description: L1_W094: SPAR-seq of 108 multi-exon gene regions in N2A cells, Wbp7 knockdown (T0094), replicate 1


status: Public on Jul 15 2022

type: SRA

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description: L1_W095: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zmynd8 knockdown (T0095), replicate 1

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Mouse neuroblastoma cells

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

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

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

tag: tissue

value: Mouse neuroblastoma cells

tag: cell line


title: M327

type: RNA

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

country: USA

institute: Baylor College of Medicine

description: NanoString nCounter assay

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

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

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

label: not provided

organism: Homo sapiens

source_name: pediatric liver cancer

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

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

tag: disease state

value: Hepatoblastoma

value: liver

tag: status

value: Alive after Transplant

tag: histology

value: HB FPA

tag: age

tag: Sex

value: M

tag: stage (pretext)


title: inflorescence stem, ref3-3, rep3

city: West Lafayette

first: Clint

last: Chapple

address: 175 S. University St.

department: Biochemistry

institute: Purdue University

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

organism: Arabidopsis thaliana

source_name: basal 0.5-2 cm of inflorescence stem

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

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

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

value: basal 0.5-2 cm of inflorescence stem

tag: ecotype

tag: genotype

value: harvest at 28-day-old


title: patient 21, first biopsy, glomeruli [X21AG_1]

city: Columbus

first: Samir

last: Parikh

state: OH

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

department: Nephrology

institute: Ohio State University

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

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

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

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

source_name: Lupus Nephritis

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

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

tag: ln class

value: Class IV

value: F

tag: age (yrs)

tag: proteinuria (g/24hr)

tag: serum creatinine (mg/dl)

tag: clinical response group

value: Partial Response


title: patient 38, first biopsy, glomeruli [X38A.G_3]

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

value: Class III

value: No Response


title: M325

description: NanoString nCounter assay

value: DOD


description: L1_W093: SPAR-seq of 108 multi-exon gene regions in N2A cells, Brpf1 knockdown (T0093), replicate 1


title: patient 24, first biopsy, glomeruli [X24AG]

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


title: patient 14, first biopsy, glomeruli [X14AG_8]

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


title: patient 17, first biopsy, glomeruli [X17AG_7]

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


title: M323

description: NanoString nCounter assay

value: DOD after Transplant


title: inflorescence stem, ref3-3, rep4


title: inflorescence stem, ref3-3, rep1


description: L1_W092: SPAR-seq of 108 multi-exon gene regions in N2A cells, Smarcc2 knockdown (T0092), replicate 1


title: M425

description: NanoString nCounter assay

value: Biphasic NOS


title: patient 13, first biopsy, glomeruli [X13AG]


title: inflorescence stem, ref3-2, rep4


title: M326

description: NanoString nCounter assay

value: Alive


description: L1_W091: SPAR-seq of 108 multi-exon gene regions in N2A cells, Luc7l3 knockdown (T0091), replicate 1

value: Mouse neuroblastoma cells


title: inflorescence stem, ref3-2, rep3


description: L1_W090: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppig knockdown (T0090), replicate 1


title: patient 27, first biopsy, glomeruli [X27AG_9]

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


title: inflorescence stem, ref3-3, rep2


title: patient 10, first biopsy, glomeruli [X10AG]

value: Mixed (III/IV+V)


title: M341

description: NanoString nCounter assay

value: Hepatoblastoma

value: liver

value: Relapsed


title: M324

description: NanoString nCounter assay

value: HB FPA

value: M


description: L1_W089: SPAR-seq of 108 multi-exon gene regions in N2A cells, Htatsf1 knockdown (T0089), replicate 1


description: L1_W088: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cenpn knockdown (T0088), replicate 1


title: inflorescence stem, ref3-2, rep1

value: basal 0.5-2 cm of inflorescence stem

value: harvest at 28-day-old


title: patient 58, first biopsy, glomeruli [X58AG_8]

value: Class IV

value: F

value: complete response


title: inflorescence stem, WT, rep8

value: wild type


description: L1_W086: SPAR-seq of 108 multi-exon gene regions in N2A cells, Parp3 knockdown (T0086), replicate 1


title: M340

description: NanoString nCounter assay


title: M381

description: NanoString nCounter assay


title: inflorescence stem, WT, rep7


description: L1_W087: SPAR-seq of 108 multi-exon gene regions in N2A cells, Add3 knockdown (T0087), replicate 1


title: M339

description: NanoString nCounter assay


title: M322

description: NanoString nCounter assay


description: L1_W085: SPAR-seq of 108 multi-exon gene regions in N2A cells, Aptx knockdown (T0085), replicate 1


description: L1_W084: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ddx11 knockdown (T0084), replicate 1


title: patient 50, first biopsy, glomeruli [X50AG_10]

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


title: patient 5, first biopsy, glomeruli [X5AG_7]

value: No Response


title: inflorescence stem, ref3-2, rep2


title: patient 51, first biopsy, glomeruli [X51AG_7]


title: inflorescence stem, WT, rep6


title: M313

description: NanoString nCounter assay


title: inflorescence stem, WT, rep5


title: M319

description: NanoString nCounter assay


title: patient 49, first biopsy, glomeruli [X49AG_10]


title: patient 48, first biopsy, glomeruli [X48AG_9]

value: Class III


title: M310

description: NanoString nCounter assay

value: DOD

value: Biphasic NOS


description: L1_W083: SPAR-seq of 108 multi-exon gene regions in N2A cells, Klf9 knockdown (T0083), replicate 1

value: Mouse neuroblastoma cells


title: inflorescence stem, WT, rep3


title: inflorescence stem, WT, rep4


title: patient 37, first biopsy, glomeruli [X37AG_5]

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


title: patient 55, first biopsy, glomeruli [X55AG_9]


title: inflorescence stem, WT, rep1


description: L1_W081: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cebpg knockdown (T0081), replicate 1


title: inflorescence stem, WT, rep2


title: patient 39, first biopsy, glomeruli [X39AG_1]

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


title: M303

description: NanoString nCounter assay

value: Alive after Transplant


title: patient 32, first biopsy, glomeruli [X32AG]

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

value: Mixed (III/IV+V)


description: L1_W080: SPAR-seq of 108 multi-exon gene regions in N2A cells, Baz1b knockdown (T0080), replicate 1


title: M342

description: NanoString nCounter assay

value: Hepatoblastoma

value: liver

value: Equivocal NOS


title: M412

description: NanoString nCounter assay


title: M307

description: NanoString nCounter assay

value: M


title: patient 30, first biopsy, glomeruli [X30AG]


description: L1_W077: SPAR-seq of 108 multi-exon gene regions in N2A cells, Top1mt knockdown (T0077), replicate 1


title: M318

description: NanoString nCounter assay

value: Relapsed


title: M334

description: NanoString nCounter assay


title: CCD841, control

city: TOYAMA CITY

first: Hiroshi

last: Mihara

state: Toyama

address: 2630, Sugitani

country: Japan

institute: University Of Toyama

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

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

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

source_name: CCD841, control

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

extract_protocol: The total RNA was isolated from cells and purified using RNeasy Kit (QIAGEN) according to the manufacturer's instructions.

tag: source

value: normal colonic tissue, epithelial-like

tag: treatment

value: control


description: L1_W079: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mlf1ip knockdown (T0079), replicate 1

tag: tissue


description: L1_W082: SPAR-seq of 108 multi-exon gene regions in N2A cells, Atf3 knockdown (T0082), replicate 1

tag: cell line


title: rraga wildtype sibling macrophage sample biological replicate 3

city: Stanford

first: Harini

last: Iyer

state: California

address: 279 Campus Drive, B300 Beckman Center

department: Developmental Biology

institute: Stanford University

data_processing:
Raw data of FASTQ format were processed through Novogene in-house PERL scripts
Clean reads were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data
Q20, Q30, and GC content of all clean data were calculated
Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome.
Mapped reads of each sample were assembled by StringTie v1.3.3b
featureCount v1.5.0 was used to count the read numbers mapped to each gene.
Differential expression analysis was performed using the DESeq2R package (1.20.0)
Genome_build: GRCz11
Supplementary_files_format_and_content: text file contains gene counts, normalized (FPKM) reads for genes identified by gene name and ENSEMBL ID

molecule: polyA RNA

organism: Danio rerio

source_name: Macrophages

growth_protocol: Zebrafish embryos were raised at 28.5 ºC in embryo water with methylene blue and PTU

extract_protocol:
RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions.
Takara SMART-Seq v4 Ultra Low Input RNA Kit

treatment_protocol: Embryos were scored as mutant or wildtype using a confocal microscope at 4 and 5 days post fertilization. Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.

value: rraga wild type

tag: strain

value: TL

tag: developmental stage

value: 6 days post fertilization

tag: cell type

value: Macrophages


description: L1_W078: SPAR-seq of 108 multi-exon gene regions in N2A cells, Arid4b knockdown (T0078), replicate 1


description: L1_W076: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cebpb knockdown (T0076), replicate 1


title: M317

description: NanoString nCounter assay

tag: disease state

tag: status

tag: histology

tag: age


title: patient 26, first biopsy, glomeruli [X26AG_2]

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

value: Class III

tag: Sex

value: F

value: complete response


title: rraga wildtype sibling macrophage sample biological replicate 2

tag: genotype


title: rraga wildtype sibling macrophage sample biological replicate 4


title: patient 20, first biopsy, glomeruli [X20AG_8]

