse_EB_6D_3A2


title: C288_B5_Mouse_EB_3D_3A2


title: C300_E3_Mouse_EB_6D_3A2


title: C300_E1_Mouse_EB_6D_3A2


title: C300_E11_Mouse_EB_6D_3A2


title: C300_E12_Mouse_EB_6D_3A2


title: C300_H1_Mouse_EB_6D_3A2


title: C300_G3_Mouse_EB_6D_3A2


title: C288_A2_Mouse_EB_3D_3A2


title: C300_H3_Mouse_EB_6D_3A2


title: C288_B4_Mouse_EB_3D_3A2


title: C300_G7_Mouse_EB_6D_3A2


title: C300_D7_Mouse_EB_6D_3A2


title: C300_D6_Mouse_EB_6D_3A2


title: C300_D3_Mouse_EB_6D_3A2


title: C300_D4_Mouse_EB_6D_3A2


title: C300_E4_Mouse_EB_6D_3A2


title: C300_F8_Mouse_EB_6D_3A2


title: C300_F5_Mouse_EB_6D_3A2


title: C300_F11_Mouse_EB_6D_3A2


title: C300_G6_Mouse_EB_6D_3A2


title: C300_D2_Mouse_EB_6D_3A2


title: C300_F7_Mouse_EB_6D_3A2


title: C300_C9_Mouse_EB_6D_3A2


title: C300_F10_Mouse_EB_6D_3A2


title: C300_C6_Mouse_EB_6D_3A2


title: C300_E7_Mouse_EB_6D_3A2


title: C300_C5_Mouse_EB_6D_3A2


title: C300_C3_Mouse_EB_6D_3A2


title: C300_C2_Mouse_EB_6D_3A2


title: C300_D10_Mouse_EB_6D_3A2


title: C300_E2_Mouse_EB_6D_3A2


title: C300_B8_Mouse_EB_6D_3A2


title: C300_B9_Mouse_EB_6D_3A2


title: C300_C8_Mouse_EB_6D_3A2


title: C300_B4_Mouse_EB_6D_3A2


title: C300_B6_Mouse_EB_6D_3A2


title: C300_B5_Mouse_EB_6D_3A2


title: C300_D9_Mouse_EB_6D_3A2


title: C300_B3_Mouse_EB_6D_3A2


title: C300_D11_Mouse_EB_6D_3A2


title: C300_D12_Mouse_EB_6D_3A2


title: C300_C10_Mouse_EB_6D_3A2


title: C300_C1_Mouse_EB_6D_3A2


title: C300_B2_Mouse_EB_6D_3A2


title: C300_C7_Mouse_EB_6D_3A2


title: C300_D5_Mouse_EB_6D_3A2


title: C300_B7_Mouse_EB_6D_3A2


title: C300_B11_Mouse_EB_6D_3A2


title: C300_B10_Mouse_EB_6D_3A2


title: C300_E10_Mouse_EB_6D_3A2


title: C300_C4_Mouse_EB_6D_3A2


title: C300_C11_Mouse_EB_6D_3A2


title: C300_D1_Mouse_EB_6D_3A2


title: C300_B1_Mouse_EB_6D_3A2


title: C300_A6_Mouse_EB_6D_3A2


title: C315_H9_Mouse_EB_3D_WT

value: WT


title: C300_C12_Mouse_EB_6D_3A2


title: C315_H12_Mouse_EB_3D_WT


title: C300_B12_Mouse_EB_6D_3A2


title: C315_H7_Mouse_EB_3D_WT


title: C300_A11_Mouse_EB_6D_3A2


title: C315_G9_Mouse_EB_3D_WT


title: C300_A12_Mouse_EB_6D_3A2


title: C315_G2_Mouse_EB_3D_WT


title: C315_G3_Mouse_EB_3D_WT


title: C315_G1_Mouse_EB_3D_WT


title: C315_G5_Mouse_EB_3D_WT


title: C315_G10_Mouse_EB_3D_WT


title: C315_G12_Mouse_EB_3D_WT


title: C315_G11_Mouse_EB_3D_WT


title: C315_F9_Mouse_EB_3D_WT


title: C300_A9_Mouse_EB_6D_3A2


title: C315_G4_Mouse_EB_3D_WT


title: C315_G8_Mouse_EB_3D_WT


title: C315_F6_Mouse_EB_3D_WT


title: C315_G6_Mouse_EB_3D_WT


title: C315_F2_Mouse_EB_3D_WT


title: C315_H8_Mouse_EB_3D_WT


title: C315_F12_Mouse_EB_3D_WT


title: C315_F11_Mouse_EB_3D_WT


title: C315_E9_Mouse_EB_3D_WT


title: C315_G7_Mouse_EB_3D_WT


title: C315_E8_Mouse_EB_3D_WT


title: C315_E6_Mouse_EB_3D_WT


title: C315_F5_Mouse_EB_3D_WT


title: C315_D9_Mouse_EB_3D_WT


title: C315_E11_Mouse_EB_3D_WT


title: C315_D6_Mouse_EB_3D_WT


title: C315_F1_Mouse_EB_3D_WT


title: C315_F3_Mouse_EB_3D_WT


title: C315_D1_Mouse_EB_3D_WT


title: C315_E12_Mouse_EB_3D_WT


title: C315_F10_Mouse_EB_3D_WT


title: C315_E10_Mouse_EB_3D_WT


title: C315_E1_Mouse_EB_3D_WT


title: C315_E5_Mouse_EB_3D_WT


title: C315_C8_Mouse_EB_3D_WT


title: C315_D8_Mouse_EB_3D_WT


title: C315_D3_Mouse_EB_3D_WT


title: C315_E4_Mouse_EB_3D_WT


title: C315_D7_Mouse_EB_3D_WT


title: C315_F8_Mouse_EB_3D_WT


title: C315_E2_Mouse_EB_3D_WT


title: C315_E3_Mouse_EB_3D_WT


title: C315_C6_Mouse_EB_3D_WT


title: C315_C4_Mouse_EB_3D_WT


title: C315_C5_Mouse_EB_3D_WT


title: C315_C3_Mouse_EB_3D_WT


title: C315_C10_Mouse_EB_3D_WT


title: C315_D2_Mouse_EB_3D_WT


title: C315_B7_Mouse_EB_3D_WT


title: C315_D12_Mouse_EB_3D_WT


title: C315_B6_Mouse_EB_3D_WT


title: C315_D4_Mouse_EB_3D_WT


title: C315_D11_Mouse_EB_3D_WT


title: C315_B5_Mouse_EB_3D_WT


title: C315_C12_Mouse_EB_3D_WT


title: C315_B2_Mouse_EB_3D_WT


title: C315_C1_Mouse_EB_3D_WT


title: C315_B3_Mouse_EB_3D_WT


title: C315_B4_Mouse_EB_3D_WT


title: C315_A8_Mouse_EB_3D_WT


title: C315_C11_Mouse_EB_3D_WT


title: C315_A9_Mouse_EB_3D_WT


title: C315_B11_Mouse_EB_3D_WT


title: C315_D10_Mouse_EB_3D_WT


title: C313_H5_Mouse_EB_3D_3B126


title: C313_H9_Mouse_EB_3D_3B126


title: C315_C2_Mouse_EB_3D_WT


title: C313_G7_Mouse_EB_3D_3B126


title: C315_B12_Mouse_EB_3D_WT


title: C313_G6_Mouse_EB_3D_3B126


title: C313_G5_Mouse_EB_3D_3B126


title: C313_G10_Mouse_EB_3D_3B126


title: C313_G11_Mouse_EB_3D_3B126


title: C315_A7_Mouse_EB_3D_WT


title: C315_B8_Mouse_EB_3D_WT


title: C315_B10_Mouse_EB_3D_WT


title: C315_A4_Mouse_EB_3D_WT


title: C313_F4_Mouse_EB_3D_3B126


title: C313_F7_Mouse_EB_3D_3B126


title: C313_F6_Mouse_EB_3D_3B126


title: C313_H11_Mouse_EB_3D_3B126


title: C313_F3_Mouse_EB_3D_3B126


title: C313_G8_Mouse_EB_3D_3B126


title: C313_F9_Mouse_EB_3D_3B126


title: C313_F1_Mouse_EB_3D_3B126


title: C313_E4_Mouse_EB_3D_3B126


title: C315_A6_Mouse_EB_3D_WT


title: C313_G4_Mouse_EB_3D_3B126


title: C313_F11_Mouse_EB_3D_3B126


title: C313_F8_Mouse_EB_3D_3B126


title: C315_B1_Mouse_EB_3D_WT


title: C313_E3_Mouse_EB_3D_3B126


title: C313_F10_Mouse_EB_3D_3B126


title: C313_F12_Mouse_EB_3D_3B126


