title: Meta1 - IM17

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes with number of unique UMIs greater than a threshold (Klein et al., 2015) were selected, resulting in the processed data table.
The code-barcode reference is embedded within the inDrops processing pipeline - https://github.com/indrops/indrops. This site includes a reference file for barcode to id conversion.
Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015)
Biological read: read1 - 3' end
Assembly: Mouse: GRCm38.85
Supplementary files format and content: Delimited tables, with cells and genes, as columns and rows, filtered

source_name: Stomach

growth_protocol: gastroid growth conditions

extract_protocol:
Mouse epithelial cell suspensions were obtained by standard dissociation (refer to Min et al, 2019). Viable cells were enriched with MACS. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification.
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths.

treatment_protocol: gastroids grown from cells isolated from Mist1-Kras mice 1 month after induction

value: Stomach

value: gastroid

value: epithelial


title: IT4 SLI-var19-K2 unpanned_2

status: Public on Jun 14 2024

type: SRA

city: Hamburg

first: Johannes

last: Allweier

address: Bernhard-Nocht-Straße 74

country: Germany

institute: Bernhard Nocht Institute for Tropical Medicine

library_source: transcriptomic

data_processing:
Raw reads were mapped with hisat2 (version 2.2.1) to the respective reference genomes sourced from PlasmoDB (Amos et al., 2022). Mapped reads were sorted and indexed with samtools (version 1.17). Reads mapped to genomic features were counted using featureCounts (version 2.0.4). For var genes, only reads mapping to exon 1 were considered, for rifs, reads to the entire coding region were included. Python3 (version 3.11.4) and bioinfokit (version 2.1.2) were used to normalize the reads to transcripts per million (TPM).Differential gene expression analysis for panned against unpanned parasites was performed in R with the DESeq2 (version 1.42.0) package.
Assembly: IT4: Release 58; 3D7: Release 62
Supplementary files format and content: processed_data.xlsx; featureCounts, DESeq2

molecule: total RNA

organism: Plasmodium falciparum

source_name: P. f. infected human erythrocytes

growth_protocol: P. falciparum parasites (3D7 (Walliker et al., 1987) and IT4 (Jensen and Trager, 1978) were cultured using standard procedures (Trager and Jensen, 1976). The parasites were maintained in RPMI1640 supplemented with 0.5% Albumax and human 0+ erythrocytes, at a haematocrit of 5% at 37°C under an atmosphere consisting of 1% O2, 5% CO2, and 94% N2.

extract_protocol:
Synchronous ring-stage parasites with a parasitemia of 3 - 5%, dissolved in 5 pellet volumes of Trizol (Thermo Fischer). RNA isolation with Qiagen miRNeasy Mini Kit according to the manufacturer’s instructions. RNA integrity was assessed using the Agilent 2100® bioanalyzer system with the RNA 6000 Pico Kit. All samples had a RIN > 8.
Ribosomal RNA was removed using QIAseq FastSelect RNA Removal Kit. Libraries were prepared with the QIASeq Stranded mRNA Library Kit and sequenced on an Illumina NextSeq 550 system with NextSeq 500/550 Mid Output Kit v2.5 (150 cycles).

tag: tissue

value: P. f. infected human erythrocytes

tag: cell line

tag: genotype

value: SLI integrant


title: RNAseq_CRISPRa_48h_premature_HOXDeRNA_KD_rep2

city: Boston

first: Evgeny

last: Deforzh

state: MA

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

country: USA

institute: Brigham and Women's Hospital

data_processing:
Fastqsanger files were trimmed to remove Illumina adapters with Trimmomatic (version 0.39)
and aligned to the GRCh37/hg19 genome using HISAT 2.2.1 with the annotation Homo_sapiens.GRCh37.75.gtf (hg19)
bigwigs were generated with BamCoverage function from deeptools 3.5.0
Assembly: hg19
Supplementary files format and content: bigwigs

molecule: polyA RNA

organism: Homo sapiens

source_name: NHA

growth_protocol: NHA cells were maintained in serum-free neurobasal media supplemented with N-2 and B-27 Plus Supplements (Gibco™), 3 mM Gibco® GlutaMAX™ Supplement, 50 units/ml penicillin and 50 units/ml streptomycin (Gibco™), 2 μg/ml heparin (Sigma-Aldrich), 20 ng/ml FGF2 (Sigma-Aldrich), and 20 ng/ml EGF (Sigma-Aldrich).

extract_protocol:
Total RNA was isolated with Norgen Biotek kit followed by treatment with DNAse I (Promega) at 37°C for 30 minutes.
Purified total RNA was delivered to Novogene for mRNA library preparation
mRNA-Seq (polyA selection)

treatment_protocol: NHA cells were transduced with 2 components of CRISPRa activation system (Dharmacon), which includes dCas9-VPR and sgRNA for 2 weeks followed by siRNA transfection

value: NHA

tag: cell type

value: Immortalized human astrocytes (Sonoda 2001)

value: immortalized by E6/E7/hTERT

tag: treatment

value: CRISPRa with VPR-dCAS9 and sgRNAs for 2 weeks followed by siRNA treatment


title: R1-DHS_K562_replicate1

city: Seattle

first: Christopher

last: Yin

state: WA

address: 3946 W Stevens Wy NE

department: Electrical & Computer Engineering

institute: University of Washington

data_processing:
Sequence reads were trimmed for 3' adaptor sequence/low-quality sequencing using cutadapt package. (parameters: maximum error rate = 0.8, minimum length = 10, maximum length = 10, no_indels)
UMIs from trimmed sequences were collapsed using starcode (parameters: seq_trim=0, umi_len=10)
Number of unique UMIs per barcode sequence calculated, and UMI counts summed across all barcodes corresponding to the same enhancer, using a custom Python script
Assembly: n/a, synthetic DNA used
Supplementary files format and content: csv containing enhancer sequence, barcode sequences for this enhancer, and unnormalized read counts for each library

growth_protocol: HepG2 cells were obtained from ATCC (HB-8065) and cultured in EMEM (ATCC 30-2003) + 10% FBS + 1% Pen/Strep at 37°C and 5% CO2. K562 cells were obtained from ATCC (CCL-243) and cultured in RPMI (Gibco 11875093) + 10% FBS + 1% Pen/Strep at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from cells 48h after transfection using the Monarch total RNA miniprep kit (NEB T2010S). For DNA libraries, barcode region of plasmid was extracted via PCR.
mRNA was isolated from total RNA extracts using the magnetic mRNA Isolation Kit (NEB S1550S) then reverse transcribed with the Maxima H Minus Reverse Transcriptase (Thermo EP0753) using a UMI-containing RT primer. Plasmid DNA was prepared with the same UMI-containing primer.

treatment_protocol: For HepG2 libraries, 600k (R1 libraries) or 1 million (R2) cells were seeded in 6-well plates or 6 cm plates respectively. 24 hours later, cells were transfected with Lipofectamine 3000 (Invitrogen L3000001) and 5 (R1) or 10 (R2) ug of library DNA following the manufacturer’s instructions. For R2, media was replaced 6 hours later. Cells were then grown for 48 hours after transfection. For K562 libraries, 1.5 million K562 cells per replicate were electroporated with 10 ug DNA using the Neon Transfection System (Invitrogen MPK5000), transferred to 6-well plates (R1) or 6 cm plates (R2) with RPMI + FBS (no Pen/Strep), and incubated for 48 hours.


title: Meta1 - IM15

library_source: transcriptomic single cell

organism: Mus musculus


title: 20230824_KSA069_NCIH1048_DMSO_rep4

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

library_source: genomic

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation. For ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively. For ChIP Data, reads were aligned, then duplicates removed and read quality filtered using using Bowtie2 v2.29, Sambamba v0.7.1, and SAMtools v0.1.19.
For ChIP and ATACseq data, tracks were generated using deepTools bamCoverage (--normalizeUsing CPM -bs 40), ATACseq data was first filtered insert sizes between 38 and 100 bp. For RNAseq data, tracks were generated using deepTools bamCoverage (--normalizeUsingRPKM).
Assembly: hg19
Supplementary files format and content: Cut&Run and ATACseq bigWig files give the normalized coverage of DNA fragments across the genome in RPM, and gene count tables give raw RNA read counts mapped to exons of given genes. RNAseq bigWig files give the give the normalized coverage of DNA fragments across the genome in RPKM.

molecule: genomic DNA

extract_protocol:
For ChIP-Seq: Cells were fixed with 2mM DSG 40min RT then 1.0% PFA 10min RT, then sonicated for 12 minutes  For ATAC-Seq: 200K cells were incubated in hypotonic buffer and lysis buffer, then were resuspended in transposase reaction mixture for 30 min at 37°C with gentle shaking followed by DNA purification and 8 cycles of amplification  For RNA-Seq: All RNA was collected using the RNeasy Mini Kit (Qiagen). RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols
ChIP-seq libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. ChIP-seq was sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters.  ATAC-seq samples were sequenced on NextSeq 500 (Illumina) or NovaSeq 6000 (Illumina) using 37 bp pair-end sequencing parameters.  RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on  NextSeq 6000 (Illumina) using 37 bp pair-end sequencing parameters.

value: DMSO


title: EAE A13

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

description: BD Rhapsody Express

data_processing:
The FASTQ format of sequencing raw data were processed with BD Rhapsody WTA Analysis pipeline (version 1.11) on SevenBridges Genomics online platform (SevenBridges).
Assembly: mm10
Supplementary files format and content: st files include UMI counts for each cell barcode and genes

source_name: Lung

extract_protocol:
After perfusion of the mice with PBS, lung was prepared and kept in cold DMEM/F12 media. Three lungs of each group was collected together and dissociated as single cell by 37C incubation for 30min in dissociation buffer(papapin and liberase DH in DMEM/F12 media). After the dissociation, cells were counted using Luna-II automated cell counter (Logos Biosystems) and captured using the BD Rhapsody system.
BD Rhapsody Express system (BD) was used for the single cell capture and mRNA harvest. Single cell whole transcriptome libraries were prepared according to the manufacturer’s instructions using BD Rhapsody WTA Reagent kit (BD, 633802) and sequenced on the Illumina NextSeq 500 using High Output Kit v2.5 (150 cycles, Illumina) aiming sequencing depth of >20,000 reads per cell for each sample.

