title: nup211-so, thiamine treated, biol rep 3 [Sample_6]

first: Hualin

last: Zhong

address: 695 Park Ave

department: Department of Biological Sciences

institute: Hunter College, The City University of New York

data_processing:
Sequencing reads were aligned to the Schizosaccharomyces pombe 972h- reference genome using the STAR spliced read aligner (Dobin et al., 2013).
GFF3 and FASTA files downloaded from the Ensemble Fungi genome browser (https://fungi.ensembl.org/Schizosaccharomyces_pombe) were used to build the reference genome index.
The resulting Binary Alignment Map (BAM) files were then used to generate count matrices from reads aligned to the genome using the summarizeOverlaps function from the GenomicAlignments package in R (Lawrence et al., 2013).
Count matrices were further analyzed using the R package DESeq2 (Love et al., 2014; Love et al., 2016).
Assembly: GCA_000002945.2
Supplementary files format and content: The comma separated file counts.csv contains raw count matrices generated from the BAM files corresponding to each sample
Supplementary files format and content: The comma separated file DEseq2Results.csv contain normalized abundance measurements (logFoldChange, baseMean,padj., etc) obtained from DEseq2 along with gene annotations (name, description, location).

organism: Schizosaccharomyces pombe

growth_protocol: nup211-so cells were grown in Edinburgh Minimal Media (EMM) supplemented with adenine and leucine. To repress nup211 expression, cells were grown in EMM containing 30uM (10 ug/ml) thiamine (EMM+T)

extract_protocol:
Fission yeast cell walls were digested using 250 µg of lyticase (Sigma) for 1.0-2.5 hours at 30°C. Total RNAs were extracted from the cells using the RNeasy Kit (Qiagen).
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instructions

treatment_protocol: To reduce nup211 expression, nup211-so cells were grown in media containing 30uM (10 ug/ml) thiamine (EMM+T). Cells were grown for 24 hours, washed once with EMM, and inoculated in fresh EMM+T at OD600 = 0.05. The cells were then allowed to grow for an additional 24 hours before harvesting.

tag: genotype

value: thiamine treated


title: DNA from Kazakh individual 248

status: Public on Oct 04 2024

type: genomic

city: Astana

first: Ulykbek

last: Kairov

address: Kabanbay batyr ave.53

department: Center for Life Sciences

country: Kazakhstan

institute: National Laboratory Astana, Nazarbayev University

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 248

hyb_protocol: DNA was loaded onto BeadChips arrays

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Normalized signal intensity and genotype were computed using Illumina's GenomeStudio v.2 software. GSA MG v2 was used for genotyping
Genotype: AA,AB,BB,or NC (no call)

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: 200 ng of Genomic DNA was amplified overnight at 37 degrees.  DNA was fragmented via FMS and precipitated with 2-propanol and PM1. Then DNA is resuspended

extract_protocol: DNA isolation from frozen blood was performed with Gentra Purgene Blood kit (Qiagen)

tag: health status

value: Healthy

tag: tissue

value: blood


title: plasma_NSCLC_tumour presence [P5F0]

type: RNA

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

hyb_protocol: The hybridization to probes were performed at 65°C for 24 hours following the manufacturer’s protocol.

scan_protocol: The hybridized probes were purified on nCounter Prep Station and counted on Digital Analyzer.

data_processing: Data was analyzed by nSolver 4.0 software. Data was normalized using 5 miRNA more stable following normFinder analysis

label: Biotin label and molecular barcode

molecule: total RNA

source_name: plasma in tumour presence

label_protocol: From ~ 30-100ng (or 3ul) of each RNA sample was added to the miRNA-tag ligation reaction for annealing, followed by ligation and purification.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from plasma patients before any treatment and when considered tumour free using Plasma slurry kit (Norgen)

treatment_protocol: not applicable

tag: condition

value: tumour presence

tag: histology

value: Lung adenocarcinoma

tag: tnm

tag: Sex

value: Female

tag: age


title: plasma_NSCLC_tumour free [P1F1]

source_name: plasma tumour free

value: tumour free


title: nup211-so, thiamine treated, biol rep 2 [Sample_5]

type: SRA

city: New York

state: NY

country: USA

library_source: transcriptomic

tag: cell line

tag: treatment


title: DNA from Kazakh individual 247

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 247


title: plasma_NSCLC_tumour free [P13F1]


title: nup211-so, thiamine treated, biol rep 1 [Sample_4]


title: nup211-so, no treatment control, biol rep 3 [Sample_3]

value: no treatment


title: DNA from Kazakh individual 246

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 246


title: plasma_NSCLC_tumour presence [P1F0]

value: Lung squamous cell carcinoma


title: nup211-so, no treatment control, biol rep 2 [Sample_2]


title: DNA from Kazakh individual 250

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 250


title: DNA from Kazakh individual 245

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 245


title: Smartseq2_Lipstic_TdLN_259

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

library_source: transcriptomic single cell

data_processing:
For 10x genomics sequencing, fastq files were aligned to the mouse genome (mm39) using the Cell Ranger pipeline (v. 7.0.1).
Data was processed using the Seurat package in R, with cells containing more than 5% mitochondrial reads excluded.
Normalization was performed using the SCTransform function.
Differential expression was analyzed using Wilcoxon-Rank-Test with Bonferroni correction.
For Smartseq2, reads were aligned to the mouse genome (GRCm38.p6) using STAR aligner.
Quantification matrices were generated using RSEM, processed in the Seurat pipeline, and filtered based on mitochondrial content.
Cells were clustered and visualized in t-SNE space using Seurat.
Assembly: mm39
Supplementary files format and content: Tab-separated matrix files for gene counts, normalized data.

organism: Mus musculus

growth_protocol: All tumor cell lines were grown in DMEM supplemented with 1% L-Glutamine and 1% Penicillin/Streptomycin.

extract_protocol:
Freshly collected tumor-draining lymph nodes (tdLNs) and tumors were processed for single-cell isolation. Tumors were digested with collagenase D and DNase I, and lymph nodes were digested with collagenase D. Single-cell suspensions were then prepared, stained, and sorted by FACS based on surface markers, as detailed in the Methods section.
Single-cell RNA-seq libraries were constructed using the Chromium platform (10x Genomics) following the manufacturer’s instructions. The RNA from sorted cells was processed for library construction, aiming for specific read lengths for each segment of sequencing. Libraries for bulk RNA-seq were prepared using the Smart-Seq2 method.

treatment_protocol: Mice were injected with various tumor cell lines as described. Antibody treatments (e.g., anti-IL-27, anti-CD40L, anti-CTLA-4, anti-PD-1, or anti-MHC-II) were administered at specified doses and time points. LIPSTIC substrate biotin–LPETG was injected as described for labeling intratumoral APC-T cell interactions.

tag: mouse name

value: naïve

tag: timepoint

tag: plate date


title: nup211-so, no treatment control, biol rep 1 [Sample_1]


title: plasma_NSCLC_tumour free [P19F1]

value: Male


title: HL-1mito_TRAP1_RIP

city: Hefei,

first: Xu

last: Liu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

country: China

description: RIP-seq

library_source: other

data_processing:
For mecciRNA identification, the clean data were filtered by bowtie2 (v 1.2.1) to remove reads mapped to rDNA. The left reads were mapped to the reference genome by bwa-men (v 0.7.17). The discontinuously mapped reads were extracted and mapped again to mitochondrial genome by bowtie (v 1.2.1). mecciRNA candidates were predicted by pepline mentioned in our article.
For ng-circRNA identification, the clean reads not aligned to rDNA sequences filtered by bowtie2 were mapped to the reference genome by bwa-mem. circRNA candidates were predicted by CIRI2 (v 2.0.6).
Assembly: hg38, mm10
Supplementary files format and content: csv or txt files include count values for each Sample

molecule: other

extract_protocol:
The isolated mitochondria, total cells were lysed in TRizol reagent (Life Technologies). RNA from  mitochondia, whole cell, mitochondrial fractions and RNA-IP were extracted by using TRizol reagent according to the manufacturer’s instructions.
For samll RNA seq, the small RNA bands in fractions 2-4 and the input were excised from the gel and RNAs were purified. Small RNA libraries were constructed with NEBNext Multiplex Small RNA Library Prep Set for Illumina following the manufacturer’s protocol. For total RNA and mitochondrial RNA sequencing, rRNA is removed from the total RNA sample using TruSeq Stranded Total RNA Library Prep Gold (Illumina), and sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommendations. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs. For TRAP1 RIP and ATP5B RIP, sequencing libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommendations. For other RIP-seq, NEB Next Ultra RNA Library Prep Kit was used for library construction of immunoprecipitated RNA. The libraries were subjected to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system. Each library generated a depth of ~10 G read pairs.

value: WT


title: plasma_NSCLC_tumour free [P5F1]


title: Smartseq2_Lipstic_TdLN_258


title: DNA from Kazakh individual 244

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 244


title: DHPS-knockdown spheroids supplemented with aspartate, replicate 3

city: Leuven

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB/KU Leuven

data_processing:
After quantification with qPCR, libraries were sequenced on a NovaSeq 6000 System (Illumina) using the NovaSeq 6000 S4 Reagent kit v1.5 (ref. 20028312, Illumina), generating 2x150bp paired-end reads. The resulting reads were trimmed for adaptors and low-quality base calls using Trim Galore! (v0.6.6), after which quality control was performed with FastQC (v0.11.9). High-quality reads were then mapped to the mm39 reference mouse genome (GRCm39) using STAR (v2.6.1), and quantified using Salmon (v1.4.0).
Gene counts for all samples collected under all 4 conditions of interest (ASPshSCR, NoASPshSCR, ASPshGRIN2D, ASPshDHPS) were processed simultaneously within the DESeq2 (v1.34.0) framework. For this, Salmon-derived counts were first rounded to the closest integers, after which genes with no expression in at least 2 out of 3/4 replicates for at least one of the 4 conditions were excluded from the analysis. Integer counts for the remaining 19525 genes were then modelled within DESeq2 to determine log fold changes between the ASPshSCR and NoASPshSCR conditions. The resulting (ASPshSCR vs NoASPshSCR) log fold changes (log2FC) and their associated p-values for each gene were then combined to derive a ranking metric RM = - log2FC × log10(p-value), whereby highly positive/negative values of RM indicate respectively genes with highly up/downregulated expression in the presence vs absence of aspartate.
Pre-ranked gene-set enrichment analysis (GSEA) between the ASPshSCR and NoASPshSCR conditions was then performed, using the R package fgsea (multilevel implementation with 10,000 initial permutations and no lower bound for p-value estimation), based on the ranking metric RM, and considering a collection of 3065 mouse gene sets. The latter comprised all HALLMARK and CURATED (C2) gene sets in the Broad Institute Molecular Signatures Database (MSigDB) except for those in category C2:CGP (obtained via the R package msigdbr), plus all KEGG metabolism gene sets (obtained by querying KEGG's REST API). Only gene sets containing between 3 and 1500 genes were considered in this analysis. Gene sets with positive normalized enrichment scores (NES) were then identified and ranked based on their NES.
Assembly: mm39 build GRCm39
Supplementary files format and content: The raw-count matrix for all 14 samples included in the study is provided as a tab-separated text file (rawCounts.txt), after rounding Salmon-derived counts to the closest integers and filtering out genes with no expression in at least 2 out of 3/4 replicates for at least one of the 4 conditions considered in the study. The first two columns of this file contain respectively gene stable IDs and symbols. For genes without defined symbols, stable IDs are used in their place. Genes with different stable IDs but annotated to identical symbols are designated by appending .X to the latter, where X = 2...N, with N being the total number of times the same symbol is annotated to different stable IDs. Text-based tab-separated tables are also provided with the results of DESeq2-based differential expression analysis (DESeq2results.txt) and GSEA (GSEAresults.txt). The latter are accompanied by a text file (DESeq2GSEAColumnDescription.txt) describing the contents of the various columns in each of the two files, and a gmt file with the gene-set collection used for GSEA (GeneSets_mmHC2KEGGmet.gmt).

