title: HDLECs_CtrlsiRNA_1

description: Raw counts


title: G402_Tet_GFP_Doxycycline_Rep3

status: Public on Nov 29 2023

type: SRA

city: Chicago

first: Marc

last: Morgan

state: IL

address: 303 East Superior St, SQI 7-511

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
Basecalls were performed using bcl2fastq v2.17
ChIP-seq and RNA-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 UCSC hg38 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg38 using Tophat version 2.0.9.  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.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg38
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: SYO1, G402 and DLD1 cells were grown in DMEM supplemented with 15% fetal bovine serum.

extract_protocol:
RNA was prepared usng a Qiagen Rneasy Miniprep kit. ChIP DNA was purified using a Zymo ChIP clean and concentrator kit.
ChIP-sequencing 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. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were subjected to treatment wih Doxycycline at 2ug/ml and JQ1 and 1uM for 24 or 48 hours.

tag: cell type

value: Malignant Rhabdoid Tumor

tag: genotype

value: wild-type


title: Control Male.9 [M9]

first: Mark

last: Maienschein-Cline

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description:
M9
HBV.fa

library_source: genomic

data_processing:
Raw paired-end sequence data were merged without trimming using the software package PEAR. Merged reads were mapped to the HBV reference DNA sequence (HBV.fa) using Bismark. Methylation status was called at each CpG using Bismark, and total counts, methylated counts, and percent methylation were computed for each CpG position.
Assembly: Custom (supplementary file HBV.fa)
Supplementary files format and content: methyl_levels.txt: Tab-delimited text file of total coverage, methylated read coverage, and percent methylation for each sample.
Supplementary files format and content: HBV.fa: fatsa file of hepatitis B virus sequence used as reference genome

molecule: genomic DNA

organism: Hepatitis B virus

source_name: Liver

extract_protocol: Bisulfite treatment of protein-free genomic DNA for methylation analysis was performed using the EZ DNA Methylation-Lightning Kit (D5030; Zymo Research, Inc., Irvine, CA, USA) according to the manufacturer's instructions.  The three major viral amplicons covering 62 of the 99 CpG sequences in the HBV DNA genome were targeted using PCR amplification of the bisulfite-treated DNA, followed by sequencing of the amplicons on an Illumina MiSeq instrument.  Preparation of DNA for high-throughput amplicon sequencing was performed in two PCR steps in a protocol termed targeted amplicon sequencing (TAS)  The primer pairs targeting the bisulfite converted HBV DNA were (i) 5’-ACACTGACGACATGGTTCTACACCCCCACTAACTAAAAC-3’ (oligo CS1FP2; HBV nucleotide coordinates 1198-1214) and 5’- TACGGTAGCAGAGACTTGGTCTGGGTAATATTTGGTGG-3’ (oligo CS2RP2; HBV nucleotide coordinates 1645-1630), (ii) 5’-ACACTGACGACATGGTTCTACAAGTTATAGAGTATTTGGTGT-3’  (oligo CS1FP5a; HBV nucleotide coordinates 2244-2263) and 5’-TACGGTAGCAGAGACTTGGTCTCCCAATAAAATTCCCCA-3’ (oligo CS2RP5a; HBV nucleotide coordinates 2491-2475), and (iii) 5’-ACACTGACGACATGGTTCTACAACCTCCAATCACTCAC-3’ (oligo CS1FP9; HBV nucleotide coordinates 325-340) and 5’-TACGGTAGCAGAGACTTGGTCTGTTAAATAGTGGGGGAAAG-3’ (oligo CS2RP9; HBV nucleotide coordinates 730-712).

tag: tissue

value: Liver


title: leaf, 10 hpi, resistant, rep2

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression after 10 hpi in resistant NIL rep 2

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method .

molecule: total RNA

organism: Triticum aestivum

source_name: leaf, resistant, 10 hpi, rep-2

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Wheat seed were sown in small pots in equal mix of autoclaved soil and soil rite. The pots were kept in climate controlled growth chamber with 16h light and 8 h dark cycle with 80-90 % humidity. Temprature was maintained at 25ºC during light phase and 20ºC during dark phase.

extract_protocol: RNA was prepared using the TRIzol following the manufacturer's recommendations.

treatment_protocol: 25 days old seedlings were injected with stem rust spore suspension ( ~ 6X10¬5 spores/ml in water and 1 ppm tween 20 detergent) using a hypodermal syringe, plants were then initially kept undisturbed for 24 hours in dark and 90% humidity, and then to normal growth (16h light, 8 h dark) conditions. Leaf tissue was collected at 0, 10 & 72 hpi time points.

value: Leaf

tag: age

value: 25 day

tag: phenotype

value: resistant NIL

tag: infection

value: stem rust race

tag: time

value: 10 hpi


title: leaf, 10 hpi, resistant, rep1

description: Gene expression after 10 hpi in resistant NIL rep 1

source_name: leaf, resistant, 10 hpi, rep-1


title: CAGE-seq_BT549 cells, KJ-PYR-9 treatment, BioRep3

city: Odense

first: Simon

middle: Toftholm

last: Jakobsen

state: Syddanmark

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing: Analysis of the data was performed within the CageFigthR software

source_name: Cell line

growth_protocol: BT549 cells were maintained in RPMI supplemented with 10% FBS and antibiotics and culutred at 37oC and 5% CO2

extract_protocol: CAGE-seq analysis performed following a previously described protocol (Cvetesic et al., 2018). In brief, sample RNA was mixed with carrier RNA followed by first-strand cDNA synthesis. The ends of the RNA were oxidized, biotinylated and RNA fragments not overlapping first-strand cDNA were RNase digested. This provided a library of fragments where the biotinylated 5’cap was pulled down using streptavidin paramagnetic beads. The cap-trapped cDNA strand was then released by RNase treatment and the linker was ligated to the first cDNA strand followed by second-strand cDNA synthesis. The carrier was degraded, and the libraries were then purified using SPRI paramagnetic beads, PCR amplified and subjected to sequencing on Illumina NextSeq 550 to a minimum of 35M reads per sample.

treatment_protocol: 40μM KJ-PYR-9 (dissolved in DMSO) for 3hr

value: Cell line

tag: cell line

value: TNBC

value: WT

tag: treatment


title: leaf, 72 hpi, susceptible, rep2

description: Gene expression after 72 hpi in susceptible NIL  rep 2

source_name: leaf, susceptible, 72 hpi, rep-2

value: susceptible NIL

value: 72 hpi


title: Tet2&3-deficient Male.4 [M8]

description:
M8
HBV.fa


title: DLD1_Tet_ELOA3_JQ1_Rep1

value: Colorectal Carcinoma


title: CAGE-seq_BT549 cells, KJ-PYR-9 treatment, BioRep2


title: Tet2&3-deficient Male.3 [M7]

description:
M7
HBV.fa


title: leaf, 72 hpi, resistant, rep1

description: Gene expression after 72 hpi in resistant NIL rep 1

source_name: leaf, resistant, 72 hpi, rep-1


title: leaf, 10 hpi, susceptible, rep1

description: Gene expression after 10 hpi in susceptible NIL  rep 1

source_name: leaf, susceptible, 10 hpi, rep-1


title: CAGE-seq_BT549 cells, KJ-PYR-9 treatment, BioRep1


title: leaf, 0 hpi, resistant, rep1

description: Gene expression after 0 hpi in resistant NIL rep 1

source_name: leaf, resistant, 0 hpi, rep-1

value: control

value: 0 hpi


title: CAGE-seq_BT549 cells, VEH treatment, BioRep3

value: VEH


title: leaf, 0 hpi, resistant, rep2

description: Gene expression after 0 hpi in resistant NIL rep 2

source_name: leaf, resistant, 0 hpi, rep-2


title: DLD1_Tet_ELOA3_DMSO_Rep1


title: leaf, 10 hpi, susceptible, rep2

description: Gene expression after 10 hpi in susceptible NIL  rep 2

source_name: leaf, susceptible, 10 hpi, rep-2


title: DLD1_Tet_GFP_JQ1_and_Doxycycline_Rep2


title: 1000 ppm CO2 PSI-PI 4

city: Turku

first: Mehmet

last: Kilic

address: FI-20014 TURUN YLIOPISTO

department: Molecular Plant Biology

country: Finland

institute: University of Turku

description: 1000 ppm CO2 PSI-PI 4

data_processing:
Salmon (v0.12; Patro et al., 2017) for quantification.
Transcripts were aggregated to the gene level using tximport R package.
Raw counts were obtained with DESeq2 R package.
Assembly: TAIR10.49
Supplementary files format and content: Tab-limited text file includes raw counts for each sample
Supplementary files format and content: Tab-limited text file includes log2 and P values for comparisons of PSI-PI treatments against GL conditions; and 0, 100 and 1000 ppm CO2 against 400 ppm CO2 for  both GL and PSI-PI.

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis thaliana plants were grown in 8 h day under 100 µmol photons m-2s-1 for 6-7 weeks.

extract_protocol:
RNA was isolated with innuPREP plant RNA isolation kit (Analytik Jena) according to manufacturers instructions.
RNA libraryies were sent to BGI Europe Genomic Center for sequencing

treatment_protocol: GL plants were exposed to growth light for 3 hours. PSI-PI plants were exposed to treatment cycle [3 repetions of (5 s of 35 µmol photons m-2s-1 light, 660 nm wave length -> 1 s of 1000 µmol photons m-2s-1 light, all wave lengths) , then treated with 30 s of 100 µmol photons m-2s-1 light, all wave lengths] for 3 hours according to Tikkanen and Grebe 2018.

value: PSI photoinhibition


title: 1000 ppm CO2 PSI-PI 3

description: 1000 ppm CO2 PSI-PI 3


title: Tet3-deficient Male.3 [M4]

description:
M4
HBV.fa


title: leaf, 0 hpi, susceptible, rep2

description: Gene expression after 0 hpi in susceptible NIL  rep 2

source_name: leaf, susceptible, 0 hpi, rep-2


title: CAGE-seq_BT549 cells, VEH treatment, BioRep2


title: DLD1_Tet_GFP_JQ1_and_Doxycycline_Rep1

value: wild-type


title: 1000 ppm CO2 PSI-PI 2

description: 1000 ppm CO2 PSI-PI 2


title: CAGE-seq_BT549 cells, VEH treatment, BioRep1


title: Control Male.8 [M5]

description:
M5
HBV.fa

value: Liver


title: Tet2-deficient Male.3 [M2]

description:
M2
HBV.fa


title: leaf, 0 hpi, susceptible, rep1

description: Gene expression after 0 hpi in susceptible NIL  rep 1

source_name: leaf, susceptible, 0 hpi, rep-1

value: Leaf


title: DLD1_Tet_GFP_Doxycycline_Rep1


title: ATAC-seq_BT549 cells, KJ-PYR-9 treatment, BioRep2

data_processing:
Sequencing data was demulitplexed using bcl2fastq before aligned to the human genome version GRCh38.
Samtools was used to remove PCR duplicates and low quality reads, before MACS2 was used to call peaks using defult settings.
Homer was used to generate files for plotting the data of the regions of interest.
Supplementary files format and content: hg38

extract_protocol:
50,000 cells were lysed in ATAC-RSB (resuspension buffer) (10mM Tris-HCL pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20) supplemented with 0.1% IgePal-CA630 and 0.01% Digitonin before being washed three times in cold ATAC-RSB buffer. Nuclei were pelleted and resuspended in 50μL transposition mixture (17.75μL PBS, 5uL Nuclease Free Water, 25uL TD 2x reaction buffer, 0.5uL 1% digitonin, 0.5uL 10% Tween-20, 1.25μL TDE1 (Illumina, 20034197)) and incubated at 37oC in a thermomixer at 1000RPM for 30min. DNA was cleaned using Qiagen PCR Purification kit before PCR amplification for 10 cycles using Illumina index primers, 25μL Q5 High Fidelity 2x master mix (New England BioLabs, M0492) in a final volume of 50μL. Samples were size selected and purified using Ampure XP beads (Bechman Coulter, A63881).
Next-generation sequencing was performed using Illumina Novaseq 6000 to get ~25M 50bp paired-end reads per sample


