title: C7-April-2023-Plate4-PEM_S299

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: D4-April-2023-Plate4-PEM_S306

status: Public on Dec 02 2024

type: SRA

city: Edmonton

first: Patrick

middle: E.

last: MacDonald

state: Alberta

address: 6-040 Li Ka Shing Centre

department: Pharmacology

country: Canada

institute: University of Alberta

library_source: transcriptomic single cell

data_processing:
Fastq files were trimmed using TrimGalore version 0.6.5 with auto-detection of adapter sequence
Aligned to the GRCh38 human genome, Ensembl release 104,and counted using STAR version 2.7.11a
Counts were decontaminatedusing celda (1.20.0) decontX in R (4.4.1)
Assembly: GRCh38, Ensembl release 104
Supplementary files format and content: Combined csv count table of all cells; raw counts with ENSG identifiers
Supplementary files format and content: Processed RData file containing a Seurat object with all cells, with gene symbols, decontaminated and normalized counts
Supplementary files format and content: Python h5ad file containing all cells, with gene symbols, decontaminated counts

molecule: total RNA

organism: Homo sapiens

source_name: islets

extract_protocol:
Isolated human islets were dispersed to single cells, and whole cell patch clamp electrophysiology was performed. Following, the cells were collected and sent for scRNA-seq (SmartSeq).
SmartSeq3

tag: donor

tag: plate

tag: cellid

tag: cell type

value: islets

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record

tag: age

tag: Sex

value: male

tag: bmi


title: E7-April-2023-Plate4-PEM_S319

value: ND

value: female


title: Carotid Artery Ligation - Control rep 3

city: shanghai

first: shasha

last: sun

address: No. 1665 Kangjiang Road

country: China

institute: Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine

library_source: transcriptomic

data_processing:
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data. HISAT2 was used to align the clean reads to the mouse reference genome mm9 with default pa- rameters. HTSeq was subsequently employed to convert aligned short reads into read counts for each gene model.
Differential expression was assessed by DEseq/DESeq2/edgeR/DEGseq using read counts as input. The Benjamini–Hochberg multiple test correction method was enabled. Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.05.
All the differentially expressed genes were used for heat map analysis and KEGG ontology enrichment analyses. For KEGG enrichment anal- ysis, a P-value < 0.05 was used as the threshold to determine significant enrichment of the gene sets.
Assembly: mm9
Supplementary files format and content: gene_exp.xlsx

molecule: polyA RNA

organism: Mus musculus

source_name: Carotid Artery

extract_protocol:
Total mRNA was extracted using the Trizol Reagent (Thermo, 15596026).
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the man- ufacturer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately.

tag: tissue

value: Carotid Artery


title: EPIC01RNA_Healthy_Control

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

country: USA

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA sequencing data was processed using the nf-core/rnaseq pipeline (version 3.8.1)
The quality of sequences were assessed using FASTQC (verson 0.11.9) and the low quality bases and adapter sequences were then trimmed and filtered using Cutadapt (version 3.4). Ribosomal RNA sequences were subsequently removed from the aligned data using SortMeRNA (version 4.3.4
The resulting alignments were sorted and indexed using SAMtools (verson 1.15.1)
the quality of the RNA sequencing data, several tools were employed, including RseqQC (version 3.0.1), Qualimap (version 2.2.2-dev), dupRadar (version 1.18.0), and Preseq (version 3.1.1).
differential gene expression analysis was performed using DESeq2 (version 1.30.1)

source_name: Saliva

extract_protocol:
Total RNA was extracted using Qiagen RNeasy purification procedure and mRNA was purified using oligo(dT)-attached magnetic beads.
First, the mRNA molecules were fragmented and converted into cDNA through reverse transcription using random hexamer primers. Following this, the cDNA fragments were processed by end-repair, adenylation, and adapter ligation, and then amplified through PCR to enrich the cDNA fragments. After purification, the library's quality was assessed using the Agilent Technologies 2100 bioanalyzer. Finally, the double-stranded PCR products were denatured, circularized using a splint oligo sequence, and amplified with phi29 DNA polymerase to generate DNA nanoballs (DNBs), each containing more than 300 copies of a single molecule, forming the final library.

tag: race

value: Black

value: Female

tag: condition

value: Healthy

value: Saliva


title: Carotid Artery Ligation - Nrf3 Knockout rep 1


title: C6-April-2023-Plate4-PEM_S298

tag: cellsize f


title: SupT1 infected, Nanopore, 8hpi, rep1

city: Würzburg

first: Neva

last: Caliskan

address: Josef-Schneider-Str. 2/D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description:
Library name: Nanopore_8h_1
Nanopore_8h_1
Nanopore_seq_HCMV_splice_isoforms.xlsx
HIV1_NL43-corrected_w_TSO.fa
HIVNL43_all_iso.bed
HIVNL43_all_iso.gtf

data_processing:
DMS-Seq: Reads were trimmed using cutadapt v 1.18 and aligned to the reference sequence using bowtie2. Further analysis was carried out using the rf-count and rf-norm modules of RNA Framework package v2.7.2.
Nanopore: Acquired Nanopore data was base called in “sup” mode with Guppy version 6.5.7 and filtered for minimal qscore of 10. Isoforms were identified with Isoquant version 3.3.0 using a GTF file containing all previously reported isoforms (HIVNL43_all_iso.gtf). Only uniquely identified isoforms were counted. To identify those isoforms that may express the novel peptides, the nucleotide sequence of all reported isoforms was searched for the iORFs or/and first AUG and in silico translated using Biopython 1.79 in a custom python script.
Assembly: GCF_000001405.36, AF324493
Supplementary files format and content: DMS-Seq: The mutationMap files are in RC (RNA Count) format according to the RNA framework standard (https://rnaframework-docs.readthedocs.io/en/latest/rf-count/).
Supplementary files format and content: Nanopore: The enclosed excel file contains a list of all potential HIV transcripts isoforms with Nanopore read-counts supporting each isoform. Furthermore, information on the two identified iORFs are indicated for each isoform. The enclosed fasta file, bed file and gtf file were used for the transcript isoform deconvolution.

molecule: cytoplasmic RNA

organism:
Homo sapiens
Human immunodeficiency virus 1

extract_protocol:
Nanopore: To analyze the HIV transcriptome in infected SupT1 cells at 8, 16 and 24 hpi 30 μg of Trizol extracted RNA was treated with 3 μL of Turbo DNase in 150 μL total volume for 30 min at 37 °C. RNA was purified with Macherey-Nagel PCR Clean-up kit using NTC buffer according to manufacturer’s instructions.
DMS-Seq: For in vivo DMS modification of HIV-1 gRNA, 40 mL of SupT1 cells were infected with VSV pseudotyped HIV-1 (ΔEnv). 24 h post infection, 5 mL of cells were probed with 85 mM of dimethyl sulfate (DMS) for 6 min at 37°C, placed immediately on ice and the reaction was quenched by addition of 100 mM of β-mercaptoethanol. Cells were pelleted by centrifugation for 5 min at 400 g, 4°C and washed with PBS. The cell pellet was directly resuspended in 1 mL of TRI reagent (Sigma-Aldrich) and total RNA was extracted according to the manufacturer’s instructions. Ten μg of total cellular RNA were treated with 4 U of TURBO DNase (ThermoFisher Scientific) for 30 min at 37°C. The RNA was purified using NucleoSpin Gel and PCR Clean- Up (Macherey-Nagel, NTC buffer), according to the manufacturer´s instructions.
Nanopore: 1 ug of RNA was reverse transcribed with SuperScript IV (Invitrogen) using primer GTACAGGCAAAAAGCAGCTGCT according to manufacturer’s instructions in a 10 μL reaction. The cDNA was purified with Macharey-Nagel PCR Clean-up kit using NTC buffer and eluted in 20 μL H2O. RNA was digested in a 10 μL reaction containing 3 μL cDNA product with 0.5 μL RNase A (NEB) and 0.5 μL RNase T1 (NEB) and incubation at 37 °C for 30 min, followed by column purification as described above. Next, PCR amplification of 20 μL of the RNase-digested, purified cDNA in a 100 μL reaction with Primestar GXL (Takara) using primers GGTCTCTCTGGTTAGACCAGATCTGAG and GTACAGGCAAAAAGCAGCTGCT was performed with 12 cycles of denaturation at 98 °C for 10 sec, annealing at 55 °C for 15 sec and extension at 68 °C for 2 min. PCR products were purified with a 1:1 ratio of Mag-Bind TotalPure NGS beads (Omega Bio-Tek) according to the manufacturer’s recommendations and eluted in 14 μL H2O. Next, 80 ng PCR product in 5 μ was end repaired by addition of 0.7 μL NEBNext End Repair buffer (NEB) and 0.3 μL NEBNext End Repair Enzyme Mix (NEB), mixed thoroughly by pipetting and incubated for 5 min at 25 °C followed by 5 min at 65 °C. Nanopore native ligation barcoding barcodes (ONT SQK-NBD114.96) were ligated by transfer of 3.5 μL of end-repaired product into a new well, followed by addition of 1.5 μL of barcode and 5 μL of Blunt/TA ligation master mix (NEB). After incubation at 25 °C for 20 min, 1 μL of EDTA (SQK802 NBD114.96) was added, samples were pooled and purified with 0.4 volumes of Ampure XP beads (SQK-NBD114.96). Barcoded DNA was eluted in 31 μL of H2O. To ligate the motor protein 30 μL of the barcoded DNA was mixed with 10 μ of 5x Quick Ligation Buffer (NEB), 5 μL of NA and 5 μL of high concentration T4 DNA ligase (NEB) was added. After incubation for 20 min at 25 °C, 0.4 volumes of Ampure XP beads (SQK-NBD114.96) were added, beads were washed twice with 125 μL Short Fragment Buffer (SFB, SQK-NBD114.96) and eluted in 14 μL of Elution Buffer (EB, SQK-NBD114.96). DNA concentration was quantified with AccuClear Ultra High Sensitivity dsDNA Quantitation Solution (Biotium) and 10 fmol was prepared for sequencing on a R10.4.1 Flongle flow cell (FLO-FLG114) by addition of 15 μL sequencing buffer (SB) and 10 μL loading beads (LIB). Data was acquired on a MinION Mk1b with MinKNOW version 23.04.3.
DMS-Seq: Reverse transcription was performed on 1 μg of purified RNA mixed with 0.5 mM dNTPs, 0.25 μM of RT primer (5´- CTT GTC TAT CGG CTC CTG CTT C - 3´) in a final volume of 12 μL. The RNA was denatured at 65°C for 5 min and placed on ice. The reverse transcription reaction was performed by addition of 1 mM of MnCl2, 1x MarathonRT buffer (Tris-HCl 50 mM, pH 8.3; KCl 200 mM; Glycerol 20%), 0.2 μL RNasin (Promega) and 40 U of MarathonRT 93 in 25 μL final volume. The reactions were incubated for 8 h at 42°C. Newly synthesized cDNAs were diluted 8 times and PCR amplified: 10 μL of diluted cDNA were mixed with 0.2 mM dNTPs, 0.25 μM of both Forward (5´ - TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CTA CCA TAA TGA TAC AGA AAG GC - 3´) and Reverse (5´ - GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGT CTC TTC CCC AAA CCT GAA G - 3´) primers, 10 μL of Q5 Buffer 5x, and 1 U Q5 polymerase (NEB) in 50 μL final volume. The initial denaturation was performed at 98 °C for 2 min, followed by 25 cycles of 10 sec at 98°C, 20 sec at 55°C and 30 sec 721 at 72°C before a final extension at 72°C for 5 min. Amplicon quality was controlled on an agarose gel 1%. DNA amplicons were purified by solid-phase reversible immobilization (SPRI) using Mag-Bind TotalPure NGS beads (Omega Biotek) following the manufacturer´s instruction, with a DNA to beads ratio of 1:0.8. Nextera indexes were added by PCR, 80 ng of purified DNA were mixed with 1x Q5 Buffer, 0.2 mM dNTPs, 0.02 U of Q5 polymerase and 2.5 μL of Nextera Index (Illumina) in a 14 μL reaction. The initial denaturation was performed at 98 °C for 2 min, followed by 5 cycles of 30 sec at 98°C, 30 sec at 62°C and 1 min at 72°C before a final extension at 72°C for 5 min. Quality of libraries was assessed by agarose gel electrophoresis. Equal amounts of each sample were pooled together followed by a final SPRI purification (DNA to beads ratio of 1:0.8). Paired-end PE150 sequencing was carried out on an Illumina Novaseq instrument (Novogene).

