title: output-XETG00098__0018582__rep4_atn_post__20231129__015936

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: University of British Columbia

description: fresh frozen single-cell spatial transcriptomics

hyb_protocol: Probe hybridization was performed at 50°C overnight using the pre-designed, 247-probe Xenium Mouse Brain Gene Expression panel (10X Genomics, Cat. #1000462) in conjunction with a custom 50-probe add-on panel (10X Genomics, Cat.#1000646) against select thalamic target genes. Next, slides underwent wash steps to remove any unhybridized probes, followed by a 2-hour ligation step at 37°C to anneal probes to their specific mRNA target. The probes were then enzymatically amplified via rolling circle amplification PCR for 2 hours at 37°C. After washing, quenching steps were performed to reduce background autofluorescence, followed by a DAPI nuclear stain. The slide cassettes were subsequently loaded onto the Xenium Analyzer instrument

scan_protocol: Following instrument initialization, slides and consumables were loaded onto the Xenium Analyzer, and regions of interest were selected after a preliminary sample scan. Once the Xenium Analyzer run begins, slides undergo iterative rounds of image acquisition where probe-specific fluorescent oligos are added, hybridized to the amplified probe sequence, imaged and gently removed. mRNA-specific puncta were decoded into their corresponding gene IDs and assigned a quality score. Using the DAPI nuclear stain, cell boundaries were segmented and transcripts were spatially assigned to cells at a sub-50nm XY localization precision. After approximately 2 days of imaging and analysis, Xenium data was collected for further analysis.

data_processing: Xenium In Situ Analyzer performs automated onboard analysis which includes DAPI-based segmentation of nuclei via deep-learning, then expansion of the segmentation masks. A cell-by-gene matrix of segmented nuclei is generated for analysis. Post-processing in R with custom scripts and Seurat

source_name: brain hemisection

extract_protocol: Brain hemispheres were embedded into OCT and snap frozen in methylbutane cooled by liquid nitrogen after brain removal. Samples were processed according to recommendations in the Xenium In Situ for Fresh Frozen Tissues – Tissue Preparation Guide (10X Genomics): 10 μm anterior (bregma = -0.58mm), intermediate (bregma = -0.70mm to -0.82mm) and posterior (bregma = -0.94mm) hemisections were sectioned using a cryostat and placed within the 12x24mm sample frame on a Xenium slide. Slides were subsequently stored at -80°C until use. For use, slides were fixed and permeabilized as per the Xenium In Situ for Fresh Frozen Tissues – Fixation & Permeabilization protocol (10X Genomics).

value: brain

value: WT


title: ccRCC with PC destruction 2

status: Public on Feb 17 2024

type: RNA

city: Kashihara

first: Takuto

last: Shimizu

state: Nara

address: 840 Shijo-cho

department: Department of Urology

country: Japan

institute: Nara Medical University

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, HPRT1, LDHA, RPL1
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test group average/control group average(i.e., i-Cap2-3/i-Cap1) ratios.

label: SYBR Green

molecule: total RNA

organism: Rattus norvegicus

source_name: renal cell carcinoma

label_protocol: PCR assays were performed using RT2 Profiler PCR Array (QIAGEN,Venlo, Netherland) , Rat Extracellular Matrix & Adhesion Molecules <PARN-013-ZD> ,  following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (QIAGEN, Venlo, Netherland). Quantitative real-time PCR were performed (Light Cycler 480, Roche) 40 cycles of denaturation at 95˚C for 15 s; annealing and a final extension at 60˚C for 1 min.

extract_protocol: Total RNA was extracted with miRneasy FFPE (QIAGEN, Venlo, Netherland)Kit followed by DNase I treatment.

tag: sample type

value: i-Cap 2-3 (PC destruction)


title: output-XETG00098__0018582__rep3_atn_post__20231129__015936

country: Canada

organism: Mus musculus

tag: tissue

tag: genotype


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 tnladS 3

type: SRA

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

country: Germany

institute: Twincore

description: Ribosome protected RNA

library_source: transcriptomic

data_processing:
cutadapt , min read length 22
bowtie 2 - mapping to P. aeruginosa PA14 (NC_008463.1) reference genome, option “--very-sensitive-local”.
featureCounts
Supplementary files format and content: bed files - reads per gene (featureCounts)
Library strategy: Ribo-Seq

organism: Pseudomonas aeruginosa UCBPP-PA14

growth_protocol: planctonic growth in LB medium at 37°C, OD600 of 0.6

extract_protocol:
RNA footprints were isolated from monosome fractions with Tri-Reagent (Zymo clean and concentrator). Total bacterial RNA from the same culture was extracted using the RNeasy Mini Kit from Qiagen.
NEBNext Multiplex small RNA library prep for Illumina (E7300) using custom multiplex primers.

tag: strain


title: P2_RET-EGFP_M_DRG_B

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

data_processing:
Genome build: GRCm38.p2
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Supplementary file format and content: Text file with raw gene and cpm counts, and rpkm values

source_name: P2 male Ret-EGFP mouse FACSd T11-S1 DRG sample B

extract_protocol:
1) Dissect the appropriate level DRGs from the mice carrying a fluorescence reporter of interest, dissociate according to the age appropriate DRG dissociation procedures described on the GUDMAP website under the Jain Group protocols.
2) Add 7-AAD at 1ug/ml concentration, if needed, 10min before sorting to estimate viability and estimating gating parameters (also use fluorescence negative set to establish compensation controls and settings to recover populations of interest).  We have had good success using MoFlo, Sony or AriaII, at 100um nozzle size, and 30psi.
3) Collect directly in 750ul TRIzol-LS (Life Technologies, cat# 10296-010). Can store at -80°C or continue with RNA isolation. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols). After Trizol extraction the RNA was purified with Qiagen RNeasy micro kit and then stored at -80°C until further processing for QC and library preparation for RNA sequencing.
4) Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to use a total of 10ng in 9ul unless indicated otherwise for library preparation and RNA sequencing.
1) 10ng total RNA (in 9Âµl) was reverse transcribed and amplified using the SMARTerÂ® Ultraâ„¢ Low Input RNA for IlluminaÂ® Sequencing - HV (Clontech, cat# 634828) according to the manufacturerâ€™s instructions. 2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator. 3) The libraries were prepared using VeraSeqâ„¢ ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles. PCR conditions were 98Â°C for 30s; 12 cycles of 98Â°C for 10s, 64Â°C for 30s, 72Â°C for 30s; 72Â°C for 5 minutes and then hold at 4Â°C. The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer contains the unique reverse complement of the respective index nucleotides. The sequence of the reverse primer where "N" denotes the reverse complement of 7 nucleotides of the index is CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA.  Refer to the details of the BAM file for the sequence of the index used.

