title: MYCN-amp/FGFR1-N546K, mouse2149

description: Library name: FISCH_02149

value: R26.FSF.FGFR1-N546K tg/wt, Th-IRES Cre tg/wt; Th-MYCN tg/wt


title: pre.7

status: Public on Jan 28 2026

type: SRA

city: Stockholm

first: Carolina

last: Nylén

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

description: Library name: P30460_1013_S120_L007_Aligned.sortedByCoord.out.bam

library_source: transcriptomic

data_processing:
Quality and adapter trimming of reads was performed using Cutadapt (v3·5). Sample quality was assessed using FastQC (v0·11·8) and MultiQC (v1·14). Reads were aligned to the Ensembl GRCh38/GRCm38 reference genome using STAR (v2·7·9d). Counts for each gene were obtained using featureCounts (v1·5·1).
Assembly: Ensembl GRCh38/GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

molecule: total RNA

organism: Homo sapiens

source_name: Vastus lateralis

extract_protocol:
Total RNA from skeletal muscle biopsies was isolated using E.Z.N.A. Total RNA Kit I, #R6834-02, Omega Bio-Tek, USA, and treated with E.Z.N.A. Tissue DNA kit, #D3396-02, Omega Bio-Tek, USA.
Libraries were generated using TruSeq Stranded Total RNA (Illumina) and sequenced on an Illumina Novaseq 6000 Sequencing System (Illumina).

tag: tissue

value: Vastus lateralis

tag: Sex

value: Female

tag: subjectid

tag: age

tag: time point

value: pre


title: pre.10

description: Library name: P30460_1018_S125_L007_Aligned.sortedByCoord.out.bam


title: post.8

description: Library name: P30460_1014_S121_L007_Aligned.sortedByCoord.out.bam

value: post


title: post.6

description: Library name: P30460_1010_S117_L007_Aligned.sortedByCoord.out.bam


title: pre.4

description: Library name: P30460_1007_S114_L007_Aligned.sortedByCoord.out.bam


title: MYCN-amp/FGFR1-N546K, mouse17

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

country: Germany

institute: University Children’s Hospital of Cologne

description: Library name: FIM_00017

data_processing:
Quantification of RNA sequencing data was carried out using Kallisto (version 0.44.0) with parameters --bootstrap-samples 100 --bias, and the GRCm38 reference genome. Raw Kallisto transcript level read counts were transformed to gene level counts using the R package tximport (version 1.20.0).
Normalization of Kallisto gene level read counts and further processing was carried out in R (version 4.2.2) using the package DESeq2 (version 1.32.0). Only genes with at least 10 reads in 8 mice were used for further analysis (8 being the size of the smallest subgroup of mice).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw read counts for each mouse
Supplementary files format and content: tab-delimited text file includes DESeq2 VST expression values for each mouse

organism: Mus musculus

source_name: Tumor

extract_protocol:
RNA isolation from fresh-frozen tissue was performed with TRIzol (Ambion). RNA concentration was measured by QubitTM Assay (Invitrogen) and quality was assessed by 2100 Bioanalzyer (Agilent).
Libraries were prepared using the Illumina Stranded TruSeq RNA sample preparation Kit. After library validation and quantification (Agilent Tape Station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

value: Tumor

tag: genotype


title: pre.3

description: Library name: P30460_1005_S112_L007_Aligned.sortedByCoord.out.bam


title: MYCN-nonamp/FGFR1-N546K, mouse_T11_6d

description: Library name: T11_6d

value: R26.FSF.FGFR1-N546K tg/wt, Th-IRES Cre tg/wt


title: MYCN-amp/FGFR1-N546K, mouse2138

description: Library name: FISCH_02138


title: pre.6

description: Library name: P30460_1011_S118_L007_Aligned.sortedByCoord.out.bam


title: pre.8

description: Library name: P30460_1015_S122_L007_Aligned.sortedByCoord.out.bam


title: MYCN-amp/FGFR1-N546K, mouse84 kidney

description: Library name: FIM_00084_kidney


title: MYCN-amp/FGFR1-N546K, mouse84 pelvis

description: Library name: FIM_00084_pelvis


title: Rab37 KO CD45+, lung tumor

city: Tainan

first: You-En

last: Yang

address: No.1, University Road, Tainan 701

department: Department of Pharmacology

country: Taiwan

institute: National Cheng Kung University

description:
Library name: Tumor_Rab37_KO
10X Genomics

library_source: transcriptomic single cell

data_processing:
Libraries were prepared using the Chromium Single Cell 3’ Reagent Kit v2 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
The isolated lung tumors from WT and Rab37 KO mice were minced into small fragments (~1 mm³) in ice-cold HBSS and resuspended in digestion buffer (HBSS with Mg²⁺/Ca²⁺ supplemented with 2 mg/ml collagenase type I and 40 U/ml Dispase I). Samples were incubated at 37 °C for 30 min with gentle agitation. The digested tissue was passed through a 70-µm cell strainer, washed and resuspended in PBS, and red blood cells were removed using RBC lysis buffer when necessary. Cells were then stained with a fixable Viability Dye and fluorochrome-conjugated anti-CD45 antibody for 20 min at 4 °C, washed, and resuspended in FACS buffer (HBSS without Ca²⁺/Mg²⁺, 2% v/v FCS, 5 mM EDTA). Live CD45⁺ cells were sorted from WT and Rab37 KO normal lung tissue or tumors on a FACS  using unstained and fluorescence-minus-one controls from C57BL/6 mice as negative controls. Sorted CD45⁺ cells were washed in HBSS-/- and finally resuspended in HBSS-/- supplemented with 0.04% w/v BSA at an appropriate concentration for single-cell RNA-seq library preparation.
Single-cell RNA-seq libraries were generated using the Chromium Single Cell 3′ Reagent Kits v2 (10x Genomics) according to the manufacturer’s instructions. Briefly, sorted live CD45⁺ cells from WT and Rab37 KO lung tumors were resuspended in the 10x master mix and loaded onto a Chromium chip together with partitioning oil and barcoded gel beads to produce gel bead-in-emulsions (GEMs). Within each GEM, cell lysis occurred and poly-A RNA was reverse-transcribed into cDNA carrying an Illumina Read 1 (R1) primer sequence, a Unique Molecular Identifier (UMI), and a 10x cell barcode. Barcoded cDNA from all GEMs was then pooled, cleaned up with Silane DynaBeads, and amplified by PCR. Appropriately sized cDNA fragments were selected using SPRIselect reagent and used for library construction. During library preparation, Illumina Read 2 (R2) primer sequence, paired-end constructs containing P5 and P7 adapter sequences, and a sample index were added to generate the final sequencing-ready libraries.

value: Lung

tag: cell type

value: immune cells

value: Rab37 KO


title: MYCN-amp/FGFR1-N546K, mouse23 pelvis

description: Library name: FIM_00023_pelvis


title: post.5

description: Library name: P30460_1008_S115_L007_Aligned.sortedByCoord.out.bam


title: Rab37 KO CD45+, normal lung

description:
Library name: Normal_Rab37_KO
10X Genomics


title: Glima3-IP

city: Jinan

first: Shun

last: Wang

address: BEIYUAN road 247

country: China

institute: The Second Hospital of Shandong University

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences, remaining reads were then aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”.
Differential m6A peak were identified using exomePeak R package under parameters:
“PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200” . GO and KEGG analysis were performed using clusterProfiler R package (v3.6.0).
m6A-RNA-related genomic features were visualized using Guitar R package (v1.16.0).
Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Assembly: GRCh38
Supplementary files format and content: All.count.txt

source_name: glioma tissue

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018).
The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). 100μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The reaction was stopped by adding 10X EDTA (0.5M EDTA). Methylated RNA immunoprecipitation was performed using EpiTM m6A immunoprecipitation kit (Epibiotek, R1804). Briefly, the fragmented RNA was incubated with anti-m6A monoclonal antibody (abcam,ab208577) for 3 h at 4℃ and then with protein A/G magnetic beads (Invitrogen, 8880210002D/10004D) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was purified using TRIzol™ Reagent (Invitrogen, 15596018). The library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequence.

value: glioma tissue

tag: antibody

value: m6A RNA


title: MYCN-amp/FGFR1-N546K, mouse36 kidney

description: Library name: FIM_00036_kidney


title: MYCN-amp/FGFR1-N546K, mouse23 kidney

description: Library name: FIM_00023_kidney


title: post.7

description: Library name: P30460_1012_S119_L007_Aligned.sortedByCoord.out.bam


title: pre.9

description: Library name: P30460_1016_S123_L007_Aligned.sortedByCoord.out.bam


title: pre.5

description: Library name: P30460_1009_S116_L007_Aligned.sortedByCoord.out.bam


title: post.3

description: Library name: P30460_1004_S111_L007_Aligned.sortedByCoord.out.bam


title: Glima2-input


title: post.4

description: Library name: P30460_1006_S113_L007_Aligned.sortedByCoord.out.bam


title: cerebral cortex 4-week wild-type male 4

city: Bar Harbor

first: Robert

last: Burgess

state: ME

address: 600 Main St

country: USA

institute: The Jackson Laboratory

description: Library name: GT21-31054

data_processing:
Analysis of RNAseq data in fastq format was performed using an open source Nextflow pipeline (v3.5) at The Jackson Laboratory comprised of tools to perform read quality assessment, alignment, and quantification (Ewels et al., 2020). The pipeline takes as input fastq files for a single sample and outputs read alignment counts.  FastQC (0.11.9) was used for quality checks and Trim Galore (0.6.7) was used to remove adapters and sequences with low quality (Fred<20). Sequence reads that passed quality control were aligned to mouse reference (GRCm38) using STAR (v2.7) and gene expression estimates were made using RSEM (v1.3) with default parameters. Differential expression analysis was performed using a differential expression script in R developed by Computational Sciences at The Jackson Laboratory based on the EdgeR package (Robinson et al., 2010). We selected FDR <0.05 and absolute Log2FC >0.5 as cutoffs for differential expression.
Assembly: GRCm38
Supplementary files format and content: Table format (gene expression counts)

source_name: cerebral cortex

growth_protocol: All mice were kept under standard housing and husbandry conditions with food and water provided ad libitum and 12/12 hour light/dark cycles. All control and mutant mice were on a C57BL/6J background. Control mice for all mutants were either wild-type littermates or age-matched C57BL/6J mice from the same colony and housed together.

extract_protocol:
Total RNA was isolated from tissue using the NucleoMag RNA Kit (Macherey-Nagel) and the KingFisher Flex purification system (ThermoFisher). Tissues were homogenized in MR1 buffer (Macherey-Nagel) using a gentleMACS dissociator (Miltenyi Biotec Inc).  RNA isolation was performed according to the manufacturer’s protocol. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA ScreenTape Assay (Agilent Technologies).
Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions.

