title: TCF_rep2

status: Public on Jun 01 2021

city: West Lafayette

first: Majid

last: Kazemian

state: Indiana

address: 610 Purdue Mall

institute: Purdue university

description: Single-cell RNA-seq

data_processing:
Data quality control was performed using FastQC v0.11.8. RNA expression levels in each library were estimated by “rsem-calculate-expression” from RSEM v1.3.0 (PMID: 21816040) using default parameters except “--bowtie-n 1 –bowtie-m 100 –seed-length 28”.
The bowtie index required by RSEM software was generated by “rsem-prepare-reference” on all RefSeq genes, obtained from UCSC table browser on April 2017.
EdgeR v3.24.3 (PMID: 19910308) and DESeq2 v1.26.0 (PMID: 25516281) packages were used to identify differentially expressed genes among samples.
Gene set enrichment analysis (GSEA) was performed using GSEA version 3.0 (PMID: 16199517). Genesets for testing were sourced from “hallmark genesets” curated by the MSigDB v7.0 (GSEA). Heatmaps were drawn using Morpheus (Broad Institute).
The 10X Genomics Cellranger (v2.0.2) mkfastq was applied to demultiplex the Illumina BCL output into FASTQ files.
Cellranger count was then applied to each FASTQ file to align reads to mm10 reference genome, generate the .hd5 and .bam files, and generate barcode and UMI counts.
To calculate the RNA velocity, the .loom files are generated from the .bam files from the cellranger by velocyto.py (PMID: 30089906).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: .txt files: RSEM output.
Supplementary_files_format_and_content: .h5 files: hd5, Cell Ranger output.
Supplementary_files_format_and_content: .loom files: Velocyto.py output.
Supplementary_files_format_and_content: .rds files: Rdata saved for each single-cell RNAseq sample.

source_name: CD25+ Treg cells

growth_protocol: CD25+YFP+ Tregs were FACS sorted from MACS-pre-purified CD4+ T cells isolated from MLN of mice.

extract_protocol:
Total RNA was isolated using the PicoPure RNA Isolation Kit (Arcturus) following the manufacturer’s instructions. Single-cell RNA-seq samples: Whole live cells were washed twice in 1x PBS + 0.04% BSA and immediately submitted to the Core for Single Cell sorting. The cells were first counted and measured for viability using the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter), as well as a basic hemocytometer with light microscopy. The barcoded Gel Beads were thawed from -80C and the reverse transcription master mix was prepared according to the manufacturer’s instruction for Chromium Single Cell 3’ v2 library kit (10x Genomics).
Libraries were generated and sequenced by the University of Chicago Genomics Facility.

value: CD4+ T cells


title: CRE_rep2

type: SRA

country: USA

description: Single-cell RNA-seq

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: genotype

tag: cell type


title: TCF_rep1

description: Single-cell RNA-seq


title: APC_rep1

description: Single-cell RNA-seq


title: CRE_rep1

description: Single-cell RNA-seq


title: W12 cells - H3K27ac_rep4

status: Public on Sep 01 2021

city: Bethesda

first: Alison

middle: Anne

last: McBride

state: MD

address: 33 North Drive

department: DIR

institute: NIAID

description: Processed data files normalised to "W12 cells - input DNA_20861_rep2"

library_source: genomic

data_processing:
Reads were trimmed with Cutadapt version 1.18. All reads aligning to the ENCODE hg19 v1 blacklist regionswere identified by alignment with BWA version 0.7.17 and removed with Picard SamToFastq, https://broadinstitute.github.io/picard/. Remaining reads were aligned to an hg19 reference genome using BWA.
Reads with a mapQ score less than 6 were removed with SAMtools version 1.6 and PCR duplicates were removed with Picard MarkDuplicates.
Peaks were called by comparing each ChIP sample to its matching input sample.
For FANCD2, the mean fragment size was estimated by Phantompeakqualtools version 2.0. Peaks were called using SICER version 1.1 with the following parameters: redundancy threshold of 100, effective genome fraction of 0.75, window size of 25,000 bp, and gap size of 50,000 bp.
H3K27ac and Brd4 peaks were called using macsBroad (macs version 2.1.1 from 2016/03/09) with the following parameters: --broad-cutoff 0.01 -f "BAMPE".
Data was converted into bigwigs for viewing and normalized by reads per genomic content (RPGC) using deepTools version 3.0.1 using the following parameters: --binSize 25 --smoothLength 75 --effectiveGenomeSize 2700000000 --centerReads --normalizeUsing RPGC. RPGC-normalized input values were subtracted from RPGC-normalized ChIP values of matching cell type genome-wide using Deeptools with --binSize 25.
Genome_build: hg19
Supplementary_files_format_and_content: broadPEAK and bigwig files

molecule: genomic DNA

organism: Homo sapiens

source_name: Cervical keratinocytes

growth_protocol: W12 cervical keratinocytes were maintained in F-medium (3:1 [vol/vol] F-12–Dulbecco’s modified Eagle’s medium, 5% fetal bovine serum, 0.4 μg/ml hydrocortisone, 5 μg/ml insulin, 8.4 ng/ml cholera toxin, 10 ng/ml epidermal growth factor, 24 μg/ml adenine, 100 U/ml penicillin and 100 μg/ml streptomycin) in the presence of irradiated 3T3-J2 feeder cells. C33-A and HeLa cell lines were maintained in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal bovine serum, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
Cells were crossed-linked with 1% formaldehyde and chromatin was isolated and sheared to 100–500 bp DNA fragments using a Bioruptor sonicator (Diagonode) on high power settings. Chromatin samples were incubated overnight at 4°C with antibody and the resulting chromatin immunocomplexes were precipitated with blocked Dynabeads Protein G (Invitrogen), subjected to multiple wash steps and the chromatin eluted in elution buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA [pH 8.0], 1% SDS). Chromatin was reverse cross-linked overnight at 65°C in 0.2 M NaCl, followed by RNase A and proteinase K treatment, and the DNA purified using the ChIP DNA Clean & Concentrator kit (Zymo Research).
Libraries were prepared using Kapa Hyper Preps (Roche) according to the manufacturer's instructions and sequenced on the Illumina HiSeq 4000 following the manufacturer's protocol.

treatment_protocol: To induce replication stress, C33-A and HeLa cells were treated for 24 hours with 0.2 µM aphidicolin (Sigma A0781).

value: Integrated HPV16 positive cervical keratinocytes

tag: cell line

tag: chip-seq antibody

tag: treatment

value: Untreated


title: APC_rep2

description: Single-cell RNA-seq


title: WT_rep3

molecule: total RNA


title: WT_rep1


title: WT_rep2


title: TCF7KO_rep3


title: TCF7KO_rep2


title: TCF7KO_rep1


title: normal_2_scRNA_2

status: Public on Aug 17 2020

city: La Jolla

first: Sheng

last: Zhong

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

description:
scRNA-seq
Single-cell RNA sequencing assay

data_processing:
10X Genomics cellranger (v3.0) was used to process sequencing data produced from Chromium Single Cell Gene Expression
Genome_build: hg38
Supplementary_files_format_and_content: Three processed data files per each sample: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of genes (features) detected; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample.

source_name: Human mesenteric arterial Endothelial Cells from healthy donor 2, file 2

extract_protocol:
Single-cell suspension was prepared by using the 10XGenomics Chromium Controller
10X Genomics Single Cell 3' v3. gene expression

treatment_protocol: Primary endothelial cells were freshly isolated from human mesenteric arteries

value: Endothelial cells freshly isolated from human mesenteric arteries

tag: disease state

value: healthy donor


title: T2D_2_scRNA_2

source_name: Human mesenteric arterial Endothelial Cells from Type 2 Diabetes donor 2, file 2

value: Endothelial Cells from Type 2 Diabetes


title: normal_1_scRNA_1

source_name: Human mesenteric arterial Endothelial Cells from healthy donor 1, file 1


title: T2D_1_scRNA_2

source_name: Human mesenteric arterial Endothelial Cells from Type 2 Diabetes donor 1, file 2


title: normal_2_scRNA_3

source_name: Human mesenteric arterial Endothelial Cells from healthy donor 2, file 3


title: normal_2_scRNA_4

source_name: Human mesenteric arterial Endothelial Cells from healthy donor 2, file 4


title: T2D_1_scRNA_1

source_name: Human mesenteric arterial Endothelial Cells from Type 2 Diabetes donor 1, file 1


title: normal_2_scRNA_1

source_name: Human mesenteric arterial Endothelial Cells from healthy donor 2, file 1


title: B6_rep2

description: Single-cell RNA-seq

value: Wildtype C57BL/6J (B6)


title: eri-6 small RNAseq rep1

status: Public on Jan 14 2020

city: Boston

first: Sylvia

last: Fischer

address: 300 Longwood Avenue

department: Division of Infectious Diseases

institute: Boston Children's Hospital

data_processing:
Reads were trimmed for adaptor sequence and mapped to the C. elegans genome. total RNA dseq reads mapping to rRNA and tRNA were removed before analysis.
small RNA reads were trimmed and selected to be 18 nts or longer using Trimgalore. Filter Fastq was used to sekect reads 28nts or shorter. sequencing was analyzed using bwa (aln -n=0.01, aln -o=0, aln -e=0 and featurecounts; differential expression was analyzed using DEseq2
total RNA sequencing was analyzed using Tophat2 (with minimum intron size=20 (-i), maximum intron size 50,000 (-I) and allowing for 1 mismatch (-N 1), with multiread correction), Cufflinks, Cuffmerge and Cuffdiff with multiread correct.
mRNAseq was analyzed using Tophat2 (with minimum intron size=20 (-i), maximum intron size 50,000 (-I) and allowing for 1 mismatch (-N 1)), Cufflinks, Cuffmerge and Cuffdiff.
Genome_build: WBcel235
Supplementary_files_format_and_content: Normalized counts (DEseq2 output) for small RNA, FPKM (Cuffdiff output for mRNA and total RNA)

organism: Caenorhabditis elegans

source_name: whole animal adult

growth_protocol: Embryos were isolated using standard alkaline/hypochlorite treatment and hatched o/n at 20ºC. L1s were dropped onto NGM plates seeded with OP50 and grown for 71 hrs at 20ºC.

extract_protocol:
Animals were washed off plates and washed twice with M9. Trizol was added to the worm pellet and frozen in liq N2. After thawing, the animals were ground using a motorized pestle fitting in an eppendorf tube, followed by Trizol extraction,  chloroform extraction and isopronanol precipitation.
18-28 nt RNA was size-selected on a 15% TBE-urea polyacrylamide gel, and eluted from gel. Small RNA was treated with RNA 5'polyphosphatase, followed by liagtion of the 3' adaptor. After hybridization of the Reverse Transcription primer, the 5' adaptor was ligated. cDNA was generated using Superscript III, and was amplified using Phusion polymerase.  The correct size product was isolated from a 10% TBE polyacrylamide gel.
Total RNA libraries were prepared using epicentre Ribo-Zero magnetic kit, followed by use of the NEBNext Ultra RNA Library Prep Kit for Illumina2 kit.
mRNAseq libraries were prepared using NEBNext Ultra magnetic isolation module and NEBNext Ultra Directional RNA Library Prep Kit

treatment_protocol: For RNAi experiments: L1s were dropped onto NGM plates seeded with HT115 expressing dsRNA for drh-1, nrde-3 or control; animals werwe harvested after 71 hrs of growth at 20ºC.

tag: strain

tag: age

value: 70 hrs post L1 arrest

tag: developmental stage

value: young adult with embryos


title: adr-1 eri-6; adr-2 small RNAseq rep1

description: adr-1;adr-2;eri-6_vs_wt_smallRNA_morn_counts


title: eri-6 small RNAseq rep2


title: adr-1; adr-2 small RNAseq rep2


title: adr-1 eri-6; adr-2 small RNAseq rep2


title: adr-1; adr-2 small RNAseq rep1


title: SF11681

status: Public on Jul 07 2020

city: San Francisco

first: Aaron

last: Diaz

department: Neurological Surgery

institute: University of California, San Francisco

description:
Single Cell RNA-Seq
Raw data not available due to privacy concerns

data_processing:
For 10x scRNA-Seq and snRNA-Seq data, we utilized CellRanger (version 3.0.2) for data pre-processing and gene expression quantification, following the guidelines from the CellRanger website.
The presence/absence of somatic CNVs was assessed with CONICSmat.
The CellRanger ATAC software (version 1.1.0) was used for read alignment, deduplication, and identifying transposase cut sites.
We selected the highest quality barcodes for each case based on two criteria: 1) minumum 100 cells present in a  feature; 2) minimum 200 features present in a cell. Created via Seurat’s CreateSeuratObject function (min.cells=100,  min.features=200)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix file (mtx) includes sparse matrix of read counts, unique cell barcode files (tsv), and feature file (tsv)

source_name: Brain

extract_protocol:
Nuclei were extracted from frozen tissues following the “Frakenstein” protocol developed by Luciano Martelotto, Ph.D., Melbourne, Centre for Cancer Research, Victorian Comprehensive Cancer Centre, and available from 10X Genomics
For fresh tissues, 10.2 μL of live cells, at a concentration of 1700 live-cells/μL,were loaded into the10X Chromium Single Cell capture chip. For frozen tissues, ~15,000 nuclei were loaded per capture. Single-cell/nucleus capture, reverse transcription, cell lysis, and library preparation were performed per manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq using apaired-end 100bp protocol.

