title: Control_rep1

city: Changchun

first: Yingshuang

state: Jilin

address: NO.1163 Xinmin Street

institute: Jilin University School of Public Health

data_processing:
Illumina HiSeq 4000 software used for basecalling.
After ribosomal RNA was removed, TopHat2 (version 2.1.1) was used to map to the reference genome.
After alignment with the reference genome, the reads that could be mapped to the genome were filtered out, and the rest were used to identify the circRNA.
The circRNAs were blast searched against circBase for annotation. Those that could not be annotated were considered novel circRNAs.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts and annotation for every circRNA and every sample

source_name: Monocyte macrophage

extract_protocol:
Total RNA was extracted using TRIzol reagent (Takara, Tokyo, Japan) following the manufacturer’s instructions. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the RNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq4000 at the (LC Sciences, USA) following the vendor’s recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: RAW264.7 cell

value: untreated


title: spleen_KO_3

status: Public on May 28 2021

type: SRA

city: beijing

first: Minghang

last: Yu

address: No.10 Xitoutiao, You An Men

country: China

institute: Capital Medical University

library_source: transcriptomic

data_processing:
The library was sequenced in a paired-end 150-bp cycle using Illumina HiSeqTM 2500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie Hista2
The expression level of protein-coding genes was calculated using FPKM  method(Roberts, A., Trapnell, C., Donaghey, J. et al. Genome Biol 12, R22,2011), which is the number of Fragments from a protein-coding gene Per kilobase length Per Million Fragments.
Genome_build: mm9

molecule: total RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
NK cells((CD3-CD19-NKp46+NK1.1+) ) were purified from the spleen of mice using FACS sorting (BD FACSAria III, San Jose, USA).RNA was harvested using Trizol reagent.
RNA-seq libraries were prepared using the NEB Next RNA library prep kit for Illumina using TruSeq indexes according to the manufacturer’s protocol

tag: strain

tag: tissue

value: spleen

tag: age

tag: genotype

value: Ezh2fl/fl; Ncr1iCre


title: Heart Endothelial 3 mo rep1

city: Portland OR

first: Anthony

middle: Paul

last: Barnes

state: OR

address: HRC 545B, 3181 SW Sam Jackson Park Rd

country: USA

institute: OHSU

data_processing:
Sample demulitiplexing was done using Bcl2Fastq (Illumina)
single analysis used Cellranger (10x Genomics)
Seurat 2.3.4 and R version 3.4.2
Genome_build: mouse mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every cell for every sample

source_name: Heart Endothelial 3 mo

growth_protocol: Acute cells were harvested for this study

extract_protocol:
sequencing libraries of captured single cells were generated using the V2 barcoding chemistry of 10X Genomic library kit in accordance with manufacturers protocol
single cell sequencing, 50,000 reads per cell

treatment_protocol: Organs were dissected, minced and digested in media containing Collagenase II and DNAase I. Endothelial cells were enriched using anti-CD31 magnetic beads with Magnetic Assisted Cell Sorting (MACS) (AutoMACS, Miltinyi Biotec). For increased purity, the post- MACS sorted cells were subjected to fluorescent-activated cell sorting using a positive sort for anti-CD31, and negative sort against anti-GP38 and anti-CD45. Purified ECs were loaded onto the 10X Chromium platform for single cell sequencing.

value: 3 months

value: wild type

value: Heart

tag: cell type

value: Endothelial cell


title: Control_rep3

last: Wang

tag: cell line

tag: treatment


title: H3K4me2 ChIP-seq, canola oil-rich diet group

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University

description: mothers fed a canola oil-rich diet (Ca/Co)

library_source: genomic

data_processing:
Illumina Casava software was used for basecalling.
Sequencing quality was initially checked by running FastQC.
Sequencing reads were aligned against mm9 by using Bowtie2. BAM files were normalized by depth after removal of PCR duplicates and blacklisted regions. Peaks were called using MACS2 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig (.bw) files ChIP-seq data were included.

molecule: genomic DNA

source_name: Mammary tissue

extract_protocol:
Mammary tissue was dissected into small pieces and crosslinked using formaldehyde (1% w/v, methanol-free) followed by homogenization and chromatin preparation using a Covaris sonicator (Covaris, Woburn, MA). Chromatin was immunoprecipitated using an appropriate antibody, washed, reverse-crosslinked, and DNA isolated using the phenol-chloroform method. Precipitated DNA was QC’ed by quantitative PCR using Mouse ChIP Control qPCR Primer Sets (Active Motiff, Carlsbad, CA).
For ChIP-sequencing, 10ng precipitated DNA was used to prepare the library using Illumina TruSeq ChIP library preparation kit. Libraries were quantified for cluster generation using KAPA Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Sequencing was performed using Illumina HiSeq2500 using 50-bp single-end rapid run format.

value: BALB/c mice

tag: chip antibody

value: anti H3K4me2 (Active Motif)

tag: diet

value: canola oil-rich


title: H3K4me2 ChIP-seq, corn oil-rich diet group

description: mothers fed a corn oil-rich diet (Co/Co)

value: corn oil-rich


title: Input sample


title: H3K18ac ChIP-seq, canola oil-rich diet group

value: anti H3K18ac (Active Motif)


title: OK4_2_Kidney Endothelial 24 mo rep3-2

description:
RNA170124AB_OK4_S18_L004
processed data file: CombinedKidneyCounts.csv
replicate 3-2

data_processing:
Tophat2 with default parameters was used to align the sequenced reads against the mouse genome
HTSeq python software with default parameters was used to quantify the transcripts of the aligned reads
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Kidney Endothelial 24 mo

extract_protocol:
cDNA libraries using SmartSeq V4 chemistry (Takara)
Ovation random priming protocol from Nugen

treatment_protocol: Organs were dissected, minced and digested in media containing Collagenase II and DNAase I. Endothelial cells were enriched using anti-CD31 magnetic beads with Magnetic Assisted Cell Sorting (MACS) (AutoMACS, Miltinyi Biotec). For increased purity, the post- MACS sorted cells were subjected to fluorescent-activated cell sorting using a positive sort for anti-CD31, and negative sort against anti-GP38 and anti-CD45. Purified ECs for bulk RNA-seq were sorted into buffer RLT from Qiagen and stored at -80ºC degrees until total RNA extraction. Total RNA was extracted from cells and stored in buffer RLT using the RNAeasy Micro Kit (Qiagen). Quality and quantity of extracted RNA were assessed using the Agilent 2100 BioAnalyzer RNA 6000 Pico chip.

value: 24 months

value: Kidney


title: RT_rep3


title: H3K18ac ChIP-seq, corn oil-rich diet group


title: RT_rep1


title: Heart Endothelial 24 mo rep1

source_name: Heart Endothelial 24 mo


title: Club cells from 4 Atgl KO/cTg  mice [A0C-3260-3263]

type: RNA

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

description: Gene expression data from club cells withouth ATGL

hyb_protocol: Affymetrix Mouse Gene 2.0 ST Array (Cat No. 902118); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip® fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software AGCC 4.0.0)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.

label: Biotin

source_name: Knock-out cells

label_protocol: 50ng for NuGen Ovation Pico WTA System V2, M01224v2 (NuGEN Technologies Inc; San Carlos, CA; Cat No. 3302-24)

growth_protocol: All animals were kept on a regular light-dark cycle (14 h light-10 h dark) at 22±1 °C in a specific pathogen-free environment, and were fed a standard laboratory chow diet ad libitum.

extract_protocol: 200 μL of chloroform was put on the 1 mL of trizol containing the club cells and centrifuged. Further steps  for isolation were followed according to the kit protocol. Kit used: miRNeasy Micro Kit (Qiagen, Hilden, Germany; Cat No 217084) including DNAse treatment on the column with RNase-Free DNase Set (Qiagen, Hilden, Germany; Cat No 79254)

treatment_protocol: No specific treatments were involved. For isolation of the cells, animals were first deeply anesthesised and sacrificed. Club cells were  isolated from the extracted lung according to the standard protocol. Isolated cells were then used for RNA extraction.

tag: genotype/variation

value: Atgl KO/cTg

value: 42-45 weeks

tag: tissue/cell type

value: Club cells from Lung


title: SB-3: PMN-Arf6flox

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation. After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files. Microarray hybridization was carried out at the Microarrays Facility of the Research Center of Laval University CRCHUL.

data_processing: Background subtraction and normalization of probe set intensities were performed using the method of Robust Multiarray Analysis (Irizarry et al, 2003), as impelemented by TAC 4.0 software..

source_name: Arf6-KO Leucocytes that have migrated into the mouse air pouches injected with LPS

label_protocol: Total RNA (100 ng per sample) was labeled using the GeneChip® WT Plus Reagent Kit protocol and hybridized to the arrays as described by the manufacturer (Affymetrix, Thermofisher).

extract_protocol: Total RNA was isolated from PMNs. Total RNA extraction was performed with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol, and potential genomic DNA contamination was eliminated with the RNase-free DNase set (Qiagen). Total RNA was eluted in RNAse-free water and its concentration was quantified with a NanoDrop 1000 microvolume spectrophotometer (Thermo Scientific). Ribonucleic acid quality was assessed with the Eukaryote Total RNA Pico Series II kit (Agilent) on a 2100 Bioanalyzer by the transcriptomic core facility of the CHUQ. The minimal accepted number for RNA integrity was 7.

treatment_protocol: Leucocytes that have migrated into the mouse air pouches injected with LPS were collected from the Arf6 cKO and the control groups (homozygous Cre+/+ and flox+/+Cre-/- mice, respectively). For each mouse genotype, three independent groups of 5 mice were used. Air pouch PMNs were pooled and purified by negative selection as described above. The cell suspensions were 98% Ly6G positive as estimated by flow cytometry

value: Leucocytes

value: control flox+/+Cre-/-


title: C57BL6_SMC_ChIP_input_control_48h

city: Tucson

first: Casey

last: Romanoski

state: AZ

address: 1230 N Cherry Ave

institute: U. Arizona

description: non-immunoprecipitated chromatin (input)

data_processing:
RNA-seq reads were mapped to mm10 with STAR
reads were organized in HOMER using its preferred data structure using the makeTagDirectory function
Expression matrices were calculated in homer using the analyzeRepeats function counting tags in the mm10 RefSeq gene body annotations with either no normalization, for input into DESeq2, or with -rpkm, for visualization in heatmaps.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Reads from ChIP-seq experiments were mapped to the mm10 build of the mouse genome with Bowtie2
ChIP-seq H3K27ac-defined genomic regions were identified relative to un-immunoprecipitated, fixed chromain, or ‘input’, as a negative control. Peaks were called using HOMER with the findPeaks program using the -histone option.
Genome_build: mm10
Supplementary_files_format_and_content: peak files

source_name: Vascular smooth muscle cells

growth_protocol:
Cells were grown in DMEM containing 10% FBS, 100 units/ml penicillin, and 100 ug/ml streptomycin.
Cells were grown in DMEM containing 10% FBS, 100 units/ml penicillin, and 100 ug/ml streptomycin.
Cells were grown in DMEM containing 10% FBS, 100 units/ml penicillin, and 100 ug/ml streptomycin.