title: ATAC-seq_BT549 cells, KJ-PYR-9 treatment, BioRep1


title: DLD1_Tet_ELOA3_DMSO_Rep2


title: DLD1_Tet_GFP_Doxycycline_Rep2


title: 1000 ppm CO2 GL 4

description: 1000 ppm CO2 GL 4

value: Growth light


title: Tet2&3-deficient Male.2 [M6]

description:
M6
HBV.fa


title: Tet2&3-deficient Male.1 [M19]

description:
M19
HBV.fa


title: ATAC-seq_BT549 cells, VEH treatment, BioRep2


title: DLD1_Tet_GFP_JQ1_Rep2


title: ATAC-seq_BT549 cells, VEH treatment, BioRep1


title: Control Male.6 [M18]

description:
M18
HBV.fa


title: 1000 ppm CO2 GL 2

description: 1000 ppm CO2 GL 2


title: DLD1_Tet_GFP_JQ1_Rep1


title: DLD1_Tet_GFP_DMSO_Rep2


title: Control Male.7 [M3]

description:
M3
HBV.fa


title: 1000 ppm CO2 GL 1

description: 1000 ppm CO2 GL 1


title: 1000 ppm CO2 PSI-PI 1

description: 1000 ppm CO2 PSI-PI 1


title: DLD1_Tet_GFP_DMSO_Rep1


title: Tet3-deficient Male.1 [M15]

description:
M15
HBV.fa


title: Tet3-deficient Male.2 [M16]

description:
M16
HBV.fa


title: 400 ppm CO2 PSI-PI 4

description: 400 ppm CO2 PSI-PI 4


title: SYO1_sgELOA3_Tet_ELOA3_JQ1_and_Doxycycline_Rep1

value: Synovial Sarcoma

value: ELOA3 sgRNA


title: flox, choroid, CD45+

city: OKLAHOMA CITY

first: Jiyang

last: Cai

state: OK

address: 940 STANTON L YOUNG BLVD OUHSC

department: Physiology

institute: UNIVERSITY OF OKLAHOMA HEALTH SCIENCES CENTER

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and mtrix files

organism: Mus musculus

source_name: eye

extract_protocol:
RPE/choroid tissues were digested with collagenase and dispase, labeled with cell viability dye and anti-CD45 antibody, and sorted by flow cytometry
Lbirary was performed according to manufacter's instructions (single cell 3' v2 protocol, 10x Genomics)

treatment_protocol: NaIO3 20 mg/kg body weight, intraperitoneal injection

value: eye

value: IL-17ra fl


title: 400 ppm CO2 PSI-PI 3

description: 400 ppm CO2 PSI-PI 3


title: SYO1_sgELOA3_Tet_ELOA3_JQ1_and_Doxycycline_Rep2


title: Control Male.4 [M14]

description:
M14
HBV.fa


title: AKI stRNAseq

city: Su Zhou

first: Jun

last: Liu

address: No.92, Zhongnan Street, Industrial Park District

country: China

institute: Children’s Hospital of Soochow University

description: 10X genomics

data_processing:
Raw sequencing data were processed with the Cellranger pipeline (version 3.1.0, 10X Genomics) and mapped to the murine reference genome to generate digital gene expression (DGE) matrices. Cells from different batches were merged together, and expressions were normalized to generate a final gene expression matrix.
The raw data from the Spatial Transcriptomics (ST) assay were processed using SpaceRanger (v2.0.1) to generate the ST spots matrix by performing a series of procedures, including alignment, filtering, barcode counting, and UMI counting. Spots with fewer than 200 genes were excluded from further analysis. Normalization across spots was performed with the SCTransform function (0.3.5), and anchors between the spatial transcriptomics spots were identified using the R package “Seurat” (v4.3.0) in R (v4.2.2). Dimension reduction and clustering were performed using PCA. The first ten PCs were used to generate clusters.
Assembly: mm10
Supplementary files format and content: tab-separated text files

source_name: kidney

extract_protocol:
For single-cell suspension preparation, freshly collected mouse kidneys were rinsed twice with RPMI1640 (Gibco), minced into 3-5 mm3 pieces, and subjected to enzymatic digestion using Multi Tissue Dissociation Kits (130-110-204, Miltenyi Biotec) for 30 min under rotation at 250 rpm/min. Afterward, the cell suspension was filtered and centrifuged at 300 g at 4°C. The cell pellet was collected, resuspended in 1 mL RBC lysis buffer (Sigma) to remove RBCs, and then washed twice with RPMI1640. Cell viability was assessed using Trypan Blue (Gibco), and dead cells were removed using magnetic bead separation with a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) if the cell viability was less than 85%.
At least 20,000 cells per sample were applied to a single-cell master mix with lysis buffer and reverse transcription reagents, following the User Guide of 10X Genomics Chromium Single Cell 3’ Reagent Kits (10X Genomics). The libraries were subjected to high-throughput sequencing on a NovaSeq6000 platform.

value: kidney

value: kidney cells

value: wild type

value: I/R


title: 400 ppm CO2 PSI-PI 2

description: 400 ppm CO2 PSI-PI 2


title: SYO1_sgELOA3_Tet_GFP_JQ1_and_Doxycycline_Rep2


title: AKI scRNAseq

description: 10X genomics


title: 1000 ppm CO2 GL 3

description: 1000 ppm CO2 GL 3


title: Control Male.3 [M13]

description:
M13
HBV.fa


title: 400 ppm CO2 PSI-PI 1

description: 400 ppm CO2 PSI-PI 1


title: Control Male.5 [M17]

description:
M17
HBV.fa


title: KO, choroid, CD45+

description: 10x Genomics

value: IL-17RA CKO


title: Control Male.2 [M1]

description:
M1
HBV.fa


title: Tet2-deficient Male.2 [M12]

description:
M12
HBV.fa


title: 400 ppm CO2 GL 4

description: 400 ppm CO2 GL 4


title: Sham scRNAseq

description: 10X genomics

value: sham


title: SYO1_sgCtrl_Tet_ELOA3_JQ1_and_Doxycycline_Rep2


title: DLD1_Tet_ELOA3_JQ1_Rep2

value: Colorectal Carcinoma


title: Dbx2_constitutive_rep8

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
Sequence read quality was evaluated using FastQC version 0.11.8 (Babraham Institute, Cambridge, UK), followed by trimming using bbduk software to remove adapter sequences, poly-A tails and low-quality end bases (Q < 20)
Reads were then mapped to the mouse Ensembl GRCm38 (mm10) build reference genome with STAR version 2.5.0a (Dobin et al., 2013); gene annotations corresponding to Ensembl annotation release 96 were used to build a transcriptome index, which was provided to STAR during the alignment.
Data normalization and differential gene expression analysis were performed using Bioconductor R package edgeR version 3.36 (Robinson et al., 2010) assigning the cell line batch as a covariate to fit the generalized log-linear model of generalized log-linear model
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized CPM values for each Sample

source_name: brain, subventricular zone

extract_protocol:
Total RNA was purified from frozen cell pellets of control and Dbx2-overexpressing non-adherent cultures using Qiagen RNeasy kits
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions. The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NextSeq500 (Illumina) with a read length of 101 bp.

value: brain, subventricular zone

value: NSPCs derived from the SVZ

value: proliferating neural/stem progenitor cells

tag: transgene

value: 3 months old


title: SYO1_sgELOA3_Tet_GFP_JQ1_and_Doxycycline_Rep1


title: Dbx2_constitutive_rep7


title: 400 ppm CO2 GL 3

description: 400 ppm CO2 GL 3

value: Leaf


title: 400 ppm CO2 GL 2

description: 400 ppm CO2 GL 2

value: Growth light


title: Control Male.1 [M10]

description:
M10
HBV.fa

value: Liver


title: sham stRNAseq

description: 10X genomics


title: Control Female.9 [F9]

description:
F9
HBV.fa


title: Dbx2_constitutive_rep5


title: 400 ppm CO2 GL 1

description: 400 ppm CO2 GL 1


title: SYO1_sgCtrl_Tet_ELOA3_JQ1_and_Doxycycline_Rep1

value: Synovial Sarcoma

value: wild-type


title: Dbx2_constitutive_rep6


title: Tet2&3-deficient Female.4 [F8]

description:
F8
HBV.fa


title: 100 ppm CO2 PSI-PI 4

description: 100 ppm CO2 PSI-PI 4

value: PSI photoinhibition


title: SYO1_sgELOA3_Tet_ELOA3_JQ1_Rep2

value: ELOA3 sgRNA


title: 100 ppm CO2 PSI-PI 3

description: 100 ppm CO2 PSI-PI 3


title: SYO1_sgCtrl_Tet_GFP_JQ1_and_Doxycycline_Rep1


title: Tet2&3-deficient Female.3 [F7]

description:
F7
HBV.fa


title: SYO1_sgELOA3_Tet_ELOA3_JQ1_Rep1


title: Dbx2_constitutive_rep4


title: Dbx2_constitutive_rep3


title: Tet2&3-deficient Female.2 [F6]

description:
F6
HBV.fa


title: 100 ppm CO2 PSI-PI 2

description: 100 ppm CO2 PSI-PI 2


title: 100 ppm CO2 PSI-PI 1

description: 100 ppm CO2 PSI-PI 1


title: SYO1_sgELOA3_Tet_GFP_JQ1_Rep2


title: Tet2-deficient Male.1 [M11]

description:
M11
HBV.fa


title: Control Female.8 [F5]

description:
F5
HBV.fa


title: SYO1_sgELOA3_Tet_GFP_JQ1_Rep1


title: Tet3-deficient Female.3 [F4]

description:
F4
HBV.fa


title: Dbx2_constitutive_rep1


title: GFP_CTR_rep8

value: GFP


title: 100 ppm CO2 GL 3

description: 100 ppm CO2 GL 3


title: Control Female.7 [F3]

description:
F3
HBV.fa


title: Tet2-deficient Female.3 [F2]

description:
F2
HBV.fa


title: GFP_CTR_rep7


title: SYO1_sgCtrl_Tet_GFP_JQ1_and_Doxycycline_Rep2


title: SYO1_sgCtrl_Tet_ELOA3_JQ1_Rep1


title: SYO1_sgCtrl_Tet_ELOA3_JQ1_Rep2


title: SYO1_sgCtrl_Tet_GFP_JQ1_Rep2


title: GFP_CTR_rep6


title: 100 ppm CO2 GL 1

description: 100 ppm CO2 GL 1


title: GFP_CTR_rep5


title: 0 ppm CO2 PSI-PI 4

description: 0 ppm CO2 PSI-PI 4


title: 100 ppm CO2 GL 2

description: 100 ppm CO2 GL 2


title: Tet2&3-deficient Female.1 [F19]

description:
F19
HBV.fa


title: Control Female.6 [F18]

description:
F18
HBV.fa


title: GFP_CTR_rep4


title: SYO1_sgCtrl_Tet_GFP_JQ1_Rep1


title: SYO1_sgELOA3_Tet_ELOA3_Doxycycline_Rep2


title: Dbx2_constitutive_rep2


title: 100 ppm CO2 GL 4

description: 100 ppm CO2 GL 4


title: SYO1_sgELOA3_Tet_ELOA3_Doxycycline_Rep1


title: Control Female.5 [F17]

description:
F17
HBV.fa


title: 0 ppm CO2 PSI-PI 3

description: 0 ppm CO2 PSI-PI 3


title: 0 ppm CO2 PSI-PI 2

description: 0 ppm CO2 PSI-PI 2


title: Tet3-deficient Female.2 [F16]

description:
F16
HBV.fa


title: GFP_CTR_rep3


title: SYO1_sgELOA3_Tet_GFP_Doxycycline_Rep2


title: 0 ppm CO2 PSI-PI 1

description: 0 ppm CO2 PSI-PI 1


title: GFP_CTR_rep2


title: Tet3-deficient Female.1 [F15]

description:
F15
HBV.fa


title: GFP_CTR_rep1


title: 0 ppm CO2 GL 4

description: 0 ppm CO2 GL 4


title: Control Female.4 [F14]

description:
F14
HBV.fa


title: SYO1_sgCtrl_Tet_ELOA3_Doxycycline_Rep2


title: 0 ppm CO2 GL 3

description: 0 ppm CO2 GL 3


title: SYO1_sgCtrl_Tet_ELOA3_Doxycycline_Rep1


title: Control Female.3 [F13]

description:
F13
HBV.fa


title: 0 ppm CO2 GL 2

description: 0 ppm CO2 GL 2


title: Control Female.2 [F1]

description:
F1
HBV.fa


title: SYO1_sgCtrl_Tet_GFP_Doxycycline_Rep2


title: 0 ppm CO2 GL 1

description: 0 ppm CO2 GL 1


title: SYO1_sgCtrl_Tet_GFP_Doxycycline_Rep1


title: Tet2-deficient Female.1 [F11]

description:
F11
HBV.fa


title: Tet2-deficient Female.2 [F12]

description:
F12
HBV.fa


title: Control Female.1 [F10]

description:
F10
HBV.fa


title: tumor tissues rep1

city: Chengdu

first: Ying

last: Wang

address: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University No. 14, Sec.3, Renminnan Road, Chengdu, Sichuan

institute: West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan

description: TA

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (6x8K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Axon GenePix 4000B microarray scanner. Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Quantile normalization and subsequent data processing were performed using the R software package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: tumor tissues of head and neck squamous cell carcinoma

label_protocol: Total RNA from each group sample was amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar’s Super RNA Labeling protocol (Arraystar Inc.). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (6x7K, Arraystar).

