title: 6G_M_1545


title: 7J_M_2459

status: Public on Jul 07 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

tag: age

tag: strain


title: 6G_M_1542

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3


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title: 7J_M_2460


title: 6G_M_1544


title: 6G_M_1543


title: 6G_M_1539


title: 6G_M_1540


title: 7J_M_2457


title: 7J_M_2462


title: 7J_M_2454


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title: 6F_M_562


title: 6F_M_564


title: 6F_M_561


title: 6F_M_559


title: 6F_M_558


title: 6F_M_560


title: 6F_M_571


title: 6F_M_570


title: 6F_M_556


title: 6F_M_553


title: 6F_M_552


title: 6F_M_554


title: 6F_M_550


title: 6F_M_557


title: 6F_M_555


title: 6F_M_551


title: 6F_M_549


title: 6F_M_565


title: 6F_M_543


title: 6F_M_546


title: 6F_M_545


title: 6F_M_544


title: 6F_M_547


title: 6F_M_542


title: 6F_M_548


title: 6F_M_538


title: 6F_M_535


title: 6F_M_536


title: 6F_M_539


title: 6F_M_534


title: 6F_M_533


title: 6F_M_532


title: 6F_M_531


title: 6F_M_530


title: 6F_M_529


title: 6F_M_541


title: 6F_M_526


title: 6F_M_523


title: 6F_M_540


title: 6F_M_525


title: 6F_M_524


title: 6F_M_634


title: 6F_M_521


title: 6F_M_527


title: 6F_M_528


title: 6F_M_515


title: 6F_M_514


title: 6F_M_520


title: 6F_M_516


title: 6F_M_513


title: 6F_M_537


title: 6F_M_522


title: 6F_M_511


title: 6F_M_518


title: 6F_M_509


title: 6F_M_444


title: 6F_M_512


title: 6F_M_443


title: 6F_M_442


title: 6F_M_440


title: 6F_M_441


title: 6F_M_517


title: 6F_M_439


title: 6F_M_438


title: 6F_M_510


title: 6F_M_437


title: 6F_M_435


title: 6F_M_436


title: 6F_M_445


title: 6F_M_433


title: 6F_M_434


title: 6F_M_432


title: 6F_M_431


title: 6F_M_430


title: 6F_M_426


title: 6F_M_429


title: 6F_M_428


title: 6F_M_424


title: 6F_M_423


title: 6F_M_427


title: 6F_M_425


title: 6F_M_422


title: 6F_M_416


title: 6F_M_421


title: 6F_M_417


title: 6F_M_418


title: 6F_M_419


title: 6F_M_420


title: 6F_M_414


title: 6F_M_412


title: 6F_M_415


title: 6F_M_413


title: 6F_M_410


title: 6F_M_411


title: 6F_M_409


title: 6F_M_408


title: 6F_M_407


title: 6F_M_403


title: 6F_M_406


title: 6F_M_405


title: 6F_M_402


title: 6F_M_399


title: 6F_M_401


title: 6F_M_397


title: 6F_M_398


title: 6F_M_394


title: 6F_M_396


title: 6F_M_400


title: 6F_M_395


title: 6F_M_393


title: 6F_M_387


title: 6F_M_386


title: 6F_M_385


title: 6F_M_388


title: 6F_M_390


title: 6F_M_391


title: 6F_M_389


title: 6F_M_392


title: 6F_M_383


title: 6F_M_382


title: 6F_M_189


title: 6F_M_190


title: 6F_M_188


title: 6F_M_384


title: 6F_M_187


title: 6F_M_404


title: 6F_M_186


title: 6F_M_185


title: 6F_M_183


title: 6F_M_181


title: 6F_M_180


title: 6F_M_179


title: 6F_M_177


title: 6F_M_178


title: 6F_M_184


title: 6F_M_182


title: 6F_M_176


title: 6F_M_172


title: 6F_M_169


title: 6F_M_174


title: 6F_M_171


title: 6F_M_167


title: 6F_M_175


title: 6F_M_173


title: 6F_M_170


title: 6F_M_166


title: 6F_M_164


title: 6F_M_165


title: 6F_M_163


title: 6F_M_519


title: 6F_M_160


title: 6F_M_158


title: 6F_M_159


title: 6F_M_157


title: 6F_M_156


title: 6F_M_155


title: 6F_M_168


title: 6F_M_153


title: 6F_M_148


title: 6F_M_151


title: 6F_M_150


title: 6F_M_161


title: 6F_M_146


title: 6F_M_145


title: 6F_M_144


title: 6F_M_147


title: 6F_M_162


title: 6F_M_141


title: 6F_M_142


title: 6F_M_136


title: 6F_M_137


title: 6F_M_134


title: 6F_M_138


title: 6F_M_135


title: 6F_M_143


title: 6F_M_140


title: 6F_M_131


title: 6F_M_130


title: 6F_M_132


title: 6F_M_152


title: 6F_M_149


title: 6F_M_128


title: 6F_M_129


title: 6F_M_127


title: 6F_M_126


title: 6F_M_125


title: 6F_M_124


title: 6F_M_154


title: 6F_M_123


title: 6F_M_139


title: 6F_M_119


title: 6F_M_133


title: 6F_M_120


title: 6F_M_122


title: 6F_M_116


title: 6F_M_121


title: 6F_M_115


title: 6F_M_109


title: 6F_M_111


title: 6F_M_110


title: 6F_M_113


title: 6F_M_112


title: 6F_M_114


title: 6F_M_107


title: 6F_M_106


title: 6F_M_100


title: 6F_M_103


title: 6F_M_97


title: 6F_M_102


title: 6F_M_101


title: 6F_M_105


title: 6F_M_98


title: 6F_M_118


title: 6F_M_117


title: 6F_M_93


