description: L2_W187: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dhx57 knockdown (T0955), replicate 1


status: Public on Jul 15 2022

type: SRA

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description: L2_W163: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ap1s3 knockdown (T0931), replicate 1

library_source: transcriptomic

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).

molecule: total RNA

organism: Mus musculus

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: L2_W180: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srbd1 knockdown (T0948), replicate 1


description: L2_W177: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gemin8 knockdown (T0945), replicate 1


description: L2_W173: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zbtb44 knockdown (T0941), replicate 1


description: L2_W169: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eme1 knockdown (T0937), replicate 1


description: L2_W165: SPAR-seq of 108 multi-exon gene regions in N2A cells, Actr8 knockdown (T0933), replicate 1


description: L2_W190: SPAR-seq of 108 multi-exon gene regions in N2A cells, Esrp2 knockdown (T0958), replicate 1


description: L2_W168: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp958 knockdown (T0936), replicate 1


description: L2_W161: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp934 knockdown (T0929), replicate 1


description: L2_W160: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srek1 knockdown (T0928), replicate 1


description: L2_W162: SPAR-seq of 108 multi-exon gene regions in N2A cells, Suv420h2 knockdown (T0930), replicate 1


description: L2_W157: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sfr1 knockdown (T0925), replicate 1


description: L2_W150: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3h10 knockdown (T0918), replicate 1


description: L2_W151: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ankrd17 knockdown (T0919), replicate 1


description: L2_W170: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tmem63a knockdown (T0938), replicate 1


description: L2_W166: SPAR-seq of 108 multi-exon gene regions in N2A cells, Morn4 knockdown (T0934), replicate 1


description: L2_W155: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp668 knockdown (T0923), replicate 1


description: L2_W152: SPAR-seq of 108 multi-exon gene regions in N2A cells, AI314976 knockdown (T0920), replicate 1


description: L2_W185: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ercc6l knockdown (T0953), replicate 1


description: L2_W154: SPAR-seq of 108 multi-exon gene regions in N2A cells, Baz1a knockdown (T0922), replicate 1


description: L2_W153: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0921), replicate 1


description: L2_W146: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp629 knockdown (T0914), replicate 1


description: L2_W147: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp871 knockdown (T0915), replicate 1


description: L2_W149: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp445 knockdown (T0917), replicate 1


description: L2_W156: SPAR-seq of 108 multi-exon gene regions in N2A cells, Aqr knockdown (T0924), replicate 1


description: L2_W142: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prmt7 knockdown (T0910), replicate 1


description: L2_W144: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zbtb12 knockdown (T0912), replicate 1


description: L2_W164: SPAR-seq of 108 multi-exon gene regions in N2A cells, Asf1a knockdown (T0932), replicate 1


description: L2_W148: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm47 knockdown (T0916), replicate 1


description: L2_W159: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbfox1 knockdown (T0927), replicate 1


description: L2_W140: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp652 knockdown (T0908), replicate 1


description: L2_W143: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ash2l knockdown (T0911), replicate 1


description: L2_W138: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp574 knockdown (T0906), replicate 1


description: L2_W141: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0909), replicate 1


description: L2_W139: SPAR-seq of 108 multi-exon gene regions in N2A cells, Celf6 knockdown (T0907), replicate 1


description: L2_W158: SPAR-seq of 108 multi-exon gene regions in N2A cells, Arrdc1 knockdown (T0926), replicate 1


description: L2_W145: SPAR-seq of 108 multi-exon gene regions in N2A cells, Arrb2 knockdown (T0913), replicate 1


description: L2_W137: SPAR-seq of 108 multi-exon gene regions in N2A cells, Bend3 knockdown (T0905), replicate 1


description: L2_W135: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0903), replicate 1


description: L2_W136: SPAR-seq of 108 multi-exon gene regions in N2A cells, Klhdc4 knockdown (T0904), replicate 1


description: L2_W131: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp825 knockdown (T0899), replicate 1


description: L2_W132: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp646 knockdown (T0900), replicate 1


description: L2_W133: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrnp48 knockdown (T0901), replicate 1


description: L2_W134: SPAR-seq of 108 multi-exon gene regions in N2A cells, Asf1b knockdown (T0902), replicate 1


description: L2_W130: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zmym6 knockdown (T0898), replicate 1


description: L2_W128: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ncapd3 knockdown (T0896), replicate 1


description: L2_W127: SPAR-seq of 108 multi-exon gene regions in N2A cells, Arid5b knockdown (T0895), replicate 1


description: L2_W124: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cpsf7 knockdown (T0892), replicate 1


description: L2_W123: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0891), replicate 1


description: L2_W126: SPAR-seq of 108 multi-exon gene regions in N2A cells, Arid2 knockdown (T0894), replicate 1


description: L2_W125: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ddx39b knockdown (T0893), replicate 1


description: L2_W120: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cobra1 knockdown (T0888), replicate 1


description: L2_W121: SPAR-seq of 108 multi-exon gene regions in N2A cells, Banf1 knockdown (T0889), replicate 1


description: L2_W122: SPAR-seq of 108 multi-exon gene regions in N2A cells, Actr5 knockdown (T0890), replicate 1


description: L2_W119: SPAR-seq of 108 multi-exon gene regions in N2A cells, Adarb2 knockdown (T0887), replicate 1


description: L2_W118: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snd1 knockdown (T0886), replicate 1


description: L2_W116: SPAR-seq of 108 multi-exon gene regions in N2A cells, Arrdc4 knockdown (T0884), replicate 1


description: L2_W117: SPAR-seq of 108 multi-exon gene regions in N2A cells, Adarb1 knockdown (T0885), replicate 1


description: L2_W114: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp868 knockdown (T0882), replicate 1


description: L2_W113: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mau2 knockdown (T0881), replicate 1


description: L2_W115: SPAR-seq of 108 multi-exon gene regions in N2A cells, Anks1 knockdown (T0883), replicate 1


description: L2_W112: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sun2 knockdown (T0880), replicate 1


description: L2_W109: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pif1 knockdown (T0877), replicate 1


description: L2_W108: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cwc22 knockdown (T0876), replicate 1


description: L2_W110: SPAR-seq of 108 multi-exon gene regions in N2A cells, Csdc2 knockdown (T0878), replicate 1


description: L2_W129: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ncaph knockdown (T0897), replicate 1


description: L2_W107: SPAR-seq of 108 multi-exon gene regions in N2A cells, Clp1 knockdown (T0875), replicate 1


description: L2_W104: SPAR-seq of 108 multi-exon gene regions in N2A cells, Bbx knockdown (T0872), replicate 1


description: L2_W106: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3hav1l knockdown (T0874), replicate 1


description: L2_W105: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3h11a knockdown (T0873), replicate 1


description: L2_W103: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pstk knockdown (T0871), replicate 1


description: L2_W102: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dus3l knockdown (T0870), replicate 1


description: L2_W101: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrnp35 knockdown (T0869), replicate 1


description: L2_W098: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp809 knockdown (T0866), replicate 1


description: L2_W099: SPAR-seq of 108 multi-exon gene regions in N2A cells, Adam5 knockdown (T0867), replicate 1


description: L2_W100: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ino80e knockdown (T0868), replicate 1


description: L2_W094: SPAR-seq of 108 multi-exon gene regions in N2A cells, Apitd1 knockdown (T0862), replicate 1


description: L2_W097: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0865), replicate 1


description: L2_W095: SPAR-seq of 108 multi-exon gene regions in N2A cells, Celf5 knockdown (T0863), replicate 1


description: L2_W093: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zcrb1 knockdown (T0861), replicate 1


description: L2_W092: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nkap knockdown (T0860), replicate 1


description: L2_W111: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gpank1 knockdown (T0879), replicate 1


description: L2_W090: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf23 knockdown (T0858), replicate 1


description: L2_W089: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3h15 knockdown (T0857), replicate 1


description: L2_W086: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp593 knockdown (T0854), replicate 1


description: L2_W087: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3h6 knockdown (T0855), replicate 1


description: L2_W088: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ska1 knockdown (T0856), replicate 1


description: L2_W085: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tspyl4 knockdown (T0853), replicate 1


description: L2_W084: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf14 knockdown (T0852), replicate 1


description: L2_W083: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smchd1 knockdown (T0851), replicate 1


description: L2_W081: SPAR-seq of 108 multi-exon gene regions in N2A cells, Spty2d1 knockdown (T0849), replicate 1


description: L2_W080: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zcchc17 knockdown (T0848), replicate 1


description: L2_W082: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zcchc12 knockdown (T0850), replicate 1


description: L2_W079: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nsun6 knockdown (T0847), replicate 1


description: L2_W078: SPAR-seq of 108 multi-exon gene regions in N2A cells, Isy1 knockdown (T0846), replicate 1


description: L2_W076: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zmat5 knockdown (T0844), replicate 1


description: L2_W096: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0864), replicate 1


description: L2_W073: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gpatch4 knockdown (T0841), replicate 1


description: L2_W074: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zkscan17 knockdown (T0842), replicate 1


description: L2_W077: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp566 knockdown (T0845), replicate 1


description: L2_W071: SPAR-seq of 108 multi-exon gene regions in N2A cells, Skiv2l2 knockdown (T0839), replicate 1


description: L2_W070: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp672 knockdown (T0838), replicate 1