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

tag: ln class

tag: age (yrs)


title: M311

description: NanoString nCounter assay

tag: stage (pretext)

value: COG 1


title: patient 23, first biopsy, glomeruli [X23AG_9]

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

tag: proteinuria (g/24hr)

tag: serum creatinine (mg/dl)

tag: clinical response group


title: Patient 15, first biopsy, glomeruli [X15AG_5]


title: Patient 12, first biopsy, glomeruli [X12AG_8]


title: rraga wildtype sibling macrophage sample biological replicate 1


title: rraga mutant macrophage sample biological replicate 4

value: rraga mutant


description: L1_W075: SPAR-seq of 108 multi-exon gene regions in N2A cells, Scaf11 knockdown (T0075), replicate 1

tag: tissue

value: Mouse neuroblastoma cells


title: M309

description: NanoString nCounter assay

value: Hepatoblastoma

value: DOD


title: M306

description: NanoString nCounter assay

value: liver

value: Alive

value: Equivocal NOS


description: L1_W074: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cd2ap knockdown (T0074), replicate 1

tag: cell line


description: L1_W073: SPAR-seq of 108 multi-exon gene regions in N2A cells, Polr2d knockdown (T0073), replicate 1


title: patient 11, first biopsy, glomeruli [X11AG_5]


title: rraga mutant macrophage sample biological replicate 3

tag: strain


description: L1_W072: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2t knockdown (T0072), replicate 1


title: M305

description: NanoString nCounter assay

value: Alive after Transplant


title: CCD841, E.coli supernatant exposure

source_name: CCD841, E.coli supernatant exposure

tag: source

value: normal colonic tissue, epithelial-like

tag: treatment

value: E.coli supernatant exposure


title: M304

description: NanoString nCounter assay

tag: disease state

value: M


title: M301

description: NanoString nCounter assay

tag: status


title: rraga mutant macrophage sample biological replicate 2

value: TL

tag: developmental stage

value: 6 days post fertilization

tag: cell type


title: Patient 6, first biopsy, glomeruli [X06AG_1]

value: Class IV

tag: Sex


description: L1_W071: SPAR-seq of 108 multi-exon gene regions in N2A cells, Parp2 knockdown (T0071), replicate 1


title: Patient 7, first biopsy, glomeruli [X7AG_7]

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

value: Mixed (III/IV+V)

value: F


title: rraga mutant macrophage sample biological replicate 1

tag: genotype

value: Macrophages


description: L1_W070: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbms3 knockdown (T0070), replicate 1


title: wildtype larvae zymosan A injected biological replicate 3

data_processing:
Raw data of FASTQ format were processed through Novogene in-house perl scripts
Clean reads were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data
Q20, Q30, and GC content of all clean data were calculated
Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome.
Mapped reads of each sample were assembled by StringTie v1.3.3b
featureCount v1.5.0 was used to count the read numbers mapped to each gene.
Differential expression analysis was performed using the DESeq2R package 1.20.0
Genome_build: GRCz11
Supplementary_files_format_and_content: text file contains gene counts, normalized (FPKM) reads for genes identified by gene name, ENSEMBL ID and other details

source_name: Zebrafish larvae

extract_protocol:
RNA was extracted using the Takara NucleoSpin RNA Plus kit using the manufacturer's instructions.
NEBNext Ultra II RNA Library Prep Kit

treatment_protocol: wildtype and tfeb; tfe3a; tfe3b mutants were injected with ZymosanA, examined using confocal microscope, and snap frozen prior to RNA extraction. rraga mutants were scored using confocal microscope and snap frozen prior to RNA extraction.

value: wild type

value: zymosan A injected

value: 4 days post fertilization


title: wildtype larvae zymosan A injected biological replicate 2


description: L1_W069: SPAR-seq of 108 multi-exon gene regions in N2A cells, Bcas2 knockdown (T0069), replicate 1

value: Mouse neuroblastoma cells


description: L1_W068: SPAR-seq of 108 multi-exon gene regions in N2A cells, Foxn3 knockdown (T0068), replicate 1


title: Patient 2, First Biopsy, Glomeruli [X02AG_5]

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

tag: ln class

value: complete response


title: Patient 1, First biopsy, Glomeruli [X1A.G_3]

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

tag: age (yrs)


description: L1_W067: SPAR-seq of 108 multi-exon gene regions in N2A cells, Apc knockdown (T0067), replicate 1


title: wildtype larvae uninjected biological replicate 3

value: uninjected


description: L1_W066: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ranbp3 knockdown (T0066), replicate 1


description: L1_W065: SPAR-seq of 108 multi-exon gene regions in N2A cells, Birc6 knockdown (T0065), replicate 1


title: wildtype larvae uninjected biological replicate 2


title: wildtype larvae uninjected biological replicate 1


description: L1_W064: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cdyl knockdown (T0064), replicate 1


title: rraga mutant larvae biological replicate 3

value: rraga mutant


description: L1_W063: SPAR-seq of 108 multi-exon gene regions in N2A cells, Brd7 knockdown (T0063), replicate 1


title: wildtype larvae zymosan A injected biological replicate 1


title: rraga mutant larvae biological replicate 2


description: L1_W062: SPAR-seq of 108 multi-exon gene regions in N2A cells, Zfp869 knockdown (T0062), replicate 1


title: rraga mutant larvae biological replicate 1


title: phoR ko 4.5 B

city: CHANDIGARH

first: Dibyendu

last: Sarkar

address: SECTOR 39A

country: India

institute: CSIR-IMTECH

description: For growth under acid stress, cells at OD600 of 0.6 were pelleted, washed twice with 7H9 medium buffered with 100 mM MOPS or 2N HCl for pH 7.0 or pH 4.5, respectively, re-suspended in media of indicated pH, and finally the cells were grown further for 2 hours at 37°C.

data_processing:
Basecalling, demultiplication and adaptor trimming was performed by Illumina HiSeq control software
Quality of raw reads was assessed by using FastQC tool
Clean reads that passed the quality filter were mapped to the reference genome (Mycobacterium tuberculosis H37Rv accession number NC_000962.3) using Hisat2.
Differential gene expression analysis of samples with respect to control was performed using Cuffdiff program (v2.2.1).
Genome_build: NC_000962.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Mycobacterium tuberculosis H37Rv

source_name: ∆phoR Acidic stress

growth_protocol: M. tuberculosis H37Rv strains were grown at 37°C in Middlebrook 7H9 broth (Difco) containing 0.2% glycerol, 0.05% Tween-80 and 10% Middlebrook ADC (albumin-dextrose-catalase).

extract_protocol:
RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. Briefly, 25 ml of bacterial culture was grown (in the indicated pH) to mid-log phase (OD600= 0.4 to 0.6) and combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen).
Total RNA was isolated using Direct-zol RNA MiniPrep kit (Zymo Research Corporation), the purity of isolated RNA was determined using the NanoDrop (Thermo Scientific), quantified using Qubit (Invitrogen), and RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies).  Library construction, RNA-sequencing and data analysis have been carried out by Agrigenome Labs Private Limited (Cochin), India. Briefly, The rRNA was removed using ‘si-tools Pan-prokaryote ribopool probes,’ and further library preparation was carried out using TruSeq Stranded RNA library prep kit. Prepared libraries were sequenced using Illumina HiSeq x10 platform, and 150-bp paired-end reads were generated. Thereads that passed quality control were mapped onto the reference genome of M. tuberculosis H37Rv using Hisat2 (version-2.0.5).  The abundance of transcripts in individual samples was estimated using Cufflinks (v2.2.1).

treatment_protocol: Cultures were grown till mid log phase and then divided into two halves. One part was exposed to acidic stress (pH 4.5) and other one to normal conditions (pH 7.0) for 2 hours. RNA was isolated and processed for RNA sequencing.

value: phoR-ko

value: Acidic stress


description: L1_W061: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2o knockdown (T0061), replicate 1


title: Human metastatic ovarian carcinoma, rep3(patient 03), input [03-cm.Input]

city: Xi'an City

first: Hongxi

last: Zhao

state: Shaanxi Province

address: Xinsi Road, Baqiao District

country: China

institute: The Fourth Military Medical University

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
Clean reads of all libraries were aligned to the reference genome  by Hisat2 software (v2.0.4)
Methylated sites on RNAs (peaks) were identified by MACS software
Assembly: HG38
Supplementary files format and content: XLS sheet "Gene Expression Profiling.xlsx" ,"LncRNA Expression Profiling.xlsx", and "CircRNA Expression Profiling.xlsx" illustrated the raw counts(column B to column G) and normalized score(column H to column M, calculated by edgeR) of each transcripts from the input samples. Additional gene annotation information was also provided in column N to column Q.
Supplementary files format and content: XLS sheet "Methylated_RNA_sites.mRNA.xlsx","Methylated_RNA_sites.lncRNA.xlsx", and "Methylated_RNA_sites.circRNA.xlsx"  illustrated the m6A methylation sites information,  including m6A peak start site, peak stop site, peak ID, m6A peak score, peak length, generated by MACS software(see column B to column F). Additional statistical enrichment information and gene annotation information was also provided
Supplementary files format and content: BED files that illustrated the m6A peak start site, peak stop site, peak ID, m6A peak score, generated by MACS software.