title: 6F_M_90


title: 6F_M_88


title: 6F_M_86


title: 6F_M_108


title: 6F_M_89


title: 6F_M_87


title: 6F_M_92


title: 6F_M_85


title: 6F_M_83


title: 6F_M_82


title: 6F_M_81


title: 6F_M_96


title: 6F_M_84


title: 6F_M_78


title: 6F_M_75


title: 6F_M_72


title: 6F_M_80


title: 6F_M_76


title: 6F_M_91


title: 6F_M_71


title: 6F_M_95


title: 6F_M_79


title: 6F_M_70


title: 6F_M_68


title: 6F_M_67


title: 6F_M_66


title: 6F_M_65


title: 6F_M_60


title: 6F_M_77


title: 6F_M_63


title: 6F_M_64


title: 6F_M_61


title: 6F_M_69


title: 6F_M_62


title: 6F_M_57


title: 6F_M_74


title: 6F_M_58


title: 6F_M_55


title: 6F_M_54


title: 6F_M_56


title: 6F_M_53


title: 6F_M_50


title: 6F_M_52


title: 6F_M_49


title: 6F_M_48


title: 6F_M_51


title: 6F_M_47


title: 6F_M_46


title: 6F_M_45


title: 6F_M_44


title: 6F_M_43


title: 6F_M_73


title: 6F_M_42


title: 6F_M_37


title: 6F_M_41


title: 6F_M_36


title: 6F_M_104


title: 6F_M_33


title: 6F_M_39


title: 6F_M_59


title: 6F_M_35


title: 6F_M_30


title: 6F_M_27


title: 6F_M_28


title: 6F_M_26


title: 6F_M_29


title: 6F_M_25


title: 6F_M_20


title: 6F_M_23


title: 6F_M_21


title: 6F_M_24


title: 6F_M_19


title: 6F_M_18


title: 6F_M_22


title: 6F_M_17


title: 6F_M_14


title: 6F_M_15


title: 6F_M_38


title: 6F_M_16


title: 6F_M_32


title: 6F_M_12


title: 6F_M_11


title: 6F_M_8


title: 6F_M_40


title: 6F_M_6


title: 6F_M_7


title: 6F_M_5


title: 6F_M_31


title: 6F_M_2


title: 6F_M_1


title: GRIS-BD Experiment 14-TAG

city: Xinxiang

first: Tianhan

last: Li

state: Henan

address: No.601, Hualan Road

country: China

institute: Xinxiang Medical University

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
Set up BD rhapsody local pepline on linux operating system according to the manufacter's instruction, then load with WTA and TAG raw data and run, finally analysis the processed data (“_RSEC_MolsPerCell.csv” and “_Sample_Tag_Calls.csv”) using Segeq software.
Supplementary files format and content: tab-separated values file and matrix files

molecule: total RNA

source_name: Spleen

extract_protocol:
sort CD45+ cells from single cell suspension of spleen
each group was labelled with sample tag, then built the whole transcriptome analysis (WTA) and sample tag library (TAG) according to the manufacter's instructions (BD Rhapsody™ Single-Cell Analysis System Instrument User Guide (Doc ID 214062))

treatment_protocol: C57BL/6 female mice were divided into three groups of three mice each injected with saline, 6 mg/kg remimazolam for 4 h or 8 h, respectively. Then  the spleens of mice were collected and gently dissociated in RPMI 1640 medium containing 10% FBS on ice using 1 ml syringe plunger on 100 μm cell strainer (BD), all samples were transferred into 15 mL tubes, respectively. Cell samples from spleens were stained with antibody mixture and CD45+CD3+CD5+ T cells were sorted for single cell sequencing.

tag: tissue

value: Spleen

tag: cell type

value: CD45+CD3+CD5+ cell

tag: treatment

value: 6 mg/kg remimazolam for 0h, 4h or 8h


title: GRIS-BD Experiment 14-WTA

description: BD Rhapsody


title: 6F_M_3


title: 6F_M_4


title: P0 islets, DMSO, rep 5

city: Solna

first: Olov

last: Andersson

state: Stockholm

address: Biomedicum Quarter 5D, Tomtebodavagen 16

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description: batch 5

library_source: transcriptomic

data_processing:
Quality control. Raw reads of fastq format were firstly processed through in-house perl scripts. Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reads mapping to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Quantification of gene expression level. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Matrix table with raw read count values for each gene and each sample.

source_name: pancreatic islet

growth_protocol: Islets were maintained in RPMI 1640 medium supplemented with 11 mM glucose, 10% fetal bovine serum, and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using the Quick-RNA Microprep Kit (Zymo research).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNAwas synthesized using random hexamer primers,followed by the second strand cDNA synthesis.

treatment_protocol: Islets were treated either with DMSO or 10 µM Adjudin for 1 day.