value: Lung

tag: strain

tag: Sex

value: female

value: wildtype

value: EAE + A13


title: IT4 SLI-var19-K2 unpanned_1


title: RNAseq_CRISPRa_48h_premature_HOXDeRNA_KD_rep1


title: 20230824_KSA068_NCIH1048_DMSO_rep3


title: IT4 SLI-var19-K2 5x panned over ICAM1_4


title: IT4 SLI-var19-K2 5x panned over ICAM1_3


title: 20230824_KSA067_NCIH211_FHD609_rep3


title: EAE Cont

description: BD Rhapsody Express

value: EAE


title: RNAseq_CRISPRa_40h_premature_HOXDeRNA_KD_rep2


title: RNAseq_CRISPRa_48h_mature_HOXDeRNA_KD_rep1


title: Cont

description: BD Rhapsody Express


title: 20230824_KSA066_NCIH211_FHD609_rep2


title: IT4 SLI-var19-K2 5x panned over ICAM1_1


title: IT4 SLI-var19-K2 5x panned over ICAM1_2


title: 20230824_KSA065_NCIH211_FHD609_rep1


title: 20230824_KSA064_NCIH211_DMSO_rep4


title: RNAseq_CRISPRa_40h_premature_HOXDeRNA_KD_rep1


title: 3D7 SLI-var2csa-HA

value: 3D7 Spielmann Lab


title: RNAseq_CRISPRa_32h_premature_HOXDeRNA_KD_rep2


title: RNAseq_CRISPRa_32h_premature_HOXDeRNA_KD_rep1


title: 3D7 SLI-var0809100-HA


title: RNAseq_CRISPRa_48h_mature_HOXDeRNA_KD_rep2


title: kidney graft biopsy 195

first: Konrad

last: Buscher

address: Albert Schweitzer Campus A1

institute: University Hospital Muenster

data_processing:
Low-quality end trimming was performed using Trimmomatic version 0.39. The minimum read length was 15 bp.
The filtered reads were aligned to the Ensembl GRCm39 reference genome using HISAT2 version 2.1.0 and were sorted using SAMtools version 1.9.
We calculated the normalized read counts for each gene using DESeq2
Assembly: GRCm39
Supplementary files format and content: Raw read counts are provided as tab delimited text file

source_name: kidney

growth_protocol: The kidney allograft sample was obtained using a 18G needle biopsy.

extract_protocol:
The biopsy was directly placed in RNAlater solution (Thermo Fisher) at 4°C for a maximum of 2 hours prior to RNA isolation. Adjacent tissue such as fat or muscle was removed and the renal core of the biopsy was chopped into small pieces using a sterile scalpel. Next, the RNA was isolated using the column-based GenElute Total RNA Miniprep kit (Sigma Aldrich)
RNA quality was checked using the 4200 Tapestation (Agilent). Only samples with RNA integrity numbers greater than 6 were used. TruSeq WGS libraries were prepared according to manufactures instructions.

treatment_protocol: No treatment prior to RNA extraction

value: kidney


title: 20230824_KSA062_NCIH1048_FHD286_rep3


title: RNAseq_CRISPRa_24h_premature_HOXDeRNA_KD_rep2


title: kidney graft biopsy 196


title: kidney graft biopsy 245


title: 3D7 SLI-var0425800-HA_3


title: 3D7 SLI-var0425800-HA_2


title: 20230824_KSA061_NCIH1048_FHD286_rep2


title: kidney graft biopsy 244


title: 20230824_KSA060_NCIH1048_FHD286_rep1


title: kidney graft biopsy 236


title: RNAseq_CRISPRa_24h_rep2

value: CRISPRa with VPR-dCAS9 and sgRNAs for 2 weeks


title: 20230824_KSA059_NCIH1048_DMSO_rep2


title: 3D7 SLI-var0425800-HA_1


title: Control U937 cells treated LPS

type: RNA

city: Tainan

first: Chang-Jung

last: Chen

address: Sheng-Li Road

country: Taiwan

institute: National Cheng Kung University Medical College

description: Control U937 cells, treated with LPS, were collected after 72 hours.

hyb_protocol: Scanned on an Agilent Microarray scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: U937 cells treated LPS

label_protocol: Oligoarray control targets and hybridization buffer (Agilent Two-color Microarray-BasedGene Expression Analysis V5) were added, and samples were applied to microarrays enclosed in Agilent microarray hybridization chambers. After hybridization, slides were washed sequentially

growth_protocol: U937 cells were cultured in RPMI 1640 medium (Hyclone; SH30027.02) supplemented with 10% fetal bovine serum (Hyclone; SH30071.03), 2 mM L-glutamine (Simply; Cat. No CC515-0100), 100 units/mL Antibiotic-Antimycotic (Simply; Cat. No CC501-0100), and 1M HEPES (Simply; Cat. No CC519-0100) at 37℃ in a humidified atmosphere of 5% CO2.

extract_protocol: The Low Input Quick Amp Labeling Kit, Two-Color generates fluorescent cRNA (complimentary RNA) with a sample input RNA range between 10 ng and 200 ng of total RNA or a minimum of 5 ng of poly A+ RNA for two-color processing. The method uses T7 RNA Polymerase Blend (red cap), simultaneously amplifying target material and incorporating Cyanine 3-CTP or Cyanine 5-CTP. Amplification is typically at least 100-fold from total RNA to cRNA with the use of this kit.

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: age

value: 37 years

tag: sample type

value: Pleural effusion

tag: gender

value: Male


title: kidney graft biopsy 231


title: 20230824_KSA058_NCIH1048_DMSO_rep1


title: 3D7 SLI-MEEDvar0425800-HA_3

value: P. f. infected human erythrocytes

value: 3D7 Lavstsen Lab

value: SLI integrant


title: RNAseq_CRISPRa_16h_rep2

value: NHA

value: Immortalized human astrocytes (Sonoda 2001)

value: immortalized by E6/E7/hTERT


title: U937 cells co Panc-1 cells

description: U937 cells cocultured with Panc-1 cells, were collected after 72 hours.

source_name: U937 cells co Panc-1 cells


title: 20230824_KSA063_NCIH211_DMSO_rep3

value: DMSO


title: kidney graft biopsy 226


title: RNAseq_CRISPRa_24h_premature_HOXDeRNA_KD_rep1

value: CRISPRa with VPR-dCAS9 and sgRNAs for 2 weeks followed by siRNA treatment


title: 20230824_KSA057_NCIH526_FHD286_rep3


title: 3D7 SLI-MEEDvar0425800-HA_1


title: kidney graft biopsy 223


title: RNAseq_CRISPRa_16h_rep1


title: 20230824_KSA055_NCIH526_FHD286_rep1


title: 20230824_KSA056_NCIH526_FHD286_rep2


title: IT4 SLI_BioID-Pos2


title: IT4 SLI_BioID-Pos3


title: RNAseq_CRISPRa_8h_rep1


title: RNAseq_CRISPRa_24h_rep1


title: IT4 SLI_BioID-Pos1


title: RNAseq_CRISPRa_8h_rep2


title: kidney graft biopsy 220


title: kidney graft biopsy 219


title: 20230824_KSA052_NCIH526_DMSO_rep1


title: kidney graft biopsy 209


title: 20230824_KSA053_NCIH526_DMSO_rep2


title: IT4 wildtype

value: wildtype


title: kidney graft biopsy 202


title: 3D7 SLI-MEEDvar0425800-HA_2


title: RNAseq_CRISPRa_0h_rep1


title: kidney graft biopsy 194


title: ChIRP_CRISPRa_48h_premature_HOXDeRNA_KD_rep1

data_processing:
Fastqsanger files were mapped to hg19 genome using bowtie2 (default settings)
bigwigs were generated with BamCoverage function from deeptools 3.5.0
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: GSC and NHA Cells were maintained in serum-free neurobasal media supplemented with N-2 and B-27 Plus Supplements (Gibco™), 3 mM Gibco® GlutaMAX™ Supplement, 50 units/ml penicillin and 50 units/ml streptomycin (Gibco™), 2 μg/ml heparin (Sigma-Aldrich), 20 ng/ml FGF2 (Sigma-Aldrich), and 20 ng/ml EGF (Sigma-Aldrich).

extract_protocol:
Monarch PCR and DNA Clean Up Kit (#T1030L, NEB)
Illumina NGS libraries were prepared using the NEBNext Ultra II DNA Kit (NEB, E7645S)
ChiRP-Seq (genomic DNA)

treatment_protocol: NHA cells were transduced with 2 components of CRISPRa activation system (Dharmacon), which includes dCas9-VPR and sgRNA for 2 weeks followed by siRNA transfection or transfection with plasmids


title: ChIRP_CRISPRa_48h_premature_HOXDeRNA_KD_rep2


title: IT4 SLI-var66


title: 20230824_KSA051_CORL311_FHD286_rep3


title: IT4 SLI-var04


title: RNAseq_CRISPRa_0h_rep2


title: blood sample from stimulated rat at 8 months post status epilepticus,  LOW number of seizures, biological replicate 5

city: Warsaw

first: Kinga

last: Szydlowska

state: Select State

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biolo

description: Gene expression data from blood 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.
gc-rma signal

label: biotin

organism: Rattus norvegicus

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 3 time points and snap frozen. miRNA was isolated from 500 µl of blood using miRNeasy Kit (#217084, Qiagen). The whole miRNA isolation procedure was performed as described by the kit manufacturer. In the end of the procedure RNA was eluted to 100 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: whole blood

tag: blood collection tube coating

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

value: Sprague Dawley


title: 20230824_KSA050_CORL311_FHD286_rep2


title: kidney graft biopsy 185

value: kidney


title: 20230824_KSA054_NCIH526_DMSO_rep3


title: blood sample from stimulated rat at 8 months post status epilepticus,  LOW number of seizures, biological replicate 2


title: blood sample from stimulated rat at 8 months post status epilepticus,  LOW number of seizures, biological replicate 1


title: 20230824_KSA049_CORL311_FHD286_rep1


title: 20230824_KSA048_CORL311_DMSO_rep3


title: A-375 cells, LJH685, 72h, exp1

city: Montreal

first: Simon-Pierre

last: Gravel

state: QC

address: 2940 ch. de la polytechnique

department: Faculty of pharmacy

country: Canada

institute: University of Montreal

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35
Trimmed sequences were aligned to the reference human genome version GRCh38 (gene annotation from Gencode version 37, based on Ensembl 103) using STAR version 2.7.1a
Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain normalized gene and transcript level expression, in TPM values, for these stranded RNA libraries
DESeq2 version 1.30.1 was then used to normalize gene readcounts.
Again using DESeq2, we introduced a second factor into the model to take into account the sample pairing effect by using a Likelyhood ratio test to compare between the full model and a reduced model with the goal of isolating the condition effect.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include DESEQ2 normalized counts for each sample

source_name: melanoma cell line

growth_protocol: Cell lines were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total cellular RNA was isolated using the Monarch Total RNA Miniprep Kit (#T2010, NEB, Ipswich, MA, USA) following the manufacturer’s protocol
Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche, Basel, CHE) using a poly-A selection

treatment_protocol: MeWo and A-375 cells were treated for 72 h with DMSO 0.1% or RSK inhibitors (BI-D1870 or LJH685, respectively) at 3µM.