extract_protocol:
cells were fixed at room temperature with 1% paraformaldehyde in PBS for 10 min, and then quenched with glycine. Between 3 and 5 million cells were used for each ChIP. Fixed lysates were sonicated using a BioRuptor Standard (Diagenode)
Lysates were immunoprecipitated using antibodies bound to a 2:1 mixture of Protein A Dynabeads (Invitrogen #10002D) and Protein G Dynabeads (Invitrogen #10004D). Following immunopreciptation, crosslinking was reversed. dsDNA ends were repaired with T4 DNA Polymerase (Enzymatics #P7080L). Barcode adapters (BIOO Scientific NEXTflex, Austin, TX, #514104) were ligated onto the ends of sequences using T4 DNA Ligase (Enzymatics #L-6030-HC-L). Libraries were then amplified by PCR (Phusion Hot Start II, ThermoFisher Scientific, #F549L) and purified (Zymo #D5205) for high-throughput sequencing.
RNA was extracted from cultured VSMCs using the Quick-RNA Micro Prep kit from ZymoResearch (Irvine, CA, #R1051), including optional DNase I treatment.
mRNA was selected through poly-A isolation using Oligo d(T)25 beads (New England BioLabs, Ipswich, MA, #S1419S). Selected RNA was fragmented, followed by single strand cDNA synthesis using a SuperScript III First-Strand Synthesis System (ThermoFisher Scientific # 18080051), followed by second strand synthesis using DNA Polymerase I (Qiagen/Enzymatics, Beverly, MA, #P7050L). dsDNA ends were repaired with T4 DNA Polymerase (Enzymatics #P7080L). Barcode adapters (BIOO Scientific NEXTflex, Austin, TX, #514104) were ligated onto the ends of sequences using T4 DNA Ligase (Enzymatics #L-6030-HC-L) and samples were treated with Uracil DNA Glycosylase (UDG) (Enzymatics #G5010L). Libraries were then amplified by PCR (Phusion Hot Start II, ThermoFisher Scientific, #F549L) and purified (Zymo #D5205) for high-throughput sequencing.
cells were fixed at room temperature with 1% paraformaldehyde in PBS for 10 min, and then quenched with glycine. Between 3 and 5 million cells were used for each ChIP. Fixed lysates were sonicated using a BioRuptor Standard (Diagenode)
Lysates were immunoprecipitated using antibodies bound to a 2:1 mixture of Protein A Dynabeads (Invitrogen #10002D) and Protein G Dynabeads (Invitrogen #10004D). Following immunopreciptation, crosslinking was reversed. dsDNA ends were repaired with T4 DNA Polymerase (Enzymatics #P7080L). Barcode adapters (BIOO Scientific NEXTflex, Austin, TX, #514104) were ligated onto the ends of sequences using T4 DNA Ligase (Enzymatics #L-6030-HC-L). Libraries were then amplified by PCR (Phusion Hot Start II, ThermoFisher Scientific, #F549L) and purified (Zymo #D5205) for high-throughput sequencing.

treatment_protocol:
Treated VSMCs were incubated with Chol:MβCD (20 ug/ml) in 0.2% BSA for 24 or 48 h. Untreated samples were incubated with 0.2% BSA for 0, 24, or 48 h without Chol:MβCD.
Treated VSMCs were incubated with Chol:MβCD (20 ug/ml) in 0.2% BSA for 24 or 48 h. Untreated samples were incubated with 0.2% BSA for 0, 24, or 48 h without Chol:MβCD.
Treated VSMCs were incubated with Chol:MβCD (20 ug/ml) in 0.2% BSA for 24 or 48 h. Untreated samples were incubated with 0.2% BSA for 0, 24, or 48 h without Chol:MβCD.

value: untreated

value: murine vascular smooth muscle cells

tag: time point (hrs)


title: Heart Endothelial 3 mo rep2

value: 3 months

value: wild type


title: OK3_Kidney Endothelial 24 mo rep2

description:
RNA170124AB_OK1_S4_L004
processed data file: CombinedKidneyCounts.csv
replicate 2


title: C57BL6_SMC_ChIP_input_control_24h


title: Control_rep2

value: RAW264.7 cell


title: SB-2: PMN-Arf6flox


title: iSABs

city: Dummerstorf

first: Anne-Marie

last: Galow

address: Wilhelm-Stahl-Alle 2

country: Germany

institute: Leibniz-Institute for farm animal biology

data_processing:
BCL files generated by Illumina sequencing systems were demultiplexed and converted to standard FASTQ files using the mkfastq function from Cell Ranger (v.6.1.0)
Alignment was conducted with STAR (v.2.7) and reads were processed to generate expression (UMI count) matrices using the cellranger count function (Cell Ranger v.6.1.0) with default parameters.
Genome_build: mm10 (Ensembl release 98)
Supplementary_files_format_and_content: Raw UMI count matrices were generated as described above and are provided as supplementary file. Count matrices represent comma-separated gene expression values, where each column represents a single cell and each row represents a single gene.

molecule: polyA RNA

source_name: cell line

growth_protocol: double transfected stem cells (TBX3+MHCneoPGKhygro) were selected via addition of 10 µg/ml blasticidin (InvivoGen) and 250 µg/ml hygromycin (InvivoGen) before generating Embryoid Bodies (EBs) using a Spherical plate 5D (Kugelmeiers LTD). Antibiotic selection of “induced-sinoatrial-bodies'' (iSABs) started on day 12 of differentiation by adition of 400 µg/ml G418 (Biochrom). Cells were cultured for 29days before single cell sequencing analysis.

extract_protocol:
iSABs were separated using the Primary Cardiomyocyte Isolation Kit (Thermo Fisher Scientific) and resuspended in PBS with 0.04% BSA to 1.000 cells/μl. Single cells were then captured in droplet emulsions using the GemCode Single-Cell Instrument (10x Genomics) with a target output of 2.000 cells.
Libraries for scRNA-seq were constructed according to the 10x Genomics protocol using the GemCode Single-Cell 3′ Gel Bead and Library V3 Kit. Amplified cDNA and final libraries were evaluated on the 2100 Bioanalyzer instrument (Agilent) using a High Sensitivity NGS Analysis Kit (Advanced Analytical). Amplification yielded in 3.3pg/µl cDNA and final libraries contained cDNA fragments with an average size around 450bp. The subsequent sequencing was conducted on the HighSeq4000 Sequencing System using the HiSeq SBS and HiSeq PE Cluster Kit V4 (all Illumina, San Die-go, CA. USA).

value: pacemaker cell

tag: culture time


title: RT_rep2


title: OK4_Kidney Endothelial 24 mo rep3

description:
RNA170124AB_OK3_S13_L003
processed data file: CombinedKidneyCounts.csv
replicate 3


title: C57BL6_SMC_ChIP_input_control_0h


title: OK1_Kidney Endothelial 24 mo rep1

description:
RNA170124AB_OK1_S4_L001
processed data file: CombinedKidneyCounts.csv
replicate 1


title: YK3_Kidney Endothelial 3 mo rep2

description:
RNA170124AB_YK3_S11_L003
processed data file: CombinedKidneyCounts.csv
replicate 2

source_name: Kidney Endothelial 3 mo


title: YK4_Kidney Endothelial 3 mo rep3

description:
RNA170124AB_YK4_S16_L004
processed data file: CombinedKidneyCounts.csv
replicate 3


title: OB4_Brain Endothelial 24 mo rep3

description:
RNA170124AB_OB4_S15_L003
processed data file: CombinedBrainCounts.csv
replicate 3

source_name: Brain Endothelial 24 mo

value: Brain


title: C57BL6_SMC_ChIP_input_cholesterol_24h

value: cholesterol


title: C57BL6_SMC_ChIP_input_cholesterol_48h


title: control-48h-rep3

description: SMC-control-cholesterol-rna-rpkm-tpb1-noCondense-analyzeRepeats.xlsx

extract_protocol:
RNA was extracted from cultured VSMCs using the Quick-RNA Micro Prep kit from ZymoResearch (Irvine, CA, #R1051), including optional DNase I treatment.
mRNA was selected through poly-A isolation using Oligo d(T)25 beads (New England BioLabs, Ipswich, MA, #S1419S). Selected RNA was fragmented, followed by single strand cDNA synthesis using a SuperScript III First-Strand Synthesis System (ThermoFisher Scientific # 18080051), followed by second strand synthesis using DNA Polymerase I (Qiagen/Enzymatics, Beverly, MA, #P7050L). dsDNA ends were repaired with T4 DNA Polymerase (Enzymatics #P7080L). Barcode adapters (BIOO Scientific NEXTflex, Austin, TX, #514104) were ligated onto the ends of sequences using T4 DNA Ligase (Enzymatics #L-6030-HC-L) and samples were treated with Uracil DNA Glycosylase (UDG) (Enzymatics #G5010L). Libraries were then amplified by PCR (Phusion Hot Start II, ThermoFisher Scientific, #F549L) and purified (Zymo #D5205) for high-throughput sequencing.
RNA was extracted from cultured VSMCs using the Quick-RNA Micro Prep kit from ZymoResearch (Irvine, CA, #R1051), including optional DNase I treatment.
mRNA was selected through poly-A isolation using Oligo d(T)25 beads (New England BioLabs, Ipswich, MA, #S1419S). Selected RNA was fragmented, followed by single strand cDNA synthesis using a SuperScript III First-Strand Synthesis System (ThermoFisher Scientific # 18080051), followed by second strand synthesis using DNA Polymerase I (Qiagen/Enzymatics, Beverly, MA, #P7050L). dsDNA ends were repaired with T4 DNA Polymerase (Enzymatics #P7080L). Barcode adapters (BIOO Scientific NEXTflex, Austin, TX, #514104) were ligated onto the ends of sequences using T4 DNA Ligase (Enzymatics #L-6030-HC-L) and samples were treated with Uracil DNA Glycosylase (UDG) (Enzymatics #G5010L). Libraries were then amplified by PCR (Phusion Hot Start II, ThermoFisher Scientific, #F549L) and purified (Zymo #D5205) for high-throughput sequencing.
cells were fixed at room temperature with 1% paraformaldehyde in PBS for 10 min, and then quenched with glycine. Between 3 and 5 million cells were used for each ChIP. Fixed lysates were sonicated using a BioRuptor Standard (Diagenode)
Lysates were immunoprecipitated using antibodies bound to a 2:1 mixture of Protein A Dynabeads (Invitrogen #10002D) and Protein G Dynabeads (Invitrogen #10004D). Following immunopreciptation, crosslinking was reversed. dsDNA ends were repaired with T4 DNA Polymerase (Enzymatics #P7080L). Barcode adapters (BIOO Scientific NEXTflex, Austin, TX, #514104) were ligated onto the ends of sequences using T4 DNA Ligase (Enzymatics #L-6030-HC-L). Libraries were then amplified by PCR (Phusion Hot Start II, ThermoFisher Scientific, #F549L) and purified (Zymo #D5205) for high-throughput sequencing.


