title: HFD.WT2

first: Yuhao

last: Wang

state: Zhejiang

address: No.268 Kaixuan Road

institute: Zhejiang University

description: Processed OTU.txt

data_processing:
Sequences were joined, depleted of barcodes then sequences <150bp removed, sequences with ambiguous base calls removed. Sequences were denoised, OTUs generated and chimeras removed. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). Final OTUs were taxonomically classified using BLASTn against a curated database derived from RDPII and NCBI (www.ncbi.nlm.nih.gov, http://rdp.cme.msu.edu).
assembly: RDPII and NCBI
Tab-delimited text file with OTU counts for each sample.
Library strategy: 16S DNA-seq

source_name: Feces

extract_protocol:
Fecal DNA was extracted and purified from freshly collected feces using the FastDNA Spin Kit (MP Biomedicals 116560-200).
Sequencing libraries were prepared using the HotStarTaq Plus Master Mix Kit (Qiagen).

tag: strain/background

value: Wild-type

value: Feces

tag: housing condition

value: SPF

tag: diet

value: High-fat diet


title: HFD.WT1

status: Public on Jul 15 2022

type: SRA

city: Hangzhou

country: China

description: Processed OTU.txt

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: genotype

tag: tissue


title: HFD.SNTG5

description: Processed OTU.txt

value: Villin-Snhg9 Tg


title: HFD.WT4

description: Processed OTU.txt


title: HepG2 cell, leucine deprivation sample under leucine deprivation condition, bio rep2

type: RNA

city: Tokyo

first: Sihui

last: Ma

address: Yayoi 1-1-1

country: Japan

institute: The university of Tokyo

description: Gene expression data of HepG2 cell under leucine deprivation condition

hyb_protocol: After washing and staining, array scanning was performed using GeneChip Hybridization and Affymetrix Gene Array Scanner 3000

data_processing: The data were analyzed with Transcriptome Analysis Console using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HepG2 cell, leucine deprivation condition

label_protocol: For global miRNA expression profiling, total RNA (1000 ng) was labeled using the FlashtagTM RNA Labeling Kit.

growth_protocol: Human hepatocellular carcinoma cells (HepG2) were obtained from the American Type Culture Collection (Rockville, MD, USA) and cultured in Dulbecco's modified Eagle's medium (DMEM; Sigma-Aldrich, St. Louis, MO, USA) containing 10% (v/v) fetal bovine serum (Sigma-Aldrich) and 1% (v/v) penicillin-streptomycin (Sigma-Aldrich) at 37 °C and 5% (v/v) CO2 atmosphere.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HepG2 cells were seeded on 6-well plates at 70–80% confluent density and cultured for 24 h in antibiotic-free DMEM.  For leucine starvation, the cells were grown in minimum essential medium (Sigma-Aldrich) lacking leucine but supplemented with 10% (v/v) fetal bovine serum. Before starvation, the cells were rinsed twice with phosphate-buffered saline (Gibco, Waltham, MA, USA).For overexpression experiments, ATF4-overexpressing plasmid and pcDNA3.1 empty vector were transfected into HepG2 cells using Invitrogen Lipofectamine 2000 (Thermo Fisher Scientific) following the manufacturer's instructions. After 6 h, the culture medium was replaced with a complete medium and incubated for further 24 h.

tag: cell line

tag: treatment

value: leucine deprivation


title: HepG2 cell, control sample for leucine deprivation condition, bio rep2

description: Gene expression data of HepG2 cell under leucine deprivation condition, control

scan_protocol: After washing and staining, array scanning was performed using GeneChip Hybridization and Affymetrix Gene Array Scanner 3000

source_name: HepG2 cell, leucine deprivation condition, control

value: leucine deprivation, control


title: HepG2 cell, leucine deprivation sample under leucine deprivation condition, bio rep1


title: HeLa TGS1 CRISPR mutant clone 1

city: Rome

first: Grazia Daniela

last: Raffa

address: P.le Aldo Moro 5

country: Italy

institute: Sapienza Università di Roma

library_source: transcriptomic

data_processing:
Primary data acquisition was performed by MinKNOW.
Basecalling and demultiplexing of Fast5 files obtained by sequencing were performed using Guppy v4.2.2.
Reads with Q-score >7 were mapped to hg38 genome using Minimap2 v2.17 with parameters -ax splice.
To assemble and quantify transcripts from Nanopore reads we used FLAIR v1.4. BAM files obtained with Minimap2 were converted into BED12 files using the bam2Bed12.py utility included in FLAIR. After this, splice junctions of reads were corrected using FLAIR correct module using both the GENCODE v33 GTF file and short Illumina reads of the  corresponding samples. BED12 files were then filtered to maintain only reads with at least one splice junction.
Filtered BED12 files from all samples were used to assemble the transcriptome using the FLAIR collapse module, providing the GENCODE GTF file to annotate the results and requiring at least 10 supporting reads to identify novel transcripts. Transcripts from both the GENCODE and FLAIR GTF files were quantified using the FLAIR quantify module.
Genome_build: hg38
Supplementary_files_format_and_content: GTF file describing the transcriptome assembled by FLAIR.
Supplementary_files_format_and_content: Tab-delimited text file including TPM values in each sample calculated for each transcript assembled by FLAIR.

molecule: polyA RNA

source_name: HeLa

growth_protocol: HeLa S3 cells were cultured in DMEM supplemted with 10% Fetal Bovine Serum and Penicillin-Streptomycin at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted with Trizol reagent (Ambion), treated with Ambion™ DNase I (RNase-free) extracted with phenol/chloroform. RNA samples were quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA).
RNA libraries were prepared for Oxford Nanopore MinION  sequencing using PCR-cDNA Barcoding (SQK-PCB109) protocol.

tag: cell type

value: Cervical adenocarcinoma

tag: strain


title: HFD.WT3

description: Processed OTU.txt


title: HepG2 cell, ATF4 transfect sample for ATF4 overexpression condition

description: Gene expression data of HepG2 cell under ATF4 overexpression condition

source_name: HepG2 cell, ATF4 overexpression condition

value: ATF4 overexpression


title: HFD.SNTG2

description: Processed OTU.txt


title: HFD.SNTG3

description: Processed OTU.txt


title: chow.WT2

description: Processed OTU.txt

value: Chow


title: HepG2 cell, control sample for leucine deprivation condition, bio rep1


title: HFD.SNTG1

description: Processed OTU.txt


title: chow.SNTG3

description: Processed OTU.txt


title: chow.SNTG1

description: Processed OTU.txt


title: chow.WT3

description: Processed OTU.txt


title: chow.WT1

description: Processed OTU.txt


title: TX_2i_mESCs_5069 [IMPLICON]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

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

extract_protocol:
Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) or the AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s instructions and eluted into TE buffer or H2O.
The IMPLICON protocol consists of 2 PCR reactions. In the first reaction each sample is amplified with each primer pair in individual reactions: 30ng (2μl of 66μl eluted bisulfite treated DNA) of bisulfite treated DNA is amplified with 1.2μl of 10μM primer pool (final 1.5μM) containing both forward and reverse primers in 4μl of 2x KAPA HiFi Uracil+ ReadyMix in a final volume of 8μl. DNA was amplified using the following conditions: initial denaturation at 95°C for 5min, 30 cycles of 98°C denaturation for 20 seconds, variable annealing temperature for 15 seconds and extension at 72°C for 60 seconds; followed by a final extension at 72°C for 10 minutes. All PCR reactions for each individual sample were pooled together and samples cleaned-up using 1.5x AMPure XP beads and eluted in 20μl H2O. In the second PCR reaction, barcoded Illumina adapters are attached to the pooled PCR samples ensuring that each sample pool receives a unique reverse barcoded adapter. The 20μl PCR pool was amplified using 1μl of 10μM Illlumina PE1.0 primer (same for all samples) and 1μl of 10μM Illumina iTAG primer (distinct for each sample) and 25μl 2x KAPA HiFi Uracil+ ReadyMix in a 50μl volume reaction using the following conditions: initial denaturation at 98°C for 45 seconds, 5 cycles of 98°C denaturation for 15 seconds, 65°C annealing for 30 seconds and extension at 72°C for 30 seconds; followed by a final extension at 72°C for 5 minutes. Reactions were cleaned-up with 1x AMPure XP beads and eluted in 20μl. Libraries were verified by running 1:30 dilutions on Agilent bioanalyser.

treatment_protocol: 1μg of genomic DNA was bisulfite converted using the EZ DNA methylation Gold kit (Zymo Research) according to manufacturer’s instructions with either magnetic bead or column clean-up and eluted/resuspended in 66μl elution buffer to obtain a final concentration of ~15ng/μl bisulfite converted DNA.