description: L2_W075: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rnf181 knockdown (T0843), replicate 1


description: L2_W069: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3h13 knockdown (T0837), replicate 1


description: L2_W066: SPAR-seq of 108 multi-exon gene regions in N2A cells, 2610305D13Rik knockdown (T0834), replicate 1


description: L2_W068: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpm knockdown (T0836), replicate 1


description: L2_W067: SPAR-seq of 108 multi-exon gene regions in N2A cells, 2410141K09Rik knockdown (T0835), replicate 1


description: L2_W065: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp954 knockdown (T0833), replicate 1


description: L2_W091: SPAR-seq of 108 multi-exon gene regions in N2A cells, 2810432D09Rik knockdown (T0859), replicate 1


description: L2_W063: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dscc1 knockdown (T0831), replicate 1


description: L2_W060: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rnpc3 knockdown (T0828), replicate 1


description: L2_W061: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppwd1 knockdown (T0829), replicate 1


description: L2_W062: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf6 knockdown (T0830), replicate 1


description: L2_W059: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cdkn2aip knockdown (T0827), replicate 1


description: L2_W058: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm42 knockdown (T0826), replicate 1


description: L2_W057: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0825), replicate 1


description: L2_W072: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zcchc7 knockdown (T0840), replicate 1


description: L2_W056: SPAR-seq of 108 multi-exon gene regions in N2A cells, Spc24 knockdown (T0824), replicate 1


description: L2_W054: SPAR-seq of 108 multi-exon gene regions in N2A cells, N6amt2 knockdown (T0822), replicate 1


description: L2_W055: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hormad1 knockdown (T0823), replicate 1


description: L2_W052: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpa3 knockdown (T0820), replicate 1


description: L2_W053: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp799 knockdown (T0821), replicate 1


description: L2_W051: SPAR-seq of 108 multi-exon gene regions in N2A cells, N6amt1 knockdown (T0819), replicate 1


description: L2_W049: SPAR-seq of 108 multi-exon gene regions in N2A cells, Specc1l knockdown (T0817), replicate 1


description: L2_W047: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tox4 knockdown (T0815), replicate 1


description: L2_W048: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2f knockdown (T0816), replicate 1


description: L2_W064: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpf knockdown (T0832), replicate 1


description: L2_W044: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm4b knockdown (T0812), replicate 1


description: L2_W046: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrnp25 knockdown (T0814), replicate 1


description: L2_W043: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pabpc6 knockdown (T0811), replicate 1


description: L2_W041: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sohlh2 knockdown (T0809), replicate 1


description: L2_W042: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbmx2 knockdown (T0810), replicate 1


description: L2_W036: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cdca5 knockdown (T0804), replicate 1


description: L2_W035: SPAR-seq of 108 multi-exon gene regions in N2A cells, Swi5 knockdown (T0803), replicate 1


description: L2_W040: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm12b knockdown (T0808), replicate 1


description: L2_W037: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrpll knockdown (T0805), replicate 1


description: L2_W038: SPAR-seq of 108 multi-exon gene regions in N2A cells, Wdr77 knockdown (T0806), replicate 1


description: L2_W033: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sltm knockdown (T0801), replicate 1


description: L2_W034: SPAR-seq of 108 multi-exon gene regions in N2A cells, Larp6 knockdown (T0802), replicate 1


description: L2_W031: SPAR-seq of 108 multi-exon gene regions in N2A cells, Toe1 knockdown (T0799), replicate 1


description: L2_W032: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ccdc99 knockdown (T0800), replicate 1


description: L2_W050: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mis12 knockdown (T0818), replicate 1


description: L2_W030: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hepacam knockdown (T0798), replicate 1


description: L2_W028: SPAR-seq of 108 multi-exon gene regions in N2A cells, 2610101N10Rik knockdown (T0796), replicate 1


description: L2_W027: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0795), replicate 1


description: L2_W025: SPAR-seq of 108 multi-exon gene regions in N2A cells, Noa1 knockdown (T0793), replicate 1


description: L2_W024: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpq knockdown (T0792), replicate 1


description: L2_W026: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nsl1 knockdown (T0794), replicate 1


description: L2_W022: SPAR-seq of 108 multi-exon gene regions in N2A cells, Paf1 knockdown (T0790), replicate 1


description: L2_W019: SPAR-seq of 108 multi-exon gene regions in N2A cells, Chd8 knockdown (T0787), replicate 1


description: L2_W039: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0807), replicate 1


description: L2_W045: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0813), replicate 1


description: L2_W021: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp710 knockdown (T0789), replicate 1


description: L2_W020: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ddx17 knockdown (T0788), replicate 1


description: L2_W018: SPAR-seq of 108 multi-exon gene regions in N2A cells, Setd5 knockdown (T0786), replicate 1


description: L2_W016: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mphosph8 knockdown (T0784), replicate 1


description: L2_W013: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nup43 knockdown (T0781), replicate 1


description: L2_W014: SPAR-seq of 108 multi-exon gene regions in N2A cells, Stox2 knockdown (T0782), replicate 1


description: L2_W029: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rcc2 knockdown (T0797), replicate 1


description: L2_W015: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp688 knockdown (T0783), replicate 1


description: L2_W011: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zmat2 knockdown (T0779), replicate 1


description: L2_W010: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mael knockdown (T0778), replicate 1


description: L2_W012: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ncapd2 knockdown (T0780), replicate 1


description: L2_W009: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm25 knockdown (T0777), replicate 1


description: L2_W008: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp647 knockdown (T0776), replicate 1


description: L2_W007: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zbtb8a knockdown (T0775), replicate 1


description: L2_W005: SPAR-seq of 108 multi-exon gene regions in N2A cells, 2610027L16Rik knockdown (T0773), replicate 1


description: L2_W023: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srek1ip1 knockdown (T0791), replicate 1


description: L2_W004: SPAR-seq of 108 multi-exon gene regions in N2A cells, Glyr1 knockdown (T0772), replicate 1


description: L2_W003: SPAR-seq of 108 multi-exon gene regions in N2A cells, Puf60 knockdown (T0771), replicate 1


description: L2_W002: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tut1 knockdown (T0770), replicate 1


description: L1_W767: SPAR-seq of 108 multi-exon gene regions in N2A cells, 0610007P08Rik knockdown (T0767), replicate 1


description: L2_W017: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ddx26b knockdown (T0785), replicate 1


description: L1_W766: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srpk1 knockdown (T0766), replicate 1


description: L1_W764: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zcchc18 knockdown (T0764), replicate 1


description: L1_W768: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0768), replicate 1


description: L1_W765: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mapk1 knockdown (T0765), replicate 1


description: L1_W762: SPAR-seq of 108 multi-exon gene regions in N2A cells, Syce2 knockdown (T0762), replicate 1


description: L1_W763: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ftsjd2 knockdown (T0763), replicate 1


description: L1_W758: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sarnp knockdown (T0758), replicate 1


description: L1_W759: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zwilch knockdown (T0759), replicate 1


description: L1_W755: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ralyl knockdown (T0755), replicate 1


description: L1_W756: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thap3 knockdown (T0756), replicate 1


description: L1_W761: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ints12 knockdown (T0761), replicate 1


description: L2_W001: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0769), replicate 1


description: L1_W753: SPAR-seq of 108 multi-exon gene regions in N2A cells, Lrwd1 knockdown (T0753), replicate 1


description: L1_W754: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gsg2 knockdown (T0754), replicate 1


description: L1_W748: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gsk3b knockdown (T0748), replicate 1


description: L1_W750: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mfsd11 knockdown (T0750), replicate 1


description: L1_W751: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf38a knockdown (T0751), replicate 1


description: L1_W743: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm15b knockdown (T0743), replicate 1


description: L1_W745: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cir1 knockdown (T0745), replicate 1


description: L1_W752: SPAR-seq of 108 multi-exon gene regions in N2A cells, Raver1 knockdown (T0752), replicate 1


description: L1_W749: SPAR-seq of 108 multi-exon gene regions in N2A cells, Akt1 knockdown (T0749), replicate 1


description: L1_W747: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rnf113a2 knockdown (T0747), replicate 1


description: L1_W739: SPAR-seq of 108 multi-exon gene regions in N2A cells, 2310036O22Rik knockdown (T0739), replicate 1


description: L1_W741: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm43 knockdown (T0741), replicate 1


description: L1_W760: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mak16 knockdown (T0760), replicate 1


description: L1_W740: SPAR-seq of 108 multi-exon gene regions in N2A cells, Plk1 knockdown (T0740), replicate 1


description: L1_W744: SPAR-seq of 108 multi-exon gene regions in N2A cells, Magohb knockdown (T0744), replicate 1


description: L1_W746: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pbrm1 knockdown (T0746), replicate 1


description: L1_W736: SPAR-seq of 108 multi-exon gene regions in N2A cells, Wdr83 knockdown (T0736), replicate 1


description: L1_W737: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thoc7 knockdown (T0737), replicate 1


description: L1_W757: SPAR-seq of 108 multi-exon gene regions in N2A cells, Arrb1 knockdown (T0757), replicate 1


description: L2_W006: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp623 knockdown (T0774), replicate 1


description: L1_W730: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nip7 knockdown (T0730), replicate 1


description: L1_W729: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0729), replicate 1