title: YB3_Brain Endothelial 3 mo rep2

description:
RNA170124AB_YB3_S12_L003
processed data file: CombinedBrainCounts.csv
replicate 2

source_name: Brain Endothelial 3 mo


title: C57BL6_SMC_ChIP_H3K27ac_cholesterol_24h

description: DNA from H3K27ac ChIP-seq

tag: antibody


title: control-48h-rep2


title: OB1_Brain Endothelial 24 mo rep1

description:
RNA170124AB_OB1_S10_L002
processed data file: CombinedBrainCounts.csv
replicate 1


title: YK1_Kidney Endothelial 3 mo rep1

description:
RNA170124AB_YK1_S2_L001
processed data file: CombinedKidneyCounts.csv
replicate 1


title: YB4_Brain Endothelial 3 mo rep3

description:
RNA170124AB_YB4_S8_L002
processed data file: CombinedBrainCounts.csv
replicate 3


title: C57BL6_SMC_ChIP_H3K27ac_control_24h

description: DNA from H3K27ac ChIP-seq


title: C57BL6_SMC_ChIP_H3K27ac_control_48h

description: DNA from H3K27ac ChIP-seq


title: control-24h-rep3


title: control-24h-rep1


title: control-24h-rep2


title: OH4_Heart Endothelial 24 mo rep3

description:
RNA170124AB_OH4_S17_L004
processed data file: CombinedHeartCounts.csv
replicate 3

value: Heart


title: OH1_Heart Endothelial 24 mo rep1

description:
RNA170124AB_OH1_S3_L001
processed data file: CombinedHeartCounts.csv
replicate 1


title: YH4_2_Heart Endothelial 3 mo rep3-2

description:
RNA170124AB_YH4_S5_L004
processed data file: CombinedHeartCounts.csv
replicate 3-1

value: 4 months


title: OB3_Brain Endothelial 24 mo rep2

description:
RNA170124AB_OB3_S14_L003
processed data file: CombinedBrainCounts.csv
replicate 2

value: 24 months


title: control-0h-rep3


title: C57BL6_SMC_ChIP_H3K27ac_cholesterol_48h

description: DNA from H3K27ac ChIP-seq


title: OH3_Heart Endothelial 24 mo rep2

description:
RNA170124AB_OH3_S9_L002
processed data file: CombinedHeartCounts.csv
replicate 2


title: cholesterol-48-rep2


title: YH1_Heart Endothelial 3 mo rep1

description:
RNA170124AB_YH1_S1_L001
processed data file: CombinedHeartCounts.csv
replicate 1


title: cholesterol-48-rep3


title: C57BL6_SMC_ChIP_H3K27ac_control_0

description: DNA from H3K27ac ChIP-seq


title: cholesterol-24h-rep3


title: cholesterol-24h-rep2


title: YH3_Heart Endothelial 3 mo rep2

description:
RNA170124AB_YH3_S6_L002
processed data file: CombinedHeartCounts.csv
replicate 2


title: YH4_1_Heart Endothelial 3 mo rep3

description:
RNA170124AB_YH4_S5_L001
processed data file: CombinedHeartCounts.csv
replicate 3


title: Sstr2KOP14: P14 Sstr2 KO Allelic Series

city: Baltimore

first: Kurt

last: Weir

address: 733 North Broadway

institute: Johns Hopkins School of Medicine

description: MULTI-seq dataset with samples from an allelic series of genotypes in a single expression library

data_processing:
Library strategy: scRNA-seq
fastq generation: cellranger-3.1.0 mkfastq
read alignment and expression quantification: cellranger-3.1.0 count
gene expression and cell clustering: Seurat v3 sctransform workflow
Genome_build: mm10
Supplementary_files_format_and_content: *metadata.tsv: tsv of scRNA-seq metadata
Supplementary_files_format_and_content: *SCT_counts.mtx: mtx file of dgTMatrix of gene by cell expression using seurat sct workflow. Genes are rows, cells are columns
Supplementary_files_format_and_content: *RNA_counts.mtx: mtx file of dgTMatrix of gene by cell raw expression. Genes are rows, cells are columns
Supplementary_files_format_and_content: *genes.tsv: tsv of genes quantified in Explant_SCT_counts.mtx
Supplementary_files_format_and_content: *RNA_genes.tsv: tsv of genes quantified in Explant_RNA_counts.mtx

source_name: Retina

extract_protocol:
Retinas and explants were removed and dissociated with the Worthington papain dissociation kit. Samples were barcoded with lipi-modified oligos according to the MULTI-seq protocol and pooled into a single cell stock for each of the samples listed above.
GEM generation and library preparation were performed with the 10x Chromium controller and Chromium Single Cell 3′ Reagent Kit.

tag: sample type

value: mixed (multiplexed)

value: Postnatal day 14

value: in vivo


title: Sstr2KOP0: P0 Sstr2 KO Allelic Series

value: Postnatal day 0


title: cholesterol-48-rep1


title: Hippocampal_area_CA1_control

city: San Joan d'Alacant

first: Jose

middle: P

last: Lopez-Atalaya

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias

country: Spain

institute: CSIC-UMH

description:
Sample_30D
single-nucleus gene expression profiling (snRNA-seq)
mRNA
Calb1::Cre (www.jax.org/strain/023531)
Tdtomato mice (www.jax.org/strain/007905)

data_processing:
Sequencer: Illumina HiSeq 2500. Basecalling pipeline: HiSeq Control Software 2.2.58. HiSeq Sequencing v4 Chemistry. Read Length: 75 paired end.
Quality control of sequenced reads was performed using FastQC (Babraham Institute). Sequenced samples were processed using the Cell Ranger (v.2.2.0) pipeline (10x Genomics) and aligned to the GRCm38 (mm10) mouse reference genome customized to count reads in nuclear precursor mRNA (pre-mRNA) (gene annotation version 94). We retrieved 3,661 high quality nuclei in control sample and 3,078 in epileptic sample. Mean reads per nucleus were 71,449 in control and 96,150 in epileptic sample. Median genes per nucleus were 1,599 in control and 1,256 in epileptic sample. Minimum UMI counts per nucleus were 710 in control and 540 in epileptic sample.
Genome_build: GRCm38.94
Supplementary_files_format_and_content: Single-nucleus RNA-seq datasets. Each dataset contains three files: barcodes.tsv (a tab-separated values file with nuclear barcodes present in dataset); genes.tsv (a tab-separated values file with IDs of quantified genes (Mouse ENSEMBL Gene ID and Gene Symbol)); matrix.mtx (a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the nuclear barcodes). A standard or sparse matrix can be generated where genes.tsv file corresponds to the genes or row names of the matrix, while barcodes.tsv corresponds to the nuclei or columns.

extract_protocol:
Single nuclei from 2 control and 2 epileptic Calb1::CrexTdtomato young adult male mice were acutely isolated. Animals were sacrificed 12 weeks after the kainate/saline administration by cervical dislocation and brains were dissected and cut in 300um thick slices in a vibratome covered by ice cold HBBS1x. Dorsal CA1 region were manually dissected from 4 consecutive slices and put altogether into 400uL of ice cold MACS buffer (0,5%BSA, 2mM EDTA, PBS1x). CA1 portions were transferred to a dounce homogenizer (20404 Lab Unlimited) containing 400uL of MACS buffer and were homogenized 12-15 times each with the pestle. The cell suspension was transferred to a 2mL Eppendorf tube and centrifuge 15min 500G 4ºC. Cell pellets were resuspended in 500uL of lysis buffer (10mM Tris-HCL, 10mM NaCl, 3mM MgCl2, 0,1% IGEPAL) and kept 5 minutes on ice. Samples were then spun down at 500xg for 30 min in a pre-chilled centrifuge. The nuclei pellet was resuspended in PBS1x 1%BSA and then 15,000 nuclei were sorted on a BD FACS Aria III. The whole process was carried out at 4ºC.
FACS purified nuclei from mouse hippocampal CA1 area were processed through all steps to generate stable cDNA libraries. For every sample, 15,000 nuclei were loaded into a Chromium Single Cell A Chip (10x Genomics) and processed following the manufacturer’s instructions. Single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v2 and i7 Multiplex kit (10x Genomics). Pooled libraries were then loaded on a HiSeq2500 instrument (Illumina) and sequenced to obtain 75 bp paired-end reads.

treatment_protocol: Young adult (6-7 weeks old) male transgenic mice (Calb1::Cre (https://www.jax.org/strain/023531) x Tdtomato mice (https://www.jax.org/strain/007905)) were treated with multiple intraperitoneal injections of kainate (5 mg/kg) at hourly intervals until they reached status epilepticus. The status was defined as a condition of continuous seizures lasting longer than 30 min. Diazepam (4 mg/kg) was injected 1 h post-status to stop convulsions. Animals received intraperitoneal injections of 2.5 ml 5% dextrose in saline and their diet was supplemented with fruit and powder milk during the following 2–3 days. After 4-5 days, mice behaved normally and were housed individually. Control animals were injected with vehicle (either saline or DMSO) and received treatments similar to epileptic animals. Single-nucleus RNA-seq was performed after 12 weeks post-status when animals were in the chronic epileptic phase. Seizures were observed either during handling or recorded electrophysiologically in a subset of animals. Control animals did never exhibit seizures.

value: Calb1::Cre x Tdtomato mice

value: Adult (6-7 weeks)

tag: Sex

value: Male

value: Hippocampal CA1 pyramidal cell layer

tag: condition

value: Control


title: YB1_Brain Endothelial 3 mo rep1

description:
RNA170124AB_YB1_S7_L002
processed data file: CombinedBrainCounts.csv
replicate 1

tag: strain

value: 3 months

value: wild type


title: control-0h-rep1

value: untreated

value: murine vascular smooth muscle cells


title: control-0h-rep2


title: KO_NK_MCMV_13

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

institute: Moffitt Cancer Center

description: Bcl11b KO

data_processing:
Fastq files were trimmed using Seqtk
Trimmed fastq files were aligned to the mm10 genome via Hisat2
Raw counts were extracted from bam files using htseq
Differential analysis was performed on raw counts with DESeq2
Normalized counts were calculated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Normalized_counts.txt contains normalized count values for each sample generated by DESeq2.

source_name: Splenic Ly49h+ NK cells

extract_protocol:
Tissue were lysed and RNA was isolated using Qiagen Rneasy Plus Micro Kit (Qiagen #74034). RNA quality was determined on a bioanalyzer (Agilent RNA 6000 Nano #5067-1511)
Libraries were prepared using New England Biolabs NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (cat# E7770S) according to the manufacturer's instructions. Library quality and concentration was checked on a bioanalyzer (Agilent High Sensitivity DNA Kit #5067-4626) and by Qubit (Qubit™ dsDNA HS Assay Kit #Q32854). Libraries were sequenced on a NextSeq500.

treatment_protocol: Congenically distinct WT and Bcl11b KO NK cells were adoptively co-transfered into Ly49H deficient hosts that were infected the following day with MCMV. Cells were sorted from the spleen at day 7.

value: Bcl11b KO

value: KO


title: Hippocampal_area_CA1_epilepsy

description:
Sample_27A
single-nucleus gene expression profiling (snRNA-seq)
mRNA
Calb1::Cre (www.jax.org/strain/023531)
Tdtomato mice (www.jax.org/strain/007905)

tag: tissue

value: Epilepsy


title: KO_NK_MCMV_12

description: Bcl11b KO


title: MULTI-Seq_Sstr2: Explant Sstr2 Treatment Series

description: MULTI-seq dataset with samples from a range of treatment conditions in a single expression library

source_name: Retinal Explant

growth_protocol: Embryonic day 14 retinas were dissected from  embryos of time pregnant mothers and grown on Nuclepore membranes for 6 days on growth media

treatment_protocol: Treated with an Sstr2 small molecule agonist at concentrations listed in characteristic: treatment in the growth media

tag: age

value: ex vivo Sstr2 agonist 0 nM, 5 nM, 50 nM, 500 nM


title: KO_NK_MCMV_11

description: Bcl11b KO

tag: genotype


title: WT_NK_MCMV_12

description: Bcl11b WT

value: Bcl11b WT

value: WT


title: cholesterol-24h-rep1

description: SMC-control-cholesterol-rna-rpkm-tpb1-noCondense-analyzeRepeats.xlsx

value: cholesterol

tag: cell type


title: WT_NK_MCMV_13

description: Bcl11b WT


title: MOLM13-Cas9_YBX1-sgRNA2_RNAseq_rep4

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) genome using STAR (v2.7.5a), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: *.tdf: IGVtools tiled data files.
Supplementary_files_format_and_content: YBX1_CRISPR-ko_MOLM13_RNAseq_190225_DESeq2_DiffExp_summary_rmdup.xlsx: DESeq2 differentially expressed gene summary + normalized counts + gene z-scores.

