title: PCNA in elg1∆ cells in S phase:  eSPAN

value: anti-PCNA (ab871) followed by anti-BrdU  (B44, BD Biosciences)


title: 8CSE-65 [8 cell stage]

status: Public on Mar 28 2020

type: SRA

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

country: France

institute: Ecole Normale Superieure

library_source: genomic

data_processing:
Library strategy: HiC-Seq
All data were mapped to the mouse genome mm10, , using the BL6-EiJ / CAST SNPs from the mouse genome project (v5 SNP142), and the gene annotation from ensembl (v92).
Data were processed with HiC-Pro 7 (v2.11.0) in allele specific mode. Only pairs with both reads having MAPQ>30 were kept. Allele status is marked in the validPairs file in the 13th column, as x-x for each read in the pair, with 1 being BL6, 2 CAST, 0 unassigned and 3 inconsistent.
Cell cycle phasing was done by comparing the the proportion of short range contact (between 25kb and 2Mb) versus long range contact (between 2Mb and 12Mb). An ellipsoid was fitted to the single cell points as in 8 . The reference in polar coordinates was set to the segment passing by the center of the ellipsoid and the point of coordinates [0.15, 0.35], which correspond to the beginning of the left-ascending part of the single cell trajectory. Cells in G/S were defined as those in the angle between 0 and -0.35π (65° counter-clockwise).
Genome_build: mm10
Supplementary_files_format_and_content: HiC valid pairs

molecule: genomic DNA

organism: Mus musculus

source_name: 8 cell stage

growth_protocol: Five-week-old female C57BL/6J were purchased from Charles River (L’Arbresle). Animal care and use for this study were performed in accordance with the recommendations of the European community (2010/63/UE). All experimental protocols were approved by the ethics committee of Institut Curie CEEA-IC118 under the number APAFIS#8812-2017020611033784v2 given by national authority in compliance with the international guidelines. Single cell HiC was applied to blastomeres of embryos collected from crosses between C57BL/6J (B6) females and CAST/EiJ males. In the case of 1-cell (1c), 2-cell (2c), 4-cell (4c) some embryos were collected after female superovulation. Embryos were harvested from the reproductive tracts in M2 medium at defined time periods according to mating and/or hCG administration (given in this order): 14h or 21h for 1C (PN3 or PN4), 37h or 44h for late 2C, 48h or 55h for 4C, 55h or 62h for 8-cell (8C) and 80h for blastocyst stages (approximately 60 to 64 cells)(64C). B6 pure oocytes were collected at E0. 5 after superovulating females, 15h after hCG injection. The collected embryos were included in the analyses only if they showed a normal morphology and the correct number of blastomeres for their developmental stage.

extract_protocol:
]following fixation, and brief rinses in 1X PBS solution 1% acetylated BSA (Sigma), blastomeres were permeabilized for 30 min on ice in 10 mM Tris-HCl (pH 8), 10 mM NaCl, 0. 2% IGEPAL CA-630 containing complete EDTA-free protease inhibitor cocktail (Roche). Cells were transferred to a protein Low Binding tube (Sigma) containing 0. 3% SDS diluted with 1. 24 x NEBuffer3 for 60 min at 37 ̊C with constant agitation. Triton X-100 was added to 2% final and incubation was extended for 60 min, before addition of 625U of Mbo I (New England Biolabs) and overnight incubation. To label the digested DNA ends, 28. 4uM final of dC/G/TPs and biotin-14 dATP were added with 25U DNA polymerase I, large (Klenow) fragment (New England Biolabs) for 60 min with constant agitation. After spinning, blastomeres were treated with 10 U of T4 DNA ligase (Thermo Fisher) in presence of 1X reaction buffer with 1XBSA ( both by New England Biolabs) at 16 ̊C for at least 4 hours. After spinning, blastomeres were resuspended with PBS 1x and BSA 1 mg/mL to dispatch them individually into PCR tubes (in strips; one per tube) before storage at -80 ̊C until further processing.
To prepare single-cell Hi-C libraries from single nuclei in PCR strips, 5 μl of PBS was added to each well and crosslinks reversed by incubating at 65 ̊C overnight. Hi-C concatemer DNA was fragmented and linked with sequencing adapters using the Nextera XT DNA Library Preparation Kit (Illumina), by adding 10 μl of Tagment DNA Buffer and 5 μl of Amplicon Tagment Mix, incubating at 55 ̊C for 20 min, then cooling down to 10 ̊C, followed by addition 5 μl of Neutralize Tagment Buffer and incubation for 5 min at room temperature. Hi-C ligation junctions were then captured by Dynabeads M-280 streptavidin beads (Thermo Fisher; 20 μl of original suspension per single-cell sample). Beads were prepared by washing with 1 x BW buffer (5 mM Tris-Cl pH 7. 5, 0. 5 mM EDTA, 1 M NaCl), resuspended in 4 x BW buffer (20 mM Tris-Cl pH 7. 5, 2 mM EDTA, 4 M NaCl; 8 μl per sample), and then mixed with the 25 μl sample and incubated at room temperature overnight with gentle agitation. The beads were then washed four times with 200 μl of 1 x BW buffer, twice with 200 μl of 10 mM Tris-Cl pH 7. 5 at room temperature, and resuspended in 25 μl of 10 mM Tris-Cl pH 7. 5. Single-cell Hi-C libraries were amplified from the beads by adding 15 μl of Nextera PCR Master Mix, 5 μl of i7 Index primer of choice and 5 μl of i5 Index primer of choice. Samples were then incubated at 72 ̊C for 3 min, 95 ̊C for 30 sec followed by the thermal cycling at 95 ̊C for 10 sec, 55 ̊C for 30 sec and 72 ̊C for 30 sec for 18 cycles, then incubated at 72 ̊C for 5 min. The supernatant was separated from the beads and purified one by one with AMPure XP beads (Beckman Coulter; 0. 6 times volume of the supernatant) according to manufacturer's instructions and eluted with 30 μl each of 10 mM Tris-Cl pH 8. 5. The eluate was purified once more with AMPure XP beads (equal volume to the previous eluate) and eluted with 11 μl of 10 mM Tris-Cl pH 8. 5.

treatment_protocol: Zona pellucida and polar body were removed using acid tyrod and/or gentle pipetting (except in few cases for blastocyst stage). Embryos were incubated in Ca2+- and Mg2+-free M2 medium for 5 to 30 min to remove the polar body in zygotes or to isolate individual cells at subsequent stages. For the blastocyst stage, incubation with Ca2+- and Mg2+-free M2 medium was replaced with a 5-min incubation in TrypLE (Invitrogen). After incubation, each blastomere was mechanically dissociated, rinsed three times in PBS/acetylated BSA (Sigma) before being fixed for 10 min in a 2% formaldehyde solution at room temperature. Fixation was stopped by transferring the cells to a 127 mM glycine final solution (5 min on ice).

tag: strain

value: BL6-NJ x CAST-EiJ

tag: age

value: Five-week-old

tag: Sex

value: female


title: PCNA in elg1∆ cells in S phase:  ChIP-ssSeq

city: London

first: Hon Wing

last: Liu

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1) (Martin M, 2011) with parameters “-a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=25 –quality-cutoff=20”. As a result of the protocol used for the library preparation, a second round of trimming was performed using cutadapt with the parameter “-U 10” to remove the last 10bp of read 2.
BWA (version 0.6.2) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the trimmed reads to the yeast sacCer3 genome assembly downloaded from the UCSC (Karolchik et al., 2004).
Alignments were filtered to remove read pairs that were discordant, mapped to different chromosomes, ambiguously mapped, had an insert size outside the range 120-200 bp, and mismatch > 4 in any reads.
Alignments were split by strand using a custom script, and normalised bedGraph coverage tracks representing the signal per million mapped paired-reads were generated using BEDTools genomeCoverageBed (version 2.26.0) (Quinlan & Hall, 2010) with the parameters “-bg -pc -du -strand <STRAND> -scale <SCALE_FACTOR>”. BedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).
Genome_build: sacCer3
Supplementary_files_format_and_content: Genome-wide strand-specific bigWig files were generated by treating each pair of reads as a single fragment, and normalised to 1 million reads.

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in rich YPD media, arrested into G1 for 2 hours 45 minutes with alpha-factor, and either released to medium containing YPD either without HU for 26 minutes (S phase), or released into YPD supplemented with 0.1M HU for 40 minutes (HU).

extract_protocol:
Preparation of BrdU-IP, ChIP and eSPAN DNA according to a published eSPAN protocol (Yu et al., 2018).  Briefly, cells were grown under the specified conditions and then fixed with 1% formaldehyde.  Cells were lysed and nuclear extracts harvested, followed by chromatin immunoprecipitation.  Purified ChIP DNA was then denatured and subject to another round of BrdU-IP.  In parallel, BrdU-IP was also performed with Input DNA.  Libraries were then amplified from purified eSPAN DNA, alongside ChIP, BrdU-IP and Input DNA, and were subject to high throughput sequencing by the Ilumina HiSeq 2500 and 4000 platforms.
Sequencing libraries were prepared using the Accel-NGS® 1S Plus DNA Library Kit as per manufacturer's protocol.

treatment_protocol: Cells were cross-linked with 1% Formaldehyde for 20 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 5 minutes.

tag: tissue

value: yeast cells

tag: genotype

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ ura3::3xURA3::tetO112 tetR-GFP::HIS3 pADH1-hENT1-TK::TRP1 elg1<delta>::LEU2

tag: chip antibody

value: anti-Pk (ab15828, abcam)


title: F_P1_normal_CD45_1_DC23_M23

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

library_source: transcriptomic

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

molecule: polyA RNA

source_name: distal lung

extract_protocol:
scRNA-Seq
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

value: distal lung

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: 8CSE-67 [8 cell stage]


title: 8CSE-64 [8 cell stage]


title: 8CSE-74 [8 cell stage]


title: PCNA in elg1∆ cells in S phase:  BrdU-IP-ssSeq

value: anti-BrdU (B44, BD Biosciences)


title: F_P1_normal_CD45_1_DC23_J10

value: Mac II


title: 8CSE-62 [8 cell stage]


title: 8CSE-60 [8 cell stage]


title: 8CSE-61 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_J8

value: T cell


title: PCNA in ctf18∆ cells in S phase:  Input

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ ura3::3xURA3::tetO112 tetR-GFP::HIS3 pADH1-hENT1-TK::TRP1 ctf18<delta>::KANMX6


title: PCNA in ctf18∆ cells in S phase:  eSPAN


title: 8CSE-6 [8 cell stage]


title: F_E18.5_normal_CD45_1_DC23_B15

value: Mac I


title: PCNA in ctf18∆ cells in S phase:  ChIP-ssSeq


title: F_P21_normal_CD45_1_DC23_F5

value: Mac V


title: 8CSE-57 [8 cell stage]


title: PCNA in ctf18∆ cells in S phase:  BrdU-IP-ssSeq


title: 8CSE-59 [8 cell stage]


title: 8CSE-58 [8 cell stage]


title: 8CSE-56 [8 cell stage]


title: Ctf18-HA in S phase (TOTAL):  Input


title: 8CSE-66 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_B12


title: F_P21_normal_CD45_1_DC23_C18


title: 8CSE-55 [8 cell stage]


title: Ctf18-HA in S phase (TOTAL):  ChIP-Seq

value: anti-HA (ab9110, abcam)


title: 8CSE-54 [8 cell stage]

value: BL6-NJ x CAST-EiJ


title: 8CSE-53 [8 cell stage]

value: Five-week-old


title: 8CSE-63 [8 cell stage]

value: female


title: 8CSE-52 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_M9


title: 8CSE-51 [8 cell stage]


title: Ctf18-HA in S phase (TOTAL):  BrdU-IP-Seq

value: yeast cells


title: F_P1_normal_CD45_1_DC23_B1


title: 8CSE-50 [8 cell stage]


title: Tunicamycin sample 4

city: New York

first: Jonathan

middle: W.

last: Snow

state: New York

address: 3009 Broadway

country: USA

institute: Barnard College

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The reads were then mapped to the A. mellifera reference genome available on NCBI using the STAR aligner.
The RNA-seq aligner is executed using a splice aligner, which detects splice junctions and incorporating them to help align the entire read sequences. BAM files were generated as a result of this step.
Gene hit counts were calculated using Feature counts from the Subread package.
After mapping and total gene hit counts calculation, the total gene hit counts table was used for downstream differential expression analysis using DESeq2 and groups were compared.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: comma-separated values, normalized read ouns for paired samples

organism: Apis mellifera

source_name: honey bee midgut

extract_protocol:
Midguts were removed, stored in RNAlater, and RNA was harvested using Trizol reagent. RNA was submitted to additional quality control analysis before mRNA was enriched by polyA selectio
Llibrary preparation was performed using a NEBNext Ultra RNA library preparation kit. Sequencing was then performed using Illumina HiSeq platform.