treatment_protocol: Total RNA was extracted from 20 pooled DRGs dissected from a Ret-EGFP embryo at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Tg(Ret-EGFP)SJ/

value: dorsal root ganglion,peripheral nervous system

tag: developmental stage

tag: Sex

value: male

tag: pooled sample

value: yes

tag: pool size

value: Pooled sample of 20 FACSd DRGs from 1 male embryo


title: H3K36me2_sh1_IP

city: Changsha

first: Zongyao

last: Ren

address: No.88 Xiangya Road

country: China

institute: Central South University

library_source: genomic

data_processing:
Fastp (version 0.23.0, Shifu Chen 2018) software was used for data quality control.The data was processed by removing adapter contamination, filtering out short reads (<15bp), low-quality reads (<Q15 with >40% of bases with low quality), and reads with >5 N bases.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Intranscription factorChIP-seq analysis with both Input and IP samples, we used Input as the background and called peaks on the IP sample using Macs2 in narrow peak mode. Macs2 is important for peak calling because it models the length of theprotein bindingsequence and determines therelative abundanceof peaks based on the length of that sequence and the number of pair-end reads mapped to it. In chromatin ChIP-seq analysis with both Input and IP samples, we also used Input as the background and called peaks on the IP sample using Epic2.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: excel, Fold_enrichment, Pvalue and FDR (except for Input sample)

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: H9 embryonic stem cells (ESCs) were utilized and cultured in a standard environment of 37°C with 5% CO2. The ESCs were cultured in a 12-well plate coated with Matrigel (Corning) and maintained with mTeSR-Plus medium (STEMCELL Technologies). Once the cells reached 80-90% confluence, they were dissociated using ReLeSR (STEMCELL Technologies) and passaged at a ratio of 1:20. The culture medium was replaced every other day.

extract_protocol:
Tissue or cells are cross-linked with formaldehyde to form covalent bonds between proteins and DNA. The cells are then lysed to releasecytoplasmic contentsand collect the nuclei. DNA-protein complexesare extracted from the lysate, and the DNA is fragmented into 200-1000bp pieces. The target protein-DNA complex is immunoprecipitated and washed. The complex is then eluted, and the DNA-protein cross-links are reversed, and DNA is extracted. The quality of theprecipitated DNAis checked, and the protein is detected using Western blotting. Finally, theimmunoprecipitated DNAis used to construct a library.
DNA from the IP was end-repaired and had an A-tail added. Sequencing adapters were then added to the repaired DNA. Target-sized fragments were recovered using magnetic beads and PCR amplified to obtain a library for sequencing. The library was quality checked using gel electrophoresis and quantified using Qubit 2.0 to ensure proper concentration for sequencing. Once the library passed quality control, it was sequenced on an Illumina sequencer, with different libraries sequenced based on their effective concentration and desired data output.

treatment_protocol: When the embryonic stem cells (ESCs) were suitable for passaging, accutase was added to digest the cells, and the cells were passaged at a ratio of 1:20. After overnight incubation, the lentivirus was added to infect the cells (MOI=20). The infected cells were screened with puromycin (1ug/ml) for 48 hours, and the screening was continued for 5-7 days.

tag: cell line

tag: cell type

value: Neural progenitor cells

tag: chip antibody

value: H3K36me2 (GeneTex, #GTX54108)


title: Huh7 cells, SBFI103, 48 hrs, replicate 1

city: New Haven

first: Jonathan

last: Sun

state: CT

address: 10 Amistad St

country: USA

institute: Yale University

data_processing:
Using the PartekFlow® software, version 8.0.19.0405 (Partek, Inc., St. Louis, MO) the reads were aligned with the STAR algorithm to the mouse genome mmu10.
To estimate the transcript expression abundance we used Quantify to annotation model (Partek E/M) algorithm.
Assembly: hg19
Supplementary files format and content: counts

growth_protocol: Huh7 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). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were with performed TrueSeq Small RNA Library preparation (Illumina).RNA libraries were sequenced for 45 cycles on Illumina HiSeq 2000 platform (1 x 75bp read length)

treatment_protocol: Treatment with siRNA (10nM Ctrl or FABP5 siRNA) or inhibitor (5uM SBFI-103) in culture media for 48 hours

value: Hepatoma cells

value: FABP5 inhibition

tag: time

value: 48 hrs


title: Huh7 cells, SBFI103, 48 hrs, replicate 2


title: H3K36me2_NC_Input

value: none (input)


title: 15M Control Diet

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned against mouse genome mm9 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R (version 3.0) using Seurat v3. Cells were filtered for more than 500 genes detected in each cell, 20,000 or less total number of molecules detected within a cell and 5% or less mitochondrial gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test, and clusters were calculated with 30 PCs
Differential expression analysis was done using wilcox
Assembly: mmp10
Supplementary files format and content: Cell-gene-barcode matrices

source_name: Parenchymal and Non-parenchymal fraction of the liver

extract_protocol:
The liver of diet-fed mice were perfused with collagenase and dissociated to separate out parenchymal (hepatocytes, cholangiocytes) and non-parenchymal (endothelial cells, immune cells etc..) fractions. Parenchymal fractions were purified using a 30% percoll gradient. Non-parenchymal fraction were enriched for live cells by flourescent activated cell sorting. Purified parenchymal and non-parenchymal cells were combined at a 1:1 ratio before submission for sequencing.
Single cells were encapsulated into droplets and processed following standard manufacturer’s specification, using 10X Genomics GemCode technology. Cells were loaded on a 10x Genomics Chromium controller instrument to generate single-cell Gel Beads in emulsion (GEMS) at the Yale Center for Genome Analysis. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM followed by complementary DNA (cDNA) generation using the single-Cell 3’ Regent Kits version 2 (10X Genomics). Libraries were sequenced on an Illumina HiSeq 4000 as 2x 100 paired-end reads.

value: Liver cells

tag: age

value: 17M old


title: ccRCC with PC destruction 1

description: Test


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 tnladS 2

description: Ribosome protected RNA


title: LCMV-WE, replicate 1 + LCMV-Docile, replicate 1, mRNA derived cDNA

city: Clayton

first: Kim

last: Good-Jacobson

state: Victoria

address: Gr Fl Reception (Bldg 77) 23 Innovation Walk

country: Australia

institute: Monash University

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

data_processing:
library strategy: CITE-seq
Cellranger (v5.0.1) multi was used to process the gene expression, cite-seq and VDJ libraries simultaneously. The following details were provided for the feature reference file: C0301,C0301_TotalSeqC,R2,5PNNNNNNNNNN(BC),ACCCACCAGTAAGAC,Antibody Capture, C0302,C0302_TotalSeqC,R2,5PNNNNNNNNNN(BC),GGTCGAGAGCATTCA,Antibody Capture.
C0301 corresponds to hashtag antibody 1(used on acute samples) and C0302 corresponds to hashtag antibody 2 (used on chronic samples)
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis). Seurat's HTO Demux function was used to demultiplex the samples and then Seurat was used for quality control, filtering, dimensionality reduction and clustering of the gene expression data.
The Immcantation suite (v 4.1.0) was used for VDJ analysis.
Assembly: mm10

