title: 304_115_mouse_144_postappl_day_28_AAV6_2-Stuffer


title: 304_114_mouse_151_postappl_day_21_AAV6_2-TGFb1

status: Public on Jul 15 2022

type: SRA

city: Biberach an der Riß

first: Holger

last: Klein

state: Rhineland Palatinate

address: Birkendorfer Str. 65

department: global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

library_source: transcriptomic

data_processing:
RNA-Seq reads were aligned to mouse genomes using the STAR Aligner v2.5.2a 73 with their corresponding Ensembl 86 reference genomes 74. Sequenced read quality was checked with FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and alignment quality metrics were calculated using the RNASeQC v1.1875. Following read alignment, duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment 75. The gene expression profiles were quantified using Cufflinks software version 2.2.1 76 to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) as well as read counts from the featureCounts software package 77. Differential expression analysis was performed with the uniquely mapping read counts as input for the Bioconductor LIMMA analysis R package with voom normalization 78. Descriptive analyses such as PCA and hierarchical clustering were carried out to identify possible outliers. Differential expression between treatment and respective controls at each time points were carried out using limma with a significance threshold of p adj ≤ 0.05 and abs(log2FC) ≥0.5. Two samples out of 120 in total were excluded for not passing QC criteria.
miRNA-Seq: Sequenced read quality was checked with FastQC (FastQC version 0.11.2). Subsequently, miRNA-sequencing read adapters were detected using minion and trimmed using reaper from the kraken package, version 13–274 79. The trimmed reads were aligned to the Ensembl v86 mouse genome using the STAR Aligner (version 2.5.2a) using the following parameters: --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1 (parameters taken from personal communication with the STAR author A. Dobin). Aligned reads were filtered for mature miRNA lengths of between (or equal to) 16 and 26 bp in size. The SAM files from STAR were converted to BAM files using samtools 0.1.18 80. The aligned miRNA reads were then quantified using subread from the featureCounts package (version 1.4.5-PR1) 77 and the miRBase 21 as a reference 81.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: FeatureCounts files contain gene-level mRNA read quantification generated on Ensembl86 mouse annotation
Supplementary_files_format_and_content: Aligned.out.mature.miRNA.bam.featureCounts files contain miRNA read quantification generated on miRbase 21 mouse annotation

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
For total lung RNA preparation, the left lung was flash frozen in liquid nitrogen immediately after dissection. Frozen lungs were homogenized in 2 mL precooled RLT buffer (Qiagen, Hilden, Germany) + 1 % β-mercaptoethanol (Sigma-Aldrich) using the Peqlab Precellys 24 Dual Homogenizer and 7 mL-ceramic bead tubes (#91-PCS-CK28L, Peqlab, Erlangen). 150 µL homogenate were then mixed with 550 µL QIAzol Lysis Reagent (#79306, Qiagen). After addition of 140 µL chloroform (Sigma-Aldrich), the mixture was shaken vigorously for 15 sec and centrifuged for 5 min at 12,000 xg and 4 °C. 350 µL of the upper aqueous phase (containing RNA) were then further purified using the miRNeasy 96 Kit (#217061, Qiagen) according to the manufacturer’s instructions. After purification, RNA concentration was determined using a Synergy HT multimode microplate reader and the Take3 module (BioTek Instruments, Winooski, VT, USA). RNA quality was assessed using the 2100 Bioanalyzer (Agilent Technologies).
cDNA libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) and 200 ng of total RNA. Following purification and PCR enrichment of the cDNAs, the library was diluted to 2 nM and clustered on the flow cell at 9.6 pM, using the TruSeq SR Cluster Kit v3-cBot-HS (#GD-401-3001, Illumina) and the cBot instrument (Illumina). Sequencing of 52 bp single reads and seven bases index reads was performed on an Illumina HiSeq 2000 using the TruSeq SBS Kit v3-HS (#FC-401-3002, Illumina). Approximately 20 million reads were obtained per sample. For miRNA, the TruSeq Small RNA Library Preparation Kit was used (Illumina) to prepare the cDNA library: As a result of miRNA processing by Dicer, miRNAs contain a free 5’-phosphate and 3’-hydroxal group, which were used to ligate specific adapters prior to first and second strand cDNA synthesis. By PCR, the cDNAs were then amplified and indexed. Using magnetic Agencourt AMPure XP bead-purification (#A63881, Beckman Coulter), large DNAs were separated and small RNAs were enriched. Similar to mRNA, the samples were finally clustered at 9.6 pM and sequenced, while being spiked into mRNA sequencing samples.

treatment_protocol: Male 9-12 wk. old C57Bl/6 mice (120 in total) were obtained from Charles River Laboratories (Sulzfeld, Germany) and allowed to acclimate for one week prior to intratracheal administration of either 2.5x1011 vg of AAV-TGFβ1 or AAV-stuffer, 1 mg/kg Bleomycin or NaCl solution in a volume of 50 µL, which was carried out under light anesthesia (3-4 % isoflurane). For pharmacological inhibition of the type I TGFβ1 receptor (ALK5), the inhibitor SB-525334 was diluted in 0.5 % Natrosol and orally administered to the mice (28 in total) from day seven after AAV administration at 30 mg/kg in a once or twice daily dosing regimen. Body weight was monitored daily and animals with a loss of body weight greater than 20 % were taken out of the experiment and euthanized.

tag: strain

tag: treatment

tag: day


title: 304_118_mouse_147_postappl_day_28_AAV6_2-Stuffer


city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description: L1_W403: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp1r12a knockdown (T0403), replicate 1

data_processing:
CASAVA 1.8 was used for base calling.
Fastq files contain demultiplexed reads which were assigned to the appropriate treatment by matching to expected forward and reverse barcodes (sequenced in dedicated reads; not supplied).
Forward and reverse event reads were mapped to custom junction libraries representing all expected splice variants (supplied as processed files), using bowtie with settings --best -v 3 -k 1 --trim3 26 --trim5 10. Trimming was done to remove lower-quality, uninformative ends and because forward reads had a missing base call at position 11 due to a power outage. Junction libraries were first constructed from NCBIm37/mm9 gene annotations, and then refined based on the results of de novo mapping of the reads from one full Illumina lane from each cell line using tophat (default settings with -i 40 and providing Ensembl transcript annotations for NCBIm37), after quality trimming (minimum MAPQ of 33) from the 3'-end with the fastx toolkit. Mapped reads were counted per junction.
Alternative splicing analysis: Percent-spliced-in (PSI) values were calculated for each alternative exon, or part thereof in the case of alternative 5'-/3'-splice sites ('event'), from read tallies as follows: PSI was calculated independently from forward and reverse reads as the percentage of reads supporting inclusion divided by the total number of reads for the event. For alternative 5'/3'-ss events that were part of an alternative exon (Foxm1.A2, Mta1.A1, Uspl1.A3), the PSI was instead calculated with reference to the total reads supporting inclusion of that exon in order to assess independent regulation of alternative splice site usage. Only the read direction in which all reads unambiguously supported either inclusion or exclusion of an event was used, and the average if that applied for both. Exploratory analysis revealed that PSI values showed low-level batch effects per 96-well plate which we moderated by subtracting a weighted plate median in which negative controls (siNT and mock treatment) were given 20x more weight than other samples. To derive variances, and because PSI values are not nearly normally distributed but roughly follow a beta distribution, we elected to fit a beta distribution to each pair of replicate treatments, as well as to all negative controls from both replicates, using maximum-likelihood fitting as implemented in the fitdistr() function from the R package MASS {Venables & Ripley, Modern Applied Statistics with S (2002)}. Iterative optimization of shape parameters was initiated with settings x=PSI, shape1=1, shape2=1, method=”L-BFGS-B”, lower=0.01, and upper=mean number of reads supporting each PSI value. A modified Strictly Standardized Mean Difference (SSMD {Zhang, Genomics (2007)}) was then calculated based on the formula: SSMD = (μt – μc)/SQRT(vart + varc) where μt and μc are the means (corresponding to the PSI), and vart and varc the variances of the beta distributions fitted to the treatment replicates and negative controls, respectively. Events for which not all reads from at least one direction were informative (Mff.A2, Tead1.A2) were excluded from further analysis, as were events in individual treatments with less than 20 reads in one or both replicates (~9% of all event x treatment combinations). Additionally, the following events were removed from further splicing analysis: expression only events or constitutive exons, Fgf4, Gapdh, Srpk2, Srrm4; events with consistently low read counts: Atg13.A1, H2afy.A2, Tcf7l1 (N2A only), Dnmt3b (N2A only); or because measured inclusion was biased by differential length of isoforms:, Fgfr1, Sall4.
Expression analysis: Read counts from all splice variants of each gene were used to estimate relative mRNA expression levels, reads per million reads (RPMs). Differential expression analysis based on raw read counts was performed using the generalized linear models workflow from the R package edgeR. Plate, position (edge/interior) and treatment were used as design factors (where all treatments of each type of control were treated as replicates.) Models fitted using estimateDisp() to estimate the common, trended, and tag-wise dispersion for the CGR8 and N2A data separately. Subsequently, differences attributable to treatment, plate, or position contrasts were extracted with glmLRT() and represented as log2-fold changes with associated FDR. Fold-changes for treatments are relative to the siNT and mock-treatment controls.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are either tab-delimited  tables (.tab) or FASTA files (.fa).   JunctionLibrary_design.csv contains information about sequence and 1-based coordinates of all elements that make up each event, along with vast-tools ID (vastEVENT) and information about how elements are connected. See https://github.com/UBrau/SPARpipe for information about library design.  Junctions108_11-101_fwd.fa and Junctions108_11-101_rev.fa contain all possible junctions given the event elements and read length for forward and reverse reads, respectively.  Events108_11-101.tab indicates which junctions were used to calculate PSI for each element.  Treatments_fullScreen.csv contains information about all 1536 control and experimental knockdowns.  ExprContrasts_fullScreen.csv contains the design factors for differential expression analysis.  ReadsPerEvents.tab.gz contains raw read counts per treatment and event element.  PSI.raw.tab.gz contains raw PSI for each treatment and event element.  dPSI.norm.tab.gz contains normalized and filtered dPSI.  SSMD.norm.tab.gz contains normalized and filtered SSMD.  Expression.Treatment.tab.gz contains results from differential expression analysis (differential expression due to treatment).