tag: cell line

value: T-cell


title: Carotid Artery Ligation - Control rep 2


title: EPIA01RNA_Patient_OSA

value: OSA


title: EPIC10DNA_Healthy_Control

library_source: genomic

data_processing:
The quality check of whole genome bi-sulfite sequencing data was performed using FASTQC (verson 0.11.7)
Low quality bases were trimmed using  Trim Galore (version 0.6.0) and the adapters were removed using Cutadapt (version 2.1.0)
Bismark computational tools (version 0.18.2) were used to map bisulfite converted sequence reads and to determine cytosine methylation states
Reads that align to the exact same genomic position on the same strand (i.e., duplicate reads) were removed using SAMtools (version 1.9.0)
Differentially methylated regions (DMRs) were identified using methylKit  (version 1.8.1 in R version 3.5.3). To identify differential methylated regions, a threshold of q ≤ 0.01 and a minimum methylation difference of 25% were employed

molecule: genomic DNA

extract_protocol:
Total DNA was extracted using Qiagen RNeasy purification procedure and mRNA was purified using oligo(dT)-attached magnetic beads.
The DNA was broken down into smaller fragments using sonication, resulting in fragment sizes ranging from 100 to 300 base pairs. Following that, a process called end-repair was carried out to prepare the fragments for further analysis. Methylated sequencing adapters were then added to the 3' ends of the DNA fragments. To convert the non-methylated DNA into bisulfite-converted DNA, we used the EZ DNA Methylation-Gold kit from Zymo Research in California, USA, following the instructions provided by the manufacturer.


title: Carotid Artery Ligation - Control rep 1


title: C5-April-2023-Plate4-PEM_S297

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)


title: Femoral Artery Injury - Nrf3 Knockout rep 3

source_name: Femoral Artery

value: Femoral Artery


title: EPIC09DNA_Healthy_Control


title: Femoral Artery Injury - Nrf3 Knockout rep 2


title: B6-April-2023-Plate4-PEM_S288

tag: donor

tag: glycinecurrentwashout(pa/pf)


title: EPIA03RNA_Patient_OSA


title: B7-April-2023-Plate4-PEM_S289

tag: plate

tag: cellid


title: EPIC08DNA_Healthy_Control


title: EPIA02RNA_Patient_OSA


title: Femoral Artery Injury - Control rep 3


title: EPIC06DNA_Healthy_Control


title: Femoral Artery Injury - Control rep 2


title: biofilm, 72 h, rep2

city: Ljubljana

first: Manca

last: Volk

address: Jamnikarjeva 101

country: Slovenia

institute: Biotechnical faculty, University of Ljubljana

data_processing:
Raw reads containing the following were removed: i) adapters, ii) undetermined bases (N) > 10%, and iii) low-quality bases (Qscore ≤ 5). Read quality metrics were assessed using FastQC.
Reads were aligned to the C. jejuni subsp. jejuni NCTC 11168 (ATCC 700819) reference genome and counted using STAR 2.7.10b with default parameters.
Differential gene expression was analyzed in R 4.3.0 using the edgeR 3.42.4 and limma 3.56.2 packages. Raw counts were converted to log2 counts per million (log2 CPM) and statistics calculated using the limma-voom protocol.
Assembly: NC_002163.1
Supplementary files format and content: Excel file with gene functional annotation, differential expression analysis results (logFC, adj p-val) and normalised counts
Supplementary files format and content: tab-delimited text file with normalised counts

organism: Campylobacter jejuni subsp. jejuni

growth_protocol: Microaerobic conditions at 42 °C

extract_protocol:
RNA was isolated using a modified cetyltrimethylammonium bromide (CTAB) isolation protocol and purified using the Direct-zol RNA MiniPrep Kit (Zymo Research). Total RNA war treated with TURBO DNA-free Kit (Invitrogen).
The preparation of a strand-speciﬁc transcriptome library and sequencing on the Illumina NovaSeq platform with 150 bp paired-end reads were conducted by Novogene (China).

tag: strain

tag: group

value: biofilm, 72 h


title: biofilm, 48 h, rep4

value: biofilm, 48 h


title: biofilm, 48 h, rep3


title: biofilm, 72 h, rep4


title: EPIC07DNA_Healthy_Control


title: EPIC04DNA_Healthy_Control


title: biofilm, 72 h, rep3


title: biofilm, 72 h, rep1


title: A7-April-2023-Plate4-PEM_S279

tag: cell type

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record


title: Femoral Artery Injury - Control rep 1

tag: tissue


title: C4-April-2023-Plate4-PEM_S296

tag: age

tag: Sex

tag: bmi


title: biofilm, 48 h, rep2


title: Episomal_MPRA_DNA3

city: Indianapolis

first: Nathan

middle: J

last: VanDusen

state: IN

department: Pediatrics

institute: Indiana University School of Medicine

description:
DNA
DNA3_GEN00141101_S03
Episomal_MPRA_readcounts.csv

library_source: other

data_processing:
Reads were trimmed down to the barcode-containing region using Trimmomatic
The shell tool Grep was used to count the number of reads containing each barcode.
Supplementary files format and content: HDR_MPRA_readcounts.csv: Table containing the raw number of reads for each enhancer, for the Tnni1 integrated MPRA.
Supplementary files format and content: Episomal_MPRA_readcounts.csv: Table containing the raw number of reads for each enhancer-promoter pair, for the episomal MPRA.

molecule: other

organism: Adeno-associated virus

source_name: uninjected AAV

growth_protocol: Mouse in vivo

extract_protocol:
DNA: Proteinase K digestion followed by isopropanol precipitation. RNA: extracted by Trizol and purified by Zymo RNA Clean and Concentrator column with DNAse digestion.
RNA was reverse transcribed with Oligo-dT, reporter transcripts were selectively amplfied, and NGS adapters added during two rounds of PCR.
NGS adapter addition by two sequential rounds of PCR

treatment_protocol: AAV injection at birth

value: uninjected AAV

tag: genotype

tag: treatment

value: AAV


title: Episomal_MPRA_DNA2

description:
DNA
DNA2_GEN00141100_S02
Episomal_MPRA_readcounts.csv


title: A5-April-2023-Plate4-PEM_S277

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)


title: A6-April-2023-Plate4-PEM_S278

tag: donor

tag: plate

tag: glycinecurrentwashout(pa/pf)


title: EPIC05DNA_Healthy_Control

tag: race

tag: condition


title: EPIC03DNA_Healthy_Control


title: biofilm, 48 h, rep1

tag: strain

tag: group


title: A4-April-2023-Plate4-PEM_S276

tag: cellid

tag: cell type

tag: time from_plating_(h)

tag: glucose mm

tag: experimental record


title: Femoral Artery Injury - Nrf3 Knockout rep 1

tag: tissue


title: B5-April-2023-Plate4-PEM_S287

tag: age

tag: Sex

tag: bmi


title: Episomal_MPRA_DNA1

description:
DNA
DNA1_GEN00141099_S01
Episomal_MPRA_readcounts.csv

tag: genotype

tag: treatment


title: EPIC01DNA_Healthy_Control


title: biofilm, 24 h, rep4

value: biofilm, 24 h


title: EPIA09DNA_Patient_OSA


title: B4-April-2023-Plate4-PEM_S286

tag: donor

tag: plate

value: islets

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)


title: biofilm, 24 h, rep3

tag: strain

tag: group


title: EPIA06DNA_Patient_OSA

tag: race

tag: condition


title: G3-Nov-2022-Plate2-PEM_S127

tag: cellid

tag: cell type

tag: time from_plating_(h)

tag: glucose mm

value: male

tag: glycinecurrentwashout(pa/pf)


title: 22Rv1 shPlexinD1#2-rep 1

city: Spokane

first: Boyang

last: Wu

state: Washington

address: 412 E. Spokane Falls Blvd

institute: Washington State University

description:
RP6_1
TMM_normalized_reads_count_per_million_22rv1_kdvsctrl.txt

data_processing:
The paired-end sequencing was performed on an Illumina HiSeq 3000.
Data quality check was done on Illumina SAV.
Bowtie2 version 2.1.0 was used for mapping to the human genome hg19 transcript set.
RSEM v1.2.15 was used to calculate the count and estimate the gene expression level.
Trimmed Mean of M-values (TMM) method in the edgeR package was used for gene expression normalization.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TMM values for each Sample

extract_protocol:
The total RNA was extracted by RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: Prostate cancer cells


title: EPIA08DNA_Patient_OSA

tag: Sex

tag: tissue


title: plankton, 16 h, rep4

value: plankton, 16 h


title: biofilm, 24 h, rep2


title: EPIA07DNA_Patient_OSA


title: LNCaP Vector

description:
lib_B
TMM_normalized_reads_count_per_million_lncap_oevsctrl.txt

source_name: LNCaP

value: LNCaP

tag: genotype

value: Vector


title: LNCaP OE

description:
lib_A
TMM_normalized_reads_count_per_million_lncap_oevsctrl.txt

value: PlexinD1 OE


title: F3-Nov-2022-Plate2-PEM_S122

tag: donor

tag: plate

tag: experimental record

value: ND

tag: age

tag: bmi


title: 22Rv1 shPlexinD1#2-rep 2

description:
RP6_2
TMM_normalized_reads_count_per_million_22rv1_kdvsctrl.txt


title: biofilm, 24 h, rep1

tag: strain

tag: group


title: EPIA05DNA_Patient_OSA

tag: race

value: Black

value: Female

tag: condition

value: Saliva


title: plankton, 16 h, rep3


title: EPIA04DNA_Patient_OSA

value: OSA


title: 22Rv1 shPlexinD1#1-rep 2

description:
RP4_2
TMM_normalized_reads_count_per_million_22rv1_kdvsctrl.txt

tag: cell type


title: H3-Nov-2022-Plate2-PEM_S132

tag: cellid

tag: time from_plating_(h)