source_name: Human metastatic ovarian carcinoma

extract_protocol:
Total RNA was subjected to immunoprecipitation with the GenSeq® m6A-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified.
RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).

treatment_protocol: In situ ovarian carcinoma tissue samples and metastatic ovarian carcinoma tissue samples were obtained from Tangdu Hospital affiliated to The Fourth Military Medical University, Xi'an City, Shaanxi Province, China.

value: Human metastatic ovarian carcinoma


title: Human metastatic ovarian carcinoma, rep2(patient 02), input [02-cm.Input]


title: Human ovarian carcinoma in situ, rep1(patient 01), MeRIP [01-c.IP]

source_name: Human ovarian carcinoma in situ

value: Human ovarian carcinoma in situ


title: Human metastatic ovarian carcinoma, rep1(patient 01), input [01-cm.Input]


title: Human metastatic ovarian carcinoma, rep1(patient 01), MeRIP [01-cm.IP]


title: Human ovarian carcinoma in situ, rep2(patient 02), MeRIP [02-c.IP]


title: Human metastatic ovarian carcinoma, rep2(patient 02), MeRIP [02-cm.IP]


title: Human ovarian carcinoma in situ, rep2(patient 02), input [02-c.Input]


title: Human metastatic ovarian carcinoma, rep3(patient 03), MeRIP [03-cm.IP]


title: tfeb; tfe3a; tfe3b triple mutant larvae zymosan A injected biological replicate 3

value: tfeb; tfe3a; tfe3b triple mutant

value: TL


title: phoR ko 4.5 A


title: PDR patients who had received preoperative anti-VEGF treatment 20

city: Zunyi

first: Lan

last: Zeng

state: Guizhou

address: No.98, Fenghuang Road

institute: The First People’s Hospital of Zunyi

hyb_protocol: Performed by Genminix Informatics Co., Ltd. (Shanghai, China) in accordance with the manufacturer’s instructions

scan_protocol: Microarrays were scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0.2 software using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Group B

growth_protocol: First People’s Hospital of Zunyi

extract_protocol: total RNA was extracted using TRIzol LS reagent combined with miRNeasy Micro Kit

treatment_protocol: Vitreous sample (approximately 1mL) was carefully and slowly collected at the beginning of surgery into a 2mL sterile syringe using the 25-gauge vitreous cutter and manual suction before opening the intraocular irrigation system.

value: vitreous

value: proliferative diabetic retinopathy (PDR)

value: preoperative anti-VEGF treatment


description: L1_W060: SPAR-seq of 108 multi-exon gene regions in N2A cells, Setd8 knockdown (T0060), replicate 1


title: untreated PDR patients 63

source_name: Group C

label_protocol: Performed by Genminix Informatics Co., Ltd. (Shanghai, China) in accordance with the manufacturer’s instructions

value: untreated


title: PDR patients who had received preoperative anti-VEGF treatment 18


title: tfeb; tfe3a; tfe3b triple mutant larvae zymosan A injected biological replicate 2


title: untreated PDR patients 47


title: PDR patients who had received preoperative anti-VEGF treatment 54


title: control patient 1

source_name: Group A

value: control


title: untreated PDR patients 13


title: phoR ko 7.0 B

source_name: ∆phoR Normal condition

value: Normal condition


description: L1_W059: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nup98 knockdown (T0059), replicate 1


title: control patient 16


title: phoR ko 7.0 A


title: control patient 7


title: tfeb; tfe3a; tfe3b triple mutant larvae uninjected biological replicate 3

value: 4 days post fertilization


title: tfeb; tfe3a; tfe3b triple mutant larvae zymosan A injected biological replicate 1

value: zymosan A injected


title: Human ovarian carcinoma in situ, rep1(patient 01), input [01-c.Input]


description: L1_W056: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp2r1b knockdown (T0056), replicate 1

value: Mouse neuroblastoma cells


title: WT 4.5 A

source_name: WT Acidic stress

value: WT


title: WT 7.0 B

source_name: WT Normal condition


title: WT 4.5 B


description: L1_W057: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0057), replicate 1

source_name: Mouse neuroblastoma cells


title: Human ovarian carcinoma in situ, rep3(patient 03), MeRIP [03-c.IP]


title: tfeb; tfe3a; tfe3b triple mutant larvae uninjected biological replicate 2

value: uninjected


description: L1_W055: SPAR-seq of 108 multi-exon gene regions in N2A cells, Aggf1 knockdown (T0055), replicate 1


description: L1_W058: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nfrkb knockdown (T0058), replicate 1


title: tfeb; tfe3a; tfe3b triple mutant larvae uninjected biological replicate 1


title: Human ovarian carcinoma in situ, rep3(patient 03), input [03-c.Input]


title: OVCAR3, Combo

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0
Assembly: GRCh38
Supplementary files format and content: Matrix files

extract_protocol:
Cells were maintained at 37°C and 5% CO 2 and cultured in DMEM 1X (Gibco, #11995065) containing 10% FBS (R&D Systems, #S11150) without antibiotics. Cells used in the study were passaged for less than 15 passages. 50 mM stock solution of RAC inhibitor (NSC23766, Sigma #553502) was made in DMSO. 5 mM stock solution of EZH2 inhibitor (GSK126, Biovision #2282) was made in DMSO. For all the experiments using these inhibitors, an equivalent amount of DMSO or RAC1i or EZH2i or combination of both was added to cells and incubated for 48 hrs at 37°C and 5% CO 2. For the collection of cells, trypsin was used to dissociate cells from the culture surface. Cells were resuspended in PBS with a target concentration of 700-1200/ul and with >90% alive.
Approximately 10,000 cells per sample were targeted for input to the 10X Genomics  6 Chromium system using the Chromium Next GEM Single Cell 3’ Kit v3.1 at the Indiana University School of Medicine (IUSM) Center for Medical Genomics satellite core in Bloomington. The libraries were sequenced at the IUSM Center for Medical Genomics using a NovaSeq 6000 with a NovaSeq S2 reagent kit v1.0 (100 cycles) with approximately 450 million read pairs per sample.

value: Ovarian cancer

value: GSK126 and NSC23766


title: OVCAR3, RACi

description: 10X Genomics


title: OVCAR3, EZH2i

description: 10X Genomics

value: GSK126, Biovision #2282


description: L1_W053: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrnp200 knockdown (T0053), replicate 1


title: MUT301

city: Davis

first: Bruce

middle: W.

last: Draper

state: CA

address: University of California Davis One Shields Ave.

department: MCB

institute: University of California, Davis

data_processing:
Paired end reads were trimmed using BBduk, mapped using STAR aligner, and gene hits counted with htseq-count
Genome_build: GRCz11
Supplementary_files_format_and_content: raw data counts generated by htseq for each sample and gene

source_name: 3etv_whole embryo

extract_protocol:
single embryos were flash frozen with liquid nitrogen, and RNA was harvested using Trizol reagent, then purified and Dnase treated with Zymogen RNA Clean and concentrator columns.
mRNA libraries were prepared for sequencing using standard Illumina protocols for Poly-A enriched, strand specific libraries

tag: Stage

value: whole embryo


title: OVCAR3, DMSO

description: 10X Genomics

value: DMSO


title: RNA-seq MEF XiΔXist shYY1 Rep2

city: Durham

first: Eda

last: Yildirim

state: NC

address: DUMC Box 3709

department: Cell Biology

institute: Duke University School of Medicine

description:
XiΔXist MEFs treated with shRNA targeting YY1
MEF_XistKO_shYY1_RNAseq_129S1_SvImJ_count.txt
MEF_XistKO_shYY1_RNAseq_CAST_EiJ_count.txt

data_processing:
Biological replicates of RNA-seq data were pooled to maximize sequencing depth.
RNA-seq reads were aligned to a N-masked mouse reference genome (in which all SNPs between 129S1/SvImJ and CAST/EiJ genome are replaced by “N”).
Reads with low alignment quality (MAPQ < 30) were removed, and the remaining aligned reads were split to 129S1/SvImJ or CAST/EiJ allele using SNPsplit.
Allelically aligned reads for each gene were counted by featureCounts (v1.6.3).
Assembly: GRCm38/mm10
Supplementary files format and content: txt, allele-specific read counts for each gene.

source_name: RNA-seq

growth_protocol: Mouse embryonic fibroblasts (MEFs) were cultured in DMEM media containing 10% fetal bovine serum, 10 mM HEPES, 0.1 mM MEM Non-Essential Amino Acids (NEAA), 1% Penicillin/streptomycin and 0.2% 2-Mercaptoethanol.

extract_protocol:
Total RNA from MEF cells (3x106) were isolated using TRIzol reagent (Invitrogen).
RNA-seq libraries were prepared using KAPA RNA HyperPrep kit (Roche, 8098093702).