extract_protocol:
Spheroids were collected and washed in ice-cold cycloheximide-supplemented PBS, lysed in hypotonic buffer (2.5mM MgCl2, 5mM TRIS pH 7.5, 1.5mM KCl supplemented with RNAse and protease inhibitors), and permeabilized by sequential addition of 0.5% Triton X-100 and 0.5% SDS. Lysates were then centrifuged for 7 minutes at 16,000 x g. For each condition, supernatants containing the cytosolic lysates were immediately lysed in Trizol (TriPure Isolation Reagent), snap-frozen in liquid nitrogen, and kept at -80°C for RNA extraction and mRNA library preparation.
mRNA library preparation was performed using the Illumina Stranded mRNA Prep kit (ref. 20040534).

treatment_protocol: Control (shSCR), GRIN2D-knockdown (shGRIN2D), and DHPS-knockdown (shDHPS) 4T1 spheroids were cultured for 5 days in lung-like medium (LLM) supplemented with 700 µM aspartate (ASP) and, in the case of control spheroids, also in the absence of aspartate supplementation (NoASPshSCR).

tag: cell type

value: Triple-Negative Breast Cancer

value: DHPS-knockdown

value: LLM + 700 µM aspartate


title: DHPS-knockdown spheroids supplemented with aspartate, replicate 4


title: Smartseq2_Lipstic_TdLN_257


title: DNA from Kazakh individual 243

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 243


title: IgG for HL-1mito_TRAP1_RIP

institute: University of Science and Technology of China

description: RIP-seq


title: DHPS-knockdown spheroids supplemented with aspartate, replicate 1


title: DHPS-knockdown spheroids supplemented with aspartate, replicate 2


title: Smartseq2_Lipstic_TdLN_260


title: DNA from Kazakh individual 241

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 241


title: GRIN2D-knockdown spheroids supplemented with aspartate, replicate 2


title: DNA from Kazakh individual 242

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 242


title: Smartseq2_Lipstic_TdLN_256


title: GRIN2D-knockdown spheroids supplemented with aspartate, replicate 3


title: Smartseq2_Lipstic_TdLN_254


title: GRIN2D-knockdown spheroids supplemented with aspartate, replicate 1


title: Control spheroids not supplemented with aspartate, replicate 4

value: Control

value: LLM without aspartate supplementation


title: Smartseq2_Lipstic_TdLN_255


title: Smartseq2_Lipstic_TdLN_253


title: Control spheroids not supplemented with aspartate, replicate 2


title: DNA from Kazakh individual 239

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 239


title: DNA from Kazakh individual 240

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 240


title: Smartseq2_Lipstic_TdLN_252


title: Control spheroids supplemented with aspartate, replicate 4


title: Control spheroids not supplemented with aspartate, replicate 3


title: DNA from Kazakh individual 238

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 238


title: Control spheroids supplemented with aspartate, replicate 2


title: Control spheroids supplemented with aspartate, replicate 1


title: Smartseq2_Lipstic_TdLN_251


title: Control spheroids supplemented with aspartate, replicate 3


title: skin wound-6,siRNA-3,D3

city: 湛江

first: haili

last: huang

state: 广东

address: 广东省湛江市霞山区广东医科大学附属医院

institute: Guangdong medical university

data_processing:
The data generated from Illumina/BGI platform were used for bioinformatics analysis.
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: HISAT2
Supplementary files format and content: tab-delimited text files include FPKM  for each Sample

source_name: Skin wound

growth_protocol: Establishment of wound model: mice were anesthetized, depilated, sterilized, and then excised with a scalpel from 0.6×0.6 cm round skin, including the epidermis and dermis.

extract_protocol:
Total RNA was extracted from the skin using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA).Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions.

treatment_protocol: 1days post of injury(dpi1), the experimental and control groups were given peri-wound injections of SFRP2-siRNA and NC-siRNA interventions, respectively, and were given routine care. During the acute inflammatory phase of dpi4, the mice were executed by cervical dislocation method, and the wound tissues were sent to the test sequence by liquid nitrogen freezing.

value: Skin wound

value: dbdb


title: skin wound-5,siRNA-2,D3

address: 广东省湛江市霞山区广东医科大学附属医院


title: DNA from Kazakh individual 235

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 235

value: Healthy

value: blood


title: Smartseq2_Lipstic_TdLN_250


title: DNA from Kazakh individual 234

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 234


title: skin wound-3,NC-3,D3

address: 广东省湛江市霞山区广东医科大学附属医院

value: NC-siRNA


title: Smartseq2_Lipstic_TdLN_249


title: Smartseq2_Lipstic_TdLN_248


title: DNA from Kazakh individual 231

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 231


title: skin wound-1,NC-1,D3

address: 广东省湛江市霞山区广东医科大学附属医院


title: skin wound-2,NC-2,D3

address: 广东省湛江市霞山区广东医科大学附属医院


title: RAW264.7,siRAB6-3,6H

address: 广东省湛江市霞山区广东医科大学附属医院

growth_protocol: RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the cell using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA).Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions.

treatment_protocol: Lipofectamine 8000 and 60nM of siRNA were diluted in serum-free and antibiotic-free DMEM, transfected for 6 hours, then changed to complete culture medium. After 12 hours, 100ng/ml of lipopolysaccharide was added. RNA extraction from RAW264.7 cells was performed after 24 hours of polarization.

value: Mouse Monocyte - macrophage Leukemia Cells


title: Smartseq2_Lipstic_TdLN_247


title: DNA from Kazakh individual 230

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 230


title: RAW264.7,siRAB6-1,6H

address: 广东省湛江市霞山区广东医科大学附属医院


title: DNA from Kazakh individual 229

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 229


title: Smartseq2_Lipstic_TdLN_245


title: RAW264.7,siRNA-2,6H

address: 广东省湛江市霞山区广东医科大学附属医院


title: RAW264.7,siRAB6-2,6H

address: 广东省湛江市霞山区广东医科大学附属医院


title: Smartseq2_Lipstic_TdLN_246


title: DNA from Kazakh individual 228

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 228


title: RAW264.7,siRNA-3,6H

address: 广东省湛江市霞山区广东医科大学附属医院


title: DNA from Kazakh individual 237

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 237


title: RAW264.7,NC-3,6H

address: 广东省湛江市霞山区广东医科大学附属医院


title: RAW264.7,NC-2,6H

address: 广东省湛江市霞山区广东医科大学附属医院


title: DNA from Kazakh individual 226

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 226


title: skin wound-4,siRNA-1,D3

address: 广东省湛江市霞山区广东医科大学附属医院


title: DNA from Kazakh individual 225

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 225


title: STING-/- hypoxia_2

city: Gainesville

first: Andrew

last: Bryant

state: Florida

address: 1345 Center Dr

department: Pulmonary

institute: University of Florida

description: 10x Genomics

data_processing:
The raw sequencing reads were aligned with mouse genome mm10 provided on CellRanger website by 10X Genomics. The mapped reads were then used for unique molecular identifier (UMI) counting, following the standard CellRanger pipeline for quality control as recommended by the manufacturer (10X Genomics).
Assembly: mm10
Supplementary files format and content: cloupe files

source_name: Left lung

extract_protocol:
Mouse whole lungs were perfused with 10mL PBS to remove blood cells. Lung tissues were then cut into small pieces and incubated in 3mL RPMI 1640 with 10% FBS (Gibco #A4766801), 5% Liberase (Sigma Aldrich #05401127001), and 1000U/mL DNAse I (Sigma Aldrich #9003989) for 1h at 100rpm and 37oC. Tissues were triturated with 3mL syringes and 18G needles until complete dissociation. Cells are filtered through 70mm cell strainer, washed 3 times with DPBS 2% FBS and 1M EDTA (KD Medical #RGF-3130) to remove debris. The remaining red blood cells were lysed with ammonium chloride lysis buffer (KD Medical #50-1019080).
Single cells were captured in the 10X Genomic Chromium Single Cell 3’ Solution, and RNAseq libraries were prepared following manufacturer’s protocol. The libraries were subjected to high-throughput sequencing on an Illumina NovaSeq 6000 platform, targeting 6000-8000 cells per sample with a sequencing depth of 20 million reads of 150-bp paired-end reads.

treatment_protocol: Exposure to 10% oxygen in a normobaric ventilated chamber

value: Left lung

value: Whole lung cells

value: Global STING knock-out

value: Chronic Hypoxia


title: Smartseq2_Lipstic_TdLN_244

value: naïve


title: STING-/- normoxia_2

description: 10x Genomics

value: Normoxia


title: RAW264.7,NC-1,6H

address: 广东省湛江市霞山区广东医科大学附属医院


title: DNA from Kazakh individual 224

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 224


title: Control hypoxia_2

description: 10x Genomics


title: Control normoxia_2

description: 10x Genomics


title: Smartseq2_Lipstic_TdLN_243


title: Smartseq2_Lipstic_TdLN_241


title: STING-/- normoxia

description: 10x Genomics


title: STING-/- hypoxia

description: 10x Genomics


title: Smartseq2_Lipstic_TdLN_242


title: RAW264.7,siRNA-1,6H

address: 广东省湛江市霞山区广东医科大学附属医院


title: Smartseq2_Lipstic_TdLN_240


title: Control hypoxia

description: 10x Genomics


title: DNA from Kazakh individual 222

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 222


title: Control normoxia

description: 10x Genomics


title: DNA from Kazakh individual 221

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 221


title: DHPS-knockdown spheroids supplemented with aspartate, sub-polysomal fraction of replicate 4