value: female

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)


title: C3-Nov-2022-Plate2-PEM_S107

tag: glucose mm

tag: Sex

tag: glycinecurrentwashout(pa/pf)


title: EPIA03DNA_Patient_OSA

tag: tissue


title: E3-Nov-2022-Plate2-PEM_S117

tag: donor

tag: plate

tag: experimental record


title: B3-Nov-2022-Plate2-PEM_S102

tag: age

tag: bmi


title: plankton, 16 h, rep1

tag: strain

tag: group


title: EPIA02DNA_Patient_OSA

tag: race

tag: condition


title: D3-Nov-2022-Plate2-PEM_S112

tag: cellid

tag: cell type

tag: time from_plating_(h)


title: 22Rv1 shCon-rep 1

description:
RC_1
TMM_normalized_reads_count_per_million_22rv1_kdvsctrl.txt

tag: cell line

tag: genotype

value: shCon


title: 22Rv1 shPlexinD1#1-rep 1

description:
RP4_1
TMM_normalized_reads_count_per_million_22rv1_kdvsctrl.txt


title: C4-2B ENZR shPlexinD1#2

description:
shP6
TMM_normalized_reads_count_per_million_enzr_kdvsctrl.txt

tag: treatment

value: enzalutamide-resistant


title: C4-2B ENZR shPlexinD1#1

description:
shP4
TMM_normalized_reads_count_per_million_enzr_kdvsctrl.txt


title: plankton, 16 h, rep2


title: biofilm, 16 h, rep2

value: biofilm, 16 h


title: HEK293T PCIF1 knockout, technical replicate 1

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

description: For csv output, the columns are chromosone id, 1-based position, strand, numer of A, T, C, G started readas

data_processing:
The read pairs were firstly quality trimmed by cutadapt (-m 32 -j 4 -q 20 -e 0.25 -a AGATCGGAAGAGCACACGTC -A ATATN{8}AGATCGGAAGAGCGTCGTG).
Then the UMI along with the fixed ATAT spacer sequences were extracted by umi_tools.
In silico converted read pairs (read1 A-to-G, read2 T-to-C) were aligned by HISAT2 against A-to-G converted (for positive strand) and T-to-C converted (for negative strand) reference genome and transcriptome first (key options: -k 5 –fr –rna-strandness FR –no-temp-splicesite –no-mixed). Then the unique alignments were extracted and the in silico converted reads were inverse-transformed to the original format.
The 5’ most ends of read1 were called and the ReCappable-seq pipeline was performed to find out the enriched transcription start nucleotides.  Non-conversion rates of the transcription start nucleotides were calculated by A counts over A and G counts.
Assembly: GRCh38
Supplementary files format and content: csv
Library strategy: CROWN-Seq

extract_protocol:
Cellular total RNA in TRIzol LS (ThermoFisher 10296028) was extracted by Direct-zol RNA Miniprep kit (Zymo #R2070).  mRNA was purified by NEBNext Oligo d(T)25 Beads (NEB #E7499) based on mRNA purification from total RNA protocol of Dynabeads Oligo (dT)25 (Ambion #61002).
0.8-1.5 μg oligo(dT) selected RNA was used as input.  RNA was first diluted in 14 μl water.  To perform glyoxal protection, 6 µl 8.8 M glyoxal and 20 μl DMSO were then added to the diluted RNA and well mixed.  The 40 µl mix was first incubated at 50 ºC for 30 minutes, then 10 μl boric acid was added to the mix.  The 50 µl mix was then incubated for an additional 30 minutes at 50 ºC.  After protection, the 50 μl protected RNA was mixed with 50 μl deamination buffer (25 μl 1500 mM NaNO2, 4 μl 500 mM MES, pH 6.0, 10 μl 8.8 M glyoxal, and 11 μl water).  The deamination reaction was performed at 16 ºC for 8 hours.  After deamination, the RNA was recovered by ethanol precipitation.  To remove the glyoxal adduct from the RNA, the RNA pallet was dissolved in 50 μl deprotection buffer (500 mM TEAA pH=8.6, 47.5% deionized formamide) and was incubated at 95 ºC for 10 minutes.  After incubation, the reaction was brought to 250 μl with water.  Converted RNA was purified by ethanol precipitation and eluted in 39 μl water for 5’ end enrichment.  The converted RNA was stored at -80 ºC before 5’ end enrichment.      To eliminate the contamination of RNA with 5’-triphosphate and 5’-monophosphate, 5 µl 10X CutSmart buffer, 5 µl Quick CIP (5 U/µl) (NEB #M0525L), and 1 µl Superase*IN RNase inhibitor (ThermoFisher #AM2696) were added to the 39 μl converted RNA to set up a dephosphorylation reaction.  The dephosphorylation reaction was performed at 37 °C for 30 minutes.  The reaction was cleaned up using Zymo RCC-5 column and the RNA was eluted in 42 µl water.  To de-cap the m7G capped RNA, a 50 µl decapping reaction was set up by adding 5 µl 10X yDcpS buffer, 2 µl (200 U) yDcpS (NEB #M0463S), and 1 µl Superase*IN to the 42 µl dephosphorylated RNA.  The decapping reaction was performed at 37 ºC for 1 hour.  This unique decapping enzyme liberates m7GMP, resulting in mRNAs with a 5’-diphosphate.   Reaction was cleaned and eluted as before.  The reaction was cleaned up using Zymo RCC-5 column and the RNA was eluted in 33.5 µl water.  The 5’-diphosphorylated mRNAs were recapped with desthiobiotin-GTP (DTB-GTP, NEB #N0761S) using vaccinia capping enzyme (5 μL VCE buffer, 0.5 μL inorganic pyrophosphatase (NEB #M0361S), 5 μL DTB-GTP (5 mM; NEB N0761S), 50 U VCE, 1 µl Superase*IN) at 37 °C for 1 hour.  The reaction was cleaned up using Zymo RCC-5 column and the RNA was eluted in 30 µl water.  Now the RNA is ready for streptavidin enrichment.    Streptavidin beads (NEB #S1421S) were washed in a high salt wash buffer (10 mM Tris-HCl pH 7.5, 2 M NaCl, 1 mM EDTA) and resuspended in the high salt buffer at 4 mg/mL.  To enrich the RNA and tag the 5’ and 3’ end by the specific adapter, the 30 µl recapped RNA was first mixed with 30 µl streptavidin beads and incubated at room temperature for 45 minutes with agitation.  Beads were washed twice in high salt buffer, twice in a lower salt buffer (10 mM Tris-HCl pH 7.5, 250 mM NaCl, 1 mM EDTA), and twice in PNK wash buffer (20 mM Tris-HCl pH 7.5, 10 mM MgCl2, 0.2% Tween).  To remove 3’ phosphates resulting from fragmentation during conversion, beads were resuspended in 50 µl PNK reaction without ATP (5 µl 10X PNK buffer, 1 µl T4 PNK (#M0201S), 1 µl Superase*IN, 43 µl water), and incubate at 37 °C for 30 minutes with agitation.  The beads were then washed once in PNK wash buffer, once in 2 M NaCl wash, and twice in PNK wash.  Next, RNA was ligated to a 74 nt-long 3’ adapter (/5’rApp/AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAAAAAAAAAAAAACCCCCCCCCCAAAAAAAAAAAAAAA/3AmMO/) in the following 40 μl 3’ ligation mix: 4 μL T4 RNA ligase buffer, 2 μl T4 RNA ligase 2 truncated KQ (NEB #M0373L), 1 µl Superase*IN, 2 μl extended-L7 adapter (20 μM stock, see Key Resource table), 16 μl of 50% PEG-8000) and incubated at 25 °C for 2 hours.  After incubation, the reaction buffer was removed by washing once with high salt buffer and twice with PNK wash buffer.  To remove the exceeded adapter, the beads were incubated in 50 μl adapter digestion reaction (40 μl waater, 5 µl 10X RNA ligase buffer, 1 µl RecJf (NEB #M0264S), 1 5’ Deadenylase (NEB #M0331S), 1 µl Superase*IN) at 30 °C for 15 minutes then at 37 °C for 15 minutes.  The beads were washed once with PNK wash, once with high salt buffer and twice with low salt buffer.  To elute the DTB labeled RNA, beads were then suspended 30 µl low salt wash buffer containing 1 mM free D-biotin (ThermoFisher #B20656) and incubate at room temperature for 1 hour. The DTB labeled RNA were purified with ethanol-AMPure XP (RNA:beads:ethanol=1:2:3) and elute in 30 µl water.  To increase stringency, the streptavidin bead enrichment was repeated omitting enzymatic steps and instead washing three times with high salt and then three times with lower salt wash, and the eluate cleaned again by ethanol-AMPure XP.  The DTB-GTP cap was removed using 0.5 U/µl RppH in 1X ThermoPol buffer (NEB #M0356S) and incubating at 37 °C for 1 hour.  The resulting 5’-monophosphate RNA fragments were purified by ethanol-AMPure XP and eluted in 10 μl water.  1 μl (10 pmol) reverse transcription primer (AGACGTGTGCTCTTCCGATCT) was pre-annealed to the templates by heating up to 90 °C for 30 seconds, then 65 °C for 5 minutes, and chilled at 4 °C for over 30 seconds. 30 pmol of a 5’ adapter was ligated for 3 hours at 25 °C with 2 U/μl T4 RNA ligase 1 (NEB #M0437M).  This RNA adapter contains an 8 nt UMI followed by a fixed sequence (AUAU) at its 3’ end.  The UMI allows robust duplicate removal, and the fixed sequence provides an anchor point to correctly identify the first nucleotide of the mRNA.  40 μl ligation product was used.  Reverse transcription was carried out at 50 °C for 45 minutes in a 50 μl reaction containing 0.5 mM dNTPs, 5 mM DTT, 20 U RNaseOUT, 50 mM Tris-HCl pH 8.3, 75 mM KCl, and 300 U SuperScript III.  To perform indexing PCR, 40 μl Phusion master mix (NEB # M0532L) was added to the reverse transcription product, along with 5 μl i5 indexing primer and 5 μl i7 indexing primer (NEB #E7600S). Cycling conditions were typically 98 °C 2 minutes, then 16 cycles of 98 °C 15 seconds, 65 °C 30 seconds, 72 °C 30 seconds, with a final 5 minute 72 °C extension.  Two rounds of 0.9X AMPureXP beads purifications were performed to remove primers.

