title: RNAseq.VERO.SMARCA4KO.EmptyVector.Rep1

status: Public on Oct 11 2022

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

data_processing:
Cut & Tag, ATAC-Seq, and human RNA-seq samples were sequenced with the Illumina NextSeq 500 technology, and VERO RNA-seq samples were sequenced with Illumina NovaSeq 6000 technology.
RNAseq reads were aligned to the reference genomes hg19 and chlSab2 (NCBI annotation release 100), using STAR aligner v2.7.3a [1] with parameters --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 --quantMode GeneCounts, and bigWig files were generated using the deeptools v3.1.3 bamCoverage function [2] with the normalizeUsingRPKM parameter.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
For the ATACseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For Cut and Tag libraries, the CutRunTools pipeline was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Assembly: chlSab2, NCBI annotation release 100, hg19
Supplementary files format and content: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million and gene count tables give raw read counts mapped to exons of given genes.

organism: Chlorocebus sabaeus

source_name: VERO E6

growth_protocol: Vero E6 cells were grown in DMEM (Gibco, 11960-44), supplemented with 10% FBS (Gibco), 1X GlutaMAX (Gibco, 35050-061), and 100 U/mL penicillin-streptomycin (Gibco, 15140-122).

extract_protocol:
Omni-ATAC protocol was used to probe DNA accessibility with slight modifications covered below 54. 100,000 cells per sample were trypsinized and washed with cold PBS to remove trypsin. Cell pellets were lysed in 50μl cold resuspension buffer (RSB) supplemented with fresh NP40 (final 0.1% v/v), Tween-20 (final 0.1% v/v), Digitonin (final 0.01% v/v) (RSB recipe: 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2). Lysis step was quenched with 1 mL of RSB supplemented with Tween-20 (final 0.1% v/v) and nuclei were pelleted at 500g for 10 min at 4°C after incubating on ice for 3 minutes. Nuclei were resuspended in 50μl transposition reaction mix containing 25 μl 2X Tagment DNA buffer (Illumina), 2.5μl Tn5 transposase, 16.5μl 1X PBS, 0.5μl 1% digitonin (final 0.01% v/v), 0.5μl 10% Tween-20 (final 0.1% v/v), and 5μl nuclease-free water. Transposition reaction was incubated at 37°C for 30 min with constant shaking (1000 rpm) on a thermomixer. Tagmented DNA was purified using the Qiagen MinElute Reaction Cleanup Kit. Standard ATAC-seq amplification protocol with 7 cycles of amplification was used to amplify tagmented libraries. Libraries were sequenced on Next-seq 500 (Illumina) using 37 bp pair-end sequencing.
RNAs were extracted using Direct-zol RNA MiniPrep Kit and submitted to the Yale Center for Genome Analysis for library preparation. RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 instrument with the goal of at least 25 × 106 reads per sample. Reads were aligned to reference genome chlSab2, NCBI annotation release 100, using STAR aligner v2.7.3a(Dobin et al., 2013) with parameters --winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 --quantMode GeneCounts. Differential expression was obtained using the R package DESeq2 v1.32(Dobin et al., 2013; Love et al., 2014). Bigwig files were generated using deeptools v3.1.3(Ramírez et al., 2016) with parameter --normalizeUsing RPKM
CUT&Tag was carried out using a protocol developed by Epicypher in 8-strip PCR tubes with slight modifications as described below. Briefly, Concanavalin A (ConA) coated magnetic beads were activated with Bead Activation Buffer containing 20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2; beads were stored on ice until used. 300,000 cells/sample were trypsinized and pelleted by centrifugation at room temperature (600g for 3 min). Cells were lysed using cold Nuclear Extraction Buffer containing 20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol supplemented with fresh 0.5 mM Spermidine, and cOmplete, Mini, EDTA-free Protease Inhibitor (Roche) for 2 min. Nuclei were pelleted by centrifugation (600g for 3 min), resuspended in 100ul/sample Resuspension buffer (20 mM HEPES–KOH, pH 7.9, 150mM NaCl supplemented with fresh 0.5 mM Spermidine, and cOmplete, Mini, EDTA-free Protease Inhibitor) and incubated with activated ConA beads at room temperature for 15 min. The nuclei-ConA bead complex was resuspended in Antibody 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), 0.01% Digitonin, and 0.5ug primary antibody/sample. Following overnight incubation at 4°C on a nutator, supernatant was discarded, and beads were washed once with Digitonin 150 Buffer containing 20 mM HEPES, pH 7.5, 150 mM NaCl, supplemented with fresh 0.5 mM Spermidine, Protease Inhibitor (Roche), and 0.01% Digitonin. The ConA-nuclei complexes were then incubated with Digitonin 150 buffer supplemented with 0.5ug/sample Secondary antibody for 1hr at room temperature on a nutator. They were then washed with Digitonin 150 Buffer twice before resuspension in 50uL cold Digitonin300 Buffer containing 20 mM HEPES, pH 7.5, 300 mM NaCl, supplemented with fresh 0.5 mM Spermidine, protease inhibitor, and 0.01% Digitonin. 2.0 µL CUTANA pAG-Tn5 (Epicypher) was added to each sample and incubated on a nutator for 1hr at room temperature. Following incubation, beads were washed twice with cold Digitonin300 Buffer. Targeted chromatin tagmentation and library amplification were carried out according to Epicypher’s protocol.
RNA-seq libraries were prepared with Illumina’s TruSeq standard mRNA Sample Prep Kit using standard protocols. ATAC-seq libraries were prepared using a standard protocol (Buenrostro et al., Current Protocols (2013)).

treatment_protocol: Lentiviral particles were packaged in 293TX cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). Vero E6 cells were lentivirally infected with either Empty vector, SMARCA4 WT or SMARCA4 K785R for 24h and then selected with 5ug/ml Puromycin for 4 days. Cells were harvested for genomics experiments using standard protocols. For Huh7.5 and Calu3 Compound 12 (C12) treatment studies, cells were treated with DMSO vehicle or 1.25uM C12 for 3 days.

tag: cell line

value: VERO E6

value: SMARCA4 knockout + Empty Vector Control


title: RNAseq.VERO.SMARCA4KO.SMARCA4K785R.Rep2

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

tag: genotype

value: SMARCA4 knockout + SMARCA4 K785R


title: RNAseq.VERO.WT.Rep2

value: wild type


title: RNAseq.VERO.SMARCA4KO.SMARCA4K785R.Rep1


title: Control_1

status: Public on Oct 12 2022

city: Jinan

first: Jing

last: Li

address: No. 44-1 Wenhua Road West

country: China

institute: Shandong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Homo_sapiens Ensembl release-96
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: dental pulp stem cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Dental pulp stem cells

tag: individual

value: Donor 1

tag: treatment

value: Control lentivirus infection


title: RNAseq.VERO.SMARCA4KO.SMARCA4WT.Rep2

value: SMARCA4 knockout + SMARCA4 WT


title: RNAseq.VERO.WT.Rep1


title: Normoxia-LECs-mm10-rep1

city: Milwaukee

first: Akiko

last: Mammoto

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

data_processing:
Genome alignment and expression count (STAR) were performed using Basepair.
Genome_build: mm10
Supplementary_files_format_and_content: Expression count txt files include Transcript ID, Gene Symbol, Expression Count, Fragments Per Kilobase Million (FPKM), and Transcripts Per Kilobase Million (TPM) for each sample.

organism: Mus musculus

source_name: Lung

extract_protocol:
Mouse lung endothelial cells were isolated from C57BL6 mouse lungs (8 week old, male) using anti-CD31 conjugated magnetic beads. RNA was extracted using QIAGEN RNeasy mini kit (Cat# 74104). 1 ug of total RNA as used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was collected from endothelial cells isolated from mouse lungs 3 weeks after hypoxia and normoxia treated mouse lungs

tag: strain

tag: tissue

value: lung

value: endothelial cell

value: Normoxia

tag: age

value: 8 week old

tag: Sex

value: male


title: RNAseq.VERO.SMARCA4KO.SMARCA4WT.Rep1


title: RNAseq.VERO.SMARCA4KO.EmptyVector.Rep2


title: SGt_2hr

city: St Augustine

first: Leonid

middle: L

last: Moroz

state: FL

address: 9505 Ocean Shore Blvd

institute: University of Florida

data_processing:
Base calling and initial adapter trimming performed by Illumina Real Time Analysis v2
Additional adapter trimming and alignment to annotated genome performed using Trimmomatic (v0.32) and STAR (v2.3).
Quantification to produce transcripts per million mapped reads (TPMs) was produced by Rsubread (v1.22.3) and edgeR (v3.14.0)
BioProject for the genome:PRJNA13635
Refernce Genome: AASC00000000.3 Aplysia californica
Reference assembly: GCA_000002075.2, (assembly AplCal3.0)
RefSeq assembly accession: GCF_000002075.1 (latest)
Supplementary_files_format_and_content: TPMs for all single neurons samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all developmental stage samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all tissue samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all neuroplasticity samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE

organism: Aplysia californica

source_name: Isolated Tissue

extract_protocol:
Tissue were dissected and RNA isolated with QIAGEN Rneasy. Single neurons were processed without RNA extraction to cDNA.
cDNA was constructed with reverse transcriptase, sequencing library was made using NEBNEXT Ultra I or II Library Construction for Illumina.

