title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rcan2 knockdown (T1104), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: ACGACATC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Eif2c2 knockdown (T1109), replicate 2

status: Public on Feb 02 2017

type: SRA

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description:
Forward (i5) barcode: CTAAGCCT, reverse (i7) barcode: GTCAAGTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab

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 20. 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: NCBIm37/mm9
Supplementary_files_format_and_content: Processed files are either tab-delimited  tables (.tab) or FASTA files (.fa). KnockdownAnnotation.tab contains treatment annotations and well/plate positions. ScreenJuncUp.20-77.tab and ScreenJuncDn.20-77.tab contain the custom junction upstream and downstram junction libraries, respectively, and ScreenEvent_junctions.tab contains the information which junctions were used to calculate PSI for each event. PSI.SSMD.CGR8.tab and PSI.SSMD.N2A.tab contain raw PSI of each replicate and final SSMD. Reads_perEvent_CGR8.tab and Reads_perEvent_N2A.tab contain raw read counts on which expression analyis was based, and Expression.CGR8.treatments.tab and Expression.N2A.treatments.tab contain modeled relative abundance and fold-change with associated FDR for each treatment type.

molecule: total RNA

organism: Mus musculus

source_name: Neuroblastoma cells

growth_protocol: CGR8 mouse embryonic stem cells (ESCs) were cultured as described previously on gelatin-coated plates (Gabut et al., Cell (2011), Han  et al., Nature (2013)). Mouse neuroblastoma (N2A) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin. All cell lines were 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 50 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, CGR8 and N2A cells were seeded in 96-well plates, 3000 and 5000 cells per well, respectively. Cells were transfected with the SMARTpool siRNAs at 50 nM final concentration using DharmaFECT1 reagent (Dharmacon), as recommended by the manufacturer.

tag: cell line


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Eif4b knockdown (T1103), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TGTCTCAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dmap1 knockdown (T1106), replicate 2

description:
Forward (i5) barcode: CTAAGCCT, reverse (i7) barcode: AGGTACGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dhx8 knockdown (T1108), replicate 2

description:
Forward (i5) barcode: CTAAGCCT, reverse (i7) barcode: ATCCGGTA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Tspyl2 knockdown (T1102), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CGCGTAAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Gpatch1 knockdown (T1099), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: GACATGAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Thoc5 knockdown (T1098), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TCCTCTTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, G3bp2 knockdown (T1124), replicate 2

description:
Forward (i5) barcode: CTAAGCCT, reverse (i7) barcode: TGTCCACT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hmg20b knockdown (T1097), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CTAGTCCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dhx35 knockdown (T1107), replicate 2

description:
Forward (i5) barcode: CTAAGCCT, reverse (i7) barcode: TCAGGAGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Frg1 knockdown (T1115), replicate 2

description:
Forward (i5) barcode: CTAAGCCT, reverse (i7) barcode: GGTAATGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siMbnl (T1095), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TTGGCGTA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hp1bp3 knockdown (T1096), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CACTTCAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hnrnpl knockdown (T1094), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: AGGTTCCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, H3f3a knockdown (T1093), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: AAGCTTCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Incenp knockdown (T1091), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: GATGGTAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Gemin6 knockdown (T1092), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: ACTGTCAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zc3h12d knockdown (T1100), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TACGCCTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hdgfrp2 knockdown (T1117), replicate 2

