title: Y13.Enrich

value: Enrich


title: SAP-2

status: Public on Dec 20 2023

type: SRA

city: Jinan

first: Shulei

last: Zhao

state: China

address: Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwu Weiqi Rd, Jinan 250021, China.

department: Gastroenterology

country: China

description:
BD
RX20221125-6

library_source: transcriptomic single cell

data_processing:
the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.
Unique molecular identifier (UMI) count matrix of 2 SAP and 3 JZL184and 3 CON samples were retrieved form the raw sequence data. The R package Seurat were used to convert the UMI count matrix into a Seurat object (Butler et al. 2018) (version 4.0.4). The low-quality cells with UMI numbers <1000, and detected genes < 500 and over 15% mitochondrial-derived UMI counts were removed. Genes that were detected in less than 5 cells were removed. The filtered UMI count matrix of each sample were used for downstream analyses.
After quality control, log normalization were performed to the UMI count matrix. FindIntegration Anchors function of Seurat were conducted to create potential Anchors through top 2000 variable genes.
IntegrateData function was perofored to integrate data of different samples. Based on the integrated data matrix, dimensionality reduction was achieved by performing the principal omponent analysis (PCA)
top 50 PCs were selected for downstream analysis based on the plots by performing Elbowplot function in Seurat. FindClusters function in Seurat were performed to identify the main cell clusters with default resolution parameter (res = 0.6)
Supplementary files format and content: tab-delimited text files and  matrix files

molecule: total RNA

organism: Rattus norvegicus

source_name: ileal tissue

extract_protocol:
Newly collected fresh ileal tissue were washed in ice-cold RPMI1640，cut into small pieces (<1 mm) with the sterile scissors on ice. The tissues were dissociated using Collagenase Ⅱ (Sigma, V900892-100MG), Trypsin (Hyclone, SH30042.01) and DNase I (Sigma, DN25-1G). The obtained single-cell solution was sieved through a 70 μM cell strainer (Corning). Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Solarbio, R1010)
Single-cell cDNA libraries were generated as described in detail (Single cell 3’ whole transcriptome amplification protocol, BD Rhapsody) using successfully prepared single-cell suspensions. In brief, freshly single-cell suspensions were washed three times, and counted and subsequently loaded onto a cartridge, lysed inside the wells followed by mRNA capture on cell capture beads according to manufacturer instructions. Cell capture beads were retrieved and washed prior to performing reverse transcription and treatment with Exonuclease I. cDNA underwent extension using the WTA extension primers, purified, and then purified using SPRIselect magnetic beads (Beckman Coulter). Quantity of PCR products was determined by Qubit 4.0 with Qubit dsDNA HS Assay (Q32854)

tag: tissue

value: ileal tissue

tag: strain background

value: Sprague-Dawley (SD)

tag: Sex

value: male

tag: group

value: severe acute pancreatitis (SAP) model

tag: treatment

value: vehicle


title: Y12.Input

city: Shanghai

first: Dean

last: Li

address: Haike Road 100

institute: Chinese Academy of Science

library_source: transcriptomic

data_processing:
All sequencing reads were processed with Trim Galore (v0.6.6) with the parameters “--nextseq 30 --paired” to remove the adapter sequences (AGATCGGAAGAGC) from NovaSeq-platforms, and reads longer than 20 bp were kept. Reads that passed the quality control procedure were kept and mapped to the Homo sapiens genome (GRCh38) and Drosophila melanogaster genome (dmel-all-chromosome-r6.36) using STAR (v2.7.6a) with default parameters, respectively. Uniquely mapped read pairs were counted against annotations from Homo sapiens (Ensembl: GRCh38.94) and Drosophila melanogaster (Flybase: dmel-all-r6.36) using featureCounts (v2.0.1) with parameters “-p -B -C” and summarized as gene-level counts, respectively.
Assembly: GRCh38 and dmel-all-chromosome-r6.36
Supplementary files format and content: Counts from featurecounts output were merged into csv table with each gene in rows and each sample in columns.

molecule: polyA RNA

organism: Homo sapiens

source_name: Peripheral mononuclear blood cell

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa, catalog: 9108). NAD-RNAs were captured following method detailed in ONE-seq manuscript (https://doi.org/10.1093/nar/gkac1136). Briefly, total RNAs were subjected to one-step chemo-enzymatic biotinylation, followed by streptavidin capture and the NudC-catalyzed elution, to specifically recover NAD-capped RNAs for epitranscriptomic profiling.
RNA libraries were prepared according to instructions of Abclonal mRNA-seq Library Prep Kit for Illumina (RK20302)
RNA-Seq; 150bp paired-end

tag: cell type

value: Peripheral mononuclear blood cell

tag: age group

value: Young

value: Discovery

tag: assay

value: Input

tag: age

value: 26 years

tag: gender

value: Female


title: MAGL-3

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

description:
BD
RX20221125-10

value: monoacylglycerol lipase (MAGL) inhibitor (JZL184)


title: OPC, Day3, mock, rep.1

city: Fujisawa

first: Masato

last: Yugami

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: Research

country: Japan

institute: Takeda Pharmaceutical Company

data_processing:
OmicSoft ArrayStudio (v11, QIAGEN)
Sequence reads were mapped to mm10 and counted by RNA-seq pipeline workflow in OmicSoft ArrayStudio
Differentially expressed genes were identified by DESeq(V2) one way method in OmicSoft Studio function
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include statistics values for each comparison

organism: Mus musculus

source_name: primary oligodendrocyte precursor cells

growth_protocol: Mouse primary oligodendrocyte precursor cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 80 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit for NeoPrep followingthe manufacturer's protocol.

tag: strain

tag: cell line

value: primary oligodendrocyte precursor cells

tag: genotype

value: WT

tag: time


title: Y12.Enrich


title: WT, DSB, Stationary 3day, biol rep6

city: Boston

first: Xin

last: Wang

state: MA

address: 300 Longwood Ave,

country: USA

institute: Boston children's hospital

description:
The library has the forward index: AGC and reverse index: CTA. A total of  20256 colony number was in this library.
Stationary WT 3 day rep6

library_source: genomic

data_processing:
Large insertion detection: https://github.com/gucascau/iDSBins.git
Large insertion feature: https://github.com/gucascau/LargeInsertionFeature.git
Reference: Yeast EndoG regulates mitochondrial DNA transfer to nucleus
Reference: Methods of Yeast EndoG regulates mitochondrial DNA transfer to nucleus
Assembly: saccharomyces_cerevisiae_R64-2-1_20150113
Supplementary files format and content: BED file that contain the single donor.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"
Supplementary files format and content: BED file for poly insertions.  Each column represents : "Donor  Chromosome",  "Donor Start","Donor End", " CaseID", "Score", "Donor Strand ", and  "Representative Read"

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: No

growth_protocol: For amplicon sequencing analysis in normal conditions, cells were grown in YEPD (1% yeast extract, 2% peptone, 2% dextrose) o/n to saturation. Cells were washed twice in YEP-Raffinose (1% yeast extract, 2% peptone, 2% raffinose) media and inoculated in 10 ml of YEP-Raffinose and grown overnight. Once cells reached the density of 2x10e7/ml, they were plated on YPE-Gal plates (1% yeast extract, 2% peptone, 2.5% agar, 2% galactose, galactose was filter sterilized and added to the autoclaved media). For all analyses in stationary phase cells, we followed a previously established protocol for yeast growth (Hu et al., 2013). Yeasts were initially streaked out on YEPD plates and individual colonies were inoculated in 3 ml SC media (1.72g/L yeast nitrogen base without amino acids (USBiological, cat# Y2030), 2g/L amino acid mix (Bufferad, cat#S0051), 0.5% ammonium sulfate, 2% dextrose) and incubated overnight at 30 °C. The culture was diluted into fresh 50 mL SC media in 250 mL flasks to an OD600 of 0.1. Logarithmic growth phase control cells were plated when the culture reached 1x107 cells/ml. Cells were incubated on a shaker for 24 hrs (day 1), 3 days, 8 days, 16 days or as specified in individual experiments and plated on YEPGal plates for HO induction. Colonies were collected at after 5 days of incubation for analysis of NHEJ products. Populations of old yeast mother cells were isolated as previously described (Tsuchiyama et al., 2013) with the following modifications. 3x10e8 yeast cells from a fresh log-phase culture in YEPD were treated with 3 mg of Sulfo-NHS-LC-Biotin (Thermo Scientific) and were used to seed a 1L culture in YEP-Raffinose. Seeded cultures were incubated with shaking at 30 °C for 15 hours to age biotin-labeled cells. The aged biotin-labeled cells were isolated using 1 mL Dynabeads Biotin Binder (Thermo Scientific). Three rounds of aging and sorting were conducted to obtain old mother cells with an average replicative age of around 20. Control young cells were obtained from last sorting and wash.

extract_protocol:
All colonies from YEP-Galactose plates were collected, pooled together and mixed vigorously. ~80 μl cells were spun down and the genomic DNA was extracted using standard glass beads and phenol chloroform. The genomic DNA was treated with RNase A overnight. The genomic DNA was dissolved with water and adjusted to a concentration of 10 ng/μl.
The construction of the sequencing library was adapted from Illumina’s amplicon sequencing protocol #15044223 Rev. B. Two rounds of PCR were performed to construct the sequencing library. For each sample, 3.2 μl genomic DNA, 0.5 μl 10 μM primers and 12.5 μl KAPA HiFi HotStart ReadyMix (Roche, 7958927001) was used for the first round of PCR for a total volume of 25 μl. The forward primers are 66-mers that contain (5’ to 3’): 33 bases Illumina adapter sequence, 3 bases unique home index, and 30 bases targeting the Mata locus which is located 11 bp upstream the HO cleavage site. The reverse primers are 66-mers that contain (5’ to 3’): 34 bases Illumina adapter sequence, 3 bases unique home index, and 29 bases targeting the MATa locus which is located 18 bp downstream the HO cleavage site. The following conditions were used for the first round of PCR: 95 °C for 5 min; 22 cycles of 98 °C for 20 s, 65 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. 18μl PCR product was purified with 20μl AMPure XP beads (Beckman Coulter, A63880) and eluted with 52.5 μl 10 mM Tris pH 8.5. For the second round of PCR, 5 μl purified PCR product, 5 μl Nextera XT V2 Index (Illumina, FC-131-2001) primer N7xx, 5 μl index primer S5xx, and 25 μl KAPA HiFi HotStart ReadyMix were used. The total volume of PCR is 50 μl. The following conditions were used for PCR: 95 °C for 5 min; 8 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 3 min; 72 °C for 10 min. 40 μl PCR product was purified with 48 μl AMPure XP beads and eluted with 27.5 μl 10 mM Tris pH 8.5. The DNA concentration of each sample was determined with Qubit dsDNA BR Assay Kit (ThermoFisher, Q32850) and the average size of the DNA was determined with TapeStation. The DNA was diluted to 4 nM using 10 mM Tris pH 8.5. An equal amount of DNA was pooled from ~20 samples into the library. The pooled library and PhiX library (Illumina, FC‐110‐3001) were denatured with 0.2 M NaOH separately and diluted with pre-chilled HT1 to 12 pM. 540μl pooled library and 60 μl PhiX were mixed, incubated at 96 °C for 2 min and immediately placed in an ice-water bath for 5 min.
The denatured combined library was loaded into the MiSeq Reagent Kit v3 (600 cycle) (Illumina, MS-102-3003) for amplicon sequencing.

treatment_protocol: For growing cells once cells reached the density of 2x10e7/ml, they were plated on YPE-Gal plates (1% yeast extract, 2% peptone, 2.5% agar, 2% galactose, galactose was filter sterilized and added to the autoclaved media). For stationary phase cells, cells were plated after 1,2,3,8,16 days of incubation in SC media on YEPGalactose plates. Colonies were collected at after 5 days of incubation for analysis of NHEJ products. For aged cells and control young cells, they were plated on YPE-Gal plates.