source_name: Mouse neuroblastoma cells

growth_protocol: Mouse neuroblastoma (N2A) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin and maintained at 37°C with 5% CO2.

extract_protocol:
Forty-eight hours post-transfection, total RNA were purified from cultured cells using RNeasy Plus 96 Kit (Qiagen), as per the manufacturer’s instructions.
For each sample, a multiplex RT-PCR assay was first applied to simultaneously amplify 108 AS and/or expression events in a single reaction. The multiplex RT-PCR reaction was carried out in 96-well plates using the OneStep RT-PCR kit (Qiagen) as recommended by the manufacturer, with the following changes: reactions were performed in a volume of 20 uL with 2 uL of the purified total RNA as input, and a mixture of 50 pairs of primers was added to each reaction with a final concentration of 0.25 uM for each individual forward and reverse primer. Four identical Veriti 96-well Thermal Cyclers (Applied Biosystems) were used with the following conditions: 50°C for 30 minutes, 95°C for 15 minute, 30 cycles of 94°C for 40 seconds, 58°C for 1 minute (slow ramp rate), 72°C for 3 minutes, and a final extension step at 72°C for 10 minutes. Two sets of barcodes were incorporated into forward and reverse primers, respectively, after the universal adaptors and added to the amplicons in the second PCR reaction to allow demultiplexing all reads that were derived from a particular treatment. Primers sequences were: forward primer, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT (N denotes i5 barcode); reverse primer, CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (N denotes i7 primer). The second PCR was performed using Phusion High-Fidelity DNA Polymerase (Thermo Scientific), as per the manufacturer’s instructions. For each 20 uL of reaction, 1 uL of the multiplex RT-PCR reaction products was used as templates. The thermal cycling conditions were as follows: 98°C for 30 seconds, 15 cycles of 98°C for 10 seconds, 65°C for 30 seconds, 72°C for 30 seconds, and a final extension step at 72°C for 5 minutes. The resulting libraries were pooled and sequenced.

treatment_protocol: Twenty-four hours prior to transfection, N2A cells were seeded in 96-well plates at 5000 cells per well. Cells were transfected with the SMARTpool siRNAs at 50 nM final concentration using DharmaFECT1 reagent (Dharmacon), as recommended by the manufacturer.

tag: tissue

value: Mouse neuroblastoma cells

tag: cell line


description: L1_W402: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbms1 knockdown (T0402), replicate 1


title: 304_120_mouse_149_postappl_day_28_AAV6_2-TGFb1


description: L1_W404: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp2r5a knockdown (T0404), replicate 1


description: L1_W397: SPAR-seq of 108 multi-exon gene regions in N2A cells, Piwil1 knockdown (T0397), replicate 1


description: L1_W398: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rev3l knockdown (T0398), replicate 1


description: L1_W394: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rangap1 knockdown (T0394), replicate 1


title: 304_109_mouse_137_postappl_day_21_AAV6_2-Stuffer


title: 304_117_mouse_146_postappl_day_28_AAV6_2-Stuffer


title: 304_121_mouse_140_postappl_day_28_AAV6_2-TGFb1


description: L1_W392: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarca5 knockdown (T0392), replicate 1


title: 304_112_mouse_141_postappl_day_21_AAV6_2-TGFb1


title: 381_5_mouse_5_postappl_day_3_NaCl

value: NaCl


description: L1_W396: SPAR-seq of 108 multi-exon gene regions in N2A cells, Poll knockdown (T0396), replicate 1


title: 304_113_mouse_142_postappl_day_21_AAV6_2-TGFb1


description: L1_W395: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sfpq knockdown (T0395), replicate 1


description: L1_W399: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf8 knockdown (T0399), replicate 1


title: 304_110_mouse_138_postappl_day_21_AAV6_2-Stuffer


description: L1_W390: SPAR-seq of 108 multi-exon gene regions in N2A cells, Plrg1 knockdown (T0390), replicate 1


description: L1_W393: SPAR-seq of 108 multi-exon gene regions in N2A cells, Polr2a knockdown (T0393), replicate 1


description: L1_W389: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sf3a1 knockdown (T0389), replicate 1


description: L1_W391: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pinx1 knockdown (T0391), replicate 1


title: 304_111_mouse_150_postappl_day_21_AAV6_2-TGFb1


description: L1_W386: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarca4 knockdown (T0386), replicate 1


description: L1_W387: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf4 knockdown (T0387), replicate 1


title: 304_108_mouse_136_postappl_day_21_AAV6_2-Stuffer


description: L1_W385: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0385), replicate 1


title: 304_103_mouse_131_postappl_day_14_PBS

value: PBS


description: L1_W384: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0384), replicate 1


description: L1_W383: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pabpn1 knockdown (T0383), replicate 1


title: 304_107_mouse_135_postappl_day_21_AAV6_2-Stuffer


title: 304_101_mouse_129_postappl_day_14_AAV6_2-TGFb1


description: L1_W382: SPAR-seq of 108 multi-exon gene regions in N2A cells, Npas1 knockdown (T0382), replicate 1


description: L1_W381: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nr2f2 knockdown (T0381), replicate 1


title: 304_106_mouse_134_postappl_day_21_AAV6_2-Stuffer


title: 304_104_mouse_132_postappl_day_14_PBS


title: 304_105_mouse_133_postappl_day_14_PBS


title: 304_98_mouse_126_postappl_day_14_AAV6_2-TGFb1


description: L1_W380: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppil1 knockdown (T0380), replicate 1


description: L1_W379: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nbn knockdown (T0379), replicate 1


title: 304_97_mouse_125_postappl_day_14_AAV6_2-Stuffer


description: L1_W388: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rorc knockdown (T0388), replicate 1


title: 304_99_mouse_127_postappl_day_14_AAV6_2-TGFb1


title: 304_96_mouse_124_postappl_day_14_AAV6_2-Stuffer


title: 304_100_mouse_128_postappl_day_14_AAV6_2-TGFb1


description: L1_W378: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mtf2 knockdown (T0378), replicate 1


title: 304_94_mouse_122_postappl_day_14_AAV6_2-Stuffer


title: 304_95_mouse_123_postappl_day_14_AAV6_2-Stuffer


description: L1_W377: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppargc1a knockdown (T0377), replicate 1


description: L1_W376: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mxi1 knockdown (T0376), replicate 1


description: L1_W373: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prim1 knockdown (T0373), replicate 1


description: L1_W374: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mecp2 knockdown (T0374), replicate 1


title: 304_92_mouse_120_postappl_day_7_AAV6_2-TGFb1


title: 304_102_mouse_130_postappl_day_14_AAV6_2-TGFb1


title: 304_93_mouse_121_postappl_day_14_AAV6_2-Stuffer


description: L1_W372: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phox2a knockdown (T0372), replicate 1


description: L1_W375: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbd1 knockdown (T0375), replicate 1


title: 304_87_mouse_115_postappl_day_7_AAV6_2-Stuffer


title: 304_84_mouse_112_postappl_day_7_AAV6_2-Stuffer


description: L1_W368: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppan knockdown (T0368), replicate 1


description: L1_W371: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mcm3 knockdown (T0371), replicate 1


title: 304_88_mouse_116_postappl_day_7_AAV6_2-TGFb1


description: L1_W370: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nr1h2 knockdown (T0370), replicate 1


title: 304_83_mouse_111_postappl_day_7_AAV6_2-Stuffer


title: 304_86_mouse_114_postappl_day_7_AAV6_2-Stuffer


title: 304_85_mouse_113_postappl_day_7_AAV6_2-Stuffer


title: 304_81_mouse_109_postappl_day_3_AAV6_2-TGFb1


title: 304_80_mouse_108_postappl_day_3_AAV6_2-TGFb1


description: L1_W369: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nol3 knockdown (T0369), replicate 1


title: 304_82_mouse_110_postappl_day_3_AAV6_2-TGFb1


title: 304_90_mouse_118_postappl_day_7_AAV6_2-TGFb1


description: L1_W366: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppm1g knockdown (T0366), replicate 1


title: 304_79_mouse_107_postappl_day_3_AAV6_2-TGFb1


description: L1_W362: SPAR-seq of 108 multi-exon gene regions in N2A cells, Matr3 knockdown (T0362), replicate 1


description: L1_W364: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mnt knockdown (T0364), replicate 1


title: 304_91_mouse_119_postappl_day_7_AAV6_2-TGFb1


description: L1_W365: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ncoa3 knockdown (T0365), replicate 1


description: L1_W358: SPAR-seq of 108 multi-exon gene regions in N2A cells, Msh3 knockdown (T0358), replicate 1


description: L1_W359: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nr6a1 knockdown (T0359), replicate 1


description: L1_W363: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pcbp2 knockdown (T0363), replicate 1


title: 304_89_mouse_117_postappl_day_7_AAV6_2-TGFb1


description: L1_W357: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nr1d1 knockdown (T0357), replicate 1


title: 304_74_mouse_102_postappl_day_3_AAV6_2-Stuffer


title: 304_78_mouse_106_postappl_day_3_AAV6_2-TGFb1


description: L1_W361: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nsd1 knockdown (T0361), replicate 1


title: 304_75_mouse_103_postappl_day_3_AAV6_2-Stuffer


description: L1_W352: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pcna knockdown (T0352), replicate 1


title: 304_77_mouse_105_postappl_day_3_AAV6_2-Stuffer


title: 304_68_mouse_72_postappl_day_28_Bleomycin

value: Bleomycin


description: L1_W360: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mcm6 knockdown (T0360), replicate 1


description: L1_W367: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nfe2l2 knockdown (T0367), replicate 1


title: 304_76_mouse_104_postappl_day_3_AAV6_2-Stuffer


title: 304_67_mouse_71_postappl_day_28_Bleomycin


description: L1_W351: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf2 knockdown (T0351), replicate 1


title: 304_66_mouse_70_postappl_day_28_NaCl


description: L1_W356: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prkrir knockdown (T0356), replicate 1


title: 304_73_mouse_101_postappl_day_3_AAV6_2-Stuffer


description: L1_W355: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ndel1 knockdown (T0355), replicate 1


description: L1_W354: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nfe2l1 knockdown (T0354), replicate 1


title: 304_64_mouse_68_postappl_day_28_NaCl


description: L1_W349: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mef2d knockdown (T0349), replicate 1


description: L1_W353: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mcm4 knockdown (T0353), replicate 1