treatment_protocol: Honey bees were fed sucose solution containning 24 uM Tunicamycin (0.5%DMSO) or 0.5% DMSO alone for 24 hours.

value: midgut

tag: treatment

value: 24 uM Tunicamycin (0.5%DMSO) for 24 hours


title: F_P1_normal_CD45_1_DC23_G5

value: distal lung


title: 8CSE-5 [8 cell stage]

tag: strain


title: 8CSE-49 [8 cell stage]

tag: age


title: F_P21_normal_CD45_1_DC23_A6

value: F

value: B cell


title: Tunicamycin sample 2


title: F_E18.5_normal_CD45_1_DC23_K6

value: immune


title: Tunicamycin sample 3


title: F_E18.5_normal_CD45_1_DC23_F8


title: 8CSE-44 [8 cell stage]

tag: Sex


title: 8CSE-43 [8 cell stage]


title: 8CSE-41 [8 cell stage]


title: 8CSE-42 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_J1

tag: tissue

value: neutrophil


title: F_E18.5_normal_CD45_1_DC23_D18


title: F_E18.5_normal_CD45_1_DC23_D1

value: Mac II


title: 8CSE-4 [8 cell stage]


title: 8CSE-37 [8 cell stage]


title: F_E18.5_normal_CD45_1_DC23_L3

value: Mac IV


title: 8CSE-45 [8 cell stage]


title: 8CSE-39 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_H19


title: 8CSE-38 [8 cell stage]


title: 8CSE-35 [8 cell stage]


title: SL210199  rna-seq

city: Charlottesville

first: Pankaj

last: Kumar

state: VA

address: JPA, 1312A Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

description: RNA-seq data for Male neocortex sample SL210199

data_processing:
align to genome with STAR. The alignment parameter was "STAR --readFilesCommand zcat --runThreadN 32 --genomeDir INDEX --genomeLoad LoadAndKeep --readFilesIn SL210194_1.fq.gz SL210194_2.fq.gz --outFileNamePrefix SL210194.star. --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 50000000000 --outSAMstrandField intronMotif –outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000"
count reads mapping to genes with featureCounts. # Program:featureCounts v1.5.0; Command:"featureCounts" "-a" "GTF" "-o" "counts.txt" "-p" "-B" "-T" "16" "-t" "exon" "-g" "gene_id" "SL210194.star.Aligned.sortedByCoord.headfix.bam" "SL210195.star.Aligned.sortedByCoord.headfix.bam" "SL210196.star.Aligned.sortedByCoord.headfix.bam" "SL210197.star.Aligned.sortedByCoord.headfix.bam" "SL210198.star.Aligned.sortedByCoord.headfix.bam" "SL210199.star.Aligned.sortedByCoord.headfix.bam"
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: counts

molecule: total RNA

organism: Rattus norvegicus

source_name: neocortex

extract_protocol:
Total RNA was isolated from the neocortex of E18 SD and the cortex (normotopic neocortex and heterotopic dysplastic cortex) of tish rats in triplicate (three animals per group) and extracted using the trizol/chloroform protocol and the PureLink RNA Mini Kit (Invitrogen).
Sequencing and library preparation were performed by Hudson Alpha (Huntsville, AL).

treatment_protocol: Isolated RNA was treated with DNAse (New England Biolabs) and RNA concentrations were measured with a Nanodrop Lite (Thermo Scientific).

value: neocortex

value: Male

tag: gestational age

tag: genotype

value: tish


title: 8CSE-48 [8 cell stage]


title: 8CSE-46 [8 cell stage]


title: 8CSE-47 [8 cell stage]


title: 8CSE-36 [8 cell stage]


title: 8CSE-34 [8 cell stage]


title: 8CSE-33 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_E3

tag: sequencing run


title: 8CSE-32 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_G1

tag: gender

value: Mac V


title: SL210196  rna-seq

description: RNA-seq data for Male cortex sample SL210196

source_name: cortex

value: cortex

value: SD


title: 8CSE-31 [8 cell stage]

value: BL6-NJ x CAST-EiJ

value: Five-week-old

value: female


title: 8CSE-30 [8 cell stage]


title: SL210195  rna-seq

description: RNA-seq data for Female cortex sample SL210195

value: Female


title: SL210194  rna-seq

description: RNA-seq data for Male cortex sample SL210194


title: 8CSE-29 [8 cell stage]


title: 8CSE-28 [8 cell stage]


title: SL210198  rna-seq

description: RNA-seq data for Female neocortex sample SL210198


title: F_E18.5_normal_CD45_1_DC23_M2

value: distal lung

tag: plate

value: Mac I


title: F_P21_normal_CD45_1_DC23_D16

value: F

tag: well

value: B cell


title: F_P21_normal_CD45_1_DC23_P8

tag: timepoint

value: immune


title: SL210197  rna-seq

description: RNA-seq data for Male neocortex sample SL210197

tag: cell type


title: 8CSE-27 [8 cell stage]


title: 8CSE-24 [8 cell stage]


title: 8CSE-26 [8 cell stage]


title: 8CSE-21 [8 cell stage]


title: 8CSE-23 [8 cell stage]


title: F_E18.5_normal_CD45_1_DC23_I9

tag: cell subtype


title: MDA-MB-231 cells, VCPT76A-1

city: Hong Kong

first: Kaiyuan

last: ZHU

address: Tat Chee Avenue. Kowloon Tong.

country: China

institute: City University of Hong Kong

data_processing:
Sequencing was carried out using a 2x150 bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the sequencing instrument.In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to obtain high quality clean data. For the mapping, reference genome sequences and gene model annotation files of relative species were firstly downloaded from the genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index the reference genome sequence. Finally, clean data were aligned to the reference genome via software Hisat2 (v2.0.1). For the expression analysis, transcripts in fasta format were converted from known gff annotation files and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data. Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. The estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, and Padj of genes were set <0.1 to detect differential expressed ones.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx files include RPKM values for each Sample.

organism: Homo sapiens

source_name: MDA-MB-231 cells, VCPT76A

growth_protocol: VCPWT and VCPT76A expressed MDA-MB-231 cells maintained in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S) in the 37℃ incubator, 5% CO2 was supplied. Cells were passaged every 2-3 days.

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen). Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.), or 1% agarose gel. Total RNA (1 μg) with RIN value above 6.5 was used for library preparation.
The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming were performed using First-Strand Synthesis Reaction Buffer and Random Primers. First-strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cells to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using a Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Then libraries with different indices were multiplexed and loaded on an Illumina sequencing instrument according to manufacturer’s instructions

treatment_protocol: 10 million Flag-VCPWT or Flag-VCPT76A MDA-MB-231cells were diluted in 100 µL PBS mixed with an equal volume of Matrigel (BD Biosciences) and inoculated via subcutaneous route into the flank of 6-weeks-old female NSG mice for tumor formation.

tag: cell line

value: MDA-MB-231 human breast cancer cell line


title: MDA-MB-231 cells, VCPT76A-3


title: MDA-MB-231 cells, VCPT76A-2


title: MDA-MB-231 cells, VCPWT-3

source_name: MDA-MB-231 cells, VCPWT

value: VCPWT


title: F_P1_normal_CD45_1_DC23_F11

tag: mousename

tag: coverage


title: 8CSE-22 [8 cell stage]


title: 8CSE-2 [8 cell stage]


title: 8CSE-20 [8 cell stage]


title: MDA-MB-231 cells, VCPWT-2


title: 8CSE-3 [8 cell stage]


title: F_P1_normal_CD45_1_DC23_P13

value: neutrophil

tag: number of genes


title: 8CSE-18 [8 cell stage]

tag: strain


title: MDA-MB-231 cells, VCPWT-1


title: F_P1_normal_CD45_1_DC23_E7


title: F_P21_normal_CD45_1_DC23_L11

value: T cell


title: 8CSE-15 [8 cell stage]

tag: age


title: 8CSE-25 [8 cell stage]

tag: Sex


title: 8CSE-17 [8 cell stage]


title: F_P1_normal_CD45_1_DC23_I20

tag: tissue


title: 8CSE-16 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_N8


title: 8CSE-142 [8 cell stage]


title: F_E18.5_normal_CD45_1_DC23_O4


title: 8CSE-141 [8 cell stage]


title: 8CSE-140 [8 cell stage]


title: 8CSE-14 [8 cell stage]


title: F_P1_normal_CD45_1_DC23_I21


title: 8CSE-139 [8 cell stage]


title: 8CSE-19 [8 cell stage]


title: 8CSE-137 [8 cell stage]


title: 8CSE-132 [8 cell stage]


title: F_E18.5_normal_CD45_1_DC23_G17


title: 8CSE-136 [8 cell stage]


title: F_P1_normal_CD45_1_DC23_B15


title: 8CSE-130 [8 cell stage]


title: F_P1_normal_CD45_1_DC23_N16

value: Mac II


title: 8CSE-138 [8 cell stage]


title: 8CSE-129 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_F17

value: Mac V


title: F_P1_normal_CD45_1_DC23_O15


title: 8CSE-126 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_C6


title: 8CSE-124 [8 cell stage]


title: 8CSE-122 [8 cell stage]


title: 8CSE-123 [8 cell stage]


title: 8CSE-125 [8 cell stage]


title: 8CSE-135 [8 cell stage]


title: 8CSE-120 [8 cell stage]


title: F_E18.5_normal_CD45_1_DC23_G10


title: 8CSE-13 [8 cell stage]


title: 8CSE-121 [8 cell stage]


title: F_E18.5_normal_CD45_1_DC23_G16


title: 8CSE-119 [8 cell stage]


title: 8CSE-12 [8 cell stage]


title: 8CSE-117 [8 cell stage]


title: F_P1_normal_CD45_1_DC23_A2


title: 8CSE-118 [8 cell stage]


title: 8CSE-128 [8 cell stage]


title: 8CSE-116 [8 cell stage]


title: 8CSE-115 [8 cell stage]


title: 8CSE-113 [8 cell stage]


title: 8CSE-114 [8 cell stage]


title: F_P1_normal_CD45_1_DC23_H12


title: 8CSE-127 [8 cell stage]


title: cranial meningioma 61

type: genomic

city: Beijing

first: Dake

last: Zhang

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

description: Genomic DNA extracted from meningioma samples  was genotyped using Illumina Human Infinium CoreExome BeadChips (Illumina, San Diego, CA, USA).

hyb_protocol: DNA was amplified, fragmented and hybridized to BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip arrays were scanned using the iScan (Illumina).

data_processing: Raw intensity values were processed to obtain a normalized B allele frequency (BAF) and a Log R ratio (LRR) for each probe using the Genome Studio Software v2.0.4 (illumina, San Diego, USA)

label: Cy3 and Cy5

source_name: cranial meningioma

label_protocol: The single base extension reaction uses chain-terminating dideoxynucleotides. The A and T nucleotides are labeled with dinitrophenyl (abbreviated as DNP)and the G and C nucleotides are labeled with biotin.

extract_protocol: Genomic DNA was purified from tumor samples using a Biomek 3000 automated workstation with an E.Z.N.A Mag-Bind Tissue DNA Kit (Omega Bio-Tek, Norcross, GA, USA).