tag: progression

value: Recurrent

value: GBM, IDH1R132H WT

tag: gender

value: Male


title: B6_rep1

description: Single-cell RNA-seq


title: WT small RNAseq rep2

value: wt


title: adr-1 eri-6; adr-2 on drh-1 (RNAi) mRNAseq

value: adr-1(gv6) eri-6(mg379); adr-2(gv42)) on drh-1(RNAi)


title: adr-1 eri-6; adr-2 on control (RNAi) mRNAseq

value: adr-1(gv6) eri-6(mg379); adr-2(gv42)) on control RNAi (L4440)


title: adr-1 eri-6; adr-2 on nrde-3 (RNAi) mRNAseq

value: adr-1(gv6) eri-6(mg379); adr-2(gv42)) on bnrde-3(RNAi)


title: WT small RNAseq rep1

value: wt (+ transgene mgIs30)


title: WT on nrde-3(RNAi) mRNAseq

value: wt on nrde-3(RNAi)


title: WT on drh-1(RNAi) mRNAseq

value: wt on drh-1(RNAi)


title: T2D_2_scRNA_1

source_name: Human mesenteric arterial Endothelial Cells from Type 2 Diabetes donor 2, file 1


title: adr-1 eri-6; adr-2 total RNAseq rep2


title: adr-1 eri-6; adr-2 total RNAseq rep1


title: eri-6 total RNAseq rep2


title: normal_1_scRNA_2

source_name: Human mesenteric arterial Endothelial Cells from healthy donor 1, file 2


title: WT total RNAseq rep2


title: adr-1; adr-2 total RNAseq rep1


title: SF11612_scRNA-Seq

status: Public on Oct 12 2019

description: Single Cell RNA-Seq

data_processing:
For 10x scRNA-Seq and snRNA-Seq data, we utilized CellRanger (version 3.0.2) for data pre-processing and gene expression quantification, following the guidelines from the CellRanger website.
genome build: hg38
processed data files format and content: Matrix file (mtx) includes sparse matrix of read counts, unique cell barcode files (tsv), and feature file (tsv)

tag: tissue

value: glioma

tag: genotype/variation

value: Recurrent oligodendroglioma


title: WT total RNAseq rep1


title: adr-1; adr-2 total RNAseq rep2


title: eri-6 total RNAseq rep1


title: T47D_Hi-C_noSerum_siGTF3C5_rep2

status: Public on Nov 21 2019

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

description: Hi-C(PE)

data_processing:
We processed Hi-C data by using an in-house pipeline based on TADbit and OneD algorithms (Serra et al., 2017; Vidal et al., 2018). First, the quality of the reads was checked with FastQC to discard problematic samples and detect systematic artifacts. Trimmomatic (Bolger et al., 2014) with the recommended parameters for PE reads was used to remove adaptor sequences and poor-quality reads (ILLUMINACLIP: TruSeq3-PE.fa:2:30:12:1:true; LEADING:3; TRAILING:3; MAXINFO:targetLength:0.999; and MINLEN:36).
For mapping, a fragment-based strategy implemented in TADbit was used, which was similar to previously published protocols (Ay et al., 2015). Briefly, each side of the sequenced read was mapped in full length to GRCh38. After this step, if a read was not uniquely mapped, we assumed that the read was chimeric, owing to ligation of several DNA fragments. We next searched for ligation sites, discarding those reads in which no ligation site was found. The remaining reads were split as often as ligation sites were found. Individual split read fragments were then mapped independently. These steps were repeated for each read in the input FASTQ files. Multiple fragments from a single uniquely mapped read resulted in a number of contacts identical to the number of possible pairs between the fragments. For example, if a single read was mapped through three fragments, a total of three contacts (all-versus-all) was represented in the final contact matrix. We used the TADbit filtering module to remove non-informative contacts and to create contact matrices. The different categories of filtered reads applied were:
1. Self-circle: reads coming from a single restriction enzyme (RE) fragment and pointing to the outside.
2. Dangling end: reads coming from a single RE fragment and pointing to the inside.
3. Error: reads coming from a single RE fragment and pointing in the same direction.
4. Extra dangling end: reads coming from different RE fragments but that were sufficiently close and point to the inside; the distance threshold used was left to 500 bp (default), which was between percentiles 95 and 99 of average fragment lengths.
5. Duplicated: the combination of the start positions and directions of the reads was repeated, thus suggesting a PCR artifact; this filter removed only extra copies of the original pair.
6. Random breaks: the start position of one of the reads was too far from RE cutting site, possibly because of non-canonical enzymatic activity or random physical breaks; the threshold was set to 750 bp (default), >percentile 99.9.
From the resulting contact matrices, low-quality bins (those presenting low contact numbers) were removed, as implemented in TADbit’s ‘filter columns’ routine. A single round of ICE normalization (Imakaev et al., 2012), also known as ‘vanilla’ normalization (Rao et al., 2014), was performed. That is, each cell in the Hi-C matrix was divided by the product of the interactions in its columns and the interactions in its row. Finally, all matrices were corrected to achieve an average content of one interaction per cell.
Identification of sub-nuclear compartments and TADs
To segment the genome into A/B compartments, normalized Hi-C matrices at 100-kb resolution were corrected for decay as previously described, by grouping diagonals when the signal-to-noise ratio was below 0.05 (Rao et al., 2014). Corrected matrices were then split into chromosomal matrices and transformed into correlation matrices by using the Pearson product-moment correlation.
Normalized contacts matrices at 20-kb resolution were used to define TADs, and for visualization purposes, through a previously described method with default parameters (Crane et al., 2015; Giorgetti et al., 2016). First, for each bin, an insulation index was obtained on the basis of the number of contacts between bins on each side of a given bin. Differences in the insulation index between both sides of the bin were computed, and borders were called, searching for minima within the insulation index. The insulation score of each border was determined as previously described (Crane et al., 2015), by using the difference in the delta vector between the local maximum to the left and the local minimum to the right of the boundary bin. This procedure resulted in a set of borders for each time point and replicate. To obtain a set of consensus borders along the time course, we proceeded in two steps: (i) merging borders of replicates and overlapping merged borders (that is, for each pair of replicates, we expanded the borders one bin on each side and kept only those borders present in both replicates as merged borders) and (ii) further expanding two extra bins (100 kb) on each side and determining the overlap to obtain a consensus set of borders common to any pair of time points.
Intra-TAD contacts
Using Hi-C matrices at 5 kb resolution, we focused on TADs containing TFIIIC. We labeled each bin according to TFIIIC and CTCF occupancy as well as gene promoter annotation. Genes were classified according to RNA-seq results as "changed" or "unchanged". The former set was further divided into "up" and "down". We marked as "others" bins not overlapping any of the corresponding categories.
Then, we gathered the non-observed contacts between the different types of bins within their TAD and computed expected contacts frequencies based on the genomic distance that separate each pair (the expected distance decay was calculated excluding entries outside TADs). We used the log2 of the ratio on observed over expected as a contact score. We summarized the results via linear mixed-effects models fitted using lme4 (Ziyatdinov et al., 2018). We considered TADs as a random effect and the aforementioned bin categories (and their interactions) as fixed effects.
We fitted linear mixed models using lmer function of lme4 R package (and computed the posterior probabilities using sim function of arm R package for the corresponding interaction terms
Genome_build: hg38

extract_protocol: In situ Hi-C library preparationIn situ Hi-C was performed as previously described (Rao et al., 2014) with the following modifications: (i) 2x106 cells were used as starting material; (ii) chromatin was initially digested with 100 U MboI (New England BioLabs) for 2 h, and then another 100 U (2 h incubation) and a final 100 U were added before overnight incubation; (iii) before fill-in with bio-dATP, nuclei were pelleted and resuspended in fresh 1× NEB2 buffer; (iv) ligation was performed overnight at 24 °C with 10,000 cohesive end units per reaction; (v) de-cross-linked and purified DNA was sonicated to an average size of 300-400 bp with a Bioruptor Pico (Diagenode; seven cycles of 20 s on and 60 s off); (vi) DNA fragment-size selection was performed only after final library amplification; (vii) library preparation was performed with an NEBNext DNA Library Prep Kit (New England BioLabs) with 3  μl NEBNext adaptor in the ligation step; (viii) libraries were amplified for 8-12 cycles with Herculase II Fusion DNA Polymerase (Agilent) and were purified/size-selected with Agencourt AMPure XP beads (>200 bp). Hi-C library quality was assessed through ClaI digestion and low-coverage sequencing on an Illumina NextSeq500 instrument, after which every technical replicate (n = 2) of each biological replicate (n = 2) was sequenced at high coverage on an Illumina HiSeq2500 instrument. Data from technical replicates were pooled for downstream analysis. We sequenced >18 billion reads in total to obtain 0.78–1.21 billion valid interactions per time point per biological replicate.

tag: media

value: RPMI supplemented with 10% charcoal-treated (CT) FBS for 48 h and starvation was achieved by culturing cells in the absence of FBS for 16 h

tag: serum

value: serum-starved


title: SF11644_scRNA-Seq

description: Single Cell RNA-Seq

value: Primary

value: GBM


title: SF12017_scRNA-Seq

description: Single Cell RNA-Seq

value: Primary astrocytoma G2


title: T47D_Hi-C_noSerum_rep1

description: Hi-C(PE)


title: SF11977_scRNA-Seq

description: Single Cell RNA-Seq

value: IDHR132H WT GBM

value: Female


title: SF9259S_snRNA-Seq

description: Single Nuceli RNA seq

value: Male


title: SF11949_scRNA-Seq

description: Single Cell RNA-Seq

value: Primary oligodendroglioma G3


title: SF11136_scRNA-Seq

description: Single Cell RNA-Seq

value: Diffuse astrocytoma G2


title: SF9259R_snRNA-Seq

description: Single Nuceli RNA seq


title: SF12264_snRNA-Seq

description: Single Nuceli RNA seq


title: SF4297_snRNA-Seq

description: Single Nuceli RNA seq


title: SF6996_snRNA-Seq

description: Single Nuceli RNA seq


title: SF4400_snRNA-Seq

description: Single Nuceli RNA seq


title: SF12090_snRNA-Seq

description: Single Nuceli RNA seq


title: SF11979_snRNA-Seq

description: Single Nuceli RNA seq


title: SF10127_snRNA-Seq

description: Single Nuceli RNA seq


title: SF11331_snATAC

description: Single nuclei ATAC-Seq Bin Matrix

data_processing:
The CellRanger ATAC software (version 1.1.0) was used for read alignment, deduplication, and identifying transposase cut sites.
genome build: hg38
processed data files format and content: Matrix file (mtx) includes sparse matrix of read counts, unique cell barcode files (tsv), and feature file (tsv)