title: C313_F5_Mouse_EB_3D_3B126


title: C313_E10_Mouse_EB_3D_3B126


title: C313_G3_Mouse_EB_3D_3B126


title: C313_E8_Mouse_EB_3D_3B126


title: C313_E9_Mouse_EB_3D_3B126


title: C313_D7_Mouse_EB_3D_3B126


title: C313_D4_Mouse_EB_3D_3B126


title: C313_F2_Mouse_EB_3D_3B126


title: C313_E2_Mouse_EB_3D_3B126


title: C313_D10_Mouse_EB_3D_3B126


title: C313_D12_Mouse_EB_3D_3B126


title: C313_D2_Mouse_EB_3D_3B126


title: C313_C9_Mouse_EB_3D_3B126


title: C313_D6_Mouse_EB_3D_3B126


title: C313_E12_Mouse_EB_3D_3B126


title: C313_C6_Mouse_EB_3D_3B126


title: C313_C7_Mouse_EB_3D_3B126


title: C313_C5_Mouse_EB_3D_3B126


title: C313_E1_Mouse_EB_3D_3B126


title: C313_D3_Mouse_EB_3D_3B126


title: C313_B9_Mouse_EB_3D_3B126


title: C313_D9_Mouse_EB_3D_3B126


title: C313_D11_Mouse_EB_3D_3B126


title: C313_E6_Mouse_EB_3D_3B126


title: C313_B8_Mouse_EB_3D_3B126


title: C313_C12_Mouse_EB_3D_3B126


title: C313_C1_Mouse_EB_3D_3B126


title: C313_C3_Mouse_EB_3D_3B126


title: C313_B7_Mouse_EB_3D_3B126


title: C313_B3_Mouse_EB_3D_3B126


title: C313_C2_Mouse_EB_3D_3B126


title: C313_C4_Mouse_EB_3D_3B126


title: C313_B6_Mouse_EB_3D_3B126


title: C313_C8_Mouse_EB_3D_3B126


title: C313_B1_Mouse_EB_3D_3B126


title: C313_C10_Mouse_EB_3D_3B126


title: C313_B5_Mouse_EB_3D_3B126


title: C313_A9_Mouse_EB_3D_3B126


title: C313_B2_Mouse_EB_3D_3B126


title: C313_C11_Mouse_EB_3D_3B126


title: C313_A2_Mouse_EB_3D_3B126


title: C313_B12_Mouse_EB_3D_3B126


title: C313_A11_Mouse_EB_3D_3B126


title: C313_B10_Mouse_EB_3D_3B126


title: C313_A12_Mouse_EB_3D_3B126


title: C344_H3_Mouse_EB_8D_WT


title: C344_H8_Mouse_EB_8D_WT


title: C313_A8_Mouse_EB_3D_3B126


title: C344_H2_Mouse_EB_8D_WT


title: C344_H9_Mouse_EB_8D_WT


title: C313_A7_Mouse_EB_3D_3B126


title: C344_G8_Mouse_EB_8D_WT


title: C344_G7_Mouse_EB_8D_WT


title: C344_G4_Mouse_EB_8D_WT


title: C344_G5_Mouse_EB_8D_WT


title: C344_H4_Mouse_EB_8D_WT


title: C344_G12_Mouse_EB_8D_WT


title: C313_A3_Mouse_EB_3D_3B126


title: C344_G1_Mouse_EB_8D_WT


title: C344_G3_Mouse_EB_8D_WT


title: C344_G11_Mouse_EB_8D_WT


title: C313_B4_Mouse_EB_3D_3B126


title: C313_B11_Mouse_EB_3D_3B126


title: C344_F8_Mouse_EB_8D_WT


title: C344_G10_Mouse_EB_8D_WT


title: C344_F9_Mouse_EB_8D_WT


title: C344_F6_Mouse_EB_8D_WT


title: C344_F5_Mouse_EB_8D_WT


title: C344_F3_Mouse_EB_8D_WT


title: C344_G9_Mouse_EB_8D_WT


title: C344_F1_Mouse_EB_8D_WT


title: C344_E8_Mouse_EB_8D_WT


title: C344_F10_Mouse_EB_8D_WT


title: C344_E5_Mouse_EB_8D_WT


title: C344_E2_Mouse_EB_8D_WT


title: C344_E4_Mouse_EB_8D_WT


title: C344_E12_Mouse_EB_8D_WT


title: C344_E3_Mouse_EB_8D_WT


title: C344_E10_Mouse_EB_8D_WT


title: C344_D6_Mouse_EB_8D_WT


title: C344_D11_Mouse_EB_8D_WT


title: C344_E6_Mouse_EB_8D_WT


title: C344_F12_Mouse_EB_8D_WT


title: C344_D10_Mouse_EB_8D_WT


title: C344_D3_Mouse_EB_8D_WT


title: C344_C6_Mouse_EB_8D_WT


title: C344_C4_Mouse_EB_8D_WT


title: C344_C7_Mouse_EB_8D_WT


title: C344_F11_Mouse_EB_8D_WT


title: C344_F4_Mouse_EB_8D_WT


title: C344_C8_Mouse_EB_8D_WT


title: C313_A10_Mouse_EB_3D_3B126


title: C344_C3_Mouse_EB_8D_WT


title: C344_C9_Mouse_EB_8D_WT


title: C344_E1_Mouse_EB_8D_WT


title: C344_C1_Mouse_EB_8D_WT


title: C344_D5_Mouse_EB_8D_WT


title: C344_C10_Mouse_EB_8D_WT


title: C344_C11_Mouse_EB_8D_WT


title: C344_C5_Mouse_EB_8D_WT


title: C344_B4_Mouse_EB_8D_WT


title: C344_E11_Mouse_EB_8D_WT


title: C344_B3_Mouse_EB_8D_WT


title: C344_A9_Mouse_EB_8D_WT


title: C335_G7_Mouse_EB_6D_3B126


title: C335_G5_Mouse_EB_6D_3B126


title: C344_A8_Mouse_EB_8D_WT


title: C335_G1_Mouse_EB_6D_3B126


title: C335_G12_Mouse_EB_6D_3B126


title: C344_C12_Mouse_EB_8D_WT


title: C335_F7_Mouse_EB_6D_3B126


title: C335_F6_Mouse_EB_6D_3B126


title: C344_A3_Mouse_EB_8D_WT


title: C344_B7_Mouse_EB_8D_WT


title: C344_B2_Mouse_EB_8D_WT


title: C335_F12_Mouse_EB_6D_3B126


title: C335_G10_Mouse_EB_6D_3B126


title: C335_F8_Mouse_EB_6D_3B126


title: C344_A11_Mouse_EB_8D_WT


title: C344_B6_Mouse_EB_8D_WT


title: C335_E5_Mouse_EB_6D_3B126


title: C335_E9_Mouse_EB_6D_3B126


title: C344_B11_Mouse_EB_8D_WT


title: C344_B10_Mouse_EB_8D_WT


title: C335_E1_Mouse_EB_6D_3B126


title: C344_D1_Mouse_EB_8D_WT


title: C335_G8_Mouse_EB_6D_3B126


title: C344_B1_Mouse_EB_8D_WT


title: C344_B9_Mouse_EB_8D_WT


title: C344_B5_Mouse_EB_8D_WT


title: C335_D8_Mouse_EB_6D_3B126


title: C335_E10_Mouse_EB_6D_3B126


title: C344_B8_Mouse_EB_8D_WT


title: C344_A2_Mouse_EB_8D_WT


title: C335_D6_Mouse_EB_6D_3B126


title: C335_F4_Mouse_EB_6D_3B126


title: C335_F5_Mouse_EB_6D_3B126


title: C335_D3_Mouse_EB_6D_3B126


title: C335_D2_Mouse_EB_6D_3B126


title: C335_G11_Mouse_EB_6D_3B126


title: C335_D12_Mouse_EB_6D_3B126


title: C335_C9_Mouse_EB_6D_3B126


title: C335_C7_Mouse_EB_6D_3B126


title: C335_E2_Mouse_EB_6D_3B126


title: C335_G3_Mouse_EB_6D_3B126


title: C335_C5_Mouse_EB_6D_3B126


title: C335_C3_Mouse_EB_6D_3B126


title: C335_C12_Mouse_EB_6D_3B126


title: C335_F3_Mouse_EB_6D_3B126


title: C335_F10_Mouse_EB_6D_3B126


title: C335_B5_Mouse_EB_6D_3B126


title: C335_D5_Mouse_EB_6D_3B126


title: C335_C8_Mouse_EB_6D_3B126