source_name: Spleen

extract_protocol:
C57Bl6 mice were infected with LCMV-WE or LCMV-Docile. 28 days after infection, spleens were surgically removed from culled mice and non-RBC splenocytes were isolated. LCMV-specific B cells were magnetically enriched using an LCMV-NP tetramer system. Enriched cells were then stained with viability dye (FVS) and relevant antibodies, and 100,000 LCMV-specific B cells per sample were sorted using the BD Influx (BD Biosciences) cell sorter. After FACS, cells were spun down and resuspended in washing buffer (PBS 0.04% BSA) (50μl per ~1-2 million cells) and incubated with mouse Fc blockers (FcX, Biolegend) for 10 minutes at 4°C to block non-specific antibody binding. Following Fc blocking, each sample was incubated with either TotalSeq anti-mouse Hashtag Antibody 1 (Biolegend #155861) or 2 (Biolegend #155863) for 20 minutes at 4°C. Acute samples were tagged with Hashtag Antibody 1 and chronic samples were tagged with Hashtag Antibody 2. Following incubation, cells were washed 3x with 1ml of washing buffer to remove unbound antibodies. LCMV-WE and LCMV-Docile samples were then pooled at equal ratios in (PBS 0.04% BSA 0.2 U/ml RNAse inhibitor) at 1200 cells/ul. Cell viability >95% was confirmed via Trypan Blue staining.
Reverse transcription, cDNA amplification and library preparation for single cell gene expression and V(D)J clonotypes were performed based on the manufacturers protocol using the Chromium Single Cell 5′ Library & Gel Bead Kit v3 (10X Genomics).
Libraries were pooled at equimolar ratios and gene expression libraries were sequenced on the Illumina NovaSeq 6000 System, while HTO (hashtag oligo) and V(D)J (BCR) libraries were sequenced on Illumina NextSeq 500.

treatment_protocol: Infection with lymphocytic choriomeningitis virus (LCMV) (WE or Docile strain) for 28 days

value: Spleen

value: 28 days post-infection

value: LCMV-specific B cells

tag: disease state

value: Acute + Chronic nfection

tag: treatment

value: LCMV-WE + LCMV-Docile


title: H3K36me2_NC_IP


title: output-XETG00098__0018569__rep2_atn_ant__20231129__015936

value: brain

value: WT


title: Organoids_sh4-3

data_processing:
Quality control with SOAPnuke v1.5.2 to check the quality:
1. Remove low-quality reads (defined as reads with a base quality value <15 and >20% of total bases with low quality).
2. Remove reads with an unknown base (N) content greater than 5%.
3. Remove reads containing adapter sequences (adapter contamination).
Alignment to a reference genome or transcriptome with STAR
Quantification of gene or transcript expression with featureCounts.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol:
H9 embryonic stem cells (ESCs) were utilized and cultured in a standard environment of 37°C with 5% CO2. The ESCs were cultured in a 12-well plate coated with Matrigel (Corning) and maintained with mTeSR-Plus medium (STEMCELL Technologies). Once the cells reached 80-90% confluence, they were dissociated using ReLeSR (STEMCELL Technologies) and passaged at a ratio of 1:20. The culture medium was replaced every other day.
The method used to induce cerebral organoids was a modified version of Lancaster's protocol.

extract_protocol:
The total RNA was processed using mRNA enrichment, which involved enriching for mRNA with polyA tails using magnetic beads with OligodT.
The obtained RNA was fragmented using a fragmentation buffer, and reverse transcription was performed with random N6 primers to synthesize cDNA double strands. The synthesized double-stranded DNA was end-repaired and 5'-phosphorylated, and the 3'-end was extended with an "A" tail to form a sticky end. A bubble-shaped adapter with a protruding "T" at the 3' end was then ligated to the DNA fragments, which were PCR amplified using specific primers. The PCR products were denatured to form single-stranded DNA, which was circularized using a bridge primer to obtain a single-stranded circular DNA library.

value: Cerebral Organoids

value: KDM2A knockdown

value: Cells were treated with siRNA-4 to knockdown KDM2A


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 tngidA 3

description: Ribosome protected RNA


title: Organoids_sh4-2


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 tnladS 1

description: Ribosome protected RNA


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 tngidA 2

description: Ribosome protected RNA


title: output-XETG00098__0018569__rep2_atn_int__20231129__015936


title: output-XETG00098__0018569__rep1_atn_int__20231129__015936


title: Huh7 cells, DMSO Control, 48 hrs, replicate 3

value: Control


title: Huh7 cells, DMSO Control, 48 hrs, replicate 2

value: Hepatoma cells


title: Organoids_sh1-3

value: Cells were treated with siRNA-1 to knockdown KDM2A


title: output-XETG00098__0018569__rep1_atn_post__20231129__015936


title: Huh7 cells, DMSO Control, 48 hrs, replicate 1

value: 48 hrs


title: Organoids_sh4-1


title: RiboSeq of Pseudomonas aeruginosa UCBPP-PA14 tngidA 1

description: Ribosome protected RNA


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 tnladS 3

data_processing:
cutadapt , min read length 22
bowtie 2 - mapping to P. aeruginosa PA14 (NC_008463.1) reference genome, option “--very-sensitive-local”.
featureCounts
Supplementary files format and content: bed files - reads per gene (featureCounts)


title: Huh7 cells, shFABP5, 48 hrs, replicate 3

value: FABP5 silencing


title: Organoids_sh1-1


title: output-XETG00098__0018569__rep1_atn_ant__20231129__015936


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 tnladS 2


title: mice,testis,busulfan 30mg/kg + ULA 50mg/kg, 2

city: nantong

first: Jin

last: Dong

address: No. 9 Qixiu Road, Chongchuan District

institute: nantong university

description:
treatment
ULA2

data_processing:
RSEM (v1.3.1)
Supplementary files format and content: tab.delimited text file includes raw counts for each Sample

source_name: testis

extract_protocol:
RNA was harested using trizol. Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using DNBSEQ mRNA-Seg Library Prep Kit following manufacturer's protocols

value: testis


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 tnladS 1


title: Huh7 cells, shFABP5, 48 hrs, replicate 1


title: Organoids_sh1-2


title: Organoids_NC-3

value: Cells were treated with Scrambled shRNA


title: Organoids_NC-2


title: mice,testis,busulfan 30mg/kg + ULA 50mg/kg, 1

description:
treatment
ULA1


title: mice,testis,busulfan 30mg/kg,2

description:
busulfan model
B2


title: Huh7 cells, shControl, 48 hrs, replicate 1


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 tngidA 3


title: Huh7 cells, shControl, 48 hrs, replicate 2


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 tngidA 2


title: Huh7 cells, shControl, 48 hrs, replicate 3


title: mice,testis,busulfan 30mg/kg,1

description:
busulfan model
B1


title: RNASeq of Pseudomonas aeruginosa UCBPP-PA14 tngidA 1


title: Organoids_NC-1


title: Huh7 cells, shFABP5, 48 hrs, replicate 2


title: Callus, rap2.12-2, 7DAC, replicate 2

status: Public on Feb 16 2024

city: Seoul

first: Soon Hyung

last: Bae

state: South Korea

address: Gwanak-ro 1, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Reads were mapped to TAIR10 reference genome using STAR (v2.7.10a) with “--pOverlapNbasesMin 12 --peOverlapMMp 0.1 --twopassMode Basic” options.
Raw counts were obtained from STAR (v2.7.10a) with "--quantMode GeneCounts" option.
RSEM (v1.3.1) was used to quantify transcript abundance to obtain TPM values.
Assembly: TAIR10
Supplementary files format and content: Tab-separated values file includes TPM values for each sample