title: SF11215_snATAC

description: Single nuclei ATAC-Seq Bin Matrix


title: SF10022_snRNA-Seq

description: Single Nuceli RNA seq


title: SF11956_snATAC

description: Single nuclei ATAC-Seq Bin Matrix


title: SF11964_scRNA-Seq

description: Single Cell RNA-Seq

value: Astrocytoma


title: SF12017_snATAC

description: Single nuclei ATAC-Seq Bin Matrix

value: IDH1 Mutant astrocytoma G2


title: SF11956_scRNA-Seq

description: Single Cell RNA-Seq


title: SF11979_scRNA-Seq

description: Single Cell RNA-Seq


title: SF11612_snATAC

description: Single nuclei ATAC-Seq Bin Matrix

value: Recurrent

value: oligodendroglioma


title: SF11964_snATAC

description: Single nuclei ATAC-Seq Bin Matrix

value: IDHR132H mutant Astrocytoma


title: SF11979_snATAC

description: Single nuclei ATAC-Seq Bin Matrix

value: glioma


title: SF11949_snATAC

description: Single nuclei ATAC-Seq Bin Matrix

value: IDH1 mutant oligodendroglioma


title: RNA_B6C3F1_PB_2034

status: Public on Oct 07 2019

city: Basel

first: Remi

last: Terranova

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis Biomedical Research

description: processed data file: RNA_NormCountperMillion.txt.gz

data_processing:
Library de-multiplexing using bcl2fastq version 2.17 (Illumina).
RNA-seq read alignment: using STAR v2.4.0f1 and RefSeq mm10 reference. Read filtering using samtools (with options -q 255 and -F 512).
Expression quantification: using R GenomicAlignments (v1.6.3) (summarizeOverlap with parameters mode=Union, singleEnd=FALSE, ignore.strand=FALSE, fragments=TRUE).
Expression normalization: with EdgeR (v.3.12.1) on genes with CPM>=0.4 in at least three sample per treatment-strain group in at least one group.
DNase-seq Illumina adaptor trimming: using Cutadapt v1.8.
DNase-seq reads alignment: using Bowtie2 v2.1.0 (parameters: -I 50 -X 400 --fr --no-mixed --no-discordant) and mm10 reference.
DNase-seq read filtering: using Picard Tools MarkDuplicates v1.107(1667) and samtools to retain only properly paired, unique reads with a mapQuality score above 12.
DNase-seq peak calling: using MACS2 v2.1.1.20160309 (q-value cut-off of 0.01).
Binding quantification: using DiffBind v1.16.3 (DBA_EDGER) on consensus peaks requiring that at least 3 samples per group show a supporting peak.
Genome_build: mm10

growth_protocol: Male, 9 to 11 weeks old C57BL/6 mice were obtained from Taconic (Germany). Male, 4 to 5 weeks old B6C3F1/Ctrl (C57BL/6 female × C3H/He male) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatize for 5 days prior to being randomly divided into treatment groups (n=5 per group).

extract_protocol:
RNA-extraction: 25-50 mg of frozen liver material was used for total RNA-extraction. Samples were homogenized in TRIzol reagent (ThermoFisher, cat.No. 15596026) and total RNA was isolated by phase separation using chloroform-isoamyl alcohol. RNA precipitation with isopropyl alcohol was performed and precipitated RNA was resuspended in EB buffer (Qiagen). Samples were NanoDrop quantified and the RNA Integrity Number (RIN) measured using an Agilent RNA 6000 Nano Kit (Agilent, cat.No. 5067-1511) on a BioAnalyzer instrument. Samples with RIN above 8 were used for sequencing.
DNase-Hypersensitivity: 100-150 mg of frozen liver tissue was homogenized in ice-cold Nuclear Homogenization Buffer (NEHB) using a 7 ml dounce tissue homogenizer. Nuclei were isolated by ultracentrifugation, overlying the homogenized tissue on top of 5 ml NEHB. Isolated nuclei were rinsed three times in 1 ml ice-cold Buffer A. The pelleted nuclei were resuspended in Digestion buffer. DNase I digestion was carried out on 107 nuclei per mouse at 37 °C for 3 min using a final concentration of 50 U/ml of RQ1 RNase-free DNase I  (Promega, cat.no M6101). DNase digestion was stopped and DNA purification was performed. DNA fractionation was performed on the recovered extraction solution using a sucrose step gradient (40%, 35%, 30%, 25%, 20%, 17.5%, 15%, 12.5%, and 10% solutions in 1x Centrifugation buffer). After ultracentrifugation, the first 3 ml fraction was recovered and purified over a MinElute Purification Column (Qiagen).
RNA-seq: Illumina libraries were prepared with the TruSeq Stranded Total RNA Sample Preparation kit with Ribo-Zero Gold. We generated paired-end 76 bp reads on a HiSeq 2500 using v4 reagents (all Illumina).
DNase-seq: Next generation sequencing libraries were prepared with NuGEN Ovation Ultralow System V2 with A-tailing (TECAN, Leek, The Netherlands). Size selection of the 40 – 250 bp fraction on a BluePippin BDF3010 3% DF Marker Q2 cassette or PippinHT BEF2010 2% DF Marker M1 cassette (both Sage Science, Beverly, MA, USA), and paired-end 76 bp sequencing was performed on a HiSeq 2500 using v4 reagents (all Illumina).

treatment_protocol: PB (Sigma [St Louis, MO] #04710, 0.05% [wt/vol] in drinking water) was administered to one group through ad libitum access to drinking water for 91 days. Mice were kept on a 12 h dark/light cycle, checked daily for activity and behavior and sacrificed on the last day of dosing.

tag: Sex

value: male

value: 4 to 5 weeks

value: PB

value: Phenobarbital

tag: treatment_duration [days]

tag: treatment_dose [% w/v]

value: liver


title: RNA_B6C3F1_PB_2035


title: RNA_B6C3F1_PB_2031


title: RNA_B6C3F1_PB_2032


title: RNA_B6C3F1_Vh_1033

value: Drinking water


title: RNA_B6C3F1_Vh_1032


title: RNA_B6C3F1_Vh_1031


title: RNA_C57BL/6_PB_2025

value: 9 to 11 weeks


title: RNA_B6C3F1_PB_2033


title: RNA_B6C3F1_Vh_1035


title: RNA_C57BL/6_PB_2021


title: RNA_C57BL/6_PB_2022


title: RNA_C57BL/6_PB_2023


title: RNA_C57BL/6_Vh_1023


title: RNA_C57BL/6_Vh_1025


title: RNA_C57BL/6_Vh_1022


title: RNA_C57BL/6_Vh_1021


title: WT on control (RNAi) mRNAseq

value: 70 hrs post L1 arrest

value: young adult with embryos

tag: genotype

value: wt on control RNAi (L4440)


title: DNase_B6C3F1_PB_2035

description: processed data file: DHS_normcounts_thr3.txt.gz


title: DNase_B6C3F1_PB_2033


title: DNase_B6C3F1_Vh_1032


title: DNase_B6C3F1_PB_2031


title: DNase_B6C3F1_Vh_1033


title: DNase_B6C3F1_PB_2032


title: DNase_C57BL6_PB_2024


title: DNase_B6C3F1_Vh_1035


title: DNase_C57BL6_PB_2023


title: RNA_C57BL/6_PB_2024


title: DNase_C57BL6_PB_2022


title: DNase_C57BL6_PB_2021


title: DNase_C57BL6_Vh_1022


title: DNase_C57BL6_Vh_1021


title: DNase_C57BL6_Vh_1023


title: FACS total RNA sample 2

status: Public on Mar 29 2019

first: Derek

last: Gildea

address: 12 South Drive Rm 4009-24

institute: NHGRI/NIH

data_processing:
RNA-seq reads were alinged to zebrafish reference genome sequence using STAR (v. 2.4.2a). Reads mapping to Ensemble protein-coding genes were used for transcript abundance analysis
RNA-seq quantification was done using RSEM (v. 1.2.22)
DESeq2 was used for testing differences in transcript abundance between samples
Genome_build: GRCz10
Supplementary_files_format_and_content: raw_counts.txt: tab-delimited text matrix of raw RNA-seq read counts

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
Whole embryo and endothelial translatomes were collected using HA antibody and the translating ribosome affinity purification protocol, the endothelial transcriptome was collected through GFP+ FACs sorted endothelial cells
RNA concentration and quality were measured on a Qubit (Thermo Fisher) and on an Agilent 2100 BioAnalyzer + RNA Pico Chip (Agilent), respectively.  500 ng RNA was polyA selected or rRNA depleted using Ribo-Zero rRNA Removal Kit (Illumina) and libraries were constructed using TruSeq Stranded mRNA Library Prep Kits (Illumina).

value: Transgene positive

value: pooled embryos

tag: description

value: Angiotag transgenic, total RNA


title: FACS total RNA sample 3


title: FACS sorted sample 3

value: Angiotag transgenic, RNA from FACS-sorted endothelial cells


title: DNase_C57BL6_Vh_1025


title: Ribotag input sample 3

value: Ribotag transgenic, input RNA


title: FACS sorted sample 2


title: FACS sorted sample 1


title: DNase_B6C3F1_PB_2034


title: FACS total RNA sample 1


title: Ribotag input sample 2


title: Ribotag IP sample 3

value: Ribotag transgenic, immunoprecipitated RNA


title: Ribotag IP sample 1


title: Angiotag input sample 3

value: Angiotag transgenic, input RNA


title: Ribotag IP sample 2


title: Ribotag input sample 1


title: DNase_C57BL6_PB_2025

value: male


title: Angiotag input sample 2


title: Angiotag IP sample 3

value: Angiotag transgenic, immunoprecipitated RNA


title: Angiotag input sample 1


title: Angiotag IP sample 2


title: Angiotag IP sample 1


title: DNase_B6C3F1_Vh_1031

value: 4 to 5 weeks


title: UPenn mixed embryo batch b01

status: Public on Mar 01 2019

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

description: 10X sc-RNA-seq with cells from dissociated C. elegans embryos

data_processing:
Data was processed using the 10X Genomics CellRanger pipeline, mapping to a modified version of the reference transcriptome from WormBase version 260 (WS260). Our modifications to the refrence transcriptome consisted of extending the 3' UTR of transcripts by 0-500 bp (see Methods section of paper).
Genome_build: WS260
Supplementary_files_format_and_content: gene_by_cell_count_matrix.txt contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are background corrected UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, cell type, lineage, etc.) for each cell. gene_annotation.csv contains a data frame with gene id and gene short name.

source_name: C. elegans embryos

growth_protocol: To obtain a broad range of embryo ages, including early stages, roughly synchronized C. elegans adults (N2 strain) were obtained by releasing embryos with standard hypochlorite treatment and letting the L1 larvae hatch and undergo growth arrest on unseeded plates. Starved L1s were transferred to NGM plates seeded with E. coli OP50 bacteria. Embryos were released from these synchronized young adults using hypochlorite treatment followed by three washes with L15-10 media. To generate cell suspensions, embryos were then treated with 0.5mg/ml chitinase at room temperature until the shells were dissolved (30-40 minutes at room temperature (~22 degrees C)) followed by dissociation of the cells using a 3ml syringe fitted with 21 1/2 gauge needle until >80% of embryos were disrupted. The cell suspension was then passed through a 10µM filter, washed in phosphate buffered saline (PBS) and finally resuspended in PBS. An estimated 14,000 cells were loaded immediately on a 10X Chromium instrument. The trypan blue negative viable cell count was estimated using a hemocytometer and was >84% for all samples. To sample later stages more deeply, more tightly synchronized embryo populations (used for the 300-minute, 400-minute, and 500-minute time series shown in Fig. 1B) were obtained through two cycles of bleaching adult worms (strain VC2010, a strain derived from N2 that has been completely sequenced). On the first round of synchronization, populations of mixed stage embryos recovered by hypochlorite treatment of mixed populations were hatched overnight in egg buffer (118 mM NaCl, 48 mM KCl, 3 mM CaCl2, 3 mM MgCl2, 5 mM HEPES pH 7.2) with gentle shaking. The hatched L1s were plated onto 150 mm peptone rich NGM plates seeded with E. coli NA22 at no more than 100,000 worms per plate. When worms reached the adult stage, the number of embryos inside the adults was monitored until most had about 4 embryos on each gonad arm. The adult worms were collected and treated with hypochlorite to release embryos.  The embryos were again allowed to hatch in the absence of food at 20 °C for 12 hours yielding a more tightly synchronized population of L1 worms. Around 250,000 L1 larvae were plated onto four 100 mm petri plates seeded with NA22 bacteria and allowed to develop at 20 °C.  As the worms reached the young adult stage, the population was closely monitored. When about 20-30% of the adults had a single in either arm of the gonad, worms were subjected to hypochlorite treatment. The time hypochlorite was added to the worms was considered t=0 (see Warner et al. in press, for typical age distributions). The capture time was taken as when the cells were loaded onto the 10x Chromium capture. The embryos were allowed to develop in egg buffer until one hour prior to capture time. The embryos were collected by centrifugation, resuspended in 0.5 ml egg buffer and 1 ml chitinase (1 U/ml) and transferred to 30 mm petri dishes. The degradation of eggshell was monitored; after ~20 min (about half the eggs had lost the shell), the suspension was transferred to a 15ml falcon tube and centrifuged at 200 g for 5 min. The chitinase solution was aspirated; a solution of 200 ul pronase (15mg/ml) together with 0.5 ml egg buffer was added to the embryo pellet. The vitelline membrane was disrupted and the cells released by repeated passage through 21G1 ¼ needle attached to a 1 ml syringe. When sufficient single cells were observed the reaction was stopped by adding 1ml of egg buffer containing 1% BSA. Cells were separated from intact embryos by centrifuging the pronase treated embryos at 150 g for 5 min at 4°C. The supernatant was transferred to a 1.5 ml microcentrifuge tube and centrifuged at 500 g for 5 min at 4°C. The cell pellet was washed twice with egg-buffer containing 1% BSA.