description: L1_W728: SPAR-seq of 108 multi-exon gene regions in N2A cells, Iws1 knockdown (T0728), replicate 1


description: L1_W734: SPAR-seq of 108 multi-exon gene regions in N2A cells, 2310004I24Rik knockdown (T0734), replicate 1


description: L1_W738: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sf3b5 knockdown (T0738), replicate 1


description: L1_W725: SPAR-seq of 108 multi-exon gene regions in N2A cells, Meaf6 knockdown (T0725), replicate 1


description: L1_W742: SPAR-seq of 108 multi-exon gene regions in N2A cells, Raf1 knockdown (T0742), replicate 1


description: L1_W720: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pik3r1 knockdown (T0720), replicate 1


description: L1_W722: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dsn1 knockdown (T0722), replicate 1


description: L1_W721: SPAR-seq of 108 multi-exon gene regions in N2A cells, Plk3 knockdown (T0721), replicate 1


description: L1_W733: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf4b knockdown (T0733), replicate 1


description: L1_W731: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rrp7a knockdown (T0731), replicate 1


description: L1_W735: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mapk3 knockdown (T0735), replicate 1


description: L1_W719: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tdrd12 knockdown (T0719), replicate 1


description: L1_W732: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mcmbp knockdown (T0732), replicate 1


description: L1_W711: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0711), replicate 1


description: L1_W723: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cwc25 knockdown (T0723), replicate 1


description: L1_W709: SPAR-seq of 108 multi-exon gene regions in N2A cells, Calcoco1 knockdown (T0709), replicate 1


description: L1_W718: SPAR-seq of 108 multi-exon gene regions in N2A cells, Map2k2 knockdown (T0718), replicate 1


description: L1_W706: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rrp8 knockdown (T0706), replicate 1


description: L1_W726: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rab43 knockdown (T0726), replicate 1


description: L1_W712: SPAR-seq of 108 multi-exon gene regions in N2A cells, Map2k6 knockdown (T0712), replicate 1


description: L1_W715: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dnajc17 knockdown (T0715), replicate 1


description: L1_W704: SPAR-seq of 108 multi-exon gene regions in N2A cells, Map2k3 knockdown (T0704), replicate 1


description: L1_W702: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf38b knockdown (T0702), replicate 1


description: L1_W717: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0717), replicate 1


description: L1_W697: SPAR-seq of 108 multi-exon gene regions in N2A cells, Larp1b knockdown (T0697), replicate 1


description: L1_W713: SPAR-seq of 108 multi-exon gene regions in N2A cells, 1500010J02Rik knockdown (T0713), replicate 1


description: L1_W724: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbpms2 knockdown (T0724), replicate 1


description: L1_W695: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prkra knockdown (T0695), replicate 1


description: L1_W716: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp2cb knockdown (T0716), replicate 1


description: L1_W727: SPAR-seq of 108 multi-exon gene regions in N2A cells, 0610009D07Rik knockdown (T0727), replicate 1


description: L1_W708: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cwc15 knockdown (T0708), replicate 1


description: L1_W692: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif2ak2 knockdown (T0692), replicate 1


description: L1_W707: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tjp2 knockdown (T0707), replicate 1


description: L1_W703: SPAR-seq of 108 multi-exon gene regions in N2A cells, 2310079F23Rik knockdown (T0703), replicate 1


description: L1_W690: SPAR-seq of 108 multi-exon gene regions in N2A cells, Telo2 knockdown (T0690), replicate 1


description: L1_W714: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm19 knockdown (T0714), replicate 1


description: L1_W705: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rsrc1 knockdown (T0705), replicate 1


description: L1_W694: SPAR-seq of 108 multi-exon gene regions in N2A cells, Seh1l knockdown (T0694), replicate 1


description: L1_W688: SPAR-seq of 108 multi-exon gene regions in N2A cells, Suds3 knockdown (T0688), replicate 1


description: L1_W710: SPAR-seq of 108 multi-exon gene regions in N2A cells, Esco2 knockdown (T0710), replicate 1


description: L1_W701: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrnp27 knockdown (T0701), replicate 1


description: L1_W698: SPAR-seq of 108 multi-exon gene regions in N2A cells, Unkl knockdown (T0698), replicate 1


description: L1_W700: SPAR-seq of 108 multi-exon gene regions in N2A cells, Obfc1 knockdown (T0700), replicate 1


description: L1_W699: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0699), replicate 1


description: L1_W693: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srpk2 knockdown (T0693), replicate 1


description: L1_W687: SPAR-seq of 108 multi-exon gene regions in N2A cells, Leprel4 knockdown (T0687), replicate 1


description: L1_W682: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp2ca knockdown (T0682), replicate 1


description: L1_W686: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tctex1d2 knockdown (T0686), replicate 1


description: L1_W678: SPAR-seq of 108 multi-exon gene regions in N2A cells, Map2k1 knockdown (T0678), replicate 1


description: L1_W675: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nsmce2 knockdown (T0675), replicate 1


description: L1_W696: SPAR-seq of 108 multi-exon gene regions in N2A cells, Atr knockdown (T0696), replicate 1


description: L1_W685: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm26 knockdown (T0685), replicate 1


description: L1_W676: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pno1 knockdown (T0676), replicate 1


description: L1_W689: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kti12 knockdown (T0689), replicate 1


description: L1_W671: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zkscan5 knockdown (T0671), replicate 1


description: L1_W681: SPAR-seq of 108 multi-exon gene regions in N2A cells, Fam33a knockdown (T0681), replicate 1


description: L1_W677: SPAR-seq of 108 multi-exon gene regions in N2A cells, Esrp1 knockdown (T0677), replicate 1


description: L1_W669: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cdk4 knockdown (T0669), replicate 1


description: L1_W679: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp830 knockdown (T0679), replicate 1


description: L1_W670: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2b knockdown (T0670), replicate 1


description: L1_W680: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srpk3 knockdown (T0680), replicate 1


description: L1_W665: SPAR-seq of 108 multi-exon gene regions in N2A cells, Csnk1a1 knockdown (T0665), replicate 1


description: L1_W674: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srrm4 knockdown (T0674), replicate 1


description: L1_W684: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smndc1 knockdown (T0684), replicate 1


description: L1_W667: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mknk2 knockdown (T0667), replicate 1


description: L1_W668: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ubtf knockdown (T0668), replicate 1


description: L1_W661: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dapk3 knockdown (T0661), replicate 1


description: L1_W683: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpp knockdown (T0683), replicate 1


description: L1_W691: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mapk14 knockdown (T0691), replicate 1


description: L1_W672: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0672), replicate 1


description: L1_W664: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zbtb7a knockdown (T0664), replicate 1


description: L1_W663: SPAR-seq of 108 multi-exon gene regions in N2A cells, Patz1 knockdown (T0663), replicate 1


description: L1_W659: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cdk12 knockdown (T0659), replicate 1


description: L1_W673: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0673), replicate 1


description: L1_W662: SPAR-seq of 108 multi-exon gene regions in N2A cells, Whsc1 knockdown (T0662), replicate 1


description: L1_W658: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ttf2 knockdown (T0658), replicate 1


description: L1_W666: SPAR-seq of 108 multi-exon gene regions in N2A cells, Taf1 knockdown (T0666), replicate 1


description: L1_W653: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2g1 knockdown (T0653), replicate 1


description: L1_W660: SPAR-seq of 108 multi-exon gene regions in N2A cells, Atm knockdown (T0660), replicate 1


description: L1_W657: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cdk13 knockdown (T0657), replicate 1


description: L1_W654: SPAR-seq of 108 multi-exon gene regions in N2A cells, Akap1 knockdown (T0654), replicate 1


description: L1_W655: SPAR-seq of 108 multi-exon gene regions in N2A cells, Xpo1 knockdown (T0655), replicate 1


description: L1_W646: SPAR-seq of 108 multi-exon gene regions in N2A cells, Aurkb knockdown (T0646), replicate 1


description: L1_W640: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pik3ca knockdown (T0640), replicate 1


description: L1_W656: SPAR-seq of 108 multi-exon gene regions in N2A cells, Whsc1l1 knockdown (T0656), replicate 1


description: L1_W651: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dgkq knockdown (T0651), replicate 1


description: L1_W635: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp36l1 knockdown (T0635), replicate 1


description: L1_W638: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2m knockdown (T0638), replicate 1


description: L1_W637: SPAR-seq of 108 multi-exon gene regions in N2A cells, Brwd1 knockdown (T0637), replicate 1


description: L1_W649: SPAR-seq of 108 multi-exon gene regions in N2A cells, Xrcc5 knockdown (T0649), replicate 1


description: L1_W633: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0633), replicate 1


description: L1_W650: SPAR-seq of 108 multi-exon gene regions in N2A cells, Uhrf1 knockdown (T0650), replicate 1


description: L1_W647: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp422 knockdown (T0647), replicate 1


description: L1_W629: SPAR-seq of 108 multi-exon gene regions in N2A cells, Clk3 knockdown (T0629), replicate 1


description: L1_W632: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pfkfb3 knockdown (T0632), replicate 1


description: L1_W634: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zw10 knockdown (T0634), replicate 1


description: L1_W630: SPAR-seq of 108 multi-exon gene regions in N2A cells, Trim33 knockdown (T0630), replicate 1


