title: Columbia accession, prmt5-5, replicate 1

description:
Library name: prmt5_Col_9
Column name in processed data file: prmt5_Col_9
parental_raw_counts.csv


title: Columbia accession, prmt5-5, replicate 2

status: Public on May 27 2025

type: SRA

city: Buenos Aires

first: Ariel

last: Chernomoretz

address: Av Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

description:
Library name: prmt5_Col_11
Column name in processed data file: prmt5_Col_11
parental_raw_counts.csv

library_source: transcriptomic

data_processing:
Before carrying out read mapping, the TrimGalore wrapper was used to remove adapter sequences with Curadapt and to check read quality with FastQC.
The STAR v2.7.9a (Dobin et al. 2013) aligner was used. STAR’s “2-pass” method improved sensitivity in detecting novel junctions that were not aligned to the coordinates of isoforms present in the genome annotation.
The TAIR10 reference genome was used for reads from the Col-0 accession, while an established strategy (Winkelmüller et al. 2021) was employed for Ler. A pseudo-reference genome was generated by utilizing the single nucleotide variant (SNP) and insertion/deletion (Indel) data of Ler obtained from the 1001 Genomes Project website, starting from the Col-0 genome. The pseudogene function incorporated in the GEAN software was employed to infer the sequence of the pseudo-genome by replacing the reference allele with the alternative allele of Ler.
Assembly: TAIR10
Supplementary files format and content: csv files include raw counts matrix. For F1 samples, it was included raw counts for Col-0 and Ler genome mapping. Only reads that could be unambiguously assigned to one parent were considered.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: entire seedlings

growth_protocol: Plants were cultivated on soil at 22°C under long-day (LD; 16-h light/8-h dark cycles; 80 μmol·m-2 s-1 of white light) conditions.

extract_protocol:
Seeds were sown on MS medium containing 0.8% m/v agar, stratified for four days in the dark at 4°C, and then transferred to continuous white light at 22°C. After nine days of growth, entire seedlings were collected and total RNA was purified using the QIAGEN RNeasy Plant Mini Kit following the manufacturer’s protocol.
cDNA libraries were generated based on the Illumina TruSeq RNA Sample Preparation Guide. Polyadenylated mRNA was extracted from 3 μg of total RNA and then fragmented. Reverse transcriptase SuperScript II (SSII RT) (Thermo Fisher Scientific, Waltham, MA, USA) and random hexamers were used to synthesize cDNA. Finally, specific adapters were added to each sample and the libraries were sequenced on the Illumina GAIIx platform with 100 bp reads. Reads were analyzed using version 1.3 of the Illumina pipeline and underwent quality filtration using standard Illumina procedures.

treatment_protocol: The prmt5-5 mutant isolated in the Col-0 background was backcrossed for 7 generations with WT plants of the Ler accession, checking for the presence of the mutant allele after each cross. To generate hybrid backgrounds of WT plants (F1 Col-0 x Ler) and prmt5-5 mutant plants (F1 prmt5-5 Col x prmt5-5 Ler), multiple crosses were conducted involving WT and prmt5-5 mutant plants from the Col-0 and Ler accessions.

tag: tissue

value: entire seedlings

tag: genotype

tag: accession


title: Columbia accession, prmt5-5, replicate 3

description:
Library name: prmt5_Col_12
Column name in processed data file: prmt5_Col_12
parental_raw_counts.csv


title: Landsberg erecta accession, WT, replicate 3

description:
Library name: Ler_8
Column name in processed data file: Ler_8
parental_raw_counts.csv

value: WT

value: Ler


title: Landsberg erecta accession, prmt5-5, replicate 2

description:
Library name: prmt5_Ler_15
Column name in processed data file: prmt5_Ler_15
parental_raw_counts.csv


title: Landsberg erecta accession, WT, replicate 2

description:
Library name: Ler_7
Column name in processed data file: Ler_7
parental_raw_counts.csv


title: Landsberg erecta accession, WT, replicate 1

description:
Library name: Ler_5
Column name in processed data file: Ler_5
parental_raw_counts.csv


title: Columbia accession, WT, replicate 2

description:
Library name: Col_3
Column name in processed data file: Col_3
parental_raw_counts.csv


title: Columbia accession, WT, replicate 1

description:
Library name: Col_1
Column name in processed data file: Col_1
parental_raw_counts.csv


title: nam8D, 48h, rep3

city: Ithaca

first: Jeffrey

last: Pleiss

state: NY

address: 215 Tower Rd. Room 453

department: Molecular Biology and Genetics

country: USA

institute: Cornell University

data_processing:
Read quality was assessed using FastQC (version v0.11.5) for each fastq file
Illumina adaptor sequences were trimmed using fastp (version 0.20.0) with the following parameters: fastp -i *_R1.fastq.gz -I *_R2.fastq.gz -o *_Trimmed_R1_P.fastq.gz -O *_Trimmed_R2_P.fastq.gz --disable_trim_poly_g --adapter_sequence CTGTCTCTTATACACATCT --adapter_sequence_r2 CTGTCTCTTATACACATCT  --unpaired1 *_unpaired_Trim.fastq.gz --unpaired2 *_unpaired_Trim.fastq.gz --html *.html --json *.json --thread 2 (Chen et al., 2018)
molecular counter and unextended reads were removed using custom python scripts
Reads were aligned to the S. cerevisiae  genome (assembly R64-1-124) (Engel et al,. 2014) using STAR (version 2.7.2b) with the following parameters: STAR --genomeDir  STAR_genome_2_7 --readFilesIn *_R1_NoEmpty.fastq.gz *_R2_NoEmpty.fastq.gz  --readFilesCommand zcat --peOverlapNbasesMin 5 --peOverlapMMp 0.1 --outFilterMultimapNmax 1 --alignIntronMin 10 --alignIntronMax 1100 --outSAMattributes All --runThreadN 4 --outSAMunmapped Within KeepPairs --alignSJoverhangMin 3 --alignSplicedMateMapLmin 3 --alignMatesGapMax 3000 --outFilterMismatchNmax 999 --alignEndsType EndToEnd --outFileNamePrefix *_Filtered_ --outSAMtype BAM SortedByCoordinate (Dobin et al., 2013)
Feature counting was done using a custom python script
Assembly: SGD S. cerevisiae reference genome assembly R64-1-124
Supplementary files format and content: tab delimited text files containing sample name, intron, mature counts, and premature total counts

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: JPY28A8 strain background BY

growth_protocol: Yeast strains were grown to log phase or stationary phase in minimal media supplemented with 2% D-glucose

extract_protocol:
Total RNA was extracted using hot acid phenol as described in Collart and Oliviero,  2001
MPE-seq, Xu et al 2019, Gildea et al 2020

treatment_protocol: Cells were collected at either log phase growth or stationary phase (48hrs)

tag: cell line

value: JPY28A8 strain background BY

tag: treatment

value: saturation


title: Columbia accession, WT, replicate 3

description:
Library name: Col_4
Column name in processed data file: Col_4
parental_raw_counts.csv


title: nam8D, 48h, rep2


title: F1 Columbia X Landsberg erecta, prmt5-5, replicate 2

description:
Library name: prmt5_ColXprmt5_Ler_26
Column name in processed data file: prmt5_ColXprmt5_Ler_26_alleleCol and prmt5_ColXprmt5_Ler_26_alleleLer
F1_ColXLer_raw_counts.csv


title: nam8D, 48h, rep1

source_name: JPY28H5 strain background BY

value: JPY28H5 strain background BY


title: nam8D, Log, rep3

value: log


title: nam8D, Log, rep2


title: mud1, 48h, rep3

source_name: JPY2863 strain background BY

value: JPY2863 strain background BY


title: mud1, Log, rep2

source_name: JPY10H3 strain background BY

value: JPY10H3 strain background BY


title: WTb, 48h, rep3


title: mud1, Log, rep3


title: WTb, Log, rep3


title: nam8D, Log, rep1


title: WTb, Log, rep2


title: WTb, 48h, rep2


title: mud1, 48h, rep2


title: WTa, 48h, rep1


title: WTa, 48h, rep2


title: mud1, Log, rep1


title: mud1, 48h, rep1


title: Batch2_mud1D_48h_28A8_3

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: Quebec

address: 3201, rue Jean-Mignault

country: Canada

institute: University of Sherbrooke

description: mud1D cells in starvation phase, biological replicate #3

data_processing:
The quality of RNA-seq reads was examined with Fastqc v0.11.9
Raw reads were trimmed with Trimmomatic v0.39  with the following parameters LEADING:20 TRAILING:20 MINLEN:15
Survicing reads were aligned to S. Cerevisiae reference genome obtained from Ensembl release 104 and a customized genome annotation using STAR  v2.7.9a with the following parameters --outFilterType BySJout --outFilterMismatchNmax 5 --alignIntronMax 2500 --alignMatesGapMax 14750.
The customized yeast genome annotation was created by combining the Ensembl annotation with additional gene information including long terminal repeats, autonomously replicating sequences, retrotransposons and untranslated regions from yeastmine, using scripts at the following repository http://gitlabscottgroup.med.usherbrooke.ca/gaspard/yeast_annotation.
Gene expression levels were calculated using CoCo  v1.0.0.
Assembly: Ensembl release 104 sarCer3
Supplementary files format and content: coco_expression.xlsx contains cpm and tpm of yeast genes as well as spike-ins in all samples

growth_protocol: Cells grown in SD supplemented with histine, leucine, uracil, lysine and 2% of D-glucose

extract_protocol:
Total RNA was isolated from cells grown in log or stationary phases using hot acid phenol extraction and DNase treatment (Qiagen) was performed.
RNAseq librairies were generated from 1ug DNA-free total RNA using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760S) and following the Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490)

tag: growth phase

value: starvation

tag: biological replicate


title: Batch2_mud1D_48h_28A8_1

description: mud1D cells in starvation phase, biological replicate #1


title: Batch2_nam8D_48h_28H5_3

description: nam8D cells in starvation phase, biological replicate #3


title: Batch2_nam8D_48h_28H5_1

description: nam8D cells in starvation phase, biological replicate #1


title: Batch2_hsh49::Q24P_48h_2863_3

description: hsh49::Q24P cells in starvation phase, biological replicate #3


title: Batch2_hsh49::Q24P_48h_2863_2

description: hsh49::Q24P cells in starvation phase, biological replicate #2


title: Batch2_hsh49::Q24P_48h_2863_1

description: hsh49::Q24P cells in starvation phase, biological replicate #1


title: Batch2_WT_10H3_48h_#3

description: WT cells in starvation phase, biological replicate #3


title: WTb, 48h, rep1


title: Batch2_WT_10H3_48h_#1

description: WT cells in starvation phase, biological replicate #1


title: Batch2_WT_10H3_48h_#2

description: WT cells in starvation phase, biological replicate #2


title: Batch2_mud1D_log_28A8_1

description: mud1D cells in log phase, biological replicate #1


title: Batch2_mud1D_48h_28A8_2

description: mud1D cells in starvation phase, biological replicate #2


title: WTb, Log, rep1


title: Batch2_mud1D_log_28A8_2

description: mud1D cells in log phase, biological replicate #2


title: Batch2_nam8D_log_28H5_2

description: nam8D cells in log phase, biological replicate #2


title: Batch2_hsh49::Q24P_log_2863_2

description: hsh49::Q24P cells in log phase, biological replicate #2


title: WTa, Log, rep3


title: Batch2_hsh49::Q24P_log_2863_1

description: hsh49::Q24P cells in log phase, biological replicate #1


title: WTa, 48h, rep3


title: Batch2_mud1D_log_28A8_3

description: mud1D cells in log phase, biological replicate #3


title: WTa, Log, rep2


title: Batch2_hsh49::Q24P_log_2863_3

description: hsh49::Q24P cells in log phase, biological replicate #3


title: Batch2_WT_10H3_log_#2

description: WT cells in log phase, biological replicate #2


title: Batch2_nam8D_log_28H5_3

description: nam8D cells in log phase, biological replicate #3


title: PD1-Resistant MM523

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
Gene expression estimates were computed as Transcript Per Million (TPM) values from paired-end FASTQ files using the software Kallisto in AltAnalyze version 2.1.0, using the human Ensembl version 72 transcriptome reference.
Assembly: hg19
Supplementary files format and content: TPM Expression values (tab delimited text file)

organism: Homo sapiens

source_name: Skin

extract_protocol:
500 ng of total RNA was purified from tumor biopsies using Qiagen Rneasy Kit according to the manufacturer’s instructions.
The RNA-Seq libraries were prepared from the purified RNA by using TruSeq RNA Library Prep Kit v2 (Illumina) for gene expression analyses.
Paired-end RNA-Seq was performed with HiSeq (Illumina). An average of ~40 million paired-end reads.