tag: grade

value: III


title: 8CSE-112 [8 cell stage]


title: F_P1_normal_CD45_1_DC23_G23


title: F_P1_normal_CD45_1_DC23_B21


title: cranial meningioma 60

value: I


title: F_E18.5_normal_CD45_1_DC23_L12


title: 8CSE-111 [8 cell stage]

value: BL6-NJ x CAST-EiJ


title: F_P1_normal_CD45_1_DC23_M7


title: cranial meningioma 48

value: M


title: cranial meningioma 59


title: F_E18.5_normal_CD45_1_DC23_B8


title: 8CSE-109 [8 cell stage]

value: Five-week-old

value: female


title: 8CSE-110 [8 cell stage]


title: 8CSE-107 [8 cell stage]


title: 8CSE-11 [8 cell stage]


title: 8CSE-106 [8 cell stage]


title: cranial meningioma 47


title: F_P21_normal_CD45_1_DC23_C11

value: distal lung


title: 8CSE-108 [8 cell stage]


title: 8CSE-105 [8 cell stage]


title: 8CSE-103 [8 cell stage]


title: F_P1_normal_CD45_1_DC23_K7


title: 8CSE-102 [8 cell stage]


title: 8CSE-104 [8 cell stage]


title: 8CSE-100 [8 cell stage]


title: 8CSE-101 [8 cell stage]


title: cranial meningioma 49


title: cranial meningioma 46

value: II


title: cranial meningioma 58

value: F


title: cranial meningioma 57


title: 8CSE-10 [8 cell stage]


title: F_P21_normal_CD45_1_DC23_K23


title: 64CSE-99 [64 cell stage]

source_name: 64 cell stage


title: cranial meningioma 45


title: 64CSE-98 [64 cell stage]


title: F_P21_normal_CD45_1_DC23_E4

value: B cell


title: 64CSE-97 [64 cell stage]


title: cranial meningioma 44


title: F_P21_normal_CD45_1_DC23_J3

value: immune

value: NK cell


title: 64CSE-95 [64 cell stage]


title: 64CSE-96 [64 cell stage]


title: F_P21_normal_mesench_2_DC21_I5

value: basophil


title: 64CSE-93 [64 cell stage]


title: F_P21_normal_CD45_1_DC23_I12

value: Mac III


title: cranial meningioma 43


title: 64CSE-94 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_A10


title: 64CSE-91 [64 cell stage]


title: cranial meningioma 54


title: 64CSE-90 [64 cell stage]


title: F_P21_normal_mesench_2_DC21_L2


title: cranial meningioma 42


title: 64CSE-89 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_M2

value: Mac IV


title: 64CSE-88 [64 cell stage]


title: cranial meningioma 53


title: 64CSE-86 [64 cell stage]


title: 64CSE-87 [64 cell stage]


title: F_E18.5_normal_CD45_1_DC23_A6

value: Mac I


title: cranial meningioma 56


title: 64CSE-85 [64 cell stage]


title: cranial meningioma 41


title: 64CSE-92 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_L17


title: 64CSE-84 [64 cell stage]


title: cranial meningioma 52


title: F_P7_normal_CD45_1_DC20_N14

value: Mac V


title: 64CSE-83 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_F13


title: cranial meningioma 51


title: cranial meningioma 40


title: 64CSE-82 [64 cell stage]


title: 64CSE-78 [64 cell stage]


title: 64CSE-79 [64 cell stage]


title: cranial meningioma 39


title: 64CSE-81 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_B7

value: T cell


title: 64CSE-80 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_K20


title: 64CSE-75 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_L1


title: cranial meningioma 50

value: I


title: 64CSE-72 [64 cell stage]

value: BL6-NJ x CAST-EiJ


title: 64CSE-74 [64 cell stage]


title: 64CSE-73 [64 cell stage]


title: 64CSE-76 [64 cell stage]


title: cranial meningioma 38


title: F_P7_normal_CD45_1_DC20_N3


title: F_P7_normal_CD45_1_DC20_G14


title: cranial meningioma 329

value: M


title: 64CSE-69 [64 cell stage]

value: Five-week-old


title: 64CSE-70 [64 cell stage]

value: female


title: cranial meningioma 316


title: F_P7_normal_mesench_1_DC20_G19

value: distal lung


title: 64CSE-71 [64 cell stage]


title: 64CSE-68 [64 cell stage]


title: 64CSE-77 [64 cell stage]


title: 64CSE-67 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_A15


title: 64CSE-66 [64 cell stage]


title: cranial meningioma 328


title: 64CSE-64 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_O11


title: cranial meningioma 315


title: 64CSE-63 [64 cell stage]


title: 64CSE-62 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_A9


title: 64CSE-61 [64 cell stage]


title: 64CSE-60 [64 cell stage]


title: cranial meningioma 314


title: F_P7_normal_CD45_1_DC20_F1


title: cranial meningioma 326


title: 64CSE-59 [64 cell stage]


title: 64CSE-58 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_P9


title: 64CSE-57 [64 cell stage]


title: cranial meningioma 325


title: cranial meningioma 313


title: F_P7_normal_CD45_1_DC20_J10


title: 64CSE-55 [64 cell stage]


title: 64CSE-54 [64 cell stage]


title: 64CSE-56 [64 cell stage]


title: 64CSE-65 [64 cell stage]


title: 64CSE-52 [64 cell stage]


title: cranial meningioma 312


title: cranial meningioma 327


title: 64CSE-53 [64 cell stage]


title: cranial meningioma 324


title: 64CSE-6 [64 cell stage]


title: F_P7_normal_mesench_1_DC20_L20


title: 64CSE-51 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_M17


title: F_P7_normal_CD45_1_DC20_G23


title: 64CSE-49 [64 cell stage]


title: 64CSE-50 [64 cell stage]


title: 64CSE-48 [64 cell stage]


title: cranial meningioma 323


title: F_P7_normal_CD45_1_DC20_E1


title: cranial meningioma 311


title: 64CSE-46 [64 cell stage]


title: 64CSE-47 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_H19


title: cranial meningioma 310

value: II


title: 64CSE-44 [64 cell stage]


title: cranial meningioma 309

value: F


title: F_P7_normal_CD45_1_DC20_H5

value: DC I


title: 64CSE-45 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_H9

value: immune


title: F_P7_normal_CD45_1_DC20_C6


title: 64CSE-42 [64 cell stage]


title: 64CSE-43 [64 cell stage]


title: 64CSE-40 [64 cell stage]


title: cranial meningioma 320


title: 64CSE-41 [64 cell stage]


title: 64CSE-4 [64 cell stage]


title: cranial meningioma 319


title: 64CSE-39 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_L21


title: F_P7_normal_mesench_2_DC20_H15


title: 64CSE-38 [64 cell stage]


title: cranial meningioma 308


title: cranial meningioma 307


title: cranial meningioma 318


title: 64CSE-37 [64 cell stage]


title: 64CSE-35 [64 cell stage]


title: 64CSE-36 [64 cell stage]


title: 64CSE-34 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_G12


title: F_P7_normal_CD45_1_DC20_B6


title: 64CSE-33 [64 cell stage]


title: cranial meningioma 306


title: F_P7_normal_CD45_1_DC20_D1


title: cranial meningioma 317


title: F_P7_normal_CD45_1_DC20_C17


title: 64CSE-31 [64 cell stage]


title: 64CSE-30 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_H17


title: 64CSE-29 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_K11


title: 64CSE-27 [64 cell stage]


title: cranial meningioma 109


title: 64CSE-26 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_C23


title: cranial meningioma 97


title: 64CSE-32 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_E2


title: 64CSE-251 [64 cell stage]


title: 64CSE-250 [64 cell stage]


title: 64CSE-25 [64 cell stage]


title: cranial meningioma 96


title: 64CSE-249 [64 cell stage]


title: cranial meningioma 108


title: F_P7_normal_CD45_1_DC20_M15


title: 64CSE-247 [64 cell stage]


title: 64CSE-246 [64 cell stage]


title: 64CSE-248 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_D3


title: cranial meningioma 107

value: III


title: 64CSE-245 [64 cell stage]


title: cranial meningioma 305


title: F_P7_normal_CD45_1_DC20_B19

value: B cell


title: cranial meningioma 95


title: F_P7_normal_CD45_1_DC20_L11


title: 64CSE-243 [64 cell stage]


title: 64CSE-242 [64 cell stage]


title: 64CSE-241 [64 cell stage]


title: cranial meningioma 106


title: F_P7_normal_CD45_1_DC20_J4

value: NK cell


title: 64CSE-28 [64 cell stage]


title: 64CSE-239 [64 cell stage]


title: cranial meningioma 105


title: 64CSE-24 [64 cell stage]


title: 64CSE-240 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_D20

value: Mac III


title: 64CSE-238 [64 cell stage]


title: 64CSE-237 [64 cell stage]


title: 64CSE-235 [64 cell stage]


title: cranial meningioma 94


title: cranial meningioma 93


title: 64CSE-244 [64 cell stage]


title: cranial meningioma 104


title: F_P7_normal_mesench_2_DC20_P10

value: Mac IV


title: cranial meningioma 92


title: 64CSE-233 [64 cell stage]


title: 64CSE-231 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_L9


title: cranial meningioma 103


title: F_P7_normal_CD45_1_DC20_C9

value: neutrophil


title: 64CSE-230 [64 cell stage]


title: cranial meningioma 91


title: 64CSE-229 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_H2

value: Mac V


title: 64CSE-228 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_O19

value: DC III


title: cranial meningioma 102

value: I


title: 64CSE-226 [64 cell stage]

value: BL6-NJ x CAST-EiJ


title: F_P7_normal_CD45_1_DC20_P5

value: IL cell


title: F_P7_normal_CD45_1_DC20_A3


title: 64CSE-236 [64 cell stage]

value: Five-week-old

value: female


title: 64CSE-225 [64 cell stage]


title: 64CSE-227 [64 cell stage]


title: cranial meningioma 90

value: II


title: 64CSE-232 [64 cell stage]


title: 64CSE-224 [64 cell stage]


title: cranial meningioma 101

value: F


title: cranial meningioma 89


title: 64CSE-222 [64 cell stage]


title: 64CSE-223 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_I15

value: distal lung


title: 64CSE-221 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_E8

value: immune


title: 64CSE-23 [64 cell stage]


title: 64CSE-219 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_F22

value: T cell


title: cranial meningioma 88


title: cranial meningioma 100

value: M


title: 64CSE-218 [64 cell stage]


title: 64CSE-217 [64 cell stage]


title: cranial meningioma 99


title: 64CSE-216 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_B9


title: F_P7_normal_CD45_1_DC20_G21


title: F_P7_normal_CD45_1_DC20_A8


title: cranial meningioma 87


title: 64CSE-214 [64 cell stage]


title: 64CSE-213 [64 cell stage]


title: 64CSE-220 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_N13

value: DC II


title: 64CSE-211 [64 cell stage]


title: 64CSE-212 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_B20


title: 64CSE-21 [64 cell stage]


title: cranial meningioma 98


title: F_P7_normal_CD45_1_DC20_G7

value: Mac III


title: 64CSE-22 [64 cell stage]


title: cranial meningioma 181


title: cranial meningioma 86


title: 64CSE-209 [64 cell stage]


title: 64CSE-210 [64 cell stage]


title: 64CSE-208 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_M21

value: B cell


title: cranial meningioma 169


title: 64CSE-207 [64 cell stage]


title: 64CSE-206 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_F3

value: Mac II


title: 64CSE-215 [64 cell stage]


title: 64CSE-205 [64 cell stage]


title: cranial meningioma 180


title: 64CSE-204 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_B21


title: 64CSE-203 [64 cell stage]


title: cranial meningioma 168


title: cranial meningioma 179


title: 64CSE-202 [64 cell stage]


title: 64CSE-201 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_I3

value: NK cell


title: cranial meningioma 166


title: F_P7_normal_CD45_1_DC20_H20

value: Mac V


title: F_P7_normal_CD45_1_DC20_A7


title: cranial meningioma 177

value: I


title: 64CSE-198 [64 cell stage]

value: BL6-NJ x CAST-EiJ


title: 64CSE-197 [64 cell stage]


title: 64CSE-196 [64 cell stage]


title: 64CSE-195 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_K1

value: neutrophil


title: cranial meningioma 165


title: 64CSE-194 [64 cell stage]

value: Five-week-old


title: F_P7_normal_CD45_1_DC20_K13

value: basophil


title: 64CSE-193 [64 cell stage]

value: female


title: cranial meningioma 176

value: F


title: F_P7_normal_CD45_1_DC20_F7

value: distal lung


title: F_P7_normal_CD45_1_DC20_N8

value: immune


title: cranial meningioma 164


title: 64CSE-192 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_J3

value: T cell


title: 64CSE-190 [64 cell stage]


title: 64CSE-191 [64 cell stage]


title: 64CSE-200 [64 cell stage]


title: 64CSE-199 [64 cell stage]


title: cranial meningioma 175

value: M


title: cranial meningioma 167


title: 64CSE-188 [64 cell stage]


title: 64CSE-189 [64 cell stage]


title: 64CSE-20 [64 cell stage]


title: 64CSE-187 [64 cell stage]


title: 64CSE-186 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_F23


title: 64CSE-185 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_N18


title: cranial meningioma 163

value: II


title: 64CSE-184 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_K14


title: 64CSE-182 [64 cell stage]


title: cranial meningioma 162


title: F_P7_normal_CD45_1_DC20_B4


title: 64CSE-183 [64 cell stage]


title: 64CSE-18 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_A20


title: 64CSE-181 [64 cell stage]


title: 64CSE-180 [64 cell stage]