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols.

treatment_protocol: A total of 3 pairs of tumors and adjacent nontumor tissues were collected from clinically diagnosed patients with HNSCCand immediately stored in RNAlater (RNAlater™ Stabilization Solution, AM7021, Invitrogen™) in liquid nitrogen before undergoing further processing.

tag: disease state

value: Head and neck squamous cell carcinoma (HNSCC)

tag: sample pair

value: A


title: CD11b+ cells, IgHMOG iGBGFP, mouse 790 (replicate 3)

city: Planegg-Martinsried

first: Anneli

last: Peters

address: Großhaderner Str. 9

department: Clinical Neuroimmunology

country: Germany

institute: LMU Hospital

description: Column names: featureCounts on 729_Th_GFP: Counts, featureCounts on 772_Th_GFP: Counts, featureCounts on 790_Th_GFP: Counts, featureCounts on 727_WT_IL-6: Counts, featureCounts on 770_WT_IL-6: Counts, featureCounts on 788_WT_IL-6: Counts

data_processing:
Analysis of RNAseq data was performed on the public server at usegalaxy.eu
Fastq files were quality controlled using FastQC (version 0.74+galaxy0)
Sequence reads were trimmed for adaptor sequence/low quality (Quality cutoff: 20) and short reads (<20 bp) using Cutadapt (4.4+galaxy0)
Trimmed reads were mapped to the GRCm38/mm10 mouse genome using the RNA STAR aligner (version 2.7.10b+galaxy3) with default settings
Read counts were obtained by the featureCounts package (version 2.0.3+galaxy1)
Differential gene expression (WT iGB6 vs. IgHMOG iGBGFP) was performed using DESeq2 (version 2.11.40.7+galaxy2) with correction for gender (Secondary factor: gender)
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file of normalized counts output from the DESeq2 software
Supplementary files format and content: Tab-delimited txt file of DESeq2 results

source_name: Spleen

growth_protocol: WT or IgHMOG B cells were cultured in the iGB culture system. After 48 hours, WT cells were retrovirally transduced overnight pMSCV-IRES2-eGFP construct containing the Il6 gene, which is expressed together with an enhanced green fluorescent protein (WT iGB6). IgHMOG cells were transduced with an empty pMSCV vector (IgHMOG iGBGFP). Two days after transduction, the cells were loaded with MOG protein and adoptively transferred together with unmanipulated 2D2 CD4+ T cells into Rag1-KO mice.

extract_protocol:
CD11b+ cells were sorted from the spleens of IgHMOG iGBGFP and WT iGB6 mice 8 days after iGB-T cell co-transfer and total RNA extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions without performing on-column gDNA digestion
cDNA synthesis and library preparation were performed using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s instructions. Briefly, 8-16 ng RNA was used for cDNA synthesis and the double-stranded cDNA was amplified (17 cycles) and purified using SPRI®select beads (Beckman Coulter). 20 ng cDNA was tagged and ligated with 25-fold-diluted NEBNext® Adaptors for Illumina. The products were bead-purified and the adaptor-ligated DNA was amplified by PCR (9 cycles) using NEBNext® Single Index Primers to generate multiplexed sequencing libraries. Library quality was assessed on an Agilent 2100 Bioanalyzer using the DNA 1000 Kit (Agilent).

value: Spleen

value: CD11b+ cells

tag: strain

value: Rag1 KO

tag: Sex

value: male

value: Transfer of IgHMOG iGBGFP cells + 2D2 CD4+ T cells

value: day 8 post transfer


title: CD11b+ cells, WT iGB6, mouse 788 (replicate 3)

value: Transfer of WT iGB6 cells + 2D2 CD4+ T cells


title: SYO1_sgELOA3_Tet_GFP_Doxycycline_Rep1


title: normal tissues rep3

description: CC

source_name: normal tissues of head and neck

value: C

value: normal tissues of head and neck


title: tumor tissues rep2

description: TB

value: B

value: tumor tissues of head and neck squamous cell carcinoma


title: SYO1_sgELOA3_Tet_ELOA3_DMSO_Rep2

value: Synovial Sarcoma


title: SYO1_sgELOA3_Tet_GFP_DMSO_Rep2


title: tumor tissues rep3

description: TC


title: 0603-oct4-DD

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

data_processing:
Cell Ranger pipeline (version 4.0.0) was applied and raw reads were aligned to the human reference genome (GRCh38) using STAR aligner.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5

source_name: patient derived colorectal cancer organoid

growth_protocol: Primary colorectal cancer cell lined were established from primary CRC specimens and cultured according to previous report (Fujino, et al. PMID: 30955861)

extract_protocol:
4 days after dimerizer was removed, live cells were sorted for analysis.
Single-cell library preparation was performed following the manufacturer’s instructions for the Chromium Next GEM Single Cell 3’ Reagent Kits (v3.1) (10x Genomics, Pleasanton, CA, USA).

treatment_protocol: POU5F1-EGFP cells with inducible caspase 9 were seeded and 5μM B/B Homodimerizerwas administered for three days.

value: treated with DD for 7 days

value: colorectal cancer organoid


title: CD11b+ cells, WT iGB6, mouse 770 (replicate 2)


title: CD11b+ cells, IgHMOG iGBGFP, mouse 772 (replicate 2)


title: normal tissues rep2

description: CB


title: normal tissues rep1

description: CA


title: 0603-oct4

value: control


title: CD11b+ cells, IgHMOG iGBGFP, mouse 729 (replicate 1)

value: female


title: SYO1_sgCtrl_Tet_ELOA3_DMSO_Rep2

value: wild-type


title: SYO1_sgELOA3_Tet_GFP_DMSO_Rep1

value: ELOA3 sgRNA


title: DGRP_Mix_Sleep_Wakefulness_Run7, replicate 1, scRNA-seq

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description: 10x Genomics 3'

data_processing:
The 10x data was mapped to the Drosophila Melanogaster (BDGP6 assembly) genome using CellRanger v.3.1.0. SNP data for the DGRP lines was downloaded from http://dgrp2.gnets.ncsu.edu/ and liftOver was used to convert these to dm6 coordinates, SNPs were then filtered to include only those present uniquely in one of the lines used (88, 287, 303, 313, 359, 379, 441, 646, 892 and 908). This vcf file was used to run demuxlet from the popscle package [https://github.com/statgen/popscle] with default parameters, tools from https://github.com/aertslab/popscle_helper_tools were utilized to speed up computation.
Scanpy (v1.4.4) was used to process the 10x libraries, samples were first loaded and cells were annotated with genotypes determined by demuxlet. Demuxlet determined doublets and ambiguous cells were removed, any cells assigned to a genotype not present in that experiment were also removed. Finally, scrublet was used to remove remaining doublets using an expected doublet rate determined by the following formula based on the known doublet rate of the 10x chromium device and the number of doublets expected to be remaining after demuxlet (within-genotype doublets):  (0.008 * (n_cells / 1000)) * (num_lines / (num_lines ^ 2)). Following doublet removal, cells with less than 200 genes were removed, as well as cells with more than 20-30% UMIs assigned to mitochondrial genes. All remaining cells were combined into a single sample for further processing. Cells were normalized to a total of 10000 counts per cell and log transformed, highly variable genes were identified using default parameters and number of counts and percentage mitochondrial reads were regressed out, finally, counts were scaled to unit variance with a zero mean with a max value of 10. A principal component analysis was performed on the data and the pcacv workflow from vsn-pipelines (v0.25.0) [https://doi.org/10.5281/zenodo.3703108] was used to determine the number of principal components (PCs)(58 PCs)  to continue with for further dimensionality reduction and clustering. Both UMAP and tSNE dimensionality reductions were computed and clusters were determined using the louvain algorithm at various resolutions. Final anndata objects were converted to loom files for visualization in SCope (https://scope.aertslab.org).
Assembly: dm6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
Brains were dissected in ice-cold Schneider’s Medium with 30 mM of the transcription inhibitor Actinomycin D (Sigma-Aldrich 1410). Within 45 min after starting dissections, the brains were dissociated with an enzyme mixture of dispase (3mg/mL), collagenase (100mg/mL) and trypsin-EDTA (0.05%) in a Thermoshaker at 25C for 15 min. The dissociation was reinforced by pipetting the solution at least four times during the incubation. After washing with DPBS 15 mM Actinomycin D, resuspending the cell pellet in 100-200 ml DPBS 0.04% BSA and filtering the cell pellet with a 10mM pluriStrainer (ImTec Diagnostics_435001050).
Library preparations for the single cell RNA-seq was performed using 10X Genomics Chromium Single Cell 3’ Kit, v3.1 NextGEM chemistry (10X Genomics, Pleasanton, CA, USA). The cell count and the viability of the samples were assessed using LUNA dual florescence cell counter (Logos Biosystems). For each sample a targeted cell recovery of 10000 cells was aimed for. The dissociated cells from a fly brain are typically quite small (averaging between 1-4 um) and we have seen that this affects the counting accuracy. In order to get consistent counting accuracy, the average of cell counts from three independent measurements were consider for loading the fly cells to the 10X controller. Post cell count and QC, the samples were immediately loaded onto the Chromium Controller. Single cell RNAseq libraries were prepared using manufacturers recommendations (Single cell 3’ reagent kits v3.1 user guide; CG000204 Rev D), and at the different check points the library quality was accessed using Qubit (ThermoFisher) and Bioanalyzer (Agilent). For a targeted sequencing saturation of 50-60%, sequencing was performed at a depth of 30,000 - 60,000 reads per cell and single cell libraries were sequenced either on Illumina’s NovaSeq 6000 platform or HiSeq 2500 platform using paired-end sequencing workflow and with recommended 10X; v3.1 read parameters (28-8-0-91 cycles).
Single-cell RNA-seq (10X Genomics)

treatment_protocol: After entraining flies for three days, four to eight days-old single flies were loaded during the active period between ZT 0-2 and sleep was recorded in 12:12 LD condition in a constant environment of 55-65% humidity and 22℃. Locomotion was tracked in a high-resolution video-based Raspberry Pi-enabled device (ethoscope) (Geissmann et al., 2017). Targeted mechanical sleep deprivation was delivered in a feed-back loop triggered by 10 seconds of quiescence of a fly by the rotation of the respective tube. Flies at different points of their sleep-wake cycle and ZT time were collected and their brains dissected.

value: Brain

value: Mixed

value: Various


title: SYO1_sgELOA3_Tet_ELOA3_DMSO_Rep1


title: SYO1_sgCtrl_Tet_ELOA3_DMSO_Rep1


title: DGRP_Mix_Sleep_Wakefulness_Run6, replicate 1, scRNA-seq

description: 10x Genomics 3'


title: BEC_Sample3_post BT

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

country: France

institute: University Hospital of Montpellier, Inserm

description: Gene expression data from bronchial epithelial cell obtained post-bronchial thermoplasty treatment in severe asthma

hyb_protocol: After fragmentation and labeling, 2.8 µg DNA was targeted to be hybridized on Clariom™S HT, Human (Thermo Fisher Scientific)

scan_protocol: GeneTitan® Instrument was used for Hyb-Wash-Scan automated workflow

data_processing: Data were generated with Affymetrix Expression Console v 1.4.1.