value: melanoma cell line

value: Female 54 years old

value: RSK inhibition 72 h


title: blood sample from stimulated rat at 8 months post status epilepticus,  LOW number of seizures, biological replicate 3


title: 20230824_KSA046_CORL311_DMSO_rep1


title: blood sample from stimulated rat at 8 months post status epilepticus,  LOW number of seizures, biological replicate 4


title: ChIRP_CRISPRa_48h_mature_HOXDeRNA_KD_rep1


title: A-375 cells, LJH685, 72h, exp3


title: blood sample from stimulated rat at 7 days post status epilepticus,  LOW number of seizures, biological replicate 5


title: A-375 cells, DMSO, 72h, exp3

value: control


title: kidney graft biopsy 181


title: A-375 cells, LJH685, 72h, exp2


title: A-375 cells, DMSO, 72h, exp2


title: ChIRP_CRISPRa_24h_premature_HOXDeRNA_KD_rep2


title: ChIRP_CRISPRa_32h_premature_HOXDeRNA_KD_rep1


title: ChIRP_CRISPRa_32h_premature_HOXDeRNA_KD_rep2


title: ChIRP_CRISPRa_40h_premature_HOXDeRNA_KD_rep2


title: ChIRP_CRISPRa_48h_mature_HOXDeRNA_KD_rep2


title: 20230824_KSA043_NCIH211_FHD286_rep1


title: MeWo cells, BI-D1870, 72h, exp3

value: Male 78 years old


title: A-375 cells, DMSO, 72h, exp1


title: blood sample from stimulated rat at 7 days post status epilepticus,  LOW number of seizures, biological replicate 3


title: ChIRP_CRISPRa_24h_premature_HOXDeRNA_KD_rep1


title: 20230824_KSA047_CORL311_DMSO_rep2


title: ChIRP_CRISPRa_40h_premature_HOXDeRNA_KD_rep1


title: 20230824_KSA045_NCIH211_FHD286_rep3


title: blood sample from stimulated rat at 7 days post status epilepticus,  LOW number of seizures, biological replicate 2


title: 20230824_KSA044_NCIH211_FHD286_rep2


title: blood sample from stimulated rat at 7 days post status epilepticus,  LOW number of seizures, biological replicate 1


title: blood sample from stimulated rat at 7 days post status epilepticus,  LOW number of seizures, biological replicate 4


title: ChIRP_CRISPRa_24h_rep1

value: CRISPRa with VPR-dCAS9 and sgRNAs for 2 weeks


title: 20230718_KS140_ChIP_NCIH1048_FHD286_Input_DX2

tag: chip antibody


title: MeWo cells, BI-D1870, 72h, exp2


title: MeWo cells, BI-D1870, 72h, exp1


title: MeWo cells, DMSO, 72h, exp3


title: 20230718_KS139_ChIP_NCIH1048_FHD286_POU2F3_DX2_rep1

value: POU2F3 (CST, E5N2D, Lot 1)


title: ChIRP_CRISPRa_16h_rep1

value: NHA


title: blood sample from stimulated rat at 2 days post status epilepticus,  LOW number of seizures, biological replicate 4


title: blood sample from stimulated rat at 2 days post status epilepticus,  LOW number of seizures, biological replicate 3


title: ChIRP_CRISPRa_16h_rep2

value: Immortalized human astrocytes (Sonoda 2001)


title: MeWo cells, DMSO, 72h, exp2


title: blood sample from stimulated rat at 2 days post status epilepticus,  LOW number of seizures, biological replicate 5


title: 20230718_KS135_ChIP_NCIH1048_FHD286_RPB1_DX2_rep1

value: RPB1 (CST, 4H8, Lot 4)


title: ChIRP_CRISPRa_8h_rep2

value: immortalized by E6/E7/hTERT


title: 20230718_KS136_ChIP_NCIH1048_FHD286_H3K27ac_DX2_rep1

value: H3K27ac (CST, D5E4, Lot 8)


title: blood sample from stimulated rat at 2 days post status epilepticus,  LOW number of seizures, biological replicate 2


title: ChIRP_CRISPRa_8h_rep1


title: ChIRP_CRISPRa_0h_rep2


title: 20230824_KSA042_NCIH211_DMSO_rep2

value: DMSO


title: ChIRP_CRISPRa_24h_rep2


title: 20240402_KS239_ChIP_NCIH211_POU2F3_CST_CKX

extract_protocol:
For ChIP-Seq: Cells were fixed with 2mM disuccinimidyl glutarate 40min room temperature then 1.0% paraformaldehyde 10min room temperature, quenced with 375mM Tris HCL and then sonicated using Covaris E220 ultra-focused sonicator. 1-10ng of immunoprecipitated DNA was used for library prep.  For ATAC-Seq: 100K cells were incubated in hypotonic buffer and lysis buffer, then were resuspended in transposase reaction mixture for 30 min at 37°C with gentle shaking followed by DNA purification and 8 cycles of amplification  For RNA-Seq: All RNA was collected using the TRIzol extraction (Invitrogen) method and treated with DNAse using the DNA-free DNA Removal Kit (Invitrogen). 1ug of DNAse-treated RNA was used for the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II Directional RNA Library Prep Kit for standard Illumina sequencing.
ChIP-seq libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. ChIP-seq was sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters or NovaSeq using 50 bp pair-end sequencing parameters.  ATAC-seq samples were sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters or NovaSeq using 50 bp pair-end sequencing parameters.  RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on  Illumina NextSeq 500 using 37 bp pair-end sequencing parameters or NovaSeq using 50 bp pair-end sequencing parameters.


title: MeWo cells, DMSO, 72h, exp1


title: blood sample from stimulated rat at 2 days post status epilepticus,  LOW number of seizures, biological replicate 1

value: whole blood


title: 20240402_KS238_ChIP_NCIH211_BRG1_ab_CKX


title: 20230824_KSA041_NCIH211_DMSO_rep1


title: blood sample from stimulated rat at 8 months post status epilepticus, HIGH number of seizures, biological replicate 4

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


title: 20230718_KS132_ChIP_NCIH1048_DMSO_Input_DX2


title: ChIRP_CRISPRa_0h_rep1


title: blood sample from stimulated rat at 8 months post status epilepticus, HIGH number of seizures, biological replicate 3

value: Sprague Dawley


title: 20230718_KS137_ChIP_NCIH1048_FHD286_BRD9_DX2_rep1

value: BRD9 (CST, E4Q3F, Lot 1)


title: NHA_ChIRP_EZH2_overexpressed_rep_1

value: CRISPRa with VPR-dCAS9 and sgRNAs for 2 weeks transfected with EZH2 plasmid


title: 20230718_KS131_ChIP_NCIH1048_DMSO_POU2F3_DX2_rep1


title: NHA_ChIRP_EZH2_overexpressed_rep_2


title: 20240402_KS237_ChIP_NCIH211_BRD9_CST_CKX


title: 20230718_KS129_ChIP_NCIH1048_DMSO_BRD9_DX2_rep1


title: 20230718_KS128_ChIP_NCIH1048_DMSO_H3K27ac_DX2_rep1


title: blood sample from stimulated rat at 8 months post status epilepticus, HIGH number of seizures, biological replicate 2


title: blood sample from stimulated rat at 8 months post status epilepticus, HIGH number of seizures, biological replicate 1


title: 20240402_KS236_ChIP_NCIH211_ARID1A_CST_CKX

value: ARID1A (CST, D2A8U, Lot 4)


title: NHA_ChIRP_EZH2_Control_rep_2

value: CRISPRa with VPR-dCAS9 and sgRNAs for 2 weeks transfected with Control plasmid


title: 20240402_KS234_ChIP_NCIH526_SS18_CST_CKX

value: SS18 (CST, D6I4Z, Lot 1)


title: 20240402_KS235_ChIP_NCIH526_POU2F3_CST_CKX


title: blood sample from stimulated rat at 7 days post status epilepticus, HIGH number of seizures, biological replicate 3


title: NHA_ChIRP_EZH2_Control_rep_1


title: NHA_naive_HOXDeRNA_ChIRP-Seq_rep2

value: WT

value: Not treated


title: blood sample from stimulated rat at 7 days post status epilepticus, HIGH number of seizures, biological replicate 2


title: COR-L311_BRM014_rep2

first: Leslie

last: Duplaquet

address: 360 Longwood Ave

department: Medical Oncology

institute: DFCI

data_processing:
Sequencing reads were mapped to the hg38 genome by STAR. Statistics for differentially expressed genes were calculated by DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each samples
Supplementary files format and content: tab-delimited text file includes FPKM values for each samples

growth_protocol: NCI-H1048, NCI-H211, NCI-H526 or COR-L311 parental cells were plated at 200,000 cells/mL and treated with the small molecules indicated for 3 days

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen #74106) including a DNase digestion step according to the manufacturer’s instructions and RNA sequencing was performed
The libraries for RNA-seq are prepared using NEBNext Ultra II non-stranded kit. Paired end 150bp sequencing was performed on Novaseq6000 sequencer using S4 flow cell. Sequencing reads were mapped to the hg38 genome by STAR. Statistics for differentially expressed genes were calculated by DESeq2.

treatment_protocol: NCI-H1048, NCI-H211, NCI-H526 or COR-L311 parental cells treated with WA-68-VQ71, BRM014 at 100nM or DMSO for 72 hours in 2 biological replicates

value: Small cell lung cancer cell


title: 20240402_KS233_ChIP_NCIH526_BRD9_CST_CKX


title: 20240402_KS232_ChIP_NCIH526_BRG1_ab_CKX


title: COR-L311_WA-68-VQ71_rep2


title: NHA_naive_HOXDeRNA_ChIRP-Seq_rep1

value: NHA


title: blood sample from stimulated rat at 2 days post status epilepticus, HIGH number of seizures, biological replicate 1


title: COR-L311_DMSO_rep2


title: blood sample from stimulated rat at 7 days post status epilepticus, HIGH number of seizures, biological replicate 1


title: 20240402_KS231_ChIP_NCIH526_ARID1A_CST_CKX


title: GBM8_ChIRP_HOXDeRNA_antisense_rep2

value: Glioma Stem Cells


title: 20240222_KS191_ChIP_NCIH1048_FHD609_Input_DX1

value: Input


title: blood sample from control rat (HIGH vs. LOW) at 8 months, biological replicate 8


title: NCI-H526_WA-68-VQ71_rep2


title: GBM8_ChIRP_HOXDeRNA_antisense_rep1


title: NCI-H526_BRM014_rep2


title: 20240222_KS188_ChIP_NCIH1048_FHD286_Input_DX1


title: GBM6_ChIRP_HOXDeRNA_antisense_rep2


title: NCI-H526_DMSO_rep2


title: 20230718_KS127_ChIP_NCIH1048_DMSO_RPB1_DX2_rep1

value: RPB1 (CST, 4H8, Lot 4)


title: 20240209_KS185_ChIP_NCIH1048_DMSO_Input_DX1


title: GBM6_ChIRP_HOXDeRNA_antisense_rep1


title: blood sample from control rat (HIGH vs. LOW) at 8 months, biological replicate 7


title: blood sample from control rat (HIGH vs. LOW) at 8 months, biological replicate 6


title: 20240222_KS203_ChIP_NCIH1048_FHD609_POU2F3_CST_DX1

value: POU2F3 (CST, E5N2D, Lot 1)


title: NCI-H211_BRM014_rep2


title: blood sample from control rat (HIGH vs. LOW) at 8 months, biological replicate 5


title: NCI-H211_WA-68-VQ71_rep2


title: blood sample from control rat (HIGH vs. LOW) at 8 months, biological replicate 4


title: 20240222_KS199_ChIP_NCIH1048_FHD286_POU2F3_CST_DX1


title: GBM4_ChIRP_HOXDeRNA_antisense_rep1


title: 20240222_KS195_ChIP_NCIH1048_DMSO_POU2F3_CST_DX1

value: DMSO


title: Titration_EZH2_ChIP-seq_rG4-1_WT_1000nM_rep2

data_processing:
Fastqsanger files were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 with default parameters
PCR duplicates were removed using samtools rmdup version 1.13
resulting aligned Bam files were transformed to Bigwig format without scaling or normalization using deeptools version 3.5.0
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
ChIP-Seq was performed using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) #9003. DNA was purified using the Monarch PCR and DNA Clean Up Kit (#T1030L, NEB)
Libraries were prepared according to Illumina's instructions accompanying NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7546S, NEB).

