title: Root sample_P_7_9


title: Root sample_N_7_9

status: Public on Jan 01 2022

type: SRA

city: Taian

first: Nana

last: Ma

address: No 61 Daizong Street No 61

country: China

institute: Shandong Agricultural University

library_source: transcriptomic

data_processing:
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre).
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers.
Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters.
The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Hiseq X Ten by Gene Denovo Biotechnology Co. (Guangzhou, China).
Removing reads containing adapters;  removing reads containing more than 10% of unknown nucleotides (N); removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Zea mays

extract_protocol:
Zea Mays root were removed, flash frozen by Liquid Nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: inbred line

tag: tissue

value: root

tag: age

tag: treatment

value: nitrogen deficiency


title: drerio_G19

city: Uppsala

first: Henrik

last: Boije

address: Uppsala University, Dept. Of Neuroscience, Box 593, BMC

country: Sweden

institute: Uppsala University

description: drerio.loom

data_processing:
Alignment and mapping: Genome indexing and read alignment was performed using STAR v.2.5.4b and Velocyto v0.17.17 (La Manno et al., 2018). Fasta files for extra genes were manually added for eGFP 146 (LC337138.1), tdTomato (GeneBank: AY678269.1) and ERCC genes (Thermofisher assets: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip) and gene information was added to the species GTF file (Shaner et al., 2004; Nakajima et al., 2018). Reads were mapped to GRCm38.99 genome for mus musculus or GRCz11.98 genome for danio rerio. Genes were counted using featureCounts (subread V2.0.0) and Velocyto v0.17.17. Velocyto spliced and unspliced information was added to the final loom file as seperate layers. Full scripts are deposited at Github (http://github.com/jonetjakobsson/dmrt3-single-cell)
Genome_build: GRCm38.99
Genome_build: GRCz11.98
Supplementary_files_format_and_content: Loom file containing layers; reads, RPKM, spliced and unspliced meassures. Each row represents a well and each column represents one gene.

molecule: polyA RNA

organism: Danio rerio

source_name: Zebrafish spinal cord

extract_protocol:
For zebrafish, cells were collected 3 days post fertilization. The head and tail were removed and the middle part of the larvae was collected for sequencing. The yolk was removed by gently pipetting up and down in 100 μL of calcium-free Ringer’s solution. Larvae (n=20) were transferred to a protease solution (0.25% trypsin, 1mM EDTA, pH 8.0, PBS, 50 ml) pre-warmed at 28°C and 27 μL collagenase P in HBSS was added to the samples for 15 minutes at 28°C with homogenizing every 5 minutes by gently pipetting up and down. Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added to the tube and spun at 350 RCF for 5 minutes at 4°C. The resuspension was passed through a 20 μm cell strainer and the sample was placed on ice. Quality control was addressed by comparing live cells versus dead cells using a viability indicator for dead cells (NucRed™ Dead 647 ReadyProbes™ Reagent). For mice, the spinal cords from three E14.5 embryos were dissected in ice-cold 1X D-PBS (Thermofisher). Both the DRGs and vertebrae column were removed as much as possible. The spinal cords were pooled in one tube and dissociated using the adult brain dissociation kit (Milteny Biotec), adapted for spinal cord tissue. Briefly, 1 ml pre-heated (37ºC) enzyme solution 1 (50 µl enzyme P in 950ul buffer Z) was added to the spinal cords followed by 15ul enzyme solution 2 (5 µl enzyme A in 10 µl buffer Y). The tissue was incubated at 37ºC for 30 minutes. Every 10 minutes, the tissue was triturated 10 times with fire polished glass Pasteur pipettes pretreated in 0.5% BSA in 1X D-PBS. The pipets had a decreasing diameter staring with around 200% then 100% and finally around 20% of original opening diameter. Tissue was then transferred to 10 ml ice cold 1X D-PBS and filtered through a 40 µm cell strainer. The suspension was centrifuged at 300 RCF for 10 minutes at 4ºC and the supernatant was discarded. The cell pellet was resuspended in 900 µl 0.5% BSA in 1X D-PBS followed by 100 µl myelin removal beads (Milteny Biotec) and incubated for 15 min at 8ºC. 10 ml ice cold 1X D-PBS was added to the sample and centrifuged at 300 RCF for 10 minutes. Supernatant was discarded and the cell pellet was resuspended in 1 ml 0.5% BSA in 1X D-PBS. The sample was run through an LS-column (Milteny Biotec) on a magnetic stand and flushed with 2x1 ml 0.5% BSA in 1X D-PBS. Cell sorting was performed on a BD Melody cell sorter, and tomato positive cells were gated out in comparison to a non-fluorescent control.
cDNA synthesis and preamplification were performed using the SMART-seq2 method (Picelli et al., 2014). Briefly, cDNA was transcribed using SuperScript II reverse transcriptase, oligo(dT) primers and template switching oligonucleotides (TSO). Preamplification of the cDNA was facilitated by ISPCR primers that binds the TSO and oligo(dT). The cDNA was tagmented using the Tn5 transposase creating fragments of 200-600bp, followed by indexation using the Nextera XT sample preparation kits.

tag: developmental stage

value: spinal cord

tag: strain


title: V219

city: GuangZhou

first: Yan

last: Huang

address: 151 Yanjiang Road, Guangzhou, Guangdong, China

institute: Guangzhou Institute of Respiratory Health

description: Raw counts were normalized by TPM (transcript per million)

data_processing:
The small RNA library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Quality control: Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
Reads mapping to the reference sequence: The small RNA tags were mapped to reference sequence by Bowtie (v0.12.9) without mismatch to analyze their expression and distribution on the reference.
Known miRNA alignment: Mapped small RNA tags were used to looking for known miRNA. miRBase21.0 was used as reference, modified software mirdeep2(v2_0_0_5) and srna-tools-cli(v1.0) were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
Remove tags from these sources: To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
Small RNA annotation summary: Summarizing all alignments and annotations obtained before. In the alignment and annotation before, some small RNA tags may be mapped to more than one category. To make every unique small RNA mapped to only one annotation, we follow the following priority rule: known miRNA > rRNA > tRNA > snRNA > snoRNA > repeat > gene > NAT-siRNA > gene > novel miRNA > ta-siRNA. The total rRNA proportion was used a marker as sample quality indicator. Usually it should be less than 60% in plant samples and 40% in animal samples as high quality.
Quantification of miRNA: miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Differential expression of miRNA: Differential expression analysis of two groups was performed using the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini& Hochberg method. Corrected P-value of 0.1 was set as the threshold for  significantly differential expression by default.
Genome_build: GRCh38
Supplementary_files_format_and_content: "miRNA abundance measurements (raw counts or normalized)-yan324.xls"

organism: Homo sapiens

source_name: sputum

extract_protocol:
Exosomes were isolated from spontaneous sputum in bronchiectasis patients and induced sputum from healthy subjects. After thawing, approximately four aliquots of phosphate buffer solution were added to achieve complete homogenization, followed by 18,000 g centrifugation for 10 minutes at 4°C (Thermo Scientific, USA), which were modified by instructions, then filtered through 0.8µm filter. The supernatant was used for extraction of exosomes with the exoEasy Maxi Kit (Qiagen Inc., Hilden, Germany) based on manufacturer’s instructions. Exosomes were suspended with buffer XE (Qiagen Inc., Hilden, Germany). For exosomal miRNA sequencing, the total RNA was extracted from the cell pellets by using QIAZol lysis reagent (Qiagen Inc., Hilden, Germany) by following the instructions of the manufacturer.
RNA per sample as the input material for the miRNA library which was generated with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB Inc., USA) by following the manufacturer’s protocol. Briefly, NEB 3' & 5' Adaptor were directly and specifically ligated to the 3' and 5' end of the small RNAs (miRNA, siRNA and piRNA), which also termed the 'SR Adaptor'. After ligation at the 3' end, the reverse transcriptase Primer (RT Primer) was hybridized to the excess of 3' SR adaptor and transformed the single-stranded DNA adaptor into a double-strand DNA. The first strand cDNA was synthesized by using M-MuLV Reverse Transcriptase (RNase H-). PCR amplification was performed, followed by purification of the PCR products (DNA fragments, length: 140~160 bp) on a 8% polyacrylamide gel (100 V, 80 min). The cDNA library was constructed and its sequence length was examined by using the Aglient Bioanalyzer 2100 system (Aligent Technologies, CA, USA). The samples with an effective concentration being greater than 2nM as quantified with qPCR could be subject to exosomal miRNA sequencing by using Illumina HiSeq 2500 platform.

treatment_protocol: Induced sputum was performed in healthy subjects only. This was achieved by nebulization with 3% hypertonic saline. Because all eligible bronchiectasis patients could spontaneously produce sputum, we sampled spontaneous sputum only. We strictly controlled the quality of sputum to largely rule out the effects of saliva, which included removing saliva contamination as much as possible and selecting the highest purulent sputum for testing. All samples were assessed for quality under the light microscope (based on the counting of epithelial cells and leukocytes).

value: sputum

tag: colonization status

value: Pseudomonas aeruginosa colonization

tag: disease state

value: bronchiectasis patients in stable stage

tag: Sex

value: female


title: drerio_G18

description: drerio.loom


title: V223

value: non-Pseudomonas aeruginosa colonization

value: male


title: Root sample_N_4_6


title: KO_2_rep2

city: Freiburg

first: Yoko

middle: Fukuda

last: Yuzawa

address: Stübeweg 51

country: Germany

institute: Max-Planck Institute of Immunobiology

description: Gene expression of spleen

data_processing:
Basecalls performed using CASAVA
Reads were aligned to the mm9 genome assembly using tophat
Genome_build: mm9
Supplementary_files_format_and_content: fpkm values of UCSC genes calculated by cuffdiff comparing WT vs KO in 0 (WT_0, KO_0) and 6 (WT_2, KO_2) days of malaria infection (provided in fukao_spleen_matrix sheet)

organism: Mus musculus

source_name: miR-155 KO spleen after 6 days of malaria infection replicate2

growth_protocol: Mice were maintained in the animal facilty under specific pathogen-free conditions.