value: No

value: S. cerevisiae haploid strain

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Stationary WT 3 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Y11.Input

value: Male


title: SAP-1

description:
BD
RX20221125-5

value: ileal tissue

value: Sprague-Dawley (SD)

value: male


title: GDNF-Gel/HA-Mg group 3

city: Xi’an

first: Yuanqing

last: Cai

state: Shaanxi

address: No.157, Xiwu Road

institute: The Second Affiliated Hospital of Xi’an Jiaotong University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Ensembl_release106
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Sciatic nerve

growth_protocol: Male rats were housed in individual cages with an artificial 12:12 hr light: dark cycle at room temperature and fed with normal chow

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: GDNF-Gel/HA-Mg was implanted in sciatic nerve defect model in SD rats

value: Sciatic nerve

value: Sciatic nerve defect+GDNF-Gel/HA-Mg


title: WT, DSB, Stationary 3day, biol rep5

description:
The library has the forward index: ACG and reverse index: GTG. A total of  25760 colony number was in this library.
Stationary WT 3 day rep5


title: OPC, Day3, non-treat, rep.2


title: OPC, Day3, non-treat, rep.1


title: WT, DSB, Stationary 8day, biol rep1

description:
The library has the forward index: ATG and reverse index: GCT. A total of  59360 colony number was in this library.
Stationary WT 8 day rep1

value: Stationary WT 8 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Y11.Enrich

value: Peripheral mononuclear blood cell

value: Young

value: Discovery

value: Enrich


title: Y10.Input

value: Input

value: 29 years

value: Female


title: GDNF-Gel/HA-Mg group 1

value: WT


title: OPC, Day0, rep.1

value: primary oligodendrocyte precursor cells


title: OPC, Day0, rep.2


title: GDNF-Gel/HA-Mg group 2


title: WT, DSB, Stationary 8day, biol rep3

description:
The library has the forward index: CAC and reverse index: CAT. A total of  22080 colony number was in this library.
Stationary WT 8 day rep3

value: No

value: S. cerevisiae haploid strain

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: WT, DSB, Stationary 3day, biol rep4

description:
The library has the forward index: AGC and reverse index: CTA. A total of  26208 colony number was in this library.
Stationary WT 3 day rep4

value: Stationary WT 3 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Y10.Enrich


title: WT, DSB, Stationary 3day, biol rep2

description:
The library has the forward index: AGC and reverse index: CTA. A total of  21320 colony number was in this library.
Stationary WT 3 day rep2


title: WT, DSB, Stationary 3day, biol rep3

description:
The library has the forward index: ATG and reverse index: GCT. A total of  27160 colony number was in this library.
Stationary WT 3 day rep3


title: NC group 3

value: Sciatic nerve defect


title: NC group 2

value: Sciatic nerve


title: NC group 1


title: WT, DSB, Stationary 3day, biol rep1

description:
The library has the forward index: AAC and reverse index: GTT. A total of  63200 colony number was in this library.
Stationary WT 3 day rep1


title: Y9.Input

value: 32 years


title: Y9.Enrich


title: GFP, rep1

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

country: India

institute: NABI (National Agri-Food Biotechnology Institute)

description:
Degs_relaxed_gfp_vs_bfp_gfp.xls
Degs_relaxed_gfp_vs_bfp_yfp.xls
Degs_relaxed_gfp_vs_bfp.xls
Degs_relaxed_gfp_vs_neg.xls
Degs_relaxed_gfp_vs_yfp.xls

data_processing:
The quality of the sequencing data was assessed using FastQC
bases with fluctuating GC content were trimmed off with cutadapt
Genome mapping was performed using TopHat
A gene expression count table was generated from the aligned dataset using HTSeq
Assembly: TAIR10
Supplementary files format and content: The processed data include lists of differentially expressed genes (DEGs) for pair wise comparision between different samples. Since there are total 6 differnet samples (BFP, BFPGFP, BFPYFP, GFP, YFP, All negative), so there are maximum 5 processed files for each samples. Each file include log2 fold change and p-values for the DEGs in one sample againt another sample. FOr eg. the file "Degs_relaxed_gfp_vs_bfp.xls" contains log2 fold change in sample GFP against sample BFP.

organism: Arabidopsis thaliana

source_name: SAM

growth_protocol: Plants were grown on soil in short day conditions for 4-5 weeks before harvesting

extract_protocol:
Rneasy Mini kit (Qiagen) was used according to manufacturer’s instruction for RNA preparation
RNA-Seq Libraries for all cell-types were prepared using ‘NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

treatment_protocol: About 50 SAMs of 4-5 week old plants were quickly harvested and placed in cell-wall dissolving enzyme solution in 70um cell-strainer in a small petridish. Protoplasts samples were sorted by the EMBL flow cytometry core facility using a special setup MoFlo XDP cell sorter from Beckman Coulter equipped with a Coherent Sabr Argon gas laser emitting at 514.5nm (400mW), a Coherent Innova gas laser emitting at 488nm (300mW), and a Coherent Obis 405nm solid state laser (240mW).

value: SAM

value: GFP


title: GFP, rep3


title: GFP, rep2


title: WT, DSB, Stationary 2day, biol rep2

description:
The library has the forward index: ACC and reverse index: GAA. A total of  66560 colony number was in this library.
Stationary WT 2 day rep2

value: Stationary WT 2 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: WT, DSB, Stationary 2day, biol rep1

description:
The library has the forward index: AGG and reverse index: GGA. A total of  52480 colony number was in this library.
Stationary WT 2 day rep1


title: BFP, rep3

description:
Degs_relaxed_bfp_vs_neg.xls
Degs_relaxed_bfp_vs_bfp_yfp.xls

value: BFP


title: WT, DSB, Stationary 1day, biol rep2

description:
The library has the forward index: ACG and reverse index: GTG. A total of  69520 colony number was in this library.
Stationary WT 1 day rep2

value: Stationary WT 1 day  yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Y8.Enrich

value: Peripheral mononuclear blood cell

value: Young

value: Discovery

value: Enrich

value: 23 years


title: HEK293T, Cellular miRNAs (201113C1)

city: Koto-ku

first: Fumio

last: Maeda

state: Tokyo

department: Cellular and Molecular Biotechnology Research Institute

institute: National Institute of Advanced Industrial Science and Technology

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadat and trimmomatic.
Trimmed sequence reads were mapped to mature.fa (miRBase) using bowtie
Read count extraction and was performed using samtools_0.1.18
Assembly: mature.fa (miRBase)
Supplementary files format and content: tab-delimited text files include read counts for each Sample

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from cells using the mirVana™ miRNA Isolation Kit.
RNA libraries for RNA-seq were prepared using SMARTer smRNA-Seq Kit following manufacturer's protocols.

treatment_protocol: HEK293T cells were transfected with 15ug of plasmid DNA 1 day after seeding.

value: Human Embryonic Kidney cell

value: WT

value: plasmid transfection


title: Y7.Input

value: Input

value: 30 years

value: Male


title: BFP, rep2


title: HEK293T, Cellular miRNAs (201124C1)


title: WT, DSB, Stationary 1day, biol rep1

description:
The library has the forward index: AAC and reverse index: GTT. A total of  77600 colony number was in this library.
Stationary WT 1 day rep1

value: No

value: S. cerevisiae haploid strain

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: HEK293T, co-expression of EV-inducing protein and miRNA binding protein (201113S5)

description: plasmid transfection

value: co-transfected with the EV-inducing protein (EPN-01) and the miRNA binding protein fragment (Flag-MID-PIWI-Vpr)


title: Y7.Enrich


title: BFP, rep1

value: SAM

value: BFP


title: HEK293T, control (201113S1)

description: plasmid transfection

value: control plasmid transfection


title: TPC1 cells, si-SRPX2, rep1

city: Bengbu

first: Jiajun

last: Wu

state: None Selected

address: 浙江省杭州市拱墅区朝晖街道上塘路158号浙江省人民医院

institute: Bengbu Medical College

data_processing:
After the final transcriptome was generated, StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples)
The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change > 2 were considered differentially expressed genes.
Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: genes_fpkm_expression.xlsx

source_name: thyroid

growth_protocol: TPC1 thyroid cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent (thermofisher, 15596018). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Transcriptome expression profling was analyzed by RNA  sequencing using  NovaSeq 6000 platform (Illumina) by Shanghai Bioegene Co., Ltd.

value: thyroid cancer cells

value: SRPX2 knockdown

value: adipogenic differentiation

value: Day 2


title: TPC1 cells, si-SRPX2, rep3

address: 浙江省杭州市拱墅区朝晖街道上塘路158号浙江省人民医院


title: allneg, rep3

value: AllNeg


title: Y8.Input

value: Peripheral mononuclear blood cell

value: Young

value: Discovery

value: 23 years

value: Female


title: YFP, rep3

description:
Degs_relaxed_yfp_vs_bfp_gfp.xls
Degs_relaxed_yfp_vs_bfp_yfp.xls
Degs_relaxed_yfp_vs_bfp.xls
Degs_relaxed_yfp_vs_gfp.xls
Degs_relaxed_yfp_vs_neg.xls

value: YFP


title: YFP, rep2


title: allneg, rep2


title: YFP, rep1


title: WT, DSB, young, biol rep2

description:
The library has the forward index: CTG and reverse index: GTG. A total of  17400 colony number was in this library.
WT young 2

value: No

value: S. cerevisiae haploid strain

value: wt young yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: nuc1, DSB, replicative aging, biol rep3

description:
The library has the forward index: TGC and reverse index: GCA. A total of  7725 colony number was in this library.
Replicative nuc1 Aging rep 3

value: mutant isogenic to JKM139

value: nuc1::kanMX DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Replicative nuc1 Aging carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: WT, DSB, young, biol rep1

description:
The library has the forward index: CAG and reverse index: GAT. A total of  16360 colony number was in this library.
WT young 1

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: nuc1, DSB, replicative aging, biol rep1

description:
The library has the forward index: TAC and reverse index: CGA. A total of  18800 colony number was in this library.
Replicative nuc1 Aging rep 1

value: nuc1::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Replicative nuc1 Aging yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: nuc1, DSB, replicative aging, biol rep2

description:
The library has the forward index: TCC and reverse index: CTT. A total of  6530 colony number was in this library.
Replicative nuc1 Aging rep 2


title: Y6.Input

value: Input

value: 30 years

value: Male


title: BFPYFP, rep3

description:
Degs_relaxed_bfp_yfp_vs_bfp_gfp.xls
Degs_relaxed_bfp_yfp_vs_bfp.xls
Degs_relaxed_bfp_yfp_vs_neg.xls

value: SAM

value: BFPYFP


title: TPC1 cells, si-SRPX2, rep2

address: 浙江省杭州市拱墅区朝晖街道上塘路158号浙江省人民医院

value: thyroid cancer cells

value: SRPX2 knockdown

value: adipogenic differentiation

value: Day 2


title: BFPYFP, rep2


title: Y4.Input

value: Peripheral mononuclear blood cell

value: Young

value: Discovery

value: 28 years

value: Female


title: allneg, rep1

value: AllNeg


title: TPC1 cells, si-Control, rep3

address: 浙江省杭州市拱墅区朝晖街道上塘路158号浙江省人民医院

value: WT


title: Y6.Enrich

value: Enrich


title: TC-OKC control KO biol rep 3

city: San Francisco

first: Celine

middle: Ismay

last: Mahieu

state: California

address: 513 Parnassus Ave, HSE 740

department: Otolaryngology | Head and Neck Surgery

institute: University of California San Francisco

data_processing:
QuantSeq 3‘ mRNA-Seq Integrated Data Analysis Pipelines on Bluebee® Genomics Platform
Sequence reads were trimmed for adaptor sequence/low-quality sequence using QuantSeq FWD Data Analysis Pipelines (bbduk v35.92)
Trimmed sequence reads were mapped to hg38 using QuantSeq FWD Data Analysis Pipelines (STAR Aligner with modified ENCODE settings)
Read count extraction and normalization were performed using QuantSeq 3‘ mRNA-Seq Integrated Data Analysis Pipelines on Bluebee® Genomics Platform
Differential expression analysis on read counts was done using the DESeq2 pipeline
Assembly: Homo sapiens - human (GRCh38)
Supplementary files format and content: TSV files include baseMean values for each Sample

source_name: Primary Oral Keratinocytes (TP53/CDKN2A KO)

growth_protocol: FaDu cells were grown in EMEM with L-glutamine supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptomycin. Oral keratinocytes were collected and isolated from patient derived mucosal samples and cultured in Medium 154 and Keratinocyte SFM (1:1), supplemented with 5 mL/L Human Keratinocyte Growth Supplement, 25 mg/L Bovine Pituitary Extract, 2.5 µg/L EGF Human Recombinant and 1% P/S. Cells were maintained in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 800 ng of total RNA was used for the construction of sequencing libraries.
RNAseq libraries were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) kit according to the manufacturer’s instructions. Library quality was assessed with a High Sensitivity DNA Assay on the Agilent 2100 Bioanalyzer.