value: pancreatic islet

tag: developmental stage

value: postnatal day 0

value: DMSO

tag: time

value: 1 day treatment


title: P0 islets, Adjudin, rep 4

description: batch 4

value: Adjudin


title: P0 islets, DMSO, rep 7

description: batch 7


title: P0 islets, DMSO, rep 6

description: batch 6


title: P0 islets, Adjudin, rep 5

description: batch 5


title: P0 islets, Adjudin, rep 3

description: batch 3


title: P0 islets, DMSO, rep 3

description: batch 3


title: 6F_M_13


title: P0 islets, Adjudin, rep 2

description: batch 2


title: P0 islets, DMSO, rep 2

description: batch 2


title: P0 islets, Adjudin, rep 6

description: batch 6


title: P0 islets, Adjudin, rep 1

description: batch 1


title: 6F_M_10


title: P0 islets, DMSO, rep 4

description: batch 4


title: P0 islets, DMSO, rep 1

description: batch 1


title: db/db islets, Adjudin, rep 8

description: batch 8

value: 12 to 13 weeks old

value: BKS(D)-Leprdb/JOrlRj

tag: Sex

value: male


title: db/db islets, DMSO, rep 7

description: batch 7


title: db/db islets, DMSO, rep 8

description: batch 8


title: db/db islets, Adjudin, rep 7

description: batch 7


title: db/db islets, DMSO, rep 6

description: batch 6


title: 6F_M_0


title: db/db islets, Adjudin, rep 5

description: batch 5


title: db/db islets, DMSO, rep 4

description: batch 4


title: db/db islets, DMSO, rep 3

description: batch 3


title: db/db islets, DMSO, rep 5

description: batch 5


title: db/db islets, Adjudin, rep 2

description: batch 2


title: db/db islets, Adjudin, rep 1

description: batch 1


title: db/db islets, DMSO, rep 2

description: batch 2


title: hIL-4Ra specific Plasma cells Bone Marrow, scRNAseq

city: Tarrytown

middle: Cooper

last: Devlin

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The single cell-count matrix was filtered for by calculating the ratio of the total number of annotated genes divided by the log10 of the total number of UMIs counted. Cells with a gene to UMI ratio below about 0.1 were filtered out. Cells with more than four times the interquartile range of the total number of UMIs were filtered out. Cells with more than about 80% of reads map to a mitochondrial gene were filtered out. High quality cells with a gene to UMI ratio above about 0.1, with less than about four times the interquartile range of the total number of UMIs counted, and with less than 80% of reads mapping to a mitochondrial gene were retained. The count matrices from each individual sample capture were normalized to a total count of 10,000 and batch corrected using the Harmony algorithm to generate a combined uniform manifold approximation and projection (UMAP). Unsupervised clustering by the Leiden algorithm was then used to determine cell type clusters and a Wilcox test was used to identify specific cell type and cluster marker genes.
Assembly: VELOCIMMUNE® 3
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
Mice were immunized with hIL-4Rα antigen and then boosted four days prior to takedown. Single cell suspensions of bone marrow, spleen, and lymph nodes were generated, and RBC lysis was performed. Spleen and lymph nodes were pooled, and surface Fc was blocked with 1:10 diluted Fc Block (BD Biosciences) for 15min at +4°C. Spleen and lymph nodes were then stained using an antibody cocktail to gate for Ag+/IgG+ B cells. For bone marrow, B cells and plasma cells were isolated using EasySep mouse pan-B cell isolation kit (STEMCELL) by negative selection to remove unwanted cells (CD4, CD8, CD11c, CD49b, CD90.2, Ly-6C/G (Gr-1), TER119).  For the purified cells, after surface Fc was blocked as described above, cells were coated with NHS-biotin. Plasma Cells were then incubated with a StAv-aIgk trap for 1hr at +37°C with shaking at 400rpm. Following secretion trap, cells were washed and stained with an antibody mix containing surface markers to gate on plasma cells, anti-IgG FITC (BD Biosciences and Southern Biotech) for detection of secreted IgG, and barcoded hIL-4Rα PE in PBS/5% BSA for 30min at +4°C. Cells were sorted on BD Symphony S6 using flow cytometry.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Cells captured by secretion trap were suspended in PBS with 0.04% w/v BSA and loaded onto a Chromium® Controller device (10x Genomics) at 15,000 cells per lane. Partitions of the cells in barcoded beads were formed and the cells lysed. Reverse transcription was performed followed by breakdown of the partition. RNA-seq, Feature Barcode, and V(D)J libraries were prepared using a Chromium® Next GEM Single Cell 5’ Kit, v.2 (10x Genomics). After amplification of the libraries, cDNA was split into separate RNA-seq, Feature Barcode, and V(D)J aliquots. To enrich the V(D)J aliquot for BCR sequences, the Chromium® Automated Single Cell Mouse and Human BCR Amplification & Library Construction Kit (10x Genomics) was used. Feature Barcode libraries for DNA-barcoded Antigens or DNA-barcoded cell surface proteins were prepared using a Chromium® 5’ Feature Barcode Library Construction kit (10x Genomics). Paired-end sequencing was performed on an Illumina NovaSeq® 6000 sequencing system for RNA-seq, feature barcode, and V(D)J libraries. For RNA-seq and Feature Barcode libraries, the Cell Ranger Single-Cell Software Suite, version 6.1.1 (10x Genomics) was used to perform sample de-multiplexing, alignment, filtering, and UMI counting.

value: Plasma cells

value: bone marrow

value: VELOCIMMUNE 3

value: 36 weeks


title: db/db islets, DMSO, rep 1

description: batch 1


title: hIL-4Ra specific cells, Spleen and draining Lymph Node, scRNAseq

description: 10x Genomics

source_name: spleen

value: B/Plasma cells

value: spleen


title: 6F_M_9


title: WGBS_DIV18_NSD1-sh1_biorep1

city: Saint Louis

first: Nicole

last: Hamagami

state: MO

address: 4487 McPherson Ave. Unit C

department: Neuroscience

institute: Washington University in St. Louis

data_processing:
Reads were adaptor trimmed and mapped to the mm9 genome using bowtie2 alignment and subsequently deduplicated.
Reads were called for methylation using BS-seeker2
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Methylation levels across regions were assessed using bedtools map -o sum, summing the number of reads mapping to Cs (supporting mC) and the number of reads mapping to Cs + Ts (supporting C) in the region, then dividing those two numbers (% mC/C in region)
Regions were adjusted for nonconversion rate by substracting % methylation in Lambda spike-ins per-sample from the calculated %mC/C value
Bedgraphs of nonconversion corrected %mC/C values were converted to bigWigs
Assembly: mm9
Supplementary files format and content: bigWig

growth_protocol: Neurobasal medium supplemented with 5% fetal bovine serum, GlutaMAX, B27 Supplement and Antibiotic-Antimycotic. Cells were maintained at 37oC with 5% CO2

extract_protocol:
DNA was extracted using the Allprep DNA/RNA Mini Kit (Qiagen).
50ng of DNA was sonicated using the S220 Ultrasonicator (Covaris) and subsequently bisulfite converted using the EZ DNA Methylation-Direct Kit (Zymo Research Corporation). WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift) and complemented with Methyl-Seq Combinatorial Dual Indexing Kit (Swift). Libraries were amplified using 10 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRISelect beads from Beckman Coulter. Libraries were validated using the Agilent DNA D1000 Screntape Assay Kit.