organism: Homo sapiens

source_name: MOLM13+Cas9 cultured cells

growth_protocol: MOLM13 cells were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher). MOLM13 cells were stably transduced with Cas9 (Lenti‐Cas9‐2A‐Blast, Addgene: #73310) and selected with Blasticidine (5ug/ml). After Lentiviral transduction with 2 different guide RNAs targeting YBX1 or non-targeting control (pUSEPR-vector, Puromycine+RFP) cells were cultured in Puromycine (1ug/ml).

extract_protocol:
For RNA isolation from cell were FACS sorted for high RFP-expressing cells (guide expressing cells), 0.5x10^6 cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions for cell ine experiments.
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 37bp, paired-end reads.

tag: cell line

tag: timepoint

value: 7 days post transduction

tag: sgrna

value: CRISPR-Cas9-mediated YBX1-ko (sgRNA2)


title: MOLM13-Cas9_YBX1-sgRNA2_RNAseq_rep3

description: YBX1_CRISPR-ko_MOLM13_RNAseq_190225_DESeq2_DiffExp_summary_rmdup.xlsx


title: MOLM13-Cas9_YBX1-sgRNA2_RNAseq_rep2


title: MOLM13-Cas9_YBX1-sgRNA1_RNAseq_rep2

value: CRISPR-Cas9-mediated YBX1-ko (sgRNA1)


title: MOLM13-Cas9_YBX1-sgRNA1_RNAseq_rep3


title: MOLM13-Cas9_empty-vector-control_RNAseq_rep3

value: non-targeting sgRNA vector


title: MOLM13-Cas9_YBX1-sgRNA2_RNAseq_rep1


title: MOLM13-Cas9_YBX1-sgRNA1_RNAseq_rep1


title: MOLM13-Cas9_YBX1-sgRNA1_RNAseq_rep4


title: MOLM13-Cas9_empty-vector-control_RNAseq_rep2


title: MOLM13-Cas9_empty-vector-control_RNAseq_rep4


title: MOLM13_YBX1-ChIP

description:
Molm13_Yb1-CHIP_vs_Molm13_input.hg19.macs_peaks.annotated.txt
Molm13_Yb1-CHIP_vs_Molm13_input.hg19.macs_peaks.motifs.tar

data_processing:
Raw Illumina NextSeq BCL files converted to FASTQs using Illumina bcl2fastq v02.14.01.07 and reads trimmed using Trimmomatic v0.36 (phred quality threshold 33).
FastQ files were uploaded to the Basepair-server (basepairtech.com).
Alignment and ChIP-seq QC was performed using the basepair (Bowtie2) utilizing the default settings.
Peak calling was performed using MACS (v.1.4) within the basepair platform utilizing the default settings.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig: Sample signal files for visualization.
Supplementary_files_format_and_content: Molm13_Yb1-CHIP_vs_Molm13_input.hg19.macs_peaks.annotated.txt: YBX1 peak calling results as the original MACS output.
Supplementary_files_format_and_content: Molm13_Yb1-CHIP_vs_Molm13_input.hg19.macs_peaks.motifs.tar: Tar archive containing HOMER output for determining enriched motifs associated with YBX1-peaks.

source_name: MOLM13 cultured cells

growth_protocol: MOLM13 cells were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher).

extract_protocol:
The cells were collected and washed twice in ice-cold PBS followed by crosslinking in 1% formaldehyde (methanol free) for 5 minutes. Excess of formaldehyde was quenched by addition of Tris pH 8.0 to 100nM final and Glycine 125 mM final. Chromatin was sheared using Covaris E220 for 20 min with power 140; duty 5; bursts 200/sec. We then used 5ul aliquot of sheared chromatin to decrosslink in order to test completeness of shearing. Chromatin was considered passed QC if fragments 100-600bp were >90%. For immunoprecipitation we used approximately chromatin from 1-10x10^6 cells, 5-10ug of specific antibody and 10-20ul of Protein-A/G magnetic beads (Dynal). In 16 hours the immune complexes were washed in Mixed Micelle Buffer, buffer 500, LiCl/detergent solution and TE buffers. DNA was eluted from the beads using 100mM NaHCO3 100mM NaCl 1% SDS and purified using AmpureXP beads.
1-10 ng of ChIP'ed DNA was used for Illumina compatible library generation using ThruPlex DNA-seq kit with 10 to 14 cycles of amplification with single end barcodes.
Sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 37bp, paired-end reads.

value: steady-state

tag: treatment

tag: chip antibody


title: Day 10 axially elongating human iPSC-derived organoids [RPI4]

city: San Francisco

first: Todd

last: McDevitt

state: CA

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

description: Human axially elongating organoids

data_processing:
Demultiplex with CellRanger v3.0.2
Align to GRCh38 with CellRanger v3.0.2
Generate raw counts matrix with CellRanger v3.0.2
Demultiplex MultiSeq barcodes with v2.20.0
Call MultiSeq barcodes with deMULTIplex v1.0.2
Subset final counts matrix corresponding to MultiSeq Barcode 9 using Seurat v3.1.5
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix Market Format final counts of the MultiSeq reads corresponding to axially elongating worms
Supplementary_files_format_and_content: Matrix Market Format raw counts for all samples before demultiplexing
Supplementary_files_format_and_content: Comma separated value formated final MultiSeq barcode assignments

source_name: Human iPSC

growth_protocol: Neural differentiation following Libby et al 2020

extract_protocol:
Multi-seq barcoding following McGinnis et al 2018 followed by 10x Chromium Single Cell Barcoding v2
10x Chromium Single Cell Library Prep v2 and Multi-seq Library Prep following McGinnis et al 2018

treatment_protocol: Differentiation following 2 uM CHIR pretreatment in 10 cm dishes for 10 days

value: elongating organoids


title: Elongating organoid day 10 [4 uM CHIR Day 10 - Replicate 3]

description: Elongating neural organoid at day 10 of differentiation

data_processing:
Demultiplex with bcl2fastq v2.20.0
Align to GRCh37 with hisat2 v2.1.0
Generate counts matrices with featureCounts v1.6.2
Genome_build: GRCh37
Supplementary_files_format_and_content: Comma separated value count files

source_name: human iPSC derived neural organoids

extract_protocol:
Extraction using Qiagen Rneasy Mini Kit
Library prep using Takara Biosciences SMARTer Stranded Total RNA Sample Prep Kit

treatment_protocol: Differentiation following Libby et al 2020 with either 0 uM or 4 uM CHIR treatment for 10 days, sampling every other day after initial aggregation

tag: time point

value: day 10

tag: agent

value: 4 uM CHIR


title: MOLM13-Cas9_empty-vector-control_RNAseq_rep1


title: Elongating organoid day 10 [4 uM CHIR Day 10 - Replicate 2]


title: WT_NK_MCMV_11

description: Bcl11b WT


title: MOLM13_Chromatin-input


title: Elongating organoid day 10 [4 uM CHIR Day 10 - Replicate 1]


title: Non-elongating organoid day 10 [0 uM CHIR Day 10 - Replicate 3]

description: Non-elongating neural organoid at day 10 of differentiation

value: non-elongating organoids

value: 0 uM CHIR


title: CD34_3

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Paired-end reads in Fastq files were first trimmed (stringency 2) using Trim Galore! (v0.4.0) and aligned to the human genome build GRChg38 from Ensembl using STAR (Dobin et al., 2013) with the “--outFilterMultimapNmax 100 --winAnchorMultimapNmax 100” options.
Repeat and gene expression was quantified with TETranscripts version 2.00 (Jin et al., 2015).
Genome_build: GRChg38
Supplementary_files_format_and_content: AML_vs_CD34.cntTable.txt: Tab-delimited text file includes raw counts.

source_name: blood

growth_protocol: Blood samples of pre-therapeutic and newly diagnosed AML patients were obtained from the Hematology, Oncology and Stem cell Transplantation department of the University of Freiburg, Medical Center. Leukemic blast cells were isolated from buffy coats by MACS sorting with both anti-CD34 and anti-CD117 MicroBeads (Miltenyibiotec).

extract_protocol:
Total RNA from around 0.5-1x10^6 cells was isolated with Trizol (Sigma), digested with TurboDNase (Ambion), washed and resuspended in H2O. The RNA integrity was confirmed with an RNA Bioanalyzer (Agilent).
Comparable amounts (250ng – 1ug) of total RNA was converted into non-poly(A) selected, ribosomal RNA depleted (TruSeq RNA Library Prep Kit v2) cDNA libraries following Illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: blood

tag: diagnosis

value: control


title: CD34_8


title: TM03

value: Leukemic blast cells

value: AML


title: TM04


title: CD34_1


title: CD34_5


title: TM016


title: TM11


title: TM10


title: TM005


title: CD34_2


title: H1299-mutSMARCA4_Dox_H3K27me3 Rep2

city: Barcelona

first: Antonio

last: Gomez

address: Pg Vall d'Hebron 119-129

department: Rheumatology research Group

institute: VHIR

data_processing:
For ChIP-sequencing data analysis, reads were aligned to the human reference genome hg38, using Bowtie v1.2.2, with default parameters and disallowing multi-mapping (–m 1)35.PCR duplicates were removed using PICARD (http://broadinstitute.github.io/picard/).  Ambiguous and multi-mapped reads were discarded. Peaks were called using MACS2 v2.1.136.  To avoid false positives, peaks were discarded if they were present in the ChIP-seq of  SMARCA4 in the SMARCA4-deficient cells. Genomic peak annotation was performed with  the R package ChIPpeakAnno v3.15, considering the region ± 2 kb around the TSS as the  promoter37. All analyses considered peaks overlapping with promoter regions, unless otherwise  specified. Peak lists were then transformed to gene target lists. For ChIP-sequencing data analysis, reads were aligned to the human reference genome hg38, using Bowtie v1.2.2, with default parameters and disallowing multi-mapping (–m 1)35.PCR duplicates were removed using PICARD (http://broadinstitute.github.io/picard/).  Ambiguous and multi-mapped reads were discarded. Peaks were called using MACS2 v2.1.136.  To avoid false positives, peaks were discarded if they were present in the ChIP-seq of  SMARCA4 in the SMARCA4-deficient cells. Genomic peak annotation was performed with  the R package ChIPpeakAnno v3.15, considering the region ± 2 kb around the TSS as the  promoter37. All analyses considered peaks overlapping with promoter regions, unless otherwise  specified. Peak lists were then transformed to gene target lists.
Genome_build: hg38

source_name: Lung

extract_protocol: For ChIP, cells were grown in P-150 cm cell dishes and fixed with 1%  methanol-free formaldehyde (Thermo Scientific) for 10 min at room temperature, then  quenched by 125 mmol/L glycine for 15 min at room temperature, washed with ice-cold PBS  twice and centrifuged at 200g, 4°C for 5 min. The pellet was resuspended in 1 mL of cell lysis  buffer (10 mmol/L Tris-HCl, 10 mmol/L NaCl, 0.5% NP-40, protease inhibitor) and kept at  4°C, rotating for 30 min. After centrifugation, the pellet was resuspended in 1 mL of nuclear  lysis buffer (1% SDS, 10 mmol/L EDTA, 50 mmol/L Tris-HCl pH 8.0, protease inhibitor) and  kept at 4°C for 60 min. After another centrifugation, the lysate was sonicated with a Covaris  M220 instrument to yield chromatin fragments of an average size of 0.25–1.00 kb, and then  frozen at -20ºC for 30 min. The chromatin was thawed on ice and centrifuged at 2,500 g. For  each ChIP reaction, 60 μL of Magna ChIP™ Protein A+G Magnetic Beads (Merck Millipore)  was used in accordance with the manufacturer’s protocol. Before addition of the sheared  chromatin to the beads, Triton X-100 and Na-deoxycholate was added to a final concentration  of 10% each. 1% of the chromatin volume was used for input. At least two independent ChIP  experiments were performed. Immunoprecipitated chromatin was deep-sequenced in the Genomics Unit of the Centre  for Genomic Regulation (CRG, Barcelona, Spain) using the Illumina HiSeq 2500 system  (Illumina). Briefly, library preparation included end-repair, generation of dA overhangs,  adapter ligation, size selection and removal of non-ligated adapters by agarose gene  electrophoresis and amplification (18 cycles) before loading the samples into the sequencer.

