title: Microbiota from stool CER_16 T1

description:
Library name: BC50
65s rRNA v3-v4 sequencing of human stool


title: Cell_2564

status: Public on Sep 19 2025

type: SRA

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: SmartSeq2_Gene_log_normalized_counts.rds

library_source: transcriptomic

data_processing:
Raw fastq files were obtained by bcltoFastq conversion (version 2.20.0.422)
Fastq files were aligned to the mm10 reference genome using STAR aligner (version 2.7.9a) with the argument ‘STARsolo’. This argument allowed simultaneous mapping of reads and quantification of gene expression. The reference genome and gene transfer format (GTF) file were downloaded from 10x genomic webpage at (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz).
The output of ‘STARsolo’ was loaded into R (version 4.1.0) using the Bioconducter package DropletUtils (version 1.12.1).
Downstream analyses were done in R using SingleCellExperiment (version 5271.14.1) and Seurat (version 4.0.6).
Cells with <2000 detected genes, >15% mitochondrial content and > 10% hemoglobin percentage were excluded.
For isoform analysis, fastq files of selected 432 cells (46 cells from HE-HSC (AGM), 198 from HE-LMP (YSm), and 188 cells from HE-EMP (YSb)) were aligned and quantifed using Salmon 1.4.0  in Mapping mode. GRCm39 M32 mouse reference genome, transcriptome, and GTF file were downloaded from GENCODE website. Resulting quant.sf files were fed into IsoformSwitchAnalyzer  2.01.07 where importIsoformExpression function was used to give TMM normalized abundance values.
Assembly: GRCm39 M32 Gencode reference for Isoform Analysis and mm10 10X genomics reference for gene level analysis
Supplementary files format and content: RDS file having log normalized counts for each sample-gene level analyses (1494 cells)
Supplementary files format and content: RDS file having TMM normalized abundance for each sample used for isoform analyses (432 cells)

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Single cells were FACS sorted into 384-well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol.
cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher). Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems)

tag: tissue

tag: sequencing run


title: Cell_2611


title: Cell_2565


title: Microbiota from stool CER_15 T1

city: Florence

first: Sara

last: Bertorello

address: Viale Gaetano Pieraccini 6

country: Italy

institute: University of Florence

description:
Library name: BC49
64s rRNA v3-v4 sequencing of human stool

library_source: genomic

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
qiime demux summarize  --i-data trim-seqs.qza --o-visualization quality.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trim-seqs.qza --p-trunc-len-f 253 --p-trunc-len-r 219 --o-table Featuredada.qza --o-representative-sequences data-trunc.qza --o-denoising-stats denoising-stats.qza
bowtie2 -x INDEXED_GRCh38_analysis_set_BOWTIE2/GRCh38_noalt_as  -U dna-sequences.fasta --un filtered.fasta
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
R software for further analysis
Supplementary files format and content: filtered.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: otu_table.csv: CSV text file containing the abundance table
Supplementary files format and content: taxonomy.csv: TSV text file containing the complete taxonomic classification of the reference sequence
Library strategy: 16S rRNA-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Stool

extract_protocol:
Total DNA was extracted from stools, amplified to collect amplicons of variable V3–V4 region of the bacterial 16S rRNA gene were sequenced in paired-end mode (2 × 300 cycles) on the AVITI™ System.
For detailed library preparation please contact IGA Technology Services (Udine, Italy)

value: Stool


title: Cell_2561


title: Microbiota from stool CER_11 T1

description:
Library name: BC46
61s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_12 T1

description:
Library name: BC47
62s rRNA v3-v4 sequencing of human stool


title: Cell_2562


title: Cell_2559


title: Microbiota from stool CER_10 T1

description:
Library name: BC45
60s rRNA v3-v4 sequencing of human stool


title: Cell_2558

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: Microbiota from stool CER_09 T1

description:
Library name: BC44
59s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_08 T1

description:
Library name: BC43
58s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_19 T1

description:
Library name: BC53
68s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_07 T1

description:
Library name: BC42
57s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_06 T1

description:
Library name: BC41
56s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_05 T1

description:
Library name: BC40
55s rRNA v3-v4 sequencing of human stool


title: Cell_2548


title: Microbiota from stool CER_04 T1

description:
Library name: BC39
54s rRNA v3-v4 sequencing of human stool


title: Cell_2545


title: Microbiota from stool CER_03 T1

description:
Library name: BC38
53s rRNA v3-v4 sequencing of human stool


title: Cell_2542


title: Cell_2543


title: Cell_2546


title: Microbiota from stool CER_39 T0

description:
Library name: BC36
51s rRNA v3-v4 sequencing of human stool


title: Cell_2560


title: Cell_2540


title: Cell_2539


title: Microbiota from stool CER_14 T1

description:
Library name: BC48
63s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_38 T0

description:
Library name: BC35
50s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_36 T0

description:
Library name: BC33
48s rRNA v3-v4 sequencing of human stool


title: Cell_2557

description: SmartSeq2_Gene_log_normalized_counts.rds


title: Microbiota from stool CER_37 T0

description:
Library name: BC34
49s rRNA v3-v4 sequencing of human stool


title: Cell_2550


title: Microbiota from stool CER_34 T0

description:
Library name: BC31
46s rRNA v3-v4 sequencing of human stool


title: Cell_2530


title: Cell_2536


title: Cell_2531


title: Cell_2532


title: Cell_2524


title: Cell_2525


title: Microbiota from stool CER_32 T0

description:
Library name: BC29
44s rRNA v3-v4 sequencing of human stool


title: Cell_2523


title: Microbiota from stool CER_02 T1

description:
Library name: BC37
52s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_31 T0

description:
Library name: BC28
43s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_27 T0

description:
Library name: BC25
40s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_30 T0

description:
Library name: BC27
42s rRNA v3-v4 sequencing of human stool


title: Cell_2515

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: Cell_2493


title: Microbiota from stool CER_35 T0

description:
Library name: BC32
47s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_26 T0

description:
Library name: BC24
39s rRNA v3-v4 sequencing of human stool


title: Cell_2472


title: Cell_2463


title: Cell_2471


title: Cell_2459


title: Microbiota from stool CER_24 T0

description:
Library name: BC22
37s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_23 T0

description:
Library name: BC21
36s rRNA v3-v4 sequencing of human stool


title: Cell_2456


title: Microbiota from stool CER_33 T0

description:
Library name: BC30
45s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_22 T0

description:
Library name: BC20
35s rRNA v3-v4 sequencing of human stool


title: Cell_2455


title: Cell_2457


title: Cell_2454


title: Microbiota from stool CER_18 T0

description:
Library name: BC16
31s rRNA v3-v4 sequencing of human stool


title: Cell_2452


title: Microbiota from stool CER_20 T0

description:
Library name: BC18
33s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_19 T0

description:
Library name: BC17
32s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_28 T0

description:
Library name: BC26
41s rRNA v3-v4 sequencing of human stool


title: Cell_2482


title: Microbiota from stool CER_17 T0

description:
Library name: BC15
30s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_16 T0

description:
Library name: BC14
29s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_25 T0

description:
Library name: BC23
38s rRNA v3-v4 sequencing of human stool


title: Cell_2451


title: Cell_2450

description: SmartSeq2_Gene_log_normalized_counts.rds


title: Microbiota from stool CER_14 T0

description:
Library name: BC12
27s rRNA v3-v4 sequencing of human stool


title: Cell_2448


title: Microbiota from stool CER_21 T0

description:
Library name: BC19
34s rRNA v3-v4 sequencing of human stool


title: Cell_2447

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: Cell_2441


title: Microbiota from stool CER_15 T0

description:
Library name: BC13
28s rRNA v3-v4 sequencing of human stool


title: Cell_2444


title: Cell_2445


title: Microbiota from stool CER_11 T0

description:
Library name: BC10
25s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_09 T0

description:
Library name: BC8
23s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_12 T0

description:
Library name: BC11
26s rRNA v3-v4 sequencing of human stool


title: Cell_2440


title: Microbiota from stool CER_07 T0

description:
Library name: BC6
21s rRNA v3-v4 sequencing of human stool


title: Cell_2437


title: Microbiota from stool CER_06 T0

description:
Library name: BC5
20s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_05 T0

description:
Library name: BC4
19s rRNA v3-v4 sequencing of human stool


title: Cell_2432


title: Microbiota from stool CER_08 T0

description:
Library name: BC7
22s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_03 T0

description:
Library name: BC2
17s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_04 T0

description:
Library name: BC3
18s rRNA v3-v4 sequencing of human stool


title: Cell_2436


title: Cell_2431


title: Cell_2428


title: Microbiota from stool CER_02 T0

description:
Library name: BC1
16s rRNA v3-v4 sequencing of human stool


title: Cell_2429


title: 208125290049_R06C02

type: genomic

city: Hamburg

first: Melanie

last: Schoof

address: Martinistr. 52

country: Germany

institute: Research Institute Childrens Cancer Center Hamburg

hyb_protocol: DNA was bisulfite conversed by the EZ DNA Methylation Kit (Zymo Research)

scan_protocol: The samples were hybridized in the Infinium Mouse Methylation BeadChip microarray following the manufacturer’s instructions.

data_processing:
idat files were processed using the OpenSesame pipeline from the Sesame package
openSesame normalized beta values (see Supplementary file Geo_mset.txt at the foot of the GSE record)