treatment_protocol: Cells were treated with lentivirally expressed shRNAs at MOI of 3 on days in vitro (DIV) 1. Cells were grown in vitro until DIV 18.

tag: cell line

value: cultured cortical neurons

tag: biological replicate

value: NSD1 sh1


title: WGBS_DIV18_NSD1-sh2_biorep2

value: NSD1 sh2


title: db/db islets, Adjudin, rep 6

description: batch 6

value: pancreatic islet


title: Liver, 4.4 ug/L aqueous atorvastatin rep 2

city: Ocean Springs

first: Jeremy

last: Johnson

state: Mississippi

address: 103 McIlwain Dr.

institute: University of Southern Mississippi

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GCF_017654675.1 using CLC genomic workbench
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GCF_017654675.1
Supplementary files format and content: .xlsx files containing RPKM values for each sample

organism: Xenopus laevis

source_name: Liver

extract_protocol: RNeasy Mini Kit (Qiagen #74106)

value: Liver

value: tadpoles

value: atorvastatin


title: WGBS_8wk_ctx_nsd1_cKO_biorep2

source_name: cerebral cortex

tag: genotype

value: Nsd1 flx/flx; Nestin-cre +/- (NSD1 cKO)

value: F

value: cerebral cortex

value: 8 week


title: WGBS_DIV18_NSD1-sh2_biorep1


title: WGBS_8wk_ctx_nsd1_cKO_biorep3


title: WGBS_DIV18_nsd1_Ctrl-sh_biorep1_A

value: Ctrl sh


title: Liver, 4.4 ug/L aqueous atorvastatin rep 1


title: WGBS_DIV18_nsd1_Ctrl-sh_biorep1_B


title: Liver, 4.4 ug/L aqueous atorvastatin rep 3


title: db/db islets, Adjudin, rep 4

description: batch 4

value: 12 to 13 weeks old

value: BKS(D)-Leprdb/JOrlRj

value: male

value: Adjudin

value: 1 day treatment


title: db/db islets, Adjudin, rep 3

description: batch 3


title: Liver, Control replicate 3

value: Control


title: WGBS_8wk_ctx_nsd1_cKO_biorep1

value: M


title: Liver, Control replicate 2


title: WGBS_8wk_ctx_nsd1_ctrl_biorep3

value: Nsd1 flx/flx; Nestin-cre -/- (NSD1 ctrl)


title: P0 islets, Adjudin, rep 7

description: batch 7

value: pancreatic islet

value: postnatal day 0


title: WGBS_DIV18_NSD1-sh1_biorep2

value: cultured cortical neurons

value: NSD1 sh1


title: WGBS_8wk_ctx_nsd1_ctrl_biorep1


title: WGBS_DIV18_nsd1_Ctrl-sh_biorep2


title: LUBMET7

city: Winston-Salem

first: Qianqian

last: Song

state: NC

address: 1 Medical Center Boulevard

department: Cancer Genomics and Precision Oncology

institute: Wake Forest Baptist Comprehensive Cancer Center

data_processing:
Run cellranger mkfastq on the Illumina BCL output folder to generate FASTQ files.
Run cellranger count on each library that was demultiplexed by cellranger mkfastq.
Run cellranger aggr to aggregate multiple libraries from a single experiment that were analyzed by cellranger count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Cellular suspensions were loaded on a Chromium Single Cell Controller (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs. Single-cell RNA-Seq libraries were prepared using Chromium™ Single Cell 3’ Library & Gel Bead Kit (10x Genomics, P/N-120237).  GEM-RT was performed in a Biometra Thermal cycler with TempAssure PCR 8-tube strip (USA Scientific, P/N 1402-4700): 53 °C for 45 min, 85 °C for 5 min; held at 4 °C.
Constructed using the reagents in the Chromium™ Single Cell 3’ Library & Gel Bead Kit, following these steps: (1) end repair and A-tailing; (2) adapter ligation; (3) post-ligation cleanup with SPRIselect; (4) sample index PCR and cleanup.  The barcode sequencing libraries were quantified using the Qubit 3.0 (Thermo Fisher, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: treatment-naïve

tag: cancer type

value: Brain Metastasis

value: Female


title: BRBMET3


title: BRBMET2


title: WGBS_8wk_ctx_nsd1_ctrl_biorep2

value: F

value: cerebral cortex


title: BRBMET87


title: SW948_BI00894999_35nM_4h_rep2

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

data_processing:
Multiplexed samples were sequenced on an Illumina NextSeq 500 system. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Data was processed with a pipeline building upon the implementation of the ENCODE "Long RNA-seq" pipeline: In brief, single-end sequencing reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (source 1000 Genomes Project - GRCh38_full_analysis_set_plus_decoy_hla.fa,  excluding alternate contigs, chromosome mapping via grch38_ucsc2ensembl.txt) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. Finally, differential expression analysis was performed on the counts derived from featureCount using limma/voom.
Assembly: GRCh38
Supplementary files format and content: Processed data files contain sample-wise results produced by FeaturesCounts and include raw count values for each gene.

source_name: SW948 cancer cell line

growth_protocol: The cell lines were grown in the media recommended by the vendor.