title: cranial meningioma 161


title: cranial meningioma 172


title: F_P7_normal_CD45_1_DC20_E10

value: Mac III


title: 64CSE-179 [64 cell stage]


title: cranial meningioma 173


title: 64CSE-177 [64 cell stage]


title: 64CSE-175 [64 cell stage]


title: 64CSE-176 [64 cell stage]


title: 64CSE-178 [64 cell stage]


title: cranial meningioma 160


title: 64CSE-174 [64 cell stage]


title: cranial meningioma 171


title: F_P7_normal_CD45_1_DC20_J17


title: cranial meningioma 174


title: F_P7_normal_CD45_1_DC20_C12


title: 64CSE-173 [64 cell stage]


title: cranial meningioma 159


title: cranial meningioma 170


title: 64CSE-17 [64 cell stage]


title: 64CSE-171 [64 cell stage]


title: 64CSE-169 [64 cell stage]


title: cranial meningioma 158

value: III


title: F_P7_normal_CD45_1_DC20_L18


title: F_P7_normal_CD45_1_DC20_F21


title: F_P7_normal_CD45_1_DC20_C14

value: Mac IV


title: 64CSE-168 [64 cell stage]


title: 64CSE-234 [64 cell stage]


title: 64CSE-167 [64 cell stage]


title: 64CSE-166 [64 cell stage]


title: cranial meningioma 269


title: cranial meningioma 281


title: cranial meningioma 280


title: F_P7_normal_CD45_1_DC20_I5


title: F_P7_normal_CD45_1_DC20_H21

value: Mac II


title: 64CSE-164 [64 cell stage]


title: 64CSE-172 [64 cell stage]


title: 64CSE-165 [64 cell stage]


title: cranial meningioma 268


title: 64CSE-163 [64 cell stage]


title: 64CSE-170 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_M1

value: Mac V


title: 64CSE-161 [64 cell stage]


title: 64CSE-162 [64 cell stage]


title: 64CSE-160 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_D14


title: F_P7_normal_CD45_1_DC20_P16


title: 64CSE-16 [64 cell stage]


title: 64CSE-159 [64 cell stage]


title: cranial meningioma 279

value: I


title: 64CSE-158 [64 cell stage]

value: BL6-NJ x CAST-EiJ


title: cranial meningioma 267


title: F_P7_normal_CD45_1_DC20_D4


title: 64CSE-157 [64 cell stage]


title: cranial meningioma 278


title: F_P7_normal_CD45_1_DC20_E3

value: neutrophil


title: 64CSE-154 [64 cell stage]

value: Five-week-old


title: 64CSE-155 [64 cell stage]


title: 64CSE-156 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_L16

value: B cell


title: 64CSE-152 [64 cell stage]

value: female


title: F_P7_normal_CD45_1_DC20_H14

value: F


title: cranial meningioma 266


title: 64CSE-153 [64 cell stage]


title: cranial meningioma 265


title: cranial meningioma 277


title: cranial meningioma 276


title: 64CSE-151 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_N22

value: distal lung


title: F_P7_normal_CD45_1_DC20_P15

value: immune


title: 64CSE-150 [64 cell stage]


title: 64CSE-15 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_H18


title: 64CSE-149 [64 cell stage]


title: 64CSE-148 [64 cell stage]


title: cranial meningioma 264


title: 64CSE-147 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_F12


title: 64CSE-146 [64 cell stage]


title: 64CSE-145 [64 cell stage]


title: cranial meningioma 275


title: 64CSE-144 [64 cell stage]


title: 64CSE-143 [64 cell stage]


title: cranial meningioma 263


title: cranial meningioma 274


title: F_P7_normal_CD45_1_DC20_O14


title: 64CSE-140 [64 cell stage]


title: cranial meningioma 262


title: cranial meningioma 273


title: 64CSE-139 [64 cell stage]


title: 64CSE-137 [64 cell stage]


title: 64CSE-136 [64 cell stage]


title: 64CSE-138 [64 cell stage]


title: 64CSE-134 [64 cell stage]


title: 64CSE-141 [64 cell stage]


title: 64CSE-133 [64 cell stage]


title: cranial meningioma 260


title: 64CSE-132 [64 cell stage]


title: 64CSE-131 [64 cell stage]


title: 64CSE-142 [64 cell stage]


title: cranial meningioma 272


title: 64CSE-130 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_G17


title: F_P7_normal_CD45_1_DC20_A21


title: cranial meningioma 271


title: 64CSE-135 [64 cell stage]


title: 64CSE-14 [64 cell stage]


title: 64CSE-129 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_G10


title: F_P7_normal_CD45_1_DC20_B13


title: F_P7_normal_CD45_1_DC20_I9


title: cranial meningioma 261


title: 64CSE-127 [64 cell stage]


title: cranial meningioma 259


title: 64CSE-128 [64 cell stage]


title: 64CSE-126 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_I20


title: cranial meningioma 270


title: cranial meningioma 258


title: F_P7_normal_CD45_1_DC20_M22


title: 64CSE-124 [64 cell stage]


title: 64CSE-123 [64 cell stage]


title: cranial meningioma 255


title: F_P7_normal_CD45_1_DC20_K22


title: 64CSE-125 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_A22


title: F_P7_normal_CD45_1_DC20_D12


title: 64CSE-120 [64 cell stage]


title: 64CSE-121 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_F6


title: cranial meningioma 242


title: 64CSE-12 [64 cell stage]


title: cranial meningioma 254


title: 64CSE-119 [64 cell stage]


title: 64CSE-118 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_F2

value: T cell


title: cranial meningioma 241

value: M


title: F_P7_normal_CD45_1_DC20_J23


title: 64CSE-117 [64 cell stage]


title: 64CSE-116 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_O7


title: cranial meningioma 253


title: 64CSE-115 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_H16


title: 64CSE-113 [64 cell stage]


title: 64CSE-114 [64 cell stage]


title: 64CSE-122 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_F14


title: 64CSE-112 [64 cell stage]


title: cranial meningioma 240


title: cranial meningioma 252


title: 64CSE-109 [64 cell stage]


title: 64CSE-11 [64 cell stage]


title: 64CSE-110 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_K18


title: cranial meningioma 251


title: cranial meningioma 239

value: II


title: F_P7_normal_CD45_1_DC20_E17


title: F_P7_normal_CD45_1_DC20_F15


title: cranial meningioma 238


title: cranial meningioma 249


title: F_P7_normal_mesench_2_DC20_J23


title: F_P7_normal_CD45_1_DC20_A17


title: 64CSE-104 [64 cell stage]


title: 64CSE-105 [64 cell stage]


title: 64CSE-107 [64 cell stage]


title: 64CSE-103 [64 cell stage]


title: 64CSE-102 [64 cell stage]


title: 64CSE-106 [64 cell stage]


title: 64CSE-101 [64 cell stage]


title: 64CSE-100 [64 cell stage]


title: 64CSE-111 [64 cell stage]


title: F_P7_normal_CD45_1_DC20_F5


title: 64CSE-10 [64 cell stage]


title: 4CSE-99 [4 cell stage]

source_name: 4 cell stage


title: 64CSE-108 [64 cell stage]


title: cranial meningioma 236


title: 4CSE-98 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_J15

value: NK cell


title: F_P7_normal_CD45_1_DC20_A12


title: 4CSE-97 [4 cell stage]


title: cranial meningioma 247


title: 4CSE-96 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_B15


title: 4CSE-95 [4 cell stage]


title: cranial meningioma 235


title: 4CSE-93 [4 cell stage]


title: cranial meningioma 246


title: 4CSE-92 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_H13


title: cranial meningioma 248


title: cranial meningioma 245


title: 4CSE-91 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_E12


title: 4CSE-90 [4 cell stage]


title: 4CSE-9 [4 cell stage]


title: cranial meningioma 237


title: 4CSE-88 [4 cell stage]


title: 4CSE-89 [4 cell stage]


title: 4CSE-87 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_P8


title: 4CSE-94 [4 cell stage]


title: 4CSE-86 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_N1


title: 4CSE-85 [4 cell stage]


title: cranial meningioma 231


title: cranial meningioma 233


title: 4CSE-84 [4 cell stage]


title: cranial meningioma 244


title: F_P7_normal_CD45_1_DC20_L14


title: 4CSE-83 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_E16

value: Mac III


title: F_P7_normal_CD45_1_DC20_O1


title: cranial meningioma 243


title: cranial meningioma 234


title: 4CSE-81 [4 cell stage]


title: 4CSE-80 [4 cell stage]


title: 4CSE-8 [4 cell stage]


title: cranial meningioma 230


title: F_P7_normal_CD45_1_DC20_C5

value: Mac IV


title: 4CSE-78 [4 cell stage]


title: 4CSE-76 [4 cell stage]


title: 4CSE-77 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_M12


title: 4CSE-75 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_F11


title: 4CSE-82 [4 cell stage]


title: cranial meningioma 132


title: F_P7_normal_CD45_1_DC20_N6


title: 4CSE-72 [4 cell stage]


title: 4CSE-74 [4 cell stage]


title: 4CSE-71 [4 cell stage]


title: 4CSE-73 [4 cell stage]


title: cranial meningioma 119


title: 4CSE-70 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_O13


title: F_P7_normal_CD45_1_DC20_A16


title: F_P7_normal_CD45_1_DC20_J12


title: cranial meningioma 130


title: F_P7_normal_CD45_1_DC20_J8


title: 4CSE-68 [4 cell stage]


title: 4CSE-7 [4 cell stage]


title: 4CSE-67 [4 cell stage]


title: 4CSE-69 [4 cell stage]


title: cranial meningioma 118


title: cranial meningioma 121


title: cranial meningioma 133


title: cranial meningioma 129


title: F_P7_normal_CD45_1_DC20_G8


title: 4CSE-66 [4 cell stage]


title: cranial meningioma 131


title: cranial meningioma 117


title: F_P7_normal_CD45_1_DC20_B5


title: cranial meningioma 128


title: 4CSE-60 [4 cell stage]


title: 4CSE-64 [4 cell stage]


title: cranial meningioma 116


title: F_P7_normal_CD45_1_DC20_J22


title: 4CSE-61 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_C19


title: 4CSE-65 [4 cell stage]


title: 4CSE-59 [4 cell stage]


title: 4CSE-63 [4 cell stage]


title: F_P7_normal_mesench_1_DC20_G12

value: basophil


title: cranial meningioma 127


title: 4CSE-58 [4 cell stage]


title: cranial meningioma 115


title: 4CSE-56 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_K23


title: 4CSE-55 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_B12


title: 4CSE-54 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_L13


title: cranial meningioma 125


title: 4CSE-52 [4 cell stage]


title: F_P7_normal_mesench_1_DC20_G18

value: Mac V


title: cranial meningioma 113

value: I


title: 4CSE-51 [4 cell stage]

value: BL6-NJ x CAST-EiJ


title: F_P7_normal_CD45_1_DC20_J18


title: 4CSE-5 [4 cell stage]


title: 4CSE-50 [4 cell stage]


title: 4CSE-49 [4 cell stage]


title: cranial meningioma 124


title: 4CSE-57 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_E13


title: cranial meningioma 112


title: F_P7_normal_CD45_1_DC20_N2


title: 4CSE-47 [4 cell stage]


title: 4CSE-53 [4 cell stage]


title: cranial meningioma 126


title: 4CSE-46 [4 cell stage]


title: 4CSE-45 [4 cell stage]


title: cranial meningioma 123


title: cranial meningioma 111


title: F_P7_normal_CD45_1_DC20_P21

value: IL cell


title: 4CSE-43 [4 cell stage]

value: Five-week-old


title: 4CSE-44 [4 cell stage]


title: 4CSE-42 [4 cell stage]


title: cranial meningioma 110


title: 4CSE-41 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_G13


title: cranial meningioma 85


title: 4CSE-4 [4 cell stage]


title: 4CSE-39 [4 cell stage]


title: 4CSE-40 [4 cell stage]


title: 4CSE-48 [4 cell stage]


title: cranial meningioma 73


title: F_P7_normal_CD45_1_DC20_H22


title: 4CSE-38 [4 cell stage]


title: 4CSE-37 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_E18

value: neutrophil


title: F_P7_normal_CD45_1_DC20_L4

value: Mac II


title: cranial meningioma 84

value: F


title: 4CSE-36 [4 cell stage]

value: female


title: 4CSE-35 [4 cell stage]


title: 4CSE-33 [4 cell stage]


title: cranial meningioma 72


title: 4CSE-34 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_M4

value: distal lung

value: immune


title: cranial meningioma 83

value: M


title: 4CSE-32 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_H11


title: F_P7_normal_CD45_1_DC20_K7


title: 4CSE-30 [4 cell stage]