extract_protocol: Single cell capture and library preparation followed 10X Genomics published protocols.  For each channel, 14,000 C elegans cells were mixed with reverse transcriptase reaction solution and loaded immediately onto the capture chip to minimize the time C. elegans cells spent in reverse transcription cocktail. The exception was the first 500 minute sample, when 14,000, 4,666, and 1,555 cells were loaded on each channel.

value: embryo


title: UW synchronized 500 min post bleach batch 2

value: VC2010, derived from N2


title: UW synchronized 500 min post bleach batch 1


title: UW synchronized 300 min post bleach


title: UW synchronized 400 min post bleach


title: UPenn mixed embryo batch b02


title: UPenn mixed embryo batch r17


title: ChIP_input_PCF11andCPSF73_R1

status: Public on Feb 28 2019

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

data_processing:
ChIP-seq reads were mapped with bowtie2 with hg19 genome index.
Macs2 was used to detect significant enrichments – broad peaks, q-value < 0.01.
For visualisation genome-wide coverage within 50 bp was calculated normalised for sequencing depth (rpm). Reads were calibarted additionally for D.melanogaster content. BigWig files were generated to visualize the data in the UCSC browser.
Genome_build: hg19
Supplementary_files_format_and_content: Bed: Table with three columns: chr, start, end; contains peak coordinates
Supplementary_files_format_and_content: bigWig: created form bedGraph file (table: chr, start, end, value) with the bedGraphToBigWig utility available form UCSC; scores represent sequencing-depth normalized read density or log2(IP/input)

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum.

extract_protocol:
ChIP was performed as described in accompanying paper. Antibodies used are indicated for each sample.
Sample 1-12: genomic libraries were prepared using NEBNext ChIP-Seq master-mix kit. Sample 13-25: Diagenode MicroPlex library preparation kit v2 (C05010012) was used to prepare libraries for sequencing, following manufacturer’s instructions.

treatment_protocol: siRNAs from Dharmacon were transfected for 48 hrs according to RNAiMAX reagent protocol at the concentrations indicated.

tag: cell line

value: HeLa cells

tag: molecule subtype

value: input DNA

tag: genotype/treatment

value: siLUC (5 nM) input for both PCF11 ChIP R1 and CPSF73 ChIP siLUC R1

tag: antibody

tag: calibration

value: Drosophila spike-in


title: ChIP_PCF11-Ct_R1

value: PCF11 bound DNA

value: siLUC (5 nM)

value: Rabbit polyclonal anti-PCF11 (PCF11-Ct) Abcam Cat# ab134391


title: HeLa, mock treated

status: Public on Dec 04 2018

city: Rochester

first: Christian

middle: Karl

last: Pfaller

state: MN

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

description:
total RNA, rRNA depleted
Cuffnorm_gene_FPKM_tracking.tabular.gz

data_processing:
Base-calling was performed with RTA version 2.7.3 (Illumina).
Reads were aligned with Bowtie2 (v.2.2.6.2, sensitive end-to-end).
Single nucleotide variant calling was performed using the SAMtools (v. 1.3) and BCFtools (v. 1.3). Produced SNV list was passed to the GIREMI (v. 0.2.0), which splitted it into two groups: RNA editing positions and SNPs, dbSNP build 138 was used for the GIREMI statistical model evaluation.
A list of ADAR1-edited genes (A>G substitutions) was generated by comparing the number of editing sites in HeLa cells with the number in ADAR1-KO cells and ranked according to the highest differential. The following exclusion criteria were applied sequentially: (1) Genes were discarded, if the number of editing sites was smaller than 8 in HeLa cells; (2) genes were discarded, if the ratio of detected editing sites #ADAR1-KO/#HeLa was >0.5; (3) genes were discarded, if the number of editing sites per 100,000 bp gene length was <10; and (4) genes were discarded, if #HeLa/(#ADAR1-KO+1) was <1.75.
WIG files with base counts over ADAR1-edited regions were generated with IGVTools (count --bases -w 1).
Gene expression quantification was performed on all 12 samples using the Cufflinks suite (v. 2.2.1.0): Assembled transcripts were generated using Cufflinks and a final transcriptome assembly was generated from this using Cuffmerge. Mapped reads were quantified on this assembly using Cuffquant and normalized expression levels were calculated using Cuffnorm.
Genome_build: NCBI GRCh38.p7 (hg38): GCA_000001405.25
Supplementary_files_format_and_content: *.RES, GIREMI variant analysis output file (tab delimited); *.WIG, IGVTools base count file (tab delimited); *.tabular, FPKM quantification of gene expression levels, 12 samples matrix.

source_name: HeLa cell line

growth_protocol: Cells were cultivated in 6-well plates in 2 ml D-MEM +10% FBS and 1x Penicillin/Streptomycin

extract_protocol:
Trizol RNA extraction, isopropanol precipitation, rRNA depletion w/ Ribominus Kit (Life Technologies)
RNA libraries were prepared using 100 ng of total RNA according to the manufacturer’s instructions for the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA, Cat# RS-122-2201).  The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA). Libraries were sequenced at 60-110 million reads per sample following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit (Illumina, Cat# PE-410-1001). The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit (Illumina, Cat# FC-410-1002 and FC-410-1001) and HCS v 3.3.52 collection software. Base-calling is performed using Illumina’s RTA version 2.7.3.

treatment_protocol: untreated, MeV-vac2(GFP)-infected (MOI=3, 24 h), MeV-CKO(GFP)-infected (MOI=3, 24 h), or IFNA/D-treated (1,000 U/ml) for 24 h prior to RNA extraction

value: HeLa cell line

value: parental HeLa


title: HeLa-ADAR1KO, mock treated

source_name: HeLa CRISPR/Cas9 clone E7

value: HeLa CRISPR/Cas9 clone E7

value: CRISPR/Cas9 knock-out of ADAR1-p150 + ADAR1-p110


title: MGH36-P9-C04

status: Public on Nov 06 2016

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
Paired-end, 38-base reads were mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6", which allows alignment of sequences with single base changes such as point mutation in the IDH1  gene. Expression values were calculated from SAM files using RSEM v1.2.3 in paired-end mode  using parameters "--estimate-rspd --paired end -sam -p 6", from which TPM values for each gene  were extracted.
Expression levels were quantified as Ei,j=log2(TPMi,j/10+1), where TPMi,j refers to transcriptper-million  for gene i in sample j, as calculated by RSEM41. TPM values are divided by 10 since  we estimate the complexity of single cell libraries in the order of 100,000 transcripts and would  like to avoid counting each transcript ~10 times, as would be the case with TPM, which may  inflate the difference between the expression level of a gene in cells in which the gene is detected  and those in which it is not detected.
For each cell, we quantified two quality measures: the number of genes for which at least one  read was mapped, and the average expression level of a curated list of housekeeping genes. We then conservatively excluded all cells with either fewer than 3,000 detected genes or an average housekeeping expression (E, as defined above) below 2.5. We then distinguished oligodendroglioma from non-malignant cells by inferrence of copy number variations and excluded the non-malignant cells. For the remaining cells we calculated  the aggregate expression of each gene as log2(average(TPMi,1...n)+1), and excluded genes with an  aggregate expression below 4, leaving a set of 8008 analyzed genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing the normalized expression levels (E) for 8008 analyzed genes across 2,594 oligodendroglioma cells that passed QC.

source_name: oligodendroglioma single cell

growth_protocol: no culutring (freshly-resected tumor samples)

extract_protocol:
RNA from single cells was first purified with Agencourt  RNAClean XP beads (Beckman Coulter)
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli  2014) with the following modifications.oligo-dT were used to prime reverse transcription with  Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle  PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent  Agencourt AMPure XP bead purification as described. Libraries were tagmented using the  Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon  request). Libraries from 384 cells with unique barcodes were combined and sequenced using a  NextSeq 500 sequencer (Illumina).

treatment_protocol: Fresh tumor tissue was minced with a scalpel and enzymatically dissociated using a gentle papain-based brain tumor dissociation kit (Miltenyi Biotec). Large pieces of debris were removed with a 100 micron strainer, and dissociated cells were layered carefully onto a 5mL density gradient (Lympholyte-H, Cedar Lane labs), which was centrifuged at 2,000 rpm for 10 min at room temperature to pellet dead cells and red blood cells. The interface containing live cells was saved and used for staining and flow cytometry. Tumor cells were blocked in 1% bovine serum albumin in Hanks buffered saline solution (BSA /  HBSS), and then stained first with CD45-Vioblue direct antibody conjugate (Miltenyi Biotec) for  30 min at 4C. Cells were washed with cold PBS, and then resuspended in 1 mL of BSA / HBSS  containing 1uM calcein AM (Life Technologies) and 0.33uM TO-PRO-3 iodide (Life  Technologies) to co-stain for 30 min before sorting. Fluorescence-activated cell sorting was  performed on FACSAria Fusion Special Order System (Becton Dickinson) using 488nm (calcein  AM, 530/30 filter), 640nm (TO-PRO-3, 670/14 filter), and 405nm (Vioblue, 450/50 filter) lasers.   Fluorescence-minus-one controls were included with all tumors, as well as heat killed controls in  early pilot experiments, which were crucial to ensure proper identification of the TO-PRO-3  positive compartment and ensure sorting of the live cell population. Standard, strict forward  scatter height versus area criteria were used to discriminate doublets and gate only singlets.  Viable cells were identified by staining positive with calcein AM but negative for TO-PRO-3.  Single cells were sorted into 96-well plates containing cold buffer TCL buffer (Qiagen)  containing 1% beta-mercaptoethanol, snap frozen on dry ice, and then stored at -80C prior to  whole transcriptome amplification, library preparation and sequencing.