tag: tissue type

value: salivary gland


title: SGc


title: Ac11_AG_1hr

source_name: Isolated Ganglion

value: ganglion


title: Ac11_CG_1hr


title: Ac11_RPlG_1hr


title: Ac11_BG_1hr


title: Ac11_RPeG_1hr


title: Ac9_RPlG_1hr


title: Ac9_BG_1hr


title: Ac9_CG_1hr


title: Ac10_LPlG_2hr


title: Ac10_CG_2hr


title: Ac9_LPeG_1hr


title: Ac8_LPeG_1hr


title: Ac10_AG_2hr


title: Ac9_AG_1hr


title: Ac8_CG_1hr


title: Ac8_AG_1hr


title: Ac8_BG_1hr


title: Ac7_BG_1hr


title: Ac10_LPeG_2hr


title: Ac7_CG_1hr


title: Ac7_AG_1hr


title: Ac6_RPlG_2hr


title: Ac7_RPlG_1hr


title: Ac6_LPlG_2hr


title: Ac6_CG_2hr


title: Ac5_RPlG_2hr


title: Ac5_RPeG_2hr


title: Ac5_LPeG_control


title: Ac4_BG_2hr


title: Ac5_AG_2hr


title: Ac5_CG_2hr


title: Ac4_LPeG_2hr


title: Ac10_BG_2hr


title: Ac7_RPeG_1hr


title: Ac7_LPeG_control


title: Ac3_BG_0.5hr


title: Ac4_CG_2hr


title: Ac3_CG_0.5hr


title: Ac2_RPlG_0.5hr


title: Ac3_LPeG_0.5hr


title: Ac3_AG_0.5hr


title: Ac2_BG_0.5hr


title: Ac2_RPeG_0.5hr


title: Ac2_LPeG_control


title: Ac1_LPlG_0.5hr


title: Ac4_AG_2hr


title: Ac6_LPeG_2hr


title: Ac6_RPeG_2hr


title: Ac5_BG_2hr


title: Ac1_BG_0.5hr


title: Ac2_AG_0.5hr


title: Ac6_AG_2hr


title: Ac2_CG_0.5hr


title: Ac1_CG_0.5hr


title: Ac1_LPeG_0.5hr


title: Ac1_AG_0.5hr


title: Ac3_LPlG_0.5hr


title: Ac3c_RPlG


title: Ac3c_LBG


title: Ac3c_RPeG


title: Ac3c_CG


title: Ac3c_AG


title: Ac3c_LPeG


title: Ac3c_LPlG


title: Ac2c_RPlG


title: Ac2c_LPlG


title: Ac2c_RBG


title: Ac2c_LPeG


title: Ac2c_CG


title: Ac2c_RPeG


title: Ac2c_LBG


title: Ac3c_RBG


title: Ac1c_LPlG


title: Ac1c_RPlG


title: Ac1c_CG


title: Ac2c_AG


title: Ac1c_LBG


title: Ac1c_RPeG


title: stomach

value: stomach


title: cephalic_aorta

value: cephalic aorta


title: radula

value: radula


title: sperm_sack

value: sperm sack


title: Ac1c_RBG


title: Ac1c_AG


title: Ac1c_LPeG


title: body_wall_nerves

value: body wall nerves


title: body_wall_muscle

value: body wall muscle


title: esophagus

value: esophagus


title: ink_gland

value: ink gland


title: skin

value: skin


title: spermateca

value: spermateca


title: penis_muscle

value: penis muscle


title: buccal_muscle

value: buccal muscle


title: Sm_Ant_CerG_2

source_name: Single Neurons Isolated from CNS

value: CNS

value: neuron


title: Sm_Ant_CerG_1


title: R_Pd_cilia_7


title: R_Pd_cilia_8


title: R_Pd_cilia_5


title: R_Pd_cilia_9


title: R_Pd_cilia_4


title: R_Pd_cilia_21


title: R_Pd_cilia_20


title: R_Pd_cilia_2


title: R_Pd_cilia_19


title: R_Pd_cilia_1


title: R_Pd_cilia_3


title: R_Pd_cilia_18


title: R_Pd_cilia_15


title: R_Pd_cilia_14


title: R_Pd_cilia_16


title: R_Pd_cilia_17


title: R_Pd_cilia_13


title: R_Pd_cilia_11


title: R_Pd_cilia_10


title: C_cluster_7


title: C_cluster_5


title: C_cluster_4


title: C_cluster_6


title: R_MCC


title: R_Pd_cilia_6


title: C_cluster_2


title: R_A_cluster_4


title: R_A_cluster_5


title: R_A_cluster_2


title: R_A_cluster_3


title: R_A_cluster_1


title: Pl_FMRF_9


title: Pl_FMRF_8


title: R2


title: Pl_FMRF_6


title: R_Pd_cilia_12


title: Pl_FMRF_3


title: Pl_FMRF_2


title: Pl_FMRF_4


title: Pl_FMRF_12


title: Pl_FMRF_11


title: Pl_FMRF_10


title: C_cluster_3


title: Near_R2_5


title: Near_R2_3


title: Near_R2_6


title: Near_R2_2


title: R14


title: Pl_FMRF_7


title: Near_L7_2


title: Near_R14


title: Near_R2_1


title: Pl_FMRF_5


title: L_VC_9


title: Near_F2


title: Near_L11_1


title: Med_E_cluster


title: Pl_FMRF_1


title: L_VC_8


title: L_VC_7


title: L_VC_4


title: C_cluster_1


title: L_VC_6


title: L_VC_5


title: L_VC_2


title: L_VC_13


title: L_VC_11


title: L_VC_1


title: L_VC_3


title: L_VC_14


title: L_VC_10


title: L_VC_12


title: Lg_E_cluster


title: LPL1


title: Gill_Motor_Neuron


title: L_G_cluster


title: G_cluster_6


title: L_MCC


title: G_cluster_7


title: G_cluster_5


title: G_cluster_3


title: G_cluster_4


title: G_cluster_2


title: G_cluster_1


title: F_cluster_2


title: Behind_E2


title: F_cluster_1


title: AboveR14_2


title: B_cluster


title: AboveR14_1


title: RPLg_1_T2


title: B4_1_T2


title: R15_2_T2


title: L13_1_T2


title: L12_1_T2


title: L10_1_T2


title: R14_1_T2


title: R6_1_T2


title: L2_1_T2


title: Abd_1_T2


title: R3_2_T2


title: R3_1_T2


title: L7_5_T2


title: Abd_9_T2


title: L7_3_T2


title: Near_R2_7


title: R2_6_T2


title: Abd_10_T2


title: R2_4_T2


title: L11_4_T2


title: R2_5_T2


title: Near_R2_4


title: Ac6_BG_2hr


title: LCQg_1_T2


title: L11_3_T2


title: B4_1_T1


title: RPLg_1_T1


title: LCQg_1_T1


title: R15_2_T1


title: L13_1_T1


title: L12_1_T1


title: L10_1_T1


title: L11_4_T1


title: R14_1_T1


title: L11_1_T1


title: L7_5_T1


title: L7_2


title: L7_3_T1


title: L7_4


title: L7_1


title: Abd_9_T1


title: Abd_10_T1


title: L11_1_T2


title: Abd_3


title: Abd_1_T1


title: Abd_2


title: R3_2_T1


title: R3_1_T1


title: R2_6_T1


title: R6_1_T1


title: R2_4_T1


title: L2_1_T1


title: ESC_Lmna_H222P_hom_ATAC_seq_Rep1

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

library_source: genomic

data_processing:
ATAC-seq reads were trimmed of adapters using Trimmomatic-0.39 and then mapped to mm10 mouse genome with Bowtie2.
Following removal of unmapped reads by SAMtools (-F 1804 -f 2), PCR artefacts were excluded by the MarkDuplicates.jar from Picard-tools-1.119.
BamCoverage function of deepTools with normalization to RPKM was used to generate the bigwig files for visualization of ATAC-seq reads in the genome browser IGV (-bs 20 --smoothLength 40 --normalizeUsing RPKM -e). Afterwards, fastq.gz files of each 2 replicates were merged and processing was performed like described.
Assembly: mm10
Supplementary files format and content: Excel file and BigWig files

molecule: genomic DNA

source_name: ESC

growth_protocol: E14 Tg(Nkx2-5-EmGFP) ES cells were maintained on mitomycin  treated mouse embryonic fibroblasts (MEF) in DMEM high glucose supplemented with 15% fetal bovine serum, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol , 0.1 mM non-essential amino acids , 1 mM sodium pyruvate , 4.5 mg/ml D-glucose, 1% Penicillin-Streptomycin and 1000U/ml of leukemia inhibitory factor . mESCs were dissociated by 0.05% trypsin-EDTA , preplated for 45 min to remove the feeders and collected for RNA-seq.

extract_protocol: Nuclei of ESC control and Lmna KO lines were isolated and permeabilised for tagmentation to receive nucleosomes. DNA fragments were detached from nucleosomes, amplified and size selected by bead purification to yield fragment size ranging from 150-1000bp. Fragment distribution was checked by bioanalyzer.

tag: cell line background

value: E14 Tg(Nkx2-5-EmGFP)

value: ES

tag: antibody


title: ESC_Lmna_G609G_het_ATAC_seq_Rep2


title: ESC_Lmna_G609G_hom_ATAC_seq_Rep1


title: L11_3_T1


title: L7_L11


title: ESC_Lmna_G609G_het_ATAC_seq_Rep1


title: ESC_Lmna_ctr_fromMUT_ATAC_seq_Rep2

value: WT


title: Day10_CM_LMNA_PLKO_RNA_seq_Rep3

data_processing:
RNA-Seq reads were mapped to the mm10 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000)
amples were quantified using analyzeRepeats.pl (mm10 –count exons –strand both –noadj).
Differential expression was quantified and normalized using DESEq2. Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR.
Excel was used to filter differentially regulated genes (fold change ≥1.5; log2 fold change ≤-0.58, ≥0.58; p-value < 0.05.)
Genome_build: mm10
Supplementary_files_format_and_content: Excel differential expression data

growth_protocol: mESCs were maintained on mouse feeders in Knockout DMEM medium  containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement , 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, 1% Penicillin-Streptomycin and 1,000 U/ml of leukemia inhibitory factor. Before differentiation, mESCs were dissociated and grown on 0.1% gelatin  coated 10-cm dishes in Neurobasal medium: DMEM/F12 (1:1) medium supplemented with 2000U/ml LIF and 10 ng/ml BMP4 for 2 days. Differentiation was initiated by aggregation in low attachment bacterial dishes at a cell density of 75000 cells/ml in IMDM: F12 medium (3:1). After 48 h aggregates were dissociated and re-aggregated in the presence of Activin A (5 ng/ml), VEGF (5 ng/ml) and BMP4 (0.1-0.8 ng/ml,Bmp4 concentration was optimized for each lot). 40 h following the second aggregation, aggregates were dissociated and plated as a monolayer in Stempro-34 medium , supplemented with 2 mM L-Glutamine, L-Ascorbic Acid (50µg/ml) and VEGF (5 ng/ml), bFGF (10 ng/ml), and FGF10 (25 ng/ml) growth factors. Day8 monolayer CMs were trypsinized and 50% of the cells were re-seeded on 0.1% gelatin coated 24-well plate in the presence of 8µg/ml polybrene together with virus produced in Stempro-34 medium. The medium was changed to normal Stempro-34 medium 24 hours after virus transduction and CMs were harvested at d10.

extract_protocol:
Total RNA was isolated using QiaZOl RNA extraction kit from Qiagen
BGI

treatment_protocol: LMNA KD at Day8 and sample collected at day 10

value: cardiomyocyte

value: Lmna KD


title: ESC_Lmna_ctr_fromMUT_ATAC_seq_Rep1


title: Day10_sorted_CM_LMNA_ctr_RNA_seq_Rep3

growth_protocol: E14 Tg(Nkx2-5-EmGFP) ES cells were maintained on mitomycin  treated mouse embryonic fibroblasts (MEF) in DMEM high glucose supplemented with 15% fetal bovine serum, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol , 0.1 mM non-essential amino acids , 1 mM sodium pyruvate , 4.5 mg/ml D-glucose, 1% Penicillin-Streptomycin and 1000U/ml of leukemia inhibitory factor . mESCs were differentiated into cardiomyocytes by hanging droplets method . Briefly, differentiation through the hanging drop method was initiated following mESCs dissociation by 0.05% trypsin-EDTA and suspension at 33000 cells/ml in mESC growth medium without LIF in 15 μl drops. After two day the resulting embryoid bodies (EBs) were transferred to low attachment culture dishes . At day10, EBs were dissociated and  CMs were FACS sorted by Nkx2-5-GFP expression and performed RNA-seq.

tag: time point


title: Day10_CM_LMNA_PLKO_RNA_seq_Rep1


title: Day10_CM_LMNA_KD_RNA_seq_Rep1


title: Day10_sorted_CM_LMNA_KO_RNA_seq_Rep3

value: Lmna KO


title: Day10_sorted_CM_LMNA_KO_RNA_seq_Rep1


title: Day10_sorted_CM_LMNA_ctr_RNA_seq_Rep1


title: Day10_sorted_CM_LMNA_KO_RNA_seq_Rep2


title: R2_5_T1


title: Day10_EBs_LMNA_KO_RNA_seq_Rep3

growth_protocol: E14 Tg(Nkx2-5-EmGFP) ES cells were maintained on mitomycin  treated mouse embryonic fibroblasts (MEF) in DMEM high glucose supplemented with 15% fetal bovine serum, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol , 0.1 mM non-essential amino acids , 1 mM sodium pyruvate , 4.5 mg/ml D-glucose, 1% Penicillin-Streptomycin and 1000U/ml of leukemia inhibitory factor . mESCs were differentiated into cardiomyocytes by hanging droplets method . Briefly, differentiation through the hanging drop method was initiated following mESCs dissociation by 0.05% trypsin-EDTA and suspension at 33000 cells/ml in mESC growth medium without LIF in 15 μl drops. After two day the resulting embryoid bodies (EBs) were transferred to low attachment culture dishes . At day10, EBs  were collected for RNA-seq.

tag: tissue/cell type

value: Embryonic bodies


title: Day10_CM_LMNA_KD_RNA_seq_Rep2


title: Day10_CM_LMNA_KD_RNA_seq_Rep3


title: ESC_Lmna_H222P_hom_ATAC_seq_Rep2


title: Day10_EBs_LMNA_KO_RNA_seq_Rep2


title: Day10_EBs_LMNA_ctr_RNA_seq_Rep3


title: Day10_sorted_CM_LMNA_ctr_RNA_seq_Rep2


title: Day10_EBs_LMNA_ctr_RNA_seq_Rep2


title: Day10_EBs_LMNA_ctr_RNA_seq_Rep1


title: Day6_CPC_sorted_LMNA_KO_RNA_seq_Rep2

growth_protocol: E14 Tg(Nkx2-5-EmGFP) ES cells were maintained on mitomycin  treated mouse embryonic fibroblasts (MEF) in DMEM high glucose supplemented with 15% fetal bovine serum, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol , 0.1 mM non-essential amino acids , 1 mM sodium pyruvate , 4.5 mg/ml D-glucose, 1% Penicillin-Streptomycin and 1000U/ml of leukemia inhibitory factor . mESCs were differentiated into cardiomyocytes by hanging droplets method . Briefly, differentiation through the hanging drop method was initiated following mESCs dissociation by 0.05% trypsin-EDTA and suspension at 33000 cells/ml in mESC growth medium without LIF in 15 μl drops. After two day the resulting embryoid bodies (EBs) were transferred to low attachment culture dishes . At day6, EBs were dissociated and CPCs were FACS sorted by Nkx2-5-GFP expression and performed RNA-seq.

value: cardiac progenitor cells (CPC)


title: Day6_CPC_sorted_LMNA_KO_RNA_seq_Rep3


title: Day6_CPC_sorted_LMNA_ctr_RNA_seq_Rep3


title: Day10_CM_LMNA_PLKO_RNA_seq_Rep2


title: Day6_CPC_sorted_LMNA_KO_RNA_seq_Rep1


title: Day6_CPC_sorted_LMNA_ctr_RNA_seq_Rep1


title: ESC_LMNA_KO_RNA_seq_Rep3


title: Day6_CPC_sorted_LMNA_ctr_RNA_seq_Rep2


title: ESC_LMNA_KO_RNA_seq_Rep1


title: ESC_LMNA_KO_RNA_seq_Rep2


title: Day10_EBs_LMNA_KO_RNA_seq_Rep1


title: ESC_LMNA_ctr_RNA_seq_Rep3


title: ESC_LMNA_ctr_RNA_seq_Rep2


title: ESC_LMNA_ctr_RNA_seq_Rep1


title: CA1352_d6_EtOH rep 4

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

data_processing:
Bowtie version 1.2.2 was used to map reads with the following settings: bowtie -I 0 -X 500 -k 1 -m 2 -S -p 2
HTSeq version 0.11.2 was used to count reads mapping to the WS273 canonical geneset (file name c_elegans.PRJNA13758.WS273.canonical_geneset.gtf downloaded from Wormbase)
edgeR version 3.24.4 was used for differential expression analysis. Count data was restricted to include protein-coding genes, and further restricted to include only genes with counts greater than 10 in at least four libraries.
The RUVseq package was used to determine factors of unwanted variation prior to differential expression analysis based on spike-ins. First, betweenLaneNormalization was used for upper-quartile normalization (which = ”upper”). Next, RUVg was used with k = 1 to improve normalization by normalizing based on the spike-ins. edgeR was then used for differential expression analysis, incorporating the factors of unwanted variation from RUVseq. glmFit and glmLRT commands (which fit a GLM and execute a likelihood ratio test in edgeR) were used to determine significant differences for pairs of conditions of interest.
Genome_build: WS273
Supplementary_files_format_and_content: Count files for each library; these are the non-normalized input into edgeR for differential expression analysis. An excel final with edgeR output from pairwise differential expression is also included.