label: biotin

source_name: Bronchial epithelial cells

label_protocol: Fragmentation and labeling were performed to produce ss-cDNA with the GeneChip® WT Terminal Labeling Kit according to the GeneChip™ Whole Transcript (WT) Reagent kit manual MAN0018137. Sense-strand cDNA was synthesized from 94 ng of total RNA

growth_protocol: Bronchial epithelial cells (BEC) isolated from bronchial biopsies of severe asthmatics before bronchial thermoplasty and 12-18 months post- bronchial thermoplasty were cultivated in specific epithelium culture medium.

extract_protocol: RNeasy Mini Kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Patients having suboptimal asthma control despite daily doses of at least 500 µg of fluticasone and at least 100 µg of salmeterol (or equivalents) were included in bronchial thermoplasty protocol at the Institute of cardiology and pneumology of Quebec asthma clinic. Bronchial biopsies were collected before bronchial thermoplasty and during a follow-up evaluation occurring at 12-48 months  after treatment.

value: Bronchial tissue

tag: patient diagnosis

value: severe asthma

value: post-bronchial thermoplasty treatment


title: BEC_Sample2_post BT


title: DGRP_Mix_Sleep_Wakefulness_Run5, replicate 1, scRNA-seq

description: 10x Genomics 3'


title: TLB, scRNAseq

status: Public on Nov 28 2023

city: Vancouver

first: Peter

last: Zandstra

state: British Columbia

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

description:
Targeted sequencing of captured lineage barcodes
Targeted_LineageBarcodes

data_processing:
The Cell Ranger function mkfastq was used for FASTQ generation, and Cell Ranger count was applied using default parameters for trimming, alignment and counting using hg19 as the reference genome. (cellranger v6.0.1)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hematopoietic

extract_protocol:
For the sample coresponding to the passage day, adherent and floating cells were sequenced separately. Each sample was pelleted by centrifugation at 300x g for 5 minutes. Replicate wells were pooled together and washed with PBS. Samples were Fc blocked (BD, 564220) and labelled with zombie-UV viability dye (BioLegend, 423108) on ice in the dark for 20 minutes. Next, each sample was labelled with 0.1 ug of a cell hashing antibody (TotalSeq-B anti-human Hashtag antibodies 1 through 8, BioLegend). Cells were labelled for 30 minutes on ice in the dark. Next, samples were washed 3 times with HF buffer and counted prior to pooling. Samples were combined in to two pools, one for the EHT time points and another for the progenitor T cell differentiation time points. To enrich for Zombie-UV-negative viable cells, the EHT time point pool was subject to Fluorescent Activated Cell Sorting (FACS) using a MoFlo Astrios (Beckman Coulter).
Cell pools were counted and loaded on the Chromium Controller (10x genomics) using the Chromium Single Cell 3’ Reagents kit (v3.1) and libraries were generated according to the manufacturer’s instructions. Libraries were sequenced on the NextSeq2000 (Read 1: 28bp Index1: 10bp Index 2: 10bp Read 2: 90bp)

value: Hematopoietic

value: Hematopoietic stem and progenitor cells, myeloid progenitors, erythroid and megakaryocyte progenitors, mast progenitors, progenitor T cells


title: SYO1_sgCtrl_Tet_GFP_DMSO_Rep1


title: TimecourseD, scRNAseq

description:
poly A RNA
Timecourse_poolD

value: Endothelial cells, hematopoietic stem and progenitor cells, myeloid progenitors, erythroid and megakaryocyte progenitors, mast progenitors, progenitor T cells


title: TB, dissected, stag2b NZ207, scRNA-seq

city: Dunedin

first: Michael

last: Meier

state: Region

address: 56 Hanover St

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
FASTQs were quality and adapter trimmed and mapped to zebrafish genome and count tables were calculated using CellRanger(v7.1.0) filtered for empty droplets.
Assembly: GRCz11
Supplementary files format and content: Tab separated value files and matrix files

organism: Danio rerio

source_name: tailbud

extract_protocol:
Tailbuds were manually dissected and then dissociated using collagenase P and trypsin
Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Libraries used 10X Chromium chemistry v2.

value: tailbud

value: 16 hpf

value: stag2b NZ207


title: TB, dissected, wild type, scRNA-seq

value: AB wild type


title: TimecourseC, scRNAseq

description:
poly A RNA
Timecourse_poolC


title: LBC_T1, scRNAseq

description:
poly A RNA
LineageBarcoded_T1


title: BEC_Sample1_post BT


title: SYO1_sgCtrl_Tet_GFP_DMSO_Rep2

value: Synovial Sarcoma


title: TimecourseA, scRNAseq

description:
poly A RNA
Timecourse_poolA


title: Calu-3 cells, uninfected, replicate 5

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Base calling was performed with Dragen BCLConvert (v3.7.4).
Read alignment was performed in performed in R (v4.1.2) using the Rsubread package (v2.6.4). A genome index was built using a custom combined human and SARS-CoV-2 genome using the buildindex function and alignment was performed using sunjunc, with default settings.
A custom GTF file consisting of human and SARS-CoV-2 data was used for mapping. This GTF file was processed using the Annotations scripts from the Intron-reads repository (https://github.com/charitylaw/Intron-reads) in order to define exon and gene body regions. Counts were obtained using featureCounts from Rsubread (v2.8.1), with isPairedEnd and useMetaFeatures set to TRUE, allowMultiOverlap set to FALSE and strandSpecific 2. Intron counts were obtained by subtracting exon counts from gene body counts.
Exon- and intron-level differential gene expression analyses followed the methods of the index package (v1.0), using the edgeR (v3.36.0) and limma (v3.50.0) packages.
Assembly: hg38
Supplementary files format and content: Comma-delimited text files including exon and intron counts for each gene for every sample.

molecule: cytoplasmic RNA

growth_protocol: Calu-3 cells were cultured at 37°C and 5% CO2 and were maintained in MEM supplemented with 10% v/v foetal calf serum (FCS) and 2 mM L-glutamine, 1x sodium pyruvate and 1x non-essential amino acids.

extract_protocol:
Cytoplasmic RNA was extracted using Cytoplasmic & Nuclear RNA Purification Kit (Norgen; Cat. 21000, 37400) according to manufacturer’s instructions.
Total RNA libraries were prepared, starting with 500 ng of total RNA, according to the Illumina Tru-Seq Stranded Total RNA-Seq protocol (1000000040499) with RiboZero depletion, using unique dual indexes. 150 base paired-end sequencing was performed on a NextSeq 2000 P3 chip, loading pooled libraries at a concentration of 1,000 pM (protocol 1000000109376).

treatment_protocol: Calu-3 cells were left untreated, infected with SARS-CoV-2 (MOI = 0.1) for 48 hr, or treated with human IFNβ (PBL Assay Science; 100 IU/ml) for 6 hr.

value: Unif

tag: replicate


title: Calu-3 cells, uninfected, replicate 3


title: Calu-3 cells, SARS-CoV-2, replicate 3


title: Calu-3 cells, IFNb, replicate 5

value: IFNb


title: BEC_Sample3_before BT

description: Gene expression data from bronchial epithelial cell obtained before bronchial thermoplasty treatment in severe asthma

value: before treatment


title: Calu-3 cells, IFNb, replicate 3


title: Calu-3 cells, SARS-CoV-2, replicate 2


title: Calu-3 cells, SARS-CoV-2, replicate 5


title: CD11b+ cells, WT iGB6, mouse 727 (replicate 1)

value: Spleen

value: CD11b+ cells

value: Rag1 KO

value: female

value: Transfer of WT iGB6 cells + 2D2 CD4+ T cells

value: day 8 post transfer


title: Calu-3 cells, uninfected, replicate 2


title: BEC_Sample2_before BT

value: Bronchial tissue

value: severe asthma


title: Calu-3 cells, SARS-CoV-2, replicate 1


title: Calu-3 cells, uninfected, replicate 1


title: Calu-3 cells, IFNb, replicate 1


title: LBC_T2, scRNAseq

description:
poly A RNA
LineageBarcoded_T2

value: Hematopoietic

value: Hematopoietic stem and progenitor cells, myeloid progenitors, erythroid and megakaryocyte progenitors, mast progenitors, progenitor T cells


title: IRF3 KO THP-1 cells, IFNb, replicate 4 [4C_IFNb]

data_processing:
Base calling was performed with Dragen BCLConvert (v3.7.4).
Read alignment was performed in performed in R (v4.1.2) using the Rsubread package (v2.6.4). A genome index was built using a custom combined human and EMCV genome using the buildindex function and alignment was performed using sunjunc, with default settings.
A custom GTF file consisting of human and EMCV data was used for mapping. This GTF file was processed using the Annotations scripts from the Intron-reads repository (https://github.com/charitylaw/Intron-reads) in order to define exon and gene body regions. Counts were obtained using featureCounts from Rsubread (v2.8.1), with isPairedEnd and useMetaFeatures set to TRUE, allowMultiOverlap set to FALSE and strandSpecific 2. Intron counts were obtained by subtracting exon counts from gene body counts.
Exon- and intron-level differential gene expression analyses followed the methods of the index package (v1.0), using the edgeR (v3.36.0) and limma (v3.50.0) packages.
Assembly: hg38
Supplementary files format and content: Comma-delimited text files including exon and intron counts for each gene for every sample.

growth_protocol: THP-1 cells were cultured at 37°C and 5% CO2 and were maintained in RPMI supplemented with 10% v/v foetal calf serum (FCS) and 2 mM L-glutamine.

treatment_protocol: THP-1 cell were incubated with 10 ng/ml PMA overnight, then left untreated, infected with EMCV (MOI = 2) for 20 hr, or treated with human IFNβ (Rebif; 100 IU/ml) for 6 hr.

value: IRF3 KO


title: IRF3 KO THP-1 cells, EMCV, replicate 4 [4B_EMCV]

value: EMCV


title: IRF3 KO THP-1 cells, EMCV, replicate 3 [3B_EMCV]


title: IRF3 KO THP-1 cells, IFNb, replicate 3 [3C_IFNb]

description:
Replicate 3 of IFNb treatment was performed in technical duplicate.
3C_IFNb


title: IRF3 KO THP-1 cells, IFNb, replicate 2 [2C_IFNb]


title: IRF3 KO THP-1 cells, EMCV, replicate 2 [2B_EMCV]


title: BEC_Sample1_before BT


title: IRF3 KO THP-1 cells, uninfected, replicate 2 [2A_Unif]


title: IRF3 KO THP-1 cells, uninfected, replicate 1 [1A_Unif]


title: IRF3 KO THP-1 cells, EMCV, replicate 1 [1B_EMCV]


title: Calu-3 cells, IFNb, replicate 2


title: Zmat3 -/- Puma -/- p21 -/- 1

city: Barcelona

first: Gerard

last: Romero

state: Catalonia

address: Doctor Aiguader, 88

department: Dpt of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS/UPF)

country: Spain

institute: Universitat Pompeu Fabra

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de- multiplexing utilised bcl2fastq conversion software v2.15.0.4.
Raw FASTQ files were processed, and quality control performed using the nf-core/rnaseq (v. 3.10.1). Reads were pseudo-aligned and quantified using the Salmon option.
We filtered out genes: i) with obsolete Entrez Gene IDs, ii) ribosomal RNA (rRNA), iii) non-protein coding immunoglobulin genes iv) the Xist gene and v) genes that are on chromosome Y. Next, we filtered out lowly expressed genes by discarding those that did not show a minimum reliable level of expression of 20 counts per million reads of the smallest library size, in at least all the samples of the smallest group.
The DESeq2 package (v. 1.40.0) was used for the differential expression analysis. We adjusted for the sex as a batch effect correction and surrogate variables were calculated with SVA.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files incudes raw counts for each sample

source_name: thymus

extract_protocol:
RNA was extracted from thymocytes using the miRNeasy Micro Kit (Qiagen) according to the manufacturer's protocol, including a DNase digestion step. An input of total 100 ng total RNA for each sample was indexed separately using the TruSeq RNA Prep Kit v2 (Illumina).
Each library was quantified using the Agilent Tapestation. The indexed libraries were pooled and diluted to 750 pM for paired end sequencing (2 x 116 cycles) on the NextSeq 2000 instrument using the P3 200 cycle High Output Kit (Illumina) according to the manufacturer’s instructions.