value: Skin

tag: cell type

value: Melanoma


title: PD1-Resistant MM507


title: PD1-Resistant MM506


title: Batch2_WT_10H3_log_#3

description: WT cells in log phase, biological replicate #3


title: PD1-Resistant MM490


title: Batch2_WT_10H3_log_#1

description: WT cells in log phase, biological replicate #1


title: PD1-Resistant MM395


title: PD1-Resistant MM-352


title: PD1-Resistant MM-384


title: Untreated MM-313

value: Untreated


title: Batch2_nam8D_log_28H5_1

description: nam8D cells in log phase, biological replicate #1


title: PD1-Resistant - MM_387-A7


title: PD1-Resistant MM-337


title: PD1-Resistant MM-386


title: Untreated MM-325


title: Untreated MM-206


title: Untreated MM-219


title: Untreated MM-179


title: PD1-Resistant MM-329


title: Untreated MM-195


title: Untreated MM-218


title: Untreated MM-251


title: Untreated MM-163


title: Untreated MM-230


title: Untreated MM-157


title: Untreated MM-189


title: PD1-Resistant MM406


title: Untreated MM-224


title: MM337-M7-Cobimetinib + Regorafenib

value: Cobimetinib + Regorafenib


title: PD1-Resistant MM-448


title: Untreated MM-348


title: MM337-M5-Vehicle

value: Vehicle


title: Untreated MM-178


title: MM337-M3-Cobimetinib + Regorafenib


title: MM337-M1-Vehicle


title: MM505-M7-Cobimetinib + Regorafenib


title: MM505-M12-Vehicle


title: MM505-M10-Vehicle


title: MM505-M11-Cobimetinib + Regorafenib


title: MTP3_4_biol rep 5

city: Houston

first: Hu

last: Chen

state: TX

address: 1250 Moursund St,

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
Adapter sequences were removed from raw sequencing reads using Trimmomatic v0.39 at default parameters.
Trimmed reads were aligned to GRCh38.p12 version 28 human genome assembly from GENCODE using STAR v2.7.9.a using all default parameters except –sjdbOverhang149.
Finally, differential gene expression analyses on the read counts were performed using DESeq2 in R environment.
Assembly: GRCh38
Supplementary files format and content: The number of reads mapped to each gene using the "--quantMode GeneCounts" option in STAR during mapping.

growth_protocol: PC3 cells were maintained in RPMI suppplemented with 10% FBS at 37oC, 90%RH, and 5% CO2. Cells were passaged at 80% confluency and split 1:5 at each passage.

extract_protocol:
Total RNA was extracted from using Qiagen Rneasy Plus Kit with gDNA eliminating columns. 2 ug of total RNA was provided to for library construction.
mRNA libraries for RNA-seq were prepared by Azenta/Genewiz using PolyA selection with ERCC spike ins

treatment_protocol: PC3 cells were seeded into 12 well plates to acheive 70% confluency and incubated over night. The following day, adherent cells were washed with DPBS and supplemented with fresh media containing indicated treatments conditions. Total volume of treatments per well was 1.2mL

value: Prostate cancer cell line

value: 20 uM MTP3, 24hr


title: MTP3_3_biol rep 4


title: MTP3_1_biol rep 2


title: MTP3_2_biol rep 3


title: MTP3_biol rep 1


title: PD1-Resistant MM409


title: HO3395_4_biol rep 5


title: HO3395_2_biol rep 3


title: DMSO_3_biol rep 4

value: DMSO, contol, 24hr


title: HO3395_biol rep 1

value: WT


title: DMSO_2_biol rep 3


title: HO3395_1_biol rep 2


title: MM337-M4-Cobimetinib + Regorafenib


title: DMSO_4_biol rep 5


title: MM337-M6-Vehicle


title: DMSO_biol rep 1


title: genotype: CNAG_07922, librarydate: 2018-01-16, sample: 2568

city: St Louis

first: Chase

last: Mateusiak

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University, St Louis

description: Library name: sample_2568

data_processing:
Reads were aligned with Novoalign (version 4.03.02) and quantified with HTSeq (0.9.1) using the FungiDB KN99 alpha genome sequence. Quality control ensued in two phases. In Phase I, custom scripts were used to verify the Crypto C. neoformans strain in each sample by calculating CDS coverage over putatively deleted genes and the corresponding selectable deletion cassette, ensuring that the former were absent and the latter present. Strains that passed this step were labeled as ‘passing’ if they contained at least 1e6 reads aligned to protein coding regions and less than 7% of all reads failed to align.
In Phase 2, we evaluated replicate agreement using the Regularized Log Expression (RLE). First, we used DESeq2 (version 1.34.0) to estimate the effect of the library date (the known batch effect). We removed the batch effect using the DESeq coefficients for the library dates such that the data was standardized to a single date, resulting in adjusted expression levels on a log2 normalized scale. To compute the RLE value for a given gene, the median expression level of that gene, across all samples in a replicate set, was subtracted from the expression level of that the gene in each sample. For each sample, we then calculated the interquartile range of the distribution of these RLE values across genes. If the interquartile range of RLEs of a given sample was greater than 1, indicating that more than half of genes deviated from their respective medians by a factor of 2 in adjusted count, the sample was considered an outlier and failed for replicate agreement.
Assembly: ASM221672v1
Supplementary files format and content: gzipped tab separated (tsv) raw counts and DESeq2 sizeFactor normalized counts

organism: Cryptococcus neoformans

growth_protocol: Strains were removed from -80C to YPD agar no more than 5 days before the experiment, grown at 30C for 2 nights , and a single colony was inoculated into 4 mL YPD and grown overnight  at 30C shaking at 230 rpm. One day before the experiment, 1 mL of the ON culture was inoculated into 100 mL YPD and grown as above. At the beginning of the experiment, this culture was spun down, washed in 25 mL PBS, and resuspended in 10 mL PBS. 2 x 10^8 cells were then inoculated into each of four T75 flasks containing preconditioned medium  and incubated under the conditions specified for the experiment. A single flask was harvested for each time point (30, 90, 180, and 1440 min after inoculation), with 1.5 mL of culture removed for imaging and the remaining 18.5 mL used for RNA-Seq. The latter was transferred into a tube on ice containing 2 mL RNA Stop solution (5% tris-saturated phenol in ethanol), the cells were sedimented (3000g, 5 min, 4C), supernatant fraction decanted, and the pellet was frozen in liquid nitrogen and stored at -80C. All flasks were prepared and then preconditioned for 24 hours at the designated temperature and pH concentration before use. Cultures were then inoculated as above and the T75 flasks (MIDSCI TP90076) incubated without rotation.

extract_protocol:
Frozen cell pellets were thawed on ice and 875m  TRIzol (Ambion 15-596-018) was added. Cells were then lysed with 750 ml 0.5mm silica-zirconia beads for 3 min in a Minibeadbeater (Biospec Products) and RNA isolated following the Trizol manufacturer’s protocol. Residual DNA was removed with the Turbo DNA-free Kit (Life Technologies AM1907) and polyA+ RNA isolated from ~1 mg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit from Illumina and samples were pooled at 10 nM. The pools were sequenced on a NextSeq 500 using the High75v2 kit as a 1x75 with 7bp Index1 and 6bp Index2 with 1% PhiX.  Fastq files were demultiplexed using the Illumina bcl2fastq2 allowing 1 bp mismatch.