title: 304_70_mouse_77_postappl_day_28_Bleomycin


title: 304_69_mouse_76_postappl_day_28_Bleomycin


title: 304_71_mouse_79_postappl_day_28_Bleomycin


description: L1_W350: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nusap1 knockdown (T0350), replicate 1


description: L1_W344: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ybx1 knockdown (T0344), replicate 1


description: L1_W348: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mcm7 knockdown (T0348), replicate 1


title: 304_72_mouse_96_postappl_day_28_Bleomycin


description: L1_W342: SPAR-seq of 108 multi-exon gene regions in N2A cells, Spen knockdown (T0342), replicate 1


description: L1_W347: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mlh1 knockdown (T0347), replicate 1


description: L1_W346: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ncor2 knockdown (T0346), replicate 1


title: 304_65_mouse_69_postappl_day_28_NaCl


title: 304_62_mouse_66_postappl_day_28_NaCl


title: 304_56_mouse_58_postappl_day_21_Bleomycin


title: 304_55_mouse_57_postappl_day_21_Bleomycin


description: L1_W339: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pcbp4 knockdown (T0339), replicate 1


title: 304_57_mouse_59_postappl_day_21_Bleomycin


description: L1_W338: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mre11a knockdown (T0338), replicate 1


title: 304_54_mouse_56_postappl_day_21_Bleomycin


title: 304_63_mouse_67_postappl_day_28_NaCl


description: L1_W345: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0345), replicate 1


title: 304_61_mouse_65_postappl_day_28_NaCl


description: L1_W343: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ndrg2 knockdown (T0343), replicate 1


title: 304_59_mouse_62_postappl_day_21_Bleomycin


title: 304_53_mouse_54_postappl_day_21_NaCl


description: L1_W335: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pou6f1 knockdown (T0335), replicate 1


description: L1_W341: SPAR-seq of 108 multi-exon gene regions in N2A cells, Orc6 knockdown (T0341), replicate 1


title: 304_52_mouse_53_postappl_day_21_NaCl


description: L1_W333: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0333), replicate 1


title: 304_58_mouse_60_postappl_day_21_Bleomycin


title: 304_49_mouse_50_postappl_day_21_NaCl


description: L1_W334: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prim2 knockdown (T0334), replicate 1


description: L1_W332: SPAR-seq of 108 multi-exon gene regions in N2A cells, Msh6 knockdown (T0332), replicate 1


description: L1_W340: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mcts1 knockdown (T0340), replicate 1


description: L1_W331: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ndrg1 knockdown (T0331), replicate 1


description: L1_W337: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbd2 knockdown (T0337), replicate 1


description: L1_W336: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ncor1 knockdown (T0336), replicate 1


title: 304_51_mouse_52_postappl_day_21_NaCl


description: L1_W330: SPAR-seq of 108 multi-exon gene regions in N2A cells, Paxip1 knockdown (T0330), replicate 1


title: 304_60_mouse_64_postappl_day_21_Bleomycin


title: 304_50_mouse_51_postappl_day_21_NaCl


title: 304_48_mouse_49_postappl_day_21_NaCl


description: L1_W329: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nr1d2 knockdown (T0329), replicate 1


title: 304_47_mouse_48_postappl_day_14_Bleomycin


description: L1_W326: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nras knockdown (T0326), replicate 1


title: 304_43_mouse_44_postappl_day_14_Bleomycin


description: L1_W328: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mcm5 knockdown (T0328), replicate 1


title: 304_45_mouse_46_postappl_day_14_Bleomycin


description: L1_W325: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nr2f6 knockdown (T0325), replicate 1


title: 304_44_mouse_45_postappl_day_14_Bleomycin


description: L1_W323: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbtd1 knockdown (T0323), replicate 1


description: L1_W321: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nfyb knockdown (T0321), replicate 1


title: 304_42_mouse_23_postappl_day_14_Bleomycin


description: L1_W320: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phip knockdown (T0320), replicate 1


title: 304_40_mouse_41_postappl_day_14_Bleomycin


title: 304_37_mouse_38_postappl_day_14_NaCl


title: 304_38_mouse_39_postappl_day_14_Bleomycin


title: 304_41_mouse_42_postappl_day_14_Bleomycin


description: L1_W322: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mef2a knockdown (T0322), replicate 1


title: 304_36_mouse_37_postappl_day_14_NaCl


description: L1_W324: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbd3 knockdown (T0324), replicate 1


title: 304_35_mouse_36_postappl_day_14_NaCl


title: 304_34_mouse_35_postappl_day_14_NaCl


description: L1_W327: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0327), replicate 1


title: 304_46_mouse_47_postappl_day_14_Bleomycin


title: 304_33_mouse_34_postappl_day_14_NaCl


title: 304_31_mouse_32_postappl_day_7_Bleomycin


description: L1_W317: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nde1 knockdown (T0317), replicate 1


description: L1_W319: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mll1 knockdown (T0319), replicate 1


description: L1_W315: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0315), replicate 1


description: L1_W316: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mcm2 knockdown (T0316), replicate 1


title: 304_29_mouse_30_postappl_day_7_Bleomycin


description: L1_W318: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nr4a1 knockdown (T0318), replicate 1


title: 304_28_mouse_29_postappl_day_7_Bleomycin


description: L1_W312: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phox2b knockdown (T0312), replicate 1


description: L1_W309: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nfyc knockdown (T0309), replicate 1


title: 304_39_mouse_40_postappl_day_14_Bleomycin


title: 304_32_mouse_33_postappl_day_14_NaCl


description: L1_W305: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mdm4 knockdown (T0305), replicate 1


description: L1_W311: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mcm3ap knockdown (T0311), replicate 1


description: L1_W313: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nfil3 knockdown (T0313), replicate 1


description: L1_W307: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hspa4l knockdown (T0307), replicate 1


title: 304_30_mouse_31_postappl_day_7_Bleomycin


title: 304_27_mouse_28_postappl_day_7_Bleomycin


title: 304_20_mouse_21_postappl_day_7_NaCl


title: 304_26_mouse_27_postappl_day_7_Bleomycin


title: 304_24_mouse_25_postappl_day_7_Bleomycin


title: 304_22_mouse_43_postappl_day_7_Bleomycin


description: L1_W303: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mllt10 knockdown (T0303), replicate 1


description: L1_W306: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kat2b knockdown (T0306), replicate 1


description: L1_W308: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppargc1b knockdown (T0308), replicate 1


title: 304_23_mouse_87_postappl_day_7_Bleomycin


description: L1_W310: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mxd4 knockdown (T0310), replicate 1


description: L1_W298: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phc1 knockdown (T0298), replicate 1


title: 304_17_mouse_18_postappl_day_7_NaCl


description: L1_W314: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mki67ip knockdown (T0314), replicate 1


title: 304_25_mouse_26_postappl_day_7_Bleomycin


title: 304_15_mouse_16_postappl_day_3_Bleomycin


title: 304_14_mouse_15_postappl_day_3_Bleomycin


title: 304_18_mouse_19_postappl_day_7_NaCl


title: 304_19_mouse_20_postappl_day_7_NaCl


title: 304_21_mouse_22_postappl_day_7_NaCl


description: L1_W299: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pes1 knockdown (T0299), replicate 1


title: 304_16_mouse_17_postappl_day_7_NaCl


description: L1_W300: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pafah1b1 knockdown (T0300), replicate 1


description: L1_W301: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pbx3 knockdown (T0301), replicate 1


description: L1_W297: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nxt1 knockdown (T0297), replicate 1


description: L1_W304: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tgs1 knockdown (T0304), replicate 1


title: 304_12_mouse_13_postappl_day_3_Bleomycin


title: 304_13_mouse_14_postappl_day_3_Bleomycin


title: 304_11_mouse_12_postappl_day_3_Bleomycin


description: L1_W293: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mki67 knockdown (T0293), replicate 1


title: 304_9_mouse_10_postappl_day_3_Bleomycin


title: 304_10_mouse_11_postappl_day_3_Bleomycin


description: L1_W295: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nktr knockdown (T0295), replicate 1


description: L1_W294: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbd4 knockdown (T0294), replicate 1


description: L1_W302: SPAR-seq of 108 multi-exon gene regions in N2A cells, Npm1 knockdown (T0302), replicate 1


description: L1_W292: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mybl2 knockdown (T0292), replicate 1


title: 304_8_mouse_8_postappl_day_3_Bleomycin


description: L1_W291: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pbx2 knockdown (T0291), replicate 1


description: L1_W290: SPAR-seq of 108 multi-exon gene regions in N2A cells, Msh2 knockdown (T0290), replicate 1


title: 304_7_mouse_7_postappl_day_3_Bleomycin


description: L1_W289: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0289), replicate 1


title: 304_5_mouse_5_postappl_day_3_NaCl


description: L1_W286: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kin knockdown (T0286), replicate 1


description: L1_W296: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf1 knockdown (T0296), replicate 1


title: 304_6_mouse_6_postappl_day_3_NaCl


description: L1_W288: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0288), replicate 1


description: L1_W287: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hspa8 knockdown (T0287), replicate 1


description: L1_W284: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ivns1abp knockdown (T0284), replicate 1


description: L1_W285: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmgn1 knockdown (T0285), replicate 1


title: 304_1_mouse_1_postappl_day_3_NaCl


description: L1_W283: SPAR-seq of 108 multi-exon gene regions in N2A cells, Foxd3 knockdown (T0283), replicate 1