tag: cell type

value: oligodendroglioma single cell


title: MGH36-P9-C05


title: MGH36-P9-C11


title: MGH36-P9-C12


title: MGH36-P9-C01


title: MGH36-P9-C02


title: MGH36-P9-C09


title: MGH36-P9-C08


title: MGH36-P9-B09


title: MGH36-P9-B12


title: MGH36-P9-B08


title: MGH36-P9-B11


title: MGH36-P9-B07


title: MGH36-P9-D01


title: MGH36-P9-C10


title: MGH36-P9-B05


title: MGH36-P9-A12


title: MGH36-P9-B06


title: MGH36-P9-B03


title: MGH36-P9-B04


title: MGH36-P9-B02


title: MGH36-P9-A11


title: MGH36-P9-B01


title: MGH36-P9-A10


title: MGH36-P9-C06


title: MGH36-P9-A09


title: MGH36-P9-C03


title: MGH36-P9-A08


title: MGH36-P9-B10


title: MGH36-P9-C07


title: MGH36-P9-A07


title: MGH36-P8-H12


title: MGH36-P9-A05


title: MGH36-P8-H11


title: MGH36-P8-H08


title: MGH36-P9-A03


title: MGH36-P9-A01


title: MGH36-P9-A02


title: MGH36-P9-A04


title: MGH36-P8-H07


title: MGH36-P8-H10


title: MGH36-P9-A06


title: MGH36-P8-H06


title: MGH36-P8-H04


title: MGH36-P8-H03


title: MGH36-P8-H05


title: MGH36-P8-G09


title: MGH36-P8-G10


title: MGH36-P8-H02


title: MGH36-P8-G11


title: MGH36-P8-H01


title: MGH36-P8-G08


title: MGH36-P8-G07


title: MGH36-P8-G06


title: MGH36-P8-G04


title: MGH36-P8-G05


title: MGH36-P8-H09


title: MGH36-P8-G03


title: MGH36-P8-G01


title: MGH36-P8-F11


title: MGH36-P8-F10


title: MGH36-P8-F09


title: MGH36-P8-F07


title: MGH36-P8-F04


title: MGH36-P8-F08


title: MGH36-P8-F06


title: MGH36-P8-G12


title: MGH36-P8-F01


title: MGH36-P8-E09


title: MGH36-P8-E11


title: MGH36-P8-E10


title: MGH36-P8-E04


title: MGH36-P8-E06


title: MGH36-P8-E12


title: MGH36-P8-E05


title: MGH36-P8-E01


title: MGH36-P8-E03


title: MGH36-P8-E02


title: MGH36-P8-D12


title: MGH36-P8-D11


title: MGH36-P8-G02


title: MGH36-P8-F12


title: MGH36-P8-D10


title: MGH36-P8-D09


title: MGH36-P8-D08


title: MGH36-P8-F05


title: MGH36-P8-D07


title: MGH36-P8-F03


title: MGH36-P8-D05


title: MGH36-P8-D04


title: MGH36-P8-D06


title: MGH36-P8-D01


title: MGH36-P8-D02


title: MGH36-P8-F02


title: MGH36-P8-E08


title: MGH36-P8-D03


title: MGH36-P8-C11


title: MGH36-P8-C09


title: MGH36-P8-C10


title: MGH36-P8-C08


title: MGH36-P8-C12


title: MGH36-P8-E07


title: MGH36-P8-C05


title: MGH36-P8-C03


title: MGH36-P8-B11


title: MGH36-P8-C04


title: MGH36-P8-C01


title: MGH36-P8-B12


title: MGH36-P8-C07


title: MGH36-P8-B09


title: MGH36-P8-B10


title: MGH36-P8-C02


title: MGH36-P8-B08


title: MGH36-P8-B07


title: MGH36-P8-B03


title: MGH36-P8-B04


title: MGH36-P8-B05


title: MGH36-P8-B06


title: MGH36-P8-A11


title: MGH36-P8-A10


title: MGH36-P8-B02


title: MGH36-P8-B01


title: MGH36-P8-A12


title: MGH36-P8-A09


title: MGH36-P8-A06


title: MGH36-P8-A03


title: MGH36-P8-A08


title: MGH36-P8-A07


title: MGH36-P8-C06


title: MGH36-P8-A04


title: MGH36-P8-A05


title: MGH36-P7-H12


title: MGH36-P8-A02


title: MGH36-P7-H11


title: MGH36-P7-H08


title: MGH36-P7-H07


title: MGH36-P7-H06


title: MGH36-P7-H05


title: MGH36-P7-H09


title: MGH36-P7-H03


title: MGH36-P7-H02


title: MGH36-P7-G12


title: MGH36-P7-G11


title: MGH36-P7-G10


title: MGH36-P7-G09


title: MGH36-P7-H01


title: MGH36-P7-G08


title: MGH36-P7-G07


title: MGH36-P7-G06


title: MGH36-P7-G04


title: MGH36-P7-G03


title: MGH36-P8-A01


title: MGH36-P7-G05


title: MGH36-P7-G02


title: MGH36-P7-H10


title: MGH36-P7-G01


title: MGH36-P7-F09


title: MGH36-P7-F10


title: MGH36-P7-F11


title: MGH36-P7-F07


title: MGH36-P7-F05


title: MGH36-P7-F06


title: MGH36-P7-F04


title: MGH36-P7-F12


title: MGH36-P7-H04


title: MGH36-P7-F08


title: MGH36-P7-F01


title: MGH36-P7-F02


title: MGH36-P7-E12


title: MGH36-P7-E08


title: MGH36-P7-E10


title: MGH36-P7-E09


title: MGH36-P7-F03


title: MGH36-P7-E06


title: MGH36-P7-E07


title: MGH36-P7-E05


title: MGH36-P7-E04


title: MGH36-P7-E03


title: MGH36-P7-E01


title: MGH36-P7-D12


title: MGH36-P7-D11


title: MGH36-P7-E02


title: MGH36-P7-D10


title: MGH36-P7-D09


title: MGH36-P7-D08


title: MGH36-P7-D07


title: MGH36-P7-D05


title: MGH36-P7-D03


title: MGH36-P7-D02


title: MGH36-P7-D04


title: MGH36-P7-C12


title: MGH36-P7-E11


title: MGH36-P7-C11


title: MGH36-P7-C10


title: MGH36-P7-C09


title: MGH36-P7-C08


title: MGH36-P7-C05


title: MGH36-P7-C06


title: MGH36-P7-C02


title: MGH36-P7-C03


title: MGH36-P7-C04


title: MGH36-P7-B11


title: MGH36-P7-B12


title: MGH36-P7-B10


title: MGH36-P7-B09


title: MGH36-P7-D06


title: MGH36-P7-B06


title: MGH36-P7-B08


title: MGH36-P7-B05


title: MGH36-P7-B04


title: MGH36-P7-D01


title: MGH36-P7-B03


title: MGH36-P7-B07


title: MGH36-P7-B01


title: MGH36-P7-A09


title: MGH36-P7-A08


title: MGH36-P7-A12


title: MGH36-P7-C07


title: MGH36-P7-A07


title: MGH36-P7-A10


title: MGH36-P7-A11


title: MGH36-P7-A06


title: MGH36-P7-B02


title: MGH36-P7-C01


title: MGH36-P7-A03


title: MGH36-P7-A02


title: MGH36-P7-A01


title: MGH36-P6-H12


title: MGH36-P7-A04


title: MGH36-P6-H09


title: MGH36-P6-H10


title: MGH36-P6-H05


title: MGH36-P6-H06


title: MGH36-P6-H07


title: MGH36-P6-H03


title: MGH36-P6-H04


title: MGH36-P6-H01


title: MGH36-P6-H02


title: MGH36-P6-G11


title: MGH36-P6-G07


title: MGH36-P6-G12


title: MGH36-P6-G08


title: MGH36-P6-G10


title: MGH36-P6-G06


title: MGH36-P6-G05


title: MGH36-P6-G04


title: MGH36-P6-G02


title: MGH36-P6-G01


title: MGH36-P6-G03


title: MGH36-P6-F11


title: MGH36-P6-H08


title: MGH36-P6-F12


title: MGH36-P6-F10


title: MGH36-P6-F09


title: MGH36-P6-H11


title: MGH36-P6-F08


title: MGH36-P6-F07


title: MGH36-P6-F06


title: MGH36-P6-F04


title: MGH36-P6-F03


title: MGH36-P6-F05


title: MGH36-P6-E12


title: MGH36-P7-A05


title: MGH36-P6-F01


title: MGH36-P6-F02


title: MGH36-P6-E11


title: MGH36-P6-G09


title: MGH36-P6-E09


title: MGH36-P6-E10


title: MGH36-P6-E08


title: MGH36-P6-E07


title: MGH36-P6-E05


title: MGH36-P6-E06


title: MGH36-P6-E04


title: MGH36-P6-E02


title: MGH36-P6-D11


title: MGH36-P6-D10


title: MGH36-P6-D09


title: MGH36-P6-D07


title: MGH36-P6-E01


title: MGH36-P6-D08


title: MGH36-P6-D05


title: MGH36-P6-D03


title: MGH36-P6-D04


title: MGH36-P6-E03


title: MGH36-P6-D02


title: MGH36-P6-D01


title: MGH36-P6-C12


title: MGH36-P6-C08


title: MGH36-P6-C10


title: MGH36-P6-C09


title: MGH36-P6-C07


title: MGH36-P6-C05


title: MGH36-P6-C04


title: MGH36-P6-C02


title: MGH36-P6-B12


title: MGH36-P6-B11


title: MGH36-P6-D12


title: MGH36-P6-B10


title: MGH36-P6-D06


title: MGH36-P6-B06


title: MGH36-P6-C03


title: MGH36-P6-B09


title: MGH36-P6-B03


title: MGH36-P6-B08


title: MGH36-P6-B02


title: MGH36-P6-B04


title: MGH36-P6-A11


title: MGH36-P6-A12


title: MGH36-P6-B05


title: MGH36-P6-B01


title: MGH36-P6-C06


title: MGH36-P6-A10


title: MGH36-P6-B07


title: MGH36-P6-A09


title: MGH36-P6-C11


title: MGH36-P6-A08


title: MGH36-P6-A06


title: MGH36-P6-C01


title: MGH36-P6-A05


title: MGH36-P4-H12


title: MGH36-P4-H11


title: MGH36-P6-A02


title: MGH36-P4-H10


title: MGH36-P6-A01


title: MGH36-P4-H07


title: MGH36-P4-H05


title: MGH36-P4-H08


title: MGH36-P4-H06


title: MGH36-P4-H03


title: MGH36-P4-H04


title: MGH36-P4-G10


title: MGH36-P4-H02


title: MGH36-P4-G09


title: MGH36-P6-A07


title: MGH36-P4-G12


title: MGH36-P4-G05


title: MGH36-P4-G04


title: MGH36-P4-G08


title: MGH36-P4-G03


title: MGH36-P4-G07


title: MGH36-P6-A04


title: MGH36-P4-G06


title: MGH36-P4-G02


title: MGH36-P4-G01


title: MGH36-P4-F12


title: MGH36-P4-F08


title: MGH36-P4-F10


title: MGH36-P4-F09


title: MGH36-P4-F11


title: MGH36-P4-G11


title: MGH36-P4-F03


title: MGH36-P4-F04


title: MGH36-P4-E12


title: MGH36-P4-F01


title: MGH36-P4-H01


title: MGH36-P6-A03


title: MGH36-P4-F02


title: MGH36-P4-F05


title: MGH36-P4-F06


title: MGH36-P4-E11


title: MGH36-P4-E06


title: MGH36-P4-E08


title: MGH36-P4-E10


title: MGH36-P4-E09


title: MGH36-P4-E04


title: MGH36-P4-E03


title: MGH36-P4-E05


title: MGH36-P4-E02


title: MGH36-P4-E07


title: MGH36-P4-H09


title: MGH36-P4-D11


title: MGH36-P4-E01


title: MGH36-P4-F07


title: MGH36-P4-D08


title: MGH36-P4-D09


title: MGH36-P4-D06


title: MGH36-P4-D05


title: MGH36-P4-D04


title: MGH36-P4-D03


title: MGH36-P4-D01


title: MGH36-P4-C12


title: MGH36-P4-C09


title: MGH36-P4-C11


title: MGH36-P4-C06


title: MGH36-P4-C07


title: MGH36-P4-C05


title: MGH36-P4-C03


title: MGH36-P4-D10


title: MGH36-P4-B11


title: MGH36-P4-D12


title: MGH36-P4-C02


title: MGH36-P4-B08


title: MGH36-P4-B12


title: MGH36-P4-D07


title: MGH36-P4-B06


title: MGH36-P4-B04


title: MGH36-P4-B09


title: MGH36-P4-B05


title: MGH36-P4-B03


title: MGH36-P4-B01


title: MGH36-P4-A12


title: MGH36-P4-D02


title: MGH36-P4-C10


title: MGH36-P4-B02


title: MGH36-P4-A11


title: MGH36-P4-A10


title: MGH36-P4-C04


title: MGH36-P4-C08


title: MGH36-P4-B10


title: MGH36-P4-A05


title: MGH36-P4-A08


title: MGH36-P4-A07


title: MGH36-P4-A06


title: MGH36-P4-A01


title: MGH36-P4-A03


title: MGH36-P4-A04


title: MGH36-P4-B07


title: MGH36-P3-H10


title: MGH36-P4-A02


title: MGH36-P3-H12


title: MGH36-P3-H11


title: MGH36-P3-H09


title: MGH36-P3-H06


title: MGH36-P3-H07


title: MGH36-P3-H01


title: MGH36-P3-G12


title: MGH36-P3-H03


title: MGH36-P3-G11


title: MGH36-P3-G10


title: MGH36-P3-H05


title: MGH36-P3-H08


