title: G93A_Dia_SC_D_NaBu3

city: Arlington

first: Ang

last: Li

address: 655 W Mitchell St, SEIR 244

department: Kinesiology

institute: University of Texas at Arlington

data_processing:
SOAPnuke was applied to trim adapter sequence and filter low quanlity reads, which contain more than 20% low-quality base (base quality less than or equal to 15) or contain more than 5% unknown base.
Bowtie2 was applied to align clean reads to the gene set, a database built by BGI in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM. differential expression analysis was performed using the DESeq2 with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Tab delimited text files include TPM values for each sample

source_name: diaphragm

growth_protocol: FACS-isolated satellite cells were cultured in growth medium (DMEM supplemented with 20% FBS + 1% Pen/Strep + 1% chick embryonic extract) for four days (samples labeled with "G"). To induce differentiation, cells were washed three times with PBS and cultured in differentiation medium (DMEM supplemented with 2% HS+ 1% Pen/Strep) for two more days (samples labeled with "D").

extract_protocol:
RNAs were extracted using Direct-zol RNA Miniprep Kit (Zymo Research)
RNA library preparation for DNBSeq is conducted following protocol BGI-NGS-JK-RNA-001

treatment_protocol: The samples labelled with "NaBu3" were treated with 0.5 mM NaBu (final concentration) for 3 days (from Day 4 in growth medium to Day 2 in differentiation medium).

value: diaphragm

value: primary culture from sorting

value: satellite cells

value: growth medium 4 days (last day with 0.5 mM NaBu) + differentiation medium 2 days (with 0.5 mM NaBu)


title: WAT, high-fat diet, water, rep5

status: Public on Dec 11 2023

type: SRA

city: Ya'an

first: Songqi

last: Duan

state: Sichuan

address: No.46, Xinkang Road, Yucheng District

department: College of Food Science

country: China

institute: Sichuan Agricultural University

library_source: transcriptomic

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (v0.23.2) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (v2.2.1).
The gene expression levels were quantified using featureCounts (v2.0.6) based on the aligned BAM files generated by HISAT2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain raw counts values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: White adipose tissue

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

tag: tissue

value: White adipose tissue

tag: diet

value: high fat diet

tag: group

value: water


title: G93A_Dia_SC_D_Ctrl

state: TX

country: USA

molecule: total RNA

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: growth medium 4 days + differentiation medium 2 days


title: WAT, high-fat diet, water, rep4


title: WAT, high-fat diet, tea, rep4

value: tea


title: 5679_YM3B_1-1-B11-E2

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: YM3B human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Male

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: 5679_YM3B_1-1-B11-E1


title: G93A_HL_SC_D_NaBu3

source_name: hindlimb muscle

value: hindlimb muscle


title: WAT, high-fat diet, water, rep3


title: G93A_HL_SC_D_Ctrl


title: 5679_YM3B_1-1-B11-E14


title: WAT, high-fat diet, water, rep2


title: G93A_EOM_SC_D

source_name: extraocular muscle

value: extraocular muscle


title: 5679_YM3B_1-1-B11-E13


title: 5679_YM3B_1-1-B11-F2


title: ATAC_B6_HFD_6 [F_B6_16_3]

city: Kuopio

first: Juho

middle: Mikael

last: Mononen

address: Yliopistonranta 1E

department: Faculty of Health Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
For ATAC-seq samples from the C57Bl/6J and 129S1/SvImJ strains reads were trimmed with Trimmomatic (v0.36) using long TruSeq3-SE.v2 adapters and as essential settings: ILLUMINACLIP:0:30:10, LEADING:3, TRAILING:3, MINLEN:35.
Alignment was done using to strain-specific genomes, generated with g2gtools (v0.2.9) and MGPv5 SNPs and InDels, using STAR (v2.5.4b) with ‘--alignIntronMax 1 --alignEndsType "EndToEnd"’.
Reads were filtered for true pairs and MAPQ>20 with Samtools v 1.9. Duplicates were removed using Picard (v2.8.13) MarkDuplicates.
Peaks were called with HMMRATAC (v1.2.10) using ‘--means 75,200,400,600 --upper 20 --lower 10’.
For F1 samples we used ASEReadCounter* pipeline (https://github.com/gimelbrantlab/ASEReadCounter_star).
Genome_build: mm10
Supplementary_files_format_and_content: Sample-wise peaks: Summits were widened to peaks with Bedtools (v2.27.1) using ‘slop -b 75’. Peaks were shifted to mm10 coordinates using g2gtools. ENCODE blacklisted regions were removed from the regions.
Supplementary_files_format_and_content: Raw counts: Consensus peak set was formed from the peak centers using modified kernel density estimation -based approach (Tuoresmäki et al. PLoS One 2014;9(4):e96105). Reads were shortened to 1bp tags at 5’-ends and counted using csaw (v1.28.0).
Supplementary_files_format_and_content: F1 allelic counts: Counts were obtained from ASEReadCounter* pipeline. Counts were generated using the consensus peak set from ATAC-seq samples from the C57Bl/6J and 129S1/SvImJ strains. The table contains counts for peaks and aggregated counts for SNPs in these peaks.
Supplementary_files_format_and_content: BigWigs: BAM files shifted to mm10 coordinates were downsampled after and merged by group using Samtools. BigWigs were generated using Deeptools (v3.4.2) bamCoverage with '--normalizeUsing CPM --outFileFormat bigwig --binSize 10'.

source_name: Liver

extract_protocol:
Nuclei were isolated using a Dounce homogenizer and 1× homogenization buffer (320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 1× protease inhibitors (Roche, cOmplete), and 1 mM β-mercaptoethanol). After tissue homogenization, nuclei were recovered by OptiPrep/iodixanol (Sigma-Aldrich) density gradient centrifugation.
Libraries were generated following Omni-ATAC protocol (Corces MR. et al. Nat Methods. 2017;14(10):959-962) with minor adjustments. Nuclei were resuspended in transposition mix (25 µl 2× TD buffer, 2.5 µl transposase, 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O). After the transposition reaction, DNA was purified with DNA Clean & Concentrator-5 Kit (Zymo Research). Ten microliters of purified transposed DNA were amplified for 9-11 cycles (predetermined) using 25µl of 2 × Ultra II Q5 Master Mix (New England BioLabs) and 1 µl of both amplification primers (Buenrostro JD et al. Nat Methods. 2013;10(12):1213-1218; 1.25 μM final concentration). For cleanup and to remove primer dimers and large (>1,000 bp) fragments from the libraries, SPRIselect beads (Beckman Coulter) were used.

tag: strain

value: HFD

tag: mouse id

value: Liver

tag: replicate


title: WAT, high-fat diet, water, rep1


title: 5679_YM3B_1-1-B11-D2


title: WAT, high-fat diet, tea, rep1


title: G93A_EOM_SC_G

value: growth medium 4 days


title: ATAC_B6_HFD_5 [F_B6_16_1]


title: WAT, chow diet, tea, rep5

value: chow


title: ATAC_B6_HFD_4 [F_B6_1_5]


title: 5679_YM3B_1-1-B11-D1


title: G93A_Dia_SC_D

value: diaphragm

value: primary culture from sorting


title: WAT, chow diet, tea, rep4


title: ATAC_F1_2 [ATAC_F1_no2]

value: F1 (129S1/SvImJ x C57BL/6J)


title: ATAC_B6_HFD_3 [F_B6_1_4]


title: 5679_YM3B_1-1-B11-D14


title: G93A_Dia_SC_G

value: satellite cells


title: ATAC_F1_1 [ATAC_F1_no1]


title: G93A_HL_SC_D


title: 5679_YM3B_1-1-B11-D13


title: ATAC_B6_HFD_2 [F_B6_1_3]


title: ATAC_B6_HFD_1 [F_B6_1_1]


title: 5679_YM3B_1-1-B11-C2


title: ATAC_B6_HFD_7 [F_B6_16_4]


title: 5679_YM3B_1-1-B11-C1


title: WAT, chow diet, tea, rep1

value: White adipose tissue


title: ATAC_SV_HFD_6 [F_SV_113_5]