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
Quant-seq libraries were prepares using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina from Lexogene (#015.96) according to manufacturer's instructions.

treatment_protocol: See samples section.

tag: disease

value: colon carcinoma

tag: replicate

tag: ID


title: SW948_BI00894999_35nM_4h_rep1


title: SW948_BI00894999_10nM_4h_rep1


title: SW948_DMSO_4h_rep2


title: SW948_BI00894999_10nM_4h_rep2


title: Mhc2_hi_0h_186

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description:
Mhc2_hi_0h
Mhc2_Cd206_baseline_raw_expression_matrix.csv

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v3.1.1). Then, low quality cells (expressing less than 500 genes or more than 9000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for dural Cd206_hi cells and Mhc2_hi cells at base line condition.

source_name: mouse dura mhc2_hi cell

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted dural Cd206_hi cells and Mhc2_hi cells were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

value: mouse dura mhc2_hi cell

value: FACS sorted

tag: molecule type

value: single cell RNA


title: LUBMET1

source_name: Adjacent tumor


title: Mhc2_hi_0h_187


title: Mhc2_hi_0h_183


title: Mhc2_hi_0h_190


title: Liver, Control replicate 1

value: Liver

value: tadpoles


title: Mhc2_hi_0h_184


title: SW620_BI00894999_35nM_4h_rep2

source_name: SW620 cancer cell line


title: Mhc2_hi_0h_182


title: Mhc2_hi_0h_189


title: SW620_BI00894999_35nM_4h_rep1


title: Mhc2_hi_0h_191


title: SW948_DMSO_4h_rep1


title: Mhc2_hi_0h_181


title: Mhc2_hi_0h_185


title: Mhc2_hi_0h_192


title: SW620_BI00894999_10nM_4h_rep2


title: Mhc2_hi_0h_180


title: SW620_BI00894999_10nM_4h_rep1


title: Mhc2_hi_0h_179


title: Mhc2_hi_0h_188


title: Mhc2_hi_0h_178


title: SW620_DMSO_4h_rep2


title: SW620_DMSO_4h_rep1


title: Mhc2_hi_0h_177


title: Mhc2_hi_0h_176


title: Mhc2_hi_0h_175


title: NCI-H716_BI00894999_35nM_4h_rep1

source_name: NCI-H716 cancer cell line


title: NCI-H716_BI00894999_35nM_4h_rep2


title: Mhc2_hi_0h_174


title: Mhc2_hi_0h_172


title: Mhc2_hi_0h_173


title: NCI-H716_DMSO_4h_rep1


title: NCI-H716_BI00894999_10nM_4h_rep2


title: NCI-H716_DMSO_4h_rep2


title: LS513_BI00894999_35nM_4h_rep1

source_name: LS513 cancer cell line


title: LS513_BI00894999_35nM_4h_rep2


title: Mhc2_hi_0h_165


title: LS513_DMSO_4h_rep2


title: Mhc2_hi_0h_169


title: NCI-H716_BI00894999_10nM_4h_rep1


title: Mhc2_hi_0h_167


title: Mhc2_hi_0h_168


title: LS513_DMSO_4h_rep1


title: Mhc2_hi_0h_170


title: Mhc2_hi_0h_171


title: LS411N_BI00894999_35nM_4h_rep2

source_name: LS411N cancer cell line


title: Mhc2_hi_0h_166


title: Mhc2_hi_0h_164


title: LS411N_BI00894999_10nM_4h_rep2


title: Mhc2_hi_0h_163


title: LS411N_BI00894999_35nM_4h_rep1


title: Mhc2_hi_0h_162


title: LS411N_BI00894999_10nM_4h_rep1


title: Mhc2_hi_0h_161


title: LS411N_DMSO_4h_rep2


title: Mhc2_hi_0h_160


title: Mhc2_hi_0h_157


title: Mhc2_hi_0h_154


title: Mhc2_hi_0h_152


title: Mhc2_hi_0h_153


title: HT55_BI00894999_35nM_4h_rep1

source_name: HT55 cancer cell line


title: Mhc2_hi_0h_155


title: Mhc2_hi_0h_156


title: LoVo_DMSO_4h_rep2

source_name: LoVo cancer cell line

value: LoVo


title: Mhc2_hi_0h_150


title: Mhc2_hi_0h_149


title: HT55_BI00894999_10nM_4h_rep2


title: Mhc2_hi_0h_148


title: LoVo_BI00894999_35nM_4h_rep1


title: LoVo_DMSO_4h_rep1


title: HT55_DMSO_4h_rep2


title: LS513_BI00894999_10nM_4h_rep2


title: HT55_BI00894999_10nM_4h_rep1


title: LoVo_BI00894999_35nM_4h_rep2


title: HT55_DMSO_4h_rep1


title: Mhc2_hi_0h_159


title: Mhc2_hi_0h_158


title: Mhc2_hi_0h_147


title: LoVo_BI00894999_10nM_4h_rep2


title: Mhc2_hi_0h_146


title: HCT-8_BI00894999_35nM_4h_rep2

source_name: HCT-8 cancer cell line


title: LS411N_DMSO_4h_rep1


title: LoVo_BI00894999_10nM_4h_rep1


title: Mhc2_hi_0h_151


title: HT55_BI00894999_35nM_4h_rep2


title: LS513_BI00894999_10nM_4h_rep1


title: HCT-8_BI00894999_35nM_4h_rep1


title: HCT-8_BI00894999_10nM_4h_rep2


title: Mhc2_hi_0h_144


title: Mhc2_hi_0h_143


title: HCT-8_BI00894999_10nM_4h_rep1


title: Mhc2_hi_0h_145


title: Mhc2_hi_0h_141


title: HCT-8_DMSO_4h_rep2


title: Mhc2_hi_0h_142


title: Mhc2_hi_0h_140


title: HCT-8_DMSO_4h_rep1


title: DLD-1_BI00894999_35nM_4h_rep1

source_name: DLD-1 cancer cell line


title: Mhc2_hi_0h_139