description:
Forward (i5) barcode: CTAAGCCT, reverse (i7) barcode: AACCTACG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Exosc3 knockdown (T1088), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: GAAGACGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Eif4a1 knockdown (T1090), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: GACACTGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Prpf40a knockdown (T1087), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CTTCCTTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Thumpd3 knockdown (T1089), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: AAGCCGAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp771 knockdown (T1085), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CTAGCAAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Gtf3a knockdown (T1086), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CTCATCTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siNT (T1101), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TAGGTTGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hbp1 knockdown (T1078), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CCTAGCAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dazap1 knockdown (T1074), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TCGAAGCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Tra2a knockdown (T1075), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: AGGTCTTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Flywch1 knockdown (T1076), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: ACCAACGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dgcr8 knockdown (T1072), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: ATCGCGAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hnrnph2 knockdown (T1079), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TCGTTGGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Gemin5 knockdown (T1081), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: AGACCAGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Larp7 knockdown (T1080), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CCTTATGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dnajc8 knockdown (T1073), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: GCGCAATT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hnrnpa2b1 knockdown (T1084), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TTCCGCAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hmgb2 knockdown (T1069), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TGTGGTGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hemt1 knockdown (T1068), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TGTCCTCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Gemin7 knockdown (T1067), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: ATAACCGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, mock (T1083), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: ACTCAGTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dhx15 knockdown (T1065), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CGAACCTA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Kat2a knockdown (T1062), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: GGTTGCTA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dazl knockdown (T1061), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: GGTATTCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Grwd1 knockdown (T1060), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TTCCTAGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hist3h2ba knockdown (T1059), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CAGAGTGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, H1fx knockdown (T1082), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: GGCGAATA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Eif2s1 knockdown (T1077), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: GAGTCTCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hmgb1 knockdown (T1064), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CTTCTGCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Esrrb knockdown (T1063), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CCTTGGTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, mock (T1056), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TCGTTCGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Mbd6 knockdown (T1052), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TCTGAGAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Leng9 knockdown (T1058), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CACTCAGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Mxd3 knockdown (T1221), replicate 2

description:
Forward (i5) barcode: AGATCGTC, reverse (i7) barcode: AGCATCGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp828 knockdown (T1051), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GAAGCTAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Smc3 knockdown (T1047), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TTGGTTCC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Mms22l knockdown (T1070), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CAGTTGTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpped1 knockdown (T1050), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CACTCTCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cherp knockdown (T1048), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: ACCACTAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp473 knockdown (T1054), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: ACTCTGAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cstf2t knockdown (T1046), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: ACCTGATG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siNT (T1057), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CCAATACG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Crnkl1 knockdown (T1055), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TAGCGGAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dicer1 knockdown (T1066), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: CCGCATAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpeb4 knockdown (T1045), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TCCTCAAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rif1 knockdown (T1044), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GGCGTTAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpeb1 knockdown (T1042), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: ACGTTGCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cxxc1 knockdown (T1043), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GGATAAGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Parp8 knockdown (T1039), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CGAATTCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Capn7 knockdown (T1041), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TCTGGACA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Utp3 knockdown (T1038), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CCTAGCTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cdca8 knockdown (T1040), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TATAGCCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ddx5 knockdown (T1037), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TTCCGGTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpne1 knockdown (T1053), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GTCTAGTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpeb2 knockdown (T1034), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TACCAAGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Nudt21 knockdown (T1035), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CCATCGTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpsf3 knockdown (T1036), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CTGAGAGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Celf4 knockdown (T1049), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CTACCTAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rcor1 knockdown (T1033), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GGTTCCAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Samd4b knockdown (T1027), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CAACGAAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Enox1 knockdown (T1028), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TTGGCCTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zcchc10 knockdown (T1032), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TCGAGTAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ddx46 knockdown (T1029), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GGATGGAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, C1qbp knockdown (T1031), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: AGCAGTTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Macrod1 knockdown (T1024), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GTTCGTAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cbx7 knockdown (T1025), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CTGACTCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ccar1 knockdown (T1026), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CTTGACCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Mysm1 knockdown (T1021), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: ATCGAAGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Clns1a knockdown (T1023), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: AGGATGGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ddx50 knockdown (T1022), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TTATGGCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ddx39 knockdown (T1019), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TGACAGAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Eif4a3 knockdown (T1018), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GTTCAGCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cbx2 knockdown (T1015), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: AGGTGAAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Bicc1 knockdown (T1016), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: AGACTCAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siMbnl (T1017), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: TTATCCGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Setd3 knockdown (T1014), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CGGCTATA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpsf2 knockdown (T1013), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: GGTACGTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Slu7 knockdown (T1012), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: ATGCAACC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, D4Wsu53e knockdown (T1011), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: CATCCTTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cdyl2 knockdown (T1010), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: AGAGGACT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cstf1 knockdown (T1008), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GCATCCAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Slx4 knockdown (T1007), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CTAGACCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Mis18bp1 knockdown (T1009), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: ACAGGTGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Carm1 knockdown (T1030), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: AGCTAGCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp12 knockdown (T1006), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: AGTGTCTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siNT (T1005), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GATGTCCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Casc3 knockdown (T1002), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ATCGTAGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Brms1l knockdown (T1003), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CTGATCAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Sf3b3 knockdown (T1001), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GTCTACAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siMbnl (T0999), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CTCTCACA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Capn5 knockdown (T0998), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: TGCTCATC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zbtb24 knockdown (T0994), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GACAGTCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Mthfsd knockdown (T1000), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: AGGAAGCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ccnl2 knockdown (T0997), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CCTTGCAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Wdhd1 knockdown (T1020), replicate 2