value: Mouse embryonic stem cell

tag: Sex

value: Female

tag: group

value: control mESC type generated in 2i conditions


title: HFD.SNTG4

description: Processed OTU.txt


title: BS1014_PD1_48_ADT

status: Public on Jul 16 2022

city: Basel

first: Marina

last: Natoli

state: Basel city

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

description:
Antibody-derived oligonucleotide library matched to mRNA samples
Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
Cell Ranger v5.0 was used for demultiplexing, alignment, filtering, barcode counting and UMI counting
Assembly: hg18
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: Lung Tumour

extract_protocol:
10x Genomics protocol for 3′ gene expression profiling with feature barcoding (CG000206, Rev A)
3' paired end scRNAseq with CITE-seq

treatment_protocol: Libraires were prepared following the 10x Genomics protocol for 3′ gene expression profiling with feature barcoding (CG000206, Rev A) and cDNA or library quality was assessed using a 4200 TapeStation System (Agilent).

tag: patient id

value: Lung Tumour

tag: treatment time

tag: library type

value: ADT

tag: antibodies/tags

value: TotalSeqB TBNK cocktail BioLegend cat. 399902


title: M_FBS2_miPSCs [IMPLICON]

value: Mouse induced pluripotent stem cell

value: Male

value: miPSC type generated using FBS


title: chow.WT4

description: Processed OTU.txt

value: Wild-type

value: Feces

value: SPF


title: dsGFP4

city: Xinxiang

first: Libo

last: Hou

state: Henan

address: 110 Room, College of Fisheries, 46 Jianshe East Road

institute: Henan normal university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

organism: Eriocheir sinensis

source_name: hemolymph

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hemolymph

value: hemocytes

tag: time point

value: GFP knockdown


title: chow.SNTG4

description: Processed OTU.txt

value: Villin-Snhg9 Tg


title: F_FBS5_miPSCs [IMPLICON]


title: F_FBS3_miPSCs [IMPLICON]


title: chow.SNTG5

description: Processed OTU.txt

value: Chow


title: F_FBS2_miPSCs [IMPLICON]


title: Tx_2i_mESCs_4836 [IMPLICON]

value: Mouse embryonic stem cell


title: M_KSR6_miPSCs_4836 [IMPLICON]

value: miPSC type generated using KSR


title: M_KSR2_miPSCs_4836 [IMPLICON]


title: M_KSR1_miPSCs_4836 [IMPLICON]


title: chow.SNTG2

description: Processed OTU.txt


title: M_FBS3_miPSCs [IMPLICON]


title: Male_MEFs_4836 [IMPLICON]

value: Mouse embryonic fibroblasts

value: male

value: Parental male mouse embryonic fibroblasts


title: M_FBS4_miPSCs [IMPLICON]


title: F_KSR6_miPSCs_4836 [IMPLICON]

value: Female


title: M_FBS5_miPSCs [IMPLICON]

value: Mouse induced pluripotent stem cell


title: M_KSR5_miPSCs_4836 [IMPLICON]

value: Male


title: M_FBS1_miPSCs [IMPLICON]

value: miPSC type generated using FBS


title: Female_MEFs_4836 [IMPLICON]

value: female

value: Parental female mouse embryonic fibroblasts


title: M_KSR3_miPSCs_4836 [IMPLICON]


title: JB10_CD_Adenoma

city: Bethesda

first: Prashant

last: Chittiboina

state: MD

address: 3D20, 10 Center Drive

department: NINDS

country: USA

institute: NIH

data_processing:
Paired-end sequence files (.fastq) per sample were quality inspected using the FastQC tool 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) then adaptor clipped (TruSeq3-PE-2.fa:2:30:10) and trimmed to remove 5' nucleotide bias (HEADCROP:12) and low quality calls (TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:15) using the Trimmomatic tool 0.39
Surviving intact pairs of reads per sample were then imported into the CLCbio Genomics Workbench v11 (https://www.qiagenbioinformatics.com/) and reference mapped by sample in stranded fashion against the current instance of the human genome (GRCh38) using the "RNA-Seq Analysis" tool supported therein under default parameters.
Expression in counts per known annotated gene (Homo_sapiens.GRCh38.96.chr.gff3) were then exported from the tool.
Analysis of bulk RNA sequencing data for paired core-margin samples was performed using the edgeR package on total exon counts per gene.
A paired analysis was performed with GLM-based approach was used with design matrix including patient and sample type. Genes were filtered by expression with filterByExpr, dispersion estimated with estimateDisp, and the GLM fit with glmFit. The log ratio test was used to detect differences between core vs margin or CD vs nonCD samples using glmLRT, and significant genes were recorded at FDR<0.01 and log fold-change > 1.5.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include nrmalized values for each Sample

source_name: Pituitary cells

extract_protocol:
Paired human adenoma and normal pituitary gland were procured from surgery and immediately flash frozen in 1 mL of Qiazol (Qiagen, Germany) within Lysing Matrix E tubes (MP Biomedicals, Santa Ana, CA) in dry ice. We thawed the contents and homogenized the tissues using a Fast Prep-24 Homogenizer, (MP Biomedicals) for 20 seconds at 4.5 m/s. Total RNA was extracted using an RNeasy Mini Kit (Qiagen, Germany). RNA quantity and quality were measured by NanoDrop ND-1000, and integrity assessed by agarose gel electrophoresis. PolyA+ mRNA isolation, size fragmentation, cDNA synthesis, size selection, and next gen sequencing were performed at the National Intramural Sequencing Center, Bethesda, MD
RNA-Seq libraries were constructed from 1 μg total RNA after rRNA depletion using Ribo-Zero GOLD (Illumina). The Illumina TruSeq RNA Sample Prep V2 Kit was used according to manufacturer’s instructions.

value: Pituitary cells

value: Adenoma


title: F_KSR5_miPSCs_4836 [IMPLICON]


title: F_KSR4_miPSCs_4836 [IMPLICON]


title: F_KSR2_miPSCs_4836 [IMPLICON]


title: F_KSR3_miPSCs_4836 [IMPLICON]


title: F_KSR1_miPSCs_4836 [IMPLICON]


title: M_KSR3_miPSCs_4666 [IMPLICON]


title: M_KSR5_miPSCs_4666 [IMPLICON]


title: F_FBS1_miPSCs [IMPLICON]


title: M_KSR4_miPSCs_4666 [IMPLICON]


title: Male_MEFs_4666 [IMPLICON]


title: M_KSR6_miPSCs_4666 [IMPLICON]


title: M_KSR2_miPSCs_4666 [IMPLICON]


title: F_KSR5_miPSCs_4666 [IMPLICON]


title: F_KSR4_miPSCs_4666 [IMPLICON]


title: M_KSR4_miPSCs_4836 [IMPLICON]


title: F_KSR1_miPSCs_4666 [IMPLICON]


title: WT2

description: Processed tg_wt.txt

data_processing:
Reads were mapped against mm10 using tophat with default parameters and FPKMs were calculated using cuffdiff with default parameters.
assembly: mm10 (GRCm38)
Tab-delimited text file with FPKM for each sample.

source_name: Ileum

extract_protocol:
RNA was extracted from ileum using Rneasy Mini Kit (Qiagen 74104).
Sequencing libraries were prepared using TruSeq RNA sample preparation kit v2 (Illumina).

value: Wild-type

value: Ileum

value: SPF


title: Female_MEFs_4666 [IMPLICON]


title: Sntg2

description: Processed tg_wt.txt

value: Villin-Snhg9 Tg

value: Chow


title: TCRseq

city: Stanford

first: Juliane

last: Lohmeyer

address: 269 W. Campus Drive

institute: Stanford University

data_processing:
Sequencing reads were checked using FastQC v.0.11.7. Estimated transcript counts and transcripts per million (TPM) for the mouse genome assembly GRCm38 (mm10) were obtained using the pseudo-aligner Kallisto. Transcript-level abundance was quantified and summarized into gene level using the tximport R package. Differential gene expression was performed using the DESeq2 R package version 1.22.221. TCRα and TCRβ sequence analysis was performed with VDJFasta
Assembly: mouse genome assembly GRCm38 (mm10)
Supplementary files format and content: RNAseq: csv file with normalized counts for each sample
Supplementary files format and content: TCRseq: csv file with counts and proportion for each TCR sequence and sample
Library strategy: TCR-seq

source_name: spleen + lymph nodes

extract_protocol:
RNA was extracted using the TRizol RNA isolation method combined with the RNeasy MinElute Cleanup (Qiagen).
The Clontech SMARTer v4 Kit (Takara Bio USA, Inc.) was used to generate full-length cDNA prior to library preparation with the Nextera XT DNA Library Prep Kit (Illumina, Inc.). For TCR sequencing, libraries were prepared from the synthesized full-length cDNA using the nested PCR method reported previously (Han et al., Saligrama et al.)