value: PCIF1 KO


title: SNCA_R1

city: Esch sur Alzette

first: Alise

last: Zagare

state: Belval

address: 7 Avenue des Hauts-Fourneaux

country: Luxembourg

institute: University of Luxembourg

data_processing:
Gene-level differential expression analysis was conducted in R (version 3.5.1) using the Bioconductor package edgeR (Robinson et al., 2009), and filtering out genes with low expression counts using the filterByExpr-function with default parameters
Assembly: Ensembl 96 human
Supplementary files format and content: Tab-delimited text file with raw feature counts

source_name: Midbrain organoids

growth_protocol: Nickels et al, 2020

extract_protocol:
Total RNA was isolated from a pool of 5 organoids using Trizol reagent (cat. no. 15596026, ThermoFisher)
1 µg of total RNA was used for library preparation using TruSeq stranded mRNA library preparation kit (cat. no. 20020594, Illumina)

value: Midbrain organoids


title: biofilm, 16 h, rep1


title: 22Rv1 shCon-rep 2

description:
RC_2
TMM_normalized_reads_count_per_million_22rv1_kdvsctrl.txt


title: A3-Nov-2022-Plate2-PEM_S97

value: islets

tag: glucose mm

tag: Sex

value: male

tag: cellsize f

tag: glycinecurrent(pa/pf)

tag: glycinecurrent+strychnine(pa/pf)

tag: glycinecurrentwashout(pa/pf)


title: WT_R3

value: WT


title: biofilm, 16 h, rep4


title: C4-2B ENZR-rep 2

description:
C42BENZLG_2
TMM_normalized_reads_count_per_million_lncap_enzr.txt

value: Prostate cancer cells

value: parental


title: EPIA01DNA_Patient_OSA

tag: tissue


title: HEK293T FTO knockout, technical replicate 1

value: FTO KO


title: WT_R2


title: biofilm, 16 h, rep3

tag: strain


title: Afidopyropen treatment 2

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
Low-quality reads (those with a mass value of less than 15 bases accounting for more than 40% of the total base number of the reads were defined as low-quality reads) were removed to obtain clean reads.
High-quality clean reads were de novo assembled using Trinity, followed by clustering of transcripts to deredundancy using CD-HIT to obtain unigene.
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html), and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: de novo transcriptome assembly
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Semiaphis heraclei

source_name: whole body

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

value: whole body

value: Afidopyropen treatment


title: HEK293T wildtype, technical replicate 2

value: wild-type


title: A549 wildtype, technical replicate 2


title: Afidopyropen treatment 3


title: WT_R1


title: SNCA_R3


title: A549 wildtype, technical replicate 1


title: SNCA_R2


title: C4-2B ENZR-rep 1

description:
C42BENZLG_1
TMM_normalized_reads_count_per_million_lncap_enzr.txt


title: C4-2B ENZR shCon

description:
shCtrl
TMM_normalized_reads_count_per_million_enzr_kdvsctrl.txt


title: HEK293T wildtype, technical replicate 1


title: Acetone treatment 3

value: Acetone treatment


title: LNCaP- rep 1

description:
LNCaPLG_1
TMM_normalized_reads_count_per_million_lncap_enzr.txt

value: LNCaP


title: LNCaP-rep 2

description:
LNCaPLG_2
TMM_normalized_reads_count_per_million_lncap_enzr.txt


title: Acetone treatment 2


title: Afidopyropen treatment 1


title: KOLF2_HAND1_KO_BSA_IgG_R1

city: Farmington

first: Paul

last: Robson

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory For Genomic Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Human induced pluripotent stem cell

tag: chip antibody


title: BS16017

description: 10x Genomics

data_processing:
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.16.0.10 (Illumina) and FASTQ files associated with the gene expression libraries were aligned to the GRCh38.93 reference genome (10x Genomics GRCh38 reference 3.0.0 [including all transcribed unitary pseudogenes]) using the version 3.1.0 Cell Ranger count pipeline (10x Genomics). All libraries were then combined using the Cellranger aggr pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human induced pluripotent stem cell

extract_protocol: Cells were washed and suspended in PBS containing 0.04% BSA and immediately processed as follows. Cell viability was assessed on a Countess II automated cell counter (ThermoFisher), and up to 12,000 cells were loaded onto one lane of a 10X Chromium Controller. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform79 v2 chemistry and according to the manufacturer’s protocol (#CG00103) with modifications for generating the hashtag library80. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and each library was sequenced independently on a separate lane of an Illumina HiSeq 4000 HO flow cell, targeting 6,000 barcoded cells with an average sequencing depth of 50,000 reads per cell.


title: PR19058

description: 10x Genomics


title: LSK_mut3_H3K9me3

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

data_processing:
reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009)
Assembly: mm10
Supplementary files format and content: bigWig files were generated from Homer tag directories using makeBigWig.pl

source_name: Fetal Liver

extract_protocol:
5000 FACS-sorted LSK cells from E13.5 Setdb1vav and control fetal livers were resuspended in 20 μL of EZ nuclei isolation lysis buffer (Sigma) containing 0.1% Triton, 0.1% deoxycholate, 1x cOmplete EDTA-free Protease Inhibitor Cocktail (Roche Diagnostics), 1 mM PMSF, flash frozen and kept at -80 °C. Chromatin fragmentation and immunoprecipitation was performed following the ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP) protocol with minor modifications (Brind’Amour et al., 2015). After thawing, 10% of the volume (2 μL) of a 1% Triton/1% deoxycholate solution was added and chromatin was fragmented using MNase (Biolabs) enzyme at 1.5 U/μL in MNase digestion buffer (1X MNase Reaction Buffer, 100 mM DTT, 50% PEG 6000, and ultrapure H20) for 7.5 minutes at 21°C. Reaction was stopped by adding 10% of the reaction volume of 100 μM EDTA and 1% Triton/1% deoxycholate solution. To 120 μL fragmentated chromatin, 380 μL of complete immunoprecipitation buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1x cOmplete EDTA-free Protease Inhibitor Cocktail, 1 mM PMSF) was added and rotated for 1h at 4°C. 100 μL of sample was taken as input. The remaining 400 μL chromatin was pre-cleared and immunoprecipitated using 5 μL beads coated with 0.25 μg antibody overnight at 4°C. Chromatin-bound beads were first washed 3X with 500 μL low salt wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% SDS) and then 3X with high salt wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS). Immunoprecipitated DNA was eluted in 30 μL freshly prepared ChIP elution buffer (100 mM NaHCO3, 1% SDS) for 1.5 hours at 65°C. To maximize the elution, additional 70 μL freshly prepared ChIP elution buffer was added to the beads. DNA isolation was carried out by Agencourt AMPure XP beads (Beckman Coulter).
MicroPlex Library Preparation Kit v2 (Diagenode, cat. C05010012)

value: Fetal Liver

value: LSK

tag: developmental stage

value: Setdb1 p/p;vav-cre

tag: facs sorting_markers


title: LSK_mut2_H3K9me3


title: KOLF2_HAND1_KO_BSA_IgG_R2


title: Acetone treatment 1


title: KOLF2_WT_BSA_IgG_R3


title: PR17028

description: 10x Genomics


title: LSK_mut1_H3K9me3


title: BS16012

description: 10x Genomics


title: Larval ring gland, post-NRC starvation, rep3

city: Guangzhou

first: Suning

last: Liu

state: Guangdong

address: No.55, West of Zhongshan Avenue, Tianhe District

institute: South China Normal University

data_processing:
Paired fastq sequencing reads were aligned to the annotated D. melanogaster reference genome (BDGP release 6) using HISAT2, StringTie and Bowtie. The resulting alignment files were reconstructed with Cufflinks. Expression levels were quantified as FPKM.
Assembly: D. melanogaster reference genome (BDGP release 6)
Supplementary files format and content: Excel, the expression level of genes in the RGs at different conditions

organism: Drosophila melanogaster

source_name: Ring gland

extract_protocol:
Total RNA was extracted using the miRNeasy Micro Kit (QIAGEN, Germany), then stored at ~80 °C. RNA quality, especially DNA contamination, was monitored on 1.5% agarose gels. RNA concentration was measured using NanoDrop 2000 (Thermo Fisher Scientific, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, USA).
Libraries were generated using NEBNext® Ultra™ small RNA Sample Library Prep Kit for Illumina® (NEB, USA) and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The libraries prepared were sequenced on an Illumina Hiseq platform and paired-end reads were generated.

value: Ring gland


title: Larval ring gland, post-NRC starvation, rep2


title: LSK_con3_H3K9me3

value: Setdb1 +/p;vav-cre


title: Larval ring gland, post-NRC starvation, rep1


title: LSK_con1_H3K9me3


title: Larval ring gland, pre-NRC starvation, rep3


title: BS16007

description: 10x Genomics


title: Patient 6-1, scRNA-seq

city: CHICAGO

first: Yu

last: Luan

state: Illinois

address: 303 E. Superior Simpson Querrey 7-518

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description:
Sonicated-P6
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Supplementary files format and content: hg38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: peritumoral brain

extract_protocol:
Isolated cells were washed with PBS containing 0.04% bovine serum albumin and filtered through a 40-μm cell strainer. Cell concentration and viability were determined by a Countess II Automated Cell Counter with a final cell concentration of 700-1,200 cells/ul.
Single-cell RNA-seq libraries were generated using the Chromium Single Cell 3′ Reagent Kit (10X Genomics). Single-cell suspension was mixed with RT-PCR master mix and loaded together with Single Cell 3′ Gel Beads and Partitioning Oil into a Single Cell 3′ Chip (10X Genomics). The cDNA was amplified and further used to construct 3’ gene expression library according to the manufacturer’s instructions. The size profiles of pre-amplified cDNA and sequencing libraries were examined by the Agilent High Sensitivity 2100 Systems (Agilent). The scRNA-seq library was sequenced on the Illumina NextSeq 500/550 platform.

treatment_protocol: Biopsy of non-eloquent peri-tumoral brain was performed when feasible/justified as per standard neurosurgical technique. A skull implantable ultrasound device was positioned over the brain via a bone window, delivering 25 ms pulses every two seconds for 270 seconds at a maximum pressure output of 1.03 MPa. Immediately afterwards, fluorescein was infused intravenously with chemotherapy (i.e. ABX or CBP) over 30 minutes. Peri-tumoral brain was defined as brain parenchyma that was not enhancing per the contrast MRI used for stereotaxic navigation. Sonicated peri-tumoral brain was identified by fluorescent microscopy following infusion of fluorescein and non-sonicated peri-tumoral brain based on absence of fluorescence in this setting.