title: 304_2_mouse_2_postappl_day_3_NaCl


title: TX_2i_mESCs_rep2 [RNA-Seq]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
IMPLICON-seq
Standard Illumina base-calling pipeline.
As first step in the processing, the first 8 bp of Read 2 were removed and written into the readID of both reads as an in-line barcode, or UMI (Unique Molecular Identifier). This UMI was then later used during the de-duplication step with "deduplicate bismark --barcode mapped_file.bam".
Raw sequence reads were then trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.5, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 2.3; parameters: --paired). Trimmed reads were aligned to the mouse genome in paired-end mode. Alignments were carried out with Bismark v0.22.3 (Krueger and Andrews, 2011)  CpG methylation calls were extracted from the mapping output using the Bismark methylation extractor. Deduplication was then carried out with deduplicate_bismark, using the --bacode option to take UMIs into account (see above)). For hybrid mouse strain experiments, the data was aligned to a hybrid genome of C57Bl/6 (genome 1)/CAST (genome 2)(the genome was prepared with the SNPsplit package (v0.3.4, https://github.com/FelixKrueger/SNPsplit)). Following alignment and deduplication, reads were split allele-specifically with SNPsplit.
Genome_build: GRCm38
RNA-Seq
Standard Illumina base-calling pipeline.
Sequenced RNA-seq reads were trimmed for adaptor sequence and low-quality sequence with Trim Galore (v0.6.1), and then mapped to the GRCm38 genome using HISAT2 v2.1.0 with parameters --dta --no-softclip --no-mixed --no-discordant. The resulting hits were filtered to remove mappings with a MAPQ scores of < 20.
Allele-specific alignments were performed by mapping to an N-masked C57Bl/6 (genome 1) and CAST_EiJ (genome 2) which was based on the GRCm38 genome, and generated using the SNPsplit package (v0.3.4; https://github.com/FelixKrueger/SNPsplit). Reads that were then sorted allele-specifically either genome and excluding those containing conflicting SNP information. Aligned reads were imported into the Seqmonk software (http://www.bioinformatics.babraham.ac.uk/ projects/seqmonk) for all downstream analysis using standard parameters. Data was quantified at the mRNA level using strand-specific quantification of mRNA probes using the RNA-seq quantification pipeline in Seqmonk. Differentially expressed genes were determined using both EdgeR (p-value of 0.05 with multiple testing correction) and intensity difference filter (p-value 0.05 with multiple testing correction), with the intersection between the two lists giving high confidence differentially expressed genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: The RNAseq report was generated by SeqMonk (v1.46.0). It is a tab delimited text file showing log2RPM values for each sample

extract_protocol:
Total RNA was extracted from cells using NZYOL™ RNA Isolation Reagent (Nzytech) and treated with DNase I (Roche) according to manufacturer’s instructions.
RNA was used for 250–300 bp insert cDNA library following manufacturer’s recommendations. Libraries were sequenced on the Illimina HiSeq 2000 platform using paired-end 150-bp mode.

treatment_protocol: DNAse I-treated total RNA from biological triplicates of female MEFs, M3, M5, F2, F4 miPSCs and Tx 2i mESCs were checked by 2100 Agilent Bioanalyser. Only samples with RIN score above 9 were sent for sequencing.

tag: cell type

value: Mouse embryonic stem cell

tag: Sex

value: Female

tag: group

value: control mESC type generated in 2i conditions


description: L1_W282: SPAR-seq of 108 multi-exon gene regions in N2A cells, Foxd1 knockdown (T0282), replicate 1


title: M_KSR5_miPSCs_rep3 [RNA-Seq]

value: Mouse induced pluripotent stem cell

value: Male

value: miPSC type generated using KSR


description: L1_W279: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kif2c knockdown (T0279), replicate 1


title: M_KSR5_miPSCs_rep1 [RNA-Seq]


description: L1_W281: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kifap3 knockdown (T0281), replicate 1


description: L1_W280: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kras knockdown (T0280), replicate 1


title: M_KSR3_miPSCs_rep2 [RNA-Seq]


description: L1_W278: SPAR-seq of 108 multi-exon gene regions in N2A cells, Id2 knockdown (T0278), replicate 1


title: M_KSR5_miPSCs_rep2 [RNA-Seq]


description: L1_W276: SPAR-seq of 108 multi-exon gene regions in N2A cells, Foxh1 knockdown (T0276), replicate 1


title: 304_4_mouse_4_postappl_day_3_NaCl


description: L1_W277: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpul1 knockdown (T0277), replicate 1


title: 304_3_mouse_3_postappl_day_3_NaCl


title: M_KSR3_miPSCs_rep3 [RNA-Seq]


title: Female_MEFs_rep3 [RNA-Seq]

value: Mouse embryonic fibroblasts

value: female

value: Parental female mouse embryonic fibroblasts


title: Female_MEFs_rep1 [RNA-Seq]


description: L1_W275: SPAR-seq of 108 multi-exon gene regions in N2A cells, Foxj2 knockdown (T0275), replicate 1


description: L1_W273: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kifc5b knockdown (T0273), replicate 1


title: TX_2i_mESCs_rep3 [RNA-Seq]


title: M_KSR3_miPSCs_rep1 [RNA-Seq]


title: F_KSR4_miPSCs_rep2 [RNA-Seq]


title: F_KSR4_miPSCs_rep3 [RNA-Seq]


description: L1_W272: SPAR-seq of 108 multi-exon gene regions in N2A cells, Krr1 knockdown (T0272), replicate 1


title: F_KSR4_miPSCs_rep1 [RNA-Seq]


description: L1_W270: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kdm5a knockdown (T0270), replicate 1


description: L1_W271: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ing1 knockdown (T0271), replicate 1


title: Female_MEFs_rep2 [RNA-Seq]


title: TX_2i_mESCs_rep1 [RNA-Seq]


title: F_KSR2_miPSCs_rep2 [RNA-Seq]


description: L1_W266: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ndc80 knockdown (T0266), replicate 1


description: L1_W267: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdac5 knockdown (T0267), replicate 1


description: L1_W264: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdac7 knockdown (T0264), replicate 1


description: L1_W269: SPAR-seq of 108 multi-exon gene regions in N2A cells, Fxr1 knockdown (T0269), replicate 1


description: L1_W268: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hand2 knockdown (T0268), replicate 1


description: L1_W274: SPAR-seq of 108 multi-exon gene regions in N2A cells, H2afx knockdown (T0274), replicate 1


description: L1_W261: SPAR-seq of 108 multi-exon gene regions in N2A cells, Foxm1 knockdown (T0261), replicate 1


description: L1_W265: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kif22 knockdown (T0265), replicate 1


description: L1_W263: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpk knockdown (T0263), replicate 1


title: F_KSR2_miPSCs_rep1 [RNA-Seq]


title: F_KSR2_miPSCs_rep3 [RNA-Seq]


title: Patient 66 [IM 66]

type: RNA

city: Atlanta

first: Milad

last: Rad

state: GA

address: 266 Ferst Dr NW

department: School of Electrical and Computer Engineering

country: USA

institute: Georgia Institute of Technology

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The Human Immunology v2 NanoString nCounter Gene Expression CodeSet was used (NanoString, Seattle, WA). All NanoString-based measurements were conducted at the Emory University Integrated Genomics Core facility using an amplification step for low abundant RNA applied to all samples as previously described.

data_processing: Digital images are processed within the nCounter instrument, and the Reporter Probe counts are tabulated in a comma separated value (CSV) format for convenient data analysis with Nanostring’s free nSolver Analysis Software.

label: biotin

organism: Homo sapiens

source_name: neutrophils

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

extract_protocol: RNA was isolated from neutrophils using the Nucleospin RNA II kit with on-column genomic DNA digestion according to the manufacturer’s protocol (Takara, Mountain View, CA). RNA sizing quantification and quality control was performed in the Emory Integrated Genomics Core on an Agilent 2100 bioanalyzer using Pico and Nano Agilent kits and a Tecan optical density plate reader to measure the concentration of the RNA.28 A low input RNA amplification kit was used. Only children with paired poly(I:C) gene expression data were used in the NanoString gene expression analysis.

tag: disease state

value: asthma

value: neutrophils

tag: cluster


title: Patient 71 [IM 71]


title: Patient 63 [IM 63]


title: Patient 70 [IM 70]


title: Patient 68 [IM 68]


description: L1_W255: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmbs knockdown (T0255), replicate 1


description: L1_W259: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hist1h1c knockdown (T0259), replicate 1


description: L1_W256: SPAR-seq of 108 multi-exon gene regions in N2A cells, Fxr2 knockdown (T0256), replicate 1


title: Patient 55 [IM 55]


title: Patient 60 [IM 60]


title: Patient 59 [IM 59]


title: Patient 62 [IM 62]


description: L1_W257: SPAR-seq of 108 multi-exon gene regions in N2A cells, H2afz knockdown (T0257), replicate 1


description: L1_W260: SPAR-seq of 108 multi-exon gene regions in N2A cells, G3bp1 knockdown (T0260), replicate 1


title: Patient 57 [IM 57]


title: Patient 58 [IM 58]


title: Patient 61 [IM 61]


description: L1_W250: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hspa2 knockdown (T0250), replicate 1


description: L1_W252: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdac11 knockdown (T0252), replicate 1


title: Patient 51 [IM 51]


title: Patient 50 [IM 50]


description: L1_W254: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmga1 knockdown (T0254), replicate 1


description: L1_W258: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hivep2 knockdown (T0258), replicate 1


title: Patient 48 [IM 48]


title: Patient 47 [IM 47]


description: L1_W249: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0249), replicate 1


title: Patient 52 [IM 52]


description: L1_W245: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdac6 knockdown (T0245), replicate 1


description: L1_W253: SPAR-seq of 108 multi-exon gene regions in N2A cells, Khsrp knockdown (T0253), replicate 1


title: Patient 44 [IM 44]


title: Patient 53 [IM 53]


title: Patient 49 [IM 49]


description: L1_W248: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmgxb4 knockdown (T0248), replicate 1


description: L1_W251: SPAR-seq of 108 multi-exon gene regions in N2A cells, Klf4 knockdown (T0251), replicate 1


description: L1_W246: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ing3 knockdown (T0246), replicate 1


title: Patient 42 [IM 42]


title: Patient 43 [IM 43]


description: L1_W243: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ilf3 knockdown (T0243), replicate 1


description: L1_W247: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hat1 knockdown (T0247), replicate 1


description: L1_W241: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdac1 knockdown (T0241), replicate 1


title: Patient 41 [IM 41]


description: L1_W242: SPAR-seq of 108 multi-exon gene regions in N2A cells, H2afy2 knockdown (T0242), replicate 1


description: L1_W262: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prmt2 knockdown (T0262), replicate 1


description: L1_W240: SPAR-seq of 108 multi-exon gene regions in N2A cells, Khdrbs1 knockdown (T0240), replicate 1


description: L1_W238: SPAR-seq of 108 multi-exon gene regions in N2A cells, Fus knockdown (T0238), replicate 1


description: L1_W239: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ing4 knockdown (T0239), replicate 1


title: Patient 37 [IM 37]


title: Patient 36 [IM 36]


description: L1_W237: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0237), replicate 1


title: Patient 39 [IM 39]


description: L1_W236: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kif23 knockdown (T0236), replicate 1


title: Patient 32 [IM 32]


title: Patient 30 [IM 30]


description: L1_W232: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hr knockdown (T0232), replicate 1