organism: Arabidopsis thaliana

source_name: hypocotyl explant-derived callus

extract_protocol:
Total RNA was extracted from calli using TransZol Up according to the manufacturer’s recommendations.
RNA-seq libraries were constructed from 1 μg total RNA using the TruSeq RNA library kit.

value: hypocotyl explant-derived callus


title: Callus, rap2.12-2, 7DAC, replicate 3


title: Callus, Col-0, 7DAC, replicate 3


title: Callus, rap2.12-2, 7DAC, replicate 1


title: Callus, Col-0, 7DAC, replicate 2


title: Callus, 7DAC, hypocotyl, replicate 3


title: Callus, 7DAC, hypocotyl, replicate 2


title: Callus, 7DAC, hypocotyl, replicate 1


title: Callus, 0DAC, hypocotyl, replicate 2


title: Callus, 0DAC, hypocotyl, replicate 1


title: Callus, 0DAC, hypocotyl, replicate 3


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-127]

city: Lyon

first: Anne-Pierre

last: Morel

state: Rhone-Alpes

address: 28, rue Laennec, Cheney D 2nd floor

country: France

institute: Cancer Research Center of Lyon

data_processing:
Raw reads were aligned on the human genome with STAR.
Gene expression was quantified with STAR gene count, following the annotations of gencode v29.
Samples with less than 50000 reads were excluded.
Assembly: GRCh38
Supplementary files format and content: STAR gene count

source_name: HME-RASi

extract_protocol:
Briefly, freshly harvested single cells were sorted into 96-well plates containing the lysis buffer (0.2% Triton X-100, 1U/  l RNase inhibitor, Thermo Fisher Scientific). RT was performed using SuperScript II (Thermo Fisher Scientific) in the presence of 1   M oligo-dT30VN (IDT), 1   M Template-switching oligonucleotides (QIAGEN), and 1 M betaine.
Full-length scRNAseq libraries were prepared using the Smart-seq2 protocol (Picelli et al., 2013) with minor modifications. cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Roche) and IS PCR primer (IDT), with 23 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). A total of 140 pg of the amplified cDNA was fragmented using Nextera XT (Illumina) and amplified with Nextera XT indexes (Illumina). Products of each well of the 96-well plate were pooled and purified twice with Agencourt Ampure XP beads (Beckmann Coulter). Final libraries were quantified and checked for fragment size distribution using a Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled sequencing of Nextera libraries was carried out using a HiSeq4000 (Illumina) to an average sequencing depth of 0.5 million reads per cell. Sequencing was carried out as paired-end reads of 75 bp length (PE75) with library indexes corresponding to cell barcodes.

value: HME-RASi

value: mammary epithelial cells RAS inductible

tag: sequencing plate

tag: nbcells


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-139]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-163]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-151]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-115]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-187]


title: A375_2D_high_1

city: Koto-ku

first: Hitomi

last: Shirahama

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation for Cancer Research

description: A375 cells at high density in a two-dimensional system

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hours at 45℃ on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (Thermo Fisher Scientific, MA, USA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Thermo Fisher Scientific).

data_processing: Normalization of microarray data was carried out by the Robust Multichip Average (RMA) method using R software with affy package.

label: biotin

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual) from 100 ng total RNA.

extract_protocol: Total RNA was extracted from cultured cells using QIAshredder and RNeasy Mini Kit (QIAGEN, CA, USA).

treatment_protocol: A375 cells were cultured in a two-dimensional system at high density (around 100% confluency) and maintained in RPMI-1640 supplemented with 5% fetal bovine serum and 100 µg/mL kanamycin.

tag: treatement


title: 5637 R2_12

city: Chicago

first: Kyle

last: Schachtschneider

state: IL

address: 2201 West Campbell Park Drive

institute: Sus Clinicals Inc

description:
expression results for human bladder cancer cell lines with and without gemcitabine treatment
5637 human cells were cultured in RPMI medium.

hyb_protocol: The RNeasy Mini Kit was used to purify the amplified cRNA samples, according to the manufacturer instructions (Agilent). Then we Used the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1 (or higher) to quantify the cRNA. Next Prepared the 10× Blocking Agent, Prepared hybridization samples, Prepared the hybridization assembly and then Hybridized, all following the steps of the manufacturer instructions (Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Manual). For the Wash, we Added Triton X-102 to Gene Expression wash buffers, Prewarm Gene Expression Wash Buffer 2, Prepare the equipment and Wash the microarray slides, also following the steps of the manufacturer instructions (Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Manual). Microarray slides “HD Human GE 4 × 44K v2 Microarray” (1 slide, part number: G2519F-026652) and “Porcine (V2) Gene Expression Microarray, 4 × 44K” (1 slide, part number: G2519F-026440) were used for hybridization.

scan_protocol: The Scaned of the slides was performed in a SureScan/Agilent C microarray scanner and Agilent Scan Control software v7.0.03. Then we Extracted data using Agilent Feature Extraction Software. All steps were performed according to the manufacturer instructions (Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Manual)

data_processing:
Microarray slide analysis was performed in the software GeneSpring GX (Agilent Technologies Inc, Santa Clara, CA, USA). The software uses lowess normalization to adjust for internal differences between channels.
Untreated and treated groups of each cell line were first compared to each other using p (<0,05) and fold change to identify differentially expressed genes (DEGs) (2). DEGs were then compared between the human and Oncopig samples to identify common transcriptional changes in response to gemcitabine exposure.

source_name: Gemcitabine Treated Human Bladder Cancer Cell Line (5637)

label_protocol: We used the Low Input Quick Amp Labeling Kit, according to the manufacturer instructions (Agilent). Two-Color generates fluorescent cRNA (complimentary RNA) with a sample input RNA range between 10 ng and 200 ng of total RNA or a minimum of 5 ng of poly A+ RNA for two-color processing. The method uses T7 RNA Polymerase Blend (red cap), which simultaneously amplifies target material and incorporates Cyanine 3-CTP or Cyanine 5-CTP. Amplification is typically at least a 100-fold from total RNA to cRNA with the use of this kit. The steps were performed  following the manufacturer instructions (Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Manual).