title: 4CSE-31 [4 cell stage]


title: cranial meningioma 71

value: II


title: 4CSE-3 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_M11


title: cranial meningioma 82


title: F_P7_normal_CD45_1_DC20_C18


title: 4CSE-79 [4 cell stage]


title: 4CSE-28 [4 cell stage]


title: 4CSE-29 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_J21

value: DC I


title: cranial meningioma 70


title: 4CSE-27 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_B14

value: Mac III


title: 4CSE-25 [4 cell stage]


title: cranial meningioma 69


title: cranial meningioma 81


title: F_P7_normal_CD45_1_DC20_N17

value: B cell


title: 4CSE-23 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_N20


title: 4CSE-24 [4 cell stage]


title: 4CSE-21 [4 cell stage]


title: 4CSE-22 [4 cell stage]


title: cranial meningioma 80


title: 4CSE-20 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_D15


title: cranial meningioma 68


title: 4CSE-19 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_C4


title: 4CSE-2 [4 cell stage]


title: 4CSE-18 [4 cell stage]


title: cranial meningioma 79


title: 4CSE-17 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_M9


title: cranial meningioma 67


title: 4CSE-26 [4 cell stage]


title: 4CSE-16 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_A4


title: 4CSE-15 [4 cell stage]


title: 4CSE-145 [4 cell stage]


title: 4CSE-146 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_O8


title: cranial meningioma 78


title: F_P7_normal_CD45_1_DC20_J13

value: T cell


title: 4CSE-144 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_C10

value: basophil


title: cranial meningioma 66


title: cranial meningioma 77

value: I


title: cranial meningioma 65


title: 4CSE-143 [4 cell stage]

value: BL6-NJ x CAST-EiJ


title: 4CSE-142 [4 cell stage]


title: 4CSE-141 [4 cell stage]


title: 4CSE-140 [4 cell stage]


title: 4CSE-14 [4 cell stage]


title: cranial meningioma 76


title: F_P7_normal_CD45_1_DC20_C2


title: 4CSE-139 [4 cell stage]


title: cranial meningioma 64


title: 4CSE-138 [4 cell stage]


title: 4CSE-137 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_B22


title: cranial meningioma 75


title: 4CSE-135 [4 cell stage]


title: 4CSE-134 [4 cell stage]


title: cranial meningioma 74


title: cranial meningioma 63


title: F_P7_normal_CD45_1_DC20_D11

value: Mac V


title: 4CSE-131 [4 cell stage]

value: Five-week-old


title: F_P7_normal_CD45_1_DC20_N15


title: F_P7_normal_CD45_1_DC20_B23


title: 4CSE-13 [4 cell stage]


title: cranial meningioma 62


title: F_P7_normal_CD45_1_DC20_B16


title: cranial meningioma 157


title: F_P7_normal_CD45_1_DC20_C11

value: Mac IV


title: F_P7_normal_CD45_1_DC20_A18


title: 4CSE-128 [4 cell stage]


title: 4CSE-133 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_E6


title: 4CSE-136 [4 cell stage]


title: 4CSE-132 [4 cell stage]


title: 4CSE-126 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_M23

value: neutrophil


title: cranial meningioma 145

value: F


title: 4CSE-130 [4 cell stage]

value: female


title: 4CSE-124 [4 cell stage]


title: 4CSE-122 [4 cell stage]


title: cranial meningioma 156


title: cranial meningioma 144


title: 4CSE-129 [4 cell stage]


title: cranial meningioma 143


title: 4CSE-121 [4 cell stage]


title: 4CSE-6 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_I12

value: distal lung


title: 4CSE-127 [4 cell stage]


title: 4CSE-120 [4 cell stage]


title: 4CSE-12 [4 cell stage]


title: 4CSE-125 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_B2

value: immune


title: F_P7_normal_CD45_1_DC20_N16


title: cranial meningioma 142


title: 4CSE-123 [4 cell stage]


title: 4CSE-117 [4 cell stage]


title: cranial meningioma 154

value: M


title: 4CSE-118 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_P11

value: Mac II


title: 4CSE-115 [4 cell stage]


title: 4CSE-114 [4 cell stage]


title: 4CSE-116 [4 cell stage]


title: cranial meningioma 153


title: 4CSE-113 [4 cell stage]


title: 4CSE-62 [4 cell stage]


title: cranial meningioma 141


title: 4CSE-112 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_M16


title: F_P7_normal_CD45_1_DC20_D8


title: 4CSE-111 [4 cell stage]


title: 4CSE-110 [4 cell stage]


title: 4CSE-119 [4 cell stage]


title: 4CSE-11 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_I23


title: cranial meningioma 140


title: 4CSE-109 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_K10


title: cranial meningioma 151


title: 4CSE-107 [4 cell stage]


title: 4CSE-108 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_C20


title: cranial meningioma 139

value: II


title: 4CSE-105 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_D7


title: 4CSE-106 [4 cell stage]


title: 4CSE-103 [4 cell stage]


title: cranial meningioma 150


title: cranial meningioma 138


title: F_P7_normal_CD45_1_DC20_I19


title: F_P7_normal_CD45_1_DC20_O17


title: cranial meningioma 152


title: cranial meningioma 149


title: 4CSE-10 [4 cell stage]


title: F_P7_normal_CD45_1_DC20_M6

value: Mac III


title: 4CSE-104 [4 cell stage]


title: 4CSE-100 [4 cell stage]


title: cranial meningioma 137


title: 4CSE-101 [4 cell stage]


title: 2CSE-99 [2 cell stage]

source_name: 2 cell stage


title: F_P7_normal_CD45_1_DC20_I8


title: 4CSE-1 [4 cell stage]


title: 2CSE-98 [2 cell stage]


title: 2CSE-97 [2 cell stage]


title: cranial meningioma 148


title: F_P7_normal_CD45_1_DC20_M18


title: 2CSE-96 [2 cell stage]


title: cranial meningioma 136


title: 2CSE-95 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_D13


title: 2CSE-94 [2 cell stage]


title: 2CSE-93 [2 cell stage]


title: cranial meningioma 147


title: 4CSE-102 [4 cell stage]


title: cranial meningioma 205


title: cranial meningioma 135


title: F_P7_normal_CD45_1_DC20_M10

value: B cell


title: F_P7_normal_CD45_1_DC20_E22


title: cranial meningioma 146


title: F_P7_normal_CD45_1_DC20_L7


title: cranial meningioma 134


title: F_P7_normal_CD45_1_DC20_E23


title: 2CSE-90 [2 cell stage]


title: 2CSE-89 [2 cell stage]


title: 2CSE-9 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_H3


title: 2CSE-83 [2 cell stage]


title: cranial meningioma 193


title: 2CSE-8 [2 cell stage]


title: 2CSE-86 [2 cell stage]


title: 2CSE-92 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_A6


title: 2CSE-91 [2 cell stage]


title: 2CSE-72 [2 cell stage]


title: cranial meningioma 192


title: 2CSE-70 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_G16


title: cranial meningioma 204


title: 2CSE-71 [2 cell stage]


title: 2CSE-7 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_B1


title: 2CSE-87 [2 cell stage]


title: 2CSE-88 [2 cell stage]


title: cranial meningioma 191


title: 2CSE-69 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_O6


title: 2CSE-68 [2 cell stage]


title: cranial meningioma 202


title: F_P7_normal_CD45_1_DC20_P4


title: 2CSE-82 [2 cell stage]


title: cranial meningioma 190


title: 2CSE-59 [2 cell stage]


title: 2CSE-60 [2 cell stage]


title: 2CSE-66 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_C7


title: 2CSE-6 [2 cell stage]


title: cranial meningioma 201


title: 2CSE-57 [2 cell stage]


title: cranial meningioma 189


title: cranial meningioma 200


title: 2CSE-58 [2 cell stage]


title: 2CSE-56 [2 cell stage]


title: 2CSE-55 [2 cell stage]


title: 2CSE-54 [2 cell stage]


title: 2CSE-53 [2 cell stage]


title: cranial meningioma 203


title: cranial meningioma 188


title: 2CSE-67 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_G5


title: F_P7_normal_CD45_1_DC20_E21


title: 2CSE-52 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_N9


title: F_P7_normal_CD45_1_DC20_P1


title: F_P7_normal_CD45_1_DC20_A13

value: NK cell


title: 2CSE-50 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_D2


title: cranial meningioma 187


title: 2CSE-5 [2 cell stage]


title: 2CSE-47 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_B11


title: 2CSE-49 [2 cell stage]


title: cranial meningioma 186


title: 2CSE-46 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_L6


title: F_P7_normal_CD45_1_DC20_P14


title: 2CSE-45 [2 cell stage]


title: cranial meningioma 197


title: 2CSE-43 [2 cell stage]


title: 2CSE-42 [2 cell stage]


title: 2CSE-44 [2 cell stage]


title: 2CSE-41 [2 cell stage]


title: 2CSE-51 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_M13

value: T cell


title: 2CSE-40 [2 cell stage]


title: cranial meningioma 185

value: I


title: F_P7_normal_CD45_1_DC20_J6

value: DC I


title: cranial meningioma 199


title: 2CSE-48 [2 cell stage]

value: BL6-NJ x CAST-EiJ


title: cranial meningioma 198


title: cranial meningioma 196


title: 2CSE-39 [2 cell stage]

value: Five-week-old


title: cranial meningioma 184


title: 2CSE-4 [2 cell stage]


title: 2CSE-38 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_H10

value: Mac V


title: 2CSE-36 [2 cell stage]


title: 2CSE-37 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_I1


title: cranial meningioma 195


title: 2CSE-35 [2 cell stage]


title: 2CSE-33 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_M3


title: F_P7_normal_CD45_1_DC20_L20


title: cranial meningioma 194


title: F_P7_normal_CD45_1_DC20_N10


title: 2CSE-31 [2 cell stage]


title: 2CSE-32 [2 cell stage]


title: cranial meningioma 182


title: 2CSE-3 [2 cell stage]


title: cranial meningioma 377


title: F_P7_normal_CD45_1_DC20_O3


title: F_P7_normal_CD45_1_DC20_I14


title: 2CSE-29 [2 cell stage]


title: 2CSE-28 [2 cell stage]


title: cranial meningioma 365


title: F_P7_normal_CD45_1_DC20_H1


title: 2CSE-27 [2 cell stage]


title: 2CSE-26 [2 cell stage]


title: cranial meningioma 183


title: 2CSE-24 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_O22


title: cranial meningioma 364


title: F_P7_normal_CD45_1_DC20_G2


title: 2CSE-23 [2 cell stage]


title: cranial meningioma 375


title: cranial meningioma 376


title: 2CSE-20 [2 cell stage]


title: 2CSE-25 [2 cell stage]


title: 2CSE-30 [2 cell stage]


title: 2CSE-21 [2 cell stage]


title: 2CSE-34 [2 cell stage]


title: cranial meningioma 363


title: F_P7_normal_CD45_1_DC20_M19


title: F_P7_normal_CD45_1_DC20_E14


title: 2CSE-19 [2 cell stage]


title: 2CSE-2 [2 cell stage]


title: cranial meningioma 374


title: 2CSE-18 [2 cell stage]


title: 2CSE-17 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_M20

value: DC II


title: 2CSE-16 [2 cell stage]


title: cranial meningioma 362


title: cranial meningioma 373

value: F


title: F_P7_normal_CD45_1_DC20_L8


title: 2CSE-145 [2 cell stage]

value: female


title: 2CSE-15 [2 cell stage]


title: 2CSE-22 [2 cell stage]


title: cranial meningioma 361


title: F_P7_normal_CD45_1_DC20_O5

value: distal lung


title: F_P7_normal_CD45_1_DC20_L23

value: immune

value: neutrophil


title: cranial meningioma 372


title: 2CSE-142 [2 cell stage]


title: 2CSE-144 [2 cell stage]


title: 2CSE-141 [2 cell stage]


title: cranial meningioma 360


title: 2CSE-139 [2 cell stage]


title: 2CSE-14 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_F10


title: F_P7_normal_CD45_1_DC20_G3


title: cranial meningioma 371


title: cranial meningioma 359

value: M


title: F_P7_normal_CD45_1_DC20_E9


title: F_P7_normal_CD45_1_DC20_D23


title: 2CSE-138 [2 cell stage]


title: 2CSE-137 [2 cell stage]


title: 2CSE-135 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_C1


title: 2CSE-143 [2 cell stage]


title: 2CSE-133 [2 cell stage]