value: yeast

tag: strain

value: deletion CNAG_07922

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min

tag: time

value: 90 min


title: genotype: CNAG_07940, librarydate: 2018-01-16, sample: 2547

description: Library name: sample_2547

value: deletion CNAG_07940


title: genotype: CNAG_07940, librarydate: 2018-01-26, sample: 1739

description: Library name: sample_1739


title: genotype: CNAG_07922, librarydate: 2018-01-26, sample: 1738

description: Library name: sample_1738


title: genotype: CNAG_07922, librarydate: 2018-01-16, sample: 2546

description: Library name: sample_2546


title: genotype: CNAG_07922, librarydate: 2018-01-26, sample: 1716

description: Library name: sample_1716


title: genotype: CNAG_07901, librarydate: 2018-01-16, sample: 2567

description: Library name: sample_2567

value: deletion CNAG_07901


title: HO3395_3_biol rep 4


title: genotype: CNAG_07901, librarydate: 2020-10-05, sample: 704

description: Library name: sample_704


title: genotype: CNAG_07528, librarydate: 2016-06-09, sample: 2010

description: Library name: sample_2010

value: deletion CNAG_07528


title: genotype: CNAG_07528, librarydate: 2020-10-30, sample: 2304

description: Library name: sample_2304


title: genotype: CNAG_07528, librarydate: 2018-08-14, sample: 375

description: Library name: sample_375


title: genotype: CNAG_07528, librarydate: 2016-06-09, sample: 2011

description: Library name: sample_2011


title: genotype: CNAG_07528, librarydate: 2016-11-10, sample: 39

description: Library name: sample_39


title: genotype: CNAG_07528, librarydate: 2016-11-10, sample: 38

description: Library name: sample_38


title: DMSO_1_biol rep 2


title: genotype: CNAG_07528, librarydate: 2016-11-10, sample: 37

description: Library name: sample_37


title: genotype: CNAG_07443, librarydate: 2021-03-10, sample: 2684

description: Library name: sample_2684

value: deletion CNAG_07443


title: genotype: CNAG_07443, librarydate: 2018-01-26, sample: 1714

description: Library name: sample_1714


title: genotype: CNAG_07940, librarydate: 2018-01-16, sample: 2569

description: Library name: sample_2569


title: genotype: CNAG_07443, librarydate: 2018-01-16, sample: 2566

description: Library name: sample_2566


title: genotype: CNAG_06921, librarydate: 2021-05-06, sample: 2829

description: Library name: sample_2829

value: deletion CNAG_06921


title: genotype: CNAG_07940, librarydate: 2018-01-26, sample: 1717

description: Library name: sample_1717


title: genotype: CNAG_07443, librarydate: 2021-03-10, sample: 2683

description: Library name: sample_2683


title: genotype: CNAG_07443, librarydate: 2018-01-16, sample: 2544

description: Library name: sample_2544


title: genotype: CNAG_06921, librarydate: 2021-05-06, sample: 2830

description: Library name: sample_2830


title: genotype: CNAG_06871, librarydate: 2018-07-06, sample: 1769

description: Library name: sample_1769

value: deletion CNAG_06871


title: genotype: CNAG_06921, librarydate: 2021-04-28, sample: 2814

description: Library name: sample_2814


title: genotype: CNAG_06871, librarydate: 2018-01-16, sample: 2548

description: Library name: sample_2548


title: genotype: CNAG_07901, librarydate: 2018-01-26, sample: 1715

description: Library name: sample_1715


title: genotype: CNAG_06921, librarydate: 2021-04-28, sample: 2813

description: Library name: sample_2813


title: genotype: CNAG_06871, librarydate: 2018-01-26, sample: 1740

description: Library name: sample_1740


title: genotype: CNAG_07901, librarydate: 2018-10-18, sample: 150

description: Library name: sample_150


title: genotype: CNAG_07528, librarydate: 2016-06-09, sample: 2009

description: Library name: sample_2009


title: genotype: CNAG_06871, librarydate: 2018-05-25, sample: 1364

description: Library name: sample_1364


title: genotype: CNAG_06751, librarydate: 2018-01-16, sample: 2528

description: Library name: sample_2528

value: deletion CNAG_06751


title: genotype: CNAG_06871, librarydate: 2018-01-26, sample: 1718

description: Library name: sample_1718


title: genotype: CNAG_06751, librarydate: 2018-01-16, sample: 2550

description: Library name: sample_2550


title: genotype: CNAG_06751, librarydate: 2018-01-26, sample: 1698

description: Library name: sample_1698


title: genotype: CNAG_06751, librarydate: 2018-05-25, sample: 1362

description: Library name: sample_1362


title: genotype: CNAG_06719, librarydate: 2018-01-16, sample: 2529

description: Library name: sample_2529

value: deletion CNAG_06719


title: genotype: CNAG_06719, librarydate: 2018-01-16, sample: 2551

description: Library name: sample_2551


title: genotype: CNAG_06719, librarydate: 2018-01-26, sample: 1721

description: Library name: sample_1721


title: genotype: CNAG_06719, librarydate: 2018-01-26, sample: 1699

description: Library name: sample_1699


title: genotype: CNAG_06483, librarydate: 2021-05-06, sample: 2828

description: Library name: sample_2828

value: deletion CNAG_06483


title: genotype: CNAG_06425, librarydate: 2018-01-16, sample: 2552

description: Library name: sample_2552

value: deletion CNAG_06425


title: genotype: CNAG_06483, librarydate: 2021-05-06, sample: 2827

description: Library name: sample_2827


title: genotype: CNAG_06483, librarydate: 2021-04-28, sample: 2811

description: Library name: sample_2811


title: genotype: CNAG_06483, librarydate: 2021-04-28, sample: 2812

description: Library name: sample_2812


title: genotype: CNAG_06871, librarydate: 2018-01-16, sample: 2570

description: Library name: sample_2570


title: genotype: CNAG_06425, librarydate: 2018-01-26, sample: 1722

description: Library name: sample_1722


title: genotype: CNAG_06425, librarydate: 2018-01-26, sample: 1700

description: Library name: sample_1700


title: genotype: CNAG_06425, librarydate: 2018-01-16, sample: 2530

description: Library name: sample_2530


title: genotype: CNAG_06339, librarydate: 2018-01-16, sample: 2553

description: Library name: sample_2553

value: deletion CNAG_06339


title: genotype: CNAG_06339, librarydate: 2018-01-16, sample: 2531

description: Library name: sample_2531


title: genotype: CNAG_06339, librarydate: 2016-10-04, sample: 2498

description: Library name: sample_2498


title: genotype: CNAG_06339, librarydate: 2018-01-26, sample: 1701

description: Library name: sample_1701


title: genotype: CNAG_06327, librarydate: 2018-01-16, sample: 2554

description: Library name: sample_2554

value: deletion CNAG_06327


title: genotype: CNAG_06327, librarydate: 2016-10-04, sample: 2497

description: Library name: sample_2497


title: genotype: CNAG_06339, librarydate: 2018-01-26, sample: 1723

description: Library name: sample_1723


title: genotype: CNAG_06327, librarydate: 2016-10-04, sample: 2495

description: Library name: sample_2495


title: genotype: CNAG_06327, librarydate: 2016-10-04, sample: 2496

description: Library name: sample_2496


title: genotype: CNAG_06276, librarydate: 2012-01-23, sample: 614

description: Library name: sample_614

value: deletion CNAG_06276


title: genotype: CNAG_06276, librarydate: 2012-03-19, sample: 226

description: Library name: sample_226

value: yeast


title: genotype: CNAG_06327, librarydate: 2018-01-26, sample: 1724

description: Library name: sample_1724


title: genotype: CNAG_06276, librarydate: 2012-03-19, sample: 227

description: Library name: sample_227


title: genotype: CNAG_06276, librarydate: 2012-03-19, sample: 225

description: Library name: sample_225


title: genotype: CNAG_06483, librarydate: 2021-06-08, sample: 2919

description: Library name: sample_2919


title: genotype: CNAG_06252, librarydate: 2020-09-02, sample: 837

description: Library name: sample_837

value: deletion CNAG_06252


title: genotype: CNAG_06252, librarydate: 2020-09-10, sample: 2063

description: Library name: sample_2063

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: genotype: CNAG_06156, librarydate: 2020-10-30, sample: 2300

description: Library name: sample_2300

value: deletion CNAG_06156

value: 90 min


title: genotype: CNAG_06252, librarydate: 2020-10-07, sample: 1049

description: Library name: sample_1049


title: genotype: CNAG_06252, librarydate: 2020-10-05, sample: 674

description: Library name: sample_674


title: genotype: CNAG_06156, librarydate: 2016-06-09, sample: 2006

description: Library name: sample_2006


title: genotype: CNAG_06156, librarydate: 2016-06-09, sample: 2008

description: Library name: sample_2008


title: genotype: CNAG_06134, librarydate: 2021-03-10, sample: 2673

description: Library name: sample_2673

value: deletion CNAG_06134


title: genotype: CNAG_06156, librarydate: 2016-06-09, sample: 2007

description: Library name: sample_2007


title: genotype: CNAG_06339, librarydate: 2016-10-04, sample: 2499

description: Library name: sample_2499


title: genotype: CNAG_06134, librarydate: 2021-01-13, sample: 1784

description: Library name: sample_1784


title: genotype: CNAG_06134, librarydate: 2021-01-13, sample: 1783

description: Library name: sample_1783


title: genotype: CNAG_06134, librarydate: 2018-08-14, sample: 377

description: Library name: sample_377


title: genotype: CNAG_06134, librarydate: 2021-03-10, sample: 2674

description: Library name: sample_2674


title: genotype: CNAG_06327, librarydate: 2018-01-16, sample: 2532

description: Library name: sample_2532


title: genotype: CNAG_06097, librarydate: 2018-01-16, sample: 2556

description: Library name: sample_2556

value: deletion CNAG_06097


title: genotype: CNAG_06097, librarydate: 2018-01-16, sample: 2534

description: Library name: sample_2534


title: genotype: CNAG_06097, librarydate: 2018-01-26, sample: 1704

description: Library name: sample_1704


title: genotype: CNAG_05861, librarydate: 2018-01-16, sample: 2535

description: Library name: sample_2535

value: deletion CNAG_05861


title: genotype: CNAG_05861, librarydate: 2013-03-13, sample: 2115

description: Library name: sample_2115


title: genotype: CNAG_05861, librarydate: 2013-03-13, sample: 2116

description: Library name: sample_2116


title: genotype: CNAG_05861, librarydate: 2018-01-26, sample: 1705

description: Library name: sample_1705


title: genotype: CNAG_05861, librarydate: 2018-01-16, sample: 2557

description: Library name: sample_2557


title: genotype: CNAG_05861, librarydate: 2018-01-26, sample: 1727

description: Library name: sample_1727


title: genotype: CNAG_05785, librarydate: 2017-11-01, sample: 1131

description: Library name: sample_1131

value: deletion CNAG_05785


title: genotype: CNAG_06252, librarydate: 2018-10-18, sample: 155

description: Library name: sample_155


title: genotype: CNAG_05785, librarydate: 2018-10-23, sample: 141

description: Library name: sample_141


title: genotype: CNAG_05785, librarydate: 2018-11-02, sample: 142

description: Library name: sample_142


title: genotype: CNAG_05642, librarydate: 2017-11-13, sample: 2180

description: Library name: sample_2180

value: deletion CNAG_05642


title: genotype: CNAG_05642, librarydate: 2017-11-01, sample: 1153

description: Library name: sample_1153


title: genotype: CNAG_05538, librarydate: 2021-03-10, sample: 2679

description: Library name: sample_2679

value: deletion CNAG_05538


title: genotype: CNAG_05642, librarydate: 2017-11-01, sample: 1130

description: Library name: sample_1130


title: genotype: CNAG_05642, librarydate: 2017-11-13, sample: 2203

description: Library name: sample_2203


title: genotype: CNAG_06097, librarydate: 2018-01-26, sample: 1726

description: Library name: sample_1726


title: genotype: CNAG_05436, librarydate: 2016-06-09, sample: 2012

description: Library name: sample_2012

value: deletion CNAG_05436


title: genotype: CNAG_05436, librarydate: 2016-06-09, sample: 2013

description: Library name: sample_2013


title: genotype: CNAG_05538, librarydate: 2018-10-23, sample: 140

description: Library name: sample_140


title: genotype: CNAG_05436, librarydate: 2016-11-10, sample: 36

description: Library name: sample_36


title: genotype: CNAG_05436, librarydate: 2016-06-09, sample: 2014

description: Library name: sample_2014


title: genotype: CNAG_05538, librarydate: 2018-08-14, sample: 382

description: Library name: sample_382


title: genotype: CNAG_05431, librarydate: 2012-03-26, sample: 2429

description: Library name: sample_2429

value: deletion CNAG_05431


title: genotype: CNAG_05436, librarydate: 2016-11-10, sample: 34

description: Library name: sample_34


title: genotype: CNAG_05431, librarydate: 2012-03-26, sample: 2427

description: Library name: sample_2427


title: genotype: CNAG_05538, librarydate: 2018-07-06, sample: 1766

description: Library name: sample_1766


title: genotype: CNAG_05431, librarydate: 2012-03-26, sample: 2428

description: Library name: sample_2428


title: Batch2_nam8D_48h_28H5_2

description: nam8D cells in starvation phase, biological replicate #2

value: starvation


title: genotype: CNAG_05431, librarydate: 2011-02-05, sample: 2022

description: Library name: sample_2022


title: genotype: CNAG_05785, librarydate: 2018-05-25, sample: 1358

description: Library name: sample_1358


title: genotype: CNAG_05431, librarydate: 2012-09-06, sample: 1612

description: Library name: sample_1612


title: genotype: CNAG_05420, librarydate: 2016-10-04, sample: 2460

description: Library name: sample_2460

value: deletion CNAG_05420


title: genotype: CNAG_05420, librarydate: 2015-11-16, sample: 2285

description: Library name: sample_2285


title: genotype: CNAG_05420, librarydate: 2016-10-04, sample: 2459

description: Library name: sample_2459


title: genotype: CNAG_05431, librarydate: 2012-09-06, sample: 1611

description: Library name: sample_1611


title: genotype: CNAG_05431, librarydate: 2012-09-06, sample: 1613

description: Library name: sample_1613


title: genotype: CNAG_05420, librarydate: 2016-10-04, sample: 2461

description: Library name: sample_2461


title: genotype: CNAG_05420, librarydate: 2015-11-16, sample: 2284

description: Library name: sample_2284


title: genotype: CNAG_05420, librarydate: 2015-11-16, sample: 2283

description: Library name: sample_2283


title: genotype: CNAG_05420, librarydate: 2013-10-08, sample: 1879

description: Library name: sample_1879


title: genotype: CNAG_05420, librarydate: 2013-10-08, sample: 1880

description: Library name: sample_1880


title: genotype: CNAG_05420, librarydate: 2012-05-01, sample: 562

description: Library name: sample_562


title: genotype: CNAG_05420, librarydate: 2012-05-01, sample: 561

description: Library name: sample_561


title: genotype: CNAG_05420, librarydate: 2012-05-01, sample: 560

description: Library name: sample_560


title: genotype: CNAG_05392, librarydate: 2016-10-04, sample: 2485

description: Library name: sample_2485

value: deletion CNAG_05392


title: genotype: CNAG_05420, librarydate: 2012-05-01, sample: 539

description: Library name: sample_539


title: genotype: CNAG_05420, librarydate: 2012-05-01, sample: 538

description: Library name: sample_538


title: genotype: CNAG_05392, librarydate: 2018-08-14, sample: 376

description: Library name: sample_376


title: genotype: CNAG_05392, librarydate: 2020-10-30, sample: 2306

description: Library name: sample_2306


title: genotype: CNAG_05392, librarydate: 2016-10-04, sample: 2483

description: Library name: sample_2483


title: genotype: CNAG_05420, librarydate: 2012-05-01, sample: 540

description: Library name: sample_540


title: genotype: CNAG_05380, librarydate: 2017-11-01, sample: 1152

description: Library name: sample_1152

value: deletion CNAG_05380


title: genotype: CNAG_05392, librarydate: 2016-10-04, sample: 2484

description: Library name: sample_2484

value: yeast


title: genotype: CNAG_05380, librarydate: 2018-08-14, sample: 380

description: Library name: sample_380


title: genotype: CNAG_05375, librarydate: 2017-11-13, sample: 2201

description: Library name: sample_2201

value: deletion CNAG_05375


title: genotype: CNAG_05380, librarydate: 2017-11-13, sample: 2202

description: Library name: sample_2202

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: genotype: CNAG_05375, librarydate: 2017-11-01, sample: 1151