description: L1_W648: SPAR-seq of 108 multi-exon gene regions in N2A cells, Trim24 knockdown (T0648), replicate 1


description: L1_W631: SPAR-seq of 108 multi-exon gene regions in N2A cells, Traf6 knockdown (T0631), replicate 1


description: L1_W636: SPAR-seq of 108 multi-exon gene regions in N2A cells, Uhrf2 knockdown (T0636), replicate 1


description: L1_W641: SPAR-seq of 108 multi-exon gene regions in N2A cells, Fn3krp knockdown (T0641), replicate 1


description: L1_W628: SPAR-seq of 108 multi-exon gene regions in N2A cells, Aurkc knockdown (T0628), replicate 1


description: L1_W643: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zeb2 knockdown (T0643), replicate 1


description: L1_W642: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2v2 knockdown (T0642), replicate 1


description: L1_W652: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp7 knockdown (T0652), replicate 1


description: L1_W627: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp523 knockdown (T0627), replicate 1


description: L1_W644: SPAR-seq of 108 multi-exon gene regions in N2A cells, Exosc10 knockdown (T0644), replicate 1


description: L1_W645: SPAR-seq of 108 multi-exon gene regions in N2A cells, Yy1 knockdown (T0645), replicate 1


description: L1_W639: SPAR-seq of 108 multi-exon gene regions in N2A cells, Uhmk1 knockdown (T0639), replicate 1


description: L1_W623: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zmynd11 knockdown (T0623), replicate 1


description: L1_W621: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0621), replicate 1


description: L1_W625: SPAR-seq of 108 multi-exon gene regions in N2A cells, Chek1 knockdown (T0625), replicate 1


description: L1_W626: SPAR-seq of 108 multi-exon gene regions in N2A cells, Brd2 knockdown (T0626), replicate 1


description: L1_W619: SPAR-seq of 108 multi-exon gene regions in N2A cells, Akt2 knockdown (T0619), replicate 1


description: L1_W610: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zbtb17 knockdown (T0610), replicate 1


description: L1_W620: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2d2 knockdown (T0620), replicate 1


description: L1_W617: SPAR-seq of 108 multi-exon gene regions in N2A cells, Csnk2a1 knockdown (T0617), replicate 1


description: L1_W618: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tpr knockdown (T0618), replicate 1


description: L1_W612: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zmat3 knockdown (T0612), replicate 1


description: L1_W604: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2c knockdown (T0604), replicate 1


description: L1_W607: SPAR-seq of 108 multi-exon gene regions in N2A cells, Clk2 knockdown (T0607), replicate 1


description: L1_W605: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nek2 knockdown (T0605), replicate 1


description: L1_W611: SPAR-seq of 108 multi-exon gene regions in N2A cells, Clk4 knockdown (T0611), replicate 1


description: L1_W614: SPAR-seq of 108 multi-exon gene regions in N2A cells, Usf2 knockdown (T0614), replicate 1


description: L1_W613: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mknk1 knockdown (T0613), replicate 1


description: L1_W603: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0603), replicate 1


description: L1_W606: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp161 knockdown (T0606), replicate 1


description: L1_W602: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2l6 knockdown (T0602), replicate 1


description: L1_W608: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2r2 knockdown (T0608), replicate 1


description: L1_W599: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2h knockdown (T0599), replicate 1


description: L1_W622: SPAR-seq of 108 multi-exon gene regions in N2A cells, Bub1 knockdown (T0622), replicate 1


description: L1_W601: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2s knockdown (T0601), replicate 1


description: L1_W598: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2e1 knockdown (T0598), replicate 1


description: L1_W616: SPAR-seq of 108 multi-exon gene regions in N2A cells, Akap8 knockdown (T0616), replicate 1


description: L1_W600: SPAR-seq of 108 multi-exon gene regions in N2A cells, Wt1 knockdown (T0600), replicate 1


description: L1_W597: SPAR-seq of 108 multi-exon gene regions in N2A cells, Braf knockdown (T0597), replicate 1


description: L1_W596: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp191 knockdown (T0596), replicate 1


description: L1_W615: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0615), replicate 1


description: L1_W595: SPAR-seq of 108 multi-exon gene regions in N2A cells, Usf1 knockdown (T0595), replicate 1


description: L1_W594: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif4h knockdown (T0594), replicate 1


description: L1_W609: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zic3 knockdown (T0609), replicate 1


description: L1_W592: SPAR-seq of 108 multi-exon gene regions in N2A cells, Uchl5 knockdown (T0592), replicate 1


description: L1_W593: SPAR-seq of 108 multi-exon gene regions in N2A cells, Trim28 knockdown (T0593), replicate 1


description: L1_W585: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zbtb7b knockdown (T0585), replicate 1


description: L1_W583: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp238 knockdown (T0583), replicate 1


description: L1_W624: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tubg1 knockdown (T0624), replicate 1


description: L1_W589: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp41 knockdown (T0589), replicate 1


description: L1_W584: SPAR-seq of 108 multi-exon gene regions in N2A cells, Trp53 knockdown (T0584), replicate 1


description: L1_W588: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfx knockdown (T0588), replicate 1


description: L1_W579: SPAR-seq of 108 multi-exon gene regions in N2A cells, Araf knockdown (T0579), replicate 1


description: L1_W586: SPAR-seq of 108 multi-exon gene regions in N2A cells, Bub1b knockdown (T0586), replicate 1


description: L1_W582: SPAR-seq of 108 multi-exon gene regions in N2A cells, Xrcc1 knockdown (T0582), replicate 1


description: L1_W580: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tnpo1 knockdown (T0580), replicate 1


description: L1_W578: SPAR-seq of 108 multi-exon gene regions in N2A cells, Csnk2a2 knockdown (T0578), replicate 1


description: L1_W591: SPAR-seq of 108 multi-exon gene regions in N2A cells, Usp3 knockdown (T0591), replicate 1


description: L1_W581: SPAR-seq of 108 multi-exon gene regions in N2A cells, Trp53bp1 knockdown (T0581), replicate 1


description: L1_W590: SPAR-seq of 108 multi-exon gene regions in N2A cells, Xbp1 knockdown (T0590), replicate 1


description: L1_W574: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarce1 knockdown (T0574), replicate 1


description: L1_W575: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tfap4 knockdown (T0575), replicate 1


description: L1_W577: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0577), replicate 1


description: L1_W568: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sox9 knockdown (T0568), replicate 1


description: L1_W569: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tdrd7 knockdown (T0569), replicate 1


description: L1_W573: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tardbp knockdown (T0573), replicate 1


description: L1_W571: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tiparp knockdown (T0571), replicate 1


description: L1_W567: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ssrp1 knockdown (T0567), replicate 1


description: L1_W576: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0576), replicate 1


description: L1_W572: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarcd1 knockdown (T0572), replicate 1


description: L1_W570: SPAR-seq of 108 multi-exon gene regions in N2A cells, Taf15 knockdown (T0570), replicate 1


description: L1_W566: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smc4 knockdown (T0566), replicate 1


description: L1_W565: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tinf2 knockdown (T0565), replicate 1


description: L1_W587: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cdk11b knockdown (T0587), replicate 1


description: L1_W564: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smyd2 knockdown (T0564), replicate 1


title: DSB RAFT HEK293T rep2

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description: Replicate 2

library_source: genomic

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
EcoRI/PstI primer was ligated to DSBs sites, so sequenced reads were trimmed from EcorI/PstI primer sequence and low quality/too short sequences by cutadapt v. 3.5 using the following options: --trim-n --times=5 --minimum-length=20 --quality-cutoff=26 --discard-untrimmed --pair-filter=both -g CCGAATTCTCCTTATACTGCAGGGG -G CCGAATTCTCCTTATACTGCAGGGG. This options ensure that read have EcorI/PstI 5' adapter at the any of reads, and thus, contains DSB. All other reads have been eliminated.
At the next step all already trimmed sequences were trimmed from all possible combinations of 5' and/or 3' adapters: -a CCCAAGCTTAAGCGGCCGCAAACX -a GTTTGCGGCCGCTTAAGCTTGGGX -a CCCCTGCAGTATAAGGAGAATTCGGX -g XCCCAAGCTTAAGCGGCCGCAAAC -g XGTTTGCGGCCGCTTAAGCTTGGG -g XCCCCTGCAGTATAAGGAGAATTCGG   -A CCCAAGCTTAAGCGGCCGCAAACX -A GTTTGCGGCCGCTTAAGCTTGGGX -A CCCCTGCAGTATAAGGAGAATTCGGX   -G XCCCAAGCTTAAGCGGCCGCAAAC -G XGTTTGCGGCCGCTTAAGCTTGGG -G XCCCCTGCAGTATAAGGAGAATTCGG
At the last adapter removal step we removed all incomplete 5' and/or 3' adapters: -g file:5adapters.fa -G file:5adapters.fa -a file:3adapters.fa -A file:3adapters.fa -a CCCCTGCAGTATAAGGAGAATTCGG -A CCCCTGCAGTATAAGGAGAATTCGG.
Trimmed reads were mapped to hg19p13 by bwa 0.7.17-r1188 using the mem algorithm. All non-aligned reads were removed from resulting alignment file by samtools 1.14 with -F 4 option.
Mapping and alignment results were converted to resulting tables using samtools 1.14 and ad hoc Perl scripts.
bedtools intersectBed 2.29.1 was applied to find and remove exact intersections (parameters -v -f 1.0) between each replicate and low complexity and/or repeat regions from the DFAM database. At the next step, intersections between replicates were found by intersectBed again. In-house Perl scripts were used to convert the resulting file to bedGraph format and to add to it sequences by coordinates from the reference genome. BEDOPS 2.4.40 bedmap, partition as well as Linux awk were used to merge the bedGraph genome tracks with intersected segments.
All data processing steps were performed for H.sapiens hg38p12 build too.
Assembly: Homo Sapiens hg19/GRCh37.p13 genome with included to chr14 from address 1 Human ribosomal DNA U13369
Assembly: Homo Sapiens hg38/GRCh38.p12 genome with included to chr14 from address 1 Human ribosomal DNA U13369
Supplementary files format and content: Tab-delimited text file include the following features of each mapping: begin, end, length, coverage, number of reads, sequence. bedGraph files for intersection are supplied too.
Library strategy: DNA-seq