title: cranial meningioma 370

value: III


title: F_P7_normal_CD45_1_DC20_O20


title: cranial meningioma 358

value: II


title: 2CSE-136 [2 cell stage]


title: 2CSE-134 [2 cell stage]


title: 2CSE-132 [2 cell stage]


title: 2CSE-131 [2 cell stage]


title: cranial meningioma 369


title: 2CSE-140 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_P12

value: B cell


title: 2CSE-13 [2 cell stage]


title: 2CSE-129 [2 cell stage]


title: 2CSE-128 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_C13


title: 2CSE-127 [2 cell stage]


title: cranial meningioma 356


title: 2CSE-126 [2 cell stage]


title: 2CSE-125 [2 cell stage]


title: 2CSE-123 [2 cell stage]


title: 2CSE-124 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_A2

value: Mac III


title: cranial meningioma 367


title: F_P7_normal_CD45_1_DC20_A19


title: 2CSE-121 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_D16


title: 2CSE-122 [2 cell stage]


title: cranial meningioma 355


title: 2CSE-119 [2 cell stage]


title: cranial meningioma 366


title: 2CSE-12 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_J11


title: 2CSE-120 [2 cell stage]


title: cranial meningioma 368


title: cranial meningioma 354


title: 2CSE-117 [2 cell stage]


title: 2CSE-118 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_K3


title: F_P7_normal_CD45_1_DC20_K5

value: T cell


title: F_P7_normal_CD45_1_DC20_G11


title: 2CSE-116 [2 cell stage]


title: cranial meningioma 353

value: I


title: cranial meningioma 341


title: cranial meningioma 352


title: F_P7_normal_CD45_1_DC20_G15


title: 2CSE-115 [2 cell stage]


title: 2CSE-114 [2 cell stage]


title: 2CSE-113 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_M5


title: cranial meningioma 357


title: cranial meningioma 340


title: 2CSE-110 [2 cell stage]


title: 2CSE-11 [2 cell stage]


title: 2CSE-108 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_H4


title: 2CSE-107 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_I4


title: cranial meningioma 351


title: 2CSE-112 [2 cell stage]


title: 2CSE-106 [2 cell stage]


title: cranial meningioma 339


title: F_P7_normal_CD45_1_DC20_O18

value: NK cell


title: 2CSE-105 [2 cell stage]

value: BL6-NJ x CAST-EiJ


title: cranial meningioma 350


title: 2CSE-109 [2 cell stage]

value: Five-week-old


title: 2CSE-104 [2 cell stage]


title: 2CSE-103 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_I10


title: cranial meningioma 348


title: F_P7_normal_CD45_1_DC20_I22

value: Mac V


title: cranial meningioma 336


title: 2CSE-101 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_J1

value: DC III


title: cranial meningioma 338

value: F


title: 2CSE-10 [2 cell stage]

value: female


title: 1CSE-98 [1 cell stage]

source_name: 1 cell stage


title: 1CSE-99 [1 cell stage]


title: 1CSE-97 [1 cell stage]


title: 1CSE-92 [1 cell stage]


title: cranial meningioma 349


title: 2CSE-111 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_I7

value: distal lung

value: Mac II


title: cranial meningioma 335


title: 2CSE-102 [2 cell stage]


title: 1CSE-9 [1 cell stage]


title: cranial meningioma 346


title: F_P7_normal_CD45_1_DC20_B18

value: immune


title: cranial meningioma 337

value: M


title: F_P7_normal_CD45_1_DC20_A23


title: 2CSE-1 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_C22


title: 1CSE-88 [1 cell stage]


title: 1CSE-87 [1 cell stage]


title: 2CSE-100 [2 cell stage]


title: F_P7_normal_CD45_1_DC20_K4


title: 1CSE-94 [1 cell stage]


title: 1CSE-89 [1 cell stage]


title: cranial meningioma 334


title: F_P7_normal_CD45_1_DC20_L5


title: cranial meningioma 345


title: cranial meningioma 333


title: 1CSE-84 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_I18

value: neutrophil


title: 1CSE-83 [1 cell stage]


title: 1CSE-82 [1 cell stage]


title: cranial meningioma 344


title: 1CSE-86 [1 cell stage]


title: 1CSE-80 [1 cell stage]


title: 1CSE-81 [1 cell stage]


title: 1CSE-85 [1 cell stage]


title: 1CSE-8 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_P13

value: Mac IV


title: 1CSE-79 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_G22


title: 1CSE-78 [1 cell stage]


title: cranial meningioma 331


title: F_P7_normal_CD45_1_DC20_A14


title: 1CSE-77 [1 cell stage]


title: cranial meningioma 343


title: cranial meningioma 332

value: II


title: 1CSE-75 [1 cell stage]


title: 1CSE-76 [1 cell stage]


title: cranial meningioma 342


title: F_P7_normal_CD45_1_DC20_P23


title: 1CSE-74 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_N7


title: 1CSE-73 [1 cell stage]


title: 1CSE-72 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_N12


title: F_P7_normal_CD45_1_DC20_O9


title: F_P7_normal_CD45_1_DC20_O10


title: cranial meningioma 330


title: cranial meningioma 304


title: 1CSE-7 [1 cell stage]


title: 1CSE-71 [1 cell stage]


title: 1CSE-69 [1 cell stage]


title: 1CSE-67 [1 cell stage]


title: 1CSE-66 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_G6


title: cranial meningioma 293


title: cranial meningioma 303


title: 1CSE-65 [1 cell stage]


title: 1CSE-68 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_L15


title: F_P7_normal_CD45_1_DC20_C15


title: 1CSE-63 [1 cell stage]


title: cranial meningioma 292


title: 1CSE-62 [1 cell stage]


title: 1CSE-64 [1 cell stage]


title: cranial meningioma 291


title: 1CSE-61 [1 cell stage]


title: 1CSE-60 [1 cell stage]


title: 1CSE-70 [1 cell stage]


title: 1CSE-59 [1 cell stage]


title: cranial meningioma 301


title: 1CSE-6 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_K17


title: F_P7_normal_CD45_1_DC20_J2


title: cranial meningioma 290


title: F_P7_normal_CD45_1_DC20_O16


title: 1CSE-58 [1 cell stage]


title: 1CSE-56 [1 cell stage]


title: 1CSE-57 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_N21


title: 1CSE-55 [1 cell stage]


title: cranial meningioma 250


title: F_P7_normal_CD45_1_DC20_C21


title: 1CSE-54 [1 cell stage]


title: cranial meningioma 289


title: cranial meningioma 302


title: 1CSE-52 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_J19


title: cranial meningioma 300


title: 1CSE-50 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_C16


title: F_P7_normal_CD45_1_DC20_M14

value: Mac III


title: 1CSE-49 [1 cell stage]


title: cranial meningioma 299


title: 1CSE-5 [1 cell stage]


title: 1CSE-48 [1 cell stage]


title: 1CSE-46 [1 cell stage]


title: 1CSE-47 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_E4


title: 1CSE-45 [1 cell stage]


title: cranial meningioma 298


title: cranial meningioma 287


title: 1CSE-43 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_K16


title: cranial meningioma 286


title: 1CSE-41 [1 cell stage]


title: 1CSE-40 [1 cell stage]


title: cranial meningioma 297


title: F_P7_normal_CD45_1_DC20_I2


title: cranial meningioma 285


title: cranial meningioma 288


title: 1CSE-51 [1 cell stage]


title: 1CSE-4 [1 cell stage]


title: 1CSE-39 [1 cell stage]


title: 1CSE-38 [1 cell stage]


title: cranial meningioma 284


title: F_P7_normal_CD45_1_DC20_L2


title: F_P7_normal_CD45_1_DC20_N11

value: mast cell


title: 1CSE-37 [1 cell stage]


title: cranial meningioma 295

value: I


title: 1CSE-36 [1 cell stage]


title: 1CSE-44 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_B8

value: T cell


title: 1CSE-35 [1 cell stage]

value: BL6-NJ x CAST-EiJ


title: 1CSE-42 [1 cell stage]

value: Five-week-old


title: 1CSE-53 [1 cell stage]


title: cranial meningioma 294


title: F_P7_normal_CD45_1_DC20_I17

value: Mac V


title: F_P7_normal_CD45_1_DC20_O4


title: 1CSE-30 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_N23


title: 1CSE-33 [1 cell stage]


title: 1CSE-32 [1 cell stage]


title: cranial meningioma 229


title: 1CSE-3 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_D19


title: 1CSE-28 [1 cell stage]


title: 1CSE-29 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_F8


title: 1CSE-34 [1 cell stage]


title: cranial meningioma 217


title: 1CSE-27 [1 cell stage]


title: 1CSE-26 [1 cell stage]


title: cranial meningioma 228


title: F_P7_normal_CD45_1_DC20_K9


title: F_P7_normal_CD45_1_DC20_P6

value: B cell


title: cranial meningioma 283

value: F


title: 1CSE-24 [1 cell stage]

value: female


title: F_P7_normal_CD45_1_DC20_P3

value: distal lung


title: 1CSE-23 [1 cell stage]


title: cranial meningioma 216


title: 1CSE-22 [1 cell stage]


title: 1CSE-31 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_J16


title: cranial meningioma 282


title: cranial meningioma 227


title: F_P7_normal_CD45_1_DC20_L12


title: cranial meningioma 215


title: F_P7_normal_CD45_1_DC20_K6

value: IL cell


title: cranial meningioma 226


title: 1CSE-25 [1 cell stage]


title: 1CSE-18 [1 cell stage]


title: 1CSE-16 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_F16

value: immune


title: 1CSE-17 [1 cell stage]


title: 1CSE-2 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_H6

value: basophil


title: 1CSE-19 [1 cell stage]


title: 1CSE-14 [1 cell stage]


title: 1CSE-13 [1 cell stage]


title: 1CSE-12 [1 cell stage]


title: cranial meningioma 225

value: M


title: 1CSE-11 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_M8

value: neutrophil


title: 1CSE-15 [1 cell stage]


title: cranial meningioma 213


title: 1CSE-21 [1 cell stage]


title: 1CSE-20 [1 cell stage]


title: cranial meningioma 224


title: 1CSE-104 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_I16


title: F_P7_normal_CD45_1_DC20_K21


title: 1CSE-103 [1 cell stage]


title: cranial meningioma 212


title: melanoma5_CD8_PD-1hiCTLA-4hi

city: San Francisco

first: Kelly

middle: Maria

last: Mahuron

state: CA

address: 513 Parnassus Avenue, HSW 1201B

institute: UCSF

data_processing:
Following clipping of adapter sequences, reads were aligned to Ensembl hg19 GRCh37.75 with Tophat (v 2.0.12)
SAM files were generated with SAMtools from alignment results
Reads were counted with htseq-count 0.6.1p1 with the union option and -stranded=no
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing raw read counts for each gene

source_name: melanoma lesion 5

growth_protocol: Cells were sort-purified from collagenase-digested human melanoma tumors