description: Library name: sample_1151


title: genotype: CNAG_05375, librarydate: 2018-05-25, sample: 1356

description: Library name: sample_1356


title: genotype: CNAG_05222, librarydate: 2016-10-04, sample: 2474

description: Library name: sample_2474

value: deletion CNAG_05222


title: genotype: CNAG_05375, librarydate: 2017-11-01, sample: 1128

description: Library name: sample_1128

value: 90 min


title: genotype: CNAG_05255, librarydate: 2017-11-01, sample: 1150

description: Library name: sample_1150

value: deletion CNAG_05255


title: genotype: CNAG_05420, librarydate: 2013-10-08, sample: 1878

description: Library name: sample_1878


title: genotype: CNAG_05255, librarydate: 2018-05-25, sample: 1355

description: Library name: sample_1355


title: genotype: CNAG_05222, librarydate: 2016-10-04, sample: 2475

description: Library name: sample_2475


title: genotype: CNAG_05255, librarydate: 2017-11-01, sample: 1127

description: Library name: sample_1127


title: genotype: CNAG_05255, librarydate: 2017-11-13, sample: 2200

description: Library name: sample_2200


title: genotype: CNAG_05222, librarydate: 2016-10-04, sample: 2476

description: Library name: sample_2476


title: genotype: CNAG_05176, librarydate: 2017-11-13, sample: 2176

description: Library name: sample_2176

value: deletion CNAG_05176


title: genotype: CNAG_05170, librarydate: 2017-11-13, sample: 2175

description: Library name: sample_2175

value: deletion CNAG_05170


title: genotype: CNAG_05176, librarydate: 2017-11-01, sample: 1126

description: Library name: sample_1126


title: genotype: CNAG_05176, librarydate: 2017-11-01, sample: 1149

description: Library name: sample_1149


title: genotype: CNAG_05170, librarydate: 2017-11-01, sample: 1125

description: Library name: sample_1125


title: genotype: CNAG_05170, librarydate: 2018-05-25, sample: 1353

description: Library name: sample_1353


title: genotype: CNAG_05170, librarydate: 2017-11-01, sample: 1148

description: Library name: sample_1148


title: genotype: CNAG_05176, librarydate: 2018-05-25, sample: 1354

description: Library name: sample_1354


title: genotype: CNAG_05112, librarydate: 2017-11-01, sample: 1147

description: Library name: sample_1147

value: deletion CNAG_05112


title: genotype: CNAG_05112, librarydate: 2017-11-01, sample: 1124

description: Library name: sample_1124


title: genotype: CNAG_05380, librarydate: 2017-11-01, sample: 1129

description: Library name: sample_1129


title: genotype: CNAG_05112, librarydate: 2017-11-13, sample: 2174

description: Library name: sample_2174


title: genotype: CNAG_05049, librarydate: 2017-11-13, sample: 2195

description: Library name: sample_2195

value: deletion CNAG_05049


title: genotype: CNAG_05093, librarydate: 2018-05-25, sample: 1352

description: Library name: sample_1352

value: deletion CNAG_05093


title: genotype: CNAG_05049, librarydate: 2017-11-13, sample: 2172

description: Library name: sample_2172


title: genotype: CNAG_05112, librarydate: 2017-11-13, sample: 2197

description: Library name: sample_2197


title: genotype: CNAG_05093, librarydate: 2017-11-13, sample: 2196

description: Library name: sample_2196


title: genotype: CNAG_05093, librarydate: 2017-11-01, sample: 1123

description: Library name: sample_1123


title: genotype: CNAG_05049, librarydate: 2017-11-01, sample: 1145

description: Library name: sample_1145


title: genotype: CNAG_05049, librarydate: 2017-11-01, sample: 1122

description: Library name: sample_1122


title: genotype: CNAG_04908, librarydate: 2012-03-19, sample: 217

description: Library name: sample_217

value: deletion CNAG_04908


title: genotype: CNAG_04908, librarydate: 2012-03-19, sample: 216

description: Library name: sample_216


title: genotype: CNAG_05170, librarydate: 2017-11-13, sample: 2198

description: Library name: sample_2198


title: genotype: CNAG_04895, librarydate: 2021-04-28, sample: 2809

description: Library name: sample_2809

value: deletion CNAG_04895


title: genotype: CNAG_04895, librarydate: 2021-05-06, sample: 2825

description: Library name: sample_2825


title: genotype: CNAG_04908, librarydate: 2012-03-19, sample: 218

description: Library name: sample_218


title: genotype: CNAG_04864, librarydate: 2016-10-04, sample: 2455

description: Library name: sample_2455

value: deletion CNAG_04864


title: genotype: CNAG_04908, librarydate: 2012-01-23, sample: 606

description: Library name: sample_606


title: genotype: CNAG_04895, librarydate: 2021-05-06, sample: 2826

description: Library name: sample_2826


title: genotype: CNAG_04895, librarydate: 2021-04-28, sample: 2810

description: Library name: sample_2810


title: genotype: CNAG_04864, librarydate: 2015-08-10, sample: 1859

description: Library name: sample_1859


title: genotype: CNAG_05093, librarydate: 2017-11-01, sample: 1146

description: Library name: sample_1146


title: genotype: CNAG_04864, librarydate: 2016-10-04, sample: 2453

description: Library name: sample_2453


title: genotype: CNAG_04864, librarydate: 2015-08-10, sample: 1858

description: Library name: sample_1858


title: genotype: CNAG_04864, librarydate: 2015-08-10, sample: 1857

description: Library name: sample_1857


title: genotype: CNAG_04864, librarydate: 2012-02-13, sample: 1376

description: Library name: sample_1376


title: genotype: CNAG_04864, librarydate: 2012-02-13, sample: 1377

description: Library name: sample_1377


title: genotype: CNAG_04864, librarydate: 2012-02-13, sample: 1375

description: Library name: sample_1375


title: genotype: CNAG_04841, librarydate: 2020-09-02, sample: 865

description: Library name: sample_865

value: deletion CNAG_04841


title: genotype: CNAG_04841, librarydate: 2018-08-14, sample: 385

description: Library name: sample_385


title: genotype: CNAG_04841, librarydate: 2020-09-10, sample: 2095

description: Library name: sample_2095


title: genotype: CNAG_04841, librarydate: 2020-10-30, sample: 2346

description: Library name: sample_2346


title: genotype: CNAG_04841, librarydate: 2018-10-23, sample: 137

description: Library name: sample_137


title: genotype: CNAG_04807, librarydate: 2017-11-13, sample: 2194

description: Library name: sample_2194

value: deletion CNAG_04807


title: genotype: CNAG_04807, librarydate: 2017-11-01, sample: 1144

description: Library name: sample_1144


title: genotype: CNAG_04807, librarydate: 2017-11-13, sample: 2170

description: Library name: sample_2170


title: genotype: CNAG_04864, librarydate: 2016-10-04, sample: 2454

description: Library name: sample_2454


title: genotype: CNAG_04774, librarydate: 2017-11-01, sample: 1142

description: Library name: sample_1142

value: deletion CNAG_04774


title: genotype: CNAG_04804, librarydate: 2017-11-13, sample: 2171

description: Library name: sample_2171

value: yeast

value: deletion CNAG_04804


title: genotype: CNAG_04804, librarydate: 2017-11-01, sample: 1120

description: Library name: sample_1120

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: genotype: CNAG_04804, librarydate: 2017-11-01, sample: 1143

description: Library name: sample_1143


title: genotype: CNAG_04774, librarydate: 2017-11-13, sample: 2169

description: Library name: sample_2169


title: genotype: CNAG_04637, librarydate: 2021-01-13, sample: 1791

description: Library name: sample_1791

value: deletion CNAG_04637


title: genotype: CNAG_04804, librarydate: 2017-11-13, sample: 2193

description: Library name: sample_2193

value: 90 min


title: genotype: CNAG_04637, librarydate: 2018-01-16, sample: 2565

description: Library name: sample_2565


title: genotype: CNAG_04807, librarydate: 2017-11-01, sample: 1121

description: Library name: sample_1121


title: genotype: CNAG_04637, librarydate: 2018-01-26, sample: 1713

description: Library name: sample_1713


title: genotype: CNAG_04774, librarydate: 2017-11-13, sample: 2192

description: Library name: sample_2192


title: genotype: CNAG_04774, librarydate: 2017-11-01, sample: 1119

description: Library name: sample_1119


title: genotype: CNAG_04630, librarydate: 2017-11-13, sample: 2191

description: Library name: sample_2191

value: deletion CNAG_04630


title: genotype: CNAG_04637, librarydate: 2020-10-05, sample: 702

description: Library name: sample_702


title: genotype: CNAG_04841, librarydate: 2018-11-02, sample: 138

description: Library name: sample_138


title: genotype: CNAG_04630, librarydate: 2017-11-13, sample: 2168

description: Library name: sample_2168


title: genotype: CNAG_04588, librarydate: 2017-11-01, sample: 1139

description: Library name: sample_1139

value: deletion CNAG_04588


title: genotype: CNAG_04594, librarydate: 2017-11-13, sample: 2190

description: Library name: sample_2190

value: deletion CNAG_04594


title: genotype: CNAG_04588, librarydate: 2021-03-10, sample: 2677

description: Library name: sample_2677


title: genotype: CNAG_04594, librarydate: 2017-11-01, sample: 1140

description: Library name: sample_1140


title: genotype: CNAG_04594, librarydate: 2017-11-13, sample: 2167

description: Library name: sample_2167


title: genotype: CNAG_04588, librarydate: 2018-05-25, sample: 1350

description: Library name: sample_1350


title: genotype: CNAG_04630, librarydate: 2017-11-01, sample: 1118

description: Library name: sample_1118


title: genotype: CNAG_04588, librarydate: 2021-03-10, sample: 2678

description: Library name: sample_2678


title: genotype: CNAG_04588, librarydate: 2017-11-13, sample: 2166

description: Library name: sample_2166


title: genotype: CNAG_04630, librarydate: 2017-11-01, sample: 1141

description: Library name: sample_1141


title: genotype: CNAG_04594, librarydate: 2017-11-01, sample: 1117

description: Library name: sample_1117


title: genotype: CNAG_04586, librarydate: 2017-11-13, sample: 2188

description: Library name: sample_2188

value: deletion CNAG_04586


title: genotype: CNAG_04586, librarydate: 2018-05-25, sample: 1349

description: Library name: sample_1349


title: genotype: CNAG_04586, librarydate: 2017-11-13, sample: 2165

description: Library name: sample_2165


title: genotype: CNAG_04586, librarydate: 2017-11-01, sample: 1138

description: Library name: sample_1138


title: genotype: CNAG_04583, librarydate: 2021-10-26, sample: 3212

description: Library name: sample_3212

value: deletion CNAG_04583


title: genotype: CNAG_04518, librarydate: 2017-11-01, sample: 1137

description: Library name: sample_1137

value: deletion CNAG_04518


title: genotype: CNAG_04518, librarydate: 2017-11-13, sample: 2187

description: Library name: sample_2187


title: genotype: CNAG_04583, librarydate: 2021-05-06, sample: 2824

description: Library name: sample_2824


title: genotype: CNAG_04583, librarydate: 2021-04-28, sample: 2808

description: Library name: sample_2808


title: genotype: CNAG_04586, librarydate: 2017-11-01, sample: 1115

description: Library name: sample_1115


title: genotype: CNAG_04457, librarydate: 2017-11-01, sample: 1113

description: Library name: sample_1113

value: deletion CNAG_04457


title: genotype: CNAG_04457, librarydate: 2017-11-01, sample: 1136

description: Library name: sample_1136


title: genotype: CNAG_04457, librarydate: 2017-11-13, sample: 2163

description: Library name: sample_2163


title: genotype: CNAG_04518, librarydate: 2017-11-01, sample: 1114

description: Library name: sample_1114


title: genotype: CNAG_04398, librarydate: 2017-11-13, sample: 2185

description: Library name: sample_2185

value: deletion CNAG_04398


title: genotype: CNAG_04352, librarydate: 2020-10-30, sample: 2340

description: Library name: sample_2340

value: deletion CNAG_04352


title: genotype: CNAG_04353, librarydate: 2013-03-13, sample: 2110

description: Library name: sample_2110

value: deletion CNAG_04353


title: genotype: CNAG_04352, librarydate: 2021-01-13, sample: 1788

description: Library name: sample_1788


title: genotype: CNAG_04398, librarydate: 2017-11-01, sample: 1135

description: Library name: sample_1135


title: genotype: CNAG_04352, librarydate: 2018-05-25, sample: 1347

description: Library name: sample_1347


title: genotype: CNAG_04352, librarydate: 2017-11-01, sample: 1134

description: Library name: sample_1134


title: genotype: CNAG_04345, librarydate: 2012-01-03, sample: 2404

description: Library name: sample_2404

value: deletion CNAG_04345


title: genotype: CNAG_04345, librarydate: 2012-01-03, sample: 2403

description: Library name: sample_2403


title: genotype: CNAG_04583, librarydate: 2021-06-08, sample: 2920

description: Library name: sample_2920


title: genotype: CNAG_04457, librarydate: 2017-11-13, sample: 2186

description: Library name: sample_2186


title: genotype: CNAG_04345, librarydate: 2012-03-12, sample: 169

description: Library name: sample_169


title: genotype: CNAG_04345, librarydate: 2012-03-12, sample: 168

description: Library name: sample_168


title: genotype: CNAG_04184, librarydate: 2017-11-01, sample: 1133

description: Library name: sample_1133

value: deletion CNAG_04184


title: genotype: CNAG_04176, librarydate: 2021-10-26, sample: 3211

description: Library name: sample_3211

value: yeast

value: deletion CNAG_04176


title: genotype: CNAG_04352, librarydate: 2017-11-01, sample: 1111

description: Library name: sample_1111

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: genotype: CNAG_04176, librarydate: 2021-10-26, sample: 3210