treatment_protocol: homozygous mutant mice lacking the Pcdhgc5 gene were compared to wild type littermates

value: cerebral cortex

value: wild-type male


title: MYCN-nonamp/FGFR1-N546K, mouse_T12_6d

description: Library name: T12_6d


title: WT CD45+, lung tumor

description:
Library name: Tumor_WT
10X Genomics

value: WT


title: MYCN-amp/FGFR1-N546K, mouse36 pelvis

description: Library name: FIM_00036_pelvis


title: MYCN-amp/FGFR1-N546K, mouse18

description: Library name: FIM_00018


title: MYCN-amp/FGFR1-N546K, mouse15

description: Library name: FIM_00015


title: cerebral cortex 4-week wild-type male 3

description: Library name: GT21-31052


title: cerebral cortex 4-week mutant female 3

description: Library name: GT21-31051

value: homozygous mutant female


title: pre.2

description: Library name: P30460_1003_S110_L007_Aligned.sortedByCoord.out.bam


title: WT CD45+, normal lung

description:
Library name: Normal_WT
10X Genomics


title: Nomal2-IP

value: Normal


title: pre.1

description: Library name: P30460_1002_S109_L007_Aligned.sortedByCoord.out.bam


title: cerebral cortex 4-week wild-type male 5

description: Library name: GT21-31055


title: cerebral cortex 4-week mutant male 3

description: Library name: GT21-31056

value: homozygous mutant male


title: Nomal2-input


title: Nomal1-IP


title: Nomal3-Input


title: cerebral cortex 4-week mutant male 1

description: Library name: GT21-31049


title: AngII+ML264

city: Shijiazhuang

first: siming

last: Bu

state: CHINA

address: Zhongshan East Road

institute: Hebei Medical university

description: Library name: AngII+ML264

library_source: genomic

data_processing:
Jointly models the non-uniform coverage and genomic distance scaling of contact counts to compute statistical significance estimates. In order to show the specific loop structure, we need to combine Enhance/Superenhancer of the database to peaks quantification of loop region. HiC Plotter can draw maps of all chromosomes with different resolutions. The “all.validpair” files generated after HiC-Pro processing were converted into “hic” file, which can be visualized by juicebox.
Assembly: mm10
Supplementary files format and content: AngII+ML264.hic
Supplementary files format and content: AngII.hic
Library strategy: HiChIP

molecule: genomic DNA

source_name: VSMCs

extract_protocol:
The HiChIP-seq protocol was conducted and H3K27ac (Invitrogen, PA5-85524, 9 μL per ChIP) antibody was used in vehicle control and Klf5 inhibitor ML264-pretreated mouse VSMCs under AngII treatment (10-7 mol/L). Briefly, cells were cross-linked in 1.5% formaldehyde and were pelleted, washed and centrifugation.
Capture HiChIP processing FASTQ files (paired-end Illumina data) were processed with the HiC-Pro v2.11.1 using Bowtie2 v2.3.5.1 for mapping short reads to the reference genome mm10 / hg19. After the mapping, filtering and deduplication steps of the HiC-Pro pipeline, normalized matrices were generated at 500 kb, or 10 kb resolutions. A large number of loop structures can be identified by Fit HiChIP analysis software.

value: VSMCs


title: RICU220112-2_001A [Thrombocytopenia(-)]

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

institute: TCVGH

data_processing:
sequence reads were mapped to the human reference genome GRCh38 by HISAT2 (version 2.2.0)
Read counts were calculated by featureCounts (Version 2.0.0)
Assembly: GRCh38
Supplementary files format and content: tab delimited text file include raw read counts for each sample

source_name: PBMC

extract_protocol:
PAXgene Blood miRNA Kit
Universal Plus mRNA-Seq library preparation kit with NuQuant

value: PBMC

tag: time

tag: condition

value: Thrombocytopenia(-)

tag: patient


title: cerebral cortex 4-week mutant female 1

description: Library name: GT21-31045


title: sod2_ir2d, male 2

city: Saint Louis

first: Shuhua

last: Fu

state: MO

address: 660 S. Euclid Avenue Campus Box 8103

institute: Washington University in St. Louis

description:
Library name: lib333
sample.146
mm_M_norm_result_k5.txt

data_processing:
Raw reads of RNA-seq libraries were processed using the RNA-seq pipeline (https://github.com/Zhang-lab/RNA-seq_QC_analysis) which consists of data processing, quality control, integrative analysis, and data visualization.
Mouse genome mm10 with STAR version 2.5.4b (Dobin et al., 2013). Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount (version 1.4.6) (Liao et al., 2013), with mm10 gene annotation ENCODE M20.
Assembly: mm10 genome annotation ENCODE M20
Supplementary files format and content: TXT format, readcount table

source_name: Left Ventricle

extract_protocol:
Total RNA was isolated from murine ventricles using TRIzol reagent (Invitrogen), per manufacturer instructions, and DNAse-treated using the TURBO DNA-free Kit (Ambion).
cDNA libraries were constructed using Takara-Clontech SMARTer cDNA kit per manufacterer's instructions.

treatment_protocol: Murine IR treatment was performed using the small animal radiation research platform (SARRP, Xstrahl Inc.). Mice received 25 Gy radiation targetd to the entire heart. Radiation was delivered at a 3.9 Gy/min dose rate in a single fraction of 25 Gy.

value: Left Ventricle

value: male

tag: treatment

value: 2 days post 25 Gy IR


title: Glima2-IP

value: Tumor


title: Glima3-Input


title: Nomal1-input


title: RICU220119-3_002A [Thrombocytopenia(-)]


title: RICU220119-2_002A [Thrombocytopenia(-)]


title: pJT126-flexiNR_D5_JT039_R2_Unbound

city: Stanford

first: Abby

middle: R

last: Thurm

state: CA

address: 443 Via Ortega Rm 036

institute: Stanford University

description: Library name: HT-Prot8

data_processing:
Bowtie2 alignment, log2(OFF:ON) ratio calculation based on counts per fraction, replicate combination
Assembly: custom Bowtie2 index of library members
Supplementary files format and content: .csv files of libray member counts per fraction and normalized log2(OFF:ON) ratios per replicate

growth_protocol: 5% CO2, 37C, RPMI media supplemented with 10% FBS and 1% PSG

extract_protocol:
QiaAmp DNEasy genomic DNA extraction kit
targeted PCR of genomic DNA to produce DNA amplicons

treatment_protocol: 2 or 5 days of doxycycline recruitment

tag: cell line

value: lymphoid


title: Glima1-IP


title: cerebral cortex 4-week mutant female 2

description: Library name: GT21-31047


title: pJT126-flexiNR_D5_JT039_R2_Bound

description: Library name: HT-Prot7


title: post.1

description: Library name: P30460_1001_S108_L007_Aligned.sortedByCoord.out.bam

value: Vastus lateralis

value: Female

value: post


title: RICU220106-1_002A [Thrombocytopenia(-)]


title: cerebral cortex 4-week wild-type male 1

description: Library name: GT21-31048

value: cerebral cortex


title: Nomal3-IP

value: glioma tissue

value: m6A RNA


title: RICU211125-2_002A [Thrombocytopenia(-)]


title: sod2_ir2d, male 1

description:
Library name: lib332
sample.141
mm_M_norm_result_k5.txt


title: AngII

description: Library name: AngII


title: pJT126-flexiNR_D2_DY032_R2_Bound

description: Library name: HT-Prot3


title: RICU211019-1_002A [Thrombocytopenia(-)]


title: pJT126-flexiNR_D2_DY032_R2_Unbound

description: Library name: HT-Prot4


title: cerebral cortex 4-week mutant male 2

description: Library name: GT21-31053


title: sod2_ir2d, female 3

description:
Library name: lib331
sample.136
mm_F_norm_result_k2.txt

value: female


title: Glima1-input


title: WT No Affinity Capture repeat 1, fraction 3

city: Heidelberg

first: Alessia

last: Ruggieri

address: Im Neuenheimer Feld 344

department: Dpt. of Infectious Diseases, Molecular Virology

institute: Heidelberg University

description:
Library name: Sample 10
fractionated total RNA, fraction 3

data_processing:
The 80 nt long single-end reads were first aligned to human rRNA sequences as downloaded from the UCSC Genome Browser using bowtie v1.2.2 (PMID: 19261174).
Reads that did not align to rRNA were further aligned to the human genome (hg38) using STAR v2.5.4b (PMID: 23104886), providing a gtf file with the exonic coordinates of the basic set of Gencode V38.
Finally, reads that did not align to human genomic sequences were aligned to the DENV2 NGC full plasmid sequence with bowtie. In all alignment steps, up to two mismatches were allowed.
Assembly: hg38
Supplementary files format and content: The number of reads that could be successfully aligned in each alignment step (rRNA, hg38, DENV2) and the number of unmapped reads is given in the csv file readCounts.csv.

source_name: liver

growth_protocol: Huh7 cells were maintained at 37 °C, 5% CO2 in Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 10 % fetal calf serum (Capricorn), 1% nonessential amino acids, 100 U/ml penicillin and 100 μg/ml streptomycin (all from Gibco).

extract_protocol:
Total RNA from DENV2-infected Huh7was extracted following the ViREn protocol. Total RNA was subjected to 5-20% sucrose gradient ultracentrifugation, and RNA fractionated. After fractionation, DENV2 sfRNA (in fraction 3) and gRNA (in fraction 11) was postively selected using affinity capture magnetic beads (Element Zero Biolabs).
Sequencing libraries were produced with the NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on a NextSeq550 System (Illumina).

treatment_protocol: DENV2 New Guinea C (NGC) infection MOI of 10 for 48h

value: liver

value: hepatoma cells

value: WT

value: DENV2 New Guinea C infection


title: cerebral cortex 4-week wild-type female 1

description: Library name: GT21-31046

value: wild-type female


title: WT Affinity Capture repeat 2, fraction 3

description:
Library name: Sample 8
DENV gRNA enirched total RNA, fraction 3


title: RICU211230-1_001A [Thrombocytopenia(-)]

value: PBMC

value: Thrombocytopenia(-)


title: pJT126-flexiNR_D2_DY032_R1_Unbound

description: Library name: HT-Prot2


title: cerebral cortex 4-week wild-type male 2

description: Library name: GT21-31050

value: wild-type male


title: sod2_ir2d, female 2

description:
Library name: lib330
sample.131
mm_F_norm_result_k2.txt

value: Left Ventricle

value: 2 days post 25 Gy IR


title: fvb_ir2d, female 3

description:
Library name: lib326
sample.111
mm_F_norm_result_k2.txt


title: RICU220114-1_001A [Thrombocytopenia(-)]


title: pJT126-flexiNR_D5_JT039_R1_Unbound

description: Library name: HT-Prot6

value: lymphoid


title: fvb_ir2d, female 2

description:
Library name: lib325
sample.106
mm_F_norm_result_k2.txt


title: RICU211012-1_001A [Thrombocytopenia(-)]


title: fvb_ir2d, male 1

description:
Library name: lib327
sample.116
mm_M_norm_result_k5.txt

value: male


title: RICU211117-1_001A [Thrombocytopenia(-)]


title: WT No Affinity Capture repeat 3, fraction 11

description:
Library name: Sample 6
fractionated total RNA, fraction 11


title: fvb_ir2d, female 1

description:
Library name: lib324
sample.101
mm_F_norm_result_k2.txt


title: WT No Affinity Capture repeat 3, fraction 3

description:
Library name: Sample 12
fractionated total RNA, fraction 3


title: WT Affinity Capture repeat 3, fraction 11

description:
Library name: Sample 3
DENV gRNA enirched total RNA, fraction 11


title: RICU210604-2_001A [Thrombocytopenia(-)]


title: RICU210406-1_002A [Thrombocytopenia(-)]


title: RICU210930-1_002A [Thrombocytopenia(-)]


title: pJT126-flexiNR_D5_JT039_R1_Bound

description: Library name: HT-Prot5


title: RICU210330-4_001A [Thrombocytopenia(-)]


title: WT Affinity Capture repeat 1, fraction 3

description:
Library name: Sample 7
DENV gRNA enirched total RNA, fraction 3


title: WT Affinity Capture repeat 3, fraction 3

description:
Library name: Sample 9
DENV gRNA enirched total RNA, fraction 3


title: fvb_ir2d, male 2

description:
Library name: lib328
sample.121
mm_M_norm_result_k5.txt


title: H51, unstimulated, natural killer

city: Brisbane

first: Zuleima

last: Pava Imitola

state: Queensland

address: 300 Herston road

country: Australia

institute: QIMR Berghofer

data_processing:
Transcriptomic data was processed using STAR aligner, samtools, and HTSeq
Assembly: GRCh38
Supplementary files format and content: csv file containing the raw counts obtained by Htseq. Columns are libraries rows are genenames

source_name: Natural killer

extract_protocol:
RNA was extracted from isolated cell population lysates using the QIAGEN PicoPureTM RNA isolation kit (Applied Biosystems™, KIT0204)
RNA sequencing libraries were constructed using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (E6420S) and NEBNext® Multiplex Oligos for Illumina®(96 Unique Dual Index Primer Pairs) (E6440S).