growth_protocol: Oncopig BCCL cells were cultured in DMEM medium (Vitrocell Embriolife, Campinas, Brazil) and 5637 cells were cultured in RPMI medium. Both mediums were supplemented with 10% fetal bovine serum. The cells grew in a controlled atmosphere at 37ºC, 95% humidity and 5% CO2. The experiments were performed after cells reached the sub-confluence stage (<90%). Cells were then seeded in 6-well plates at a density of 2x10^5 cells

extract_protocol: After the treatment period of 48h, cells were washed with PBS and total RNA from the samples was extracted using TRIzol reagent, following manufacturer instructions (Invitrogen). Then, Qiagen RNeasy Kits (QIAGEN GmbH, Hilden, Germany) were used to isolate and purify the RNA according to manufacturer's recommendations. The quality and integrity of total RNA was verified by Nanovue Spectrophotometer (GE Healthcare) and Agilent 2100 bioanalyzer kit (Agilent Technologies, Santa Clara, CA, USA). cDNA synthesis was performed using 10 µl of total RNA at 100 ng/µl added to 10 µl of the High Capacity cDNA Reverse Transcription kit (Applied Biosystems ™, UK). The reaction condition was 25oC for 10 minutes, 37oC for two hours, 85 o C for 5 minutes and 4 o C to finish the reaction, followed by storage of the samples at –20 o C.

treatment_protocol: RNA extractions of human and Oncopig cells were performed in 6-well plates at a density of 2x10^5 cells per well after exposure to the chemotherapeutic gemcitabine at 1 µM for 48h. The control group consisted of cells exposed to medium only for 48h as well.

source_name: Untreated Human Bladder Cancer Cell Line (5637)

value: Human Bladder Cancer Cell Line (5637)

value: untreated


title: 5637 R1_00

value: exposure to the chemotherapeutic gemcitabine at 1 µM for 48h


title: 5637 R3_13


title: A375_2D_low_2

description: A375 cells at low density in a two-dimensional system

treatment_protocol: A375 cells were cultured in a two-dimensional system at low density (around 30% confluency) and maintained in RPMI-1640 supplemented with 5% fetal bovine serum and 100 µg/mL kanamycin.


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-186]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-103]


title: Callus, Col-0, 7DAC, replicate 1

tag: tissue


title: A375_3D_2

description: A375 cells in a three-dimensional system

treatment_protocol: A375 cells were cultured in a three-dimensional system and maintained in advanced DMEM/F12 supplemented with 0.1 µg/mL fibroblast growth factor basic, 0.2 µg/mL epidermal growth factor, 1x GlutaMAX™ supplement, and 100 µg/mL kanamycin.


title: A375_2D_low_1

value: A375 cells at low density in a two-dimensional system


title: A375_3D_1

value: A375 cells in a three-dimensional system


title: A375_2D_high_2

value: A375 cells at high density in a two-dimensional system


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-150]


title: DLD_1_pH6_5

city: SASEBO

first: KYOKO

last: FUJIMOTO

state: NAGASAKI

address: 2825-7 HUIS TEN BOSCH

department: PHARMACY

institute: NAGASAKI INTERNATIONAL UNIVERSITY

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.


title: DLD_1_control

source_name: DLD-1, control


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-138]


title: DLD_1_pH6_8


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-114]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-161]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-102]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-126]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-185]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-137]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-113]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-101]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-184]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-149]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-174]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-162]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-172]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-136]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-124]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-112]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-160]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-100]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-183]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-171]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-147]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-135]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-123]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-111]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-182]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-99]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-146]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-134]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-125]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-158]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-170]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-122]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-157]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-181]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-121]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-97]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-109]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-148]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-169]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-159]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-84]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-72]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-60]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-48]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-36]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-12]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-95]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-24]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-83]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-110]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-71]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-94]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-11]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-23]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-70]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-145]


title: p2_J0_single cell_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-133]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-58]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-46]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-69]


title: p1_J0_bulk_HME-RAS-ER_200c [HFFTNBBXY_8_IDT-DUI-NXT-1]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-10]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-96]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-22]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-93]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-81]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-33]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-9]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-57]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-68]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-32]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-59]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-20]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-56]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-91]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-21]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-8]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-45]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-79]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-82]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-19]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-55]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-43]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-31]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-67]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-90]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-34]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-7]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-78]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-77]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-89]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-30]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-6]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-66]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-65]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-41]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-53]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-29]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-17]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-76]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-5]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-88]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-52]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-28]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-40]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-64]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-75]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-4]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-63]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-51]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-27]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-87]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-15]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-18]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-74]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-50]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-3]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-86]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-38]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-14]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-85]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-62]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-2]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-26]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-61]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-37]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-73]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-25]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-96]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-84]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-72]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-60]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-48]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-36]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-12]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-13]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-71]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-47]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-83]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-59]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-24]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-23]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-95]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-94]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-11]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-70]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-46]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-58]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-35]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-34]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-22]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-82]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-93]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-81]


title: p1_J0_bulk_HME-RAS-ER_1c [HFFTNBBXY_8_IDT-DUI-NXT-49]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-10]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-21]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-92]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-33]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-68]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-80]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-45]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-69]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-56]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-9]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-91]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-20]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-79]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-67]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-55]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-43]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-7]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-31]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-78]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-90]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-57]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-42]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-54]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-66]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-30]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-18]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-6]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-65]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-89]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-41]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-44]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-32]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-8]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-5]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-88]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-76]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-17]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-19]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-64]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-52]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-28]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-40]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-4]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-75]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-16]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-63]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-51]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-87]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-39]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-77]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-15]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-3]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-86]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-74]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-53]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-62]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-29]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-38]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-14]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-50]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-26]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-85]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-49]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-61]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-2]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-1]


title: p7_J7_bulk_HME-RAS-ER_200c [HFFTNBBXY_7_IDT-DUI-NXT-289]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-37]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-13]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-372]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-384]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-336]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-27]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-348]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-324]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-312]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-300]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-360]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-371]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-359]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-347]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-383]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-335]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-323]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-311]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-299]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-370]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-382]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-73]


title: p9_J3_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-25]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-358]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-334]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-310]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-322]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-298]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-369]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-345]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-381]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-333]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-309]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-297]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-368]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-321]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-356]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-380]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-344]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-296]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-379]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-308]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-367]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-320]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-331]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-355]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-343]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-307]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-319]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-342]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-330]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-354]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-295]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-346]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-366]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-378]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-294]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-318]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-353]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-365]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-377]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-306]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-376]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-329]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-340]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-364]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-328]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-352]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-316]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-375]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-341]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-317]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-293]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-292]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-363]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-339]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-351]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-327]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-315]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-303]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-291]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-374]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-305]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-332]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-362]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-338]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-350]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-290]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-326]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-314]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-302]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-325]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-373]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-304]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-276]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-349]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-301]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-264]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-288]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-252]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-240]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-313]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-204]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-216]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-275]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-228]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-287]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-263]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-361]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-251]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-227]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-239]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-215]