description: Library name: sample_3210


title: genotype: CNAG_04176, librarydate: 2021-04-28, sample: 2806

description: Library name: sample_2806


title: genotype: CNAG_04345, librarydate: 2012-01-03, sample: 2405

description: Library name: sample_2405


title: genotype: CNAG_04176, librarydate: 2021-04-28, sample: 2805

description: Library name: sample_2805


title: genotype: CNAG_04518, librarydate: 2018-05-25, sample: 1348

description: Library name: sample_1348


title: genotype: CNAG_04093, librarydate: 2012-03-19, sample: 219

description: Library name: sample_219

value: deletion CNAG_04093


title: genotype: CNAG_04093, librarydate: 2012-01-23, sample: 609

description: Library name: sample_609

value: 90 min


title: genotype: CNAG_04012, librarydate: 2020-10-30, sample: 2338

description: Library name: sample_2338

value: deletion CNAG_04012


title: genotype: CNAG_04093, librarydate: 2012-01-23, sample: 608

description: Library name: sample_608


title: genotype: CNAG_04345, librarydate: 2012-03-12, sample: 167

description: Library name: sample_167


title: genotype: CNAG_04184, librarydate: 2017-11-01, sample: 1110

description: Library name: sample_1110


title: genotype: CNAG_04012, librarydate: 2018-05-25, sample: 1346

description: Library name: sample_1346


title: genotype: CNAG_04184, librarydate: 2017-11-13, sample: 2160

description: Library name: sample_2160


title: genotype: CNAG_03998, librarydate: 2017-09-07, sample: 195

description: Library name: sample_195

value: deletion CNAG_03998


title: genotype: CNAG_03914, librarydate: 2020-10-30, sample: 2334

description: Library name: sample_2334

value: deletion CNAG_03914


title: genotype: CNAG_03998, librarydate: 2017-08-09, sample: 784

description: Library name: sample_784


title: genotype: CNAG_03914, librarydate: 2017-10-03, sample: 1489

description: Library name: sample_1489


title: genotype: CNAG_04398, librarydate: 2017-11-13, sample: 2162

description: Library name: sample_2162


title: genotype: CNAG_03914, librarydate: 2017-09-07, sample: 194

description: Library name: sample_194


title: genotype: CNAG_03902, librarydate: 2012-01-03, sample: 2402

description: Library name: sample_2402

value: deletion CNAG_03902


title: genotype: CNAG_04012, librarydate: 2017-10-03, sample: 1470

description: Library name: sample_1470


title: genotype: CNAG_03902, librarydate: 2012-03-12, sample: 165

description: Library name: sample_165


title: genotype: CNAG_03902, librarydate: 2012-01-03, sample: 2400

description: Library name: sample_2400


title: genotype: CNAG_03902, librarydate: 2012-03-12, sample: 164

description: Library name: sample_164


title: genotype: CNAG_03894, librarydate: 2020-09-10, sample: 2055

description: Library name: sample_2055

value: deletion CNAG_03894


title: genotype: CNAG_04353, librarydate: 2013-03-13, sample: 2108

description: Library name: sample_2108


title: genotype: CNAG_03894, librarydate: 2020-09-10, sample: 2053

description: Library name: sample_2053


title: genotype: CNAG_04353, librarydate: 2013-03-13, sample: 2109

description: Library name: sample_2109


title: genotype: CNAG_03894, librarydate: 2019-11-10, sample: 276

description: Library name: sample_276


title: genotype: CNAG_03894, librarydate: 2013-03-13, sample: 2118

description: Library name: sample_2118


title: genotype: CNAG_03849, librarydate: 2012-05-01, sample: 659

description: Library name: sample_659

value: deletion CNAG_03849


title: genotype: CNAG_03849, librarydate: 2012-05-01, sample: 660

description: Library name: sample_660


title: genotype: CNAG_03998, librarydate: 2017-10-03, sample: 1469

description: Library name: sample_1469


title: genotype: CNAG_04012, librarydate: 2017-10-03, sample: 1491

description: Library name: sample_1491


title: genotype: CNAG_04184, librarydate: 2021-03-10, sample: 2676

description: Library name: sample_2676


title: genotype: CNAG_03998, librarydate: 2017-10-03, sample: 1490

description: Library name: sample_1490


title: genotype: CNAG_04352, librarydate: 2017-11-13, sample: 2184

description: Library name: sample_2184


title: genotype: CNAG_04012, librarydate: 2017-09-07, sample: 196

description: Library name: sample_196


title: genotype: CNAG_04398, librarydate: 2017-11-01, sample: 1112

description: Library name: sample_1112


title: genotype: CNAG_04093, librarydate: 2012-03-19, sample: 220

description: Library name: sample_220


title: genotype: CNAG_04093, librarydate: 2012-03-19, sample: 221

description: Library name: sample_221


title: genotype: CNAG_03741, librarydate: 2020-10-07, sample: 1065

description: Library name: sample_1065

value: deletion CNAG_03741


title: genotype: CNAG_04184, librarydate: 2021-03-10, sample: 2675

description: Library name: sample_2675


title: genotype: CNAG_03914, librarydate: 2017-10-03, sample: 1468

description: Library name: sample_1468


title: genotype: CNAG_03741, librarydate: 2017-09-07, sample: 193

description: Library name: sample_193


title: genotype: CNAG_03741, librarydate: 2017-08-09, sample: 782

description: Library name: sample_782


title: genotype: CNAG_03894, librarydate: 2013-03-13, sample: 2119

description: Library name: sample_2119


title: genotype: CNAG_03894, librarydate: 2019-11-10, sample: 977

description: Library name: sample_977


title: genotype: CNAG_03902, librarydate: 2012-01-03, sample: 2401

description: Library name: sample_2401


title: genotype: CNAG_03710, librarydate: 2016-06-09, sample: 2004

description: Library name: sample_2004

value: deletion CNAG_03710


title: genotype: CNAG_03902, librarydate: 2012-03-12, sample: 166

description: Library name: sample_166


title: genotype: CNAG_03894, librarydate: 2020-10-30, sample: 2294

description: Library name: sample_2294


title: genotype: CNAG_03894, librarydate: 2019-10-23, sample: 1328

description: Library name: sample_1328


title: genotype: CNAG_03741, librarydate: 2017-10-03, sample: 1488

description: Library name: sample_1488


title: genotype: CNAG_03914, librarydate: 2018-05-25, sample: 1345

description: Library name: sample_1345


title: genotype: CNAG_03710, librarydate: 2016-11-10, sample: 32

description: Library name: sample_32


title: genotype: CNAG_03710, librarydate: 2016-11-10, sample: 10

description: Library name: sample_10


title: genotype: CNAG_03561, librarydate: 2017-09-07, sample: 192

description: Library name: sample_192

value: deletion CNAG_03561


title: genotype: CNAG_03894, librarydate: 2013-03-13, sample: 2117

description: Library name: sample_2117


title: genotype: CNAG_03849, librarydate: 2012-05-01, sample: 658

description: Library name: sample_658


title: genotype: CNAG_03561, librarydate: 2018-05-25, sample: 1344

description: Library name: sample_1344


title: genotype: CNAG_03409, librarydate: 2020-09-10, sample: 2089

description: Library name: sample_2089

value: deletion CNAG_03409


title: genotype: CNAG_03409, librarydate: 2020-10-30, sample: 2332

description: Library name: sample_2332


title: genotype: CNAG_03741, librarydate: 2020-10-05, sample: 692

description: Library name: sample_692


title: genotype: CNAG_03741, librarydate: 2017-10-03, sample: 1467

description: Library name: sample_1467


title: genotype: CNAG_03409, librarydate: 2017-09-07, sample: 190

description: Library name: sample_190


title: genotype: CNAG_03401, librarydate: 2020-09-10, sample: 2087

description: Library name: sample_2087

value: deletion CNAG_03401


title: genotype: CNAG_03401, librarydate: 2017-08-09, sample: 778

description: Library name: sample_778


title: genotype: CNAG_03401, librarydate: 2017-09-07, sample: 189

description: Library name: sample_189


title: genotype: CNAG_03366, librarydate: 2021-10-26, sample: 3213

description: Library name: sample_3213

value: deletion CNAG_03366


title: genotype: CNAG_03366, librarydate: 2021-06-08, sample: 2918

description: Library name: sample_2918

value: yeast


title: genotype: CNAG_03409, librarydate: 2017-08-09, sample: 779

description: Library name: sample_779


title: genotype: CNAG_03431, librarydate: 2021-04-28, sample: 2802

description: Library name: sample_2802

value: deletion CNAG_03431


title: genotype: CNAG_03431, librarydate: 2021-05-06, sample: 2817

description: Library name: sample_2817

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: genotype: CNAG_03710, librarydate: 2016-11-10, sample: 31