tag: sample id

value: Natural killer

value: unstimulated


title: H51, stimulated, natural killer

value: stimulated with P. falciparum


title: RICU210924-1_001A [Thrombocytopenia(-)]


title: H50, unstimulated, natural killer


title: H50, stimulated, natural killer


title: WT No Affinity Capture repeat 2, fraction 3

description:
Library name: Sample 11
fractionated total RNA, fraction 3


title: sod2_ir2d, female 1

description:
Library name: lib329
sample.126
mm_F_norm_result_k2.txt


title: RICU210121-1_001A [Thrombocytopenia(-)]


title: H49, unstimulated, natural killer


title: pJT126-flexiNR_D2_DY032_R1_Bound

description: Library name: HT-Prot1


title: RICU210610-2_002A [Thrombocytopenia(-)]


title: WT No Affinity Capture repeat 2, fraction 11

description:
Library name: Sample 5
fractionated total RNA, fraction 11


title: H49, stimulated, natural killer


title: H44, stimulated, natural killer


title: WT No Affinity Capture repeat 1, fraction 11

description:
Library name: Sample 4
fractionated total RNA, fraction 11


title: sod2_ir6w, male 1

description:
Library name: lib322
sample.91
mm_M_norm_result_k5.txt

value: 6 weeks post 25 Gy IR


title: H44, unstimulated, natural killer


title: RICU201230-2_001A [Thrombocytopenia(-)]


title: fvb_ir6w, male 1

description:
Library name: lib317
sample.66
mm_M_norm_result_k5.txt


title: sod2_ir6w, female 3

description:
Library name: lib321
sample.86
mm_F_norm_result_k2.txt

value: female


title: RICU201230-1_001A [Thrombocytopenia(-)]


title: H41, unstimulated, natural killer


title: WT Affinity Capture repeat 1, fraction 11

description:
Library name: Sample 1
DENV gRNA enirched total RNA, fraction 11

value: liver


title: RICU201223-1_002A [Thrombocytopenia(-)]


title: sod2_ir6w, female 2

description:
Library name: lib320
sample.81
mm_F_norm_result_k2.txt


title: H25, stimulated, natural killer


title: RICU210126-1_002A [Thrombocytopenia(-)]


title: RICU210106-2_002A [Thrombocytopenia(-)]


title: fvb_ir6w, male 2

description:
Library name: lib318
sample.71
mm_M_norm_result_k5.txt


title: RICU201216-1_001A [Thrombocytopenia(-)]


title: H23, stimulated, natural killer


title: RICU210106-1_002A [Thrombocytopenia(-)]


title: H23, unstimulated, natural killer


title: H40, unstimulated, natural killer


title: WT Affinity Capture repeat 2, fraction 11

description:
Library name: Sample 2
DENV gRNA enirched total RNA, fraction 11

value: hepatoma cells


title: sod2_ir6w, male 2

description:
Library name: lib323
sample.96
mm_M_norm_result_k5.txt


title: fvb_ir6w, female 2

description:
Library name: lib315
sample.56
mm_F_norm_result_k2.txt

value: WT


title: sod2_ir6w, female 1

description:
Library name: lib319
sample.76
mm_F_norm_result_k2.txt


title: RICU201215-1_002A [Thrombocytopenia(-)]


title: H41, stimulated, natural killer


title: H48, unstimulated, natural killer


title: H40, stimulated, natural killer


title: H22, stimulated, natural killer


title: H18, unstimulated, natural killer


title: H48, stimulated, natural killer


title: H25, unstimulated, natural killer


title: sod2_sham, male 3

description:
Library name: lib313
sample.46
mm_M_norm_result_k5.txt

value: Sham


title: fvb_ir6w, female 3

description:
Library name: lib316
sample.61
mm_F_norm_result_k2.txt


title: H10, stimulated, natural killer


title: fvb_ir6w, female 1

description:
Library name: lib314
sample.51
mm_F_norm_result_k2.txt


title: H10, unstimulated, natural killer


title: sod2_sham, male 1

description:
Library name: lib311
sample.36
mm_M_norm_result_k5.txt


title: RICU201208-1_001A [Thrombocytopenia(-)]


title: sod2_sham, female 2

description:
Library name: lib310
sample.31
mm_F_norm_result_k2.txt


title: PEO1, sipNC, E2, 8h, 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: siNC_E2_8h-2_S8

data_processing:
QC was performed with MultiQC and reads were trimmed to remove the adapters from reads using cutadapt. RNA-seq data was aligned using bowtie2 algorithm via RSEM V1.3.3 to make estimated expression raw counts.
Assembly: Human Hg19
Supplementary files format and content: RSEM estimated raw counts in text tab delimitted format

growth_protocol: RPMI-1640, 10% FBS, 1% pen/strep.

extract_protocol:
Total RNA was extracted from cells using QIAshredder columns (QIAGEN) and RNeasy Mini kit (QIAGEN), followed by DNase digestion.
Libraries for RNA-seq were prepared using the Quant Seq 3’ mRNA-Seq V2 Library Prep Kit FWD (Lexogen, Vienna, Austria) as per manufacturer’s instructions starting with an input of 200ng of RNA and 16 cycles of final PCR amplification.  Overall library size was determined using the 4200 Tapestation and the High-sensitivity DNA 5000 assay (Agilent, Santa Clara, CA) and libraries were quantitated using the Qubit 2.0 Fluorometer (Thermo Fisher, Waltham, MA).

treatment_protocol: Cells were cultured in phenol red-free media and 10% charcoal-stripped FBS for 48 hours before E2 (10 nM) treatment.

value: Ovarian cancer cell

value: siControl

value: 10 nM E2 8h


title: RICU201125-1_002A [Thrombocytopenia(-)]

value: PBMC

value: Thrombocytopenia(-)


title: PEO1, sipNC, E2, 8h, 3

description: Library name: siNC_E2_8h-3_S9


title: sod2_sham, male 2

description:
Library name: lib312
sample.41
mm_M_norm_result_k5.txt

value: Left Ventricle


title: PEO1, sipNC, E2, 2h, 3

description: Library name: siNC_E2_2h-3_S6

value: 10 nM E2 2h


title: RICU201118-1_001A [Thrombocytopenia(-)]


title: PEO1, sipNC, E2, 8h, 1

description: Library name: siNC_E2_8h-1_S7


title: sod2_sham, female 1

description:
Library name: lib309
sample.26
mm_F_norm_result_k2.txt


title: PEO1, sipNC, E2, 0h, 1

description: Library name: siNC_E2_0h-1_S1

value: unt


title: PEO1, sipNC, E2, 2h, 2

description: Library name: siNC_E2_2h-2_S5


title: RICU201015-1_001A [Thrombocytopenia(-)]


title: H18, stimulated, natural killer

value: Natural killer


title: fvb_sham, male 2

description:
Library name: lib308
sample.21
mm_M_norm_result_k5.txt

value: male


title: RICU201022-1_002A [Thrombocytopenia(-)]


title: fvb_sham, female 3

description:
Library name: lib306
sample.11
mm_F_norm_result_k2.txt


title: PEO1, sip53, E2, 8h, 2

description: Library name: sip53_E2_8h-2_S17


title: PEO1, sipNC, E2, 0h, 2

description: Library name: siNC_E2_0h-2_S2


title: RICU201030-1_002A [Thrombocytopenia(-)]


title: PEO1, sip53, E2, 8h, 3

description: Library name: sip53_E2_8h-3_S18


title: fvb_sham, female 2

description:
Library name: lib305
sample.6
mm_F_norm_result_k2.txt


title: fvb_sham, female 1

description:
Library name: lib304
sample.1
mm_F_norm_result_k2.txt


title: fvb_sham, male 1

description:
Library name: lib307
sample.16
mm_M_norm_result_k5.txt


title: PEO1, sip53, E2, 2h, 3

description: Library name: sip53_E2_2h-3_S15


title: PEO1, sipNC, E2, 2h, 1

description: Library name: siNC_E2_2h-1_S4


title: PEO1, sip53, E2, 8h, 1

description: Library name: sip53_E2_8h-1_S16


title: PEO1, sip53, E2, 2h, 2

description: Library name: sip53_E2_2h-2_S14


title: PEO1, sip53, E2, 0h, 3

description: Library name: sip53_E2_0h-3_S12


title: PEO1, sip53, E2, 2h, 1

description: Library name: sip53_E2_2h-1_S13


title: Fibroblasts, extracted and cultured after radiation,BuOE,rep 2

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Library name: BR-2

data_processing:
Bisulfite-seq methylation data were quality-trimmed using Trim Galore and Cutadapt version 2.9. The filtered data were processed with Bisulfite Mapper and Methylation Caller (Bismark) version 0.24.0, which includes alignments to the GENCODE Mus musculus reference genome and cytosine methylation calls.
These methylation calls were subsequently analyzed using methylKit version 1.30.0 in R version 4.3.0. The methylation calls were filtered by coverage, where bases that have coverage below 10 reads and more than 99.99th percentile of coverage in each sample were discarded.
To remove CpG sites that have no or little variation among samples and are not informative for downstream analyses, data were further filtered with standard deviation filtering on percent methylation values, which is equivalent to Beta values. CpG sites with standard deviations larger than one were kept. Differential methylation analyses were done using a logistic regression for each pairwise comparison of interest with correction for overdispersion, and the Chi-squared test was used for testing between models, and the resulting p-values were adjusted using the Benjamini-Hochberg FDR method.
Differentially methylated sites with adjusted p-values smaller than 0.05 were considered significant.
Assembly: GENCODE M30 (GRCm39)
Supplementary files format and content: Tab-delimited files (per sample) with the following columns: CpG ID, Chromosome number of unplaced scaffold ID, Start locus, End locus, methylation percentage (0 - 100).

source_name: prostate

extract_protocol:
Mice were sacrificed and prostates were removed immediately post-mortem. Organs were briefly minced using a scalpel in Hank’s buffered saline solution (HBSS) without calcium and magnesium, and fragments were centrifuged for 3 minutes at 400xg. Prostate  fragments were resuspended in type I collagenase (Sigma-Aldrich, Saint Louis, MO, SCR103) in HBSS with calcium and magnesium and incubated at 37°C. Every five minutes, fragments were mixed by serially pipetting through a 25 ml, 10 ml, 5 ml, and 2 ml pipette until fragments could pass easily through the 2 ml pipette tip. Fragments were washed twice in HBSS without calcium and magnesium and then cultured using DMEM supplemented with 10% FBS, 1% penicillin/streptomycin, and 1% non-essential amino acids.
At two months post-radiation, fibroblasts were isolated from prostates and cultured for three days. DNA was isolated from fibroblasts using a FitAmp Blood and Cultured Cell DNA extraction kit (Epigentek, P-1018-050) and samples were sent to Epigentek (Farmingdale, NY) for reduced representation bisulfite sequencing (RRBS)

treatment_protocol: 8-10 week old male C57BL/6 mice were obtained from Taconic Biosciences (Germantown, NY). For those mice undergoing radiation, pelvic radiation was performed using an RS 2000 irradiator (Rad Source RS-2000, Buford, GA). Mice were given 37.5 Gy over the course of 5 days in fractions of 7.5 Gy at a dose rate of 1.2 Gy/min. Pelvic radiation was achieved using lead shielding to ensure only the pelvic region received radiation under anesthesia. Mice were regularly observed for potential radiation damage and toxicity throughout the course of the experiment.