treatment_protocol: CRISPR-RNPs were used to KO indicated genes at >90% KO efficiency as confirmed through TIDE analysis. Cells were maintained under normal growth conditions and RNA was collected 6 days post transfection of Cas9-RNPs.

value: Tonsil derived primary keratinocytes, engineered to carry TP53/CDKN2A KO mutations

value: 11q13 control KO

value: Epithelial

tag: disease

value: Non-cancer


title: Y5.Input

value: Input

value: 25 years


title: Y5.Enrich


title: WT, DSB, replicative aging, biol rep3

description:
The library has the forward index: CTG and reverse index: CCA. A total of  12573 colony number was in this library.
Replicative WT Aging 3

value: No

value: S. cerevisiae haploid strain

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Replicative WT Aging yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: TPC1 cells, si-Control, rep2

address: 浙江省杭州市拱墅区朝晖街道上塘路158号浙江省人民医院

value: thyroid cancer cells

value: adipogenic differentiation

value: Day 2


title: Y4.Enrich

value: Peripheral mononuclear blood cell

value: Young

value: Discovery

value: 28 years

value: Female


title: TPC1 cells, si-Control, rep1

address: 浙江省杭州市拱墅区朝晖街道上塘路158号浙江省人民医院

value: WT


title: BFPYFP, rep1

value: SAM

value: BFPYFP


title: Y3.Input

value: Input

value: 31 years

value: Male


title: TC-OKC control KO biol rep 1

value: Primary Oral Keratinocytes (TP53/CDKN2A KO)

value: Tonsil derived primary keratinocytes, engineered to carry TP53/CDKN2A KO mutations

value: 11q13 control KO

value: Epithelial

value: Non-cancer


title: TC-OKC control KO biol rep 2


title: Y3.Enrich

value: Enrich


title: TC-OKC CCND2 KO biol rep 2

value: CCND2 KO


title: Y2.Enrich

value: Peripheral mononuclear blood cell

value: Young

value: 29 years


title: Y1.Input

value: Discovery

value: 27 years


title: TC-OKC CCND2 KO biol rep 1


title: Y2.Input

value: Female


title: BFPGFP, rep2

description:
Degs_relaxed_bfp_gfp_vs_bfp_yfp.xls
Degs_relaxed_bfp_gfp_vs_bfp.xls
Degs_relaxed_bfp_gfp_vs_neg.xls

value: SAM

value: BFPGFP


title: BFPGFP, rep1


title: Y1.Enrich


title: Ribo-seq_MSC, mutant#2, rep2

city: Los Angeles

first: Supawadee

last: Jariyasakulroj

address: Alcazar street

institute: University of Southern California

data_processing:
Sequence reads were trimmed for 3'adaptor sequence/low-quality sequence using trimmomatic v0.36 (MINLEN: 18)
The different libraries were split using splitFastq.pl script
The PCR dulicates were removed using readCollapse script
Sequence reads were trimmed for 5' header sequence/low-quality sequence using trimmomatic v0.36 (MINLEN: 20)
Trimmed reads were aligned to the rRNA/tRNA using Bowtie2 (v.2.3.4.3), only unmapped reads were retained
The remaining reads were mapped to GRCh38 with HISAT2 (v2.2.1) software
Read count extraction were performed using featureCounts (v2.0.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample
Library strategy: Ribo-seq (ribosome profiling sequencing)

source_name: human iPS derived mesenchymal stem cells

growth_protocol: Human iPS derived MSCs were induced from human iPS derived neural crest cells

extract_protocol:
Cell media was aspirated and cells were washed with ice-cold PBS. After removing PBS thoroughly, the dish was added 400 uL, which was then placed on wet ice for 5 min. Cells were then scraped off to a 1.5 mL tube and added NP40 (10%) for complete lysis for 10 min. The lysate was cleared by centrifugation at 2,000 g 4 °C for 10 min and then 20,000 g 4°C for 10 min. Lysate RNA was measured with Qubit HS RNA kit and certain amount of lysates were used for digestion at concentration (600 ng RNase A + 75 U RNase T1/ug RNA) at 25°C for 30 min. Stop the reaction by chilling on ice and add 50 U SUPERase In RNase inhibitior (2.5 uL/sample) and 0.5 M EDTA (100x). Following nuclease digestion, monosomes were purified using ultracentrifugation in a SW55i rotor at 55,000 rpm at 4°C for 5 h. PNK treatment was performed after pellet RNA recovery. Then 15% polyacrylamide TBE-Urea gel was used to isolate RPFs (26-34 nt) and the RPFs were recovered for library preparation.
Library was prepared using optimized PARIS protocol (Lu. et al. Cell, 2016). The step of ribosomal rRNA depletion was performed after circularization step using pre-synthesized biotinylated probes whose sequences were from the protocol (Ingolia. et al. Nature protocol, 2012).

treatment_protocol: MSCs were maintained in ɑ-MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

value: mesenchymal stem cells

value: Snord118 mutant heterozygote


title: ap1cal mir 16hr  rep3

description:
ap1Cal_Mir_16_vs_Ap1_16.xls
ap1Cal_Mir_16_vs_LHG_16.xls

data_processing:
The quality of the sequencing data was assessed using FastQC
bases with fluctuating GC content were trimmed off with cutadapt
Genome mapping was performed using TopHat
A gene expression count table was generated from the aligned dataset using HTSeq
Assembly: TAIR10
Supplementary files format and content: The processed data include lists of differentially expressed genes (DEGs) for pair wise comparision between different samples. Since there are total 3 differnet samples (ap1cal, ap1cal with LHG4, and ap1cal with mir), so there are 2 processed files for each samples. Each file include log2 fold change and p-values for the DEGs in one sample againt another sample. For eg. the file "ap1Cal_Mir_16_vs_Ap1_16.xls" contains log2 fold change in sample "ap1cal with mir" against sample "ap1cal'.

growth_protocol: Plants were grown under long day conditions till flowering

extract_protocol:
Rneasy Mini kit (Qiagen) was used according to manufacturer’s instruction
the libraries were prepared with 1μg of total RNA using ‘TruSeq Stranded mRNA Library Prep Kit from Illumina’.

treatment_protocol: For inducible gene perturbations in the IM, 10 μMDEX solution containing 0.015% Silwet L-77 was applied once to the IM and tissues were collected after required time point for RNA-Seq

value: pUBQ10>>mir165a in ap1cal

value: Dex 16hr


title: pif1-m2 dna2, DSB, non aging, biol rep3

description:
The library has the forward index: CAG and reverse index: GAT. A total of  6000 colony number was in this library.
pif1-m2 dna2 3

value: No

value: mutant isogenic to JKM139

value: dna2::kanMX pif1-m2 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: pif1-m2 dna2 yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: pif1-m2 dna2, DSB, non aging, biol rep5

description:
The library has the forward index: TTG and reverse index: CTG. A total of  23104 colony number was in this library.
pif1-m2 dna2 5


title: nuc1, DSB, non aging, biol rep1

description:
The library has the forward index: TGC and reverse index: GCA. A total of  11440 colony number was in this library.
nuc1 1

value: nuc1::klTRP1 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: nuc1 yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: nuc1, DSB, non aging, biol rep2

description:
The library has the forward index: TTC and reverse index: GTC. A total of  14120 colony number was in this library.
nuc1 2


title: Ribo-seq_MSC, mutant#1, rep1

value: human iPS derived mesenchymal stem cells


title: WT, DSB, replicative aging, biol rep1

description:
The library has the forward index: AAC and reverse index: GAA. A total of  26400 colony number was in this library.
Replicative WT Aging 1

value: S. cerevisiae haploid strain

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: Replicative WT Aging cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: pif1-m2 dna2, DSB, non aging, biol rep4

description:
The library has the forward index: CAG and reverse index: GAT. A total of  12000 colony number was in this library.
pif1-m2 dna2 4


title: WT, DSB, replicative aging, biol rep2

description:
The library has the forward index: ATC and reverse index: CGT. A total of  30720 colony number was in this library.
Replicative WT Aging 2

value: Replicative WT Aging yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: ap1cal mir 16hr  rep2

value: SAM


title: Ribo-seq_MSC, wildtype#2, rep2

value: WT


title: FaDu control KO biol rep 1

source_name: FaDu (HTB-43)

value: FaDu (HTB-43)

value: Pharyngeal Squamous Cell Carcinoma

value: 11q13 control KO

value: Epithelial

value: Cancer


title: FaDu control KO biol rep 2


title: ap1cal mir 16hr  rep1

value: pUBQ10>>mir165a in ap1cal

value: Dex 16hr


title: ap1cal mir 12hr  rep4

description:
ap1Cal_Mir_12_vs_Ap1_12.xls
ap1Cal_Mir_12_vs_LHG_12.xls

value: Dex 12hr


title: TC-OKC CCND1 KO biol rep 2

value: Primary Oral Keratinocytes (TP53/CDKN2A KO)

value: Tonsil derived primary keratinocytes, engineered to carry TP53/CDKN2A KO mutations

value: CCND1 KO

value: Non-cancer


title: ap1cal mir 12hr  rep3


title: FaDu MIR548K KO biol rep 2

value: MIR548K KO


title: BFPGFP, rep3

value: BFPGFP


title: MSC, mutant#2, rep2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic v0.36
Trimmed sequence reads were mapped to GRCh38 with HISAT2 (v2.2.1) software
Read count extraction were performed using featureCounts (v2.0.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

extract_protocol:
RNA was extracted using TRIzol (ThermoFisher). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit following manufacturer's protocols.

value: human iPS derived mesenchymal stem cells

value: mesenchymal stem cells

value: Snord118 mutant heterozygote


title: ap1cal mir 12hr  rep2

value: SAM


title: pif1-m2 dna2, DSB, non aging, biol rep6

description:
The library has the forward index: ACC and reverse index: GAA. A total of  76160 colony number was in this library.
pif1-m2 dna2 6

value: No

value: mutant isogenic to JKM139

value: dna2::kanMX pif1-m2 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: pif1-m2 dna2 yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: Ribo-seq_MSC, wildtype#1, rep1

value: WT


title: FaDU ORAOV1 KO biol rep 2

value: FaDu (HTB-43)

value: Pharyngeal Squamous Cell Carcinoma

value: ORAOV1 KO

value: Epithelial

value: Cancer


title: TC-OKC CCND1 KO biol rep 1

value: Primary Oral Keratinocytes (TP53/CDKN2A KO)

value: Tonsil derived primary keratinocytes, engineered to carry TP53/CDKN2A KO mutations

value: CCND1 KO

value: Non-cancer


title: FaDu MIR548K KO biol rep 1

value: MIR548K KO


title: MSC, mutant#1, rep1

value: human iPS derived mesenchymal stem cells

value: mesenchymal stem cells

value: Snord118 mutant heterozygote


title: pif1-m2 dna2, DSB, non aging, biol rep2

description:
The library has the forward index: CAG and reverse index: GAT. A total of  40000 colony number was in this library.
pif1-m2 dna2 2

value: No

value: mutant isogenic to JKM139


title: pif1-m2 dna2, DSB, non aging, biol rep1

description:
The library has the forward index: CAG and reverse index: GAT. A total of  40000 colony number was in this library.
pif1-m2 dna2 1

value: dna2::kanMX pif1-m2 DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: pif1-m2 dna2 yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: WT, DSB, non aging, biol rep6