title: C335_B2_Mouse_EB_6D_3B126


title: C335_B3_Mouse_EB_6D_3B126


title: C335_B4_Mouse_EB_6D_3B126


title: C335_D4_Mouse_EB_6D_3B126


title: C335_B1_Mouse_EB_6D_3B126


title: C335_B12_Mouse_EB_6D_3B126


title: C335_B10_Mouse_EB_6D_3B126


title: C335_C10_Mouse_EB_6D_3B126


title: C335_A7_Mouse_EB_6D_3B126


title: C335_D10_Mouse_EB_6D_3B126


title: C335_F2_Mouse_EB_6D_3B126


title: C335_B9_Mouse_EB_6D_3B126


title: C335_A3_Mouse_EB_6D_3B126


title: C335_E11_Mouse_EB_6D_3B126


title: C335_C2_Mouse_EB_6D_3B126


title: C334_H7_Mouse_EB_6D_WT


title: C334_H9_Mouse_EB_6D_WT


title: C334_H6_Mouse_EB_6D_WT


title: C335_B11_Mouse_EB_6D_3B126


title: C334_H5_Mouse_EB_6D_WT


title: C335_C6_Mouse_EB_6D_3B126


title: C335_C4_Mouse_EB_6D_3B126


title: C334_H11_Mouse_EB_6D_WT


title: C334_H2_Mouse_EB_6D_WT


title: C334_G5_Mouse_EB_6D_WT


title: C335_C11_Mouse_EB_6D_3B126


title: C334_H10_Mouse_EB_6D_WT


title: C335_B7_Mouse_EB_6D_3B126


title: C334_G4_Mouse_EB_6D_WT


title: C334_G12_Mouse_EB_6D_WT


title: C334_G2_Mouse_EB_6D_WT


title: C334_G10_Mouse_EB_6D_WT


title: C335_B6_Mouse_EB_6D_3B126


title: C334_F8_Mouse_EB_6D_WT


title: C334_F7_Mouse_EB_6D_WT


title: C335_A5_Mouse_EB_6D_3B126


title: C334_F3_Mouse_EB_6D_WT


title: C335_A2_Mouse_EB_6D_3B126


title: C334_F1_Mouse_EB_6D_WT


title: C334_G8_Mouse_EB_6D_WT


title: C334_E3_Mouse_EB_6D_WT


title: C334_E2_Mouse_EB_6D_WT


title: C334_E11_Mouse_EB_6D_WT


title: C334_H4_Mouse_EB_6D_WT


title: C334_G3_Mouse_EB_6D_WT


title: C334_G1_Mouse_EB_6D_WT


title: C334_G11_Mouse_EB_6D_WT


title: C334_F5_Mouse_EB_6D_WT


title: C334_D8_Mouse_EB_6D_WT


title: C334_D7_Mouse_EB_6D_WT


title: C334_F12_Mouse_EB_6D_WT


title: C334_D5_Mouse_EB_6D_WT


title: C334_F2_Mouse_EB_6D_WT


title: C334_D3_Mouse_EB_6D_WT


title: C334_G9_Mouse_EB_6D_WT


title: C334_F4_Mouse_EB_6D_WT


title: C334_G6_Mouse_EB_6D_WT


title: C334_H3_Mouse_EB_6D_WT


title: C334_C8_Mouse_EB_6D_WT


title: C334_D2_Mouse_EB_6D_WT


title: C334_E8_Mouse_EB_6D_WT


title: C334_E4_Mouse_EB_6D_WT


title: C334_B6_Mouse_EB_6D_WT


title: C334_E6_Mouse_EB_6D_WT


title: C334_C10_Mouse_EB_6D_WT


title: C334_F11_Mouse_EB_6D_WT


title: C334_E10_Mouse_EB_6D_WT


title: C334_E5_Mouse_EB_6D_WT


title: C334_C1_Mouse_EB_6D_WT


title: C334_B1_Mouse_EB_6D_WT


title: C334_B10_Mouse_EB_6D_WT


title: C334_D4_Mouse_EB_6D_WT


title: C334_B11_Mouse_EB_6D_WT


title: C334_C3_Mouse_EB_6D_WT


title: C334_A6_Mouse_EB_6D_WT


title: C334_A2_Mouse_EB_6D_WT


title: C334_D6_Mouse_EB_6D_WT


title: C335_E3_Mouse_EB_6D_3B126


title: C334_A7_Mouse_EB_6D_WT


title: C334_A1_Mouse_EB_6D_WT


title: C334_C5_Mouse_EB_6D_WT


title: C334_A4_Mouse_EB_6D_WT


title: C334_C4_Mouse_EB_6D_WT


title: C334_B12_Mouse_EB_6D_WT


title: C334_A10_Mouse_EB_6D_WT


title: C334_E12_Mouse_EB_6D_WT


title: C334_C7_Mouse_EB_6D_WT


title: C334_B9_Mouse_EB_6D_WT


title: C343_F4_Mouse_EB_8D_WT


title: C334_A11_Mouse_EB_6D_WT


title: C343_D2_Mouse_EB_8D_WT


title: C343_E3_Mouse_EB_8D_WT


title: C334_A3_Mouse_EB_6D_WT


title: C343_E1_Mouse_EB_8D_WT


title: C334_A5_Mouse_EB_6D_WT


title: C343_E5_Mouse_EB_8D_WT


title: C343_D12_Mouse_EB_8D_WT_OLDNPM


title: C343_C3_Mouse_EB_8D_WT


title: C343_C2_Mouse_EB_8D_WT


title: C343_C12_Mouse_EB_8D_WT_OLDNPM


title: C343_C4_Mouse_EB_8D_WT


title: C343_D1_Mouse_EB_8D_WT


title: C343_B4_Mouse_EB_8D_WT


title: C343_E2_Mouse_EB_8D_WT


title: C343_E12_Mouse_EB_8D_WT_OLDNPM


title: C343_B12_Mouse_EB_8D_WT_OLDNPM


title: C343_A5_Mouse_EB_8D_WT


title: C343_B11_Mouse_EB_8D_WT


title: C343_B1_Mouse_EB_8D_WT


title: C340_G5_Mouse_EB_8D_3B126


title: C340_G8_Mouse_EB_8D_3B126


title: C340_G9_Mouse_EB_8D_3B126


title: C343_C10_Mouse_EB_8D_WT


title: C343_A3_Mouse_EB_8D_WT


title: C340_G1_Mouse_EB_8D_3B126


title: C340_G4_Mouse_EB_8D_3B126


title: C340_F7_Mouse_EB_8D_3B126


title: C340_G3_Mouse_EB_8D_3B126


title: C340_F6_Mouse_EB_8D_3B126


title: C340_F4_Mouse_EB_8D_3B126


title: C340_G10_Mouse_EB_8D_3B126


title: C343_B3_Mouse_EB_8D_WT


title: C340_F9_Mouse_EB_8D_3B126


title: C340_F1_Mouse_EB_8D_3B126


title: C340_F12_Mouse_EB_8D_3B126_07NPM


title: C340_F8_Mouse_EB_8D_3B126


title: C340_F5_Mouse_EB_8D_3B126


title: C340_E8_Mouse_EB_8D_3B126


title: C340_E9_Mouse_EB_8D_3B126


title: C340_F3_Mouse_EB_8D_3B126


title: C340_E5_Mouse_EB_8D_3B126


title: C340_E12_Mouse_EB_8D_3B126_07NPM


title: C340_E7_Mouse_EB_8D_3B126


title: C340_E6_Mouse_EB_8D_3B126


title: C340_E3_Mouse_EB_8D_3B126


title: C340_F2_Mouse_EB_8D_3B126


title: C340_D2_Mouse_EB_8D_3B126


title: C340_D6_Mouse_EB_8D_3B126


title: C340_D3_Mouse_EB_8D_3B126


title: C340_E2_Mouse_EB_8D_3B126


title: C340_D9_Mouse_EB_8D_3B126


title: C340_D5_Mouse_EB_8D_3B126


title: C340_C5_Mouse_EB_8D_3B126


title: C340_E4_Mouse_EB_8D_3B126


title: C340_D1_Mouse_EB_8D_3B126


title: C340_D10_Mouse_EB_8D_3B126


title: C340_E1_Mouse_EB_8D_3B126


title: C340_C7_Mouse_EB_8D_3B126


title: C340_C2_Mouse_EB_8D_3B126


title: C340_D12_Mouse_EB_8D_3B126_07NPM


title: C340_D4_Mouse_EB_8D_3B126


title: C340_F10_Mouse_EB_8D_3B126


title: C340_B10_Mouse_EB_8D_3B126