title: G93A_HL_SC_G


title: WAT, chow diet, water, rep5

value: water


title: 5679_YM3B_1-1-B11-C14


title: WT_EOM_SC_G

value: WT


title: WT_Dia_SC_D

value: growth medium 4 days + differentiation medium 2 days


title: WAT, chow diet, water, rep4


title: 5679_YM3B_1-1-B11-C13

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: ATAC_SV_HFD_4 [F_SV_113_1]


title: WT_Dia_SC_G


title: 5679_YM3B_1-1-B11-B2

value: Male


title: WAT, chow diet, water, rep3


title: WAT, chow diet, tea, rep3

value: tea


title: ATAC_SV_HFD_3 [F_SV_109_5]


title: WAT, chow diet, water, rep2


title: ATAC_SV_HFD_2 [F_SV_109_3]


title: WAT, chow diet, tea, rep2


title: 5679_YM3B_1-1-B11-B1

value: nuclear RNA + genomic DNA


title: WAT, chow diet, water, rep1


title: WT_EOM_SC_D

value: extraocular muscle


title: WT_HL_SC_D

value: hindlimb muscle


title: 5679_YM3B_1-1-B11-B13


title: 5679_YM3B_1-1-B11-B14


title: ATAC_SV_HFD_1 [F_SV_109_2]

value: HFD

value: Liver


title: ATAC_B6_Chow_6 [C_B6_61_4]

value: Chow


title: EarlyTumour

city: Liverpool

first: Kim

last: Clarke

address: Crown Street

country: United Kingdom

institute: University of Liverpool

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: features, cell barcodes and mtx files in tsv.gz and mtx.gz format

source_name: macrophage

extract_protocol:
For advanced metastasis, livers were perfused with F4/80-FITC antibody in vivo before dissection. Freshly dissected livers were minced finely and incubated in digestion buffer (1mg/ml collgenase P in Ca2+/Mg2+ containing HBSS) in a shaking incubator at 37 degrees for 30 minutes. Cell extract was further digested with 0.25% trypsin-EDTA at 37 degrees for 5 minutes. After removal of RBCs, cells were then resuspended in PBS + 0.5% BSA and stained with viability dye and CD45, CD11b, F4/80-APC antibodies. Liver F4/80+ cells were then isolated using FACS.
Library construction was performed according to the manufacter’s instructions (single cell 3.1’ v3 protocol, 10x Genomics).

value: macrophage

tag: time

value: early mets

tag: location


title: 5679_YM3B_1-1-B11-A2


title: Naïve

value: no tumour


title: ATAC_B6_Chow_5 [C_B6_61_2]


title: Distal

value: late mets

value: distant from tumour


title: ATAC_SV_HFD_5 [F_SV_113_3]


title: 5679_YM3B_1-1-B11-A1


title: ATAC_B6_Chow_4 [C_B6_61_1]


title: OHT_4

city: Shanghai

first: Weng

address: No. 2005, Songhu Road, Yangpu District, Shanghai

institute: fudan university

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using STAR version 2.7.10.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: SVFs was cultured in Medium A (Dulbecco’s modified Eagle’s medium (DMEM) with low glucose (1 g/L), 5% neonatal bovine serum, 100 U/ml penicillin, and 100 mg/ml streptomycin) at 37oC in an atmosphere of 8.8% CO2 and maintained in less than 50% confluence. Cells were subjected to a standard cocktail hormone as previously described.

extract_protocol:
RNA-Seq analysis of global gene expression profiling was conducted at Anoroad (Beijing, China).
3μgRNApooled from 3 different samples of the same treatment was used to generate sequencing libraries using UltraTMRNA Library Prep Kit for Illumina (NEB, #7530L).

treatment_protocol: For inducible deletion of Med20, SVFs-derived adipocytes (Rosa-CreERT2;Med20f/f), on day 6 of differentiation, were treated with 4-OHT (10 μM) for 4 days.

value: Med20 knockout


title: 5679_YM3B_1-1-B11-A14


title: ATAC_B6_Chow_3 [C_B6_58_4]


title: Proximal

value: proximal to tumour


title: 5679_YM3B_1-1-B11-A13


title: ATAC_B6_Chow_2 [C_B6_58_3]


title: DMSO

value: WT

value: DMSO


title: WT_HL_SC_G

value: primary culture from sorting

value: satellite cells

value: growth medium 4 days


title: SUM149 AHR KO 3

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from AHR KO SUM149 cells.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the Robust Multiarray Average (RMA) with R version 3.2.3 and the Brainarray affy (version 1.48.0) and hugene20sthsentrezgcdf (version 20.0.0) R packages.

label: biotin

source_name: AHR KO SUM149

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: SUM149 cells were cultured in F-12 K Medium (Mediatech, Herndon, VA) containing 5 % FBS (Sigma-Aldrich), 0.5 μg/mL hydrocortisone (Sigma-Aldrich), 2 mM L-glutamine (Mediatech), 100 IU penicillin/100 μg/mL streptomycin (Mediatech), 10 μg/mL insulin (Sigma-Aldrich), and 5 μg/mL Plasmocin (Invivogen, San Diego, CA). MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (Mediatech) containing 10% FBS, 100 IU/ml penicillin, 100 μg/ml streptomycin (Mediatech), and 2 mM L-glutamine (Mediatech). The Culture conditions were maintained at 37°C, 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) according to manufacturer's recommendations. cDNA was generated using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA). Diluted cDNA was used for quantitative polymerase chain reaction (qPCR) analyses. The predesigned TaqMan primers (Applied Biosystems, Foster City, CA) were used in conjunction with Taqman Universial Master Mix II (Applied Biosystems, Foster City, CA, #4440038) and the StepOne Real Time PCR Systems (Applied Biosystems, Foster City, CA) following manufacturer's recommendations. Relative mRNA expression was quantified using the comparative Ct (ΔΔCt) method according to the ABI manual (Applied Biosystems, Foster City, CA). Amplification of glyceraldehyde-3-phosphate dehydrogenase (Gapdh) served as an internal reference in each reaction.

treatment_protocol: Human AHR knock-out SUM149 and MDA-MB-231 cell lines were created using lentiCRISPR v2 (Addgene no. 52961, Cambridge, MA) which contains Cas9 and a guide RNA cloning site (BsmBI). Two target sequences (5′‐CCTACGCCAGTCGCAAGCGG‐3′ and 5′‐CCGAGCGCGTCCTCATCGCG‐3′) for AHR knock-out were used. The target sequences are located in the first exon of the AHR gene. Lentivirus particles were generated in the HEK293NT cells by co-transfecting the AHR lentiCRISPR v2 and the packaging plasmids (pLenti-P2A and pLenti-P2B, Cat. # LV003, Applied Biological Materials Inc. Richmond, BC, Canada), by using Lipofectamine 2000 (Invitrogen, Grand Island, NY), according to the manufacturer’s instructions. Virus-containing media was collected daily up to 72 hours and filtered through a 0.45 μm filter. SUM149 and MDA-MB-231 cells were transduced with lentiviruses in the presence of 5 µg/ml polybrene. Forty-eight hours after transduction, cells were serial diluted plating in 96 well plates and selected with 2 µg/ml Puromycin for 10 days. The efficiency of AHR knockout was validated by DNA sequencing and immunoblot analyses.

tag: cell line background

value: breast cancer cell line

value: AHR KO


title: FIR+ (40 Gy), BR1

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201 S. University St, Hansen Life Sciences Building, Room 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.6.2) with the following parameters: “-s 0 –p –Q 10”.
The data was filtered out if they had a raw read count of less than 10 in half or more of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Genome_build: hg38
Supplementary_files_format_and_content: analysis with raw count (excel) from edgeR

source_name: LNCaP cells_FIR+ (40 Gy)

growth_protocol: LNCaP cells were purchased from ATCC (Manassas, VA, USA) and cultured in RPMI1640 with 10% FBS and other antibiotics.

extract_protocol:
RNA was isolated using Trizol Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LNCap treated with a cumulative dose of 40 Gy FIR

value: LNCaP

value: androgen-sensitive human prostate adenocarcinoma cells


title: FIR+ (40 Gy), BR2

value: treated with a cumulative dose of 40 Gy FIR


title: ATAC_SV_Chow_4 [C_SV_120_1]

value: Chow

tag: tissue

value: Liver


title: FIR+ (40 Gy), BR3


title: ATAC_B6_Chow_1 [C_B6_58_1]

tag: diet


title: PDLSC_Fibroblast

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
The alignment was performed using hisat2 against the human reference genome GRch38
Gene counts were obtained using featureCounts.
Assembly: GRch38
Supplementary files format and content: A csv file containing raw count values for each sample

source_name: Fibroblast

growth_protocol: Osteoblasts and fibroblasts were sequenced

extract_protocol: Illumina libraries were prepared using according to manufacturer specifications

value: wild type

value: Fibroblast


title: PDLSC_Osteoblast

source_name: Osteoblast

value: Osteoblast


title: SUM149 AHR KO 2


title: SUM149 control 2

description: Gene expression data from control SUM149 cells.