value: prostate

value: fibroblasts

value: BuOE and radiation


title: PEO1, sip53, E2, 0h, 2

description: Library name: sip53_E2_0h-2_S11


title: PEO1, sipNC, E2, 0h, 3

description: Library name: siNC_E2_0h-3_S3


title: RICU201013-1_002A [Thrombocytopenia(-)]


title: PEO1, sip53, E2, 0h, 1

description: Library name: sip53_E2_0h-1_S10


title: input-7-PEO1-H3K27AC_ChIP

description: Library name: input-7-PEO1-H3K27AC_S41

data_processing:
Sequencing reads were quality checked with FASTQC (v0.11.9)  and aligned to the GRCh37 (hg19) genome assembly using bowtie2.
HOMER software package was used to call peaks in pull-down samples compared to input samples.
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.

extract_protocol:
10 million cells were crosslinked with 1% formaldehyde for 10 min and quenched with 0.125 M glycine for 10 min. After cell lysis, chromatin was sonicated using a Covaris Ultrasonicator. ChIP DNA was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research).
ChIP DNA was used to prepare libraries for Next Generation Sequencing using the NEBNext Ultra II DNA kit (New England Biolabs, Ipswich, MA), according to manufacturer’s directions. Overall library size was determined using the 4200 Tapestation and the High-sensitivity DNA 5000 assay (Agilent, Santa Clara, CA) and libraries were quantitated using the Qubit 2.0 Fluorometer (Thermofisher, Waltham, MA). Libraries were pooled and Next Generation Sequencing with a paired-end 2x60 bp run length was done on the Nextseq 2000 (Illumina, San Diego, CA).


title: RICU200915-2_002A [Thrombocytopenia(-)]


title: Fibroblasts, extracted and cultured after radiation,BuOE,rep 1

description: Library name: BR-1


title: input-4-PEO1-sip53-E2_ChIP

description: Library name: input-4-PEO1-sip53-E2_S38


title: RICU201023-1_001A [Thrombocytopenia(-)]


title: input-2-PEO1-sip53_ChIP

description: Library name: input-2-PEO1-sip53_S36


title: RICU200917-1_002A [Thrombocytopenia(-)]


title: RICU201006-1_001A [Thrombocytopenia(-)]


title: Fibroblasts, extracted and cultured after radiation,PBS, rep 2

description: Library name: PR-3

value: PBS and raditation


title: RICU200910-1_001A [Thrombocytopenia(-)]


title: RICU200908-2_001A [Thrombocytopenia(-)]


title: input-1-PEO1-siNC_ChIP

description: Library name: input-1-PEO1-siNC_S35


title: RICU200727-1_002A [Thrombocytopenia(-)]


title: 6-PEO1-sip53-SP1-IP_ChIP

description: Library name: 6-PEO1-sip53-SP1-IP_S29


title: RICU200721-1_001A [Thrombocytopenia(-)]


title: 5-PEO1-siNC-SP1-IP_ChIP

description: Library name: 5-PEO1-siNC-SP1-IP_S28


title: 4-PEO1-sip53-E2-ERa-IP_ChIP

description: Library name: 4-PEO1-sip53-E2-ERa-IP_S27


title: Fibroblasts, extracted and cultured after radiation,PBS, rep 1

description: Library name: PR-2


title: input-3-PEO1-siNC-E2_ChIP

description: Library name: input-3-PEO1-siNC-E2_S37


title: 3-PEO1-siNC-E2-ERa-IP_ChIP

description: Library name: 3-PEO1-siNC-E2-ERa-IP_S26


title: 8-PEO1-sip53-E2-SP1-IP_ChIP

description: Library name: 8-PEO1-sip53-E2-SP1-IP_S31


title: Fibroblasts, extracted and cultured after radiation,PBS, rep 3

description: Library name: PR-4


title: RICU200623-1_002A [Thrombocytopenia(-)]


title: RICU200616-1_001A [Thrombocytopenia(-)]


title: Fibroblasts, extracted and cultured after radiation,BuOE,rep 3

description: Library name: BR-3


title: Fibroblasts, extracted and cultured,BuOE,rep 1

description: Library name: B-1

value: BuOE


title: pSMAL-CellTag-V3

city: Seattle

first: Guangrong

last: Qin

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Library name: pSMAL-CellTag-V3

data_processing:
Base quality was checked using FASTQC, followed by use of a customized script to identify CellTags from the paired reads as follows: First, nucleotides with Q-scores <30 at the 3’ end of Read1 (R1) were trimmed, and the complement of Read2 (R2) was generated to provide a 5’ to 3’ sequence to use as a search string to identify the CellTag-V1 barcode region sequence motif  GGT(********)GAATT. A parallel search was performed in R1 sequence data using GGT(*****) as a seed to search for the last 11 nucleotides of R1 that overlapped the CellTag barcode region. CellTags identified in R1 and R2 were then compared to identify the subset that unambiguously identified identical, unique tag sequences
Supplementary files format and content: csv format. The processed file includes the quantification of Cell Tags per sample.

organism: synthetic construct

source_name: ctrl

extract_protocol:
Genomic DNA was purified from timed samples using a QiaQuick gDNA extraction kit, then lentiviral barcodes were PCR-amplified from gDNA using vector-specific primer pairs.
The resulting lentiviral CellTag-V1 amplicon DNA was UMI-indexed prior to Illumina short read NGS sequencing using variants of workflows developed by the Morris Lab (Biddy et al. 2018; https://github.com/morris-lab) and Trapnell Lab (Jose McFaline, UW Genome Sciences, Seattle WA and Columbia University). CellTag barcodes were identified in fastq files extracted from raw NGS paired end reads using bcl2fastq and the primer pairs as seed sequences. In brief, Read2 (3’ to 5’) covered the 8 base CellTag sequence, with Read1 (5’ to 3’) providing an overlapping segment of the CellTag 3’ end sequence.

value: ctrl


title: RICU200122-1_002A [Thrombocytopenia(-)]


title: Fibroblasts, extracted and cultured,BuOE,rep 2

description: Library name: B-2


title: Fibroblasts, extracted and cultured,BuOE,rep 3

description: Library name: B-4


title: 2-PEO1-sip53-ERa-IP_ChIP

description: Library name: 2-PEO1-sip53-ERa-IP_S25


title: Fibroblasts, extracted and cultured,PBS, rep 3

description: Library name: P-4

value: PBS


title: Fibroblasts, extracted and cultured,PBS, rep 2

description: Library name: P-3


title: 11-PEO1-H3K27AC-IP_ChIP

description: Library name: 11-PEO1-H3K27AC-IP_S34

value: Ovarian cancer cell


title: RICU191224-2_002A [Thrombocytopenia(-)]


title: 1-PEO1-siNC-ERa-IP_ChIP

description: Library name: 1-PEO1-siNC-ERa-IP_S24


title: pSMAL-CellTag-V2

description: Library name: pSMAL-CellTag-V2


title: GSC-0827_D40-mock1

description: Library name: GSC-0827_D40-mock1


title: pSMAL-CellTag-V1

description: Library name: pSMAL-CellTag-V1


title: Fibroblasts, extracted and cultured,PBS, rep 1

description: Library name: P-2


title: GSC-0827_D40-IR

description: Library name: GSC-0827_D40-IR


title: RICU200116-1_001A [Thrombocytopenia(-)]


title: GSC-0827_D30-neg

description: Library name: GSC-0827_D30-neg


title: GSC-0827_D30-mock1

description: Library name: GSC-0827_D30-mock1


title: 7-PEO1-siNC-E2-SP1-IP_ChIP

description: Library name: 7-PEO1-siNC-E2-SP1-IP_S30


title: GSC-0827_D20-mock1

description: Library name: GSC-0827_D20-mock1


title: GSC-0827_D40-neg

description: Library name: GSC-0827_D40-neg


title: GSC-0827_D20-IR

description: Library name: GSC-0827_D20-IR


title: GSC-0827_D20-neg

description: Library name: GSC-0827_D20-neg


title: GSC-0827_D30-IR

description: Library name: GSC-0827_D30-IR


title: RICU191125-1_002A [Thrombocytopenia(-)]


title: Fibroblasts, extracted and cultured after radiation,BuOE

description:
Library name: BuOErad
BR1

data_processing:
RNA-seq reads were first trimmed with Trim Galore version 0.6.4, which includes filtering reads shorter than 30 bp and low-quality ends from reads (Phred score: <20) and the option of removing reads with Ns. The quality of reads before and after trimming was checked with FastQC version 0.12.166. The filtered reads were then used to quantify transcripts in Salmon version 1.4.0 mapping-based mode using a decoy-aware transcriptome built from the GENCODE Mus musculus genome and transcriptome release M30 (GRCm39). Transcript expression values were normalized using the trimmed mean of M-values (TMM) method in edgeR version 4.2.2 to correct composition biases between libraries. The subsequent values were used to compute the log2 count-per-million (CPM) of samples and log2 fold changes for the groups of interest.
Assembly: GENCODE M30 (GRCm39)
Supplementary files format and content: A featureCounts tab-delimited data matrix which has 5 columns: an ENSEMBL ID in the first column and raw counts in the subsequent columns for each sample. The header has as columns (empty)\t followed by sample names.

extract_protocol:
Mice were sacrificed and prostates and bladders were removed immediately post-mortem. Organs were briefly minced using a scalpel in Hank’s buffered saline solution (HBSS) without calcium and magnesium, and fragments were centrifuged for 3 minutes at 400xg. Prostate or bladder fragments were resuspended in type I collagenase (Sigma-Aldrich, Saint Louis, MO, SCR103) in HBSS with calcium and magnesium and incubated at 37°C. Every five minutes, fragments were mixed by serially pipetting through a 25 ml, 10 ml, 5 ml, and 2 ml pipette until fragments could pass easily through the 2 ml pipette tip. Fragments were washed twice in HBSS without calcium and magnesium and then cultured using DMEM supplemented with 10% FBS, 1% penicillin/streptomycin, and 1% non-essential amino acids.
RNA was isolated using the Qiagen RNeasy mini kit as per protocol (cat. no. 74104). RNA sequencing was performed by City of Hope (Duarte, CA). Bulk RNA sequencing was performed on the NovaSeq 6000 (Illumina, San Diego, CA) with S4 reagent kit v1.5


title: GSC-0827_D12-mock3

description: Library name: GSC-0827_D12-mock3


title: GSC-0827_D12-mock2

description: Library name: GSC-0827_D12-mock2


title: RICU191008-2_002A [Thrombocytopenia(-)]


title: RICU191217-2_001A [Thrombocytopenia(-)]


title: GSC-0827_D12-neg

description: Library name: GSC-0827_D12-neg


title: Fibroblasts, extracted and cultured,BuOE

description:
Library name: BuOE
B1


title: shCTR HT1/2/3

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

description: Library name: GA

data_processing:
Cells from each sample were pooled and loaded into 10X Chromium. Gene expression together with Hashtag oligo (HTO) libraries were processed using Cell Ranger (v5.0.0) in multi-mode.
Assembly: mm10
Supplementary files format and content: A Seurat R object contains single cell gene expressions, dimension reductions, cell clustering and cell phenotypes.