extract_protocol:
Total RNA was extracted using Qiashredder and Rneasy kit.
polyA(+) RNA was isolated by Dynabeads mRNA Purification Kit (Invitrogen) and fragmented by incubation at 94°C for 3min in fragmentation buffer (40mM TrisOAc pH8.2, 100mMKOAc, 30mM MgOAc).  cDNA was synthesized using SuperScriptTM III First-Strand Synthesis System for RT-PCR (Invitrogen) with random hexamers for first-strand, Second Strand Buffer (Invitrogen) and dNTPs with dTTP replaced by dUTP (Roche) for second-strand. End repair, dA-Tailing, and adapter-ligation were performed by NEBNext ChIP-Seq Sample Prep Master Mix Set1 (NEB). After size selection and Uracil–DNA glycosylase (NEB) treatment, cDNA was enriched by Phusion polymerase. We used the standard Illumina adaptors, PCR and sequencing primers.

treatment_protocol: WT and miR-155 KO mice were infected by P. berghei ANKA

value: malaria infection

value: Spleen

tag: gender

value: post natal week 8

tag: genotype/variation

value: miR-155 KO


title: WT_2_rep2

description: Gene expression of spleen

source_name: WT spleen after 6 days of malaria infection replicate2

value: WT


title: WT_2_rep1

description: Gene expression of spleen

source_name: WT spleen after 6 days of malaria infection replicate1


title: KO_2_rep1

description: Gene expression of spleen

source_name: miR-155 KO spleen after 6 days of malaria infection replicate1


title: Root sample_N_1_3


title: drerio_G17

description: drerio.loom


title: KO_0_rep1

description: Gene expression of spleen

source_name: miR-155 KO spleen without infection replicate1

value: without infection


title: drerio_G16

description: drerio.loom


title: V217


title: Root sample_K_7_9

value: potassium deficiency


title: WT_0_rep2

description: Gene expression of spleen

source_name: WT spleen without infection replicate2


title: drerio_G15

description: drerio.loom


title: V214


title: drerio_G20

description: drerio.loom


title: Root sample_K_4_6


title: drerio_G14

description: drerio.loom


title: V211


title: 120h antenna

city: Bronx

first: Zhe Jun

last: Ji

state: NY

address: 1300 Morris Park Avenue

country: USA

institute: Albert Einstein College of Medicine

data_processing:
reads mapped to Drosophila dm3 genome suing TopHat
expression levels quantified using Cufflinks
Genome_build: dm3
Supplementary_files_format_and_content: RNAseq200404ST1 contains FPKM values for 10893 expressed genes

organism: Drosophila melanogaster

source_name: antenna portion of eye-antenna imaginal disc

growth_protocol: larvae cultured at 25°C on yeast-glucose media

extract_protocol:
tissue extracted in Trizol
poly A selection, reverse transcription with random hexamer primers, addition of termnal A residue, ligation of LM-PCR adapters, ~300 bp size selection, PCR and gel purification

treatment_protocol: dissection from live larvae

value: 120 +/- 1h after egg laying


title: V202


title: stress_2

city: Beijing

first: Lei

last: Qin

address: ZhongGuanCunNan Street 5

institute: Beijing Institute of Technology

description: stress_2 FPKM

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence  using software SOAPnuke (v1.4.0)(parameter: -l 5 -q 0.5 -n 0.1)
Reads were then mapped to Saccharomyces_cerevisiae_S288C whole genome  using software HISAT2 (v2.1.0) (parameter: --dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2（PE）)
Clean reads were aligned using software Bowtie2 (v2.2.5) (parameter: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200)
Genes were anotated with PHI-base using DIAMOND (v0.8.31) (parameter: --evalue 1e-5 --outfmt 6 --max-target-seqs 1 --more-sensitive) (screening factor: query coverage >= 50%、identity >= 40%). Gene expressions were calculated using RSEM (v1.2.8).
Genome_build: GCF_000146045.2_R64 (Saccharomyces_cerevisiae_S288C)
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae_stress_10h

growth_protocol: Strains were incubated in 20 mL YPD medium (2 % peptone, 1 % yeast extract, 2% or 10% glucose) at an initial OD600 of 0.5 and grown at 30°C or 36°C, and 200 rpm for 10 h.

extract_protocol:
RNA was extracted using the TRIzol® method following the manufacturer’s protocol. Bulk cells or filamentous fungus are grounded to a powder using liquid nitrogen, and the powder was transferred into the 2ml tube contains 1.5ml Trizol reagent. The mix was shaked for 3min, and kept for 5min at room temperature, then was Centrifuged at 10,000×g for 5min at 4°C. The supernatant was added 200μL of chloroform/isoamyl alcohol (24:1) with 1ml lysis reagents. After centrifuged at 10,000×g for 10min at 4°C, the supernatant was transferred into another new tube with equal volume of isopropanol and put in the refrigerator at -20°C for 1h. After centrifuged at 13600×g for 20min at 4°C, the supernatant was precipitated by 1 mL of 75% ethanol and let dry for 3-5min. The RNA pellet was dissolved with 30-100μL of DEPC water or RNase-free water. The concentration of the extracted RNA samples was determined using a Nanodrop system (NanoDrop, Madison, USA), and the integrity of the RNA was examined by the RNA integrity number (RIN) using an Agilent 2100 bioanalyzer (Agilent, Santa Clara, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Cells were harvested by centrifuge and followed by washing in sterile water.

value: CY

value: stress condition (36°C, 10% glucose) for 10hrs


title: KO_0_rep2

description: Gene expression of spleen

source_name: miR-155 KO spleen without infection replicate2


title: drerio_G12

description: drerio.loom

value: spinal cord


title: V192

value: sputum


title: stress_1

description: stress_1 FPKM


title: non-stress_2

description: non-stress_2 FPKM

source_name: S. cerevisiae_non-stress_10h

value: non-stress condition (30°C, 2% glucose) for 10hrs


title: drerio_G11

description: drerio.loom


title: V191

value: bronchiectasis patients in stable stage


title: V215

value: Pseudomonas aeruginosa colonization

value: female


title: 96h eye

source_name: eye portion of eye-antennal imaginal disc

value: 96 +/- 1h after egg laying


title: 72h eye-antenna-mouthparts

source_name: eye-antennal imaginal disc with associated cuticular mouthparts

value: 72 +/- 1h after egg laying


title: drerio_G1

description: drerio.loom


title: non-stress_1

description: non-stress_1 FPKM


title: V185


title: V190

value: non-Pseudomonas aeruginosa colonization


title: WPP eye-antenna

source_name: eye-antennal imaginal disc

value: at white puparium formation

value: eye-antennal imaginal disc


title: WT_0_rep1

description: Gene expression of spleen

source_name: WT spleen without infection replicate1

value: Spleen

value: post natal week 8

value: WT


title: Root sample_K_1_3

value: root

value: potassium deficiency


title: drerio_F9

description: drerio.loom


title: V178


title: 120h eye-antenna

value: 120 +/- 1h after egg laying


title: MCF7 cells, shRNACOP1-3

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

description: ERalpha positive cells, see this link for a list of mutations found in this cell line: https://cansarblack.icr.ac.uk/cell-line/MCF-7/mutations

data_processing:
Basecalling performed using Illumina bcl2fastq v2.17
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 097.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include raw counts for annotations for all Sample

source_name: Untreated COP1-depleted MCF7 cells

growth_protocol: Cells were maintained in a medium lacking any estrogens before stimulations

extract_protocol:
Total RNAs were extracted using Trizol. RNA sequencing was performed on libraries prepared from total RNA samples. Three biological replicates were analyzed for each condition. RNA integrity was verified on a Bioanalyser 2100 with RNA 6000 Nano chips (Agilent technologies, CA, USA). RNA integrity number score was above 9 for every sample
Libraries were prepared using Truseq® stranded mRNA Sample Preparation Kits (Illumina, CA, USA) following manufacturer’s instructions. Libraries were validated using QIAxcel Advanced System and quantified by qPCR using the KAPA library quantification kit. Libraries were multiplexed and sequenced on an Illumina NextSeq500 sequencer to generate more than ~25,000,000 paired-end reads (2 × 150 bases) per library.

treatment_protocol: E2 was added or not (10 nM) for 5 hours in the culture medium

tag: cell line

tag: cell type

value: Breast cancer-derived cells

value: No treatment

tag: genotype


title: V175

value: sputum

value: male


title: MCF7 cells, shRNACOP1-3-5h

source_name: E2-stimulated COP1-depleted MCF7 cells

value: estrogens (E2 ) for 5 hours (10 nM)