label: Cy3 and Cy5

source_name: Primarytumor

label_protocol: Standard Illumina label protocol

extract_protocol: extraction of DNA by Maxwell DNA isolation

value: Primarytumor

tag: genotype


title: Cell_2427


title: 208125290049_R05C02


title: 208125290049_R03C02


title: Microbiota from stool CER_10 T0

description:
Library name: BC9
24s rRNA v3-v4 sequencing of human stool


title: 208125290049_R04C02


title: Cell_2417


title: Cell_2423


title: Cell_2419


title: Cell_2422


title: Cell_2421


title: Cell_2418


title: 208125290049_R02C02


title: Cell_2415


title: 207592480059_R05C01

value: DMG


title: 207592480059_R06C01


title: Cell_2413


title: Cell_2412


title: Cell_2414


title: 207592480059_R05C02


title: Cell_2411


title: 207592480059_R04C01


title: 207592480059_R04C02


title: Cell_2410


title: Cell_2430


title: 207592480059_R03C01


title: 207592480059_R02C02


title: Cell_2409


title: 207592480059_R02C01


title: 207592480059_R06C02


title: 207592480059_R01C02


title: Cell_2404


title: Cell_2403


title: 207592480059_R01C01


title: 207097260029_R06C02


title: 207097260029_R06C01


title: 207097260029_R05C02


title: Cell_2394


title: Cell_2396


title: Cell_2402


title: 207097260029_R05C01


title: 207592480059_R03C02


title: 207097260029_R03C02


title: Cell_2393


title: Cell_2392


title: 207097260029_R02C02


title: Cell_2398


title: Cell_2391


title: 207097260029_R01C02


title: Cell_2389


title: Cell_2388


title: 206975990041_R06C02

source_name: Immune

value: Immune


title: Cell_2387


title: Cell_2385


title: 206975990041_R05C01


title: Cell_2384


title: 206975990041_R04C01


title: Cell_2407


title: Cell_2383


title: 206975990041_R03C02


title: Cell_2381


title: Cell_2380


title: Cell_2379


title: 206975990041_R02C02


title: 206975990041_R03C01


title: Cell_2390


title: 206975990041_R01C02


title: Cell_2378


title: Cell_2377


title: 206975990041_R02C01


title: 206975990041_R01C01


title: Cell_2376


title: Cell_2373


title: Cell_2375


title: 206522590004_R05C02


title: 206522590004_R06C02


title: Cell_2372


title: 206975990041_R06C01


title: 206522590004_R04C02


title: 206975990041_R05C02


title: 206975990041_R04C02


title: 205668270029_R05C01


title: Cell_2371


title: 207097260029_R04C02


title: 205668270029_R06C01


title: Cell_2368


title: Cell_2366


title: Cell_2363


title: Cell_2367


title: 205489430007_R06C01


title: Cell_2362


title: 205489430007_R03C01


title: Cell_2357


title: Cell_2359


title: 205489430007_R05C01


title: 205659810062_R04C01


title: 205489430007_R02C02


title: Cell_2356


title: Cell_2355


title: 205291550034_R06C02

source_name: primarytumor

value: primarytumor


title: 205489430007_R01C02


title: Cell_2354


title: 205291550034_R06C01


title: 205489430003_R03C01, Primarytumor, TP53


title: 205668270029_R04C01


title: Cell_2350


title: 205489430003_R02C01, Primarytumor, TP53


title: 205668270008_R01C01


title: Cell_2349


title: Cell_2348


title: 206448030020_R05C02, Primarytumor, P53


title: Cell_2361


title: Cell_2343


title: 205333480132_R02C02, Thalamus, Wildtype_P7

source_name: Thalamus

value: Thalamus


title: 206448030020_R04C02, Primarytumor, P53


title: Cell_2345


title: Cell_2344


title: 205333480132_R01C02, Thalamus, Wildtype_P7


title: Cell_2341


title: 204887840026_R03C02, Thalamus, Wildtype_P7


title: 204887840026_R02C02, Thalamus, Wildtype_P7


title: 205333480118_R02C02

value: SHH


title: 204887840026_R01C02, Thalamus, Wildtype_P7


title: Cell_2335


title: Cell_2340


title: Cell_2338


title: 205333480135_R03C02, Thalamus, Wildtype_P28


title: Cell_2334


title: 205291550050_R05C01, Primarytumor, TP53


title: 205333480135_R01C02, Thalamus, Wildtype_P28


title: Cell_2337


title: 205291550082_R03C02, Thalamus, Wildtype_P28


title: 205333480135_R02C02, Thalamus, Wildtype_P28


title: Cell_2332


title: Cell_2351


title: Cell_2333


title: Cell_2331


title: 205291550082_R02C02, Thalamus, Wildtype_P28


title: Cell_2353


title: Cell_2330


title: 205291550082_R01C02, Thalamus, Wildtype_P28


title: 205333480092_R03C02, Thalamus, Wildtype_P21


title: 205333480132_R03C02, Thalamus, Wildtype_P7


title: Cell_2328


title: Cell_2329


title: Cell_2327


title: 205333480092_R01C02, Thalamus, Wildtype_P21


title: 205333480092_R02C02, Thalamus, Wildtype_P21


title: Cell_2324


title: 205291550061_R03C02, Thalamus, Wildtype_P21


title: 205291550061_R02C02, Thalamus, Wildtype_P21


title: 205291550061_R01C02, Thalamus, Wildtype_P21


title: Cell_2325


title: Cell_2323


title: Cell_2322


title: Cell_2319


title: 205537640002_R03C02, Thalamus, Wildtype_P14


title: Cell_2318


title: 205537640002_R02C02, Thalamus, Wildtype_P14


title: 205537640002_R01C02, Thalamus, Wildtype_P14


title: 205333490001_R03C02, Thalamus, Wildtype_P14


title: Cell_2316


title: Cell_2314


title: Cell_2315


title: Cell_2310


title: Cell_2309


title: 205333490001_R02C02, Thalamus, Wildtype_P14


title: 205291550098_R01C02, Thalamus, Wildtype_P0


title: 205333490001_R01C02, Thalamus, Wildtype_P14


title: 205291550098_R03C02, Thalamus, Wildtype_P0


title: Cell_2308


title: 205291550084_R02C02, Thalamus, Wildtype_P0


title: 205291550098_R02C02, Thalamus, Wildtype_P0


title: Cell_2312


title: 205291550046_R03C02, Primarytumor, SS18_SSX2_sg_Pten


title: 205291550084_R03C02, Thalamus, Wildtype_P0


title: 206448030002_R05C02, 2Dcellline, SS18_SSX2_Pten


title: 205291550046_R02C02, Primarytumor, SS18_SSX2_sg_Pten


title: 205291550084_R01C02, Thalamus, Wildtype_P0


title: Cell_2302


title: Cell_2304


title: Cell_2303


title: 205489430003_R03C02, SAMprimarycells, SS18_SSX2_Pten

source_name: SAMprimarycells

value: SAMprimarycells


title: Cell_2301


title: Cell_2297


title: 205291550046_R01C02, Primarytumor, SS18_SSX2_Pten


title: Cell_2299


title: 205291550050_R03C01, Primarytumor, SS18_SSX1


title: 205489430003_R04C02, SAMprimaryfragments, SS18_SSX2_Pten

source_name: SAMprimaryfragments

value: SAMprimaryfragments


title: Cell_2307


title: Cell_2298


title: Cell_2295


title: Cell_2305


title: Cell_2292


title: 205489430003_R02C02, 3Dcellline, SS18_SSX2_Pten


title: 206448030002_R02C01, Primarytumor, SS18_SSX1_Pten


title: Cell_2289


title: Cell_2287


title: 206448030002_R05C01, Primarytumor, SS18_SSX1_Pten


title: Cell_2306


title: Cell_2290


title: Cell_2285


title: 206448030002_R04C01, Primarytumor, SS18_SSX1_Pten


title: 205668270008_R05C01, Primarytumor, Lmax1a_cre_P53f_f_Rbf_f


title: 206448030002_R03C01, Primarytumor, SS18_SSX1_Pten


title: Cell_2288


title: 206448030002_R06C01, Primarytumor, SS18_SSX1_Pten


title: 205659810063_R02C01, Primarytumor, hGFAP_cre_P53Fl_Fl_lsl_MYCNFl_wt_CAG_Gli2


title: 206448030002_R01C02, Primarytumor, SS18_SSX1_Pten


title: Cell_2286


title: Cell_2284


title: Cell_2280


title: 205668270008_R04C01, Primarytumor, Lmax1a_cre_P53f_f_Rbf_f


title: Cell_2283


title: Cell_2278


title: 205659810063_R06C02, Primarytumor, hGFAP_cre_P53Fl_Fl_lsl_MYCNFl_wt_CAG_Gli2


title: 205668270029_R02C01, Primarytumor, BRAF_VEKIN


title: Cell_2276


title: 205659810063_R03C01, Primarytumor, hGFAP_cre_P53Fl_Fl_lsl_MYCNFl_wt_CAG_Gli2


title: Cell_2282


title: 205659810062_R04C02, Primarytumor, hGFAP_cre_P53Fl_Fl_lsl_MYCNFl_wt_CAG_Gli2


title: Cell_2281


title: 205659810062_R02C02, Primarytumor, hGFAP_cre_P53Fl_Fl_lsl_MYCNFl_wt_CAG_Gli2


title: 205668270008_R06C01, Primarytumor, Lmax1a_cre_P53f_f_Rbf_f


title: Cell_2277


title: 205668270039_R04C02, Primarytumor, LSL_PLAG1(+_d)_hGFAP_Cre


title: Cell_2279


title: 205333490087_R04C01, Primarytumor, BRAF_Cdkn2aKO


title: 205668270039_R03C02, Primarytumor, LSL_PLAG1(+_d)_hGFAP_Cre


title: 205668270008_R03C02, Primarytumor, NMYC

value: NMYC


title: 205333490087_R03C01, Primarytumor, BRAF_Cdkn2aKO


title: 205333490087_R02C01, Primarytumor, BRAF_Cdkn2aKO


title: Cell_2274


title: Cell_2272


title: Cell_2270


title: Cell_2271


title: Cell_2267


title: Cell_2269


title: 205668270039_R01C01, Primarytumor, BRAF_VEKIN


title: 205668270008_R06C02, Primarytumor, NMYC_ALK


title: Cell_2268


title: Cell_2266


title: Cell_2265


title: 205668270008_R05C02, Primarytumor, NMYC_ALK


title: Cell_2275


title: 205668270008_R04C02, Primarytumor, NMYC_ALK


title: Cell_2263


title: 205333480133_R01C01, Primarytumor, Wildtype_adult


title: Cell_2264


title: 205333480098_R05C02, Primarytumor, Wildtype_adult


title: Cell_2262


title: Cell_2261


title: 205333480098_R04C02, Primarytumor, Wildtype_adult


title: 205333480098_R03C02, Primarytumor, Wildtype_adult


title: Cell_2260


title: 205333480098_R01C02, Primarytumor, Wildtype_adult


title: Cell_2259


title: Cell_2258


title: 205668270008_R01C02, Primarytumor, NMYC


title: 205668270008_R02C02, Primarytumor, NMYC


title: 206448030020_R03C02, Primarytumor, SMARCB1_P53


title: Cell_2257


title: 205489430003_R06C01, Primarytumor, SMARCB1_P53


title: 205489430003_R05C01, Primarytumor, SMARCB1_P53


title: 205333480098_R06C01, Primarytumor, NF1_sg_P53


title: 205333480098_R04C01, Primarytumor, NF1_sg_P53


title: 205333480098_R05C01, Primarytumor, NF1_sg_P53


title: Cell_2254


title: Cell_2256


title: Cell_2253


title: Cell_2251


title: 206448030014_R06C01, SAMprimaryfragments, Nf1_P53


title: Cell_2250


title: 206448030014_R05C01, SAMprimarycells, Nf1_P53


title: 206448030014_R04C01, 3Dcellline, Nf1_P53


title: Cell_2248


title: 205333480098_R02C02, Primarytumor, Wildtype_adult


title: 206448030014_R03C01, 2Dcellline, Nf1_P53


title: Cell_2247


title: 206448030014_R02C02, SAM3DP6, Nf1_P53


title: Cell_2246


title: 206448030014_R02C01, Primarytumor, Nf1_P53


title: 206448030014_R01C02, SAM2DP6, Nf1_P53


title: 205489430003_R01C01, Allograft, Nf1_P53

source_name: Allograft

value: Allograft


title: 205489430003_R01C02, Primarytumor, SMARCB1_P53


title: Cell_2255


title: Cell_2243


title: Cell_2245


title: Cell_2252


title: Cell_2244


title: Cell_2241


title: 207097260029_R02C01, Primarytumor, Blbp_cre_Ctnnb1Fl_Fl_TP53Fl_Fl


title: Cell_2240


title: Cell_2239


title: 207097260029_R03C01, AllograftP1, Blbp_cre_Ctnnb1_P53_Pik3caE545K


title: 207097260029_R04C01, AllograftP1, Blbp_cre_Ctnnb1_P53_Pik3caE545K


title: 205489430007_R06C02, Allograft, Blbp_cre_Ctnnb1_P53_Pik3caE545K


title: Cell_2249


title: 205489430007_R05C02, Allograft, Blbp_cre_Ctnnb1_P53_Pik3caE545K


title: Cell_2238


title: Cell_2236


title: 205489430007_R04C02, Allograft, Blbp_cre_Ctnnb1_P53_Pik3caE545K


title: 205659810062_R02C01, Allograft, Blbp_cre_Ctnnb1_Brg1


title: 205659810062_R06C01, Allograft, Blbp_cre_Ctnnb1_Brg1


title: Cell_2234


title: Cell_2235


title: Cell_2233


title: Cell_2232


title: 205659810062_R01C02, Allograft, Blbp_cre_Ctnnb1_Brg1


title: 205668270038_R02C01, Primarytumor, SHH


title: Cell_2230


title: 205668270038_R03C01, Primarytumor, SHH


title: Cell_2229


title: 207097260029_R01C01, Primarytumor, Blbp_cre_Ctnnb1Fl_Fl_TP53Fl_Fl


title: 205668270038_R01C01, Primarytumor, SHH


title: Cell_2242


title: 205333480118_R06C01, NA, SHH


title: 205333480118_R05C01, NA, SHH


title: Cell_2225


title: 205333480118_R04C01, NA, SHH


title: Cell_2226


title: Cell_2224


title: 205333480118_R03C01, NA, SHH


title: 205333480118_R02C01, NA, SHH


title: Cell_2222


title: 205333480118_R01C02, NA, SHH


title: Cell_2219


title: Cell_2220


title: 205668270038_R06C01, Primarytumor, SHH_Ptch1+___Atoh1_EGFP


title: Cell_2221


title: 205333480118_R01C01, NA, SHH


title: Cell_2218


title: 205668270038_R05C01, Primarytumor, SHH_Ptch1+___Atoh1_EGFP


title: Cell_2217


title: Cell_2216


title: 205668270035_R05C02, Primarytumor, SHH_Ptch1+___Atoh1_EGFP


title: Cell_2215


title: Cell_2228


title: 205668270035_R04C02, Primarytumor, SHH_Ptch1+___Atoh1_EGFP


title: 205668270038_R04C01, Primarytumor, SHH_Ptch1+___Atoh1_EGFP


title: 205668270035_R03C02, Primarytumor, SHH_Ptch1+___Atoh1_EGFP


title: Cell_2214


title: Cell_2213


title: 205489430002_R03C02, Primarytumor, Ptch1KO


title: 205489430002_R04C02, Primarytumor, Ptch1KO


title: 205333480032_R02C01, Primarytumor, Ptch1KO


title: Cell_2212


title: Cell_2210


title: 205333480032_R01C01, Primarytumor, Ptch1KO


title: Cell_2209


title: myotubes, siLaminsA/C, Hours72, stretch,rep 4

city: Paris

first: Catherine

last: Coirault

address: 47 bd de l'Hôpital

country: France

institute: Inserm

description:
Library name: Ssi_4_1
run2

data_processing:
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on hg38 reference genome and quantification with gencode v37 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: hg38
Supplementary files format and content: Format TSV: gene and transcript counts in each sample

molecule: total RNA

source_name: myotubes

growth_protocol: Human immortalized muscle cell precursors, clone 8220, were cultured with 5% CO2 at 37°C in growth medium consisting of 1 vol 199 Medium/4 vol DMEM (Life Technologies, Carlsbad, CA, USA) supplemented with 20% fetal calf serum (Life technologies, Carlsbad, CA, USA), 5 ng/mL hEGF (Life Technologies, Carlsbad, CA, USA), 0.5 ng/mL βFGF, 0.1 mg/mL dexamethasone (Sigma-Aldrich, St. Louis, MO, USA), 50 μg/mL fetuin (Life Technologies, Carlsbad,CA, USA), 5 μg/mL insulin (Life Technologies, Carlsbad, CA, USA), and 50 mg/mL Gentamycin (Gibco™, Life Technologies, Carlsbad, CA, USA).

extract_protocol:
The siRNA transfections were done with Lipofectamine RNAiMAX (Life Technologies, Carlsbad, CA, 13778-150) according to manufacturer’s instructions 24h and 48h after switching confluent myoblasts to differentiation medium using 50 nM of siRNA. Gene or protein of interest was analyzed 72 h after the first transfection
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Differentiation into myotubes was induced by switching confluent myoblasts to differentiation medium containing DMEM (Gibco) and 50 mg/mL gentamycin. Gentamycin was removed when siRNA treatment is applied.