source_name: lung lysate

extract_protocol:
The lung lobes were minced on a glass slide and then digested (collagenase IV (Sigma Aldrich C5138), DNAse I (Sigma Aldrich, DN25) in RPMI with 10% FBS) for 35 minutes at 37 degrees celsius. Digestion was stopped with EDTA (1 mM). Digested tissue were filtered into a single cell suspension through a 100 micron filter followed by red blood cell lysis (BD Pharm Lyse 555899). Cells were then washed and suspended in a staining buffer. Cells were then stained with live dead staining (Zombie UV fixabable viability dye, Biolegend #423107) and PeCy7 anti-CD45 (see flow cytometry methods section for staining protocol). Approximately 500,000 lung immune cells from each condition (2 mice per condition) were sorted as live+ IV-CD45 - CD45+ and 50,000 tumor cells were sorted as live+ CD45- GFP+.
Followed 10x ECCITE-seq standard library construction protocol.

value: lung lysate

value: shCtr

value: Doxycycline in the food Bio-Serv, S3888


title: RICU191014-1_001A [Thrombocytopenia(-)]

value: PBMC

value: Thrombocytopenia(-)


title: RICU191021-1_002A [Thrombocytopenia(-)]


title: RICU191001-1_001A [Thrombocytopenia(-)]


title: GSC-0827_D7-mock2

description: Library name: GSC-0827_D7-mock2


title: GSC-0827_D7-mock1

description: Library name: GSC-0827_D7-mock1


title: GSC-0827_D7-mock3

description: Library name: GSC-0827_D7-mock3


title: RICU190911-1_002A [Thrombocytopenia(-)]


title: GSC-0827_D12-mock1

description: Library name: GSC-0827_D12-mock1


title: Fibroblasts, extracted and cultured,PBS

description:
Library name: PBS
P1


title: Primary neurons,shKIF3A+TTBK2 Overexpress,Day5 rep2

city: changchun

first: Zhang

last: Renfeng

state: jilin

address: 218 Ziqiang Street

institute: Jilin University Second Hospital: The Second Hospital of Jilin University

description: Library name: KT2

data_processing:
Rawdata (raw reads) of fastq format were firstly processed through fastp  software.
In this step, clean data (clean reads) were obtained by  removing reads containing adapter, reads containing ploy-N and low  quality reads from raw data.
At the same time, Q20, Q30 and GC content  the clean data were calculated. All the downstream analyses were based  on the clean data with high quality.
Reference genome and gene model annotation files were downloaded  from genome website. Use HISAT2 (2.2.1) to build the index of the  reference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotation file to  create splice-aware alignments, providing better alignment accuracy  compared to other non-splice alignment tools.
For DESeq2 with biological replicates: Differential expression analysis for  two conditions/groups was performed using the DESeq2 R package  (1.42.0). DESeq2 provides statistical programs for determining  differential expression in digital gene expression data using models  based on negative binomial distribution. The resulting P-value is  adjusted using the Benjamini and Hochberg’s methods to control the  error discovery rate. The threshold of significant differential expression： padj <= 0.05 ＆ |log2(foldchange)| >= 1.  For edgeR without biological replicates: Prior to differential gene  expression analysis, for each sequencing library, read counts were adjusted using the edgeR R package (4.0.16) by scaling normalization  factors to eliminate differences in sequencing depth between samples,  followed by differential expression analysis. The resulting P value is  adjusted using the Benjamini and Hochberg’s methods to control the  error discovery rate. The threshold of significant differential expression： padj <= 0.05 ＆ |log2(foldchange)| >= 1.
Supplementary files format and content: gene_count, gene_fpkm
Assembly: Mus Musculus(GRCm39/mm39):
Assembly: http://ftp.ensembl.org/pub/release-107/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa
Assembly: http://ftp.ensembl.org/pub/release-107/gtf/mus_musculus/Mus_musculus.GRCm39.107.gtf.gz.

source_name: spinal cord

growth_protocol: Neuronal cells were isolated from the spinal cord of fetal rats at 15 days of gestation. Cells were cultured at a density of 1.5*10^6/well (six-well plate) . Neuronal growing media included DMEM (Gibco, USA) and FBS (Gibco, USA), and neuronal media included Neurobasal medium (Gibco, USA), 2% B27neural supplement (Gibco-Invitrogen, USA), 1 mM L- glutamine solution (Sigma-Aldrich, G7513, USA) and 100 ng/ml penicillin-streptomycin (Gibco-Invitrogen, USA). Neuronal cells were changed every 2 days and a half, and subsequent experiments were performed on day 5 to identify neuronal cells by immunofluorescence assay.All animal experiments were conducted in accordance with the Guidelines for the Protection and Utilization of Laboratory Animals (KT202003066) approved by the Animal Protection and Utilization Committee of Jilin University.

extract_protocol:
Total RNA was extracted by the trizol method
Messenger RNAwaspurified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was  synthesized using random hexamer primers. Then the second strand  cDNA was synthesized using dUTP, instead of dTTP. The directional  library was ready after end repair, A-tailing, adapter ligation, size  selection, USER enzyme digestion, amplification, and purification. The  library was checked with Qubit and real-time PCR for quantification and  bioanalyzer for size distribution detection

treatment_protocol: The experiment was divided into five groups, including: NC, shKIF3A, shTTBK2, OETTBK2, shKIF3A+OETTBK2. Cells were seeded on day 5 of the plate and infected using adenovirus, using the 1/2-volume infection method, half of the medium in the original well plate was removed, and the corresponding viral solution was added according to the MOI=100.

value: spinal cord

tag: strain

value: Primary neurons

value: KIF3A Knockdown+TTBK2 Overexpress

value: Adenovirus infection

tag: batch


title: Primary neurons,shKIF3A+TTBK2 Overexpress,Day5 rep1

description: Library name: KT1


title: RICU190909-1_002A [Thrombocytopenia(-)]


title: GSC-0827_D7-neg

description: Library name: GSC-0827_D7-neg


title: GSC-0827_D7-IR

description: Library name: GSC-0827_D7-IR


title: RICU191118-1_001A [Thrombocytopenia(-)]


title: GSC0827_D0-mock2

description: Library name: GSC0827_D0-mock2


title: RICU190905-1_001A [Thrombocytopenia(-)]


title: Fibroblasts, extracted and cultured after radiation,PBS

description:
Library name: PBSrad
PR1

value: prostate

value: PBS and radiation


title: GSC0827_D0-mock3

description: Library name: GSC0827_D0-mock3


title: GSC-0131_D40-IR

description: Library name: GSC-0131_D40-IR


title: GSC0827_D0-neg

description: Library name: GSC0827_D0-neg


title: GSC0827_D0-mock1

description: Library name: GSC0827_D0-mock1


title: Primary neurons,TTBK2 Overexpress,Day5 rep2

description: Library name: TG2

value: TTBK2 Overexpress


title: shLCN2 HT2/3

description: Library name: GB

value: live+ IV-CD45 - CD45+ and 50,000 tumor cells were sorted as live+ CD45- GFP+.


title: GSC-0131_D20-IR

description: Library name: GSC-0131_D20-IR


title: Primary neurons,shKIF3A+TTBK2 Overexpress,Day5 rep3

description: Library name: KT3


title: GSC-0827_D12-IR

description: Library name: GSC-0827_D12-IR


title: RICU190902-1_001A [Thrombocytopenia(-)]


title: GSC-0131_D30-neg

description: Library name: GSC-0131_D30-neg


title: GSC-0131_D12-mock2

description: Library name: GSC-0131_D12-mock2


title: RICU181224-2_001A [Thrombocytopenia(-)]


title: RICU190114-2_002A [Thrombocytopenia(-)]


title: Primary neurons,shTTBK2,Day5 rep3

description: Library name: TC3

value: TTBK2 Knockdown


title: RICU190102-1_002B [Thrombocytopenia(-)]


title: GSC-0131_D40-neg

description: Library name: GSC-0131_D40-neg


title: GSC-0131_D12-neg

description: Library name: GSC-0131_D12-neg


title: GSC-0131_D30-IR

description: Library name: GSC-0131_D30-IR


title: Primary neurons,TTBK2 Overexpress,Day5 rep3

description: Library name: TG3


title: GSC-0131_D20-neg

description: Library name: GSC-0131_D20-neg


title: Primary neurons,shTTBK2,Day5 rep2

description: Library name: TC2


title: Primary neurons,shControl,Day5 rep3

description: Library name: NC3

value: WT


title: GSC-0131_D7-mock2

description: Library name: GSC-0131_D7-mock2


title: GSC-0131_D12-mock3

description: Library name: GSC-0131_D12-mock3


title: Primary neurons,shKIF3A,Day5 rep1

description: Library name: KC1

value: KIF3A Knockdown


title: Primary neurons,shKIF3A,Day5 rep2

description: Library name: KC2


title: GSC0131_D0-mock2

description: Library name: GSC0131_D0-mock2


title: GSC-0131_D7-mock1

description: Library name: GSC-0131_D7-mock1


title: GSC0131_D0-mock1

description: Library name: GSC0131_D0-mock1


title: RICU220316-1_001A [Thrombocytopenia(+)]

value: Thrombocytopenia(+)


title: RICU220324-1_002A [Thrombocytopenia(+)]


title: GSC0131_D0-neg

description: Library name: GSC0131_D0-neg


title: RICU190108-1_001A [Thrombocytopenia(-)]


title: RICU220414-2_002A [Thrombocytopenia(+)]


title: GSC-0131_D12-IR

description: Library name: GSC-0131_D12-IR


title: Primary neurons,shKIF3A,Day5 rep3

description: Library name: KC3


title: RICU220329-1_001A [Thrombocytopenia(+)]


title: GSC-0131_D7-mock3

description: Library name: GSC-0131_D7-mock3


title: GSC-0131_D12-mock1

description: Library name: GSC-0131_D12-mock1


title: RICU220407-2_001A [Thrombocytopenia(+)]


title: WT

city: Guangzhou

first: Shunyan

last: Kan

address: No.601, West Huangpu Avenue

country: Afghanistan

institute: Jinan University

description: Library name: Sample1

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: B16-F0 melanoma

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: B16-F0 melanoma

value: TIL-Treg


title: GSC-0131_D7-IR

description: Library name: GSC-0131_D7-IR


title: GSC-0131_D7-neg

description: Library name: GSC-0131_D7-neg


title: TIL_Treg_Foxp3_high3

description: Library name: Sample7

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: Ensembl_GRCm39_111
Supplementary files format and content: tab-delimited text file includes read count values for each Sample