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Spin Columns
cDNA was created from 220 pg of input RNA using the SMARTer Ultra Low input kit, sequencing 50 bp paired end unstranded reads

value: melanoma

tag: tumor site

value: Involved regional lymph node

tag: treatment status

value: naive

tag: sort purification strategy

value: Cells were sort-purified as live, singlet, CD45+, CD3+, CD4-CD8+ PD-1+CTLA-4+


title: melanoma4_CD8_PD-1hiCTLA-4hi

source_name: human melanoma


title: melanoma3_CD8_PD-1hiCTLA-4hi


title: cranial meningioma 214

tag: gender

value: I


title: cranial meningioma 223


title: melanoma2_CD8_PD-1hiCTLA-4hi


title: F_P7_normal_CD45_1_DC20_D9

tag: sequencing run

tag: plate

tag: well

value: T cell


title: 1CSE-102 [1 cell stage]

value: BL6-NJ x CAST-EiJ

value: Five-week-old


title: cranial meningioma 211


title: F_P7_normal_CD45_1_DC20_N5

tag: timepoint

tag: cell type

tag: cell subtype


title: melanoma1_CD8_PD-1hiCTLA-4hi

value: Cutaneous primary tumor


title: F_P7_normal_CD45_1_DC20_O12

value: F

value: Mac V

tag: mousename

tag: coverage


title: F_P7_normal_CD45_1_DC20_H23

value: distal lung

value: Mac III

tag: number of genes


title: melanoma5_CD8_PD-1loCTLAlo

value: Cells were sort-purified as live, singlet, CD45+, CD3+, CD4-CD8+ PD-1-CTLA-4-


title: 1CSE-101 [1 cell stage]

tag: strain

tag: age

value: female


title: 1CSE-10 [1 cell stage]

tag: Sex


title: melanoma4_CD8_PD-1loCTLAlo

tag: tissue


title: F_P7_normal_CD45_1_DC20_C3

value: immune

value: B cell


title: 1CSE-1 [1 cell stage]


title: F_P7_normal_CD45_1_DC20_O21

value: IL cell


title: melanoma3_CD8_PD-1loCTLAlo

value: melanoma

tag: tumor site

value: Involved regional lymph node


title: M_C17_RNAseq

city: East Lansing

first: Hua

last: Xiao

state: Michigan

address: 567 WILSON RD, RM 2201

department: Physiology

institute: Michigan State University

description: non-treated, raw files were directly concatenated from L001 and L002 files for one raw read file

data_processing:
Raw data was hard-trimmed using Trimmomatic 0.33 (Bolger et al., 2014), for 20 week old cohort parameters "MINLEN:50 CROP:75 HEADCROP:15" were used, for 39 week old cohort parameters "MINLEN:100 CROP:110 HEADCROP:10" were used
Trimmed reads were mapped to reference genome Ensembl GRCm38.p5 using TopHat2
Transcript of each sample was assembled with Cufflinks using mapped reads
Final transcriptome assembly for 20 week old cohort or 39 week old cohort was generated with Cuffmerge using assembled transcripts of all 20 week old samples or 39 week old samples, separately
Normalized FPKM value of each genes for each sample were calculated by Cuffnorm taking final transcriptome assembly and mapped reads of each sample as input
Genome_build: Ensembl GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include normalized (within whole experiment) RPKM values for each gene for each sample

source_name: liver

growth_protocol: All mice were housed in Optimice cages at Michigan State University animal facility on a 12:12-h light-dark cycle and fed standard rodent diet ad libitum

extract_protocol:
RNA was isolated from total liver tissue using TRIzol reagent and was further purified with the RNeasy Mini Kit (Qiagen) and assessed for quality using a Nanodrop (ThermoFisher) and a Bioanalyzer 2100 via Eukaryote total RNA Pico assay (Agilent)
20 week old cohort library preparation was carried out by the Michigan State University Research Technology Support Facility. 250~300bp insert cDNA library preparation for 39 week old cohort was carried out by Novogene

treatment_protocol: All liver samples were freshly frozen by liquid nitrogen immediately after dissection and stored in -80 freezer.

value: liver

value: 20 week

tag: genotype

value: wild type


title: F_P7_normal_CD45_1_DC20_K12


title: cranial meningioma 220

tag: grade

value: I


title: cranial meningioma 210

tag: gender


title: F_P7_normal_CD45_1_DC20_F17

tag: sequencing run

value: T cell


title: melanoma1_CD8_PD-1loCTLAlo

value: Cutaneous primary tumor

tag: treatment status

value: naive

tag: sort purification strategy


title: cranial meningioma 209

value: F


title: cranial meningioma 221


title: M_76_RNAseq


title: 1CSE-100 [1 cell stage]

value: BL6-NJ x CAST-EiJ

value: Five-week-old


title: cranial meningioma 222


title: melanoma2_CD8_PD-1loCTLAlo

value: Cells were sort-purified as live, singlet, CD45+, CD3+, CD4-CD8+ PD-1-CTLA-4-


title: cranial meningioma 208


title: F_P7_normal_CD45_1_DC20_L3

value: distal lung

tag: plate

tag: well

tag: timepoint

value: neutrophil


title: M_75_RNAseq


title: cranial meningioma 219


title: M_74_RNAseq


title: HC3

city: Los Angeles

first: Kindra

middle: M

last: Kelly-Scumpia

address: 615 Charles E Young Dr Rm 246

institute: UCLA

data_processing:
Sequenced reads were demultiplexed and aligned to the human reference genome hg19 (UCSC) using TopHat (version 2.0.6) and Bowtie2 (version 2.0.2).
The HTseq package was then used to assign uniquely mapped reads to exons and genes using the gene annotation file for build hg19 from Ensembl in order to generate raw count data.
Once raw count data was generated, data normalization and differential expression analysis using a negative binomial model was performed in the R statistical programming environment using the DESeq (version 1.5) Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: 1 csv file of normalized counts and another csv for raw counts from all samples

source_name: enriched HLADR-CD33+ cells

growth_protocol: Human HLADR-CD33+ cells were obtained by magnetic bead separation of PBMC from multiple leprosy patients and healthy donors.

extract_protocol:
Total RNA was then isolated using Trizol followed by clean up with RNeasy Minikit (Qiagen) according to manufacturer’s protocol and quantified by Bioanalyzer.  All samples had a RNA integrity above 7.0 as determined by Bioanalyzer (Agilent Technologies).
Library preparation was performed TruSeq Sample Preparation Kit (Illumina) as per manufacturer’s protocols.
Final libraries were reassessed for quality (Qubit), multiplexed at six or seven samples per lane (10µM each library), and sequenced on a HiSeq 2500 sequencer (Illumina) at 50bp single-end reads protocol.

treatment_protocol: Cells were untreated

value: blood

tag: cell type

value: HLADR-CD33+ cells

tag: diagnosis

value: Healthy

tag: donor id


title: HC2


title: cranial meningioma 207

value: M


title: M_73_RNAseq

tag: strain

value: liver


title: F_P7_normal_CD45_1_DC20_E11

value: immune

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: cranial meningioma 218

tag: age

value: III


title: M_72_RNAseq

tag: tissue

value: 20 week

tag: genotype

value: wild type


title: F_P7_normal_CD45_1_DC20_J14

tag: sequencing run

tag: gender


title: ENL4

value: Leprosy


title: RR4


title: M_C16_RNAseq


title: cranial meningioma 206

value: F

tag: grade

value: I


title: F_P7_normal_CD45_1_DC20_I11

tag: plate


title: M_71_RNAseq


title: cranial meningioma 389


title: cranial meningioma 400


title: HC1


title: ENL3


title: F_P7_normal_CD45_1_DC20_D22

tag: well


title: cranial meningioma 388


title: F_P7_normal_CD45_1_DC20_D18

tag: timepoint

value: IL cell


title: RP-2

city: Seoul

first: Minwoo

last: Park

address: 25, Seonyu-ro 13-gil, youngdeungpo-gu

department: Research & Development

country: South Korea

institute: ebiogen

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Muscle

growth_protocol: Female C57BL/6 mice, 4 weeks of age, were purchased from Central Lab. Animal Inc. (Seoul, Korea) and used in all experiments. During a seven-day acclimation period prior to the experiments, the mice were housed in a temperature-controlled room with a 12-h light-dark cycle and fed a standard laboratory diet in the animal facility of the Chung-Ang University (Seoul, Korea).

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Normal group was injected 4 times with saline every other day while orally administered with distilled water for 9 consecutive days. Cisplatin group was intraperitoneally injected 4 times with 3mg/kg cisplatin, suspended in saline every other day while orally administered with distilled water for 9 consecutive days.  RP group was injected 4 times with 3 mg/kg cispaltin every other day while orally administered with 100 mg/kg RP suspended in distilled water for 9 consecutive days.

value: Gastrocnemius Muscle

tag: Sex

value: Female

tag: group

value: cisplatin and RP-treated group

value: 4 weeks


title: RP-3


title: F_P7_normal_CD45_1_DC20_F4

value: distal lung

tag: cell type

value: T cell


title: RP-1

tag: strain


title: cranial meningioma 387


title: RR3

value: blood

value: HLADR-CD33+ cells

tag: diagnosis

tag: donor id


title: F_P7_normal_CD45_1_DC20_H7

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage


title: cranial meningioma 386

tag: age


title: F_P7_normal_CD45_1_DC20_K19

tag: tissue

value: B cell

tag: number of genes


title: Cisplatin-3

value: cisplatin-treated  group


title: cranial meningioma 397

tag: gender


title: ENL2


title: F_P7_normal_CD45_1_DC20_F20

tag: sequencing run


title: ENL1


title: Cisplatin-1


title: cranial meningioma 385

tag: grade


title: F_P7_normal_CD45_1_DC20_I21

tag: plate

tag: well


title: Cisplatin-2

tag: Sex


title: RR1


title: cranial meningioma 396


title: F_P7_normal_CD45_1_DC20_H15

tag: timepoint

value: neutrophil


title: Untreated, Normal-3

tag: group

value: Normal


title: M_656_RNAseq

description: metformin-treated, received metformin (Sigma Aldrich) dissolved in drinking water at a dosage of approximately 250mg/kg/day from 8 weeks of age until 39 weeks of age

tag: strain

value: liver

value: 39 week

tag: genotype


title: Untreated, Normal-2


title: F_P7_normal_CD45_1_DC20_G4

value: F

tag: cell type


title: RR5

tag: diagnosis

value: Leprosy

tag: donor id


title: cranial meningioma 384

value: M

value: I


title: M_546_RNAseq


title: F_P7_normal_CD45_1_DC20_O2

tag: cell subtype

tag: mousename

tag: coverage


title: RR2

tag: tissue


title: Untreated, Normal-1

value: Gastrocnemius Muscle

value: Female

tag: age

value: 4 weeks


title: cranial meningioma 395

tag: gender


title: cranial meningioma 383

tag: grade


title: M_535_RNAseq


title: F_P7_normal_CD45_1_DC20_J7

value: distal lung

tag: sequencing run

tag: plate

value: T cell

tag: number of genes


title: F_P7_normal_CD45_1_DC20_D6

tag: well

tag: timepoint

value: immune

value: NK cell


title: M_534_RNAseq

tag: strain


title: cranial meningioma 394

value: II


title: F_P7_normal_CD45_1_DC20_I13


title: cranial meningioma 382


title: cranial meningioma 393


title: F_P7_normal_CD45_1_DC20_D10


title: M_533_RNAseq

tag: genotype

value: wild type


title: M_532_RNAseq


title: cranial meningioma 381


title: M_530_RNAseq


title: PCNA in WT cells in S Phase:  Input Replicate 3

source_name: yeast strains in small batch culture

value: yeast cells

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ ura3::3xURA3::tetO112 tetR-GFP::HIS3 pADH1-hENT1-TK::TRP1

tag: chip antibody


title: cranial meningioma 392


title: PCNA in WT cells in S Phase:  Input Replicate 2


title: M_849_RNAseq

description: non-treated

value: liver


title: cranial meningioma 391


title: M_783_RNAseq

description: non-treated

value: 39 week


title: cranial meningioma 379

value: F


title: M_643_RNAseq

description: non-treated


title: stage V act. OFF (repl. 2): NF54/MAP-2GFPDD stage V activated gametocytes OFF Shield-1, replicate 2

type: RNA

city: Basel

first: Till

middle: Steffen

last: Voss

address: Socinstrasse 59

department: Medical Parasitology and Infection Biology

country: Switzerland

institute: Swiss Tropical and Public Health Institute

hyb_protocol: Microarray hybridizations were carried out as described in (Painter HJ, Altenhofen LM, Kafsack BF, Llinás M: Whole-genome analysis of Plasmodium spp. Utilizing a new Agilent technologies DNA microarray platform. Methods Mol Biol. 2013;923:213-9). In short, 500ng Cy5-labeled test cDNA and 500ng Cy3-labeled reference pool cDNA were hybridized on a P. falciparum 8x15K Agilent gene expression microarray (Agilent design ID Agilent-085039) for 16 hours at 65°C in an Agilent hybridisation oven (G2545A).

scan_protocol: Microarrays were scanned as described in [Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5]. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: The raw microarray data representing relative transcript abundance ratios between each test sample and the reference pool (Cy5/Cy3 log2 ratios) were subjected to lowess normalization and background filtering as implemented by the Acuity 4.0 program (Molecular Devices). Flagged features and features with either Cy3 or Cy5 intensities lower than two-fold the background were discarded.

organism: Plasmodium falciparum 3D7

source_name: RNA extracted from NF54/MAP-2GFPDD stage V gametocytes (day13)

label_protocol: Labeling was carried out as described in [Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5]

growth_protocol: NF54/MAP-2GFPDD stage V gametocytes cultured in presence of Shield-1 were split on day 12 of gametocytogenesis and Shield-1 was removed from one of the paired populations, resulting in samples “stage V ON” and “stage V OFF”. 24 hours later (day 13), the paired populations were split again and in one half each gametogenesis was activated by incubation with XA-containing activation medium for 10 min. These samples are termed “stage V act. ON” and “stage V act. OFF”. All cultures (30 mL, 5% haematocrit, approx. 2% gametocytemia) were subsequently spun for 5 min at 2000 g and the resulting RBC pellet was resuspended in 9 mL Trizol pre-warmed to 37°C.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions.