title: MGH36-P4-C01


title: MGH36-P3-G09


title: MGH36-P3-G08


title: MGH36-P3-G06


title: MGH36-P4-A09


title: MGH36-P3-G01


title: MGH36-P3-G05


title: MGH36-P3-G03


title: MGH36-P3-G04


title: MGH36-P3-G02


title: MGH36-P3-H02


title: MGH36-P3-F11


title: MGH36-P3-G07


title: MGH36-P3-F12


title: MGH36-P3-F09


title: MGH36-P3-F08


title: MGH36-P3-F07


title: MGH36-P3-F06


title: MGH36-P3-F10


title: MGH36-P3-F05


title: MGH36-P3-H04


title: MGH36-P3-F03


title: MGH36-P3-F04


title: MGH36-P3-F01


title: MGH36-P3-F02


title: MGH36-P3-E11


title: MGH36-P3-E10


title: MGH36-P3-E06


title: MGH36-P3-E07


title: MGH36-P3-E08


title: MGH36-P3-E09


title: MGH36-P3-E05


title: MGH36-P3-E04


title: MGH36-P3-D07


title: MGH36-P3-D10


title: MGH36-P3-D09


title: MGH36-P3-D11


title: MGH36-P3-D06


title: MGH36-P3-D08


title: MGH36-P3-D12


title: MGH36-P3-E03


title: MGH36-P3-D04


title: MGH36-P3-D05


title: MGH36-P3-C12


title: MGH36-P3-E12


title: MGH36-P3-C11


title: MGH36-P3-D03


title: MGH36-P3-C10


title: MGH36-P3-D01


title: MGH36-P3-D02


title: MGH36-P3-C08


title: MGH36-P3-C09


title: MGH36-P3-C02


title: MGH36-P3-C06


title: MGH36-P3-C07


title: MGH36-P3-C05


title: MGH36-P3-C04


title: MGH36-P3-C03


title: MGH36-P3-E02


title: MGH36-P3-B11


title: MGH36-P3-E01


title: MGH36-P3-B12


title: MGH36-P3-B10


title: MGH36-P3-B07


title: MGH36-P3-B08


title: MGH36-P3-B05


title: MGH36-P3-B06


title: MGH36-P3-B04


title: MGH36-P3-A12


title: MGH36-P3-B03


title: MGH36-P3-A11


title: MGH36-P3-A10


title: MGH36-P3-B09


title: MGH36-P3-B01


title: MGH36-P3-A08


title: MGH36-P3-A07


title: MGH36-P3-A06


title: MGH36-P3-B02


title: MGH36-P3-A05


title: MGH36-P3-A04


title: MGH36-P3-C01


title: MGH36-P3-A03


title: MGH36-P10-H11


title: MGH36-P10-H09


title: MGH36-P10-H08


title: MGH36-P3-A01


title: MGH36-P3-A02


title: MGH36-P10-H10


title: MGH36-P10-H07


title: MGH36-P10-H03


title: MGH36-P10-H06


title: MGH36-P10-H05


title: MGH36-P10-H02


title: MGH36-P10-H04


title: MGH36-P10-G10


title: MGH36-P10-G11


title: MGH36-P10-G07


title: MGH36-P10-G12


title: MGH36-P10-G03


title: MGH36-P10-H01


title: MGH36-P10-G05


title: MGH36-P10-F12


title: MGH36-P10-F11


title: MGH36-P3-A09


title: MGH36-P10-H12


title: MGH36-P10-G09


title: MGH36-P10-G08


title: MGH36-P10-G04


title: MGH36-P10-F10


title: MGH36-P10-F07


title: MGH36-P10-F06


title: MGH36-P10-G02


title: MGH36-P10-G01


title: MGH36-P10-F09


title: MGH36-P10-F01


title: MGH36-P10-E12


title: MGH36-P10-F08


title: MGH36-P10-E10


title: MGH36-P10-F04


title: MGH36-P10-F02


title: MGH36-P10-E08


title: MGH36-P10-E11


title: MGH36-P10-F05


title: MGH36-P10-F03


title: MGH36-P10-G06


title: MGH36-P10-E06


title: MGH36-P10-E05


title: MGH36-P10-E09


title: MGH36-P10-D12


title: MGH36-P10-D11


title: MGH36-P10-D08


title: MGH36-P10-D04


title: MGH36-P10-D05


title: MGH36-P10-D07


title: MGH36-P10-E04


title: MGH36-P10-E01


title: MGH36-P10-D01


title: MGH36-P10-D09


title: MGH36-P10-D10


title: MGH36-P10-E03


title: MGH36-P10-D06


title: MGH36-P10-E07


title: MGH36-P10-D02


title: MGH36-P10-C10


title: MGH36-P10-D03


title: MGH36-P10-C11


title: MGH36-P10-E02


title: MGH36-P10-C05


title: MGH36-P10-C08


title: MGH36-P10-C09


title: MGH36-P10-C06


title: MGH36-P10-C04


title: MGH36-P10-C03


title: MGH36-P10-C02


title: MGH36-P10-C07


title: MGH36-P10-B10


title: MGH36-P10-B11


title: MGH36-P10-B12


title: MGH36-P10-C01


title: MGH36-P10-C12


title: MGH36-P10-B09


title: MGH36-P10-B06


title: MGH36-P10-B05


title: MGH36-P10-B03


title: MGH36-P10-B04


title: MGH36-P10-B08


title: MGH36-P10-A11


title: MGH36-P10-B02


title: MGH36-P10-A10


title: MGH36-P10-B07


title: MGH36-P10-A07


title: MGH36-P10-B01


title: MGH36-P10-A09


title: MGH36-P10-A06


title: MGH36-P10-A04


title: MGH36-P10-A05


title: MGH36-P10-A02


title: MGH36_P5_H11


title: MGH36-P10-A01


title: MGH36_P5_H09


title: MGH36_P5_H12


title: MGH36_P5_H06


title: MGH36_P5_H08


title: MGH36-P10-A12


title: MGH36_P5_H04


title: MGH36_P5_H07


title: MGH36_P5_G12


title: MGH36_P5_H01


title: MGH36_P5_H02


title: MGH36_P5_H03


title: MGH36-P10-A08


title: MGH36_P5_G09


title: MGH36_P5_G10


title: MGH36_P5_G05


title: MGH36_P5_G08


title: MGH36_P5_G07


title: MGH36_P5_G11


title: MGH36_P5_G03


title: MGH36_P5_G06


title: MGH36-P10-A03


title: MGH36_P5_G02


title: MGH36_P5_H10


title: MGH36_P5_F11


title: MGH36_P5_F12


title: MGH36_P5_F10


title: MGH36_P5_H05


title: MGH36_P5_G04


title: MGH36_P5_G01


title: MGH36_P5_F07


title: MGH36_P5_F06


title: MGH36_P5_F04


title: MGH36_P5_F08


title: MGH36_P5_F05


title: MGH36_P5_F02


title: MGH36_P5_E11


title: MGH36_P5_F03


title: MGH36_P5_E12


title: MGH36_P5_F01


title: MGH36_P5_E05


title: MGH36_P5_E10


title: MGH36_P5_E06


title: MGH36_P5_E09


title: MGH36_P5_E04


title: MGH36_P5_E08


title: MGH36_P5_E03


title: MGH36_P5_D11


title: MGH36_P5_D03


title: MGH36_P5_E01


title: MGH36_P5_D06


title: MGH36_P5_D02


title: MGH36_P5_D01


title: MGH36_P5_F09


title: MGH36_P5_D05


title: MGH36_P5_D08


title: MGH36_P5_D09


title: MGH36_P5_D07


title: MGH36_P5_D12


title: MGH36_P5_C12


title: MGH36_P5_C11


title: MGH36_P5_D10


title: MGH36_P5_C08


title: MGH36_P5_C10


title: MGH36_P5_C06


title: MGH36_P5_E07


title: MGH36_P5_C07


title: MGH36_P5_C05


title: MGH53-P5-D09


title: MGH53-P5-D08


title: MGH53-P5-D11


title: MGH53-P5-D10


title: MGH36_P5_C04


title: MGH36_P5_E02


title: MGH53-P5-D07


title: MGH36_P5_D04


title: MGH36_P5_C09


title: MGH53-P5-D05


title: MGH53-P5-D02


title: MGH53-P5-D03


title: MGH53-P5-D04


title: MGH53-P5-D01


title: MGH53-P5-C10


title: MGH53-P5-C12


title: MGH53-P5-D06


title: MGH53-P5-C08


title: MGH53-P5-C09


title: MGH53-P5-C04


title: MGH53-P5-C11


title: MGH53-P5-C07


title: MGH53-P5-C02


title: MGH53-P5-B12


title: MGH53-P5-C03


title: MGH53-P5-C05


title: MGH53-P5-B10


title: MGH53-P5-B09


title: MGH53-P5-B06


title: MGH53-P5-B05


title: MGH53-P5-B03


title: MGH53-P5-B04


title: MGH53-P5-B02


title: MGH53-P5-A12


title: MGH53-P5-A11


title: MGH53-P5-A10


title: MGH53-P5-A06


title: MGH53-P5-B11


title: MGH53-P5-A08


title: MGH53-P5-A07


title: MGH53-P5-B01


title: MGH53-P5-C01


title: MGH53-P5-C06


title: MGH53-P5-A04


title: MGH53-P4-H11


title: MGH53-P4-H09


title: MGH53-P5-A03


title: MGH53-P5-B07


title: MGH53-P5-A02


title: MGH53-P4-H12


title: MGH53-P5-A01


title: MGH53-P4-H07


title: MGH53-P4-H08


title: MGH53-P4-H10


title: MGH53-P5-B08


title: MGH53-P4-H03


title: MGH53-P4-H02


title: MGH53-P5-A05


title: MGH53-P4-H05


title: MGH53-P4-H01


title: MGH53-P4-H06


title: MGH53-P5-A09


title: MGH53-P4-G12


title: MGH53-P4-G10


title: MGH53-P4-G08


title: MGH53-P4-G09


title: MGH53-P4-G05


title: MGH53-P4-G06


title: MGH53-P4-G07


title: MGH53-P4-G02


title: MGH53-P4-G04


title: MGH53-P4-G03


title: MGH53-P4-F08


title: MGH53-P4-F12


title: MGH53-P4-F04


title: MGH53-P4-G01


title: MGH53-P4-F03


title: MGH53-P4-F05


title: MGH53-P4-F10


title: MGH53-P4-F07


title: MGH53-P4-F09


title: MGH53-P4-F02


title: MGH53-P4-F01


title: MGH53-P4-E11


title: MGH53-P4-E12


title: MGH53-P4-H04


title: MGH53-P4-E09


title: MGH53-P4-E08


title: MGH53-P4-G11


title: MGH53-P4-E07


title: MGH53-P4-E06


title: MGH53-P4-F11


title: MGH53-P4-E04


title: MGH53-P4-D12


title: MGH53-P4-E05


title: MGH53-P4-F06


title: MGH53-P4-E03


title: MGH53-P4-E02


title: MGH53-P4-E01


title: MGH53-P4-D08


title: MGH53-P4-D06


title: MGH53-P4-D11


title: MGH53-P4-D09


title: MGH53-P4-D05


title: MGH53-P4-D02


title: MGH53-P4-D03


title: MGH53-P4-D01


title: MGH53-P4-E10


title: MGH53-P4-C10


title: MGH53-P4-C12


title: MGH53-P4-D07


title: MGH53-P4-D10


title: MGH53-P4-D04


title: MGH53-P4-C11


title: MGH53-P4-C09


title: MGH53-P4-C07


title: MGH53-P4-C08


title: MGH53-P4-C06


title: MGH53-P4-C05


title: MGH53-P4-C03


title: MGH53-P4-C01


title: MGH53-P4-B10


title: MGH53-P4-B06


title: MGH53-P4-B12


title: MGH53-P4-B07


title: MGH53-P4-B11


title: MGH53-P4-B04


title: MGH53-P4-B03


title: MGH53-P4-B05


title: MGH53-P4-B08


title: MGH53-P4-C02


title: MGH53-P4-A10


title: MGH53-P4-A12


title: MGH53-P4-B02


title: MGH53-P4-A11


title: MGH53-P4-A09


title: MGH53-P4-A02


title: MGH53-P4-A01


title: MGH53-P4-A07


title: MGH53-P4-A06


title: MGH53-P4-A05


title: MGH53-P2-H11


title: MGH53-P4-C04


title: MGH53-P4-A04


title: MGH53-P4-B01


title: MGH53-P2-H08


title: MGH53-P2-H10


title: MGH53-P4-B09


title: MGH53-P2-H09


title: MGH53-P2-H07


title: MGH53-P4-A03


title: MGH53-P4-A08


title: MGH53-P2-H03


title: MGH53-P2-H06


title: MGH53-P2-H02


title: MGH53-P2-G11


title: MGH53-P2-H05


title: MGH53-P2-H04


title: MGH53-P2-H12


title: MGH53-P2-G08


title: MGH53-P2-G10


title: MGH53-P2-G07


title: MGH53-P2-G09


title: MGH53-P2-G12


title: MGH53-P2-G02


title: MGH53-P2-G05


title: MGH53-P2-G06


title: MGH53-P2-G04


title: MGH53-P2-G03


title: MGH53-P2-F10


title: MGH53-P2-F11


title: MGH53-P2-F06


title: MGH53-P2-F09


title: MGH53-P2-F12


title: MGH53-P2-F07


title: MGH53-P2-F05


title: MGH53-P2-F03


title: MGH53-P2-H01


title: MGH53-P2-F04


title: MGH53-P2-F08


title: MGH53-P2-E11


title: MGH53-P2-F02