description:
The library has the forward index: AGC and reverse index: CTA. A total of  23856 colony number was in this library.
WT 6

value: S. cerevisiae haploid strain

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: WT yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: WT, DSB, non aging, biol rep5

description:
The library has the forward index: AGG and reverse index: GGA. A total of  15120 colony number was in this library.
WT 5


title: WT, DSB, non aging, biol rep3

description:
The library has the forward index: TGC and reverse index: TGC. A total of  16000 colony number was in this library.
WT 3


title: ap1cal mir 8hr  rep4

description:
ap1Cal_Mir_8_vs_Ap1_8.xls
ap1Cal_Mir_8_vs_LHG_8.xls

value: SAM

value: pUBQ10>>mir165a in ap1cal

value: Dex 8hr


title: MSC, wildtype#1, rep1

value: WT


title: WT, DSB, non aging, biol rep4

description:
The library has the forward index: TGC and reverse index: TGC. A total of  16000 colony number was in this library.
WT 4


title: FaDU ORAOV1 KO biol rep 1

value: FaDu (HTB-43)

value: Pharyngeal Squamous Cell Carcinoma

value: ORAOV1 KO

value: Epithelial

value: Cancer


title: FaDu CCND2 KO biol rep 2

value: CCND2 KO


title: MSC, wildtype#2, rep2

value: human iPS derived mesenchymal stem cells

value: mesenchymal stem cells


title: SA06: PC9-Tr-BrM-S100A9-inh

city: New York

first: Swarnali

last: Acharyya

state: NY

address: 1130 ST NICHOLAS AVE, HERBERT IRVING COMP CANCER, Room 401A,

department: Pathology and Cell Biology

institute: Columbia University

data_processing:
Raw RNA-seq reads were aligned to the human genome (GRCh38) using STAR version 4.0.1 in two-pass mode
Raw gene-level read counts were generated using STAR and collecting the unstranded read counts for each sample
For downstream processing and statistical testing, raw reads were imported into R (v4.0.1) and DESeq2 (v 1.28.1) was used to normalize read counts to library size and perform differential expression analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read counts, as summarized by STAR

source_name: EGFR-mutant lung cancer cell line

extract_protocol:
Total RNA was extracted using trizol and Qiagen RNAeasy RNA extraction kit per manufacturers instructions without modification
Poly-A selected RNA was used to generate Illumina TruSeq compatable sequencing libraries

value: EGFR-mutant lung cancer cell line

tag: condition

value: Tr-BrM


title: SA05: PC9-Tr-BrM-S100A9-inh


title: ap1cal mir 4hr  rep3

description:
ap1Cal_Mir_4_vs_Ap1_4.xls
ap1Cal_Mir_4_vs_LHG_4.xls

value: Dex 4hr


title: FaDu CCND2 KO biol rep 1


title: ap1cal mir 4hr  rep4


title: ap1cal mir 4hr  rep1


title: WT, non-DSB, non aging, biol rep1

description:
The library has the forward index: TCG and reverse index: GTC. A total of  32000 colony number was in this library.
WT noDSB

value: No

value: S. cerevisiae haploid strain

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO

value: WT yeast cells that did not generate a single double-strand break (DSB) per genome at the MATa locus.


title: FaDu CCND1 KO biol rep 2

value: CCND1 KO


title: CA1 hippcampus, treated, 72h, replicate 3

city: Bonn

first: Ashley

last: van Waardenberg

address: Venusberg-Campus 1

country: Germany

institute: i-Synapse

data_processing:
For building genome indices and mapping, STAR version 2.7.8a was used. For genome indices, gtf and genome fasta files were provided to STAR as parameters –sjdbGTFfile and –geneFastaFiles with --runMode genomeGenerate to generate indices. --sjdbOverhand was set to 99 (read length – 1). All other parameters remained default.
Adapter trimming was performed using trimgalore version 0.6.6 (implemented in python version 3.8.5) and run in paired-end mode (using the –paired parameter). Adapters trimmed were “–illumina”. Sequence end soft clipping was performed using the default phred score of 20 and paired reads less than 20bp for both reads were discarded. All other parameters were default.
For mapping of RNA reads, STAR was run with parameter “--runMode alignReads”and paired (trimmed) reads input to the --readFilesIn parameter. Inputs for “—sjdbGTFfile” and “—genomeDir” parameters were the index described and gtf file described above. Non-default parameters were: --outSAMtype BAM Unsorted; --outFilterMultimapNmax 20; --outFilterMismatchNmax 999; --outFilterMismatchNoverReadLmax 0.04; --outFilterType BySJout; --alignIntronMin 20; --alignIntronMax 1000000; --alignMatesGapMax 1000000; --alignSJoverhangMin 8; --alignSJDBoverhangMin 1; --sjdbScore 1.
Bam files were sorted with samtools version 1.10 and reads summarized using htseq-count version 0.13.5 (implemented with python version 3.8.5). Non-default htseq-count parameters included: --format bam; --order=pos; --stranded no. All other parameters remained default.
After an initial assessment of lane or pair specific biases, reads from multiple lanes of the same samples were merged into a single fastq files for each of the paired fastq files.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and raw counts for each sample

source_name: Brain

extract_protocol:
Mice were deeply anesthetized following decapitation and the brain was rapidly removed. Hippocampal slices were prepared by slicing the brain into coronal slices (400 μm) on a Thermo scientific HM650V microtome in ice-cold Phosphate Buffer Solution  (140 mM NaCl, 10 mM phosphate buffer, and 3 mM KCl, pH 7.4 solution). CA1 hippocampus region was carefully microdissected under a microscope. Samples were subsequently mechanically homogenized for total RNA isolation.
Total RNA was isolated using the miRNeasy micro kit (Qiagen) according to the manufacturer’s protocol. The quality and integrity of total RNA was assessed using a Tapestation 2200 (Agilent Technologies). Purification of mRNA was performed using polyT oligo-attached magnetic beads. After purification, mRNA was used for library preparation using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s protocol. Sequencing was carried out on a HiSeq1500 system (Illumina) using cycle paired-end sequencing.

treatment_protocol: For SE induction, adult (≥60 days old, weight ≥ 20 g) C57Bl/6N mice (Charles River) were pretreated with a subcutaneous injection of 1 mg/kg scopolamine methyl nitrate (Sigma), followed 20 minutes later by a subcutaneous injection of 335 mg/kg pilocarpine hydrochloride (Sigma), as previously described (Pitsch et al., 2017; Pitsch et al., 2012; Pohlentz et al., 2022). Forty min after the onset of SE, animals received an injection of diazepam (4 mg/kg, s.c.; Ratiopharm). Control (non-SE) animals were treated identically, but received saline instead of pilocarpine. Of the animals injected with pilocarpine, only those that developed SE (SE-experienced) were used for subsequent analyses.

value: Brain

tag: section

value: CA1 Hippocampus

value: C57Bl/6N mice (Charles River)

value: 335 mg/kg pilocarpine hydrochloride


title: ap1cal LHG4 16hr  rep3

description:
ap1Cal_LHG_16_vs_Ap1_16.xls
ap1Cal_Mir_16_vs_LHG_16.xls

tag: tissue

value: SAM

value: pUBQ10::GR-LHG4 in ap1cal

value: Dex 16hr


title: HEK293T, co-expression of EV-inducing protein and miRNA binding protein

value: Human Embryonic Kidney cell

value: WT

value: co-transfected with the EV-inducing protein (EPN-01) and the miRNA binding protein fragment (Flag-MID-PIWI-Vpr)


title: SA03: PC9-Tr-BrM-control

value: EGFR-mutant lung cancer cell line

value: Tr-BrM

value: control


title: CA1 hippcampus, treated, 72h, replicate 2


title: WT, DSB, non aging, biol rep1

description:
The library has the forward index: TGC and reverse index: TGC. A total of  16000 colony number was in this library.
WT 1

value: No

value: S. cerevisiae haploid strain

value: WT yeast cells carrying a galactose-inducible HO endonuclease that generates a single double-strand break (DSB) per genome at the MATa locus.


title: FaDu CCND2 KO biol rep 3

value: FaDu (HTB-43)

value: Pharyngeal Squamous Cell Carcinoma

value: CCND2 KO

value: Epithelial

value: Cancer


title: ap1cal mir 8hr  rep1

value: SAM

value: pUBQ10>>mir165a in ap1cal

value: Dex 8hr


title: ap1cal LHG4 16hr  rep2

value: pUBQ10::GR-LHG4 in ap1cal

value: Dex 16hr


title: SA02: PC9-Tr-BrM-control


title: CA1 hippcampus, treated, 72h, replicate 1

value: Brain

value: CA1 Hippocampus

value: C57Bl/6N mice (Charles River)

value: 335 mg/kg pilocarpine hydrochloride


title: WT, DSB, non aging, biol rep2

description:
The library has the forward index: TGC and reverse index: TGC. A total of  16000 colony number was in this library.
WT 2

value: No

value: DELho hml::ADE1 MATa hmr::ADE1 ade1 leu2-3,112 lys5 trp1::hisG ura3-52 ade3::GAL10::HO


title: ap1cal LHG4 16hr  rep1


title: ap1cal mir 8hr  rep3


title: HEK293T, control

value: Human Embryonic Kidney cell

value: WT

value: control plasmid transfection


title: FaDu CCND1 KO biol rep 1

value: FaDu (HTB-43)

value: Pharyngeal Squamous Cell Carcinoma

value: CCND1 KO


title: CA1 hippcampus, untreated, 72h, replicate 3

value: saline


title: PANC-1 TAMs rep3

city: Guangzhou

first: Leyi

last: Huang

state: Guangdong

address: 107 Yan Jiang West Road, Guangzhou, P.R. China

institute: Sun Yat-sen University

data_processing:
Illumina Casava  bcl2fastqv2.19 software used for basecalling.
Fragments Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a protocol from  Mortazavi A et al., Nat Methods, 2008.We first applied StringTie (version:1.3.0) to the Fragments of each gene after Hisat2 comparison, then normalized with TMM (mean of M values) , and finally calculates the FPKM value for each gene with Perl.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tumor-associated Macrophages

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat#74004, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were conducted with standard Illumina protocols, using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina® (Vazyme, China), Agencourt ® AMPure XP Beads(Beckman, USA),Qubit™ dsDNA HS Assay Kit(Invitrogen, USA) and Agilent High Sensitivity DNA Kit(Agilent, USA).

value: monocytes derived macrophages

value: culture with PANC-1 condition medium


title: ap1cal LHG4 12hr  rep4

description:
ap1Cal_LHG_12_vs_Ap1_12.xls
ap1Cal_Mir_12_vs_LHG_12.xls

value: SAM

value: pUBQ10::GR-LHG4 in ap1cal

value: Dex 12hr


title: SA04: PC9-Tr-BrM-S100A9-inh

value: EGFR-mutant lung cancer cell line

value: Tr-BrM


title: SA14: PC9-BrM-control

value: BrM

value: control


title: CA1 hippcampus, untreated, 72h, replicate 2

value: Brain

value: CA1 Hippocampus

value: C57Bl/6N mice (Charles River)


title: CA1 hippcampus, untreated, 72h, replicate 1


title: SA13: PC9-BrM-control


title: PANC-1 TAMs rep1


title: ap1cal LHG4 12hr  rep3


title: SA12: PC9-BrM-control


title: ap1cal LHG4 12hr  rep2


title: SA01: PC9-Tr-BrM-control


title: ap1cal LHG4 8hr  rep3

description:
ap1Cal_LHG_8_vs_Ap1_8.xls
ap1Cal_Mir_8_vs_LHG_8.xls

value: Dex 8hr


title: MIA PaCa-2 TAMs rep3

value: culture with MIA PaCa-2 condition medium


title: CA1 hippcampus, treated, 36h, replicate 3

value: 335 mg/kg pilocarpine hydrochloride


title: CA1 hippcampus, treated, 36h, replicate 2


title: ap1cal LHG4 8hr  rep2


title: CA1 hippcampus, untreated, 36h, replicate 3


title: MDMs rep3

source_name: Macrophages

value: untreated


title: MIA PaCa-2 TAMs rep1


title: CA1 hippcampus, treated, 36h, replicate 1


title: CA1 hippcampus, untreated, 36h, replicate 2

value: saline


title: ap1cal LHG4 8hr  rep1


title: PANC-1 TAMs rep2

value: monocytes derived macrophages


title: CA1 hippcampus, untreated, 36h, replicate 1


title: ap1cal LHG4 4hr  rep4

description:
ap1Cal_LHG_4_vs_Ap1_4.xls
ap1Cal_Mir_4_vs_LHG_4.xls

value: Dex 4hr


title: MDMs rep2


title: MDMs rep1


title: ap1cal LHG4 4hr  rep2

value: SAM


title: CA1 hippcampus, treated, 24h, replicate 3


title: MIA PaCa-2 TAMs rep2


title: ap1cal LHG4 4hr  rep3

value: pUBQ10::GR-LHG4 in ap1cal


title: BxPC-3 TAMs rep3

value: culture with BxPC-3 condition medium


title: CA1 hippcampus, treated, 24h, replicate 2


title: RPTEC_stiff_CM_03

type: RNA

city: Asan-si

first: Dayeon

last: Kang

address: 22, Soonchunhyang-ro, Sinchang-myeon

country: South Korea

institute: Soon Chun Hyang University

description:
miRNA
TC5

hyb_protocol: For analysing of miRNA expression, the digital multiplexed nanoString nCounter human miRNA expression assay (nanoString Technologies) was performed with Human miRNA Panel Kit according to the manufacturer’s protocol.