source_name: control SUM149

value: control


title: SUM149 AHR KO 1


title: untreated, BR3

source_name: LNCaP cells_untreated

value: untreated


title: DPSC_Osteoblast


title: ATAC_SV_Chow_5 [C_SV_120_4]


title: ATAC_SV_Chow_3 [C_SV_119_3]


title: SUM149 control 1


title: MDA-MB-231 AHR KO 3

description: Gene expression data from AHR KO MDA-MB-231 cells.

source_name: AHR KO MDA-MB-231


title: ATAC_SV_Chow_2 [C_SV_119_2]


title: ATAC_SV_Chow_1 [C_SV_119_1]


title: untreated, BR2


title: untreated, BR1


title: DPSC_scRNAseq

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
The raw reads were aligned to the human reference genome GRCh38, and the gene expression was then quantified using 10x's Cell Ranger (version 4.0) following the recommended pipeline
Assembly: GRch38
Supplementary files format and content: A csv file containing raw count values for each sample

source_name: Teeth

extract_protocol:
Teeth from systemically healthy individuals (aged 21-27 years) with an indication for third molar extraction with intact periodontium, roots, and pulp, without periodontal inflammation, caries, and dental calculus, were obtained. Both the periodontal ligament (PDL) and dental pulp (DP) tissue samples were obtained using the protocol described in Iwata et al. (2010) and Yang et al. (2013). Briefly, teeth were washed with a solution containing 0.1% Amphotericin B 250 µg/mL + 1% PenStrep, (both from Gibco, Life Technologies, NY, United States) in α-Minimum Essential Medium (α-MEM, Life Technologies, NY, United States). PDL samples were obtained by scraping the middle third of the root. The DP tissue was collected after sectioning the tooth at the cementoenamel junction using a diamond bur (DandZ., Wiesbaden, Germany). Isolated pieces from PDL and DP were digested with 4 mg/mL dispase + 3 mg/mL collagenase Type I (Sigma-Aldrich, MO, United States) diluted in α-MEM for 1 hour (37 ˚C). Samples were periodically resuspended for 30 s at every 20 min interval. After digestion, cells were seeded in 6-well plates with specific culture media (α-MEM + 10% fetal bovine serum + 0.292 mg/mL glutamine + 1% PenStrep) and left in the incubator (37 ˚C with 5% CO2 and 95% air humidity) for 24 h. After this period, non-adherent cells and tissue fragments were washed out, and the medium was replaced every 48 h until the primary culture reached 75% confluency. Then, cells were split into 75 cm2 culture flasks until they reached passages 3 to 5.
Illumina libraries were prepared following the manufacturer specifications of 10X GENOMICS Chromium System

value: Teeth

value: dental pulp stem cells


title: SUM149 control 3


title: MDA-MB-231 AHR KO 1


title: PAEC, PAH, 27

status: Public on Dec 10 2023

first: Bradley

last: Maron

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham & Women's Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence.
Assembly: not provided
Supplementary files format and content: *.count.txt: Tab-delimited text files include read counts for each Sample.

organism: Rattus norvegicus

source_name: Lung

extract_protocol: For details of cell isolation, please see Wertheim BM et al., PLoS One 2019 Feb 27;14(2):e0211909. doi: 10.1371/journal.pone.0211909. eCollection 2019. PMID 30811450, PMCID PMC6392245.

value: Sprague Dawley

value: Lung

value: Primary pulmonary artery endothelial cell

value: Monocrotaline PAH


title: PAEC, PAH, 24


title: DPSC_Fibroblast


title: PAEC, PAH, 23


title: MDA-MB-231 control 3

description: Gene expression data from control MDA-MB-231 cells.

source_name: control MDA-MB-231

value: breast cancer cell line


title: PAEC, vehicle, 8

value: Vehicle control


title: PAEC, PAH, 19


title: MDA-MB-231 control 1


title: PAEC, PAH, 20


title: PAEC, vehicle, 2


title: PAEC, vehicle, 9


title: PAEC, vehicle, 6


title: PAEC, PAH, 26


title: MDA-MB-231 AHR KO 2

value: AHR KO


title: PAEC, vehicle, 4


title: PDLSC_scRNAseq

value: periodontal ligament stem cells


title: MDA-MB-231 control 2


title: PAEC, vehicle, 1


title: ABE_RELA_ex7_SD_biorep_3

city: Champaign

first: Pablo

last: Pinera

state: Illinois

address: 2332 West John Street, Apt. D

department: Bioengineering

institute: University of Illinois at Urbana-Champaign

description:
REL_ABE_ex7_SD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

data_processing:
Crispresso2 utilized for base calling and base editing frequency quantification for all DNA NGS files. Sequences were filtered for 90% homology with a phred33 read qualitty of >30. Sequencecs were aligned to an inputted PCR amplicon with the gRNA region of interest
RNAstar utilized for exon junction analysis, creating bam and SJ outputs to visualize and quantify RNA splicing. 2-pass mapping was used with a MAPQ quality score of 60
Assembly: chr38
Supplementary files format and content: Excel sheet containing editing data sorted by figure number; .txt file containing nucleotide frequencies
Supplementary files format and content: DNA base editing analysis outputted in .txt files containing nucleotide frequencies in gRNA windows
Supplementary files format and content: RNAstar files outputted as .txt files containing splice junctions and quantification of junction occurance

source_name: kidney

extract_protocol:
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits and utilized manufacturer protocols
Targeted genomic and exon high throughput sequencing with nextera indexing primers

value: kidney

value: epithelial

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w  RELA ex7 SD Targeting gRNAs


title: ABE_RELA_ex7_SASD_biorep_3

description:
REL_ABE_ex7_SASD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w  RELA ex7 SA and SD Targeting gRNAs


title: ABE_RELA_ex7_SD_biorep_1

description:
REL_ABE_ex7_SD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_RELA_ex7_SASD_biorep_1

description:
REL_ABE_ex7_SASD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_RELA_ex7_SA_biorep_3

description:
REL_ABE_ex7_SA_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w  RELA ex7 SA Targeting gRNA


title: ABE_RELA_ex7_SD_biorep_2

description:
REL_ABE_ex7_SD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_RELA_ex7_SASD_biorep_2

description:
REL_ABE_ex7_SASD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_RELA_ex7_GFP_control_biorep_3

description:
REL_ABE_ex7_GFP_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected GFP Plasmid


title: ABE_RELA_ex7_SA_biorep_2

description:
REL_ABE_ex7_SA_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_RELA_ex7_GFP_control_biorep_1

description:
REL_ABE_ex7_GFP_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_LMNA_ex11_GFP_control_biorep_3

description:
LMNA_ex11_GFP_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_RELA_ex7_GFP_control_biorep_2

description:
REL_ABE_ex7_GFP_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_LMNA_ex11_GFP_control_biorep_1

description:
LMNA_ex11_GFP_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_LMNA_ex11_GFP_control_biorep_2

description:
LMNA_ex11_GFP_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_LMNA_ex11_SD_biorep_3

description:
LMNA_ABE_ex11_SD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w LMNA ex11 SD Targeting gRNA


title: ABE_LMNA_ex11_SD_biorep_1

description:
LMNA_ABE_ex11_SD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_LMNA_ex11_SD_biorep_2

description:
LMNA_ABE_ex11_SD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_LMNA_ex11_SASD_biorep_3

description:
LMNA_ABE_ex11_SASD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w LMNA ex11 SA and SD Targeting gRNAs


title: ABE_LMNA_ex11_SA_biorep_1

description:
LMNA_ABE_ex11_SA_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w LMNA ex11 SA Targeting gRNA


title: ABE_LMNA_ex11_SASD_biorep_1

description:
LMNA_ABE_ex11_SASD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_LMNA_ex11_SASD_biorep_2