value: MEF

value: Xi[delta]Xist shYY1

value: Female

value: 129S1/SvImJ x CAST/EiJ


title: MUT302


description: L1_W052: SPAR-seq of 108 multi-exon gene regions in N2A cells, Chd9 knockdown (T0052), replicate 1


title: RNA-seq MEF XiΔXist shYY1 Rep1


title: WLD303

source_name: WT_whole embryo


description: L1_W051: SPAR-seq of 108 multi-exon gene regions in N2A cells, Bclaf1 knockdown (T0051), replicate 1


title: WLD302


title: RNA-seq MEF XiΔXist Rep2

description:
Xist deletion on Xi
MEF_XistKO_RNAseq_129S1_SvImJ_count.txt
MEF_XistKO_RNAseq_CAST_EiJ_count.txt

value: Xi[delta]Xist


title: WLD301


description: L1_W049: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hdac4 knockdown (T0049), replicate 1


title: RPE1_H2O2- TDP1 CUT&RUN rep2

city: Sheffield

first: Sherif

last: El-Khamisy

state: South Yorkshire

address: Firth Court, University of Sheffield, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

description: MH = Untreated/H2O2-, 90R = H2O2 treated 90 minute recovery, I = IgG, N = NuMA (TDIF), T = TDP1

library_source: genomic

data_processing:
library strategy: CUT&RUN
Data mapped using bwa mem version 0.7.17 (parameters: -M -k 25)
Data was filtered prior to downstream analyses. Reads with a quality score of less than 30 were also removed using samtools view (parameters: -q 30)
bigwigs were generated using MACS2 version 2.1.1.2. Fragment pileup and control (IgG) lambda were output to BEDgraph files using MACS2 peak calling (parameters: -B –SPMR). The sample and control lambda BEDgraph signal tracks were then compared using MACS2 bdgcomp (parameters: -m FE), and the resulting bedgraph files converted to bigwigs
Metagene profiles were generated using bam2geneprofile from CGAT scripts using gene annotations derived from Ensembl 85, with reporter set to genes and no normalisation
Assembly: hg38
Supplementary files format and content: Fold-change relative to IgG bigwigs

molecule: genomic DNA

source_name: Human retinal pigment epithelial cell line

growth_protocol: RPE-1 cells with a stably integrated spCas9 (tet-on promoter) and NuMA (TDIF) sgRNA were cultured in Dulbecco’s Modified Eagle Medium F-12 Nutrient Mixture (HAM) (DMEM/F-12(1:1) (1X) + Glutamax supplemented with a final concentration of 10% tetracycline-free fetal bovine serum and 1% penicillin/streptomycin. Briefly, the RPE-1 cells contained a doxycycline-inducible spCas9 and was infected with a pLenti-sgRNA against NuMA (TDIF) using virus expressed in HEK293T cells and selected using puromycin. A final concentration of 0.005 mg/ml Puromycin was always added to ensure the selection of cells containing the NuMA (TDIF) sgRNA, while up to 0.001 mg/ml Doxycycline was added daily for 2-3 consecutive days to induce the spCas9 in the RPE-1 cells to knock out NuMA (TDIF). The cells were grown at 37°C in a humidified atmosphere containing 5% carbon dioxide.

extract_protocol:
Around 500,000 cells were immobilized on BioMag Plus Concanavalin A beads (Cat. No.: BP531-3) and then incubated with the required antibodies overnight at 4°C, in a buffer containing Digitonin to permeabilize the cells. After washing the cells immobilized on the beads, Protein A/G MNase fusion protein was added and incubated for 1 hour at 4°C to bind to the antibodies. Following washes, cells were incubated with CaCl2 on ice for 45 minutes to activate the MNase to cleave the DNA. A 2X STOP Buffer containing EDTA is then added to stop the cleavage and release the chromatin to the solution. The released fragments were then treated with Proteinase K and purified with phenol  chloroform and precipitated with ethanol before being subjected to library prep.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina with Sample Purification Beads (Cat. No.: E7103L) and NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (Cat. No.: E7335L). Briefly, the DNA ends were end repaired, 5'phosphorylated and dA-tailing was done using the NEBNext Ultra II End Prep Enzyme Mix, then adaptors were ligated and Uracils were excised using the USER enzyme. The DNA was then cleaned up and enriched by PCR for 12 cycles and then cleaned up with the sample purification beads, before being sequenced on the Illumina NovaSeq 6000.

treatment_protocol: Cells were either left untreated or treated with 10 µM hydrogen peroxide (H2O2) in cold PBS for 10 minutes in the dark, on ice and then washed with PBS. Cells were then allowed to recover in H2O2-free media for 90 minutes at 37°C.

tag: sample type

value: NuMA (TDIF) CUT&RUN


title: RPE1_H2O2+ 90 min recovery TDP1 CUT&RUN rep2

value: Human retinal pigment epithelial cell line


title: RPE1_H2O2+ 90 min recovery TDP1 CUT&RUN rep1


title: RPE1_H2O2- TDP1 CUT&RUN rep1


title: RPE1_H2O2+ 90 min recovery NuMA (TDIF) CUT&RUN rep2


title: RNA-seq MEF XiΔXist shSCR Rep2

description:
XiΔXist MEFs treated with scramble shRNA
MEF_XistKO_shSCR_RNAseq_129S1_SvImJ_count.txt
MEF_XistKO_shSCR_RNAseq_CAST_EiJ_count.txt

value: Xi[delta]Xist shSCR


title: MUT303


description: L1_W046: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ube2q1 knockdown (T0046), replicate 1


title: RPE1_H2O2- NuMA (TDIF) CUT&RUN rep2


title: MUT101


title: MUT103


title: RNA-seq MEF WT Rep2

description:
Wild type
MEF_WT_RNAseq_129S1_SvImJ_count.txt
MEF_WT_RNAseq_CAST_EiJ_count.txt


title: RPE1_H2O2+ 90 min recovery NuMA (TDIF) CUT&RUN rep1


title: MUT102


description: L1_W054: SPAR-seq of 108 multi-exon gene regions in N2A cells, Parp1 knockdown (T0054), replicate 1


title: RNA-seq MEF XiΔXist Rep1


title: WT 7.0 A

value: Normal condition


title: WLD102


title: RNA-seq MEF XiΔXist shSCR Rep1


description: L1_W050: SPAR-seq of 108 multi-exon gene regions in N2A cells, Brd8 knockdown (T0050), replicate 1

value: Mouse neuroblastoma cells


title: RPE1_H2O2+ 90 min recovery IgG CUT&RUN rep2

value: IgG CUT&RUN


description: L1_W047: SPAR-seq of 108 multi-exon gene regions in N2A cells, Elmod3 knockdown (T0047), replicate 1


description: L1_W048: SPAR-seq of 108 multi-exon gene regions in N2A cells, Atrx knockdown (T0048), replicate 1


title: RPE1_H2O2- IgG CUT&RUN rep2


description: L1_W043: SPAR-seq of 108 multi-exon gene regions in N2A cells, Pds5b knockdown (T0043), replicate 1


title: H3K27ac ChIP-seq XiΔXist Rep2

description:
Xist deletion on Xi
MEF_XistKO_H3K27ac_129.bigwig
MEF_XistKO_H3K27ac_CAST.bigwig

data_processing:
Biological replicates of ChIP-seq data were pooled to maximize sequencing depth.
ChIP-seq reads were aligned to a N-masked mouse reference genome (in which all SNPs between 129S1/SvImJ and CAST/EiJ genome are replaced by “N”).
Reads with low alignment quality (MAPQ < 30) were removed, and the remaining aligned reads were split to 129S1/SvImJ or CAST/EiJ allele using SNPsplit.
Bigwig files were prepared using deepTools without normalization.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig, allele-specific genome track.

source_name: MEF

extract_protocol:
DNA was purified using MiniElute PCR purification kit (QIAGEN, 28006).
ChIP-seq libraries were prepared using KAPA HyperPrep kit (KAPA, 07962347001).

treatment_protocol: ChIP experiments were performed as previously described with minor modifications (Kadota and Nagata, 2014). MEFs (~3x106) were crosslinked with 1% formaldehyde for 10 min (H3K27me3 and H3K27ac ChIP) or 15min (YY1 ChIP) at RT. The reaction was stopped by adding glycine (final concentration, 125 mM) for 5 min at RT. Crosslinked cells were lysed and the chromatin was digested to fragmetns smaller than 1000bp by sonication or MNase treatment. The digested chromatin was incuabted with 2 ul of anti-H3K27me3 (mAbcam6002; Abcam), anti-YY1 (Cell Signaling, 46395) or anti-H3K27ac (Abcam, ab4729) antibody 4ºC overnight with rotation, followed by incubation with pre-washed Protein A/G agarose (Thermo Scientific, 20423) or Protein G magnetic beads (Invitrogen, 10003D) for 1-2 hours at 4ºC. The agarose/beads was sequentially washed with low salt wash buffer (20 mM Tris-HCl, pH 7.9, 100 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) for 10 min, high salt wash buffer (20 mM Tris-HCl, pH 7.9, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) for 10 min, the LiCl buffer (10 mM Tris-HCl, pH 7.9, 250 mM LiCl, 1% NP-40, 1% deoxycholate acid, 1 mM EDTA) for 10 min, and twice with TE buffer for 5 min. DNA-protein complexes were eluted in elution buffer (1% SDS, 0.1 M NaHCO3). Reverse crosslinking was performed by incubating samples in 200 mM of NaCl at 65ºC overnight followed by Proteinase K (20 mg/ml) treatment for 2 hrs at 55ºC.