title: drerio_F8

description: drerio.loom

source_name: Zebrafish spinal cord

value: spinal cord


title: drerio_G13

description: drerio.loom


title: 120h eye

value: eye portion of eye-antennal imaginal disc


title: 96h antenna

value: 96 +/- 1h after egg laying

value: antenna portion of eye-antenna imaginal disc


title: 96h eye-antenna


title: V174

source_name: sputum

value: Pseudomonas aeruginosa colonization

value: bronchiectasis patients in stable stage

value: female


title: MCF7 cells, shRNACOP1-2


title: MCF7 cells, shRNACOP1-2-5h


title: drerio_F7

description: drerio.loom


title: V173

value: non-Pseudomonas aeruginosa colonization


title: drerio_F6

description: drerio.loom


title: MCF7 cells, shRNACOP1-1


title: 72h eye-antenna

value: 72 +/- 1h after egg laying

value: eye-antennal imaginal disc


title: drerio_G10

description: drerio.loom


title: 120h Larvae

source_name: whole larva

value: whole larva


title: V167


title: MCF7 cells, shRNACOP1-1-5h


title: 96h Larvae


title: V164


title: drerio_F5

description: drerio.loom


title: MCF7 cells, shRNAcontrol3

source_name: Untreated Control MCF7 cells

value: control


title: 72h Larvae


title: drerio_F3

description: drerio.loom


title: V161


title: MCF7 cells, shRNAcontrol3-5h

source_name: Control MCF7 cells treated for 5 hours with E2

value: Breast cancer-derived cells


title: V155


title: drerio_F24

description: drerio.loom


title: drerio_F4

description: drerio.loom


title: drerio_F23

description: drerio.loom


title: V152


title: MCF7 cells, shRNAcontrol2-5h


title: V153


title: V141


title: MCF7 cells, shRNAcontrol1

value: No treatment


title: MCF7 cells, shRNAcontrol1-5h


title: drerio_F20

description: drerio.loom


title: drerio_F21

description: drerio.loom


title: V135

value: sputum


title: drerio_F2

description: drerio.loom


title: drerio_F19

description: drerio.loom


title: V132


title: 7-6

city: Greenville

first: Weihua

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
Kallisto for pseudo-alignment to Ensembl human transcriptome GRCh38
DESeq2 for differential gene expression
Genome_build: GRCh38
Supplementary_files_format_and_content: An Excel file including TPM of each gene for all 6 samples

source_name: PBMCs

growth_protocol: Purified PBMCs (2×10^6/well) were cultured in 24-well plates containing RPMI 1640 supplemented with 10% (v/v) heat-inactivated FBS, 60 mg/L (100 U/mL) penicillin, 100 μg/mL streptomycin, 25 mM of HEPES, and 0.29 g/L L-glutamine.

extract_protocol:
Cells were harvested and total RNA was isolated using Trizol reagent (Gibco BRL, Rockville, Maryland) according to the manufacturer’s instructions. The RNA concentrations were quantified by triplicate optical density readings
TruSeq Stranded LT Total RNA kit

treatment_protocol: PBMCs were stimulated with 100 ng/mL of recombinant interleukin 4 (rIL-4) and 1 μg/mL of anti-CD40 mAb. PBMCs were cultured normally or with 10 μg/mL arctigenin for 10days.

value: PBMCs

value: allergy

value: IL-4/anti-CD40 stimulation+ arctigenin


title: MCF7 cells, shRNAcontrol2


title: 7-5

value: IL-4/anti-CD40 stimulation


title: 7-4


title: V102


title: drerio_F18

description: drerio.loom

value: spinal cord


title: 7-3


title: V090


title: drerio_F22

description: drerio.loom


title: drerio_F17

description: drerio.loom


title: V139

value: male


title: Lmo2_lines.261: Lmo2 cell line 3

type: RNA

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw intensity values were background corrected and normalized by the neqc method. Probes were filtered as ‘not expressed’ if they failed to achieve a BeadStudio detection P value of 0.05 on at least one array. Manufacturer probe annotation was used. Linear models were fitted to genes using Bioconductor R package limma. Differences in expression were assessed with empirical Bayes moderated t-statistics. Genes were considered to have different expression if they achieved a false-discovery rate of less than 0.05 and also a fold change greater than 1.5 folds.

source_name: Mouse cell line

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen).Approximately 300 ng of total RNA was labelled and hybridised to Illumina MouseWG-6 v2.0 Expression BeadChips (Illumina) according to Illumina standard protocols.

value: Lmo2 cell line


title: TG.966: Lmo2 transgenic sample rep 1

source_name: Mouse thymus

value: Thymus


title: TG.973: Lmo2 transgenic sample rep 2


title: 7-2


title: TG.970: Lmo2 transgenic sample rep 3


title: Lmo2_lines.175: Lmo2 cell line 2


title: WT.971: Wild type sample rep 2


title: V089

value: Pseudomonas aeruginosa colonization

value: bronchiectasis patients in stable stage


title: 7-1


title: drerio_F16

description: drerio.loom


title: WT.972: Wild type sample rep 3


title: Lmo2_lines.3: Lmo2 cell line 1


title: drerio_F14

description: drerio.loom


title: drerio_F13

description: drerio.loom


title: wild type third instar larval optic lobe rep 10

city: Paris

first: NIKOLAOS

last: KONSTANTINIDES

address: 15 rue Helene Brion

country: France

institute: Institut Jacques Monod

data_processing:
We mapped the sequenced libraries to the D. melanogaster genome assembly BDGP6.88 using CellRanger 3.0.1. We kept only genes that were expressed in at least 3 cells across all cells and cells with counts for at least 200 genes for further analysis.
We used the procedure implemented in Seurat v.3 to remove batch effects from our sequenced libraries. We used default parameters except for the dimensionality for which we used value 150.
The dataset was then clustered with a resolution of 2.
This (larval) dataset was then merged to a published pupal dataset (stage P15: accession number GSE142789) using default parameters.
150 PCs were used subsequently for generating the UMAP.
Genome_build: D. melanogaster genome assembly BDGP6.88
Supplementary_files_format_and_content: R Seurat object with both L3 and P15 data (as described and analyzed in the paper)

source_name: third instar larval optic lobe

growth_protocol: Embryo and larvae were kept under standard conditions

extract_protocol:
Droplet-based purification, amplification and barcoding of single-cell transcriptomes were performed using Chromium Single Cell 3′Reagent Kit v2 (10x Genomics) as described in the manufacturer’s manual (Chromium Single Cell 3′Reagent Kits v2 User Guide – Rev D), with a target recovery of 7,000 cells per experiment.
We prepared 10 libraries using Chromium Single Cell 3′Reagent Kit v2 (10x Genomics) as described in the manufacturer’s manual (Chromium Single Cell 3′Reagent Kits v2 User Guide – Rev D)

treatment_protocol: Developing central nervous systems from male and female flies were dissected from Canton-S wandering third instar larvae in PBS. The optic lobes were separated from the central brain using Vannas Spring Scissors with a 2mm cutting edge (Fine Science Tools Cat no. 15000-04). The optic lobes were dissociated into single cell suspension by incubating in 2mg/mL collagenase and 2mg/mL dispase in PBS for 15 minutes at 25C. The enzymes were then carefully removed and replaced with PBS + 0.1% BSA. The brains are soft but remain intact if pipetted slowly. The brains were pipetted up and down many times (> 100) until most large chunks of tissue are dissociated. The cells/tissue were kept cold by putting the tubes in ice. The cells were then filtered using 20um cell strainers. The concentration of the cell suspension was then measured staining the cells with 1/2000 Hoeschst, using an epifluorescent microscope and a 0.02-mm deep cytometer.

value: Canton-S


title: WT.969: Wild type sample rep 1


title: 0 h vs. 19 h Stx2 treatment

city: Yonago

first: Fumiko

last: Obata

state: Tottori

address: 86 Nichicho

department: Bacteriology

country: Japan

institute: Tottori University

description: 0 h vs. 19 h Stx2 treatment

hyb_protocol: samples were hybridized on the whole human genome oligonucleotide microarray (44K oligonucleotide DNA microarray, Agilent)

scan_protocol: Scanned on an Agilent G2505A scanner. The Feature Extraction and Image Analysis software was used to locate and delinate spots in the array.

data_processing: Agilent Feature Extraction Software was used for background subtraction and normalization.

source_name: RPTEC cells, 0 h (no Stx2)

label_protocol: total RNA samples were used for the preparation of Cy5- and Cy3-labeled cDNA probes.

growth_protocol: Primary human renal proximal tubular epithelial cells (RPTEC) were maintained in renal epithelial cell growth medium supplemented with human epidermal growth factor, hdrocortisone, epinephrine, insulin, tri-iodothyronine, transferrin, GA-1000 and FBS.

extract_protocol: Total RNA was extracted using RNAgents total RNA isolation system (Promega) following manufacturer's instructions

value: RPTEC

source_name: treated with Stx2 (10 ng/mL)


title: V081

value: female


title: V083

value: non-Pseudomonas aeruginosa colonization


title: V071


title: V070


title: 0 h vs. 6 h Stx2 treatment

description: 0 h vs. 6 h Stx2 treatment


title: wild type third instar larval optic lobe rep 9


title: 0 h vs. 13 h Stx2 treatment

description: 0 h vs. 13 h Stx2 treatment


title: 0 h (no Stx2) mouse kidney, biological rep3

description: Gene expression data from 0 h (not treated with Stx2) mouse kidney

hyb_protocol: Labelled cRNA were hybridized on GeneChip Mouse Genome 430A 2.0 Array according to Affymetrix instruction. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data from CEL files were normalized with robust multi-chip averaging (RMA), and calculation of RNA copy numbers and fold changes against 0 h were performed in R (v.3.6.0) with affy package and RankProd 2.0.

label: biotin

label_protocol: Biotinylated cRNA were synthesized according to the Affymetrix protocol using 5 ug total RNA.

growth_protocol: Mice, C57BL/6, male, 19-22 g, specific pathogen-free. Three mice per time point were used.

extract_protocol: Total RNA extraction was performed with Rneasy Midi kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Stx2 (5 ng/20 g body weight) was injected intraperitoneally, and kidneys were collected at 2, 4, 6, 8, 12, 24, 48 and 72 hours. Control kidneys without Stx2 (0 h samples) were collected. PBS (vehicle)-injected mice kidneys were also collected at 72 h as no LPS contamination control.

value: kidney from naive mouse

value: C57BL/6 (wild type)

tag: weight


title: drerio_F15

description: drerio.loom


title: drerio_F12

description: drerio.loom


title: drerio_F10

description: drerio.loom


title: drerio_F11

description: drerio.loom


title: wild type third instar larval optic lobe rep 7


title: wild type third instar larval optic lobe rep 8


title: wild type third instar larval optic lobe rep 6


title: V062

value: sputum


title: V056


title: wild type third instar larval optic lobe rep 5


title: drerio_F1

description: drerio.loom


title: V063


title: drerio_E9

description: drerio.loom


title: wild type third instar larval optic lobe rep 4


title: V040


title: V038


title: NC_2

city: Kunming

first: Jing

last: Sun

state: Yunnan

address: NO. 935,JIAO LIN ROAD

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Gene expression data from human platelets stimuated by PBS in vitro.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip HuGene1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip2 Scanner 3000 7G

data_processing: Raw data from the generated .CEL files were imported into Affymetrix Expression Console using the RMA method.