value: thymus

value: thymocytes

value: Zmat3, Puma & p21 KO


title: Zmat3 -/- 1

value: Zmat3 KO


title: Wild-type 3

value: WT


title: Zmat3 -/- Puma -/- p21 -/- 2


title: Zmat3 -/- 2


title: Zmat3 -/- Puma -/- p21 -/- 3


title: Wild-type 2


title: Zmat3 -/- 3


title: Wild-type 4


title: IRF3 KO THP-1 cells, uninfected, replicate 4 [4A_Unif]

value: Unif


title: IRF3 KO THP-1 cells, uninfected, replicate 3 [3A_Unif]


title: Visium_heart_7dPI

first: Fabio

last: Rossi

state: BC

description:
probe-targeted RNA
Cross-section of the cardiac infarct

data_processing:
Demultiplexed FASTQ reads were aligned to the mouse reference genome, mm10 (GRCm38.p5, primary assembly) using the 10X Genomics Space Ranger v.2.0.1 pipeline. Default and recommended parameters were adopted.
Downstream processing and analysis was completed with Seurat as described in the spatial data vignette using SCTransform.
Assembly: mm10 (GRCm38.p5)
Supplementary files format and content: HDF5 file containing gene count matrices (and HTO if applicable)
Library strategy: Spatial transcriptomics

source_name: Adult mouse hearts

extract_protocol:
Mice were anesthetized with 0.5 mg/g tribromoethanol (Avertin) IP.  Following transcardiac perfusion with 20 mL of PBS-EDTA (2mM), whole hearts were excised and their atria were trimmed off. For spatial RNAseq, heart samples were washed with cold PBS upon harvest and directly snap frozen in OCT compound. Using a Leica cryostat, a 10-um transverse section of the heart was mounted onto a glass slide. The section was then fixed in cold methanol prior to H&E staining (7 minutes hematoxylin and 1 minute eosin incubations) and imaged with a Nikon Eclipse Ni microscope. Further processing of tissue sections was performed in accordance with the Visium CytAssist user guide (CG000495) using the Visium CytAssist Spatial Gene Expression Kit (PN-100051).
For spatial RNAseq, cDNA libraries were generated using the 10x Genomics Visium Spatial Gene Expression 3’ Library Construction V2 Kit, followed by sequencing on an Illumina NextSeq 2000 using the P2 100 Cycle kit to a depth of 40,000 mean reads per spot.

treatment_protocol: Experimental induction of myocardial infarctions was performed on animals ventilated with a mixture of oxygen and isofluorane until surgical anesthesia. Skin was surgically scrubbed with alcohol and Bupivacaine was administered subcutaneously at the incision site. An incision through the rib cage was made and held open with a retractor to visualize the heart. Using an 8-0 polypropylene suture, a branch of the left anterior descending (LAD) artery was ligated. Wound was then closed using a 6-0 vicryl suture in a horizontal mattress pattern.12 Buprenorphine (20 uL/g) and saline (1 mL) were administered subcutaneously every 8 hours.

value: Heart ventricles collected 7 days after MI

value: Pdgfra-EGFP


title: Visium_heart_14dPI

value: Heart ventricles collected 14 days after MI


title: Visium_heart_3dPI

value: Heart ventricles collected 3 days after MI


title: IRF3 KO THP-1 cells, IFNb, replicate 3 [1C_IFNb]

description:
Replicate 3 of IFNb treatment was performed in technical duplicate.
1C_IFNb

value: IFNb


title: Visium_heart_undamaged

description:
probe-targeted RNA
Cross-section of the undamaged heart

data_processing:
Assembly: mm10 (GRCm38.p5)
Supplementary files format and content: HDF5 file containing gene count matrices (and HTO if applicable)
Library strategy: Spatial transcriptomics

value: Heart ventricles collected at steady state


title: H3K4me3_4dpi, rep3 NextSeq 2000

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

description: H3K4me3_4dpi, rep3

data_processing:
Reads were aligned to the mouse genome (mm10) using Bowtie2 with options ‘--very-sensitive -X 1000 --dovetail -1’
Duplicates were removed using Picard (http://broadinstitute.github.io/picard/).
Assembly: mm10
Supplementary files format and content: The bigwig files (.bw) are generated by converting the bam files to bigwig using bamCoverage with CPM normalization.
Supplementary files format and content: Peak calling for histone PTMs was performed using MACS2 without Isotype controls as input files. Narrow peaks for H3K27ac, H3K4me1 and H3K4me3 and broad peaks for H3K27me3 were used with FDR set to 0.01. Called peaks were filtered using the mm10-blacklist.v2 file.
Supplementary files format and content: For Sox4 CUT&RUN samples, which had relatively high background, peak calling was performed using MACS2 with combined Isotype controls of the corresponding time points as input files with FDR set to 0.1.  Narrow peaks were used, and the called peaks were filtered using the mm10-blacklist.v2 file.

source_name: Liver

extract_protocol:
After washing in wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl (Sigma), 0.5 mM spermidine (Sigma) and EDTA-free protease inhibitors (Roche)) twice by centrifugation at 600 ×g at 4 °C for 3 minute
The cells were resuspended in 150 ul wash buffer, 15 ul Concanavalin A-coated magnetic beads (EpiCypher) was added, and the cells/bead conjugate was bound to a magnet.
After removal of the supernatant, the cells were resuspended in 50 ul antibody reaction buffer (wash buffer with 5% digitonin and 0.5 M EDTA), 0.5 ul antibody was added, and incubated at 4 °C overnight. Following two washes in 200 ul permeabilization buffer (wash buffer with 5% digitonin), beads were resuspended in 50 ul permeabilization buffer.
Then, 2.5 ul pAG-MNase (EpiCypher) was added, and the samples were incubated at RT for 10 minutes.
While on the magnet, the supernatant was removed, and the samples were washed twice in 200 ul cold permeabilization buffer. Following resuspension in 50 ul permeabilization buffer, 1 ul 100 mM CaCl2 was added to activate MNase, and MNase digestion was performed at 4 °C for 2 hours.
The reaction was stopped by adding 33 ul STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 10 ug/ml RNase A, 50 ug/ml glycogen), and 1 ul E-Coli spike-in DNA (0.5 ng/ul) (EpiCypher) to each tube.
After incubation at 37 °C for 10 minutes, beads were bound to the magnet, and the supernatant was transferred to a new tube.
The DNA was cleaned up with the NEB Monarch kit (NEB), eluted in 12 ul elution buffer, and used as CUT&RUN DNA.
Library preparation was performed using NEBNext Ultra II End Prep kit (NEB) with a slightly modified protocol.
Briefly, after adaptor ligation, HA-Sox4 CUT&RUN DNA samples were purified with 1.75× AMPure XP beads (Beckman), while histone and IgG CUT&RUN samples were purified with 1.1× AMPure XP beads.
14-cycle PCR with index primers (NEB) was performed (initial denaturation: 1 cycle of 98 °C for 45 seconds; annealing/extension: 14 cycles of 98 °C for 15 seconds and 60 °C for 10 seconds; final extension: 72 °C for 1 minute).
Finally, the library was purified with AMPure XP beads (for HA-Sox4 0.8× followed by 1.2×; for histone and isotype control 0.9×).
For samples with adaptor contamination, further AMPure bead cleanup or gel extraction was performed.

treatment_protocol: AAV8-TBG-HA-Sox4-P2A-Cre (Sox4) was retro-orbitally injected at 1e12 gc/mouse. Eighteen hours and four days post injection, hepatocytes were harvsted.

value: Liver

value: Hepatocyte

value: AAV8-TBG-Sox4-P2A-Cre injected; harvested 4 days post injection


title: H3K4me3_18hpi, rep3 NextSeq 2000

description: H3K4me3_18hpi, rep3

value: AAV8-TBG-Sox4-P2A-Cre injected; harvested 18 hours post injection


title: H3K4me1_4dpi, rep3 NextSeq 2000

description: H3K4me1_4dpi, rep3


title: Zmat3 -/- 4


title: H3K4me3_18hpi, rep2 NextSeq 2000

description: H3K4me3_18hpi, rep2


title: H3K4me1_18hpi, rep2 NextSeq 2000

description: H3K4me1_18hpi, rep2


title: H3K4me1_4dpi, rep2 NextSeq 2000

description: H3K4me1_4dpi, rep2


title: H3K4m27me3_4dpi, rep3 NextSeq 2000

description: H3K4m27me3_4dpi, rep3


title: H3K27ac_4dpi, rep3 NextSeq 2000

description: H3K27ac_4dpi, rep3


title: Wild-type 1


title: H3K4m27me3_18hpi, rep3 NextSeq 2000

description: H3K4m27me3_18hpi, rep3


title: H3K4me1_18hpi, rep3 NextSeq 2000

description: H3K4me1_18hpi, rep3


title: Isotype_4dpi, rep2 NextSeq 2000

description: Isotype_4dpi, rep2


title: Isotype_4dpi, rep3 NextSeq 2000

description: Isotype_4dpi, rep3


title: Sox4_4dpi, rep1 NextSeq 2000

description: Sox4_4dpi, rep1


title: Isotype_18hpi, rep3 NextSeq 2000

description: Isotype_18hpi, rep3


title: Isotype_4dpi, rep1 NextSeq 2000

description: Isotype_4dpi, rep1


title: Isotype_18hpi, rep2 NextSeq 2000

description: Isotype_18hpi, rep2


title: Sox4_4dpi, rep2 NextSeq 2000

description: Sox4_4dpi, rep2


title: Isotype_18hpi, rep1 NextSeq 2000

description: Isotype_18hpi, rep1


title: H3K27ac_18hpi, rep3 NextSeq 2000

description: H3K27ac_18hpi, rep3


title: Sox4_18hpi, rep3 NextSeq 2000

description: Sox4_18hpi, rep3


title: Sox4_4dpi, rep3 NextSeq 2000

description: Sox4_4dpi, rep3


title: Sox4_18hpi, rep2 NextSeq 2000

description: Sox4_18hpi, rep2


title: H3K4me3_4dpi, rep2 NextSeq 2000

description: H3K4me3_4dpi, rep2


title: Sox4_18hpi, rep1 NextSeq 2000

description: Sox4_18hpi, rep1


title: pUC57-Halo, repeat 3

city: Beijing

first: Qiang

last: Huo

address: Yuanmingyuan West Road

institute: China Agricultural University

data_processing:
Illumina software used for base calling
Trimmomatic (version 0.39) was used to trim the fastq files as follows: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, HEADCROP:0, MINLEN:75 and bowtie2 (version: 2.4.1)  was used to align them to the B73 v4 reference genome with the following parameters: -I 75 -X 1000 --no-discordant --no-mixed.
Peaks were called using GEM v3.4 with the following parameters: --d Read_Distribution_default.txt --k_min 4 --k_max 12 --outNP --q 3 --nrf --outNP --outHOMER –outMEME. Blacklisted peaks were subtracted to created to create final narrowPeak file.
Supplementary files format and content: Zea mays ssp mays B73 v4
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: DAP-seq

organism: Zea mays

source_name: leaf

growth_protocol: B73 inbred line cultivated in the greenhouse of China Agricultural University (Beijing, China)

extract_protocol:
gDNA was extracted from maize B73 14 DAG leaf. gDNA libraries was prepared using TIANSeq DirectFast Library Kit (illumina) (cat. no. NG101, TIANGEN) according to the manufacturer’s instructions.
gDNA libraries was prepared using TIANSeq DirectFast Library Kit (illumina) (cat. no. NG101, TIANGEN) according to the manufacturer’s instructions. Full length maize transcription factors’ coding sequences were cloned from maize 14 DAG leaf cDNA into the NotI and AscI sites of pUC57-Halo using MultlF Seamless Assembly Mix (cat. no. RM20523, ABclonal). Protein expression was using TNT SP6 High-YIELD Wheat Germ Master Protein Expression System (cat. no. L3260; Promega) according to the manufacturer’s instructions. Halo-fusion protein was bound to Magne HaloTag Beads (cat. no. G7281; Promega) and washed three times using TBSN buffer( 100 mM Tris buffer, pH 7.5, 50 mM NaCl, 0.005 % NP40). Then, 500 ng gDNA libraries was added and incubated at room temperature for 1.5 h. After incubation the beads was washed four times. Resuspended the beads in 30µl of EB buffer to recover DNA. The recovered DNA was were cleaned up with Silane magnetic beads, and amplified via PCR. The PCR products were cleaned up with Silane magnetic beads and sequenced using an NovaSeq platform (Illumina) by BerryGnomics.