description:
LMNA_ABE_ex11_SASD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_LMNA_ex11_SA_biorep_2

description:
LMNA_ABE_ex11_SA_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_CBE_JAG1_ex12_GFP_control_biorep_3

description:
JAG_ex12_GFP_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_LMNA_ex11_SA_biorep_3

description:
LMNA_ABE_ex11_SA_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_CBE_JAG1_ex12_GFP_control_biorep_2

description:
JAG_ex12_GFP_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_RELA_ex7_SA_biorep_1

description:
REL_ABE_ex7_SA_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_JAG1_ex12_SD_biorep_1

description:
JAG_ABE_ex12_SD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w JAG1 ex12 SD Targeting gRNA


title: ABE_CBE_JAG1_ex12_GFP_control_biorep_1

description:
JAG_ex12_GFP_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_JAG1_ex12_SD_biorep_2

description:
JAG_ABE_ex12_SD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_JAG1_ex12_SD_biorep_3

description:
JAG_ABE_ex12_SD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_JAG1_ex12_SA_biorep_3

description:
JAG_ABE_ex12_SA_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w JAG1 ex12 SA Targeting gRNA


title: ABE_JAG1_ex12_SA_biorep_2

description:
JAG_ABE_ex12_SA_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_JAG1_ex12_SA_biorep_1

description:
JAG_ABE_ex12_SA_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_JAG1_ex12_SASD_biorep_2

description:
JAG_ABE_ex12_SASD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w JAG1 ex12 SA and SD Targeting gRNAs


title: CBE_JAG1_ex12_SD_biorep_3

description:
J_ex12_CBE_SD_03
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w JAG1 ex12 SD Targeting gRNA


title: ABE_JAG1_ex12_SASD_biorep_1

description:
JAG_ABE_ex12_SASD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_JAG1_ex12_SD_biorep_1

description:
J_ex12_CBE_SD_01
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_JAG1_ex12_SD_biorep_2

description:
J_ex12_CBE_SD_02
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_JAG1_ex12_SA_biorep_3

description:
J_ex12_CBE_SA_03
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w JAG1 ex12 SA Targeting gRNA


title: CBE_JAG1_ex12_SA_biorep_2

description:
J_ex12_CBE_SA_02
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_JAG1_ex12_SASD_biorep_3

description:
J_ex12_CBE_SASD_03
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w JAG1 ex12 SA and SD Targeting gRNAs


title: CBE_JAG1_ex12_SASD_biorep_1

description:
J_ex12_CBE_SASD_01
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_HSF1_ex11_SD_biorep_1

description:
HSF_ABE_ex11_SD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w HSF1 ex 11 SD Targeting gRNA


title: ABE_HSF1_ex11_SASD_biorep_3

description:
HSF_ABE_ex11_SASD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w HSF1 ex 11 SA and SD Targeting gRNAs


title: ABE_HSF1_ex11_GFP_control_biorep_2

description:
HSF1_ex11_GFP_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: kidney


title: ABE_HSF1_ex11_GFP_control_biorep_3

description:
HSF1_ex11_GFP_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: epithelial


title: ABE_HSF1_ex11_SD_biorep_3

description:
HSF1_ABE_ex11_SD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_HSF1_ex11_SASD_biorep_2

description:
HSF1_ABE_ex11_SASD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_HSF1_ex11_GFP_control_biorep_1

description:
HSF1_ex11_GFP_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_HSF1_ex11_SASD_biorep_1

description:
HSF1_ABE_ex11_SASD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_HSF1_ex11_SA_biorep_3

description:
HSF1_ABE_ex11_SA_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w HSF1 ex 11 SA Targeting gRNA


title: ABE_HSF1_ex11_SA_biorep_2

description:
HSF1_ABE_ex11_SA_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_EGFR_ex23_GFP_control_biorep_3

description:
EGFR_ex23_GFP_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_HSF1_ex11_SA_biorep_1

description:
HSF1_ABE_ex11_SA_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_EGFR_ex23_GFP_control_biorep_1

description:
EGFR_ex23_GFP_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_JAG1_ex12_SASD_biorep_3

description:
JAG_ABE_ex12_SASD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_EGFR_ex23_SASD_biorep_2

description:
EGFR_CBE_EX23_SASD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w EGFR ex23 SA  and SD Targeting gRNAs


title: CBE_EGFR_ex23_SASD_biorep_1

description:
EGFR_CBE_ex23_SASD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_EGFR_ex23_SA_biorep_3

description:
EGFR_CBE_ex23_SA_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w EGFR ex23 SA Targeting gRNA


title: CBE_EGFR_ex23_SASD_biorep_3

description:
EGFR_CBE_EX23_SASD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_EGFR_ex23_SD_biorep_1

description:
EGFR_CBE_ex23_SD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w EGFR ex23 SD Targeting gRNA


title: CBE_EGFR_ex23_SD_biorep_3

description:
EGFR_CBE_ex23_SD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_EGFR_ex23_SD_biorep_2

description:
EGFR_CBE_ex23_SD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_JAG1_ex12_SA_biorep_1

description:
J_ex12_CBE_SA_01
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_EGFR_ex23_SA_biorep_2

description:
EGFR_CBE_ex23_SA_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: BE2M17_ABE_APP_ex17_SD_biorep_3

description:
BE2M17_APP_SD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

source_name: neuroblastoma

value: neuroblastoma

value: Lipofectamine 2000 transfected and Puromycin Selected  SpRY-ABE8e Plasmid  w APP ex17 SD Targeting gRNA


title: BE2M17_ABE_APP_ex17_SD_biorep_2

description:
BE2M17_APP_SD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_JAG1_ex12_SASD_biorep_2

description:
J_ex12_CBE_SASD_02
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_HSF1_ex11_SD_biorep_2

description:
HSF1_ABE_ex11_SD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: BE2M17_ABE_APP_ex17_SASD_biorep_3

description:
BE2M17_APP_SASD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected and Puromycin Selected  SpRY-ABE8e Plasmid  w APP ex17 SA and SD Targeting gRNAs


title: BE2M17_ABE_APP_ex17_SD_biorep_1

description:
BE2M17_APP_SD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: BE2M17_ABE_APP_ex17_SASD_biorep_2

description:
BE2M17_APP_SASD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_EGFR_ex23_SA_biorep_1

description:
EGFR_CBE_ex23_SA_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: BE2M17_ABE_APP_ex17_SA_biorep_2

description:
BE2M17_APP_SA_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected and Puromycin Selected  SpRY-ABE8e Plasmid  w APP ex17 SA Targeting gRNA


title: BE2M17_ABE_APP_ex17_ROSA_control_biorep_3

description:
BE2M17_APP_ROSA_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected and Puromycin Selected  SpRY-ABE8e Plasmid  w ROSA Targeting gRNA


title: BE2M17_ABE_APP_ex17_ROSA_control_biorep_2

description:
BE2M17_APP_ROSA_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: BE2M17_ABE_APP_ex17_SA_biorep_1

description:
BE2M17_APP_SA_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_EGFR_ex23_GFP_control_biorep_2

description:
EGFR_ex23_GFP_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected GFP Plasmid


title: CBE_BAP1_ex2_GFP_control_biorep_3

description:
BAP1_ex2_GFP_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: BE2M17_ABE_APP_ex17_ROSA_control_biorep_1

description:
BE2M17_APP_ROSA_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: BE2M17_ABE_APP_ex17_SA_biorep_3

description:
BE2M17_APP_SA_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_BAP1_ex2_GFP_control_biorep_2

description:
BAP1_ex2_GFP_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_BAP1_ex2_GFP_control_biorep_1

description:
BAP1_ex2_GFP_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_BAP1_ex2_SD_biorep_3

description:
BAP1_CBE_ex2_SD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w BAP1 ex2 SD Targeting gRNA


title: CBE_BAP1_ex2_SD_biorep_2

description:
BAP1_CBE_ex2_SD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_BAP1_ex2_SASD_biorep_3

description:
BAP1_CBE_ex2_SASD_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w BAP1 ex2 SA and SD Targeting gRNAs


title: CBE_BAP1_ex2_SASD_biorep_2

description:
BAP1_CBE_ex2_SASD_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_BAP1_ex2_SA_biorep_3