value: peritumoral brain

tag: disease

value: Recurrent Glioblastoma (IDH WT)

value: Female

value: Low-intensity pulsed ultrasound

tag: patient


title: LSK_input

tag: cell type


title: Larval ring gland, pre-NRC starvation, rep2


title: Patient 5-2, scRNA-seq

description:
Non-Sonicated-P5
10x Genomics


title: MPP_mut3_RNA

data_processing:
Paired end RNA-seq reads were mapped to the mouse genome (mm10) using STAR (Dobin et al., 2013).
Expression of genes in FPKM was calculated with RSEM (Li et al., 2011).
Assembly: mm10

extract_protocol:
RNA was extracted using the PicoPure RNA Isolation Kit (cat no. KIT0204) according to the manufacturer instructions, but eluted in 11  μl prewarmed H2O (37◦C)
protocol Smarter ultra low input-v4 (Clontech 634888) and Microplex-v2 (Diagenode C05010012) - 10ng input RNA

treatment_protocol: Fetal liver has been dissected, single fetal liver cells have been subjected to RBC lysis and hematopoietic cells have been enriched for Lin- cells by MACS. Around 500-1000  LT-HSCs and 20000 MPPs were FACS sorted in 100 μl of Extraction Buffer from PicoPure RNA Isolation Kit (cat no. KIT0204)


title: KOLF2_WT_BSA_input_R2

tag: cell line


title: BS16001

description: 10x Genomics


title: LSK_con2_H3K9me3

tag: genotype


title: Patient 5-1, scRNA-seq

description:
Sonicated-P5
10x Genomics

tag: treatment


title: Larval ring gland, feeding, rep3


title: MPP_mut1_RNA


title: KOLF2_HAND1_KO_BSA_H3K4me3_R2

description: H3K4me3.consensus_peaks.annotatePeaks.txt


title: KOLF2_WT_BSA_input_R1


title: KOLF2_HAND1_KO_BSA_input_R2


title: MPP_con3_RNA


title: Patient 6-2, scRNA-seq

description:
Non-Sonicated-P6
10x Genomics


title: Larval ring gland, feeding, rep2


title: KOLF2_WT_BSA_IgG_R2


title: Patient 3-1, scRNA-seq

description:
Sonicated-P3
10x Genomics

value: Recurrent Glioblastoma (IDH Mutant)

value: Male


title: KOLF2_HAND1_KO_BSA_HAND1_R2


title: Patient 3-2, scRNA-seq

description:
Non-Sonicated-P3
10x Genomics


title: MPP_con1_RNA


title: PHILO, Tomato, H3K9ac, 2hJA, rep2

city: Piscataway

first: Mark

last: Zander

address: 190 Frelinghuysen Rd

institute: Rutgers State University of New Jersey

data_processing:
ChIP-seq reads were aligned to the TAIR10 (Arabidopsis thaliana), SLM_r2.0.pmol (Solanum lycopersicum), cs10 (Cannabis sativa) using Bowtie2 (version 2.4.1).
To generate ChIP-seq coverage plots, bamCoverage (binSize 5) from deepTools (version 3.5.2) was used.
Histone marks domains were identified with epic2 (version 0.0.52) using default parameters and IgG samples as controls.
Assembly: TAIR10 (Arabidopsis thaliana), SLM_r2.0.pmol (Solanum lycopersicum), cs10 (Cannabis sativa)
Supplementary files format and content: bigwig, domain.csv

organism: Solanum lycopersicum

source_name: two-week-old whole seedling

growth_protocol: Ten-day-old Col-0 Arabidopsis seedlings, two-week-old Micro-Tom tomato (Solanum lycopsericum) seedlings, and two-week-old Otto II Boax hemp (Cannabis sativa)seedlings grown under a 16 h light/8 h dark cycle were used for PHILO ChIP-seq analysis.

extract_protocol:
Tissues were crosslinked with 1% formaldehyde solution for 2 x 10 min. After quenching, samples were shock-frozen, ground and chromatin was subsequently extracted. Chromatin was sonicated with a Diagenode Bioruptor.
Libraries were prepared as follows. End repair (5 μl of End Repair Reaction Buffer + 2.5 μl of End Repair Enzyme Mix from the NEBNext End Repair Module (New England Biolabs)), A-tailing (2.5 µl NEBnext dA-Tailing Reaction Buffer + 1.5 µl Klenow Fragment (3'5' exo-) (New England Biolabs)), adapter ligation(1 µl TruSeq DNA Unique Dual Indexes (UDIs) v2 (Illumina), 2.5 µl T4 DNA Ligase Reaction Buffer + 1.25 µl T4 DNA Ligase (New England Biolabs)), and PCR enrichment (12.5 µl NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs).

treatment_protocol: no treatment

value: anti-H3K9ac (39137, Active Motif)

value: Micro-Tom


title: KOLF2_HAND1_KO_BSA_input_R1


title: KOLF2_HAND1_KO_BSA_HAND1_R1


title: PHILO, Tomato, H3K9ac, 2hJA, rep3


title: Larval ring gland, pre-NRC starvation, rep1


title: KOLF2_WT_BSA_IgG_R1


title: Patient 2-2, scRNA-seq

description:
Non-Sonicated-P2
10x Genomics


title: PHILO, Tomato, H3K9ac, 2hJA, rep1


title: MPP_mut2_RNA


title: Patient 4-2, scRNA-seq

description:
Non-Sonicated-P4
10x Genomics


title: Patient 2-1, scRNA-seq

description:
Sonicated-P2
10x Genomics


title: Patient 1-2, scRNA-seq

description:
Non-Sonicated-P1
10x Genomics


title: PHILO, Tomato, H3K9ac, ctrl, rep2


title: Patient 4-1, scRNA-seq

description:
Sonicated-P4
10x Genomics


title: Patient 1-1, scRNA-seq

description:
Sonicated-P1
10x Genomics


title: PHILO, Tomato, H3K9ac, ctrl, rep1


title: LT-HSC_con3_RNA


title: PHILO, Tomato, IgG, rep3

value: IgG (#015-000-003, Jackson ImmunoResearch)


title: Larval ring gland, feeding, rep1


title: KOLF2_WT_BSA_HAND1_R2


title: LT-HSC_mut3_RNA


title: KOLF2_HAND1_KO_BSA_H3K4me3_R1


title: KOLF2_WT_BSA_input_R3


title: LT-HSC_con1_RNA


title: MPP_con2_RNA


title: LSK_mut2_ATAC

extract_protocol:
ATAC-seq was done as previously described (Buenrostro et al., 2013). Briefly, 10000 FACS sorted cells were washed in 1xPBS, re-suspended in 50 ul of lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40,) and spun at 500g for 10 min at 4 °C to collect nuclei. Nuclei were subsequently re-suspended in 50 µl Transposase reaction containing 25µL 2x tagmentation buffer, 22.5 µl water, 2.5 µl Tn5 Transposase (Illumina Nextera DNA Library Preparation Kit, cat. FC-121-1030). Reactions were incubated for 30 min at 37° C in a thermomixer shaking at 300 rpm and DNA purified using Qiagen PCR clean-up MinElute kit (Qiagen).
The transposed DNA was subsequently amplified in 50µl reactions with custom primers as described (Buenrostro et al., 2013). After 4 cycles libraries were then monitored with qPCR: 5 µl PCR sample in a 15 µl reaction with the same primers. qPCR output was monitored for the ΔRN; 0.25 ΔRN cycle number was used to estimate the number of additional cycles of the PCR reaction needed for the remaining PCR samples. Amplified libraries were purified with the Qiagen PCR clean-up MinElute kit (Qiagen) and size selected for fragments less than 600 bp using the Agencourt AMPure XP beads (Beckman Coulter). Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis.


title: PHILO, Tomato, IgG, rep1


title: ST_mock_rep3

data_processing:
*library strategy: CROWN-seq
To obtain reads for individual libraries from the pooled sequencing results, we performed two steps processing by Cutadap3. First, we removed the low-quality reads by parameters: cutadapt -a ANNNNNNNNNNNNAGATCGGAAGAGCACACGTC -A NNTAAGATCGGAAGAGCGTCGTG --max-n 0 -m 32 -q 20 -e 0.25. Second, we extract different libraries by pattern recognition: cutadapt -g [sample #1]=GCGA -g [sample #2]=GTGC -g [sample #3]=ATCA -g [sample #4]=GGAC. The extracted reads were stored in different FASTQ files for further analysis.
To analyze individual libraries, we first remove the AT adapter sequences at the beginning of read1. Then the UMI sequences in both read1 and read2 were extracted by UMI-tools4 (umitools extract --bc-pattern2 NNNNNNNNN -p NN).
To map the reads to reference genome, we first in silico A-to-G and T-to-C converted reference genome of pig (Ensembl Sscrofa11.1 r110) and PRV (GCA_000843825.1). We then built HISAT2 indexes on these converted reference genome. The reads were mapped to the converted reference genome by the CROWN-seq alignment pipeline (https://github.com/jhfoxliu/CROWN-Seq). Notably, only unique alignments were used in analyses.
After alignment, we removed PCR duplications by UMI-tools. We then calculated the coverages of the 5’ end mapped to reference genome, which represents the positions of transcription-start nucleotides.
For A-started transcripts, m6Am level was calculated as the number of A (m6Am) reads versus the sum of A reads and G (Am) reads. To annotate snRNA genes, we used snRNA annotations in Ensembl Sscrofa11.1 r110.
Assembly: Ensembl Sscrofa11.1 r110; GCA_000843825.1
Supplementary files format and content: CSV, base counts for transcription-start nucleotides
Supplementary files format and content: TXT, base counts for transcription-start nucleotides

organism: Sus scrofa

source_name: ST

growth_protocol: Swine testicle (ST) cells were cultured in MEM (Gibco) supplemented with 10 % fetal calf serum (FCS), 1 mM sodium pyruvate, 105 U/l penicillin, 100 mg/l streptomycin and 50 mg/l gentamycin. HEK293T cells were cultured in DMEM (Gibco) supplemented with 10 % FCS, 105 U/l penicillin, 100 mg/l streptomycin and 50 mg/l gentamycin. Both cell lines were obtained from the American Type Culture Collection (ATCC) and were tested to be free of mycoplasma contamination via de LookOut Mycoplasma PCR detection kit (Sigma-Aldrich). Wild-type NIA3 PRV strain and an isogenic UL13null mutant (M137) were previously described and were kindly donated by the ID-DLO (The Netherlands) (De Wind et al., 1992; de Wind et al., 1990).