source_name: human plateltes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Platelets were cultured in 1640 containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 U/mL streptomycin.  Platelets were cultured in 1640 containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 U/mL streptomycin

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Platelets were isolated by Ficoll-Hypaque density gradient centrifugation Kit (Solarbio,China,P6390, ). Cells were then adjusted to the concentration of 1×106/ml and incubated for 2h at at 24℃ and 5% CO2 with the 1ml/1×106 cells EBV-containing supernatant of the B95.8 marmoset cell line in vitro.

tag: tissue/cell type

value: platelets


title: wild type third instar larval optic lobe rep 3


title: NC_1


title: drerio_E7

description: drerio.loom


title: EBV_1

description: Gene expression data from human platelets infected by EBV in vitro.

source_name: human plateltes infected by EBV

value: infected by EBV


title: NC_3


title: EBV_3


title: V036


title: EBV_2


title: V031


title: wild type third instar larval optic lobe rep 1


title: drerio_E6

description: drerio.loom


title: drerio_E5

description: drerio.loom


title: V015


title: drerio_E4

description: drerio.loom


title: V012


title: V011


title: drerio_E8

description: drerio.loom


title: IDTC colony-2

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

hyb_protocol: Affymetrix Human Gene 1.0 ST Array (Cat No. 901085); GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC_3_1_1.)

data_processing: Geneexpression Console v.1.1, Affymetrix (Expression Console  EC_1_1_2) using Affymetrix default analysis settings for generation of CEL-files.

label: Biotin

source_name: cell line

label_protocol: The Ambion® WT Expression Kit; For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays, 09/2009 Rev C (Cat No. 4411973 ), Affymetrix WT Terminal Labeling Kit 30rxn (Cat No. 900671)

growth_protocol: Cells were grown RPMI media supplimented with 5% FCS, 2mM L –Glutamine and 2x Penstrep

extract_protocol: mRNA was  extracted  using RNeasy mini kit Qiagen

treatment_protocol: Cells were treated with 500nM PLX4032 for 60 days period with media containing inhibitor being changed every 3 days

value: BRAF mutant melanoma


title: V006


title: drerio_E24

description: drerio.loom


title: 3-10

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Expression values were computed using STAR and featureCounts
Genome_build: CanFam3.1
Supplementary_files_format_and_content: text files holding raw counts

organism: Canis lupus familiaris

source_name: visceral adipose tissue

extract_protocol:
VAT was collected by laparotomy before and after ACTH treatment. Total RNA was isolated from VAT tissue with the RNeasy Lipid Tissue Mini Kit (Qiagen GmbH, Hilden, Germany).
The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolecularly and sequenced in an Illumina NovaSeq sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.
Illumina TruSeq stranded mRNA protocol

treatment_protocol: Permanent administration of tetracosactide, a synthetic analog of ACTH, was performed with osmotic pumps for 25 weeks. Pumps were replaced every 4 weeks. Tetracosactide dosage started at 1.3-1.95 μg/kg/day, increasing to a final dosage of 6-10 μg/kg/day.

tag: animal id

tag: treatment status

value: Post-ACTH

value: M

value: visceral adipose tissue


title: 3-9

tag: tissue


title: HeLa_AS32a_Replicate2

city: Frederick

first: Lisheng

last: Dai

state: MD

address: 1050 Boyles St.

institute: NCI-Frederick

description: wild type cells transfected with Drosha splice variant AS32a_Replicate 2

data_processing:
PacBio sequencing was processed by the Iso-Seq standard pipeline.
Small RNA sequencing was processed by customized scripts. Reads without the 3′ adaptor sequences or shorter than 18 nt were discarded
Genome_build: GRCH38 or miRBase21
Supplementary_files_format_and_content: BED files or TXT files

growth_protocol: Cells were maintained in DMEM (high glucose) (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Hyclone), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco).

extract_protocol:
RNA was extracted from cell lines using Trizol
Sequencing libraries were prepared using standard protocols. Samll RNA library was constructed by NEBNext® Multiplex Small RNA Library Prep Set according to the manufacturer's’ protocol
PacBio Sequencing or MiSeq

treatment_protocol: No treatment or Transfection

value: HeLa

tag: passage


title: 3-8

value: F


title: drerio_E3

description: drerio.loom

value: spinal cord


title: wild type third instar larval optic lobe rep 2


title: V005

value: Pseudomonas aeruginosa colonization

value: bronchiectasis patients in stable stage

value: male

tag: age


title: HeLa_Vector_Replicate2

description: wild type cells transfected with empty vector_Replicate 2


title: drerio_E23

description: drerio.loom

tag: developmental stage


title: 3-6


title: V004

value: female


title: DroshaKO_AS32a_Replicate2

description: Drosha KO cells trasnfected with Drosha splice variant AS32a_Replicate 2


title: Parent_3

tag: treatment

value: control


title: 3-7


title: IDTC colony-3


title: Parent_1


title: drerio_E22

description: drerio.loom

tag: strain


title: Parent_2


title: 3-5

value: Pre-ACTH


title: V002

tag: colonization status

value: non-Pseudomonas aeruginosa colonization

tag: disease state


title: DroshaKO_AS27a_Replicate2

description: Drosha KO cells trasnfected with Drosha splice variant AS27a_Replicate 2


title: IDTC colony-1


title: drerio_E21

description: drerio.loom


title: 3-4

tag: gender


title: H93

value: sputum

value: healthy subjects

tag: Sex


title: 3-3


title: DroshaKO_Vector_Replicate2

description: Drosha KO cells trasnfected with empty vector_Replicate 2


title: DroshaKO_FL_Replicate2

description: Drosha KO cells trasnfected with Drosha plasmids_Replicate 2


title: drerio_E2

description: drerio.loom


title: 3-2


title: drerio_E20

description: drerio.loom


title: drerio_E19

description: drerio.loom


title: 3-1


title: 293T_Vector_Replicate2


title: drerio_E18

description: drerio.loom


title: HeLa_AS32a_Replicate1

description: wild type cells transfected with Drosha splice variant AS32a_Replicate 1


title: drerio_E17

description: drerio.loom


title: H82


title: SLE2H3K27me3

city: Jinan

first: Yu

last: Xia

state: Shandong

address: 324 Jingwu Street

department: Department of Central Laboratory

institute: Shandong Provincial Hospital affiliated to Shandong University

description: ChIP-seq of Homo sapiens, H3K27me3, adult female monocytes, SLE2

library_source: genomic

data_processing:
reads were quality-filtered according to the Illumina pipeline. The data was aligned to the human reference genome (ucsc.hg19) by bowtie2 (version 2.2.3) and binding sites were identified by MACS2 (version 2.1.1).
Genome_build: hg19
Supplementary_files_format_and_content: peaks file

molecule: genomic DNA

source_name: primary monocyte

extract_protocol:
Nuclear extracts from about one million cells and chromatin was sheared to an average size of 200 bp with asonicator (Bioruptor Pico, Diagenode).
ChIP libraries were prepared using standard Illumina protocols.

value: peripheral blood

value: CD14+ monocytes

value: Systemic Lupus Erythematosus (SLE) patient

tag: chip antibody

value: Histone H3K27me3 antibody (pAb)  (ActiveMotif, Catalog No:39155)

value: adult


title: SLE2H3K27ac

description: ChIP-seq of Homo sapiens, H3K27ac, adult female monocytes, SLE2

tag: cell type

value: Histone H3K27ac antibody (pAb)  (ActiveMotif, Catalog No:39133)


title: HeLa_Vector_Replicate1

description: wild type cells transfected with empty vector_Replicate 1

value: HeLa


title: H81


title: H40


title: drerio_E16

description: drerio.loom

value: spinal cord


title: DroshaKO_AS32a_Replicate1

description: Drosha KO cells trasnfected with Drosha splice variant AS32a_Replicate 1


title: SLE2H3K4me3

description: ChIP-seq of Homo sapiens, H3K4me3, adult female monocytes, SLE2

value: Histone H3K4me3 antibody (pAb)  (ActiveMotif, Catalog No:39915)


title: drerio_E15

description: drerio.loom


title: H39

description: Raw counts were normalized by TPM (transcript per million)


title: SLE1H3K27me3

description: ChIP-seq of Homo sapiens, H3K27me3, adult female monocytes, SLE1


title: H29


title: 293T_Drosha_AS32a_Replicate2


title: drerio_E14

description: drerio.loom


title: H92


title: H86


title: DroshaKO_FL_Replicate1

description: Drosha KO cells trasnfected with Drosha plasmids_Replicate 1


title: SLE1H3K27ac

description: ChIP-seq of Homo sapiens, H3K27ac, adult female monocytes, SLE1


title: SLE1H3K4me3

description: ChIP-seq of Homo sapiens, H3K4me3, adult female monocytes, SLE1


title: DroshaKO_Vector_Replicate1

description: Drosha KO cells trasnfected with empty vector_Replicate 1


title: CTR2_ATAC

description: ATAC-seq of Homo sapiens, adult female monocytes, CTR1

data_processing:
The data was mapped to the human reference genome (ucsc.hg19) by bowtie2 (version 2.2.3) and binding sites were identified by MACS2 (version 2.1.1) with the parameter ‘-q 0.05 --nomodel --extsize 150 --keep-dup all --call-summits’.
Genome_build: hg19
Supplementary_files_format_and_content: bed files

extract_protocol:
The cells were lysed in1×Lysis Buffer to get the nuclei.
TruePrep™DNA Library Prep Kit V2 for Illumina (Vazyme Biotech) was used to construct the transposase-treated libraries.