value: spleen + lymph nodes

value: primary

value: T cell


title: WT1

description: Processed tg_wt.txt


title: F_KSR2_miPSCs_4666 [IMPLICON]

value: miPSC type generated using KSR


title: M_KSR1_miPSCs_4666 [IMPLICON]


title: CV1

description: Processed cv_gf.txt

source_name: Ileum epithelial cells

extract_protocol:
RNA was extracted from intestinal epithelial cells isolated by laser capture microdissection. Extracted RNA was purified using PicoPure RNA Isolation Kit (Life Technology 12204-01).
Sequencing libraries were prepared using TruSeq RNA sample preparation kit v2 (Illumina).

value: Ileum epithelial cells


title: CV2

description: Processed cv_gf.txt


title: GF2

description: Processed cv_gf.txt

value: Germ-free


title: G- mouse 70 - Ecad high

city: Amsterdam

first: Roebi

middle: de

last: Bruijn

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Reads were mapped to the genome with Hisat version: 2.1.0
Read counts were determined with Icount, which is based on HTSeq-count, using mode union
Assembly: Mus_musculus.GRCm38_87
Supplementary files format and content: ensembl gene id vs 8 samples plus gene annotation columns

source_name: brain metastasis

extract_protocol:
FACS sorted samples were frozen at -80C in FACS collection medium and Trizol LS reagent (Invitrogen, Cat. No 10296010). RNA was harvested with Trizol LS reagent according to the manufacturer´s protocol. To help with the visualization of the pellet we used GlycoBlue Coprecipitant (Invitrogen, Cat. No AM9516) as described by the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: wild type

tag: disease state

value: breast cancer

value: brain metastasis tumor

tag: e-cadherin status

value: Ecad high


title: H- mouse 70 - Ecad low

value: Ecad low


title: F_KSR3_miPSCs_4666 [IMPLICON]

value: Mouse induced pluripotent stem cell

value: Female


title: E- mouse 67 - Ecad high


title: C- mouse 57 - Ecad high


title: B- mouse 58 - Ecad low


title: D- mouse 57 - Ecad low


title: ASO

city: 都城市

first: 超

last: 章

state: 宮崎県

address: 下川東4丁目28号1番

institute: 霧島酒造株式会社

hyb_protocol: Each labeled cRNA of 1.65 µg was fragmented using the Gene Expression Hybridization Kit and applied to the Whole Mouse Genome Microarray Ver2.0 slide for 17 h hybridization at 65 °C.

scan_protocol: Gene expression analyses were performed using the array analysis software GenePix Pro. A microarray scanner GenePix 4000B, was used to produce an array image scan digitized with the array analysis software GenePix Pro.

data_processing: The signal data for the features (spots of the array) were imported into GeneSpring 12.6 (Agilent Technologies, Inc.) and further analyzed with the software. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.The signal data from the arrays were normalized using the 75th percentile method, and baseline transformation was performed with the median of the control samples.

organism: Mus

source_name: hippocampus, administered orally,15day

label_protocol: Two hundred-nanogram samples of total RNA pooled in equal amounts of five samples from each group were synthesized with cDNA, Cy3-labeled cRNA, and purified using the Low Input Quick Amp Labeling Kit. The concentration of labeled cRNA and Cy3 incorporation was calculated from the absorbance at 260, 280, 550, and 320 nm, and we confirmed that the standard value (Cy3-CTP incorporation > 6 pmol/g) was reached.

growth_protocol: The experiment was divided into three groups: the normal control group (NCO), the Aβ25-35 injected-control group (ACO), and the Aβ25-35 injected-shochu oil group (ASO). The experimental substance was administered orally to mice for 15 days, with distilled water (the medium) given to those in the NCO and ACO groups. Shochu oil (administered to the ASO group) was administered orally at 2,000 mg/kg/day. Each mouse in the NCO group was given 5 μL of distilled water, Each mouse in the ACO and the SCO groups was intracerebroventricularly injected 5 μL (10 nmol) of the Aß25-35 solution on the 8th day after oral administration began. The Y-maze spontaneous alternation experiment was conducted on day 16. Samples for RNA extraction were derived from RNAlater-treated frozen hippocampus stored after measurement of the Y-maze spontaneous alternation (n = 10).

extract_protocol: Total RNA was isolated using RNAiso plus following the manufacturer’s instructions. To balance the data reproducibility and cost performance, we pooled the RNA from two mice as one set and obtained five sets from ten mice in each group. After centrifugation, the RNA was precipitated from the aqueous layer, washed, and dissolved in DNase/RNase-free distilled water. Next, the extracted total RNA liquid phase was mixed with DNase/RNase-free distilled water and purified with the RNeasy MinElute Cleanup Kit. RNA concentration and integrity were assessed by spectrophotometry and gel electrophoresis. The total RNA obtained was measured for absorbance at 260 nm and 280 nm, and the ratio of absorbance at 260 nm and 280 nm was used to assess the purity of RNA. A ratio of over 2.0 was generally accepted as “pure” for RNA. The extracted total RNA was stored frozen (< -70 °C).

treatment_protocol: After the measurement of spontaneous alternation behavior in the Y-maze experiment, mice were euthanized with CO2 gas, and decapitated. The hippocampus, which was collected from the isolated brain, was pretreated by immersion in RNAlater RNA Stabilization Reagent (RNAlater). The RNAlater-treated hippocampus was stored frozen (< -70 °C).

value: Slc:ddY mice

value: hippocampus

tag: gender

value: male

tag: age

value: Aβ25-35 injected-shochu oil group


title: F- mouse 67 - Ecad low

tag: genotype


title: F_KSR6_miPSCs_4666 [IMPLICON]


title: ACO

tag: tissue

value: Aβ25-35 injected-control group


title: F_FBS4_miPSCs [IMPLICON]

value: miPSC type generated using FBS


title: Sntg1

description: Processed tg_wt.txt

tag: strain/background

value: Villin-Snhg9 Tg

value: Ileum

tag: housing condition

value: SPF

tag: diet

value: Chow


title: GF1

description: Processed cv_gf.txt

value: Wild-type

value: Ileum epithelial cells

value: Germ-free


city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description: L4_W767: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1535), replicate 2

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

source_name: Mouse neuroblastoma cells

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

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

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

value: Mouse neuroblastoma cells

tag: cell line


description: L4_W768: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1536), replicate 2


description: L4_W766: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1534), replicate 2


title: NCO

tag: strain

tag: treatment

value: control


description: L4_W760: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp295 knockdown (T1528), replicate 2


description: L4_W763: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp553 knockdown (T1531), replicate 2


description: L4_W761: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zscan12 knockdown (T1529), replicate 2


description: L4_W764: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2a knockdown (T1532), replicate 2


description: L4_W758: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zbtb43 knockdown (T1526), replicate 2


title: A- mouse 58 - Ecad high

value: FVB

value: wild type

value: breast cancer

value: brain metastasis tumor

value: Ecad high


description: L4_W759: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp617 knockdown (T1527), replicate 2


description: L4_W762: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp97 knockdown (T1530), replicate 2


description: L4_W757: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3h8 knockdown (T1525), replicate 2


description: L4_W756: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1524), replicate 2


description: L4_W755: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1523), replicate 2


description: L4_W754: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1522), replicate 2


description: L4_W753: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbmxl2 knockdown (T1521), replicate 2


description: L4_W750: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp326 knockdown (T1518), replicate 2


description: L4_W751: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3h3 knockdown (T1519), replicate 2


description: L4_W752: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zscan21 knockdown (T1520), replicate 2


description: L4_W749: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp628 knockdown (T1517), replicate 2


description: L4_W765: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1533), replicate 2


description: L4_W748: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp282 knockdown (T1516), replicate 2


description: L4_W746: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ythdf3 knockdown (T1514), replicate 2


description: L4_W745: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp236 knockdown (T1513), replicate 2


description: L4_W744: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1512), replicate 2


description: L4_W741: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm44 knockdown (T1509), replicate 2


description: L4_W743: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1511), replicate 2


description: L4_W747: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp263 knockdown (T1515), replicate 2


description: L4_W742: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1510), replicate 2


description: L4_W737: SPAR-seq of 108 multi-exon gene regions in N2A cells, Wbp4 knockdown (T1505), replicate 2


description: L4_W739: SPAR-seq of 108 multi-exon gene regions in N2A cells, Xab2 knockdown (T1507), replicate 2


description: L4_W738: SPAR-seq of 108 multi-exon gene regions in N2A cells, Parp12 knockdown (T1506), replicate 2


description: L4_W740: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp358 knockdown (T1508), replicate 2