description:
BAP1_CBE_ex2_SA_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w BAP1 ex2 SA Targeting gRNA


title: CBE_BAP1_ex2_SASD_biorep_1

description:
BAP1_CBE_ex2_SASD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_BAP1_ex2_SA_biorep_1

description:
BAP1_CBE_ex2_SA_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SD3_biorep_3

description:
APP_ABE_ex17_SD3_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w APP ex 17 SD Targeting gRNA


title: ABE_APP_ex17_SD3_biorep_1

description:
APP_ABE_ex17_SD3_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SD3_biorep_2

description:
APP_ABE_ex17_SD3_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SD1_biorep_3

description:
APP_ABE_ex17_SD1_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SD2_biorep_2

description:
APP_ABE_ex17_SD2_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SD2_biorep_3

description:
APP_ABE_ex17_SD2_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SD2_biorep_1

description:
APP_ABE_ex17_SD2_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: BE2M17_ABE_APP_ex17_SASD_biorep_1

description:
BE2M17_APP_SASD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SD1_biorep_1

description:
APP_ABE_ex17_SD1_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SASD3_biorep_3

description:
APP_ABE_ex17_SASD3_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w APP ex 17 SA and SD Targeting gRNAs


title: ABE_APP_ex17_SASD3_biorep_2

description:
APP_ABE_ex17_SASD3_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: kidney


title: ABE_APP_ex17_SD1_biorep_2

description:
APP_ABE_ex17_SD1_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: epithelial


title: ABE_APP_ex17_SASD3_biorep_1

description:
APP_ABE_ex17_SASD3_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SASD2_biorep_1

description:
APP_ABE_ex17_SASD2_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SASD1_biorep_2

description:
APP_ABE_ex17_SASD1_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SASD2_biorep_2

description:
APP_ABE_ex17_SASD2_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SASD1_biorep_3

description:
APP_ABE_ex17_SASD1_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SASD1_biorep_1

description:
APP_ABE_ex17_SASD1_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SA_biorep_2

description:
APP_ABE_ex17_SA_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-ABE8e Plasmid  w APP ex 17 SA Targeting gRNA


title: ABE_APP_ex17_SA_biorep_3

description:
APP_ABE_ex17_SA_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_BAP1_ex2_SD_biorep_1

description:
BAP1_CBE_ex2_SD_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_SA_biorep_1

description:
APP_ABE_ex17_SA_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_GFP_control_biorep_3

description:
APP_ABE_ex17_GFP_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_BAP1_ex2_SA_biorep_2

description:
BAP1_CBE_ex2_SA_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_GFP_control_biorep_1

description:
APP_ABE_ex17_GFP_1
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: ABE_APP_ex17_GFP_control_biorep_2

description:
APP_ABE_ex17_GFP_2
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: APP331_OFF_Target_SD_site5_biorep_3

description:
APP331_09_3
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site5_biorep_1

description:
APP331_09_1
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site5_biorep_2

description:
APP331_09_2
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site4_biorep_1

description:
APP331_08_1
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site3_biorep_3

description:
APP331_07_3
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site3_biorep_2

description:
APP331_07_2
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: ABE_APP_ex17_SASD2_biorep_3

description:
APP_ABE_ex17_SASD2_3
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: APP331_OFF_Target_SD_site4_biorep_2

description:
APP331_08_2
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site2_biorep_3

description:
APP331_06_3
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site2_biorep_2

description:
APP331_06_2
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site4_biorep_3

description:
APP331_08_3
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site3_biorep_1

description:
APP331_07_1
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site1_biorep_2

description:
APP331_05_2
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site2_biorep_1

description:
APP331_06_1
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site1_biorep_1

description:
APP331_05_1
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site5_biorep_2

description:
APP331_04_2
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site5_biorep_3

description:
APP331_04_3
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SD_site1_biorep_3

description:
APP331_05_3
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site5_biorep_1

description:
APP331_04_1
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site3_biorep_2

description:
APP331_02_2
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site4_biorep_1

description:
APP331_03_1
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site3_biorep_3

description:
APP331_02_3
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site4_biorep_2

description:
APP331_03_2
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site2_biorep_3

description:
APP331_01_3
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site3_biorep_1

description:
APP331_02_1
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site2_biorep_2

description:
APP331_01_2
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site2_biorep_1

description:
APP331_01_1
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site1_biorep_3

description:
APP331_00_3
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site1_biorep_1

description:
APP331_00_1
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: APP331_OFF_Target_SA_site1_biorep_2

description:
APP331_00_2
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: AHCY_ex9_GFP_control_biorep_3

description:
A_ex9_GFP_03
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: AHCY_ex9_GFP_control_biorep_2

description:
A_ex9_GFP_02
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_AHCY_ex9_SD_biorep_2

description:
A_CBE_ex9_SD_02
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w AHCY ex9 SD Targeting gRNAs


title: CBE_AHCY_ex9_SD_biorep_3

description:
A_CBE_ex9_SD_03
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_AHCY_ex9_SD_biorep_1

description:
A_CBE_ex9_SD_01
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_AHCY_ex9_SASD_biorep_1

description:
A_CBE_ex9_SASD_01
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid   w AHCY ex9 SA and SD Targeting gRNAs


title: CBE_AHCY_ex9_SA_biorep_3

description:
A_CBE_ex9_SA_03
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid  w AHCY ex9 SA Targeting gRNAs


title: CBE_AHCY_ex9_SASD_biorep_2

description:
A_CBE_ex9_SASD_02
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max  Plasmid  w AHCY ex9 SA and SD Targeting gRNAs


title: CBE_AHCY_ex9_SASD_biorep_3

description:
A_CBE_ex9_SASD_03
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: CBE_AHCY_ex9_SA_biorep_2

description:
A_CBE_ex9_SA_02
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: Lipofectamine 2000 transfected SpRY-CBE4max Plasmid   w AHCY ex9 SA Targeting gRNAs


title: APP331_OFF_Target_SA_site4_biorep_3

description:
APP331_03_3
DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and nucleotide frequency


title: CBE_AHCY_ex9_SA_biorep_1

description:
A_CBE_ex9_SA_01
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification


title: Total  RNA of Msm cells in the log phase Rep -1

city: Newyork

first: Xiangwu

last: Ju

address: 1230 York Avenue

institute: The Rockefeller University

description: Total RNA

data_processing:
Basecalls performed using CASAVA version 1.7
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to Msm(NC_008596.1) by using Bowtie2 v2.3.4.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Mycobacterium smegmatis str. MC2 155 NC_008596.1

organism: Mycolicibacterium smegmatis

source_name: whole cell

growth_protocol: Mycobacterium smegmatis (Msm) MC2155 was grown in Middlebrook 7H9 medium supplemented with 0.2% (v/v) glycerol, 0.05% (v/v) Tween80 and 10% (v/v) albumin-dextrose-catalase (ADC).

extract_protocol:
Bacterial cells were quenched by adding 1x vol of GTC buffer (600 g L-1 guanidium thiocyanate, 5 g L-1 N-laurylsarcosine and 7.1 g L-1 sodium citrate and 0.7% (v/v) 2-mercaptoethanol) to the culture medium immediately before the harvest and placed it at room temperature for 15 min. Cell pellets were collected by centrifugation (4,000 g for 10 min at 4 °C), then thoroughly resuspended in 100 μl of TE buffer (10 mM Tris-HCl and 1 mM EDTA, pH8.0). After adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and 300 mg of glass beads (Sigma,  G1145), the cells were immediately lysed by bead beating with the Precellys Evolution homogenizer at the highest speed 10,000 rpm for 4x 45s cycles with interval of 60s at 4°C. Then the RNA was extracted following TRIzol RNA purification protocol.
SEnd-seq strategy was used to prepare the SEnd-seq library

treatment_protocol: RNA  samples were collected when Msm cells reached to log phase or stationary phase.