value: healthy


title: drerio_E12

description: drerio.loom

data_processing:
Alignment and mapping: Genome indexing and read alignment was performed using STAR v.2.5.4b and Velocyto v0.17.17 (La Manno et al., 2018). Fasta files for extra genes were manually added for eGFP 146 (LC337138.1), tdTomato (GeneBank: AY678269.1) and ERCC genes (Thermofisher assets: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip) and gene information was added to the species GTF file (Shaner et al., 2004; Nakajima et al., 2018). Reads were mapped to GRCm38.99 genome for mus musculus or GRCz11.98 genome for danio rerio. Genes were counted using featureCounts (subread V2.0.0) and Velocyto v0.17.17. Velocyto spliced and unspliced information was added to the final loom file as seperate layers. Full scripts are deposited at Github (http://github.com/jonetjakobsson/dmrt3-single-cell)
Genome_build: GRCm38.99
Genome_build: GRCz11.98
Supplementary_files_format_and_content: Loom file containing layers; reads, RPKM, spliced and unspliced meassures. Each row represents a well and each column represents one gene.

extract_protocol:
For zebrafish, cells were collected 3 days post fertilization. The head and tail were removed and the middle part of the larvae was collected for sequencing. The yolk was removed by gently pipetting up and down in 100 μL of calcium-free Ringer’s solution. Larvae (n=20) were transferred to a protease solution (0.25% trypsin, 1mM EDTA, pH 8.0, PBS, 50 ml) pre-warmed at 28°C and 27 μL collagenase P in HBSS was added to the samples for 15 minutes at 28°C with homogenizing every 5 minutes by gently pipetting up and down. Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added to the tube and spun at 350 RCF for 5 minutes at 4°C. The resuspension was passed through a 20 μm cell strainer and the sample was placed on ice. Quality control was addressed by comparing live cells versus dead cells using a viability indicator for dead cells (NucRed™ Dead 647 ReadyProbes™ Reagent). For mice, the spinal cords from three E14.5 embryos were dissected in ice-cold 1X D-PBS (Thermofisher). Both the DRGs and vertebrae column were removed as much as possible. The spinal cords were pooled in one tube and dissociated using the adult brain dissociation kit (Milteny Biotec), adapted for spinal cord tissue. Briefly, 1 ml pre-heated (37ºC) enzyme solution 1 (50 µl enzyme P in 950ul buffer Z) was added to the spinal cords followed by 15ul enzyme solution 2 (5 µl enzyme A in 10 µl buffer Y). The tissue was incubated at 37ºC for 30 minutes. Every 10 minutes, the tissue was triturated 10 times with fire polished glass Pasteur pipettes pretreated in 0.5% BSA in 1X D-PBS. The pipets had a decreasing diameter staring with around 200% then 100% and finally around 20% of original opening diameter. Tissue was then transferred to 10 ml ice cold 1X D-PBS and filtered through a 40 µm cell strainer. The suspension was centrifuged at 300 RCF for 10 minutes at 4ºC and the supernatant was discarded. The cell pellet was resuspended in 900 µl 0.5% BSA in 1X D-PBS followed by 100 µl myelin removal beads (Milteny Biotec) and incubated for 15 min at 8ºC. 10 ml ice cold 1X D-PBS was added to the sample and centrifuged at 300 RCF for 10 minutes. Supernatant was discarded and the cell pellet was resuspended in 1 ml 0.5% BSA in 1X D-PBS. The sample was run through an LS-column (Milteny Biotec) on a magnetic stand and flushed with 2x1 ml 0.5% BSA in 1X D-PBS. Cell sorting was performed on a BD Melody cell sorter, and tomato positive cells were gated out in comparison to a non-fluorescent control.
cDNA synthesis and preamplification were performed using the SMART-seq2 method (Picelli et al., 2014). Briefly, cDNA was transcribed using SuperScript II reverse transcriptase, oligo(dT) primers and template switching oligonucleotides (TSO). Preamplification of the cDNA was facilitated by ISPCR primers that binds the TSO and oligo(dT). The cDNA was tagmented using the Tn5 transposase creating fragments of 200-600bp, followed by indexation using the Nextera XT sample preparation kits.


title: 293T_Drosha_AS32a_Replicate1


title: drerio_E11

description: drerio.loom


title: CTR1_ATAC

description: ATAC-seq of Homo sapiens, adult female monocytes, CTR2


title: drerio_E10

description: drerio.loom


title: preNC_dgRNA-KO_rep2

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
For each read, we trimmed the first six nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45 bp, the entire pair was discarded.
Trimmed reads were mapped to the human reference genome (hg19) using BWA-MEM v0.7.17 using default parameters. Only reads with mapping  quality scores equal or higher than 20 were kept. Duplicated read pairs were removed to allow only unique fragments using Picard  MarkDuplicates v2.8.2.
Peak and motif finding was performed using HOMER v4.10 with default parameters for transcription factors.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig for each sample (bw), tabulated text file with Homer peakcaller output (peak)

source_name: WA01 ES cells

growth_protocol: Human ESC/iPSC colonies digested with Accutase cell detachment solution (Innovative Cell Technologies) were re-suspended in differentiation medium plus CHIR 99021 (3 µM; #4423 Tocris Bioscience) plated at 20,000 cells per cm2 on Matrigel-coated surfaces. Differentiation medium contained DMEM/F12 medium supplemented with 2% B27 supplement (Life Technologies), 1× Glutamax (Life Technologies) and 0.5% bovine serum albumin (wt/vol) (A9647, Sigma-Aldrich). The ROCK inhibitor Y-27632 (10 µM; Tocris Bioscience) was added for the first two days.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with anti-FOXB1 antibody.
Approximately 10 – 15 ng CHIP DNA (around 15 μL) for each sample was used for CHIP-seq library construction following manufacturer instructions for NEBNext® UltraTM II DNA Libarry Prep Kit for Illumina (New England Biolabs). In brief, CHIP DNA was ended repaired at 20oC for 30 min followed by incubation at 65oC for 30 min. Ligation of adaptor (NEBNext Adaptor for Illumina) was then performed at 20oC for 15 min followed by U excision at 37oC for 15 min.  Adaptor ligated and U-excised DNA was then cleaned up using AMPure XP beads (Beckman Coulter), washed twice with freshly prepared 80% ethanol and eluted in 17 μL of 10 mM Tris-HCl. PCR amplification was used to add the following indices GTCCGC, GTGAAA, GTGGCC, GTTTCG, CGTACG, and GAGTGG  (NEBNExt Index 18 to 23) to the cleaned up DNA followed by another clean up step with AMPure XP Beads as described above. DNA was eluted in 30 μL 0.1X TE. The amount and quality of DNA was measured on Qubit 3.0 Fluorometer (Life Technologies) using Qubit™ dsDNA HS Assay Kit and Bioanalyzer (Agilent) using High Sensititivity DNA chip.

treatment_protocol: FOXB1 dgRNA-KO cell line was generated by targeted deletion of the sequence encoding the DNA binding domain of FOXB1 gene by CRISPR/Cas9 technology

value: Pre-neural crest cells

tag: cell line

value: WA01 ES cells

tag: differentiation day

value: day 3

tag: genotype

value: FOXB1 dgRNA-KO

tag: antibody


title: SLE2_ATAC

description: ATAC-seq of Homo sapiens, adult female monocytes, SLE2

value: female


title: preNC_Input

value: Wildtype

value: no antibody


title: drerio_E1

description: drerio.loom

source_name: Zebrafish spinal cord


title: DroshaKO_AS27a_Replicate1

description: Drosha KO cells trasnfected with Drosha splice variant AS27a_Replicate 1


title: SLE1_ATAC

description: ATAC-seq of Homo sapiens, adult female monocytes, SLE1

value: peripheral blood


title: preNC_dgRNA-KO_rep1


title: preNC_WT_rep2


title: drerio_D9

description: drerio.loom


title: preNC_WT_rep1


title: NC_sgRNA-KO_rep2

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 were trimmed using in-house scripts.  If, after trimming, the read was shorter than 45-bp, the whole read was discarded.
Trimmed reads were mapped to the human reference genome (hg19) with a known transcriptome index (UCSC Known Gene annotation) with Tophat v2.1.1 using the very-sensitive preset, first strand library type, and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results.
Tophat alignments were then processed by Cuffdiff v2.2.1 to obtain differential gene expression using first strand library type, providing gene model annotation and the genome sequence file for detection and correction of sequence-specific bias that random hexamer can cause during library preparation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKMs, fold changes, and p-values for each condition. Cuffdiff output format.

extract_protocol:
Total RNAs were extracted using TRIzol reagent (Life Technologies) according to Manufacturer's instructions. Extracted RNAs were dissolved in H2O and kept at -80oC until ready for library construction.
Libraries were prepared from poly-adenylated (poly-A) mRNAs using a custom kit based on the Illumina’s mRNA-seq kit (Illumina, part # RS-122-2101)

treatment_protocol: FOXB1 sgRNA-Het and sgRNA-KO cell lines were generated using CRISPR/Cas9 technology by targeting the translational start site of FOXB1 gene using a single guide RNA.