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 100-200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

value: Tumor

value: TIL

value: Treg


title: Primary neurons,shTTBK2,Day5 rep1

description: Library name: TC1

value: spinal cord


title: GBM8_D30-mock2

description: Library name: GBM8_D30-mock2


title: RICU220216-1_002A [Thrombocytopenia(+)]

value: PBMC


title: GSC0131_D0-mock3

description: Library name: GSC0131_D0-mock3


title: RICU220210-1_001A [Thrombocytopenia(+)]


title: GBM8_D30-mock3

description: Library name: GBM8_D30-mock3


title: GBM8_D30-IR

description: Library name: GBM8_D30-IR


title: GBM8_D40-mock3

description: Library name: GBM8_D40-mock3


title: RICU220407-1_002A [Thrombocytopenia(+)]


title: Primary neurons,TTBK2 Overexpress,Day5 rep1

description: Library name: TG1

value: Primary neurons


title: GBM8_D20-mock2

description: Library name: GBM8_D20-mock2


title: GBM8_D20-mock3

description: Library name: GBM8_D20-mock3


title: RICU220301-1_002A [Thrombocytopenia(+)]


title: TIL_Treg_Foxp3_low4

description: Library name: Sample4


title: Primary neurons,shControl,Day5 rep2

description: Library name: NC2

value: Adenovirus infection


title: GBM8_D20-IR

description: Library name: GBM8_D20-IR


title: GBM8_D40-mock2

description: Library name: GBM8_D40-mock2


title: GBM8_D20-neg

description: Library name: GBM8_D20-neg


title: GBM8_D40-neg

description: Library name: GBM8_D40-neg


title: KO

description: Library name: Sample2

value: KO


title: Primary neurons,shControl,Day5 rep1

description: Library name: NC1


title: TIL_Treg_Foxp3_low3

description: Library name: Sample3


title: GBM8_D40-IR

description: Library name: GBM8_D40-IR


title: GBM8_D30-neg

description: Library name: GBM8_D30-neg


title: GBM8_D15-IR

description: Library name: GBM8_D15-IR


title: TIL_Treg_Foxp3_high2

description: Library name: Sample6


title: RICU211228-2_001A [Thrombocytopenia(+)]


title: GBM8_D15-neg

description: Library name: GBM8_D15-neg


title: GBM8_D40-mock1

description: Library name: GBM8_D40-mock1


title: GBM8_D30-mock1

description: Library name: GBM8_D30-mock1


title: RICU220104-1_002A [Thrombocytopenia(+)]


title: GBM8_D15-mock2

description: Library name: GBM8_D15-mock2


title: GBM8_D7-mock3

description: Library name: GBM8_D7-mock3


title: RICU211227-1_001A [Thrombocytopenia(+)]


title: GBM8_D20-mock1

description: Library name: GBM8_D20-mock1


title: RICU220225-1_001A [Thrombocytopenia(+)]


title: Tu_WT_Treg3

description: Library name: Sample24

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id)
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCm39_release110
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.


title: TIL_Treg_Foxp3_low1

description: Library name: Sample1


title: TIL_Treg_Foxp3_high1

description: Library name: Sample5


title: RICU220126-3_002A [Thrombocytopenia(+)]


title: TIL_Treg_Foxp3_low2

description: Library name: Sample2


title: RICU211214-1_001A [Thrombocytopenia(+)]


title: RICU220121-3_001A [Thrombocytopenia(+)]


title: Tu_WT_Treg1

description: Library name: Sample22


title: GBM8_D15-mock3

description: Library name: GBM8_D15-mock3


title: GBM8_D7-neg

description: Library name: GBM8_D7-neg


title: GBM8_D0-mock3

description: Library name: GBM8_D0-mock3


title: Tu_WT_B3

description: Library name: Sample21

value: B cell


title: GBM8_D0-neg

description: Library name: GBM8_D0-neg


title: RICU220103-1_002A [Thrombocytopenia(+)]


title: Tu_WT_Treg2

description: Library name: Sample23


title: RICU211208-3_002A [Thrombocytopenia(+)]


title: GBM8_D7-mock2

description: Library name: GBM8_D7-mock2


title: RICU211221-1_002A [Thrombocytopenia(+)]


title: GBM8_D7-mock1

description: Library name: GBM8_D7-mock1


title: GBM8_D15-mock1

description: Library name: GBM8_D15-mock1


title: GBM8_D7-IR

description: Library name: GBM8_D7-IR


title: GBM4_D40-mock2

description: Library name: GBM4_D40-mock2


title: Tu_WT_B2

description: Library name: Sample20


title: RICU211201-3_001A [Thrombocytopenia(+)]


title: GBM8_D0-mock1

description: Library name: GBM8_D0-mock1


title: Tu_WT_B1

description: Library name: Sample19


title: GBM4_D40-IR

description: Library name: GBM4_D40-IR


title: GBM4_D30-neg

description: Library name: GBM4_D30-neg


title: LN_WT_Treg1

description: Library name: Sample16

source_name: lymph node

value: lymph node


title: RICU211124-1_001A [Thrombocytopenia(+)]


title: GBM4_D30-mock2

description: Library name: GBM4_D30-mock2


title: GBM4_D40-neg

description: Library name: GBM4_D40-neg


title: GBM8_D0-mock2

description: Library name: GBM8_D0-mock2


title: RICU211201-1_002A [Thrombocytopenia(+)]


title: RICU211208-2_002A [Thrombocytopenia(+)]


title: GBM4_D20-mock2

description: Library name: GBM4_D20-mock2


title: GBM4_D20-mock3

description: Library name: GBM4_D20-mock3


title: LN_WT_Treg3

description: Library name: Sample18


title: RICU211130-2_001A [Thrombocytopenia(+)]


title: LN_WT_Treg2

description: Library name: Sample17


title: GBM4_D20-mock1

description: Library name: GBM4_D20-mock1


title: LN_WT_B3

description: Library name: Sample15


title: GBM4_D30-mock1

description: Library name: GBM4_D30-mock1


title: GBM4_D20-IR

description: Library name: GBM4_D20-IR


title: GBM4_D30-IR

description: Library name: GBM4_D30-IR


title: RICU211102-1_002A [Thrombocytopenia(+)]


title: LN_WT_B1

description: Library name: Sample13


title: RICU210520-1_001A [Thrombocytopenia(+)]


title: GBM4_D7-mock3

description: Library name: GBM4_D7-mock3


title: RICU210527-1_002A [Thrombocytopenia(+)]


title: RICU210504-1_002A [Thrombocytopenia(+)]


title: GBM4_D7-mock2

description: Library name: GBM4_D7-mock2


title: RICU211026-1_001A [Thrombocytopenia(+)]


title: Tu_KO_Treg2

description: Library name: Sample11


title: Tu_KO_Treg1

description: Library name: Sample10


title: GBM4_D7-neg

description: Library name: GBM4_D7-neg


title: GBM4_D0-mock1

description: Library name: GBM4_D0-mock1


title: RICU210429-2_001A [Thrombocytopenia(+)]


title: LN_WT_B2

description: Library name: Sample14


title: GBM4_D0-mock3

description: Library name: GBM4_D0-mock3


title: GBM4_D20-neg

description: Library name: GBM4_D20-neg


title: Tu_KO_Treg3

description: Library name: Sample12


title: N.orthonotus_ID318_veryold_brain

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

description: WGBS

data_processing:
Raw reads were subjected to adapter and quality trimming using cutadapt (v2.4; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read.
The trimmed reads were aligned to the Nothobranchius furzeri and Nothobranchius orthonotus reference genomes using using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). A sorted BAM file was obtained and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10).
Methylation rates were called for autosomes only using mcall from the MOABS package (v1.3.2; default parameters).
Supplementary files format and content: bigWig file of 10-200X coverage filtered methylation rate BED file (<chr> <start> <end> <methylation rate>)

organism: Nothobranchius orthonotus

source_name: brain

extract_protocol:
Genomic DNA was extracted using the PureLink Genomic DNA Mini Kit.
gDNA was sheared by sonication and then bisulfite converted using the Zymo EZ DNA Methylation Gold Kit. Bisulfite converted DNA was then immediately processed using the Swift Biosciences Accel-NGS Methyl-Seq library kit according to manufacturer's instructions

value: brain

tag: age group

value: very old


title: RICU201208-2_002A [Thrombocytopenia(+)]

tag: tissue


title: RICU201105-1_002A [Thrombocytopenia(+)]


title: N.orthonotus_ID303_veryold_brain

description: WGBS


title: N.orthonotus_ID305_veryold_brain

description: WGBS


title: GBM4_D7-IR

description: Library name: GBM4_D7-IR


title: GBM4_D7-mock1

description: Library name: GBM4_D7-mock1


title: Tu_KO_B2

description: Library name: Sample8


title: GBM4_D0-mock2

description: Library name: GBM4_D0-mock2


title: N.orthonotus_ID288_veryold_brain

description: WGBS


title: GBM4_D0-neg

description: Library name: GBM4_D0-neg


title: N.orthonotus_ID289_old_brain

description: WGBS

value: old


title: N.orthonotus_ID296_veryold_brain

description: WGBS


title: Tu_KO_B3

description: Library name: Sample9


title: N.orthonotus_ID282_old_brain

description: WGBS


title: RICU201201-2_001A [Thrombocytopenia(+)]


title: LN_KO_Treg3

description: Library name: Sample6


title: N.orthonotus_ID312_old_brain

description: WGBS


title: N.orthonotus_ID292_old_brain

description: WGBS


title: Tu_KO_B1

description: Library name: Sample7


title: RICU201029-1_001A [Thrombocytopenia(+)]


title: RICU201021-1_001A [Thrombocytopenia(+)]


title: LN_KO_Treg2

description: Library name: Sample5


title: RICU201028-1_002A [Thrombocytopenia(+)]


title: RICU200909-1_002A [Thrombocytopenia(+)]


title: N.orthonotus_ID295_old_brain

description: WGBS


title: LN_KO_Treg1

description: Library name: Sample4


title: N.orthonotus_ID327_young_brain

description: WGBS

value: young


title: N.orthonotus_ID328_young_brain

description: WGBS


title: LN_KO_B3

description: Library name: Sample3


title: N.orthonotus_ID276_young_brain

description: WGBS


title: RICU200902-1_001A [Thrombocytopenia(+)]

value: Thrombocytopenia(+)


title: LN_KO_B2

description: Library name: Sample2


title: No.17_18

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description:
Library name: No.17_18
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

data_processing:
1. Cell segmentation with ssDNA images
2. SCTransform
Assembly: AmexG v6.0
Supplementary files format and content: 19 AnnData H5AD files (one for each slice, including segmented cell bin matrix, cell coordinates and annotation metadata.), 19 GEM files (spot-level spatial gene expression matrices in long-format), and 19 ssDNA images (preprocessed and aligned ssDNA images)
Library strategy: Spatial Transcriptomics

organism: Ambystoma mexicanum

source_name: Metencephalon

extract_protocol:
Stereo-seq protocol by BGI
Stereo-seq library construction by BGI

value: Metencephalon

value: Metamorphosis


title: RICU200901-2_002A [Thrombocytopenia(+)]

data_processing:
sequence reads were mapped to the human reference genome GRCh38 by HISAT2 (version 2.2.0)
Read counts were calculated by featureCounts (Version 2.0.0)
Assembly: GRCh38
Supplementary files format and content: tab delimited text file include raw read counts for each sample

extract_protocol:
PAXgene Blood miRNA Kit
Universal Plus mRNA-Seq library preparation kit with NuQuant


title: N.orthonotus_ID283_young_brain

description: WGBS


title: RICU200417-1_002A [Thrombocytopenia(+)]


title: No.13_15

description:
Library name: No.13_15
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

source_name: Telencephalon/Diencephalon

value: Telencephalon/Diencephalon


title: No.14

description:
Library name: No.14
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

source_name: Diencephalon

value: Diencephalon


title: N.orthonotus_ID277_young_brain

description: WGBS


title: RICU200410-1_001A [Thrombocytopenia(+)]


title: No.8_10

description:
Library name: No.8_10
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

source_name: Metencephalon/Pituitary

value: Metencephalon/Pituitary

value: Adult


title: No.12_16_19

description:
Library name: No.12_16_19
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