tag: genotype/variation

value: Plasmodium falciparum conditional mutant NF54/MAP-2GFPDD

tag: sample type

value: cDNA

tag: culture conditions

value: 100uM xanthurenic acid

tag: time point

value: activated stage V gametocytes (day 13)

value: whole organism

source_name: reference pool RNA

value: cDNA reference pool extracted from wild type parasites (8-48hpi)


title: stage V OFF (repl. 1): NF54/MAP-2GFPDD stage V gametocytes OFF Shield-1, replicate 1

value: stage V gametocytes (day 13)


title: PCNA in WT cells in S Phase:  eSPAN Replicate 1

value: anti-PCNA (ab871) followed by anti-BrdU  (B44, BD Biosciences)


title: stage V OFF (repl. 2): NF54/MAP-2GFPDD stage V gametocytes OFF Shield-1, replicate 2


title: stage V act. OFF (repl. 1): NF54/MAP-2GFPDD stage V activated gametocytes OFF Shield-1, replicate 1


title: PCNA in WT cells in S Phase:  eSPAN Replicate 2


title: cranial meningioma 390

value: I


title: stage V act. ON (repl. 1): NF54/MAP-2GFPDD stage V activated gametocytes ON Shield-1, replicate 1

value: 625nM Shield-1; 100uM xanthurenic acid


title: PCNA in WT cells in S Phase:  ChIP-ssSeq Replicate 2

value: anti-Pk (ab15828, abcam)


title: cranial meningioma 378


title: stage V ON (repl. 1): NF54/MAP-2GFPDD stage V gametocytes ON Shield-1, replicate 1

value: 625nM Shield-1


title: cranial meningioma 1


title: Plate 1009901028

city: Stanford

first: Yuan

last: Xue

address: 318 Campus Drive

institute: Stanford University

description:
NS24_schistosome_atlas_reads_v13.tsv.gz
NS24_schistosome_atlas_TPM_v13.tsv.gz

data_processing:
Paired-end reads were mapped to S. mansoni genome version WBPS13 (WormBase Parasite) using Salmon (version 0.14.0) with â--validateMappingsâ flag. Read counts from the two separate sequencing lanes were then summed for samples that originated from the same well during sort.
We performed downstream preprocessing and analysis on the estimated read counts in the Salmon output. Reads were initially mapped to exonic regions of the genome. To calculate total gene counts, exonic read counts corresponding to each gene were summed together.
To eliminate low-quality cells, we filtered out cells with fewer than 520 genes detected, leaving 7,657 cells remaining. This number was arbitrarily chosen based on the histogram of number of genes detected per cell.
Genome_build: Schitosoma mansoni WBPS 13
Supplementary_files_format_and_content: Gzip compressed tab-separated values (tsv.gz). Contains read count matrix, estimated TPM, and other meta output of Salmon

organism: Schistosoma mansoni

source_name: S. mansoni juveniles retrieved from infected female Swiss Webster mice at 3.5 weeks post-infection

growth_protocol: Worms were cultured at 37ËC in Basch Media 169 supplemented with 1X Antibiotic-Antimycotic.

extract_protocol:
S. mansoni juveniles were retrieved from infected female Swiss Webster mice (NR-21963) by hepatic portal vein perfusion with 37Â°C DMEM + 5% heat inactivated FBS at 3.5 weeks post-infection.
Smart-seq2 followed by Illumina Nextera XT library construction kit.
Each sample was sequenced on two separate lanes on a NovaSeq 6000, thus producing two pairs of fastqs for each single cell.

tag: developmental stage

value: S. mansoni juveniles

tag: host

value: Swiss Webster female mice (NR-21963)

tag: time

value: retrieved from infected female mice at 3.5 weeks post-infection

tag: cell type

value: all body cells


title: Plate 1009901027


title: PCNA in WT cells in S Phase:  BrdU-IP-ssSeq Replicate 3

tag: tissue

value: yeast cells

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ ura3::3xURA3::tetO112 tetR-GFP::HIS3 pADH1-hENT1-TK::TRP1

value: anti-BrdU (B44, BD Biosciences)


title: M_746_RNAseq

description: non-treated

value: liver

tag: age

value: 39 week

value: wild type


title: Plate 1009901026


title: cranial meningioma 13

tag: gender

value: F

tag: grade


title: stage V act. ON (repl. 2): NF54/MAP-2GFPDD stage V activated gametocytes ON Shield-1, replicate 2

value: Plasmodium falciparum conditional mutant NF54/MAP-2GFPDD

value: cDNA

value: activated stage V gametocytes (day 13)

value: whole organism

value: cDNA reference pool extracted from wild type parasites (8-48hpi)


title: PCNA in WT cells in S Phase:  BrdU-IP-ssSeq Replicate 2


title: M_645_RNAseq

description: non-treated


title: M_531_RNAseq


title: PCNA in WT cells in S Phase:  eSPAN Replicate 3

value: anti-PCNA (ab871) followed by anti-BrdU  (B44, BD Biosciences)


title: Plate 1009901025

value: S. mansoni juveniles


title: stage V ON (repl. 2): NF54/MAP-2GFPDD stage V gametocytes ON Shield-1, replicate 2

value: 625nM Shield-1

value: stage V gametocytes (day 13)


title: cranial meningioma 12

value: I


title: Plate 1009901029

value: Swiss Webster female mice (NR-21963)

value: retrieved from infected female mice at 3.5 weeks post-infection

value: all body cells


title: cranial meningioma 11


title: M_552_RNAseq

description: non-treated

value: liver


title: Plate 1009901024


title: Rfc1-Pk in S phase:  eSPAN

value: yeast cells

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ pADH1-hENT1-TK::TRP1 RFC1-Pk9::KANMX6

value: anti-Pk followed by anti-BrdU (B44, BD Biosciences)


title: M_644_RNAseq

description: non-treated

value: 39 week

value: wild type


title: PCNA in WT cells in S Phase:  ChIP-ssSeq Replicate 3

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ ura3::3xURA3::tetO112 tetR-GFP::HIS3 pADH1-hENT1-TK::TRP1

value: anti-Pk (ab15828, abcam)


title: Rfc1-Pk in S phase:  ChIP-ssSeq


title: Plate 1009901023


title: M_553_RNAseq

description: non-treated


title: M_641_RNAseq

description: non-treated


title: Plate 1009901022


title: PCNA in rfc1-aid cells in S phase:  Input

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ ura3::3xURA3::tetO112 tetR-GFP::HIS3 pADH1-hENT1-TK::TRP1 ade2::pADH1-OsTir1-Myc9 RFC1-PK3-miniAID3::KANMX6


title: cranial meningioma 8

value: M


title: P_23_4 [RNA-Seq]

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

data_processing:
It was necessary to run all samples in each of two runs to generate 50,000,000 reads/sample
Data quality was visualized with FastQC reports. Because the data were of high quality and sequences did not contain any sequencing adapter, no trimming was performed.
genome assembly downloaded from Ensembl using Hisat2 (2.1.0)
Coverage files were generated with Bedtools (v2.26.0) and the mapping was visualized in Integrated Genomics Viewer.
RNA abundance at the gene level was obtained by counting the reads mapped to each gene using featureCounts (v1.5.3), using bovine Ensembl annotation (Release 95).
Normalization and differential expression analysis was performed using the DESeq2 package, with a likelihood ratio test (an “ANOVA-like” test compatible with sequencing data) followed by a Benjamini-Hochberg correction.
Genome_build: ARS-UCD1.2 genome assembly
Supplementary_files_format_and_content: microsoft office excel, includes RPKM values and P and Padj values

organism: Bos taurus

source_name: Corpus luteum (ovary)

extract_protocol:
Samples of RNA were isolated using the miRcury tissue total RNA isolation kit (Exiqon) according to the manufacturer’s protocol. This kit isolates miRNA with total RNA. RNA quantity and quality were assessed using a Biorad Experion; all samples had an RNA quantity index (RQI) greater than 8.5, which is well within the range of good quality samples. A260/230 ratios were all >2.00, and 260/280 ratios were all >1.98.
The TruSeq Stranded mRNA library kit was used

tag: time point (day of pregnancy)

value: Corpus luteum (ovary)


title: P_23_3 [RNA-Seq]


title: PCNA in rfc1-aid cells in S phase:  eSPAN

value: anti-PCNA (ab871) followed by anti-BrdU  (B44, BD Biosciences)


title: Plate 1009901021

value: S. mansoni juveniles


title: cranial meningioma 6

value: F

value: I


title: P_23_2 [RNA-Seq]


title: P_23_1 [RNA-Seq]


title: cranial meningioma 5


title: Plate 1009901019

value: Swiss Webster female mice (NR-21963)

value: retrieved from infected female mice at 3.5 weeks post-infection


title: PCNA in rfc1-aid cells in S phase:  ChIP-ssSeq


title: PCNA in rfc1-aid cells in S phase:  BrdU-IP-ssSeq

value: anti-BrdU (B44, BD Biosciences)


title: P_20_4 [RNA-Seq]


title: Plate 1009901020

value: all body cells


title: PCNA in ctf18∆elg1∆ cells in S phase:  Input

value: yeast cells

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ ura3::3xURA3::tetO112 tetR-GFP::HIS3 pADH1-hENT1-TK::TRP1 ctf18<delta>::KANMX6 elg1<delta>::LEU2


title: cranial meningioma 9


title: P_20_3 [RNA-Seq]


title: Plate 1009901017


title: P_20_2 [RNA-Seq]


title: Plate 1009901018


title: PCNA in ctf18∆elg1∆ cells in S phase:  ChIP-ssSeq


title: cranial meningioma 4


title: PCNA in ctf18∆elg1∆ cells in S phase:  eSPAN

value: anti-PCNA (ab871) followed by anti-BrdU (B44, BD Biosciences)


title: P_20_1 [RNA-Seq]


title: cranial meningioma 2


title: PCNA in ctf18∆elg1∆ cells in S phase:  BrdU-IP-ssSeq


title: Plate 1009901015


title: cranial meningioma 7

value: II


title: cranial meningioma 37


title: cranial meningioma 25


title: P_17_4 [RNA-Seq]


title: Ctf18-HA in S phase:  eSPAN

value: anti-HA followed by anti-BrdU (B44, BD Biosciences)


title: cranial meningioma 3


title: Plate 1009901012


title: P_17_3 [RNA-Seq]


title: cranial meningioma 24


title: P_17_2 [RNA-Seq]


title: Ctf18-HA in S phase:  Input


title: cranial meningioma 36


title: Plate 1009901014


title: Ctf18-HA in S phase:  ChIP-ssSeq

value: anti-HA (ab9110, abcam)


title: Plate 1009901013


title: Ctf18-HA in S phase:  BrdU-IP-ssSeq


title: Plate 1009901011


title: P_17_1 [RNA-Seq]


title: P_14_4 [RNA-Seq]


title: Plate 1009901016


title: Rfc1-Pk in ctf18∆ cells in HU:  Input

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ pADH1-hENT1-TK::TRP1 ctf18<delta>::LEU2  RFC1-PK9::KANMX6


title: Plate 1009901010


title: cranial meningioma 35


title: P_14_3 [RNA-Seq]


title: Rfc1-Pk in ctf18∆ cells in HU:  eSPAN

value: anti-Pk followed by anti-BrdU (B44, BD Biosciences)


title: Plate 1009901009


title: cranial meningioma 34


title: P_14_2 [RNA-Seq]

value: Corpus luteum (ovary)


title: cranial meningioma 23

value: M


title: Rfc1-Pk in ctf18∆ cells in HU:  ChIP-ssSeq

value: anti-Pk (ab15828, abcam)


title: Plate 1009901008

value: S. mansoni juveniles


title: Rfc1-Pk in ctf18∆ cells in HU:  BrdU-IP-ssSeq


title: cranial meningioma 33

value: F

value: I


title: P_14_1 [RNA-Seq]


title: Plate 1009901007

value: Swiss Webster female mice (NR-21963)

value: retrieved from infected female mice at 3.5 weeks post-infection


title: cranial meningioma 22


title: cranial meningioma 21


title: Plate 1009901006

value: all body cells


title: Rfc1-Pk in HU:  eSPAN

value: yeast cells

value: MATa, ade2-1, trp1-1, can1-100, leu2-3, 112, his3-11,15, ura3-52, GAL, psi+ pADH1-hENT1-TK::TRP1 RFC1-Pk9::KANMX6


title: Plate 1009901005


title: Rfc1-Pk in HU:  Input


title: cranial meningioma 32


title: Plate 1009901004


title: cranial meningioma 20