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: All strains were maintained well-fed on OP50 at 20°C for several generations. For LRB387, CA1200, and CA1352, approximately 10 L4s were picked onto five 10 cm NGM plates with OP50 for each biological replicate. For LRB389, which grows slower, approximately 15 gravid adults were picked onto seven 10 cm NGM plates with OP50 for each biological replicate. After 4 days, plates from all four strains were hypochlorite treated in parallel. For each strain, three 50 mL Erlenmeyer flasks were used, each with 10,000 embryos resuspended at 1/uL in 10 mL. Flasks were put in a shaker at 180 rpm at 20°C. After 36 hours of L1 arrest (48 hours after bleach), the 36-hour samples were collected by spinning down the 10 mL culture for each strain at 3,000 rpm, aspirating off excess S-basal, and then transferring the worms in ~100 uL to a 1.5 mL Eppendorf tube. The volume of the sample was further reduced by spinning again at 3,000 rpm and pipetting off excess liquid to bring the final volume down to approximately 10 uL. Samples were flash frozen in liquid nitrogen and stored at -80°C until RNA isolation. At 36 hours, 100 uM auxin or ethanol was added to each of the remaining flasks. After 132 hours of L1 arrest, auxin and ethanol samples were collected as described for the 36-hour samples.

extract_protocol:
RNA was isolated using TRIzol following the manufacturer's protocol with notable exceptions. Only 100 uL of Trizol was used, and 5 ug linear polyacrylamide (Sigma Aldrich) was included as a neutral carrier for RNA precipitation. RNA was eluted in nuclease-free water and incubated at 55°C for approximately four minutes to resuspend the pellet.
NEBNext Ultra II RNA Library Prep kit was used to perform polyA selection on total RNA and prepare libraries for sequencing. ThermoFisher ERCC Spike-In mix was added based on total RNA. The libraries were enriched with 14 or 15 cycles of PCR, depending on batch.

treatment_protocol: CA1200 [ieSi57 [eft-3p::TIR1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)] II], CA1352 [ieSi64 [gld-1p::TIR1::mRuby::gld-1 3’UTR + Cbr-unc-119(+)] II], LRB387 [ieSi64 II; ama-1(syb1513) IV], and LRB389 [ieSi57 II; ama-1(syb1513) IV]

tag: developmental stage

value: L1 larvae

tag: time point (hours)

tag: auxin treatment

value: ethanol


title: CA1352_d6_aux rep 4

value: auxin


title: CA1352_d6_EtOH rep 1


title: CA1352_d6_EtOH rep 2


title: CA1352_d6_aux rep 3


title: CA1352_d2 rep 1


title: CA1200_d6_EtOH rep 4


title: CA1352_d6_aux rep 1


title: CA1200_d6_EtOH rep 3


title: CA1200_d6_aux rep 3


title: CA1352_d2 rep 3


title: CA1200_d6_EtOH rep 2


title: CA1200_d6_aux rep 4


title: CA1200_d6_aux rep 2


title: CA1352_d2 rep 4


title: CA1200_d6_aux rep 1


title: CA1200_d6_EtOH rep 1


title: CA1352_d6_aux rep 2


title: CA1352_d6_EtOH rep 3


title: CA1200_d2 rep 3


title: CA1200_d2 rep 2


title: CA1352_d2 rep 2


title: ama1_CA1352_d6_EtOH rep 2


title: ama1_CA1352_d6_EtOH rep 4


title: CA1200_d2 rep 1


title: ama1_CA1352_d6_EtOH rep 3


title: ama1_CA1352_d6_EtOH rep 1


title: CA1200_d2 rep 4


title: ama1_CA1352_d6_aux rep 2


title: ama1_CA1352_d6_aux rep 4


title: ama1_CA1352_d6_aux rep 1


title: ama1_CA1352_d2 rep 4


title: ama1_CA1352_d2 rep 3


title: ama1_CA1352_d6_aux rep 3


title: Near_L11_2


title: ama1_CA1200_d6_EtOH rep 4


title: ama1_CA1200_d6_aux rep 3


title: ama1_CA1200_d6_EtOH rep 3


title: ama1_CA1352_d2 rep 2


title: ama1_CA1200_d6_EtOH rep 1


title: ama1_CA1352_d2 rep 1


title: ama1_CA1200_d2 rep 1


title: ama1_CA1200_d6_aux rep 1


title: ama1_CA1200_d6_aux rep 4


title: ama1_CA1200_d6_EtOH rep 2


title: ama1_CA1200_d2 rep 3


title: ama1_CA1200_d6_aux rep 2


title: ama1_CA1200_d2 rep 2


title: Near_L7_1


title: 211R: muscle, healthy, fresh

city: La Jolla

first: Samuel

middle: Richard

last: Ward

state: CA

address: 9500 Gilman Drive (0863)

department: Orthopaedic Surgery, Radiology, and Bioengineering

institute: University of California San Diego

description: 10x Genomics Visium

data_processing:
Space Ranger 1.2.0
Loupe Browser v.6.0.0
Ensembl release 104 (Oryctolagus_cuniculus.OryCun2.0.104.chr.gtf)
Assembly: OryCun2.0 (Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa
Supplementary files format and content: tsv: barcodes, features
Supplementary files format and content: mtx: matrix
Supplementary files format and content: jpg: H&E staining
Supplementary files format and content: json: spot pixel coordinates

organism: Oryctolagus cuniculus

source_name: M. supraspinatus

extract_protocol:
Permeabilization protocol by 10x Genomics CG000238 Rev E. 18 min incubation time.
10x Genomics Protocol CG000239 Rev E

treatment_protocol: snapfrozen in liquid nitrogen-cooled isopentane and stored at -80°C

value: M. supraspinatus

value: Harvested and snapfrozen


title: 14R: muscle, healthy, stored 6 years

description: 10x Genomics Visium


title: 14L: muscle, 16 weeks tenotomy, stored 6 years

description: 10x Genomics Visium

value: Harvested and snapfrozen at 16w after tenotomy


title: 6L: muscle, 2 weeks tenotomy, stored 6 years

description: 10x Genomics Visium

value: Harvested and snapfrozen at 2w after tenotomy


title: MG-ZT-no

city: NY

first: Saeed

last: Tavazoie

address: 1150 St Nicholas

institute: Columbia University

data_processing:
demultiplexing (flag samples based on index)
merge files (from different lanes on the flow cell)
clip illumina adaptors &transposon sequence and id target sequence
quality score filtering (drop read if target is less than 15bps and trim low quality ends of reads)
Genome_build: bowtie align reads to to given database genome
Supplementary_files_format_and_content: count total reads aligned per sample; score locations

organism: Escherichia coli

source_name: thyA- library at start of selection

growth_protocol: 2 hours pregrowth of library in high thymidine

extract_protocol:
Genomic DNA was isolated from the samples collected during the selection using the DNEasy Blood and Tissue Kit (Qiagen) and purified using Zymo genomic DNA clean & concentrate kit (Zymo Research). The isolated and purified DNA was digested with MspI and/or HinP1. After purification again using a Zymo clean and concentrate kit, a Y-linker (Girgis, Liu, Ryu, & Tavazoie, 2007) was annealed and ligated to the DNA and the samples were purified using Agencourt AMPure beads (Beckman Coulter). The Y-linker was annealed by combining the primers with annealing buffer in a PCR tube at 90°C for 2 min, followed by cooling to 30°C at a rate of ~2 degrees per minute. After snap cooling, the Y-linker was promptly used or frozen for future use. A second Illumina bar code was added by PCR (the first was added to the transposon fragment itself before library generation). After another bead cleanup was a second PCR amplification, which added dual indexes for sequencing. After a final bead cleanup, samples were pooled and sequenced using a NextSeq 500 sequencer (Illumina).
: Using Gibson assembly, we redesigned the EZ-Tn5 Transposon Vector (Epicentre) so that the transposon insertion has, in addition to the kanamycin cassette, an Illumina sequencing adapter. MG1655 thyA- cells were prepared for transformation and electroporated with 2μL of the generated transposomes. After 1h, serial dilutions were made of a small aliquot onto LB/kanamycin/thymidine plates in order to gauge the number of successful transformants. The remainder of the cell mixture was added to 250mL of LB/kanamycin/thymidine and grown to amplify the mutants. After 8h, the library was pelleted and resuspended in a small volume of 15% glycerol (diluted in LB), subsequently aliquoted, snap-frozen, and stored at -80°C.
EZ-Tn5 Transposon Vector (Epicentre)

treatment_protocol: washed twice in 1x phosphate buffered saline (PBS), and placed in thymidine-free media. Samples were collected at three time points during the selection: “Start”, “0h”, and “3h”.

value: start of selection


title: MG-ZT-OH

source_name: thyA- library at 0H thymidine starvation after outgrowth

value: 0H thymidine starvation after outgrowth


title: ama1_CA1200_d2 rep 4


title: Parental control

data_processing:
demultiplexing (flag samples based on index)
merge files (from different lanes on the flow cell)
clip illumina adaptors and id target sequence
quality score filtering (drop read if target is less than 15bps and trim low quality ends of reads)
Genome_build: Rockhopper (version 2.03) was used on each RNA read by itself to get quantitation and statistics on expression levels

source_name: mdss-control

growth_protocol: Both strains were diluted 1:200 from overnight cultures into high thymidine and grown for 2h at 30°C before strains were washed twice and placed in new media

extract_protocol:
After incubation with RNAprotect Bacteria Reagent (Qiagen), samples were stored at -80°C. Total RNA was made from the pellets using the Total RNA Purification Plus Kit (Norgen) according to the manufacturer’s recommended protocol for Gram-negative bacteria. Ribosomal RNA was removed from these samples using the Ribo-Zero rRNA Removal Kit (Illumina).
Indexed libraries were prepared from the resulting RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). Samples were pooled and sequenced on a NextSeq 500 sequencer (Illumina).

treatment_protocol: Three samples were taken for each strain: a high thymidine sample 2h into growth, a sample 30 minutes into thymidine starvation, and a control was washed twice similar to the starved sample but placed back into high thymidine and collected after 30 minutes.

value: control for starved pelleting and wash

tag: genetic background

value: MDS42 background


title: Parental Starved

source_name: mdss-starved

value: 30 mins into thymidine starvation


title: Evolved control


title: MG-ZT-3H

source_name: thyA- library at 3H thymidine starvation after outgrowth

value: 3H thymidine starvation after outgrowth


title: sen1top2-1_IP_bTMP_32

city: Milano

first: Mohamood Adhil

last: Mohammed Iqbal

state: Lombardia

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

description: Negative supercoiling scored by bTMP intercalation at underbound DNA using bTMP-ChIP-seq

data_processing:
The raw reads were filtered based on the quality value (-q 20 and –p 30) using FASTX Toolkit. The filtered reads were aligned to the reference genome (SacCer 2011) using bowtie2 aligner. The PCR duplicates were removed from the aligned BAM files using PICARD tools. The BAM files were sorted and indexed for the peak calling using SAMTOOLS. The bedgraph files were generated by comparing bam files of IP and Input (IP read coverage/Input read coverage) result in the ratio for every base across the whole genome using DEEPTOOLS (bamCompare) (Ramirez et al., 2014). Finally, peak calling was performed using MACS with the following parameters (--gsize=1.21e+7 -q 0.05 –nomodel)
Assembly: SacCer 2011

organism: Saccharomyces cerevisiae

source_name: Yeast strains

growth_protocol: For S phase samples : Log in YPG, G1 cell cyle arrest in YPD+Alpha factor and release in S phase,23oC, at 45'-50' time point harvested as S phase time point. For Log sample: Log in YPG, moved to YPD for 2.5hrs and harvested for bTMP-seq. For top2-s allele combiantion: Log in YPG, moved to YPD for 1.5hrs at 25oC and temprature increased to 32oC for 1hr .