tag: background

tag: gene id

value: pUC57-Halo vector

value: 14 DAG

value: leaf


title: pUC57-Halo, repeat 2


title: EREB84


title: 1d030858


title: EREB148


title: NACTF4


title: HSFTF20


title: WRKY53


title: NACTF23


title: NACTF110


title: pUC57-Halo, repeat 1


title: THX35


title: MYB127


title: NACTF32


title: MYBR77


title: MYB32


title: MYBR32


title: MYB35


title: HB49


title: TU1


title: HB45


title: MYBR21


title: MYBR43


title: YY1


title: HSFTF5


title: WOX13A


title: HB98


title: DOF47


title: BZIP3


title: BZIP71


title: BZIP125


title: OHP1


title: BZIP48


title: BZIP10


title: BZIP49


title: BZIP14


title: BHLH164


title: MYC7


title: BZIP92


title: EREB72


title: EREB109


title: EREB19


title: BZIP102


title: EREB195


title: EREB190


title: BZIP58


title: MYBR26


title: EREB83


title: O2


title: Mutant ZmEREB108, replicate 2

data_processing:
Trimmomatic  (version 0.39) was used to trim the sequence reads and Hisat2 (version 2.2.1) was used to align them to the B73 v4 reference genome.
Supplementary files format and content: Zea mays ssp mays B73 v4
Supplementary files format and content: Matrix table with raw counts for every sample (column) and gene (rows)

source_name: Endosperm

growth_protocol: Wild type and mutant plant kernels cultivated in the greenhouse of China Agricultural University (Beijing, China)

extract_protocol:
5-10 of 8 DAP endosperms of wild type and mutant were pooled for extracting total RNA with an RNAprep Pure Plant Kit (cat. no. DP441, TIANGEN)
MP3RNA-seq

value: Endosperm

tag: cultivar

value: 8 DAP

tag: genotype

value: mutant


title: Mutant ZmEREB108, replicate 1

tag: tissue

tag: age


title: Wild type ZmEREB108, replicate 2

value: wild type


title: Wild type ZmEREB108, replicate 3


title: Wild type ZmEREB108, replicate 1


title: Mutant ZmMYBR29, replicate 2


title: Mutant ZmMYBR29, replicate 1


title: Wild type ZmMYBR29, replicate 3


title: Wild type ZmMYBR29, replicate 2


title: Wild type ZmMYBR29, replicate 1


title: Mutant ZmMYBR19, replicate 3


title: Mutant ZmMYBR19, replicate 1


title: Wild type ZmMYBR19, replicate 3


title: Wild type ZmMYBR19, replicate 2


title: B73 7DAP endosperm,  replicate 3

description:
7DAP3
Rowcount.txt

data_processing:
Trimmomatic  (version 0.39) was used to trim the sequence reads and STAR was used to align them to the B73 v4 reference genome. We computed gene expression levels for uniquely mapped reads by Using featureCounts (version 2.0.1).
Supplementary files format and content: Zea mays ssp mays B73 v4
Supplementary files format and content: Matrix table with raw counts for every sample (column) and gene (rows)

growth_protocol: B73 inbried line kernels cultivated in the greenhouse of China Agricultural University (Beijing, China)

extract_protocol:
Twenty of 6, 7, 8 DAP endosperms of B73 were pooled for extracting total RNA with an RNAprep Pure Plant Kit (cat. no. DP441, TIANGEN)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: 7 DAP


title: B73 7DAP endosperm,  replicate 2

description:
7DAP2
Rowcount.txt


title: B73 6DAP endosperm,  replicate 3

description:
6DAP3
Rowcount.txt

value: 6 DAP


title: B73 7DAP endosperm,  replicate 1

description:
7DAP1
Rowcount.txt


title: B73 6DAP endosperm,  replicate 2

description:
6DAP2
Rowcount.txt


title: B73 6DAP endosperm,  replicate 1

description:
6DAP1
Rowcount.txt


title: B73 6DAP protoplasts endosperm

description:
6DAPPRO
rowcount_pro.txt


title: B73 7DAP no-protoplasts endosperm

description:
7DAPEN
rowcount_pro.txt


title: B73 7DAP protoplasts endosperm

description:
7DAPPRO
rowcount_pro.txt


title: Mutant ZmEREB108, replicate 3


title: 7DAP endosperm, replicate 3, scRNAseq

description: 10x Genomics

data_processing:
Raw data were compared, barcoded and quantified by UMI using the Chromium 10x Cell Ranger software package. Samples were normalized and cell clusters were determined using Seurat.
Assembly: Zea mays ssp mays B73 v4
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol: Endosperm from maize 80-100 maize kernels from 6 to 8 DAP. Endosperm were incubated in a enzymatic solution to digest cell walls and produce protoplasts. Protoplasts were filtered using a cell strainer and used as input for the 10x Chromium Single Cell 3' V3 pipeline. Libraries were prepared using Chromium Single Cell 3' Reagent Kit V3.


title: Mutant ZmMYBR29, replicate 3


title: 7DAP endosperm, replicate 2, scRNAseq

description: 10x Genomics


title: B73 6DAP no-protoplasts endosperm

description:
6DAPEN
rowcount_pro.txt


title: HC227

city: San Francisco

first: Qin

last: Ma

state: CA

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

data_processing:
The low quality reads were filtered by Trimmomatic, then the reads were uniquely mapped to the reference genome (hg38, UCSC) using the Bismark software. The bisulfite conversion rates were calculated using the lambda DNA.
Assembly: hg38
Supplementary files format and content: Methylation level for each CpG covered by a minimum of 3 reads. We counted the number of 'C' bases from sequencing reads as  methylated (denoted as NC) and the number of 'T' bases as unmodified (denoted as NT). The methylation level was estimated as NC/(NC + NT) in each CpG site. For each CpG there are four columns of data including chromosome name, location of the left CpG sits, location of the right CpG site, methylation level.

source_name: peripheral blood

extract_protocol:
Genomic DNA was extracted from peripheral blood using standard methods. Briefly, the yellow-top vacutainer tubes were centrifuged, aspirated off most of the serum, treated with red blood cell lysis buffer. Then the cells were lysed using nuclei lysis buffer and proteinase K, and the genomic DNA was precipitated using ammonium acetate and ethanol. Finally, the DNA pellet was washed, dried, and dissolved.
Genomic DNA was fragmented, end-repaired, A-tailed, and ligated to methylated adaptors. The ligated samples will be pooled together to perform MHC capture using validated capture probes and custom panel from Twist Bioscience following the target enrichment standard hybridization protocol (Twist Bioscience). The pooled fragments were then bisulfite converted using the EZ DNA Methylation Gold kit (Zymo Research) at 64℃ for 2.5 hours and amplified using the KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit.

value: peripheral blood

tag: subject status

value: healthy control


title: Mutant ZmMYBR19, replicate 2


title: HC223


title: HC225


title: 6DAP endosperm, replicate 1, scRNAseq

description: 10x Genomics


title: Wild type ZmMYBR19, replicate 1


title: HC221


title: HC226


title: HC224


title: HC228


title: HC222


title: HC219


title: HC220


title: HC218


title: HC217


title: HC213


title: HC212


title: HC209


title: HC208


title: HC210


title: HC215


title: HC211


title: HC206


title: HC205


title: HC202


title: HC203


title: HC102


title: HC216


title: HC96


title: HC97


title: HC100


title: HC101


title: HC201


title: HC92


title: HC98


title: HC214


title: HC204


title: HC95


title: HC89


title: HC88


title: HC87


title: HC99


title: HC207


title: HC91


title: HC83


title: HC85


title: HC86


title: HC84


title: HC82


title: HC81


title: HC93


title: HC79


title: HC78


title: HC94


title: HC77


title: HC90


title: HC75


title: HC70


title: HC72


title: HC71


title: HC74


title: HC69


title: HC65


title: HC68


title: HC64


title: HC76


title: HC62


title: HC66


title: HC63


title: HC61


title: HC59


title: HC67


title: HC80


title: HC58


title: HC56


title: HC60


title: HC53


title: HC51


title: HC52


title: HC73


title: HC48


title: HC49


title: HC50


title: HC47


title: HC43


title: HC45


title: HC44


title: HC42


title: HC41


title: HC39


title: HC40


title: HC38


title: HC33


title: HC55


title: HC54


title: HC35


title: HC36


title: HC34


title: HC37


title: HC31


title: HC32


title: HC30


title: HC27


title: HC25


title: HC26


title: HC24


title: HC23


title: HC46


title: HC21


title: HC18


title: HC19


title: HC14


title: HC13


title: HC22


title: HC20


title: HC15


title: HC28


title: HC12


title: HC16


title: HC11


title: HC9


title: HC10


title: HC8


title: HC7


title: HC6


title: HC4


title: HC3


title: HC5


title: HC17


title: MS233

value: multiple sclerosis (MS) patient


title: HC2


title: MS232


title: HC1


title: MS230


title: MS229


title: MS228


title: MS227


title: MS222


title: MS226


title: MS225


title: MS219


title: MS221


title: MS224


title: MS214


title: MS216


title: MS231


title: MS218


title: MS215


title: MS209


title: MS210


title: MS211


title: MS208


title: MS217


title: MS213


title: MS223


title: MS206


title: MS220


title: MS207


title: MS205


title: MS201


title: P201732520

city: Seattle

first: Cathy

middle: M

last: Tangen

state: WA

address: 1100 Fairview Avenue N, J6-311

institute: Fred Hutchinson Cancer Center

hyb_protocol: Labelled cDNA was combined with dimethyl sulfoxide, hybridization buffer and nuclease free water and hybridised onto a HG-U133_Plus_2 Array (ThermoFisher) for 18hrs at 40oC.  Following hybridization, all arrays were washed using buffers of varying salt concentrations and stained with streptavidin-phycoerythrin conjugate (SAPE) .    All reaction components are contained within the hybridization, wash and stain kit (ThermoFisher).

scan_protocol: The arrays were scanned on the GeneChip scanner system (Thermofisher) using an epiflourescent, confocal microscope.  A solid-state laser contained within the GeneChip system was used to excite fluorophores bound to the hybridized cDNA molecules. The fluorescent values were firstly converted into an electronic signal and then to a numerical value representing the fluorescent intensity.

data_processing: CEL file intensities have been normalised to probeset level using Robust Multichip Average (RMA) consisting background adjustment, quantile normalisation and summarisation pre-processing (Bolstad et al, 2003).

source_name: FFPE

label_protocol: Biotin

extract_protocol: All FFPE tissues were first de-paraffinized with a xylene followed by ethanol dehydration. Tissue samples were then disrupted during an optimised overnight incubation with a Proteinase K. Nucleic acids were bound to a glass fibre filter in the presence of a chaotropic salt under conditions that were optimized specifically for RNA & miRNA recovery. Bound RNA was subjected to a series of wash steps to remove contaminating cellular components, and any residual DNA was digested by incubation with DNaseI followed by further wash steps to improve the final purity of the RNA, which was then eluted from the glass fibres in a small volume of water.