source_name: Olfactory Bulb/Diencephalon/Pituitary

value: Olfactory Bulb/Diencephalon/Pituitary


title: PP Tfh, SPF, rep3

city: Nam-gu, Pohang-si

first: Haeun

last: Ko

state: Gyeongsangbuk-do

address: 77, Cheongam-ro

department: Life Science

country: South Korea

institute: POSTECH

description: Library name: PP_Tfh_3

data_processing:
STAR (v2.7.10b) and RSEM(v1.3.3) were used for alignment and transcript quantification of raw RNA sequencing data.
GeTMM method was applied to normalize the expected read counts while accounting for differences in sequencing depth and gene length.
Differentially expressed genes (DEGs) analysis was conducted using DESeq2 R package (DESeq2 version 1.42.1; R version 4.1.2) (Log2 fold-change > 1 and P < 0.01).
Assembly: mm38
Supplementary files format and content: Read counts are shown in SPvsPP Tfh RNAseq count. tsv
Supplementary files format and content: GeTMM value are shown in SPvsPP Tfh RNAseq GeTMM.tsv

source_name: Peyer's patches

extract_protocol:
Tfh (CD4+CXCR5+PD1+GITR-CD44+) from the spleen and Peyer's patches of WT mice were sorted by a MoFlo Astrios (Beckman Coulter). Total RNA was extracted with TRIzol (GeneAll) according to the manufacturer's instruction.
The library for RNA sequencing was generated using the SMART-Seq mRNA Kit/NEXtera XT DNA Library Preparation Kit (Illumina). RNA-Seq

value: Peyer's patches

value: Tfh (CD4+CXCR5+PD1+GITR-CD44+)

value: Wild type


title: SP Tfh, SPF, rep1

description: Library name: SP_Tfh_1

source_name: Spleen

value: Spleen


title: No.4

description:
Library name: No.4
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

source_name: Telencephalon

value: Telencephalon


title: RICU200824-1_001A [Thrombocytopenia(+)]

source_name: PBMC

value: PBMC


title: RICU190827-1_001A [Thrombocytopenia(+)]


title: PP Tfh, SPF, rep2

description: Library name: PP_Tfh_2


title: No.7

description:
Library name: No.7
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals


title: RICU190903-1_002A [Thrombocytopenia(+)]


title: SP Tfh, SPF, rep2

description: Library name: SP_Tfh_2


title: hBMSCs, GelHA3, 14day

city: 北京

first: Yunfeng

last: Zhao

state: --- Select One ---

address: Beijing

institute: Air Force Medical Center

description:
Library name: Sample 3
HA3

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: hg38
Supplementary files format and content: txt file include TPM values for each sample

molecule: cytoplasmic RNA

source_name: bone marrow

extract_protocol:
The total RNA of each group was extracted to construct RNA sequencing libraries.
RNA sequencing was performed at Hangzhou cosmos wisdom Biotechnology Co., Ltd. (Hangzhou, China) using NovaSeq Xplus (Illumina, San Diego, CA, USA).

value: bone marrow

value: hBMSCs

value: mesenchymal stem cells

value: osteogenic differentiation


title: No.11

description:
Library name: No.11
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

source_name: Olfactory Bulb

value: Olfactory Bulb


title: hBMSCs, GelHA1, 14day

description:
Library name: Sample 1
HA1


title: SP Tfh, SPF, rep3

description: Library name: SP_Tfh_3


title: hBMSCs, GelHA2, 14day

description:
Library name: Sample 2
HA2


title: PDX, N+L-2

city: Guishan, Taoyuan

first: Chiao-Yun

last: Lin

address: 5 Fu-Shin St

institute: Department of Obstetrics and Gynecology

data_processing:
The RNA raw reads were aligned with the human–mouse fusion reference genome (GRCh38.85 and GRCm38.100) by using the STAR aligner for transcript quantification.
Reads that aligned with the mouse genome were removed before downstream differential expression gene analysis was performed.
The differentially expressed genes (DEGs) (adjusted p value < 0.05) were subjected to functional annotation through the Gene ontology (GO) enrichment tool of clusterProfiler (R package)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: patient derived xenograft

extract_protocol:
Total RNA was extracted from the cell lines and tumors using a TOOLSmart RNA extractor, 1ug of RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SureSelect Human All Exon V6 kit following manufacturer's protocols.

value: stage III/IV OCCC Tissue

value: niraparib+lenvatinib


title: hBMSCs, GelHABT3, 14day

description:
Library name: Sample 6
HABTO3


title: Patient 022, Tumour Tissue

city: Townsville

first: Lionel

last: Hebbard

state: QLD

address: 1 James Cook Dr, Douglas QLD 4811

institute: James Cook University

description: Library name: T022

data_processing:
Trimmomatic v0.39; STAR v2.7.11b; RSEM v1.3.3
GATK v4.6.1.0; Picard Tools v3.1.1; VEP v.113.0
Assembly: GRCh38
Supplementary files format and content: RSEM isoforms and genes results files
Supplementary files format and content: Mutect2 vcf files, filtered and annotated

source_name: Hepatocellular Carcinoma

extract_protocol:
Tissue was snap frozen immediately after resection. RNA extractions were performed using Isolate II RNA Mini Kit (BIO-52073, Meridian Bioscience).
polyA Enrichment; Fragmentation; Reverse Transcription; cDNA synthesis; End Repair and A-tailing; Adapter ligation; Size selection; PCR Amplification

value: Hepatocellular Carcinoma


title: Patient 021, Tumour Tissue

description: Library name: T021


title: hBMSCs, GelHABT2, 14day

description:
Library name: Sample 5
HABTO2


title: PDX, N+L-1


title: No.2_3

description:
Library name: No.2_3
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

source_name: Olfactory Bulb/Telencephalon

value: Olfactory Bulb/Telencephalon


title: CD1 mouse, sham, male, biol rep 9

description: Library name: lib134

data_processing:
Raw reads of RNA-seq libraries were processed using the RNA-seq pipeline (https://github.com/Zhang-lab/RNA-seq_QC_analysis) which consists of data processing, quality control, integrative analysis, and data visualization.
Assembly: human genome hg38 with gene annotation ENCODE V27. mouse genome mm10 with gene annotation ENCODE M20.
Supplementary files format and content: TXT format, readcount table

molecule: nuclear RNA

source_name: Left Ventricle

growth_protocol: iCell Cardiomyocytes^2 were maintained per the manufacturer's instructions.  GCaMP6 hiPSC-CMs were differentiated into cardiomyocytes via GSK-3 inhibition/Wnt activation followed by TNKS inhibition/Wnt inhibition, followed by purification via lactate-mediated metabolic selection, and were then maintained in RPMI 1640 + 2% B-27 Supplement at 37 C with 5% CO2.

extract_protocol:
Cell preparation, antibody binding, tagmentation, and DNA extraction and purification were performed using the Active Motif CUT&Tag kit (Active Motif, 53171) according to the manufacturer’s instructions. The following antibodies were used: H3K27me3 (Active Motif, 39155), H3K27ac (Active Motif, 39685), H3K4me3 (Active Motif, 39159), H3K4me1 (Cell Signaling Technology, 5326), or IgG isotype control (Cell Signaling Technology, 66362S).
cDNA libraries were constructed using the Active Motif CUT&Tag kit with Nextera primers per manufacturer's instructions.

treatment_protocol: IR treatment was performed using the small animal radiation research platform (SARRP, Xstrahl Inc.). hiPSC-CMs received 25 Gy to the entire cell culture surface area. Radiation was delivered at a 3.9 Gy/min dose rate in a single fraction of 25 Gy.

value: Left Ventricle

value: PCM1+ cardiomyocyte nuclei

value: WT

value: Sham


title: No.9

description:
Library name: No.9
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

value: Metencephalon

value: Adult


title: CD1 mouse, sham, male, biol rep 8

description: Library name: lib133


title: PDX, Lenvatinib-2

value: lenvatinib


title: hBMSCs, GelHABT1, 14day

description:
Library name: Sample 4
HABTO1


title: Patient 012, Tumour Tissue

description: Library name: T012


title: Patient 014, Tumour Tissue

description: Library name: T014


title: CD1 mouse, sham, male, biol rep 6

description: Library name: lib131


title: CD1 mouse, ir6w, male, biol rep 7

description: Library name: lib129

value: 25 Gy IR


title: PDX, Control-1

value: control


title: CD1 mouse, ir6w, male, biol rep 6

description: Library name: lib128


title: Patient 009, Tumour Tissue

description: Library name: T009


title: CD1 mouse, sham, male,  biol rep 5

description: Library name: lib130


title: PDX, Lenvatinib-1


title: C3_Discovery_187

type: genomic

city: Potsdam

first: Amandeep

last: Singh

state: Brandenburg

address: Arthur-Scheunert-Allee 114-116

department: EOD

institute: German Institute of Human Nutrition

hyb_protocol: The bisulfite treatment and hybridisation was carried out by Life & Brain GmbH

scan_protocol: iscan, carried out by Life & Brain GmbH

data_processing: ChAMP package in R environment

label: other

source_name: Blood cells

label_protocol: Labeling was carried out by Life & Brain GmbH

extract_protocol: precipitation with sodium acetate

treatment_protocol: Genomic DNA was extracted from blood cells.

tag: Sex

value: M

value: Blood cells


title: CD1 mouse, sham, male, biol rep 7

city: Saint Louis

first: Shuhua

last: Fu

address: 660 S. Euclid Avenue Campus Box 8103

institute: Washington University in St. Louis

description: Library name: lib132


title: Patient 020, Tumour Tissue

description: Library name: T020


title: PP Tfh, SPF, rep1

description: Library name: PP_Tfh_1

value: Peyer's patches

value: Tfh (CD4+CXCR5+PD1+GITR-CD44+)

value: Wild type


title: LN_KO_B1

description: Library name: Sample1

source_name: lymph node

value: lymph node

value: B cell

value: KO


title: Patient 008, Tumour Tissue

description: Library name: T008

value: Hepatocellular Carcinoma


title: PDX, Control-2

value: stage III/IV OCCC Tissue


title: PDX, Niraparib-1

value: niraparib


title: No.1

description:
Library name: No.1
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

value: Olfactory Bulb


title: Patient 018, Tumour Tissue

description: Library name: T018


title: No.5_6

description:
Library name: No.5_6
Five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals

value: Diencephalon


title: Patient 015, Tumour Tissue

description: Library name: T015


title: CD1 mouse, ir6w, male, biol rep 4

description: Library name: lib126

value: Left Ventricle

value: PCM1+ cardiomyocyte nuclei

value: WT


title: Patient 010, Tumour Tissue

description: Library name: T010


title: Patient 006, Tumour Tissue

description: Library name: T006


title: C5_Discovery_186

value: F


title: PDX, Niraparib-2


title: Patient 005, Tumour Tissue

description: Library name: T005


title: Patient 017, Tumour Tissue

description: Library name: T017


title: Patient 019, Tumour Tissue

description: Library name: T019


title: C3_Discovery_184


title: CD1 mouse, ir6w, male, biol rep 3

description: Library name: lib125

value: 25 Gy IR


title: CD1 mouse, sham, male, biol rep 4

description: Library name: lib073

value: Sham


title: C6_Discovery_185

value: M

value: Blood cells


title: Patient 004, Tumour Tissue

description: Library name: T004


title: Patient 007, Tumour Tissue

description: Library name: T007


title: CD1 mouse, ir6w, male, biol rep 5

description: Library name: lib127


title: Patient 019, Normal Liver

description: Library name: N019

source_name: Liver

value: Liver


title: Patient 018, Normal Liver

description: Library name: N018


title: C6_Discovery_181


title: Patient 002, Tumour Tissue

description: Library name: T002


title: C6_Discovery_183


title: Patient 022, Normal Liver

description: Library name: N022


title: C3_Discovery_182


title: Patient 003, Tumour Tissue

description: Library name: T003


title: CD1 mouse, sham, male, biol rep 2

description: Library name: lib071


title: Patient 012, Normal Liver

description: Library name: N012


title: C5_Discovery_179


title: C6_Discovery_178


title: CD1 mouse, sham, male, biol rep 1

description: Library name: lib070


title: CD1 mouse, sham, female, biol rep 3

description: Library name: lib068


title: Patient 015, Normal Liver

description: Library name: N015


title: CD1 mouse, sham, male, biol rep 3

description: Library name: lib072


title: Patient 010, Normal Liver

description: Library name: N010


title: CD1 mouse, sham, female, biol rep 1

description: Library name: lib066


title: Patient 017, Normal Liver

description: Library name: N017


title: CD1 mouse, ir6w, male, biol rep 2

description: Library name: lib065


title: Patient 014, Normal Liver

description: Library name: N014


title: C3_Discovery_180


title: Patient 020, Normal Liver

description: Library name: N020


title: Patient 001, Tumour Tissue

description: Library name: T001


title: Patient 009, Normal Liver

description: Library name: N009


title: C5_Discovery_176


title: Patient 021, Normal Liver

description: Library name: N021


title: Patient 007, Normal Liver

description: Library name: N007


title: CD1 mouse, sham, female, biol rep 4

description: Library name: lib069


title: Patient 004, Normal Liver

description: Library name: N004


title: Patient 008, Normal Liver

description: Library name: N008


title: CD1 mouse, ir6w, male, biol rep 1

description: Library name: lib064


title: CD1 mouse, ir6w, male, biol rep 8

description: Library name: lib063


title: Patient 002, Normal Liver

description: Library name: N002


title: C5_Discovery_174


title: C5_Discovery_173


title: C3_Discovery_177


title: 1822, NaDCA0.1%, rep2

city: Itabashi-ku

first: Takahiro

last: Namiki

state: Tokyo

address: 30-1 Oyaguchikamicho

department: Pathology and Microbiology

country: Japan

institute: Nihon University School of Medicine

description: Library name: Candida tropicalis-1822 NaDCA0.1_

data_processing:
Cyclic DNA was created with the MGIEasy Dual Barcode Circularization kit (MGI Tech) sequencing was performed with a High-throughput Pair-End Sequencing Primer Kit (App-D) (MGI Tech). DNA nanoballs were constructed with a DNBSEQ-G400RS High-throughput Sequencing Kit (MGI Tech) and a High-throughput Pair-End Sequencing Primer Kit (App-D) (MGI Tech) according to the manufacturer’s instructions.
The prepared libraries were subsequently sequenced on a DNBSEQ-G400 (MGI Tech) using primers from the High-throughput Pair-End Sequencing Primer Kit (App-D) (MGI Tech) to generate 2×150 bp reads. Raw reads were trimmed with cutadapt (ver. 4.0) to remove adapters and low-quality bases (quality score<20 and <75 bps, respectively).
Assembly: Candida tropicalis ATCC MYA-3404/T1C for all Candida tropicalis strains and Candida albicans SC5314 for Candida albicans JCM1542
Supplementary files format and content: Raw fastq.gz data files.

organism: Candida tropicalis

source_name: cell

growth_protocol: Incubated in YPD broth before stimulation.

extract_protocol:
Ribonucleic acid (RNA) was extracted via ReliaPrepTM RNA Miniprep Systems (Promega, US). In addition to vortexing with 0.3–0.4 mm zirconia beads (As One, Japan) for two and a half minutes after mixing with isopropanol, the manufacturer’s protocol was followed.
The quality of the extracted RNA was measured with a NanoDrop One C (Thermo Fisher, US) and 5200 Fragment Analyzer (Agilent Technologies, US). Samples with an RNA integrity number (RIN) > 7.0 were selected for library preparation. RNA-seq libraries were prepared using the MGIEasy Fast RNA Library Prep Set (MGI Tech, China) according to the manufacturer’s protocol.
The quality of the library was checked with an Agilent 2100 bioanalyzer and a high-sensitivity DNA kit (Agilent Technologies).

treatment_protocol: Incubated in RPMI1640 containing 10%FBS with or without 0.1% of sodium deoxycholate (NaDCA) in a 37ºC+5% carbondioxide chamber for 6 hours.

value: cell

value: Yeast

value: NaDCA 0.1%


title: JCM1542, control, rep2

description: Library name: Candida albicans-JCM1542 control

organism: Candida albicans

value: Control


title: C6_Discovery_172


title: Patient 006, Normal Liver

description: Library name: N006


title: 1712, NaDCA0.1%, rep2

description: Library name: Candida tropicalis-1712 NaDCA0.1_


title: 1822, control, rep2

description: Library name: Candida tropicalis-1822 control


title: C5_Discovery_175


title: Patient 001, Normal Liver

description: Library name: N001


title: Patient 005, Normal Liver

description: Library name: N005


title: C6_Discovery_171


title: 1712, control, rep2

description: Library name: Candida tropicalis-1712 control


title: CD1 mouse, ir6w, female, biol rep 3

description: Library name: lib060


title: CD1 mouse, ir6w, female, biol rep 4

description: Library name: lib061


title: C6_Discovery_170


title: Patient 003, Normal Liver

description: Library name: N003


title: CD1 mouse, sham, male, biol rep 9

description: Library name: lib081

data_processing:
Raw ATAC-seq reads were aligned to the human (hg38) or mouse (mm10) reference genome and processed using AIAP, which includes four key steps: data processing, quality control, integrative analysis, and data visualization.
To generate a unified peak set, narrow peak files from all ATAC-seq libraries were merged using the merge function in the BEDTools suite.
Read counts for each ATAC-seq peak were quantified using the BEDTools coverage command.
To correct batch effects in read counts, RUVr normalization (RUVSeq R package, k = 2) was applied.
Assembly: hg38 and mm10
Supplementary files format and content: bigWig: dense, continuous data used in genome browser track
Supplementary files format and content: txt: normalized read counts of OCRs


title: 8, control, rep2

description: Library name: Candida tropicalis-8 control


title: C6_Discovery_169


title: CD1 mouse, ir6w, female, biol rep 1

description: Library name: lib058


title: 8, NaDCA0.1%, rep2

description: Library name: Candida tropicalis-8 NaDCA0.1_


title: A, control, rep2

description: Library name: Candida tropicalis-A control

value: A


title: CD1 mouse, ir6w, female, biol rep 2

description: Library name: lib059


title: A, NaDCA0.1%, rep2

description: Library name: Candida tropicalis-A NaDCA0.1_


title: JCM1542, NaDCA0.1%, rep2

description: Library name: Candida albicans-JCM1542 NaDCA0.1_


title: C6_Discovery_168


title: JCM1541, NaDCA 0.1%, rep2

description: Library name: Candida tropicalis-JCM1541 NaDCA0.1_


title: CD1 mouse, ir6wk, female, biol rep 2

description: Library name: lib054


title: JCM1541, control, rep2

description: Library name: Candida tropicalis-JCM1541 control


title: FGC0743_s_1_TTAGGC

first: Lin

last: Guo

address: 1020 Locust Street

institute: Thomas Jefferson University

library_source: other

data_processing:
Sequence reads were trimmed for adaptor sequence.
The resulting sequences were aligned to human genome and E. coli genome using Bowtie and the annotated peaks were analyzed by a program HOMER for motif finding.
Assembly: build hg19 and E. Coli
Supplementary files format and content: txt files include the enriched motifs found in the samples aligned to E. coli genome.
Supplementary files format and content: txt files include the enriched motifs found in the samples aligned to human genome.

molecule: other

organism: Escherichia coli

source_name: E. coli B F– ompT hsdS(r – m –) dcm+ Tetr gal λ(DE3) endA Hte [argU ileY BB leuW Camr]

growth_protocol: Transformed E. coli were grown at 37°C in 1L of LB media until OD600=0.5-0.6.

extract_protocol:
N-terminally tagged GST-FUS was overexpressed in BL21(DE3)RIL E. coli. The E. coli cells were then lysed by sonication on ice in PBS and protease inhibitors (cOmplete, EDTA-free, Roche Applied Science). The protein was purified over Glutathione Sepharose 4 Fast Flow beads (GE Healthcare) and eluted from the beads using FUS assembly buffer (50mM Tris-HCl pH 8, 200mM trehalose, 1mM DTT, and 20mM reduced glutathione). RNA that was bound to GST-FUS during protein purification was extracted by adding DNase I and then Proteinase K to the sample followed by phenol-chloroform extraction, and precipitation in 100% ethanol with 70% ethanol wash.
For preparing cDNA libraries for high-throughput sequencing, we used the NEBNext® Small RNA Library Prep Set for Illumina® and followed the manufacturer's instructions. Library quality was checked with the Agilent 2100 BioAnalyzer.
The sample was sequenced on the Illumina HiSeq2000 platform using hiSeq-50SR.

treatment_protocol: Protein expression was induced with addition of 1mM IPTG and then bacterial cultures were incubated for 16h at 16°C.

value: BL21-CodonPlus(DE3)-RIL strain

value: Bacterial cells

value: Transformed with pDuet-FUS and induced expression of GST-FUS with IPTG


title: FGC0743_s_1_ACAGTG


title: C5_Discovery_166


title: C3_Discovery_165


title: FGC0743_s_1_CGATGT


title: C6_Discovery_164


title: CD1 mouse, ir6wk, male, biol rep 7

description: Library name: lib055

value: Left Ventricle


title: Hs578T, siYTHDC1, rep2

city: guangzhou

first: zhenghao

last: Lai

address: yanjiang road

institute: sun yat-san memorial hospital

description: Library name: Hs578T-siYTHDC1-2

data_processing:
Qubit 3.0
Using Qubit 3.0 to initially quantify concentrations, the Agilent 2100 system initially assessed library fragment size.
After meeting expectations,the effective concentration of the library was accurately quantified using the Bio-RAD CFX 96 Fluorescent Quantitative PCR Instrument.

source_name: breast cancer

growth_protocol: MDA-MB-231 and Hs578T cells were cultured in DMEM (Gibco) supplemented with 10% FBS (Shanghai ExCell Biology Inc.) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA was harvested using Trizol. The Nanodrop2000 microspectrophotometer detects sample purity and concentration;
(1) Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; (4) Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; (5) PCR enrichment was performed to obtain cDNA libraries.

value: breast cancer


title: CD1 mouse, sham, male, biol rep 8

description: Library name: lib051

value: PCM1+ cardiomyocyte nuclei

value: WT


title: CD1 mouse, sham, female, biol rep 1

description: Library name: lib052


title: Hs578T, siYTHDC1, rep1

description: Library name: Hs578T-siYTHDC1-1


title: CD1 mouse, ir6wk, male, biol rep 6

description: Library name: lib053

value: 25 Gy IR


title: MDA-MB-231, siYTHDC1, rep2

description: Library name: 231-siYTHDC1-2


title: CD1 mouse, sham, female, biol rep 2

description: Library name: lib057

value: Sham


title: Hs578T, siNC, rep2

description: Library name: Hs578T-siNC-2

value: siNC


title: FGC0743_s_1_TGACCA


title: C3_Discovery_162

value: F

value: Blood cells


title: C6_Discovery_167

value: M


title: C5_Discovery_161


title: CD1 mouse, ir6wk, female, biol rep 1

description: Library name: lib056


title: Hs578T, siNC, rep3

description: Library name: Hs578T-siNC-3


title: MDA-MB-231, siNC, rep3

description: Library name: 231-siNC-3


title: C3_Discovery_163


title: MDA-MB-231, siYTHDC1, rep3

description: Library name: 231-siYTHDC1-3


title: Hs578T, siNC, rep1

description: Library name: Hs578T-siNC-1


title: CD1 mouse, sham, male, biol rep 6

description: Library name: lib123


title: MDA-MB-231, siNC, rep1

description: Library name: 231-siNC-1


title: C6_Discovery_159