tag: clone

tag: cell type

value: myotubes

value: lamin A/C knockdown

tag: treatment

value: myogenic differentiation

tag: time

value: Day 3


title: 205668270039_R06C01, Primarytumor, Ptch1KO_Trp53KO


title: 205489430002_R05C02, Primarytumor, Ptch1KO_Trp53KO


title: myotubes, siLaminsA/C, Hours72, stretch,rep 3

description:
Library name: Ssi_1_3
run2


title: myotubes, siLaminsA/C, Hours72, stretch,rep 2

description:
Library name: Ssi_1_2
run2


title: Cell_2208


title: Cell_2207


title: Cell_2206


title: 205668270035_R06C01, Hyperplasia, Ptch1KO_Atoh1_EGFP

source_name: Hyperplasia

value: Hyperplasia


title: myotubes, siLaminsA/C, Hours72, stretch,rep 1

description:
Library name: Ssi_1_1
run2


title: 205668270035_R02C02, Hyperplasia, Ptch1KO_Atoh1_EGFP


title: myotubes, siLaminsA/C, Hours72, static,rep 8

description:
Library name: Nsi-4
run2


title: Cell_2205


title: 205668270035_R01C02, Hyperplasia, Ptch1KO_Atoh1_EGFP


title: myotubes, siLaminsA/C, Hours72, static,rep 7

description:
Library name: Nsi-3
run2


title: myotubes, siLaminsA/C, Hours72, static, rep5

description:
Library name: Nsi-0
run2


title: Cell_2204


title: Cell_2203


title: HCT-p53KO-Nutlin-Sp1-ChIP-1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome using STAR (v2.7.9a).
Assembly: hg19
Supplementary files format and content: CPM-normalized bigWig files were generated using Deeptools (v3.5.1). Score represents the normalized coverage of DNA fragment at a given coordinate.

growth_protocol: McCoy’s 5A (Corning) with 10% FBS and 1% pen/strep

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes then quenched with glycine. After cell lysis, chromatin was sonicated using a a focused-ultrasonicator (Covaris, ME220).
Libraries for ChIP-seq were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) as per manufacturer’s instructions starting with 1 ng of ChIP DNA and 12 cycles of final PCR amplification. Library size was assessed using the 4200 Tapestation and the High-Sensitivity DNA assay (Agilent, Santa Clara, CA).  Concentration was determined using the Qubit Fluorometer 2.0. (Thermo Fisher Scientific, Waltham, MA).

tag: chip antibody

tag: cell line

value: Human colorectal carcinoma


title: Cell_2211


title: 205785610013_R03C02, Primarytumor, Ptch1


title: HCT-p53KO-Nutlin-Input-2


title: Cell_2202


title: 205489430002_R06C02, Primarytumor, Ptch1KO_Trp53KO


title: 205785610013_R02C02, Primarytumor, Ptch1


title: HCT-p53KO-Nutlin-Input-1


title: HCT-p53KO-Nutlin-H3K27Ac-ChIP-2

value: H3K27ac (ab4729, Abcam)


title: Cell_2201


title: 205785610013_R01C02, Primarytumor, Ptch1

value: Primarytumor


title: 205333480032_R04C02, Primarytumor, Ptch1(+_d)_Bcor(p_p)_Atoh_Cre


title: HCT-p53KO-Control-Sp1-ChIP-2

value: Untreated


title: HCT-p53KO-Control-Input-2


title: HCT-p53KO-Control-Sp1-ChIP-1


title: Cell_2200


title: myotubes, siLaminsA/C, Hours72, static,rep6

description:
Library name: Nsi-2
run2


title: HCT-p53KO-Nutlin-H3K27Ac-ChIP-1


title: 205333480032_R03C02, Primarytumor, Ptch1(+_d)_Bcor(p_p)_Atoh_Cre


title: Cell_2198


title: Cell_2197


title: HCT-p53KO-Control-H3K27Ac-ChIP-2


title: HCT-p53KO-Nutlin-Sp1-ChIP-2


title: HCT-WT-Nutlin-p53-ChIP-2

value: p53 (DO-1, Santa Cruz)

value: WT/WT


title: HCT-WT-Nutlin-p53-ChIP-1


title: Cell_2196


title: Cell_2195


title: HCT-p53KO-Control-H3K27Ac-ChIP-1


title: 205333480032_R06C01, Primarytumor, Ptch1_Elp1KO


title: 205333480032_R05C01, Primarytumor, Ptch1_Elp1KO


title: HCT-WT-Nutlin-Sp1-ChIP-1


title: HCT-WT-Nutlin-Sp1-ChIP-2


title: HCT-WT-Nutlin-Input-2


title: Cell_2194


title: 205333480032_R01C02, Primarytumor, Ptch1_Elp1KO


title: HCT-WT-Nutlin-Input-1


title: Cell_2193


title: HCT-WT-Nutlin-H3K27Ac-ChIP-2


title: HCT-WT-Nutlin-H3K27Ac-ChIP-1


title: HCT-p53KO-Control-Input-1


title: 205333480032_R03C01, Primarytumor, Ptch1_BcorKO


title: HCT-WT-Control-p53-ChIP-2


title: HCT-WT-Control-p53-ChIP-1


title: 205333480032_R04C01, Primarytumor, Ptch1_BcorKO


title: Cell_2192


title: HCT-WT-Control-Sp1-ChIP-2


title: 207017570061_R06C01, Primarytumor, Math1_CreERT_Gli2A


title: Cell_2191


title: HCT-WT-Control-Input-2


title: HCT-WT-Control-Sp1-ChIP-1


title: 205333480032_R02C02, Primarytumor, Ptch1(+_d)_Bcor(p_p)_Atoh_Cre


title: HCT-WT-Control-Input-1


title: 207017570061_R05C01, Primarytumor, Math1_CreERT_Gli2A


title: Cell_2188


title: HCT-WT-Control-H3K27Ac-ChIP-2


title: HCT-WT-Control-H3K27Ac-ChIP-1


title: 207017570061_R04C01, Primarytumor, Math1_CreERT_Gli2A


title: HCT-G334R-Nutlin-p53-ChIP-2


title: 207017570061_R03C02, Primarytumor, Math1_CreERT_Gli2A


title: HCT-G334R-Nutlin-p53-ChIP-1


title: HCT-G334R-Nutlin-Sp1-ChIP-2


title: Cell_2186


title: Cell_2187


title: HCT-G334R-Nutlin-Sp1-ChIP-1


title: HCT-G334R-Nutlin-Input-2


title: HCT-G334R-Nutlin-Input-1


title: 207017570061_R01C02, Primarytumor, Math1_CreERT_Gli2A


title: HCT-G334R-Nutlin-H3K27Ac-ChIP-2


title: HCT-G334R-Control-p53-ChIP-2


title: Cell_2183


title: 205333480031_R05C01, Primarytumor, Math1_cre_SmoM2


title: Cell_2190


title: Cell_2182


title: HCT-G334R-Control-Sp1-ChIP-1


title: HCT-G334R-Control-Input-2


title: 205038970012_R03C01, Primarytumor, Math1_cre_SmoM2


title: 205333480031_R04C01, Primarytumor, Math1_cre_SmoM2


title: Cell_2181


title: HCT-G334R-Control-H3K27Ac-ChIP-2


title: HCT-G334R-Control-Input-1


title: Cell_2180


title: 207017570061_R02C02, Primarytumor, Math1_CreERT_Gli2A


title: 205038970012_R02C01, Primarytumor, Math1_cre_SmoM2


title: Cell_2185


title: HCT-G334R-24hr-3

data_processing:
Reads were aligned using Bowtie2  against mm10 version of the human genome, and RNA-Seq by Expectation Maximization (RSEM) was used to quantify transcripts and estimate fragments per kilobase of transcript per million fragments mapped values using Ensembl transcriptome information.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts of each sample.

extract_protocol:
RNA was isolated using QIAshredder columns (Qiagen) and the RNeasy Mini Kit (Qiagen).  On-column DNaseI digestion was performed.
Libraries for 3′ mRNA-seq were generated from 100 ng total RNA using the QuantSeq FWD library preparation kit (Lexogen) according to the manufacturer's directions.


title: 205038970012_R01C01, Primarytumor, Math1_cre_SmoM2


title: HCT-G334R-24hr-2


title: Cell_2179


title: HCT-G334R-Control-H3K27Ac-ChIP-1


title: HCT-G334R-24hr-1


title: Cell_2178


title: Cell_2184


title: HCT-G334R-6hr-3


title: 205333480031_R06C01, Primarytumor, Math1_cre_SmoM2


title: HCT-G334R-Control-p53-ChIP-1


title: HCT-G334R-Nutlin-H3K27Ac-ChIP-1


title: 205537640001_R03C02, Primarytumor, Math1_cre_Ptch1Fl_Fl


title: HCT-G334R-6hr-2


title: Cell_2177


title: HCT-G334R-6hr-1


title: HCT-G334R-Control-Sp1-ChIP-2


title: 205537640001_R02C02, Primarytumor, Math1_cre_Ptch1Fl_Fl


title: HCT-G334R-Control-3

value: control


title: Cell_2176


title: 205537640001_R01C02, Primarytumor, Math1_cre_Ptch1Fl_Fl


title: HCT-G334R-Control-2


title: HCT-G334R-Control-1


title: 207017570061_R03C01, Primarytumor, Math1_Cre_Gli2A


title: HCT-WT-24hr-3


title: Cell_2175


title: Cell_2174


title: HCT-WT-24hr-1


title: HCT-WT-6hr-3


title: Cell_2173


title: 207017570061_R01C01, Primarytumor, Math1_Cre_Gli2A


title: HCT-WT-6hr-2


title: 207017570061_R02C01, Primarytumor, Math1_Cre_Gli2A


title: HCT-WT-24hr-2


title: HCT-WT-6hr-1


title: 205785610013_R03C01, Primarytumor, Elp1WT_Ptch1


title: HCT-WT-Control-2


title: HCT-WT-Control-1


title: Cell_2170


title: Cell_2171


title: 205785610013_R01C01, Primarytumor, Elp1WT_Ptch1


title: Cell_2168


title: 1928_A03_spleen_01, day 6

first: Regina

middle: M.

last: Young

state: Pennsylvania

address: 3400 Civic Center BLVD

department: CCI

institute: University of Pennsylvania

description:
Library name: 1928_A03_spleen_01
Illumina 150x150 bp

data_processing:
Kallisto and DESeq2
Supplementary files format and content: DESeq2 normlized count matrix in txt format
Assembly: GRCm39

source_name: Spleen

growth_protocol: PDA7940bWT cells were cultured in R10 media consisting of RPMI-1640 (Gibco, Life Technologies) with 10% FBS, 2% HEPES (Gibco), 1% of GlutaMAX (Gibco), and 1% of penicillin/streptomycin(Gibco, Life Technologies).  B6.SJL-Ptprca/BoyAiTac (B6.SJL congenic) mouse splenocytes were enriched for CD3+ cells by magnetic bead separation (STEMCELL Technologies). T cells were activated with mouse CD3/CD28 Dynabeads (Thermo Fisher Scientific) in the presence of 50 U/ml recombinant human IL-2 (Peprotech) for 48 hr before spinfection on retronectin-coated (Takara Bio) plates. Cells were collected for injection two days after transduction.

extract_protocol:
Zymo research RNA mini prep kit
Illumina Stranded mRNA prep

treatment_protocol: Male C57BL/6NTac (B6) and B6.SJL-Ptprca/BoyAiTac (B6.SJL congenic) mice aged 6 weeks were purchased from Taconic Farms. B6 and B6.SJL congenic mice were used at 8-10 weeks old. The murine pancreatic PDA7940bWT cell lines were established from the KrasLSL.G12D/+p53R172H/+ (KPC) mouse pancreatic tumor model.  PDA7940bWT cells (1e6) were injected (subcutaneous) into B6 mice and 7 days later B6.SJL congenic derived CAR T cells (1e6) were injected (intraveneously).  Spleens were harvested from tumor-bearing C57BL/6 mice. Single cell suspensions were stained using anti-mouse FITC-CD45.1 antibody (Miltenyi Biotech; 130-124-211) and magnetically sorted using the EasySep™ Mouse FITC Positive Selection Kit II according to manufacturer’s guidelines (STEMCELL).

value: Spleen

value: B6.SJL congenic derived CAR T cells

value: CD19/28z-A03BBz CAR T cells

value: WT

value: Tumor-Bearing Mice

value: day 6


title: 205785610013_R02C01, Primarytumor, Elp1WT_Ptch1


title: 1928_A03_spleen_02, day 6

description:
Library name: 1928_A03_spleen_02
Illumina 150x150 bp


title: A03_spleen_03, day 6

description:
Library name: A03_spleen_03
Illumina 150x150 bp

value: A03BBz CAR T cells


title: Cell_2169


title: 205785610013_R05C01, Primarytumor, Elp1cKO_Ptch1


title: A03_spleen_02, day 6

description:
Library name: A03_spleen_02
Illumina 150x150 bp


title: Cell_2167

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: A03_spleen_01, day 6

description:
Library name: A03_spleen_01
Illumina 150x150 bp


title: 205785610013_R06C01, Primarytumor, Elp1cKO_Ptch1


title: 9_260521

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

institute: CIML

description: Library name: Sample 22

data_processing:
Alignments of fastq files obtained after sequencing were generated with STAR 2.7.9a software using the GRCm38 reference genome. The number of reads mapped to each gene was determined with featureCounts v2.0.1 using Mus_musculus.GRCm38.100.gtf annotation file.
Assembly: GRCm38
Supplementary files format and content: Table output from the featureCounts

source_name: lung

extract_protocol:
Total RNAs from lung cells were extracted using RNeasy Plus Mini Kit (Qiagen) following the manufacturer protocol.
500 ng of lung RNA/sample were used to prepare libraries for sequencing by using KAPA RNA HyperPrep Kits (Roche).

treatment_protocol: Harvested organs were incubated in RNAlater (Thermofisher) at 4°C overnight, then frozen at -80°C until RNA isolation. RNA was isolated from the lungs of uninfected and IAV-infected control and pDC-less mice (160 PFU, days 0, 3 and 6 after infection).