title: Mhc2_hi_0h_137


title: DLD-1_BI00894999_35nM_4h_rep2


title: DLD-1_DMSO_4h_rep1


title: Mhc2_hi_0h_135


title: DLD-1_BI00894999_10nM_4h_rep2


title: Mhc2_hi_0h_136


title: Mhc2_hi_0h_134


title: ATAC-Seq CDC1 rep3

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

institute: Lund University

data_processing:
bcl2fastq2 v2.20 was used to convert BCL files generated by Illumina NextSeq to standard FASTQ file formats
Reads were further mapped to the GRCh38 reference genome using HISAT2 v2.0.4 (Kim D, Langmead B, Nature Methods, 2015) with the following parameters: --very-sensitive -k 20.
Peak calling was performed with Genrich (v0.6.1, available at https://github.com/jsh58/Genrich, parameters: -m 30 -j -y -r -e chrM) separately for each sample. Combined peak list for all samples we further obtained by using PEPATACr R library (Smith P, Corces MR, bioRxviv, 2020).
Finally read counts on a combined peak list were calculated with bedtools multicov (Quinlan A, Hall I, Bioinformatics, 2010). The resulting read counts were further processed with R package DESeq2 (Love M, Genome Biology, 2014)
Assembly: hg38
Supplementary files format and content: count table (.txt) and metadata table (.txt)

growth_protocol: Cells were maintained in Dulbecco´s Eagle Modified (DMEM) RPMI-1640, Ham´s Nutrient F10 Mixture (F10) and Ham´s Nutrient F12 Mixture (F12) growth medium supplemented with 10% (v/v) FBS, Glutamax and Penicillin/Streptomycin solution (100U/ml penicillin, 100mg/ml streptomycin). All cells were cultured in humid environment at 37°C and 5% CO2.

extract_protocol:
5,000–10,000 cells from defined populations were separated via FACS and processed to prepare sequencing library as described previously (Buenrostro, Curr Protoc Mol Biol, 2015). Briefly, Sorted cells were centrifuged, washed, and resuspended in lysis buffer to extract nuclei. Nuclei were centrifuged and resuspended in Tn5 transposition reaction mix for 30 min at 37C. Transposed DNA was purified and stored at -20C.
Libraries were constructed as described previously (Buenrostro, Curr Protoc Mol Biol, 2015). The quality was assessed using a High Sensitivity DNA Chip (Agilent Technologies), and library was sequenced using a NextSeq 500/550 High Output Kit (150 Cycles) on a NextSeq 500 (Illumina).

treatment_protocol: Cells were sorted by FACS.

tag: tumour type

tag: transduction

tag: sorted cells


title: DLD-1_BI00894999_10nM_4h_rep1


title: ATAC-Seq CDC1 rep1


title: Mhc2_hi_0h_132

tag: strain


title: Mhc2_hi_0h_133

tag: cell type


title: ATAC-Seq T98G d9 CD45+HLA-DR+ rep3

value: glioblastoma

value: The cells were transduced with SFFV-hPIB-EGFP lentiviral particles to induce reprogramming (4h to overnight).

value: Cells were collected 9 days after viral transduction


title: Mhc2_hi_0h_131

tag: treatment


title: ATAC-Seq T98G d9 CD45+HLA-DR+ rep2


title: Mhc2_hi_0h_138


title: DLD-1_DMSO_4h_rep2


title: Mhc2_hi_0h_130


title: Mhc2_hi_0h_128


title: ATAC-Seq T98G d9 CD45+HLA-DR+ rep1


title: Mhc2_hi_0h_129


title: ATAC-Seq T98G d9 HLA-DR+ rep3

value: HLA-DR+


title: ATAC-Seq T98G d7 CD45+HLA-DR+ rep2

value: Cells were collected 7 days after viral transduction


title: ATAC-Seq T98G d9 HLA-DR+ rep1


title: ATAC-Seq CDC1 rep2


title: ATAC-Seq T98G d7 CD45+HLA-DR+ rep1


title: Mhc2_hi_0h_127


title: Mhc2_hi_0h_123


title: Mhc2_hi_0h_124


title: Mhc2_hi_0h_121


title: ATAC-Seq T98G d5 CD45+HLA-DR+ rep2

value: Cells were collected 5 days after viral transduction


title: ATAC-Seq T98G d7 HLA-DR+ rep1


title: Mhc2_hi_0h_125


title: ATAC-Seq T98G d5 HLA-DR+ rep2


title: Mhc2_hi_0h_122


title: Mhc2_hi_0h_120


title: ATAC-Seq T98G d5 HLA-DR+ rep1


title: ATAC-Seq T98G d5 CD45+HLA-DR+ rep1


title: Mhc2_hi_0h_119


title: Mhc2_hi_0h_118


title: ATAC-Seq T98G d3 CD45+HLA-DR+ rep3

value: Cells were collected 3 days after viral transduction


title: ATAC-Seq T98G d3 CD45+HLA-DR+ rep1


title: ATAC-Seq T98G d9 HLA-DR+ rep2


title: ATAC-Seq T98G d3 CD45+HLA-DR+ rep2


title: Mhc2_hi_0h_116


title: Mhc2_hi_0h_117


title: ATAC-Seq T98G d7 CD45+HLA-DR+ rep3


title: Mhc2_hi_0h_126


title: ATAC-Seq T98G d3 HLA-DR+ rep3


title: Mhc2_hi_0h_115


title: Mhc2_hi_0h_114


title: ATAC-Seq T98G d3 HLA-DR+ rep2


title: ATAC-Seq T98G rep3

value: The cells were transduced with control SFFV-MCS-EGFP lentiviral particles (4h to overnight).