tag: antibody

value: Lung

value: male

value: 43 years adult

tag: source

value: Non-Small cell lung cancer

value: doxycycline


title: TM019


title: TM010


title: Elongating organoid day 7 [4 uM CHIR Day 7 - Replicate 1]

description: Elongating neural organoid at day 7 of differentiation

value: day 7


title: H1299-mutSMARCA4_Not_induced_H3K27me3 Rep2

tag: Sex


title: Elongating organoid day 5 [4 uM CHIR Day 5 - Replicate 2]

description: Elongating neural organoid at day 5 of differentiation

value: day 5


title: Non-elongating organoid day 7 [0 uM CHIR Day 7 - Replicate 2]

description: Non-elongating neural organoid at day 7 of differentiation


title: Elongating organoid day 7 [4 uM CHIR Day 7 - Replicate 3]


title: Elongating organoid day 7 [4 uM CHIR Day 7 - Replicate 2]


title: Non-elongating organoid day 7 [0 uM CHIR Day 7 - Replicate 3]


title: H1299-wtSMARCA4_Dox_H3K27me3 Rep2


title: Non-elongating organoid day 10 [0 uM CHIR Day 10 - Replicate 2]


title: Non-elongating organoid day 10 [0 uM CHIR Day 10 - Replicate 1]


title: Non-elongating organoid day 7 [0 uM CHIR Day 7 - Replicate 1]


title: H1299-wtSMARCA4_Dox_SAHA_H3K27me3 Rep2

value: doxycycline+SAHA


title: H1299-mutSMARCA4_Dox_SAHA_H3K27me3 Rep2


title: H1299-wtSMARCA4_Not_induced_H3K27me3 Rep2


title: Elongating organoid day 5 [4 uM CHIR Day 5 - Replicate 1]

value: elongating organoids


title: Non-elongating organoid day 5 [0 uM CHIR Day 5 - Replicate 3]

description: Non-elongating neural organoid at day 5 of differentiation


title: Elongating organoid day 5 [4 uM CHIR Day 5 - Replicate 3]


title: Elongating organoid day 3 [4 uM CHIR Day 3 - Replicate 3]

description: Elongating neural organoid at day 3 of differentiation

value: day 3


title: Non-elongating organoid day 5 [0 uM CHIR Day 5 - Replicate 2]


title: Non-elongating organoid day 5 [0 uM CHIR Day 5 - Replicate 1]


title: Elongating organoid day 3 [4 uM CHIR Day 3 - Replicate 2]

value: 4 uM CHIR


title: H1299-mutSMARCA4_Dox_SAHA_H3K27Ac Rep2


title: Elongating organoid day 3 [4 uM CHIR Day 3 - Replicate 1]


title: ΔAmyR-3

city: Qingdao

first: yueyan

last: hu

address: Binhai road 72

institute: Shandong university

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) for differential expression analysis.
Genome_build: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Penicillium oxalicum

source_name: AmyR deletion strain in starch

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% starch as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% starch as carbon resources for 18h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.  After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AmyR deletion strain

tag: medium

value: Modified Mendal’s medium with 2% starch as carbon resource

tag: culture time

value: 18h after transferring washed mycelia to the new medium

value: Fungal mycelia


title: Non-elongating organoid day 3 [0 uM CHIR Day 3 - Replicate 2]

description: Non-elongating neural organoid at day 3 of differentiation

value: non-elongating organoids

value: 0 uM CHIR


title: ΔAmyR-2

tag: strain

tag: tissue


title: ΔHat1-2

source_name: Hat1 deletion strain in starch

value: Hat1  deletion strain


title: ΔAmyR-1


title: ΔHat1-1

value: Hat1 deletion strain


title: ΔHat1-3


title: H1299-mutSMARCA4_Dox_H3K27Ac Rep2

value: Lung

value: male

tag: age

value: 43 years adult


title: H1299-mutSMARCA4_Not_induced_H3K27Ac Rep2

value: Non-Small cell lung cancer


title: H1299-wtSMARCA4_Dox_SAHA_H3K27Ac Rep2


title: H1299-mutSMARCA4_Dox_SAHA_EZH2 Rep2


title: WT-3

source_name: Wild type strain in starch

value: 114-2(wild type)


title: Non-elongating organoid day 3 [0 uM CHIR Day 3 - Replicate 3]

tag: cell type


title: H1299-mutSMARCA4_Dox_EZH2 Rep2

tag: cell line

value: doxycycline


title: Non-elongating organoid day 3 [0 uM CHIR Day 3 - Replicate 1]


title: H1299-wtSMARCA4_Dox_SAHA_EZH2 Rep2

value: doxycycline+SAHA


title: H1299-wtSMARCA4_Dox_H3K27Ac Rep2


title: H1299-wtSMARCA4_Not_induced_H3K27Ac Rep2


title: Elongating organoid day 1 [4 uM CHIR Day 1 - Replicate 3]

description: Elongating neural organoid at day 1 of differentiation

value: elongating organoids

value: day 1


title: WT-1


title: WT-2


title: H1299-wtSMARCA4_Dox_EZH2 Rep2


title: H1299-mutSMARCA4_Not_induced_EZH2 Rep2


title: Elongating organoid day 1 [4 uM CHIR Day 1 - Replicate 2]

value: 4 uM CHIR


title: control group circRNA 3

city: Guangzhou

first: Rui

last: Chen

address: 466 Xin Gang Zhong Road

department: Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute

institute: Guangdong Second Provincial General Hospital

hyb_protocol: Mouse circRNAs array hybridization was performed based on the standard protocols of Arraystar Mouse circRNA Array V2.

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

data_processing: The scanned images were analyzed with Agilent feature extraction software (version 11.0.1.1).

source_name: cell line C2C12

label_protocol: Samples labeling were performed based on the standard protocols of Arraystar Mouse circRNA Array V2.

extract_protocol: According to the TRIzol regent (Life Technologies, USA) manufacturer's instructions, total RNA was extracted from the mouse C2C12 cells.

treatment_protocol: C2C12 was cultured in DMEM high glucose supplemented with 10% fetal bovine serum, 100 U/mL of penicillin, and 100 μg/mL of streptomycin in 5% CO2 at 37°C. When the cells reached 80–90% confluence, they were differentiated by incubation in DMEM containing 2% horse serum. CoCl2（200 μM）were added to cells for 48 h prior to cell collection.

tag: differentiation

value: myotube


title: Invitro-4-2

city: Ann Arbor

first: Keerthikka

last: Ravi

state: Michigan

address: 1105 N University st

department: Molecular, Cellular and Developmental Biology

institute: University of Michigan

data_processing:
FastQC version 0.11.9 used to check quality of sequenced reads
Trimmomativ version 0.6.5 used to trim reads of poor quality, estting the parameters as LEADING and TRAILING set at 20 and MINLEN set at 100
Trimgalore version 0.6.5 used to remove adapter reads from the in vivo  sample reads.
Fastx_trimmer to trim the adapter sequences at the 3' end of the in vitro sample reads.
Bowtie2 version 2.3.4.3 used to align the sequenced reads to the reference genome
samtools verison 1.7 used to covert the SAM alignmnet output files to BAM format
Bioconductor packages GenomicAlignments and GenomicFeatures were used to generate the count file for the reads
DESeq2 used for analysing differnetial gene expression generating an FPKM file for all smaples as well as significanr log2 fold change in expression.
Genome_build: Reference sequence used for alignemnet - GenBank accession no CP017687
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Diffential gene expression for all genes, expression at 37°C vs expression at 4°C
Supplementary_files_format_and_content: Diffential gene expression for all genes, in vivo expression  vs expression at 37°C in vitro

organism: Pseudomonas lundensis

source_name: Aerobic culture in LB broth

growth_protocol: AU1044 was innoculated in LB broth from frozen stock and grown overnight aerobically at 37°C. 4 20mL flasks of LB broth each at 4°C and 37°C aerobic conditions were innoculated with the 100µl of cells from the over night culture. Cells were harvested for RNA isolation once thery reached early stationary phase (OD of 2.1 at 600nm). For the in vivo samples, 6 germ free Balb/c mice went through gastric colonisation of AU1044 through oral gavage. Cecal content of the mice was harvested after 14 days of innoculation and used for Bacterial RNA isolation.

extract_protocol:
For the in vitro samples, protease treament followed by RNA isolation was performed as per the bacterial RNA isolation protocol from Qiagen Rneasy Kit. For the in vivo samples, Trizol/Rneasy hybrid protocol by Mauricio Rodriguez-Lanetty was followed
NEBNext Ultra II DNA library prep was used for cDNA library preperation.

tag: culture method

value: Aerobic culture in LB broth


title: Invitro-37-4

description:
res_37v4.txt
res_iv_37.txt


title: H1299-wtSMARCA4_Not_induced_EZH2 Rep2


title: H1299-wtSMARCA4_Not_induced_BRG1 Rep2


title: Invitro-4-3


title: Non-elongating organoid day 1 [0 uM CHIR Day 1 - Replicate 1]

description: Non-elongating neural organoid at day 1 of differentiation


title: Non-elongating organoid day 1 [0 uM CHIR Day 1 - Replicate 3]


title: Invitro-4-1


title: Invitro-37-2

description:
res_37v4.txt
res_iv_37.txt


title: Invitro-37-3

description:
res_37v4.txt
res_iv_37.txt


title: control group circRNA 2

tag: treatment


title: CoCl2 group circRNA 2

value: CoCl2 treatment


title: H1299-mutSMARCA4_Dox_BRG1 Rep2


title: H1299-mutSMARCA4_Dox_SAHA_input

value: input


title: H1299-mutSMARCA4_Not_induced_BRG1 Rep2


title: Invitro-37-1

description:
res_37v4.txt
res_iv_37.txt


title: Elongating organoid day 1 [4 uM CHIR Day 1 - Replicate 1]


title: Non-elongating organoid day 1 [0 uM CHIR Day 1 - Replicate 2]

value: non-elongating organoids

value: 0 uM CHIR


title: 20E-OV replicate 3

city: Paris

first: NIKOLAOS

last: KONSTANTINIDES

address: 15 rue Helene Brion

country: France

institute: Institut Jacques Monod

data_processing:
The reads were trimmed for quality and adapter sequence using Trimmomatic (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Reads from both sample sets were mapped with STAR (v.2.5.3a) (Dobin et al. 2013) on the Harpegnathos genome version 8.5 (Shields et al. 2018)
The reads were counted using ht-seq union mode (Anders et al. 2015)
Genome_build: Harpegnathos genome version 8.5 (Shields et al 2018)
Supplementary_files_format_and_content: Htseq output for all samples are provided in the txt file.