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK 293 cells were seeded in 10 cm culture plates 1-2 days before experiment in DMEM containing 10% FBS, and used at approximately 60-80% confluency.

extract_protocol:
About 6 millions of HEK293T cells in 2 ml of culture medium were pelleted by centrifugation at 2000 rpm, resuspended in 0.3 ml of the same medium, gently mixed at 42°C with an equal volume of a 1% agarose L (LKB) in PBS solution, and distributed on a mold containing 100-microliters wells. The mold was placed on ice for 2-5 min, covered with parafilm. The agarose plugs were then placed in Petri dishes with 5 ml of solution containing 0.5 M EDTA (pH 9.5), 1% sodium laurylsarcosine, and 1-2 mg of proteinase K solution per ml for 40-48 hr at 50°C, and stored at 4°C in the same solution. Each DNA-agarose plus usually contained about 15 microgramms of DNA corresponding to about 1 millions of cells.  To test the quality of isolated DNA the fractionation in the pulsed-field gels. Portions of the original agarose-DNA plugs (5-50 microliters) containing 1-10 microgramms of DNA were used for electrophoresis without any restriction enzyme digestion. The DNA samples were run in 0.8% agarose gels on an LKB Pulsaphor system using hexagonal electrode and switching times of 25 or 450 sec.  For elution of DNA preparations the fractionation in 1% agarose conventional mini-gel was performed. One-half of DNA-agarose plug was washed in 1xTE 3 times (for 15 min each) following by 3 times washing in the same solution containing 17.4 microgramms/ml PMSF in ethanol. After fractionation in the mini-gel, the ethidium-bromide stained DNA band was excised and electoeluted inside the dialysis cellulose membrane bag. After overnight dialysis without stirring against 1 liter of 0.01 x TE at 4°C, the DNA was concentrated with PEG (4°C) and redialyzed.  Library preparation:  About 1.5 microgramms of isolated DNA, forum DNA, (see above) was ligated with 70 ng of double-stranded oligonucleotide containing EcoRI and PstI sites (25 bp long 5’-phosphorylated 5’ pCCCCTGCAGTATAAGGAGAATTCGGG 3’ oligonucleotide annealed with 26 bp long 5’ biotinylated 5’ bio-CCGAATTCTCCTTATACTGCAGGGG 3’ oligonucleotide) in 150 microliters of solution containing 0.1 M NaCl, 50 mM Tris HCl (pH 7.4), 8 mM MgCl2, 9 mM 2-mercaptoethanol, 7 microM ATP, 7.5 % PEG, and 40 units of T4 DNA ligase at 20°C for 16 hr. After heating at 65°C for 10 min the DNA preparation was digested with Sau3A enzyme to shorten the forum domain to the termini attached to the ligated oligonicleotide. The selection of such termini was performed in 0.5 ml eppendorf tubes using 300 microliters of suspension containing streptavidin magnespere paramagnetic particles, SA-PMP (Promega) according to the manufacturer's recommendations. After extensive washing with 0.5xSSC removing DNA fragments corresponding to internal parts of forum domains, the forum termini (FT) DNA preparation was eluted from the SA-PMP using digestion with EcoRI enzyme in final volume of 50?mictolitres (double-stranded FT). The FT were then ligated with 100x molar excess of double-stranded Sau3A adaptor (5’-phosphorylated 5’ pGATCGTTTGCGGCCGCTTAAGCTTGGG 3’ oligonucleotide annealed with 5’ CCCAAGCTTAAGCGGCCGCAAAC 3’ oligonucleotide). In some experiments (FT) DNA preparation was eluted from the SA-PMP using heating by incubation at 100°C for 3 min in 50 microliters of 0.01xTE (single-stranded FT). Before heating the FT preparation was ligated with100x molar excess of double-stranded Sau3A adaptor in suspension with SA-PMP (see above). Both final DNA samples (double-stranded FT or single-stranded FT) were used for PCR amplifications. 40 cycle PCR amplification in 30 microlitersl of a solution containing 67 mM Tris-HCl (pH 8.4); 6 mM MgCl2; 10 mM 2-mercaptoethanol; 16.6 mM ammonium sulfate; 6.7 microM EDTA; 5 microg/ml BSA; 1 mM dNTPs; 1 microg of primer corresponding to Sau3A adaptor (5’ CCCAAGCTTAAGCGGCCGCAAAC 3’); 1 microg of primer corresponding to biotinilated oligonucleotide (5’ CCGAATTCTCCTTATACTGCAGGGG 3’) and 1 u of Taq polymerase was performed using Eppendorf Mastercycler Personal. Amplification conditions were 90°C for melting, 65°C for annealing and 72°C for extension, for 1 min each.
Both final DNA samples (double-stranded FT or single-stranded FT) were used for PCR amplifications. 40 cycle PCR amplification in 30 microlitersl of a solution containing 67 mM Tris-HCl (pH 8.4); 6 mM MgCl2; 10 mM 2-mercaptoethanol; 16.6 mM ammonium sulfate; 6.7 microM EDTA; 5 microg/ml BSA; 1 mM dNTPs; 1 microg of primer corresponding to Sau3A adaptor (5’ CCCAAGCTTAAGCGGCCGCAAAC 3’); 1 microg of primer corresponding to biotinilated oligonucleotide (5’ CCGAATTCTCCTTATACTGCAGGGG 3’) and 1 u of Taq polymerase was performed using Eppendorf Mastercycler Personal. Amplification conditions were 90°C for melting, 65°C for annealing and 72°C for extension, for 1 min each. Deep sequencing of libraries were performed using HiSeq1500 (Illumina) in Paired-End mode using 100-nt long reads.

treatment_protocol: The cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemente+B29d with 10% FBS penicillin (100 U/ml), streptomycin (100ug/ml) and L-glutamine (4 mM).

value: kidney

tag: age

value: embryo

tag: genotype

value: wild type


title: BLA, ER, biol rep 1

city: Cincinnati

first: Marissa

middle: Ann

last: Smail

state: Ohio

address: 4227 Allendorf Drive, Apt 1

department: Pharmacology and Systems Physiology

country: USA

institute: University of Cincinnati

data_processing:
Reads were aligned using Hisat2 aligner in R 4.0
Counts were generated using Rsubread (R.3.8)
Counts were normalized using Deseq2
Assembly: RGSC7.2
Supplementary files format and content: excel files include matrix of normalized counts for each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: brain

extract_protocol:
RNA was harvested using RNA Mini kits kits (Qiagen). ~300ng of total RNA (which contained equal representation from 10 animals' RNA samples) was used for the construction of sequencing libraries.  Samples underwent polyA RNA isolation using the NEBNext Poly(A) mRNA Magnetic Isolation Module prior to library preparation.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra Directional RNA Library prep kit following manufacturer's protocols.

treatment_protocol: Adult male Sprague-Dawley rats were subjected to standard housing, environmentally enriched, or enrichment removed conditions.  Brains were collected and micropunches of the basolateral amygdala (BLA) were used for subseqent analysis.  Proportional samples from 10 rats per group were pooled for sequencing, yielding one biological replicate for each condition.

value: brain

tag: treatment

value: enrichment removed


title: BLA, EE, biol rep 1

value: environmentally enriched


description: L1_W559: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tia1 knockdown (T0559), replicate 1


description: L1_W561: SPAR-seq of 108 multi-exon gene regions in N2A cells, Top2a knockdown (T0561), replicate 1


description: L1_W563: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcf3 knockdown (T0563), replicate 1


title: DSB RAFT HEK293T rep1

description: Replicate 1


title: BLA, ER, biol rep 6

extract_protocol:
RNA was harvested using RNAqueous-Micro isolation kits (Qiagen). ~400ng of total RNA was used for the construction of sequencing libraries.  Samples underwent polyA RNA isolation using the NEBNext Poly(A) mRNA Magnetic Isolation Module prior to library preparation.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra Directional RNA Library prep kit following manufacturer's protocols.

treatment_protocol: Adult male Sprague-Dawley rats were subjected to standard housing, environmentally enriched, or enrichment removed conditions.  Brains were collected and micropunches of the basolateral amygdala (BLA) were used for subseqent analysis.