title: MGH53-P2-E09


title: MGH53-P2-E10


title: MGH53-P2-E06


title: MGH53-P2-E08


title: MGH53-P2-F01


title: MGH53-P2-E05


title: MGH53-P2-G01


title: MGH53-P2-E04


title: MGH53-P2-E02


title: MGH53-P2-D11


title: MGH53-P2-E01


title: MGH53-P2-E07


title: MGH53-P2-E03


title: MGH53-P2-D08


title: MGH53-P2-D10


title: MGH53-P2-D09


title: MGH53-P2-D07


title: MGH53-P2-D04


title: MGH53-P2-D05


title: MGH53-P2-D06


title: MGH53-P2-C12


title: MGH53-P2-E12


title: MGH53-P2-D01


title: MGH53-P2-D03


title: MGH53-P2-C08


title: MGH53-P2-C07


title: MGH53-P2-C06


title: MGH53-P2-C10


title: MGH53-P2-C04


title: MGH53-P2-C05


title: MGH53-P2-C03


title: MGH53-P2-C02


title: MGH53-P2-D12


title: MGH53-P2-C01


title: MGH53-P2-B12


title: MGH53-P2-B10


title: MGH53-P2-B09


title: MGH53-P2-B08


title: MGH53-P2-D02


title: MGH53-P2-B07


title: MGH53-P2-B06


title: MGH53-P2-B05


title: MGH53-P2-B04


title: MGH53-P2-C11


title: MGH53-P2-B03


title: MGH53-P2-B02


title: MGH53-P2-A12


title: MGH53-P2-B01


title: MGH53-P2-A11


title: MGH53-P2-A08


title: MGH53-P2-A09


title: MGH53-P2-A10


title: MGH53-P2-A07


title: MGH53-P2-A04


title: MGH53-P2-A02


title: MGH53-P2-A01


title: MGH53-P2-A05


title: MGH53-P1-H12


title: MGH53-P2-B11


title: MGH53-P1-H10


title: MGH53-P2-C09


title: MGH53-P2-A03


title: MGH53-P1-H09


title: MGH53-P1-H06


title: MGH53-P1-H07


title: MGH53-P1-H05


title: MGH53-P1-H04


title: MGH53-P1-H03


title: MGH53-P1-H02


title: MGH53-P1-H01


title: MGH53-P1-G11


title: MGH53-P1-G12


title: MGH53-P1-G08


title: MGH53-P2-A06


title: MGH53-P1-G05


title: MGH53-P1-G07


title: MGH53-P1-G04


title: MGH53-P1-G10


title: MGH53-P1-G03


title: MGH53-P1-G09


title: MGH53-P1-G01


title: MGH53-P1-F10


title: MGH53-P1-F09


title: MGH53-P1-H08


title: MGH53-P1-F08


title: MGH53-P1-G02


title: MGH53-P1-F07


title: MGH53-P1-F11


title: MGH53-P1-F06


title: MGH53-P1-F04


title: MGH53-P1-F12


title: MGH53-P1-F02


title: MGH53-P1-F03


title: MGH53-P1-F01


title: MGH53-P1-E12


title: MGH53-P1-E11


title: MGH53-P1-E10


title: MGH53-P1-E09


title: MGH53-P1-E08


title: MGH53-P1-E07


title: MGH53-P1-E03


title: MGH53-P1-E04


title: MGH53-P1-E06


title: MGH53-P1-E05


title: MGH53-P1-H11


title: MGH53-P1-D12


title: MGH53-P1-E02


title: MGH53-P1-E01


title: MGH53-P1-D11


title: MGH53-P1-F05


title: MGH53-P1-D04


title: MGH53-P1-D10


title: MGH53-P1-D06


title: MGH53-P1-D08


title: MGH53-P1-D03


title: MGH53-P1-D09


title: MGH53-P1-C11


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title: MGH53-P1-D02


title: MGH53-P1-D01


title: MGH53-P1-C10


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title: MGH53-P1-C05


title: MGH53-P1-C06


title: MGH53-P1-G06


title: MGH53-P1-C04


title: MGH53-P1-B11


title: MGH53-P1-C02


title: MGH53-P1-C03


title: MGH53-P1-B12


title: MGH53-P1-C01


title: MGH53-P1-B09


title: MGH53-P1-B10


title: MGH53-P1-D05


title: MGH53-P1-B08


title: MGH53-P1-B05


title: MGH53-P1-B07


title: MGH53-P1-A12


title: MGH53-P1-C09


title: MGH53-P1-A11


title: MGH53-P1-A07


title: MGH53-P1-C12


title: MGH53-P1-C07


title: MGH53-P1-A10


title: MGH53-P1-B01


title: MGH53-P1-B03


title: MGH53-P1-A06


title: MGH53-P1-B02


title: MGH53-P1-B06


title: MGH53-P1-A09


title: MGH53-P1-A05


title: MGH53-P1-A04


title: MGH53-P1-A08


title: MGH53-P1-A02


title: MGH53-P1-A03


title: MGH53-P1-A01


title: MGH53-P12-H12


title: MGH53-P12-H09


title: MGH53-P12-H10


title: MGH53-P12-H08


title: MGH53-P12-H11


title: MGH53-P12-H05


title: MGH53-P1-B04


title: MGH53-P12-H06


title: MGH53-P12-H04


title: MGH53-P12-H02


title: MGH53-P12-H01


title: MGH53-P12-G09


title: MGH53-P12-G08


title: MGH53-P12-G05


title: MGH53-P12-G06


title: MGH53-P12-G04


title: MGH53-P12-G01


title: MGH53-P12-G02


title: MGH53-P12-F12


title: MGH53-P12-F09


title: MGH53-P12-F08


title: MGH53-P12-F10


title: MGH53-P12-F07


title: MGH53-P12-F05


title: MGH53-P12-F06


title: MGH53-P12-H07


title: MGH53-P12-F04


title: MGH53-P12-F02


title: MGH53-P12-F01


title: MGH53-P12-H03


title: MGH53-P12-E12


title: MGH53-P12-E11


title: MGH53-P12-G12


title: MGH53-P12-G10


title: MGH53-P12-F03


title: MGH53-P12-G07


title: MGH53-P12-E09


title: MGH53-P12-G11


title: MGH53-P12-E10


title: MGH53-P12-E08


title: MGH53-P12-E07


title: MGH53-P12-G03


title: MGH53-P12-F11


title: MGH53-P12-E05


title: MGH53-P12-E01


title: MGH53-P12-E03


title: MGH53-P12-D12


title: MGH53-P12-D11


title: MGH53-P12-E04


title: MGH53-P12-D10


title: MGH53-P12-D09


title: MGH53-P12-D08


title: MGH53-P12-D07


title: MGH53-P12-D06


title: MGH53-P12-D04


title: MGH53-P12-D03


title: MGH53-P12-D02


title: MGH53-P12-D01


title: MGH53-P12-C11


title: MGH53-P12-C10


title: MGH53-P12-C09


title: MGH53-P12-E06


title: MGH53-P12-C08


title: MGH53-P12-C04


title: MGH53-P12-C06


title: MGH53-P12-C05


title: MGH53-P12-E02


title: MGH53-P12-C03


title: MGH53-P12-C07


title: MGH53-P12-C02


title: MGH53-P12-C01


title: MGH53-P12-B09


title: MGH53-P12-B06


title: MGH53-P12-B08


title: MGH53-P12-D05


title: MGH53-P12-B07


title: MGH53-P12-B11


title: MGH53-P12-B03


title: MGH53-P12-B05


title: MGH53-P12-B10


title: MGH53-P12-B02


title: MGH53-P12-B04


title: MGH53-P12-C12


title: MGH53-P12-A12


title: MGH53-P12-B01


title: MGH53-P12-A09


title: MGH53-P12-A10


title: MGH53-P12-A07


title: MGH53-P12-A08


title: MGH53-P12-A05


title: MGH53-P12-A06


title: MGH53-P12-A01


title: MGH53-P12-A02


title: MGH53-P12-A11


title: MGH53-P11-H12


title: MGH53-P11-H11


title: MGH53-P11-H10


title: MGH53-P11-H09


title: MGH53-P12-A03


title: MGH53-P12-A04


title: MGH53-P11-H08


title: MGH53-P11-H06


title: MGH53-P11-H05


title: MGH53-P11-H04


title: MGH53-P12-B12


title: MGH53-P11-G12


title: MGH53-P11-H02


title: MGH53-P11-H01


title: MGH53-P11-G09


title: MGH53-P11-G11


title: MGH53-P11-G08


title: MGH53-P11-G06


title: MGH53-P11-G05


title: MGH53-P11-G04


title: MGH53-P11-G03


title: MGH53-P11-G02


title: MGH53-P11-F12


title: MGH53-P11-G01


title: MGH53-P11-F11


title: MGH53-P11-F07


title: MGH53-P11-F09


title: MGH53-P11-F08


title: MGH53-P11-F10


title: MGH53-P11-F04


title: MGH53-P11-F05


title: MGH53-P11-F06


title: MGH53-P11-H07


title: MGH53-P11-F02


title: MGH53-P11-F03


title: MGH53-P11-H03


title: MGH53-P11-E09


title: MGH53-P11-G10


title: MGH53-P11-E10


title: MGH53-P11-E12


title: MGH53-P11-E11


title: MGH53-P11-G07


title: MGH53-P11-E03


title: MGH53-P11-E07


title: MGH53-P11-E04


title: MGH53-P11-E02


title: MGH53-P11-E06


title: MGH53-P11-E05


title: MGH53-P11-E01


title: MGH53-P11-D12


title: MGH53-P11-D10


title: MGH53-P11-D08


title: MGH53-P11-D06


title: MGH53-P11-D09


title: MGH53-P11-D05


title: MGH53-P11-F01


title: MGH53-P11-C12


title: MGH53-P11-D04


title: MGH53-P11-D02


title: MGH53-P11-C11


title: MGH53-P11-E08


title: MGH53-P11-D01


title: MGH53-P11-D03


title: MGH53-P11-C10


title: MGH53-P11-C07


title: MGH53-P11-C06


title: MGH53-P11-C08


title: MGH53-P11-C05


title: MGH53-P11-C09


title: MGH53-P11-C02


title: MGH53-P11-C04


title: MGH53-P11-C01


title: MGH53-P11-D07


title: MGH53-P11-C03


title: MGH53-P11-B11


title: MGH53-P11-B10


title: MGH53-P11-D11


title: MGH53-P11-B07


title: MGH53-P11-B08


title: MGH53-P11-B06


title: MGH53-P11-B05


title: MGH53-P11-B04


title: MGH53-P11-B03


title: MGH53-P11-B09


title: MGH53-P11-B02


title: MGH53-P11-A12


title: MGH53-P11-A10


title: MGH53-P11-A11


title: MGH53-P11-A08


title: MGH53-P11-A09


title: MGH53-P11-A07


title: MGH53-P11-A06


title: MGH53-P11-A04


title: MGH53-P11-A03


title: MGH53-P11-A01


title: MGH53-P10-H12


title: MGH53-P11-B12


title: MGH53-P10-H11


title: MGH53-P10-H10


title: MGH53-P10-H05


title: MGH53-P10-H09


title: MGH53-P11-A02


title: MGH53-P10-H03


title: MGH53-P10-H04


title: MGH53-P10-H06


title: MGH53-P10-H08


title: MGH53-P10-G08


title: MGH53-P10-H02


title: MGH53-P10-G10


title: MGH53-P10-H01


title: MGH53-P10-G09


title: MGH53-P10-H07


title: MGH53-P11-A05


title: MGH53-P11-B01


title: MGH53-P10-G07


title: MGH53-P10-G05


title: MGH53-P10-G11


title: MGH53-P10-G04


title: MGH53-P10-G03


title: MGH53-P10-G02


title: MGH53-P10-G06


title: MGH53-P10-F10


title: MGH53-P10-F12


title: MGH53-P10-F09


title: MGH53-P10-F08


title: MGH53-P10-G01


title: MGH53-P10-G12


title: MGH53-P10-F06


title: MGH53-P10-F05


title: MGH53-P10-F01


title: MGH53-P10-F04


title: MGH53-P10-F03


title: MGH53-P10-F07


title: MGH53-P10-F02


title: MGH53-P10-E12


title: MGH53-P10-E11


title: MGH53-P10-E07


title: MGH53-P10-E09


title: MGH53-P10-E06


title: MGH53-P10-E08


title: MGH53-P10-E10


title: MGH53-P10-E05


title: MGH53-P10-E02


title: MGH53-P10-E03


title: MGH53-P10-E01


title: MGH53-P10-D10


title: MGH53-P10-D09


title: MGH53-P10-D12


title: MGH53-P10-D11


title: MGH53-P10-D08


title: MGH53-P10-D07


title: MGH53-P10-F11


title: MGH53-P10-C10


title: MGH53-P10-D05


title: MGH53-P10-C11


title: MGH53-P10-D06


title: MGH53-P10-C08


title: MGH53-P10-E04


title: MGH53-P10-D01


title: MGH53-P10-D02


title: MGH53-P10-D03


title: MGH53-P10-C05


title: MGH53-P10-C07


title: MGH53-P10-C09


title: MGH53-P10-C06


title: MGH53-P10-C12


title: MGH53-P10-C03


title: MGH53-P10-B11


title: MGH53-P10-B12