value: Immortalized human astrocytes (Sonoda 2001)

value: immortalized by E6/E7/hTERT

value: Recombinant PRC2 proteins were mixed with plasmids containing SOX2 or OLIG2 promoters and WT rG4-1 RNA fragments


title: blood sample from control rat (HIGH vs. LOW) at 8 months, biological replicate 3

value: whole blood

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

value: Sprague Dawley


title: NCI-H211_DMSO_rep2


title: 20240222_KS202_ChIP_NCIH1048_FHD609_SS18_CST_DX1


title: blood sample from control rat (HIGH vs. LOW) at 8 months, biological replicate 2


title: NCI-H1048_WA-68-VQ71_rep2


title: Titration_EZH2_ChIP-seq_rG4-1_WT_1000nM_rep1


title: NCI-H1048_BRM014_rep2


title: 20240222_KS198_ChIP_NCIH1048_FHD286_SS18_CST_DX1


title: blood sample from control rat (HIGH vs. LOW) at 8 months, biological replicate 1


title: Titration_EZH2_ChIP-seq_rG4-1_WT_500nM_rep2


title: NCI-H1048_DMSO_rep2


title: blood sample from control rat (HIGH vs. LOW) at 7 days, biological replicate 7


title: 20240222_KS194_ChIP_NCIH1048_DMSO_SS18_CST_DX1


title: blood sample from control rat (HIGH vs. LOW) at 7 days, biological replicate 6


title: Titration_EZH2_ChIP-seq_rG4-1_WT_500nM_rep1


title: GBM4_ChIRP_HOXDeRNA_antisense_rep2


title: Titration_EZH2_ChIP-seq_rG4-1_WT_200nM_rep2


title: 20240222_KS187_ChIP_NCIH1048_FHD286_BRD9_CST_DX1

value: BRD9 (CST, E4Q3F, Lot 1)


title: 20240222_KS190_ChIP_NCIH1048_FHD609_BRD9_CST_DX1


title: blood sample from control rat (HIGH vs. LOW) at 7 days, biological replicate 5


title: COR-L311_WA-68-VQ71_rep1


title: COR-L311_BRM014_rep1


title: Titration_EZH2_ChIP-seq_rG4-1_WT_200nM_rep1


title: 20240402_KS247_ChIP_NCIH1048_DMSO_BRD9_CST_DX1_reseq_PE


title: COR-L311_DMSO_rep1


title: blood sample from control rat (HIGH vs. LOW) at 7 days, biological replicate 4


title: 20240222_KS189_ChIP_NCIH1048_FHD609_BRG1_ab_DX1


title: Titration_EZH2_ChIP-seq_rG4-1_WT_100nM_rep2


title: Titration_EZH2_ChIP-seq_rG4-1_WT_100nM_rep1


title: NCI-H526_BRM014_rep1


title: blood sample from control rat (HIGH vs. LOW) at 7 days, biological replicate 3


title: NCI-H526_WA-68-VQ71_rep1


title: Titration_EZH2_ChIP-seq_rG4-1_WT_50nM_rep2


title: 20240222_KS186_ChIP_NCIH1048_FHD286_BRG1_ab_DX1


title: blood sample from control rat (HIGH vs. LOW) at 7 days, biological replicate 2


title: 20240402_KS246_ChIP_NCIH1048_DMSO_BRG1_ab_DX1_reseq_PE


title: NCI-H526_DMSO_rep1


title: blood sample from control rat (HIGH vs. LOW) at 7 days, biological replicate 1


title: blood sample from control rat (HIGH vs. LOW) at 2 days, biological replicate 7


title: parental +Dox/IAA biol rep 3

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
condition 2 - parental treated
parental@Dox@IAA@3@S21

data_processing:
Sequencing: Sequence-libraries of each sample were equimolarly pooled and sequenced on Illumina NextSeq 500 (76 bp, Single Reads, v1.5) at the VIB Nucleomics Core (www.nucleomics.be).
Preprocessing: Low-quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15. Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.36.1. With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina.
Mapping: The preprocessed reads were aligned with STAR aligner v2.5.2b to the reference genome of Homo sapiens (GRCh38). Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments.
Counting: The number of reads in the alignments that overlap with gene features was counted with featureCounts 1.5.3. Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id.
Assembly: Homo sapiens Ensembl GRCh38.88
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cells were grown in low glucose-DMEM medium supplemented with 10% FBS and penicilline/streptomycin

extract_protocol:
RNA was extracted with the Mammalian Total RNA Miniprep kit (GenElute from SIGMA)
RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent). Per sample, an amount of 1 microgram of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were equimolarly pooled and sequenced on an Illumina NextSeq 500 instrument (High Output, 75 bp, Single Reads, v2) at the VIB Nucleomics core (www.nucleomics.be).

treatment_protocol: Cells were treated for 48h with 2 µg/ml doxycycline and 500 µM IAA

value: HCT116 Tet-OsTIR1 (parental)

value: Dox/IAA


title: Titration_EZH2_ChIP-seq_rG4-1_mutant_1000nM_rep2

value: Recombinant PRC2 proteins were mixed with plasmids containing SOX2 or OLIG2 promoters and mutated rG4-1 RNA fragments


title: blood sample from control rat (HIGH vs. LOW) at 2 days, biological replicate 6


title: Titration_EZH2_ChIP-seq_rG4-1_mutant_1000nM_rep1


title: SDS22- biol rep 3

description:
condition 3 - SDS22 degron non treated
SDS22@3@S19

value: HCT116 Tet-OsTIR1 SDS22 WT (SDS22)

value: Untreated


title: NCI-H211_DMSO_rep1

value: Small cell lung cancer cell

value: WT


title: NCI-H1048_BRM014_rep1


title: Titration_EZH2_ChIP-seq_rG4-1_mutant_500nM_rep2

value: NHA


title: parental - biol rep 3

description:
condition 1 - parental non treated
parental@3@S17


title: blood sample from control rat (HIGH vs. LOW) at 2 days, biological replicate 4


title: SDS22 +Dox/IAA biol rep 2

description:
condition 4 - SDS22 degron treated
SDS22@Dox@IAA@2@S15


title: blood sample from control rat (HIGH vs. LOW) at 2 days, biological replicate 3


title: Titration_EZH2_ChIP-seq_rG4-1_mutant_200nM_rep2


title: NCI-H1048_WA-68-VQ71_rep1


title: Titration_EZH2_ChIP-seq_rG4-1_WT_50nM_rep1


title: NCI-H1048_DMSO_rep1


title: Titration_EZH2_ChIP-seq_rG4-1_mutant_200nM_rep1


title: parental +Dox/IAA biol rep 2

description:
condition 2 - parental treated
parental@Dox@IAA@2@S13


title: blood sample from control rat (HIGH vs. LOW) at 2 days, biological replicate 2


title: NCI-H211_BRM014_rep1


title: SDS22 +Dox/IAA biol rep 3

description:
condition 4 - SDS22 degron treated
SDS22@Dox@IAA@3@S23


title: SDS22- biol rep 2

description:
condition 3 - SDS22 degron non treated
SDS22@2@S11


title: Lung 4, fibrotic, recipient

city: Saint Louis

first: Marco

last: Colonna

state: Missouri

address: 660 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St Louis School of Medicine

description: Lung tissue was procured from organ donors and explants from transplant recipients suffering from pulmonary fibrosis.  Patients provided informed consent. Lungs from healthy donors and fibrotic recipients were mechanically disrupted and digested in complete RPMI medium containing 1 mg ml–1 Collagenase IV (Sigma, C-5138) at 37 °C for 45 min under agitation. Cells were filtered through 70-μm cell strainers and stained for sorting or flow cytometry analysis. Lineage-negative cells were sorted from the lungs as CD45+, lymphocyte gate, singlets, alive and CD3–CD19–CD14–.

data_processing:
Processing was performed with the 10X Chromium cellranger pipeline version 6.0.1 using default settings
Assembly: GRCh38
Supplementary files format and content: tsv.gz of Filtered feature-barcode matrix with raw counts for each sample

extract_protocol:
Using the Chromium Single Cell 3′ Reagent Kit v2 or v3User Guide, single cell suspensions were partitioned into nanoliter droplets called Gel-bead-in-Emulsions (GEMs) to achieve single cell resolution. The cDNA generated within each individual GEM is tagged with a common 16nt 10x barcode and a 12nt unique molecular barcode during the RT reaction. Purified cDNA was amplified for 11 cycles before being purified using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. 10uL of purified cDNA was used to generate the Illumina library for sequencing.
For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

value: Lung

value: innate lymphoid cells


title: Titration_EZH2_ChIP-seq_rG4-1_mutant_100nM_rep2

value: Immortalized human astrocytes (Sonoda 2001)


title: blood sample from control rat (HIGH vs. LOW) at 2 days, biological replicate 1


title: NCI-H211_WA-68-VQ71_rep1


title: blood sample from control rat (HIGH vs. LOW) at 2 days, biological replicate 5


title: Titration_EZH2_ChIP-seq_rG4-1_mutant_100nM_rep1

value: immortalized by E6/E7/hTERT


title: blood sample from stimulated rat at 8 months post status epilepticus, LATE seizures development, biological replicate 4


title: Lung 3, control, donor


title: parental - biol rep 2

description:
condition 1 - parental non treated
parental@2@S9


title: Titration_EZH2_ChIP-seq_rG4-1_mutant_50nM_rep2


title: SDS22 +Dox/IAA biol rep 1

description:
condition 4 - SDS22 degron treated
SDS22@Dox@IAA@S7


title: blood sample from stimulated rat at 8 months post status epilepticus, LATE seizures development, biological replicate 3


title: Lung 2, fibrotic, recipient


title: Titration_EZH2_ChIP-seq_rG4-1_mutant_50nM_rep1


title: Titration_EZH2_ChIP-seq_rG4-1_mutant_500nM_rep1


title: parental +Dox/IAA biol rep 1

description:
condition 2 - parental treated
parental@Dox@IAA@S5


title: SDS22- biol rep 1

description:
condition 3 - SDS22 degron non treated
SDS22@@S3


title: N1425-4 LPL 1, control ileum

description: LPL cells were extracted by digesting tissue in complete RPMI medium containing 1 mg ml–1 Collagenase IV at 37 °C for 45 min under agitation. Cells were filtered and subjected to density gradient centrifugation using 40% and 70% Percoll solutions. LPL sample was sorted as CD45+, lymphocyte gate, singlets, alive and CD3–CD19–.