title: BLA, SH, biol rep 1

value: standard housing


description: L1_W558: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srf knockdown (T0558), replicate 1


description: L1_W556: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tfpt knockdown (T0556), replicate 1


title: BLA, ER, biol rep 4


title: BLA, ER, biol rep 3


title: BLA, ER, biol rep 2


title: BLA, EE, biol rep 6


title: BLA, EE, biol rep 5


description: L1_W552: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tbl1x knockdown (T0552), replicate 1


description: L1_W553: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarcd2 knockdown (T0553), replicate 1


description: L1_W557: SPAR-seq of 108 multi-exon gene regions in N2A cells, Syn1 knockdown (T0557), replicate 1


description: L1_W551: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrpn knockdown (T0551), replicate 1


description: L1_W554: SPAR-seq of 108 multi-exon gene regions in N2A cells, Supt6h knockdown (T0554), replicate 1


title: BLA, EE, biol rep 3


description: L1_W562: SPAR-seq of 108 multi-exon gene regions in N2A cells, Synj2 knockdown (T0562), replicate 1


title: BLA, ER, biol rep 1


title: BLA, EE, biol rep 4


description: L1_W555: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smn1 knockdown (T0555), replicate 1


description: L1_W560: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sept2 knockdown (T0560), replicate 1


description: L1_W549: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tada3 knockdown (T0549), replicate 1


description: L1_W550: SPAR-seq of 108 multi-exon gene regions in N2A cells, Terf2 knockdown (T0550), replicate 1


description: L1_W547: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcf12 knockdown (T0547), replicate 1


title: BLA, EE, biol rep 2


title: BLA, SH, biol rep 6


title: BLA, EE, biol rep 1


description: L1_W548: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tax1bp1 knockdown (T0548), replicate 1


title: BLA, ER, biol rep 5


description: L1_W545: SPAR-seq of 108 multi-exon gene regions in N2A cells, Setd7 knockdown (T0545), replicate 1


description: L1_W546: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sox4 knockdown (T0546), replicate 1


title: BLA, SH, biol rep 5


description: L1_W543: SPAR-seq of 108 multi-exon gene regions in N2A cells, Suv39h1 knockdown (T0543), replicate 1


title: BLA, SH, biol rep 2


title: BLA, SH, biol rep 3


title: BLA, SH, biol rep 4


title: BLA, SH, biol rep 1


description: L1_W542: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tef knockdown (T0542), replicate 1


description: L1_W541: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tbx3 knockdown (T0541), replicate 1


description: L1_W540: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srrm2 knockdown (T0540), replicate 1


description: L1_W538: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sos1 knockdown (T0538), replicate 1


description: L1_W539: SPAR-seq of 108 multi-exon gene regions in N2A cells, Top3a knockdown (T0539), replicate 1


description: L1_W537: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0537), replicate 1


description: L1_W544: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tial1 knockdown (T0544), replicate 1


description: L1_W536: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarcc1 knockdown (T0536), replicate 1


description: L1_W535: SPAR-seq of 108 multi-exon gene regions in N2A cells, Syncrip knockdown (T0535), replicate 1


description: L1_W530: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sox8 knockdown (T0530), replicate 1


description: L1_W531: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prmt5 knockdown (T0531), replicate 1


description: L1_W532: SPAR-seq of 108 multi-exon gene regions in N2A cells, Top2b knockdown (T0532), replicate 1


description: L1_W527: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tfam knockdown (T0527), replicate 1


title: Wildtype_Rep2

type: RNA

city: Hirosaki

first: Sho

last: Fujii

state: Aomori

address: Bunkyocho 3

department: Department of Biology, Faculty of Agriculture and Life Science

country: Japan

institute: Hirosaki University

hyb_protocol: Fragmented labeled cRNA was pooled and hybridized to Agilent Arabidopsis V4 4x44K Microarray (G2519F; Agilent) at 65°C for 17 h. Washing and dyring was performed following manufacturer's suggestions.

scan_protocol: The microarrays were scanned with an Agilent microarray scanner (Agilent) at 535 nm for Cy3.

data_processing: The array images were analyzed by the Feature Extraction software (Agilent) using the default settings. Feature extracted data was analysied using GeneSpring GX 11.5 (Agilent). Features flagged as absent or with expression value below 100 in all conditions were eliminated from further analyses. Raw data was normalized using the 75th percentile shift for each chip and the signal level of each probe in pgp1-2 samples was calculated with baseline normalization against the corresponding wild type samples.

organism: Arabidopsis thaliana

source_name: Wild type, replicate 2

label_protocol: 0.2 μg of total RNA was amplified by using a Low Input Quick-Amp Labeling kit (Agilent) and labeled with Cy3 (CyDye, Agilent) during the in vitro transcription process. 1.65 μg of Cy3-labled cRNA was fragmented by incubating at 60°C for 30 minutes.

growth_protocol: Arabidopsis seedlings were grown on agar (0.8% w/v)-solidified medium containing 3% (w/v) sucrose under continuous light illumination.

extract_protocol: Total RNA was extracted from frozen samples by using QIAGEN RNeasy Plant Mini Kit.

treatment_protocol: Seedlings grown for 7 d (wild type) or 14 d (pgp1-2) under 30 μmol photons m-2 s-1 was incubated for additional 7 d under 15 μmol photons m-2 s-1.

tag: ecotype

value: WT

value: whole seedling


title: Glast+ astrocyte_Drd2mGFAP cKO_basal

city: Shanghai

first: Yue

last: Wu

address: 320 Yueyang Road

department: Institute of Neuroscience

country: China

institute: Chinese Academy of Sciences

description: Gene expression data from Glast+ astrocyte from spinal cord of Drd2mGFAP cKO mice at basal

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

label: biotin

source_name: Glast+ astrocyte, Drd2mGFAP cKO, bassal

label_protocol: Biotinylated cDNA were prepared using Affymetrix WT PLUS Reagent Kit (Cat#902280, Affymetrix, Santa Clara, CA, US) following manufacture's recommendations.

growth_protocol: The mice were maintained on a 12 h light/dark cycle at 23°C with food and water available ad libitum. Animal maintenance and handling were approved by the Institutional Animal Care and Use Committee (IACUC No. NA-004-2016) and were in accordance with the US National Institutes of Health Guide for the Care and Use of   Laboratory Animals.

extract_protocol: Total RNA was harvested using Trizol reagent.

treatment_protocol: The recipient mice were subcutaneously injected with myelin oligodendrocyte glycoprotein (MOG 35-55, 200 μg/animal) emulsified in CFA containing 5 mg/ml killed Mycobacterium tuberculosis (DIFCO), and intraperitoneally injected with pertussis toxin (400 ng/animal, Sigma-Aldrich) on day 0 and 2. The Glast+ astrocyte from spinal cord was isolated using Miltenyi Biotec Anti-GLAST (ACSA-1) MicroBead Kit following manufacture's recommendations at basal and EAE day17.

value: Glast+ astrocyte from spinal cord

tag: strain

value: 2-3 months

value: Drd2mGFAP conditional knockout

tag: condition

value: basal


title: Glast+ astrocyte_control_basal

description: Gene expression data from Glast+ astrocyte from spinal cord of control mice at basal

source_name: Glast+ astrocyte, control, bassal

value: wt


title: 381_122_mouse_152_postappl_day_28_AAV6_2-TGFb1

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

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

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: day


title: 381_121_mouse_140_postappl_day_28_AAV6_2-TGFb1


title: Glast+ astrocyte_Drd2mGFAP cKO_EAE day17

description: Gene expression data from Glast+ astrocyte from spinal cord of Drd2mGFAP cKO mice on EAE day 17

source_name: Glast+ astrocyte, Drd2mGFAP cKO, EAE day17

value: EAE day 17


title: pgp1_Rep2

source_name: pgp1, replicate 2


title: 381_123_mouse_153_postappl_day_28_AAV6_2-TGFb1


title: Glast+ astrocyte_control_EAE day17

description: Gene expression data from Glast+ astrocyte from spinal cord of control mice on EAE day 17

source_name: Glast+ astrocyte, control, EAE day17


title: pgp1_Rep1

source_name: pgp1, replicate 1


title: Wildtype_Rep1

source_name: Wild type, replicate 1


description: L1_W524: SPAR-seq of 108 multi-exon gene regions in N2A cells, Terf2ip knockdown (T0524), replicate 1


description: L1_W528: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcerg1 knockdown (T0528), replicate 1


description: L1_W526: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tarbp2 knockdown (T0526), replicate 1


description: L1_W534: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sox2 knockdown (T0534), replicate 1


title: pgp1_Rep3

source_name: pgp1, replicate 3


description: L1_W529: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sp2 knockdown (T0529), replicate 1


description: L1_W525: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0525), replicate 1


title: Wildtype_Rep3

source_name: Wild type, replicate 3


title: 381_119_mouse_148_postappl_day_28_AAV6_2-Stuffer


description: L1_W533: SPAR-seq of 108 multi-exon gene regions in N2A cells, Slc6a8 knockdown (T0533), replicate 1


title: 381_118_mouse_147_postappl_day_28_AAV6_2-Stuffer


title: 381_124_mouse_161_postappl_day_28_AAV6_2-TGFb1


description: L1_W521: SPAR-seq of 108 multi-exon gene regions in N2A cells, Set knockdown (T0521), replicate 1