description:
Forward (i5) barcode: ACTGCATA, reverse (i7) barcode: AGTGAGTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rbm41 knockdown (T0992), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CATGGATC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Enox2 knockdown (T0996), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: TCTCGTCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zbtb46 knockdown (T0990), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GAACCTAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Clk1 knockdown (T0991), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CGCCTTAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, D2Ertd750e knockdown (T0989), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GACTTGTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, mock (T0987), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GTTGCAAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zwint knockdown (T0984), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ATGCGCAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpeb3 knockdown (T0982), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CATCAGCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cic knockdown (T0980), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: AGAGACAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Phf21a knockdown (T0986), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: AGTGGTCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ddx1 knockdown (T0979), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ATTACGCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Trmt1 knockdown (T0981), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GTCAGAGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rbm34 knockdown (T0978), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GGTTATGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Boll knockdown (T0977), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: AGCTGTAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Csn3 knockdown (T0974), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ACTCCTGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpsf1 knockdown (T0995), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GTGACACT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ddx3x knockdown (T0993), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: TGAGGTGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Chd1l knockdown (T0973), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GTAGTCGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Txnl4b knockdown (T0971), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ATGCTTCC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, D1Pas1 knockdown (T0967), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: TCAGCACA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zbtb40 knockdown (T0968), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CGAATTGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, D19Bwg1357e knockdown (T0988), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GCATAACC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Carhsp1 knockdown (T0970), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ACGTGATC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cstf2 knockdown (T0966), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: TGCTAGGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Chd3 knockdown (T0976), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: GTACGATC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ddx19a knockdown (T0965), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: TCAGACTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Deb1 knockdown (T0985), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: TGTCCAGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpsf4 knockdown (T0964), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ACCACTTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Lemd2 knockdown (T0962), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: TCCTTGCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Setd1a knockdown (T0956), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: GCATCCTT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Bud13 knockdown (T0983), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CTAGCTTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ddx41 knockdown (T0963), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: AGACGACA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zbtb38 knockdown (T0954), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: ATGGCCTA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cpsf4l knockdown (T0975), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: ACACTCAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, mock (T0960), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: GATGAGGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp459 knockdown (T0957), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TACGCGAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp768 knockdown (T0969), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: TTCCTTGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ercc6l knockdown (T0953), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: ACCTAGGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Dhx57 knockdown (T0955), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: GCGGATAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Camk4 knockdown (T0972), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CGATGGAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Esrp2 knockdown (T0958), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: GACTGAGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siNT (T0961), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: TCCAACGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Cdk2 knockdown (T1004), replicate 2