value: lung

value: pDC-less

value: IAV-infected mouse

tag: time(days)


title: 9_160621

description: Library name: Sample 21


title: 205785610013_R04C01, Primarytumor, Elp1cKO_Ptch1


title: Cell_2166


title: 8_260521

description: Library name: Sample 20


title: Cell_2165


title: 205668270037_R06C02, Primarytumor, p53DN_srcCA


title: 8_100321

description: Library name: Sample 18


title: 8_250321

description: Library name: Sample 19


title: 7_260521

description: Library name: Sample 17


title: HCT-WT-Control-3

value: Human colorectal carcinoma


title: 205668270037_R05C02, Primarytumor, p53DN_srcCA


title: 7_250321

description: Library name: Sample 16


title: 1928_A03_spleen_03, day 6

description:
Library name: 1928_A03_spleen_03
Illumina 150x150 bp


title: 7_160621

description: Library name: Sample 15


title: 205668270037_R04C02, Primarytumor, p53DN_srcCA


title: Cell_2163


title: 6_260521

description: Library name: Sample 14

value: uninfected mouse


title: 205668270037_R03C02, Primarytumor, p53DN_srcCA

value: Primarytumor


title: Cell_2162


title: Cell_2161


title: 6_250321

description: Library name: Sample 13


title: 5_260521

description: Library name: Sample 12

value: PacsinDTA


title: 5_100321

description: Library name: Sample 11


title: 205668270037_R02C02, Primarytumor, p53DN_srcCA


title: 205668270037_R01C02, Primarytumor, p53DN_srcCA


title: 4_260521

description: Library name: Sample 10


title: 4_160621

description: Library name: Sample 9


title: 4_100321

description: Library name: Sample 8

value: SiglechiCre


title: 205668270031_R06C02, Primarytumor, LRL_Myc_Trp53DN_Ptf1a_Cre


title: Cell_2159


title: 3_160621

description: Library name: Sample 6


title: Cell_2164


title: 2_100321

description: Library name: Sample 4


title: 3_250321

description: Library name: Sample 7


title: 205668270029_R04C02, Primarytumor, LRL_Myc_Trp53DN_Ptf1a_Cre


title: Cell_2158


title: 2_250321

description: Library name: Sample 5


title: 1_260521

description: Library name: Sample 3


title: 205668270029_R05C02, Primarytumor, LRL_Myc_Trp53DN_Ptf1a_Cre


title: Cell_2157


title: 1_250321

description: Library name: Sample 2


title: Cell_2156


title: D6-TgK18-2045

description: Library name: Sample 18

treatment_protocol: Harvested organs were incubated in RNAlater (Thermofisher) at 4°C overnight, then frozen at -80°C until RNA isolation. RNA was isolated from the lungs of uninfected and SARS-CoV2 infected  K18:hACE2 mice (1.1 10^5 PFU, days 0, 1, 2, 4 and 6 after infection).

value: SARS-CoV2 infected mouse

value: Day 6


title: 1_100321

description: Library name: Sample 1


title: 205668270029_R03C02, Primarytumor, LRL_Myc_Trp53DN_Gad2_IRES_Cre


title: 205668270039_R05C02, Primarytumor, LRL_Myc_Trp53DN_Atoh1_Cre


title: D6-TgK18-1787

description: Library name: Sample 17


title: Cell_2160


title: Cell_2154


title: 205668270029_R06C02, Primarytumor, LRL_Myc_Trp53DN_Atoh1_Cre


title: D4-TgK18-1808

description: Library name: Sample 14

value: Day 4


title: D4-TgK18-1855

description: Library name: Sample 15


title: 205668270031_R06C01, Primarytumor, Gr3__MYCNSchulte


title: Cell_2153


title: D4-TgK18-1807

description: Library name: Sample 13


title: D4-TgK18-2046

description: Library name: Sample 12


title: Cell_2151


title: D2-TgK18-1889

description: Library name: Sample 11

value: Day 2


title: D2-TgK18-1809

description: Library name: Sample 8


title: 205668270031_R04C01, Primarytumor, Gr3__MYCNSchulte


title: D2-TgK18-1859

description: Library name: Sample 10


title: D2-TgK18-1829

description: Library name: Sample 9


title: Cell_2148


title: D2-TgK18-2047

description: Library name: Sample 7


title: 205668270031_R03C02, AllograftP1, Gr3__AllograftMYCNSchulte


title: Cell_2155


title: Cell_2147


title: D1-TgK18-1884

description: Library name: Sample 5

value: Day 1


title: D1-TgK18-2039

description: Library name: Sample 6


title: D1-TgK18-1825

description: Library name: Sample 4


title: 205668270031_R02C02, AllograftP1, Gr3__AllograftMYCNSchulte


title: D4-TgK18-1843

description: Library name: Sample 16


title: Cell_2146


title: 205668270031_R01C02, AllograftP1, Gr3__AllograftMYCNSchulte


title: NI-TgK18-2040

description: Library name: Sample 3

value: Day 0


title: NI-TgK18-1888

description: Library name: Sample 2


title: 205307790110_R06C02, Primarytumor, Glt1_tTA_TRE_MYCN_Luc


title: 205668270031_R05C01, Primarytumor, Gr3__MYCNSchulte


title: NI-TgK18-1826

description: Library name: Sample 1


title: Cell_2144

description: SmartSeq2_Gene_log_normalized_counts.rds


title: Cell_2152


title: WT Female 34 8 Week LNAME

city: Chicago

first: Alireza

last: Khoddam

state: IL

address: 303 E Superior St 8-400

department: Cardiology

institute: Northwestern University

description:
Library name: DV_24_10
10x genomics

library_source: transcriptomic single cell

data_processing:
for bulk RNA-seq: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2[2] as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. For scRNA-Seq: Sequencing data were aligned to mouse reference using the Cell Ranger 3.0.2 pipeline.
Assembly: Mouse mm10
Supplementary files format and content: csv contains raw counts for each sample (bullk RNA-seq). AnnData Object containing raw counts of scRNA seq data.

source_name: aorta

extract_protocol:
For bulk RNA-seq: mice were perfused with PBS, whole aortas were extraced and cleaned of peri-aortic fat. For scRNA-seq: A working enzyme solution was prepared on ice by combining Liberase TM (Roche #05401127001, Basel, Basel-Stadt, Switzerland) at 2 units/mL final concentration, Elastase (Worthington #LS002279, Columbus, OH, USA) at 2 units/mL final concentration, and DNase I at 60 units/mL (Roche #10104159001, Basel, Basel-Stadt, Switzerland) in HBSS with Ca2+ and Mg2+ (Gibco #14025092, Waltham, MA, USA).  After euthanization in a CO2 chamber for 2 minutes, mice were perfused with 10 mL HBSS (Gibco #14025092, Waltham, MA, USA) via left ventricular puncture, and the aorta was harvested. The aortas underwent extensive cleaning of periaortic fat and excess tissue while submerged in MACS Separation Buffer (Miltenyi Biotec #130-091-221, Bergisch Gladbach, Rhineland, Germany). The aorta was split open and minced using iris scissors, transferred to 1mL of the enzyme solution described above, and incubated at 37°C for 45 minutes while shaking at 300 RPM. The reaction digestion reaction was stopped by adding 5 mL of 2% FBS (Gibco #A38401-01, Waltham, MA, USA) in HBSS (Gibco #14025092, Waltham, MA, USA). The cell suspension was passed through a 70-μm strainer into a 50 mL conical tube, and residual liquid was collected by centrifugation 300 × g for 10 minutes. Isolated cells were transferred into a microcentrifuge tube and centrifuged at 300 × g for 5 minutes. All but 100 μL of supernatant was removed and cells were resuspended in the remaining 100 μL volume.
For bulk RNA-seq: RNA was isolated using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, North Rhine-Westphalia, Germany) using the manufacturer protocol. For scRNA-seq: Single-cell mRNA libraries were built using the Chromium Next GEM Single Cell 3’ Library Construction V4 Kit.

value: aorta

value: 8-week LNAME treatment


title: Cell_2143


title: WT Female 33 8 Week LNAME

description:
Library name: DV_24_9
10x genomics


title: 205307790110_R05C02, Primarytumor, Glt1_tTA_TRE_MYCN_Luc


title: Cell_2142


title: 205333480031_R06C02, Primarytumor, cMyctransplantedcerebellarcells

value: cMyctransplantedcerebellarcells


title: WT Male 35 8 Week LNAME

description:
Library name: DV_24_11
10x genomics


title: Cell_2141


title: WT Male 28 8 Week LNAME

description:
Library name: DV_24_4
10x genomics


title: Cell_2140


title: Het Female 36 8 Week LNAME

description:
Library name: DV_24_12
10x genomics


title: Het Female 37 8 Week LNAME

description:
Library name: DV_24_13
10x genomics


title: WT Male 29 8 Week LNAME

description:
Library name: DV_24_5
10x genomics


title: Het Male 31 8 Week LNAME

description:
Library name: DV_24_7
10x genomics


title: 205333480031_R04C02, Primarytumor, cMyctransplantedcerebellarcells


title: 205333480031_R05C02, Primarytumor, cMyctransplantedcerebellarcells


title: Het Male 30 8 Week LNAME

description:
Library name: DV_24_6
10x genomics


title: 205307790110_R03C02, Primarytumor, Cmyc+Brg1


title: YPG, rip1∆, biol rep 2

city: Vienna

first: Trinh

last: Phan-Canh

email: phancanht99@univie.ac.at, phancanhtrinh@gmail.com, karl.kuchler@univie.ac.at, karl.kuchler@univie.ac.at

state: Vienna

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs Vienna, Campus Vienna Biocenter

country: Austria

institute: Medical University of Vienna

description: Library name: R11

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v2.8 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1). The reads were then mapped to C. auris genome (B8441) using NextGenMap (Sedlazeck et al., 2013), settings: -b -Q 30.
Optical read duplicates were removed using Picard tools (Broad Institute, https://broadinstitute.github.io/picard/, settings: MarkDuplicates REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT). Read counting was done using HTseq (Anders et al., 2014) in the union mode and the genomic annotation from C. auris B8441 (settings: -f bam -t gene -i ID).
Assembly: Differential gene expression analysis was done using the glm approach in edgeR (Robinson et al., 2009)
Supplementary files format and content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)
Assembly: Candida auris B8441 - Genome version: s01-m01-r22 from Candida Genome Database
Supplementary files format and content: Matrix files raw count and FPKM are provided for all samples

organism: Candidozyma auris

growth_protocol: YPD or YP-2%Glycerol (YPG), 37°C, 200 rpm, exponential phase

extract_protocol:
The total RNA was isolated from frozen samples using TRIZOL reagent.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: comparing different genotypes

value: planktonic cell at exponential phase

value: YPG


title: YPG, rip1∆, biol rep 3

description: Library name: R12


title: Cell_2136


title: WT Female 32 8 Week LNAME

description:
Library name: DV_24_8
10x genomics


title: YPG, WT, biol rep 3

description: Library name: R9

value: WT


title: YPG, rip1∆, biol rep 1

description: Library name: R10


title: YPG, WT, biol rep 2

description: Library name: R8


title: Cell_2135


title: YPG, WT, biol rep 1

description: Library name: R7


title: 205307790110_R04C02, Primarytumor, Glt1_tTA_TRE_MYCN_Luc


title: 206448030020_R01C01, Primarytumor, ETV6_NTRK3_P53


title: YPD, rip1∆, biol rep 3

description: Library name: R6

value: YPD


title: Cell_2134


title: YPD, rip1∆, biol rep 2

description: Library name: R5


title: 206448030004_R05C01, SAM2DP6, ETV6_NTRK3_P53


title: Cell_2131


title: YPD, WT, biol rep 2

description: Library name: R2


title: Cell_2137


title: YPD, rip1∆, biol rep 1

description: Library name: R4


title: Cell_2133


title: Cell_2130


title: YPD, WT, biol rep 1

description: Library name: R1


title: 205307790110_R02C02, Primarytumor, Cmyc+Brg1


title: Cell_2138


title: 206448030004_R03C01, SAMprimarycells, ETV6_NTRK3_P53

value: SAMprimarycells


title: CT SCM 3

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description: Library name: CT tdTomato+ SCM 3 - 2064719

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to mouse genome assembly (mm10) (STAR v2.7.1a).
The gene level expression values were quantified (RSEM v1.31) based on  GENCODE annotation (mouse release M22) .
Assembly: GRCm38(mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: FACS sorted tdTomato positive sternocleiodmastoid muscle

extract_protocol:
For FACS sorted SCM muscle, SCM muscles were manually dissected from surrounding tissue, manually dissociated and then digested for 1 hour at 37C in 2U/mL Collagenase B (Roche, #11088831001), Dispase II (Roche, # 04942078001), 50 mM HEPES/KOH pH 7.4, 150 mM NaCl. Cells were then resuspended in 2x volume 10% FBS  in PBS to inactivate digestion enzymes. Samples were filtered through 70 uM filter, spun and supernatant spun again. Then filtered through a 40 uM filter to yield a single cell suspension. Samples were spun down and resuspended in 5% FBS PBS prior to sorting on a FACS Aria for tdTomato+ cell populations with DAPI as a live/dead marker. Data were analyzed with FACSDiva and FlowJo software. Following FACS sorting RNA was isolated from tdTomato+ cells with miRNeasy microelute kit (Qiagen) per manufacturer's instructions.
For FACS sorted samples low input RNA unstranded sequencing was used. One nanogram of total RNA was used to create SPIA-cDNA with a Tecan Ocation RNA seuqncing stem v2 protocol (Tecan, #7102-32) per manufacturer's instructions. 500 ng of purified cDNA was sheered ina Covaris LE220 focused ultra sonicator using a 96 microtube-50 AFA fiberr plate and target base pair size of 300 bp. Following sheering libraries were created using KAPA Hyper-Prep kit (Roche, #KK8504) per manufacturer's instructions based on initial cDNA input. UDI DNA indexes were used from Illumina (20022370).