title: C340_B1_Mouse_EB_8D_3B126


title: C340_C8_Mouse_EB_8D_3B126


title: C340_B11_Mouse_EB_8D_3B126


title: C340_C6_Mouse_EB_8D_3B126


title: C340_B9_Mouse_EB_8D_3B126


title: ME48h_3BKO_B77_3B_rep2

data_processing:
Following quality controls (performed with FastQC v0.11.2), sequencing reads were aligned to the mouse reference genome (mm10/GRCm38 Ensembl release 84) using HiSat2 v2.2.1 (Kim 2019) . Pre-built indexes based on the Ensembl transcript annotation (release 84) for guided alignment to transcriptome were retrieved from the HiSat2 web site ( https://cloud.biohpc.swmed.edu/index.php/s/grcm38_tran/download). Gene expression levels were quantified with featureCounts v1.6.1 (Liao 2015) using the Ensembl release 84 transcript annotation (ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/Mus_musculus.GRCm38.84.gtf.gz). Multi-mapped reads were excluded from quantification.
Assembly: mm10/GRCm38
Supplementary files format and content: Tab-delimited text file of normalized read counts per gene/samples.

source_name: Mouse Meso-Endodermal Progenitors

growth_protocol: E14 mouse WT and mutant (Dnmt3a -/-   and Dnmt3b -/-) ESCs were cultured in high-glucose DMEM (Euroclone) supplemented with 15% FBS (Millipore Corp., Billerica, MA, USA), 0.1 mmol/l nonessential amino acids (Invitrogen), 1 mmol/l sodium pyruvate (Invitrogen), 0.1 mmol/l β-mercaptoethanol, 1500 U/ml Leukemia Inhibitory Factor (LIF; Millipore), 25 U/ml penicillin, and 25 μg/ml streptomycin. For EpiSC induction, a single-cell suspension was seeded onto Geltrex (A1413202 GIBCO)-coated plates at a density of 10,000 cells cm-2 in N2B27 medium supplemented with 20ng/ml ActivinA (PHC9564 GIBCO) and 12 ng/ml bFGF (PHG0026 GIBCO). The cells were passaged 1:3 as small clumps using Collagenase IV (17104019 GIBCO). EpiSCs were collected for DNA and RNA analyses after 14 days of induction followed by daily medium changes. N2B27 medium is composed by 50% advanced DMEM/F12 (12634028 GIBCO) and 50% Neurobasal medium (21103049 GIBCO), supplemented with 0.5% N2 Supplement (17502048 GIBCO), 1% B27 Supplement (17504044 GIBCO), 0.033% BSA solution (A9647 SIGMA), 50 uM β-mercaptoethanol (M3148 Sigma), 2mM Glutamax (35050038 GIBCO), 100U/ml penicillin and 100 ug/ml streptomycin (DE17-602E LONZA). For Meso-endoderm directed lineage specific differentiation, EpiSCs were plated as small clumps onto Geltrex-coated plates in EpiSCs medium for 24 hours. The day after, medium was replaced with N2NB27 medium consisted of 50% advanced DMEM/F12 (12634028 GIBCO) and 50% Neurobasal medium (21103049 GIBCO), supplemented with 0.5% N2 Supplement (17502048 GIBCO), 1% B27 supplement minus Vitamin A (12587010 GIBCO) and 3 uM iGSK3β (CHIR99021 SIGMA). Cells were fed daily until the end of differentiation.

extract_protocol:
Total RNA was extracted by using TRIzol reagent (Invitrogen), according to manufacturer’s protocol.
Total RNA was isolated using TRIzol reagent (Invitrogen), according to the manufacturer’s protocol. Quantity and quality of the starting RNA were checked by Qubit and Bioanalyzer (Agilent). 1 μg of total RNA was subjected to poly(A) selection, and libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75 bp reads).

value: EpiLC-derived ME progenitors

value: Dnmt3b -/- (3BKO)

value: Transfected with pEF6-Dnmt3b

tag: condition

value: ME T48h

tag: clone


title: C340_C3_Mouse_EB_8D_3B126


title: ME48h_3BKO_B126_3B_rep2


title: C340_C12_Mouse_EB_8D_3B126_07NPM


title: C340_B5_Mouse_EB_8D_3B126


title: ME48h_3BKO_B126_rep2

value: Transfected with pEF6-Empty


title: ME24h_3BKO_B77_3B_rep2

value: ME T24h


title: C340_C9_Mouse_EB_8D_3B126


title: ME48h_3BKO_B77_rep2


title: ME48h_3BKO_B77_3B_rep1


title: ME24h_3BKO_B77_rep2


title: EpiLC_3BKO_B126_rep2

source_name: Mouse Epiblast-Like Cells

value: ES-E14 derived EpiLCs

value: EpiLC


title: EpiLC_3BKO_B77_3B_rep1


title: ME48h_3BKO_B126_rep1


title: ME48h_3BKO_B77_rep1


title: ME24h_3BKO_B126_3B_rep2


title: ME24h_3BKO_B126_rep2


title: EpiLC_3BKO_B126_3B_rep1


title: ESC_B77_CRISPRoff

data_processing:
Following quality controls, sequencing reads were processed with Trim Galore! v0.5.0 to perform quality and adapter trimming (parameters: --stringency 3 –q 20 --paired). Trimmed reads were next aligned to the mouse reference genome (UCSC mm10/GRCm38) using Bismark v0.22.3.The bisulfite-converted genome was created using the bismark_genome_preparation utility (parameters: --genomic_composition --bowtie2). Read mapping was performed with the bismark command (parameters: --nucleotide_coverage). Duplicated alignments were removed with the deduplicate_bismark utility and methylation calling was carried out using the bismark_methylation_extractor utility (parameters: --ignore 1 --bedGraph --counts --gzip). Cytosine methylation reports with the top and bottom strand methylation evidence pooled into a single CpG dinucleotide entity were obtained using the coverage2cytosine utility (parameters: --zero_based --gzip --merge_CpG).
Assembly: mm10/GRCm38
Supplementary files format and content: BigWig files containing CpG methylation scores at single-base resolution.