scan_protocol: Abundances of specific target molecules were quantified on the nCounter Digital Analyzer by counting the individual fluorescent barcodes and assessing the target molecules. For each assay, a high-density scan encompassing 555 fields of view was performed. The data was collected using the nCounter Digital Analyzer after taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera.

data_processing: To analysis the miRNA data, we used the nSolver(version 4.0) software analysis, freely available from nanoString Technologies.

label: biotin

source_name: hTERT-immortalized renal proximal tubule epithelial cell

label_protocol: NanoString’s nCounter CodeSet chemistry utilizes target-specific Reporter and Capture Probes, collectively referred to as a CodeSet, that directly hybridize to a target of interest. Each probe pair consists of a color-coded Reporter and a Capture Probe to which a target-specific sequence has been covalently attached.

growth_protocol: RPTEC/TERT1 cells were cultured in DMEM: F-12 Medium supplemented with the hTERT Immortalized RPTEC Growth Kit, 0.1 mg/ml geneticin, and 0.2% FBS at 37°C in a humidified 5% CO2 atmosphere. RPTEC/TERT1 cells were plated on soft and stiff polyacrylamide gel plates. Cells were then incubated for 5 days at 37°C in a humidified atmosphere containing 5% CO2, with the medium replaced every 2 days.

extract_protocol: Total RNA was extracted using Qiagen miRNeasy Kits (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: For conditioned medium (CM) treatment, RPTEC culture medium was replaced with CM on day 4 and incubated for 24 h

value: stiff

tag: agent

value: BMSC-CM


title: RPTEC_soft_CM_02

description:
miRNA
SC4

value: soft

value: hTERT-immortalized renal proximal tubule epithelial cell


title: RPTEC_stiff_CM_02

description:
miRNA
TC4


title: RPTEC_stiff_CM_01

description:
miRNA
TC3


title: RPTEC_soft_CM_03

description:
miRNA
SC5


title: BxPC-3 TAMs rep2


title: BxPC-3 TAMs rep1


title: CA1 hippcampus, treated, 24h, replicate 1

value: Brain


title: ap1cal 16hr  rep2

description:
ap1Cal_LHG_16_vs_Ap1_16.xls
ap1Cal_Mir_16_vs_Ap1_16.xls

value: Dex 16hr


title: RPTEC_stiff_notreat_03

description:
miRNA
TN5


title: H12: H1650-Tr-BrM-S100A9-inh

value: EGFR-mutant lung cancer cell line

value: Tr-BrM


title: RPTEC_stiff_notreat_02

description:
miRNA
TN4


title: ap1cal 12hr  rep3

description:
ap1Cal_LHG_12_vs_Ap1_12.xls
ap1Cal_Mir_12_vs_Ap1_12.xls

value: Dex 12hr


title: H11: H1650-Tr-BrM-S100A9-inh


title: CA1 hippcampus, treated, 12h, replicate 2

value: CA1 Hippocampus

value: C57Bl/6N mice (Charles River)

value: 335 mg/kg pilocarpine hydrochloride


title: ap1cal 12hr  rep2


title: RPTEC_soft_notreat_03

description:
miRNA
SN5


title: RPTEC_soft_CM_01

description:
miRNA
SC3


title: ap1cal 16hr  rep4


title: CA1 hippcampus, untreated, 12h, replicate 3

value: saline


title: ap1cal 12hr  rep1


title: H9: H1650-Tr-BrM-control

value: control


title: ap1cal 16hr  rep3

value: SAM


title: ap1cal 8hr  rep4

description:
ap1Cal_LHG_8_vs_Ap1_8.xls
ap1Cal_Mir_8_vs_Ap1_8.xls

value: Dex 8hr


title: CA1 hippcampus, untreated, 12h, replicate 2


title: CA1 hippcampus, untreated, 12h, replicate 1


title: RPTEC_soft_notreat_01

description:
miRNA
SN3


title: H8: H1650-Tr-BrM-control


title: CA1 hippcampus, treated, 12h, replicate 3


title: ap1cal 4hr  rep3

description:
ap1Cal_LHG_4_vs_Ap1_4.xls
ap1Cal_Mir_4_vs_Ap1_4.xls

value: Dex 4hr


title: H7: H1650-Tr-BrM-control


title: ap1cal 8hr  rep1


title: CA1 hippcampus, treated, 12h, replicate 1


title: RPTEC_stiff_notreat_01

description:
miRNA
TN3

value: stiff


title: CA1 hippcampus, treated, 6h, replicate 3


title: CA1 hippcampus, treated, 6h, replicate 2


title: JIMT-1 aCT1-3

city: Indianapolis

first: Elizabeth

last: Yeh

state: Indiana

address: 635 Barnhill Drive, Medical Science Building A418

department: Pharmacology and Toxicology

institute: Indiana University School of Medicine

data_processing:
NanoString nSolver 4.0 software was used for analysis of gene expression values
Nanostring nSolver 4.0 software computed normalized log2 count and normalized linear count

source_name: Human HER2+ Breast Cancer Cells (JIMT-1)

growth_protocol: Cells grown in DMEM (Corning 10-017-CV) supplemented with 10% fetal bovine serum, 200 nM glutamine (Thermo Scientific), and penicillin/streptomycin (Thermo Scientific).

extract_protocol: Used GeneJET RNA purifcation kit (K0732) to isolate RNA from cells.

treatment_protocol: JIMT-1 cells treated with 250 µM aCT1 or PBS for 24 hours.

value: HER2+ breast cancer cell


title: JIMT-1 aCT1-1


title: ap1cal 4hr  rep2


title: CA1 hippcampus, treated, 6h, replicate 1


title: H10: H1650-Tr-BrM-S100A9-inh


title: H2: H1650-BrM-control

value: BrM


title: RPTEC_soft_notreat_02

description:
miRNA
SN4

value: soft

value: hTERT-immortalized renal proximal tubule epithelial cell


title: H3: H1650-BrM-control


title: H1: H1650-BrM-control


title: o-iPSCs WT rep2

status: Public on Dec 19 2023

city: Taipei

first: Wei-Ni

last: Lyu

state: Daan

address: 4th Floor, No. 81, Changxing Street

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

description:
E8_P34_S4
Bornean orangutan

data_processing:
The raw fastq files were assessed using FastQC v0.11.9, and the results were summarized using MultiQC v1.13.
Trimmomatic v0.39 was utilized for adapter removal and quality filtering of low-quality bases.
The trimmed and untrimmed reads were then aligned to the Pongo abelii Susie_PABv2 reference genome with Ensembl v108 annotations using STAR v2.7.10b.
The featureCounts command line was employed to count the mapped reads for genes using the Rsubread v2.0.1 package.
Assembly: Pongo abelii Susie_PABv2
Supplementary files format and content: all_feature_pab.txt: Tab-delimited text file includes raw counts for each Sample.

organism: Pongo pygmaeus

source_name: induced pluripotent stem cells

extract_protocol:
Total RNA is isolated by TRIzol® reagent (15596026) and treated with RNase-free DNase I (M6101, Promega, Madison, WI, USA) to remove genomic DNA.
RNA libraries for RNA-seq were prepared using SureSelect 415 XT HS2 mRNA Library Preparation kit following the manufacturer's protocols.

value: induced pluripotent stem cells


title: o-iPSCs treated rep2

description:
A4iLAF_P7
Bornean orangutan

value: 4i/L/A culture system


title: o-iPSCs treated rep1

description:
A4iLAF_P5_S5
Bornean orangutan


title: o-iPSCs WT rep1

description:
E8_P33
Bornean orangutan


title: JIMT-1 aCT1-2


title: ap1cal 8hr  rep2


title: ap1cal 4hr  rep1


title: JIMT-1 control 1

value: Control


title: LPSBLF3

city: Shijiazhuang

first: Yantao

address: No.389, Zhongshan East Road, Shijiazhuang City

department: Department of Critical Care Medicine

institute: The First Affiliated Hospital of Hebei University of Chinese Medicine

data_processing:
The raw data was filtered with SOAPnuke (v1.5.2) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.1.0).
The expression level of genes was calculated by RSEM (v1.2.8).
Assembly: mm10
Supplementary files format and content: FileincludeCount and FPKM valuesforeachsample

source_name: lung tissues

growth_protocol: Male BALB/c mice (6–8 weeks old, 20 g, n = 24) were purchased from Hubei Experimental Animal Research Center and raised under the following conditions: temperature, 24°C–26°C; humidity, 40%–60%, and 12-h light/dark cycle. Food and water were provided ad libitum.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT)-attached magnetic beads. Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first-strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.

treatment_protocol: A total of 24 mice were randomly divided into 4 groups (n = 6): control, lung injury (LPS, 50 μL, 1 μg/μL), bLF (bLF, 200 mg/kg/day), and treatment (LPS+bLF). After 14 days of modeling, lung tissues of 12 mice from the control, LPS, bLF, and LPS+bLF groups (n = 3) were used for RNA-seq analysis.