description: L4_W733: SPAR-seq of 108 multi-exon gene regions in N2A cells, Unk knockdown (T1501), replicate 2


description: L4_W735: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp9 knockdown (T1503), replicate 2


description: L4_W730: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1498), replicate 2


description: L4_W734: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp57 knockdown (T1502), replicate 2


description: L4_W731: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1499), replicate 2


description: L4_W732: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1500), replicate 2


description: L4_W728: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp90 knockdown (T1496), replicate 2


description: L4_W726: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cxcl12 knockdown (T1494), replicate 2


description: L4_W727: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp180 knockdown (T1495), replicate 2


description: L4_W724: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp68 knockdown (T1492), replicate 2


description: L4_W725: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zzz3 knockdown (T1493), replicate 2


description: L4_W723: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3hav1 knockdown (T1491), replicate 2


description: L4_W721: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp36l2 knockdown (T1489), replicate 2


description: L4_W722: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp36 knockdown (T1490), replicate 2


description: L4_W720: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1488), replicate 2


description: L4_W719: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1487), replicate 2


description: L4_W718: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1486), replicate 2


description: L4_W715: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp277 knockdown (T1483), replicate 2


description: L4_W716: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp62 knockdown (T1484), replicate 2


description: L4_W714: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp316 knockdown (T1482), replicate 2


description: L4_W713: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp955a knockdown (T1481), replicate 2


description: L4_W712: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp260 knockdown (T1480), replicate 2


description: L4_W736: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp451 knockdown (T1504), replicate 2


description: L4_W729: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1497), replicate 2


description: L4_W708: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1476), replicate 2


description: L4_W710: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp207 knockdown (T1478), replicate 2


description: L4_W707: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1475), replicate 2


description: L4_W711: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1479), replicate 2


description: L4_W706: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1474), replicate 2


description: L4_W702: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zcchc8 knockdown (T1470), replicate 2


description: L4_W704: SPAR-seq of 108 multi-exon gene regions in N2A cells, U2af2 knockdown (T1472), replicate 2


description: L4_W705: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nova1 knockdown (T1473), replicate 2


description: L4_W701: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp317 knockdown (T1469), replicate 2


description: L4_W703: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfr knockdown (T1471), replicate 2


description: L4_W697: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ythdf2 knockdown (T1465), replicate 2


description: L4_W698: SPAR-seq of 108 multi-exon gene regions in N2A cells, Wtap knockdown (T1466), replicate 2


description: L4_W700: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp239 knockdown (T1468), replicate 2


description: L4_W717: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1485), replicate 2


description: L4_W694: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1462), replicate 2


description: L4_W693: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mex3a knockdown (T1461), replicate 2


description: L4_W691: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp467 knockdown (T1459), replicate 2


description: L4_W695: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1463), replicate 2


description: L4_W690: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp330 knockdown (T1458), replicate 2


description: L4_W696: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1464), replicate 2


description: L4_W688: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp385a knockdown (T1456), replicate 2


description: L4_W689: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sf1 knockdown (T1457), replicate 2


description: L4_W684: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1452), replicate 2


description: L4_W709: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp13 knockdown (T1477), replicate 2


description: L4_W699: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1467), replicate 2


description: L4_W685: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp1 knockdown (T1453), replicate 2


description: L4_W682: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1450), replicate 2


description: L4_W676: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp319 knockdown (T1444), replicate 2


description: L4_W692: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zrsr2 knockdown (T1460), replicate 2


description: L4_W681: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zmym1 knockdown (T1449), replicate 2


description: L4_W687: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3h7a knockdown (T1455), replicate 2


description: L4_W683: SPAR-seq of 108 multi-exon gene regions in N2A cells, untreated (T1451), replicate 2


description: L4_W679: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ybx2 knockdown (T1447), replicate 2


description: L4_W686: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ythdf1 knockdown (T1454), replicate 2


description: L4_W678: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp35 knockdown (T1446), replicate 2


description: L4_W671: SPAR-seq of 108 multi-exon gene regions in N2A cells, Stag1 knockdown (T1439), replicate 2


description: L4_W670: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tnrc6a knockdown (T1438), replicate 2


description: L4_W674: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp59 knockdown (T1442), replicate 2


description: L4_W677: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zkscan3 knockdown (T1445), replicate 2


description: L4_W673: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1441), replicate 2


description: L4_W675: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp46 knockdown (T1443), replicate 2


description: L4_W669: SPAR-seq of 108 multi-exon gene regions in N2A cells, U2af1l4 knockdown (T1437), replicate 2


description: L4_W672: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1440), replicate 2


description: L4_W668: SPAR-seq of 108 multi-exon gene regions in N2A cells, Alyref knockdown (T1436), replicate 2


description: L4_W665: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thap1 knockdown (T1433), replicate 2


description: L4_W666: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thoc3 knockdown (T1434), replicate 2


description: L4_W667: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrpe knockdown (T1435), replicate 2


description: L4_W663: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tipin knockdown (T1431), replicate 2


description: L4_W662: SPAR-seq of 108 multi-exon gene regions in N2A cells, Stag3 knockdown (T1430), replicate 2


description: L4_W661: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tnks knockdown (T1429), replicate 2


description: L4_W660: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tmpo knockdown (T1428), replicate 2


description: L4_W658: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrpg knockdown (T1426), replicate 2


description: L4_W659: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sugp1 knockdown (T1427), replicate 2


description: L4_W657: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf9 knockdown (T1425), replicate 2


description: L4_W680: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zbtb22 knockdown (T1448), replicate 2


description: L4_W654: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smc6 knockdown (T1422), replicate 2


description: L4_W656: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sugp2 knockdown (T1424), replicate 2


description: L4_W652: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf6 knockdown (T1420), replicate 2


description: L4_W653: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srrm1 knockdown (T1421), replicate 2


description: L4_W651: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrpa knockdown (T1419), replicate 2


description: L4_W650: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rad54l2 knockdown (T1418), replicate 2


description: L4_W643: SPAR-seq of 108 multi-exon gene regions in N2A cells, Shprh knockdown (T1411), replicate 2


description: L4_W646: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nhp2l1 knockdown (T1414), replicate 2


description: L4_W644: SPAR-seq of 108 multi-exon gene regions in N2A cells, U2af1 knockdown (T1412), replicate 2


description: L4_W645: SPAR-seq of 108 multi-exon gene regions in N2A cells, Taf9 knockdown (T1413), replicate 2


description: L4_W648: SPAR-seq of 108 multi-exon gene regions in N2A cells, Scand1 knockdown (T1416), replicate 2


description: L4_W664: SPAR-seq of 108 multi-exon gene regions in N2A cells, Stag2 knockdown (T1432), replicate 2


description: L4_W647: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sp6 knockdown (T1415), replicate 2


description: L4_W641: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf1 knockdown (T1409), replicate 2


description: L4_W642: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kdm6a knockdown (T1410), replicate 2


description: L4_W639: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rsph1 knockdown (T1407), replicate 2


description: L4_W638: SPAR-seq of 108 multi-exon gene regions in N2A cells, Txnl4a knockdown (T1406), replicate 2


description: L4_W636: SPAR-seq of 108 multi-exon gene regions in N2A cells, Usp39 knockdown (T1404), replicate 2


description: L4_W637: SPAR-seq of 108 multi-exon gene regions in N2A cells, Vmn1r11 knockdown (T1405), replicate 2


description: L4_W635: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tra2b knockdown (T1403), replicate 2


description: L4_W632: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpk knockdown (T1400), replicate 2


description: L4_W634: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snapc4 knockdown (T1402), replicate 2


description: L4_W633: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1401), replicate 2


description: L4_W631: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ssb knockdown (T1399), replicate 2


description: L4_W655: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sox11 knockdown (T1423), replicate 2


description: L4_W630: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sgol1 knockdown (T1398), replicate 2


description: L4_W629: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sept8 knockdown (T1397), replicate 2


description: L4_W649: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smc2 knockdown (T1417), replicate 2


description: L4_W628: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sox13 knockdown (T1396), replicate 2


description: L4_W640: SPAR-seq of 108 multi-exon gene regions in N2A cells, Supt16h knockdown (T1408), replicate 2


description: L4_W625: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrpa1 knockdown (T1393), replicate 2


description: L4_W626: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrpd1 knockdown (T1394), replicate 2


description: L4_W623: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrpb knockdown (T1391), replicate 2


description: L4_W624: SPAR-seq of 108 multi-exon gene regions in N2A cells, Stau1 knockdown (T1392), replicate 2


description: L4_W622: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sf3a2 knockdown (T1390), replicate 2


description: L4_W619: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sin3b knockdown (T1387), replicate 2