tag: chip antibody

value: anti-H3K27ac (Abcam, ab4729)


title: WLD101

value: WT


title: WLD103


title: RPE1_H2O2+ 90 min recovery IgG CUT&RUN rep1


title: RNA-seq MEF WT Rep1


title: RPE1_H2O2- NuMA (TDIF) CUT&RUN rep1


description: L1_W042: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf18 knockdown (T0042), replicate 1


title: H3K27ac ChIP-seq WT Rep2

description:
Wild type
MEF_XistKO_H3K27ac_129.bigwig
MEF_XistKO_H3K27ac_CAST.bigwig


title: H3K27ac ChIP-seq XiΔXist Rep1


title: H3K27ac ChIP-seq WT Rep1


title: H2O2+ NuMA (TDIF) CUT&RUN rep3

description: MH = Untreated/H2O2-, PH = H2O2 treated, IG = IgG T = NuMA (TDIF)

source_name: Neuroblastoma cell line

growth_protocol: SH-SY5Y cells were cultured in DMEM/F12 (1:1) (1X) + GlutaMAX supplemented with 1X non-essential amino acids, 100 U/ml penicillin and 100 μg/ml streptomycin and 10% fetal bovine serum. Differentiation was performed by culturing in 2.5% fetal bovine serum supplemented with 20μM retinoic acid for 6 days. Cells were grown at 37°C in a humidified atmosphere containing 5% carbon dioxide (CO2).

extract_protocol:
Around 500,000 cells were immobilized on BioMag Plus Concanavalin A beads (Cat. No.: BP531-3) and then incubated with the required antibodies overnight at 4°C, in a buffer containing Digitonin to permeabilize the cells. After washing the cells immobilized on the beads, Protein A/G MNase fusion protein was added and incubated for 1 hour at 4°C to bind to the antibodies. Following washes, cells were incubated with CaCl2 on ice for 45 minutes to activate the MNase to cleave the DNA. A 2X STOP Buffer containing EDTA is then added to stop the cleavage and release the chromatin to the solution. The released fragments were then treated with Proteinase K and purified with phenol  chloroform and precipitated with ethanol before being subjected to library prep.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina with Sample Purification Beads (Cat. No.: E7103L) and NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (Cat. No.: E7335L). Briefly, DNA ends were end repaired, 5'phosphorylated and dA-tailing was done using the NEBNext Ultra II End Prep Enzyme Mix, then adaptors were ligated and Uracils were excised using the USER enzyme. The DNA was then cleaned up and enriched by PCR for 9 cycles and then cleaned up with the sample purification beads, before being sequenced on the Illumina NovaSeq 6000.

value: Neuroblastoma cell line


description: L1_W040: SPAR-seq of 108 multi-exon gene regions in N2A cells, Brca1 knockdown (T0040), replicate 1


title: YY1 ChIP-seq XiΔXist Rep3

description:
Xist deletion on Xi
MEF_XistKO_YY1_129.bigwig
MEF_XistKO_YY1_CAST.bigwig

value: anti-YY1 (Cell Signaling, 46395)


description: L1_W039: SPAR-seq of 108 multi-exon gene regions in N2A cells, Mbnl1+2 knockdown (T0039), replicate 1


title: YY1 ChIP-seq WT Rep4

description:
Wild type
MEF_WT_YY1_129.bigwig
MEF_WT_YY1_CAST.bigwig


description: L1_W038: SPAR-seq of 108 multi-exon gene regions in N2A cells, Gtf2f1 knockdown (T0038), replicate 1


description: L1_W041: SPAR-seq of 108 multi-exon gene regions in N2A cells, Rbbp6 knockdown (T0041), replicate 1


title: YY1 ChIP-seq XiΔXist Rep2


description: L1_W044: SPAR-seq of 108 multi-exon gene regions in N2A cells, Klf8 knockdown (T0044), replicate 1


description: L1_W045: SPAR-seq of 108 multi-exon gene regions in N2A cells, control non-targeting knockdown (T0045), replicate 1


title: YY1 ChIP-seq WT Rep3


title: No epitope control ChIP-seq on wildtype Pf3D7 at 30 hpi input

city: STATE COLLEGE

first: Timothy

middle: J

last: Russell

state: PA

address: W122 Millennium Science Complex

institute: Pennsylvania State University

data_processing:
Reads in each DNA library were trimmed to remove low quality base calls and Illumina adaptor sequences using Trimmomatic 0.32.3.
Reads were mapped to the P. falciparum 3D7 genome (Pf 3D7 v36) using BWA-MEM 0.4.1.
Duplicate reads were removed using samtools 1.1.2.
MACS2 (version 2.1.1.20160309) was used to call peaks with a q value cutoff of 0.01.
Deeptools BamCoverage 3.5.1.0.0 was used to generate bigwig files from mapped .bam files.
Assembly: PlasmoDB-36_Pfalciparum3D7_Genome.fasta
Supplementary files format and content: bigwig for all libraries, narrowpeak calls for immunoprecipitate over input

organism: Plasmodium falciparum

growth_protocol: Parasites were grown at 37°C, 5% O2, 7% CO2 using RPMI1640 media supplemented with hypoxanthine and .5% Albumax II (Thermo). AP2-EXP::GFP and AP2-EXP::HA were maintained in media supplemented with 2.5nM WR99210

extract_protocol:
ChIP was performed as described in PMID: 32198457. Briefly, nuclear material was extracted following cross-linking in 1% formaldehyde. Chromatin was sonicated using an M220 ultrasonicator (Covaris) at 5% duty cycle, 75 W peak incident power, 200 cycles per burst, treatment time 300 seconds. Input chromatin was set aside to use as a control, and the remaining material was immunoprecipitated overnight using anti-HA or anti-GFP antibody. RNA and protein were removed by enzymatic digestion and DNA was isolated using the Qiagen MinElute kit.
ChIP-seq DNA libraries were prepared as described in PMID: 32198457 using the NEBNext II DNA library kit (New England Biolabs) according to the manufacturer’s instructions. Quality was assessed using an Agilent 2100 Bioanalyzer or TapeStation. AMPure XP beads (Beckmann Coulter) were used to size select and purify DNA between NEBNext II library preparation steps.

value: trophozoite

value: Abcam Ab290 anti-GFP


title: RPE1_H2O2- IgG CUT&RUN rep1

description: MH = Untreated/H2O2-, 90R = H2O2 treated 90 minute recovery, I = IgG, N = NuMA (TDIF), T = TDP1


title: H2O2+ NuMA (TDIF) CUT&RUN rep2


title: YY1 ChIP-seq WT Rep2

value: MEF


title: ChIP-seq on AP2-EXP in the AP2-EXP::GFP Pf3D7 background at 30 hpi replicate 1 immunoprecipitate


title: ChIP-seq on AP2-EXP in the AP2-EXP::GFP Pf3D7 background at 30 hpi replicate 2 immunoprecipitate


title: ChIP-seq on AP2-EXP in the AP2-EXP::GFP Pf3D7 background at 30 hpi replicate 1 input


title: No epitope control ChIP-seq on wildtype Pf3D7 at 30 hpi immunoprecipitate


title: H2O2- NuMA (TDIF) CUT&RUN rep2


title: day02.RNA.ZIC3ko.Rep3

city: La Jolla

first: Christopher

last: Benner

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
RNA-seq at Day 2 (mesoderm) ZIC3 KO rep 3
fpkm.txt.gz

data_processing:
base-calling use bcl2fastq version 2.17
Reads were aligned with bowtie2 (ATAC/ChIPseq) or STAR (RNAseq) to the human hg19 genome using default parameters. Only reads that mapped uniquely to the genome (MAPQ >=10) were considered for downstream analyses. ATAC/ChIPseq peaks were found using HOMER's getDifferentialPeaksReplicates.pl and gene expression FPKM values were calculated using HOMER's analyzeRepeats.pl program using GENCODE transcript annotations.
Genome_build: hg19
Supplementary_files_format_and_content: BED files with peak positions (hg19), FPKM transcript levels in a tab-delimited text file

source_name: ES derived mesoderm

growth_protocol: Human pluripotent stem cells were grown in E8 on Geltrex-coated plates and differentiated into cardiomyocytes and intervening staged using modulation of WNT signalling

extract_protocol:
ATAC-seq was performed as previously described (PMID: 29434377). ChIP-seq experiments for all histone marks at all time points were performed as previously described (PMID: 22763441). Detailed protocols for ChIP-seq including antibodies used and antibodies validations performed are available at www.encodedcc.org associated with each experiment described here. They can also be found at the links below. Standard ChIP-seq, Tissue fixation & sonication: https://www.encodeproject.org/documents/3125496b-c833-4414-bf5f84dd633eb30d/@@download/attachment/Ren_Tissue_Fixation_and_Sonication_v060614.pdf, Immunoprecipitation: https://www.encodeproject.org/documents/89795b31-e65a-42ca-9d7bd75196f6f4b3/@@download/attachment/Ren%20Lab%20ENCODE%20Chromatin%20Immunoprecipitation%20Protocol_V2.pdf. For RNA-seq, total RNA was extracted with Trizol according to protocol (Thermo Scientific, 15596-026).
ATAC-seq libraries were created using Nextera Tn5 transposase with Illumina adapters and PCR-amplified as previously described (PMID: 29434377). ChIP-seq libraries were created as described here: https://www.encodeproject.org/documents/4f73fbc3-956e-47ae-aa2d41a7df552c81/@@download/attachment/Ren_ChIP_Library_Preparation_v060614.pdf. RNA-seq libraries were constructed using standard Illumina TruSeq LT library prep.

treatment_protocol: ZIC3 knock out lines were generated through CRISPR/Cas9-mediated targeting of exon1 that is common to ZIC3 isoforms

value: ES derived mesoderm

tag: differentiation time

value: H9 MLC2v:H2B

tag: perturbation

value: ZIC3 KO


description: L1_W037: SPAR-seq of 108 multi-exon gene regions in N2A cells, Atf6 knockdown (T0037), replicate 1