description:
Forward (i5) barcode: GTAAGGAG, reverse (i7) barcode: CTTGTGCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Setd1b knockdown (T0952), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TCAGGTGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Baz2a knockdown (T0959), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: ACTCAGAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Adar knockdown (T0949), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TCACCAGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Arglu1 knockdown (T0951), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TTGCGCAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zgpat knockdown (T0947), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: CTCTCAGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Srbd1 knockdown (T0948), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: CTGAAGAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zc3h12a knockdown (T0943), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: AGAGAGTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Gemin8 knockdown (T0945), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: AGCATCCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Prmt6 knockdown (T0946), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TCGATCGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Raver2 knockdown (T0944), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: CATCGTTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Samd14 knockdown (T0942), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: CACTAGAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zbtb44 knockdown (T0941), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: AGTCCTCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Srrt knockdown (T0940), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: GGATTAGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Tbl1xr1 knockdown (T0939), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: AGGAACGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Hmgxb3 knockdown (T0950), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: CCATCGAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Eme1 knockdown (T0937), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: GTTGTCCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Tmem63a knockdown (T0938), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TGTGGTCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, 5930416I19Rik knockdown (T0935), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: CAGAGACA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Morn4 knockdown (T0934), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: CGATGCAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp958 knockdown (T0936), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TCGTCAAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Asf1a knockdown (T0932), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: CCTACCAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Suv420h2 knockdown (T0930), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TGACACTG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Actr8 knockdown (T0933), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TAGGAAGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Srek1 knockdown (T0928), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TACCGGTA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Arrdc1 knockdown (T0926), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: ATCCTTCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Aqr knockdown (T0924), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TACCTTGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ap1s3 knockdown (T0931), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TGGACATC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp934 knockdown (T0929), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: CAACAGCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rbfox1 knockdown (T0927), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TCCAGATG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siMbnl (T0921), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TTGGATCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp668 knockdown (T0923), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: ATGCAAGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Sfr1 knockdown (T0925), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TGCTTGCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Baz1a knockdown (T0922), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: ACCTGAAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, AI314976 knockdown (T0920), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TGACGACT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp445 knockdown (T0917), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: GTGTTGAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ankrd17 knockdown (T0919), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: AGGTCTAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Rbm47 knockdown (T0916), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: GGCCATAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp871 knockdown (T0915), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: TCCAACCT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zc3h10 knockdown (T0918), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: AACGAACG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Arrb2 knockdown (T0913), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: AATAGGCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ash2l knockdown (T0911), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CTCAACTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siNT (T0909), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CGTAGGAA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Prmt7 knockdown (T0910), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TAATGCCG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp652 knockdown (T0908), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GATGGATG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp574 knockdown (T0906), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CTGTTGTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Bend3 knockdown (T0905), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: AGCTTCGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, siMbnl (T0903), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CCTATTGC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Arid2 knockdown (T0894), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GTGAAGAC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: ReNcell CX neural progenitor 4

city: Chapel Hill

first: Shawn

middle: D.

last: Hingtgen

state: NC

address: 4212 Marsico Hall, 125 Mason Farm Road

department: UNC Eshelman School of Pharmacy, UNC Biomedical Research Imaging Center

country: USA

institute: University of North Carolina at Chapel Hill

description: EMD Millipore, cat # SCC008

data_processing:
Paired-end fastqs were aligned to hg38 using version 2.4.2a of STAR.
Transcript abundance estimates were calculated using version 0.4.2 of Salmon.
Genome_build: hg38
Supplementary_files_format_and_content: Relative transcript abundances in Transcripts Per Million (TPM)

organism: Homo sapiens

source_name: ReNcell CX neural progenitor

extract_protocol:
total RNA, Qiagen RNAeasy MiniKit with on-column DNAseI treatment
KAPA Biosystems stranded RNA library with polyA-enrichment, Illumina 6mer single-barcodes

tag: cell type

value: brain-derived neural progenitor cells


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Asf1b knockdown (T0902), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CTACCAAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: ReNcell CX neural progenitor 2

description: EMD Millipore, cat # SCC008


title: ReNcell CX neural progenitor 3

description: EMD Millipore, cat # SCC008


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp646 knockdown (T0900), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CTTGTCCA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zmym6 knockdown (T0898), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GACACAGA
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ncaph knockdown (T0897), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CCATAACG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: NHF1-hTERT hiNSC 4

description: lentiviral transduction with hSox2/rtTA plasmid

source_name: modified NHF1-hTERT fibroblasts

value: human iNSCs


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Snrnp48 knockdown (T0901), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GAGATCAG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: NHF1-hTERT hiNSC 3


title: ReNcell CX neural progenitor 1

description: EMD Millipore, cat # SCC008


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Ncapd3 knockdown (T0896), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: TAGGATCC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp825 knockdown (T0899), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: GCTACGAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zfp629 knockdown (T0914), replicate 2

description:
Forward (i5) barcode: AGAGTAGA, reverse (i7) barcode: CGGCAATT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Zbtb12 knockdown (T0912), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: ATATGGCC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Arid5b knockdown (T0895), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CCAAGCAT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Celf6 knockdown (T0907), replicate 2

description:
Forward (i5) barcode: TATCCTCT, reverse (i7) barcode: CTTGGTTC
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: KR_48