title: 381_120_mouse_149_postappl_day_28_AAV6_2-TGFb1


title: 381_117_mouse_146_postappl_day_28_AAV6_2-Stuffer


title: 381_116_mouse_145_postappl_day_28_AAV6_2-Stuffer


description: L1_W522: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tbx2 knockdown (T0522), replicate 1


description: L1_W519: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0519), replicate 1


description: L1_W523: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tlr5 knockdown (T0523), replicate 1


title: 381_115_mouse_144_postappl_day_28_AAV6_2-Stuffer


description: L1_W517: SPAR-seq of 108 multi-exon gene regions in N2A cells, Timeless knockdown (T0517), replicate 1


title: 381_112_mouse_141_postappl_day_21_AAV6_2-TGFb1


title: 381_114_mouse_151_postappl_day_21_AAV6_2-TGFb1


title: 381_111_mouse_150_postappl_day_21_AAV6_2-TGFb1


description: L1_W520: SPAR-seq of 108 multi-exon gene regions in N2A cells, Stat6 knockdown (T0520), replicate 1


description: L1_W515: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcf4 knockdown (T0515), replicate 1


title: 381_113_mouse_142_postappl_day_21_AAV6_2-TGFb1


description: L1_W518: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcp1 knockdown (T0518), replicate 1


description: L1_W516: SPAR-seq of 108 multi-exon gene regions in N2A cells, Supt5h knockdown (T0516), replicate 1


description: L1_W512: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tfdp1 knockdown (T0512), replicate 1


title: 381_109_mouse_137_postappl_day_21_AAV6_2-Stuffer


title: 381_107_mouse_135_postappl_day_21_AAV6_2-Stuffer


title: 381_108_mouse_136_postappl_day_21_AAV6_2-Stuffer


description: L1_W511: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sox15 knockdown (T0511), replicate 1


title: 381_106_mouse_134_postappl_day_21_AAV6_2-Stuffer


description: L1_W513: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sip1 knockdown (T0513), replicate 1


description: L1_W510: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarcal1 knockdown (T0510), replicate 1


description: L1_W508: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tbx1 knockdown (T0508), replicate 1


title: 381_104_mouse_132_postappl_day_14_PBS

value: PBS


title: 381_103_mouse_131_postappl_day_14_PBS


description: L1_W509: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sp3 knockdown (T0509), replicate 1

value: Mouse neuroblastoma cells


title: 381_102_mouse_130_postappl_day_14_AAV6_2-TGFb1


title: 381_110_mouse_138_postappl_day_21_AAV6_2-Stuffer


description: L1_W507: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0507), replicate 1


title: 381_101_mouse_129_postappl_day_14_AAV6_2-TGFb1


description: L1_W514: SPAR-seq of 108 multi-exon gene regions in N2A cells, Taf12 knockdown (T0514), replicate 1


title: 381_100_mouse_128_postappl_day_14_AAV6_2-TGFb1


description: L1_W506: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sp1 knockdown (T0506), replicate 1


title: 381_105_mouse_133_postappl_day_14_PBS


description: L1_W504: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcf7l1 knockdown (T0504), replicate 1


title: 381_99_mouse_127_postappl_day_14_AAV6_2-TGFb1


description: L1_W502: SPAR-seq of 108 multi-exon gene regions in N2A cells, Taf11 knockdown (T0502), replicate 1


title: 381_95_mouse_123_postappl_day_14_AAV6_2-Stuffer


title: 381_98_mouse_126_postappl_day_14_AAV6_2-TGFb1


title: 381_97_mouse_125_postappl_day_14_AAV6_2-Stuffer


title: 381_96_mouse_124_postappl_day_14_AAV6_2-Stuffer


description: L1_W501: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sirt2 knockdown (T0501), replicate 1


description: L1_W500: SPAR-seq of 108 multi-exon gene regions in N2A cells, Son knockdown (T0500), replicate 1


description: L1_W499: SPAR-seq of 108 multi-exon gene regions in N2A cells, Terf1 knockdown (T0499), replicate 1


description: L1_W498: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcf15 knockdown (T0498), replicate 1


description: L1_W497: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tceb3 knockdown (T0497), replicate 1


title: 381_92_mouse_120_postappl_day_7_AAV6_2-TGFb1


title: 381_93_mouse_121_postappl_day_14_AAV6_2-Stuffer


description: L1_W496: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tada2a knockdown (T0496), replicate 1


title: 381_94_mouse_122_postappl_day_14_AAV6_2-Stuffer


title: 381_91_mouse_119_postappl_day_7_AAV6_2-TGFb1


title: 381_89_mouse_117_postappl_day_7_AAV6_2-TGFb1


title: 381_90_mouse_118_postappl_day_7_AAV6_2-TGFb1


title: 381_88_mouse_116_postappl_day_7_AAV6_2-TGFb1


description: L1_W495: SPAR-seq of 108 multi-exon gene regions in N2A cells, Top1 knockdown (T0495), replicate 1


description: L1_W494: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sirt1 knockdown (T0494), replicate 1


description: L1_W505: SPAR-seq of 108 multi-exon gene regions in N2A cells, Top3b knockdown (T0505), replicate 1


description: L1_W503: SPAR-seq of 108 multi-exon gene regions in N2A cells, Suv39h2 knockdown (T0503), replicate 1


title: 381_87_mouse_115_postappl_day_7_AAV6_2-Stuffer


description: L1_W493: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thrap3 knockdown (T0493), replicate 1


description: L1_W492: SPAR-seq of 108 multi-exon gene regions in N2A cells, Topors knockdown (T0492), replicate 1


title: 381_86_mouse_114_postappl_day_7_AAV6_2-Stuffer


title: 381_85_mouse_113_postappl_day_7_AAV6_2-Stuffer


title: 381_80_mouse_108_postappl_day_3_AAV6_2-TGFb1


description: L1_W489: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcea3 knockdown (T0489), replicate 1


description: L1_W491: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcf7 knockdown (T0491), replicate 1


description: L1_W485: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcfl5 knockdown (T0485), replicate 1


title: 381_83_mouse_111_postappl_day_7_AAV6_2-Stuffer


description: L1_W488: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarcb1 knockdown (T0488), replicate 1


description: L1_W490: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tlr2 knockdown (T0490), replicate 1


description: L1_W484: SPAR-seq of 108 multi-exon gene regions in N2A cells, Topbp1 knockdown (T0484), replicate 1


description: L1_W482: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thoc1 knockdown (T0482), replicate 1


title: 381_84_mouse_112_postappl_day_7_AAV6_2-Stuffer


description: L1_W487: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tcea1 knockdown (T0487), replicate 1


title: 381_81_mouse_109_postappl_day_3_AAV6_2-TGFb1


description: L1_W479: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ran knockdown (T0479), replicate 1


title: 381_77_mouse_105_postappl_day_3_AAV6_2-Stuffer


title: 381_74_mouse_102_postappl_day_3_AAV6_2-Stuffer


title: 381_78_mouse_106_postappl_day_3_AAV6_2-TGFb1


description: L1_W480: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0480), replicate 1


description: L1_W476: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rad54l knockdown (T0476), replicate 1


description: L1_W481: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0481), replicate 1


title: 381_75_mouse_103_postappl_day_3_AAV6_2-Stuffer


description: L1_W478: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ring1 knockdown (T0478), replicate 1


description: L1_W477: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbbp7 knockdown (T0477), replicate 1


title: 381_69_mouse_76_postappl_day_28_Bleomycin

value: Bleomycin


title: 381_79_mouse_107_postappl_day_3_AAV6_2-TGFb1


title: 381_82_mouse_110_postappl_day_3_AAV6_2-TGFb1


description: L1_W475: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm15 knockdown (T0475), replicate 1


title: 381_72_mouse_96_postappl_day_28_Bleomycin


description: L1_W474: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm11 knockdown (T0474), replicate 1


description: L1_W483: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sin3a knockdown (T0483), replicate 1


title: 381_71_mouse_79_postappl_day_28_Bleomycin


description: L1_W486: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sept7 knockdown (T0486), replicate 1


title: 381_70_mouse_77_postappl_day_28_Bleomycin


title: 381_67_mouse_71_postappl_day_28_Bleomycin


title: 381_68_mouse_72_postappl_day_28_Bleomycin


description: L1_W473: SPAR-seq of 108 multi-exon gene regions in N2A cells, Psen1 knockdown (T0473), replicate 1


title: 381_66_mouse_70_postappl_day_28_NaCl

value: NaCl


title: 381_76_mouse_104_postappl_day_3_AAV6_2-Stuffer


description: L1_W472: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rxrb knockdown (T0472), replicate 1


title: 381_73_mouse_101_postappl_day_3_AAV6_2-Stuffer


title: 381_65_mouse_69_postappl_day_28_NaCl


description: L1_W471: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pole knockdown (T0471), replicate 1


description: L1_W470: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zbtb32 knockdown (T0470), replicate 1


title: 381_64_mouse_68_postappl_day_28_NaCl


description: L1_W468: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp1cc knockdown (T0468), replicate 1


description: L1_W467: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rpl5 knockdown (T0467), replicate 1


description: L1_W469: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rhobtb2 knockdown (T0469), replicate 1


title: 381_61_mouse_65_postappl_day_28_NaCl


title: 381_63_mouse_67_postappl_day_28_NaCl


title: 381_62_mouse_66_postappl_day_28_NaCl


title: 381_60_mouse_64_postappl_day_21_Bleomycin


description: L1_W464: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rest knockdown (T0464), replicate 1