value: lung tissues

value: BALB/c

tag: Sex

value: male

value: LBS+BLF


title: LPSBLF2


title: BLF3

value: BLF


title: LPSBLF1


title: JIMT-1 control 3


title: BLF1


title: JIMT-1 control 2


title: LPS3

value: LPS


title: LPS1


title: Liver_EC_WT_CDAA_rep3.fastq.gz

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

institute: Medizinische Fakultät Mannheim

data_processing:
Trimmomatics was used to trim raw fastq reads.
Trimmed reads were aligned to the reference using the short read aligner STAR (https://code.google.com/p/rna-star/). With the following parameters (STAR --genomeDir $geno_mm10 --runThreadN 8 --alignIntronMin 20 --alignIntronMax 500000)
sam files were converted to taq libraries by the help of makeTaqLibrariy from homer and quantified with analyzeRepeats.pl, with the following parameters (rna mm10 -strand both -count exons)
Differential expression analysis was performed using Deseq2 from R. Differentially expressed Genes were selected with (0.75<FC>1.5 and FDR<0.05).
Genome_build: mm10
Supplementary_files_format_and_content: Excel files from the Differential expressed genes were used to produce the heatmaps

source_name: isolated liver endothelial cells

growth_protocol: Sox9fl/fl mice were crossed with Cdh5-Cre+/- and interbred homozygous for Sox9fl/fl and hemizygous for Cre

extract_protocol:
Total RNA was isolated using Macherey-Nagel column kit
BGI

treatment_protocol: Mice were injected with 0.5 mg Tamoxifen for 5 consecutive days 14 days prior to diet start

value: mixed background

value: liver

value: 4 M

value: ctrl


title: Liver_EC_WT_Chow_rep2.fastq.gz


title: LPS2


title: BLF2


title: Liver_EC_WT_Chow_rep1.fastq.gz


title: Liver_EC_KO_Chow_rep2.fastq.gz

value: Sox9 knock-out


title: Liver_EC_WT_CDAA_rep1.fastq.gz


title: Liver_EC_WT_Chow_rep3.fastq.gz


title: Liver_EC_KO_Chow_rep1.fastq.gz


title: Liver_EC_WT_CDAA_rep2.fastq.gz


title: control3

value: NC


title: Liver_EC_KO_Chow_rep3.fastq.gz


title: Liver_EC_KO_CDAA_rep2.fastq.gz


title: 02lung_EC_WT_NaCl_rep2

source_name: isolated pulmonal endothelial cells

treatment_protocol: Mice were injected with 0.5 mg Tamoxifen for 5 consecutive days 14 days prior to diet start or injection

value: lung

value: NaCl


title: Liver_EC_KO_CDAA_rep1.fastq.gz


title: 02lung_EC_WT_NaCl_rep3


title: 02lung_EC_WT_NaCl_rep1


title: control1


title: 02lung_EC_WT_BLM_rep3

value: BLM


title: 02lung_EC_WT_BLM_rep2


title: Liver_EC_KO_CDAA_rep3.fastq.gz


title: 02lung_EC_WT_BLM_rep1


title: 02lung_EC_Sox9_KO_NaCl_rep3


title: 02lung_EC_Sox9_KO_NaCl_rep1


title: 02lung_EC_Sox9_KO_NaCl_rep2


title: 02lung_EC_Sox9_KO_BLM_rep3


title: 02lung_EC_Sox9_KO_BLM_rep2


title: control2


title: 02lung_EC_Sox9_KO_BLM_rep1


title: 01heart_EC_WT_HFPEF_rep3

source_name: isolated cardiac endothelial cells

value: heart

value: HFPEF


title: 01heart_EC_WT_Chow_rep3

value: Chow


title: 01heart_EC_WT_Chow_rep2


title: 01heart_EC_WT_HFPEF_rep2


title: 01heart_EC_Sox9_KO_HFPEF_rep2


title: 01heart_EC_WT_Chow_rep1


title: 01heart_EC_Sox9_KO_Chow_rep3


title: 01heart_EC_Sox9_KO_HFPEF_rep3


title: 01heart_EC_Sox9_KO_Chow_rep1


title: 01heart_EC_Sox9_KO_HFPEF_rep1


title: 01heart_EC_Sox9_KO_Chow_rep2


title: 03Heart_EC_KO_TAC_r3

growth_protocol: hprt-Sox9fl/fl or Sox9fl/fl mice, resp., were crossed with Cdh5-Cre+/- and interbred homozygous for hprt-Sox9fl/fl and hemizygous for Cre

treatment_protocol: Mice were injected with 0.5 mg Tamoxifen for 5 consecutive days either 1 M prior to organ harvest or 14 days prior to 1 W TAC or sham operation

value: Transversal Aorta constriction


title: 03Heart_EC_KO_Sh_r1


title: 03Heart_EC_KO_Sh_r2


title: 03Heart_EC_KO_TAC_r2


title: 03Heart_EC_bWT_TAC_r3


title: 03Heart_EC_KO_TAC_r1


title: 03Heart_EC_bWT_TAC_r2


title: 03Heart_EC_bWT_TAC_r1


title: 03Heart_EC_KO_Sh_r3


title: 03Heart_EC_aWT_Sh_r1


title: 02Liver_EC_OE_r2

source_name: isolated hepatic endothelial cells

value: Sox9 overexpression


title: 02Liver_EC_OE_r1


title: 02Liver_EC_CTR_r3


title: 03Heart_EC_aWT_Sh_r2


title: 01heart_EC_WT_HFPEF_rep1


title: 03Heart_EC_aWT_Sh_r3


title: 02Liver_EC_CTR_r2


title: 02Liver_EC_OE_r3


title: 02Liver_EC_CTR_r1


title: 01Lung_EC_OE_r3


title: 01Lung_EC_OE_r1


title: 01Lung_EC_OE_r2


title: 01Lung_EC_CTR_r1


title: 01Lung_EC_CTR_r2


title: 01Lung_EC_CTR_r3


title: Sox9_hprt_VECad_Cre_CTR_heart_EC_rep3

growth_protocol: hprt-Sox9fl/fl mice were crossed with Cdh5-Cre+/- and interbred homozygous for hprt-Sox9fl/fl and hemizygous for Cre

treatment_protocol: Mice were injected with 0.5 mg Tamoxifen for 5 consecutive days 1 M prior to organ harvest


title: Sox9_hprt_VECad_Cre_OE_heart_EC_rep3


title: Sox9_hprt_VECad_Cre_OE_heart_EC_rep2


title: Sox9_hprt_VECad_Cre_OE_heart_EC_rep1


title: Sox9_hprt_VECad_Cre_CTR_heart_EC_rep2


title: 4301 Protein | 001 | Tumour

type: protein

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

hyb_protocol: DSP eluates were hybridised as per manufacturers instructions in nCounter Readout User Manual.

scan_protocol: Hybridised samples were loaded into Nanostring prep station and processed as per DSP Slide Prep User Manual. N counter was performed with default parameters, and counts from Ncounter uploaded back to DSP instrument

data_processing: Counts were aligned and ERCC corrected automatically on the DSP instrument. This QC data was exported for analysis.

molecule: protein

source_name: NSCLC

label_protocol: DSP experiments were performed as per manufacturers DSP Slide Prep User Manual instructions. Slides were deparafinised, antigen retrieval by HIER, and overnight staining with antibody cocktail as per "DSP Slide Prep User Manual". Slides were images and samples collected on DSP instrument

extract_protocol: Clinical FFPE samples on individual slides were obtained with appropriate ethics approval

tag: roi

tag: segment

value: Tumour

tag: area

tag: aoinucleicount

tag: response

value: Responder

tag: followup

tag: status

value: Alive


title: 4301 Protein | 003 | Tumour

value: Non-responder

value: Deceased


title: 4301 Protein | 001 | Stroma

value: Stroma


title: 4301 Protein | 002 | Stroma


title: 4301 Protein | 004 | Tumour


title: 4301 Protein | 004 | Stroma


title: 4301 Protein | 005 | Tumour


title: 4301 Protein | 006 | Stroma


title: 4301 Protein | 006 | Tumour


title: 4301 Protein | 007 | Stroma


title: 4301 Protein | 007 | Tumour


title: 4301 Protein | 008 | Tumour


title: 4301 Protein | 003 | Stroma


title: 4301 Protein | 009 | Stroma


title: 4301 Protein | 005 | Stroma


title: 4301 Protein | 010 | Stroma


title: 4301 Protein | 010 | Tumour


title: Sox9_hprt_VECad_Cre_CTR_heart_EC_rep1

tag: strain

value: mixed background

tag: age

value: ctrl


title: 4301 Protein | 008 | Stroma


title: 4301 Protein | 011 | Tumour


title: 4301 Protein | 013 | Tumour


title: 4301 Protein | 011 | Stroma


title: 4301 Protein | 014 | Tumour


title: 4301 Protein | 014 | Stroma


title: 4301 Protein | 012 | Tumour


title: 4301 Protein | 012 | Stroma


title: 4301 Protein | 013 | Stroma


title: 4301 Protein | 002 | Tumour


title: 4301 Protein | 015 | Tumour


title: 4301 Protein | 016 | Stroma


title: 4301 Protein | 016 | Tumour


title: 4301 Protein | 017 | Tumour


title: 4301 Protein | 015 | Stroma


title: 4301 Protein | 017 | Stroma


title: 4301 Protein | 020 | Stroma


title: 4301 Protein | 018 | Stroma


title: 4301 Protein | 009 | Tumour


title: 4301 Protein | 020 | Tumour


title: 4301 Protein | 018 | Tumour


title: 4301 Protein | 021 | Stroma


title: 4301 Protein | 047 | Tumour


title: 4301 Protein | 047 | Stroma


title: 4301 Protein | 021 | Tumour


title: 4301 Protein | 019 | Stroma


title: 4301 Protein | 048 | Tumour


title: 4301 Protein | 048 | Stroma


title: 4301 Protein | 022 | Tumour


title: 4301 Protein | 023 | Tumour


title: 4301 Protein | 024 | Stroma


title: 4301 Protein | 025 | Tumour


title: 4301 Protein | 022 | Stroma


title: 4301 Protein | 025 | Stroma


title: 4301 Protein | 026 | Tumour

value: LB16 948 TL B


title: 4301 Protein | 024 | Tumour


title: 4301 Protein | 027 | Tumour

value: LB15 746  TL A


title: 4301 Protein | 026 | Stroma


title: 4301 Protein | 028 | Tumour

value: LB11 551 TL C


title: 4301 Protein | 027 | Stroma


title: 4301 Protein | 029 | Tumour


title: 4301 Protein | 028 | Stroma


title: 4301 Protein | 019 | Tumour


title: 4301 Protein | 030 | Tumour


title: 4301 Protein | 029 | Stroma


title: 4301 Protein | 031 | Tumour

value: LB18 159 TL B


title: 4301 Protein | 030 | Stroma


title: 4301 Protein | 032 | Stroma


title: 4301 Protein | 034 | Tumour


title: 4301 Protein | 033 | Tumour


title: 4301 Protein | 031 | Stroma


title: 4301 Protein | 033 | Stroma


title: 4301 Protein | 032 | Tumour


title: 4301 Protein | 035 | Tumour


title: 4301 Protein | 023 | Stroma


title: 4301 Protein | 035 | Stroma


title: 4301 Protein | 036 | Stroma


title: 4301 Protein | 036 | Tumour


title: 4301 Protein | 037 | Stroma


title: 4301 Protein | 038 | Tumour


title: 4301 Protein | 037 | Tumour


title: 4301 Protein | 038 | Stroma


title: 4301 Protein | 039 | Stroma


title: 4301 Protein | 040 | Tumour


title: 4301 Protein | 039 | Tumour


title: 4301 Protein | 041 | Stroma


title: 4301 Protein | 042 | Stroma


title: 4301 Protein | 042 | Tumour


title: 4301 Protein | 043 | Stroma


title: 4301 Protein | 044 | Stroma


title: 4301 Protein | 043 | Tumour


title: 4301 Protein | 045 | Tumour


title: 4301 Protein | 034 | Stroma


title: 4301 Protein | 046 | Tumour


title: 4301 Protein | 046 | Stroma


title: 4301 Protein | 041 | Tumour


title: Msn2Full_HO_TEF_1

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Demultiplexing with AdapterRemoval, --trim3p 0 21.
Identification of UMI with umi_tools extract, --bc-pattern=NNNNNNNNN.
Mapping the reads with bowtie2, -p8 --local --very-sensitive --trim-to 30 -x.
Sorting and indexing with samtools.
Deduplication of UMI with umi_tools dedup.
Calculation of coverage with bedtools coverage -counts -s -a.
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.txt: Processed data files contain counts mapped with bedtools coverage in format of (chromosome, chromosome location (start), chromosome location (stop), systemic name, number, strand, counts).

organism: Saccharomyces cerevisiae BY4741

source_name: cultured yeast cells

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose.

extract_protocol:
RNA-seq: Modified protocol of the nucleospin 96 RNA kit (Macherey-Nagel, Duren, Germany). Specifically, cell lysis was done in a 96 deep-well plate by adding 450 μl of lysis buffer containing 1 M sorbitol (Sigma-Aldrich), 100 mM EDTA, and 0.45 μl lyticase (10 IU/μl). The plate was incubated at 30°C for 30 minutes in order to break the cell wall and then centrifuged for 10 minutes at 2,500 rpm, and the supernatant was removed. From this point, extraction proceeded as in the protocol of nucleospin 96 RNA kit, only substituting β-mercaptoethanol with DTT 1M.
RNA libraries were created as described before (Chapal et al., 2019).