title: 206448030004_R04C01, SAMprimaryfragments, ETV6_NTRK3_P53

value: SAMprimaryfragments


title: CT SCM 1

description: Library name: CT tdTomato+ SCM 1 - 2064703

value: FACS sorted tdTomato positive sternocleiodmastoid muscle


title: CT SCM 2

description: Library name: CT tdTomato+ SCM 2 - 2064705


title: AT SCM 2

description: Library name: AT tdTomato+ SCM 2 - 2064709


title: Cell_2128


title: Cell_2129


title: AT SCM 1

description: Library name: AT tdTomato+ SCM 1 - 2064707


title: 206448030004_R02C01, 3Dcellline, ETV6_NTRK3_P53


title: Human skin biopsy_32

first: Carmen

last: AL YOUSSEF

state: Paris

address: 24 rue du faubourg saint jacques

department: Institut Cochin

institute: Inserm, U1016

description: Library name: T78646

data_processing:
Reads were aligned to the human genome build hg38/GRCh38.p7 using BWA [18], and duplicated reads were removed with Sambamba [19]. Somatic single nucleotide variants (SNVs) and small insertions/deletions (indels) were called with MuTect2 (v2.0) [20] against a panel of normal samples. Variants were annotated using Ensembl’s VEP (release 101) [21] for functional consequences (SIFT 2.2, PolyPhen 2.2.2) and cross-referenced with public (dbSNP153, GnomAD v2.1, COSMIC v91) and in-house databases.
Somatic variants were filtered using quality, read support, allele fraction, and population frequency thresholds. We analyzed 48 UV-induced cSCC driver genes, identified significantly recurrent mutations with MutSigCV, validated candidate variants with the Illumina pipeline and IGV, and annotated clinically relevant mutations using CIVIC.
Assembly: Reads were aligned to the human genome build hg38/GRCh38.p7 using the Burrows-Wheeler Aligner (BWA) tool.
Supplementary files format and content: Small variants vcf files, includes SNPs and small indels variants that passed quality filters

source_name: skin

extract_protocol:
DNA was extracted from two 20 m FFPE sections using the truXTRAC FFPE Total Nucleic Acid Plus Kit (Covaris Ltd., Woburn, Massachusetts, USA). Concentrations were measured with a Qubit fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts, USA). DNA fragmentation was performed using Adaptive Focused Acoustics Technology from Covaris according to the manufacturer’s instructions. DNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA).
Libraries were prepared using 100 ng of DNA and TruSight Oncology 500 kit (Illumina Inc., San Diego, California, USA), involving A-base addition, adapter ligation, and hybridisation with probes targeting 523 genes. Library concentrations were measured fluorometrically using a Qubit fluorometer, and sequenced on an Illumina NextSeq 500 (Illumina) using paired-end 101-base reads, generating fastq files.

value: skin

value: skin cell


title: 206448030004_R01C01, 2Dcellline, ETV6_NTRK3_P53


title: Cell_2127


title: 206448030002_R06C02, Primarytumor, ETV6_NTRK3_P53

value: Primarytumor


title: Human skin biopsy_31

description: Library name: T76893


title: Human skin biopsy_30

description: Library name: T52822


title: 206448030004_R06C01, SAM3DP6, ETV6_NTRK3_P53


title: Cell_2126


title: YPD, WT, biol rep 3

description: Library name: R3


title: 206448030002_R01C01, Primarytumor, ETV6_NTRK3_P53


title: Human skin biopsy_29

description: Library name: SCC_O_01620298


title: Cell_2125


title: Human skin biopsy_28

description: Library name: SCC_N_new


title: Human skin biopsy_27

description: Library name: SCC_M_97-2094-1B


title: 206448030001_R06C02, Primarytumor, ETV6_NTRK3_P53


title: Human skin biopsy_26

description: Library name: SCC_F_13-933-1A


title: Cell_2124


title: Human skin biopsy_25

description: Library name: P775669


title: 206448030001_R06C01, Primarytumor, ETV6_NTRK3_P53


title: AT SCM 3

description: Library name: AT tdTomato+ SCM 3 - 2156406


title: Human skin biopsy_23

description: Library name: P678428-A13


title: Cell_2123


title: 206448030001_R05C02, Primarytumor, ETV6_NTRK3_P53


title: Cell_2122


title: Human skin biopsy_22

description: Library name: P668009-A22


title: 206448030001_R05C01, Primarytumor, ETV6_NTRK3_P53


title: Cell_2121


title: Human skin biopsy_21

description: Library name: P551523-11


title: 206448030001_R04C02, Primarytumor, ETV6_NTRK3_P53


title: Human skin biopsy_18

description: Library name: 133103-B1


title: Human skin biopsy_20

description: Library name: G43_543


title: Cell_2120


title: Human skin biopsy_19

description: Library name: 995533-3J


title: Human skin biopsy_24

description: Library name: P701367-A37


title: Human skin biopsy_17

description: Library name: 124252-24


title: Human skin biopsy_16

description: Library name: 046479-01


title: Human skin biopsy_15

description: Library name: 7480


title: 206448030001_R03C02, Primarytumor, ETV6_NTRK3_P53


title: Human skin biopsy_14

description: Library name: 7058


title: Cell_2118


title: Human skin biopsy_13

description: Library name: 6173


title: Human skin biopsy_12

description: Library name: 97-2094-1B


title: 206448030001_R03C01, Primarytumor, ETV6_NTRK3_P53


title: Cell_2117


title: 206448030001_R02C02, Primarytumor, ETV6_NTRK3_P53


title: Human skin biopsy_11

description: Library name: 18NA02195


title: 206448030001_R01C02, Primarytumor, ETV6_NTRK3_P53


title: Human skin biopsy_10

description: Library name: 18NA01510


title: Human skin biopsy_9

description: Library name: 16TH_11630-13


title: Human skin biopsy_8

description: Library name: 16NA05530


title: Cell_2115


title: Cell_2116


title: 205333490087_R03C02, Primarytumor, Trp53KO_Rb1KO_p107KO


title: Cell_2114


title: Human skin biopsy_6

description: Library name: 16H17317


title: 205333490087_R02C02, Primarytumor, Trp53KO_Rb1KO_p107KO


title: 206448030001_R04C01, Primarytumor, ETV6_NTRK3_P53


title: Human skin biopsy_4

description: Library name: 14H03170


title: Cell_2119


title: 207363410039_R06C01, Allograft, TFG_MET

value: Allograft


title: Human skin biopsy_5

description: Library name: 14TH_11846-02


title: Human skin biopsy_7

description: Library name: 16NA02560


title: Cell_2112


title: 207363410039_R05C01, Primarytumor, TFG_MET


title: Cell_2113


title: Cell_2111


title: niPS KLF7_rep4

city: Padua

first: Elena

last: Carbognin

state: --- Select One ---

address: via Ugo Bassi 58b

department: Biology

institute: University of Padua

data_processing:
trimming was performed using BBDuk from BBTools v38.87
alignment was performed with STAR 2.7.6a
quantification was performed with Salmon v1.6.0
Assembly: Human GRCh38.p13 Ensembl release 105
Supplementary files format and content: raw counts in .txt format

source_name: naive hiPSCs

growth_protocol: Cells were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs; DR4 ATCC) in PXGL medium (N2B27 (DMEM/F12 [Gibco 11320-074], and Neurobasal in 1:1 ratio [Gibco 21103-049], with 1:200 N2 Supplement [Gibco 17502-048], and 1:100 B27 Supplement [Gibco 17504-044], 2 mM L-glutamine [Gibco 25030-024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem), 2 μM Gö6983 (Axon Medchem) and 10 ng/ml human LIF (produced in-house)) or in RSeT medium (Stem Cell Technologies 05969 ). Human naive PSCs were passaged as single cells every 4 days at split ratio 1:3 or 1:4 following dissociation with TrypLE (Gibco 12563-029) for 10 minutes at room temperature (RT). ROCK inhibitor (Y27632, Axon Medchem 1683) was added in the naïve medium only for 24h after passaging.

extract_protocol:
Total RNA was isolated using Total RNA Purification kit (Norgen Biotek), according to manufactorer's protocol.
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) is used for library construction.

treatment_protocol: For reprogramming from fibroblasts to primed iPSCs, fibroblasts were seeded at day 0 at 15 cells per mm2 in DMEM/10% FBS on microfluidic channels coated with 25 μg ml−1 Vitronectin (for 1 hour at room temperature. On day 1, 9 hours before the first mRNAs transfection, E6 medium (Chen et al., 2011) supplemented with FGF2 100ng ml−1, 1% KSR, ROCKi 5μM, LSD1i 0.1μM and 200ng ml-1 B18R was applied. Cells were transfected daily at 6PM and fresh medium was given daily at 9AM. The transfection mix was prepared according to the StemMACSTM mRNA Transfection Kit (Miltenyi Biotec, 130- 104-463) and using modified mRNAs (coding cocktail components) and NM-microRNAs (Stemgent StemRNA-NM Reprogramming Kit). Individual modified mRNAs (OCT4, SOX2, NANOG, LIN28A, KLF7, KLF4, MYC) were made in-house by in vitro transcription using mRNA synthesis with HiScribeTM T7 ARCA mRNA Kit. During the 8 days of transfection, the dose of mRNAs was gradually increased according to cell proliferation rate and transfection-induced cell mortality. From day 9, cells were cultured in mTeSR (StemCell Technologies 05850) for 6 days to allow stabilisation of hiPSC colonies. Fresh medium was given twice a day at 9AM and 6PM. For chemical resetting from primed to naive PSC, cells were seeded at 10000 cells/cm2 on mitotically inactivated MEFs in E8 medium with 10µM ROCKi (added only for 24 hours). Two days after plating (day 0), medium was changed to PDL/HDACi (N2B27 with 1µM PD0325901, 10ng/ml human LIF and 1mM VPA (HDACi)). Following 3 days in PDL/HDACi, medium was changed to PXGL for a further 10-11 days before passing in PXGL medium on MEFs.