title: p7_J7_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-337]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-203]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-274]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-250]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-262]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-238]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-202]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-273]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-226]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-261]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-214]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-237]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-285]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-225]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-213]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-284]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-201]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-260]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-286]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-200]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-236]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-224]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-211]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-212]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-283]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-271]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-259]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-282]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-247]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-223]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-249]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-222]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-246]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-281]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-199]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-272]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-235]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-258]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-221]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-210]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-248]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-269]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-257]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-209]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-197]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-280]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-232]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-220]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-244]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-208]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-196]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-279]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-270]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-234]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-267]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-231]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-198]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-219]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-195]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-255]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-243]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-245]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-278]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-207]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-233]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-206]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-218]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-194]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-266]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-242]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-230]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-254]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-277]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-268]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-265]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-256]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-241]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-253]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-229]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-205]


title: P3_J20_bulk_HME-RAS-ER_200c [HFFTNBBXY_7_IDT-DUI-NXT-97]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-217]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-120]


title: P4_J20_single cell_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-193]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-167]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-166]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-191]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-179]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-190]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-142]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-118]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-107]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-154]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-189]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-165]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-141]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-117]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-152]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-176]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-164]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-128]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-116]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-187]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-175]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-186]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-151]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-115]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-103]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-174]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-114]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-185]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-162]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-173]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-161]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-149]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-113]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-136]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-184]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-153]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-112]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-159]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-171]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-101]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-135]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-148]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-146]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-111]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-98]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-110]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-182]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-147]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-133]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-109]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-145]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-372]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-360]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-324]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-336]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-348]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-384]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-300]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-312]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-371]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-359]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-347]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-335]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-323]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-311]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-299]


title: P3_J20_bulk_HME-RAS-ER_1c [HFFTNBBXY_7_IDT-DUI-NXT-183]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-358]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-334]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-322]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-346]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-310]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-382]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-298]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-369]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-357]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-333]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-321]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-297]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-380]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-309]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-344]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-332]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-320]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-379]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-308]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-367]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-296]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-355]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-370]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-331]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-319]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-343]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-307]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-381]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-354]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-295]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-366]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-342]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-330]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-345]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-377]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-356]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-294]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-368]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-365]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-353]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-341]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-329]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-317]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-305]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-293]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-352]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-364]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-340]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-328]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-376]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-316]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-378]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-304]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-363]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-327]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-318]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-351]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-292]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-339]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-315]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-306]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-303]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-291]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-374]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-338]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-326]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-362]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-314]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-290]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-302]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-373]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-361]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-325]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-289]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-276]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-375]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-301]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-252]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-337]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-264]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-240]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-228]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-263]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-287]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-216]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-275]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-313]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-239]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-350]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-204]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-251]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-215]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-227]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-238]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-203]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-250]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-226]


title: p10_J3_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-349]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-262]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-274]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-214]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-273]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-285]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-202]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-237]


title: iPSC-derived retinal pigment epithelium, RP13-2-Cas9, bio_rep_3

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

institute: University of Leeds

data_processing:
RNA paired-end sequencing quality control was assessed through FastQC and multiQC. An average of 40 million reads were sequenced per sample. Both adapters and low quality bases (QV < 20) were trimmed from reads’ extremities using Trimmomatic (v 0.36) with a minimum read length of 30 bp. All libraries were mapped against the Human GRCh38 release-105 reference genome through STAR aligner (v 2.7.10a) with default parameters. STAR-generated sorted BAM output files were used for assigning read counts to gene features with featureCounts (v 2.0.1) with the following parameters: -p -B -C -M -O --fraction -s 2. We relied on Homo_sapiens.GRCh38.105.gtf annotation file.
Read counts’ table generated by featureCounts was then used as input for differential expression (DE) analyses relying on the DeSeq2 negative binomial distribution model through a local fitting type and a 0.05 FDR threshold. DE pairwise comparisons were performed either per cell line per patient or per cell line on pooled patients, always setting Mutant:Cas9-WTC as the fold-change ratio to be assessed. The same read count table was also submitted to a multi-dimensional scaling (MDS) analysis using the plotMDS function from the EdgeR package. (https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html) was employed for an overall DE visualization through volcano plots. All tools described in this paragraph were run under the R environment version 4.1.0.
Assembly: Ensembl Homo_sapiens.GRCh38.105

molecule: polyA RNA

source_name: iPSC-derived retinal pigment epithelium

extract_protocol:
Trizol suspensions of iPSCs, RPEs, kidney and retinal organoids were homogenized using 26-gauge syringe needles followed by standard Trizol RNA extraction. Extracted RNA was further purified using DNAse TURBO, and RNA purity and concentration was evaluated on TapeStation (Agilent Technologies)
Illumina TruSeq Stranded mRNA Libraries from total RNA

value: iPSC-derived retinal pigment epithelium


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-261]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-249]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-284]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-225]


title: iPSC-derived retinal pigment epithelium, RP13-2-Cas9, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-272]


title: iPSC-derived retinal organoid, RP13-2-Cas9, bio_rep_2

source_name: iPSC-derived retinal organoid

value: iPSC-derived retinal organoid


title: iPSC-derived retinal organoid, RP13-2-Cas9, bio_rep_3


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-213]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-201]


title: iPSC-derived kidney organoid, RP13-2-Cas9, bio_rep_3

source_name: iPSC-derived kidney organoid

value: iPSC-derived kidney organoid


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-260]


title: iPSC-derived kidney organoid, RP13-2-Cas9, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-286]


title: iPSC, RP13-2-Cas9, bio_rep_2

source_name: iPSC

value: iPSC


title: iPSC, RP13-2-Cas9, bio_rep_3


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-248]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-212]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-224]


title: iPSC, RP13-2-Cas9, bio_rep_1


title: iPSC-derived kidney organoid, RP13-2-Cas9, bio_rep_1


title: iPSC-derived retinal pigment epithelium, RP13-2-Cas9, bio_rep_1


title: iPSC-derived retinal pigment epithelium, RP13-2, bio_rep_3


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-271]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-200]


title: iPSC-derived retinal organoid, RP13-2, bio_rep_3


title: iPSC-derived kidney organoid, RP13-2, bio_rep_3


title: iPSC, RP13-2, bio_rep_3


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-259]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-235]


title: iPSC-derived retinal pigment epithelium, RP13-2, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-247]


title: iPSC-derived kidney organoid, RP13-2, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-199]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-211]


title: iPSC-derived retinal organoid, RP13-2, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-282]


title: iPSC-derived retinal pigment epithelium, RP13-2, bio_rep_1


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-258]


title: iPSC-derived retinal organoid, RP13-2-Cas9, bio_rep_1


title: iPSC, RP13-2, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-236]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-270]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-283]


title: iPSC-derived kidney organoid, RP13-2, bio_rep_1


title: iPSC-derived retinal organoid, RP13-2, bio_rep_1


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-246]