data_processing:
After quantification with qPCR, libraries were sequenced on a NovaSeq 6000 System (Illumina) using the NovaSeq 6000 S4 Reagent kit v1.5 (ref. 20028312, Illumina), generating 2x150bp paired-end reads. The resulting reads were trimmed for adaptors and low-quality base calls using Trim Galore! (v0.6.6), after which quality control was performed with FastQC (v0.11.9). High-quality reads were then mapped to the mm39 reference mouse genome (GRCm39) using STAR (v2.6.1), and quantified using Salmon (v1.4.0).
Gene counts for all 4 matched polysomal/sub-polysomal sample pairs collected under all 4 conditions of interest (ASPshSCR, NoASPshSCR, ASPshGRIN2D, ASPshDHPS) were processed simultaneously within the DESeq2 (v1.34.0) framework. For this, Salmon-derived counts were first rounded to the closest integers, after which genes with no expression in at least 3 out of 4 replicates for at least one of the 8 condition/fraction combinations were excluded from the analysis. Integer counts for the remaining 17757 genes were then modelled within DESeq2, using a design accounting for the paired nature of the polysomal/sub-polysomal fractions for each replicate and condition, of the form  Counts ~ Condition+Condition:Replicate+Condition:Fraction,  where : denotes an interaction, Condition denotes either of ASPshSCR, NoASPshSCR, ASPshGRIN2D, or ASPshDHPS, Fraction denotes either of the sub-polysomal (reference level) or polysomal fractions, and Replicate=1⋯4. Based on this design, the coefficients for the interaction terms Condition:Fraction directly represent the average log fold changes (log2FC) in mRNA levels between the polysomal/sub-polysomal fractions for each of the 4 conditions of interest. The differences between these log fold changes for the ASPshSCR condition and those for all other 3 conditions thus provide a measure of whether protein translation for a specific gene is altered in the presence of aspartate (ASPshSCR vs NoASPshSCR) or due to either NMDA-receptor activity (ASPshSCR vs ASPshGRIN2D) or hypusine production (ASPshSCR vs ASPshDHPS). These log fold-change differences were determined directly within DESeq2, further being subject to shrinkage using the ashr adaptive shrinkage estimator. The resulting shrunken log fold-change differences (Δlog2FC) and their associated p-values were then combined to derive a translation ranking metric TRM = - Δlog2FC × log10(p-value), whereby highly positive/negative values of TRM indicate genes for which protein translation is highly up/downregulated, respectively.
Pre-ranked gene-set enrichment analysis (GSEA) was then performed, using the R package fgsea (multilevel implementation with 10,000 initial permutations and no lower bound for p-value estimation), for each of the 3 comparisons of interest, based on the ranking metric TRM, and considering a collection of 3065 mouse gene sets. The latter comprised all HALLMARK and CURATED (C2) gene sets in the Broad Institute Molecular Signatures Database (MSigDB) except for those in category C2:CGP (obtained via the R package msigdbr), plus all KEGG metabolism gene sets (obtained by querying KEGG's REST API). Only gene sets containing between 3 and 1500 genes were considered in this analysis. Gene sets with positive normalized enrichment scores (NES) in all 3 comparisons were then identified and ranked based on their average NES among all comparisons.
To build the word cloud with the top enriched terms based on increased translation in ASP shSCR vs all other 3 conditions, combined, average shrunken log fold-change differences (Δlog2FC) between the ASP shSCR condition and all other 3 conditions were first determined for each gene, again directly within DESeq2. The latter were then used, together with their associated p-values, to derive a global translation ranking metric, analogously as described above. This global translation ranking metric was then used to perform GSEA, identically as described above, after which upregulated gene sets were ranked based on their NES. Gene-set names were then split into individual words, or terms, and each of these terms were assigned a ranking percentile RP based on the ranking of their associated gene set, rounded up to multiples of 0.1%. A score for each individual term in each gene set was then computed as 100/RP (thus covering the range 1–1000), after which an overall score for each term was determined by averaging its scores among all gene sets in which the term appeared. The latter overall scores were then used as weights to create the word cloud, after excluding common and/or uninformative terms.
Assembly: mm39 build GRCm39
Supplementary files format and content: The raw-count matrix for all 32 samples included in the study is provided as a tab-separated text file (rawCounts.txt), after rounding Salmon-derived counts to the closest integers and filtering out genes with no expression in at least 3 out of 4 replicates for at least one of the 8 condition/fraction combinations considered in the study. The first two columns of this file contain respectively gene stable IDs and symbols. For genes without defined symbols, stable IDs are used in their place. Genes with different stable IDs but annotated to identical symbols are designated by appending .X to the latter, where X = 2...N, with N being the total number of times the same symbol is annotated to different stable IDs. Text-based tab-separated tables are also provided with the results of DESeq2-based Δlog2FC analysis (Deltalog2FCresults.txt) and GSEA (GSEAresults.txt). The latter are accompanied by a text file (Deltalog2FCGSEAColumnDescription.txt) describing the contents of the various columns in each of the two files, and a gmt file with the gene-set collection used for GSEA (GeneSets_mmHC2KEGGmet.gmt).

extract_protocol:
Spheroids were collected and washed in ice-cold cycloheximide-supplemented PBS, lysed in hypotonic buffer (2.5mM MgCl2, 5mM TRIS pH 7.5, 1.5mM KCl supplemented with RNAse and protease inhibitors), and permeabilized by sequential addition of 0.5% Triton X-100 and 0.5% SDS. Lysates were then centrifuged for 7 minutes at 16,000 x g. For each condition, supernatants containing the cytosolic lysates were then loaded on top of a non-linear sucrose gradient (5% - 34% - 55%) and further ultracentrifuged at 200,000 x g for 2 hours at 4 °C. Total RNA input (~10% of the cytosolic lysate) was kept for RNA extraction and immediately lysed in Trizol (TriPure Isolation Reagent) and snap-frozen in liquid nitrogen. Polysome fractions were collected using a piston gradient fractionator. Matched polysomal (efficiently translated mRNA; associated with >3 ribosomes) and sub-polysomal (associated with <3 ribosomes) gradient fractions from 4 independent spheroid pellets per condition were then lysed in Trizol, snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction.
mRNA library preparation was performed using the Illumina Stranded mRNA Prep kit (ref. 20040534).

value: Triple-Negative Breast Cancer


title: DHPS-knockdown spheroids supplemented with aspartate, sub-polysomal fraction of replicate 2

value: DHPS-knockdown


title: DNA from Kazakh individual 220

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 220


title: DHPS-knockdown spheroids supplemented with aspartate, sub-polysomal fraction of replicate 3

value: LLM + 700 µM aspartate


title: DHPS-knockdown spheroids supplemented with aspartate, sub-polysomal fraction of replicate 1


title: Smartseq2_Lipstic_TdLN_237


title: Smartseq2_Lipstic_TdLN_238


title: DHPS-knockdown spheroids supplemented with aspartate, polysomal fraction of replicate 4


title: DNA from Kazakh individual 219

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 219


title: DNA from Kazakh individual 218

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 218


title: DHPS-knockdown spheroids supplemented with aspartate, polysomal fraction of replicate 3


title: DHPS-knockdown spheroids supplemented with aspartate, polysomal fraction of replicate 2


title: DHPS-knockdown spheroids supplemented with aspartate, polysomal fraction of replicate 1


title: DNA from Kazakh individual 223

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 223


title: GRIN2D-knockdown spheroids supplemented with aspartate, sub-polysomal fraction of replicate 4


title: DNA from Kazakh individual 217

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 217


title: Smartseq2_Lipstic_TdLN_235


title: GRIN2D-knockdown spheroids supplemented with aspartate, sub-polysomal fraction of replicate 3


title: Smartseq2_Lipstic_TdLN_234


title: DNA from Kazakh individual 216

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 216


title: GRIN2D-knockdown spheroids supplemented with aspartate, sub-polysomal fraction of replicate 2


title: Smartseq2_Lipstic_TdLN_233


title: Smartseq2_Lipstic_TdLN_239


title: GRIN2D-knockdown spheroids supplemented with aspartate, sub-polysomal fraction of replicate 1


title: GRIN2D-knockdown spheroids supplemented with aspartate, polysomal fraction of replicate 4


title: GRIN2D-knockdown spheroids supplemented with aspartate, polysomal fraction of replicate 3


title: Smartseq2_Lipstic_TdLN_232


title: DNA from Kazakh individual 213

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 213


title: GRIN2D-knockdown spheroids supplemented with aspartate, polysomal fraction of replicate 1


title: Control spheroids not supplemented with aspartate, sub-polysomal fraction of replicate 3

value: Control


title: DNA from Kazakh individual 214

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 214


title: Control spheroids not supplemented with aspartate, sub-polysomal fraction of replicate 4

value: LLM without aspartate supplementation


title: Smartseq2_Lipstic_TdLN_231


title: DNA from Kazakh individual 212

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 212


title: Control spheroids not supplemented with aspartate, sub-polysomal fraction of replicate 2


title: Control spheroids not supplemented with aspartate, sub-polysomal fraction of replicate 1


title: Smartseq2_Lipstic_TdLN_236


title: Control spheroids not supplemented with aspartate, polysomal fraction of replicate 4


title: DNA from Kazakh individual 211

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 211


title: DNA from Kazakh individual 210

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 210


title: Control spheroids not supplemented with aspartate, polysomal fraction of replicate 3


title: Control spheroids not supplemented with aspartate, polysomal fraction of replicate 2


title: Smartseq2_Lipstic_TdLN_227


title: Control spheroids not supplemented with aspartate, polysomal fraction of replicate 1


title: DNA from Kazakh individual 209

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 209


title: Control spheroids supplemented with aspartate, sub-polysomal fraction of replicate 4


title: Smartseq2_Lipstic_TdLN_228


title: DNA from Kazakh individual 215

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 215


title: Control spheroids supplemented with aspartate, sub-polysomal fraction of replicate 2


title: Control spheroids supplemented with aspartate, sub-polysomal fraction of replicate 3


title: DNA from Kazakh individual 208

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 208


title: GRIN2D-knockdown spheroids supplemented with aspartate, polysomal fraction of replicate 2


title: Control spheroids supplemented with aspartate, sub-polysomal fraction of replicate 1


title: Smartseq2_Lipstic_TdLN_226


title: Smartseq2_Lipstic_TdLN_225

value: Tumor


title: Smartseq2_Lipstic_TdLN_230


title: Control spheroids supplemented with aspartate, polysomal fraction of replicate 4


title: DNA from Kazakh individual 207

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 207


title: Control spheroids supplemented with aspartate, polysomal fraction of replicate 3


title: DNA from Kazakh individual 206

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 206


title: Smartseq2_Lipstic_TdLN_224


title: Control spheroids supplemented with aspartate, polysomal fraction of replicate 1


title: Smartseq2_Lipstic_TdLN_229


title: Smartseq2_Lipstic_TdLN_223


title: Control spheroids supplemented with aspartate, polysomal fraction of replicate 2