description: L4_W618: SPAR-seq of 108 multi-exon gene regions in N2A cells, Clasrp knockdown (T1386), replicate 2


description: L4_W616: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ttc14 knockdown (T1384), replicate 2


description: L4_W617: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sf3b4 knockdown (T1385), replicate 2


description: L4_W611: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thap4 knockdown (T1379), replicate 2


description: L4_W612: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smc5 knockdown (T1380), replicate 2


description: L4_W621: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1389), replicate 2


description: L4_W610: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sirt3 knockdown (T1378), replicate 2


description: L4_W620: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrnp70 knockdown (T1388), replicate 2


description: L4_W609: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf4 knockdown (T1377), replicate 2


description: L4_W613: SPAR-seq of 108 multi-exon gene regions in N2A cells, Spag5 knockdown (T1381), replicate 2


description: L4_W614: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sf3b1 knockdown (T1382), replicate 2


description: L4_W608: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf12 knockdown (T1376), replicate 2


description: L4_W607: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tspyl1 knockdown (T1375), replicate 2


description: L4_W604: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thap7 knockdown (T1372), replicate 2


description: L4_W606: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smu1 knockdown (T1374), replicate 2


description: L4_W605: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sirt6 knockdown (T1373), replicate 2


description: L4_W627: SPAR-seq of 108 multi-exon gene regions in N2A cells, Adad1 knockdown (T1395), replicate 2


description: L4_W601: SPAR-seq of 108 multi-exon gene regions in N2A cells, Stau2 knockdown (T1369), replicate 2


description: L4_W603: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1371), replicate 2


description: L4_W599: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrpb2 knockdown (T1367), replicate 2


description: L4_W600: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eftud2 knockdown (T1368), replicate 2


description: L4_W598: SPAR-seq of 108 multi-exon gene regions in N2A cells, Celf3 knockdown (T1366), replicate 2


description: L4_W602: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sept6 knockdown (T1370), replicate 2


description: L4_W597: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tdrd3 knockdown (T1365), replicate 2


description: L4_W596: SPAR-seq of 108 multi-exon gene regions in N2A cells, Stra13 knockdown (T1364), replicate 2


description: L4_W615: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1383), replicate 2


description: L4_W595: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sf3b2 knockdown (T1363), replicate 2


description: L4_W594: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dynlt3 knockdown (T1362), replicate 2


description: L4_W592: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thumpd1 knockdown (T1360), replicate 2


description: L4_W587: SPAR-seq of 108 multi-exon gene regions in N2A cells, Strbp knockdown (T1355), replicate 2


description: L4_W593: SPAR-seq of 108 multi-exon gene regions in N2A cells, Strap knockdown (T1361), replicate 2


description: L4_W591: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf5 knockdown (T1359), replicate 2


description: L4_W586: SPAR-seq of 108 multi-exon gene regions in N2A cells, Slc11a1 knockdown (T1354), replicate 2


description: L4_W583: SPAR-seq of 108 multi-exon gene regions in N2A cells, Taf8 knockdown (T1351), replicate 2


description: L4_W585: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrpc knockdown (T1353), replicate 2


description: L4_W580: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smc1a knockdown (T1348), replicate 2


description: L4_W581: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrpd3 knockdown (T1349), replicate 2


description: L4_W584: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snw1 knockdown (T1352), replicate 2


description: L4_W579: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tfip11 knockdown (T1347), replicate 2


description: L4_W577: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1345), replicate 2


description: L4_W578: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tdrd1 knockdown (T1346), replicate 2


description: L4_W575: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm4 knockdown (T1343), replicate 2


description: L4_W589: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smyd5 knockdown (T1357), replicate 2


description: L4_W590: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sycp3 knockdown (T1358), replicate 2


description: L4_W573: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rod1 knockdown (T1341), replicate 2


description: L4_W571: SPAR-seq of 108 multi-exon gene regions in N2A cells, Orc3 knockdown (T1339), replicate 2


description: L4_W570: SPAR-seq of 108 multi-exon gene regions in N2A cells, Orc4 knockdown (T1338), replicate 2


description: L4_W572: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf5a knockdown (T1340), replicate 2


description: L4_W588: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tdrd6 knockdown (T1356), replicate 2


description: L4_W569: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm17 knockdown (T1337), replicate 2


description: L4_W568: SPAR-seq of 108 multi-exon gene regions in N2A cells, Orc2 knockdown (T1336), replicate 2


description: L4_W567: SPAR-seq of 108 multi-exon gene regions in N2A cells, Polr2h knockdown (T1335), replicate 2


description: L4_W564: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rp9 knockdown (T1332), replicate 2


description: L4_W582: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sirt7 knockdown (T1350), replicate 2


description: L4_W565: SPAR-seq of 108 multi-exon gene regions in N2A cells, Polr2k knockdown (T1333), replicate 2


description: L4_W562: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rps13 knockdown (T1330), replicate 2


description: L4_W566: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf8 knockdown (T1334), replicate 2


description: L4_W563: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mex3d knockdown (T1331), replicate 2


description: L4_W576: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1344), replicate 2


description: L4_W557: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pole3 knockdown (T1325), replicate 2


description: L4_W561: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rcor2 knockdown (T1329), replicate 2


description: L4_W559: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pogk knockdown (T1327), replicate 2


description: L4_W560: SPAR-seq of 108 multi-exon gene regions in N2A cells, Repin1 knockdown (T1328), replicate 2


description: L4_W558: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf15 knockdown (T1326), replicate 2


description: L4_W552: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pole4 knockdown (T1320), replicate 2


description: L4_W553: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ptbp2 knockdown (T1321), replicate 2


description: L4_W551: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbmx knockdown (T1319), replicate 2


description: L4_W555: SPAR-seq of 108 multi-exon gene regions in N2A cells, Poldip3 knockdown (T1323), replicate 2


description: L4_W550: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rdm1 knockdown (T1318), replicate 2


description: L4_W548: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbmxl1 knockdown (T1316), replicate 2


description: L4_W574: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sec13 knockdown (T1342), replicate 2


description: L4_W544: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sfmbt2 knockdown (T1312), replicate 2


description: L4_W545: SPAR-seq of 108 multi-exon gene regions in N2A cells, Scaf8 knockdown (T1313), replicate 2


description: L4_W546: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rpa1 knockdown (T1314), replicate 2


description: L4_W542: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pold2 knockdown (T1310), replicate 2


description: L4_W547: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm10 knockdown (T1315), replicate 2


description: L4_W543: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ptcd1 knockdown (T1311), replicate 2


description: L4_W541: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pspc1 knockdown (T1309), replicate 2


description: L4_W540: SPAR-seq of 108 multi-exon gene regions in N2A cells, Papola knockdown (T1308), replicate 2


description: L4_W538: SPAR-seq of 108 multi-exon gene regions in N2A cells, Polr1b knockdown (T1306), replicate 2


description: L4_W539: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rps26 knockdown (T1307), replicate 2


description: L4_W554: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prr3 knockdown (T1322), replicate 2


description: L4_W536: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pole2 knockdown (T1304), replicate 2


description: L4_W556: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm7 knockdown (T1324), replicate 2


description: L4_W535: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pdcd7 knockdown (T1303), replicate 2


description: L4_W537: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1305), replicate 2


description: L4_W534: SPAR-seq of 108 multi-exon gene regions in N2A cells, Psip1 knockdown (T1302), replicate 2


description: L4_W532: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rrs1 knockdown (T1300), replicate 2


description: L4_W529: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pmf1 knockdown (T1297), replicate 2


description: L4_W549: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppie knockdown (T1317), replicate 2


description: L4_W531: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rragc knockdown (T1299), replicate 2


description: L4_W526: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rnf41 knockdown (T1294), replicate 2


description: L4_W530: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mex3b knockdown (T1298), replicate 2


description: L4_W533: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pola2 knockdown (T1301), replicate 2


description: L4_W524: SPAR-seq of 108 multi-exon gene regions in N2A cells, Satb1 knockdown (T1292), replicate 2


description: L4_W523: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rnf2 knockdown (T1291), replicate 2


description: L4_W525: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1293), replicate 2


description: L4_W527: SPAR-seq of 108 multi-exon gene regions in N2A cells, Orc1 knockdown (T1295), replicate 2


description: L4_W528: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pdcd11 knockdown (T1296), replicate 2


description: L4_W522: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf17 knockdown (T1290), replicate 2


description: L4_W521: SPAR-seq of 108 multi-exon gene regions in N2A cells, Scrt1 knockdown (T1289), replicate 2


description: L4_W516: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rnf138 knockdown (T1284), replicate 2


description: L4_W519: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1287), replicate 2


description: L4_W517: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rcor3 knockdown (T1285), replicate 2


description: L4_W511: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf39 knockdown (T1279), replicate 2