tag: cell type

value: cultured yeast cells

tag: type

tag: fusion

value: HO

tag: loci

tag: delta native tf

value: FALSE

tag: promoter


title: Crz1Full_HO_TEF_1


title: Sko1Full_HO_TEF_1


title: Pdr8Full_HO_TEF_1


title: Met31Full_HO_TEF_1


title: Reb1Full_HO_TEF_2


title: Msn2Full_HO_TEF_2


title: Mig3Full_HO_TEF_1


title: Vhr1Full_HO_TEF_2


title: Vhr1Full_HO_TEF_1


title: 4301 Protein | 045 | Stroma


title: Abf1Full_HO_TEF_2


title: Ino2Full_HO_TEF_2


title: Ino2Full_HO_TEF_1


title: Gcn4Full_HO_TEF_1


title: Abf1Full_HO_TEF_1


title: Sko1Full_HO_TEF_2


title: 4301 Protein | 044 | Tumour


title: Yap1Full_HO_TEF_1


title: Crz1Full_HO_TEF_2


title: Gcn4Full_HO_TEF_2


title: Reb1Full_HO_TEF_3


title: Met31Full_HO_TEF_2


title: Nrg2Full_HO_TEF_1


title: Yap1Full_HO_TEF_2


title: Gln3Full_HO_TEF_1


title: Rpn4Full_HO_TEF_1


title: Reb1Full_HO_TEF_1


title: Nrg2Full_HO_TEF_2


title: Rpn4Full_HO_TEF_2


title: Gal4Full_HO_TEF_1


title: 4301 Protein | 040 | Stroma


title: Cst6Full_HO_TEF_1


title: Cst6Full_HO_TEF_2


title: Msn2Full_HO_TEF_3


title: Yap1Full_lib_HOdYap1_B03_1

value: TRUE

value: synthetic


title: Gal4Full_lib_HOdGal4_B04_1


title: Gal4Full_lib_HOdGal4_C05_1


title: Yap1Full_lib_HOdYap1_G04_1


title: Gal4Full_HO_TEF_2


title: Yap1Full_lib_HOdYap1_TEF_1


title: Gal4Full_lib_HOdGal4_D11_1


title: Yap1Full_lib_HOdYap1_D04_1


title: Yap1Full_lib_HOdYap1_H12_1


title: Nrg2Full_HO_TEF_3


title: Gal4Full_lib_HOdGal4_TEF_1


title: Yap1Full_lib_HOdYap1_G02_1


title: Yap1Full_lib_HOdYap1_B12_1


title: Gal4Full_lib_HOdGal4_C01_1


title: Gln3Full_HO_TEF_3


title: Gln3Full_HO_TEF_2


title: Pdr8Full_HO_TEF_2


title: Yap1Full_lib_HOdYap1_C06_1


title: Yap1Full_lib_HOdYap1_C04_1


title: Yap1Full_lib_HOdYap1_E06_1


title: Gal4Full_lib_HOdGal4_C02_1


title: Gal4Full_lib_HOdGal4_B01_1


title: Gal4Full_lib_HOdGal4_A06_1


title: Gal4Full_lib_HOdGal4_A12_1


title: Yap1Full_lib_HOdYap1_A06_1


title: Yap1Full_lib_HOdYap1_A10_1


title: Yap1Full_lib_HOdYap1_B05_1


title: Yap1Full_lib_HOdYap1_H06_1


title: Yap1Full_lib_HOdYap1_C09_1


title: Gal4Full_lib_HOdGal4_A10_1


title: Gal4Full_lib_HOdGal4_A09_1


title: Gal4Full_lib_HOdGal4_A01_1


title: Gal4Full_lib_HOdGal4_B03_1


title: Yap1Full_lib_HOdYap1_B10_1


title: Yap1Full_lib_HOdYap1_H01_1


title: Gal4Full_lib_HOdGal4_C06_1


title: Gal4Full_lib_HOdGal4_B10_1


title: Yap1Full_lib_HOdYap1_C02_1


title: Yap1Full_lib_HOdYap1_G12_1


title: Gal4Full_lib_HOdGal4_B12_1


title: Gal4Full_lib_HOdGal4_C07_1


title: Yap1Full_lib_HOdYap1_C12_1


title: Yap1Full_lib_HOdYap1_G11_1


title: Yap1Full_lib_HOdYap1_F02_1


title: Yap1Full_lib_HOdYap1_B08_1


title: Yap1Full_lib_HOdYap1_TEF_2


title: Yap1Full_lib_HOdYap1_F05_1


title: Gal4Full_lib_HOdGal4_B07_1


title: Yap1Full_lib_HOdYap1_TEF_3


title: Gal4Full_lib_HOdGal4_B05_1


title: Gal4Full_lib_HOdGal4_D05_1


title: Yap1Full_lib_HOdYap1_A05_1


title: Gal4Full_lib_HOdGal4_D08_1


title: Gal4Full_lib_HOdGal4_B09_1


title: Gal4Full_lib_HOdGal4_A04_1


title: Gal4Full_lib_HOdGal4_B06_1


title: Gal4Full_lib_HOdGal4_C08_1


title: Yap1Full_lib_HOdYap1_A01_1


title: Yap1Full_lib_HOdYap1_D01_1


title: Yap1Full_lib_HOdYap1_C07_1


title: Yap1Full_lib_HOdYap1_E01_1


title: Yap1Full_lib_HOdYap1_G06_1


title: Gal4Full_lib_HOdGal4_TEF_3


title: Gal4Full_lib_HOdGal4_D07_1


title: Gal4Full_lib_HOdGal4_D10_1


title: Gal4Full_lib_HOdGal4_C12_1


title: Yap1Full_lib_HOdYap1_C08_1


title: Gal4Full_lib_HOdGal4_C04_1


title: Yap1Full_lib_HOdYap1_H10_1


title: Gal4Full_lib_HOdGal4_B11_1


title: Yap1Full_lib_HOdYap1_G07_1


title: Yap1Full_lib_HOdYap1_A09_1


title: Gal4Full_lib_HOdGal4_A11_1


title: BY_1

value: Control


title: Gal4Full_lib_HOdGal4_B02_1


title: Gal4Full_lib_HOdGal4_D02_1


title: Gal4Full_lib_HOdGal4_TEF_2


title: Gal4Full_lib_HOdGal4_D12_1


title: Yap1Full_lib_HOdYap1_A04_1


title: BY_3


title: BY_5


title: Yap1Full_lib_HOdYap1_G03_1


title: Yap1Full_lib_HOdYap1_A07_1


title: Yap1Full_lib_HOdYap1_F08_1


title: BY_2


title: Gal4Full_lib_HOdGal4_A07_1


title: Gal4Full_lib_HOdGal4_D04_1


title: Gal4Full_lib_HOdGal4_D03_1


title: Yap1DBD_Gal11_HOdYap1_3


title: Yap1DBD_Gal11_HOdYap1_1


title: Yap1DBD_Gal11_HOdYap1_2


title: Gal4Full_lib_HOdGal4_A05_1


title: Gcn4DBD_Gal11_HOdGcn4_5


title: Gcn4DBD_Gal11_HOdGcn4_2


title: Gcn4DBD_Gal11_HOdGcn4_4


title: Yap1DBD_Gal11_HOdYap1_4


title: BY_7


title: Yap1Full_lib_HOdYap1_H05_1


title: BY_8


title: Gcn4DBD_Gal11_HOdGcn4_6


title: BY_10


title: BY_9


title: Rpn4DBD_Gal11_HOdRpn4_1


title: BY_4


title: Gcn4DBD_Gal11_HOdGcn4_1


title: Gcn4DBD_Gal11_HOdGcn4_3


title: Gal4Full_lib_HOdGal4_B08_1


title: Rpn4DBD_Gal11_HOdRpn4_2


title: BY_6


title: Msn2DBD_Gcn4AD_lib_nativeloc_F05_1

value: native


title: Msn2DBD_Gcn4AD_lib_nativeloc_F07_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_C09_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_H08_1


title: Msn2DBD_Gal4AD_lib_nativeloc_E11_1


title: Msn2DBD_Gal4AD_lib_nativeloc_A06_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_G01_1


title: Msn2DBD_Gal4AD_lib_nativeloc_C04_1


title: Msn2DBD_Gal4AD_lib_nativeloc_D11_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_F06_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_G07_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_F08_1


title: Msn2DBD_Gal4AD_lib_nativeloc_D10_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_nativeprom_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_B01_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_D06_1


title: Msn2DBD_Gal4AD_lib_nativeloc_C12_1


title: Msn2DBD_Gal4AD_lib_nativeloc_A08_1


title: Msn2DBD_Gal4AD_lib_nativeloc_nativeprom_1


title: Msn2DBD_Gal4AD_lib_nativeloc_A02_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_H05_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_C04_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_B06_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_C01_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_E01_1


title: BY_11


title: Msn2DBD_Gal4AD_lib_nativeloc_B08_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_C07_1


title: Msn2DBD_Gal4AD_lib_nativeloc_A05_1


title: Msn2DBD_Gal4AD_lib_nativeloc_E01_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_A05_1


title: Msn2DBD_Gal4AD_lib_nativeloc_A10_1


title: BY_12


title: Msn2DBD_Gcn4AD_lib_nativeloc_D02_1


title: Msn2DBD_Gal4AD_lib_nativeloc_C03_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_H12_1


title: Msn2DBD_Gal4AD_lib_nativeloc_D02_1


title: Msn2DBD_Gal4AD_lib_nativeloc_C02_1


title: Msn2DBD_Gal4AD_lib_nativeloc_C09_1


title: Msn2DBD_Gal4AD_lib_nativeloc_C07_1


title: Msn2DBD_Gal4AD_lib_nativeloc_E06_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_E02_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_D01_1


title: Msn2DBD_Gal4AD_lib_nativeloc_G05_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_B08_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_nativeprom_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_A08_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_E12_1


title: Msn2DBD_Gal4AD_lib_nativeloc_B05_1


title: Msn2DBD_Gal4AD_lib_nativeloc_G03_1


title: Msn2DBD_Gal4AD_lib_nativeloc_G06_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_A07_1


title: Msn2DBD_Gal4AD_lib_nativeloc_F11_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_F02_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_A12_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_C12_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_F12_1


title: Msn2DBD_Gal4AD_lib_nativeloc_E03_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_B10_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_B11_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_A10_1


title: Msn2DBD_Gal4AD_lib_nativeloc_H09_1


title: Msn2DBD_Gal4AD_lib_nativeloc_B02_1


title: Msn2DBD_Gal4AD_lib_nativeloc_C06_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_H10_1


title: Msn2DBD_Gal4AD_lib_nativeloc_D04_1


title: Msn2DBD_Gal4AD_lib_nativeloc_H03_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_B09_1


title: Msn2DBD_Gal4AD_lib_nativeloc_B10_1


title: Msn2DBD_Gal4AD_lib_nativeloc_A07_1


title: Msn2DBD_Gal4AD_lib_nativeloc_nativeprom_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_G12_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_E11_1


title: Msn2DBD_Gal4AD_lib_nativeloc_G02_1


title: BY_13


title: Msn2DBD_Gcn4AD_lib_nativeloc_H02_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_H06_1


title: Msn2DBD_Gal4AD_lib_nativeloc_B11_1


title: BY_14


title: Msn2DBD_Gcn4AD_lib_nativeloc_G11_1


title: Msn2DBD_Gal4AD_lib_nativeloc_A11_1


title: Msn2DBD_Gal4AD_lib_nativeloc_H04_1


title: Crz1DBD_Gcn4AD_TEF_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_D12_1


title: Sko1DBD_Gcn4AD_TEF_1


title: Rpn4DBD_Gcn4AD_TEF_1


title: Cst6DBD_Gcn4AD_TEF_1


title: Vhr1DBD_Gal4AD_TEF_1


title: Pdr8DBD_Gal4AD_TEF_1


title: Nrg2DBD_Gcn4AD_TEF_1


title: Sko1DBD_Gal4AD_TEF_1


title: Gln3DBD_Gal4AD_TEF_1


title: Pdr8DBD_Gal4AD_TEF_2


title: Abf1DBD_Gal4AD_TEF_1


title: Met31DBD_Gcn4AD_TEF_1


title: Reb1DBD_Gal4AD_TEF_1


title: Pdr8DBD_Gcn4AD_TEF_1


title: Gln3DBD_Gcn4AD_TEF_1


title: Crz1DBD_Gal4AD_TEF_1


title: Msn2DBD_Gal4AD_lib_nativeloc_H08_1


title: Pdr8DBD_Gcn4AD_TEF_2


title: Nrg2DBD_Gal4AD_TEF_1


title: Abf1DBD_Gcn4AD_TEF_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_TEF_1


title: Cst6DBD_Gal4AD_TEF_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_G07_1


title: Rpn4DBD_Gal4AD_TEF_1


title: BY_15


title: BY_16


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_B04_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_G07_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_B06_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_B02_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_F12_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_E06_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_TEF_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_G01_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_H01_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_E02_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_G04_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_F07_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_C08_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_TEF_2


title: Gal4DBD_Gcn4AD_lib_HOdGal4_TEF_3


title: Gal4DBD_Gal4AD_lib_HOdGal4_C12_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_F01_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_B07_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_F09_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_H08_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_G11_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_C07_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_TEF_4


title: Gal4DBD_Gcn4AD_lib_HOdGal4_TEF_5


title: Gal4DBD_Gal4AD_lib_HOdGal4_G06_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_D06_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_F01_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_D11_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_F06_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_G04_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_H04_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_H08_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_D01_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_A01_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_TEF_2


title: Gal4DBD_Gal4AD_lib_HOdGal4_TEF_3


title: Gal4DBD_Gal4AD_lib_HOdGal4_G02_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_H07_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_A09_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_B12_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_B10_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_B04_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_D05_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_A06_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_TEF_4