treatment_protocol: These are baseline bladder tissue results prior to any chemotherapy being received by the patients in the clinical trial

tag: treatment arm

value: DDMVAC+CYST

tag: disease

value: muscle-invasive bladder cancer

value: Clinical Stage -T2


title: MS202


title: MS204


title: MS116


title: MS114


title: MS203


title: MS117


title: P201702278

value: GC+CYST


title: P201771305


title: P201676404_F2


title: P201676404


title: P201675503


title: P201615426


title: P201700054

value: Clinical Stage -T3 or T4a


title: P201601164


title: MS115


title: MS107


title: MS113


title: MS112


title: P201670456_F2


title: MS111


title: P201629921


title: MS109


title: P201629818


title: P201670456


title: P201627722


title: P201605294


title: P201672800


title: MS104


title: MS106


title: MS100


title: MS108


title: MS101


title: P201663777


title: MS102


title: MS97


title: P201677959


title: P201673036


title: P201656212


title: MS103


title: MS105


title: MS95


title: P201620651


title: MS94


title: MS99


title: P201602163


title: P201618688


title: MS98


title: P201606550


title: HC29


title: P201672804


title: P201637008_F2


title: MS88


title: MS93


title: MS84


title: MS92


title: MS96


title: P201663951


title: P201636138


title: MS91


title: P201679861


title: P201611842


title: P201654117


title: P201687658


title: P201627232


title: P201634238


title: P201637366


title: P201625922


title: MS83


title: MS90


title: P201637008


title: MS86


title: MS87


title: MS85


title: MS75


title: P201617902


title: P201643272


title: MS212


title: MS74


title: MS73


title: MS72


title: MS71


title: P201629823


title: MS82


title: P201674717


title: P201610811


title: MS69


title: MS81


title: P201621419


title: MS80


title: P201654107


title: MS79


title: MS66


title: MS78


title: P201620134


title: P201644034


title: P201639970


title: P201675571_F2


title: P201630725


title: P201622083


title: P201699555


title: P201626254


title: P201626254_F2


title: MS76


title: MS77


title: MS70


title: MS62


title: MS68


title: MS59


title: MS67


title: P201674610


title: P201634229


title: P201666833


title: P201627751


title: P201611714


title: P201662727


title: P201638659


title: MS65


title: P201610706


title: P201675571


title: MS64


title: MS56


title: MS63


title: MS61


title: MS60


title: MS57


title: MS54


title: MS53


title: P201608579


title: MS55


title: MS50


title: MS51


title: MS52


title: MS49


title: MS58


title: P201638938


title: P201610581


title: P201575060


title: MS47


title: MS46


title: P201637222


title: MS48


title: MS45


title: P201643882


title: P201584036


title: P201580646


title: P201537829


title: P201517416


title: P201577864


title: MS44


title: MS43


title: P201666524


title: P201564532


title: P201579303


title: P201571488


title: P201555953


title: MS42


title: MS41


title: MS40


title: P201563555


title: MS39


title: MS38


title: P201513530


title: P201513419


title: MS36


title: MS35


title: MS34


title: MS33


title: MS32


title: MS31


title: P201574614


title: P201552627


title: P201555405


title: P201511368


title: P201559680


title: MS30


title: P201588314


title: MS37


title: MS29


title: P201546727


title: P201514523


title: MS27


title: MS26


title: MS28


title: P201527495


title: MS25


title: MS24


title: MS23


title: P201514523_F2


title: MS20


title: MS18


title: P201595248


title: P201521727_F2


title: MS17


title: P201471010


title: P201735826


title: MS14


title: MS15


title: MS22


title: P201720100


title: P201550563


title: MS12


title: P201559772


title: P201736627


title: P201743980


title: P201764296


title: MS9


title: P201510632


title: P201521727


title: P201781082


title: P201750226


title: P201784204


title: P201755521


title: P201751910


title: P201748536


title: MS8


title: MS13


title: MS19


title: MS11


title: MS16


title: P201702259


title: MS10


title: MS7


title: MS4


title: MS6


title: MS5


title: P201773543


title: MS1


title: MS2


title: P201753572


title: P201750638


title: CD146_CSPG4_tdTomato_7dPI

description: CD45- CD31- PI- CD146+ cells

data_processing:
Demultiplexed FASTQ reads were aligned to the mouse reference genome, mm10 (GRCm38.p5, primary assembly) with transgenic sequences including tdTomato, YFP, and DsRed appended using the 10X Genomics Cellranger v4.0.0. Default and recommended parameters were adopted. The resulting gene-barcode matrices were processed and analyzed in Seurat (Satija Lab, v3.2.0). Further demultiplexing with hashtag oligos (using 0.99 quantile as a threshold for positivity) was applied to remove cross-sample multiplets.
For scRNAseq, quality control metrics including the number of genes expressed (>200), total unique molecular identifier (UMI; <7000-15,000), and proportion of mitochondrial transcripts (<10-15%) were tailored to each dataset to remove cells of poor quality. Data was then processed using principal component analysis, Louvain clustering, and dimensionality reduction with UMAP (30 PCs). Differential gene expression using the Wilcoxon rank sum test was performed on filtered and normalized counts.
Assembly: mm10 (GRCm38.p5)
Supplementary files format and content: HDF5 file containing gene count matrices (and HTO if applicable)

extract_protocol:
Mice were anesthetized with 0.5 mg/g tribromoethanol (Avertin) IP.  Following transcardiac perfusion with 20 mL of PBS-EDTA (2mM), whole hearts were excised and their atria were trimmed off. For single-cell RNAseq (scRNAseq), excised ventricles were cut into 2 mm pieces and digested in Collagenase type II solution (Millipore Sigma C6885; 500uL per heart at 2.5 U/mL) containing 5 mM CaCl2 for 30 minutes at 37°C. Digested lysate was quenched and centrifuged at 140-g to remove the supernatant. This was followed by a second round of digestion in a solution (500 uL per heart) containing Collagenase D (Millipore Sigma 11088882001; 1.5 U/ml), Dispase II (Millipore Sigma 04942078001; 2.4 U/ml) and 5 mM CaCl2 for 1 hour at 37°C. Digested lysate was quenched and filtered through 40-μm strainer filters. Filtrate was centrifuged at 500-g and washed again with cold FACS buffer prior to incubation with primary antibodies for 30 minutes. Stained cells are double-sorted using a BD Influx (Becton Dickinson) into DMEM (Gibco 11965-092) containing 20% fetal bovine serum (FBS; Sigma F1051). Cell-hashing with oligo-tagged antibodies against MHC class I and CD45 (BioLegend 155801/155803/155805/155807) were applied in some samples.
For scRNAseq, viable cells were delivered into a Chromium Controller (10X Genomics), captured and libraried with the Chromium single cell 3’ reagent kit v2 or v3 (10X Genomics) as per the manufacturer's protocol. Sample integrity was assessed on the Agilent Bioanalyzer 2100 system using the RNA 6000 Pico or Nano kit (Agilent, 5067-1511 and 5067-1513, respectively). cDNA libraries were sequenced on Illumina Nextseq 500 using the High Output 75 Cycle kits to a minimum depth of 30,000 mean reads per cell.

treatment_protocol: Cre recombination was induced by intraperitoneal (IP) injections of TAM (Sigma-Aldrich T5648) at 3 mg/kg in 100uL of corn oil for 5 consecutive days, followed by at least 10 days of washout period. Experimental induction of myocardial infarctions was performed on animals ventilated with a mixture of oxygen and isofluorane until surgical anesthesia. Skin was surgically scrubbed with alcohol and Bupivacaine was administered subcutaneously at the incision site. An incision through the rib cage was made and held open with a retractor to visualize the heart. Using an 8-0 polypropylene suture, a branch of the left anterior descending (LAD) artery was ligated. Wound was then closed using a 6-0 vicryl suture in a horizontal mattress pattern. Buprenorphine (20 uL/g) and saline (1 mL) were administered subcutaneously every 8 hours.

value: Heart ventricles collected 10-14 days after tamoxifen administration and 7 days post-MI

tag: cell type

value: CD146+ cells (mural cells and Schwann cells)


title: CD146_HIC1_YFP_CSPG4_DSRED_42dPI

description: CD45- CD31- PI- CD146+ cells

value: Heart ventricles collected 10-14 days after tamoxifen administration and 42 days post-MI


title: P201749306


title: P201770486


title: P201713716


title: P201713639


title: MS3


title: P201661650


title: P201607895


title: HIC1_tdTomato_7dPI

description: CD45- CD31- PI- tdTomato+ cells (mural cells enrichment by CD146)

value: Hic1-labelled cells (tdTomato+ cells)


title: CD146_HIC1_YFP_undamaged

description: CD45- CD31- PI- CD146+ cells

value: Heart ventricles collected 10-14 days after tamoxifen administration


title: CD146_HIC1_YFP_7dPI

description: CD45- CD31- PI- CD146+ cells


title: P201758996


title: Hashed_CD146_HIC1_YFP_CSPG4_DSRED_3dPI

description: CD45- CD31- PI- CD146+ cells

value: Heart ventricles collected 10-14 days after tamoxifen administration and 3 days post-MI


title: P201787135


title: P201768928


title: P201759655


title: P201625399


title: P201669179


title: Hashed_HIC1_tdTomato_undamaged


title: H3K4me1_4dpi, rep1 NextSeq 500

description: H3K4me1_4dpi, rep1

value: Liver

value: Hepatocyte

tag: treatment

value: AAV8-TBG-Sox4-P2A-Cre injected; harvested 4 days post injection


title: P201644895


title: H3K4me3_18hpi, rep1 NextSeq 500

description: H3K4me3_18hpi, rep1

value: AAV8-TBG-Sox4-P2A-Cre injected; harvested 18 hours post injection


title: H3K4me3_4dpi, rep1 NextSeq 500

description: H3K4me3_4dpi, rep1


title: P201666573


title: H3K4m27me3_4dpi, rep2 NextSeq 500

description: H3K4m27me3_4dpi, rep2


title: H3K4m27me3_4dpi, rep1 NextSeq 500

description: H3K4m27me3_4dpi, rep1


title: P201649699


title: P201677124


title: P201546672


title: P201577803


title: P201531182


title: P201599657


title: H3K4m27me3_18hpi, rep2 NextSeq 500

description: H3K4m27me3_18hpi, rep2


title: H3K27ac_4dpi, rep2 NextSeq 500

description: H3K27ac_4dpi, rep2


title: H3K27ac_4dpi, rep1 NextSeq 500

description: H3K27ac_4dpi, rep1


title: H3K4m27me3_18hpi, rep1 NextSeq 500

description: H3K4m27me3_18hpi, rep1


title: H3K4me1_18hpi, rep1 NextSeq 500

description: H3K4me1_18hpi, rep1


title: P201577658


title: Isotype_4dpi, rep3 NextSeq 500

description: Isotype_4dpi, rep3


title: H3K27ac_18hpi, rep1 NextSeq 500

description: H3K27ac_18hpi, rep1


title: H3K27ac_18hpi, rep2 NextSeq 500

description: H3K27ac_18hpi, rep2


title: Isotype_4dpi, rep2 NextSeq 500

description: Isotype_4dpi, rep2


title: Isotype_4dpi, rep1 NextSeq 500

description: Isotype_4dpi, rep1


title: P201540848


title: Isotype_18hpi, rep3 NextSeq 500

description: Isotype_18hpi, rep3


title: P201528766


title: Isotype_18hpi, rep2 NextSeq 500

description: Isotype_18hpi, rep2


title: P201761388


title: P201599766


title: P201763604


title: Sox4_4dpi, rep2 NextSeq 500

description: Sox4_4dpi, rep2


title: P201590938


title: Isotype_18hpi, rep1 NextSeq 500

description: Isotype_18hpi, rep1


title: P201796801


title: Sox4_4dpi, rep1 NextSeq 500

description: Sox4_4dpi, rep1


title: P201418282


title: Sox4_4dpi, rep3 NextSeq 500

description: Sox4_4dpi, rep3


title: Sox4_18hpi, rep2 NextSeq 500

description: Sox4_18hpi, rep2


title: Sox4_18hpi, rep1 NextSeq 500

description: Sox4_18hpi, rep1


title: Rainbow trout_infection_6

city: Sopot

first: Magdalena

last: Malachowicz

address: Powstańców Warszawy

country: Poland

institute: Institute of Oceanology Polish Academy of Sciences

description: Biological replicate 6 of 7.