extract_protocol:
Protein-ChIP-seq, ChIP-seq analysis for proteins was carried out as described (Achar et al., 2020; Bermejo et al., 2009) with few modifications. Cells were cross-linked with 1% formaldehyde in culture medium for 30 min at room temperature followed by quenching with 0.125 M glycine for 5 min and transferred to ice for 20 min. Cells were washed twice with ice-cold 1xPBS and lysed in 1ml of lysis buffer (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1%Triton X-100, 0.1%Na-deoxycholate) using Zirconia beads. Cells were lysed with PowerLyzer 24 Homogenizer at 4000 rpm for 20 sec for 8 rounds. In between each round the cells were kept on ice for 5 mins. The samples were collected from glass beads and centrifuged to collect the pellet at 13400 RCF for 10 mins at 4oC. The samples are sonicated to an average size of 100-150bp using covaris focused ultrasonicator E220 with milliTUBE 1ml AFA Fiber (Parameters: Duty Factor 6, burst/cycle 200, Peak Watt 200, Time 2400 seconds). The samples were centrifuged at 16000 RCF for 5mins at 4oC and supernatant was collected. The lysate was then centrifuged to remove cell debris and the chromatin fractions were incubated with respective Dynabeads protein beads coated with respective antibody overnight at 4oC. The immune complexes were washed with the following buffers 2 times with ChIP-lysis buffer (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate), 2 times with lysis buffer + high salt (ChIP lysis buffer +360 mM NaCl), 2 times with ChIP-wash buffer (250mM LiCl, 10mM Tris pH8.0, 0.5%Na-deoxycholate, 0.5%NP-40, 1mM EDTA) and 2 times with 1xTE (20mM Tris pH8.0, 2mM EDTA). The protein-DNA complexes were eluted from the beads using 250 μl elution buffer (1%SDS, 50mM Tris pH8.0, 10mM EDTA) at 65oC for 20 min followed by the addition of proteinase K at 500 μg/ml and overnight incubation at 65oC. Input DNA was isolated from sheared chromatin input (1/100 of the material used for ChIP). The IP and Input samples were purified with DNA clean and concentration kit from Zymoresearch and eluted in elution buffer from the kit. The input samples were analyzed in Agilent bioanalyzer for optimum fragmentation. Both Input and IP samples were processed for sequencing and ChIP–seq libraries were prepared according to the manufacturer’s protocols. The Input and IP samples were ligated with illumina barcodes and amplified using Kapa library amplification kit, followed by size selection with AMPure XP Beads. ASPRI clean-up with a 1.5xAMPure XP Bead: DNA ratio was performed and final libraries were eluted and sequenced using Illumina Nextseq 550 System with NextSeq 500/550 High or medium Output Kit v2.5 where each sample (IP and Input) contained approximately 10 million paired end reads.   bTMP-seq. To map genome wide negative supercoiling, we used the previously described method (Achar et al., 2020; Naughton et al., 2013) and modified it for sequencing. Biotinylated-TMP synthesis performed as previously described method (Saffran et al., 1988). 1-8 x109 cells were treated with Sodium azide (0.1%) and kept on ice for 20 mins. Cells were collected by centrifugation and the pellets were treated with 800μl of Polyethylene glycol (PEG 50%), 100μl of lithium acetate (1M) and 100μl of DMSO-Dimethyl sulfoxide. Permeabilized yeast cells were incubated with bTMP (calculate as 400μg per 2x109 cells) in dark for 90 min and then cross-linked by 365nm UV light at 2000 energy (Millijoules/cm2) 4 times to form psoralen adducts between two DNA strands. Cells were washed twice with ice-cold 1xPBS and lysed with 1ml lysis buffer (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1%TritonX-100, 0.1% Na-deoxycholate) using Zirconia beads. Cells were lysed with PowerLyzer 24 Homogenizer at 4000rpm for 20sec 8 times. In between each round the cells were kept on ice for 5 minutes. Further, the crosslinked chromatin was sheared to an average size of 100-150bp by covaris focused ultrasonicator E220 and the sonicated samples were incubated with 30μl of 20% SDS, Proteinase K 25μl, RNAseA 5μl and then incubated overnight at 50oC. DNA was purified using QIAquick PCR purification kit. The concentration of the DNA was measured using nano drop. Input DNA was collected from the purified sheared chromatin (1/100 of the material was collected as Input) and stored at -20oC. The purified DNA was incubated with Dynabeads MyOne streptavidin overnight at 4oC. The beads were washed twice with each of the following buffers; wash buffer-I (20mM Tris-HCl pH8, 2mM EDTA, 150mM NaCl, 1%Triton-X, 0.1% SDS), wash buffer-II (20mM Tris-HCl pH 8, 2mM EDTA, 500mM NaCl, 1% Triton-X, 0.1% SDS), wash buffer III (250mM LiCl, 10mM Tris pH8.0, 0.5%Na-deoxycholate, 0.5% NP-40, 1mM EDTA) and 1xTE (20mM Tris pH 8.0, 2mM EDTA). The bTMP–DNA complexes were eluted from the beads using 250μl elution buffer (95% formamide, 10mM EDTA) at 90oC for 20 min and the eluted samples were cleaned with concentration kit from Zymoresearch. From this step onwards, Input and IP DNA were subjected to Whole Genome Amplification using SeqPlex DNA amplification kit (Sigma-Aldrich) and processed for next generation sequencing.
Both Input and IP samples were processed for sequencing and ChIP–seq libraries were prepared according to the manufacturer’s protocols. The Input and IP samples were ligated with illumina barcodes and amplified using Kapa library amplification kit, followed by size selection with AMPure XP Beads. ASPRI clean-up with a 1.5xAMPure XP Bead: DNA ratio was performed and final libraries were eluted and sequenced using Illumina Nextseq 550 System with NextSeq 500/550 High or medium Output Kit v2.5 where each sample (IP and Input) contained approximately 10 million paired end reads.

value: Yeast strains

tag: chip-antibody

value: bTMP-ChIP-seq (streptavidin-Biotin)

tag: genotype

value: bTMP-seq_log at 32oC


title: sen1rrm3top2-1_IP_bTMP_32


title: sen1rrm3top2-1_Input_bTMP_32


title: WT_IP_bTMP_32

value: wild type


title: sen1_Input_bTMP_32


title: sen1rrm3_Input_bTMP_32


title: rrm3_Input_bTMP_32


title: sen1rrm3_IP_bTMP_32


title: rrm3top2-1_IP_bTMP_32


title: WT_Input_bTMP_32

value: wild tyoe


title: rrm3_IP_bTMP_32


title: sen1_IP_bTMP_32


title: sen1rrm3top1_Input_bTMP

value: bTMP-seq_log cells


title: sen1rrm3top1_IP_bTMP


title: sen1top1_Input_bTMP


title: rrm3top1_Input_bTMP


title: rrm3top1_IP_bTMP


title: top2-1_Input_bTMP_32


title: sen1top1_IP_bTMP


title: top2-1_IP_bTMP_32


title: Parental log

source_name: mdss-log

value: in log phase


title: Evolved Starved


title: Evolved log


title: top1_IP_bTMP


title: rrm3top2-1_Input_bTMP_32


title: top1_Input_bTMP


title: sen1rrm3_IP_bTMP


title: sen1rrm3_Input_bTMP


title: sen1top2-1_Input_bTMP_32


title: rrm3_Input_bTMP


title: sen1rrm3_Input_bTMP_S

value: bTMP-seq (S-phase)


title: sen1_Input_bTMP


title: sen1rrm3_IP_bTMP_S


title: sen1_IP_bTMP


title: WT_Input_bTMP


title: rrm3_Input_bTMP_S


title: WT_IP_bTMP


title: WT_IP_bTMP_S


title: WT_Input_bTMP_S


title: rrm3_IP_bTMP_S


title: sen1_Input_bTMP_S


title: rrm3_IP_bTMP


title: rrm3_Input_Rpb1_S

description: RNA Pol II occupacy scored by Rpb1-ChIP-seq during S phase of cell cycle

value: Rpb1-ChIP-seq (S-phase)


title: sen1_Input_Rpb1_S


title: rrm3_IP_Rpb1_S


title: sen1_IP_Rpb1_S


title: WT_IP_Rpb1_S


title: sen1_IP_bTMP_S


title: WT_Input_Rpb1_S


title: HeLa cell line

city: HANGZHOU

first: XIUWEN

last: TANG

address: YUHANGTONG ROAD

department: BIOCHEMISTRY AND GENETICS

institute: ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE

data_processing:
FastQC software
The differential splicing events between the NRF2 knock-down A549 NSCLC cells versus control A549 cells, NRF2-knockdown HeLa cells (HeLa#B30CRNrf2 ) against control HeLa cells, NRF2 overexpression of NRF2-knockdown HeLa cells (HeLa#B30CRNrf2-NRF2) against NRF2-knockdown HeLa cells, and SMN overexpression of NRF2-knockdown HeLa cells (HeLa#B30CRNrf2-NRF2) versus NRF2-knockdown HeLa cells were analyzed using rMATS (replicate multivariate analysis of transcript splicing) software. Alternative splicing events such as skipped exons, retained introns, mutually exclusive exons, alternative 5' splice sites, and alternative 3' splice sites were identified using Fisher’s exact test in rMATS with the p-value <0.01 and FDR <0.1.
Mapping of high-throughput sequencing reads to the human reference genome version hg19 (UCSC) was performed by STAR software.
The Cufflinks package was used to assemble the mapped reads into transcripts to generate transcriptome assembly.
The differential splicing events were analyzed using rMATS (replicate multivariate analysis of transcript splicing) software
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files (A3SS.MATS.JunctionCountOnly.txt, A5SS.MATS.JunctionCountOnly.txt, MXE.MATS.JunctionCountOnly.txt, RI.MATS.JunctionCountOnly.txt, and SE.MATS.JunctionCountOnly.txt) include alternative splicing events for each sample, alternative 3' splice sites, alternative 5' splice sites, mutually exclusive exons, retained introns, and skipped exons respectively. tab-delimited text file (Select_Inpas_results.txt) includes alternative Polyadenylation Sites for each sample

source_name: HeLa cells

growth_protocol: 1x10^5 cells/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 48 hours

extract_protocol:
RNA was isolated from siGFP-C5, siNrf2-C27, HeLa cells, NRF2-knockdown HeLa cells (HeLa#B30CRNrf2 ), NRF2 overexpression of NRF2-knockdown HeLa cells (HeLa#B30CRNrf2-NRF2), and SMN overexpression of NRF2-knockdown HeLa cells (HeLa#B30CRNrf2-SMN)  using TRIzol from Invitrogen (Shanghai, China).
An Illumina Hisq 3000 high-throughput sequencer was used for paired-end sequencing, and quality control analysis of the pre-processed data was performed using FastQC software.

tag: cell line

value: HeLa

tag: tissue source

value: cervix

value: wild-type

tag: sample label

value: (Hela)


title: sen1rrm3_IP_Rpb1_S

tag: tissue

tag: treatment


title: siGFP-C5

data_processing:
FastQC software
The differential splicing events between the NRF2 knock-down A549 NSCLC cells versus control A549 cells were analyzed using rMATS (replicate multivariate analysis of transcript splicing) software. Alternative splicing events such as skipped exons, retained introns, mutually exclusive exons, alternative 5' splice sites, and alternative 3' splice sites were identified using Fisher’s exact test in rMATS with the p-value <0.01 and FDR <0.1.
Mapping of high-throughput sequencing reads to the human reference genome version hg19 (UCSC) was performed by STAR software.
The Cufflinks package was used to assemble the mapped reads into transcripts to generate transcriptome assembly.
The differential splicing events were analyzed using rMATS (replicate multivariate analysis of transcript splicing) software
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files (A3SS.MATS.JunctionCountOnly.txt, A5SS.MATS.JunctionCountOnly.txt, MXE.MATS.JunctionCountOnly.txt, RI.MATS.JunctionCountOnly.txt, and SE.MATS.JunctionCountOnly.txt) include alternative splicing events for each sample, alternative 3' splice sites, alternative 5' splice sites, mutually exclusive exons, retained introns, and skipped exons respectively. tab-delimited text file (Select_Inpas_results.txt) includes alternative Polyadenylation Sites for each sample

source_name: A549 NSCLC cells

growth_protocol: 1x105 cells/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 48 hours

extract_protocol:
RNA was isolated from siGFP-C5 and siNrf2-C27 using TRIzol from Invitrogen (Shanghai, China).
An Illumina Hisq 3000 high-throughput sequencer was used for paired-end sequencing, and quality control analysis of the pre-processed data was performed using FastQC software.

tag: cell type

value: Non-Small Cell Lung Cancer (NSCLC) cell line

tag: genotype/variation


title: HeLa#B30CRNrf2


title: siNrf2-C27


title: rrm3sen1_Input_RNA-DNA_S

type: genomic

description: Genome wide RNA:DNA hybrids mapped by DRIP-Chip. Cell released in S-phase at 45'

hyb_protocol: Hybridized to Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array (Sc03b_MR) according to the Affymetrix standard protocol

scan_protocol: Standard Affymetrix Protocol.

data_processing: The CEL files are processed using rMAT R package for normalization, MAT score calculation and calling enriched regions or peaks. The following commands and parameters are used; i) (Normalization) SetNorm = NormalizeProbes(Set, method="MAT", robust=T, all=T, standard=TRUE, verbose=FALSE), where 'Set' is the probe map object created using CEL file and probe annotation file (Sc03b_MR_v04.bpmap) ii) (MAT score calculation) RD = computeMATScore(SetNorm, dMax=300, verbose=FALSE, cName = InputColumnName), iii) (Calling Enriched Region) peak = callEnrichedRegions(RD, dMax=300, dMerge=300, nProbesMin=8, method=method, threshold=1.5, verbose=FALSE). Bed file containing the enriched regions with respective MAT score and BedGraph file containing the score for short interval bases. Both bed and bedGraph files are generated using rMAT R package and these files are UCSC genome compatible with sacCer3 reference.

label: biotin

source_name: yeast culture

label_protocol: In case of ChIP-chip, BrdU-chip and DRIP-Chip, samples were measured using nanodrop and 5000ng of Input and IP was used for the further steps. Both IP and input DNA were amplified using the GenomePlex complete whole-genome amplification kit, they were then biotin-labelled. Biotin labelling was performed using 4.85μl of 10XOne-Phor-All Buffer, 25mM CoCl2, 2.9μl DNAase reaction mix 1.5μl and 5μg of DNA (IP or Input) with ddH2O in 40.75μl. Samples were vortexed, pulse-spun and incubated in thermocycler at 37oC for 30 seconds and then transferred to 95oC for 15 minutes. Samples were transferred to new 1.5ml Eppendorf tube and DNA labelling was performed using 5μl of TdT reaction buffer, 1μl Biotin-N11-ddATP (1nMole/μl) and 1μl terminal transferase (400U/μl). Samples were incubated at 37oC for 1hr.