value: whole cell

value: Msm MC2155

value: bacteria

value: WT

value: log phase growth


title: Total RNA of Mtb mc2 cells  control group for rho knockdown   -1

description: Total RNA

data_processing:
Basecalls performed using CASAVA version 1.7
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to Mtb(NC_018143.2 ) by using Bowtie2 v2.3.4.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Mycobacterium tuberculosis H37RV, NC_018143.2
wig files

organism: Mycobacterium tuberculosis

growth_protocol: Mycobacterium tuberculosis (Mtb) H37Rv was grown at 37 °C in a minimal medium (Difco Middlebrook 7H9 broth) supplemented with 0.5% (v/v) glycerol, 0.05% (v/v) tyloxapol, 0.2 g L-1 casamino acids, 0.024 g L-1 pantothenic acid and 10% (v/v) OADC (BD). The double auxotrophic Mtb mc2 6206 strain (H37Rv ΔpanCD ΔleuCD)21 was grown in minimal medium with an additional 50 mg L-1 L-leucine (Sigma) and 24 mg mL-1  pantothenic acid (Sigma).

treatment_protocol: RNA  samples were collected when Mtb cells reached to log phase or stationary phase, or Mtb cells upon treatments of indicated antibiotics at different time points.

value: MeOH


title: primary RNA of Msm cells in the log phase Rep -2

description: primary RNA (5'PPP RNA)


title: Total  RNA of Msm cells in the log phase Rep -2

description: Total RNA


title: Total RNA of Mtb mc2 cells  after 96h of  rho knockdown   -2

description: Total RNA

value: Atc


title: Total RNA of Mtb mc2 cells  after 96h of  rho knockdown   -1

description: Total RNA


title: Total RNA of Mtb mc2  cells  after 30 min of rifampicin treatment rep-1

description: Total RNA

value: rifampicin


title: Total RNA of Mtb mc2  cells  after 10 min of streptomycin treatment rep-1

description: Total RNA

value: streptomycin


title: Total RNA of Mtb mc2 cells  control group for rho knockdown   -2

description: Total RNA


title: Total RNA of Mtb mc2  cells  after 20 min of rifampicin treatment rep-1

description: Total RNA


title: Total RNA of Mtb mc2  cells  after 10 min of rifampicin treatment rep-1

description: Total RNA


title: Total RNA of Mtb mc2  cells  after 30 min of linezolid treatment rep-2

description: Total RNA

value: linezolid


title: AHCY_ex9_GFP_control_biorep_1

description:
A_ex9_GFP_01
RNeasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

value: kidney

value: epithelial

value: Lipofectamine 2000 transfected GFP Plasmid


title: Total RNA of Mtb mc2  cells  after 10 min of linezolid treatment rep-1

description: Total RNA


title: Total RNA of Mtb mc2  cells  after 30 min of DMSO treatment rep-1

description: Total RNA

value: DMSO


title: Total RNA of Mtb mc2  cells  after 20 min of linezolid treatment rep-1

description: Total RNA


title: Total RNA of Mtb mc2  cells  after 30 min of DMSO treatment rep-2

description: Total RNA


title: Total RNA of Mtb cells in the stationary phase Rep -2

description: Total RNA

value: stationary phase growth


title: primary RNA of Mtb cells in the stationary phase Rep -2

description: primary RNA (5'PPP RNA)


title: primary RNA of Mtb mc2 cells  after 96h of  rho knockdown   rep-1

description: primary RNA (5'PPP RNA)

value: rho knockdown


title: primary RNA of Mtb cells in the statioanry phase Rep -1

description: primary RNA (5'PPP RNA)


title: Total RNA of Mtb cells in the stationary phase Rep -1

description: Total RNA


title: primary RNA of Msm cells in the log phase Rep -1

description: primary RNA (5'PPP RNA)

data_processing:
Basecalls performed using CASAVA version 1.7
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to Msm(NC_008596.1) by using Bowtie2 v2.3.4.1, and single end full length sequence was generated by  the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Mycobacterium smegmatis str. MC2 155 NC_008596.1
wig files


title: primary RNA of Mtb mc2 cells  without rho knockdown  rep-1

description: primary RNA (5'PPP RNA)


title: Total RNA of Mtb mc2  cells  after 10 min of clarithromycin treatment rep-1

description: Total RNA

value: clarithromycin


title: RRBS 9I

city: Kraków

first: Alicja

last: Wierzbicka

address: ul. Sarego 2

country: Poland

institute: National Research Institute of Animal Produstion

data_processing:
Quality control (fastQC)
Filtration of low quality reads (phred quality <20). Minimal length of reads set to 35. Removal of adaptors (Flexbar)
The files were processed using the R package (version 4.3) to obtain input data for Methylkit v. 1.26.0 software. Methylkit software was used to identify differentially methylated sites (DMS) with a cutoff value of at least 25% methylation difference between two groups and q-value < 0.05. Gene annotations were obtained from the Sscrofa11.1 Ensembl GTF annotation.
Supplementary files format and content: fasq and xlsx

organism: Sus scrofa domesticus

extract_protocol:
Collected tissues were stored at -80°C. Total DNA from 16 lung samples (8 females and 8 males) was isolated using the Wizard® Genomic DNA Purification Kit (Promega, USA). Libraries for methyl-seq were prepared using the Ovation® RRBS Methyl-Seq System 1-16 kit (Tecan, USA).
Libraries for methyl-seq were prepared using the Ovation® RRBS Methyl-Seq System 1-16 kit (Tecan, USA) in line with the recomendations.

value: Lung

value: female

value: Standard cholecalciferol


title: RRBS 51II

value: Increased cholecalciferol


title: RRBS 3II


title: blood sample from stimulated rat at 90 days post status epilepticus, biological replicate 12 [D90_SE_12]

city: Warsaw

first: Kinga

last: Szydlowska

address: Pasteura 3

institute: Nencki Institute of Experimental Biology

description: Gene expression data from plasma of adult rats after amygdala stimulation

hyb_protocol: Hybridization was done for 20 hours in +48 °C (AF-900454 GeneChip Hybridization Control Kit, Affymetrix). It was followed by the wash and stain protocol (AF-901910 FlashTagTM Biotin HSR RNA Labeling Kit, Affymetrix). The whole procedure was performed using GeneAtlas™ instrument from Affymetrix (#00-0393).

scan_protocol: The whole procedure was performed using GeneAtlas™ instrument from Affymetrix.

data_processing: Data analysis of the miRNA 4.1 Array Strips identifying up- and down-regulated miRNAs was performed with RStudio (R v. 3.3.2) using Bioconductor (Gentleman et al. 2004, R_Core_Team 2012), oligo and limma (G 2005) packages. The microarray data were normalized with the Robust Multi-array Average (RMA) algorithm (oligo package version 1.22.0) (Carvalho and Irizarry 2010). For the expression analysis, the calculated p-values were based on moderated t-statistics. Furthermore, the Benjamini and Hochberg multiple testing adjustment method was applied to the p-values (FDR – False Discovery Rate). A one-way ANOVA was used to establish  miRNA with differential levels between the tested groups.  The correlation, unsupervised clustering and PCA (principal component analyses) were performed in the RStudio (R version 3.3.2) (R_Core_Team 2012). PCA was performed on microarray probes using package stats and the lattice package (Sakar D 2008). For the heatmap clustering of miRNAs with significantly different level (p < 0.05), miRNAs were ordered with the clustering complete-linkage method, together with the Pearson correlation distance measure. The heatmap diagrams were generated with the gplots package (Warnes GR 2012). Pearson correlation test was used to analyze the correlations between miRNAs with significantly different level (p < 0.05) between stimulated and sham-operated control animals. The fuzzy c-means algorithm implemented in the Mfuzz package (Kumar & E Futschik, 2007) was used to perform clusterization on all probes.  Data analysis of the miRNA 4.1 Array Strips identifying up- and down-regulated miRNAs was performed with RStudio (R v. 3.3.2) using Bioconductor (Gentleman et al. 2004, R_Core_Team 2012), oligo and limma (G 2005) packages. The microarray data were normalized with the Robust Multi-array Average (RMA) algorithm (oligo package version 1.22.0) (Carvalho and Irizarry 2010). For the expression analysis, the calculated p-values were based on moderated t-statistics. Furthermore, the Benjamini and Hochberg multiple testing adjustment method was applied to the p-values (FDR – False Discovery Rate). A one-way ANOVA was used to establish  miRNA with differential levels between the tested groups.  The correlation, unsupervised clustering and PCA (principal component analyses) were performed in the RStudio (R version 3.3.2) (R_Core_Team 2012). PCA was performed on microarray probes using package stats and the lattice package (Sakar D 2008). For the heatmap clustering of miRNAs with significantly different level (p < 0.05), miRNAs were ordered with the clustering complete-linkage method, together with the Pearson correlation distance measure. The heatmap diagrams were generated with the gplots package (Warnes GR 2012). Pearson correlation test was used to analyze the correlations between miRNAs with significantly different level (p < 0.05) between stimulated and sham-operated control animals. The fuzzy c-means algorithm implemented in the Mfuzz package (Kumar & E Futschik, 2007) was used to perform clusterization on all probes.