description: L1_W233: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmgn3 knockdown (T0233), replicate 1


title: Patient 40 [IM 40]


title: Patient 31 [IM 31]


description: L1_W244: SPAR-seq of 108 multi-exon gene regions in N2A cells, Jund knockdown (T0244), replicate 1


description: L1_W234: SPAR-seq of 108 multi-exon gene regions in N2A cells, Men1 knockdown (T0234), replicate 1


title: Patient 23 [IM 23]


title: Patient 26 [IM 26]


title: Patient 25 [IM 25]


description: L1_W230: SPAR-seq of 108 multi-exon gene regions in N2A cells, Junb knockdown (T0230), replicate 1


title: Patient 24 [IM 24]


title: Patient 27 [IM 27]


description: L1_W231: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0231), replicate 1


description: L1_W229: SPAR-seq of 108 multi-exon gene regions in N2A cells, Klf13 knockdown (T0229), replicate 1


title: Patient 20 [IM 20]


title: Patient 21 [IM 21]


description: L1_W228: SPAR-seq of 108 multi-exon gene regions in N2A cells, Fmr1 knockdown (T0228), replicate 1


title: Patient 18 [IM 18]


description: L1_W224: SPAR-seq of 108 multi-exon gene regions in N2A cells, Xrcc6 knockdown (T0224), replicate 1


description: L1_W235: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kdm5b knockdown (T0235), replicate 1


description: L1_W223: SPAR-seq of 108 multi-exon gene regions in N2A cells, H2afy knockdown (T0223), replicate 1


description: L1_W222: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gtf2f2 knockdown (T0222), replicate 1


title: Patient 17 [IM 17]


title: Patient 16 [IM 16]


description: L1_W226: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ing2 knockdown (T0226), replicate 1


description: L1_W221: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ilf2 knockdown (T0221), replicate 1


description: L1_W225: SPAR-seq of 108 multi-exon gene regions in N2A cells, Jun knockdown (T0225), replicate 1


description: L1_W227: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf10 knockdown (T0227), replicate 1


description: L1_W220: SPAR-seq of 108 multi-exon gene regions in N2A cells, H3f3b knockdown (T0220), replicate 1


title: Patient 13 [IM 13]


description: L1_W219: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0219), replicate 1


description: L1_W218: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdlbp knockdown (T0218), replicate 1


title: Patient 10 [IM 10]


title: Patient 12 [IM 12]


description: L1_W216: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prmt1 knockdown (T0216), replicate 1


title: Patient 7 [IM 7]


title: Patient 15 [IM 15]


title: Patient 6 [IM 6]


description: L1_W217: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hlcs knockdown (T0217), replicate 1


title: Patient 19 [IM 19]


title: Patient 5 [IM 5]


title: Patient 4 [IM 4]


title: Patient 14 [IM 14]


title: Patient 2 [IM 2]


description: L1_W213: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdac2 knockdown (T0213), replicate 1


description: L1_W214: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmgb3 knockdown (T0214), replicate 1


description: L1_W211: SPAR-seq of 108 multi-exon gene regions in N2A cells, Fosl2 knockdown (T0211), replicate 1


description: L1_W212: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmgn2 knockdown (T0212), replicate 1


description: L1_W215: SPAR-seq of 108 multi-exon gene regions in N2A cells, Igf2bp1 knockdown (T0215), replicate 1


description: L1_W208: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kat5 knockdown (T0208), replicate 1


title: Patient 8 [IM 8]


title: Patient 1 [IM 1]


description: L1_W210: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ik knockdown (T0210), replicate 1


title: Pre-implantation kidney donor control 10 [Avg_16YT]

city: Columbus

first: Samir

last: Parikh

state: OH

address: 395 W 12th Avenu, -Address 2-

department: Nephrology

institute: Ohio State University

description: Nanostring RAW 14.xlsx, Nanostring RAW 17.xlsx

hyb_protocol: Reporter and Capture probes against 579 mRNAs were obtained from Nanostring Technologies Seattle, WA. Data were collected and analyzed using the nCounter Digital Analyzer.

scan_protocol: The number of barcodes hybridized to specific RNA targets on cartridges were directly counted by the nCounter™ Digital Analyzer with 579 fields of view setting.

data_processing: For nanostring data, raw counts were normalized to the positive spike-in controls and then log2 transformed. To reduce technical bias, genes with an expression level below the mean plus two standard deviations of the negative controls were filtered out. Quantile normalization was applied to the remaining transcripts (522 for glomeruli and 502 for TI).  Linear mixed effect models were used to identify differentially expressed genes by taking into account the correlation between repeated measures before and after treatment. To improve the stability of variance estimation, moderated t-tests were employed for differential expression detection.

label: not provided

source_name: Healthy Control

label_protocol: To ensure there was similar starting material for each sample for expression analysis, pre-amplification conditions were determined by GAPDH RT-PCR cycle number. Extracted RNA was submitted for expression analysis using the Nanostring nCounter® GX human Immunology Panel (Nanostring Technologies, Seattle, WA). The panel consists of 579 immune response genes, 6 positive controls, 6 negative controls and 15 housekeeping genes.

extract_protocol: Formalin-fixed and paraffin-embedded (FFPE) kidney biopsy tissue was cut into 6-7 10μm sections. After deparaffinization, all available glomeruli and TI were separated by laser microdissection (PALM MicroBeam, Zeiss Labs, Germany), captured and digested with proteinase K. From each biopsy, a median glomerular cross-sectional area of 1,250,000 μm2, corresponding to ≈40 glomerular cross-sections, and a tubulointerstitial area of 3,500,000  μm2 was collected. DNA was removed with DNase. RNA was precipitated and extracted with RNeasy MinElute spin columns (Qiagen, Redwood City, California, USA).

tag: ln class

value: Healthy control


description: L1_W207: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdgf knockdown (T0207), replicate 1


title: Pre-implantation kidney donor control 9 [Avg_15YT]

description: Nanostring RAW 16.xlsx, Nanostring RAW 20.xlsx


title: Pre-implantation kidney donor control 8 [Avg_10YT]

description: Nanostring RAW 16.xlsx, Nanostring RAW 21.xlsx


title: Patient 3 [IM 3]


title: Pre-implantation kidney donor control 6 [X6XNT_9T]

description: Nanostring RAW 19.xlsx


description: L1_W206: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmg20a knockdown (T0206), replicate 1


description: L1_W204: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hspa5 knockdown (T0204), replicate 1


description: L1_W203: SPAR-seq of 108 multi-exon gene regions in N2A cells, Grsf1 knockdown (T0203), replicate 1


description: L1_W202: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ssh1 knockdown (T0202), replicate 1


title: Pre-implantation kidney donor control 3 [X3XNT_8T]

description: Nanostring RAW 18.xlsx


title: Pre-implantation kidney donor control 5 [Avg_5XNT]

description: Nanostring RAW 19.xlsx, Nanostring RAW 20.xlsx


title: Pre-implantation kidney donor control 4 [X4XNT_8T]

description: Nanostring RAW 18.xlsx


title: Pre-implantation kidney donor control 1 [X1XN_7T]

description: Nanostring RAW 17.xlsx


description: L1_W201: SPAR-seq of 108 multi-exon gene regions in N2A cells, Jarid2 knockdown (T0201), replicate 1


description: L1_W209: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdac3 knockdown (T0209), replicate 1


description: L1_W200: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdac10 knockdown (T0200), replicate 1


title: Patient 56, Second Biopsy, Tubulointerstitium [X56BT_1]

description:
Nanostring RAW 11.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

source_name: Lupus Nephritis

value: Class III

value: F

tag: age (yrs)

tag: proteinuria (g/24hr)

tag: serum creatinine (mg/dl)

tag: clinical response group

value: Partial Response


title: Pre-implantation kidney donor control 7 [X7XNT_11T]

description: Nanostring RAW 21.xslx


description: L1_W198: SPAR-seq of 108 multi-exon gene regions in N2A cells, Aff2 knockdown (T0198), replicate 1

value: Mouse neuroblastoma cells


title: Patient 54, Second Biopsy, Tubulointerstitium [X54BT_11]

description:
Nanostring RAW 21.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

value: Mixed (III/IV+V)


description: L1_W195: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hes6 knockdown (T0195), replicate 1


title: Pre-implantation kidney donor control 2 [X2XN_7T]

description: Nanostring RAW 17.xlsx


description: L1_W197: SPAR-seq of 108 multi-exon gene regions in N2A cells, Myod1 knockdown (T0197), replicate 1


title: Patient 29, Second Biopsy, Tubulointerstitium [X29BT_7]

description:
Nanostring RAW 17.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

value: Class IV


title: Patient 46, Second Biopsy, Tubulointerstitium [X46BT_8]

description:
Nanostring RAW 18.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 57, Second Biopsy, Tubulointerstitium [X57BT_11]

description:
Nanostring RAW 21.xslx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W193: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0193), replicate 1


description: L1_W199: SPAR-seq of 108 multi-exon gene regions in N2A cells, Foxn2 knockdown (T0199), replicate 1


description: L1_W192: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0192), replicate 1


title: Patient 22, Second Biopsy, Tubulointerstitium [X22BT_7]


title: Patient 21, Second Biopsy, Tubulointerstitium [X21BT_1]


title: Patient 35, Second Biopsy, Tubulointerstitium [X35BT_9]

description:
Nanostring RAW  3. xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

value: M


title: Patient 36, Second Biopsy, Tubulointerstitium [X36BT_3]

description:
Nanostring RAW 1.xlsx, Nanostring RAW 13.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W189: SPAR-seq of 108 multi-exon gene regions in N2A cells, Chd2 knockdown (T0189), replicate 1


description: L1_W194: SPAR-seq of 108 multi-exon gene regions in N2A cells, Aktip knockdown (T0194), replicate 1


title: Patient 28, Second Biopsy, Tubulointerstitium [X28BT_4]

description:
Nanostring RAW 14.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W205: SPAR-seq of 108 multi-exon gene regions in N2A cells, Igf2bp3 knockdown (T0205), replicate 1


description: L1_W190: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ep300 knockdown (T0190), replicate 1


title: Patient 4, Second Biopsy, Tubulointerstitium [X04BT_5]

description:
Nanostring RAW 1.xlsx, Nanostring RAW 12.xlsx, Nanostring RAW 15.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W188: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cops5 knockdown (T0188), replicate 1