growth_protocol: For BrdU-Chip_G2/M: Log in YPG, G1 cell cyle arrest in YPD+Alpha factor and release in S phase,23oC, YPD+Nocodazole to arrest cells in G2/M. For RNA:DNA hybrids Log in YPG, G1 cell cyle arrest in YPD+Alpha factor and release in S phase,23oC, at 45'-50' time point harvested as S phase time point

extract_protocol: BrdU-Chip. Yeast culture was grown O/N as log at 23oC in SC-URA medium till up to 1x107 cells/ml. The synchronization was done in YPD or YPG medium using α-Factor at 23°C. After synchronization, BrdU 200μg/ml was added for 20 min before the release. Cells were released from G1 into YPD medium containing BrdU 200μg/ml. Cell were blocked using 0.1% of Sodium Azide and kept on ice for at least 5 minutes.  Cells were pellet centrifuged and washed with 20ml of cold and sterilized 1xTE. Genomic DNA was isolated as mentioned in the genomic DNA extraction section and the DNA was re-suspended in 250 μl of 1xTE pH8. For each 200ml culture genomic DNA, 20μl Protein A dynabeads (Invitrogen) were washed twice in a costar prelubricated tube with 1ml of 1xPBS, 5mg/ml BSA, 0.1% Tween20. The beads were re-suspended in 20μl of 1x PBS, 5mg/ml BSA, 0.1% Tween20 and add 4μg of anti-BrdU antibody (MBL M1-11-3). This complex was incubated O/N at 4oC. BrdU containing genomic DNA was fragmented to 200-500bp using the bandelin UW2070 sonicator with following parameters as 20% power, 20 second/pulse for 6 times. Fragmented DNA was quantified and antibody-bead complex was washed two times with 1ml of 1xPBS, 5mg/ml BSA, 0.1% Tween20. Beads were resuspended in 20μl and split into 2 costar prelubricated tubes. The DNA was denatured at 100°C for 10 minutes and immediately put on ice and 100μl of 2xPBS and 200μl of ice cold 1xPBS, 2%BSA, 0.2%Tween-20 was added. 10μl of antibody-beads complex was added in denatured DNA and incubated O/N at 4°C rotating. Beads containing tubes were kept on magnetic grid and washed as following, 2 times with ChIP lysis buffer (50mM Hepes-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate), 2 times with (ChIP Lysis buffer +500mM NaCl), 2 times with ChIP Washing buffer (10mM Tris-HCl pH8.0, 250mM LiCl, 0.5% NP-40, 0.5% Sodium deoxycholate, 1mM EDTA) and one wash with 1xTE pH8.0 and all residual liquid was removed with vacuum pump. The beads were re-suspended in 50μl of ChIP Elution buffer (50mM Tris-HCl pH8.0, 10mM EDTA, 1%SDS) and incubated at 65°C for 10 minutes. To the eluted material (IP) and Input, 49μl of 1xTE, 1μl of Proteinase K (Stock 50mg/mL) was added and incubated at 37oC for 1hr and the DNA was purified by Qiagen PCR purification Kit and eluted with EB buffer. IP and Input samples proceeded with WGA (Whole Genome Amplification) using WGA2 GenomePlex Complete Genome Amplification (WGA) Kit as per manufacturer’s instructions. DRIP-Chip. DRIP-ChIP was performed using anti-RNA:DNA hybrid monoclonal mouse antibody S9.6 as previously described (Achar et al., 2020; Chan et al., 2014). The method was adopted with a few changes; cells were cross-linked by shaking with 1% formaldehyde in culture medium for 20 min at room temperature and the reaction was quenched with 0.125 M glycine for 5 min at RT. Cells were centrifuged and washed twice with ice-cold 1xPBS and lysed in 1 ml of lysis buffer (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1%TritonX-100, 0.1%Na-deoxycholate) using Zirconia beads. Cross-linked chromatin was sheared to an average size of 300-500 bp by 6x15-s pulses using a Biorupter sonicator. The lysate was then centrifuged to remove cell debris and collected as chromatin fraction at 4oC. The chromatin fraction was incubated with Protein-A magnetic beads coated with anti-DNA:RNA hybrid-S9.6 antibody (Boguslawski et al., 1986) overnight at 4oC . The immune complexes were washed twice with the following buffers- ChIP-lysis buffer (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate), lysis buffer+ high salt (ChIP lysis buffer + 360mM NaCl), ChIP-wash buffer (250mM LiCl, 10mM Tris pH8.0, 0.5% Na-deoxycholate, 0.5%NP-40, 1mM EDTA) and 1xTE (20mM Tris pH8.0, 2mM EDTA). The RNA:DNA hybrid complexes were eluted from the beads in 250μl elution buffer (1%SDS, 50mM Tris pH8.0, 10mM EDTA) at 65oC for 20 min followed by the addition of proteinase K at 500μg/ml and incubated overnight at 65oC. Input DNA was isolated from sheared chromatin input (1/100 of the material used for ChIP). Both IP and input samples were processed as mentioned in the section below ‘Microarray and data processing’.

tag: treatment(s)

tag: strain


title: rrm3sen1 _RNA-DNA_S

tag: antibody


title: sen1_Input_RNA-DNA_S


title: sen1_IP_RNA-DNA_S


title: rrm3_Input_RNA-DNA_S


title: rrm3_IP_RNA-DNA_S


title: sen1rrm3_Input_Rpb1_S


title: rrm3sen1 _Sup_BrdU_G2M

description: BrdU-Chip, Replication fork fusion at G2/M stage of cell cycle by Nocodazole.


title: sen1_Sup_BrdU_G2M


title: rrm3_Sup_BrdU_G2M


title: WT_IP_BrdU_G2M

value: WT


title: rrm3sen1_IP_BrdU_G2M


title: WT_Sup_BrdU_G2M


title: rrm3_IP_BrdU_G2M


title: sen1_IP_BrdU_G2M


title: KPCF_lung3

city: Chongqing Provence

first: Yu

last: He

address: No.136, Zhongshan 2nd Road, Yuzhong District

institute: Children's Hospital of Chongqing Medical University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus_musculus.GRCm38 V99
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

source_name: Lung

growth_protocol: Female BALB/c mice (6–8-weeks old) and perinatal BALB/c mice were purchased from the Animal Laboratory of Chongqing Medical University (China). Perinatal BALB/c mice were used to obtain neonatal mice for next capsaicin pretreatment to get KPCF mice.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The KCF mice were infected with RSV-A2 via intranasal inoculation under 2%–5% isoflurane and at 12 h post-RSV infection, mice were anesthetized with CO2 and sacrificed by cervical dislocation.

value: BALB/c

value: Lung

tag: age

value: 6 - 8 weeks old

value: KPCF


title: KPCFpi_spleen2

source_name: Spleen

value: Spleen


title: KPCFpi_lung1


title: KPCFpi_spleen3


title: KPCF_lung2


title: KPCFpi_lung3


title: KPCFpi_lung2


title: KPCFpi_spleen1


title: KPCF_spleen1


title: KPCF_spleen2


title: KPCFpi_intestine2

source_name: Intestine

value: Intestine


title: KPCFpi_intestine3


title: KPCF_lung1


title: KPCF_intestine3


title: KPCFpi_intestine1


title: WT_Input_RNA-DNA_S


title: KPCF_intestine2


title: KPCF_intestine1


title: WT_IP_RNA-DNA_S


title: KPCFpi_brain3

source_name: Brain

value: Brain


title: KPCFpi_brain2


title: KPCFpi_brain1


title: KPCF_spleen3


title: E13 epi NRG1 day 4 rep2

city: San Francisco

first: Sarah

last: Knox

address: 513 Parnassus Ave

institute: UCSF

data_processing:
Quality control metrics were performed on raw sequencing reads using fastp.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene
Assembly: mm10
Supplementary files format and content: Excel file that contains matrix of raw counts of all samples

source_name: salivary gland epithelium

extract_protocol:
Total RNA was collected  and purified using RNAaqueous and DNase reagents according to the manufacturer’s instructions (Ambion, Houston, TX, USA)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: salivary gland epithelium

tag: developmental stage


title: KPCF_brain3


title: E13 epi NRG1 day 4 rep1


title: KPCF_brain2


title: E16SMG fresh dissect A

source_name: salivary gland

value: salivary gland

value: untreated


title: KPCF_brain1


title: E13 epi NRG1 day 3 rep2


title: E16 Erbb3 KO rep3

value: KO


title: E16 Erbb3 KO rep4


title: E13 epi NRG1 day 2 rep1


title: E13 epi NRG1 day 2 rep2


title: E17SMG fresh dissect D


title: E16SMG fresh dissect B


title: E17SMG fresh dissect A


title: E17SMG fresh dissect B


title: E16 WT rep2


title: E16 WT rep1


title: E16SMG fresh dissect C


title: E18SMG fresh dissect C


title: E18SMG fresh dissect D


title: E16 Erbb3 KO rep1


title: E17SMG fresh dissect C


title: E16SMG fresh dissect D


title: E15SMG fresh dissect D


title: E15SMG fresh dissect A


title: E15SMG fresh dissect C


title: E15SMG fresh dissect B


title: E16 Erbb3 KO rep2


title: E16 WT rep3


title: E18SMG fresh dissect A


title: E16 WT rep4


title: E13 epi NRG1 day 3 rep1


title: E14SMG fresh dissect A


title: E14SMG fresh dissect C


title: E14SMG fresh dissect B


title: E18SMG fresh dissect B


title: E13SMG fresh dissect D


title: E13SMG fresh dissect B


title: E13SMG fresh dissect A


title: TORIN1 epi 72h D


title: TORIN1 epi 72h B


title: E13SMG fresh dissect C


title: TORIN1 epi 72h C


title: DMSO epi 72h D

value: DMSO


title: DMSO epi 72h C


title: E14 end bud NRG1 B


title: DMSO epi 72h A


title: DMSO epi 72h B


title: TORIN1 epi 72h A


title: E14 end bud NRG1 C


title: E14SMG fresh dissect D


title: E13 end bud NRG1 A


title: E14 end bud NRG1 A


title: E14 end bud Control C


title: E14 end bud Control B


title: E13 end bud Control C


title: E13 end bud NRG1 B


title: E13 end bud NRG1 C


title: E13 end bud Control B


title: E13 end bud Control A


title: KO452

city: shanghai

first: george

last: yue

address: Room 4B, the 3rd Building, No. 401, Caobao Road, Xuhui District, Shanghai, China, 200233

institute: Genergy Bio-technology (Shanghai) Co., Ltd

data_processing:
The RNA-seq library was prepared by a TruSeq RNA sample preparation kit (Illumina, US), and sequencing of the libraries was conducted on an Illumina HiSeq system. Three samples were collected from each group. The read depth was 30-50 × 106 bp for each sample. Skewer (v0.2.2) software (https://sourceforge.net) was used to dynamically remove joint sequence fragments and low-quality fragments from the 3' end of the sequencing data. FastQC (v0.11.5) software (http://www.bioinformatics) was used to conduct quality control analysis on the preprocessed data. Sequence data were mapped to the mouse reference genome GRCm38 with STAR (v2.5.3a) software (https://github.com). StringTie (v1.3.1c) software (http://ccb.jhu.edu) was used to calculate the original sequence count of known genes for all samples, and the expression levels of known genes were calculated using FPKM (fragments per kilobase of transcript per million fragments mapped).
Differentially expressed genes (DEG) analysis was conducted between WT and WAS-KO mice to identify significantly up- or downregulated genes. DEGs were assessed by DESeq 2 (v1.16.1) software (https://bioconductor.org). The Benjamini–Hochberg multiple test correction method was used. Differentially expressed genes were chosen according to | log 2 fold change | > = 1 and adjusted P value < 0.05. Functional annotation clustering was performed using TopGO software (http://www.bioconductor.org). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp) annotations were tested for enrichment, and a Benjamini–Hochberg-corrected p value < 0.05 was deemed significant. Functional analysis of disease annotation was performed via the functional annotation and classification of disease types in the DisGeNET disease database (http://www.disgenet.org) for DEGs. Reactome metabolic pathway analysis was used to annotate DEGs for metabolic pathways in the Reactome database (http://www.reactome.org/).
Assembly: http://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.chromosome.*.fa.gz
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: spleen

extract_protocol:
Was -/- (129S6/SvEvTac-Wastm1Sbs/J) (WAS-Knockout, WAS-KO) and 129S6/SvEvTac (wild-type, WT) mice were purchased from the Jackson Laboratory (Bar Harbor, Maine, ME, USA). All animals were maintained with food and water made available ad libitum and under a 12 h light/dark cycle. Ten-week-old male mice were used in this experiment, and all experiments were approved by the Medical Ethics Committee of Children’s Hospital of Chongqing Medical University. The mice were euthanized, and their spleens were isolated. Total RNA was extracted from the right spleen using an RNAqueousTM Kit (AM1912, Thermo Fisher, Germany) following the manufacturer’s instructions. Purity was determined by a NanoDrop 1000 (Thermo Scientific, Germany).
RNA libraries for RNA-seq were prepared using  illumina mRNA-Seq Library  Kit following manufacturer's protocols.

value: spleen

value: spleen cells

value: WAS knockout


title: Kdm6b_WT_RNA-seq_biol_rep_1

city: Durham

first: Anne

middle: E

last: West

state: NC

address: 311 Research Dr

department: Neurobiology

institute: Duke University

description:
PE150
Kdm6b_WT_biol_rep_1

data_processing:
RNA-seq raw fastq read files were analyzed with FastQC and processed with Trimmomatic 0.38 for quality control and adapter trimming
Trimmed reads were then aligned to the mm10 reference genome using STAR 2.7.2b. Duplicates were filtered from the resulting alignments with macs2 2.1 filterdup keeping only one duplicate
Read counts for genes were generated using the count command of the HTseq2 package, with feature type set to ‘exon’, and the Gencode mm10 GTF annotation file
DESeq2 was used for read-count normalization and differential expression analysis.
Assembly: mm10
Supplementary files format and content: exon.reads

source_name: Cerebellum

extract_protocol:
Cerebellar tissue was lysed in Trizol reagent, after which chloroform was added and phase separation was performed. The resulting aqueous layer was further processed using the Zymo Direct-zol RNA miniprep kit (Zymo #R2052). RNA purity was then measured to make sure samples had A260/280 and A260/230 values > 1.9.
Novogene mRNA library preparation

value: Cerebellum


title: WT454

value: WT


title: KO451


title: KO457


title: WT453


title: WT455


title: Kdm6b_cKO_RNA-seq_biol_rep_2

description:
PE150
Kdm6b_cKO_biol_rep_1


title: Kdm6b_cKO_RNA-seq_biol_rep_1

description:
PE150
Kdm6b_cKO_biol_rep_1


title: CGN, GSK-J4, H3K27me3, CUT&RUN, Rep 2 [CGN_GJ4_1uM_biol_rep_2]

description:
S-Prime 50bp
CGN_GJ4_1uM_biol_rep_2

data_processing:
library strategy: CUT and RUN
CUT&RUN raw fastq read files were analyzed with FastQC and processed with Trimmomatic 0.38 for quality control and adapter trimming
Trimmed reads were then aligned to the mm10 reference genome using STAR 2.7.2b. Duplicates were filtered from the resulting alignments with macs2 2.1 filterdup keeping only one duplicate
Genome coverage was calculated using bedtools v2.25.0 genomecov.
Peak calling was performed with the genome coverage file using Macs2 using the broad peak function with an FDR threshold of 0.1. A union peak file was obtained with the union function from GenomicRanges 1.48.0  R package. Raw reads were counted using this union peak file as reference with the regionCounts function from the csaw 1.30.1 R package.
DESeq2 1.36.0 was used to obtain differentially bound peaks between timepoints, using an adjusted p value cutoff of 0.05.
Assembly: mm10
Supplementary files format and content: bed

source_name: Cerebellar granule neuron

growth_protocol: Neurobasal, 2% Calf Serum, 1x glutamine, 1x penicillin/streptomycin, 1x B27. Cells were cultured at 37C at 10% CO2.