source_name: adult, male rat

label_protocol: miRNA level was profiled using miRNA 4.1 Array Strip (#902404, Santa Clara, CA, Affymetrix). Procedure was performed according to manufacturer’s recommendations. 8 µl of RNA was used to perform poly-A-tailing reaction (AF-902134 GA HWS Kit for miRNA Arrays, Affymetrix).

growth_protocol: Adult, male Sprague-Dawley rats (270-320 g) from Mossakowski Medical Research Centre Polish Academy of Sciences, in Warsaw (Poland) were used in this study. Rats were housed under controlled conditions (24 °C, humidity 50 - 60 %, 12/12 h light-dark cycle) with food and water available ad libitum. Animals were housed in pairs. Environment was enriched by using various toys (wooden or plastic balls, wooden bridges, etc.) and snacks, which were changed every week. Starting four weeks before electrical stimulation rats were subjected to regular handling every other day for 10 minutes.

extract_protocol: Blood drawn from rat tail vein was drawn at 4 time points and cecntrifuged to separate plasma. miRNA was isolated from 50 µl of plasma using miRCURY kit from Qiagen. The whole miRNA isolation procedure was performed as described by the kit manufacturer. In the end of the procedure RNA was eluted to 50 µl of RNAse free water, aliquoted and stored in -80°C.

treatment_protocol: The amygdala stimulation model of temporal lobe epilepsy was used in this study as previously described with some modifications (Guzik-Kornacka et al, 2011; Nissinen et al., 2000). Surgery was performed under isoflurane anesthesia (2-2.5 % in 100 % O2) followed by the injection of butorphanol (Butomidor, Richter Pharma AG, Wells, Austria; 0.5 mg/kg i.p.) for analgesia. A stimulating and recording bipolar wire electrode (Plastic One Inc., Roanoke, VA, # E363-3-2WT-SPC) was implanted into the left lateral nucleus of the amygdala 3.6 mm posterior and 5.0 mm lateral to bregma, 6.5 mm ventral to the surface of the brain. A stainless steel screw electrode (Plastic One Inc., Roanoke, VA, #E363/20) was implanted contralaterally into the skull over the right frontal cortex (3.0 mm anterior and 2.0 mm lateral to bregma) as a surface EEG recording electrode. Two stainless steel screw electrodes were placed bilaterally over the cerebellum (10.0 mm posterior and 2.0 mm lateral to bregma) as grounding and reference electrodes. The contacts of all electrodes were placed in a multi-channel electrode pedestal (Plastic One Inc., Roanoke, VA, #MS363) which was attached to the skull with dental acrylate (Duracryl Plus). After two weeks of recovery, animals were electrically stimulated via the intra-amygdala electrode to evoke status epilepticus. Stimulation consisted of a 100-ms train of 1-ms biphasic square-wave pulses (400 μA peak to peak) delivered at 60 Hz every 0.5 s for 30 min. If the animal did not enter status epilepticus, stimulation was continued for an additional 10 min. The status epilepticus was stopped 1 h after stimulation via an intraperitoneal injection of diazepam (20 mg/kg). If the first dose of diazepam did not suppress status epilepticus , the animal received subsequent doses of diazepam at   5 mg/kg. Time matched control animals had electrodes implanted but did not receive electrical stimulation (sham animals).

value: Sprague Dawley

value: adult

value: male

tag: blood collection tube coating

value: tubes coated with 1 mg K2EDTA #363706 BD Vacutainer

value: plasma

tag: time point

value: miRNA

tag: subdivision of stimulated animals based on seizure number

value: LOW

tag: subdivision of stimulated animals based on epilepsy development at given time point

value: EPI

tag: subdivision of stimulated animals based on time of epilepsy developmentepilepsy development

value: EARLY


title: blood sample from stimulated rat at 90 days post status epilepticus, biological replicate 13 [D90_SE_13]


title: RRBS 44II

tag: treatment


title: RRBS 33I


title: RRBS 41I


title: blood sample from stimulated rat at 90 days post status epilepticus, biological replicate 11 [D90_SE_11]

tag: age


title: Total RNA of Mtb mc2  cells  after 30 min of linezolid treatment rep-1

description: Total RNA

value: whole cell

tag: cell line

tag: cell type

value: bacteria

tag: genotype

value: WT

value: linezolid


title: RRBS 34I

value: Lung

tag: Sex


title: blood sample from stimulated rat at 90 days post status epilepticus, biological replicate 9 [D90_SE_9]

tag: strain

tag: molecule subtype

value: HIGH


title: RRBS 20II


title: blood sample from stimulated rat at 90 days post status epilepticus, biological replicate 8 [D90_SE_8]


title: blood sample from stimulated rat at 90 days post status epilepticus, biological replicate 10 [D90_SE_10]


title: RRBS 19II

value: female


title: RRBS 26I

value: Standard cholecalciferol


title: RRBS 18I


title: blood sample from stimulated rat at 90 days post status epilepticus, biological replicate 4 [D90_SE_4]

value: Sprague Dawley

value: LATE


title: blood sample from stimulated rat at 90 days post status epilepticus, biological replicate 2 [D90_SE_2]

value: adult

value: male


title: blood sample from stimulated rat at 90 days post status epilepticus, biological replicate 5 [D90_SE_5]

value: tubes coated with 1 mg K2EDTA #363706 BD Vacutainer

value: plasma


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 10 [D90_CTRL_10]

value: miRNA

value: CTRL


title: RRBS 17I


title: blood sample from stimulated rat at 90 days post status epilepticus, biological replicate 6 [D90_SE_6]

value: LOW

value: EPI


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 11 [D90_CTRL_11]


title: RRBS 12II

value: Increased cholecalciferol


title: RRBS 27II


title: RRBS 10I


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 7 [D90_CTRL_7]


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 6 [D90_CTRL_6]


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 8 [D90_CTRL_8]


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 5 [D90_CTRL_5]


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 1 [D90_CTRL_1]


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 9 [D90_CTRL_9]


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 13 [D60_SE_13]

value: EARLY


title: RRBS 11II


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 12 [D60_SE_12]


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 11 [D60_SE_11]


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 9 [D60_SE_9]


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 8 [D60_SE_8]


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 4 [D90_CTRL_4]


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 2 [D90_CTRL_2]


title: plasma sample from control rat at 90 days post status epilepticus, biological replicate 3 [D90_CTRL_3]


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 6 [D60_SE_6]


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 5 [D60_SE_5]


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 7 [D60_SE_7]


title: HNV_Control_8

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

hyb_protocol: Equimolar target/reference mixes were hybridised to custom Agilent 60-mer arrays (EPI_8X60_3P_004; Epistem) according to the manufacturer's instructions.

scan_protocol: Slides were scanned for Cy5 and Cy3 on an Agilent Technologies Microarray Scanner G2505c (Serial number US91903684) at a 3uM resolution producing a 20Bit tiff image. Array data was extracted from the scanned images using the default Agilent 2 colour extraction protocol GE2_105_Dec08 in Agilent feature extraction version 10.5.1.

data_processing: Preprocessing of the probe set intensities included background correction, normalisation (Loess), and replicate averaging, excluding control probes and feature filtering (removal of features not associated with a Gene ID and duplicate Gene IDs).

source_name: reference

label_protocol: Individual cDNA test samples were labelled with Cy5 and an equimolar pool of all amplified cDNA samples was used to incorporate Cy3 fluorophore using an RNAamp Cy3/Cy5 labelling kit (Epistem).

growth_protocol: RNA amplification was performed using 10 ng total RNA and the RNAamp RNA Nano amplification kit (Epistem, Manchester, UK). Amplified cDNA was assessed quantitatively (NanoDrop) and qualitatively (Bioanalyzer; Agilent).

extract_protocol: Skin samples were homogenised in TRIzol (ThermoFisher Scientific, Waltham, MA, USA) using a polytron homogeniser, and total RNA was isolated according to the manufacturer's protocol.