value: naive hiPSCs

value: KLF7 overexpression

value: chemical resetting


title: niPS KLF7_rep3


title: Human skin biopsy_1

description: Library name: 12-009942


title: niPS KLF7_rep2


title: 205668270039_R02C02, AllograftP3, TFG_MET_Trp53KO


title: 205668270038_R06C02, AllograftP2, TFG_MET_Trp53KO


title: niPS KLF7_rep1


title: niPS EMPTY_rep2

value: EMPTY vector overexpression


title: niPS EMPTY_rep3


title: 205668270038_R05C02, AllograftP2, TFG_MET_Trp53KO


title: niPS EMPTY_rep4


title: Cell_2105


title: Cell_2104


title: 205668270038_R04C02, AllograftP1, TFG_MET_Trp53KO


title: niPS EMPTY_rep1


title: 205668270029_R02C02, AllograftP3, TFG_MET_Trp53KO


title: Human skin biopsy_2

description: Library name: 13TH_03711-03


title: KiPS KLF7_rep3

source_name: primed hiPSCs

value: primed hiPSCs


title: Cell_2102


title: KiPS KLF7_rep4


title: Cell_2101


title: 205668270029_R01C02, AllograftP3, TFG_MET_Trp53KO


title: Human skin biopsy_3

description: Library name: 14-3956-4F


title: KiPS KLF7_rep1


title: KiPS EMPTY_rep4


title: KiPS KLF7_rep2


title: Cell_2098


title: 205668270029_R01C01, Primarytumor, TFG_MET_Trp53KO


title: Cell_2110


title: KiPS EMPTY_rep2


title: Cell_2097


title: 205537640006_R05C02, AllograftP2, TFG_MET_Trp53KO


title: KiPS EMPTY_rep1


title: Cell_2096


title: HPD06_rep3


title: HPD06_rep2


title: 205537640006_R04C02, Primarytumor, TFG_MET_Trp53KO


title: HPD01_rep3


title: Cell_2095


title: HPD06_rep1


title: HPD01_rep2


title: 205307790105_R01C02, Primarytumor, TFG_MET_Trp53KO


title: Cell_2093


title: HPD01_rep1


title: Cell_2094


title: 207215890038_R06C01, Primarytumor, ROS1_Ex35_Trp53


title: HPD00_rep3


title: 207215890038_R02C02, Primarytumor, ROS1_Ex35_Trp53


title: HPD00_rep2


title: OSK7M_P7_rep4

value: reprogramming


title: Cell_2091


title: KiPS EMPTY_rep3


title: OSK7M_P7_rep2


title: Cell_2092


title: 207215890038_R01C02, Primarytumor, ROS1_Ex35_Trp53


title: OSK7M_P7_rep3


title: OSK7M_P7_rep1


title: OSK7M_P4_rep4


title: 205333490028_R05C01, Primarytumor, QKI_NTRK2_Trp53KO


title: 205333490028_R03C01, Primarytumor, QKI_NTRK2_Trp53KO


title: OSK7M_P4_rep3


title: OSK7M_P4_rep2


title: Cell_2085


title: 207215890037_R03C01, AllograftP1, QKI_NTRK2_Cdkn2aKO


title: OSK7M_P4_rep1


title: 207215890037_R02C01, AllograftP1, QKI_NTRK2_Cdkn2aKO


title: HPD00_rep1


title: OSKM_P7_rep1


title: Cell_2083


title: OSKM_P4_rep1


title: OSKM_P4_rep3


title: 205333490028_R01C01, Primarytumor, QKI_NTRK2_Cdkn2aKO


title: OSKM_P4_rep2


title: 207215890037_R01C01, Culture, QKI_NTRK2_Cdkn2aKO

source_name: Culture

value: Culture


title: OSKM_P4_rep4


title: OSKM_P7_rep3


title: H9_rep3

source_name: hES cells

value: hES cells


title: 205333490028_R04C01, Primarytumor, QKI_NTRK2_Trp53KO

source_name: Primarytumor


title: 205333490028_R02C01, Primarytumor, QKI_NTRK2_Cdkn2aKO


title: OSKM_P7_rep2

value: WT


title: Cell_2081


title: H9_rep1


title: H9_rep2


title: Cell_2090


title: Cell_2088


title: OSKM_P7_rep4


title: 205333490003_R06C02, Primarytumor, QKI_NTRK2_Cdkn2aKO


title: BJ_rep3

source_name: human fibroblasts

value: human fibroblasts


title: Cell_2087


title: 207215890038_R06C02, Primarytumor, pT2K_C11orf95_RELA_HA_IRES_Luc_T2TP


title: BJ_rep2


title: Cell_2084


title: Cell_2080


title: 207215890037_R05C02, AllograftP1, pT2K_C11orf95_RELA_HA_IRES_Luc_T2TP


title: BJ_rep1


title: Cell_2079


title: 205668270039_R04C01, Primarytumor, PPP1CB_ALK


title: Cell_1299


title: Cell_1282


title: Cell_2077


title: Cell_1289


title: Cell_1283


title: 205333490003_R06C01, Primarytumor, PPP1CB_ALK


title: 205668270039_R03C01, Primarytumor, PPP1CB_ALK


title: Cell_1277


title: Cell_1265


title: Cell_2082


title: Cell_1279


title: Cell_2072


title: Cell_1291


title: Cell_2075


title: 205333490003_R05C02, Primarytumor, PPP1CB_ALK_Trp53KO


title: Cell_2071


title: 205333490003_R04C02, Primarytumor, PPP1CB_ALK_Trp53KO


title: Cell_1261


title: Cell_1257


title: Cell_1260


title: Cell_1253


title: Cell_1255


title: 205333490003_R03C02, Primarytumor, PPP1CB_ALK_Trp53KO


title: Cell_2068


title: Cell_1249


title: Cell_1248


title: Cell_2078


title: 207215890037_R06C01, AllograftP1, PPP1CB_ALK_Cdkn2aKO


title: Cell_2067


title: Cell_1246


title: Cell_1243


title: Cell_1244


title: 207215890037_R05C01, AllograftP1, PPP1CB_ALK_Cdkn2aKO


title: 207215890037_R04C01, Culture, PPP1CB_ALK_Cdkn2aKO


title: Cell_2066


title: Cell_1240


title: Cell_1236


title: Cell_2065


title: Cell_1234


title: Cell_2062


title: 207215890037_R01C02, AllograftP1, PPP1CB_ALK_Cdkn2aKO


title: Cell_1235


title: 205333490003_R02C02, Primarytumor, PPP1CB_ALK_Cdkn2aKO


title: Cell_1214


title: Cell_1215


title: Cell_1213


title: Cell_1212


title: Cell_2070


title: 205333490003_R01C02, Primarytumor, PPP1CB_ALK_Cdkn2aKO


title: 205291550050_R06C02, Primarytumor, PPP1CB_ALK_Cdkn2aKO


title: Cell_2060


title: Cell_1211


title: 205489430003_R06C02, Primarytumor, PDGFRA_Trp53KO


title: Cell_1208


title: Cell_2059


title: Cell_2055


title: 205489430003_R05C02, Primarytumor, PDGFRA_Trp53KO


title: Cell_1209


title: Cell_2053


title: Cell_1206


title: 205668270038_R03C02, Primarytumor, p53DN_srcCA


title: Cell_1204


title: Cell_1203


title: Cell_1207


title: 205668270038_R02C02, Primarytumor, p53DN_srcCA


title: Cell_1201


title: Cell_2052


title: 205668270038_R01C02, Primarytumor, p53DN_srcCA


title: Cell_2051


title: Cell_1199


title: 205489430002_R04C01, Primarytumor, Nf1KO_Trp53KO


title: Cell_2049


title: Cell_1195


title: Cell_1198


title: Cell_2058


title: Cell_2048


title: Cell_1197


title: Cell_1210


title: Cell_1193


title: Cell_2047


title: 205489430002_R03C01, Primarytumor, Nf1KO_Trp53KO


title: Cell_1194


title: 205307790105_R03C02, Primarytumor, NF1KO_Trp53KO


title: Cell_1202


title: Cell_1187


title: Cell_1185


title: Cell_2044


title: Cell_2046


title: 205307790105_R02C02, Primarytumor, NF1KO_Trp53KO


title: 205489430002_R02C02, Primarytumor, Nf1KO_Trp53KO_PtenKO


title: Cell_1184


title: Cell_1183


title: 207215890038_R05C02, Primarytumor, MET_FL_Trp53


title: Cell_2043


title: Cell_1182


title: Cell_1180


title: Cell_1179


title: 207215890038_R04C02, Primarytumor, MET_FL_Trp53


title: Cell_1178


title: Cell_2041


title: Cell_1174


title: Cell_2040


title: Cell_1177


title: 205333480031_R03C02, Primarytumor, hGFAP_cre_P53_MYCN


title: Cell_1169


title: Cell_1181


title: Cell_1192


title: Cell_1168


title: 207215890038_R03C02, Primarytumor, MET_FL_Trp53


title: Cell_1186


title: Cell_1164


title: 205333480031_R02C02, Primarytumor, hGFAP_cre_P53_MYCN


title: 205333480031_R01C02, Primarytumor, hGFAP_cre_P53_MYCN


title: Cell_2037


title: Cell_1163


title: 205038970012_R06C01, Primarytumor, hGFAP_cre_P53_MYCN


title: Cell_2042


title: Cell_1156


title: Cell_2035


title: Cell_1158


title: Cell_2039


title: 205038970012_R05C01, Primarytumor, hGFAP_cre_P53_MYCN


title: Cell_2033


title: Cell_1153


title: Cell_1154


title: 205038970012_R04C01, Primarytumor, hGFAP_cre_P53_MYCN


title: Cell_1146


title: Cell_1149


title: Cell_2029


title: Cell_2030


title: Cell_1138


title: 207215890038_R01C01, Primarytumor, GOPC_ROS1_Trp53


title: Cell_1120


title: Cell_1141


title: Cell_2025


title: 207215890037_R06C02, Primarytumor, GOPC_ROS1_Trp53


title: Cell_2036


title: Cell_1119


title: Cell_1161


title: Cell_1117


title: Cell_2023


title: 207215890037_R04C02, AllograftP1, FGFR1K656E_Cdkn2aKO


title: Cell_2022


title: Cell_1116


title: Cell_1155


title: Cell_1113


title: Cell_2021


title: Cell_1114


title: 207215890037_R02C02, Culture, FGFR1K656E_Cdkn2aKO


title: Cell_1112


title: Cell_2016


title: 207215890038_R02C01, Primarytumor, GOPC_ROS1_Trp53


title: 207215890037_R03C02, AllograftP1, FGFR1K656E_Cdkn2aKO


title: 205668270039_R02C01, Primarytumor, FGFR1_K656E


title: Cell_1111


title: Cell_2015


title: Cell_1103


title: 205333490003_R03C01, Primarytumor, FGFR1_K656E


title: Cell_1108


title: Cell_2013


title: Cell_1102


title: Cell_1118


title: Cell_1097


title: Cell_2011


title: Cell_1080


title: 205668270039_R05C01, Primarytumor, FGFR1_K656E_Nf1KO


title: Cell_1079


title: Cell_1087


title: 205333490028_R04C02, Primarytumor, FGFR1_K656E_Nf1KO


title: Cell_1076


title: Cell_1115


title: Cell_2010


title: 205333490028_R03C02, Primarytumor, FGFR1_K656E_Nf1KO


title: Cell_2008


title: Cell_1074


title: Cell_2007


title: Cell_1066


title: 205333490003_R05C01, Primarytumor, FGFR1_K656E_Cdkn2aKO


title: Cell_2006


title: Cell_1065


title: 205333490003_R04C01, Primarytumor, FGFR1_K656E_Cdkn2aKO


title: Cell_1060


title: Cell_1063


title: Cell_1062


title: 205333490003_R02C01, Primarytumor, FGFR_N546K


title: Cell_1059


title: Cell_1055


title: Cell_2003


title: 205333490003_R01C01, Primarytumor, FGFR_N546K


title: Cell_1053


title: Cell_2005


title: 205489430002_R06C01, Primarytumor, FGFR_N546K_Trp53KO


title: Cell_1052


title: Cell_1050


title: 205489430002_R05C01, Primarytumor, FGFR_N546K_Trp53KO


title: Cell_1075


title: Cell_1051


title: Cell_1998


title: 205489430002_R01C01, Primarytumor, FGFR1_K656E_Cdkn2aKO


title: Cell_2002


title: Cell_1030


title: Cell_1997


title: Cell_1028


title: Cell_1027


title: 205333490087_R06C02, Primarytumor, FGFR_N546K_Cdkn2aKO


title: Cell_1026


title: Cell_1992


title: Cell_1025


title: 205489430002_R01C02, Primarytumor, FGFR_N546K_Trp53KO


title: Cell_1023


title: Cell_1981


title: Cell_1024


title: 205333490087_R04C02, Primarytumor, FGFR_N546K_Cdkn2aKO


title: Cell_1022


title: 205333490087_R05C02, Primarytumor, FGFR_N546K_Cdkn2aKO


title: Cell_1979


title: 205333490087_R06C01, Primarytumor, EpisomalEGFRVIII_PTENKO_Cdkn2aKO


title: Cell_1029


title: Cell_1019


title: Cell_1978


title: Cell_1018


title: Cell_1021


title: Cell_1013


title: Cell_1016


title: Cell_1017


title: Cell_1972


title: 205333490087_R01C02, Primarytumor, EpisomalEGFRVIII_PTENKO_Cdkn2aKO


title: 205489430002_R02C01, Primarytumor, EpisomalEGFR_VIII+EGFR_PtenKO_Cdkn2aKO


title: Cell_1009


title: Cell_1011


title: Cell_1996


title: Cell_1006


title: Cell_1969


title: Cell_1005


title: 205333490087_R05C01, Primarytumor, EpisomalEGFRVIII_PTENKO_Cdkn2aKO


title: 205333490087_R01C01, Primarytumor, EpisomalEGFR_VIII+EGFR_PtenKO_Cdkn2aKO


title: Cell_1004


title: 205333480032_R06C02, Primarytumor, EpisomalEGFR_VIII+EGFR_PtenKO_Cdkn2aKO


title: Cell_1002


title: Cell_1001


title: Cell_1967


title: 205333490028_R06C02, Primarytumor, EGFR_VIII_EGFR_PtenKO_Cdkn2aKO


title: Cell_1966


title: Cell_0999


title: 205333490028_R05C02, Primarytumor, EGFR_VIII_EGFR_PtenKO_Cdkn2aKO


title: Cell_0998


title: Cell_1965


title: 205333480032_R05C02, Primarytumor, EGFR_VIII_EGFR_PtenKO_Cdkn2aKO


title: Cell_0997


title: Cell_1963


title: Cell_1971


title: 207215890038_R05C01, Primarytumor, CLIP1_ROS1_Trp53


title: Cell_0996


title: DSHM implatation, S. aureus infectious cranial defect, Day 14, Sample 2

city: 成都市

first: Zhuojun

last: Xie

state: 四川省

address: 成都市人民南路三段14号

country: China

institute: Sichuan University

description: Library name: S-2

data_processing:
Raw data
quality control
Reference genome alignment
Transcript assembly
Gene expression analysis, etc., plus advanced analyses.
Supplementary files format and content: CSV file includes Count and FPKM values for each sample

organism: Rattus norvegicus

source_name: Bone

extract_protocol:
Two weeks post-implantation, the rats were euthanized, and tissues from the defect regions were carefully dissected, rinsed with pre-chilled sterile PBS, blotted dry, and immediately transferred into cryovials containing RNA-later (5 mL, Beyotime). Samples were snap-frozen in liquid nitrogen and sent to Suzhou Genewiz Biological Technology Co., Ltd. (China) for high-throughput RNA sequencing and subsequent bioinformatics analysis.
Use NR605 kit - select rRNA removal product by species, remove rRNA, do strand-specific construction. It combines second-strand synthesis and end repair dA-Tailing, taking 3h. Or use #NR616, premixed for Illumina/MGI, reducing steps and time.

treatment_protocol: Male SD rats (aged 6–8 weeks) were used to establish infectious calvarial defect models. Briefly, anesthesia was induced via inhalation of 4% isoflurane and maintained at 2% during surgery. Following anesthesia, the scalp was incised to expose the calvaria, and symmetrical full-thickness bilateral defects (5 mm diameter) were created in the parietal bone using a sterilized metal trephine bur, with careful avoidance of dural injury. To induce infection, gelatin sponges soaked with S. aureus (0.5 mL, 1.0 × 108 CFU·mL-1) were implanted into each defect site, followed by careful suturing of the incision. Postoperatively, all animals had free access to food and water to support recovery. One week after surgery, rats were randomly divided into two groups (n = 3 per group): (a) Blank (b) DSHM During the secondary surgery, rats were positioned supine with their heads toward the operator. The calvaria defects were re-exposed, and infected tissue was thoroughly debrided to remove pus and necrotic material. Subsequently, DSHM was implanted into both defects of each rat in the experimental group, while rats in the control group was without any treatment. Incisions were then closed carefully, and rats were housed separately by group to ensure adequate post-operative care and monitoring.