value: Neural crest cells

value: day 5

value: FOXB1 sgRNA-KO


title: H26

data_processing:
The small RNA library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Quality control: Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
Reads mapping to the reference sequence: The small RNA tags were mapped to reference sequence by Bowtie (v0.12.9) without mismatch to analyze their expression and distribution on the reference.
Known miRNA alignment: Mapped small RNA tags were used to looking for known miRNA. miRBase21.0 was used as reference, modified software mirdeep2(v2_0_0_5) and srna-tools-cli(v1.0) were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
Remove tags from these sources: To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
Small RNA annotation summary: Summarizing all alignments and annotations obtained before. In the alignment and annotation before, some small RNA tags may be mapped to more than one category. To make every unique small RNA mapped to only one annotation, we follow the following priority rule: known miRNA > rRNA > tRNA > snRNA > snoRNA > repeat > gene > NAT-siRNA > gene > novel miRNA > ta-siRNA. The total rRNA proportion was used a marker as sample quality indicator. Usually it should be less than 60% in plant samples and 40% in animal samples as high quality.
Quantification of miRNA: miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Differential expression of miRNA: Differential expression analysis of two groups was performed using the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini& Hochberg method. Corrected P-value of 0.1 was set as the threshold for  significantly differential expression by default.
Genome_build: GRCh38
Supplementary_files_format_and_content: "miRNA abundance measurements (raw counts or normalized)-yan324.xls"

source_name: sputum

extract_protocol:
Exosomes were isolated from spontaneous sputum in bronchiectasis patients and induced sputum from healthy subjects. After thawing, approximately four aliquots of phosphate buffer solution were added to achieve complete homogenization, followed by 18,000 g centrifugation for 10 minutes at 4°C (Thermo Scientific, USA), which were modified by instructions, then filtered through 0.8µm filter. The supernatant was used for extraction of exosomes with the exoEasy Maxi Kit (Qiagen Inc., Hilden, Germany) based on manufacturer’s instructions. Exosomes were suspended with buffer XE (Qiagen Inc., Hilden, Germany). For exosomal miRNA sequencing, the total RNA was extracted from the cell pellets by using QIAZol lysis reagent (Qiagen Inc., Hilden, Germany) by following the instructions of the manufacturer.
RNA per sample as the input material for the miRNA library which was generated with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB Inc., USA) by following the manufacturer’s protocol. Briefly, NEB 3' & 5' Adaptor were directly and specifically ligated to the 3' and 5' end of the small RNAs (miRNA, siRNA and piRNA), which also termed the 'SR Adaptor'. After ligation at the 3' end, the reverse transcriptase Primer (RT Primer) was hybridized to the excess of 3' SR adaptor and transformed the single-stranded DNA adaptor into a double-strand DNA. The first strand cDNA was synthesized by using M-MuLV Reverse Transcriptase (RNase H-). PCR amplification was performed, followed by purification of the PCR products (DNA fragments, length: 140~160 bp) on a 8% polyacrylamide gel (100 V, 80 min). The cDNA library was constructed and its sequence length was examined by using the Aglient Bioanalyzer 2100 system (Aligent Technologies, CA, USA). The samples with an effective concentration being greater than 2nM as quantified with qPCR could be subject to exosomal miRNA sequencing by using Illumina HiSeq 2500 platform.

value: sputum

value: healthy subjects

value: male


title: drerio_E13

description: drerio.loom

value: spinal cord


title: drerio_D8

description: drerio.loom


title: FG4592 rep1_RNA-seq

city: Nanjing

first: Yuexian

last: Xing

state: Jiangsu

address: Zhongshan Road No.305

institute: Jinling Hospital

data_processing:
ATAC-seq: The fastq files were processed through Cutadapt to remove adaptors and low-quality reads and then mapped to hg19 using Bowtie2. Unmapped reads were removed. The aligned sam files were converted to bam format and sorted using samtools. After duplicate reads were excluded by Picard Mark Duplicates and ENCODE blacklist regions were removed, MACS2 was used to call broad open chromatin peaks. For visualization, bigwig files were generated using bedGraphToBigWig.
RNAseq: Expression level was estimated as transcripts per million (TPM) using Kallisto and default parameters. As a reference transcriptome, we obtained from ensemble (ftp://ftp.ensembl.org/pub/grch37/release-94/gtf/homo sapiens/). The differential analysis of gene expression was performed using sleuth.
Genome_build: ATAC-seq:hg19,RNA-seq:hg19

source_name: kidney tubule HK2 cells

growth_protocol: HK2 cell line  maintained in DMEM-F12 medium with 10% FBS (Gibco), 1% penicillin-streptomycin at 37°C in a 5% (v/v) CO2 humidified incubator.

extract_protocol:
Genomic DNA was extracted with DNA Clean & Concentrator kit(ZYMO).
Libraries were constructed according to the Illumina instruction.

treatment_protocol: The HK2 cells were divided into negative control (Control), DMSO control (DMSO), H2O2, TGF-1β and FG4592 groups. We treated HK2 cells with H2O2, TGF-B1 and FG4592 (DMSO as control only for FG4592) to establish models of renal tubular epithelial cell damage in vitro. 500μM H2O2, 8 ng/ml TGF-B1 and 50μM FG4592 were added to HK2 cells for 48 h, respectively.

value: Human proximal tubular epithelial cells


title: NC_sgRNA-KO_rep1


title: FG4592 rep2_RNA-seq


title: TGF-β1 rep2_RNA-seq


title: 293T_Vector_Replicate1


title: drerio_D6

city: Uppsala

first: Henrik

institute: Uppsala University

description: drerio.loom


title: drerio_D7

description: drerio.loom


title: NC_isoWT2_rep2

value: Isogenic wildtype 2


title: H2O2 rep2_RNA-seq


title: NC_isoWT2_rep1


title: NC_sgRNA-Het_rep1

value: FOXB1 sgRNA-Het


title: drerio_D4

description: drerio.loom


title: TGF-β1 rep1_RNA-seq


title: drerio_D5

description: drerio.loom


title: drerio_D3

description: drerio.loom


title: NC_isoWT1_rep2

value: WA01 ES cells

value: Isogenic wildtype 1


title: drerio_D24

description: drerio.loom


title: NC_isoWT1_rep1


title: drerio_D23

description: drerio.loom


title: preNC_sgRNA-KO_rep2

value: Pre-neural crest cells

value: day 3


title: drerio_D22

description: drerio.loom


title: NC_sgRNA-Het_rep2


title: Control rep2_RNA-seq


title: Control rep1_RNA-seq


title: H2O2 rep1_RNA-seq


title: DMSO rep1_RNA-seq


title: DMSO rep2_RNA-seq


title: preNC_sgRNA-KO_rep1


title: drerio_D21

description: drerio.loom


title: FG4592 rep2_ATAC-seq

tag: restriction enzyme

value: Tn5 Transposase


title: preNC_isoWT2_rep2


title: drerio_D20

description: drerio.loom

tag: tissue


title: FG4592 rep1_ATAC-seq


title: drerio_D2

description: drerio.loom


title: preNC_isoWT2_rep1


title: TGF-β1 rep2_ATAC-seq


title: preNC_sgRNA-Het_rep2


title: drerio_D19

description: drerio.loom


title: TGF-β1 rep1_ATAC-seq


title: preNC_sgRNA-Het_rep1


title: H2O2 rep2_ATAC-seq


title: preNC_isoWT1_rep2


title: drerio_D18

description: drerio.loom


title: drerio_D17

description: drerio.loom


title: drerio_D16

description: drerio.loom


title: preNC_isoWT1_rep1


title: DMSO rep2_ATAC-seq


title: drerio_D15

description: drerio.loom


title: drerio_D14

description: drerio.loom


title: 10197T

city: Jacksonville

first: Tae Hyun

last: Hwang

state: FL

address: 4500 San Pablo Rd S.

institute: Mayo Clinic

hyb_protocol: HumanHT-12 v3.0 Expression BeadChip array (Illumina) was used.

data_processing: The data were normalised using quantile normalisation with MATLAB. We then selected only the probs whose gene symbols are in our 32 gene list. Atter being transformed by logarithm base 2, for each gene symbol, we aggregate the expression values at the corresponding probs by taking their mean expression value.

source_name: Stomach

label_protocol: Illumina TotalPrep™ RNA Amplification Kit was used for synthesis of labeled cRNA.

extract_protocol: RecoverAll™ total nucleic acid isolation kit (Ambion) or the mirVana RNA Isolation Labeling Kit (Ambion) were used. Quality control was performed with NanoDrop 2000 (Thermo Fischer Scientific) and RNA Nano 6000 chip (Agilent).

tag: tumor stage

value: Male


title: drerio_D13

last: Boije

address: Uppsala University, Dept. Of Neuroscience, Box 593, BMC

description: drerio.loom


title: 10122T

tag: age


title: 10115T


title: Control rep2_ATAC-seq


title: drerio_D12

description: drerio.loom

tag: developmental stage


title: Control rep1_ATAC-seq


title: 10109T

value: Female


title: DMAG3 (miRNA-Seq)

city: Luzhou

first: Long

last: Wang

state: Sichuan

address: No.1 Section 1, Xiang Lin Road, Longmatan District, Luzhou 646000, China.

institute: Southwest Medical University

data_processing:
Illumina hiseqXten software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using HISAT2 v2.0.4 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default. The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
The mapped reads of each sample were assembled by StringTie (v1.3.3) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself.
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps. At the same time, custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified miRNA respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM

source_name: blood

growth_protocol: HEL cells were cultured with RPMI 1640 medium (Gibico, Invitrogen Corporation, Carlsbad, CA) supplemented with 10% FBS (Thermo Fisher Scientific, Waltham, MA, USA), 100 U/ml of penicillin, and 100 mg/ml of streptomycin at 37°C, with 5% CO2 and saturated humidity.