source_name: Ileum LPL

value: Ileum LPL


title: blood sample from stimulated rat at 8 months post status epilepticus, LATE seizures development, biological replicate 1

value: whole blood


title: EZH2_ChIPseq__CRISPRa_48h_premature_HOXDeRNA_KD_rep2

value: CRISPRa with VPR-dCAS9 and sgRNAs for 2 weeks followed by siRNA treatment


title: Lung 1, control, donor


title: N-7420 NKp44+ IEL 2, control ileum

description: Single-cell suspension of the mucosal tissue from the terminal ileum was separated from the muscular layer and serosa and cut into small pieces. Intraepithelial lymphocyte cells were extracted by rotating the tissue at room temperature for 40 min in Hank's balanced salt solution, 10% FCS, and 5 mM ethylenediaminetetraacetic acid (EDTA). Cells were filtered through 100-μm cell strainers, and dithiothreitol (DTT) was added at a final concentration of 5 mM. Cells were filtered and subjected to density gradient centrifugation using 40% and 70% Percoll solutions. IEL ILCs  were sorted as CD45+, lymphocyte gate, singlets, alive and CD3–CD19– NKp44+CD103+.

source_name: Ileum IEL

value: Ileum IEL


title: blood sample from stimulated rat at 7 days post status epilepticus, LATE seizures development, biological replicate 3

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

value: Sprague Dawley


title: EZH2_ChIPseq__CRISPRa_48h_premature_HOXDeRNA_KD_rep1


title: blood sample from stimulated rat at 8 months post status epilepticus, LATE seizures development, biological replicate 2


title: blood sample from stimulated rat at 7 days post status epilepticus, LATE seizures development, biological replicate 2


title: parental - biol rep 1

description:
condition 1 - parental non treated
parental@S1

value: HCT116 Tet-OsTIR1 (parental)


title: N-1234 NKp44+ IEL 1, control ileum


title: 20231128_KSA102_NCIH211_FHD609_rep6


title: blood sample from stimulated rat at 7 days post status epilepticus, LATE seizures development, biological replicate 1


title: 20231128_KSA101_NCIH211_FHD609_rep5


title: CD-1818-2 IEL 2,Crohn's disease, pooled non-inflamed and inflamed ileum

description: Single-cell suspension of the mucosal tissue from the terminal ileum was separated from the muscular layer and serosa and cut into small pieces. Intraepithelial lymphocyte cells were extracted by rotating the tissue at room temperature for 40 min in Hank's balanced salt solution, 10% FCS, and 5 mM ethylenediaminetetraacetic acid (EDTA). Cells were filtered through 100-μm cell strainers, and dithiothreitol (DTT) was added at a final concentration of 5 mM. Cells were filtered and subjected to density gradient centrifugation using 40% and 70% Percoll solutions. IEL samples were sorted as CD45+, lymphocyte gate, singlets, alive and CD3–CD19–.


title: EZH2_ChIPseq__CRISPRa_48h_mature_HOXDeRNA_KD_rep1


title: blood sample from stimulated rat at 2 days post status epilepticus, LATE seizures development, biological replicate 3

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


title: EZH2_ChIPseq__CRISPRa_48h_mature_HOXDeRNA_KD_rep2


title: EZH2_ChIPseq__CRISPRa_40h_premature_HOXDeRNA_KD_rep2


title: 20231128_KSA099_NCIH211_FHD286_rep6


title: 20231128_KSA100_NCIH211_FHD609_rep4


title: N-1425-2 IEL 1, control ileum


title: Tonsil 5

description: Tonsils were obtained from elective tonsillectomies (Children’s Hospital in Saint Louis) and provided as surgical waste with no identifiers attached. Briefly, tissue was mechanically disrupted, passed through a 0.0059-inch opening sieve, and filtered extensively through 70-μm cell strainers. Cells were enriched via negative selection with CD3 and CD19 microbeads (Miltenyi), according to the manufacturer’s recommendations. Lineage negative cells were enriched using the EasySep™ Human Pan-ILC Enrichment Kit (StemCell Technologies). After enrichment of lineage negative cells, samples from tonsils were sorted as lymphocyte gate, singlets, alive and CD45hiCD3–CD19–CD161+CD127+.

source_name: Tonsil

value: Tonsil


title: EZH2_ChIPseq__CRISPRa_32h_premature_HOXDeRNA_KD_rep2


title: 20231128_KSA098_NCIH211_FHD286_rep5


title: blood sample from stimulated rat at 2 days post status epilepticus, LATE seizures development, biological replicate 1


title: Tonsil 4

description: Tonsils were obtained from elective tonsillectomies (Children’s Hospital in Saint Louis) and provided as surgical waste with no identifiers attached. Briefly, tissue was mechanically disrupted, passed through a 0.0059-inch opening sieve, and filtered extensively through 70-μm cell strainers. CD56+ cells were enriched via positive selection with CD56 microbeads (Miltenyi), according to the manufacturer’s recommendations. Cells were sorted and pooled: CD3-CD19-CD45+NKp44+CD56+.


title: blood sample from stimulated rat at 8 months post status epilepticus, ERLY seizures development, biological replicate 5


title: EZH2_ChIPseq__CRISPRa_24h_premature_HOXDeRNA_KD_rep2


title: EZH2_ChIPseq__CRISPRa_32h_premature_HOXDeRNA_KD_rep1


title: Tonsil 3


title: 20231128_KSA096_NCIH211_DMSO_rep7

value: DMSO


title: Tonsil 2


title: EZH2_ChIPseq__CRISPRa_40h_premature_HOXDeRNA_KD_rep1


title: EZH2_ChIPseq__CRISPRa_24h_premature_HOXDeRNA_KD_rep1


title: Tonsil 1


title: 20231128_KSA094_NCIH211_DMSO_rep5


title: 20231128_KSA095_NCIH211_DMSO_rep6


title: blood sample from stimulated rat at 8 months post status epilepticus, ERLY seizures development, biological replicate 2


title: blood sample from stimulated rat at 2 days post status epilepticus, LATE seizures development, biological replicate 2


title: blood sample from stimulated rat at 8 months post status epilepticus, ERLY seizures development, biological replicate 3


title: 20231012_KSA081_NCIH1048_FHD609_rep6


title: EZH2_ChIPseq__CRISPRa_24h_rep2

value: CRISPRa with VPR-dCAS9 and sgRNAs for 2 weeks


title: Blood 2

description: Blood samples were collected from discarded leukoreduction system (LRS) chambers from apheresis procedures. Blood lymphocytes were purified via a Ficoll density gradient centrifugation. Lineage negative cells were enriched using the EasySep™ Human Pan-ILC Enrichment Kit (StemCell Technologies). After enrichment of lineage negative cells, samples from blood  were sorted as lymphocyte gate, singlets, alive and CD45hiCD3–CD19–CD161+CD127+.

source_name: Blood

value: Blood


title: blood sample from stimulated rat at 8 months post status epilepticus, ERLY seizures development, biological replicate 1


title: 20231012_KSA080_NCIH1048_FHD609_rep5


title: EZH2_ChIPseq__CRISPRa_24h_rep1


title: blood sample from stimulated rat at 7 days post status epilepticus, ERLY seizures development, biological replicate 5


title: Blood 1


title: Patient c5, Control PBMCs CD45+, 3' GEX scRNAseq

city: Essen

first: Björn

last: Scheffler

address: Hufelandstrasse 55

department: DKTK Division Translational Neurooncology at the WTZ

institute: DKFZ (German Cancer Research Center)

description: 10x Genomics, 3' GEX

data_processing:
3' data read alignment of raw reads was performed to the hg38 human reference genome (2020) and feature-barcode matrices were obtained according to the Cell Ranger pipeline (7.0.1) set to default parameters.
5' data, integrating V(D)J repertoire and gene expression data were processed utilizing the cellranger multi pipeline with the hg38 human reference genome (2020), and the human V(D)J reference (GRCh38) provided by 10x Genomics. Further analyses of count matrices were performed in the R environment (v4.2.0) using the raw file output of the 3? data and the filtered multi pipeline output of the 5'.
Assembly: hg38/GRCh38
Supplementary files format and content: CellRanger (7.0.1) Output, raw tab-separated feature and barcode files, raw matrix files; filtered feature bc martix; comma-separated filtered contig annotations files.

source_name: PBMCs

extract_protocol:
Processing of fresh samples occurred within 30 min after surgical resection and transfer in ice-cold transport media. Tumor tissues were minced and single cell suspensions prepared by homogenizing the tissue in Iscove's Modified Dulbecco's Medium (IMDM, Gibco) with 0.11 DMC U/mL neutral protease (NP, Nordmark Biochemicals, Germany) at 37°C for approximately 30 minutes in a shaker-incubator. Tissue dissociation was supported by gentle intermittent resuspension. Bone chips were continuously flushed with pre-warmed (37°C) 0.11 DMC U/mL NP in IMDM for 10-15 minutes in 15 mL canonical tubes to facilitate vital cell release. Cell suspensions were filtered by a 35 µm cell strainer. PBMC and BMMC were isolated from venous blood or from distal hip bone marrow. Aspirates were collected in 7.5 mL EDTA vacutainers or heparinized tubes, respectively. PBMC and BMMC were seprarated using the high-density medium Histopaque®-1077 by density centrifugation according to the manufacturer's suggestions.
For subsequent 10x Genomics processing, respective single cell suspensions were washed in PBS supplemented with 0.04% BSA and enriched for CD45+ cells by magnetic cell separation. Indicated samples underwent additional magnetic depletion of myeloid cells (CD14 negative flowthrough) prior to 10x Genomics processing.
Samples were processed using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) (10x Genomics, #CG0000315 Rev C) or the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) (#CG0000331 Rev E), following the manufacturer's instructions. Following a standard quality control (2100 Bioanalyzer, Agilent), paired-end sequencing of pooled libraries was performed using a NovaSeq 6000 system (Illumina).