extract_protocol:
Cells were scraped into 1X PBS + Protease Inhibitor, pelleted and washed in the same buffer, after which intact nuclei were pelleted and CUT and RUN was performed according to the Epicypher CUT and RUN kit (#14-1408) as per manufacturer guidelines
CUT and RUN libraries were prepared using the NEB Ultra II DNA Library Prep Kit for Illumina (NEB #R7645L) and NEBNext Multiplex Oligos for Illumina (NEB #E6440S). Library Cleanup was performed prior to and after PCR amplification (as noted in Epicypher CUT and RUN Kit, #14-1408), using 0.8X Kapa Hyperpure beads (Roche #08963851001)

treatment_protocol: Cells were treated with 1 uM Cytosine Arabinoside (Arac) at DIV2

value: Cerebellar granule neuron

value: H3K27me3 Active Motif 39155


title: CGN, GSK-J4, H3K27me3, CUT&RUN, Rep 3 [CGN_GJ4_1uM_biol_rep_3]

description:
S-Prime 50bp
CGN_GJ4_1uM_biol_rep_3


title: CGN, GSK-J4, H3K27me3, CUT&RUN, Rep 1 [CGN_GJ4_1uM_biol_rep_1]

description:
S-Prime 50bp
CGN_GJ4_1uM_biol_rep_1


title: CGN, DMSO, H3K27me3, CUT&RUN, Rep 3 [CGN_GJ4_0uM_biol_rep_3]

description:
S-Prime 50bp
CGN_GJ4_0uM_biol_rep_3


title: CGN, DMSO, H3K27me3, CUT&RUN, Rep 2 [CGN_GJ4_0uM_biol_rep_2]

description:
S-Prime 50bp
CGN_GJ4_0uM_biol_rep_2


title: CGN, GSK-126, H3K27me3, CUT&RUN, Rep 3 [CGN_G126_biol_rep_3]

description:
S-Prime 50bp
CGN_G126_biol_rep_3


title: CGN, DMSO, H3K27me3, CUT&RUN, Rep 3 [CGN_DMSO_biol_rep_3]

description:
S-Prime 50bp
CGN_DMSO_biol_rep_3


title: CGN, DMSO, H3K27me3, CUT&RUN, Rep 1 [CGN_DMSO_biol_rep_1]

description:
S-Prime 50bp
CGN_DMSO_biol_rep_1


title: CGN, GSK-126, H3K27me3, CUT&RUN, Rep 1 [CGN_G126_biol_rep_1]

description:
S-Prime 50bp
CGN_G126_biol_rep_1


title: CGN, GSK-126, H3K27me3, CUT&RUN, Rep 2 [CGN_G126_biol_rep_2]

description:
S-Prime 50bp
CGN_G126_biol_rep_2


title: CGN, DMSO, H3K27me3, CUT&RUN, Rep 2 [CGN_DMSO_biol_rep_2]

description:
S-Prime 50bp
CGN_DMSO_biol_rep_2


title: CGN, DIV7, H3K27me3, CUT&RUN, Rep 3 [CGN_D7_H3K27me3_biol_rep_3]

description:
S-Prime 50bp
CGN_D7_H3K27me3_biol_rep_3


title: CGN, DMSO, H3K27me3, CUT&RUN, Rep 1 [CGN_GJ4_0uM_biol_rep_1]

description:
S-Prime 50bp
CGN_GJ4_0uM_biol_rep_1


title: CGN, DIV7, H3K27me3, CUT&RUN, Rep 1 [CGN_D7_H3K27me3_biol_rep_1]

description:
S-Prime 50bp
CGN_D7_H3K27me3_biol_rep_1


title: CGN, DIV5, H3K27me3, CUT&RUN, Rep 3 [CGN_D5_H3K27me3_biol_rep_3]

description:
S-Prime 50bp
CGN_D5_H3K27me3_biol_rep_3


title: CGN, DIV5, H3K27me3, CUT&RUN, Rep 1 [CGN_D5_H3K27me3_biol_rep_1]

description:
S-Prime 50bp
CGN_D5_H3K27me3_biol_rep_1


title: CGN, DIV5, H3K27me3, CUT&RUN, Rep 2 [CGN_D5_H3K27me3_biol_rep_2]

description:
S-Prime 50bp
CGN_D5_H3K27me3_biol_rep_2


title: CGN, DIV3, H3K27me3, CUT&RUN, Rep 3 [CGN_D3_H3K27me3_biol_rep_3]

description:
S-Prime 50bp
CGN_D3_H3K27me3_biol_rep_3


title: CGN, DIV3, H3K27me3, CUT&RUN, Rep 2 [CGN_D3_H3K27me3_biol_rep_2]

description:
S-Prime 50bp
CGN_D3_H3K27me3_biol_rep_2


title: Kdm6b_WT_RNA-seq_biol_rep_2

description:
PE150
Kdm6b_WT_biol_rep_1


title: CGN, DIV3, H3K27me3, CUT&RUN, Rep 1 [CGN_D3_H3K27me3_biol_rep_1]

description:
S-Prime 50bp
CGN_D3_H3K27me3_biol_rep_1


title: CGN, DIV1, H3K27me3, CUT&RUN, Rep 3 [CGN_D1_H3K27me3_biol_rep_3]

description:
S-Prime 50bp
CGN_D1_H3K27me3_biol_rep_3


title: CGN, DIV7, H3K27me3, CUT&RUN, Rep 2 [CGN_D7_H3K27me3_biol_rep_2]

description:
S-Prime 50bp
CGN_D7_H3K27me3_biol_rep_2


title: CGN, DIV1, H3K27me3, CUT&RUN, Rep 2 [CGN_D1_H3K27me3_biol_rep_2]

description:
S-Prime 50bp
CGN_D1_H3K27me3_biol_rep_2


title: CGN, DIV1, H3K27me3, CUT&RUN, Rep 1 [CGN_D1_H3K27me3_biol_rep_1]

description:
S-Prime 50bp
CGN_D1_H3K27me3_biol_rep_1


title: lymphnode_controltumorbearing_e29d5K6_L1

city: Candiolo

first: Luigia

last: Pace

address: Strada Provinciale, 142 -KM 3.95

institute: Italian Institute for Genomic Medicine

library_source: transcriptomic single cell

data_processing:
Single-cell sequencing files (base calls) were demultiplexed with bcl2fastq2 v.2.20.0.422 with default parameters for paired-end sequencing
FASTQ files were aligned to GRCm38 mouse (mm10) genome using STAR v.2.7.3a
Transcript-per-million (TMP) counts were obtained by processing the alignment results with RSEM v.1.3.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files of transcript expression quantification obtained via RSEM

source_name: lymph node

extract_protocol:
Dextramer-Adpgk+ CD8+ T cells were FACS sorted from draining lymph nodes and tumors, harvested from non-treated tumor bearing mice, treated with αPD-1, and αPD-1 combined with GAd. Neoepitope specific- CD8+ T cells were sorted into 384-well plates, containing lyses buffer and immediately frozen.
Single cell library preparation was done as previously described (Picelli et al., 2014).