description: L4_W510: SPAR-seq of 108 multi-exon gene regions in N2A cells, Polr2c knockdown (T1278), replicate 2


description: L4_W509: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rnps1 knockdown (T1277), replicate 2


description: L4_W514: SPAR-seq of 108 multi-exon gene regions in N2A cells, Raly knockdown (T1282), replicate 2


description: L4_W515: SPAR-seq of 108 multi-exon gene regions in N2A cells, Polr2j knockdown (T1283), replicate 2


description: L4_W506: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pum2 knockdown (T1274), replicate 2


description: L4_W513: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppih knockdown (T1281), replicate 2


description: L4_W518: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm28 knockdown (T1286), replicate 2


description: L4_W507: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1275), replicate 2


description: L4_W503: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm14 knockdown (T1271), replicate 2


description: L4_W508: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rdbp knockdown (T1276), replicate 2


description: L4_W497: SPAR-seq of 108 multi-exon gene regions in N2A cells, Orc5 knockdown (T1265), replicate 2


description: L4_W505: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rpp25 knockdown (T1273), replicate 2


description: L4_W495: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm18 knockdown (T1263), replicate 2


description: L4_W512: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbpms knockdown (T1280), replicate 2


description: L4_W500: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf19 knockdown (T1268), replicate 2


description: L4_W494: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppil4 knockdown (T1262), replicate 2


description: L4_W492: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pnpt1 knockdown (T1260), replicate 2


description: L4_W502: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppil2 knockdown (T1270), replicate 2


description: L4_W501: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rufy2 knockdown (T1269), replicate 2


description: L4_W489: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm3 knockdown (T1257), replicate 2


description: L4_W504: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pum1 knockdown (T1272), replicate 2


description: L4_W498: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rex2 knockdown (T1266), replicate 2


description: L4_W520: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm8a knockdown (T1288), replicate 2


description: L4_W490: SPAR-seq of 108 multi-exon gene regions in N2A cells, Qk knockdown (T1258), replicate 2


description: L4_W493: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sart3 knockdown (T1261), replicate 2


description: L4_W483: SPAR-seq of 108 multi-exon gene regions in N2A cells, Chmp1a knockdown (T1251), replicate 2


description: L4_W491: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppil3 knockdown (T1259), replicate 2


description: L4_W482: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm39 knockdown (T1250), replicate 2


description: L4_W488: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf3 knockdown (T1256), replicate 2


description: L4_W477: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pabpc5 knockdown (T1245), replicate 2


description: L4_W496: SPAR-seq of 108 multi-exon gene regions in N2A cells, Purb knockdown (T1264), replicate 2


description: L4_W474: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif2d knockdown (T1242), replicate 2


description: L4_W479: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf13 knockdown (T1247), replicate 2


description: L4_W473: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mov10l1 knockdown (T1241), replicate 2


description: L4_W499: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm38 knockdown (T1267), replicate 2


description: L4_W487: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pogz knockdown (T1255), replicate 2


description: L4_W469: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ncbp2 knockdown (T1237), replicate 2


description: L4_W486: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rlim knockdown (T1254), replicate 2


description: L4_W480: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1248), replicate 2


description: L4_W485: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbfox2 knockdown (T1253), replicate 2


description: L4_W476: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ing5 knockdown (T1244), replicate 2


description: L4_W466: SPAR-seq of 108 multi-exon gene regions in N2A cells, Lsm4 knockdown (T1234), replicate 2


description: L4_W464: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nup155 knockdown (T1232), replicate 2


description: L4_W484: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rpa2 knockdown (T1252), replicate 2


description: L4_W470: SPAR-seq of 108 multi-exon gene regions in N2A cells, Morf4l1 knockdown (T1238), replicate 2


description: L4_W459: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nap1l5 knockdown (T1227), replicate 2


description: L4_W461: SPAR-seq of 108 multi-exon gene regions in N2A cells, Msi2 knockdown (T1229), replicate 2


description: L4_W475: SPAR-seq of 108 multi-exon gene regions in N2A cells, Myst2 knockdown (T1243), replicate 2


description: L4_W471: SPAR-seq of 108 multi-exon gene regions in N2A cells, Lsm11 knockdown (T1239), replicate 2


description: L4_W468: SPAR-seq of 108 multi-exon gene regions in N2A cells, Npm3 knockdown (T1236), replicate 2


description: L4_W481: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1249), replicate 2


description: L4_W457: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp637 knockdown (T1225), replicate 2


description: L4_W472: SPAR-seq of 108 multi-exon gene regions in N2A cells, Myef2 knockdown (T1240), replicate 2


description: L4_W454: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nup107 knockdown (T1222), replicate 2


description: L4_W478: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kdm5c knockdown (T1246), replicate 2


description: L4_W458: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mkrn1 knockdown (T1226), replicate 2


description: L4_W463: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pcbp1 knockdown (T1231), replicate 2


description: L4_W444: SPAR-seq of 108 multi-exon gene regions in N2A cells, Msi1 knockdown (T1212), replicate 2


description: L4_W447: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nup160 knockdown (T1215), replicate 2


description: L4_W465: SPAR-seq of 108 multi-exon gene regions in N2A cells, Jdp2 knockdown (T1233), replicate 2


description: L4_W442: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl2 knockdown (T1210), replicate 2


description: L4_W455: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nxf2 knockdown (T1223), replicate 2


description: L4_W467: SPAR-seq of 108 multi-exon gene regions in N2A cells, Lsm3 knockdown (T1235), replicate 2


description: L4_W462: SPAR-seq of 108 multi-exon gene regions in N2A cells, Trmt2a knockdown (T1230), replicate 2


description: L4_W441: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1209), replicate 2


description: L4_W460: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp870 knockdown (T1228), replicate 2


description: L4_W456: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pcbp3 knockdown (T1224), replicate 2


description: L4_W452: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kdm4b knockdown (T1220), replicate 2


description: L4_W450: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nxf1 knockdown (T1218), replicate 2


description: L4_W435: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kdm4c knockdown (T1203), replicate 2


description: L4_W436: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nsfl1c knockdown (T1204), replicate 2


description: L4_W449: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phax knockdown (T1217), replicate 2


description: L4_W453: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mxd3 knockdown (T1221), replicate 2


description: L4_W445: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nol6 knockdown (T1213), replicate 2


description: L4_W448: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prmt8 knockdown (T1216), replicate 2


description: L4_W446: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dpf1 knockdown (T1214), replicate 2


description: L4_W439: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nelf knockdown (T1207), replicate 2


description: L4_W431: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nup133 knockdown (T1199), replicate 2


description: L4_W429: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1197), replicate 2


description: L4_W428: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nupl2 knockdown (T1196), replicate 2


description: L4_W437: SPAR-seq of 108 multi-exon gene regions in N2A cells, Khdrbs2 knockdown (T1205), replicate 2


description: L4_W420: SPAR-seq of 108 multi-exon gene regions in N2A cells, Parn knockdown (T1188), replicate 2


description: L4_W419: SPAR-seq of 108 multi-exon gene regions in N2A cells, Msl3 knockdown (T1187), replicate 2


description: L4_W438: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf12 knockdown (T1206), replicate 2


description: L4_W421: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nono knockdown (T1189), replicate 2


description: L4_W418: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nufip1 knockdown (T1186), replicate 2


description: L4_W414: SPAR-seq of 108 multi-exon gene regions in N2A cells, Lin28a knockdown (T1182), replicate 2


description: L4_W451: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mettl3 knockdown (T1219), replicate 2


description: L4_W440: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mynn knockdown (T1208), replicate 2


description: L4_W415: SPAR-seq of 108 multi-exon gene regions in N2A cells, Luc7l knockdown (T1183), replicate 2


description: L4_W434: SPAR-seq of 108 multi-exon gene regions in N2A cells, Lsm2 knockdown (T1202), replicate 2


description: L4_W426: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mphosph10 knockdown (T1194), replicate 2


description: L4_W443: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kdm3b knockdown (T1211), replicate 2


description: L4_W425: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pabpc1 knockdown (T1193), replicate 2


description: L4_W427: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mov10 knockdown (T1195), replicate 2


description: L4_W430: SPAR-seq of 108 multi-exon gene regions in N2A cells, Myst1 knockdown (T1198), replicate 2


description: L4_W433: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kdm4a knockdown (T1201), replicate 2


description: L4_W424: SPAR-seq of 108 multi-exon gene regions in N2A cells, Luc7l2 knockdown (T1192), replicate 2


description: L4_W432: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1 knockdown (T1200), replicate 2


description: L4_W409: SPAR-seq of 108 multi-exon gene regions in N2A cells, Magoh knockdown (T1177), replicate 2