title: MGH53-P10-C04


title: MGH53-P10-C02


title: MGH53-P10-B07


title: MGH53-P10-D04


title: MGH53-P10-B09


title: MGH53-P10-C01


title: MGH53-P10-B08


title: MGH53-P10-B06


title: MGH53-P10-B05


title: MGH53-P10-B04


title: MGH53-P10-B02


title: MGH53-P10-B01


title: MGH53-P10-B03


title: MGH53-P10-A11


title: MGH53-P10-A04


title: MGH53-P10-A08


title: MGH53-P10-A07


title: MGH53-P10-A05


title: MGH53-P10-A09


title: MGH53-P10-A06


title: MGH53-P10-A12


title: MGH53-P10-A02


title: MGH53-P10-A10


title: MGH53-P10-B10


title: MGH36-P9-H12


title: MGH36-P9-H09


title: MGH36-P9-H11


title: MGH36-P9-H08


title: MGH36-P9-H10


title: MGH36-P9-H06


title: MGH36-P9-H05


title: MGH36-P9-H02


title: MGH36-P9-G12


title: MGH36-P9-H01


title: MGH36-P9-G11


title: MGH36-P9-G09


title: MGH36-P9-G08


title: MGH36-P9-G07


title: MGH36-P9-G06


title: MGH36-P9-G04


title: MGH53-P10-A03


title: MGH36-P9-G05


title: MGH53-P10-A01


title: MGH36-P9-G03


title: MGH36-P9-G10


title: MGH36-P9-G02


title: MGH36-P9-F12


title: MGH36-P9-F09


title: MGH36-P9-G01


title: MGH36-P9-H07


title: MGH36-P9-F10


title: MGH36-P9-F11


title: MGH36-P9-F03


title: MGH36-P9-F07


title: MGH36-P9-H03


title: MGH36-P9-F01


title: MGH36-P9-F06


title: MGH36-P9-F02


title: MGH36-P9-E10


title: MGH36-P9-H04


title: MGH36-P9-E11


title: MGH36-P9-E08


title: MGH36-P9-E12


title: MGH36-P9-E05


title: MGH36-P9-E04


title: MGH36-P9-F08


title: MGH36-P9-E06


title: MGH36-P9-E03


title: MGH36-P9-F05


title: MGH36-P9-E02


title: MGH36-P9-D08


title: MGH36-P9-E07


title: MGH36-P9-D11


title: MGH36-P9-E01


title: MGH36-P9-D10


title: MGH36-P9-D09


title: MGH36-P9-D12


title: MGH36-P9-F04


title: MGH36-P9-D03


title: MGH36-P9-D02


title: MGH36-P9-D07


title: MGH36-P9-D06


title: MGH97_P10_H05

data_processing:
Paired-end, 38-base reads were mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6", which allows alignment of sequences with single base changes such as point mutation in the IDH1  gene. Expression values were calculated from SAM files using RSEM v1.2.3 in paired-end mode  using parameters "--estimate-rspd --paired end -sam -p 6", from which TPM values for each gene  were extracted.
Expression levels were quantified as Ei,j=log2(TPMi,j/10+1), where TPMi,j refers to transcriptper-million  for gene i in sample j, as calculated by RSEM41. TPM values are divided by 10 since  we estimate the complexity of single cell libraries in the order of 100,000 transcripts and would  like to avoid counting each transcript ~10 times, as would be the case with TPM, which may  inflate the difference between the expression level of a gene in cells in which the gene is detected  and those in which it is not detected.
For each cell, we quantified two quality measures: the number of genes for which at least one  read was mapped, and the average expression level of a curated list of housekeeping genes. We then conservatively excluded all cells with either fewer than 3,000 detected genes or an average housekeeping expression (E, as defined above) below 2.5. We then distinguished oligodendroglioma from non-malignant cells by inferrence of copy number variations and excluded the non-malignant cells.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing the normalized expression levels (E) for 23,686 analyzed genes across 4347 oligodendroglioma cells that passed QC.

extract_protocol:
RNA from single cells was first purified with Agencourt  RNAClean XP beads (Beckman Coulter)
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli  2014) with the following modifications.oligo-dT were used to prime reverse transcription with  Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle  PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent  Agencourt AMPure XP bead purification as described. Libraries were tagmented using the  Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon  request). Libraries from 384 cells with unique barcodes were combined and sequenced using a  NextSeq 500 sequencer (Illumina).
single cell RNA-seq

tag: tumor


title: MGH97_P10_H04


title: MGH97_P10_H03


title: MGH97_P10_G12


title: MGH97_P10_G10


title: MGH97_P10_H08


title: MGH97_P7_A01


title: MGH36-P9-E09


title: MGH97_P10_H06


title: MGH97_P10_H09


title: MGH97_P10_H10


title: MGH97_P10_H11


title: MGH97_P7_A03


title: MGH97_P7_A04


title: MGH97_P7_A05


title: MGH97_P10_G11


title: MGH97_P7_A02


title: MGH97_P7_B03


title: MGH97_P7_A09


title: MGH97_P7_B01


title: MGH36-P9-D05


title: MGH97_P7_A07


title: MGH97_P7_B02


title: MGH97_P7_A11


title: MGH97_P7_B06


title: MGH97_P7_B11


title: MGH97_P7_A06


title: MGH97_P7_B04


title: MGH97_P10_H07


title: MGH97_P7_C02


title: MGH97_P7_B05


title: MGH97_P7_B10


title: MGH97_P7_C11


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title: MGH97_P7_D03


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title: MGH97_P7_F05


title: MGH97_P7_C06


title: MGH36-P9-D04


title: MGH97_P7_F08


title: MGH97_P7_E06


title: MGH97_P7_E03


title: MGH97_P7_F09


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title: MGH97_P9_H02


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title: MGH54-P9-H04


title: MGH54-P9-H03


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title: MGH54-P9-G09


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title: MGH97_P9_H04


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title: MGH54-P6-H10


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title: MGH54-P6-H12


title: MGH54-P6-F09


title: MGH54-P6-F10


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title: MGH54-P6-G12


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title: MGH54-P6-E12


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title: MGH54-P6-E02


title: MGH54-P6-D09


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title: MGH54-P6-D10


title: MGH54-P6-D08


title: MGH54-P6-F08


title: MGH54-P6-D07


title: MGH54-P6-F07


title: MGH54-P6-D06


title: MGH54-P6-D05


title: MGH54-P6-D04


title: MGH54-P6-D03


title: MGH54-P6-D02


title: MGH54-P6-D01


title: MGH54-P6-C12


title: MGH54-P6-E07


title: MGH54-P6-E08


title: MGH54-P6-C11


title: MGH54-P6-C09


title: MGH54-P6-C10


title: MGH54-P6-C08


title: MGH54-P6-C05


title: MGH54-P6-C04


title: MGH54-P6-C07


title: MGH54-P6-C06


title: MGH54-P6-C03


title: MGH54-P6-C02


title: MGH54-P6-C01


title: MGH54-P6-B10


title: MGH54-P6-B12


title: MGH54-P6-B08


title: MGH54-P6-B07


title: MGH54-P6-B11


title: MGH54-P6-B06


title: MGH54-P6-B05


title: MGH54-P6-B03


title: MGH54-P6-B02


title: MGH54-P6-A11


title: MGH54-P6-A12


title: MGH54-P6-B04


title: MGH54-P6-A07


title: MGH54-P6-A04


title: MGH54-P6-A08


title: MGH54-P6-A05


title: MGH54-P6-A09


title: MGH54-P6-B01


title: MGH54-P6-A03


title: MGH54-P6-A01


title: MGH54-P6-B09


title: MGH54-P5-H12


title: MGH54-P5-H11


title: MGH54-P5-H10


title: MGH54-P5-H08


title: MGH54-P5-H01


title: MGH54-P5-H07


title: MGH54-P5-H02


title: MGH54-P5-H04


title: MGH54-P5-H05


title: MGH54-P5-G12


title: MGH54-P6-A10


title: MGH54-P5-H06


title: MGH54-P5-H03


title: MGH54-P6-A06


title: MGH54-P5-G11


title: MGH54-P5-G10


title: MGH54-P5-G08


title: MGH54-P5-G09


title: MGH54-P5-G06


title: MGH54-P5-G05


title: MGH54-P5-G04


title: MGH54-P5-G07


title: MGH54-P6-A02


title: MGH54-P5-G02


title: MGH54-P5-G03


title: MGH54-P5-H09


title: MGH54-P5-F12


title: MGH54-P5-G01


title: MGH54-P5-F10


title: MGH54-P5-F07


title: MGH54-P5-F11


title: MGH54-P5-F05


title: MGH54-P5-F06


title: MGH54-P5-F03


title: MGH54-P5-F04


title: MGH54-P5-F02


title: MGH54-P5-E12


title: MGH54-P5-E10


title: MGH54-P7-A06


title: MGH54-P5-F01


title: MGH54-P5-E11


title: MGH54-P5-E08


title: MGH54-P5-E09


title: MGH54-P5-E07


title: MGH54-P5-E04


title: MGH54-P5-E06


title: MGH54-P5-F09


title: MGH54-P5-E05


title: MGH54-P5-D12


title: MGH54-P5-E01


title: MGH54-P5-E02


title: MGH54-P5-E03


title: MGH54-P5-D09


title: MGH54-P5-D11


title: MGH54-P5-F08


title: MGH54-P5-D08


title: MGH54-P5-D04


title: MGH54-P5-D06


title: MGH54-P5-D05


title: MGH54-P5-D01


title: MGH54-P5-C12


title: MGH54-P5-D02


title: MGH54-P5-C11


title: MGH54-P5-C09


title: MGH54-P5-C10


title: MGH54-P5-C08


title: MGH54-P5-C07


title: MGH54-P5-C06


title: MGH54-P5-C05


title: MGH54-P5-C04


title: MGH54-P5-C03


title: MGH54-P5-D10


title: MGH54-P5-C01


title: MGH54-P5-B09


title: MGH54-P5-C02


title: MGH54-P5-D07


title: MGH54-P5-B10


title: MGH54-P5-B12


title: MGH54-P5-B07


title: MGH54-P5-B11


title: MGH54-P5-B05


title: MGH54-P5-D03


title: MGH54-P5-B04


title: MGH54-P5-B03


title: MGH54-P5-B06


title: MGH54-P5-B08


title: MGH54-P5-B02


title: MGH54-P5-A11


title: MGH54-P5-B01


title: MGH54-P5-A10


title: MGH54-P5-A09


title: MGH54-P5-A08


title: MGH54-P5-A07


title: MGH54-P5-A05


title: MGH54-P5-A06


title: MGH54-P5-A04


title: MGH54-P5-A03


title: MGH54-P5-A01


title: MGH54-P2-H12


title: MGH54-P2-H09


title: MGH54-P2-H10


title: MGH54-P2-H11


title: MGH54-P2-H07


title: MGH54-P2-H06


title: MGH54-P2-H05


title: MGH54-P2-H04


title: MGH54-P5-A12


title: MGH54-P2-H02


title: MGH54-P2-G12


title: MGH54-P2-H01


title: MGH54-P2-G11


title: MGH54-P2-G07


title: MGH54-P2-G10


title: MGH54-P2-G09


title: MGH54-P2-G08


title: MGH54-P2-G04


title: MGH54-P2-G03