extract_protocol:
RNA isolations were performed using the RNeasy minikit (Qiagen) according to the manufacturer’s procedure. Purified RNA was treated with RNase-free DNase I (New England Biolabs) at 37°C for 10 min to remove contaminating DNA. To stop DNase I activity, EDTA (Invitrogen) was added at a final concentration of 5 mM and samples were incubated at 75°C for 10 min.
CROWN-seq is performed as previously described with some modifications. ~30 μg total RNA input was used for the CROWN-seq libraries. The RNA input was converted by sodium nitrite as described in the GLORI protocol1. After conversion, the m7G capped 5’ end RNA fragments were isolated based on a modified ReCappable-seq workflow2. In brief, the converted m7G capped RNAs were firstly recapped by 3´-Desthiobiotin-GTP. Then the recapped RNA fragments were enriched on streptavidin beads. Different from the original ReCappable-seq protocol, we performed on-beads 3’ adapter ligation, where a barcoded 3’ DNA adapter (/rApp/ANNNNNNNNXXXXAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAAAAAAAAAAAAAACCCCCCCCCCAAAAAAAAAAAAAAA/3AmMO/, X=barcode) was ligated to the enriched RNA fragments. We used four different barcodes to label different samples. After adapter ligation, 2-4 samples in different barcodes were pooled. This pooling strategy can increase the yield of library. The pooled RNA fragments were then treated by 5´ Deadenylase (NEB #M0331S) and RecJf (NEB #M0264S), which can remove the exceeded 3’ adapter. After a second round streptavidin enrichment, the RNA fragments were eluted into water. To ligate 5’ adapter, we used RppH (NEB #M0356S) to release the 3´-Desthiobiotin caps, which results in monophosphate 5’ ends readily for ligation. We then ligated a 5’ adapter (rCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrArUrNrN) which contain unique molecular identifier (UMI) to the RNA fragments. After adapter ligation, reverse transcription primer (GACGTGTGCTCTTCCGATCT) was annealed to the 3’ adapter (75°C 5 min, 37 °C 15 min, then 25 °C 15 min). Reverse transcription was performed with SuperScript III (Thermo Fisher #18080093). After reverse transcription, cDNA was amplified with Phusion PCR master mix (NEB #M0531S) and NEBNext multiplex oligos (NEB #E7780S). Amplified libraries were size selected by SPRIselect beads (Beckman #B23317). Size selected libraries were then sequenced by NovaSeqX in PE100 mode.

treatment_protocol: Confluent cells were infected at an MOI of 10 and lysed at 16 hpi unless otherwise mentioned.

value: ST

value: mock


title: LT-HSC_mut2_RNA


title: KOLF2_WT_BSA_H3K4me3_R2

value: Human induced pluripotent stem cell


title: PHILO, Tomato, H3K9ac, ctrl, rep3


title: LT-HSC_mut1_RNA

value: Fetal Liver


title: KOLF2_WT_BSA_H3K4me3_R3


title: KOLF2_WT_BSA_HAND1_R3


title: KOLF2_WT_BSA_H3K4me3_R1


title: CS01-2PB_2

city: Bonn

first: Ulrich

last: Schweizer

state: NRW

address: Nussallee 11

department: Institut für Biochemie und Molekularbiologie

institute: Universitätsklinikum Bonn

description:
RPF
Small RNA RNA-seq

data_processing:
For 3' Poly(A) RNA-seq, reads were trimmed with bbduk.sh following manufacturer's protocol. ref=/data/resources/polyA.fa.gz,/data/resources/truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20; For Ribo-Seq: trimGalore was used with options --length 17 --quality 20 --stringency 5 --cores 4
For 3' Poly(A) RNA-seq, Reads were aligned with STAR aligner following the manufacturer's protocol. STAR  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1   --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20   --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD  --outSAMtype BAM SortedByCoordinate --outFileNamePrefix. For Ribo-Seq, Star Aligner was used first to align against non-coding RNAs (retrieved from UCSC Table Browser) with options --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0 --alignIntronMax 1  --outSAMtype BAM Unsorted --outReadsUnmapped Fastx --outFilterMultimapNmax 100. Non-matched reads were then aligned with Star aligner against a transcriptome, recived from UCSC Table Browser with coding sequences including 3'- and 5'-UTR regions: --readFilesCommand zcat --outFilterMismatchNoverLmax 0.05 --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0 --alignIntronMax 1 --alignEndsType EndToEnd --seedSearchStartLmax 15 --outFileNamePrefix "$outName" --outSAMtype BAM Unsorted --scoreGap 1000000
For 3' Poly(A) RNA-seq, the amount of sequences aligned to transcripts was counted with cuffdiff and column for counts at the + strand was used for downstream analysis. For Ribo-Seq, reads with sizes 20, 21, 28 and 29 were used with an offset of 15nt form the 5' end to the A-site. Reads with A-site positions within the CDS of the corresponding transcript were counted and used for downstream analysis.
Genome_build: For 3' Poly(A) RNA-seq: GRCh38.101, for Ribo-Seq: hg38
Supplementary_files_format_and_content: table with 2 columns in .txt format, column1: Ensemble Gene Accession Number/Gene symbol, column2: corresponding counts

source_name: Brain microvascular endothelial cells

extract_protocol:
RPF were prepared as described in McGlincy & Ingolia 2017, with exception of ommission of any translation inbibitors. RPF were pelleted over 50% sucrose cushion. Pellet was resolved in Qiazol and RPF were extracted using miRNEasy Mini Kit (Qiagen). Sizes between 17 and 34 nt were selected by 15% TBE-Urea gel electrophoresis and treated with T4 PNK following manufacturers protocol (ThermoFisher).
Libraries were prepared with the TrueQuant SmallRNA-NGS Kit (GenXPro). Ribosomal RNA was removed with Ribo-Zero Gold (Illumina). Reads were sequenced to 30M raw reads on an Illumina NextSeq500 machine.

tag: age

value: MCT8 P321L 2PB


title: ST_mock_rep1


title: 2A2-wo_1

description:
RPF
Small RNA RNA-seq

value: MCT8 P321L-corr


title: LSK_con1_ATAC

value: LSK


title: SD, scRNA

status: Public on Dec 01 2024

city: 重庆Chongqing

first: Zeyu

last: Fu

state: 重庆Chongqing

address: 高滩岩正街

department: College of Preventive Medicine

institute: AMU

description: 10X Genomics

data_processing:
Cellranger 7.0.1
Assembly: mm10
Supplementary files format and content: loom files

source_name: Bone marrow

extract_protocol:
We prepared the bone marrow single-cell suspension by harvesting the femurs and tibias from euthanized mice, flushing the marrow into a sterile tube, gently dissociating the cells, filtering the suspension through a 70 µm cell strainer, centrifuging to pellet the cells, resuspending the pellet in an appropriate buffer, and assessing cell concentration and viability to ensure a high-quality single-cell suspension for downstream applications.
We performed single-cell library preparation by first isolating total bone marrow cells and sorting them using LK magnetic beads to enrich for specific cell populations. The sorted cells were then mixed in a 1:1 ratio with the total bone marrow cells to ensure a representative sample. The mixed cell suspension was loaded onto a microfluidic device for single-cell capture, allowing individual cells to be encapsulated in droplets. Reverse transcription was conducted within each droplet to convert the mRNA from each cell into complementary DNA (cDNA), which was subsequently amplified to generate sufficient material for library preparation. The amplified cDNA was processed to construct the sequencing library, including the addition of sequencing adapters and barcodes for identification. Quality control was performed to ensure the constructed library met the required standards for sequencing. Finally, the library was sequenced using a high-throughput sequencing platform, enabling us to analyze the gene expression profiles of individual cells and gain insights into the effects of sleep deprivation on hematopoietic stem cells and the bone marrow microenvironment.

value: Bone marrow

value: LK cells and Bone marrow 1:1

value: sleep deprivation


title: LT-HSC_con2_RNA

value: Setdb1 +/p;vav-cre


title: CS01-2PB_1

description:
RPF
Small RNA RNA-seq


title: Br_Y5_2

city: Beijing

first: Lun

address: No. 2, Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

data_processing:
NovaSeq 6000
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2 / HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
FPKM （Fragments Per Kilobases per Millionreads）values were used to show gene expression level.
Genome_build: SL 3.0; https://solgenomics.net/organism/Solanum_lycopersicum/genome
Supplementary_files_format_and_content: text files include FPKM values for each Sample

extract_protocol: Total RNA was extracted from above tomato fruits by TRIzol reagent and three biological replicates were taken.

value: fruit

tag: time

value: 25 DDA


title: PB_WT_115

value: WT


title: PHILO, Tomato, IgG, rep2


title: CS01-wo_2

description:
RPF
Small RNA RNA-seq

value: MCT8 P321L


title: CS01-wo_1

description:
RPF
Small RNA RNA-seq


title: LSK_mut1_ATAC

value: Setdb1 p/p;vav-cre


title: PHILO, Tomato, H3K4me3, rep3

value: anti-H3K4me3 (#04-475, Millipore Sigma)

value: Micro-Tom


title: PB_WT_10


title: LSK_con2_ATAC


title: ST_mock_rep2

value: ST

value: mock


title: KOLF2_WT_BSA_HAND1_R1

value: Human induced pluripotent stem cell


title: PHILO, Tomato, H3K4me3, rep2


title: CT, scRNA

description: 10X Genomics

value: control


title: PHILO, Tomato, H3K4me3, rep1


title: Br_Y5_14


title: Br_Y5_10_B


title: 2A2-wo_2

description:
RPF
Small RNA RNA-seq

value: MCT8 P321L-corr


title: PB_WT_6


title: Flow_rep5

type: RNA

city: Toronto

first: Philip

middle: A

last: Marsden

state: ON

address: 209 Victoria Street, Room 522

department: Medicine

institute: University of Toronto

description: gene expression in non-pulsatile, laminar flow conditions

hyb_protocol: Cy3-Labeled cRNA was hybridized to Custom Arraystar Human LncRNA Array v3.0 (8x 60K, Arraystar) using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Scanner G2505C

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis

source_name: HUVEC, laminar flow 48 hours

growth_protocol: HUVECs were isolated from umbilical cords of male and female births. HUVECs were cultured in supplemented Endothelial Cell Growth Media (PromoCell) for 2 passages and all biological replicates were used at passage 2-4.

extract_protocol: Total RNA was extracted from HUVECs using Rneasy Mini Kit (Qiagen). A known amount of exogenous luciferase RNA was introduced at the beginning of the extraction to evaluate efficiency of RNA extraction and first strand cDNA synthesis.

treatment_protocol: Each biological replicate was subjected to either static or non-pulsatile, laminar flow conditions (10 dynes/cm2, 48 hours, 1 Hz) using a parallel plate flow chamber in 5% CO2, 37°C.

tag: cell

value: endothelial cells

tag: gender

value: female


title: Ad-KLF2_si1_rep2

description: gene expression

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis

source_name: HUVEC, Adenovirus KLF2 and nimbuss siRNA 1

extract_protocol: Total RNA was extracted from HUVECs using Rneasy Mini Kit (Qiagen). A known amount of exogenous luciferase RNA was introduced at the beginning of the extraction to assess for RNA extraction and first strand cDNA synthesis efficiency.

treatment_protocol: Four biological replicates of HUVECs were transduced with adenoviruses expressing GFP only or murine KLF2 at a MOI of 200 for 96 hours prior to harvesting. siRNA transfection for NIMBUSS was performed using two independent siRNAs at 48 hours prior to harvesting for total cell lysates and total RNA isolation.