title: 381_57_mouse_59_postappl_day_21_Bleomycin


description: L1_W463: SPAR-seq of 108 multi-exon gene regions in N2A cells, Upf1 knockdown (T0463), replicate 1


title: 381_58_mouse_60_postappl_day_21_Bleomycin


title: 381_59_mouse_62_postappl_day_21_Bleomycin


title: 381_55_mouse_57_postappl_day_21_Bleomycin


description: L1_W465: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pms1 knockdown (T0465), replicate 1


title: 381_53_mouse_54_postappl_day_21_NaCl


title: 381_54_mouse_56_postappl_day_21_Bleomycin


description: L1_W460: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf7 knockdown (T0460), replicate 1


description: L1_W461: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rnpep knockdown (T0461), replicate 1


description: L1_W462: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarcad1 knockdown (T0462), replicate 1


title: 381_56_mouse_58_postappl_day_21_Bleomycin


title: 381_52_mouse_53_postappl_day_21_NaCl


description: L1_W457: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pcgf2 knockdown (T0457), replicate 1


description: L1_W458: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pot1a knockdown (T0458), replicate 1


description: L1_W456: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm6 knockdown (T0456), replicate 1


description: L1_W455: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hltf knockdown (T0455), replicate 1


title: 381_51_mouse_52_postappl_day_21_NaCl


title: 381_49_mouse_50_postappl_day_21_NaCl


description: L1_W466: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rad50 knockdown (T0466), replicate 1


description: L1_W454: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prdm5 knockdown (T0454), replicate 1


description: L1_W453: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp4r2 knockdown (T0453), replicate 1


title: 381_47_mouse_48_postappl_day_14_Bleomycin


title: 381_48_mouse_49_postappl_day_21_NaCl


title: 381_46_mouse_47_postappl_day_14_Bleomycin


description: L1_W452: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm5 knockdown (T0452), replicate 1


description: L1_W459: SPAR-seq of 108 multi-exon gene regions in N2A cells, Setdb1 knockdown (T0459), replicate 1


description: L1_W451: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sall1 knockdown (T0451), replicate 1


title: 381_45_mouse_46_postappl_day_14_Bleomycin


title: 381_44_mouse_45_postappl_day_14_Bleomycin


description: L1_W449: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbms2 knockdown (T0449), replicate 1


title: 381_43_mouse_44_postappl_day_14_Bleomycin


description: L1_W446: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp2r5c knockdown (T0446), replicate 1


description: L1_W447: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pold1 knockdown (T0447), replicate 1


title: 381_40_mouse_41_postappl_day_14_Bleomycin


description: L1_W445: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pop7 knockdown (T0445), replicate 1


description: L1_W448: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sart1 knockdown (T0448), replicate 1


title: 381_39_mouse_40_postappl_day_14_Bleomycin


title: 381_50_mouse_51_postappl_day_21_NaCl


title: 381_38_mouse_39_postappl_day_14_Bleomycin


description: L1_W444: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf2 knockdown (T0444), replicate 1


title: 381_37_mouse_38_postappl_day_14_NaCl


title: 381_36_mouse_37_postappl_day_14_NaCl


description: L1_W442: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf3 knockdown (T0442), replicate 1


title: 381_35_mouse_36_postappl_day_14_NaCl


description: L1_W441: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0441), replicate 1


description: L1_W443: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rec8 knockdown (T0443), replicate 1


description: L1_W439: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rara knockdown (T0439), replicate 1


description: L1_W440: SPAR-seq of 108 multi-exon gene regions in N2A cells, Polr2b knockdown (T0440), replicate 1


description: L1_W438: SPAR-seq of 108 multi-exon gene regions in N2A cells, Slbp knockdown (T0438), replicate 1


title: 381_41_mouse_42_postappl_day_14_Bleomycin


title: 381_42_mouse_23_postappl_day_14_Bleomycin


title: 381_34_mouse_35_postappl_day_14_NaCl


description: L1_W450: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pola1 knockdown (T0450), replicate 1


description: L1_W436: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sf3a3 knockdown (T0436), replicate 1


title: 381_32_mouse_33_postappl_day_14_NaCl


title: 381_31_mouse_32_postappl_day_7_Bleomycin


title: 381_30_mouse_31_postappl_day_7_Bleomycin


description: L1_W437: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp1r9b knockdown (T0437), replicate 1


description: L1_W433: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sall4 knockdown (T0433), replicate 1


description: L1_W435: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ruvbl2 knockdown (T0435), replicate 1


title: 381_27_mouse_28_postappl_day_7_Bleomycin


title: 381_28_mouse_29_postappl_day_7_Bleomycin


title: 381_29_mouse_30_postappl_day_7_Bleomycin


description: L1_W434: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rad18 knockdown (T0434), replicate 1


description: L1_W430: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rfc1 knockdown (T0430), replicate 1


description: L1_W431: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rad21 knockdown (T0431), replicate 1


description: L1_W427: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snupn knockdown (T0427), replicate 1


title: 381_25_mouse_26_postappl_day_7_Bleomycin


title: 381_24_mouse_25_postappl_day_7_Bleomycin


title: 381_20_mouse_21_postappl_day_7_NaCl


title: 381_21_mouse_22_postappl_day_7_NaCl


description: L1_W429: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0429), replicate 1


title: 381_23_mouse_87_postappl_day_7_Bleomycin


title: 381_22_mouse_43_postappl_day_7_Bleomycin


description: L1_W424: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pprc1 knockdown (T0424), replicate 1


description: L1_W426: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rps3 knockdown (T0426), replicate 1


description: L1_W423: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0423), replicate 1


title: 381_33_mouse_34_postappl_day_14_NaCl


title: 381_19_mouse_20_postappl_day_7_NaCl


description: L1_W422: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarca2 knockdown (T0422), replicate 1


title: 381_26_mouse_27_postappl_day_7_Bleomycin


description: L1_W432: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rarg knockdown (T0432), replicate 1


description: L1_W425: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ptbp1 knockdown (T0425), replicate 1


description: L1_W428: SPAR-seq of 108 multi-exon gene regions in N2A cells, Polb knockdown (T0428), replicate 1


title: 381_16_mouse_17_postappl_day_7_NaCl


description: L1_W421: SPAR-seq of 108 multi-exon gene regions in N2A cells, Piwil2 knockdown (T0421), replicate 1


description: L1_W419: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rad17 knockdown (T0419), replicate 1


title: 381_17_mouse_18_postappl_day_7_NaCl


title: 381_15_mouse_16_postappl_day_3_Bleomycin


title: 381_13_mouse_14_postappl_day_3_Bleomycin


title: 381_12_mouse_13_postappl_day_3_Bleomycin


title: 381_18_mouse_19_postappl_day_7_NaCl


title: 381_11_mouse_12_postappl_day_3_Bleomycin


description: L1_W420: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp1r10 knockdown (T0420), replicate 1


description: L1_W418: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbmy1a1 knockdown (T0418), replicate 1


description: L1_W417: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sub1 knockdown (T0417), replicate 1


title: 381_10_mouse_11_postappl_day_3_Bleomycin


title: 381_7_mouse_7_postappl_day_3_Bleomycin


description: L1_W413: SPAR-seq of 108 multi-exon gene regions in N2A cells, Psen2 knockdown (T0413), replicate 1


title: 381_6_mouse_6_postappl_day_3_NaCl


title: 381_14_mouse_15_postappl_day_3_Bleomycin


description: L1_W416: SPAR-seq of 108 multi-exon gene regions in N2A cells, Jmjd6 knockdown (T0416), replicate 1


title: 381_9_mouse_10_postappl_day_3_Bleomycin


description: L1_W414: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sfswap knockdown (T0414), replicate 1


description: L1_W412: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp2r1a knockdown (T0412), replicate 1


description: L1_W409: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbbp4 knockdown (T0409), replicate 1


description: L1_W411: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0411), replicate 1


description: L1_W407: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rnf8 knockdown (T0407), replicate 1


title: 381_4_mouse_4_postappl_day_3_NaCl


title: 304_123_mouse_153_postappl_day_28_AAV6_2-TGFb1


title: 381_3_mouse_3_postappl_day_3_NaCl


title: 304_124_mouse_161_postappl_day_28_AAV6_2-TGFb1


title: 381_2_mouse_2_postappl_day_3_NaCl


description: L1_W406: SPAR-seq of 108 multi-exon gene regions in N2A cells, Riok2 knockdown (T0406), replicate 1


description: L1_W408: SPAR-seq of 108 multi-exon gene regions in N2A cells, Polr2g knockdown (T0408), replicate 1


title: 304_122_mouse_152_postappl_day_28_AAV6_2-TGFb1


title: 381_1_mouse_1_postappl_day_3_NaCl


description: L1_W410: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pnn knockdown (T0410), replicate 1


description: L1_W415: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sall3 knockdown (T0415), replicate 1


title: 304_119_mouse_148_postappl_day_28_AAV6_2-Stuffer


description: L1_W400: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pou2f1 knockdown (T0400), replicate 1


description: L1_W405: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rfc4 knockdown (T0405), replicate 1


description: L1_W401: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rad51 knockdown (T0401), replicate 1


title: 304_116_mouse_145_postappl_day_28_AAV6_2-Stuffer