title: Patient 16, Second Biopsy, Tubulointerstitium [X16BT_5]

description:
Nanostring RAW 15.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W187: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dbp knockdown (T0187), replicate 1


description: L1_W191: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cbx1 knockdown (T0191), replicate 1


description: L1_W196: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kif4 knockdown (T0196), replicate 1


description: L1_W186: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dclre1b knockdown (T0186), replicate 1


description: L1_W185: SPAR-seq of 108 multi-exon gene regions in N2A cells, Atf6b knockdown (T0185), replicate 1


title: Patient 18, Second Biopsy, Tubulointerstitium [Avg_18BT]

description:
Nanostring RAW 12.xlsx, Nanostring RAW 17.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 38, Second Biopsy, Tubulointerstitium [Avg_38BT]

description:
Nanostring RAW 2.xlsx, Nanostring RAW 15.xlsx, Nanostring RAW 17.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

value: No Response


title: Patient 31, Second Biopsy, Tubulointerstitium [X31BT_1]

description:
Nanostring RAW 11.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 14, Second Biopsy, Tubulointerstitium [X14BT_6]

description:
Nanostring RAW 16.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W183: SPAR-seq of 108 multi-exon gene regions in N2A cells, Chd4 knockdown (T0183), replicate 1


description: L1_W184: SPAR-seq of 108 multi-exon gene regions in N2A cells, Clspn knockdown (T0184), replicate 1


description: L1_W181: SPAR-seq of 108 multi-exon gene regions in N2A cells, Med26 knockdown (T0181), replicate 1


description: L1_W179: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dhx16 knockdown (T0179), replicate 1


description: L1_W182: SPAR-seq of 108 multi-exon gene regions in N2A cells, Med14 knockdown (T0182), replicate 1


title: Patient 17, Second Biopsy, Tubulointerstitium [X17BT_3]

description:
Nanostring RAW 13.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 24, Second Biopsy, Tubulointerstitium [X24BT_6]


title: Patient 27, Second Biopsy, Tubulointerstitium [X27BT_4]

description:
Nanostring RAW 14.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W176: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ezh2 knockdown (T0176), replicate 1


description: L1_W180: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cirbp knockdown (T0180), replicate 1


title: Patient 5, Second Biopsy, Tubulointerstitium [X05BT_5]

description:
Nanostring RAW 15.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 13, Second Biopsy, Tubulointerstitium [X13BT_3]


description: L1_W174: SPAR-seq of 108 multi-exon gene regions in N2A cells, Celf2 knockdown (T0174), replicate 1


title: Patient 52, Second Biopsy, Tubulointerstitium [X52BT_10]

description:
Nanostring RAW 20.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

value: complete response


title: Patient 9, Second Biopsy, Tubulointerstitium [X09BT_4]

description:
Nansotring RAW 14.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W175: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dnmt3b knockdown (T0175), replicate 1


description: L1_W178: SPAR-seq of 108 multi-exon gene regions in N2A cells, Elavl3 knockdown (T0178), replicate 1


title: Patient 58, Second Biopsy, Tubulointerstitium [X58BT_11]

description:
Nanostring RAW 21.xslx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W177: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dek knockdown (T0177), replicate 1


title: Patient 55, Second Biopsy, Tubulointerstitium [X55BT_8]

description:
Nanostring RAW 21.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 50, Second Biopsy, Tubulointerstitium [X50BT_9]

description:
Nanostring RAW 19.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 10, Second Biopsy, Tubulointerstitium [X10BT_2]

description:
Nanostring RAW 12.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W169: SPAR-seq of 108 multi-exon gene regions in N2A cells, E2f3 knockdown (T0169), replicate 1


description: L1_W172: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cdc5l knockdown (T0172), replicate 1


title: Patient 48, Second Biopsy, Tubulointerstitium [X48BT_1]

description:
Nanostring RAW 11.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 51, Second Biopsy, Tubulointerstitium [X51BT_4]

description:
Nanostring RAW 14.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W173: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpe knockdown (T0173), replicate 1


title: Patient 53, Second Biopsy, Tubulointerstitium [X53BT_11]


title: Patient 34, Second Biopsy, Tubulointerstitium [X34BT_3]

description:
Nanostring RAW 13.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W170: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dpf2 knockdown (T0170), replicate 1


description: L1_W165: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpb knockdown (T0165), replicate 1


title: Patient 32, Second Biopsy, Tubulointerstitium [X32BT_1]


description: L1_W164: SPAR-seq of 108 multi-exon gene regions in N2A cells, Csde1 knockdown (T0164), replicate 1


description: L1_W171: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif3g knockdown (T0171), replicate 1


title: Patient 39, Second Biopsy, Tubulointerstitium [X39BT_7]

description:
Nanostring RAW 17.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 26, Second Biopsy, Tubulointerstitium [X26BT_2]


description: L1_W168: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ahctf1 knockdown (T0168), replicate 1


description: L1_W166: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cbx3 knockdown (T0166), replicate 1


title: Patient 47, Second Biopsy, Tubulointerstitium [X47BT_10]

description:
Nanostring RAW 20.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W161: SPAR-seq of 108 multi-exon gene regions in N2A cells, Chaf1a knockdown (T0161), replicate 1


description: L1_W167: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpc1 knockdown (T0167), replicate 1


title: Patient 25, Second Biopsy, Tubulointerstitium [X25BT_9]

description:
Nanostring RAW 19.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W157: SPAR-seq of 108 multi-exon gene regions in N2A cells, Elavl2 knockdown (T0157), replicate 1


description: L1_W160: SPAR-seq of 108 multi-exon gene regions in N2A cells, Col4a3 knockdown (T0160), replicate 1


title: Patient 20, Second Biopsy, Tubulointerstitium [X20BT_3]


title: Patient 11, Second Biopsy, Tubulointerstitium [X11BT_2]

description:
Nanostring RAW 12.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W163: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dctn3 knockdown (T0163), replicate 1


description: L1_W159: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eef1a1 knockdown (T0159), replicate 1


title: Patient 30, Second Biopsy, Tubulointerstitium [X30BT_6]

description:
Nanostring RAW 16.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W158: SPAR-seq of 108 multi-exon gene regions in N2A cells, Bptf knockdown (T0158), replicate 1


title: Patient 49, Second Biopsy, Tubulointerstitium [X49BT_8]

description:
Nanostring RAW 18.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 19, Second Biopsy, Tubulointerstitium [X19BT_9]


title: Patient 15, Second Biopsy, Tubulointerstitium [Avg_15BT]

description:
Nanostring RAW 15.xlsx, Nanostring RAW 18.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 37, Second Biopsy, Tubulointerstitium [X37BT_10]


description: L1_W162: SPAR-seq of 108 multi-exon gene regions in N2A cells, Elavl4 knockdown (T0162), replicate 1


title: Patient 2, Second Biopsy, Tubulointerstitium [X02BT_4]

description:
Nanostring RAW 14.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 23, Second Biopsy, Tubulointerstitium [X23BT_6]


description: L1_W155: SPAR-seq of 108 multi-exon gene regions in N2A cells, Med23 knockdown (T0155), replicate 1


title: Patient 41, First Biopsy, Tubulointerstitium [X41AT_2]


description: L1_W153: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0153), replicate 1


description: L1_W156: SPAR-seq of 108 multi-exon gene regions in N2A cells, Crebbp knockdown (T0156), replicate 1


title: Patient 56, First Biopsy, Tubulointerstitium [X56AT_1]

description:
Nanostring RAW 11.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 7, Second Biopsy, Tubulointerstitium [X07BT_10]

description:
Nanostring RAW 20.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W150: SPAR-seq of 108 multi-exon gene regions in N2A cells, H2afj knockdown (T0150), replicate 1


description: L1_W149: SPAR-seq of 108 multi-exon gene regions in N2A cells, Drap1 knockdown (T0149), replicate 1


title: Patient 40, First Biopsy, Tubulointerstitium [X40AT_8]


description: L1_W148: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cnbp knockdown (T0148), replicate 1


title: Patient 1, Second Biopsy, Tubulointerstitium [X01BT_6]

description:
Nanostring RAW 2.xlsx, Nanostring RAW 16.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W151: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ddx20 knockdown (T0151), replicate 1


description: L1_W154: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cbx8 knockdown (T0154), replicate 1


title: Patient 29, First Biopsy, Tubulointerstitium [X29AT_7]

description:
Nanostring RAW 17.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W152: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif3b knockdown (T0152), replicate 1


title: Patient 28, First Biopsy, Tubulointerstitium [X28AT_4]


description: L1_W144: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nuf2 knockdown (T0144), replicate 1


description: L1_W147: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ctnnbl1 knockdown (T0147), replicate 1


title: Patient 18, First Biopsy, Tubulointerstitium [Avg_18AT]

description:
Nanostring RAW 12.xlsx, Nanostring RAW 18.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 33, First Biopsy, Tubulointerstitium [X33AT_10]


title: Patient 35, First Biopsy, Tubulointerstitium [X35AT_9]

description:
Nanostring RAW 19.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 21, First Biopsy, Tubulointerstitium [X21AT_1]


description: L1_W145: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cstf3 knockdown (T0145), replicate 1


description: L1_W146: SPAR-seq of 108 multi-exon gene regions in N2A cells, Elavl1 knockdown (T0146), replicate 1


title: Patient 22, First Biopsy, Tubulointerstitium [X22AT_7]


title: Patient 14, First Biopsy, Tubulointerstitium [X14AT_6]

description:
Nansotring RAW 16.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W143: SPAR-seq of 108 multi-exon gene regions in N2A cells, Chd1 knockdown (T0143), replicate 1


description: L1_W142: SPAR-seq of 108 multi-exon gene regions in N2A cells, Suz12 knockdown (T0142), replicate 1


title: patient 27, First Biopsy, Tubulointerstitium [Avg_27AT]

description:
Nanostring RAW 14.xlsx, Nanostring RAW 18.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 38, First Biopsy, Tubulointerstitium [X38AT_5]

description:
Nanostring RAW 2.xlsx, Nanostring RAW 15.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 16, First Biopsy, Tubulointerstitium [X16AT_5]

description:
Nanostring RAW 15.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 24, First Biopsy, Tubulointerstitium [X24AT_6]


description: L1_W141: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0141), replicate 1


title: patient 17, First Biopsy, Tubulointerstitium [X17AT_3]

description:
Nanostring RAW  13.xslx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 31, First Biopsy, Tubulointerstitium [X31AT_1]

description:
Nanostring RAW 11.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 4, First Biopsy, Tubulointerstitium [X04AT_5]

description:
Nanostring RAW 1.xlsx, Nanostring RAW 12.xlsx, Nanostring RAW 15.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: MSCs from control under osteogenic induction at day 7

city: New Taipei City

first: Chin-Hsiu

last: Liu

address: Zhonghe road

department: Rheumatology and clinical immunology

country: Taiwan

institute: Taipei Tzu Chi General Hospital

description: Gene expression data from C MSC under osteogenic induction at day 7

hyb_protocol: After converting linear RNA into 35-200 nt biotin-labeled fragments, samples were then hybridized to GeneChip® Human Genome U133 array.