value: GFP+


title: ATAC-Seq T98G rep2


title: ATAC-Seq T98G rep1


title: Mhc2_hi_0h_110


title: Mhc2_hi_0h_109


title: Mhc2_hi_0h_112


title: Mhc2_hi_0h_111


title: B1203L d9 CD45+HLA-DR+ rep4

description:
B1203L_12
counts.Cell.Lines.txt

data_processing:
bcl2fastq2 v2.20 was used to convert BCL files generated by Illumina NextSeq to standard FASTQ file formats
Alignment to GRCm38.p5 was done using STAR v2.5.3a (Dobin A, Bioinformatics, 2013) with default settings except for the following ones: --sjdbOverhang 74 --quantMode GeneCounts.
The resulting gene counts were further processed and normalised using DESeq2 R package v1.20 (Love M, Genome Biology, 2014).
Assembly: hg38
Supplementary files format and content: count tables (.txt) and metadata tables (.txt)

growth_protocol: Cells were maintained in Dulbecco´s Eagle Modified (DMEM) RPMI-1640, Ham´s Nutrient F10 Mixture (F10) and Ham´s Nutrient F12 Mixture (F12) growth medium supplemented with 10% (v/v) FBS, Glutamax and Penicillin/Streptomycin solution (100U/ml penicillin, 100mg/ml streptomycin). All cells were cultured in humid environment at 37°C and 5% CO2. Human embryonic fibroblasts (HEF) were grown on plates coated with 0.1% gelatine and maintained in Dulbecco´s Eagles Modified growth medium supplemented with 10% FBS, Glutamax and 1% penicillin/streptomycin.

extract_protocol:
To profile reprogramming-induced transcriptomic changes in human cancer cell lines and human embryonic fibroblasts (HEF), total RNA from 3,000–5,000 FACS-sorted cells was extracted using TRIzol Reagent (ThermoFischer Scientific) following the manufacturer’s protocol. cDNA was transcribed with SMARTSeq v4 Ultra low input RNA kit (TakaraBio), amplified with 8 PCR cycles and purified with AMPure XP beads. The cDNA was quantified using High sensitivity DNA kit (Agilent) on Bioanalyzer 2100 (Agilent).
Sequencing library was prepared using Nextera XT DNA library preparation kit (Illumina) according to the manufacturer´s instructions. Briefly, cDNA was enzymatically tagmented, followed by indexing via 12 cycles of PCR. The library was normalized with beads, pooled and sequenced on Illumina NextSeq 500 platform (75bp paired-end).