description: L4_W416: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mkrn2 knockdown (T1184), replicate 2


description: L4_W417: SPAR-seq of 108 multi-exon gene regions in N2A cells, Lsm7 knockdown (T1185), replicate 2


description: L4_W412: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mus81 knockdown (T1180), replicate 2


description: L4_W407: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nup88 knockdown (T1175), replicate 2


description: L4_W408: SPAR-seq of 108 multi-exon gene regions in N2A cells, Myst4 knockdown (T1176), replicate 2


description: L4_W403: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mga knockdown (T1171), replicate 2


description: L4_W401: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pabpc4 knockdown (T1169), replicate 2


description: L4_W422: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mkrn3 knockdown (T1190), replicate 2


description: L4_W411: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1179), replicate 2


description: L4_W397: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfml knockdown (T1165), replicate 2


description: L4_W398: SPAR-seq of 108 multi-exon gene regions in N2A cells, Naa38 knockdown (T1166), replicate 2


description: L4_W394: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nxf7 knockdown (T1162), replicate 2


description: L4_W410: SPAR-seq of 108 multi-exon gene regions in N2A cells, Lsm10 knockdown (T1178), replicate 2


description: L4_W423: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1191), replicate 2


description: L4_W413: SPAR-seq of 108 multi-exon gene regions in N2A cells, Morf4l2 knockdown (T1181), replicate 2


description: L4_W405: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nap1l1 knockdown (T1173), replicate 2


description: L4_W404: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mfap1a knockdown (T1172), replicate 2


description: L4_W389: SPAR-seq of 108 multi-exon gene regions in N2A cells, Klhdc3 knockdown (T1157), replicate 2


description: L4_W384: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1152), replicate 2


description: L4_W388: SPAR-seq of 108 multi-exon gene regions in N2A cells, L3mbtl3 knockdown (T1156), replicate 2


description: L4_W386: SPAR-seq of 108 multi-exon gene regions in N2A cells, Parg knockdown (T1154), replicate 2


description: L4_W400: SPAR-seq of 108 multi-exon gene regions in N2A cells, Phf10 knockdown (T1168), replicate 2


description: L4_W399: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mcm8 knockdown (T1167), replicate 2


description: L4_W379: SPAR-seq of 108 multi-exon gene regions in N2A cells, Fer knockdown (T1147), replicate 2


description: L4_W395: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl3 knockdown (T1163), replicate 2


description: L4_W375: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dido1 knockdown (T1143), replicate 2


description: L4_W392: SPAR-seq of 108 multi-exon gene regions in N2A cells, Lsm5 knockdown (T1160), replicate 2


description: L4_W406: SPAR-seq of 108 multi-exon gene regions in N2A cells, Neurog2 knockdown (T1174), replicate 2


description: L4_W372: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdgfrp3 knockdown (T1140), replicate 2


description: L4_W402: SPAR-seq of 108 multi-exon gene regions in N2A cells, L3mbtl2 knockdown (T1170), replicate 2


description: L4_W393: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nup37 knockdown (T1161), replicate 2


description: L4_W391: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmgn5 knockdown (T1159), replicate 2


description: L4_W382: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ep400 knockdown (T1150), replicate 2


description: L4_W367: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrpdl knockdown (T1135), replicate 2


description: L4_W366: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gemin4 knockdown (T1134), replicate 2


description: L4_W385: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1153), replicate 2


description: L4_W378: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ino80b knockdown (T1146), replicate 2


description: L4_W390: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ncl knockdown (T1158), replicate 2


description: L4_W365: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dppa5a knockdown (T1133), replicate 2


description: L4_W381: SPAR-seq of 108 multi-exon gene regions in N2A cells, Exosc4 knockdown (T1149), replicate 2


description: L4_W363: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hira knockdown (T1131), replicate 2


description: L4_W374: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpr knockdown (T1142), replicate 2


description: L4_W377: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dync1li1 knockdown (T1145), replicate 2


description: L4_W376: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif2s2 knockdown (T1144), replicate 2


description: L4_W373: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dhx38 knockdown (T1141), replicate 2


description: L4_W383: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpd knockdown (T1151), replicate 2


description: L4_W360: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dhx30 knockdown (T1128), replicate 2


description: L4_W387: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nap1l4 knockdown (T1155), replicate 2


description: L4_W358: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif2c3 knockdown (T1126), replicate 2


description: L4_W371: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hells knockdown (T1139), replicate 2


description: L4_W369: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnph1 knockdown (T1137), replicate 2


description: L4_W380: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prmt3 knockdown (T1148), replicate 2


description: L4_W356: SPAR-seq of 108 multi-exon gene regions in N2A cells, G3bp2 knockdown (T1124), replicate 2


description: L4_W355: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpi knockdown (T1123), replicate 2


description: L4_W368: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hist1h2bc knockdown (T1136), replicate 2


description: L4_W364: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif2c4 knockdown (T1132), replicate 2


description: L4_W350: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dgcr14 knockdown (T1118), replicate 2


description: L4_W359: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dnd1 knockdown (T1127), replicate 2


description: L4_W357: SPAR-seq of 108 multi-exon gene regions in N2A cells, Drosha knockdown (T1125), replicate 2


description: L4_W353: SPAR-seq of 108 multi-exon gene regions in N2A cells, Epb4.1l4a knockdown (T1121), replicate 2


description: L4_W348: SPAR-seq of 108 multi-exon gene regions in N2A cells, Syf2 knockdown (T1116), replicate 2


description: L4_W354: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hras1 knockdown (T1122), replicate 2


description: L4_W347: SPAR-seq of 108 multi-exon gene regions in N2A cells, Frg1 knockdown (T1115), replicate 2


description: L4_W351: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gtl3 knockdown (T1119), replicate 2


description: L4_W345: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1113), replicate 2


description: L4_W346: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpc knockdown (T1114), replicate 2


description: L4_W362: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpa1 knockdown (T1130), replicate 2


description: L4_W370: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dnmt3l knockdown (T1138), replicate 2


description: L4_W349: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdgfrp2 knockdown (T1117), replicate 2


description: L4_W361: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpm knockdown (T1129), replicate 2


description: L4_W344: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dhx9 knockdown (T1112), replicate 2


description: L4_W342: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpt knockdown (T1110), replicate 2


description: L4_W343: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpu knockdown (T1111), replicate 2


description: L4_W338: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dmap1 knockdown (T1106), replicate 2


description: L4_W352: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ehmt1 knockdown (T1120), replicate 2


description: L4_W341: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif2c2 knockdown (T1109), replicate 2


description: L4_W339: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dhx35 knockdown (T1107), replicate 2


description: L4_W340: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dhx8 knockdown (T1108), replicate 2


description: L4_W335: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif4b knockdown (T1103), replicate 2


description: L4_W396: SPAR-seq of 108 multi-exon gene regions in N2A cells, Khdrbs3 knockdown (T1164), replicate 2


description: L4_W336: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rcan2 knockdown (T1104), replicate 2


description: L4_W337: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpab knockdown (T1105), replicate 2


description: L4_W332: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zc3h12d knockdown (T1100), replicate 2


description: L4_W334: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tspyl2 knockdown (T1102), replicate 2


description: L4_W333: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1101), replicate 2


description: L4_W331: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gpatch1 knockdown (T1099), replicate 2


description: L4_W328: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hp1bp3 knockdown (T1096), replicate 2


description: L4_W327: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1095), replicate 2


description: L4_W330: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thoc5 knockdown (T1098), replicate 2


description: L4_W329: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmg20b knockdown (T1097), replicate 2


description: L4_W325: SPAR-seq of 108 multi-exon gene regions in N2A cells, H3f3a knockdown (T1093), replicate 2


description: L4_W322: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif4a1 knockdown (T1090), replicate 2


description: L4_W323: SPAR-seq of 108 multi-exon gene regions in N2A cells, Incenp knockdown (T1091), replicate 2


description: L4_W321: SPAR-seq of 108 multi-exon gene regions in N2A cells, Thumpd3 knockdown (T1089), replicate 2


description: L4_W326: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpl knockdown (T1094), replicate 2


description: L4_W317: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp771 knockdown (T1085), replicate 2


description: L4_W324: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gemin6 knockdown (T1092), replicate 2


description: L4_W318: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gtf3a knockdown (T1086), replicate 2


description: L4_W319: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf40a knockdown (T1087), replicate 2


description: L4_W316: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnpa2b1 knockdown (T1084), replicate 2


description: L4_W315: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1083), replicate 2


description: L4_W314: SPAR-seq of 108 multi-exon gene regions in N2A cells, H1fx knockdown (T1082), replicate 2


description: L4_W311: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hnrnph2 knockdown (T1079), replicate 2