value: CD45+ cells

value: PBMCs

tag: disease

value: non-neoplastic intracranial disease


title: EZH2_ChIPseq__CRISPRa_16h_rep2

value: NHA


title: 20231012_KSA079_NCIH1048_FHD609_rep4


title: blood sample from stimulated rat at 8 months post status epilepticus, ERLY seizures development, biological replicate 4


title: 20231128_KSA097_NCIH211_FHD286_rep4


title: Patient c5, Control Cranial Bone CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX

source_name: Cranial Bone

value: Cranial Bone


title: blood sample from stimulated rat at 7 days post status epilepticus, ERLY seizures development, biological replicate 4


title: blood sample from stimulated rat at 7 days post status epilepticus, ERLY seizures development, biological replicate 3


title: Patient c4, Control PBMCs CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX


title: EZH2_ChIPseq__CRISPRa_8h_rep2

value: Immortalized human astrocytes (Sonoda 2001)

value: immortalized by E6/E7/hTERT


title: 20231012_KSA077_NCIH1048_FHD286_rep5


title: 20231012_KSA078_NCIH1048_FHD286_rep6


title: Patient c4, Control Cranial Bone CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX


title: EZH2_ChIPseq__CRISPRa_8h_rep1


title: blood sample from stimulated rat at 7 days post status epilepticus, ERLY seizures development, biological replicate 2

value: whole blood


title: 20231012_KSA076_NCIH1048_FHD286_rep4


title: blood sample from stimulated rat at 7 days post status epilepticus, ERLY seizures development, biological replicate 1


title: Patient 9, PBMCs CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX

value: glioblastoma


title: blood sample from stimulated rat at 2 days post status epilepticus, ERLY seizures development, biological replicate 3


title: Patient 9, Tumor CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX

source_name: Tumor

value: Tumor


title: blood sample from stimulated rat at 2 days post status epilepticus, ERLY seizures development, biological replicate 2

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


title: 20231012_KSA074_NCIH1048_DMSO_rep6


title: 20231012_KSA075_NCIH1048_DMSO_rep7


title: EZH2_ChIPseq__CRISPRa_0h_rep1


title: EZH2_ChIPseq__CRISPRa_0h_rep2


title: Patient 9, Cranial Bone CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX


title: 20231012_KSA073_NCIH1048_DMSO_rep5


title: EZH2_ChIPseq__CRISPRa_16h_rep1


title: NHA_ChIP_EZH2_overexpressed_rep1


title: blood sample from control rat (EARLY vs. LATE) at 8 months, biological replicate 8

value: Sprague Dawley


title: Patient 8, Cranial Bone CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX


title: 20231109_KS165_ChIP_FHD609_H3K27ac_DX2_rep1

value: H3K27ac (CST, D5E4, Lot 8)


title: Patient 7, Cranial Bone CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX


title: NHA_ChIP_EZH2_Control_rep2


title: Patient 2, Tumor CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX


title: blood sample from control rat (EARLY vs. LATE) at 8 months, biological replicate 6


title: NHA_ChIP_EZH2_Control_rep1


title: blood sample from control rat (EARLY vs. LATE) at 8 months, biological replicate 7


title: MOLM13-RES_RNA_GIL+MET_rep3

city: Monrovia

first: Jianjun

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
Human genome indices were generated utilizing gene annotations from gencode v43 and the human GRCh38 reference genome sequences. STAR (version 2.7.2b) and RSEM (version 1.2.31) software were employed for this purpose. Subsequently, raw reads obtained from RNA-seq underwent quality control assessment using FastQC (version 0.11.5, available at https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), followed by mapping to the reference genome using the previously constructed indices via STAR. After alignment, RSEM was utilized to estimate gene read counts.
For the analysis of differentially expressed genes, a criterion was applied to retain genes with read counts greater than 0 in at least 50% of the samples. These retained genes were then subjected to DESeq2 analysis, employing shrinkage estimators for dispersion and fold change. Gene enrichment and Gene Set Enrichment Analysis (GSEA) were carried out using the clusterProfiler R package.

growth_protocol: MOLM13-RES cells were cultured in RPMI 1640 medium supplemented with 10% FBS

extract_protocol:
Qiagen miRNeasy Mini Kit
Each RNA sample was supplemented with Mix1 or Mix2 in accordance with Life Technologies' guidelines, targeting an approximate 1% representation of the total RNA-Seq reads mapped to the 92 ERCC control sequences. In total, 300 ng of RNA from each sample was used for this purpose.
Sequencing was performed using an Illumina®HiSeq 2500 system, utilizing a 51 bp single-end configuration via the TruSeq SR Cluster Kit V4-cBot-HS (Illumina, San Diego, CA, USA).

treatment_protocol: Treat with DMSO, Gilteritinib, Metformin and Gilteritinib+Metformin for 24 hours, respectively

value: acute myeloid leukemia

value: Gilteritinib+Metformin


title: 20231109_KS158_ChIP_DMSO_H3K27ac_DX2_rep2

value: DMSO


title: NHA_ChIP_EZH2_overexpressed_rep2

value: CRISPRa with VPR-dCAS9 and sgRNAs for 2 weeks


title: blood sample from control rat (EARLY vs. LATE) at 8 months, biological replicate 5


title: Patient 2, Cranial Bone CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX

value: CD45+ cells


title: MOLM13-RES_RNA_GIL+MET_rep2


title: blood sample from stimulated rat at 2 days post status epilepticus, ERLY seizures development, biological replicate 1


title: 20231109_KS157_ChIP_DMSO_POU2F3_DX2_rep2

value: POU2F3 (CST, E5N2D, Lot 1)


title: Patient 1, PBMCs CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX

value: PBMCs


title: blood sample from control rat (EARLY vs. LATE) at 8 months, biological replicate 4


title: MOLM13-RES_RNA_GIL+MET_rep1


title: HUVEC_flow_APLNR_siRNA_rep3

description:
Flow_KD-3
Table_FPKM_siRNA.txt

data_processing:
Sequenced reads were aligned to the human (hg38) reference genome with TopHat (version 2.1.1)
The aligned reads were used for the transcript quantification by using HTSeq-count (version 0.6.1)
DESeq2 was used to identify differentially expressed genes across the samples
Assembly: hg38
Supplementary files format and content: txt file of FPKM values for each gene and sample

source_name: HUVEC

growth_protocol: HUVEC were maintained in endothelial cell proliferation media from provitro

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
library was generated using NEBNext (NEB, E7760L) as manufacturer's protocols.

treatment_protocol: Flow was treated utilizing ibid flow system for total 18hrs and Apelin 13 was treated for 6hrs. To achieve knockdown of APLNR, siAPLNR(Invitrogen, HSS100324) was treated using RNAiMAX(Invitrogen, 13778075) and Opti-MEM

value: HUVEC

value: Human umbilical cord vein endothelial cell

value: wildtype

value: APLNR siRNA + flow 15dyn/cm2


title: blood sample from control rat (EARLY vs. LATE) at 8 months, biological replicate 3

value: whole blood


title: Patient 1, Tumor CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX

value: glioblastoma


title: blood sample from control rat (EARLY vs. LATE) at 8 months, biological replicate 2


title: Patient 1, Cranial Bone CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX

value: Cranial Bone


title: 20231109_KS164_ChIP_FHD609_POU2F3_DX2_rep2


title: MOLM13-RES_RNA_MET_rep3

value: Metformin


title: peripheral blood cells, inactive LN 13

city: Taipei

first: Jyh-Hong

last: Lee

address: 8 Chung-Shan South Road

institute: National Taiwan University Hospital

data_processing:
Bases with low quality and the adaptor sequences from the raw data were removed using the program Fastp (version 0.20.0). The filtered reads were aligned to the reference genomes using HISAT2 (version 2.1.0).  removed using the program Fastp (version 0.20.0). The filtered reads were aligned to the reference genomes using HISAT2 (version 2.1.0).
The software FeatureCounts (v2.0.1) in the Subread package was used to quantify gene abundance. DEGs were identified using DESeq2 (version 1.28.0) or EdgeR (version 3.36.0) 58,59, depending on the presence or absence of biological replicates.

source_name: peripheral blood cell

extract_protocol:
Purified RNA was used to prepare a sequencing library using the TruSeq  Purified RNA was used to prepare a sequencing library using the TruSeq stranded mRNA library prep kit.
mRNA was purified from total RNA (1 μg) on oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. First-strand cDNA was synthesized using reverse transcriptase and random primers. After generating double-strand cDNA and adenylation of the 3’ ends of the DNA fragments, the adaptors were ligated and then the samples were purified using the AMPure XP system.

value: peripheral blood cell

value: inactive LN

tag: time


title: blood sample from control rat (EARLY vs. LATE) at 8 months, biological replicate 1

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

value: Sprague Dawley


title: 20231109_KS160_ChIP_DMSO_Input_DX2_rep3

value: DMSO


title: MOLM13-RES_RNA_MET_rep2

value: acute myeloid leukemia


title: HUVEC_flow_APLNR_siRNA_rep1

description:
Flow_KD-1
Table_FPKM_siRNA.txt


title: Patient 2, PBMCs CD45+, 3' GEX scRNAseq

description: 10x Genomics, 3' GEX

value: CD45+ cells


title: MOLM13-RES_RNA_MET_rep1


title: blood sample from control rat (EARLY vs. LATE) at 7 days, biological replicate 6


title: blood sample from control rat (EARLY vs. LATE) at 7 days, biological replicate 7


title: HUVEC_flow_Cont_siRNA_rep2

description:
Flow_Cont-2
Table_FPKM_siRNA.txt

value: Cont siRNA + flow 15dyn/cm2


title: MOLM13-RES_RNA_GIL_rep2

value: Gilteritinib


title: HUVEC_flow_Cont_siRNA_rep1

description:
Flow_Cont-1
Table_FPKM_siRNA.txt

value: HUVEC


title: HUVEC_flow_APLNR_siRNA_rep2

description:
Flow_KD-2
Table_FPKM_siRNA.txt

value: Human umbilical cord vein endothelial cell


title: peripheral blood cells, inactive LN 11


title: HUVEC_static_APLNR_siRNA_rep3

description:
Sta_KD-3
Table_FPKM_siRNA.txt

value: wildtype

value: APLNR siRNA


title: MOLM13-RES_RNA_DMSO_rep3


title: blood sample from control rat (EARLY vs. LATE) at 7 days, biological replicate 5

value: whole blood


title: MOLM13-RES_RNA_GIL_rep1


title: peripheral blood cells, inactive LN 10


title: blood sample from control rat (EARLY vs. LATE) at 7 days, biological replicate 4


title: peripheral blood cells, inactive LN 9


title: MOLM13-RES_RNA_DMSO_rep2


title: HUVEC_static_APLNR_siRNA_rep1

description:
Sta_KD-1
Table_FPKM_siRNA.txt


title: blood sample from control rat (EARLY vs. LATE) at 7 days, biological replicate 2


title: blood sample from control rat (EARLY vs. LATE) at 7 days, biological replicate 3


title: peripheral blood cells, inactive LN 8


title: peripheral blood cells, inactive LN 7


title: HUVEC_flow_Cont_siRNA_rep3

description:
Flow_Cont-3
Table_FPKM_siRNA.txt


title: HUVEC_static_APLNR_siRNA_rep2

description:
Sta_KD-2
Table_FPKM_siRNA.txt


title: peripheral blood cells, inactive LN 6


title: MOLM13-RES_RNA_GIL_rep3


title: MOLM13-RES_RNA_DMSO_rep1


title: blood sample from control rat (EARLY vs. LATE) at 7 days, biological replicate 1


title: HUVEC_static_Cont_siRNA_rep3

description:
Sta_Cont-3
Table_FPKM_siRNA.txt

value: Cont siRNA


title: peripheral blood cells, inactive LN 12


title: HUVEC_static_Cont_siRNA_rep2

description:
Sta_Cont-2
Table_FPKM_siRNA.txt


title: HUVEC_static_Cont_siRNA_rep1

description:
Sta_Cont-1
Table_FPKM_siRNA.txt


title: h1076si1

city: shenzhen

first: junquan

last: weng

address: Dongmen North Road

country: China

institute: Shenzhen People's Hospital

data_processing:
The libraries were sequenced in paired-end mode on one lane of the Illumina HiSeq2500 instrument.
R software was used to analyze differentially expressed genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
The total RNA of cells was obtained according to the instructions provided by the TRIZOL reagent
The Illumina TruSeq Stranded Total RNA Library Prep Kit (RS-122-2201) was used to construct the sequencing libraries.