description: Library name: sample_31


title: genotype: CNAG_03409, librarydate: 2017-10-03, sample: 1464

description: Library name: sample_1464


title: genotype: CNAG_03561, librarydate: 2017-10-03, sample: 1466

description: Library name: sample_1466


title: genotype: CNAG_03431, librarydate: 2021-06-08, sample: 2913

description: Library name: sample_2913


title: genotype: CNAG_03710, librarydate: 2016-06-09, sample: 2005

description: Library name: sample_2005


title: genotype: CNAG_03366, librarydate: 2021-05-06, sample: 2831

description: Library name: sample_2831


title: genotype: CNAG_03561, librarydate: 2020-10-05, sample: 690

description: Library name: sample_690


title: genotype: CNAG_03346, librarydate: 2021-01-13, sample: 1789

description: Library name: sample_1789

value: deletion CNAG_03346


title: genotype: CNAG_03710, librarydate: 2016-11-10, sample: 12

description: Library name: sample_12

value: 90 min


title: genotype: CNAG_03401, librarydate: 2017-10-03, sample: 1463

description: Library name: sample_1463


title: genotype: CNAG_03710, librarydate: 2016-11-10, sample: 11

description: Library name: sample_11


title: genotype: CNAG_03346, librarydate: 2018-01-16, sample: 2558

description: Library name: sample_2558


title: genotype: CNAG_03431, librarydate: 2021-04-28, sample: 2801

description: Library name: sample_2801


title: genotype: CNAG_03336, librarydate: 2020-09-10, sample: 2085

description: Library name: sample_2085

value: deletion CNAG_03336


title: genotype: CNAG_03366, librarydate: 2021-05-06, sample: 2832

description: Library name: sample_2832


title: genotype: CNAG_03401, librarydate: 2017-10-03, sample: 1484

description: Library name: sample_1484


title: genotype: CNAG_03336, librarydate: 2017-10-03, sample: 1461

description: Library name: sample_1461


title: genotype: CNAG_03346, librarydate: 2020-09-02, sample: 863

description: Library name: sample_863


title: genotype: CNAG_03336, librarydate: 2017-08-09, sample: 777

description: Library name: sample_777


title: genotype: CNAG_03346, librarydate: 2018-01-26, sample: 1706

description: Library name: sample_1706


title: genotype: CNAG_03279, librarydate: 2020-09-10, sample: 2059

description: Library name: sample_2059

value: deletion CNAG_03279


title: genotype: CNAG_03336, librarydate: 2017-09-07, sample: 188

description: Library name: sample_188


title: genotype: CNAG_03279, librarydate: 2020-09-02, sample: 833

description: Library name: sample_833


title: genotype: CNAG_03346, librarydate: 2020-10-05, sample: 698

description: Library name: sample_698


title: genotype: CNAG_03409, librarydate: 2017-10-03, sample: 1485

description: Library name: sample_1485


title: genotype: CNAG_03279, librarydate: 2020-10-05, sample: 670

description: Library name: sample_670


title: genotype: CNAG_03212, librarydate: 2016-06-09, sample: 2002

description: Library name: sample_2002

value: deletion CNAG_03212


title: genotype: CNAG_03212, librarydate: 2016-11-10, sample: 18

description: Library name: sample_18


title: genotype: CNAG_03212, librarydate: 2016-11-10, sample: 16

description: Library name: sample_16


title: genotype: CNAG_03212, librarydate: 2016-06-09, sample: 2001

description: Library name: sample_2001


title: genotype: CNAG_03132, librarydate: 2017-10-03, sample: 1462

description: Library name: sample_1462

value: deletion CNAG_03132


title: genotype: CNAG_03132, librarydate: 2017-09-07, sample: 187

description: Library name: sample_187


title: genotype: CNAG_03132, librarydate: 2018-05-25, sample: 1343

description: Library name: sample_1343


title: genotype: CNAG_03115, librarydate: 2016-06-09, sample: 2000

description: Library name: sample_2000

value: deletion CNAG_03115


title: genotype: CNAG_03212, librarydate: 2016-11-10, sample: 17

description: Library name: sample_17


title: genotype: CNAG_03132, librarydate: 2020-10-30, sample: 2330

description: Library name: sample_2330


title: genotype: CNAG_03336, librarydate: 2017-10-03, sample: 1483

description: Library name: sample_1483


title: genotype: CNAG_03212, librarydate: 2018-08-14, sample: 373

description: Library name: sample_373


title: genotype: CNAG_03115, librarydate: 2016-06-09, sample: 1998

description: Library name: sample_1998


title: genotype: CNAG_03132, librarydate: 2017-10-03, sample: 1482

description: Library name: sample_1482


title: genotype: CNAG_03115, librarydate: 2016-11-10, sample: 41

description: Library name: sample_41


title: genotype: CNAG_03115, librarydate: 2016-11-10, sample: 42

description: Library name: sample_42


title: genotype: CNAG_03115, librarydate: 2016-06-09, sample: 1999

description: Library name: sample_1999


title: genotype: CNAG_03336, librarydate: 2020-09-02, sample: 856

description: Library name: sample_856


title: genotype: CNAG_03086, librarydate: 2017-10-03, sample: 1481

description: Library name: sample_1481

value: deletion CNAG_03086


title: genotype: CNAG_03115, librarydate: 2016-11-10, sample: 40

description: Library name: sample_40


title: genotype: CNAG_03086, librarydate: 2020-09-10, sample: 2083

description: Library name: sample_2083


title: genotype: CNAG_03212, librarydate: 2016-06-09, sample: 2003

description: Library name: sample_2003


title: genotype: CNAG_03086, librarydate: 2017-10-03, sample: 1460

description: Library name: sample_1460


title: genotype: CNAG_03086, librarydate: 2017-09-07, sample: 186

description: Library name: sample_186


title: genotype: CNAG_03086, librarydate: 2020-09-02, sample: 854

description: Library name: sample_854


title: genotype: CNAG_03059, librarydate: 2020-10-30, sample: 2328

description: Library name: sample_2328

value: deletion CNAG_03059


title: genotype: CNAG_03059, librarydate: 2017-10-03, sample: 1480

description: Library name: sample_1480


title: genotype: CNAG_03059, librarydate: 2017-10-03, sample: 1459

description: Library name: sample_1459


title: genotype: CNAG_03059, librarydate: 2018-05-25, sample: 1342

description: Library name: sample_1342


title: genotype: CNAG_03086, librarydate: 2017-08-09, sample: 775

description: Library name: sample_775


title: genotype: CNAG_03018, librarydate: 2021-03-10, sample: 2668

description: Library name: sample_2668

value: deletion CNAG_03018


title: genotype: CNAG_03018, librarydate: 2021-01-13, sample: 1775

description: Library name: sample_1775


title: genotype: CNAG_03059, librarydate: 2017-09-07, sample: 185

description: Library name: sample_185


title: genotype: CNAG_02877, librarydate: 2017-10-03, sample: 1458

description: Library name: sample_1458

value: deletion CNAG_02877


title: genotype: CNAG_02877, librarydate: 2017-10-03, sample: 1479

description: Library name: sample_1479


title: genotype: CNAG_02877, librarydate: 2017-09-07, sample: 184

description: Library name: sample_184


title: genotype: CNAG_02774, librarydate: 2012-07-28, sample: 513

description: Library name: sample_513

value: deletion CNAG_02774


title: genotype: CNAG_02700, librarydate: 2021-03-10, sample: 2682

description: Library name: sample_2682

value: deletion CNAG_02700


title: genotype: CNAG_02723, librarydate: 2020-10-30, sample: 2324

description: Library name: sample_2324

value: deletion CNAG_02723


title: genotype: CNAG_02774, librarydate: 2012-07-28, sample: 515

description: Library name: sample_515

value: yeast


title: genotype: CNAG_02774, librarydate: 2012-07-28, sample: 514

description: Library name: sample_514


title: genotype: CNAG_02877, librarydate: 2020-10-30, sample: 2326

description: Library name: sample_2326


title: genotype: CNAG_02723, librarydate: 2018-05-25, sample: 1341

description: Library name: sample_1341


title: genotype: CNAG_02723, librarydate: 2017-09-07, sample: 183

description: Library name: sample_183


title: genotype: CNAG_02723, librarydate: 2017-10-03, sample: 1457

description: Library name: sample_1457


title: genotype: CNAG_02723, librarydate: 2017-10-03, sample: 1478

description: Library name: sample_1478


title: genotype: CNAG_02700, librarydate: 2020-10-30, sample: 2348

description: Library name: sample_2348


title: genotype: CNAG_02603, librarydate: 2017-10-03, sample: 1456

description: Library name: sample_1456

value: deletion CNAG_02603


title: genotype: CNAG_02603, librarydate: 2020-10-30, sample: 2322

description: Library name: sample_2322

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: genotype: CNAG_02603, librarydate: 2018-05-25, sample: 1340

description: Library name: sample_1340


title: genotype: CNAG_02566, librarydate: 2015-08-10, sample: 1862

description: Library name: sample_1862

value: deletion CNAG_02566


title: genotype: CNAG_02566, librarydate: 2015-08-10, sample: 1861

description: Library name: sample_1861

value: 90 min


title: genotype: CNAG_02603, librarydate: 2017-09-07, sample: 182

description: Library name: sample_182


title: genotype: CNAG_02566, librarydate: 2018-10-18, sample: 158

description: Library name: sample_158


title: genotype: CNAG_02566, librarydate: 2016-11-10, sample: 15

description: Library name: sample_15


title: Healthy lung sample 10 rep 2, snRNA-seq

first: Satish K

last: Madala

state: Ohio

address: 3230 Eden Avenue

department: Internal Medicine

institute: University Of Cincinnati

description:
Library name: C11
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed using Illumina's bcl2fastq v2.20.0.422 software with default parameters, generating individual fastq files for each sample.
These fastq files were aligned to the human reference genome (hg38) on 10x Genomics Cell Ranger v7.0.1 using 10x Genomics Cloud Analysis, which generated cell barcode, feature, and matrix files.
Assembly: hg38 (human)
Supplementary files format and content: compressed folder which contains, "barcodes.tsv", "features.tsv" and "matrix.mtx" files that are used to generate seurat object for further analysis and visualization.

molecule: nuclear RNA

source_name: Right Lower Lung Lobe

extract_protocol:
Frozen lung tissues were collected from the most basal segments of the right lower lobes, and carefully excised to obtain approximately 50 mg of tissue free of visible airway structures, vessels, mucin, or blood clots. Tissues were immediately placed into a nuclei isolation buffer (20 mM Tris-HCl pH 7.5, 292 mM NaCl, 2 mM CaCl2, 42 mM MgCl2, 1% CHAPS, and 2% BSA) and homogenized using a Dounce homogenizer to mechanically dissociate nuclei from cells. The resulting homogenate was filtered through a 40 µm strainer, and nuclei were pelleted by centrifugation at 300 × g for 2 minutes at 4°C. Nuclei were resuspended in 0.04% BSA buffer to a final concentration of 1,000 nuclei/µl.
Single-nuclei RNA sequencing (snRNA-seq) libraries were prepared using the 10x Genomics 5' Kit v2, following the manufacturer's protocol (10X Genomics). Libraries were sequenced on an Illumina NextSeq 550 platform using 75-cycle paired-end sequencing.