organism: Harpegnathos saltator

source_name: Ovary

growth_protocol: Ants were maintained in the containment room with a controlled temperature of 25°C with 12 hours of light–dark cycle.

extract_protocol:
For extracting RNA, a pipette was used to gently aspirate and agitate the tissue. After agitation, fresh Trizol was added to bring the volume to 1 ml. The mixture was placed into a new 1.5 mL microcentrifuge tube and 200 μl chloroform per 1ml Trizol was added. The tube was inverted repeatedly for 30 sec and left at room temperature for 5 min. The Trizol mixture was centrifuged for 15 min at 12,000x g at 4oC. The top clear aqueous phase (~500 μl) was transferred to a new microcentrifuge tube containing 1μl of Glycoblue (ThermoFisher, #AM9515) and 1x volume of isopropanol. The RNA/isopropanol/Glycoblue mix was then centrifuged for 30 min at 20,000x g at 4°C. The supernatant was removed and the pellet was washed twice with 70% and 80% ethanol, respectively and subsequently centrifuged for 10 min at 20,000x g at 4°C. The pellet was air dried for 5 min before dissolved in BTE buffer (10mM Bis-Tris pH 6.8, 1mM EDTA). RNA samples were treated by DNase I (Ambion, #2239) and DNase I was removed by phenol/choloform extraction and isopropanol precipitation.
For library preparation, polyA+ RNA was isolated from approximately 500 ng total RNA using NEBNext ® Poly(A) mRNA Magnetic Isolation (E7490). Libraries were prepared using NEBNext® Ultra II RNA library prep kit (E7770, E7335 and E7500), quantified before and after amplification using KAPA SYBR® Fast universal qPCR Kit (KK4854) and sequenced on Illumina Hiseq 2500.

treatment_protocol: Workers were injected with 500ng of JHA or 20E diluted in Hank's balanced salt solution (HBSS) into abdomens. The control ants were injected with ~1 μL of 10% EtOH in HBSS.

value: Ovary


title: JHA-OV replicate 3

value: JHA-injected


title: H1299-wtSMARCA4_Dox_BRG1 Rep2

value: Lung

value: male


title: JHA-OV replicate 1


title: CoCl2 group circRNA 3


title: JHA-OV replicate 2


title: 20E-OV replicate 2


title: 20E-OV replicate 1


title: EtOH-OV replicate 2

value: EtOH-injected


title: EtOH-OV replicate 1


title: EtOH-OV replicate 3


title: H1299-mutSMARCA4_Dox_input

value: 43 years adult

value: Non-Small cell lung cancer


title: H1299-wtSMARCA4_Dox_SAHA_input

value: doxycycline+SAHA


title: JHA-Fb replicate 3

source_name: Abdominal fat body

value: Abdominal fat body


title: H1299-wtSMARCA4_Dox_input

value: doxycycline


title: JHA-Fb replicate 1


title: control group circRNA 1


title: JHA-Fb replicate 2


title: H1299-mutSMARCA4_Not_induced_input


title: 20E-Fb replicate 3


title: ATAC_Don003_d17_rep3

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

description: Genome-wide library of tagmented fragments

data_processing:
Library Strategy: ATAC-seq
Mapping : bowtie -m 2 --maxIns 350, hg9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

source_name: CD34 Culture

growth_protocol: Fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 10^5 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 10^5 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x10^5 cells ml-1. Cells were counted on day 9 and diluted to 3x10^5 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 10^6 cells ml-1. Cells were counted on days 13 and 15 and diluted to 10^6 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band).

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

value: Erythroid

value: Male

tag: differentiation day

value: Day 17

tag: donor id


title: ATAC_Don003_d7_rep1

value: Day 7


title: ATAC_Don003_d13_rep1

value: Day 13


title: EtOH-Fb replicate 3


title: CoCl2 group circRNA 1

value: myotube

value: CoCl2 treatment


title: ATAC_Don003_d13_rep2


title: 20E-Fb replicate 2


title: H1299-mutSMARCA4_Dox_SAHA_H3K27me3


title: ATAC_Don003_d7_rep2


title: EtOH-Fb replicate 2


title: H1299-wtSMARCA4_Not_induced_input

value: input


title: Invitro-4-4

value: Aerobic culture in LB broth


title: EtOH-Fb replicate 1


title: ATAC_Don003_d11_rep2

value: Day 11


title: H1299-wtSMARCA4_Dox_SAHA_H3K27me3

value: Lung

value: male


title: JHA-Brain replicate 2

source_name: Non-visual brain

value: Non-visual brain

value: JHA-injected


title: ATAC_Don003_d13_rep3


title: 20E-Brain replicate 3


title: H1299-mutSMARCA4_Dox_H3K27me3

value: 43 years adult

value: Non-Small cell lung cancer


title: JHA-Brain replicate 1


title: 20E-Brain replicate 2


title: 20E-Fb replicate 1

value: Abdominal fat body


title: EtOH-Brain replicate 3

value: EtOH-injected


title: 20E-Brain replicate 1


title: H1299-wtSMARCA4_Dox_H3K27me3

value: doxycycline


title: ATAC_Don003_d10_rep2

value: Erythroid

value: Male

value: Day 10


title: ATAC_Don003_d10_rep3


title: H1299-mutSMARCA4_Not_induced_H3K27me3


title: EtOH-Brain replicate 1


title: H1299-wtSMARCA4_Not_induced_H3K27me3


title: ATAC_Don002_d7_rep2

value: Day 7


title: ATAC_Don003_d11_rep1


title: 20-099 clinical

city: College Station

first: Ellen Ruth

middle: Alexander

last: Morris

state: Texas

address: TAMU 4475

institute: Texas A&M University

data_processing:
Transcripts were trimmed using Trimmomatic
Alignment and transcript counts were performed using Salmon against the Streptococcus equi 4047 reference genome
Differential gene expression analysis was performed using edgeR, by the quasi-likelihood negative binomial generalized log-linear model
Genome_build: https://bacteria.ensembl.org/Streptococcus_equi_subsp_equi_4047_gca_000026585/Info/Index/
Genome_build: 553482
Supplementary_files_format_and_content: Salmon's quant.sf.txt - plain-text, tab-separated file

organism: Streptococcus equi subsp. equi

source_name: Bacterial colony

growth_protocol: Streptococcus equi subsp. equi was grown in Todd Hewitt broth for 4 hours (exponential phase growth) at 37°C in 5% CO2

extract_protocol:
RNA was extracted using the RiboPure™ RNA Purification kit (Invitrogen™, Carlsbad, CA, USA) for bacteria, following the manufacturer’s instructions.
RNA libraries were prepared using the Stranded Total RNA Preparation kit (Illumina©, San Diego, CA, USA) following the manufacturer’s instructions.

tag: disease state

value: Clinical


title: ATAC_Don002_d7_rep1


title: ATAC_Don003_d10_rep1


title: 20-096 clinical


title: 20-097 clinical


title: 20-098 clinical


title: H1299-wtSMARCA4_Dox_SAHA_H3K27Ac

value: doxycycline+SAHA


title: ATAC_Don002_d17_rep3

value: Day 17


title: 20-100 clinical


title: JHA-Brain replicate 3


title: ATAC_Don002_d13_rep3

value: Day 13


title: H1299-mutSMARCA4_Dox_H3K27Ac

value: Lung


title: 20-095 clinical


title: 20-094 clinical


title: ATAC_Don002_d13_rep2


title: 20-093 clinical


title: H1299-wtSMARCA4_Dox_H3K27Ac

value: male


title: 20-092 clinical


title: EtOH-Brain replicate 2

value: Non-visual brain


title: ATAC_Don002_d13_rep1


title: H1299-mutSMARCA4_Dox_SAHA_H3K27Ac


title: ATAC_Don002_d11_rep2

value: Day 11


title: 20-090 carrier

value: Carrier


title: 20-089 carrier


title: H1299-mutSMARCA4_Not_induced_H3K27Ac

value: 43 years adult

value: Non-Small cell lung cancer


title: 20-091 clinical


title: 20-088 carrier


title: 20-086 carrier


title: H1299-mutSMARCA4_Dox_SAHA_EZH2


title: H1299-wtSMARCA4_Not_induced_H3K27Ac


title: H1299-wtSMARCA4_Dox_SAHA_EZH2


title: ATAC_Don002_d11_rep1


title: 20-083 carrier


title: ATAC_Don002_d10_rep5


title: H1299-mutSMARCA4_Dox_EZH2


title: 20-085 carrier


title: 20-084 carrier


title: 20-087 carrier


title: ATAC_Don002_d10_rep4


title: 20-082 carrier


title: 20-081 carrier


title: ATAC_Don002_d10_rep3


title: 20-080 carrier


title: H1299-wtSMARCA4_Dox_EZH2


title: ATAC_Don002_d10_rep2


title: H1299-mutSMARCA4_Not_induced_EZH2


title: SLE_PBMC_scATAC-seq

city: Shenzhen

first: Haiyan

last: YU

address: No. 1017, North of Dongmen Road

institute: Shenzhen People's Hospital

data_processing:
Barcode processing: To improve data quality, a ‘whitelist’ of correct barcode sequences was applied to fix the occasional sequencing error in barcodes obtained from the ‘I2’ index read
Genome alignment: Reference-based analysis was performed using the Cell Ranger ATAC pipeline. BWA-MEM was applied with default parameters to align the trimmed read pairs that were greater than 25 bp to GRCh38
Filteing: We filtered scATAC-seq data using cut-offs of 1,000 unique nuclear fragments per cell and a transcription start site (TSS) enrichment score of 8 to exclude low-quality cells in 10x genomic Cell Ranger ATAC platform
Peak calling: First, the number of transposition events at each base pair along the genome was counted. Next, a smoothed profile of these events with a 401 bp moving window around each base pair and fitting a ZINBA-like mixture model was generated. Then, a signal threshold was set to determine whether a region was a peak signal or noise based on an odds ratio of 1/5. Finally, peaks within 500 bp of each other were merged to produce a position-sorted BED file.
Cell calling and peak-barcode matrix: For each barcode, the mapped high-quality fragments that passed all filters were recorded, and the number of fragments that overlapped any peak regions was used to separate the signal from noise. To capture the signal and noise, a mixture model of two negative binomial distributions was set, and barcodes that corresponded to real cells from the non-cell barcodes were separated by setting an odds ratio of 1000. Subsequently, a raw peak-barcode matrix consisting of the counts of fragment ends within each peak region for each barcode was produced. After filtering to contain only cell barcodes, the matrix was used in subsequent analyses, such as dimensionality reduction, clustering and visualization.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files for barcodes; mtx files for matrix; bed files for peaks