scan_protocol: The array data were acquired with GeneChip® Scanner 3000.

data_processing: The data from GFP control and GFP-PRDM1 transduced H9 hESCS were analyzed with GeneSpring GX.

label_protocol: 1 ug of total RNA was subjected to reverse transcription and biotin-conjugated nucleotide incorporation by using GeneChip ® 3' IVT Express Kit (Affymetrix).

growth_protocol: MSCs were growth in α-MEM, 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin at 37°C under 5% CO2 atmosphere

extract_protocol: Total RNA was isolated according to the manufacturer's instructions by an RNeasy spin column (Qiagen).

treatment_protocol: For osteogenic induction, α-MEM was supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 50 μg/mL ascorbate-2 phosphate, 10 nmol/L dexamethasone, and 10 mmol/L beta-glycerophosphate.

value: mesenchymal stem cells

tag: time (osteogenic induction)

value: Day 7

tag: origin

value: MSCs originated from spinal enthesal tissues of control

value: control


description: L1_W140: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ccnb1 knockdown (T0140), replicate 1


title: MSCs from patient with AS under osteogenic induction at day 3

description: Gene expression data from AS MSC under osteogenic induction at day 3

value: Day 3

value: MSCs originated from spinal enthesal tissues involved in spinal ankylosis of AS

value: ankylosing spondylitis


description: L1_W139: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdac9 knockdown (T0139), replicate 1


title: patient 9, First Biopsy, Tubulointerstitium [X09AT_4]

description:
Nansotring RAW 14.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 5, First Biopsy, Tubulointerstitium [X05AT_5]


description: L1_W138: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ubr2 knockdown (T0138), replicate 1


title: MSCs from control under osteogenic induction at day 0

description: Gene expression data from C MSC under osteogenic induction at day 0

value: Day 0


title: MSCs from patient with AS under osteogenic induction at day 7

description: Gene expression data from AS MSC under osteogenic induction at day 7


title: MSCs from control under osteogenic induction at day 3

description: Gene expression data from C MSC under osteogenic induction at day 3


title: patient 50, First Biopsy, Tubulointerstitium [X50AT_9]

description:
Nanostring RAW 19.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, ref2, rep4

city: West Lafayette

first: Clint

last: Chapple

address: 175 S. University St.

department: Biochemistry

institute: Purdue University

data_processing:
Casava1.8.2 software was used for basecalling.
Trimmomatic and/or fastx_clipper were used to remove adapters. Poor quality bases (less than Phred-20) were removed (clipped) from both the 5' and 3' ends of the Unaligned reads. Reads were then mapped to TAIR10 assembly of the Arabidopsis genome using HISAT2 (v.2.1.0) with default parameters.
Digital gene expression (counts) were determined for each sample using HTSeq-count with the following parameters: -s reverse -r pos -m intersection-nonempty -t exon -i gene_id. Data were saved as processed data file in genecounts.csv.
Differential gene expression analysis was conducted using DESeq2 (v 1.22.2) package in R. Gene expression at low levels were filtered out by removing genes with average raw counts below 30 in at least one genotype or with average normalized counts counts below 5 in our genotypes. A count table of 20974 expressed genes was used to identify 5581 differential expressed genes in at least one genotypes (ANOVA, FDR < 0.01, Fold change ≥ 2).
Assembly: TAIR10
Supplementary files format and content: Comma-separated values file includes count values for each sample.

organism: Arabidopsis thaliana

source_name: basal 0.5-2 cm of inflorescence stem

growth_protocol: Seeds were sown five per 4" x 4" pot and positions of the pots were randomized. Seeds were held at 4 °C for two days before transferring to 23 °C under a 16 hr light, 8 hr dark photoperiod. Basal 0.5-2 cm of inflorescence stem from 6 plants was collected together as one sample at noon on the 28th day after transferring to the growth chamber. Four replicates for each mutant and eight replicates for wild type were sampled.

extract_protocol:
About 100 mg ground frozen tissue was extracted for total RNA using QIAGENE RNeasy Mini kit. An on-column DNase treatment from QIAGEN was performed to remove DNA from samples.
PolyA+ RNA libraries were constructed using Illumina’s TruSeq stranded mRNA library prep kit for each sample.

treatment_protocol: Tissue were flash frozen in liquid nitrogen immediately after harvest and stored at -80 °C until extraction. Frozen samples were ground in ceramic mortars in liquid nitrogen.

value: basal 0.5-2 cm of inflorescence stem

tag: ecotype

tag: genotype

tag: age

value: harvest at 28-day-old


title: patient 53, First Biopsy, Tubulointerstitium [X53AT_11]

description:
Nanostring RAW 21.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

value: F


title: MSCs from patient with AS under osteogenic induction at day 0

description: Gene expression data from AS MSC under osteogenic induction at day 0


title: inflorescence stem, ref2, rep2

tag: tissue


title: patient 51, First Biopsy, Tubulointerstitium [X51AT_4]

description:
Nanostring RAW 14.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 49, First Biopsy, Tubulointerstitium [X49AT_11]

description:
Nanostring RAW 21.xslx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 13, First Biopsy, Tubulointerstitium [X13AT_3]

description:
Nanostring RAW 13.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W136: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm45 knockdown (T0136), replicate 1

value: Mouse neuroblastoma cells

tag: cell line


description: L1_W137: SPAR-seq of 108 multi-exon gene regions in N2A cells, Fancd2 knockdown (T0137), replicate 1


title: inflorescence stem, med5a/b ref2, rep4

value: med5a/b ref2


title: patient 48, First Biopsy, Tubulointerstitium [Avg_48AT]

description:
Nanostring RAW 11.xlsx, Nanostring RAW 17.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

value: Class III


title: patient 55, First Biopsy, Tubulointerstitium [X55AT_8]

description:
Nanostring RAW 18.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 44, First Biopsy, Tubulointerstitium [X44AT_10]

description:
Nanostring RAW 20.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

value: Class IV


title: inflorescence stem, med5a/b ref2, rep3


title: patient 47, First Biopsy, Tubulointerstitium [X47AT_10]


title: inflorescence stem, ref2, rep3


title: patient 39, First Biopsy, Tubulointerstitium [X39AT_7]

description:
Nanostring RAW 17.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W134: SPAR-seq of 108 multi-exon gene regions in N2A cells, Larp4b knockdown (T0134), replicate 1


title: patient 10, First Biopsy, Tubulointerstitium [X10AT_2]

description:
Nanostring RAW 12.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

value: Mixed (III/IV+V)

value: M

value: No Response


description: L1_W135: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0135), replicate 1


description: L1_W133: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dctn2 knockdown (T0133), replicate 1


title: patient 32, First Biopsy, Tubulointerstitium [X32AT_1]

description:
Nanostring RAW 11.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis

value: complete response


title: inflorescence stem, med5a/b ref2, rep2


title: patient 34, First Biopsy, Tubulointerstitium [X34AT_3]


description: L1_W132: SPAR-seq of 108 multi-exon gene regions in N2A cells, Fubp1 knockdown (T0132), replicate 1


title: patient 37, First Biopsy, Tubulointerstitium [X37AT_10]


description: L1_W131: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cbx4 knockdown (T0131), replicate 1


title: inflorescence stem, med5a/b ref8, rep3

value: med5a/b ref8


title: patient 26, First Biopsy, Tubulointerstitium [X26AT_2]


title: inflorescence stem, med5a/b ref2, rep1


title: patient 30, First Biopsy, Tubulointerstitium [X30AT_6]

description:
Nanostring RAW 16.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 25, First Biopsy, Tubulointerstitium [X25AT_9]

description:
Nanostring RAW 19.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, med5a/b ref8, rep4


description: L1_W130: SPAR-seq of 108 multi-exon gene regions in N2A cells, Csda knockdown (T0130), replicate 1


title: patient 20, First Biopsy, Tubulointerstitium [X20AT_3]

description:
Nanostring RAW 13.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, med5a/b ref8, rep1


title: Patient 6, First Biopsy, Tubulointerstitium [X06AT_10]


title: patient 23, First Biopsy, Tubulointerstitium [X23AT_6]


title: patient 15, First Biopsy, Tubulointerstitium [Avg_15AT]

description:
Nanostring RAW 15.xlsx, Nanostring RAW 18.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Patient 1, First Biopsy, Tubulointerstitium [X01AT_6]

description:
Nanostring RAW 2.xlsx, Nanostring RAW 16.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, med5a/b ref8, rep2


title: patient 12, First Biopsy, Tubulointerstitium [X12AT_11]

description:
Nanostring RAW 21.xslx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, ref2, rep1


title: Patient 11, First Biopsy, Tubulointerstitium [X11AT_2]


description: L1_W129: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ewsr1 knockdown (T0129), replicate 1


title: Pre-implantation kidney donor control 9 [X16YG]

description:
Nanostring RAW 5.xlsx, Nanostring RAW 6.xlsx, Nanostring RAW 7.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis

value: Healthy control


title: Pre-implantation kidney donor control 8 [X15YG]


description: L1_W127: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ints6 knockdown (T0127), replicate 1


title: inflorescence stem, med5a/b, rep4


title: Pre-implantation kidney donor control 7 [X10YG]

description:
Nanostring RAW 6.xlsx, Nanostring RAW 9.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W125: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eed knockdown (T0125), replicate 1


title: inflorescence stem, med5a/b, rep3


title: inflorescence stem, med5a/b, rep1


description: L1_W126: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cd2bp2 knockdown (T0126), replicate 1


title: Pre-implantation kidney donor control 6 [X7XNG_2]

description:
Nanostring RAW 10.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, med5a/b, rep2