value: HNSCC cells

value: SCC9 cell line


title: peripheral blood cells, inactive LN 4

value: peripheral blood cell


title: h1076C


title: HUVEC_flow_A13_rep3

description:
A13-3
Table_FPKM_A13.txt

value: flow 15dyn/cm2, Apelin 13(1uM)


title: blood sample from control rat (EARLY vs. LATE) at 2 days, biological replicate 6

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


title: h1076si2


title: peripheral blood cells, inactive LN 3

value: inactive LN


title: blood sample from control rat (EARLY vs. LATE) at 2 days, biological replicate 5

value: Sprague Dawley


title: Root, 5 dpg, PLT3

city: Wageningen

first: Merijn

last: Kerstens

address: Droevendaalsesteeg 1

department: Plant Developmental Biology

country: Netherlands

institute: Wageningen University & Research

data_processing:
Adapter trimming was performed with fastp v0.23.2, specifying --trim_poly_g and Illumina TruSeq adapters.
Reads were mapped to the TAIR10 genome with BWA-MEM v0.7.17.
Unmapped, duplicate, and mapping quality < 30 reads were removed with SAMtools v1.15 and Sambamba v0.6.6.
Peaks were called with MACS3 v3.0.0a7 using the 3xFLAG-EGFP sample as background with a q-value = 0.05 cutoff.
Assembly: TAIR10
Supplementary files format and content: narrowPeak; file with peak coordinates (except EGFP sample)
Library strategy: DAP-seq

organism: Arabidopsis thaliana

source_name: Whole roots

growth_protocol: Col-0 was grown for five days on ½ Murashige and Skoog (MS) medium including vitamins and 3% plant agar.

extract_protocol:
Roots were cut on the agar, immediately frozen in liquid nitrogen, then ground with a metal ball in a TissueLyzer LT (Qiagen). CTAB DNA extraction was used on the remaining powder.
DAP-seq libraries were prepared according to Bartlett et al., (2017) with Illumina TruSeq barcodes. 200 ng of gDNA was used as starting material for the PLT3 and EGFP samples. Libraries were amplified using 20 cycles. Post-amplification libraries were size selected at >200 bp in length using AMPure XP beads.

value: Whole roots

tag: developmental stage

value: 5 dpg

tag: dap antibody

value: Anti-FLAG M2 Magnetic Beads (M8823 SIGMA)

tag: ecotype


title: blood sample from control rat (EARLY vs. LATE) at 2 days, biological replicate 4

tag: tissue


title: peripheral blood cells, inactive LN 1


title: HUVEC_flow_A13_rep1

description:
A13-1
Table_FPKM_A13.txt

tag: cell line


title: 4701_S16_IO_0019_Hsp90i

city: Durham

first: Ria

last: Goswami

state: NC

address: 2 Genome Ct. MSRBII

department: Duke Human Vaccine Institute

institute: Duke University

data_processing:
Adaptor trimming was performed with TrimGalore toolkit which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis.
Reads were mapped to the GRCh37v75 version of the huamn genome and transcriptome using the STAR RNA-seq alignment tool.  Reads were kept for subsequent analysis if they mapped to a single genomic location
Gene counts were compiled using the HTSeq tool.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment. The patient ID was used as a cofactor in the model when comparing the drug versus control samples.  The false discovery rate was calculated to control for multiple hypothesis testing.
Genome_build: Homo Sapiens GRch37v75
Supplementary_files_format_and_content: RawCounts_DMSO_Hsp90i_pediatric_tonsil.xlsx contains raw read counts for each sample, as quantified by HTSeq after alignment. Table contains columns consisting of GeneID (ENSEMBL ID), [{SAMPLE_NAME}, {SAMPLE_NAME…..].
Supplementary_files_format_and_content: DifferentialExpression_DMOS_SNX5422_HIV_pediatric_tonsil.xlsx contains differential expression and normalized count data for SNX-5422 treated vs. DMSO treated pediatric tonsil cells. The .xlsx file consists of columns GeneID - ENSEMBL Gene ID; GeneName - Gene common name/symbol; IsCoding - status of gene as protein coding or not; baseMean - average normalized expression value across samples; logFC - log2 fold-change of drug vs. control expression; lfcSE - standard error of log2 fold-change; stat - Wald test statistic; pvalue - P-value; pad - FDR corrected pvalue; <SampleID {donor}_{DMSO} {donor}_{SNX5422}.... > - DESeq2 normalized read counts per sample per gene

source_name: Human pediatric tonsils

growth_protocol: Discarded tonsil tissues from 8 independent donors <15 years of age were obtained through Duke University School of Medicine Biorepository and Precision Pathology Center (BRPC), during routine tonsillectomy.  Tonsil tissues were washed and minced in RPMI 1640 (Gibco), containing 1X antibiotic/antimycotic mixture (Gibco), 50μg/ml Gentamicin (Gibco), 10μg/ml Cephalothin (Sigma-Aldrich) and 5μg/ml Fluconazole (Sigma-Aldrich), and tonsillar mononuclear cells (TMCs) were isolated by filtering tonsillar tissue pieces through a 70-μm mesh filter, followed by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare, Waukesha, WI).

extract_protocol:
Total cellular RNA was extracted from TMCs using RNAeasy Mini kit (Qiagen).
Total RNA quality and quantity was assessed using the Agilent Bionalyzer 2100 and the Qubit fluorometer, respectively. Poly(A) mRNA capture and construction of stranded mRNA-seq libraries from intact total RNA (RIN >7) was achieved using the commercially available KAPA Stranded mRNA-Seq Kit. In brief, mRNA transcripts were first captured from 200ng of total RNA using magnetic oligo-dT beads, fragmented using heat and magnesium, and reverse transcribed to produce dscDNA. Illumina sequencing adapters were then ligated to the dscDNA fragments and amplified to produce the final RNA-seq library. Libraries were indexed using dual molecular indices allowing for multiple libraries to be pooled and sequenced on the same sequencing lane on a HiSeq 4000 Illumina sequencing platform. Before pooling and sequencing, fragment length distribution and library quality was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent Technologies).
All libraries were then pooled in equimolar ratio and sequenced. Multiplexing 8 libraries on one lane of an Illumina HiSeq 4000 flow cell yielded about 43 million 50bp sequences per sample. Once generated, sequence data was de-multiplexed and Fastq files generated using Bcl2Fastq conversion software provided by Illumina.

treatment_protocol: 5x105 TMCs were infected with 250ng p24 equivalent of the cell-free CCR5-tropic HIV-JRFL virus. After 24hr, virus- infected cells were treated with either 0.1% DMSO or 0.1μM Hsp90i, daily for 96 hrs.

value: Tonsillar monuclear cells

value: 0.1μM Hsp90i treated


title: HUVEC_flow_rep2

description:
Flow-2
Table_FPKM_A13.txt

value: HUVEC

value: Human umbilical cord vein endothelial cell

tag: genotype

value: flow 15dyn/cm2


title: blood sample from control rat (EARLY vs. LATE) at 2 days, biological replicate 3

value: whole blood


title: HUVEC_flow_rep3

description:
Flow-3
Table_FPKM_A13.txt

tag: cell type

value: wildtype


title: 4701_S15_IO_0019_DMSO

tag: treatment

value: 0.1% DMSO treated


title: peripheral blood cells, inactive LN 2


title: blood sample from control rat (EARLY vs. LATE) at 2 days, biological replicate 1

tag: strain


title: peripheral blood cells, inactive LN 5


title: HUVEC_flow_rep1

description:
Flow-1
Table_FPKM_A13.txt


title: peripheral blood cells, active LN 10

value: active LN


title: 4701_S14_IO_0018_Hsp90i


title: blood sample from control rat (EARLY vs. LATE) at 2 days, biological replicate 7


title: blood sample from stimulated rat at 8 days post status epilepticus, biological replicate 9


title: Root, 5 dpg, EGFP

value: 3xFLAG-EGFP (negative control)


title: HUVEC_flow_A13_rep2

description:
A13-2
Table_FPKM_A13.txt

value: flow 15dyn/cm2, Apelin 13(1uM)


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

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


title: HUVEC_static_rep2

description:
Cont-2
Table_FPKM_A13.txt


title: 4701_S13_IO_0018_DMSO


title: peripheral blood cells, active LN 8

value: peripheral blood cell


title: 4701_S12_IO_0016_Hsp90i


title: blood sample from control rat (EARLY vs. LATE) at 2 days, biological replicate 2

value: Sprague Dawley


title: blood sample from stimulated rat at 8 days post status epilepticus, biological replicate 7


title: peripheral blood cells, active LN 7


title: blood sample from stimulated rat at 8 days post status epilepticus, biological replicate 6


title: peripheral blood cells, active LN 12


title: HUVEC_static_rep1

description:
Cont-1
Table_FPKM_A13.txt


title: 4701_S11_IO_0016_DMSO


title: peripheral blood cells, active LN 11


title: Input of  ChIP_GFPCpA_GFPCpADAXXKO_02

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

data_processing:
Base-calling with Illumina run time analysis software 1.12.4.2
Alignment to hg38 using bowtie2 (ver 2.3.4.1).  Narrow peaks were called using the MACS2 (version 2.1.1.20160309)  callpeak function using the sample’s respective input dataset.
The replicate concordant peaks among replicates were combined to get the highly reproducible peaks using the IDR method.
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: HeLa

extract_protocol:
Samples were digested to mononucleosomes (~20 min MNase) and ChIP'ed using anti- CENP-A or S-tag antibodies. Purified DNA fragments were sent for sequencing.
Sequencing libraries were generated using Illumina TruSeq V3 protocol and subject to 101 bp paired-end sequencing on Illumina NextSeq2000.