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
PBMCs were separated using an equal proportion of Ficoll-Paque Plus. Nuclei suspensions were obtained by adding lysis buffer (10 mM Tris-HCl, 3 mM MgCl2, 10 mM NaCl , 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 1% BSA). The final libraries were constructed via PCR with P5 and P7 primers in Illumina® bridge amplification.
scATAC-seq libraries were generated according to the Chromium Single Cell ATAC protocol (10x GENOMICS)

value: SLE patients

value: peripheral blood


title: ATAC_Don002_d10_rep1

value: Erythroid


title: H1299-wtSMARCA4_Not_induced_EZH2


title: ATAC_Don001_d7_rep2

value: Female


title: CA1_superficial_epileptic_replicate3

description:
Sample_ID_120619
Gene expression values (read counts mapped to each gene).
mRNA

data_processing:
Sequencer: Illumina HiSeq 2500 (HWI-D00733). Basecalling pipeline: HiSeq Control Software 2.2.58; Gerald version 1.8. HiSeq Sequencing Kit TruSeq v4. Read Length: 75 paired end.
Alignment quality control of sequenced samples (LCM-RNA-seq) was assessed with FastQC (v.0.11.3) (Babraham Institute) and RNA-seq tracks were visualized using IGV (v.2.3.57) (Thorvaldsdottir et al., 2013). LCM-RNA-seq reads were mapped to the rat genome (Rnor_6.0.83) using STAR (v.2.5.0c) (Dobin et al., 2013), and files were further processed with Samtools (v.0.1.19). Aligned reads were counted to gene transcripts using HTSeq (v.0.6.1) (Anders et al., 2015).
Genome_build: Rnor_6.0.83
Supplementary_files_format_and_content: *counts.txt: Tab-delimited text files include Ensembl gene identifiers (ENSRNOG) and gene-level counts (raw counts).

organism: Rattus norvegicus

source_name: Superficial CA1 hippocampal sublayer

extract_protocol:
Brains from 3 control and 3 epileptic rats were dissected, longitudinally cut in half (separating both hemispheres), wrapped in aluminum foil and immediately frozen in liquid nitrogen. All samples were conserved at -80ºC until use. The hippocampal region of each hemisphere was cut in 20μm slices in a cryostat (Leica) (chamber temperature: -20ºC; block temperature: -30ºC) and placed on 1.0mm PEN-membrane covered slides (Carl Zeiss). Slides were conserved at -20ºC until use. Right before microdissection, slides were dried with vapor of liquid nitrogen. CA1 pyramidal cell layer was microdissected with a Leica 6000 laser microdissector through a 40x non-oil immersion objective to obtain cell bodies of superficial and deep sublayers separately. Microdissected deep and superficial areas were collected in different empty caps of 0.5ml Eppendorf tubes. After microdissection, samples were processed following ARCTURUS PicoPure RNA Isolation Kit (Thermo Fisher Scientific) instructions in order to extract and isolate total RNA. Briefly, 50μl of extraction buffer was added into the cap, incubated at 42ºC for 30min, centrifuged at 800xg for 2min and stored at -80ºC. The same volume of 70% ethanol was added to the cell extract and the mixture was pipetted into a pre-conditioned RNA purification column. The column was centrifuged 2min at 100xg and 30sec at 16000xg, and washed with 100μl of Wash Buffer 1. To completely eliminate DNA, the purification column was treated with 40μl of DNase (diluted 1/8 in RDD Buffer) (Qiagen), incubated 15min and centrifuged at 8000xg for 15sec. Then the column was washed twice with 100μl of Wash Buffer 2, and centrifuged at 8000xg after the first wash and at 16000xg after the second one. Finally, RNA was eluted into a new 0.5μl Eppendorf tube by adding 11μl of elution buffer onto the column membrane, incubating the column for 1min at room temperature, and centrifuging the column for 1min at 1000xg and at 16000xg immediately after. Total RNA samples were stored at -80ºC. RNA integrity number (RIN) was similar in control (4.7 ± 0.8) and epileptic rats (5.7 ± 0.5; P=0.07; 3 replicates x 2 sublayers per group), as well as for deep (5.2 ± 0.9) and superficial sublayers (5.3 ± 0.; P=0.81; n=6 replicates per sublayers) when assayed on an Agilent 2100 Bioanalyzer.
RNA-seq libraries were produced (TruSeq Stranded mRNA Sample Preparation Kit) and sequenced (HiSeq Sequencing Kit TruSeq v4) according to manufacturer instructions in a HiSeq2500 sequencer (Illumina, Inc). Libraries were strand specific (reverse) and sequencing was performed in paired-end configuration with a read length of 75bp. Library size of read pairs for the different samples analyzed was between 47 and 59 Million reads.

treatment_protocol: Adult male Wistar rats (180 –200 g) were treated with multiple intraperitoneal injections of kainate (5 mg/kg) at hourly intervals until they reached status epilepticus. The status was defined as a condition of continuous seizures lasting longer than 30 min. Diazepam (4 mg/kg) was injected 1 h post-status to stop convulsions. Animals received intraperitoneal injections of 2.5 ml 5% dextrose in saline and their diet was supplemented with fruit and powder milk during the following 2–3 days. After 4-5 days, rats behaved normally and were housed individually. Control animals were injected with vehicle (either saline or DMSO) and received treatments similar to epileptic animals. RNA samples were collected after 6 to 8 weeks post-status when animals were in the chronic epileptic phase. Seizures were observed either during handling or recorded electrophysiologically in a subset of animals. Control animals did never exhibit seizures.

value: Wistar

value: Adult (45-50 days)

value: Male

tag: weight

value: Hippocampal CA1 pyramidal cell layer

tag: ca1 sublayer

value: Superficial

tag: condition

value: Epilepsy


title: ATAC_Don001_d17_rep3

tag: Sex

value: Day 17


title: H1299-wtSMARCA4_Not_induced_BRG1

tag: antibody

value: Lung

value: male

tag: source


title: CA1_superficial_epileptic_replicate2

description:
Sample_ID_120617
Gene expression values (read counts mapped to each gene).
mRNA

tag: strain


title: CA1_deep_epileptic_replicate3

description:
Sample_ID_120618
Gene expression values (read counts mapped to each gene).
mRNA

source_name: Deep CA1 hippocampal sublayer

tag: tissue

value: Deep


title: ATAC_Don001_d7_rep1

value: Day 7


title: H1299-wtSMARCA4_Dox_SAHA_BRG1

tag: age

value: 43 years adult

value: doxycycline+SAHA


title: ATAC_Don001_d13_rep2

tag: cell type

value: Day 13


title: Murine MLL-AF4 LMPP FL 2 + 7

city: Edinburgh

first: Katrin

last: Ottersbach

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: University of Edinburgh

description: Murine MLL-AF4 LMPP FL 2 + 7

data_processing:
Initial quality control of ATAC-seq fastq read files generated in this study was carried out using the FastQC toolkit (https://github.com/s-andrews/FastQC).
The Tn5 transposase sequence 5’- CTGTCTCTTATACACATCT-3’ was then trimmed from reads using Cutadapt (Martin et al., https://doi.org/10.14806/ej.17.1.200).
Following trimming, samples were aligned to the mouse and human reference genomes MGSCv37 (mm9) and GRCh38 (hg38) respectively using Bowtie2 (Langmead et al., PMID: 22388286) version 2.3.4.1, with a –very-sensitive –local call and paired-end settings.
The generated sam files containing aligned read pairs were then sorted and converted to bam format using the samtools suite (Li et al., PMID: 19505943). Duplicated reads were filtered using the Picard tools function MarkDuplicates (https://github.com/broadinstitute/picard). Replicate samples were subsequently merged using the samtools merge function (Li et al., PMID: 19505943). Coverage and insert size distribution was then measured for both individual replicates and merged samples using Qualimap (Okonechnikov et al., PMID: 26428292). The aligned reads (bam files) were normalised for sequencing coverage to a 1x genome depth (reads per genome coverage, RPGC), using an effective genome size of either 2150570000 base pairs for mm9 or 3049315783 base pairs for hg38, with the bamCoverage function from deepTools (PMID: 27079975) using a bin size of 10 base pairs, the extendReads parameter, chromosome X ignored for normalisation and ENCODE blacklist regions excluded (Amemiya et al., PMID: 31249361).
The resulting normalised bigwig files were visualised using Integrative Genomics Viewer (IGV) (Robinson et al., PMID: 21221095).
Genome_build: MGSCv37 (mm9) and GRCh38 (hg38)
Supplementary_files_format_and_content: normalised bigwig files

source_name: Lin- CD45+ ckit+ Sca1+ Flt3+ cells

extract_protocol:
cells were sorted from freshly isolated mouse tissues or previously frozen human tissues; single cell preparations were stained with cell surface markers and directly sorted into transposition buffer
Following the discarding of supernatant the nuclei pellet was resuspended in 50 μl transposition mix with the following Tn5 volumes according to cellular input (1000-5000 (0.5 μl Tn5), 5000-10,000 (1.0 μl Tn5), 10,000-15,000 (1.5 μl Tn5) with the remainder of the total reaction adjusted with water (25 μl 2× TD buffer, x μl transposase, 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, x μl H2O) and incubated at 37 °C for 30 min in a thermomixer with 1,000 rpm shaking. All reactions were cleaned up using the Zymo DNA Clean and Concentrator-5 Kit (Cat# D4014) with DNA eluted in 11 μl of elution buffer and PCR amplified with the NEBNext Hi-Fidelity PCR Master Mix (Cat# M0541L) with a custom dual barcoding strategy as previously described (Mezger et al. PMID: 30194434). The amplification reaction was stopped at 5 cycles and 5 μl of the pre-amplified mixture was run in a 15 μl qPCR reaction to determine the optimal number of additional cycles that corresponded to 1/3 of the maximum fluorescent intensity up to a total of 13 cycles (Buenrostro et al. PMID: 25559105). A final clean up was performed, libraries were eluted in 20 μl and quantified using the NEBNext Library Kit for Illumina (Cat# E7645L), assessed using the Agilent Bioanalyzer High Sensitivity DNA Analysis kit (Cat# 5067-4627) and finally double size selected with the Zymo Select-a-Size DNA Clean & Concentrator kit (Cat# D4084).

tag: genotype

value: foetal liver


title: H1299-mutSMARCA4_Dox_BRG1

tag: cell line

value: Non-Small cell lung cancer

value: doxycycline


title: H1299-wtSMARCA4_Dox_BRG1


title: CA1_superficial_epileptic_replicate1

description:
Sample_ID_120615
Gene expression values (read counts mapped to each gene).
mRNA

value: Wistar


title: CA1_deep_epileptic_replicate2

description:
Sample_ID_120616
Gene expression values (read counts mapped to each gene).
mRNA

value: Adult (45-50 days)


title: ATAC_Don001_d13_rep3

value: Erythroid

value: Female


title: H1299-mutSMARCA4_Dox_SAHA_BRG1


title: NC_PBMC_scATAC-seq

value: Healthy controls

value: peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)


title: Murine MLL-AF4 LMPP FL 1

description: Murine MLL-AF4 LMPP FL 1


title: CA1_deep_epileptic_replicate1

description:
Sample_ID_120614
Gene expression values (read counts mapped to each gene).
mRNA

value: Male

value: Hippocampal CA1 pyramidal cell layer

value: Epilepsy


title: ATAC_Don001_d11_rep2

value: Day 11


title: control group lncRNA 2

hyb_protocol: 1 μg of  Cy3-labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from cells using TRIZOL reagent (Life Technologies, Grand Island, NY, USA) in accordance with the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: C2C12 was cultured in DMEM high glucose supplemented with 10% fetal bovine serum, 100 U/mL of penicillin, and 100 μg/mL of streptomycin in 5% CO2 at 37°C. When the cells reached 80–90% confluence, they were differentiated by incubation in DMEM containing 2% horse serum. CoCl2 (200 uM) were added to cells for 48 h prior to cell collection.