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

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.

tag: tissue

tag: cell line


title: YY1 ChIP-seq WT Rep1

value: Female

tag: strain

value: 129S1/SvImJ x CAST/EiJ


title: H2O2+IgG CUT&RUN


title: day02.RNA.ZIC3ko.Rep2

description:
RNA-seq at Day 2 (mesoderm) ZIC3 KO rep 2
fpkm.txt.gz


title: ChIP-seq on AP2-EXP in the AP2-EXP::GFP Pf3D7 background at 30 hpi replicate 2 input


description: L1_W035: SPAR-seq of 108 multi-exon gene regions in N2A cells, Igf2bp2 knockdown (T0035), replicate 1


title: H2O2+ NuMA (TDIF) CUT&RUN rep1

value: NuMA (TDIF) CUT&RUN


title: H2O2- NuMA (TDIF) CUT&RUN rep1


title: day02.RNA.ZIC3ko.Rep1

description:
RNA-seq at Day 2 (mesoderm) ZIC3 KO rep 1
fpkm.txt.gz


title: YY1 ChIP-seq XiΔXist Rep1

value: Xi[delta]Xist


title: H2O2- NuMA (TDIF) CUT&RUN rep3


title: mouse_expt_arms_1_2_3_4_5_tcr

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description: Mixed samples: T cells derived from the bone marrow or spleen of leukemic mice after immunization or niliotinib/anti-PDL1 drug treatments

data_processing:
10X Genomics Cell Ranger (scRNAseq) software was used to demultiplex samples and generate fastq files.
Each gel bead in emulsion (GEM) was identified and all gene specific reads were mapped via cellranger "count" (ver. 5.0.1) using the mouse reference genome (mm10) or human reference genome (GRCh38), or antibody specific tags (HTOs and ADTs). T-cell receptor contigs were recovered by running Cellranger "vdj" software with a reference provided by 10X genomics.
HTO/ADT counts were generated by cellranger count using the specific antibody-oligo tags sequences used in this experiment. Experimental arms or patient samples were classified using HTO counts respectively via GMM-Demux software (ver. 0.2.1.3).
Raw counts data was imported into R (ver 4.0.3) for downstream processing, including normalization, principal components analysis, differential gene expression testing, single cell clustering, etc. primarily using the Seurat R package (ver. 4.0.1).
Genome_build: refdata-gex-mm10-2020-A, refdata-gex-GRCh38-2020-A, refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0, refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0 (all provided by 10X Genomics)
Supplementary_files_format_and_content: tab-delimited text files include raw or normalized read count values for each sample (GEX, HTO, ADT) or tab-delimited text and json files of T-cell receptor contigs (TCR)

source_name: mixed sample, expt arms 1-5, bone marrow and spleen T-cells

extract_protocol:
For the mouse studies, CD44+CD4+ T cells from the indicated arms of mice were sorted using a BD FACSAria sorter. Cells from different treatment arms were labeled with hashtag antibodies, as well as CITE-Seq antibodies to CD25, OX40, TIGIT, PD1, Tim3, LAG3 (Biolegend). Sorted CD44+CD4+ T cells were resuspended at 106 ml in 50% FBS in 1×PBS and captured using 10x Genomics Single Cell 5’ Solution. Single cell TCR sequencing was performed using the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics) according to the manufacturer’s instructions. For the human studies, cells were sorted using a BD FACSAria sorter. Ten-thousand cells from each of the three sorted fractions were pooled together and resuspended at 10^6 ml in 50% FBS in 1×PBS before capture using 10x Genomics Single Cell 5’ Solution. Single cell TCR sequencing was performed using the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics).
For 10X Genomics scRNA-seq, we generated three libraries that measure: (1) mRNA transcript expression (GEX), (2) sample/tissue-specific hashtag oligos (HTO) and protein marker levels using antibody derived tags (ADT), and (3) T cell receptor specific mRNA reperitorires. Cells were harvested and stained as described above. The sample was split into three libraries (GEX, HTO/ADT, and TCR). Reverse transcription PCR and library preparation were carried out under the Chromium Single Cell 5’ v1.1 protocol (10X Genomics) per manufacturer’s recommendations. The libraries were sequenced on the NovaSeq 6000 with 2x150 bp paired-end reads (Illumina).

treatment_protocol: For the mouse studies, C57BL/6 mice were injected with 2500 LM138 cells via tail vein. Mice were bled at 14 days post-leukemia challenge, then treated with 75mg/kg nilotinib via oral gavage 5 days/week for 2 weeks. Some mice were treated with 10mg/kg InVivoPlus anti-mouse PDL1 (BioXCell, clone: 10F.9G2), or an isotype control antibody (Rat IgG2b, kappa) via intraperitoneal injection on days 14, 16 and 18 post-leukemia establishment. For the 1-week treatment schedule, mice were treated with nilotinib 5 days/week for 1 week starting at day 14 post leukemia establishment, and with anti-PDL1 or isotype control antibodies. For the CD4 and CD8 T cell depletion studies, mice were treated with 22mg/kg InVivoPlus anti-CD4 (BioXCell, clone: GK1.5) or InVivoPlus anti-CD8 (BioXCell, clone: YTS 169.4) depleting antibodies on days 7, 9 and 11 post-leukemia establishment. For the human studies, leukemia blasts, T cells (CD45+CD3+) and other immune cells (CD45+CD3-CD10-) were isolated from bone marrow biopsy samples from five leukemia patients.

value: bone marrow and spleen

tag: treatment

value: mixed samples:injected with leukemia cell line (LM138), treated with nilotinib and/or with anti-mouse PDL1

value: single cell T cell receptor mRNA


description: L1_W033: SPAR-seq of 108 multi-exon gene regions in N2A cells, Blm knockdown (T0033), replicate 1

value: Mouse neuroblastoma cells


description: L1_W034: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ppp1r8 knockdown (T0034), replicate 1


title: RPE1_H2O2+ NuMA (TDIF) KD PolII ChIP rep2

description: MH = Untreated/H2O2-, PH = H2O2 treated, ND = No doxycyclin/WT with respect to NuMA (TDIF), PD = post-doxycyclin/NuMA (TDIF) KD, IN = Input, IG = IgG, Pol2 = RNA polymerase II

data_processing:
Data mapped using bwa mem version 0.7.17 (parameters: -M -k 25)
Data was filtered prior to downstream analyses. Duplicates were first removed from the BAM files using Picard MarkDuplicates in conjunction with samtools view to remove PCR or optical duplicates (parameters: -F 1024). Reads with a quality score of less than 30 were also removed using samtools view (parameters: -q 30)
bigwigs were generated using MACS2 version 2.1.1.2. Fragment pileup and control (input) lambda were output to BEDgraph files using MACS2 peak calling (parameters: -B –SPMR). The sample and control lambda BEDgraph signal tracks were then compared using MACS2 bdgcomp (parameters: -m FE), and the resulting bedgraph files converted to bigwigs
Metagene profiles were generated using bam2geneprofile from CGAT scripts using gene annotations derived from Ensembl 85, with reporter set to genes and no normalisation
Assembly: hg38
Supplementary files format and content: Fold-change relative to input bigwigs

extract_protocol:
The nuclei was extracted through a fractionation protocol, that first lysed the cell membrane and then the nuclei were lysed. The lysate was then sonicated using the Bioruptor Pico (Diagenode) for 12 cycles on 20 seconds on/40 seconds off to yield fragments in the size range of 100-300 bp. The lysates were cleared by centrifugation and the protein-DNA complexes of interest were enriched by overnight incubation with antibodies, followed by a 2-hour incubation with Protein G Dynabeads. After subsequent washes, the immunoprecipitated complexes were eluted, and reverse crosslinked overnight, treated with RNase A, proteinase K and then purified with phenol chloroform and the DNA was ethanol precipitated before being subjected to library prep.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina with Sample Purification Beads (Cat. No.: E7103L) and NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (Cat. No.: E7335L). Briefly, the DNA ends were end repaired, 5'phosphorylated and dA-tailing was done using the NEBNext Ultra II End Prep Enzyme Mix, then adaptors were ligated and Uracils were excised using the USER enzyme. The DNA was then cleaned up and enriched by PCR for 12 cycles and then cleaned up with the sample purification beads, before being sequenced on the Illumina NovaSeq 6000.

treatment_protocol: Cells were grown to nearly 80% confluency and then washed once with PBS, followed by the addition of media lacking the serum and allowed to grow for 48 hours. Cells were washed with PBS then treated with freshly prepared 10 µM hydrogen peroxide (H2O2) in cold PBS for 10 minutes, on ice, in the dark. After treatment, the cells were washed again with PBS. Following serum starvation or H2O2 treatment, cells were washed with PBS then incubated with media containing all the supplements including the serum, for 90 minutes. Cells were then crosslinked with 1% Paraformaldehyde for 10 minutes at room temperature, followed by a 5 minute incubation with 0.125 M Glycine. Cells were then washed twice with cold PBS, before being scraped in cold PBS and pelleted. The pellets were snap frozen in liquid nitrogen and then stored at -80°C.