value: male


title: Flow_rep4


title: Static_rep5

description: gene expression in static conditions

source_name: HUVEC, static 48 hours


title: Static_rep3

description: gene expression in static conditions


title: Ad-KLF2_si2_rep4

description: gene expression

source_name: HUVEC, Adenovirus KLF2 and nimbuss siRNA 2


title: Static_rep4

description: gene expression in static conditions


title: Flow_rep1


title: genomic DNA from sample398

type: genomic

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description: whole blood case sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples.
matrix processed value definition: Funnorm normalized

label: Cy5 and Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: diagnosis

value: case

tag: Sex

tag: bmi

tag: cellcount-mono

tag: cellcount-gran

tag: cellcount-nk

tag: cellcount-bcell

tag: snp based principle component 1

tag: snp based principle component 2


title: Ad-KLF2_siCTL_rep4

description: gene expression

source_name: HUVEC, Adenovirus KLF2 and control siRNA


title: Ad-GFP_siCTL_rep4

description: gene expression

source_name: HUVEC, Adenovirus GFP and control siRNA


title: Ad-KLF2_siCTL_rep3

description: gene expression


title: Flow_rep3


title: Ad-GFP_siCTL_rep2

description: gene expression


title: genomic DNA from sample397

description: whole blood case sample


title: Ad-KLF2_siCTL_rep2

description: gene expression


title: genomic DNA from sample396

description: whole blood control sample


title: Ad-KLF2_si1_rep4

description: gene expression


title: Ad-KLF2_si2_rep3

description: gene expression


title: Flow_rep2


title: genomic DNA from sample395

description: whole blood control sample


title: Static_rep1

description: gene expression in static conditions


title: Ad-KLF2_si2_rep1

description: gene expression


title: Static_rep2

description: gene expression in static conditions


title: genomic DNA from sample394

description: whole blood case sample


title: Ad-KLF2_si2_rep2

description: gene expression


title: Ad-GFP_siCTL_rep3

description: gene expression


title: Ad-GFP_siCTL_rep1

description: gene expression


title: genomic DNA from sample393

description: whole blood case sample


title: genomic DNA from sample391

description: whole blood control sample


title: Ad-KLF2_si1_rep1

description: gene expression


title: genomic DNA from sample390

description: whole blood control sample


title: genomic DNA from sample389

description: whole blood control sample


title: genomic DNA from sample388

description: whole blood control sample


title: genomic DNA from sample387

description: whole blood control sample


title: genomic DNA from sample386

description: whole blood control sample


title: genomic DNA from sample392

description: whole blood control sample


title: genomic DNA from sample383

description: whole blood case sample


title: genomic DNA from sample382

description: whole blood control sample


title: genomic DNA from sample384

description: whole blood case sample


title: Ad-KLF2_si1_rep3

description: gene expression


title: genomic DNA from sample385

description: whole blood control sample


title: Ad-KLF2_siCTL_rep1

description: gene expression


title: genomic DNA from sample378

description: whole blood case sample


title: genomic DNA from sample376

description: whole blood control sample


title: genomic DNA from sample375

description: whole blood control sample


title: genomic DNA from sample381

description: whole blood control sample


title: genomic DNA from sample374

description: whole blood case sample


title: genomic DNA from sample373

description: whole blood case sample


title: genomic DNA from sample371

description: whole blood control sample


title: genomic DNA from sample380

description: whole blood control sample


title: genomic DNA from sample367

description: whole blood control sample


title: genomic DNA from sample379

description: whole blood control sample


title: genomic DNA from sample362

description: whole blood case sample


title: genomic DNA from sample366

description: whole blood case sample


title: genomic DNA from sample369

description: whole blood case sample


title: genomic DNA from sample372

description: whole blood control sample


title: genomic DNA from sample370

description: whole blood case sample


title: genomic DNA from sample360

description: whole blood control sample


title: genomic DNA from sample368

description: whole blood control sample


title: genomic DNA from sample358

description: whole blood case sample


title: genomic DNA from sample359

description: whole blood control sample


title: genomic DNA from sample361

description: whole blood case sample


title: genomic DNA from sample356

description: whole blood case sample


title: genomic DNA from sample353

description: whole blood control sample


title: genomic DNA from sample365

description: whole blood case sample


title: genomic DNA from sample364

description: whole blood control sample


title: genomic DNA from sample377

description: whole blood case sample


title: genomic DNA from sample349

description: whole blood control sample


title: genomic DNA from sample363

description: whole blood control sample


title: genomic DNA from sample357

description: whole blood case sample


title: genomic DNA from sample346

description: whole blood case sample


title: genomic DNA from sample355

description: whole blood case sample


title: genomic DNA from sample354

description: whole blood control sample


title: genomic DNA from sample352

description: whole blood control sample


title: genomic DNA from sample351

description: whole blood control sample


title: genomic DNA from sample341

description: whole blood case sample


title: genomic DNA from sample342

description: whole blood case sample


title: genomic DNA from sample350

description: whole blood control sample


title: genomic DNA from sample347

description: whole blood case sample


title: genomic DNA from sample348

description: whole blood case sample


title: genomic DNA from sample334

description: whole blood case sample


title: genomic DNA from sample333

description: whole blood case sample


title: genomic DNA from sample343

description: whole blood control sample


title: genomic DNA from sample339

description: whole blood control sample


title: genomic DNA from sample344

description: whole blood control sample


title: genomic DNA from sample337

description: whole blood control sample


title: genomic DNA from sample338

description: whole blood control sample


title: genomic DNA from sample336

description: whole blood control sample


title: genomic DNA from sample335

description: whole blood control sample


title: genomic DNA from sample331

description: whole blood control sample


title: genomic DNA from sample329

description: whole blood control sample


title: genomic DNA from sample328

description: whole blood case sample


title: genomic DNA from sample326

description: whole blood control sample


title: genomic DNA from sample324

description: whole blood case sample


title: genomic DNA from sample323

description: whole blood case sample


title: genomic DNA from sample321

description: whole blood case sample


title: genomic DNA from sample319

description: whole blood control sample


title: genomic DNA from sample325

description: whole blood control sample


title: genomic DNA from sample320

description: whole blood control sample


title: genomic DNA from sample327

description: whole blood case sample


title: genomic DNA from sample340

description: whole blood control sample


title: genomic DNA from sample315

description: whole blood control sample


title: genomic DNA from sample332

description: whole blood control sample


title: genomic DNA from sample318

description: whole blood control sample


title: genomic DNA from sample311

description: whole blood case sample


title: genomic DNA from sample330

description: whole blood control sample


title: genomic DNA from sample316

description: whole blood control sample


title: genomic DNA from sample309

description: whole blood case sample


title: genomic DNA from sample307

description: whole blood control sample


title: genomic DNA from sample312

description: whole blood case sample


title: genomic DNA from sample313

description: whole blood case sample


title: genomic DNA from sample322

description: whole blood case sample


title: genomic DNA from sample304

description: whole blood case sample


title: genomic DNA from sample314

description: whole blood case sample


title: genomic DNA from sample310

description: whole blood case sample


title: genomic DNA from sample345

description: whole blood case sample


title: genomic DNA from sample306

description: whole blood control sample


title: genomic DNA from sample308

description: whole blood control sample


title: genomic DNA from sample305

description: whole blood control sample


title: genomic DNA from sample301

description: whole blood control sample


title: genomic DNA from sample297

description: whole blood control sample


title: genomic DNA from sample298

description: whole blood control sample


title: genomic DNA from sample296

description: whole blood case sample


title: genomic DNA from sample302

description: whole blood control sample


title: genomic DNA from sample300

description: whole blood case sample


title: genomic DNA from sample317

description: whole blood control sample


title: genomic DNA from sample299

description: whole blood case sample


title: genomic DNA from sample294

description: whole blood control sample


title: genomic DNA from sample291

description: whole blood case sample


title: genomic DNA from sample293

description: whole blood control sample


title: genomic DNA from sample292

description: whole blood case sample


title: genomic DNA from sample287

description: whole blood control sample


title: genomic DNA from sample285

description: whole blood case sample


title: genomic DNA from sample289

description: whole blood control sample


title: genomic DNA from sample290

description: whole blood control sample


title: genomic DNA from sample288

description: whole blood control sample


title: genomic DNA from sample284

description: whole blood case sample


title: genomic DNA from sample303

description: whole blood case sample


title: genomic DNA from sample282

description: whole blood control sample


title: genomic DNA from sample281

description: whole blood control sample


title: genomic DNA from sample280

description: whole blood case sample


title: genomic DNA from sample277

description: whole blood control sample


title: genomic DNA from sample278

description: whole blood control sample


title: genomic DNA from sample279

description: whole blood case sample


title: genomic DNA from sample295

description: whole blood case sample


title: genomic DNA from sample275

description: whole blood case sample


title: genomic DNA from sample271

description: whole blood case sample


title: genomic DNA from sample270

description: whole blood control sample


title: genomic DNA from sample268

description: whole blood control sample


title: genomic DNA from sample273

description: whole blood control sample


title: genomic DNA from sample272

description: whole blood case sample


title: genomic DNA from sample274

description: whole blood control sample


title: genomic DNA from sample269

description: whole blood control sample


title: genomic DNA from sample267

description: whole blood control sample


title: genomic DNA from sample263

description: whole blood case sample


title: genomic DNA from sample261

description: whole blood control sample


title: genomic DNA from sample262

description: whole blood control sample


title: genomic DNA from sample286

description: whole blood case sample


title: genomic DNA from sample264

description: whole blood case sample


title: genomic DNA from sample265

description: whole blood control sample


title: genomic DNA from sample266

description: whole blood control sample


title: genomic DNA from sample256

description: whole blood case sample


title: genomic DNA from sample260

description: whole blood case sample


title: genomic DNA from sample283

description: whole blood case sample


title: genomic DNA from sample258

description: whole blood control sample


title: genomic DNA from sample255

description: whole blood case sample


title: genomic DNA from sample276

description: whole blood case sample


title: genomic DNA from sample253

description: whole blood control sample


title: genomic DNA from sample257

description: whole blood control sample


title: genomic DNA from sample251

description: whole blood control sample


title: genomic DNA from sample250

description: whole blood control sample


title: genomic DNA from sample252

description: whole blood control sample


title: genomic DNA from sample248

description: whole blood control sample


title: genomic DNA from sample249

description: whole blood control sample


title: genomic DNA from sample244

description: whole blood control sample


title: genomic DNA from sample243

description: whole blood control sample


title: genomic DNA from sample247

description: whole blood control sample


title: genomic DNA from sample245

description: whole blood case sample


title: genomic DNA from sample242

description: whole blood case sample


title: genomic DNA from sample240

description: whole blood control sample


title: genomic DNA from sample237

description: whole blood case sample


title: genomic DNA from sample232

description: whole blood control sample


title: genomic DNA from sample259

description: whole blood case sample


title: genomic DNA from sample239

description: whole blood control sample


title: genomic DNA from sample230

description: whole blood control sample


title: genomic DNA from sample231

description: whole blood control sample


title: genomic DNA from sample238

description: whole blood case sample


title: genomic DNA from sample228

description: whole blood case sample


title: genomic DNA from sample227

description: whole blood case sample


title: genomic DNA from sample236

description: whole blood control sample


title: genomic DNA from sample234

description: whole blood case sample


title: genomic DNA from sample233

description: whole blood case sample


title: genomic DNA from sample241

description: whole blood case sample