title: DNA from Kazakh individual 205

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 205


title: TSF1b, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate b

description: 10x Genomics Single-Cell Gene Expression 5' v1.1

data_processing:
Single-cell libraries were sequenced on an Illumina NovaSeq 6000 System. Sequenced reads were then mapped to a customized version of the mm10 mouse genome (mm10 build GRCm38.p6, including an extra chromosome with the CD90.1 sequence included in the lentiviral vector used to transduce 4T1 cells), using the 10x Genomics Cell Ranger software, and the resulting single-cell gene expression data was analyzed within the R/Bioconductor framework.
Raw UMI count matrices for all samples were first imported and merged using Seurat v4.1.0, and immediately subject to ambient RNA correction using a customized version of the SoupX v1.6.2 pipeline. Specifically, two modifications were applied to the standard SoupX pipeline. First, the automatically determined (global) ambient contamination fractions for each of the samples were multiplicatively increased by a factor of 2, to account for the fact that, as reported in the literature, the automatic determination method tends to underestimate ambient contamination levels for single-cell RNA-sequencing data. Second, rather than assuming a fixed contamination fraction for all cells, the latter was adapted for each cell based on its specific library size (total UMI counts), to achieve a uniform distribution of subtracted counts across all cells in each sample, in keeping with the nature of the ambient RNA contamination problem.
Ambient-corrected count matrices for the different samples were then merged and converted for further processing with Monocle3-alpha v2.99.3. Low-quality cells were then filtered based on standard quality-control metrics, with thresholds chosen based on evaluating quality-control histograms. In particular, cells were filtered based on their mitochondrial RNA content (allowing for a maximum of 10%), library size (removing cells with total UMI counts below 800) and number of detected genes (removing cells expressing less than 200 genes). Genes not expressed in any of the cells remaining after quality-control filtering were ignored in all subsequent analyses.
Size-factor and variance-stabilizing normalization (based on fitting to a negative binomial distribution) were then applied to the filtered data set, and highly variable genes (HVGs) were identified based on their departure from the average normalized dispersion versus expression trend observed among all genes. After excluding mitochondrial, ribosomal-protein, and cell cycle-associated genes, the top 1000 HVGs with size-factor normalized expression levels above 0.01 were selected. Principal component analysis (PCA) was then performed on the size factor-normalized and variance-stabilized count matrix restricted to these genes only, followed by 2D UMAP dimensional reduction based on the resulting top 50 principal components (with correlation distance metric, number of neighbors = 15, and minimum distance = 0.1, and without further PCA scaling). After that, cells were clustered in the UMAP plane by applying the Louvain graph-based algorithm at high resolution (resolution = 0.001, with kNN = 7), in order to attain a fine-grained cluster structure (183 clusters).
The resulting fine-grained clusters were then manually annotated to specific cell types, based on evaluating the expression profiles of several cell type-specific markers across the different fine-grained clusters. These cell-type annotations were further refined based on applying a second (analogous) step of dimensional reduction and (sub-)clustering analysis, separately to each of the preliminarily annotated cell-types. This in turn allowed us to more easily identify and filter out ambiguously annotated sub-clusters, most notably clusters originating from heterogeneous cell multiplets, characterized by simultaneously presenting markers associated to two or more cell types. Our multiplet identification was confirmed based on the distribution of doublet scores estimated across the different cells in each separate sample using scDblFinder v1.8.0. Specifically for the case of cancer cells, the latter could be unambiguously identified upon the first clustering step based on CD90.1 expression, and no re-annotation or doublet removal were needed upon sub-clustering.
Differential expression analysis, based on comparing cancer cells under TSF or CM pre-treatment at 16 days of metastatic colonization only, was performed within the Seurat framework, using the function FindMarkers with default parameters other than preserving all genes in the output regardless of their determined fold-changes and/or their fraction of expressing cells across samples. The resulting (TSF2 vs CM2) log fold changes (log2FC) and their associated p-values for each gene were then combined with the maximum fraction of cancer cells expressing that gene among the two conditions being compared (Xmax, where Xmax=1 for genes expressed in 100% of cancer cells in either of the two conditions) to derive an adjusted ranking metric RMadj = - log2FC × log10(p-value) × Xmax, whereby highly positive/negative values of RMadj indicate genes with highly up/downregulated expression under TSF pre-treatment, respectively. Pre-ranked gene-set enrichment analysis (GSEA) was then performed using the R package fgsea (multilevel implementation with 10,000 initial permutations and no lower bound for p-value estimation), based on the ranking metric RMadj, and considering a collection of 3065 mouse gene sets. The latter comprised all HALLMARK and CURATED (C2) gene sets in the Broad Institute Molecular Signatures Database (MSigDB) except for those in category C2:CGP (obtained via the R package msigdbr), plus all KEGG metabolism gene sets (obtained by querying KEGG's REST API). Only gene sets containing between 3 and 1500 genes were considered in this analysis. Gene sets with positive normalized enrichment scores (NES) were then identified and ranked based on their NES.
Assembly: mm10 build GRCm38.p6, including an extra chromosome with the CD90.1 sequence included in the lentiviral vector used to transduce 4T1 cells.
Supplementary files format and content: The raw-count output of the 10x Genomics CellRanger pipeline is provided in the form of MatrixMarket sparse matrices with gene|barcode|counts triplets (matrix.mtx.gz), together with the corresponding gene (features.tsv.gz) and barcode (barcodes.tsv.gz) index files, within a separate tar archive for each sample (Counts_SID.tar, where SID = CM0/1/2 or TSF0/1a/1b/2 is the sample identifier). In addition, analogous supplementary files are provided containing a merged gene|barcode|counts sparse matrix for the combination of all samples (Counts_FINAL.tar), after performing ambient RNA correction, filtering out cells based on quality-control metrics (mitochondrial RNA content, library size, and number of detected genes), and removing genes not expressed in any of the cells remaining after quality-control filtering. The latter are accompanied by text-based tables (GeneMetaData_FINAL.txt, CellMetaData_FINAL.txt) with all relevant gene/cell meta data needed to reproduce the results of the final analysis, including quality-control metrics, cell-type annotations, fine-grained cluster assignments, and UMAP coordinates. A description of the full contents of these meta data tables is provided in a separate text file (MetaDataDescription_FINAL.txt). Finally, text-based tables are also provided with the results of differential expression analysis (CancerCells_TSF2vsCM2_DEAresults.txt) and GSEA (CancerCells_TSF2vsCM2_GSEAresults.txt) based on comparing cancer cells under TSF or CM pre-treatment at 16 days of metastatic colonization only (TSF2 vs CM2). The latter are accompanied by a text file (CancerCells_TSF2vsCM2_DEAGSEAColumnDescription.txt) describing the contents of the various columns in each of the two files, and a gmt file with the gene-set collection used for GSEA (GeneSets_mmHC2KEGGmet.gmt).

source_name: Lung

extract_protocol:
Upon mice euthanasia, lungs were extracted and washed in blood bank saline, dried, and minced for ~ 2 minutes using blades. Minced lung tissues were then incubated with Liberase (0.3 mg/mL) and DNAse1 (1 μg/mL) for 45 min at 37°C, with occasional vortexing. The reaction was then quenched with PBS + 3% FBS + 2mM EDTA, after which cells were filtered through a 70μm cell strainer, washed once, and incubated with Red Blood Cell Lysis buffer. After red blood cell lysis, cells were washed once more and transferred through a 40 μm cell strainer. Cells were then pooled together from the 3 independent lung dissociations performed per group, resuspended in cell-culture medium at a density of 10^6 cells/mL, and kept on ice for immediate processing into single-cell cDNA libraries.
Cell suspensions for each sample were converted to barcoded single-cell cDNA libraries using the Chromium Single Cell 5’ v1.1 Library Kit, following the manufacturer’s guidelines, and aiming for a total of 10,000 cells per library.

treatment_protocol: For collecting Tumor-Secreted Factors (TSF), 4T1 or EMT6.5 derived primary tumors were resected after 17 days from m.f.p. injection, cut into smaller pieces and incubated at 37 °C in 15 mL/g of tumor in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 50 U/mL penicillin and 50 μg/mL streptomycin. For control medium (CM) formation, the same medium was incubated in parallel without the presence of tumor cells. After 72 h, media were filtered with a 70 µm cell strainer and centrifuged at 1,000 x g for 10 minutes. Supernatants from three biologically independent tumors were pooled together to cover for biological variability and 20 mM HEPES was added. Subsequently, media were filtered with 20 µm filters and stored at 4°C for a maximum of 5 days from collection. Female BALB/C mice (6 weeks old) were then injected i.v. with 200 µL of TSF (n=3) or CM (n=3) three times per week for three weeks, and subsequently either euthanized (pre-metastatic niche, CM0/TSF0), or injected i.v. with 25,000 CD90.1-expressing 4T1 cancer cells and then euthanized 11 days (metastatic seeding, CM1/TSF1) or 16 days (metastatic colonization, CM2/TSF2) after cancer-cell injection.

tag: strain

value: BALB/c

value: Female

value: 10 weeks-old

value: Lung

value: Tumor-Secreted Factors (TSF)

tag: injected cell_line

tag: metastasis stage

value: Seeding (d11)


title: Smartseq2_Lipstic_TdLN_222


title: TSF2, Lungs from TSF Injection, Metastatic Colonization (d16)

value: 11 weeks-old

value: Colonization (d16)


title: TSF1a, Lungs from TSF Injection, Metastatic Seeding (d11), Replicate a


title: DNA from Kazakh individual 204

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 204

value: Healthy

value: blood


title: Smartseq2_Lipstic_TdLN_221


title: DNA from Kazakh individual 203

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 203


title: CM2, Lungs from CM Injection, Metastatic Colonization (d16)

value: Control Medium (CM)


title: WT hippocampi, replicate 3

city: Urbana

first: Stephanie

last: Ceman

state: Illinois

address: 506 S Mathews Ave

department: Cell and Developmental Biology

institute: University of Illinois Urbana-Champaign

data_processing:
Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used portion in bold font for adaptor trimming).
Salmon version 1.4.0 was used to quantify the abundance of each transcript using the Selective Alignment method with a decoy-aware transcriptome using the entire GRCm39 genome as the decoy.
Assembly: mm39
Supplementary files format and content: sf

source_name: hippocampus

extract_protocol:
Total RNA was isoalted using RNeasy Mini Kit, Qiagen from hippocampi of at least two P0 pups per sample.
The RNA-seq libraries were prepared using TruSeq Stranded mRNAseq Sample Prep kit, Illumina

value: hippocampus

tag: genotype

value: WT

tag: time


title: Smartseq2_Lipstic_TdLN_220


title: DNA from Kazakh individual 202

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 202

tag: health status

tag: tissue


title: WT hippocampi, replicate 2


title: Mov10 Deletion hippocampi, replicate 3

value: Mov10 Deletion


title: WT hippocampi, replicate 1


title: Smartseq2_Lipstic_TdLN_219

source_name: Biotin+

value: Biotin+


title: Mov10 Deletion hippocampi, replicate 2


title: Mov10 Deletion hippocampi, replicate 1


title: Smartseq2_Lipstic_TdLN_218


title: DNA from Kazakh individual 200

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 200


title: Smartseq2_Lipstic_TdLN_217


title: DNA from Kazakh individual 199

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 199


title: Smartseq2_Lipstic_TdLN_216


title: PAA-15-R3

city: Ithaca

first: Renato

middle: Hohl

last: Orsi

address: 324 Stocking Hall

department: Food Science

institute: Cornell University

data_processing:
Raw reads were trimmed for low quality and adaptor sequences with TrimGalore v0.6.0, a wrapper for cutadapt and fastQC, using an error rate of 10% (-e 0.1), minimum length of 50 bp (--length 50), and a minimum per base phred quality of 20 (--nextseq-trim=20).
Sequences reads were mapped to the reference genome of L. monocytogenes 10403S (NCBI accession CP002002.1) using the program STAR v2.7.0e.
SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression. Replicates (n = 3) were used as blocking factors.
A False Discovery Rate (FDR) of 0.05 was used as cutoff for statistical significance and fold changes with log2 (log2FC) < -1.0 and > 1.0 were used to identify genes that were down- or up-regulated in the presence of PAA, respectively.
Assembly: L. monocytogenes strain 10403S (NCBI accession CP002002.1)
Supplementary files format and content: tab-delimited files include raw counts for each gene in 10403S.
Supplementary files format and content: column 1: gene ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes); column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)

organism: Listeria monocytogenes

source_name: strain 10403S

growth_protocol: When the bacterial culture reached OD600 ~ 0.4, 12 ml were transferred into each of 15 ml RNAse-free tubes (VWR International) The early log phase culture was then centrifuged (6000 rpm for 15 min at room temperature-RT~25oC) and resuspended in 6 ml pre-warmed Ringer's solution (at 30oC).