value: Human retinal pigment epithelial cell line

value: NuMA (TDIF) Knockdown


title: day02.RNA.wt.Rep2

description:
RNA-seq at Day 2 (mesoderm) wild type rep 2
fpkm.txt.gz

value: wild type


title: day02.RNA.wt.Rep1

description:
RNA-seq at Day 2 (mesoderm) wild type rep 1
fpkm.txt.gz


title: day02.RNA.wt.Rep3

description:
RNA-seq at Day 2 (mesoderm) wild type rep 3
fpkm.txt.gz


title: mouse_expt_arms_1_2_3_4_5_hto_adt

value: single cell HTO and ADT feature barcodes


title: mouse_expt_arms_1_2_3_4_5_gex

value: single cell mRNA


title: H2O2- IgG CUT&RUN

description: MH = Untreated/H2O2-, PH = H2O2 treated, IG = IgG T = NuMA (TDIF)

value: Neuroblastoma cell line

value: IgG CUT&RUN


description: L1_W036: SPAR-seq of 108 multi-exon gene regions in N2A cells, Capn2 knockdown (T0036), replicate 1


description: L1_W031: SPAR-seq of 108 multi-exon gene regions in N2A cells, Srsf11 knockdown (T0031), replicate 1


title: RPE1_H2O2+ NuMA (TDIF) KD PolII ChIP rep1


title: day80.H3K4me3.Rep2

description:
H3K4me3 ChIP-seq at Day 80 (ventricular cardiomyocyte) rep 2
peaks-H3K4me3-D80.bed.gz

source_name: ES derived ventricular cardiomyocyte

value: ES derived ventricular cardiomyocyte

value: H9 MLC2v:H2B

value: H3K4me3 04-745 Millipore


title: tot_16_RNA-seq_S51A_Bort_4

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Reads were demultiplexed with Fastq Multx, trimmed using rfastp, and aligned to the mm10 reference genome using bowtie2
For expression analysis of ribosome profiling data only reads in the CDS were included and reads coming from the first 15 codons (45bp) and last 5 codons (15bp) were excluded. Additionally, only reads of size between 20-23bp or 26-32bp were counted. Counting of reads over these regions was done with featureCounts (Liao et al., 2014) followed by differential analysis with DESeq2 (Love et al., 2014).
Gene lists were generated by first by filtering genes with significant differences in RPF-read counts (RPF_FC>1.5 and padj <0.05), and then genes that changed specifically at the translation level were identified as the subset of filtered  genes with translational efficiency (TE=normalized RPF/normalized total RNA) fold changes greater than 1.5.
Genome_build: mm10
Supplementary_files_format_and_content: Counts tables contain the raw counts quantified by featureCounts and DESeq2.

growth_protocol: Cells were maintened in Elow media

extract_protocol:
Cells were quickly washed twice in ice-cold PBS, and harvested in 400uL polysome lysis buffer by scraping on ice
Ribo-seq libraries were constructed as previously described (McGlincy, 2017). rRNA was depleted using RiboCop following manufacturer's instructions (Lexogen). Total RNA libraries were built with Illumina TrySeq kit using rRNA depletion.
Novaseq S1 1x100bp

treatment_protocol: Cells were treated for 4.5h with either DMSO (vehicle) or 100nM bortezomib

value: Squamous cell carcinoma

value: Bortezomib (100nM, 4.5h)


title: RPE1_H2O2+ NuMA (TDIF) KD IgG ChIP rep2


title: RPE1_H2O2+ NuMA (TDIF) KD IgG ChIP rep1


title: RPE1_H2O2+ NuMA (TDIF) KD Input rep2


title: tot_15_RNA-seq_S51A_Bort_3


city: Toronto

first: Ulrich

last: Braunschweig

institute: University of Toronto

description: L1_W029: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ehmt2 knockdown (T0029), replicate 1


title: tot_14_RNA-seq_S51A_Bort_2


description: L1_W028: SPAR-seq of 108 multi-exon gene regions in N2A cells, Arid1a knockdown (T0028), replicate 1


title: day15.H3K4me3.Rep2

description:
H3K4me3 ChIP-seq at Day 15 (primitive cardiomyocite) rep 2
peaks-H3K4me3-D15.bed.gz

source_name: ES derived primitive cardiomyocite

value: ES derived primitive cardiomyocite


title: tot_13_RNA-seq_S51A_Bort_1


title: day80.H3K4me3.Rep1

description:
H3K4me3 ChIP-seq at Day 80 (ventricular cardiomyocyte) rep 1
peaks-H3K4me3-D80.bed.gz


description: L1_W027: SPAR-seq of 108 multi-exon gene regions in N2A cells, mock control (T0027), replicate 1


description: L1_W030: SPAR-seq of 108 multi-exon gene regions in N2A cells, Banp knockdown (T0030), replicate 1


description: L1_W032: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf40b knockdown (T0032), replicate 1


title: RPE1_H2O2- NuMA (TDIF) KD PolII ChIP rep2


title: day15.H3K4me3.Rep1

description:
H3K4me3 ChIP-seq at Day 15 (primitive cardiomyocite) rep 1
peaks-H3K4me3-D15.bed.gz


title: RPE1_H2O2+ NuMA (TDIF) KD Input rep1


title: RPE1_H2O2- NuMA (TDIF) KD PolII ChIP rep1


description: L1_W026: SPAR-seq of 108 multi-exon gene regions in N2A cells, Acin1 knockdown (T0026), replicate 1


title: day07.H3K4me3.Rep1

description:
H3K4me3 ChIP-seq at Day 7 (cardiac progenitor cells) rep 1
peaks-H3K4me3-D07.bed.gz

source_name: ES derived cardiac progenitor cells

value: ES derived cardiac progenitor cells


title: day07.H3K4me3.Rep2

description:
H3K4me3 ChIP-seq at Day 7 (cardiac progenitor cells) rep 2
peaks-H3K4me3-D07.bed.gz


description: L1_W025: SPAR-seq of 108 multi-exon gene regions in N2A cells, Bub3 knockdown (T0025), replicate 1


description: L1_W023: SPAR-seq of 108 multi-exon gene regions in N2A cells, Snrnp40 knockdown (T0023), replicate 1


title: day02.H3K4me3.Rep2

description:
H3K4me3 ChIP-seq at Day 2 (mesoderm) rep 2
peaks-H3K4me3-D02.bed.gz

value: ES derived mesoderm


title: RPE1_H2O2- NuMA (TDIF) KD IgG ChIP rep2

description: MH = Untreated/H2O2-, PH = H2O2 treated, ND = No doxycyclin/WT with respect to NuMA (TDIF), PD = post-doxycyclin/NuMA (TDIF) KD, IN = Input, IG = IgG, Pol2 = RNA polymerase II


description: L1_W020: SPAR-seq of 108 multi-exon gene regions in N2A cells, Actl6b knockdown (T0020), replicate 1


title: day05.H3K4me3.Rep2

description:
H3K4me3 ChIP-seq at Day 5 (cardiac mesoderm) rep 2
peaks-H3K4me3-D05.bed.gz

source_name: ES derived cardiac mesoderm

value: ES derived cardiac mesoderm


title: day00.H3K4me3.Rep2

description:
H3K4me3 ChIP-seq at Day 0 (ESC) rep 2
peaks-H3K4me3-D00.bed.gz

source_name: Embryonic stem cell

value: Embryonic stem cell


description: L1_W024: SPAR-seq of 108 multi-exon gene regions in N2A cells, Birc5 knockdown (T0024), replicate 1

value: Mouse neuroblastoma cells


title: RPE1_H2O2+ WT PolII ChIP rep2

value: Human retinal pigment epithelial cell line


title: day05.H3K4me3.Rep1

description:
H3K4me3 ChIP-seq at Day 5 (cardiac mesoderm) rep 1
peaks-H3K4me3-D05.bed.gz

value: wild type


description: L1_W019: SPAR-seq of 108 multi-exon gene regions in N2A cells, Arid3b knockdown (T0019), replicate 1


title: RPE1_H2O2- NuMA (TDIF) KD IgG ChIP rep1

value: NuMA (TDIF) Knockdown


title: RPE1_H2O2- NuMA (TDIF) KD Input rep2


title: RPE1_H2O2- NuMA (TDIF) KD Input rep1


title: day02.H3K4me3.Rep1

description:
H3K4me3 ChIP-seq at Day 2 (mesoderm) rep 1
peaks-H3K4me3-D02.bed.gz


description: L1_W021: SPAR-seq of 108 multi-exon gene regions in N2A cells, Nacc1 knockdown (T0021), replicate 1


description: L1_W022: SPAR-seq of 108 multi-exon gene regions in N2A cells, Atf2 knockdown (T0022), replicate 1


title: day80.H3K4me1.Rep1

description:
H3K4me1 ChIP-seq at Day 80 (ventricular cardiomyocyte) rep 1
peaks-H3K4me1-D80.bed.gz

value: H3K4me1 ab8895 Abcam


description: L1_W018: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prdm2 knockdown (T0018), replicate 1


title: tot_4_RNA-seq_Ctrl_veh_4

value: Vehicle


title: RPE1_H2O2+ WT IgG ChIP rep1


title: RPE1_H2O2+ WT PolII ChIP rep1


title: day80.H3K4me1.Rep2

description:
H3K4me1 ChIP-seq at Day 80 (ventricular cardiomyocyte) rep 2
peaks-H3K4me1-D80.bed.gz