source_name: Mouse Embryonic Sem Cells

growth_protocol: E14 mouse WT and mutant (Dnmt3a -/-   and Dnmt3b -/-) ESCs were cultured in high-glucose DMEM (Euroclone) supplemented with 15% FBS (Millipore Corp., Billerica, MA, USA), 0.1 mmol/l nonessential amino acids (Invitrogen), 1 mmol/l sodium pyruvate (Invitrogen), 0.1 mmol/l β-mercaptoethanol, 1500 U/ml Leukemia Inhibitory Factor (LIF; Millipore), 25 U/ml penicillin, and 25 μg/ml streptomycin. For EpiSC induction, a single-cell suspension was seeded onto Geltrex (A1413202 GIBCO)-coated plates at a density of 10,000 cells cm-2 in N2B27 medium supplemented with 20ng/ml ActivinA (PHC9564 GIBCO) and 12 ng/ml bFGF (PHG0026 GIBCO). The cells were passaged 1:3 as small clumps using Collagenase IV (17104019 GIBCO). EpiSCs were collected for DNA and RNA analyses after 14 days of induction followed by daily medium changes. N2B27 medium is composed by 50% advanced DMEM/F12 (12634028 GIBCO) and 50% Neurobasal medium (21103049 GIBCO), supplemented with 0.5% N2 Supplement (17502048 GIBCO), 1% B27 Supplement (17504044 GIBCO), 0.033% BSA solution (A9647 SIGMA), 50 uM β-mercaptoethanol (M3148 Sigma), 2mM Glutamax (35050038 GIBCO), 100U/ml penicillin and 100 ug/ml streptomycin (DE17-602E LONZA).

extract_protocol:
Genomic DNA was extracted from cells using the DNeasy Blood and Tissue kit (QIAGEN, 69506) following the manufacturer’s instructions.
For each condition, 1 μg genomic DNA was subjected to bisulfite conversion and cleanup according to manufacturer’s instructions using the EpiTect Bisulfite kit (Qiagen_#59104), eluting to 40 μl. 3 μl eluate was used for individual amplicons PCR amplification using AccuPrime™ Taq DNA Polymerase System (Invitrogen_#12346086). Amplicons were then purified using a MinElute PCR Purification Kit (Qiagen_#28006) and eluted to 15 μl. The Sox2 super enhancer amplicons were amplified using the primer pairs listed in Supplementary Table 8. Amplicons were sequenced on the Illumina NextSeq 500 Platform.

value: ESCs

value: ESC


title: ME24h_3BKO_B77_rep1


title: C340_B7_Mouse_EB_8D_3B126


title: ME24h_3BKO_B77_3B_rep1


title: ESC_B77_CRISPRoff_gRNAs_E3


title: ESC_B77_CRISPRoff_gRNAs_E4


title: ESC_B77_CRISPRoff_gRNAs_E1


title: EpiLC_3BKO_B77_rep2


title: EpiLC_3BKO_B77_3B_rep2


title: EpiLC_3BKO_B126_rep1


title: ESC_B126_CRISPRoff_gRNAs_E3


title: EpiLC_3BKO_B77_rep1


title: ESC_B126_CRISPRoff_gRNAs_E2


title: ESC_B77_CRISPRoff_untransfected


title: ME24h_3BKO_B126_rep1


title: ESC_B77_CRISPRoff_gRNAs_E2


title: Hippocampus, 862, H

description:
Brain_All_RNAcounts.mtx.gz
Brain_barcodes.tsv.gz
Brain_features.tsv.gz

source_name: brain (hippocampus)

tag: tissue

value: brain (hippocampus)

value: CD


title: Hippocampus, 976, H


title: ME48h_3BKO_B126_3B_rep1


title: Hippocampus, 636, H


title: Hippocampus, 637, H

value: HFD


title: Hippocampus, 485, H


title: ESC_B126_CRISPRoff


title: Hippocampus, 650, H


title: EpiLC_3BKO_B126_3B_rep2


title: EpiLC_B77


title: ESC_B126_CRISPRoff_gRNAs_E4


title: Hippocampus, 484, H


title: Hippocampus, 69, H


title: EpiLC_WT

value: Wild type (WT)


title: ME24h_3BKO_B126_3B_rep1


title: Hippocampus, 481, H


title: EpiLC_B77_3b


title: EpiLC_B126_3b


title: Hippocampus, 644, H


title: Hippocampus, 464, H


title: ESC_B126_CRISPRoff_untransfected


title: Hippocampus, 453, H


title: EpiLC_B126


title: ESC_B126_CRISPRoff_gRNAs_E1


title: Hippocampus, 660, H


title: Hippocampus, 478, H


title: 5_LSD1-mKO2 Sol VWR

city: Kumamoto

first: Hirotaka

last: Araki

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

data_processing:
Resulting reads were aligned to the UCSC mm10 reference genome by using STAR.
DESeq2 was used for quantification of gene expression changes. Top 1000 genes showing differential expression between the WT and KO mice were extracted from the genes with mean TPM >1 by using median absolute deviation (MAD).
Assembly: mm10
Supplementary files format and content: All_gene_FC.txt  in text file format.

source_name: mouse soleus muscle

growth_protocol: Mice were maintained in a temperature-controlled animal facility with a 12-h light/12-h dark cycle and fed ad libitum on a regular diet. All procedures were conducted in accordance with the guidelines of the Animal Care and Use Committee of Kumamoto University.

extract_protocol:
Total RNA from the muscles were extracted using a Trizol reagent (Invitrogen). mRNA was purified using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
cDNA library for sequencing was synthesized using NEB Next Ultra DNA Library Prep Kit for Illumina (NEB) and was sequenced on NextSeq 500 sequencer (Illumina) with 75-bps single-end reads.

treatment_protocol: Eight-week-old control or LSD1-mKO mice were single-housed in cages with free access to a vertical running wheel (Shinano Seisakusho) for 38 days. After three days of familiarization,  LSD1-KO was induced by  tamoxifen injection at a dose of 75 mg/kg for five consecutive days, and running distance was measured during the next 30 days.

tag: mouse genotype

value: VWR training

value: mouse soleus muscle


title: Hippocampus, 32, H


title: 6_LSD1-mKO3 Sol VWR


title: 3_WT3 Sol VWR

value: WT


title: Hippocampus, 479, H


title: Hippocampus, 468, H


title: Hippocampus, 467, H


title: Hippocampus, 470, H

description:
Brain_All_RNAcounts.mtx.gz
Brain_barcodes.tsv.gz
Brain_features.tsv.gz
Illumina NextSeq 500 & 2000


title: LSD1-mKO3 Sol Dex [a8]

data_processing:
Resulting reads were aligned to the UCSC mm10 reference genome by using STAR.
Edge R was used for quantification of gene expression changes, in which an FDR cut-off of 0.05 was used to determine differentially expressed genes between WT and KO mice.
Assembly: mm10
Supplementary files format and content: all_genes_FC_Gas.txt and all_genes_FC_Sol.txt  in text file format.