value: Adpgk+ CD8+ T cell

value: lymph node

value: 6-10 weeks old


title: lymphnode_controltumorbearing_e29d5L8_L1


title: tumor_controltumorbearing_e29d5O11_L1

source_name: tumor

value: tumor


title: lymphnode_controltumorbearing_e29d5K15_L1


title: tumor_controltumorbearing_e29d5N5_L1


title: tumor_controltumorbearing_e29d5N1_L1


title: lymphnode_controltumorbearing_e29d5L7_L1


title: lymphnode_controltumorbearing_e29d5K11_L1


title: tumor_controltumorbearing_e29d5O7_L1


title: lymphnode_controltumorbearing_e29d5M1_L1


title: lymphnode_controltumorbearing_e29d5K4_L1


title: lymphnode_controltumorbearing_e29d5J4_L1


title: lymphnode_controltumorbearing_e29d5J21_L1


title: lymphnode_controltumorbearing_e29d5L2_L1


title: lymphnode_controltumorbearing_e29d5J7_L1


title: lymphnode_controltumorbearing_e29d5N23_L1


title: lymphnode_controltumorbearing_e29d5L3_L1


title: lymphnode_controltumorbearing_e29d5J3_L1


title: lymphnode_controltumorbearing_e29d5J12_L1


title: lymphnode_controltumorbearing_e29d5J1_L1


title: lymphnode_controltumorbearing_e29d5I9_L1


title: lymphnode_controltumorbearing_e29d5I8_L1


title: lymphnode_controltumorbearing_e29d5I6_L1


title: lymphnode_controltumorbearing_e29d5H8_L1


title: lymphnode_controltumorbearing_e29d5K2_L1


title: lymphnode_controltumorbearing_e29d5H4_L1


title: lymphnode_controltumorbearing_e29d5H7_L1


title: lymphnode_controltumorbearing_e29d5H3_L1


title: lymphnode_controltumorbearing_e29d5G5_L1


title: lymphnode_controltumorbearing_e29d5G3_L1


title: lymphnode_controltumorbearing_e29d5G2_L1


title: lymphnode_controltumorbearing_e29d5G23_L1


title: lymphnode_controltumorbearing_e29d5H2_L1


title: lymphnode_controltumorbearing_e29d5G8_L1


title: lymphnode_controltumorbearing_e29d5J11_L1


title: lymphnode_controltumorbearing_e29d5H1_L1


title: lymphnode_controltumorbearing_e29d5G11_L1


title: lymphnode_controltumorbearing_e29d5G20_L1


title: lymphnode_controltumorbearing_e29d5F6_L1


title: lymphnode_controltumorbearing_e29d5G18_L1


title: lymphnode_controltumorbearing_e29d5F2_L1


title: lymphnode_controltumorbearing_e29d5F4_L1


title: lymphnode_controltumorbearing_e29d5F9_L1


title: lymphnode_controltumorbearing_e29d5F1_L1


title: lymphnode_controltumorbearing_e29d5G19_L1


title: lymphnode_controltumorbearing_e29d5F3_L1


title: lymphnode_controltumorbearing_e29d5F14_L1


title: lymphnode_controltumorbearing_e29d5I3_L1


title: lymphnode_controltumorbearing_e29d5F13_L1


title: lymphnode_controltumorbearing_e29d5E9_L1


title: lymphnode_controltumorbearing_e29d5E7_L1


title: lymphnode_controltumorbearing_e29d5E8_L1


title: lymphnode_controltumorbearing_e29d5E6_L1


title: lymphnode_controltumorbearing_e29d5E5_L1


title: lymphnode_controltumorbearing_e29d5H14_L1


title: lymphnode_controltumorbearing_e29d5H12_L1


title: lymphnode_controltumorbearing_e29d5E4_L1


title: lymphnode_controltumorbearing_e29d5G4_L1


title: lymphnode_controltumorbearing_e29d5E3_L1


title: lymphnode_controltumorbearing_e29d5E2_L1


title: lymphnode_controltumorbearing_e29d5E1_L1


title: lymphnode_controltumorbearing_e29d5E10_L1


title: lymphnode_controltumorbearing_e29d5E11_L1


title: lymphnode_controltumorbearing_e29d5D5_L1


title: lymphnode_controltumorbearing_e29d5D3_L1


title: lymphnode_controltumorbearing_e29d5D4_L1


title: lymphnode_controltumorbearing_e29d5E12_L1


title: lymphnode_controltumorbearing_e29d5D2_L1


title: lymphnode_controltumorbearing_e29d5D1_L1


title: lymphnode_controltumorbearing_e29d5D13_L1


title: lymphnode_controltumorbearing_e29d5D12_L1


title: lymphnode_controltumorbearing_e29d5D10_L1


title: lymphnode_controltumorbearing_e29d5C8_L1


title: lymphnode_controltumorbearing_e29d5C7_L1


title: lymphnode_controltumorbearing_e29d5C6_L1


title: lymphnode_controltumorbearing_e29d5C4_L1


title: lymphnode_controltumorbearing_e29d5C5_L1


title: lymphnode_controltumorbearing_e29d5C2_L1


title: lymphnode_controltumorbearing_e29d5C1_L1


title: lymphnode_controltumorbearing_e29d5C14_L1


title: lymphnode_controltumorbearing_e29d5C10_L1


title: lymphnode_controltumorbearing_e29d5C11_L1


title: lymphnode_controltumorbearing_e29d5E20_L1


title: lymphnode_controltumorfree_e29d5B5_L1

value: CD8+ T cell


title: lymphnode_controltumorbearing_e29d5D19_L1


title: lymphnode_controltumorfree_e29d5B7_L1


title: lymphnode_controltumorbearing_e29d5D14_L1


title: lymphnode_controltumorfree_e29d5B2_L1


title: lymphnode_controltumorfree_e29d5B4_L1


title: lymphnode_controltumorfree_e29d5B1_L1


title: lymphnode_controltumorfree_e29d5B15_L1


title: lymphnode_controltumorfree_e29d5B10_L1


title: lymphnode_controltumorbearing_e29d5C3_L1


title: lymphnode_controltumorfree_e29d5B11_L1


title: tumor_aPD1.GAd_e29d3P2_L1


title: tumor_aPD1.GAd_e29d3P3_L1


title: tumor_aPD1.GAd_e29d3P6_L1


title: tumor_aPD1.GAd_e29d3P4_L1


title: lymphnode_controltumorfree_e29d5B9_L1


title: tumor_aPD1.GAd_e29d3P7_L1


title: tumor_aPD1.GAd_e29d3P16_L1


title: tumor_aPD1.GAd_e29d3P14_L1


title: tumor_aPD1.GAd_e29d3P10_L1


title: tumor_aPD1.GAd_e29d3P1_L1


title: tumor_aPD1.GAd_e29d3O8_L1


title: tumor_aPD1.GAd_e29d3O7_L1


title: tumor_aPD1.GAd_e29d3O5_L1


title: tumor_aPD1.GAd_e29d3O4_L1


title: tumor_aPD1.GAd_e29d3O1_L1


title: tumor_aPD1.GAd_e29d3O21_L1


title: tumor_aPD1.GAd_e29d3P11_L1


title: tumor_aPD1.GAd_e29d3O18_L1


title: tumor_aPD1.GAd_e29d3O2_L1


title: tumor_aPD1.GAd_e29d3P8_L1


title: tumor_aPD1.GAd_e29d3O16_L1


title: tumor_aPD1.GAd_e29d3O10_L1


title: tumor_aPD1.GAd_e29d3O11_L1


title: tumor_aPD1.GAd_e29d3N8_L1


title: tumor_aPD1.GAd_e29d3N5_L1


title: tumor_aPD1.GAd_e29d3N7_L1


title: tumor_aPD1.GAd_e29d3N4_L1


title: tumor_aPD1.GAd_e29d3N6_L1


title: tumor_aPD1.GAd_e29d3N2_L1


title: tumor_aPD1.GAd_e29d3N20_L1


title: tumor_aPD1.GAd_e29d3N3_L1


title: tumor_aPD1.GAd_e29d3N15_L1


title: tumor_aPD1.GAd_e29d3N17_L1


title: tumor_aPD1.GAd_e29d3N14_L1


title: tumor_aPD1.GAd_e29d3N11_L1


title: tumor_aPD1.GAd_e29d3N13_L1


title: tumor_aPD1.GAd_e29d3N12_L1


title: tumor_aPD1.GAd_e29d3M9_L1


title: tumor_aPD1.GAd_e29d3M7_L1


title: tumor_aPD1.GAd_e29d3M5_L1


title: tumor_aPD1.GAd_e29d3M4_L1


title: tumor_aPD1.GAd_e29d3M6_L1


title: tumor_aPD1.GAd_e29d3M21_L1


title: tumor_aPD1.GAd_e29d3M22_L1


title: tumor_aPD1.GAd_e29d3M3_L1


title: tumor_aPD1.GAd_e29d3M19_L1


title: tumor_aPD1.GAd_e29d3M18_L1


title: tumor_aPD1.GAd_e29d3M17_L1


title: tumor_aPD1.GAd_e29d3M16_L1


title: tumor_aPD1.GAd_e29d3M15_L1


title: tumor_aPD1.GAd_e29d3M14_L1


title: tumor_aPD1.GAd_e29d3N19_L1


title: tumor_aPD1.GAd_e29d3M11_L1


title: tumor_aPD1.GAd_e29d3M12_L1


title: tumor_aPD1.GAd_e29d3L9_L1


title: tumor_aPD1.GAd_e29d3L7_L1


title: tumor_aPD1.GAd_e29d3L5_L1


title: tumor_aPD1.GAd_e29d3L4_L1


title: tumor_aPD1.GAd_e29d3L23_L1


title: tumor_aPD1.GAd_e29d3L6_L1


title: tumor_aPD1.GAd_e29d3L1_L1


title: tumor_aPD1.GAd_e29d3L12_L1


title: tumor_aPD1.GAd_e29d3L15_L1


title: tumor_aPD1.GAd_e29d3L10_L1


title: tumor_aPD1.GAd_e29d3M1_L1


title: tumor_aPD1.GAd_e29d3K6_L1


title: tumor_aPD1.GAd_e29d3K8_L1


title: tumor_aPD1.GAd_e29d3K7_L1


title: tumor_aPD1.GAd_e29d3K9_L1


title: tumor_aPD1.GAd_e29d3K4_L1


title: tumor_aPD1.GAd_e29d3N9_L1


title: tumor_aPD1.GAd_e29d3K2_L1


title: tumor_aPD1.GAd_e29d3K20_L1


title: tumor_aPD1.GAd_e29d3K21_L1


title: tumor_aPD1.GAd_e29d3M13_L1


title: tumor_aPD1.GAd_e29d3K3_L1


title: tumor_aPD1.GAd_e29d3K18_L1


title: tumor_aPD1.GAd_e29d3K5_L1


title: tumor_aPD1.GAd_e29d3K17_L1


title: tumor_aPD1.GAd_e29d3K14_L1


title: tumor_aPD1.GAd_e29d3K13_L1


title: tumor_aPD1.GAd_e29d3K10_L1


title: tumor_aPD1.GAd_e29d3K12_L1


title: tumor_aPD1.GAd_e29d3L19_L1


title: tumor_aPD1.GAd_e29d3J8_L1


title: tumor_aPD1.GAd_e29d3J9_L1


title: tumor_aPD1.GAd_e29d3L14_L1


title: tumor_aPD1.GAd_e29d3L22_L1


title: tumor_aPD1.GAd_e29d3J7_L1


title: tumor_aPD1.GAd_e29d3J6_L1


title: tumor_aPD1.GAd_e29d3J5_L1


title: tumor_aPD1.GAd_e29d3J4_L1


title: tumor_aPD1.GAd_e29d3J3_L1


title: tumor_aPD1.GAd_e29d3J21_L1


title: tumor_aPD1.GAd_e29d3K1_L1


title: tumor_aPD1.GAd_e29d3J1_L1


title: tumor_aPD1.GAd_e29d3J20_L1


title: tumor_aPD1.GAd_e29d3J18_L1


title: tumor_aPD1.GAd_e29d3J16_L1


title: tumor_aPD1.GAd_e29d3J14_L1


title: tumor_aPD1.GAd_e29d3J15_L1


title: tumor_aPD1.GAd_e29d3J13_L1


title: tumor_aPD1.GAd_e29d3J12_L1


title: tumor_aPD1.GAd_e29d3J11_L1


title: tumor_aPD1.GAd_e29d3I9_L1


title: tumor_aPD1.GAd_e29d3I8_L1


title: tumor_aPD1.GAd_e29d3J10_L1


title: tumor_aPD1.GAd_e29d3I7_L1


title: tumor_aPD1.GAd_e29d3I6_L1


title: tumor_aPD1.GAd_e29d3I4_L1


title: tumor_aPD1.GAd_e29d3I5_L1


title: tumor_aPD1.GAd_e29d3I20_L1


title: tumor_aPD1.GAd_e29d3I21_L1


title: tumor_aPD1.GAd_e29d3I22_L1


title: tumor_aPD1.GAd_e29d3I1_L1


title: tumor_aPD1.GAd_e29d3J22_L1


title: tumor_aPD1.GAd_e29d3J2_L1


title: tumor_aPD1.GAd_e29d3I19_L1


title: tumor_aPD1.GAd_e29d3I17_L1


title: tumor_aPD1.GAd_e29d3J19_L1


title: tumor_aPD1.GAd_e29d3I18_L1


title: tumor_aPD1.GAd_e29d3I16_L1


title: tumor_aPD1.GAd_e29d3I12_L1


title: tumor_aPD1.GAd_e29d3I11_L1


title: tumor_aPD1.GAd_e29d3I10_L1


title: tumor_aPD1.GAd_e29d3I13_L1


title: tumor_aPD1.GAd_e29d3H5_L1


title: tumor_aPD1.GAd_e29d3H6_L1


title: tumor_aPD1.GAd_e29d3H8_L1


title: tumor_aPD1.GAd_e29d3H7_L1


title: tumor_aPD1.GAd_e29d3H9_L1


title: tumor_aPD1.GAd_e29d3I3_L1


title: tumor_aPD1.GAd_e29d3H22_L1


title: tumor_aPD1.GAd_e29d3H4_L1


title: tumor_aPD1.GAd_e29d3H2_L1


title: tumor_aPD1.GAd_e29d3H21_L1


title: tumor_aPD1.GAd_e29d3H18_L1


title: tumor_aPD1.GAd_e29d3H15_L1


title: tumor_aPD1.GAd_e29d3H1_L1


title: tumor_aPD1.GAd_e29d3H16_L1


title: tumor_aPD1.GAd_e29d3H14_L1


title: tumor_aPD1.GAd_e29d3H13_L1


title: tumor_aPD1.GAd_e29d3H11_L1


title: tumor_aPD1.GAd_e29d3H10_L1


title: tumor_aPD1.GAd_e29d3G8_L1


title: tumor_aPD1.GAd_e29d3G7_L1


title: tumor_aPD1.GAd_e29d3G4_L1


title: tumor_aPD1.GAd_e29d3G3_L1


title: tumor_aPD1.GAd_e29d3G2_L1


title: tumor_aPD1.GAd_e29d3G24_L1


title: tumor_aPD1.GAd_e29d3G21_L1


title: tumor_aPD1.GAd_e29d3H19_L1


title: tumor_aPD1.GAd_e29d3G1_L1


title: tumor_aPD1.GAd_e29d3G13_L1


title: tumor_aPD1.GAd_e29d3G17_L1


title: tumor_aPD1.GAd_e29d3G15_L1


title: tumor_aPD1.GAd_e29d3G5_L1


title: tumor_aPD1.GAd_e29d3G14_L1


title: tumor_aPD1.GAd_e29d3G19_L1


title: tumor_aPD1.GAd_e29d3H12_L1


title: tumor_aPD1.GAd_e29d3F8_L1


title: tumor_aPD1.GAd_e29d3F4_L1


title: tumor_aPD1.GAd_e29d3G9_L1


title: tumor_aPD1.GAd_e29d3F5_L1


title: tumor_aPD1.GAd_e29d3G23_L1


title: tumor_aPD1.GAd_e29d3G18_L1


title: tumor_aPD1.GAd_e29d3G6_L1


title: tumor_aPD1.GAd_e29d3F2_L1


title: tumor_aPD1.GAd_e29d3F24_L1


title: tumor_aPD1.GAd_e29d3F23_L1


title: tumor_aPD1.GAd_e29d3F22_L1


title: tumor_aPD1.GAd_e29d3F21_L1


title: tumor_aPD1.GAd_e29d3F20_L1


title: tumor_aPD1.GAd_e29d3F19_L1


title: tumor_aPD1.GAd_e29d3F1_L1


title: tumor_aPD1.GAd_e29d3G16_L1


title: tumor_aPD1.GAd_e29d3F18_L1


title: tumor_aPD1.GAd_e29d3F14_L1


title: tumor_aPD1.GAd_e29d3F12_L1


title: tumor_aPD1.GAd_e29d3F11_L1


title: tumor_aPD1.GAd_e29d3F16_L1