title: genomic DNA from sample246

description: whole blood case sample


title: genomic DNA from sample235

description: whole blood control sample


title: genomic DNA from sample254

description: whole blood control sample


title: genomic DNA from sample222

description: whole blood case sample


title: genomic DNA from sample224

description: whole blood control sample


title: genomic DNA from sample219

description: whole blood control sample


title: genomic DNA from sample226

description: whole blood control sample


title: genomic DNA from sample218

description: whole blood control sample


title: genomic DNA from sample229

description: whole blood control sample


title: genomic DNA from sample215

description: whole blood control sample


title: genomic DNA from sample216

description: whole blood control sample


title: genomic DNA from sample214

description: whole blood control sample


title: genomic DNA from sample223

description: whole blood control sample


title: genomic DNA from sample220

description: whole blood control sample


title: genomic DNA from sample213

description: whole blood control sample


title: genomic DNA from sample217

description: whole blood control sample


title: genomic DNA from sample221

description: whole blood case sample


title: genomic DNA from sample212

description: whole blood case sample


title: genomic DNA from sample209

description: whole blood case sample


title: genomic DNA from sample205

description: whole blood control sample


title: genomic DNA from sample202

description: whole blood control sample


title: genomic DNA from sample200

description: whole blood case sample


title: genomic DNA from sample211

description: whole blood case sample


title: genomic DNA from sample225

description: whole blood control sample


title: genomic DNA from sample199

description: whole blood case sample


title: genomic DNA from sample210

description: whole blood case sample


title: genomic DNA from sample204

description: whole blood case sample


title: genomic DNA from sample198

description: whole blood control sample


title: genomic DNA from sample207

description: whole blood control sample


title: genomic DNA from sample203

description: whole blood case sample


title: genomic DNA from sample201

description: whole blood control sample


title: genomic DNA from sample206

description: whole blood control sample


title: genomic DNA from sample193

description: whole blood control sample


title: genomic DNA from sample190

description: whole blood case sample


title: genomic DNA from sample192

description: whole blood control sample


title: genomic DNA from sample189

description: whole blood case sample


title: genomic DNA from sample197

description: whole blood control sample


title: genomic DNA from sample191

description: whole blood control sample


title: genomic DNA from sample208

description: whole blood control sample


title: genomic DNA from sample195

description: whole blood control sample


title: genomic DNA from sample186

description: whole blood control sample


title: genomic DNA from sample185

description: whole blood control sample


title: genomic DNA from sample194

description: whole blood control sample


title: genomic DNA from sample187

description: whole blood control sample


title: genomic DNA from sample181

description: whole blood control sample


title: genomic DNA from sample183

description: whole blood case sample


title: genomic DNA from sample182

description: whole blood control sample


title: genomic DNA from sample196

description: whole blood control sample


title: genomic DNA from sample188

description: whole blood control sample


title: genomic DNA from sample180

description: whole blood case sample


title: genomic DNA from sample184

description: whole blood case sample


title: genomic DNA from sample176

description: whole blood control sample


title: genomic DNA from sample177

description: whole blood case sample


title: genomic DNA from sample179

description: whole blood case sample


title: genomic DNA from sample173

description: whole blood control sample


title: genomic DNA from sample178

description: whole blood case sample


title: genomic DNA from sample175

description: whole blood control sample


title: genomic DNA from sample171

description: whole blood case sample


title: genomic DNA from sample172

description: whole blood case sample


title: genomic DNA from sample174

description: whole blood control sample


title: genomic DNA from sample170

description: whole blood case sample


title: genomic DNA from sample167

description: whole blood case sample


title: genomic DNA from sample168

description: whole blood case sample


title: genomic DNA from sample169

description: whole blood case sample


title: genomic DNA from sample161

description: whole blood control sample


title: genomic DNA from sample166

description: whole blood control sample


title: genomic DNA from sample163

description: whole blood control sample


title: genomic DNA from sample153

description: whole blood case sample


title: genomic DNA from sample151

description: whole blood control sample


title: genomic DNA from sample162

description: whole blood control sample


title: genomic DNA from sample155

description: whole blood case sample


title: genomic DNA from sample149

description: whole blood control sample


title: genomic DNA from sample156

description: whole blood case sample


title: genomic DNA from sample154

description: whole blood case sample


title: genomic DNA from sample144

description: whole blood case sample


title: genomic DNA from sample146

description: whole blood control sample


title: genomic DNA from sample157

description: whole blood control sample


title: genomic DNA from sample152

description: whole blood control sample


title: genomic DNA from sample141

description: whole blood control sample


title: genomic DNA from sample164

description: whole blood control sample


title: genomic DNA from sample140

description: whole blood control sample


title: genomic DNA from sample139

description: whole blood control sample


title: genomic DNA from sample150

description: whole blood control sample


title: genomic DNA from sample147

description: whole blood control sample


title: genomic DNA from sample148

description: whole blood control sample


title: genomic DNA from sample145

description: whole blood control sample


title: genomic DNA from sample158

description: whole blood control sample


title: genomic DNA from sample143

description: whole blood case sample


title: genomic DNA from sample142

description: whole blood control sample


title: genomic DNA from sample165

description: whole blood control sample


title: genomic DNA from sample137

description: whole blood case sample


title: genomic DNA from sample160

description: whole blood case sample


title: genomic DNA from sample138

description: whole blood case sample


title: genomic DNA from sample159

description: whole blood case sample


title: genomic DNA from sample135

description: whole blood control sample


title: genomic DNA from sample130

description: whole blood control sample


title: genomic DNA from sample124

description: whole blood case sample


title: genomic DNA from sample134

description: whole blood case sample


title: genomic DNA from sample133

description: whole blood case sample


title: genomic DNA from sample123

description: whole blood case sample


title: genomic DNA from sample122

description: whole blood case sample


title: genomic DNA from sample132

description: whole blood control sample


title: genomic DNA from sample129

description: whole blood control sample


title: genomic DNA from sample131

description: whole blood control sample


title: genomic DNA from sample121

description: whole blood case sample


title: genomic DNA from sample136

description: whole blood control sample


title: genomic DNA from sample117

description: whole blood control sample


title: genomic DNA from sample127

description: whole blood control sample


title: genomic DNA from sample128

description: whole blood control sample


title: genomic DNA from sample113

description: whole blood control sample


title: genomic DNA from sample125

description: whole blood case sample


title: genomic DNA from sample110

description: whole blood case sample


title: genomic DNA from sample109

description: whole blood case sample


title: genomic DNA from sample107

description: whole blood control sample


title: genomic DNA from sample120

description: whole blood control sample


title: genomic DNA from sample118

description: whole blood control sample


title: genomic DNA from sample119

description: whole blood control sample


title: genomic DNA from sample116

description: whole blood control sample


title: genomic DNA from sample115

description: whole blood control sample


title: genomic DNA from sample104

description: whole blood control sample


title: genomic DNA from sample101

description: whole blood case sample


title: genomic DNA from sample100

description: whole blood case sample


title: genomic DNA from sample108

description: whole blood control sample


title: genomic DNA from sample102

description: whole blood case sample


title: genomic DNA from sample114

description: whole blood control sample


title: genomic DNA from sample126

description: whole blood case sample


title: genomic DNA from sample106

description: whole blood case sample


title: genomic DNA from sample112

description: whole blood case sample


title: genomic DNA from sample105

description: whole blood case sample


title: genomic DNA from sample111

description: whole blood case sample


title: genomic DNA from sample93

description: whole blood case sample


title: genomic DNA from sample92

description: whole blood case sample


title: genomic DNA from sample97

description: whole blood control sample


title: genomic DNA from sample99

description: whole blood case sample


title: genomic DNA from sample98

description: whole blood control sample


title: genomic DNA from sample96

description: whole blood control sample


title: genomic DNA from sample88

description: whole blood control sample


title: genomic DNA from sample89

description: whole blood case sample


title: genomic DNA from sample87

description: whole blood control sample


title: genomic DNA from sample95

description: whole blood control sample


title: genomic DNA from sample85

description: whole blood control sample


title: genomic DNA from sample83

description: whole blood control sample


title: genomic DNA from sample94

description: whole blood case sample


title: genomic DNA from sample77

description: whole blood control sample


title: genomic DNA from sample79

description: whole blood case sample


title: genomic DNA from sample80

description: whole blood case sample


title: genomic DNA from sample76

description: whole blood control sample


title: genomic DNA from sample91

description: whole blood case sample


title: genomic DNA from sample74

description: whole blood case sample


title: genomic DNA from sample90

description: whole blood case sample


title: genomic DNA from sample73

description: whole blood case sample


title: genomic DNA from sample70

description: whole blood control sample


title: genomic DNA from sample86

description: whole blood control sample


title: genomic DNA from sample71

description: whole blood case sample


title: genomic DNA from sample84

description: whole blood control sample


title: genomic DNA from sample67

description: whole blood control sample


title: genomic DNA from sample69

description: whole blood control sample


title: genomic DNA from sample103

description: whole blood control sample


title: genomic DNA from sample82

description: whole blood control sample


title: genomic DNA from sample62

description: whole blood case sample


title: genomic DNA from sample61

description: whole blood case sample


title: genomic DNA from sample64

description: whole blood case sample


title: genomic DNA from sample81

description: whole blood control sample


title: genomic DNA from sample75

description: whole blood control sample


title: genomic DNA from sample72

description: whole blood case sample


title: genomic DNA from sample59

description: whole blood control sample


title: genomic DNA from sample68

description: whole blood control sample


title: genomic DNA from sample65

description: whole blood control sample


title: genomic DNA from sample63

description: whole blood case sample


title: genomic DNA from sample58

description: whole blood case sample


title: genomic DNA from sample60

description: whole blood control sample


title: genomic DNA from sample57

description: whole blood case sample


title: genomic DNA from sample56

description: whole blood control sample


title: genomic DNA from sample78

description: whole blood control sample


title: genomic DNA from sample54

description: whole blood case sample


title: genomic DNA from sample46

description: whole blood case sample


title: genomic DNA from sample47

description: whole blood control sample


title: genomic DNA from sample51

description: whole blood case sample


title: genomic DNA from sample55

description: whole blood control sample


title: genomic DNA from sample52

description: whole blood case sample


title: genomic DNA from sample53

description: whole blood case sample


title: genomic DNA from sample44

description: whole blood case sample


title: genomic DNA from sample50

description: whole blood control sample


title: genomic DNA from sample43

description: whole blood case sample


title: genomic DNA from sample42

description: whole blood case sample


title: genomic DNA from sample49

description: whole blood control sample


title: genomic DNA from sample66

description: whole blood control sample


title: genomic DNA from sample40

description: whole blood control sample


title: genomic DNA from sample48

description: whole blood control sample


title: genomic DNA from sample37

description: whole blood control sample


title: genomic DNA from sample39

description: whole blood control sample


title: genomic DNA from sample41

description: whole blood case sample


title: genomic DNA from sample38

description: whole blood control sample


title: genomic DNA from sample36

description: whole blood case sample


title: genomic DNA from sample34

description: whole blood case sample