value: HeLa

value: GFPCpA Transfected HeLa DAXX KO


title: GFPCpA ChIP in GFPCpA DAXXKO rep #2

value: Santa Cruz sc-9996


title: 4701_S10_IO_0015_Hsp90i

value: Tonsillar monuclear cells


title: peripheral blood cells, active LN 6


title: peripheral blood cells, active LN 5


title: blood sample from stimulated rat at 8 days post status epilepticus, biological replicate 4


title: 4701_S9_IO_0015_DMSO


title: peripheral blood cells, active LN 9


title: blood sample from stimulated rat at 8 days post status epilepticus, biological replicate 3


title: HUVEC_static_rep3

description:
Cont-3
Table_FPKM_A13.txt


title: GFPCpA ChIP in GFPCpA DAXXKO rep #1


title: peripheral blood cells, active LN 4


title: 4701_S8_IO_0014_Hsp90i

value: 0.1μM Hsp90i treated


title: Input of  ChIP_GFPCpA_GFPCpADAXXKO_01


title: blood sample from stimulated rat at 8 days post status epilepticus, biological replicate 2


title: peripheral blood cells, active LN 3


title: peripheral blood cells, active LN 2


title: nCpA ChIP in GFPCpA DAXXKO rep #2

value: Custom Rb CENP-A


title: blood sample from stimulated rat at 8 days post status epilepticus, biological replicate 1


title: 4701_S7_IO_0014_DMSO


title: Input of  ChIP_nCpA_GFPCpADAXXKO_02


title: blood sample from stimulated rat at 8 days post status epilepticus, biological replicate 5


title: peripheral blood cells, active LN 1


title: blood sample from control rat (CTRL vs. SE) at 8 months, biological replicate 8


title: 4701_S5_IO_0013_DMSO


title: 4701_S4_IO_0012_Hsp90i


title: MDA468-Input-rep2-3

city: Dubai

first: Fahad

last: Ali

address: Bldg 14, Dubai Healthcare City

country: United Arab Emirates

institute: Mohammed Bin Rashid University of Medicine and Health Sciences

data_processing:
Fastq trimming with trim_galore v0.6.4_dev -q 20 --paired
Mapped to hg38 with bowtie2 v2.4.1 snakemake wrapper 0.71.1/bio/bowtie2/align
Mapped reads filtered for paired end = True, mismatch NM:<=4, min fragment size >=-2000 max fragment size <=2000
Duplicate reads marked but not removed, and replicate bam files were merged and subsampled to 160 million reads, or total library size if less than 160 million reads.
Peaks called with macs2 v2.2.7.1, snakemake wrapper 0.66.0/bio/macs2/callpeak  -f BAMPE -g hs --SPMR --qvalue 0.05 --keep-dup all. Peaks with fold enrichment above local background > 5 were retained for downstream analysis.
Bigwig files: bedgraph files generated with bedtools genomecov scaled by library size, converted to bw with ucsc bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: Macs2 narrowpeak files
Supplementary files format and content: Bigwig

source_name: Cell line

extract_protocol: Not provided

value: Cell line

value: Breast cancer

tag: antibody

value: FOXC1 WT


title: Input of ChIP_nCpA_GFPCpADAXXKO_01


title: MDA468-Input-rep1


title: nCpA ChIP in GFPCpA DAXXKO rep #1


title: 4701_S3_IO_0012_DMSO


title: blood sample from control rat (CTRL vs. SE) at 8 months, biological replicate 6

value: whole blood


title: blood sample from control rat (CTRL vs. SE) at 8 months, biological replicate 7


title: CpATAP ChIP in GFPCpAHeLa rep #2

value: GFPCpA Transfected HeLa


title: MDA468-Chip-rep3


title: 4701_S2_IO_0011_Hsp90i


title: MDA468-Chip-rep2


title: blood sample from control rat (CTRL vs. SE) at 8 months, biological replicate 5


title: 4701_S1_IO_0011_DMSO

value: 0.1% DMSO treated


title: Input of ChIP_CpATAP_GFPCpAHeLa_02


title: blood sample from control rat (CTRL vs. SE) at 8 months, biological replicate 3


title: 4701_S6_IO_0013_Hsp90i


title: MDA468-Chip-rep1


title: CpATAP ChIP in GFPCpAHeLa rep #1


title: blood sample from control rat (CTRL vs. SE) at 8 months, biological replicate 4


title: blood sample from control rat (CTRL vs. SE) at 8 months, biological replicate 2


title: MDA231-Input-rep2-3


title: control rep6

city: BOSTON

first: CHANG

last: CAO

address: 185 CAMBRIDGE ST.

department: CENTER FOR GENOMIC MEDICINE

institute: Mass General Brigham

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Reads were trimmed by trimmomatic v0.36 and high-quality reads were aligned to mouse reference genome (GRCm38.p6) using STAR 2.5.2b.
The reads counts were calculated by featureCounts software from the Subread package v1.5.2.
Assembly: GRCm38.p6
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: placenta

extract_protocol:
RNA was extracted from placenta using Rneasy plus mini kit (Qiagen, cat. no. 73404).
NEBNext Ultra RNA Library Prep Kit for Illumina (cat. no. E7770) was used for the construction of sequencing libraries following manufacturer’s instructions.

value: placenta

value: control

tag: Sex

value: female

value: Embryonic day 15.5


title: knockout rep14

value: KO

value: male


title: Input of ChIP_CpATAP_GFPCpAHeLa_01

value: HeLa


title: nCpA ChIP in GFPCpAHeLa rep #2


title: MDA231-Input-rep1


title: knockout rep13


title: MDA231-Chip-rep3


title: knockout rep12


title: blood sample from stimulated rat at 7 days post status epilepticus, biological replicate 8

extract_protocol: Blood drawn from rat tail vein was drawn at 3 time points and snap frozen. miRNA was isolated from 500 µl of blood using miRNeasy Kit (#217084, Qiagen). The whole miRNA isolation procedure was performed as described by the kit manufacturer. In the end of the procedure RNA was eluted to 100 µl of RNAse free water, aliquoted and stored in -80°C.

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

value: Sprague Dawley


title: nCpA ChIP in GFPCpAHeLa rep #1


title: knockout rep11


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


title: MDA231-Chip-rep2


title: MDA231-Chip-rep1


title: Input of ChIP_nCpA_GFPCpAHeLa_01


title: blood sample from stimulated rat at 7 days post status epilepticus, biological replicate 6


title: control rep5


title: CpATAP ChIP in DAXXKOHIRAKD rep #2

value: Trasfected DAXX KO + HIRA KD cells

value: Millipore Cat #MAC115


title: blood sample from stimulated rat at 7 days post status epilepticus, biological replicate 5


title: knockout rep10


title: Input of ChIP_CpATAP_DAXXKOHIRAKD_02


title: Hs578-Input-rep2-3

value: Cell line


title: Hs578-Input-rep1

value: Breast cancer


title: control rep4


title: Hs578-Chip-rep3

value: FOXC1 WT


title: blood sample from stimulated rat at 7 days post status epilepticus, biological replicate 4

value: whole blood


title: Input of ChIP_CpATAP_DAXXKOHIRAKD_01


title: blood sample from control rat (CTRL vs. SE) at 8 months, biological replicate 1


title: CpATAP ChIP in DAXXKOHIRAKD rep #1

value: Millipore Cat #MAC113


title: knockout rep9


title: Input of ChIP_nCpA_GFPCpAHeLa_02

value: GFPCpA Transfected HeLa


title: control rep3

value: placenta


title: blood sample from stimulated rat at 7 days post status epilepticus, biological replicate 3


title: blood sample from stimulated rat at 7 days post status epilepticus, biological replicate 2


title: nCpA ChIP in DAXXKOHIRAKD rep #2

value: DAXX KO + HIRA KD cells

value: Custom Rb CENP-A


title: blood sample from stimulated rat at 7 days post status epilepticus, biological replicate 1


title: Hs578-Chip-rep1


title: Input of ChIP_nCpA_DAXXKOHIRAKD_02


title: knockout rep7

value: Embryonic day 15.5


title: blood sample from control rat (CTRL vs. SE) at 7 days post status epilepticus, biological replicate 7


title: knockout rep8

value: KO


title: Hs578-Chip-rep2


title: nCpA ChIP in DAXXKOHIRAKD rep #1


title: blood sample from control rat (CTRL vs. SE) at 7 days post status epilepticus, biological replicate 6


title: Bt549-Input-rep1


title: Bt549-Input-rep2-3


title: control rep2

value: control

value: female


title: Input of ChIP_nCpA_DAXXKOHIRAKD_01

value: HeLa


title: blood sample from control rat (CTRL vs. SE) at 7 days post status epilepticus, biological replicate 5

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

value: Sprague Dawley


title: control rep1


title: Bt549-Chip-rep3


title: CpATAP ChIP in DAXXKO rep #2

value: Transfected DAXX KO cells

value: Millipore Cat #MAC115


title: Bt549-Chip-rep2

value: Cell line

value: Breast cancer


title: blood sample from control rat (CTRL vs. SE) at 7 days post status epilepticus, biological replicate 4

value: whole blood


title: Input of ChIP_CpATAP_DAXXKO_02


title: blood sample from control rat (CTRL vs. SE) at 7 days post status epilepticus, biological replicate 3


title: knockout rep6

value: male


title: Donor 3, B cells, BTKi, anti-BCR

city: Philadelphia

first: Diego

middle: A

last: Espinoza

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

description: Donor 3 aBCR BTKi

data_processing:
Data was analyzed using online platform Basepair (Link: https://www.basepairtech.com/)
Sequence reads were trimmed and mapped to hg19 using STAR algorithm (default settings on the platform)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

growth_protocol: B cells were maintained in X-vivo 10 Medium supplement with Glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Vehicle (DMSO), BTK inhibitor (1uM) or GSK3 inhibitor (1uM) were added to B cells 30 min. B cells treated with Vehicle or BTK inhibitor was either left alone or stimulated by anti-BCR for 24hrs.

tag: individual

value: Donor 3

value: Blood

value: B cells

tag: disease state

value: Healthy

value: Anti-BCR BTKi


title: knockout rep5

value: placenta

value: KO

value: Embryonic day 15.5


title: CpATAP ChIP in DAXXKO rep #1

value: HeLa

value: Millipore Cat #MAC113


title: blood sample from control rat (CTRL vs. SE) at 7 days post status epilepticus, biological replicate 1

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.
gc-rma signal

tag: blood collection tube coating

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

value: Sprague Dawley


title: Input of ChIP_CpATAP_DAXXKO_01

value: Transfected DAXX KO cells

tag: chip antibody


title: nCpA ChIP in DAXXKO rep #2

value: DAXX KO cells

value: Custom Rb CENP-A


title: Input of ChIP_nCpA_DAXXKO_02


title: knockout rep2


title: blood sample from stimulated rat at 2 days post status epilepticus, biological replicate 5

value: whole blood


title: nCpA ChIP in DAXXKO rep #1


title: knockout rep1

value: female


title: blood sample from stimulated rat at 2 days post status epilepticus, biological replicate 4


title: Donor 1, B cells, Vehicle, anti-BCR

description: Donor 1 aBCR Vehicle

value: Donor 1

value: Anti-BCR Vehicle


title: Input of ChIP_nCpA_DAXXKO_01


title: Bt549-Chip-rep1

value: Cell line

value: Breast cancer

value: FOXC1 WT


title: blood sample from stimulated rat at 2 days post status epilepticus, biological replicate 3