extract_protocol:
Total RNA was extracted by using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions.
For lncRNA sequencing libraries construction,  a total amount of 20 ng RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by rRNA Removal Kit, and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA. Briefly, fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme was used with size-selected, adaptor-ligated cDNA at 37° C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase,Universal PCR primers and Index (X) Primer. At last, products were purified(AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. For small RNA library, a total amount of 3 μg total RNA per sample was used as input material. Sequencing libraries were generated using  Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

treatment_protocol: HEL cells were treated with 40 μg/ml DMAG for 3 days

value: HEL

tag: treatment

value: DMAG


title: DMAG2 (miRNA-Seq)


title: drerio_D10

description: drerio.loom

tag: strain


title: 10107T


title: DMAG1 (miRNA-Seq)


title: 10100T


title: drerio_D1

description: drerio.loom


title: CTL3 (miRNA-Seq)

value: Control


title: DMSO rep1_ATAC-seq


title: 10072T


title: H2O2 rep1_ATAC-seq


title: drerio_D11

description: drerio.loom


title: 10029T


title: CTL1 (miRNA-Seq)


title: drerio_C6

description: drerio.loom


title: drerio_C7

description: drerio.loom


title: drerio_C9

description: drerio.loom


title: DMAG2 (RNA-Seq)


title: peripheral blood_PE_10

type: genomic

city: Shanghai

last: Liu

address: No.501, Haike Road, Zhangjiang Hi-Tech Park, Pudong, Shanghai

institute: Shanghai Institute of Materia Medica

description: Hybridized to CytoScanHD_Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The raw data was processed by Affymetrix® Chromosome Analysis Suite (ChAS). Copy number variations, single nucleotide polymorphisms and loss of heterozygosities were extracted and converted from CEL files into signal intensities using ChAS.
Copy number type: Gain and Loss; Copy number state: 0.00, 1.00, 3.00 and 4.00

source_name: peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted peripheral blood using the AxyPrep Multisource Genomic DNA Miniprep Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: group

value: Preeclampsia group

value: peripheral blood


title: CTL2 (miRNA-Seq)


title: 10020T


title: 10032T


title: drerio_C8

description: drerio.loom


title: DMAG3 (RNA-Seq)


title: drerio_C5

description: drerio.loom


title: DMAG1 (RNA-Seq)


title: 10024T


title: peripheral blood_Con_9

description: Hybridized to CytoScanHD_Array

value: Control group


title: 10013T


title: peripheral blood_PE_8

description: Hybridized to CytoScanHD_Array


title: peripheral blood_PE_5

description: Hybridized to CytoScanHD_Array


title: drerio_C3

description: drerio.loom

value: spinal cord


title: CTL3 (RNA-Seq)


title: drerio_C4

description: drerio.loom


title: peripheral blood_PE_4

description: Hybridized to CytoScanHD_Array


title: CTL2 (RNA-Seq)


title: peripheral blood_PE_6

description: Hybridized to CytoScanHD_Array


title: BB15_GATCAG

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

data_processing:
Quality and adapter trimming was done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of tomato and B. cinerea with the following settings: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Solanum lycopersicum SL4.0, B. cinerea ASM83294v1
Supplementary_files_format_and_content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

organism: Solanum lycopersicum

source_name: Inoculated fruit

extract_protocol:
At 3 dpi, fruit pericarp and epidermal tissue of the blossom end halves of healthy, mock-inoculated, and inoculated fruit were collected and immediately frozen in liquid nitrogen. Frozen tissue was ground to a fine powder in liquid nitrogen. 2 gram of ground material was used during for RNA extraction as described in Blanco-Ulate et al., 2013. Purity and concentration of the extracted RNA were determined with the use of the NanoDrop One Spectrophotometer (Thermo Scientific), followed by a more precise concentration measurement with the Qubit 3 (Invitrogen). The integrity of the RNA was confirmed via agarose gel electrophoresis.
cDNA libraries were barcoded individually and analyzed for quantity and quality with the High Sensitivity DNA Analysis Kit in the Agilent 2100 Bioanalyzer (Agilent, USA). cDNA libraries were pooled in equal amounts for sequencing (single end, 50 bp) at the Expression Analysis Core Facility (UC Davis, CA, USA) in an Illumina HiSeq 2000 sequencer.

value: Ailsa Craig

tag: ripening stage

value: RR

value: Mock-inoculated


title: 10011T


title: peripheral blood_PE_9

description: Hybridized to CytoScanHD_Array


title: drerio_C24

description: drerio.loom


title: peripheral blood_Con_8

description: Hybridized to CytoScanHD_Array


title: peripheral blood_Con_5

description: Hybridized to CytoScanHD_Array


title: CTL1 (RNA-Seq)


title: drerio_C23

description: drerio.loom


title: peripheral blood_PE_3

description: Hybridized to CytoScanHD_Array


title: peripheral blood_Con_7

description: Hybridized to CytoScanHD_Array


title: peripheral blood_PE_2

description: Hybridized to CytoScanHD_Array


title: peripheral blood_PE_1

description: Hybridized to CytoScanHD_Array


title: peripheral blood_Con_10

description: Hybridized to CytoScanHD_Array


title: drerio_C21

description: drerio.loom


title: BB12_GCCAAT

value: Healthy


title: 10009T


title: BB11_ACAGTG


title: peripheral blood_PE_7

description: Hybridized to CytoScanHD_Array


title: CD5low-CD5low.rep2

city: Beijing

first: Xiaoyang

last: Jin

state: -- Please, Select --

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, CAS

description: CD5low cDC2s are cultured with TGF-beta for 24 hours, and then sorted according to their CD5 expression level. The sample correspoonds to the CD5low part

data_processing:
Salmon (version: 0.8.2) was used to quantify the expression of each transcript.  The human transcript sequences were provided by GENCODE (release 26), and only protein-coding transcript sequences were considered. The transcript-level expression value was imported and summarized using tximport to estimate gene-level read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts and TPM (Transcripts Per Kilobase Million) value for each sample

source_name: CD5low cDC2s

extract_protocol:
According to the quality and RNA abundance of samples, construction of sequencing library takes a method suitable for single-cell RNA sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD5low to CD5low -TGF-beta cDC2


title: BB13_CAGATC


title: drerio_C20

description: drerio.loom


title: BB10_TGACCA


title: BB14_ACTTGA


title: CD5high-CD5high.rep1

description: CD5high cDC2s are cultured with TGF-beta for 24 hours, and then sorted according to their CD5 expression level. The sample correspoonds to the CD5high part

source_name: CD5high cDC2s

value: CD5high to CD5high -TGF-beta cDC2


title: drerio_C2

description: drerio.loom


title: CD5low-CD5high.rep1

description: CD5low cDC2s are cultured with TGF-beta for 24 hours, and then sorted according to their CD5 expression level. The sample correspoonds to the CD5high part

value: CD5low to CD5high -TGF-beta cDC2


title: 10005T


title: peripheral blood_Con_3

description: Hybridized to CytoScanHD_Array


title: CD5low-CD5low.rep1


title: 10008T


title: BB6_GTGAAA

value: MG


title: peripheral blood_Con_4

description: Hybridized to CytoScanHD_Array


title: 10004T

value: Male


title: peripheral blood_Con_6

description: Hybridized to CytoScanHD_Array


title: 10006T

value: Female


title: drerio_C19

description: drerio.loom


title: drerio_C18

description: drerio.loom


title: BB4_CCGTCC


title: 10012T


title: peripheral blood_Con_2

description: Hybridized to CytoScanHD_Array


title: peripheral blood_Con_1

description: Hybridized to CytoScanHD_Array


title: drerio_C22

description: drerio.loom


title: BB3_ATGTCA


title: drerio_C16

description: drerio.loom


title: BB2_AGTTCC


title: 10007T


title: BB5_GTCCGC


title: 10002T


title: drerio_C17

description: drerio.loom


title: drerio_C14

description: drerio.loom


title: drerio_C15

description: drerio.loom


title: drerio_C12

description: drerio.loom


title: methylation_sample_202

city: Heidelberg

first: David

last: Reuss

department: Neuropathology

institute: University Hospital Heidelberg

hyb_protocol: Illumina protocol

scan_protocol: Illumina scan protocol according to the manufacturer protocol

data_processing:
Bioconductor version 3.14 package minfi (Version 1.40.0) using processillumina
normalized data: Average Beta

source_name: Astrocytoma, IDH-mutant, supratentorial, low

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

tag: material

value: FFPE


title: methylation_sample_201


title: drerio_C13

description: drerio.loom


title: methylation_sample_200


title: 10001T

tag: Sex


title: drerio_C11

description: drerio.loom


title: 4786T


title: Lpcat1 KO photoreceptor cell_rep1

city: Shinjuku-ku

first: Katsuyuki

last: Nagata

address: 1-21-1 Toyama

institute: National Center for Global Health and Medicine

description: Gene expression in Lpcat1 KO photoreceptor cell

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Sure Print G3 Mouse GE 8x60K (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Lpcat1 KO, Photoreceptor cell, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.03 ug RNA using the Low Input Quick Amp Labeling kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer(TOMY, Q5000) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: photoreceptor cell

value: Lpcat1 KO


title: 4768T


title: Lpcat1 KO photoreceptor cell_rep3

source_name: Lpcat1 KO, Photoreceptor cell, replicate 3


title: drerio_C10

description: drerio.loom


title: BB1_AGTCAA


title: Lpcat1 HZ photoreceptor cell_rep2

description: Gene expression in Lpcat1 HZ photoreceptor cell

source_name: Lpcat1 HZ, Photoreceptor cell, replicate 2

value: Lpcat1 HZ


title: 4688T


title: 4865T


title: 4925T


title: 4659T


title: methylation_sample_173

source_name: Astrocytoma, IDH-mutant, supratentorial, high


title: Lpcat1 HZ photoreceptor cell_rep3

source_name: Lpcat1 HZ, Photoreceptor cell, replicate 3


title: 4655T


title: Lpcat1 KO photoreceptor cell_rep2

source_name: Lpcat1 KO, Photoreceptor cell, replicate 2


title: Lpcat1 HZ photoreceptor cell_rep4

source_name: Lpcat1 HZ, Photoreceptor cell, replicate 4


title: Lpcat1 KO photoreceptor cell_rep4

source_name: Lpcat1 KO, Photoreceptor cell, replicate 4


title: drerio_B9

description: drerio.loom

source_name: Zebrafish spinal cord


title: drerio_C1

description: drerio.loom


title: methylation_sample_146

source_name: Primary tumor of oligosarcoma


title: drerio_B7

description: drerio.loom


title: drerio_B8

description: drerio.loom


title: methylation_sample_154


title: methylation_sample_153


title: methylation_sample_143


title: methylation_sample_144


title: 4669T

source_name: Stomach


title: CD5low-CD5high.rep2


title: Lpcat1 HZ photoreceptor cell_rep1

source_name: Lpcat1 HZ, Photoreceptor cell, replicate 1


title: drerio_B6

description: drerio.loom


title: methylation_sample_142


title: drerio_B5

description: drerio.loom


title: 4626T


title: methylation_sample_145


title: 4577T


title: 4603T


title: C2C12 KPC-exo

city: Hangzhou

first: Wang

last: Lantian

state: Zhejiang

address: 88 Jiefang Road

department: Department of Surgery

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

description: Gene expression after 24hr treated by KPC-exo

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring(version14.8,Agilent Technologies)were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 2.0. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs.