value: Bone

value: Osteoblast

value: S. aureus infectious cranial defect with DSHM implantation

value: Experience (Day 14)


title: DSHM implatation, S. aureus infectious cranial defect, Day 14, Sample 3

address: 成都市人民南路三段14号

description: Library name: S-3


title: DSHM implatation, S. aureus infectious cranial defect, Day 14, Sample 1

address: 成都市人民南路三段14号

description: Library name: S-1


title: Cell_1960


title: 207215890038_R04C01, Primarytumor, CLIP1_ROS1_Trp53


title: 207215890038_R03C01, Primarytumor, CLIP1_ROS1_Trp53


title: Cell_0995


title: Blank, S. aureus infectious cranial defect, Day 14, Sample 3

address: 成都市人民南路三段14号

description: Library name: N-3

value: S. aureus infectious cranial defect without treatment

value: Blank (Day 14)


title: Blank, S. aureus infectious cranial defect, Day 14, Sample 2

address: 成都市人民南路三段14号

description: Library name: N-2


title: Cell_1968


title: Cell_1003


title: Cell_0994


title: Blank, S. aureus infectious cranial defect, Day 14, Sample 1

address: 成都市人民南路三段14号

description: Library name: N-1


title: 205785610013_R06C02, AllograftP1, H3_3K27M_PDGFRA_Trp53KO


title: Cell_1951


title: Cell_1950


title: Cell_0993


title: 205785610013_R05C02, AllograftP1, H3_3K27M_PDGFRA_Trp53KO


title: TS603_Veh_p9_rep3

first: Thomas

middle: Kieran

last: Sears

address: 303 E. Superior St.

department: Neurological Surgery

description:
Library name: TS603_Veh_p9_9_13_21
TS603_Veh_p9_9_13_21

data_processing:
Raw reads were assessed for quality using FastQC and trimmed using Trim Galore v0.4.4 and Cutadapt v 1.14.
Aligned BAM files were generated using STAR and gene counts were generated using HTSeq
Assembly: hg38
Supplementary files format and content: Processed data file includes normalized counts generated by deseq

growth_protocol: Serum-free, non-adherent gliomasphere cultures in Glioma Stem Cell Media (GSCM)

extract_protocol:
RNA was extracted using Qiagen's RNEasy Plus Mini Kit
Libraries were constructed using Illumina's TruSeq RNA Library Kit