treatment_protocol: To induce skeletal muscle-specific LSD1 knockout, 20 mg/mL tamoxifen in corn oil was administered intraperitoneally to eight-week-old male LSD1-mKO or WT mice at a dose of 75 mg/kg for five consecutive days. From the fourth day of tamoxifen administration,  dexamethasone at 1 mg/kg was intraperitoneally administered for seven consecutive days.

value: Dexamethasone treated


title: LSD1-mKO4 Sol Dex [a9]


title: WT1 Sol Dex [a1]


title: Hippocampus, 462, H


title: 2_WT2 Sol VWR


title: Hippocampus, 451, H


title: Hippocampus, 640, H


title: Hippocampus, 465, H


title: Hippocampus, 44, H


title: LSD1-mKO5 Sol Dex [a10]


title: LSD1-mKO2 Gas Dex [araki5]

source_name: mouse gastrocnemius muscle

value: mouse gastrocnemius muscle


title: Hippocampus, 482, H


title: Hippocampus, 447, H


title: WT1 Gas Dex [araki1]


title: WT2 Gas Dex [araki2]


title: 1_WT1 Sol VWR


title: LSD1-mKO3 Gas Dex [araki6]


title: 4_LSD1-mKO1 Sol VWR


title: 238_H7_EB_9D_3B_SC_Batch1

data_processing:
Following quality controls (performed with FastQC v0.11.2 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc)), sequencing reads were processed with Trim Galore! v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to perform quality and adapter trimming (parameters: --stringency 3 –q 20). Trimmed reads were next aligned to the mouse reference genome (mm10/GRCm38.p6) using STAR v2.7.1a with options: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04. Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using the GENCODE Release M23 annotation. Multi-mapped reads were excluded from quantification.
Genome_build: mm10/GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text file of raw read counts matrix per gene/cell.

source_name: Mouse Embryoid Bodies

extract_protocol:
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol.
Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads), reaching a median of ~ 578,000 generated reads per cell.

value: Embryoid Bodies (EB)

value: Dnmt3b -/- (3BKO)


title: Hippocampus, 458, H


title: LSD1-mKO2 Sol Dex [a7]


title: LSD1-mKO4 Gas Dex [araki7]


title: 238_H8_EB_9D_3B_SC_Batch1


title: 238_G7_EB_9D_3B_SC_Batch1


title: 238_H9_EB_9D_3B_SC_Batch2


title: Hippocampus, 39, H


title: 238_G5_EB_9D_3B_SC_Batch1


title: 238_G6_EB_9D_3B_SC_Batch1


title: 238_G8_EB_9D_3B_SC_Batch1


title: 238_H1_EB_9D_3B_SC_Batch1


title: WT3 Gas Dex [araki8]


title: LSD1-mKO1 Sol Dex [a6]


title: WT2 Sol Dex [a2]


title: 238_H3_EB_9D_3B_SC_Batch1


title: 238_H5_EB_9D_3B_SC_Batch1


title: LSD1-mKO5 Gas Dex [araki3]


title: LSD1-mKO1 Gas Dex [araki4]


title: 238_H6_EB_9D_3B_SC_Batch1


title: 238_H2_EB_9D_3B_SC_Batch1


title: 238_G4_EB_9D_3B_SC_Batch1


title: 238_H4_EB_9D_3B_SC_Batch1


title: 238_G9_EB_9D_3B_SC_Batch2


title: 238_G1_EB_9D_3B_SC_Batch1


title: 238_G3_EB_9D_3B_SC_Batch1


title: WT3 Sol Dex [a3]