description: L4_W312: SPAR-seq of 108 multi-exon gene regions in N2A cells, Larp7 knockdown (T1080), replicate 2


description: L4_W308: SPAR-seq of 108 multi-exon gene regions in N2A cells, Flywch1 knockdown (T1076), replicate 2


description: L4_W310: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hbp1 knockdown (T1078), replicate 2


description: L4_W309: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif2s1 knockdown (T1077), replicate 2


description: L4_W313: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gemin5 knockdown (T1081), replicate 2


description: L4_W320: SPAR-seq of 108 multi-exon gene regions in N2A cells, Exosc3 knockdown (T1088), replicate 2


description: L4_W305: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dnajc8 knockdown (T1073), replicate 2


description: L4_W307: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tra2a knockdown (T1075), replicate 2


description: L4_W300: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hemt1 knockdown (T1068), replicate 2


description: L4_W303: SPAR-seq of 108 multi-exon gene regions in N2A cells, Exosc5 knockdown (T1071), replicate 2


description: L4_W301: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmgb2 knockdown (T1069), replicate 2


description: L4_W299: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gemin7 knockdown (T1067), replicate 2


description: L4_W297: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dhx15 knockdown (T1065), replicate 2


description: L4_W298: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dicer1 knockdown (T1066), replicate 2


description: L4_W296: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hmgb1 knockdown (T1064), replicate 2


description: L4_W293: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dazl knockdown (T1061), replicate 2


description: L4_W295: SPAR-seq of 108 multi-exon gene regions in N2A cells, Esrrb knockdown (T1063), replicate 2


description: L4_W306: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dazap1 knockdown (T1074), replicate 2


description: L4_W290: SPAR-seq of 108 multi-exon gene regions in N2A cells, Leng9 knockdown (T1058), replicate 2


description: L4_W292: SPAR-seq of 108 multi-exon gene regions in N2A cells, Grwd1 knockdown (T1060), replicate 2


description: L4_W294: SPAR-seq of 108 multi-exon gene regions in N2A cells, Kat2a knockdown (T1062), replicate 2


description: L4_W288: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T1056), replicate 2


description: L4_W289: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1057), replicate 2


description: L4_W285: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cpne1 knockdown (T1053), replicate 2


description: L4_W304: SPAR-seq of 108 multi-exon gene regions in N2A cells, Dgcr8 knockdown (T1072), replicate 2


description: L4_W291: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hist3h2ba knockdown (T1059), replicate 2


description: L4_W286: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp473 knockdown (T1054), replicate 2


description: L4_W287: SPAR-seq of 108 multi-exon gene regions in N2A cells, Crnkl1 knockdown (T1055), replicate 2


description: L4_W302: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mms22l knockdown (T1070), replicate 2


description: L4_W284: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbd6 knockdown (T1052), replicate 2


description: L4_W282: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cpped1 knockdown (T1050), replicate 2


description: L4_W281: SPAR-seq of 108 multi-exon gene regions in N2A cells, Celf4 knockdown (T1049), replicate 2


description: L4_W278: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cstf2t knockdown (T1046), replicate 2


description: L4_W283: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp828 knockdown (T1051), replicate 2


description: L4_W276: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rif1 knockdown (T1044), replicate 2


description: L4_W273: SPAR-seq of 108 multi-exon gene regions in N2A cells, Capn7 knockdown (T1041), replicate 2


description: L4_W279: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smc3 knockdown (T1047), replicate 2


description: L4_W275: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cxxc1 knockdown (T1043), replicate 2


description: L4_W280: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cherp knockdown (T1048), replicate 2


description: L4_W274: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cpeb1 knockdown (T1042), replicate 2


description: L4_W272: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cdca8 knockdown (T1040), replicate 2


description: L4_W270: SPAR-seq of 108 multi-exon gene regions in N2A cells, Utp3 knockdown (T1038), replicate 2


description: L4_W269: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ddx5 knockdown (T1037), replicate 2


description: L4_W271: SPAR-seq of 108 multi-exon gene regions in N2A cells, Parp8 knockdown (T1039), replicate 2


description: L4_W268: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cpsf3 knockdown (T1036), replicate 2


description: L4_W267: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nudt21 knockdown (T1035), replicate 2


description: L4_W263: SPAR-seq of 108 multi-exon gene regions in N2A cells, C1qbp knockdown (T1031), replicate 2


description: L4_W266: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cpeb2 knockdown (T1034), replicate 2


description: L4_W265: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rcor1 knockdown (T1033), replicate 2


description: L4_W277: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cpeb4 knockdown (T1045), replicate 2


description: L4_W262: SPAR-seq of 108 multi-exon gene regions in N2A cells, Carm1 knockdown (T1030), replicate 2


description: L4_W258: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ccar1 knockdown (T1026), replicate 2


description: L4_W257: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cbx7 knockdown (T1025), replicate 2


description: L4_W256: SPAR-seq of 108 multi-exon gene regions in N2A cells, Macrod1 knockdown (T1024), replicate 2


description: L4_W259: SPAR-seq of 108 multi-exon gene regions in N2A cells, Samd4b knockdown (T1027), replicate 2


description: L4_W255: SPAR-seq of 108 multi-exon gene regions in N2A cells, Clns1a knockdown (T1023), replicate 2


description: L4_W252: SPAR-seq of 108 multi-exon gene regions in N2A cells, Wdhd1 knockdown (T1020), replicate 2


description: L4_W253: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mysm1 knockdown (T1021), replicate 2


description: L4_W254: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ddx50 knockdown (T1022), replicate 2


description: L4_W251: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ddx39 knockdown (T1019), replicate 2


description: L4_W250: SPAR-seq of 108 multi-exon gene regions in N2A cells, Eif4a3 knockdown (T1018), replicate 2


description: L4_W248: SPAR-seq of 108 multi-exon gene regions in N2A cells, Bicc1 knockdown (T1016), replicate 2


description: L4_W249: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T1017), replicate 2


description: L4_W246: SPAR-seq of 108 multi-exon gene regions in N2A cells, Setd3 knockdown (T1014), replicate 2


description: L4_W247: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cbx2 knockdown (T1015), replicate 2


description: L4_W245: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cpsf2 knockdown (T1013), replicate 2


description: L4_W243: SPAR-seq of 108 multi-exon gene regions in N2A cells, D4Wsu53e knockdown (T1011), replicate 2


description: L4_W244: SPAR-seq of 108 multi-exon gene regions in N2A cells, Slu7 knockdown (T1012), replicate 2


description: L4_W264: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zcchc10 knockdown (T1032), replicate 2


description: L4_W242: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cdyl2 knockdown (T1010), replicate 2


description: L4_W241: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mis18bp1 knockdown (T1009), replicate 2


description: L4_W239: SPAR-seq of 108 multi-exon gene regions in N2A cells, Slx4 knockdown (T1007), replicate 2


description: L4_W240: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cstf1 knockdown (T1008), replicate 2


description: L4_W261: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ddx46 knockdown (T1029), replicate 2


description: L4_W260: SPAR-seq of 108 multi-exon gene regions in N2A cells, Enox1 knockdown (T1028), replicate 2


description: L4_W238: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp12 knockdown (T1006), replicate 2


description: L4_W235: SPAR-seq of 108 multi-exon gene regions in N2A cells, Brms1l knockdown (T1003), replicate 2


description: L4_W233: SPAR-seq of 108 multi-exon gene regions in N2A cells, Sf3b3 knockdown (T1001), replicate 2


description: L4_W234: SPAR-seq of 108 multi-exon gene regions in N2A cells, Casc3 knockdown (T1002), replicate 2


description: L4_W231: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0999), replicate 2


description: L4_W228: SPAR-seq of 108 multi-exon gene regions in N2A cells, Enox2 knockdown (T0996), replicate 2


description: L4_W229: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ccnl2 knockdown (T0997), replicate 2


description: L4_W232: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mthfsd knockdown (T1000), replicate 2


description: L4_W224: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbm41 knockdown (T0992), replicate 2


description: L4_W227: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cpsf1 knockdown (T0995), replicate 2


description: L4_W225: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ddx3x knockdown (T0993), replicate 2


description: L4_W223: SPAR-seq of 108 multi-exon gene regions in N2A cells, Clk1 knockdown (T0991), replicate 2


description: L4_W221: SPAR-seq of 108 multi-exon gene regions in N2A cells, D2Ertd750e knockdown (T0989), replicate 2


description: L4_W222: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zbtb46 knockdown (T0990), replicate 2


description: L4_W216: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zwint knockdown (T0984), replicate 2


description: L4_W237: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T1005), replicate 2


description: L4_W215: SPAR-seq of 108 multi-exon gene regions in N2A cells, Bud13 knockdown (T0983), replicate 2