title: iPSC-derived retinal pigment epithelium, RP13-1C-Cas9, bio_rep_3


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-234]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-222]


title: iPSC, RP13-2, bio_rep_1


title: iPSC-derived kidney organoid, RP13-1C-Cas9, bio_rep_3


title: iPSC-derived retinal organoid, RP13-1C-Cas9, bio_rep_3


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-198]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-223]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-281]


title: iPSC, RP13-1C-Cas9, bio_rep_3


title: iPSC-derived retinal pigment epithelium, RP13-1C-Cas9, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-269]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-257]


title: iPSC-derived retinal organoid, RP13-1C-Cas9, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-245]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-221]


title: iPSC-derived retinal pigment epithelium, RP13-1C-Cas9, bio_rep_1


title: iPSC, RP13-1C-Cas9, bio_rep_2


title: iPSC-derived retinal organoid, RP13-1C-Cas9, bio_rep_1


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-210]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-233]


title: iPSC-derived retinal pigment epithelium, RP13-1C, bio_rep_3


title: iPSC-derived kidney organoid, RP13-1C-Cas9, bio_rep_1


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-197]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-256]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-268]


title: iPSC, RP13-1C-Cas9, bio_rep_1


title: iPSC-derived retinal organoid, RP13-1C, bio_rep_3


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-209]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-280]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-232]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-244]


title: iPSC-derived retinal pigment epithelium, RP13-1C, bio_rep_2


title: iPSC-derived kidney organoid, RP13-1C, bio_rep_3


title: iPSC, RP13-1C, bio_rep_3


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-220]


title: iPSC-derived retinal organoid, RP13-1C, bio_rep_2


title: iPSC-derived kidney organoid, RP13-1C, bio_rep_2


title: iPSC, RP13-1C, bio_rep_2


title: iPSC-derived kidney organoid, RP13-1C-Cas9, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-208]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-279]


title: iPSC-derived retinal organoid, RP13-1C, bio_rep_1


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-267]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-243]


title: iPSC-derived kidney organoid, RP13-1C, bio_rep_1


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-231]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-219]


title: iPSC, RP13-1C, bio_rep_1


title: iPSC-derived retinal pigment epithelium, RP13-1B-Cas9, bio_rep_3


title: iPSC-derived kidney organoid, RP13-1B-Cas9, bio_rep_3


title: iPSC-derived retinal organoid, RP13-1B-Cas9, bio_rep_3


title: iPSC, RP13-1B-Cas9, bio_rep_3


title: iPSC-derived retinal pigment epithelium, RP13-1B-Cas9, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-195]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-278]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-266]


title: iPSC, RP13-1B-Cas9, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-230]


title: iPSC-derived retinal organoid, RP13-1B-Cas9, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-196]


title: iPSC-derived retinal organoid, RP13-1B-Cas9, bio_rep_1


title: iPSC-derived retinal pigment epithelium, RP13-1B-Cas9, bio_rep_1


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-218]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-242]


title: iPSC-derived retinal pigment epithelium, RP13-1C, bio_rep_1


title: iPSC-derived kidney organoid, RP13-1B-Cas9, bio_rep_1


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-255]


title: iPSC, RP13-1B-Cas9, bio_rep_1


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-277]


title: iPSC-derived retinal pigment epithelium, RP13-1B, bio_rep_3


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-254]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-265]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-253]


title: iPSC, RP13-1B, bio_rep_3


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-241]


title: iPSC-derived kidney organoid, RP13-1B-Cas9, bio_rep_2


title: iPSC-derived retinal pigment epithelium, RP13-1B, bio_rep_2


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-194]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-207]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-193]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-205]


title: iPSC-derived retinal organoid, RP13-1B, bio_rep_2


title: iPSC-derived kidney organoid, RP13-1B, bio_rep_2


title: iPSC-derived retinal pigment epithelium, RP13-1B, bio_rep_1


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-206]


title: iPSC, RP13-1B, bio_rep_2


title: p5_J14_bulk_HME-RAS-ER_200c [HFFTNBBXY_6_IDT-DUI-NXT-97]


title: p6_J14_sc_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-229]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-192]


title: iPSC-derived kidney organoid, RP13-1B, bio_rep_1


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-168]


title: iPSC, RP13-1B, bio_rep_1


title: iPSC-derived retinal organoid, RP13-1B, bio_rep_1


title: iPSC-derived retinal organoid, RP13-1B, bio_rep_3


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-156]


title: iPSC-derived retinal pigment epithelium, RP13-1A-Cas9, bio_rep_3


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-144]


title: iPSC-derived retinal organoid, RP13-1A-Cas9, bio_rep_3


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-132]


title: iPSC-derived kidney organoid, RP13-1B, bio_rep_3


title: iPSC-derived kidney organoid, RP13-1A-Cas9, bio_rep_3


title: iPSC, RP13-1A-Cas9, bio_rep_3


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-120]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-108]


title: iPSC-derived retinal pigment epithelium, RP13-1A-Cas9, bio_rep_2


title: iPSC-derived retinal organoid, RP13-1A-Cas9, bio_rep_2


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-180]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-179]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-167]


title: p5_J14_bulk_HME-RAS-ER_1c [HFFTNBBXY_6_IDT-DUI-NXT-191]


title: iPSC-derived kidney organoid, RP13-1A-Cas9, bio_rep_2


title: iPSC, RP13-1A-Cas9, bio_rep_2


title: iPSC-derived retinal pigment epithelium, RP13-1A-Cas9, bio_rep_1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-96]


title: pbmc scRNA-seq

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

data_processing:
Sequencing alignment to the hg19 reference genome was performed using CellRanger (version 2.1.0), and spliced, unspliced, and ambiguous read counts were extracted using Velocyto.
Normalization, log transformation, and other data processing carried out in Scanpy (version 1.8.2; Wolf et al., 2018).
Assembly: hg19
Supplementary files format and content: Processed data, including cluster assignments, provided in h5ad format. Raw counts of full data available in the .raw attribute of the AnnData structure: Raw counts stored in .raw.X; Cell names are stored in .raw.obs_names; Gene names are stored in .raw.var_names.

source_name: peripheral blood mononuclear cells

growth_protocol: PBMCs were thawed in RPMI 1640 with 5% FBS, and incubated at 37°C for 1 hr for recovery to ground state. 3x105 cells were set aside for scRNA-sequencing.

extract_protocol:
Cells allocated for scRNA-seq were strained and washed with PBS containing 0.4% BSA, before strained through a 40 uM cell strainer.
Sample barcoding and library preparation was carried out using the 10x sequencing protocol.