title: 238_G2_EB_9D_3B_SC_Batch1


title: 238_G12_EB_9D_3B_SC_Batch2


title: 238_G11_EB_9D_3B_SC_Batch2


title: 238_F8_EB_9D_3B_SC_Batch1


title: 238_G10_EB_9D_3B_SC_Batch2


title: 238_F3_EB_9D_3B_SC_Batch1


title: 238_F7_EB_9D_3B_SC_Batch1


title: 238_F12_EB_9D_3B_SC_Batch2


title: 238_F9_EB_9D_3B_SC_Batch2


title: 238_E5_EB_9D_3B_SC_Batch1


title: 238_E1_EB_9D_3B_SC_Batch1


title: 238_E6_EB_9D_3B_SC_Batch1


title: 238_E7_EB_9D_3B_SC_Batch1


title: 238_F6_EB_9D_3B_SC_Batch1


title: 238_E10_EB_9D_3B_SC_Batch2


title: 238_F2_EB_9D_3B_SC_Batch1


title: 238_E12_EB_9D_3B_SC_Batch2


title: 238_E2_EB_9D_3B_SC_Batch1


title: 238_F10_EB_9D_3B_SC_Batch2


title: 238_E11_EB_9D_3B_SC_Batch2


title: 238_F11_EB_9D_3B_SC_Batch2


title: 238_E9_EB_9D_3B_SC_Batch2


title: 238_F5_EB_9D_3B_SC_Batch1


title: 238_D9_EB_9D_3B_SC_Batch2


title: 238_D4_EB_9D_3B_SC_Batch1


title: 238_D6_EB_9D_3B_SC_Batch1


title: 238_E8_EB_9D_3B_SC_Batch1


title: 238_E4_EB_9D_3B_SC_Batch1


title: 238_D1_EB_9D_3B_SC_Batch1


title: 238_F4_EB_9D_3B_SC_Batch1


title: 238_C8_EB_9D_3B_SC_Batch1


title: 238_E3_EB_9D_3B_SC_Batch1


title: 238_C6_EB_9D_3B_SC_Batch1


title: 238_D10_EB_9D_3B_SC_Batch2


title: 238_C7_EB_9D_3B_SC_Batch1


title: 238_D2_EB_9D_3B_SC_Batch1


title: 238_F1_EB_9D_3B_SC_Batch1


title: 238_C4_EB_9D_3B_SC_Batch1


title: 238_D5_EB_9D_3B_SC_Batch1


title: 238_C12_EB_9D_3B_SC_Batch2


title: 238_D8_EB_9D_3B_SC_Batch1


title: 238_D3_EB_9D_3B_SC_Batch1


title: 238_D7_EB_9D_3B_SC_Batch1


title: 238_C3_EB_9D_3B_SC_Batch1


title: 238_B9_EB_9D_3B_SC_Batch2


title: 238_B7_EB_9D_3B_SC_Batch1


title: 238_C11_EB_9D_3B_SC_Batch2


title: 238_C9_EB_9D_3B_SC_Batch2


title: 238_D11_EB_9D_3B_SC_Batch2


title: 238_D12_EB_9D_3B_SC_Batch2


title: 238_C10_EB_9D_3B_SC_Batch2


title: 238_B4_EB_9D_3B_SC_Batch1


title: 238_B2_EB_9D_3B_SC_Batch1


title: 238_C2_EB_9D_3B_SC_Batch1


title: 238_C5_EB_9D_3B_SC_Batch1


title: 238_C1_EB_9D_3B_SC_Batch1


title: 238_A9_EB_9D_3B_SC_Batch2


title: 238_A6_EB_9D_3B_SC_Batch1


title: 238_B12_EB_9D_3B_SC_Batch2


title: 238_A8_EB_9D_3B_SC_Batch1


title: 238_B11_EB_9D_3B_SC_Batch2


title: 238_A7_EB_9D_3B_SC_Batch1


title: 238_B6_EB_9D_3B_SC_Batch1


title: 238_A4_EB_9D_3B_SC_Batch1


title: S4a_modified

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

library_source: other

data_processing:
We removed adapters using cutadapt (-a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 10) (Martin, 2011). Then we joined two pair-end reads using fastq-join (Aronesty, 2013). The low-quality and duplicated reads were filtered out using fastq_quality_filter (-q 20 -p 90) and fastx_collapser, respectively (http://hannonlab.cshl.edu/fastx_toolkit/index.html). The 6 nt randomized barcodes in the 3p-end of the remaining reads were removed. The reads in fasta format were further converted into fastq format. Next, ShapeMapper2 software was applied to identify RNA structures of pri-mir-142 variants (shapemapper --min-seq-depth 1000) (Busan and Weeks, 2018). The resulting SHAPE reactivity data from ShapeMapper2 were applied to detect RNA structures using RNAstructure (Reuter and Mathews, 2010).
Assembly: Pri-mir-142 variant sequences
Supplementary files format and content: target_sequences.txt: Tab-delimited text file contains the target sequences of pri-mir-142 variants
Supplementary files format and content: S1_profile.txt: Tab-delimited text file contains the read profiles generated from S1_untreated and S1_modified samples
Supplementary files format and content: S1_shape_reactivity.txt: Tab-delimited text file contains the shape reactivity for each nucleotide of S1 variants
Supplementary files format and content: S4a_profile.txt: Tab-delimited text file contains the read profiles generated from S4a_untreated and S4a_modified samples
Supplementary files format and content: S4a_shape_reactivity.txt: Tab-delimited text file contains the shape reactivity for each nucleotide of S4a variants

molecule: other

organism: synthetic construct

source_name: In vitro transcription

extract_protocol:
Illumina adapter sequences were incorporated to the libraries using PCR.
Different variants of pri-mir-142 were folded in buffer containing 50 mM Tris-HCl pH 7.5, 100 mM NaCl, 2 mM MgCl2 at 37°C for 20 min. Next, 1M7 (1-Methyl-7-nitroisatoic anhydride) (Sigma-Aldrich, 908401) was added to the concentration of 10 mM and incubated for 75 s at 37°C to modify RNAs. The control samples were prepared in parallel, where DMSO was added instead of 1M7. After modification, RNAs were precipitated by isopropanol and washed by ethanol before being ligated to the 3' adapter (6N-RA3). Next, the reverse transcription was performed for 3 h at 42°C by SuperScript II (Invitrogen™, 18064014) using R-RA3 primer in the buffer containing 0.5 mM dNTPs, 50 mM Tris-HCl pH 8.0, 75 mM KCl, 6 mM MnCl2 and 10 mM DTT. The resulting cDNAs were later amplified two time, the first time by R-RA3 and the pri-mir-142 sequence-specific forward primer, and the second time by sequencing primers, both using Phusion Hot Start II DNA Polymerase. The final DNA products were subjected to next-generation sequencing using the Illumina Novaseq 6000 sequencer.

tag: type sample

value: 4 matched nt in CNNC are consecutive

value: modified


title: 238_A3_EB_9D_3B_SC_Batch1

tag: strain


title: S1_modified

value: 1 matched nt in CNNC


title: 238_B5_EB_9D_3B_SC_Batch1


title: 238_A5_EB_9D_3B_SC_Batch1


title: 238_B8_EB_9D_3B_SC_Batch1


title: 238_A10_EB_9D_3B_SC_Batch2


title: 238_A2_EB_9D_3B_SC_Batch1


title: 238_A1_EB_9D_3B_SC_Batch1


title: 238_A12_EB_9D_3B_SC_Batch2


title: MP_SRSF3_product_repeat1

data_processing:
We removed adapters using cutadapt (-a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 10) (Martin, 2011). Then we joined two pair-end reads using fastq-join (Aronesty, 2013). The low-quality and duplicated reads were filtered out using fastq_quality_filter (-q 20 -p 90) and fastx_collapser, respectively (http://hannonlab.cshl.edu/fastx_toolkit/index.html). The 6 nt and 4 nt randomized barcodes were discarded from the cleaved products and original substrates, respectively. We mapped the resulting reads to the built-in sequence references containing all 1,532 pri-miRNA variants using BWA (Li and Durbin, 2010). Only unique mapped reads were collected. The raw read counts were normalized as count per million.
Assembly: Pri-miRNA construct sequences
Supplementary files format and content: reference_sequences.txt: Tab-delimited text file contains the reference sequences of pri-miRNA variants
Supplementary files format and content: control_rawcount.txt: Tab-delimited text file contains the raw count of pri-miRNA variants in the control samples
Supplementary files format and content: product_rawcount.txt: Tab-delimited text file contains the raw count of cleaved products for each pri-miRNA variants in product samples
Library strategy: pri-miRNA cleavage assay

source_name: In vitro cleavage

extract_protocol:
Illumina adapter sequences were incorporated to the libraries using PCR.
In high-throughput pri-miRNA cleavage assays, 3 pmol of each randomized pri-miRNA group were incubated with 5 pmol of the MP without or with 10 pmol of SRSF3 or SRSF7 at 37°C for 2 h, in 10 μL of the standard reaction buffer as mentioned above. After the reaction, the cleaved RNA products were purified using phenol extraction followed by isopropanol precipitation. The purified RNAs were ligated with the RA5-6N adapter (GUU CAG AGU UCU ACA GUC CGA CGA UCN NNN NN) and then the resulting RA5-6N-ligated RNAs were reverse-transcribed using R-RA3 primer and SuperScript™ IV Reverse Transcriptase to generate cDNAs. The cDNAs were finally amplified using PCR with the sequencing primers into DNA libraries of the cleaved products. The pri-miRNA substrates were cloned using a circularization method. The pri-miRNAs were first reverse transcribed using SuperScript™ IV Reverse Transcriptase and cirRTP primer (5Phos/NNN NNN GAT CGT CGG ACT GTA GAA CTC TGA AC/iSp18/CCT TGG CAC CCG AGA ATT CCA). The resulting cDNAs were circularized by CircLigase™ ssDNA Ligase (Cat. No. CL4115K from Lucigen). The circularized cDNAs were eventually amplified by PCR using the sequencing primers into DNA libraries of the pri-miRNA substrates.

value: MP + SRSF3 product

tag: repeat

value: repeat 1


title: 236_H6_EB_9D_3A_SC_Batch1

value: Dnmt3a -/- (3AKO)


title: MP_product_repeat3

value: MP product

value: repeat 3


title: MP_SRSF3_product_repeat2

value: repeat 2


title: Original_substrates_repeat3

value: control


title: 236_H5_EB_9D_3A_SC_Batch1


title: MP_product_repeat1


title: 238_A11_EB_9D_3B_SC_Batch2


title: 238_B1_EB_9D_3B_SC_Batch1


title: 236_H2_EB_9D_3A_SC_Batch1


title: 238_B3_EB_9D_3B_SC_Batch1


title: 238_B10_EB_9D_3B_SC_Batch2


title: S1_untreated

value: untreated


title: MP_SRSF7_product_repeat2

value: MP + SRSF7 product


title: S4a_untreated


title: MP_SRSF7_product_repeat3


title: Original_substrates_repeat2


title: 236_G9_EB_9D_3A_SC_Batch2


title: MHCC97H  Combi

city: Amsterdam

first: Antonio

last: Mulero-Sánchez

state: Nord-Holland

address: Plesmanlaan 121

department: Molecular Carcinogenesis

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Perform alignment against reference genome hg38 (BAM-files)
Default multiplexing - Index in separate read. Not barcoded
Assembly: hg38
Supplementary files format and content: csv file, matrix table with normalized abundance

extract_protocol:
RNA was extracted using the RNeasy Mini Kit from Qiagen and analyzed using an Agilent 2100 Bioanalyzer system
[W17] polyA+ stranded RNA Library prep from tissue