extract_protocol:
Each bacterial pellet was resuspended in 250 μl Tris-EDTA (T.E.) buffer containing 50 mg/ml lysozyme and 50 mg/ml proteinase K and was incubated at 37oC for 30 min. 1 ml of TriReagent (Zymo) was added to the cell suspension followed by mechanical disruption (bead-beating with 0.1 mm acid-washed zirconium beads) A standard protocol for phenol-chloroform nucleic acid extraction was used to obtain the total RNA.RNA was treated with TurboDNase (ThermoFisher), in the presence of RNasin (Promega), to remove contaminating DNA. Subsequently, phenol-extraction was performed, followed by RNA precipitation and re-suspension of the RNA in RNAse free water (Qiagen). In order to estimate RNA concentration and purity, U.V. spectrophotometry (Nanodrop 1000, Wilmington, DE, USA) was used. The 260/280 nm and 260 /230 nm absorbance ratios were used to assess the presence of proteins and the presence of organic contaminants (e.g., Trizol, phenol, Guanidine HCL, or guanidine thiocyanate), respectively. DNAse treatment efficacy was assessed by using SYBR Green Master Mix (Applied Biosystems) for qPCR analysis of DNA levels of the housekeeping gene rpoB. RNA integrity was assessed by using the 2100 BioAnalyzer (Agilent, Santa Clara, CA).
Ribosomal RNA was depleted by hybridization from total RNA samples using the NEBNext rRNA Depletion Kit (New England Biolabs). TruSeq-barcoded RNA-seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs). Libraries were quantified with the Qubit 2.0 dsDNA High Sensitivity Kit (ThermoFisher) and the size distributions were determined with a Fragment Analyzer (Agilent, Santa Clara, CA) prior to pooling.

treatment_protocol: Subsequently, 2.0 ml of the Ringer's solution containing cells were transferred into a Nalgene tube (VWR International) containing an equal volume of pre-warmed 5 ppm PAA solution or Ringer's solution without PAA (at 30oC), following incubation at 30oC for the corresponding time (0, 5 and 15 min). To immediately stabilize RNA, after incubation for the targeted time, 4 ml of RNA protect (Qiagen) was added to each sample. Samples were mixed by hand and incubated at RT for a minimum of 5 min. Afterward, bacterial cells were pelleted by centrifugation (6.000 rpm for 15 min at RT) and pellets were stored at -80oC. Three independent growth replicates and RNA isolations were performed.

value: strain 10403S

value: PAA 15 min replicate 3


title: PAA-0-R3

value: PAA 0 min replicate 3


title: HEK293T infected with OC43, MultiSeq

city: Vienna

first: Marco

middle: Yannic

last: Hein

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs

country: Austria

institute: Medical University of Vienna

description: MultiSeq barcode on lipid-modified oligonucleotides (LMOs)

data_processing:
We processed the raw data with cellranger v. 5.0.1 using default parameters.
MultiSeq barcodes were assigned to cell barcodes as described in McGinnis et al, 2019 using scripts provided at https://github.com/chris-mcginnis-ucsf/MULTI-seq and https://github.com/Mignot-Lab/Multiseq10x.
In addition to the default cellranger filtering, we removed cells with <2,000 UMIs, cells with >5% content of mitochondrial transcripts, as well as cells whose MULTI-seq barcodes indicated multiplets or could not be unambiguously assigned to one experimental condition, resulting in 12,910 cells in the final dataset. We used leiden clustering to define three main cellular states, corresponding to uninfected cells, and cells with low and high viral loads, respectively. To assess differential gene expression between uninfected and infected cells presenting high viral load, we generated pseudo-bulk transcriptomes from sets of 100 randomly subsampled cells from either cell state.
Assembly: We used a custom transcriptome reference that combines the GRCh38 human genome and a manually curated reference for OC43 based on the published genome sequence of the VR-1558 strain (provided along with the processed files).
Supplementary files format and content: Standard cellranger output files (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz); MultiSeq barcodes for each cell, linking it to the experimental time point post infection (20221110_OC43_HEK_5p_2_cellIDs.csv); Genome sequence and GTF annotation of the OC43 ATCC VR 1588 strain (OC43_ATCC_VR_1558.fasta, OC43_ATCC_VR_1558.gtf)

organism:
Homo sapiens
Human coronavirus OC43

growth_protocol: HEK293T cells (ATCC CRL-3216) were cultured in DMEM high-glucose medium with 10 % fetal bovine serum, supplemented with 2mM glutamine, penicillin and streptomycin. OC43 (ATCC VR-1558) stock was harvested from the supernatant of infected Huh7.5.1 cells in DMEM at 34 °C without further purification.

extract_protocol:
Cells were harvested by trypsinization, quenched, and washed in PBS. We then used MULTI-seq to encode the experimental conditions (i.e. uninfected or 16, 24, 48 h.p.i) before pooling all cells and loading them onto one lane of a 10x chip (NextGEM Single-Cell V(D)J Reagents Kit v1.1, 10x Genomics), aiming for recovery of 20,000 cells. We used the 5′ workflow to distinguish the different viral subgenomic RNAs.
We followed the manufacturer’s recommendation for library preparation and sequencing, spiking in the MULTI-seq amplicons at ~8 % of the gene expression library, at ~50,000 reads per cell.

treatment_protocol: HEK293T were infected at ~80 % confluency with an MOI of 1.0 of OC43. We staggered a series of infections so that samples were harvested in parallel in an uninfected state and at 16, 24, and 48 h.p.i, respectively.

value: infection with OC43 for 16, 24, 48h, respectively

tag: library type

value: LMO


title: PAA-5-R3

value: PAA 5 min replicate 3


title: DNA from Kazakh individual 198

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 198


title: DNA from Kazakh individual 197

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 197


title: HEK293T infected with OC43, GEX

description: 10x Genomics

molecule: polyA RNA

value: mRNA


title: CM1, Lungs from CM Injection, Metastatic Seeding (d11)

value: BALB/c

value: Female

value: 10 weeks-old

value: Lung

value: Seeding (d11)


title: Smartseq2_Lipstic_TdLN_215

value: Tumor


title: Ctrl-5-R3

value: Control 5 min replicate 3


title: Ctrl-15-R3

value: WT

value: Control 15 min replicate 3


title: Smartseq2_Lipstic_TdLN_214

value: Biotin+


title: DNA from Kazakh individual 196

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 196

value: Healthy

value: blood


title: PAA-15-R2

value: strain 10403S

value: PAA 15 min replicate 2


title: DNA from Kazakh individual 201

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 201


title: DNA from Kazakh individual 195

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 195


title: PAA-5-R2

value: PAA 5 min replicate 2


title: PAA-0-R2

value: PAA 0 min replicate 2


title: ctrl-15-R2

value: Control 15 min replicate 2


title: DNA from Kazakh individual 194

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 194


title: ctrl-5-R2

value: Control 5 min replicate 2


title: Ctrl-0-R3

value: Control 0 min replicate 3


title: Smartseq2_Lipstic_TdLN_213


title: DNA from Kazakh individual 193

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 193


title: Smartseq2_Lipstic_TdLN_212


title: ctrl-0-R2

value: Control 0 min replicate 2


title: DNA from Kazakh individual 192

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 192


title: PAA-5-R1

value: PAA 5 min replicate 1


title: Smartseq2_Lipstic_TdLN_211


title: DNA from Kazakh individual 190

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 190


title: Smartseq2_Lipstic_TdLN_209


title: ctrl-15-R1

value: Control 15 min replicate 1


title: PAA-0-R1

value: PAA 0 min replicate 1


title: Smartseq2_Lipstic_TdLN_210

value: Tumor


title: DNA from Kazakh individual 189

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 189


title: ctrl-0-R1

value: WT

value: Control 0 min replicate 1


title: Smartseq2_Lipstic_TdLN_208

value: Biotin+


title: pp71_D1219_RM17

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: G494_O14_RM17_L_B_D1219_RNA1_Lib1_GL50_S57

data_processing:
Raw sequence reads were processed to digitally remove residual adapters and low-quality bases by using Trim Galore v0.6.4 (powered by Cutadapt v3.7), along with quality check using FastQC v0.11.2.
Trimmed reads were then filtered to remove globin and ribosomal sequences using Bowtie2 v2.3.4.
Paired reads were aligned to the Mmul_10 Macaca mulatta genome (Ensembl v109) and gene expression was quantified with STAR v2.7.10b using the --quantMode GeneCounts flag to generate raw gene counts.
After removing lowly expressed genes with mean gene counts below 4, trimmed mean of M-values (TMM) normalization was performed using the calcNormFactors function in edgeR to calculate the scaling factor for the adjusted library sizes.
Gene counts were then transformed into log2-counts per million (log-CPM) values by limma package with the voom function for subsequent analyses.
Assembly: Mmul_10 Macaca mulatta genome (Ensembl v109)
Supplementary files format and content: count_matrix.txt; raw count data matrix file
Supplementary files format and content: 1.norm_matrix_HGNC.txt; voom normalized count data matrix file with HGNC symbol conversion

organism: Macaca mulatta

source_name: Whole Blood

extract_protocol:
Longitudinal whole blood samples were collected into PAXgene RNA tubes (PreAnalytiX) following the manufacturer’s instructions. RNA was isolated using RNAdvance Blood Kit (Beckman) on a Biomek i7 Automated Workstation (Beckman) following the validated protocol provided with the kit that included an on-column DNase treatment.
mRNA-seq libraries were constructed using the KAPA HyperPrep Kit with RiboErase (HMR) Globin + mRNA Capture Kit (Roche Diagnostics) following the manufacturer’s recommended protocol that was adapted for the Biomek i7.

treatment_protocol: Each RM was given a prime and two boosts of one of the two vaccines: either 68-1 RhCMV/TB-6Ag or 68-1 RhCMV/Δpp71-TB-6Ag.