city: Poznań

first: Michal

last: Kabza

address: ul. Fredry 10

country: Poland

institute: Poznan University of Medical Sciences

data_processing:
Short reads were trimmed using Trimmomatic version 0.32
Reads matching rRNAs were removed using Bowtie version 1.0.1
Reads were mapped to the reference genome using STAR version 2.4.0j
Mapped reads were assembed into transcripts using StringTie version 1.0.4
Assembled reads were merged with reference annotations using Cuffmerge version 2.2.1
Expression of genes and transcripts was estimated using Kallisto version 0.42.2.1
Genome_build: GRCh38
Supplementary_files_format_and_content: Merged annotations created by Cuffmerge (GFF3 format); tab-delimited text files containing expression values of genes and transcripts (TPM values and raw estimated read counts)

source_name: Cornea

extract_protocol:
The corneas were transferred to 400 µl of lysis solution (Norgen Biotek, Thorold, ON, Canada) in a 2-mL microtube with Lysing Matrix D (MP Biomedicals, Irvine, CA, USA) and homogenized using a FastPrep®-24 Instrument (MP Biomedicals). Further total RNA extraction and purification steps were performed according to the manufacturer’s instructions supplied with a Total RNA Purification Kit (Norgen Biotek). To maximize the removal of residual DNA that could affect downstream analyses, an on-column DNase I (Zymo Research, Irvine, CA, USA) treatment was performed.
Libraries were prepared with a TruSeq Stranded Total RNA LT with Ribo-Zero™ Human/Mouse/Rat Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol, with slight modifications.

tag: disease state

value: non-KTCN

tag: study

value: replication

tag: tissue

value: cornea


title: NHF1-hTERT fibroblasts 4

source_name: immortalized cell line

value: skin fibroblasts


title: KR_52


title: KR_28


title: KR_35


title: KR_33


title: NHF1-hTERT fibroblasts 3


title: KR_27


title: NHF1-hTERT fibroblasts 2


title: NHF1-hTERT hiNSC 2


title: KR_26


title: NHF1-hTERT fibroblasts 1


title: KR_24


title: SCC_H3K27me3_ChIPSeq

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
ChIP-seq paired reads were aligned to the mm10 genome assembly using Bowtie2 with -k 1 option
H3K4me3 and H3K27Ac peaks were called using MACS (v1.4.2) at p-value threshould of 1E-05 with no-ChIP input sample as control.
Wiggle files with a 10bp resolution for H3K27me3 were generated by MACS v1.4.2 with tag shift and then rescaled to a larger of total number of uniquely alignable sequences in two datasets.
Genome_build: mm10

molecule: genomic DNA

source_name: Lung tumors

extract_protocol:
Lung tumors were pulverized, cross-linked with 1% formaldehyde in PBS for 10 min at RT, washed in 5mg/ml BSA in PBS and then in just cold PBS, re-suspended in lysis buffer [50mM Tris-HCl, pH 8.1, 10mM EDTA, 1% SDS, 1X complete protease inhibitors (Roche)], and sonicated with the Covaris E210 or S2 sonicator to obtain chromatin fragment lengths of 200-to-1500bp judged by Bioanalyzer DNA High sensitivity kit (Agilent). Fragmented chromatin was diluted in IP buffer [20mM Tris-HCl pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100] and incubated overnight at 4ºC with Protein G magnetic beads (Dynabeads: Life Technologies) that had been pre-incubated with antibodies. Immunoprecipitates were washed six times with wash buffer [50mM HEPES pH 7.6, 0.5M LiCl, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40] and twice with TE buffer. Immunoprecipitated (or no IP input) DNA was treated with RNase A and Proteinase K on the beads, recovered in 1% SDS and 0.1M NaHCO3 over a period of 5 hours at 65ºC, column purified with DNA clean and concentrator -25 (Zymo Research).
After a sonication to enrich DNA fragment lengths between 100-300bp, 5 to 10ng of DNA were used for the library construction using NEBNext Ultra DNA Library Prep Kit (NEB E7370).  Sequencing was performed on a NextSeq (Illumina) for 38 nucleotides from paired ends according to manufacturer’s instructions.