value: Hepatocelluar carcinoma cancer cells

value: WT

value: AZD8055 +Compound #57


title: MP_SRSF7_product_repeat1


title: 236_G5_EB_9D_3A_SC_Batch1

value: Embryoid Bodies (EB)


title: 236_H9_EB_9D_3A_SC_Batch2


title: MP_SRSF3_product_repeat3


title: 236_H8_EB_9D_3A_SC_Batch1


title: MHCC97H  AZD8055


title: 236_G4_EB_9D_3A_SC_Batch1


title: 236_G3_EB_9D_3A_SC_Batch1


title: Hep3B Combi


title: 236_H7_EB_9D_3A_SC_Batch1


title: seedling, WT in dark with Rifampicin, biological replicate3

city: Hannover

first: Thomas

last: Pflannschmidt

address: Herrenhäuser Straße 2

country: Germany

institute: Leibniz-Universität Hannover

description: Arabidopsis seedlings day 4 in dark; with proplastids during skotomorphogenesis

hyb_protocol: ssDNA were hybridized on an Affymetrix Chip, Arabidopsis Gene 1.0 ST Array as described in the manual (GeneChip® WT Terminal  Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit, Rev. 7, Affymetrix).

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed with RobiNA (1.2.4_build656) using default analysis settings and normalization method RMA with p-value correction after Benjamini-Hochberg method.

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings day 4 in dark with Rifampicin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® WT Terminal  Labeling and Hybridization User Manual for use with the Ambion® WT Expression Kit, Rev. 7, Affymetrix).

growth_protocol: Seeds were surface-sterilized (Ethanol) and spread on MS agar plates with 1% sucrose and powdered charcoal (4 ml / 1 l MS-medium).  The plates were kept for 72 h at 4°C in darkness and were exposed to light for 6h to induce germination. Plants grow at 21°C.

extract_protocol: Total RNA from seedlings was isolated using and RNeasy Plant Mini Kit (Qiagen) with on-column DNase I (Qiagen) treatment.

treatment_protocol: Plants grow in darkness for 4 days; wt plants (Col-0) are treated with Rifampicin (200µg/ml) in MS agar

value: whole seedling

value: wildtype

tag: ecotype

tag: age

value: 4 days


title: 236_G1_EB_9D_3A_SC_Batch1


title: 236_G2_EB_9D_3A_SC_Batch1


title: Original_substrates_repeat1


title: 236_H3_EB_9D_3A_SC_Batch1


title: MP_product_repeat2


title: Hep3B SHP2i

value: Compound #57


title: 236_H4_EB_9D_3A_SC_Batch1


title: 236_G7_EB_9D_3A_SC_Batch1


title: 236_G8_EB_9D_3A_SC_Batch1


title: 236_G12_EB_9D_3A_SC_Batch2


title: 236_G6_EB_9D_3A_SC_Batch1


title: Hep3B AZD8055


title: 236_H1_EB_9D_3A_SC_Batch1


title: Huh7 SHP2i


title: 236_F9_EB_9D_3A_SC_Batch2


title: seedling, WT in dark with Rifampicin, biological replicate2


title: MHCC97H  SHP2i


title: MHCC97H  Control

value: Untreated


title: Huh7 AZD8055


title: Huh7 Control


title: 236_F8_EB_9D_3A_SC_Batch1


title: seedling, WT in dark with Rifampicin, biological replicate1


title: Hep3B Control


title: 236_F6_EB_9D_3A_SC_Batch1


title: 236_G11_EB_9D_3A_SC_Batch2


title: 236_F7_EB_9D_3A_SC_Batch1


title: BT799_MRD_TR

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description: Chemoradiotherapy-treated, BT799 line at minimal residual disease (MRD) state

data_processing:
Raw FASTQ files were aligned to the hg19 genome using STAR aligner (STAR v2.5.2b), and the CellRanger (v2.1.1) pipeline was used to obtain the filtered gene x cell raw count matrix.
Raw count matrices were loaded into a Seurat object (Seurat R package, v 4.0.4), and filtered to retain cells with (i) 200 – 9000 recovered genes per cell and (ii) less than 60% mitochondrial content.
sctransform (sctransform R Package, v 0.3.2) was used to normalize and scale count matrix values
Genome_build: hg19
Supplementary_files_format_and_content: raw count matrix with cell-level meta data.

source_name: Primary human glioblastoma cells

growth_protocol: Neurospheres derived from minimally-cultured human GBM samples were plated on polyornithine- laminin coated plates for adherent growth. Adherent cells were replated in low-binding plates and cultured as tumorspheres, which were maintained as spheres upon serial passaging in vitro. These cells retained their self-renewal potential and were capable of in vivo tumor formation.

extract_protocol:
Single-cell library preparation was carried out as per the 10X Genomics Chromium single-cell protocol using the v2 chemistry reagent kit (10X Genomics, Plesanton, CA, USA). Cell suspensions were loaded onto individual channels of a Chromium Single-Cell Chip along reverse transcription (RT) master mix and single cell 3’ gel beads, aiming for 1000 captured cells per sample. Following generation of gel bead-in-emulsions (GEMs), cDNA was underwent a two-stage purification process with Dynal MyONE Silane beads (Thermo Fisher Scientific), followed by SPRISelect beads (Beckman Coulter). RT and cDNA amplification were performed using a 96-well Veriti Thermocycler (Life Technologies). Amplified cDNA purified using SPRIselect beads and sequencing libraries were generated with unique sample indexes (SI). Dual sided SPRIselect cleanup was used to clean up samples and size select. Libraries were sequenced on an Illumina 2500 in Highoutput mode at the Princess Margaret Genomics Centre (Toronto, ON) using the 10X Genomics recommended sequencing parameters.  Samples were quantified by Kapa Library Quantification kit (Roche) and normalized to achieve the desired median read depth per cell
10x genomics

treatment_protocol:
1x106 GBM cells (BT799 or MBT06) were injected in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mouse brains as previously described. Briefly, mice were anesthetized using gas anesthesia (Isoflurane: 2.5%). Using a 15-blade scalpel a 1.5 cm vertical midline incision was made on top of the skull. A small burr hole was then made (2-3 mm anterior to the coronal suture, 3 mm lateral to midline) using a drill held perpendicular to the skull. A Hamilton syringe was used to inject 10μL of cell suspension of GBM cells into the frontal lobe. The syringe was inserted through the burr hole at a 30o angle to a 5 mm depth. The incision was closed using interrupted stitches and sutures were sealed with a tissue adhesive. Mice were identified using ear notches and placed in recovery cages. Mice were monitored weekly for signs of illness and sacrificed at endpoint.
Once tumor engraftment was confirmed using MRI, mice were randomly assigned to control or treatment groups and chemoradiotherapy treatment was started. For mice in the combined chemoradiotherapy arm, 50 mg/kg TMZ was oral gavaged one hour before cranial irradiation was administered to mice. The mouse shield is designed such that only the head of the mice is irradiated.

tag: stage of disease

value: Recurrent disease

value: Chemoradiotherapy Treated

value: primary Human Glioblastoma cells


title: 236_G10_EB_9D_3A_SC_Batch2

value: Dnmt3a -/- (3AKO)


title: 236_F5_EB_9D_3A_SC_Batch1


title: 236_F3_EB_9D_3A_SC_Batch1


title: Huh7 Combi

tag: cell line


title: 236_F4_EB_9D_3A_SC_Batch1

tag: cell type


title: 236_F2_EB_9D_3A_SC_Batch1

tag: Stage


title: MBT06_MRD_TR

description: Chemoradiotherapy-treated, MBT06 line at minimal residual disease (MRD) state


title: BT799_MRD_CON

description: vehicle-treated, BT799 line at minimal residual disease (MRD) state

value: Vehicle Treated (Control)