value: Whole Blood

tag: animal

tag: animal age

tag: animal sex

value: Male

value: 68-1 RhCMV/{delta}pp71-TB-6Ag

tag: time point

tag: colony of_origin

value: PR


title: pp71_D1219_RM19

description: G493_O14_RM19_L_B_D1219_RNA1_Lib1_GL49_S11

tag: treatment


title: DNA from Kazakh individual 188

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 188

value: Healthy

value: blood


title: pp71_D1219_RM18

description: G492_O14_RM18_L_B_D1219_RNA1_Lib1_GL49_S44


title: pp71_D1219_RM14

description: G489_O14_RM14_L_B_D1219_RNA1_Lib1_GL51_S36

value: Female

value: ONPRC


title: Smartseq2_Lipstic_TdLN_206

tag: mouse name

tag: cell line

tag: timepoint


title: Smartseq2_Lipstic_TdLN_205

tag: plate date


title: pp71_D1219_RM15

description: G490_O14_RM15_L_B_D1219_RNA1_Lib1_GL51_S26


title: DNA from Kazakh individual 185

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 185


title: DNA from Kazakh individual 187

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 187


title: pp71_D1219_RM16

description: G491_O14_RM16_L_B_D1219_RNA1_Lib1_GL52_S87


title: DNA from Kazakh individual 186

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 186


title: TB6Ag_D1219_RM9

description: G486_O14_RM9_F_B_D1219_RNA1_Lib2_GL63_S31

value: 68-1 RhCMV/TB-6Ag


title: Smartseq2_Lipstic_TdLN_202


title: TB6Ag_D1219_RM8

description: G485_O14_RM8_F_B_D1219_RNA1_Lib1_GL53_S96


title: TB6Ag_D1219_RM6

description: G483_O14_RM6_F_B_D1219_RNA1_Lib1_GL53_S18


title: DNA from Kazakh individual 184

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 184


title: DNA from Kazakh individual 181

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 181


title: TB6Ag_D1219_RM4

description: G482_O14_RM4_F_B_D1219_RNA1_Lib1_GL50_S48


title: Smartseq2_Lipstic_TdLN_203


title: TB6Ag_D1219_RM5


title: Smartseq2_Lipstic_TdLN_207


title: ctrl-5-R1

tag: cell type

value: strain 10403S

value: Control 5 min replicate 1


title: TB6Ag_D1219_RM7

description: G481_O14_RM7_F_B_D1219_RNA1_Lib1_GL53_S48


title: PAA-15-R1

value: PAA 15 min replicate 1


title: TB6Ag_D1219_RM2

description: G480_O14_RM2_F_B_D1219_RNA1_Lib1_GL50_S14


title: DNA from Kazakh individual 179

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 179


title: Smartseq2_Lipstic_TdLN_204


title: pp71_D1219_RM13

description: G488_O14_RM13_L_B_D1219_RNA1_Lib2_GL63_S32


title: pp71_D1219_RM20

description: G487_O14_RM20_L_B_D1219_RNA1_Lib1_GL52_S25


title: Smartseq2_Lipstic_TdLN_200


title: DNA from Kazakh individual 178

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 178


title: DNA from Kazakh individual 177

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 177


title: TB6Ag_D1219_RM3

description: G478_O14_RM3_F_B_D1219_RNA1_Lib2_GL63_S29


title: TB6Ag_D1219_RM11

description: G476_O14_RM11_F_B_D1219_RNA1_Lib1_GL51_S19


title: Smartseq2_Lipstic_TdLN_198


title: Smartseq2_Lipstic_TdLN_199


title: DNA from Kazakh individual 176

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 176


title: TB6Ag_D1219_RM12

description: G477_O14_RM12_F_B_D1219_RNA1_Lib1_GL51_S45


title: TB6Ag_D1219_RM10

description: G475_O14_RM10_F_B_D1219_RNA1_Lib1_GL49_S39


title: DNA from Kazakh individual 175

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 175


title: Smartseq2_Lipstic_TdLN_201


title: pp71_D1191_RM17

description: G466_O14_RM17_L_B_D1191_RNA1_Lib1_GL50_S33


title: pp71_D1191_RM19

description: G465_O14_RM19_L_B_D1191_RNA1_Lib1_GL49_S5


title: pp71_D1191_RM18

description: G464_O14_RM18_L_B_D1191_RNA1_Lib1_GL66_S74


title: pp71_D1191_RM15

description: G462_O14_RM15_L_B_D1191_RNA1_Lib1_GL50_S54


title: pp71_D1191_RM14

description: G461_O14_RM14_L_B_D1191_RNA1_Lib1_GL53_S60


title: DNA from Kazakh individual 174

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 174


title: Smartseq2_Lipstic_TdLN_196


title: Smartseq2_Lipstic_TdLN_195


title: DNA from Kazakh individual 173

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 173


title: DNA from Kazakh individual 172

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 172


title: pp71_D1191_RM13

description: G460_O14_RM13_L_B_D1191_RNA1_Lib1_GL49_S23


title: TB6Ag_D1191_RM9

description: G458_O14_RM9_F_B_D1191_RNA1_Lib2_GL63_S28


title: Smartseq2_Lipstic_TdLN_193


title: TB6Ag_D1219_RM1

description: G479_O14_RM1_F_B_D1219_RNA1_Lib1_GL51_S57


title: pp71_D1191_RM20

description: G459_O14_RM20_L_B_D1191_RNA1_Lib1_GL50_S34


title: TB6Ag_D1191_RM8


title: DNA from Kazakh individual 170

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 170


title: TB6Ag_D1191_RM5

description: G456_O14_RM5_F_B_D1191_RNA2_Lib1_GL66_S96


title: Smartseq2_Lipstic_TdLN_197


title: TB6Ag_D1191_RM6

description: G455_O14_RM6_F_B_D1191_RNA1_Lib1_GL53_S44


title: TB6Ag_D1191_RM4

description: G454_O14_RM4_F_B_D1191_RNA1_Lib1_GL53_S8


title: TB6Ag_D1191_RM7

description: G453_O14_RM7_F_B_D1191_RNA1_Lib1_GL50_S86


title: Smartseq2_Lipstic_TdLN_192


title: DNA from Kazakh individual 169

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 169


title: TB6Ag_D1191_RM1

description: G451_O14_RM1_F_B_D1191_RNA1_Lib1_GL51_S29


title: Smartseq2_Lipstic_TdLN_194


title: Smartseq2_Lipstic_TdLN_190


title: Smartseq2_Lipstic_TdLN_191


title: pp71_D1191_RM16

description: G463_O14_RM16_L_B_D1191_RNA1_Lib1_GL50_S26


title: TB6Ag_D1191_RM3

description: G450_O14_RM3_F_B_D1191_RNA1_Lib1_GL51_S73


title: TB6Ag_D1191_RM2

description: G452_O14_RM2_F_B_D1191_RNA1_Lib2_GL63_S27


title: DNA from Kazakh individual 167

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 167


title: TB6Ag_D1191_RM11

description: G448_O14_RM11_F_B_D1191_RNA2_Lib1_GL66_S95


title: Smartseq2_Lipstic_TdLN_188


title: TB6Ag_D1191_RM10

description: G447_O14_RM10_F_B_D1191_RNA1_Lib1_GL50_S23


title: DNA from Kazakh individual 166

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 166


title: pp71_D1177_RM17

description: G438_O14_RM17_L_B_D1177_RNA1_Lib1_GL51_S67


title: TB6Ag_D1191_RM12

description: G449_O14_RM12_F_B_D1191_RNA1_Lib1_GL53_S84


title: DNA from Kazakh individual 168

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 168


title: DNA from Kazakh individual 171

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 171


title: DNA from Kazakh individual 165

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 165


title: Smartseq2_Lipstic_TdLN_187


title: pp71_D1177_RM19

description: G437_O14_RM19_L_B_D1177_RNA2_Lib1_GL62_S92


title: pp71_D1177_RM18

description: G436_O14_RM18_L_B_D1177_RNA1_Lib1_GL52_S2


title: Smartseq2_Lipstic_TdLN_186


title: DNA from Kazakh individual 164

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 164


title: pp71_D1177_RM15

description: G434_O14_RM15_L_B_D1177_RNA1_Lib1_GL52_S60


title: pp71_D1177_RM14

description: G433_O14_RM14_L_B_D1177_RNA1_Lib1_GL50_S63


title: DNA from Kazakh individual 163

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 163


title: Smartseq2_Lipstic_TdLN_189


title: Smartseq2_Lipstic_TdLN_185


title: DNA from Kazakh individual 162

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 162


title: TB6Ag_D1177_RM9

description: G430_O14_RM9_F_B_D1177_RNA1_Lib1_GL51_S5


title: TB6Ag_D1177_RM8

description: G429_O14_RM8_F_B_D1177_RNA1_Lib1_GL52_S37


title: DNA from Kazakh individual 161

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 161


title: DNA from Kazakh individual 160

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 160


title: TB6Ag_D1177_RM4

description: G426_O14_RM4_F_B_D1177_RNA1_Lib1_GL50_S39


title: TB6Ag_D1177_RM6

description: G427_O14_RM6_F_B_D1177_RNA1_Lib1_GL53_S27


title: Smartseq2_Lipstic_TdLN_181

value: naïve


title: TB6Ag_D1177_RM2

description: G424_O14_RM2_F_B_D1177_RNA1_Lib1_GL52_S92


title: TB6Ag_D1177_RM7

description: G425_O14_RM7_F_B_D1177_RNA1_Lib1_GL51_S39


title: DNA from Kazakh individual 159

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 159


title: Smartseq2_Lipstic_TdLN_180


title: DNA from Kazakh individual 158

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 158


title: TB6Ag_D1177_RM3

description: G422_O14_RM3_F_B_D1177_RNA1_Lib1_GL50_S11


title: Smartseq2_Lipstic_TdLN_184


title: TB6Ag_D1177_RM1

description: G423_O14_RM1_F_B_D1177_RNA1_Lib1_GL51_S16


title: Smartseq2_Lipstic_TdLN_179


title: Smartseq2_Lipstic_TdLN_183


title: TB6Ag_D1177_RM11

description: G420_O14_RM11_F_B_D1177_RNA1_Lib2_GL63_S25


title: Smartseq2_Lipstic_TdLN_182


title: pp71_D1177_RM13

description: G432_O14_RM13_L_B_D1177_RNA1_Lib1_GL50_S49


title: DNA from Kazakh individual 157

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 157


title: Smartseq2_Lipstic_TdLN_178


title: TB6Ag_D1177_RM12

description: G421_O14_RM12_F_B_D1177_RNA1_Lib1_GL50_S29


title: TB6Ag_D1177_RM10

description: G419_O14_RM10_F_B_D1177_RNA2_Lib1_GL53_S19


title: pp71_D1177_RM20

description: G431_O14_RM20_L_B_D1177_RNA1_Lib1_GL51_S56


title: DNA from Kazakh individual 156

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 156


title: pp71_D757_RM19

description: G409_O14_RM19_L_B_D757_RNA1_Lib1_GL53_S46


title: TB6Ag_D1177_RM5

description: G428_O14_RM5_F_B_D1177_RNA1_Lib1_GL51_S46


title: Smartseq2_Lipstic_TdLN_177


title: DNA from Kazakh individual 155

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 155


title: pp71_D757_RM17

description: G410_O14_RM17_L_B_D757_RNA2_Lib1_GL66_S93


title: Smartseq2_Lipstic_TdLN_176


title: pp71_D757_RM18

description: G408_O14_RM18_L_B_D757_RNA1_Lib1_GL53_S64


title: DNA from Kazakh individual 153

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 153


title: Smartseq2_Lipstic_TdLN_175


title: DNA from Kazakh individual 152

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 152


title: pp71_D757_RM13

description: G404_O14_RM13_L_B_D757_RNA1_Lib1_GL50_S91


title: pp71_D757_RM16

description: G407_O14_RM16_L_B_D757_RNA1_Lib1_GL52_S54