value: Lung tumors

tag: tumor subtype

value: Squamous cell carcinoma

tag: background

tag: antibody


title: KR_23


title: ADC_H3K27me3_ChIPSeq

value: Adenocarcinoma


title: KR_21


title: NHF1-hTERT hiNSC 1


title: ADC_H3K27Ac_ChIPSeq

value: H3K27Ac (Abcam ab4729)


title: SCC_H3K4me3_ChIPSeq

value: H3K4me3 (Millipore 07-473)


title: KR_18


title: KR_19


title: KR_15


title: ADC_H3K4me3_ChIPSeq


title: KR_14


title: KR_08


title: TA_rep3

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

data_processing:
Base calling: CASAVA_v1.8.2
Alignment: Reads were aligned to mm10 using Bowtie2, v2-2.1.0, -D 15 -R 2 -N 1 -L 20 -i S,1,0.50 --maxins 2000 --no-discordant --no-mixed
Peak calling: MACS2 version 2.0.10
Abundance measurement: Bedtools version 2.25.0
Genome_build: mm10
Supplementary_files_format_and_content: Broadbed including called peaks and reads of each sample in peaks

source_name: Hepatocytes

growth_protocol: 3-week old C57BL/6J mice were obtained from Jackson labs.

extract_protocol:
Eight week-old male F1 animals from control (TA) and nicotine-exposed fathers were anaesthetized using ketamine (100 mg/kg BW) and xylazine (10 mg/kg BW). Abdominal cavity was opened with a transversal incision below the rip cage. We dissected the portal vein with blunt forceps and inserted a 26 G catheter needle. After cutting the vena cava inferior cranial of the liver, we perfused the organ firstly with HBBS 1X + 200 mM  EDTA (10ml at 7ml/min) and secondly with 50ml DMEM containing collagenase type I (0.4 mg/ml) at 7 ml/min. Liver was then removed from the abdominal cavity, put in a petri dish containing culture media (DMEM, 20% FBS, 1X ITS, 1X Penicillin/Streptomycin, 0.1 uM Dexamethason, Sigma-Aldrich), and gently dissected to allow release of hepatocytes and supporting cells from connective tissue. After filtration through 70 um nylon cell strainer, cells were washed twice with PBS 1X and once with culture media (centrifugation at 500 rpm for 5 min), and plated on a 0.1% gelatin coated well. Hepatocytes were allowed to adhere to the bottom of the well for three hours.
ATAC-Seq was performed as previously descirbed (Buenrostro JD et al. Current Protocols in Molecular Biology 2015), with only slight adjustments. The volume of enzyme mix used for 50,000 cells was adjusted to 3.75 ml due to the fact that approximately 50% of all hepatocytes in culture are binuclear.

treatment_protocol: Males were immediately put on either tartaric acid (TA, 300ug/ml) or nicotine (200ug/ml nicotine free-base) in drinking water for 5 consecutive weeks with an additional week on tap water. Nicotine-exposed and control males were then allowed to mate with control females from the same shipment date. 8-week old F1 offspring from nicotine-exposed and control fathers was used for all experiments reported.

tag: strain

tag: gender

value: male

value: Liver

value: hepatocytes


title: TA_rep4


title: SCC_input

value: none (input)


title: KC_55

value: KTCN


title: KR_25


title: KC_32


title: TA_rep1


title: KR_13


title: Nicotine_rep4


title: SCC_H3K27Ac_ChIPSeq


title: Nicotine_rep3


title: TA_rep2


title: Nicotine_rep2


title: Prdm14_4C_Mll2_Y2602A

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: library strategy: 4C-seq

data_processing:
Sequencing data was acquired through the default Illumina pipeline using Casava v1.8.
ChIP-seq reads were aligned to the mouse genome (UCSC mm9) using the Bowtie aligner v0.12.9 allowing uniquely mapping reads only and allowing up to two mismatches (Langmead, 2009). RNA-seq reads were aligned to the mouse genome UCSC mm9 and to gene annotations from Ensembl 67 using TopHat v2.0.13 (Trapnell et al., 2009), using option –g 1 –x 1.
ChIP-seq reads were extended to 150 bases toward the interior of the sequenced fragment and normalized to total reads aligned (reads per million; RPM). RNA-seq reads were normalized to total reads aligned (reads per million; RPM) to generate bigWig files.
Peak detection was done using MACS v1.4.2 (Zhang et al., 2008). Associated control samples were used to determine statistical enrichment at p<1e-5. For down stream analysis, peaks were further filtered with p < 1e-8 and FDR < 0.05.
R package edgeR 3.0.8 was used to perform differential expression analysis at p-value < 1e-3 (Robinson et al., 2010).
For 4C seq, reads were demultiplexed by allowing no mismatch in library index and 1 mismatch in viewpoint sequences. The library index were trimmed before mapping. 4cseqpipe were used for alignment (van de Werken HG et al., 2012).
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq, RNA-Seq, and 4C samples

source_name: mouse embryonic stem cells

growth_protocol: Mouse V6.5 ES cells were grown in DMEM supplemented with 15% FBS (HyClone), 2 mM L-glutamine, 0.1 mM nonessential amino acids (Stemcell Technologies) and 1,000 U/ml recombinant LIF (Millipore). Hanging drop method was used to form embryoid bodies (EBs) by culturing 1000 mouse ES cells in 25 µl differentiation medium (without LIF) on the lid of 150 mm culture dish for indicated days.