title: tumor_aPD1.GAd_e29d3F13_L1


title: tumor_aPD1.GAd_e29d3F15_L1


title: tumor_aPD1.GAd_e29d3F7_L1


title: tumor_aPD1.GAd_e29d3G11_L1


title: tumor_aPD1.GAd_e29d3F10_L1


title: tumor_aPD1.GAd_e29d3E9_L1


title: tumor_aPD1.GAd_e29d3E7_L1


title: tumor_aPD1.GAd_e29d3E6_L1


title: tumor_aPD1.GAd_e29d3E4_L1


title: tumor_aPD1.GAd_e29d3F17_L1


title: tumor_aPD1.GAd_e29d3E3_L1


title: tumor_aPD1.GAd_e29d3E1_L1


title: tumor_aPD1.GAd_e29d3E24_L1


title: tumor_aPD1.GAd_e29d3E2_L1


title: tumor_aPD1.GAd_e29d3E5_L1


title: tumor_aPD1.GAd_e29d3E19_L1


title: tumor_aPD1.GAd_e29d3E18_L1


title: tumor_aPD1.GAd_e29d3E17_L1


title: tumor_aPD1.GAd_e29d3E14_L1


title: tumor_aPD1.GAd_e29d3E13_L1


title: tumor_aPD1.GAd_e29d3E11_L1


title: tumor_aPD1.GAd_e29d3E10_L1


title: tumor_aPD1.GAd_e29d3E12_L1


title: tumor_aPD1.GAd_e29d3D8_L1


title: tumor_aPD1.GAd_e29d3E8_L1


title: tumor_aPD1.GAd_e29d3D7_L1


title: tumor_aPD1.GAd_e29d3D4_L1


title: tumor_aPD1.GAd_e29d3D3_L1


title: tumor_aPD1.GAd_e29d3D5_L1


title: tumor_aPD1.GAd_e29d3D6_L1


title: tumor_aPD1.GAd_e29d3D9_L1


title: tumor_aPD1.GAd_e29d3D2_L1


title: tumor_aPD1.GAd_e29d3D24_L1


title: tumor_aPD1.GAd_e29d3D22_L1


title: tumor_aPD1.GAd_e29d3D21_L1


title: tumor_aPD1.GAd_e29d3D23_L1


title: tumor_aPD1.GAd_e29d3D20_L1


title: tumor_aPD1.GAd_e29d3D1_L1


title: tumor_aPD1.GAd_e29d3D14_L1


title: tumor_aPD1.GAd_e29d3D15_L1


title: tumor_aPD1.GAd_e29d3E16_L1


title: tumor_aPD1.GAd_e29d3D18_L1


title: tumor_aPD1.GAd_e29d3D13_L1


title: tumor_aPD1.GAd_e29d3D19_L1


title: tumor_aPD1.GAd_e29d3D16_L1


title: tumor_aPD1.GAd_e29d3D12_L1


title: tumor_aPD1.GAd_e29d3D11_L1


title: tumor_aPD1.GAd_e29d3D10_L1


title: tumor_aPD1.GAd_e29d3C9_L1


title: tumor_aPD1.GAd_e29d3C8_L1


title: tumor_aPD1.GAd_e29d3C5_L1


title: tumor_aPD1.GAd_e29d3C7_L1


title: tumor_aPD1.GAd_e29d3C3_L1


title: tumor_aPD1.GAd_e29d3C4_L1


title: tumor_aPD1.GAd_e29d3C2_L1


title: tumor_aPD1.GAd_e29d3C22_L1


title: tumor_aPD1.GAd_e29d3C23_L1


title: tumor_aPD1.GAd_e29d3C21_L1


title: tumor_aPD1.GAd_e29d3C20_L1


title: tumor_aPD1.GAd_e29d3C18_L1


title: tumor_aPD1.GAd_e29d3C1_L1


title: tumor_aPD1.GAd_e29d3C15_L1


title: tumor_aPD1.GAd_e29d3C17_L1


title: tumor_aPD1.GAd_e29d3B9_L1


title: tumor_aPD1.GAd_e29d3C14_L1


title: tumor_aPD1.GAd_e29d3C13_L1


title: tumor_aPD1.GAd_e29d3C12_L1


title: tumor_aPD1.GAd_e29d3C11_L1


title: tumor_aPD1.GAd_e29d3B8_L1


title: tumor_aPD1.GAd_e29d3B7_L1


title: tumor_aPD1.GAd_e29d3C10_L1


title: tumor_aPD1.GAd_e29d3C6_L1


title: tumor_aPD1.GAd_e29d3B3_L1


title: tumor_aPD1.GAd_e29d3B4_L1


title: tumor_aPD1.GAd_e29d3B2_L1


title: tumor_aPD1.GAd_e29d3B5_L1


title: tumor_aPD1.GAd_e29d3C24_L1


title: tumor_aPD1.GAd_e29d3B24_L1


title: tumor_aPD1.GAd_e29d3B21_L1


title: tumor_aPD1.GAd_e29d3B22_L1


title: tumor_aPD1.GAd_e29d3B15_L1


title: tumor_aPD1.GAd_e29d3B1_L1


title: tumor_aPD1.GAd_e29d3B23_L1


title: tumor_aPD1.GAd_e29d3B14_L1


title: tumor_aPD1.GAd_e29d3B13_L1


title: tumor_aPD1.GAd_e29d3B12_L1


title: tumor_aPD1.GAd_e29d3B10_L1


title: tumor_aPD1.GAd_e29d3B11_L1


title: lymphnode_controltumorfree_e29d3A9_L1


title: tumor_aPD1.GAd_e29d3A20_L1


title: tumor_aPD1.GAd_e29d3A23_L1


title: lymphnode_controltumorfree_e29d3A8_L1


title: tumor_aPD1.GAd_e29d3A22_L1


title: tumor_aPD1.GAd_e29d3A16_L1


title: tumor_aPD1.GAd_e29d3A19_L1


title: tumor_aPD1.GAd_e29d3B6_L1


title: lymphnode_controltumorfree_e29d3A14_L1


title: tumor_aPD1.GAd_e29d3A21_L1


title: tumor_aPD1.GAd_e29d2P7_L1


title: tumor_aPD1.GAd_e29d3B19_L1


title: tumor_aPD1.GAd_e29d2P2_L1


title: tumor_aPD1.GAd_e29d2P5_L1


title: tumor_aPD1.GAd_e29d2P8_L1


title: lymphnode_controltumorfree_e29d3A15_L1


title: tumor_aPD1.GAd_e29d2P17_L1


title: tumor_aPD1.GAd_e29d2P1_L1


title: tumor_aPD1.GAd_e29d2P13_L1


title: tumor_aPD1.GAd_e29d2P14_L1


title: tumor_aPD1.GAd_e29d2P11_L1


title: tumor_aPD1.GAd_e29d2O8_L1


title: lymphnode_controltumorfree_e29d3A7_L1


title: tumor_aPD1.GAd_e29d2P10_L1


title: tumor_aPD1.GAd_e29d2O7_L1


title: tumor_aPD1.GAd_e29d2O6_L1


title: tumor_aPD1.GAd_e29d2O2_L1


title: tumor_aPD1.GAd_e29d2O3_L1


title: tumor_aPD1.GAd_e29d2O5_L1


title: tumor_aPD1.GAd_e29d2O4_L1


title: lymphnode_controltumorfree_e29d3A13_L1


title: tumor_aPD1.GAd_e29d2O22_L1


title: tumor_aPD1.GAd_e29d2O1_L1


title: tumor_aPD1.GAd_e29d2O21_L1


title: tumor_aPD1.GAd_e29d2O18_L1


title: tumor_aPD1.GAd_e29d2O12_L1


title: tumor_aPD1.GAd_e29d2O11_L1


title: tumor_aPD1.GAd_e29d2P15_L1


title: tumor_aPD1.GAd_e29d2O10_L1


title: tumor_aPD1.GAd_e29d2O17_L1


title: tumor_aPD1.GAd_e29d2N9_L1


title: tumor_aPD1.GAd_e29d2P12_L1


title: tumor_aPD1.GAd_e29d2N7_L1


title: tumor_aPD1.GAd_e29d2N5_L1


title: tumor_aPD1.GAd_e29d2O14_L1


title: tumor_aPD1.GAd_e29d2N4_L1


title: tumor_aPD1.GAd_e29d2N6_L1


title: tumor_aPD1.GAd_e29d2N3_L1


title: tumor_aPD1.GAd_e29d2N24_L1


title: tumor_aPD1.GAd_e29d2N23_L1


title: tumor_aPD1.GAd_e29d2N22_L1


title: tumor_aPD1.GAd_e29d2N1_L1


title: tumor_aPD1.GAd_e29d2N18_L1


title: tumor_aPD1.GAd_e29d2N16_L1


title: tumor_aPD1.GAd_e29d2N15_L1


title: tumor_aPD1.GAd_e29d2N13_L1


title: tumor_aPD1.GAd_e29d2N14_L1


title: tumor_aPD1.GAd_e29d2O19_L1


title: tumor_aPD1.GAd_e29d2N11_L1


title: tumor_aPD1.GAd_e29d3F6_L1


title: tumor_aPD1.GAd_e29d2N10_L1


title: tumor_aPD1.GAd_e29d2M9_L1


title: tumor_aPD1.GAd_e29d2N12_L1


title: tumor_aPD1.GAd_e29d2M8_L1


title: tumor_aPD1.GAd_e29d2M6_L1


title: tumor_aPD1.GAd_e29d2M7_L1


title: tumor_aPD1.GAd_e29d2M5_L1


title: tumor_aPD1.GAd_e29d2M3_L1


title: tumor_aPD1.GAd_e29d2M4_L1


title: tumor_aPD1.GAd_e29d2M2_L1


title: tumor_aPD1.GAd_e29d2M19_L1


title: tumor_aPD1.GAd_e29d2M18_L1


title: tumor_aPD1.GAd_e29d2M20_L1


title: tumor_aPD1.GAd_e29d2M14_L1


title: tumor_aPD1.GAd_e29d2M15_L1


title: tumor_aPD1.GAd_e29d2M12_L1


title: tumor_aPD1.GAd_e29d2M13_L1


title: tumor_aPD1.GAd_e29d2M10_L1


title: tumor_aPD1.GAd_e29d2L8_L1


title: tumor_aPD1.GAd_e29d2M11_L1


title: tumor_aPD1.GAd_e29d2L7_L1


title: tumor_aPD1.GAd_e29d2L6_L1


title: tumor_aPD1.GAd_e29d2L21_L1


title: tumor_aPD1.GAd_e29d2L4_L1


title: tumor_aPD1.GAd_e29d2L1_L1


title: tumor_aPD1.GAd_e29d2L18_L1


title: tumor_aPD1.GAd_e29d2L17_L1


title: tumor_aPD1.GAd_e29d2L15_L1


title: tumor_aPD1.GAd_e29d2L14_L1


title: tumor_aPD1.GAd_e29d2L13_L1


title: tumor_aPD1.GAd_e29d2L12_L1


title: tumor_aPD1.GAd_e29d2L11_L1


title: tumor_aPD1.GAd_e29d2K9_L1


title: tumor_aPD1.GAd_e29d2L10_L1


title: tumor_aPD1.GAd_e29d2K6_L1


title: tumor_aPD1.GAd_e29d2K7_L1


title: tumor_aPD1.GAd_e29d2K5_L1


title: tumor_aPD1.GAd_e29d2K4_L1


title: tumor_aPD1.GAd_e29d2K23_L1


title: tumor_aPD1.GAd_e29d2K3_L1


title: tumor_aPD1.GAd_e29d2K2_L1


title: tumor_aPD1.GAd_e29d2L9_L1


title: tumor_aPD1.GAd_e29d2K20_L1


title: tumor_aPD1.GAd_e29d2K22_L1


title: tumor_aPD1.GAd_e29d2K14_L1


title: tumor_aPD1.GAd_e29d2K17_L1


title: tumor_aPD1.GAd_e29d2K13_L1


title: tumor_aPD1.GAd_e29d2L3_L1


title: lymphnode_aPD1_e29d2J9_L1


title: tumor_aPD1.GAd_e29d2K10_L1


title: lymphnode_aPD1_e29d2J7_L1


title: lymphnode_aPD1_e29d2J6_L1


title: lymphnode_aPD1_e29d2J4_L1


title: lymphnode_aPD1_e29d2J2_L1


title: lymphnode_aPD1_e29d2J5_L1


title: lymphnode_aPD1_e29d2J3_L1


title: lymphnode_aPD1_e29d2J23_L1


title: lymphnode_aPD1_e29d2J1_L1


title: tumor_aPD1.GAd_e29d2J19_L1


title: tumor_aPD1.GAd_e29d2J17_L1


title: tumor_aPD1.GAd_e29d2J18_L1


title: lymphnode_aPD1_e29d2J14_L1


title: tumor_aPD1.GAd_e29d2K1_L1


title: lymphnode_aPD1_e29d2J13_L1


title: lymphnode_aPD1_e29d2J12_L1


title: lymphnode_aPD1_e29d2J10_L1


title: lymphnode_aPD1_e29d2I8_L1


title: lymphnode_aPD1_e29d2I9_L1


title: lymphnode_aPD1_e29d2I7_L1


title: lymphnode_aPD1_e29d2I5_L1


title: lymphnode_aPD1_e29d2J11_L1


title: lymphnode_aPD1_e29d2I6_L1


title: lymphnode_aPD1_e29d2I4_L1


title: lymphnode_aPD1_e29d2I3_L1


title: tumor_aPD1.GAd_e29d2K11_L1


title: lymphnode_aPD1_e29d2I23_L1


title: lymphnode_aPD1_e29d2I20_L1


title: lymphnode_aPD1_e29d2I1_L1


title: tumor_aPD1.GAd_e29d2J16_L1


title: lymphnode_aPD1_e29d2I18_L1


title: lymphnode_aPD1_e29d2I19_L1


title: lymphnode_aPD1_e29d2I17_L1


title: lymphnode_aPD1_e29d2I15_L1


title: lymphnode_aPD1_e29d2I16_L1


title: lymphnode_aPD1_e29d2I12_L1


title: lymphnode_aPD1_e29d2I13_L1


title: lymphnode_aPD1_e29d2I10_L1


title: lymphnode_aPD1_e29d2H9_L1


title: lymphnode_aPD1_e29d2I11_L1


title: lymphnode_aPD1_e29d2H8_L1


title: tumor_aPD1.GAd_e29d2K12_L1


title: lymphnode_aPD1_e29d2H6_L1


title: lymphnode_aPD1_e29d2H7_L1


title: lymphnode_aPD1_e29d2H4_L1


title: lymphnode_aPD1_e29d2H3_L1


title: lymphnode_aPD1_e29d2H23_L1


title: lymphnode_aPD1_e29d2I2_L1


title: lymphnode_aPD1_e29d2H21_L1


title: lymphnode_aPD1_e29d2H2_L1


title: lymphnode_aPD1_e29d2I24_L1


title: lymphnode_aPD1_e29d2H1_L1


title: lymphnode_aPD1_e29d2H18_L1


title: lymphnode_aPD1_e29d2I21_L1


title: lymphnode_aPD1_e29d2H17_L1


title: lymphnode_aPD1_e29d2H14_L1


title: L29_4

data_processing:
Base calling and initial adapter trimming performed by Illumina Real Time Analysis v2
Additional adapter trimming and alignment to annotated genome performed using Trimmomatic (v0.32) and STAR (v2.3).
Quantification to produce transcripts per million mapped reads (TPMs) was produced by Rsubread (v1.22.3) and edgeR (v3.14.0)
BioProject for the genome:PRJNA13635
Refernce Genome: AASC00000000.3 Aplysia californica
Reference assembly: GCA_000002075.2, (assembly AplCal3.0)
RefSeq assembly accession: GCF_000002075.1 (latest)
Supplementary_files_format_and_content: TPMs for all single neurons samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all developmental stage samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all tissue samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE
Supplementary_files_format_and_content: TPMs for all neuroplasticity samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using RefSeq gene models. * indicate public data. We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE

source_name: Single Neurons Isolated from CNS

extract_protocol:
Tissue were dissected and RNA isolated with QIAGEN Rneasy. Single neurons were processed without RNA extraction to cDNA.
cDNA was constructed with reverse transcriptase, sequencing library was made using NEBNEXT Ultra I or II Library Construction for Illumina.

tag: tissue type

value: CNS

value: neuron


title: lymphnode_aPD1_e29d2H11_L1


title: lymphnode_aPD1_e29d2H12_L1


title: lymphnode_aPD1_e29d2I14_L1


title: lymphnode_aPD1_e29d2H13_L1


title: L29_3


title: LFs_10


title: lymphnode_aPD1_e29d2G9_L1


title: lymphnode_aPD1_e29d2G8_L1


title: LFs_9


title: LE_4


title: LFs_8


title: lymphnode_aPD1_e29d2G7_L1


title: lymphnode_aPD1_e29d2G6_L1


title: lymphnode_aPD1_e29d2G5_L1


title: lymphnode_aPD1_e29d2G3_L1


title: LE_3


title: lymphnode_aPD1_e29d2G24_L1


title: lymphnode_aPD1_e29d2G2_L1


title: lymphnode_aPD1_e29d2G23_L1


title: lymphnode_aPD1_e29d2G22_L1


title: lymphnode_aPD1_e29d2G21_L1


title: lymphnode_aPD1_e29d2G1_L1


title: lymphnode_aPD1_e29d2G20_L1


title: lymphnode_aPD1_e29d2G18_L1