title: pp71_D757_RM14

description: G405_O14_RM14_L_B_D757_RNA2_Lib1_GL62_S90


title: pp71_D757_RM15

description: G406_O14_RM15_L_B_D757_RNA1_Lib1_GL50_S64


title: Smartseq2_Lipstic_TdLN_174


title: TB6Ag_D757_RM9

description: G402_O14_RM9_F_B_D757_RNA1_Lib1_GL53_S67


title: pp71_D757_RM20

description: G403_O14_RM20_L_B_D757_RNA1_Lib1_GL50_S88


title: Smartseq2_Lipstic_TdLN_173


title: DNA from Kazakh individual 149

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 149


title: Smartseq2_Lipstic_TdLN_172


title: TB6Ag_D757_RM8

description: G401_O14_RM8_F_B_D757_RNA1_Lib1_GL50_S90


title: TB6Ag_D757_RM6

description: G399_O14_RM6_F_B_D757_RNA1_Lib1_GL51_S80


title: TB6Ag_D757_RM4


title: DNA from Kazakh individual 148

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 148


title: TB6Ag_D757_RM5

description: G400_O14_RM5_F_B_D757_RNA1_Lib1_GL51_S43


title: Smartseq2_Lipstic_TdLN_171


title: DNA from Kazakh individual 146

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 146


title: TB6Ag_D757_RM2

description: G396_O14_RM2_F_B_D757_RNA1_Lib1_GL49_S43


title: TB6Ag_D757_RM7

description: G397_O14_RM7_F_B_D757_RNA1_Lib1_GL49_S31


title: Smartseq2_Lipstic_TdLN_170


title: DNA from Kazakh individual 145

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 145


title: TB6Ag_D757_RM3

description: G394_O14_RM3_F_B_D757_RNA1_Lib1_GL53_S81


title: TB6Ag_D757_RM1

description: G395_O14_RM1_F_B_D757_RNA1_Lib1_GL52_S74


title: DNA from Kazakh individual 144

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 144


title: Smartseq2_Lipstic_TdLN_169


title: DNA from Kazakh individual 150

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 150


title: TB6Ag_D757_RM12

description: G393_O14_RM12_F_B_D757_RNA1_Lib1_GL50_S67


title: Smartseq2_Lipstic_TdLN_168


title: DNA from Kazakh individual 142

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 142


title: Smartseq2_Lipstic_TdLN_167


title: TB6Ag_D757_RM10

description: G391_O14_RM10_F_B_D757_RNA1_Lib1_GL50_S53


title: pp71_D750_RM19

description: G381_O14_RM19_L_B_D750_RNA1_Lib1_GL50_S61


title: pp71_D750_RM17

description: G382_O14_RM17_L_B_D750_RNA1_Lib1_GL49_S47


title: TB6Ag_D757_RM11

description: G392_O14_RM11_F_B_D757_RNA1_Lib1_GL53_S24


title: DNA from Kazakh individual 141

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 141


title: DNA from Kazakh individual 140

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 140


title: DNA from Kazakh individual 139

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 139


title: pp71_D750_RM15

description: G378_O14_RM15_L_B_D750_RNA1_Lib1_GL51_S85


title: pp71_D750_RM18

description: G380_O14_RM18_L_B_D750_RNA1_Lib1_GL50_S28


title: pp71_D750_RM16

description: G379_O14_RM16_L_B_D750_RNA1_Lib1_GL52_S5


title: pp71_D750_RM14

description: G377_O14_RM14_L_B_D750_RNA2_Lib1_GL52_S71


title: Smartseq2_Lipstic_TdLN_165

value: Tumor


title: pp71_D750_RM20

description: G375_O14_RM20_L_B_D750_RNA1_Lib1_GL52_S91


title: DNA from Kazakh individual 138

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 138


title: Smartseq2_Lipstic_TdLN_163


title: DNA from Kazakh individual 136

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 136


title: TB6Ag_D750_RM5


title: TB6Ag_D750_RM8

description: G373_O14_RM8_F_B_D750_RNA1_Lib1_GL50_S30


title: TB6Ag_D750_RM9

description: G374_O14_RM9_F_B_D750_RNA1_Lib2_GL63_S22


title: TB6Ag_D750_RM4

description: G370_O14_RM4_F_B_D750_RNA1_Lib1_GL53_S92


title: Smartseq2_Lipstic_TdLN_161


title: Smartseq2_Lipstic_TdLN_162


title: TB6Ag_D750_RM6

description: G371_O14_RM6_F_B_D750_RNA1_Lib2_GL63_S21


title: Smartseq2_Lipstic_TdLN_166


title: TB6Ag_D750_RM7

description: G369_O14_RM7_F_B_D750_RNA1_Lib1_GL53_S23


title: Smartseq2_Lipstic_TdLN_160


title: TB6Ag_D750_RM1

description: G367_O14_RM1_F_B_D750_RNA1_Lib1_GL52_S88


title: DNA from Kazakh individual 130

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 130


title: DNA from Kazakh individual 132

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 132


title: TB6Ag_D750_RM2

description: G368_O14_RM2_F_B_D750_RNA1_Lib1_GL50_S50


title: TB6Ag_D750_RM3

description: G366_O14_RM3_F_B_D750_RNA1_Lib1_GL52_S63


title: pp71_D750_RM13

description: G376_O14_RM13_L_B_D750_RNA1_Lib2_GL63_S23


title: Smartseq2_Lipstic_TdLN_159


title: DNA from Kazakh individual 129

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 129


title: TB6Ag_D750_RM11

description: G364_O14_RM11_F_B_D750_RNA1_Lib1_GL50_S81


title: TB6Ag_D750_RM12

description: G365_O14_RM12_F_B_D750_RNA1_Lib1_GL49_S24


title: Smartseq2_Lipstic_TdLN_158


title: Smartseq2_Lipstic_TdLN_164


title: DNA from Kazakh individual 128

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 128


title: pp71_D746_RM17

description: G354_O14_RM17_L_B_D746_RNA1_Lib1_GL50_S60


title: Smartseq2_Lipstic_TdLN_157


title: pp71_D746_RM19

description: G353_O14_RM19_L_B_D746_RNA1_Lib1_GL52_S46


title: DNA from Kazakh individual 127

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 127


title: DNA from Kazakh individual 133

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 133


title: pp71_D746_RM18

description: G352_O14_RM18_L_B_D746_RNA1_Lib1_GL49_S29


title: DNA from Kazakh individual 126

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 126


title: Smartseq2_Lipstic_TdLN_156


title: pp71_D746_RM16

description: G351_O14_RM16_L_B_D746_RNA1_Lib1_GL52_S67


title: pp71_D746_RM15

description: G350_O14_RM15_L_B_D746_RNA1_Lib1_GL52_S81


title: DNA from Kazakh individual 120

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 120


title: pp71_D746_RM14

description: G349_O14_RM14_L_B_D746_RNA1_Lib1_GL53_S12


title: DNA from Kazakh individual 119

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 119


title: pp71_D746_RM13

description: G348_O14_RM13_L_B_D746_RNA2_Lib2_GL63_S19


title: pp71_D746_RM20

description: G347_O14_RM20_L_B_D746_RNA1_Lib1_GL49_S42


title: DNA from Kazakh individual 118

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 118


title: TB6Ag_D750_RM10

description: G363_O14_RM10_F_B_D750_RNA1_Lib1_GL52_S35


title: Smartseq2_Lipstic_TdLN_154


title: TB6Ag_D746_RM9

description: G346_O14_RM9_F_B_D746_RNA1_Lib2_GL63_S18


title: DNA from Kazakh individual 117

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 117


title: TB6Ag_D746_RM8

description: G345_O14_RM8_F_B_D746_RNA1_Lib1_GL53_S30


title: TB6Ag_D746_RM4

description: G342_O14_RM4_F_B_D746_RNA2_Lib1_GL57_S62


title: Smartseq2_Lipstic_TdLN_153


title: TB6Ag_D746_RM5

description: G344_O14_RM5_F_B_D746_RNA1_Lib2_GL63_S17


title: Smartseq2_Lipstic_TdLN_151


title: DNA from Kazakh individual 116

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 116


title: TB6Ag_D746_RM6

description: G343_O14_RM6_F_B_D746_RNA1_Lib1_GL50_S82


title: Smartseq2_Lipstic_TdLN_150


title: TB6Ag_D746_RM2

description: G340_O14_RM2_F_B_D746_RNA1_Lib1_GL51_S50


title: DNA from Kazakh individual 114

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 114


title: TB6Ag_D746_RM3

description: G338_O14_RM3_F_B_D746_RNA1_Lib2_GL63_S16


title: TB6Ag_D746_RM12

description: G337_O14_RM12_F_B_D746_RNA1_Lib1_GL52_S58


title: Smartseq2_Lipstic_TdLN_155


title: DNA from Kazakh individual 112

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 112


title: TB6Ag_D746_RM11

description: G336_O14_RM11_F_B_D746_RNA1_Lib1_GL53_S10


title: pp71_D743_RM17

description: G326_O14_RM17_L_B_D743_RNA1_Lib1_GL51_S21


title: Smartseq2_Lipstic_TdLN_148


title: DNA from Kazakh individual 109

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 109


title: Smartseq2_Lipstic_TdLN_152


title: Smartseq2_Lipstic_TdLN_147


title: TB6Ag_D746_RM7


title: pp71_D743_RM19

description: G325_O14_RM19_L_B_D743_RNA1_Lib1_GL53_S62


title: DNA from Kazakh individual 105

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 105


title: pp71_D743_RM18

description: G324_O14_RM18_L_B_D743_RNA1_Lib1_GL53_S31


title: pp71_D743_RM13

description: G320_O14_RM13_L_B_D743_RNA2_Lib1_GL50_S17


title: DNA from Kazakh individual 108

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 108


title: TB6Ag_D746_RM10

description: G335_O14_RM10_F_B_D746_RNA1_Lib1_GL51_S91


title: pp71_D743_RM15

description: G322_O14_RM15_L_B_D743_RNA1_Lib1_GL52_S95


title: pp71_D743_RM16

description: G323_O14_RM16_L_B_D743_RNA2_Lib1_GL53_S93


title: Smartseq2_Lipstic_TdLN_144


title: Smartseq2_Lipstic_TdLN_145


title: Smartseq2_Lipstic_TdLN_146


title: Smartseq2_Lipstic_TdLN_149


title: pp71_D743_RM20

description: G319_O14_RM20_L_B_D743_RNA1_Lib1_GL49_S40


title: pp71_D743_RM14

description: G321_O14_RM14_L_B_D743_RNA1_Lib1_GL50_S77


title: TB6Ag_D743_RM9

description: G318_O14_RM9_F_B_D743_RNA1_Lib2_GL63_S14


title: DNA from Kazakh individual 101

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 101


title: TB6Ag_D746_RM1

description: G339_O14_RM1_F_B_D746_RNA1_Lib1_GL53_S78


title: Smartseq2_Lipstic_TdLN_143


title: DNA from Kazakh individual 100

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 100


title: TB6Ag_D743_RM8

description: G317_O14_RM8_F_B_D743_RNA2_Lib1_GL62_S86


title: TB6Ag_D743_RM5

description: G316_O14_RM5_F_B_D743_RNA1_Lib1_GL53_S20


title: DNA from Kazakh individual 110

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 110


title: Smartseq2_Lipstic_TdLN_142


title: DNA from Kazakh individual 99

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 99


title: Smartseq2_Lipstic_TdLN_141


title: TB6Ag_D743_RM4

description: G314_O14_RM4_F_B_D743_RNA1_Lib1_GL51_S58


title: TB6Ag_D743_RM7

description: G313_O14_RM7_F_B_D743_RNA1_Lib1_GL50_S87


title: DNA from Kazakh individual 98

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 98


title: TB6Ag_D743_RM2

description: G312_O14_RM2_F_B_D743_RNA1_Lib1_GL53_S42