value: Right Lower Lung Lobe

value: All cells

tag: Sex

value: Female

tag: age


title: Healthy lung sample 10 rep 1, snRNA-seq

description:
Library name: C10
10X Genomics


title: genotype: CNAG_02566, librarydate: 2016-11-10, sample: 13

description: Library name: sample_13


title: genotype: CNAG_02700, librarydate: 2018-11-02, sample: 135

description: Library name: sample_135


title: genotype: CNAG_02700, librarydate: 2021-03-10, sample: 2681

description: Library name: sample_2681


title: Healthy lung sample 8, snRNA-seq

description:
Library name: C8
10X Genomics

value: Male


title: Healthy lung sample 9, snRNA-seq

description:
Library name: C9
10X Genomics


title: genotype: CNAG_02566, librarydate: 2015-05-19, sample: 2353

description: Library name: sample_2353


title: genotype: CNAG_02603, librarydate: 2017-10-03, sample: 1477

description: Library name: sample_1477


title: genotype: CNAG_02566, librarydate: 2016-11-10, sample: 14

description: Library name: sample_14


title: Healthy lung sample 7, snRNA-seq

description:
Library name: C7
10X Genomics


title: genotype: CNAG_02566, librarydate: 2013-04-17, sample: 1034

description: Library name: sample_1034


title: genotype: CNAG_02566, librarydate: 2013-04-17, sample: 1033

description: Library name: sample_1033


title: Healthy lung sample 5, snRNA-seq

description:
Library name: C5
10X Genomics


title: genotype: CNAG_02516, librarydate: 2017-10-03, sample: 1476

description: Library name: sample_1476

value: deletion CNAG_02516


title: genotype: CNAG_02516, librarydate: 2018-05-25, sample: 1339

description: Library name: sample_1339


title: genotype: CNAG_02516, librarydate: 2017-10-03, sample: 1455

description: Library name: sample_1455


title: genotype: CNAG_02566, librarydate: 2015-08-10, sample: 1860

description: Library name: sample_1860


title: Healthy lung sample 3, snRNA-seq

description:
Library name: C3
10X Genomics


title: genotype: CNAG_02516, librarydate: 2017-09-07, sample: 181

description: Library name: sample_181


title: Healthy lung sample 1, snRNA-seq

description:
Library name: C1
10X Genomics


title: Healthy lung sample 2, snRNA-seq

description:
Library name: C2
10X Genomics


title: genotype: CNAG_02566, librarydate: 2013-04-17, sample: 1032

description: Library name: sample_1032


title: genotype: CNAG_02476, librarydate: 2018-01-16, sample: 2537

description: Library name: sample_2537

value: deletion CNAG_02476


title: IPF lung sample 16, snRNA-seq

description:
Library name: IPF18
10X Genomics


title: genotype: CNAG_02476, librarydate: 2018-01-26, sample: 1729

description: Library name: sample_1729


title: IPF lung sample 15, snRNA-seq

description:
Library name: IPF 17
10X Genomics


title: Healthy lung sample 4, snRNA-seq

description:
Library name: C4
10X Genomics


title: IPF lung sample 14, snRNA-seq

description:
Library name: IPF 16
10X Genomics


title: Healthy lung sample 6, snRNA-seq

description:
Library name: C6
10X Genomics


title: IPF lung sample 13 rep 1, snRNA-seq

description:
Library name: IPF 14
10X Genomics

source_name: Left Lower Lung Lobe

value: Left Lower Lung Lobe


title: genotype: CNAG_02435, librarydate: 2021-01-13, sample: 1790

description: Library name: sample_1790

value: deletion CNAG_02435


title: genotype: CNAG_02435, librarydate: 2018-01-16, sample: 2560

description: Library name: sample_2560


title: IPF lung sample 12, snRNA-seq

description:
Library name: IPF 13
10X Genomics


title: genotype: CNAG_02476, librarydate: 2018-01-16, sample: 2559

description: Library name: sample_2559


title: genotype: CNAG_02435, librarydate: 2018-01-26, sample: 1730

description: Library name: sample_1730


title: genotype: CNAG_02435, librarydate: 2020-10-30, sample: 2344

description: Library name: sample_2344


title: IPF lung sample 10, snRNA-seq

description:
Library name: IPF 11
10X Genomics


title: genotype: CNAG_02364, librarydate: 2020-09-10, sample: 2075

description: Library name: sample_2075

value: deletion CNAG_02364


title: IPF lung sample 11, snRNA-seq

description:
Library name: IPF 12
10X Genomics


title: IPF lung sample 9 rep 2, snRNA-seq

description:
Library name: IPF 10
10X Genomics


title: genotype: CNAG_02322, librarydate: 2020-10-30, sample: 2318

description: Library name: sample_2318

value: deletion CNAG_02322


title: IPF lung sample 9 rep 1, snRNA-seq

description:
Library name: IPF 9
10X Genomics


title: IPF lung sample 7, snRNA-seq

description:
Library name: IPF 7
10X Genomics


title: genotype: CNAG_02364, librarydate: 2020-09-02, sample: 846

description: Library name: sample_846


title: genotype: CNAG_02364, librarydate: 2020-10-05, sample: 686

description: Library name: sample_686


title: IPF lung sample 8, snRNA-seq

description:
Library name: IPF 8
10X Genomics


title: IPF lung sample 5, snRNA-seq

description:
Library name: IPF 5
10X Genomics

source_name: Left Upper Lung Lobe

value: Left Upper Lung Lobe


title: IPF lung sample 4, snRNA-seq

description:
Library name: IPF 4
10X Genomics


title: IPF lung sample 3, snRNA-seq

description:
Library name: IPF 3
10X Genomics


title: genotype: CNAG_02364, librarydate: 2018-08-14, sample: 379

description: Library name: sample_379


title: genotype: CNAG_02322, librarydate: 2017-10-03, sample: 1475

description: Library name: sample_1475


title: genotype: CNAG_02322, librarydate: 2017-10-03, sample: 1454

description: Library name: sample_1454


title: genotype: CNAG_02322, librarydate: 2017-09-07, sample: 180

description: Library name: sample_180


title: IPF lung sample 2, snRNA-seq

description:
Library name: IPF 2
10X Genomics


title: genotype: CNAG_02322, librarydate: 2018-05-25, sample: 1338

description: Library name: sample_1338


title: IPF lung sample 13 rep 2, snRNA-seq

description:
Library name: IPF 15
10X Genomics


title: genotype: CNAG_02305, librarydate: 2018-05-25, sample: 1337

description: Library name: sample_1337

value: deletion CNAG_02305


title: genotype: CNAG_02476, librarydate: 2018-01-26, sample: 1707

description: Library name: sample_1707

value: yeast


title: genotype: CNAG_02305, librarydate: 2018-08-14, sample: 384

description: Library name: sample_384


title: IPF lung sample 6, snRNA-seq

description:
Library name: IPF 6
10X Genomics


title: MCF10DCIS shRab27A miR-205 mimic replicate 1

city: Oklahoma city

first: Bethany

last: Hannafon

state: OK

address: 975 NE 10th Street

department: Obstetrics and Gynecology

institute: University of Oklahoma Health Sciences Center

description: Library name: MCF10DCIS shRab27A miR-205 mimic 1

data_processing:
The samples were normalized and pooled onto a 150-paired end run on an Illumina NextSeq 2000 platform to obtain 20M reads per sample. The fastq files were aligned with the Human GRCh38 genome, and differentially expressed genes were identified using Illumina’s DRAGEN v4.2.4 app at Basespace.  The output files included differential expression reports (genes.res), raw gene counts, heat maps, PCA plots, dispersion plots, and MA plots produced using DESeq 2 at the gene level for each comparison.
Assembly: Human GRCh38
Supplementary files format and content: tab-delimited text file includes normalized mRNA read counts for all samples

source_name: breast cancer cell line

extract_protocol:
Total RNA from cultured cells was prepared using TRIzol reagent (Thermo-Fisher), followed by column clean-up using the Monarch RNA Cleanup kit according to the manufacturer’s protocol for whole transcriptome isolation (New England Biolabs, T2030S). RNA quality was checked using an Agilent 2100 Bioanalyzer, and concentrations from ThermoFisher’s NanoDrop readings were used.
Stranded RNA-seq libraries were constructed using the NEBNext Poly (A) mRNA isolation kit, followed directly by the IDT XGen Broad Range RNA Library Prep Kit and the established protocols.  Library construction was performed using up to 1 µg of RNA. Each library was indexed during library construction for multiplex sequencing, and the quality and quantity were determined using Invitrogen’s Qubit 4 fluorometer and an Agilent 2100 Bioanalyzer.

value: breast cancer cell line

value: ductal carcinoma in situ


title: MCF10DCIS shRab27A miR-205 mimic replicate 2

description: Library name: MCF10DCIS shRab27A miR-205 mimic 2


title: genotype: CNAG_02305, librarydate: 2018-11-02, sample: 131

description: Library name: sample_131

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: genotype: CNAG_02066, librarydate: 2020-10-30, sample: 2316

description: Library name: sample_2316

value: deletion CNAG_02066

value: 90 min


title: MCF10DCIS shRab27A miR-205 mimic replicate 3

description: Library name: MCF10DCIS shRab27A miR-205 mimic 3


title: genotype: CNAG_02305, librarydate: 2018-10-23, sample: 130

description: Library name: sample_130


title: genotype: CNAG_02066, librarydate: 2017-10-03, sample: 1474

description: Library name: sample_1474


title: MCF10DCIS shRab27A scramble mimic replicate 2

description: Library name: MCF10DCIS shRab27A SC mimic 2


title: MCF10DCIS shRab27A scramble mimic replicate 3

description: Library name: MCF10DCIS shRab27A SC mimic 3


title: genotype: CNAG_02066, librarydate: 2018-05-25, sample: 1336

description: Library name: sample_1336


title: MCF10DCIS shRab27A scramble mimic replicate 1

description: Library name: MCF10DCIS shRab27A SC mimic 1


title: genotype: CNAG_02066, librarydate: 2017-10-03, sample: 1453

description: Library name: sample_1453


title: MCF10DCIS wildtype miR-205 mimic replicate 3

description: Library name: MCF10DCIS WT miR-205 mimic 3


title: MCF10DCIS wildtype scramble mimic replicate 3

description: Library name: MCF10DCIS WT SC mimic 3


title: MCF10DCIS wildtype miR-205 mimic replicate 1

description: Library name: MCF10DCIS WT miR-205 mimic 1


title: genotype: CNAG_01977, librarydate: 2018-01-26, sample: 1711

description: Library name: sample_1711

value: deletion CNAG_01977


title: MCF10DCIS wildtype miR-205 mimic replicate 2

description: Library name: MCF10DCIS WT miR-205 mimic 2


title: genotype: CNAG_02066, librarydate: 2017-09-07, sample: 179

description: Library name: sample_179


title: genotype: CNAG_01977, librarydate: 2018-01-16, sample: 2541

description: Library name: sample_2541


title: MCF10DCIS wildtype scramble mimic replicate 2

description: Library name: MCF10DCIS WT SC mimic 2


title: genotype: CNAG_01977, librarydate: 2018-01-16, sample: 2563

description: Library name: sample_2563


title: IPF lung sample 1, snRNA-seq

description:
Library name: IPF 1
10X Genomics

value: Right Lower Lung Lobe

value: All cells

value: Female


title: genotype: CNAG_01948, librarydate: 2021-01-13, sample: 1785

description: Library name: sample_1785

value: deletion CNAG_01948


title: PBMC, Parse v3, sample F5B

city: Seattle

first: Anna

last: Elz

state: WA

address: 1201 Eastlake Ave E

institute: Fred Hutchinson Cancer Center

description:
Library name: parse_v3_F5B
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data

data_processing:
Sequencing Depth and Downsampling: Sample sequencing was conducted to achieve a depth exceeding 25,000 reads per cell for WT libraries except for FLEX which targeted 10,000 reads per cell.  TCR libraries all targeted for 5000 reads per cell. When sequencing surpassed the targets, FASTQs were downsampled to 25,000 reads per cell for the WT libraries and 5000 reads per cells for TCR libraries using seqtk version 1.3 with random seed 100 (Li, 2012).
Generating count matrices: The software provided by each kit vendor was utilized to generate UMI count matrices from the downsampled FASTQs. Pipelines were run with default parameters unless otherwise specified. For the 10x kits, CellRanger version 8.0.0 with the multi subcommand was employed with the reference version refdata-gex-GRCh38-2024-A. Parse data was processed with splitpipe v1.2.1 using parse’s hg38_V1.1.3 reference. Fluent data was processed with PIPseeker version 3.3.0 with reference gex-reference-GRCh38-2022.04. For each sample, PIPseeker generates 5 outputs of varying sensitivity for calling cells from background. We selected the sensitivity levels on a per-sample basis informed by the knee plots and vendor guidelines. Scale data was processed through scaleRNA version 1.5 with default parameters, library structure version 1.1 and the prebuilt GRCH38 reference genome provided by Scale. FASTQs were generated at the library level by passing raw BCL folders into the first scaleRNA run. We then ran Scale’s bc_parser (distributed with the nextflow pipeline) with the `--demux` flag and options to output 2 read files and 2 index files for each sample. These were downsampled and ran with default parameters to produce the filtered expression matrix.
Assembly: GRCh38
Supplementary files format and content: The first set of processed files are pipeline outputs from downsampled data. For WT/GEX libraries, processed files include files needed to construct the counts matrix. Either h5 files, or matrix + barcode + feature files. For VDJ/TCR libraries, the processed data files have the final clone assemblies.
Supplementary files format and content: The second set of processed files are the Seurat RDS files for each kit, with all samples for that kit merged. The datasets were processed to remove low quality cells and low-abundance genes. Data was clustered at the kit level and annotated manually using reference mapping and key gene expression. See the manuscript for full details.