value: peripheral blood mononuclear cells


title: iPSC-derived retinal organoid, RP13-1A-Cas9, bio_rep_1


title: iPSC-derived kidney organoid, RP13-1A-Cas9, bio_rep_1


title: iPSC, RP13-1A-Cas9, bio_rep_1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-72]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-84]


title: iPSC-derived retinal pigment epithelium, RP13-1A, bio_rep_3


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-60]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-36]


title: iPSC-derived kidney organoid, RP13-1A, bio_rep_3


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-48]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-24]


title: iPSC, RP13-1A, bio_rep_3


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-12]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-95]


title: iPSC-derived kidney organoid, RP13-1A, bio_rep_2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-83]


title: iPSC-derived retinal organoid, RP13-1A, bio_rep_2


title: iPSC-derived retinal pigment epithelium, RP13-1A, bio_rep_2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-71]


title: iPSC, RP13-1A, bio_rep_2


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-47]


title: iPSC-derived retinal pigment epithelium, RP13-1A, bio_rep_1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-59]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-23]


title: iPSC-derived kidney organoid, RP13-1A, bio_rep_1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-11]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-94]


title: iPSC-derived retinal organoid, RP13-1A, bio_rep_3


title: iPSC, RP13-1A, bio_rep_1


title: iPSC-derived retinal organoid, RP13-1A, bio_rep_1


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-82]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-70]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-58]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-46]


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-35]


title: Fertile_endom_Input_ChIP

city: Swansea

first: David

last: James

address: Swansea University, Singleton Park

department: Medical School

institute: Swansea University

description: Healthy fertile endometrium Input ChIP-seq

data_processing:
ChIP-Seq reads were aligned to the genome hg38 using the BOWTIE2 Aligner with default settings.
Reads with more than 5 bases with Phred score less than 30 or reads containing undefined bases were removed
Peaks were called using MACS2 with default settings
Assembly: hg38
Supplementary files format and content: ChIP-Seq (HiSeq 2000 System, Illumina®).
Supplementary files format and content: bigWig files show the fragment density for 50-nt bins along the genome ('signal map') in an indexed binary format.

source_name: Human endometrium

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA fragements were isolated as per manufacturers instructions (Chromatrap® Pro-A kit).
Isolated DNA was sent to Active Motif® for library construction. AM prepared the libraries according to Illumina's instructions accompanying the True-Seq ChIP Library Preparation Kit (IP-202-1012, Illumina®).

value: Human endometrium


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-22]


title: NZW heart, biological rep1

city: Erlangen

first: Christoph

last: Daniel

address: Krankenhausstr. 8-10

department: Nephropathology

institute: FAU Erlangen-Nürnberg

description: Gene expression data from female mouse hearts with healthy kidneys.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneScan 3000 7G.

data_processing: Data were normalized using the Robust Multi-array Average (GC-RMA) algorithm, and analyzed with the Partek Genomics Suite

source_name: hearts from NZW female mice with healthy kidneys

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse hearts were collected from mice after bleeding and perfusion with 0,9% NaCl

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturers instructions

treatment_protocol: Mice were not treated, but female mice with two different genotype were used NZB_W as nephritic and NZW as healthy control mice.

tag: kidney disease

value: Healthy

tag: kidney injury

value: no kidney injury

value: heart


title: Rat lens, Galactose-3

city: Fukui

first: Masaru

last: Takashima

address: 3-9-1 Bunkyo

institute: University of Fukui

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 130μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002

scan_protocol: Gene ChIP Scanner 3000 7G System

data_processing:
Data were processed using R. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
RaGene-2_0-st.pgf
RaGene-2_0-st.mps
Generated log2 values using robust multi-array average (RMA) method with R statistical software

source_name: Rat lens, 30mM galactose, 6days, replicate3

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: The lens removed from the culture medium was ground with a biosmasher until it fell apart. Then treat the sample with TRIZOL, cDNA synthesis and amplification was performed

tag: strain

value: Sprague Dawley

value: lens

tag: condition

value: galactose-induced cataract

value: Galactose


title: p8_J7_sc_HME-RAS-ER_1c [HFJ75BBXY_7_IDT-DUI-NXT-34]

value: HME-RASi

value: mammary epithelial cells RAS inductible


title: WT1_Fertile_hESC_ChIP

description: WT1 hESC TF ChIP-seq

source_name: Human endometrial stromal cells (hESC)

growth_protocol: hESC cells were plated into 35 mm FluoroDish dishes and maintained in DMEM/F12 media (10% FBS, 1% P/S, 1 mM sodium pyruvate, 1 mM sodium bicarbonate)

extract_protocol:
Lysates were clarified from sonicated nuclei and WT1-DNA complexes were isolated with antibody as per manufacturers instructions (Chromatrap® Pro-A kit).
Isolated DNA was sent to Active Motif® for library construction. AM prepared the libraries according to Illumina's instructions accompanying the True-Seq ChIP Library Preparation Kit (IP-202-1012, Illumina®).

treatment_protocol: Confluent monolayers of hESC were treated with cAMP+P for 48h.

value: Human endometrial stromal cells (hESC)


title: NZW heart, biological rep2


title: NZB_W heart, biological rep3

description: Gene expression data from female mouse hearts with moderate kidney injury.

source_name: hearts from NZB_W female mice with moderate kidney injury

value: Lupus nephritis

value: moderate kidney injury


title: MSC ATAC

city: Indianapolis

first: Yue

last: Wang

address: 975 W. Walnut street

department: Medical Genetics

institute: Indiana University

description:
ATAC library for 50bp paired-end sequencing
filtered_feature_bc_matrix.h5
per_barcode_metadata.tsv
atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
CellRanger (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated.
These RNA+ATAC multiome data were firstly demultiplexed using genotype-free pipeline from souporcell to separate the cell barcodes from different individuals.
The 10x Genomics multiome RNA+ATAC data was processed using Seurat and Signac following the standard workflow
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mesenchymal stem cells

growth_protocol: MSCBMT™ Basal Media (PT-3238) and MSCGM™ SingleQuots Supplement Kit (PT-4105) were purchased from Lonza to ensure the cells' health in culture. The media were changed every 3 days.

extract_protocol:
Cells were then lysed with 0.1X lysis buffer for 4 minutes to isolate nuclei, based on the protocol of Demonstrated Protocol Nuclei Isolation Complex Sample ATAC GEX Se-quencing, CG000375 RevB (10X Genomics, Inc).
Following the Chromium NextGEM Multiome ATAC GEX User Guide, CG000338_RevB (10X Genomics, Inc), tagmentation of nuclei preparation was first performed. Thereafter, briefly, along with the single cell multiome gel beads and partition oil, the single nuclei master mixture containing tagmented single nuclei suspension was transferred onto a Next GEM Chip J, and the chip loaded to the Chromium Controller for GEM generation and barcoding, followed by pre-amplification PCR, ATAC library preparation, cDNA synthesis and cDNA library preparation.
single cell multiome

treatment_protocol: After the cell monolayer reached 70-80% confluency, the MSC from each of the four do-nors were collected and combined in equal numbers to create a mixed cell preparation.

tag: individual

value: Donors 1-4

value: mesenchymal stem cells

tag: genotype

value: WT


title: Rat lens, Galactose-2

source_name: Rat lens, 30mM galactose, 6days, replicate2