title: DNA from Kazakh individual 95

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 95


title: Smartseq2_Lipstic_TdLN_140


title: TB6Ag_D743_RM1

description: G311_O14_RM1_F_B_D743_RNA1_Lib1_GL53_S87


title: TB6Ag_D743_RM3


title: TB6Ag_D743_RM12

description: G309_O14_RM12_F_B_D743_RNA1_Lib1_GL52_S33


title: pp71_D1177_RM16

description: G435_O14_RM16_L_B_D1177_RNA1_Lib1_GL49_S18


title: Smartseq2_Lipstic_TdLN_139


title: pp71_D560_RM17

description: G286_O14_RM17_L_B_D560_RNA2_Lib2_GL63_S13


title: Smartseq2_Lipstic_TdLN_138


title: DNA from Kazakh individual 90

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 90


title: Smartseq2_Lipstic_TdLN_137


title: DNA from Kazakh individual 89

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 89


title: TB6Ag_D743_RM11

description: G308_O14_RM11_F_B_D743_RNA1_Lib1_GL53_S91


title: TB6Ag_D743_RM10

description: G307_O14_RM10_F_B_D743_RNA1_Lib1_GL66_S75


title: pp71_D560_RM16

description: G281_O14_RM16_L_B_D560_RNA2_Lib1_GL66_S91


title: DNA from Kazakh individual 88

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 88


title: pp71_D560_RM19

description: G285_O14_RM19_L_B_D560_RNA2_Lib1_GL53_S29


title: Smartseq2_Lipstic_TdLN_136


title: pp71_D560_RM18

description: G284_O14_RM18_L_B_D560_RNA2_Lib1_GL57_S61


title: Smartseq2_Lipstic_TdLN_135


title: DNA from Kazakh individual 87

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 87


title: Smartseq2_Lipstic_TdLN_134


title: pp71_D560_RM15

description: G280_O14_RM15_L_B_D560_RNA1_Lib1_GL50_S95


title: pp71_D560_RM13

description: G278_O14_RM13_L_B_D560_RNA1_Lib1_GL51_S53


title: pp71_D560_RM20

description: G277_O14_RM20_L_B_D560_RNA1_Lib1_GL51_S71


title: pp71_D560_RM14

description: G279_O14_RM14_L_B_D560_RNA1_Lib1_GL50_S12


title: DNA from Kazakh individual 86

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 86


title: TB6Ag_D560_RM8

description: G275_O14_RM8_F_B_D560_RNA1_Lib1_GL50_S45


title: DNA from Kazakh individual 93

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 93


title: Smartseq2_Lipstic_TdLN_133


title: TB6Ag_D560_RM9

description: G276_O14_RM9_F_B_D560_RNA1_Lib1_GL52_S31


title: TB6Ag_D743_RM6

description: G315_O14_RM6_F_B_D743_RNA1_Lib1_GL53_S58


title: DNA from Kazakh individual 85

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 85


title: TB6Ag_D560_RM6

description: G273_O14_RM6_F_B_D560_RNA1_Lib1_GL53_S95


title: DNA from Kazakh individual 84

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 84


title: TB6Ag_D560_RM5

description: G274_O14_RM5_F_B_D560_RNA1_Lib1_GL50_S70


title: TB6Ag_D560_RM4

description: G272_O14_RM4_F_B_D560_RNA1_Lib1_GL53_S45


title: DNA from Kazakh individual 83

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 83


title: Smartseq2_Lipstic_TdLN_132


title: TB6Ag_D560_RM7

description: G271_O14_RM7_F_B_D560_RNA1_Lib1_GL50_S43


title: Smartseq2_Lipstic_TdLN_131


title: TB6Ag_D560_RM2

description: G270_O14_RM2_F_B_D560_RNA1_Lib1_GL50_S38


title: TB6Ag_D560_RM1

description: G269_O14_RM1_F_B_D560_RNA1_Lib1_GL50_S66


title: Smartseq2_Lipstic_TdLN_130


title: DNA from Kazakh individual 82

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 82


title: TB6Ag_D560_RM3

description: G268_O14_RM3_F_B_D560_RNA2_Lib1_GL62_S81


title: Smartseq2_Lipstic_TdLN_129


title: DNA from Kazakh individual 80

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 80


title: TB6Ag_D560_RM12

description: G267_O14_RM12_F_B_D560_RNA1_Lib1_GL50_S10


title: TB6Ag_D560_RM11

description: G266_O14_RM11_F_B_D560_RNA1_Lib1_GL52_S82


title: Smartseq2_Lipstic_TdLN_128


title: DNA from Kazakh individual 79

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 79


title: pp71_D112_RM17

description: G253_O14_RM17_L_B_D112_RNA2_Lib1_GL66_S90


title: TB6Ag_D560_RM10

description: G265_O14_RM10_F_B_D560_RNA1_Lib1_GL52_S1


title: DNA from Kazakh individual 78

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 78


title: Smartseq2_Lipstic_TdLN_126


title: pp71_D112_RM18

description: G251_O14_RM18_L_B_D112_RNA1_Lib1_GL52_S34


title: DNA from Kazakh individual 77

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 77


title: pp71_D112_RM15

description: G247_O14_RM15_L_B_D112_RNA1_Lib1_GL53_S11


title: pp71_D112_RM16

description: G248_O14_RM16_L_B_D112_RNA1_Lib1_GL51_S4


title: pp71_D112_RM14

description: G246_O14_RM14_L_B_D112_RNA1_Lib1_GL52_S75


title: pp71_D112_RM13

description: G245_O14_RM13_L_B_D112_RNA1_Lib1_GL53_S70


title: DNA from Kazakh individual 73

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 73


title: pp71_D112_RM20

description: G244_O14_RM20_L_B_D112_RNA1_Lib1_GL51_S22


title: Smartseq2_Lipstic_TdLN_123


title: TB6Ag_D112_RM9

description: G243_O14_RM9_F_B_D112_RNA1_Lib1_GL52_S76


title: Smartseq2_Lipstic_TdLN_124


title: Smartseq2_Lipstic_TdLN_122


title: DNA from Kazakh individual 69

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 69


title: TB6Ag_D112_RM4

description: G239_O14_RM4_F_B_D112_RNA1_Lib1_GL52_S48


title: Smartseq2_Lipstic_TdLN_121


title: TB6Ag_D112_RM6

description: G240_O14_RM6_F_B_D112_RNA1_Lib2_GL63_S12


title: DNA from Kazakh individual 67

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 67


title: TB6Ag_D112_RM7

description: G238_O14_RM7_F_B_D112_RNA1_Lib1_GL52_S80


title: pp71_D112_RM19

description: G252_O14_RM19_L_B_D112_RNA1_Lib1_GL53_S77


title: TB6Ag_D112_RM2

description: G237_O14_RM2_F_B_D112_RNA1_Lib1_GL52_S72


title: Smartseq2_Lipstic_TdLN_120


title: Smartseq2_Lipstic_TdLN_127


title: TB6Ag_D112_RM1


title: DNA from Kazakh individual 65

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 65


title: DNA from Kazakh individual 75

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 75


title: TB6Ag_D112_RM3

description: G235_O14_RM3_F_B_D112_RNA1_Lib2_GL63_S10


title: Smartseq2_Lipstic_TdLN_119


title: Smartseq2_Lipstic_TdLN_125


title: TB6Ag_D112_RM5

description: G241_O14_RM5_F_B_D112_RNA1_Lib1_GL50_S46


title: TB6Ag_D112_RM8

description: G242_O14_RM8_F_B_D112_RNA1_Lib1_GL52_S79


title: DNA from Kazakh individual 64

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 64


title: DNA from Kazakh individual 71

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 71


title: TB6Ag_D112_RM12

description: G234_O14_RM12_F_B_D112_RNA1_Lib1_GL51_S92


title: Smartseq2_Lipstic_TdLN_118


title: pp71_D105_RM17

description: G220_O14_RM17_L_B_D105_RNA1_Lib1_GL53_S61


title: TB6Ag_D112_RM11

description: G233_O14_RM11_F_B_D112_RNA2_Lib1_GL57_S58


title: DNA from Kazakh individual 61

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 61


title: Smartseq2_Lipstic_TdLN_117


title: pp71_D105_RM18

description: G218_O14_RM18_L_B_D105_RNA1_Lib1_GL53_S49


title: pp71_D105_RM19

description: G219_O14_RM19_L_B_D105_RNA2_Lib1_GL52_S11


title: pp71_D105_RM16

description: G215_O14_RM16_L_B_D105_RNA2_Lib1_GL49_S36


title: Smartseq2_Lipstic_TdLN_116


title: pp71_D105_RM14

description: G213_O14_RM14_L_B_D105_RNA2_Lib1_GL62_S79


title: Smartseq2_Lipstic_TdLN_115


title: DNA from Kazakh individual 58

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 58


title: pp71_D105_RM13

description: G212_O14_RM13_L_B_D105_RNA2_Lib1_GL66_S89


title: DNA from Kazakh individual 57

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 57


title: Smartseq2_Lipstic_TdLN_114


title: pp71_D105_RM20

description: G211_O14_RM20_L_B_D105_RNA1_Lib1_GL52_S65


title: TB6Ag_D105_RM8

description: G209_O14_RM8_F_B_D105_RNA1_Lib1_GL52_S39


title: TB6Ag_D105_RM9

description: G210_O14_RM9_F_B_D105_RNA1_Lib1_GL51_S68


title: TB6Ag_D112_RM10

description: G232_O14_RM10_F_B_D112_RNA1_Lib1_GL53_S71


title: Smartseq2_Lipstic_TdLN_113


title: DNA from Kazakh individual 55

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 55


title: DNA from Kazakh individual 63

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 63


title: Smartseq2_Lipstic_TdLN_112


title: DNA from Kazakh individual 54

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 54


title: Smartseq2_Lipstic_TdLN_111


title: TB6Ag_D105_RM5

description: G208_O14_RM5_F_B_D105_RNA2_Lib1_GL51_S82


title: TB6Ag_D105_RM4

description: G206_O14_RM4_F_B_D105_RNA2_Lib1_GL50_S21


title: TB6Ag_D105_RM6

description: G207_O14_RM6_F_B_D105_RNA1_Lib1_GL51_S49


title: TB6Ag_D105_RM7

description: G205_O14_RM7_F_B_D105_RNA3_Lib1_GL62_S77


title: DNA from Kazakh individual 51

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 51


title: pp71_D105_RM15

description: G214_O14_RM15_L_B_D105_RNA2_Lib1_GL53_S47


title: Smartseq2_Lipstic_TdLN_110


title: DNA from Kazakh individual 50

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 50


title: DNA from Kazakh individual 59

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 59


title: TB6Ag_D105_RM3

description: G202_O14_RM3_F_B_D105_RNA1_Lib1_GL52_S26


title: Smartseq2_Lipstic_TdLN_109


title: TB6Ag_D105_RM12

description: G201_O14_RM12_F_B_D105_RNA2_Lib1_GL62_S76


title: TB6Ag_D105_RM11

description: G200_O14_RM11_F_B_D105_RNA2_Lib1_GL62_S74


title: DNA from Kazakh individual 49

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 49


title: Smartseq2_Lipstic_TdLN_108


title: DNA from Kazakh individual 48

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 48


title: TB6Ag_D105_RM10

description: G199_O14_RM10_F_B_D105_RNA3_Lib1_GL66_S88


title: DNA from Kazakh individual 45

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 45


title: pp71_D101_RM17

description: G187_O14_RM17_L_B_D101_RNA1_Lib1_GL50_S19


title: pp71_D101_RM18

description: G185_O14_RM18_L_B_D101_RNA1_Lib1_GL50_S32


title: pp71_D101_RM19

description: G186_O14_RM19_L_B_D101_RNA1_Lib1_GL50_S65


title: Smartseq2_Lipstic_TdLN_107


title: TB6Ag_D105_RM2


title: pp71_D101_RM13

description: G179_O14_RM13_L_B_D101_RNA1_Lib1_GL50_S83