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned in an Agilent Technologies Scanner G2505C US10353831, according to the manufacturer’s protocol GE2_1010_Sep10

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.10.1.1) following the Agilent protocol GE2_1010_Sep10. Arrays normalization was performed using the Limma package in R. The raw mean signal (gMeanSignal) was background corrected (normexp method). Next lowess and quantile normalization were performed.

organism: Oncorhynchus mykiss

source_name: Infected fish

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Total RNA was extracted using the GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich).  Concentration of extracted RNA was determined at 260 nm on microplate using the Epoch Microplate Spectrophotometer (BioTek Instruments). The RNA integrity was verified using an Agilent Bioanalyser (Agilent Technologies)

treatment_protocol: Pathogenic bacteria Aeromonas salmonicida spp. salmonicida after growing on a solid sup-port and washing were cultured. The bacteria were diluted in PBS to a concentration of 1x107/ml. Fish were injected intraperitoneally around the left pectoral fin .

value: skin

source_name: control


title: P201766238


title: P201748990


title: P201783106


title: P201712661


title: P201775693


title: P201704902


title: P201787951


title: P201789259


title: P201739908


title: P201781999


title: P201723256


title: P201724502


title: Rainbow trout_infection_1

description: Biological replicate 1 of 7.


title: Rainbow trout_infection_7

description: Biological replicate 7 of 7.


title: Rainbow trout_infection_2

description: Biological replicate 2 of 7.


title: Rainbow trout_infection_5

description: Biological replicate 5 of 7.


title: P201745861


title: Rainbow trout_infection_4

description: Biological replicate 4 of 7.


title: INPUT_HF-hKO-B

city: Lausanne

first: Gilles

last: Willemin

state: VD

address: Génopode

department: Center For Integrative Genomics

country: Switzerland

institute: Université de Lausanne

data_processing:
Reads were mapped simultaneously on both Human Hg19 and Mouse Mm10 genome releases with STAR using a merged index with the following options : --outFilterMultimapNmax 50 --outFilterMatchNminOverLread 0.4. up to 30 redundant reads were kept for further analysis.
Mouse and Human scores for Pol3 loci (+/- 150 nucleotides) were normalized according to the library size and the gene length
Factors from human spikes were used for between-samples Mouse data correction
bigWig files were generated using bamCoverage with reads extension set to 300 and bin size set to 10
Assembly: UCSC Mm10/UCSC Hg19
Supplementary files format and content: Genome-wide CPM-normalized bigWig files

growth_protocol: Male mice were fed either a Chow diet (Kliba Nafag diet #3436) or a High Fat diet (HF, with 60% of calories coming from lard – BioServ diet #F3282) from 4-5 weeks of age. Animals were housed under 12h light/dark conditions, at a constant temperature of 22°C and fed ad-libitum with free access to water.

extract_protocol:
Preparation of chromatin immunoprecipitation was as described in (Mange et al. 2017)
Preparation of  libraries and high throughput sequencing were as described in (Mange et al. 2017)

treatment_protocol: Animals were weighed, fasted overnight, refed for 4 hours, and then sacrificed to provide samples for ChIPseq, RNAseq, and proteomic analyses.

tag: diet

value: High Fat

tag: chip antibody


title: INPUT_HF-hKO-A

tag: strain


title: Rainbow trout_infection_3

description: Biological replicate 3 of 7.


title: P201791294


title: INPUT_CF-hKO-B

value: CHOW


title: P201746833

value: DDMVAC+CYST

value: muscle-invasive bladder cancer


title: INPUT_CF-hKO-C


title: P201789570

value: GC+CYST


title: P201794388

value: Clinical Stage -T2


title: P201728208


title: P201784150


title: INPUT_CF-hKO-A


title: INPUT_CF-tKO-C


title: INPUT_CF-tKO-B


title: Sox4_18hpi, rep3 NextSeq 500

description: Sox4_18hpi, rep3


title: INPUT_CF-tKO-A


title: P201714330


title: INPUT_HF-hCT-A

value: Control


title: INPUT_HF-hCT-B


title: INPUT_CF-hCT-A


title: P201720413


title: P201749533


title: INPUT_CF-hCT-B


title: P201762952


title: INPUT_CF-tCT-B


title: P201733970


title: INPUT_CF-tCT-A


title: RPC4_HF-hKO-B

value: Anti-POLR3D (CS681 Ab from Chong et al. 2001)


title: P201784321


title: P201741513


title: P201733005


title: P201722036


title: RPC4_CF-hKO-C


title: P201723659


title: RPC4_CF-hKO-A


title: RPC4_CF-hKO-B


title: P201764065


title: RPC4_CF-tKO-C


title: RPC4_HF-hKO-A


title: P201797802

value: Clinical Stage -T3 or T4a


title: P201644242


title: P201660300


title: P201764348


title: RPC4_CF-tKO-B


title: P201689763


title: P201601633


title: P201675073


title: RPC4_HF-hCT-C


title: P201641196


title: RPC4_CF-tKO-A


title: RPC4_HF-hCT-B


title: RPC4_HF-hCT-A


title: RPC4_CF-hCT-A


title: P201650005


title: RPC4_CF-hCT-B


title: P201629238


title: RPC4_CF-tCT-B


title: 14_Dgluc1mM_3

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to mouse genome using STAR spliced read aligner
Count read using HT-seq with mm10 as reference
Normalization (TMM), quantitation (log CPM) and differential expression analysis using egdeR.
Assembly: mm10
Supplementary files format and content: Counts

source_name: 2-Deoxyglusose (1 mM)

growth_protocol: Primary immature neurons were cultured from E14 mouse embryos and plated on poly-D-Lysine coated plates in the EMEM plus GlutMAX medium added with 10% fetalk bovine serum, 5% horse serum, and 1% Penicillin/Streptomycin. These neurons (two days in vitro) were treated with 2-Deoxyglucose (2-DG).

extract_protocol:
Purified RNA was extracted from these samples using Nucleospin RNA kit (Macherey-Nagel) and follwing its protocol. RNA concentration determined by Nanodrop 1000 (Thermofisher scientific).
cDNA was generated using Ovation® RNA-Seq System V2 (NuGEN) followed by the library preparation using Illumina’s TruSeq Stranded RNA (100ng) + RiboZero Gold.  The libraries were pooled and sequenced to generate 75bp paired-end reads on HiSeq™4000 system (Illumina). Minimum of 57M reads were obtained. Reads were aligned to the mouse mm10 reference genome using the STAR (ver 2.4.0) spliced read aligner (Dobin et al., 2013).

treatment_protocol: These primary immature neurons were either untreated (Control), or treated with 1mM 2-DG and 10mM 2-DG for 6h.

value: immature neurons

tag: group


title: P201672694


title: 15_Dgluc10mM_3

source_name: 2-Deoxyglusose (10 mM)


title: HF-hKO4

data_processing:
RNA and library preparation were as described in , except that samples for the HF-fed Maf1Hep-/- cohort were loaded on two lanes of a HiSeq 4000 flow cell and sequenced at 150 cycles.
Transcript quantification was done using rsem v 1.3.068. The resulting counts matrix was used for subsequent analysis.
Analysis was done in R on the three cohorts, independently; gene filtering based on the rule of 1 count per M (cpm) in at least 1 sample, library size scaling using TMM normalization (EdgeR package v 3.32.1 (Robinson et al. 2010)) and log-transformation using the Limma voom function . Unwanted variation was removed with RUVr (RUVseq package v 1.24.0, Risso et al. 2014).
Statistically significant differentially expressed genes were identified from log-transformed, TMM-scaled values using lmFit of the Limma package by fitting a linear model on the selected samples. P-values calculated using eBayes were adjusted for multiple testing using the Benjamini & Hochberg correction. RUVr-computed factors were added in the design matrix.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include rsem counts per gene for each sample

extract_protocol:
RNA and library preparation were as described in , except that samples for the HF-fed Maf1Hep-/- cohort were loaded on two lanes of a HiSeq 4000 flow cell and sequenced at 150 cycles.
RNA and library preparation were as described in , except that samples for the HF-fed Maf1Hep-/- cohort were loaded on two lanes of a HiSeq 4000 flow cell and sequenced at 150 cycles.


title: P201690589


title: P201595584


title: P201516142


title: RPC4_CF-tCT-A


title: P201674614


title: 13_CT_3

source_name: Control


title: 9_Dgluc10mM_2


title: HF-hKO3


title: HF-hKO2


title: HF-hCT5


title: 8_Dgluc1mM_2


title: 7_CT_2


title: HF-hCT4


title: HF-hCT3


title: 3_Dgluc10mM_1


title: P201665480


title: HF-hCT2


title: 2_Dgluc1mM_1


title: HF-hCT1


title: 1_CT_1


title: P201541751


title: HF-hKO1


title: KMS11 cells treated with ILF2 antisenses  for 3 weeks, Replicate 1

city: Indianapolis

first: Caleb

middle: A

last: Class

state: IN

address: 4600 Sunset Ave

department: Pharmaceutical Sciences

institute: Butler University

description: cells treated with oligonucleotides

data_processing:
FASTQ files were pseudo-aligned using Kallisto with the default options, resulting in pseudo-counts and TPM estimates for each transcript.
Genome_build: human genome GRCh38.p12 (Ensembl version 94)
Supplementary_files_format_and_content: One TSV file (Kallisto output) for each sample, including Ensembl transcript ID, transcript length, effective length, estimated counts, and estimated TPM

growth_protocol: KMS11 and JJN3 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 0.1% amphotericin B (all from Gibco). Cell cultures were maintained at 37°C in 5% CO2. Cells were constantly seeded at a density of 200,000 cells/mL independently of the type of treatment they received.

extract_protocol:
RNA was extracted from KMS11 or JJN3 cells treated with NT or ILF2 ASOs using the RNeasy kit (Qiagen).
Quality checks and quantification were performed with the 2100 Expert Bioanalyzer (Agilent). cDNA libraries were prepared at MD Anderson’s Advanced Technology Genomics Core facility using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos, CA) according to manufacturer’s specifications. Libraries were sequenced on the HiSeq 4000 System (Illumina) using the standard paired-end protocol.

treatment_protocol: KMS11 and JJN3 cells were treated with  0.5 or 1 mM ASOs for 1 or 3 weeks.

tag: cell line

value: myeloma cell

value: ILF2 ASO 09

tag: time

value: 3 weeks


title: CF-hKO3

value: Liver


title: CF-hKO2


title: CF-hKO4


title: KMS11 cells treated with NT antisenses  for 3 weeks, Replicate 3

description: cells treated with oligonucleotides

value: control NT


title: CF-hCT4


title: KMS11 cells treated with NT antisenses  for 3 weeks, Replicate 1

description: cells treated with oligonucleotides


title: KMS11 cells treated with ILF2 antisenses  for 1 week, Replicate 3

description: cells treated with oligonucleotides

value: 1 week


title: KMS11 cells treated with NT antisenses  for 3 weeks, Replicate 2

description: cells treated with oligonucleotides


title: CF-hCT3


title: CF-hCT2


title: CF-tKO5


title: CF-hKO1


title: KMS11 cells treated with ILF2 antisenses  for 1 week, Replicate 2

description: cells treated with oligonucleotides


title: KMS11 cells treated with ILF2 antisenses  for 3 weeks, Replicate 3

description: cells treated with oligonucleotides


title: KMS11 cells treated with NT antisenses  for 1 week, Replicate 2

description: cells treated with oligonucleotides


title: KMS11 cells treated with ILF2 antisenses  for 1 week, Replicate 1

description: cells treated with oligonucleotides


title: KMS11 cells treated with ILF2 antisenses  for 3 weeks, Replicate 2

description: cells treated with oligonucleotides


title: KMS11 cells treated with NT antisenses  for 1 week, Replicate 1

description: cells treated with oligonucleotides


title: CF-tKO3


title: CF-tKO4


title: JJN3 cells treated with ILF2 antisenses  for 3 weeks, Replicate 3

description: cells treated with oligonucleotides


title: CF-tKO2


title: CF-hCT1


title: JJN3 cells treated with ILF2 antisenses  for 3 weeks, Replicate 2

description: cells treated with oligonucleotides


title: CF-tKO1


title: CF-tCT7


title: JJN3 cells treated with ILF2 antisenses  for 3 weeks, Replicate 1

description: cells treated with oligonucleotides


title: CF-tCT6


title: JJN3 cells treated with NT antisenses  for 3 weeks, Replicate 2

description: cells treated with oligonucleotides


title: JJN3 cells treated with NT antisenses  for 3 weeks, Replicate 3

description: cells treated with oligonucleotides


title: CF-tCT5


title: JJN3 cells treated with NT antisenses  for 3 weeks, Replicate 1

description: cells treated with oligonucleotides


title: KMS11 cells treated with NT antisenses  for 1 week, Replicate 3

description: cells treated with oligonucleotides


title: CF-tCT4


title: JJN3 cells treated with ILF2 antisenses  for 1 week, Replicate 2

description: cells treated with oligonucleotides


title: CF-tCT3


title: JJN3 cells treated with ILF2 antisenses  for 1 week, Replicate 1

description: cells treated with oligonucleotides


title: CF-tCT2