title: RPE1_H2O2+ WT IgG ChIP rep2


title: tot_1_RNA-seq_Ctrl_veh_1


title: tot_3_RNA-seq_Ctrl_veh_3


title: tot_2_RNA-seq_Ctrl_veh_2


title: day00.H3K4me3.Rep1

description:
H3K4me3 ChIP-seq at Day 0 (ESC) rep 1
peaks-H3K4me3-D00.bed.gz


description: L1_W017: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ints7 knockdown (T0017), replicate 1


title: RPE1_H2O2+ WT Input rep2


description: L1_W016: SPAR-seq of 108 multi-exon gene regions in N2A cells, Cacna1e knockdown (T0016), replicate 1


title: day15.H3K4me1.Rep2

description:
H3K4me1 ChIP-seq at Day 15 (primitive cardiomyocite) rep 2
peaks-H3K4me1-D15.bed.gz


title: day07.H3K4me1.Rep2

description:
H3K4me1 ChIP-seq at Day 7 (cardiac progenitor cells) rep 2
peaks-H3K4me1-D07.bed.gz


title: RPE1_H2O2+ WT Input rep1

description: MH = Untreated/H2O2-, PH = H2O2 treated, ND = No doxycyclin/WT with respect to NuMA (TDIF), PD = post-doxycyclin/NuMA (TDIF) KD, IN = Input, IG = IgG, Pol2 = RNA polymerase II


description: L1_W015: SPAR-seq of 108 multi-exon gene regions in N2A cells, Brd4 knockdown (T0015), replicate 1


title: Sample_15_Ribo-Seq S51A_Bort_3

tag: molecule subtype


title: Sample_14_Ribo-Seq S51A_Bort_2


description: L1_W014: SPAR-seq of 108 multi-exon gene regions in N2A cells, Ash1l knockdown (T0014), replicate 1


title: RPE1_H2O2- WT PolII ChIP rep1


description: L1_W012: SPAR-seq of 108 multi-exon gene regions in N2A cells, Atf1 knockdown (T0012), replicate 1


title: day07.H3K4me1.Rep1

description:
H3K4me1 ChIP-seq at Day 7 (cardiac progenitor cells) rep 1
peaks-H3K4me1-D07.bed.gz


description: L1_W013: SPAR-seq of 108 multi-exon gene regions in N2A cells, Brd3 knockdown (T0013), replicate 1


title: RPE1_H2O2- WT IgG ChIP rep2


title: day05.H3K4me1.Rep2

description:
H3K4me1 ChIP-seq at Day 5 (cardiac mesoderm) rep 2
peaks-H3K4me1-D05.bed.gz


title: Sample_16_Ribo-Seq S51A_Bort_4


title: RPE1_H2O2- WT IgG ChIP rep1


title: day05.H3K4me1.Rep1

description:
H3K4me1 ChIP-seq at Day 5 (cardiac mesoderm) rep 1
peaks-H3K4me1-D05.bed.gz


title: RPE1_H2O2- WT Input rep2


title: day02.H3K4me1.Rep2

description:
H3K4me1 ChIP-seq at Day 2 (mesoderm) rep 2
peaks-H3K4me1-D02.bed.gz


title: day15.H3K4me1.Rep1

description:
H3K4me1 ChIP-seq at Day 15 (primitive cardiomyocite) rep 1
peaks-H3K4me1-D15.bed.gz


description: L1_W011: SPAR-seq of 108 multi-exon gene regions in N2A cells, Akap8l knockdown (T0011), replicate 1


title: RPE1_H2O2- WT Input rep1


description: L1_W009: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tonsl knockdown (T0009), replicate 1


title: RPE1_H2O2- WT PolII ChIP rep2


description: L1_W010: SPAR-seq of 108 multi-exon gene regions in N2A cells, Hjurp knockdown (T0010), replicate 1


title: day02.H3K4me1.Rep1

description:
H3K4me1 ChIP-seq at Day 2 (mesoderm) rep 1
peaks-H3K4me1-D02.bed.gz


title: SH-SY5Y_H2O2+ 90 min recovery NuMA (TDIF) KD OGAP-seq rep2

description: MH = Untreated/H2O2-, R90 = H2O2 treated 90 minute recovery, WT = Wild type with respect to NuMA (TDIF), KD = NuMA (TDIF) Knockdown, IN = Input, IP = OGAP-seq

data_processing:
Data mapped using bwa mem version 0.7.17 (parameters: -M -k 25)
Data was filtered prior to downstream analyses. Reads with a quality score of less than 30 were also removed using samtools view (parameters: -q 30)
bigwigs were generated using MACS2 version 2.1.1.2. Fragment pileup and control (IgG) lambda were output to BEDgraph files using MACS2 peak calling (parameters: -B –SPMR). The sample and control lambda BEDgraph signal tracks were then compared using MACS2 bdgcomp (parameters: -m FE), and the resulting bedgraph files converted to bigwigs
Metagene profiles were generated using bam2geneprofile from CGAT scripts using gene annotations derived from Ensembl 85, with reporter set to genes and no normalisation
Assembly: hg38
Supplementary files format and content: Fold-change relative to IgG bigwigs

extract_protocol:
Genomic DNA was extracted using the Qiagen Blood and Tissue Kit. The DNA was digested with OGG1 or Fpg and then the labelled with 5mM biotin labelled aldehyde-reactive probe (ARP). The DNA was subsequenetly sheared by sonication and the labelled DNA was enriched using MyOne Dynabeads, then eluted in TE Buffer. The DNA was then repaired using the PreCR Repair Mix and purified usin the MinElute Clean Up Kit.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit for Illumina with Sample Purification Beads (Cat. No.: E7103L) and NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) (Cat. No.: E7335L). Briefly, the DNA ends were end repaired, 5'phosphorylated and dA-tailing was done using the NEBNext Ultra II End Prep Enzyme Mix, then adaptors were ligated and Uracils were excised using the USER enzyme. The DNA was then cleaned up and enriched by PCR for 12 cycles and then cleaned up with the sample purification beads, before being sequenced on the Illumina NovaSeq 6000.

value: Neuroblastoma cell line


title: Sample_13_Ribo-Seq S51A_Bort_1


title: day00.H3K4me1.Rep2

description:
H3K4me1 ChIP-seq at Day 0 (ESC) rep 2
peaks-H3K4me1-D00.bed.gz


description: L1_W008: SPAR-seq of 108 multi-exon gene regions in N2A cells, Aire knockdown (T0008), replicate 1


title: day00.H3K4me1.Rep1

description:
H3K4me1 ChIP-seq at Day 0 (ESC) rep 1
peaks-H3K4me1-D00.bed.gz


description: L1_W007: SPAR-seq of 108 multi-exon gene regions in N2A cells, Atad2 knockdown (T0007), replicate 1


title: day15.H3K27me3.Rep2

description:
H3K27me3 ChIP-seq at Day 15 (primitive cardiomyocite) rep 2
peaks-H3K27me3-D15.bed.gz

value: H3K27me3 AM61017 Active Motif


title: SH-SY5Y_H2O2+ 90 min recovery NuMA (TDIF) KD OGAP-seq rep1


description: L1_W005: SPAR-seq of 108 multi-exon gene regions in N2A cells, Prpf31 knockdown (T0005), replicate 1


description: L1_W006: SPAR-seq of 108 multi-exon gene regions in N2A cells, Arl6ip4 knockdown (T0006), replicate 1


title: SH-SY5Y_H2O2+ 90 min recovery NuMA (TDIF) KD Input rep2


title: SH-SY5Y_H2O2+ 90 min recovery NuMA (TDIF) KD Input rep1


title: day07.H3K27me3.Rep2

description:
H3K27me3 ChIP-seq at Day 7 (cardiac progenitor cells) rep 2
peaks-H3K27me3-D07.bed.gz

value: H9 MLC2v:H2B


title: day80.H3K27me3.Rep1

description:
H3K27me3 ChIP-seq at Day 80 (ventricular cardiomyocyte) rep 1
peaks-H3K27me3-D80.bed.gz

value: ES derived ventricular cardiomyocyte


title: Sample_2_Ribo-Seq Ctrl_veh_2

value: Squamous cell carcinoma


title: SH-SY5Y_H2O2- NuMA (TDIF) KD OGAP-seq rep1


title: SH-SY5Y_H2O2- NuMA (TDIF) KD Input rep1


description: L1_W002: SPAR-seq of 108 multi-exon gene regions in N2A cells, Capn10 knockdown (T0002), replicate 1


title: Sample_3_Ribo-Seq Ctrl_veh_3


title: day15.H3K27me3.Rep1

description:
H3K27me3 ChIP-seq at Day 15 (primitive cardiomyocite) rep 1
peaks-H3K27me3-D15.bed.gz


description: L1_W004: SPAR-seq of 108 multi-exon gene regions in N2A cells, Tfdp2 knockdown (T0004), replicate 1


title: SH-SY5Y_H2O2+ 90 min recovery WT OGAP-seq rep2


title: Sample_1_Ribo-Seq Ctrl_veh_1


title: day07.H3K27me3.Rep1

description:
H3K27me3 ChIP-seq at Day 7 (cardiac progenitor cells) rep 1
peaks-H3K27me3-D07.bed.gz


description: L1_W003: SPAR-seq of 108 multi-exon gene regions in N2A cells, Spc25 knockdown (T0003), replicate 1


title: SH-SY5Y_H2O2- NuMA (TDIF) KD Input rep2