tag: differentiation

value: myotube


title: CoCl2 group lncRNA 3

tag: treatment

value: CoCl2 treatment


title: CoCl2 group lncRNA 1


title: CoCl2 group lncRNA 2


title: control group lncRNA 3


title: H1299-mutSMARCA4_Not_induced_BRG1

value: Lung

value: male

value: 43 years adult


title: MuFL 6/3 MA4 LMPP

description: MuFL 6/3 MA4 LMPP

value: foetal liver


title: control group lncRNA 1


title: CA1_superficial_control_replicate3

description:
Sample_ID_120613
Gene expression values (read counts mapped to each gene).
mRNA

value: Wistar

value: Superficial

value: Control


title: Developing_Root_Cortex at time 24 ammonium 3 mM experiment 4 [A4T24_3_RDC]

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

data_processing:
Base calling was made with the NovaSeq 6000 RTA3 software (Illumina). Conversion of cbcl files to fastq files were made with bcl2fastq2 Conversion Software (Illumina)
The raw reads were trimmed (quality and contamination) using SeqTrimBB software (https://github.com/rafnunser/seqtrimbb). Only the pairs in which both reads passed the quality test were further analysed (Q>20).
The reads were assembled using Trinity 2.11.0 (Haas et al., 2013, Nature Protocols 8:1494-512). Contigs lower than 400 pb were eliminated, for the rest of contigs the redundancy was reduced using CD-HIT-EST software (Fu et al., 2012, Bioinformatics 28: 3150-3152).
The final transcriptome was used as the reference for the read mapping that was performed with BWA using the MEM option (Li and Durbin, 2009, Bioinformatics 25: 1754-1760). The read count was obtained with the phyton script sam2counts (https://github.com/vsbuffalo/sam2counts).
The transcript expression was normalised by cpm. Finally the transcripts were filtered; 2 cpm in at least 2 samples (Robinson et al., 2010, Bioinformatics 26: 139-140).
Genome_build: Assemble reference transcriptome
Supplementary_files_format_and_content: Tab-delimited text files include CPM normalized counts for each sample.The column id is the sequence/sample identifier.

organism: Pinus pinaster

growth_protocol: Seeds from maritime pine (Pinus pinaster Ait.) from “Sierra Segura y Alcaraz” (Albacete, Spain) were provided by from the Área de Recursos Genéticos Forestales of the Spanish Ministerio de Agricultura, Pesca y Alimentación. Seeds were imbibed in distilled water for 24 h under continuous aeration and germinated in a plastic tray with vermiculite as a substrate. Seedlings were grown in vermiculite in plant growth chambers under 16 h light photoperiod, a luminal intensity of 100 μmol m−2 s−1, a constant temperature of 25 °C and watered twice a week with distilled water.

extract_protocol:
All the RNA extractions from the microdissection procedure were carried out using manufacturer’s instruction protocol (non‐LCM) for the RNAqueous‐Micro RNA Isolation Kit (Ambion, USA). RNA quality, DNA contamination and first quantification were performed via RNA Pico Assay for the 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Quantification was verified via a Qubit RNA BR (Broad-Range) Assay Kit (Invitrogen, Paisley, UK).  RNA samples with RNA integrity number (RIN) higher than 7 were used for subsequent RNA sequencing, mRNA amplification and cDNA synthesis.
The low input RNA-seq was carried out by Novogen (HK). The cDNA synthesis and amplification, and the library preparation was made with the SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Takara, Mountain View, CA, USA) following the manufacturer’s instructions. RNA sequencing was made in a NovaSeq 6000 sequencer according to the manufacturer’s instructions for paired-end reads (Illumina, San Diego, CA, USA). The 24 samples were sequenced producing paired-end reads of 150 bp length.

treatment_protocol: One-month old maritime pine seedlings were used for this experiment. Pine seedlings were randomly subdivided into three different groups, relocated into forestall seedbeds and irrigated with 80 mL of a solution that contains macro- and micronutrients without any nitrogen source (1.16 mM KCl; 0.63 mM KH2PO4; 0.35 mM MgSO4·7H2O; 0.17 mM CaCl2·H2O; 80 μM EDTA-FeSO4; 25.9 μM H3BO3; 10.2 μM MnCl2·4H2O; 1.3 μM ZnSO4·7H2O; 0.7 μM CuSO4·5H2O; 0.1 μM Na2MoO4·2H2O). After three days of acclimation, the control group was irrigated with 80 mL of water (C), the second group was supplied with 80 mL of 3 mM NH4Cl. Root samples were collected 24 houres after the irrigation. Seedling’s root tips were cut and tissues of 5 - 6 mm were imbibed in a specimen holder with Tissue‐Tek optimal cutting temperature embedding medium (Sakura Finetek, Alphen aan den Rijn, The Netherlands) and immediately frozen in liquid nitrogen for cryostat sectioning. LCM procedure:  1 day before cryosectioning, root tip samples were tempered at -20°C. Thirty micrometers thick sections were cut using a cryostat (CM1950, Leica Biosysyems, Wetzlar, Germany) at -20°C and mounted on PET-membrane 1.4 µm steel frame (Leica Biosysyems, Wetzlar, Germany). The PET-membrane containing samples were stored at −80°C until use.  Before microdissection, samples were fixed in cold 70% ethanol for 30 seconds, embedding medium was removed in DEPC-treated water for 2 minutes and refixed in cold 100% ethanol for 2 minutes. Afterwards, samples were air dried and used for microdissection. A laser microdissector (LMD 7000, Leica, Wetzlar, Germany) was used for microdissection. The samples obtained were placed into 0.5 mL tube caps containing 20 μL of lysis buffer from the RNAqueous-Micro RNA Isolation Kit (Ambion, USA) and all samples were placed at −80°C. Four different tissue areas were isolated by microdissection approximatively corresponding to the root cap (RC), meristem (RM), developing cortex (RDC) and developing vessels (RDV) areas.

tag: provenance

value: Segura-Alcaraz

tag: developmental stage

value: 1 month-old seedling

value: Ammonium 3 mM

tag: time

value: 24 hours

tag: experimental replicate


title: ATAC_Don001_d11_rep1

value: Erythroid

value: Female

tag: differentiation day

tag: donor id


title: Developing_Root_Cortex at time 24 ammonium 3 mM experiment 3 [A3T24_3_RDC]


title: Developing_Root_Cortex at time 24 control experiment 4 [A4T24_C_RDC]


title: ATAC_Don001_d13_rep1

tag: Sex

value: Day 13


title: ATAC_Don001_d10_rep3

value: Day 10


title: ATAC_Don001_d10_rep1


title: CA1_superficial_control_replicate2

description:
Sample_ID_120611
Gene expression values (read counts mapped to each gene).
mRNA

value: Adult (45-50 days)

value: Male

tag: weight

value: Hippocampal CA1 pyramidal cell layer

tag: ca1 sublayer

tag: condition


title: ATAC_Don001_d10_rep2


title: CA1_deep_control_replicate3

description:
Sample_ID_120612
Gene expression values (read counts mapped to each gene).
mRNA

tag: strain

tag: tissue

value: Deep


title: CA1_deep_control_replicate2

description:
Sample_ID_120610
Gene expression values (read counts mapped to each gene).
mRNA

tag: age


title: Murine WT LMPP FL 6

description: Murine WT LMPP FL 6

tag: genotype

value: wild-type


title: CA1_superficial_control_replicate1

description:
Sample_ID_120609
Gene expression values (read counts mapped to each gene).
mRNA


title: MuFL 5/4 WT LMPP

description: MuFL 5/4 WT LMPP

value: foetal liver


title: Developing_Root_Cortex at time 24 ammonium 3 mM experiment 1 [A1T24_3_RDC]


title: Blood WT LMPP 1

description: Blood WT LMPP 1


title: Developing_Root_Cortex at time 24 control experiment 3 [A3T24_C_RDC]


title: MuFL 8/8 WT LMPP

description: MuFL 8/8 WT LMPP


title: Developing_Root_Cortex at time 24 control experiment 1 [A1T24_C_RDC]


title: MuFL 4/2 MA4 LMPP

description: MuFL 4/2 MA4 LMPP


title: CA1_deep_control_replicate1

description:
Sample_ID_120608
Gene expression values (read counts mapped to each gene).
mRNA

value: Wistar


title: PDX1-CD276-high/EpCAM+

city: Richmond

first: Jiong

last: Li

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

data_processing:
RNAs were single-end sequenced on Illumina HiSeq 3000 machines
Reads was aligned using Tophat with the hg18 build of the human genome.
Transcript assembly and differential expression were determined using Cufflinks with Refseq mRNAs.
RNA-seq data was analyzed using the cummeRbund package in R.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Head and neck squamous cell carcinoma cells

growth_protocol: Two cases of Human HNSCC PDXs were maintined in NOD/SCID mice. The discarded human HNSCC primary tissues were obtained from the UCLA Translational Pathological Core and subcutaneously inoculated into flank of 6-week-old NOD/SCID mice to generate the PDXs of HNSCC.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen, cat#74104).
Sequencing libraries were generated using a KAPA RNA-Seq Library Preparation Kits (KAPA Biosystems, cat#07960140001)

treatment_protocol: To isolate single cells from HNSCC PDXs, mice were euthanized and tumors were dissected and isolated.  Tumors were chopped into small pieces with scalpels in petri dishes on ice, and then dissociated in to single cell suspension using Tumor Dissociation Kit (Miltenyi, cat# 130-095-929). The cell suspension was filtered through a 100 micro meter mesh filter and then followed by a 40 micro meter mesh filter. Red blood cells were removed using a RBC Lysis Buffer (Santa Cruz Biotechnology, cat#sc-296258). Subsequently, tumor cells were stained with the anti-CD276-PE and anti-EpCAM-APC antibodies. The CD276+/EpCAM+ and the CD276+/EpCAM- cells were isolated throug FACS sorting.

value: HNSCC PDX1

value: Head and neck squamous cell carcinoma


title: Developing_Root_Vascular at time 24 ammonium 3 mM experiment 4 [A4T24_3_RDV]

value: Segura-Alcaraz


title: Developing_Root_Vascular at time 24 ammonium 3 mM experiment 3 [A3T24_3_RDV]

value: 1 month-old seedling


title: B73_seedling_rep1

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
cellranger count (v4.0.0)
filter barcodes with less than 1000 UMIs and 500 expressed genes
filter barcodes below 1 standard deviation from the mean fraction of nuclear derived UMIs
filter barcodes above 1 standard deviation from the mean fraction of mitocondrial and chloroplast derived UMIs
Genome_build: B73 AGP v4
Supplementary_files_format_and_content: Binary triplet matrix format of geneIDs (column 1), nuclei ID (column 2), and UMI counts (column 3)

organism: Zea mays

extract_protocol:
16,000 nuclei were used to construct each library via nuclei lysis, wash, and centrifugation steps.
10X Genomics scRNA-seq Chromium Next GEM Single Cell 3' v3.1

value: Seedling