tag: tumor type

value: lung squamous carcinoma

tag: time point

tag: agent


title: B1203L d9 CD45+HLA-DR+ rep2

description:
B1203L_10
counts.Cell.Lines.txt

tag: cell line


title: Mhc2_hi_0h_106


title: Mhc2_hi_0h_107


title: B1203L d9 CD45+HLA-DR+ rep3

description:
B1203L_11
counts.Cell.Lines.txt


title: B1203L d9 CD45+ rep4

description:
B1203L_8
counts.Cell.Lines.txt


title: B1203L d9 CD45+HLA-DR+ rep1

description:
B1203L_9
counts.Cell.Lines.txt


title: Mhc2_hi_0h_104


title: B1203L d9 CD45+ rep3

description:
B1203L_7
counts.Cell.Lines.txt


title: Mhc2_hi_0h_103


title: Mhc2_hi_0h_113


title: B1203L d9 CD45+ rep1

description:
B1203L_5
counts.Cell.Lines.txt


title: B1203L d9 CD45+ rep2

description:
B1203L_6
counts.Cell.Lines.txt


title: Mhc2_hi_0h_102


title: Mhc2_hi_0h_101


title: Mhc2_hi_0h_100


title: ATAC-Seq T98G d3 HLA-DR+ rep1

tag: time


title: B1203L rep4

description:
B1203L_4
counts.Cell.Lines.txt


title: B1203L rep3

description:
B1203L_3
counts.Cell.Lines.txt


title: Mhc2_hi_0h_108


title: B1203L rep2

description:
B1203L_2
counts.Cell.Lines.txt


title: Mhc2_hi_0h_98


title: Mhc2_hi_0h_99


title: Mhc2_hi_0h_105


title: Mhc2_hi_0h_96


title: Mhc2_hi_0h_95


title: Mhc2_hi_0h_97


title: A110L d9 CD45+HLA-DR+ rep1

description:
A110L_9
counts.Cell.Lines.txt

value: lung adenocarcinoma


title: A110L d9 CD45+HLA-DR+ rep3

description:
A110L_11
counts.Cell.Lines.txt


title: A110L d9 CD45+ rep4

description:
A110L_8
counts.Cell.Lines.txt


title: B1203L rep1

description:
B1203L_1
counts.Cell.Lines.txt


title: A110L d9 CD45+ rep3

description:
A110L_7
counts.Cell.Lines.txt


title: A110L d9 CD45+HLA-DR+ rep4

description:
A110L_12
counts.Cell.Lines.txt


title: A110L d9 CD45+HLA-DR+ rep2

description:
A110L_10
counts.Cell.Lines.txt


title: Mhc2_hi_0h_93

value: mouse dura mhc2_hi cell


title: Mhc2_hi_0h_92

value: FACS sorted


title: A110L d9 CD45+ rep2

description:
A110L_6
counts.Cell.Lines.txt


title: Mhc2_hi_0h_88

value: single cell RNA


title: Mhc2_hi_0h_90


title: A110L rep4

description:
A110L_4
counts.Cell.Lines.txt


title: A110L d9 CD45+ rep1

description:
A110L_5
counts.Cell.Lines.txt


title: A110L rep2

description:
A110L_2
counts.Cell.Lines.txt


title: Mhc2_hi_0h_86


title: A110L rep3

description:
A110L_3
counts.Cell.Lines.txt


title: Mhc2_hi_0h_87


title: MCF-7 d9 HLA-DR+ rep4

description:
MCF7_8
counts.Cell.Lines.txt

value: breast adenocarcinoma


title: A110L rep1

description:
A110L_1
counts.Cell.Lines.txt


title: Mhc2_hi_0h_85


title: Mhc2_hi_0h_84


title: Mhc2_hi_0h_94


title: MCF-7 d9 HLA-DR+ rep3

description:
MCF7_7
counts.Cell.Lines.txt


title: MCF-7 d9 HLA-DR+ rep2

description:
MCF7_6
counts.Cell.Lines.txt


title: Mhc2_hi_0h_83


title: MCF-7 d9 HLA-DR+ rep1

description:
MCF7_5
counts.Cell.Lines.txt


title: Mhc2_hi_0h_82


title: Mhc2_hi_0h_91


title: MCF-7 rep2

description:
MCF7_2
counts.Cell.Lines.txt


title: MCF-7 rep4

description:
MCF7_4
counts.Cell.Lines.txt


title: MCF-7 rep3

description:
MCF7_3
counts.Cell.Lines.txt


title: Mhc2_hi_0h_80


title: Mhc2_hi_0h_77


title: Mhc2_hi_0h_78


title: Mhc2_hi_0h_79


title: Mhc2_hi_0h_89


title: MDA-MB-231 d9 CD45+HLA-DR+ rep4

description:
MDAMB231_11
counts.Cell.Lines.txt


title: Mhc2_hi_0h_75


title: Mhc2_hi_0h_76


title: Mhc2_hi_0h_73


title: MDA-MB-231 d9 CD45+HLA-DR+ rep3

description:
MDAMB231_10
counts.Cell.Lines.txt


title: MDA-MB-231 d9 CD45+ rep4

description:
MDAMB231_7
counts.Cell.Lines.txt


title: MDA-MB-231 d9 CD45+HLA-DR+ rep1

description:
MDAMB231_8
counts.Cell.Lines.txt


title: Mhc2_hi_0h_74


title: MDA-MB-231 d9 CD45+ rep3

description:
MDAMB231_6
counts.Cell.Lines.txt


title: MDA-MB-231 d9 CD45+HLA-DR+ rep2

description:
MDAMB231_9
counts.Cell.Lines.txt


title: Mhc2_hi_0h_70


title: MDA-MB-231 d9 CD45+ rep2

description:
MDAMB231_5
counts.Cell.Lines.txt


title: MDA-MB-231 d9 CD45+ rep1

description:
MDAMB231_4
counts.Cell.Lines.txt


title: Mhc2_hi_0h_71


title: Mhc2_hi_0h_72


title: MDA-MB-231 rep3

description:
MDAMB231_3
counts.Cell.Lines.txt


title: MCF-7 rep1

description:
MCF7_1
counts.Cell.Lines.txt


title: Mhc2_hi_0h_68


title: Mhc2_hi_0h_67


title: Mhc2_hi_0h_66


title: Mhc2_hi_0h_65


title: MDA-MB-231 rep1

description:
MDAMB231_1
counts.Cell.Lines.txt


title: Mhc2_hi_0h_81


title: Ovcar-8 d9 CD45+HLA-DR+ rep2

description:
OVCAR8_10
counts.Cell.Lines.txt

value: ovarian carcinoma


title: Mhc2_hi_0h_63


title: Ovcar-8 d9 CD45+HLA-DR+ rep1

description:
OVCAR8_9
counts.Cell.Lines.txt


title: Ovcar-8 d9 CD45+ rep2

description:
OVCAR8_6
counts.Cell.Lines.txt


title: Mhc2_hi_0h_62


title: Mhc2_hi_0h_61


title: Mhc2_hi_0h_60


title: Ovcar-8 d9 CD45+ rep1

description:
OVCAR8_5
counts.Cell.Lines.txt


title: Mhc2_hi_0h_59


title: Mhc2_hi_0h_58


title: Ovcar-8 rep4

description:
OVCAR8_4
counts.Cell.Lines.txt


title: Mhc2_hi_0h_69


title: Ovcar-8 rep3

description:
OVCAR8_3
counts.Cell.Lines.txt


title: MDA-MB-231 rep2

description:
MDAMB231_2
counts.Cell.Lines.txt


title: Ovcar-8 rep2

description:
OVCAR8_2
counts.Cell.Lines.txt


title: Mhc2_hi_0h_57


title: Mhc2_hi_0h_56


title: Mhc2_hi_0h_55


title: Ho-o-1u d9 CD45+HLA-DR+ rep3

description:
HO1U1_5
counts.Cell.Lines.txt

value: oral cavity carcinoma


title: Ovcar-8 rep1

description:
OVCAR8_1
counts.Cell.Lines.txt


title: Mhc2_hi_0h_64


title: Ho-o-1u d9 CD45+HLA-DR+ rep2

description:
HO1U1_4
counts.Cell.Lines.txt


title: Ho-o-1u d9 CD45+HLA-DR+ rep4

description:
HO1U1_6
counts.Cell.Lines.txt


title: Mhc2_hi_0h_53


title: Ho-o-1u d9 CD45+HLA-DR+ rep1

description:
HO1U1_3
counts.Cell.Lines.txt


title: Mhc2_hi_0h_51


title: Ovcar-8 d9 CD45+ rep4

description:
OVCAR8_8
counts.Cell.Lines.txt


title: Ho-o-1u rep2

description:
HO1U1_2
counts.Cell.Lines.txt


title: Ovcar-8 d9 CD45+ rep3

description:
OVCAR8_7
counts.Cell.Lines.txt


title: Ho-o-1u rep1

description:
HO1U1_1
counts.Cell.Lines.txt


title: Mhc2_hi_0h_50


title: Mhc2_hi_0h_49


title: Ca9-22 d9 CD45+HLA-DR+ rep3

description:
CA922_7
counts.Cell.Lines.txt


title: Ca9-22 d9 CD45+HLA-DR+ rep4

description:
CA922_8
counts.Cell.Lines.txt


title: Mhc2_hi_0h_47


title: Ca9-22 d9 CD45+HLA-DR+ rep2

description:
CA922_6
counts.Cell.Lines.txt


title: Mhc2_hi_0h_46


title: Ca9-22 d9 CD45+HLA-DR+ rep1

description:
CA922_5
counts.Cell.Lines.txt


title: Mhc2_hi_0h_45


title: Mhc2_hi_0h_54