extract_protocol:
ChIP assays were performed as previously described (Lee et al., 2006) . Briefly, 2-5x10^7 cells were crosslinked with 1% paraformaldehyde (Electron microscropy science #15710) at room temperature for 10 min and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody. Total RNA was extracted with Trizol (Invitrogen #15596), treated with DNAase I (NEB #M0303) for 20 min at room temperature and purified with RNeasy Mini kit (Qiagen #74106).Circular Chromosome Conformation Capture (4C) technique was performed as described (van de Werken et al., 2012, Methods Enzymol). Cross-linked chromatin was digested with HindIII, ligated under diluted conditions.  Cross links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions.For each viewpoint approximately 3.2 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina adaptor sequence. Multiplexed samples were sequenced on the Illumina Nextseq500 system using 75 bp single-end reads according to the manufacturer’s specifications.  4C-seq reads were sorted, aligned, and translated to restriction fragments using the 4C-seq pipeline according to (van de Werken et al., 2012, Methods Enzymol).
ChIP-seq and RNA-seq libraries were constructed by following instrucitons in KAPA HTP Library Preparation Kits (Kapa Biosystems, #KK8234) and TruSeq Stranded Total RNA Library Prep kits with Ribo-Zero Human/Mouse/Rat (Illumina, #RS-122-2201 and #RS-122-2202), respectively. Indexed primers for ChIP-seq libraries are from Bioo Scientific (#514104 ). For 4C-seq, Cross-linked chromatin was digested with HindIII, ligated under diluted conditions.  Cross links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions. For each viewpoint, approximately 3.2 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina adaptor sequence. Multiplexed samples were sequenced on the Illumina Nextseq500 system using 75 bp single-end reads according to the manufacturer’s specifications.

treatment_protocol: Mouse ES cells were infected with lentivial shRNA against either Mll2 or Menin in the presense of 4ug/ml polybrene for 12 hours and then seleted with 1.5 ug/ml puromycinfor 48h before harvest for ChIP-seq or RNA-seq experiments. For rescue experiment, mouse ES cells were electroporated with indicated plasmids and selected with 400 µg/ml G418 for 3 days.

value: V6.5 mES

tag: genotype/variation


title: Prdm14_4C_Mll2_mCXXC

description: library strategy: 4C-seq

value: Mll2 mCXXC/mCXXC


title: KC_31


title: KC_26


title: KC_25


title: ADC_input


title: KC_28


title: KC_30


title: Prdm14_4C_Mll2WT

description: library strategy: 4C-seq

value: wild type


title: Nicotine_rep1


title: KC_23


title: SPAR-Seq of multi-exon regions of 50 genes in N2A, Exosc5 knockdown (T1071), replicate 2

description:
Forward (i5) barcode: AAGGAGTA, reverse (i7) barcode: TACCATGG
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.N2A.tab
Reads_perEvent_N2A.tab
Expression.N2A.treatments.tab


title: KC_22


title: RNA_Prdm14_delta_enhancer_clone10

value: Prdm14_delta enhancer


title: KC_21

value: replication


title: KC_20

value: cornea


title: KC_34


title: RNA_Prdm14_delta_enhancer_clone4


title: RNA_Prdm14_delta_enhancer_clone3


title: RNA_Prdm1_delta_enhancer_clone22

value: Prdm1_delta enhancer


title: KC_19


title: KC_18


title: KC_17


title: RNA_Prdm1_delta_enhancer_clone20


title: RNA_Prdm1_delta_enhancer_clone5


title: Prdm14_4C_Mll2KO

description: library strategy: 4C-seq


title: KC_16


title: RNA_WT


title: KR_64

value: non-KTCN

value: discovery


title: KR_57


title: KC_15


title: KR_56