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_F10_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_F12_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_B01_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_C05_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_TEF_5


title: Gal4DBD_Gal4AD_lib_HOdGal4_G05_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_E09_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_H10_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_G12_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_E10_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_D08_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_F02_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_H10_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_H04_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_A10_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_C04_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_E10_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_B02_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_F06_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_H03_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_C07_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_D04_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_G11_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_C08_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_C10_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_C11_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_C09_1


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_H09_1


title: BY_17


title: BY_18


title: BY_19


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate1_A03_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_A04_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_B09_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_F07_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_D10_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_B06_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_TEF_1


title: BY_20


title: Gal4DBD_Gcn4AD_lib_HOdGal4_plate2_C12_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_E11_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_F03_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_F09_1


title: Gal4DBD_Gal4AD_lib_HOdGal4_E12_1


title: BY_21


title: BY_22


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_F06_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_TEF_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_C07_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_H09_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_H02_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_E07_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_F10_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_E02_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_E09_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_A03_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_A05_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_D06_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_H09_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_E03_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_C02_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_D06_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_D07_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_E08_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_B12_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_A10_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_C04_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_A11_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_D08_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_B01_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_F06_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_G12_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_D10_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_A03_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_TEF_2


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_G03_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_B10_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_D05_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_TEF_2


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_F11_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_B09_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_F04_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_B08_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_TEF_3


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_C10_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_TEF_3


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_E07_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_C10_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_F02_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_A01_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_C05_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_A12_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_C11_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_F02_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_C05_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_H02_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_F12_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_B08_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_B03_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_G08_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_D07_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_D10_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_E12_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_H09_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_E08_1


title: BY_24


title: BY_23


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_F09_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_A02_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_E06_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_D07_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_E02_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_D04_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_H05_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate2_D09_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_E10_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_G04_1


title: BY_26


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_C06_1


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_F07_1


title: Msn2Full_lib_nativeloc_F12_1


title: Msn2Full_lib_nativeloc_G06_1


title: Msn2Full_lib_nativeloc_E11_1


title: Msn2Full_lib_nativeloc_B02_1


title: Gcn4DBD_Gcn4AD_lib_HOdGcn4_plate1_G06_1


title: BY_25


title: Gcn4DBD_Gal4AD_lib_HOdGcn4_G10_1


title: Msn2Full_lib_nativeloc_G08_1


title: Msn2Full_lib_nativeloc_D06_1


title: Msn2Full_lib_nativeloc_C12_1


title: BY_27


title: Msn2Full_lib_nativeloc_G01_1


title: Msn2Full_lib_nativeloc_nativeprom_1


title: Msn2Full_lib_nativeloc_H09_1


title: Msn2Full_lib_nativeloc_H11_1


title: Msn2Full_lib_nativeloc_H07_1


title: Msn2Full_lib_nativeloc_F08_1


title: Msn2Full_lib_nativeloc_G10_1


title: Msn2Full_lib_nativeloc_H02_1


title: Msn2Full_lib_nativeloc_D04_1


title: Msn2Full_lib_nativeloc_F11_1


title: Msn2Full_lib_nativeloc_D12_1


title: Msn2Full_lib_nativeloc_F09_1


title: Msn2Full_lib_nativeloc_E05_1


title: Msn2Full_lib_nativeloc_H08_1


title: Msn2Full_lib_nativeloc_E06_1


title: Msn2Full_lib_nativeloc_H10_1


title: Msn2Full_lib_nativeloc_F10_1


title: Msn2Full_lib_nativeloc_E07_1


title: Msn2Full_lib_nativeloc_F07_1


title: Msn2Full_lib_nativeloc_D02_1


title: Msn2Full_lib_nativeloc_F04_1


title: Msn2Full_lib_nativeloc_D10_1


title: Msn2Full_lib_nativeloc_D07_1


title: Msn2Full_lib_nativeloc_G12_1


title: Msn2Full_lib_nativeloc_G11_1


title: Msn2Full_lib_nativeloc_H01_1


title: Msn2Full_lib_nativeloc_H12_1


title: Msn2Full_lib_nativeloc_C04_1


title: Msn2Full_lib_nativeloc_E10_1


title: Msn2Full_lib_nativeloc_F06_1


title: Msn2Full_lib_nativeloc_E09_1


title: Msn2Full_lib_nativeloc_D08_1


title: Msn2Full_lib_nativeloc_D09_1


title: Msn2Full_lib_nativeloc_G09_1


title: Msn2Full_lib_nativeloc_C04_2


title: Msn2Full_lib_nativeloc_G09_2


title: Msn2Full_lib_nativeloc_H12_2


title: Msn2Full_lib_nativeloc_F04_2


title: Msn2Full_lib_nativeloc_D02_2


title: Msn2Full_lib_nativeloc_D09_2


title: Msn2Full_lib_nativeloc_E10_2


title: Msn2Full_lib_nativeloc_F07_2


title: Msn2Full_lib_nativeloc_E07_2


title: Msn2Full_lib_nativeloc_E06_2


title: Msn2Full_lib_nativeloc_G11_2


title: Msn2Full_lib_nativeloc_F10_2


title: Msn2Full_lib_nativeloc_H10_2


title: Msn2Full_lib_nativeloc_D04_2


title: Msn2Full_lib_nativeloc_D08_2


title: Msn2Full_lib_nativeloc_G10_2


title: Msn2Full_lib_nativeloc_D12_2


title: Msn2Full_lib_nativeloc_F11_2


title: Msn2Full_lib_nativeloc_D07_2


title: Msn2Full_lib_nativeloc_F06_2


title: Msn2Full_lib_nativeloc_F08_2


title: Msn2Full_lib_nativeloc_H11_2


title: Msn2Full_lib_nativeloc_H02_2


title: Msn2Full_lib_nativeloc_H07_2


title: Msn2Full_lib_nativeloc_nativeprom_2


title: Msn2Full_lib_nativeloc_D06_2


title: Msn2Full_lib_nativeloc_F09_2


title: Msn2Full_lib_nativeloc_D10_2


title: Msn2Full_lib_nativeloc_H01_2


title: Msn2Full_lib_nativeloc_E05_2


title: Msn2Full_lib_nativeloc_C12_2


title: Msn2Full_lib_nativeloc_G08_2


title: Msn2Full_lib_nativeloc_F12_2


title: Msn2Full_lib_nativeloc_G06_2


title: Msn2Full_lib_nativeloc_E09_2


title: Msn2Full_lib_nativeloc_G01_2


title: Msn2Full_lib_nativeloc_B02_2


title: Msn2Full_lib_nativeloc_G12_2


title: Msn2Full_lib_nativeloc_H09_2


title: Msn2Full_lib_nativeloc_H08_2


title: Msn2Full_lib_nativeloc_E11_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_F05_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_C09_2


title: BY_28


title: Msn2DBD_Gcn4AD_lib_nativeloc_G01_2


title: Msn2DBD_Gal4AD_lib_nativeloc_E11_2


title: Msn2DBD_Gal4AD_lib_nativeloc_A06_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_H08_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_F06_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_F08_2


title: Msn2DBD_Gal4AD_lib_nativeloc_D11_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_G07_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_B01_2


title: Msn2DBD_Gal4AD_lib_nativeloc_A08_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_nativeprom_3


title: Msn2DBD_Gal4AD_lib_nativeloc_A02_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_D06_2


title: Msn2DBD_Gal4AD_lib_nativeloc_D10_2


title: Msn2DBD_Gal4AD_lib_nativeloc_G04_1


title: Msn2DBD_Gal4AD_lib_nativeloc_C12_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_E01_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_C04_2


title: Msn2DBD_Gal4AD_lib_nativeloc_nativeprom_3


title: Msn2DBD_Gcn4AD_lib_nativeloc_H05_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_B06_2


title: Msn2DBD_Gal4AD_lib_nativeloc_C04_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_C01_2


title: Msn2DBD_Gal4AD_lib_nativeloc_B08_2


title: BY_29


title: Msn2DBD_Gal4AD_lib_nativeloc_A10_2


title: Msn2DBD_Gal4AD_lib_nativeloc_C03_2


title: Msn2DBD_Gal4AD_lib_nativeloc_A05_2


title: Msn2DBD_Gal4AD_lib_nativeloc_E01_2


title: BY_30


title: Msn2DBD_Gcn4AD_lib_nativeloc_A05_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_D02_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_D01_2


title: Msn2DBD_Gal4AD_lib_nativeloc_E06_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_H12_2


title: Msn2DBD_Gal4AD_lib_nativeloc_C09_2


title: Msn2DBD_Gal4AD_lib_nativeloc_D02_2


title: Msn2DBD_Gal4AD_lib_nativeloc_C02_2


title: Msn2DBD_Gal4AD_lib_nativeloc_C07_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_B10_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_E12_2


title: Msn2DBD_Gal4AD_lib_nativeloc_G05_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_A08_2


title: Msn2DBD_Gal4AD_lib_nativeloc_G03_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_C07_2


title: Msn2DBD_Gal4AD_lib_nativeloc_F11_2


title: Msn2DBD_Gal4AD_lib_nativeloc_G06_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_F02_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_A07_2


title: Msn2DBD_Gal4AD_lib_nativeloc_B05_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_F12_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_C12_2


title: Msn2DBD_Gal4AD_lib_nativeloc_E03_2


title: Msn2DBD_Gal4AD_lib_nativeloc_H09_2


title: Msn2DBD_Gal4AD_lib_nativeloc_B02_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_D12_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_B08_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_B11_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_H10_2


title: Msn2DBD_Gal4AD_lib_nativeloc_E04_1


title: Msn2DBD_Gcn4AD_lib_nativeloc_nativeprom_4


title: Msn2DBD_Gal4AD_lib_nativeloc_E12_1


title: Msn2DBD_Gal4AD_lib_nativeloc_H03_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_E02_2


title: Msn2DBD_Gal4AD_lib_nativeloc_A07_2


title: Msn2DBD_Gal4AD_lib_nativeloc_C06_2


title: Msn2DBD_Gal4AD_lib_nativeloc_nativeprom_4


title: Msn2DBD_Gcn4AD_lib_nativeloc_G12_2


title: Msn2DBD_Gal4AD_lib_nativeloc_D04_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_H06_2


title: Msn2DBD_Gcn4AD_lib_nativeloc_H02_2


title: BY_31


title: Msn2DBD_Gcn4AD_lib_nativeloc_G11_2