treatment_protocol: 10 nM panobinostat for 24 hours

value: glioma stem-like cell

value: IDH1/2 mutant

value: DMSO vehicle for 24 hours


title: Cell_0992


title: Cell_1947


title: 205537640006_R06C02, Primarytumor, H3_3K27M_PDGFRA_Trp53KO

value: Primarytumor


title: TS603_Veh_p7_rep1

description:
Library name: TS603_Veh_p7_9_12_21
TS603_Veh_p7_9_12_21


title: Cell_1946


title: Cell_0990


title: Cell_0991


title: Cell_1944


title: Cell_0989


title: Cell_1943


title: Cell_1952


title: TS603_Veh_p8_rep2

description:
Library name: TS603_Veh_p8_9_21_21
TS603_Veh_p8_9_21_21


title: 205307790105_R02C01, Primarytumor, H3_3K27M_PDGFRA_Trp53KO


title: TS603_10nM_p7_rep1

description:
Library name: TS603_10nM_p7_9_12_21
TS603_10nM_p7_9_12_21

value: 10 nM panobinostat for 24 hours


title: 205307790105_R01C01, Primarytumor, H3_3K27M_PDGFRA_Trp53KO


title: 205307790105_R03C01, Primarytumor, H3_3K27M_PDGFRA_Trp53KO


title: TS603_10nM_p9_rep3

description:
Library name: TS603_10nM_p9_9_13_21
TS603_10nM_p9_9_13_21


title: Cell_0980


title: TS603_10nM_p8_rep2

description:
Library name: TS603_10nM_p8_9_21_21
TS603_10nM_p8_9_21_21


title: Cell_1942


title: 205307790105_R06C01, Primarytumor, H3_3K27M_Nf1KO_Trp53KO


title: TB09_Veh_p14_rep3

description:
Library name: TB09_Veh_p14_9_30_21
TB09_Veh_p14_9_30_21


title: 205307790105_R05C01, Primarytumor, H3_3K27M_Nf1KO_Trp53KO


title: Cell_0977


title: 205785610013_R04C02, AllograftP1, H3_3K27M_PDGFRA_Trp53KO


title: 205668270039_R01C02, Primarytumor, H3_3K27M_AtrxKO_Trp53KO


title: Cell_1937

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: Cell_0974


title: Cell_0963


title: Cell_0962


title: Cell_1932


title: S0923_Veh_p9_rep3

description:
Library name: S0923_Veh_p9_4_10_21
S0923_Veh_p9_4_10_21


title: 205307790105_R06C02, Primarytumor, H3_3G34R_PDGFRA_AtrxKO_Trp53KO


title: 205668270029_R03C01, Primarytumor, H3_3K27M_AtrxKO_Trp53KO


title: Cell_0968


title: Cell_0988


title: TB09_Veh_p11_rep1

description:
Library name: TB09_Veh_p11_7_10_21
TB09_Veh_p11_7_10_21


title: TB09_10nM_p14_rep2

description:
Library name: TB09_10nM_p14_8_25_21
TB09_10nM_p14_8_25_21


title: TB09_10nM_p14_rep3

description:
Library name: TB09_10nM_p14_9_30_21
TB09_10nM_p14_9_30_21


title: 205307790105_R05C02, Primarytumor, H3_3G34R_PDGFRA_AtrxKO_Trp53KO


title: Cell_1933

description: SmartSeq2_Gene_log_normalized_counts.rds


title: Cell_1934


title: Cell_0961


title: 205307790105_R04C01, Primarytumor, H3_3K27M_Nf1KO_Trp53KO


title: 205307790105_R04C02, Primarytumor, H3_3G34R_PDGFRA_AtrxKO_Trp53KO


title: Cell_0959


title: Cell_1939


title: Cell_1938


title: Cell_1929


title: TB09_Veh_p14_rep2

description:
Library name: TB09_Veh_p14_8_25_21
TB09_Veh_p14_8_25_21


title: Cell_0978


title: Cell_1941


title: S0923_Veh_p8_rep2

description:
Library name: S0923_Veh_p8_9_5_21
S0923_Veh_p8_9_5_21


title: TB09_10nM_p11_rep1

description:
Library name: TB09_10nM_p11_7_10_21
TB09_10nM_p11_7_10_21


title: S0923_Veh_p8_rep1

description:
Library name: S0923_Veh_p8_8_1_21
S0923_Veh_p8_8_1_21


title: Cell_0957


title: 205489430007_R03C02, Primarytumor, p53_NF1_PTEN


title: S0923_10nM_p9_rep3

description:
Library name: S0923_10nM_p9_4_10_21
S0923_10nM_p9_4_10_21


title: Cell_1927


title: Cell_1931


title: Cell_1928


title: Cell_0956


title: Cell_1926


title: Cell_0955


title: S0923_10nM_p8_rep1

description:
Library name: S0923_10nM_p8_8_1_21
S0923_10nM_p8_8_1_21


title: Cell_0954


title: Cell_1925


title: S0905_Veh_p8_rep3

description:
Library name: S0905_Veh_p8_5_20_21
S0905_Veh_p8_5_20_21


title: S0923_10nM_p8_rep2

description:
Library name: S0923_10nM_p8_9_5_21
S0923_10nM_p8_9_5_21


title: Cell_0953


title: Cell_1921


title: 205668270008_R02C01, Primarytumor, p53_NF1_PTEN


title: 205489430007_R01C01, Primarytumor, p53_NF1_PTEN


title: S0905_Veh_p13_rep2

description:
Library name: S0905_Veh_p13_9_7_21
S0905_Veh_p13_9_7_21


title: 205489430007_R02C01, Primarytumor, p53_NF1_PTEN


title: 205537640001_R04C01, Primarytumor, hGFAP_cre_P53


title: S0905_Veh_p13_rep1

description:
Library name: S0905_Veh_p13_9_6_21
S0905_Veh_p13_9_6_21


title: Cell_0939


title: Cell_0938


title: 205537640001_R06C01, Primarytumor, hGFAP_cre_P53


title: 205537640001_R01C01, Primarytumor, hGFAP_cre_P53


title: Cell_1918


title: S0905_10nM_p8_rep3

description:
Library name: S0905_10nM_p8_5_20_21
S0905_10nM_p8_5_20_21


title: 205333480031_R03C01, Primarytumor, hGFAP_cre_CtnnB1_SmoM2


title: Cell_0937


title: Cell_1916

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: S0905_10nM_p13_rep2

description:
Library name: S0905_10nM_p13_9_7_21
S0905_10nM_p13_9_7_21


title: 205333480031_R02C01, Primarytumor, hGFAP_cre_CtnnB1_SmoM2


title: Cell_1915


title: S0905_10nM_p13_rep1

description:
Library name: S0905_10nM_p13_9_6_21
S0905_10nM_p13_9_6_21


title: 205307790110_R06C01, Primarytumor, hGFAP_cre_CtnnB1_SmoM2


title: Cell_0936


title: 205333480031_R01C01, Primarytumor, hGFAP_cre_CtnnB1_SmoM2


title: S0827_Veh_p9_rep3

description:
Library name: S0827_Veh_p9_4_10_21
S0827_Veh_p9_4_10_21

value: IDH1/2 wildtype


title: Cell_0935


title: S0827_Veh_p10_rep2

description:
Library name: S0827_Veh_p10_9_3_21
S0827_Veh_p10_9_3_21


title: Cell_1917

description: SmartSeq2_Gene_log_normalized_counts.rds


title: Cell_0933


title: S0827_Veh_p10_rep1

description:
Library name: S0827_Veh_p10_8_1_21
S0827_Veh_p10_8_1_21


title: Cell_1913


title: 205307790110_R01C02, Primarytumor, hGFAP_cre_CtnnB1_SmoM2


title: Cell_0934


title: Cell_1910


title: Cell_0932


title: Cell_1912


title: S0827_10nM_p9_rep3

description:
Library name: S0827_10nM_p9_4_10_21
S0827_10nM_p9_4_10_21


title: Cell_1911


title: Cell_1909


title: 205333480098_R03C01, Primarytumor, KrasG12V_sg_P53


title: S0827_10nM_p10_rep2

description:
Library name: S0827_10nM_p10_9_3_21
S0827_10nM_p10_9_3_21


title: Cell_0931


title: 205333480098_R02C01, Primarytumor, KrasG12V_sg_P53


title: Cell_0930


title: 205333480098_R01C01, Primarytumor, KrasG12V_sg_P53


title: S0827_10nM_p10_rep1

description:
Library name: S0827_10nM_p10_8_1_21
S0827_10nM_p10_8_1_21


title: Cell_0929


title: 205307790110_R05C01, Primarytumor, hGFAP_cre_CtnnB1_SmoM2


title: Cell_1906


title: 205291550050_R02C01, Primarytumor, KrasG12V_sg_P53


title: 205291550050_R01C01, Primarytumor, KrasG12V_sg_P53


title: S0211_Veh_p12_rep2

description:
Library name: S0211_Veh_p12_6_13_21
S0211_Veh_p12_6_13_21


title: Cell_0927


title: 205291550046_R06C01, Primarytumor, KrasG12V_sg_P53


title: S0211_Veh_p10_rep1

description:
Library name: S0211_Veh_p10_9_20_21
S0211_Veh_p10_9_20_21


title: Cell_0926


title: 205291550046_R05C01, Primarytumor, KrasG12V_sg_P53


title: Cell_0925


title: S0211_10nM_p12_rep2

description:
Library name: S0211_10nM_p12_6_13_21
S0211_10nM_p12_6_13_21


title: 205291550046_R04C01, Primarytumor, KrasG12V_sg_P53


title: Cell_1901


title: Cell_1903


title: Cell_0924


title: Cell_1900


title: 205291550046_R03C01, Primarytumor, KrasG12V_sg_P53


title: S0211_10nM_p10_rep1

description:
Library name: S0211_10nM_p10_9_20_21
S0211_10nM_p10_9_20_21


title: Cell_0923


title: Cell_1907


title: S0211_Veh_p9_rep3

description:
Library name: S0211_Veh_p9_9_13_21
S0211_Veh_p9_9_13_21


title: Cell_1899


title: GBM43_Veh_8p6_rep3

description:
Library name: GBM43_Veh_8p6_4_10_21
GBM43_Veh_8p6_4_10_21


title: Cell_0928


title: GBM43_Veh_7p4_rep2

description:
Library name: GBM43_Veh_7p4_9_3_21
GBM43_Veh_7p4_9_3_21


title: Cell_1898


title: Cell_0922


title: Cell_1905


title: 205291550046_R01C01, Primarytumor, KrasG12V_sg_P53


title: Cell_1904


title: 206448030014_R01C01, SAM3DP6, KrasG12V_P53


title: Cell_1896

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: GBM43_Veh_7p4_rep1

description:
Library name: GBM43_Veh_7p4_8_1_21
GBM43_Veh_7p4_8_1_21


title: Cell_0920


title: Cell_0921


title: S0211_10nM_p9_rep3

description:
Library name: S0211_10nM_p9_9_13_21
S0211_10nM_p9_9_13_21


title: 206448030004_R06C02, SAM2DP6, KrasG12V_P53


title: Cell_0918


title: 206448030004_R05C02, SAMprimaryfragments, KrasG12V_P53

value: SAMprimaryfragments


title: Cell_0916


title: GBM43_10nM_8p6_rep3

description:
Library name: GBM43_10nM_8p6_4_10_21
GBM43_10nM_8p6_4_10_21


title: 206448030004_R04C02, SAMprimarycells, KrasG12V_P53

source_name: SAMprimarycells

value: SAMprimarycells


title: Cell_1893


title: GBM43_10nM_7p4_rep2

description:
Library name: GBM43_10nM_7p4_9_3_21
GBM43_10nM_7p4_9_3_21


title: Cell_1892


title: Cell_0859

description: SmartSeq2_Gene_log_normalized_counts.rds


title: 205291550046_R02C01, Primarytumor, KrasG12V_sg_P53


title: Cell_1890


title: GBM12_Veh_8p7_rep3

description:
Library name: GBM12_Veh_8p7_4_14_21
GBM12_Veh_8p7_4_14_21


title: Cell_0858


title: 206448030004_R02C02, 2Dcellline, KrasG12V_P53


title: Cell_1888


title: Cell_0857


title: Cell_1887


title: GBM12_Veh_8p2_rep1

description:
Library name: GBM12_Veh_8p2_8_1_21
GBM12_Veh_8p2_8_1_21


title: Cell_1895


title: 206448030004_R01C02, Primarytumor, KrasG12V_P53


title: Cell_0854


title: GBM12_10nM_8p2_rep2

description:
Library name: GBM12_10nM_8p2_9_3_21
GBM12_10nM_8p2_9_3_21


title: 206448030002_R02C02, Primarytumor, KrasG12V_P53


title: Cell_1886


title: Cell_1885


title: GBM43_10nM_7p4_rep1

description:
Library name: GBM43_10nM_7p4_8_1_21
GBM43_10nM_7p4_8_1_21


title: GBM12_10nM_8p7_rep3

description:
Library name: GBM12_10nM_8p7_4_14_21
GBM12_10nM_8p7_4_14_21


title: 205489430003_R04C01, Primarytumor, KrasG12V_BCOR


title: Cell_0846


title: Cell_1884


title: Cell_1883


title: 205291550050_R04C01, Primarytumor, KrasG12V_BCOR


title: BT142_Veh_p15_rep3

description:
Library name: BT142_Veh_p15_8_25_21
BT142_Veh_p15_8_25_21


title: GBM12_10nM_8p2_rep1

description:
Library name: GBM12_10nM_8p2_8_1_21
GBM12_10nM_8p2_8_1_21


title: 205291550046_R06C02, Primarytumor, KrasG12V_BCOR


title: 206448030004_R03C02, 3Dcellline, KrasG12V_P53


title: GBM12_Veh_8p2_rep2

description:
Library name: GBM12_Veh_8p2_9_3_21
GBM12_Veh_8p2_9_3_21


title: Cell_0845


title: Cell_1882


title: BT142_Veh_p12_rep2

description:
Library name: BT142_Veh_p12_9_30_21
BT142_Veh_p12_9_30_21


title: 205291550046_R05C02, Primarytumor, KrasG12V_BCOR


title: Cell_0841


title: 205291550046_R04C02, Primarytumor, KrasG12V_BCOR


title: Cell_1881


title: BT142_Veh_p12_rep1

description:
Library name: BT142_Veh_p12_7_10_21
BT142_Veh_p12_7_10_21


title: Cell_0856


title: Cell_1880


title: BT142_10nM_p15_rep3

description:
Library name: BT142_10nM_p15_8_25_21
BT142_10nM_p15_8_25_21


title: Cell_0853


title: Cell_0839


title: 205537640004_R03C01, Primarytumor, ZFTA_YAP1


title: 205537640004_R02C01, Primarytumor, ZFTA_YAP1


title: Cell_0832


title: BT142_10nM_p12_rep2

description:
Library name: BT142_10nM_p12_9_30_21
BT142_10nM_p12_9_30_21


title: Cell_1876

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: Cell_1874


title: 205537640004_R01C01, Primarytumor, ZFTA_YAP1


title: Cell_0831


title: Cell_0830


title: Cell_1873


title: BT142_10nM_p12_rep1

description:
Library name: BT142_10nM_p12_7_10_21
BT142_10nM_p12_7_10_21


title: 204934870001_R06C01, Primarytumor, ZFTA_NCOA2


title: Cell_1872


title: 204934870001_R02C02, Primarytumor, ZFTA_NCOA2


title: Cell_0822


title: Cell_1870


title: BT142 Pooled Input

description: Library name: BT142 Pooled Input

data_processing:
Quality control was performed using Trim Galore v 0.4.4, Cutadapt v1.14, and FastQC v 0.14.1
Sequences were aligned using bowtie2 v 2.5.4 to the hg38 genome in addition to the Drosophila genome
Peaks were called using MACS2 vs 2.2.9.1 and differential peaks were identfied using DiffBind v 3.18.0
All processed BigWig files are normalized to the Drosophila spike-in chromatin
Assembly: Hg38
Supplementary files format and content: BigWig

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes. Formaldehyde was quneched, cells were lysed, and samples sonicated in a Q800R3 sonicator (Qsonica)
Library's were prepared using Active Motif's ChIP-IT High Sensitivity Kit with Active Motif's Drosophila Spike-in chromatin and Spike-in Antibody for normalization.

value: glioma stem-like cells

value: DMSO Vehicle for 24 hours


title: 204934870001_R01C02, Primarytumor, ZFTA_NCOA2


title: 905 Pooled Input

description: Library name: 905 Pooled Input


title: Cell_0840


title: 923 Pooled Input

description: Library name: 923 Pooled Input


title: Cell_1869


title: 204934870001_R06C02, Primarytumor, ZFTA_MAML3


title: 827 Pooled Input

description: Library name: 827 Pooled Input


title: Cell_0820


title: Cell_0821


title: 204934870001_R05C02, Primarytumor, ZFTA_MAML3


title: Cell_1868


title: Cell_0813


title: BT142 p12 Pano rep3

description: Library name: BT142 p12 Pano

value: 10 nM Panobinostat for 24 hours


title: Cell_1867


title: 204934870001_R04C02, Primarytumor, ZFTA_MAML3


title: Cell_0812


title: BT142 p12 Veh rep3

description: Library name: BT142 p12 Veh


title: BT142 p13 Pano rep2

description: Library name: BT142 p13 Pano


title: Cell_0810


title: Cell_1865


title: Cell_0802


title: 204934870001_R04C01, Primarytumor, ZFTA_MAML2


title: BT142 p13 Veh rep2

description: Library name: BT142 p13 Veh


title: 204934870001_R03C01, Primarytumor, ZFTA_MAML2


title: BT142 p14 Pano rep1

description: Library name: BT142 p14 Pano


title: Cell_1862


title: 205537640006_R06C01, Culture, ST_EPN_RELA

value: Culture


title: Cell_1861


title: Cell_0801


title: Cell_0800


title: Cell_1859


title: 205537640006_R05C01, Culture, ST_EPN_RELA


title: 905 p8 Pano rep3

description: Library name: 905 p8 Pano


title: Cell_0794


title: 905 p8 Veh rep3

description: Library name: 905 p8 Veh


title: Cell_1854


title: 205537640006_R04C01, Culture, ST_EPN_RELA


title: 205537640006_R03C01, Culture, ST_EPN_RELA


title: 905 p13 Pano rep2

description: Library name: 905 p13 Pano


title: Cell_1866


title: 204934870001_R05C01, Primarytumor, ZFTA_MAML2


title: Cell_0793


title: Cell_1853


title: 905 p13 Veh rep2

description: Library name: 905 p13 Veh


title: 205537640006_R02C02, Culture, ST_EPN_RELA


title: 205537640006_R02C01, Culture, ST_EPN_RELA


title: Cell_0665


title: Cell_0666


title: Cell_1849


title: 205537640006_R01C02, Culture, ST_EPN_RELA


title: 905 p9 Pano rep1

description: Library name: 905 p9 Pano


title: Cell_1848


title: BT142 p14 Veh rep1

description: Library name: BT142 p14 Veh


title: Cell_0655


title: Cell_1847


title: 205537640006_R01C01, Culture, ST_EPN_RELA


title: Cell_0656


title: 923 p7 Pano rep3

description: Library name: 923 p7 Pano


title: 923 p7 Veh rep3

description: Library name: 923 p7 Veh


title: 205537640004_R06C02, Culture, ST_EPN_RELA


title: Cell_0654


title: Cell_0653


title: Cell_1852


title: 923 p9 Pano rep2

description: Library name: 923 p9 Pano


title: 905 p9 Veh rep1

description: Library name: 905 p9 Veh


title: 205537640004_R06C01, Allograft, ST_EPN_RELA

value: Allograft


title: Cell_1845


title: 205537640004_R05C02, Allograft, ST_EPN_RELA


title: 923 p9 Veh rep2

description: Library name: 923 p9 Veh


title: Cell_1842


title: Cell_0644


title: Cell_1843


title: Cell_0643


title: 205537640004_R05C01, Allograft, ST_EPN_RELA


title: Cell_0642


title: 205537640004_R04C02, Allograft, ST_EPN_RELA


title: 923 p11 Veh rep1

description: Library name: 923 p11 Veh


title: Cell_1840


title: Cell_1838


title: 827 p7 Pano rep3

description: Library name: 827 p7 Pano


title: Cell_0641


title: Cell_1846


title: 205537640004_R04C01, Allograft, ST_EPN_RELA


title: Cell_1837


title: 205537640004_R03C02, Primarytumor, ST_EPN_RELA


title: 827 p7 Veh rep3

description: Library name: 827 p7 Veh


title: Cell_0631


title: Cell_0626


title: Cell_1835


title: 205537640004_R02C02, Allograft, ST_EPN_RELA


title: Cell_0625


title: 827 p9 Pano rep2

description: Library name: 827 p9 Pano


title: 205537640004_R01C02, Primarytumor, ST_EPN_RELA


title: Cell_1833


title: Cell_1834


title: Cell_0620


title: 827 p9 Veh rep2

description: Library name: 827 p9 Veh


title: 923 p11 Pano rep1

description: Library name: 923 p11 Pano


title: 827 p10 Pano rep1

description: Library name: 827 p10 Pano


title: 205489430007_R04C01, Primarytumor, ST_EPN_RELA


title: 827 p10 Veh rep1

description: Library name: 827 p10 Veh


title: 204934870001_R03C02, Primarytumor, ST_EPN_RELA


title: Cell_0618


title: Cell_0619


title: Cell_1831


title: 204934870001_R02C01, Primarytumor, ST_EPN_YAP1


title: Cell_1829


title: 11391 LOW FAT DIET MALE baseline urothelium

city: Columbus

first: John

middle: David

last: Spencer

state: OH

address: 700 Children's Drive

institute: Nationwide Children's Hospital

data_processing:
Individual FASTQ files were trimmed for adapter sequences and filtered for a minimum quality score of Q20 using AdapterRemoval v2.2.0
Preliminary alignment using HISAT2 v2.0.6 (48) was performed to a composite reference of rRNA, mtDNA, and PhiX bacteriophage sequences obtained from NCBI RefSeq (49). Reads aligning to these references were excluded in subsequent analyses. Primary alignment was performed against the mouse genome reference GRCm38p4 using HISAT2.
Gene expression values for genes described by the GENCODE (50, 51) Gene Transfer Format (GTF) release M14 (mouse) were quantified using the featureCounts tool of the Subread package v1.5.1 (52, 53) in unstranded mode.
Quality control was performed using a modification of the QuaCRS custom workflow (54). In brief, aligned read quality was verified using RNA-SeQC (55) and RSeQC (56). The exonic rate (the percentage of reads aligning to exons), intronic rate (the percentage of reads aligning to introns), and duplication rate (the percentage of reads that were identified as PCR duplicates) were evaluated.
Coverage depths across the aligned reference were calculated with a per-base resolution using the ‘genomecov’ utility tool of Bedtools v2.27.0 (57) in BedGraph format. These files were used as input into CLEAR: a gene-by-gene analysis workflow to identify robust genes in ultra-low input RNA-seq data for downstream analyses. Determination of analysis-ready CLEAR transcripts was done as outlined in (58).
Assembly: mm10
Supplementary files format and content: comma-separated values file include CLEAR count values for each sample
Supplementary files format and content: n/a

source_name: bladder urothelium

growth_protocol: Mice were maintained on low fat or high fat rodent chow ad libitum with free access to water under controlled temperature and humidity with twelve-hour light and dark cycles.

extract_protocol:
The NucleoSpin RNA Plus XS Kit was used to extract RNA on enriched IC and PC fractions following the manufacturer’s instruction, with one modification: DNase digestion was performed in solution using DNase I. Urothelium samples were isolated mechanically from mouse bladders and RNA was isolated using Qiagen RNeasy Miniprep kit. RNA integrity was measured using Agilent 2100 Bioanalyzer with RNA pico chip. Samples with RNA integrity scores > 7 were used for RNA sequencing.
1 ng of RNA was preamplified using the Takara Clontech SMARTer v4 kit and RNA sequencing libraries were generated with the Illumina Nextera XT DNA Library Prep Kit. Samples were sequenced to a depth of 15–20 million 2 × 150 bp clusters on the Illumina HiSeq 4000 platform.

treatment_protocol: Mice were anesthetized with isoflurane prior to transurethral infection with 10^8 CFU UTI89 suspended in 50 uL sterile PBS, or sham infected with 50 uL sterile PBS. Following infection, mice were euthanized at 6 hours post infection.

value: bladder urothelium

tag: Sex

value: MALE

value: urothelial cell

value: low fat diet, sham infection with sterile PBS

tag: timepoint

value: baseline


title: 204934870001_R01C01, Primarytumor, ST_EPN_YAP1