tag: sample type

value: reference

source_name: test

value: skin biopsy

tag: disease state

value: Healthy

tag: subject

value: Control

tag: mrss


title: HNV_Control_6

tag: tissue


title: HNV_Control_7

tag: time point


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 10 [D60_SE_10]

tag: blood collection tube coating

tag: subdivision of stimulated animals based on seizure number

value: HIGH


title: PBO_Baseline_5961

value: SSc

value: Placebo

value: Baseline


title: TCZ_Baseline_9930

value: Tocilizumab


title: HNV_Control_9


title: TCZ_Baseline_5933


title: TCZ_Baseline_5934


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 3 [D60_SE_3]

value: Sprague Dawley

value: adult

value: male

value: tubes coated with 1 mg K2EDTA #363706 BD Vacutainer

tag: subdivision of stimulated animals based on epilepsy development at given time point

tag: subdivision of stimulated animals based on time of epilepsy developmentepilepsy development

value: LATE


title: PBO_Baseline_5935

tag: treatment


title: TCZ_Baseline_5932


title: PBO_Baseline_5930


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 2 [D60_SE_2]

tag: age

value: plasma

value: miRNA

value: EPI


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 4 [D60_SE_4]

value: LOW


title: blood sample from stimulated rat at 60 days post status epilepticus, biological replicate 1 [D60_SE_1]

value: EARLY


title: PBO_Baseline_5931

value: reference

value: skin biopsy


title: TCZ_Baseline_5904


title: plasma sample from control rat at 60 days post status epilepticus, biological replicate 11 [D60_CTRL_11]

value: CTRL


title: PBO_Baseline_5903

value: SSc


title: TCZ_Baseline_5902


title: plasma sample from control rat at 60 days post status epilepticus, biological replicate 10 [D60_CTRL_10]


title: PBO_Baseline_5750

value: Placebo


title: TCZ_Baseline_5900

value: Baseline


title: PBO_Baseline_5552


title: PBO_Baseline_5901


title: TCZ_Baseline_5650

value: Tocilizumab


title: plasma sample from control rat at 60 days post status epilepticus, biological replicate 4 [D60_CTRL_4]

value: Sprague Dawley


title: plasma sample from control rat at 60 days post status epilepticus, biological replicate 9 [D60_CTRL_9]

value: adult


title: plasma sample from control rat at 60 days post status epilepticus, biological replicate 2 [D60_CTRL_2]

value: male


title: plasma sample from control rat at 60 days post status epilepticus, biological replicate 3 [D60_CTRL_3]

value: tubes coated with 1 mg K2EDTA #363706 BD Vacutainer


title: plasma sample from control rat at 60 days post status epilepticus, biological replicate 8 [D60_CTRL_8]


title: plasma sample from control rat at 60 days post status epilepticus, biological replicate 1 [D60_CTRL_1]


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 12 [D30_SE_12]


title: plasma sample from control rat at 60 days post status epilepticus, biological replicate 6 [D60_CTRL_6]


title: PBO_Baseline_5651


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 13 [D30_SE_13]


title: PBO_Baseline_5554


title: PBO_Baseline_5553


title: TCZ_Baseline_5700


title: plasma sample from control rat at 60 days post status epilepticus, biological replicate 7 [D60_CTRL_7]


title: PBO_Baseline_5300


title: PBO_Baseline_5350


title: TCZ_Baseline_5550


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 8 [D30_SE_8]

value: HIGH


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 9 [D30_SE_9]

value: plasma


title: PBO_Baseline_5252


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 11 [D30_SE_11]

value: miRNA


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 10 [D30_SE_10]

value: EPI


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 7 [D30_SE_7]


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 6 [D30_SE_6]

value: LOW

value: NONEPI

value: LATE


title: PBO_Baseline_5253

value: reference

value: skin biopsy


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 5 [D30_SE_5]

value: EARLY


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 11 [D30_CTRL_11]

value: CTRL


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 1 [D30_SE_1]


title: TCZ_Baseline_5251

value: SSc

value: Baseline


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 4 [D30_SE_4]

value: Sprague Dawley


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 10 [D30_CTRL_10]

value: adult


title: TCZ_Baseline_5301

value: Tocilizumab


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 3 [D30_SE_3]

value: male

value: tubes coated with 1 mg K2EDTA #363706 BD Vacutainer


title: blood sample from stimulated rat at 30 days post status epilepticus, biological replicate 2 [D30_SE_2]

value: plasma

value: HIGH


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 8 [D30_CTRL_8]

value: miRNA


title: PBO_Baseline_5050

value: Placebo


title: HNV_Control_5

value: Healthy

value: Control


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 9 [D30_CTRL_9]


title: TCZ_Baseline_4800

value: reference


title: TCZ_Baseline_4702

value: skin biopsy


title: TCZ_Baseline_4801


title: PBO_Baseline_4703


title: TCZ_Baseline_5250


title: TCZ_Baseline_5200


title: PBO_Baseline_4700


title: TCZ_Baseline_4601


title: TCZ_Baseline_4701


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 7 [D30_CTRL_7]


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 4 [D30_CTRL_4]


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 6 [D30_CTRL_6]


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 12 [14D_SE_12]

value: LOW

value: EPI

value: EARLY


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 1 [D30_CTRL_1]

value: CTRL


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 3 [D30_CTRL_3]

value: Sprague Dawley


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 11 [14D_SE_11]

value: adult


title: TCZ_Baseline_4401

value: SSc

value: Tocilizumab

value: Baseline


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 5 [D30_CTRL_5]

value: male

value: tubes coated with 1 mg K2EDTA #363706 BD Vacutainer

value: plasma


title: plasma sample from control rat at 30 days post status epilepticus, biological replicate 2 [D30_CTRL_2]

value: miRNA


title: PBO_Baseline_4306

value: Placebo


title: PBO_Baseline_4302


title: PBO_Baseline_4307


title: TCZ_Baseline_4305


title: PBO_Baseline_4303


title: PBO_Baseline_4400


title: TCZ_Baseline_4100


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 10 [14D_SE_10]

value: HIGH


title: PBO_Baseline_4304

value: reference


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 9 [14D_SE_9]


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 8 [14D_SE_8]


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 13 [14D_SE_13]


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 7 [14D_SE_7]


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 6 [14D_SE_6]

value: NONEPI

value: LATE


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 5 [14D_SE_5]

value: LOW


title: PBO_Baseline_4300

value: skin biopsy


title: HNV_Control_4

value: Healthy

value: Control


title: PBO_Baseline_4301


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 1 [14D_SE_1]

value: Sprague Dawley

value: adult

value: EARLY


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 4 [14D_SE_4]


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 2 [14D_SE_2]


title: blood sample from stimulated rat at 14 days post status epilepticus, biological replicate 3 [14D_SE_3]


title: PBO_Baseline_4011

value: SSc

value: Baseline


title: TCZ_Baseline_3700

value: Tocilizumab


title: TCZ_Baseline_3603


title: PBO_Baseline_3601


title: TCZ_Baseline_4010


title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 11 [14D_CTRL_11]

value: male

value: tubes coated with 1 mg K2EDTA #363706 BD Vacutainer

value: plasma

value: CTRL


title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 10 [14D_CTRL_10]

value: miRNA


title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 9 [14D_CTRL_9]


title: PBO_Baseline_3602

value: reference

value: Placebo


title: TCZ_Baseline_3800


title: PBO_Baseline_3701


title: TCZ_Baseline_3502


title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 8 [14D_CTRL_8]


title: PBO_Baseline_3501


title: NST9B_CD3Neg

city: San Francisco

first: Margaret

last: Lowe

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

data_processing:
Fastq files were analyzed with Cell Ranger Version 3.0.2
Assembly: GRCh38
Supplementary files format and content: filtered feature bc matrices

source_name: blood from healthy donor

extract_protocol:
Cells were purified as live, CD45+, CD3- from skin that was enzymatically digested overnight with collagenase IV in the presence of DNAse.
sRNASeq was performed using the 10x Single Cell 5’ Chemistry

value: blood from healthy donor

tag: cell type

value: CD3 Negative Immune Cells


title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 6 [14D_CTRL_6]


title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 7 [14D_CTRL_7]


title: plasma sample from control rat at 14 days post status epilepticus, biological replicate 5 [14D_CTRL_5]