source_name: C2C12 cells, KPC-exo

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The murine pancreatic cancer cell line, developed from tumor tissue obtained from KrasLSL-G12D/+, Trp53LSL-R172H/+, Pdx1-Cre (KPC) mice, was maintained in RPMI-1640 medium, supplemented with 20% fetal bovine serum (FBS), 1% sodium pyruvate(100×), 1% MEM Non-Essential Amino Acids(NEAA 100×). The murine pancreatic ductal epithelial cell line (MPDC) was cultured in DMEM medium, supplemented with 10% FBS. C2C12 myoblasts were cultured in DMEM medium, supplemented with 10% FBS. When C2C12 myoblasts had achieved 70–80% confluence, replace the medium with DMEM containing 2% horse serum every day, which would induce the differentiation of myoblasts into myotubes in 4-6 days. The myotubes were used for the experiments.The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: C2C12 cells cultured in 25cm2 culture-flasks were treated by KPC-exo(4ug) for 24h. The C2C12 cells treated by MPDC-exo (exosomes secreted by murine pancreatic ductal epithelial cells ) were used

value: treated by KPC-exo


title: drerio_B4

description: drerio.loom


title: C2C12 MPDC-exo

description: Gene expression after24hr treated by MPDC-exo

source_name: C2C12 cells, MPDC-exo

value: control


title: 4573T


title: drerio_B3

description: drerio.loom

value: spinal cord


title: 4569T


title: Wild_Type_rep4

first: Qiulian

last: Zhou

address: Nanchen Road

department: Institute of Cardiovascular Sciences

institute: Shanghai University

description: Gene expression in C57BL/6 Wild Type mice

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: cardiac tissue,Wild Type, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All the mice were maintained on a 12 h light/dark cycle at 25°C and provided free access to commercial rodent chow and tap water.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Tissues were isolated and snap-frozen.

value: cardiac tissue

tag: gender

value: male

tag: genotype/variation

value: wild type


title: 4554T


title: Wild_Type_rep5

source_name: cardiac tissue,Wild Type, replicate 5


title: 4545T


title: Wild_Type_rep3

source_name: cardiac tissue,Wild Type, replicate 3


title: Wild_Type_rep1

source_name: cardiac tissue,Wild Type, replicate 1


title: methylation_sample_140

source_name: PMMRDIA


title: methylation_sample_138


title: methylation_sample_134


title: drerio_B24

description: drerio.loom


title: HIPK2_knockout_rep5

description: Gene expression in HIPK2-knockout mice

source_name: cardiac tissue,HIPK2 knockout, replicate 5

value: HIPK2 knockout


title: drerio_B22

description: drerio.loom


title: 4497T


title: methylation_sample_133


title: Wild_Type_rep2

source_name: cardiac tissue,Wild Type, replicate 2


title: WT9-12_K4M3_CUTRUN

city: Tianjin

first: Zhiheng

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

data_processing:
Library strategy: CUT&RUN
Bowtie2 (version 2.3.4.1) was used to align paired-end 150 bp sequence reads to human (hg38) genome
HOMER (version 4.10) findPeaks command was used to call peak
BamCoverage within deeptools (version 3.3.0) were used to generate bigwig files from bam files.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Bigwig

source_name: WT 9-12 cell

extract_protocol:
For ChIP-seq. Cells were cross-linked with 1% formaldehyde in 1 mL PBS for 10 min at RT. The crosslink was quenched by adding 67 μL of 2.5 M glycine(150 mM final). Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (200-500 bp) with Sonicator. Immunoprecipitation was performed with indicated antibodies. After elution and reversal cross-linking, DNA was purified for library preparation. For CUT&RUN. Cells were permeabilized with digitonin. DNA were cleaved in situ using a protein A-micrococcal nuclease fusion recruited by an antibody to chromatin associated protein. Then DNA was purified for library preparation.
Library construction were performed using VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-02) and VATHS DNA Adapters set2 for Illumina (Vazyme Biotech, Cat.N802-01)

tag: chip antibody

value: Millipore, 05-745R

tag: cell line


title: methylation_sample_132

value: Frozen


title: methylation_sample_131


title: drerio_B20

description: drerio.loom


title: drerio_B2

description: drerio.loom


title: methylation_sample_129


title: WT9-12_Input_ChIP

data_processing:
Bowtie2 (version 2.3.4.1) was used to align paired-end 150 bp sequence reads to human (hg38) genome
HOMER (version 4.10) findPeaks command was used to call peak
BamCoverage within deeptools (version 3.3.0) were used to generate bigwig files from bam files.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Bigwig


title: methylation_sample_139


title: 4341T


title: drerio_B23

description: drerio.loom


title: CTR2_RNA

description: RNA-seq of Homo sapiens, adult female monocytes

data_processing:
Sequencing data were mapped to the human reference genome (ucsc.hg19) using HISAT2 v2.1.0. FPKM for each gene were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM files

source_name: primary monocyte

extract_protocol:
The RNA-seq of monocytes were performed by the Smart-Seq2 method. Briefly samples were collected in tubes with lysis component and ribonuclease inhibitor. Then an Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production.
cDNAs were amplificated according to Smart-seq2 procedures for construct Illumina RNA sequencing library.

value: peripheral blood

tag: cell type

value: CD14+ monocytes

tag: disease state

value: healthy

value: adult

value: female


title: HIPK2_knockout_rep3

description: Gene expression in HIPK2-knockout mice

source_name: cardiac tissue,HIPK2 knockout, replicate 3


title: 4339T

value: Male


title: HIPK2_knockout_rep2

description: Gene expression in HIPK2-knockout mice

source_name: cardiac tissue,HIPK2 knockout, replicate 2


title: drerio_B19

description: drerio.loom

data_processing:
Alignment and mapping: Genome indexing and read alignment was performed using STAR v.2.5.4b and Velocyto v0.17.17 (La Manno et al., 2018). Fasta files for extra genes were manually added for eGFP 146 (LC337138.1), tdTomato (GeneBank: AY678269.1) and ERCC genes (Thermofisher assets: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip) and gene information was added to the species GTF file (Shaner et al., 2004; Nakajima et al., 2018). Reads were mapped to GRCm38.99 genome for mus musculus or GRCz11.98 genome for danio rerio. Genes were counted using featureCounts (subread V2.0.0) and Velocyto v0.17.17. Velocyto spliced and unspliced information was added to the final loom file as seperate layers. Full scripts are deposited at Github (http://github.com/jonetjakobsson/dmrt3-single-cell)
Genome_build: GRCm38.99
Genome_build: GRCz11.98
Supplementary_files_format_and_content: Loom file containing layers; reads, RPKM, spliced and unspliced meassures. Each row represents a well and each column represents one gene.

source_name: Zebrafish spinal cord


title: CTR1_RNA


title: HIPK2_knockout_rep4

description: Gene expression in HIPK2-knockout mice

source_name: cardiac tissue,HIPK2 knockout, replicate 4


title: methylation_sample_128


title: 4276T

source_name: Stomach


title: 4275T


title: SLE2_RNA

value: Systemic Lupus Erythematosus (SLE) patient


title: methylation_sample_127

value: FFPE


title: SLE1_RNA


title: 4262T


title: drerio_B17

description: drerio.loom


title: 4311T


title: drerio_B16

description: drerio.loom


title: HIPK2_knockout_rep1

description: Gene expression in HIPK2-knockout mice

source_name: cardiac tissue,HIPK2 knockout, replicate 1


title: methylation_sample_125


title: CTR2_HiC_Lib3

description: HiC-seq of Homo sapiens, adult female monocytes, CTR2, library rep3

data_processing:
we used integrated pipeline of HiC-Pro (V2.7.8) to process from clean fastq to contact maps with default parameters. This pipeline mainly included two-step mapping using Bowtie2 and binned to generate genome-wide interaction map. The resulting contact matrices were normalized using iterative correction and eigenvector decomposition (ICED).
The loops were called by HiCCUPS with default parameters. HiCCUPS examines each pixel in a Hi-C contact matrix and identifies those with enriched contact frequencies relative to local neighborhoods (pixels to its lower-left, pixels to its left and right, pixels above and below, and pixels within a "donut" surrounding the pixel of interest).
The R packages GENOVA was used for future advanced analysis and visualization of contact matrix. Briefly, the heatmap of ICE-normalisation contact matrix were used for visualization; the relative contact probability (RCP) was computed for each chromosome; the insulation score was used to call TADs with parameters “--is 2000000 --ids 800000 --nt 0.3”. Package hicrep and multiHiCcompare were used to do comparison analysis.
Genome_build: hg19

extract_protocol:
About one million monocytes were crosslinked by 40 ml 1% formaldehyde solution at room temperature for 10 min and 2.5 M Glycine was added to quench the crosslinking reaction. Supernatant was removed and the cells were washed three times by 1 X PBS. Crosslinked cells were resuspended in 500 µL of ice-cold Hi-C lysis buffer and rotated at 4 °C for 30 min.
in situ MboI Hi-C were assembled based on Illumina-compatible protocols.


title: CTR2_HiC_Lib2

description: HiC-seq of Homo sapiens, adult female monocytes, CTR2, library rep2