title: inflorescence stem, ref8 fah1 SmF5H, rep4

value: ref8 fah1 SmF5H


title: Pre-implantation kidney donor control 4 [X4XNG_1]

description:
Nanostring RAW 9.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: Pre-implantation kidney donor control 3 [X3XNG_1]


title: Pre-implantation kidney donor control 1 [X1XNG_10]

description:
Nanostring RAW 8.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W128: SPAR-seq of 108 multi-exon gene regions in N2A cells, Daxx knockdown (T0128), replicate 1


description: L1_W124: SPAR-seq of 108 multi-exon gene regions in N2A cells, Btaf1 knockdown (T0124), replicate 1


title: Patient 2, First Biopsy, Tubulointerstitium [X02AT_4]

description:
Nanostring RAW 14.xlsx
Tubulointerstitial RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W121: SPAR-seq of 108 multi-exon gene regions in N2A cells, Csad knockdown (T0121), replicate 1


title: inflorescence stem, ref8 fah1 SmF5H, rep2


title: Pre-implantation kidney donor control 2 [X2XNG_10]


title: patient 21, second biopsy, glomeruli [X21BG_1]

value: Partial Response


description: L1_W120: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cnot4 knockdown (T0120), replicate 1


description: L1_W123: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0123), replicate 1


title: patient 16, second biopsy, glomeruli [X16bG_9]

description:
Nanostring RAW 7.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 22, second biopsy, glomeruli [X22BG_10]


title: inflorescence stem, C4H:F5H, rep3


title: patient 4, second biopsy, glomeruli [X4BG_7]

description:
Nanostring RAW 1.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W122: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif3a knockdown (T0122), replicate 1


title: inflorescence stem, ref8 fah1 SmF5H, rep1


title: Pre-implantation kidney donor control 5 [X5XNG1_2]


title: inflorescence stem, C4H:F5H, rep4


title: patient 28, second biopsy, glomeruli [X28BG_1]


description: L1_W117: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ercc2 knockdown (T0117), replicate 1


title: patient 18, second biopsy, glomeruli [X18BG_2]


title: inflorescence stem, C4H:F5H, rep2


title: patient 27, second biopsy, glomeruli [X27BG]

description:
Nanostring RAW 7.xlsx, Nanostring RAW 8.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, ref8 fah1 SmF5H, rep3


description: L1_W118: SPAR-seq of 108 multi-exon gene regions in N2A cells, Trdmt1 knockdown (T0118), replicate 1


description: L1_W116: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dbr1 knockdown (T0116), replicate 1


title: patient 14, second biopsy, glomeruli [X14bG_8]

description:
Nanostring RAW 6.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, C4H:F5H, rep1


title: patient 31, second biopsy, glomeruli [X31BG_8]


description: L1_W119: SPAR-seq of 108 multi-exon gene regions in N2A cells, Clasp2 knockdown (T0119), replicate 1


title: inflorescence stem, fah1, rep4


title: patient 10, second biopsy, glomeruli [X10BG]

description:
Nanostring RAW 4.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 56, second biopsy, glomeruli [X56BG_10]

description:
Nanostring RAW 8.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 5, second biopsy, glomeruli [X05BG]

description:
Nanostring RAW 5.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W115: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ciz1 knockdown (T0115), replicate 1


title: patient 17, second biopsy, glomeruli [X17BG]

description:
Nanostring RAW 5.xlsx, Nanostring RAW 9.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 38, second biopsy, glomeruli [X38B.G_3]

description:
Nanostring RAW2.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 13, second biopsy, glomeruli [X13BG]


title: inflorescence stem, fah1, rep3


title: patient 55, second biopsy, glomeruli [X55BG_9]


title: patient 24, second biopsy, glomeruli [X24BG]

description:
Nanostring RAW 4.xlsx, Nanostring RAW 8.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, fah1, rep2


description: L1_W113: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dnmt1 knockdown (T0113), replicate 1


description: L1_W114: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ccnl1 knockdown (T0114), replicate 1


title: patient 51, second biopsy, glomeruli [X51BG_7]


title: patient 53, second biopsy, glomeruli [X53BG_1]

description:
Nanostring RAW 9.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, fah1, rep1


title: patient 58, second biopsy, glomeruli [X58BG_8]


title: patient 50, second biopsy, glomeruli [X50BG_10]


title: inflorescence stem, cadc cadd, rep3

value: cadc cadd


title: patient 48, second biopsy, glomeruli [X48BG_9]

description:
Nanostring RAW 7.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W112: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ezh1 knockdown (T0112), replicate 1


title: inflorescence stem, cadc cadd, rep2


description: L1_W111: SPAR-seq of 108 multi-exon gene regions in N2A cells, E2f6 knockdown (T0111), replicate 1


title: patient 49, second biopsy, glomeruli [X49BG_10]


title: patient 30, second biopsy, glomeruli [X30BG]


title: patient 39, second biopsy, glomeruli [X39BG_1]


title: patient 26, second biopsy, glomeruli [X26BG_2]

description:
Nanostring RAW 10.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: patient 32, second biopsy, glomeruli [X32BG]


description: L1_W109: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dr1 knockdown (T0109), replicate 1


description: L1_W110: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kdm1a knockdown (T0110), replicate 1


title: inflorescence stem, cadc cadd, rep4


title: patient 20, second biopsy, glomeruli [X20BG_8]

description:
Nanostring RAW 6.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W107: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpa knockdown (T0107), replicate 1


title: patient 23, second biopsy, glomeruli [X23BG_9]


title: inflorescence stem, cse-2, rep4


description: L1_W108: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dctn1 knockdown (T0108), replicate 1


title: patient 15, second biopsy, glomeruli [X15BG_5]

description:
Nanostring RAW 3.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, cse-2, rep2


title: patient 37, second biopsy, glomeruli [X37BG_5]


title: patient 7, second biopsy, glomeruli [X7BG_7]

description:
Nanostring RAW 5.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


description: L1_W105: SPAR-seq of 108 multi-exon gene regions in N2A cells, Chrac1 knockdown (T0105), replicate 1


title: M433

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine

description: NanoString nCounter assay

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then Set at 67°C for the selected hybridization time (typically 16–21 hours) and then ramp down to 4°C. To minimize the potential for evaporation, the thermal cycler lid should be set at 5° above the block temperature.

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified. Nanostring nCounter Reporter probes are imaged and counted by the nCounter Digital Analyzer System to provide a direct, digital readout of RNA molecules.

data_processing: Gene expression profiles across samples were normalized to equate positive control probes, and expression estimates were z-score normalized for each probe independently.

source_name: pediatric liver cancer

label_protocol: 10 mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of dCTP (Amersham Bioscience, Piscataway, NJ) according to the manufacturer instructions.

extract_protocol: FFPE tumor blocks cut in 10-20 micron sections (5-10 slides per sample) and one H&E slide from the Histology lab. These specimens were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist  (Dr. Terrada). Total RNA was isolated using the Rneasy Mini Kit (Qiagen). Samples were treated with deoxyribonuclease 1 and eluted in nuclease-free water. Samples with RNA integrity above 6.0 were used for our genomic studies.

value: Hepatoblastoma

value: liver

tag: status

value: DOD after Transplant

tag: histology

value: Older HB (age>8)

tag: stage (pretext)


title: patient 19, second biopsy, Glomeruli [X19BG_2]

tag: Sex

value: F


title: inflorescence stem, cse-2, rep3

value: basal 0.5-2 cm of inflorescence stem

value: harvest at 28-day-old


title: patient 11, second biopsy, glomeruli [X11BG_5]

value: Class III


title: M333

description: NanoString nCounter assay

tag: disease state

value: Alive after Transplant


title: M332

description: NanoString nCounter assay


title: patient 2, second biopsy, glomeruli [X02BG_5]

tag: ln class

value: Class IV


title: M315

description: NanoString nCounter assay


title: patient 1, second biopsy, glomeruli [X1B.G_3]

description:
Nanostring RAW 2.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis

value: M

tag: age (yrs)


description: L1_W102: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dmtf1 knockdown (T0102), replicate 1

value: Mouse neuroblastoma cells


description: L1_W106: SPAR-seq of 108 multi-exon gene regions in N2A cells, Esrra knockdown (T0106), replicate 1


title: M312

description: NanoString nCounter assay

value: Relapsed


title: inflorescence stem, 4cl1, rep4


title: inflorescence stem, 4cl1, rep3


title: M442

description: NanoString nCounter assay

value: DOD

value: HB FPA


title: inflorescence stem, cadc cadd, rep1


title: patient 56, first biopsy, glomeruli [X56AG_10]

description:
Nanostring RAW 8.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis

tag: proteinuria (g/24hr)

value: Partial Response


title: inflorescence stem, cse-2, rep1


description: L1_W101: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dnmt3a knockdown (T0101), replicate 1


title: inflorescence stem, 4cl1, rep2


description: L1_W103: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ctcf knockdown (T0103), replicate 1


title: M432

description: NanoString nCounter assay


title: inflorescence stem, 4cl1, rep1


title: patient 28, first biopsy, glomeruli [X28AG_1]

description:
Nanostring RAW 9.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis

tag: serum creatinine (mg/dl)


title: M415

description: NanoString nCounter assay


description: L1_W099: SPAR-seq of 108 multi-exon gene regions in N2A cells, Celf1 knockdown (T0099), replicate 1


description: L1_W100: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenph knockdown (T0100), replicate 1


title: inflorescence stem, pal1 pal2, rep4

value: pal1 pal2


description: L1_W104: SPAR-seq of 108 multi-exon gene regions in N2A cells, F630043A04Rik knockdown (T0104), replicate 1


title: patient 22, first biopsy, glomeruli [X22AG_10]

tag: clinical response group


title: patient 35, first biopsy, glomeruli [X35AG_2]

description:
Nanostring RAW 10.xlsx
Glomerular RNA was extracted by laser microdissection and submitted for nanostring analysis


title: inflorescence stem, pal1 pal2, rep3


title: patient 18, first biopsy, glomeruli [X18AG_2]


description: L1_W098: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cbx5 knockdown (T0098), replicate 1


description: L1_W097: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0097), replicate 1


title: inflorescence stem, pal1 pal2, rep1


title: M329

description: NanoString nCounter assay

value: Hepatoblastoma


title: M331

description: NanoString nCounter assay

value: liver

value: Alive


title: inflorescence stem, pal1 pal2, rep2


description: L1_W096: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0096), replicate 1