source_name: PBMC

extract_protocol:
Benchmark I:  3’ Whole transcriptome comparison Multiple donor leukopak frozen aliquots were purchased from Bloodworks Northwest.  PBMCs from two healthy donors F1 and F5, stored in liquid nitrogen were thawed at 37 degrees C., transferred into 10ml prewarmed thawing media (Gibco RPMI 1640 + 10% FBS) and centrifuged at 500 x g for 5 minutes at 4 degrees. Cells were washed in 10ml cold 1XPBS -MgCl and -CaCl (Gibco), followed by subsequent centrifugation at 500 x g for 5 minutes and the pellet resuspended in 10ml 1X PBS.  The CellacaMX (Revvity) live-dead assay was used to count AOPI stained cells. Viability was 83% and 88% respectively.  Each cell suspension was aliquoted for use in the 10X Genomics GEM-X and NextGEM assays in which the cell suspensions were loaded in replicate, with a targeted recovery of 20,000 and 10,000 cells, respectively.  The remaining cell suspensions were aliquoted out in technical replicates of 1 million cells and fixed using Parse’s Cell Fixation v3 User Manual (UM0027 v1.1), Fluent’s Demonstrated Protocol DSP-Methanol Fixation for Cells (FB0004708), and 10x Demonstrated Protocol Fixation of Cells and Nuclei for Chromium Fixed RNA Profiling (FLEX) (CG000478 Rev C). Separate aliquots of F1 and F5 donors were processed as above except with PBS 1% BSA for the final resuspension.  One set was fixed in technical replicates of 1 million cells following the Scale’s standard fixation kit protocol Rev. B.  The second set of aliquots was processed as above with PBS + 0.04% BSA and Promega RNase Inhibitor resuspension and no fixation for Fluent’s PIPseq V.  Benchmark II:  5’ WT, TCR single cell comparison Frozen PBMCs from four healthy donors (F1, F2, F4, and F5) of mixed sex (3 males, 1 female) and ethnicity (3 persons of Caucasian descent and 1 person of Asian descent) supplied by Bloodworks Northwest were processed in two batches one week apart (F1, F2 followed by F4, F5). Cells were thawed in a 37°C water bath before transfer to thawing media (Gibco RPMI 1640 + 10% FBS). Samples were then centrifuged at 400 x g for 10 minutes at 4°C. The supernatant was decanted, and the pellet resuspended in 10 mL of sorting media (cold Gibco 1X PBS + 1% BSA), followed by an additional centrifugation at 400 x g for 10 minutes. Each sample was next resuspended in 200 µL of stain media. Cells were stained to enrich for T-cells and to remove as many B-cells as possible. We stained the samples with human CD3, CD45, and CD19 (citation for antibodies). 7AAD was used to assess the in-flight viability of the cells during the sort. We sorted T cells using the Becton-Dickenson Symphony S6 cytometer. The final population was CD3+, CD45+, and CD19-. An aliquot of the sorted T-cells was stained with AOPI and assessed for viability and cell counts using the Nexcelom CellacaMX (Revvity).  Viabilities ranged from 88-90 % (F1 and F2) and 83-87% (F4 and F5).  An aliquot of the of each donor T-cells was utilized for 10x Genomics GEM-X 5′ v3 (CG000733 RevA) and NextGEM 5′ v2 (CG000331 RevE) assays, in which 20,000 and 10,000 cells were targeted for recovery, respectively. The remaining cell suspension, ~1.5 million cells, was fixed following Parse Evercode Cell Fixation v2 (UM0039 v2.3). Cells were frozen and later processed as directed by Evercode TCR Human WT + TCR v1 (UM0018).
Benchmark I:  3’ Whole transcriptome comparison 10x Genomics FLEX Fixed RNA profiling Per the 10x Genomics CG000527 Rev E protocol, fixed cells were incubated overnight with mRNA transcript probes targeting ~18K genes, with the left handle containing a sample specific barcode. Following probe hybridization, samples were counted and pooled equally before a series of washes to remove unbound probes.  After counting the pool, a volume targeting a recovery of 40,000 cells was combined with a master mix that contains enzymes that ligate and extend the probes during GEM incubation. This mixture was then loaded into the NEXT GEM Chip Q with gel beads and partitioning oil. Following microfluidic GEM generation on the ChromiumX, the GEMs were recovered and amplified to generate product to put into library preparation.  A portion of the amplified material was re-amplified with library specific P5 and P7 indices. 10x Genomics GEM-X 3’v4 and NextGEM v3.1 Following the 10X Genomics GEM-X 3’v4 (CG000731) and NextGEM v3.1 (CG000315) protocols, PBMCs from donor F1 and donor F5 were combined with a reverse transcript mastermix and loaded on to a microfluidic chip (Chromium GEM-X 3’ chip and NextGEM Chip G) along with partitioning oil and barcoded gel beads. Cells were partitioned into droplets containing gel beads using the ChromiumX instrument and subsequently underwent reverse transcription. The cDNA was recovered, cleaned, and amplified to create enough material for library preparation. To generate gene expression libraries, a portion of cDNA was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final amplification. Fluent Biosciences PIPseq v.4 Fixed cells were partitioned, and libraries generated using the PIPseq T20 3’ Single Cell RNA Kit v4.0PLUS User Guide (FB0002130 Rev 8.3). To target a recovery of 20,000 cells per sample, 8uls of a cell suspension at a concentration of approximately 5000 cells/ul were captured in emulsion with Particle-templated Instant Partitions (PIPs), followed by cell lysis and barcoding unique to each PIP. The emulsions were then broken, and the mRNA reverse transcribed to generate cDNA. cDNA was then amplified, isolated from the PIPs, fragmented, end repaired and A-tailed, adapter ligated, and indexed with unique P7 and P5 indices.  Fluent Biosciences PIPseq V Sample replicates of live cells (40,000 each) were loaded into PIPs for capture and barcoding as described in PIPseq V T20 3’ Single Cell RNA kit User Guide (FB0005261). To target a recovery of 20,000 cells per sample, 8ul of 5000 cells/ul were captured in emulsion with Particle-templated Instant Partitions (PIPs), followed by cell lysis and barcoding unique to each PIP. The emulsions were then broken, and the mRNA reverse transcribed to generate cDNA. cDNA was then amplified, isolated from the PIPs, fragmented, end repaired and A-tailed, adapter ligated, and indexed with unique P7 and P5 indices. Parse Evercode v3 Following the Parse protocol UMWT3300, fixed and permeabilized PBMCs were thawed, and counted using trypan blue and a hemocytometer, diluted and added to 12 wells per replicate of Plate 1 as directed by the sample loading table (48 wells total across all replicates). Following reverse transcription, cells were pooled and split an additional two times, the last of which added a barcode containing R2 and Biotin for magnetic bead enrichment Cells were pooled again, counted, and distributed into eight sublibraries each targeting under 12,500 cells where they were lysed and the biotin labelled cDNA recovered with binder beads. cDNA bound to the binder beads was washed and incubated with a template switch oligo to add a 5’ adapter to the cDNA. The cDNA was amplified and bead cleaned. A portion of this cleaned product was fragmented, adapter ligated and had p5 and p7 indices added in a final PCR. Scale Biosciences Following the Scale 1020796 Rev A protocol, fixed cells at a concentration of approximately 2000 cells/ul were added to 96 wells of barcode plate 1 and well IDs documented to map back cells to their sample of origin. The cells underwent reverse transcription and were then pooled by centrifugation into a funnel. Cells were washed and then split across a 384 well ligation plate where cells were barcoded. Cells were again pooled by centrifugation, washed, and counted to assess for recovery. The cell stock was diluted to approximately 460 cells/ul and 4uls loaded into each well of the final distribution plate, with the remainder saved at -80 degrees. In the final distribution plate, the cell membrane is broken down, cDNA is tagmented with a transposase, and the library specific P5 and P7 indexes added.  Benchmark II:  5’ WT, TCR single cell comparison 10X Genomics GEM-X 5’v3 and Next GEM 5’v2 Following the 10X Genomics GEM-X 5’v3 (CG000733) and NextGEM 5’v2 (CG000331) protocols, sorted T cells were added to a reverse transcription mastermix and loaded on to a microfluidic chip (Chromium GEM-X 5’ chip and NextGEM Chip K respectively) with partitioning oil and barcoded gel beads. Cells were partitioned into droplets containing gel beads (GEMS) and subsequently underwent reverse transcription.  The cDNA was recovered and cleaned before being amplified to create enough material for library preparation for gene expression and TCR. To generate TCR libraries, a small amount of cDNA underwent 2 rounds of PCR with a set of TCR specific primers. A portion of the PCR product was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final PCR. To generate gene expression libraries, a portion of cDNA was fragmented, adapter ligated, and an additional index with P5 and P7 handles added during a final PCR.  Parse Evercode TCR Fixed and permeabilized T cells were thawed, counted using trpyan blue and a hemocytometer, following Parse protocol UMIT2300.  Each sample was diluted according to the sample loading table and recounted before dispensing into 12 wells per sample of Plate 1 (48 wells total). Following reverse transcription, cells were pooled and split an additional two times to add barcodes, the last pool and split also adding the R2 and biotin. Cells were pooled, counted, and distributed into eight sublibraries each targeting 12,500 cells. Cells were lysed and biotin labelled cDNA recovered with binder beads.  cDNA bound to the binder beads was washed and incubated with a template switch oligo to add a 5’ adapter to the cDNA. The cDNA was amplified and bead cleaned to be usable in TCR and whole transcriptome library preparation. Whole transcription libraries undergo library preparation as described in Evercode TCR Human WT + TCR v1 (UM0018), which utilized the Parse v2 WT chemistry. The TCR library is generated from a subset of the WT cDNA in a PCR reaction targeting the V(D)J segments of the CDR3 region of the T cell.

value: PBMC

value: Parse Evercode WT v.3


title: genotype: CNAG_01948, librarydate: 2020-10-30, sample: 2310

description: Library name: sample_2310


title: PBMC, Parse v3, sample F5A

description:
Library name: parse_v3_F5A
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data


title: PBMC, Parse v3, sample F1B

description:
Library name: parse_v3_F1B
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data


title: genotype: CNAG_01977, librarydate: 2018-01-26, sample: 1733

description: Library name: sample_1733


title: PBMC, Fluent V, sample F5B

description: Library name: fluent_V_F5B

value: Fluent Biosciences PIP Seq V T20 3′


title: MCF10DCIS wildtype scramble mimic replicate 1

description: Library name: MCF10DCIS WT SC mimic 1


title: genotype: CNAG_01948, librarydate: 2021-01-13, sample: 1786

description: Library name: sample_1786


title: PBMC, Parse v3, sample F1A

description:
Library name: parse_v3_F1A
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data


title: genotype: CNAG_01889, librarydate: 2018-01-16, sample: 2555

description: Library name: sample_2555

value: deletion CNAG_01889


title: genotype: CNAG_01948, librarydate: 2020-10-05, sample: 688

description: Library name: sample_688


title: PBMC, Fluent V, sample F1B

description: Library name: fluent_V_F1B


title: PBMC, Fluent V, sample F5A

description: Library name: fluent_V_F5A


title: genotype: CNAG_01889, librarydate: 2018-01-16, sample: 2533

description: Library name: sample_2533


title: PBMC, Fluent V, sample F1A

description: Library name: fluent_V_F1A


title: genotype: CNAG_01889, librarydate: 2018-01-26, sample: 1703

description: Library name: sample_1703


title: genotype: CNAG_01889, librarydate: 2018-01-26, sample: 1725

description: Library name: sample_1725


title: PBMC, Fluent v4, sample F5A

description: Library name: fluent_v4_F5A

value: Fluent Biosciences PIP Seq T20 3′ v4


title: PBMC, Fluent v4, sample F1B

description: Library name: fluent_v4_F1B


title: genotype: CNAG_01883, librarydate: 2018-01-16, sample: 2561

description: Library name: sample_2561

value: deletion CNAG_01883


title: genotype: CNAG_01883, librarydate: 2018-01-26, sample: 1731

description: Library name: sample_1731

value: yeast


title: genotype: CNAG_01883, librarydate: 2018-01-16, sample: 2539

description: Library name: sample_2539


title: PBMC, Fluent v4, sample F1A

description: Library name: fluent_v4_F1A


title: genotype: CNAG_01883, librarydate: 2018-01-26, sample: 1709

description: Library name: sample_1709


title: genotype: CNAG_01708, librarydate: 2021-03-10, sample: 2671

description: Library name: sample_2671

value: deletion CNAG_01708


title: genotype: CNAG_01948, librarydate: 2020-10-07, sample: 1059

description: Library name: sample_1059


title: genotype: CNAG_01708, librarydate: 2021-03-10, sample: 2672

description: Library name: sample_2672


title: Sorted T-cells from PBMC, Parse v2 VDJ/TCR, sample F2

description:
Library name: parse_v2_tcr_F2
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data

value: Sorted T-cells

value: Parse Evercode v.2 TCR


title: genotype: CNAG_01708, librarydate: 2021-01-13, sample: 1781

description: Library name: sample_1781

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: Sorted T-cells from PBMC, Parse v2 VDJ/TCR, sample F1

description:
Library name: parse_v2_tcr_F1
Parse sublibraries are processed all together to split samples. The sublibraries assigned to each sample in this sheet to not contain just one sample, but all 4. All 8 sublibraries need to be passed to the Parse processing pipeline to get sample-level data


title: genotype: CNAG_01889, librarydate: 2021-10-26, sample: 3209

description: Library name: sample_3209

value: 90 min


title: genotype: CNAG_01626, librarydate: 2012-02-13, sample: 1373

description: Library name: sample_1373

value: deletion CNAG_01626


title: genotype: CNAG_01708, librarydate: 2020-10-30, sample: 2298

description: Library name: sample_2298


title: A549_rep2

city: Beijing

first: Shaodong

last: Huang

address: Peking University Health Science Center, Beijing, China

department: Department of Biomedical Informatics

country: China

institute: Peking University

data_processing:
RNA-Seq raw reads were mapped to the human genome version hg19. CircRNAs were identified by call module of CIRI-long with default parameters. Isoforms were determined by isoform collapsing modules of CIRI-long.
Assembly: hg19
Supplementary files format and content: A text file contains the summarized epxression level of circRNAs in all samples.

source_name: Lung adenocarcinoma

extract_protocol:
RNA was harvested using Takara RNAiso Plus. 2 ug of total RNA was used for librarires construction.
CircRNA libraries for RNA-seq were prepared following CIRI-long protocols. KAPA RNA HyperPrep Kit with RiboErase (HMR) was used for rRNA depletion. SMARTer PCR cDNA Synthesis Kit(Takara) was used for rolling circular reverse transcription.

value: Lung adenocarcinoma

value: Lung


title: genotype: CNAG_01551, librarydate: 2012-03-26, sample: 2421

description: Library name: sample_2421

value: deletion CNAG_01551


title: genotype: CNAG_01551, librarydate: 2012-01-30, sample: 2436

description: Library name: sample_2436