title: WT_CD4_2

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

institute: Korea Institute of Science and Technology Information

data_processing:
Quality trimming using FastQC and Fastx-toolkit
Alignment using STAR-2.6.1d to mm10
Differential expression analysis using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include expected count, FPKM, and TPM values for each sample

source_name: Lymph node

extract_protocol:
Lymph nodes were removed, flash frozen in the LN2, and RNA was harvested using Trizol reagent. Total RNA of 1 μg was extracted from each sample
The mRNA library (insert size of ~300 bp) was created using the Truseq Stranded mRNA Prep kit (Illumina)

value: FVB/NJ

value: Lymph node

value: wildtype


title: L01_AD11_050_HFO_1

status: Public on Jan 01 2022

type: SRA

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

country: USA

institute: National Instititute of Environmental Health Sciences

description:
L01_AD11
Hepatocyte_normcounts.csv

library_source: transcriptomic

data_processing:
pipeline run to convert reads to counts https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672545/
samples with counts < 100 average reads per transcript removed
normalized counts generated by cell type in DESEQ2
Genome_build: NA – Targeted Reads by BioSpyder
Supplementary_files_format_and_content: 6 normalized count matrix files in CSV with genes as rows and columns as samples.  The sample information in the hashfile.csv

molecule: total RNA

organism: Homo sapiens

source_name: Hepatocyte

extract_protocol:
described in https://www.altex.org/index.php/altex/article/view/1994
described in https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178302

tag: tissue/celltype

value: iCell Hepatocytes

tag: treatment

value: HFO

tag: dose


title: human atria, tachycardia control, 20B

type: RNA

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

description: HA CTL6 20B

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112);  Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);   Affymetrix Genechip®  fluidics station 450: protocol FS450_0002 for Cartridge Arrays

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

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

label: Biotin

source_name: isolated atrial multicellular trabeculae

label_protocol: NuGen Ovation Pico WTA System V2, M01224v2 (Cat No. 3302); Encore Biotin Module, M01111v6 (Cat No. 4200);

growth_protocol: Atrial appendages were obtained from patients undergoing CABG surgery. Trabeculae were isolated in maximal diameter of 1mm and immediatelly put in an organ bath setup were they were kept for the whole duration of the experiment.

extract_protocol: miRNeasyMICRO (Qiagen CatNo: 74004) incl DNase Treatment on column (RNase-Free DNase Set; Qiagen CatNo: 79254)

treatment_protocol: Trabeculae were either stretched to maximal phisiological length or subjected to 2,5 Hz pacing frequency for a duration of 6h.

value: tachycardia control

tag: tissue

value: atrial appendage


title: human atria, tachycardia control, 21A+21B

description: HA CTL6 21A+B


title: WT_pCREB

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

country: China

institute: Tianjin Medical University

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: freshly isolated DBA positive 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: genotype

value: WT

tag: chip antibody

value: Cell Signaling Technology, #9198

value: kidney

tag: cell type

value: Dolichos biflorus lectin (DBA) positive cells


title: fusiontg_CD4_1

city: Daejeon

country: South Korea

tag: strain

tag: age

value: CTLA4-CD28 transgene


title: Neuro2a-ZF-SCN9A_rep2

city: La Jolla

first: Prashant

last: Mali

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: University of California San Diego

data_processing:
Basecalls were performed using Illumina RTA3, and fastq files were then generated using Illumina bcl2fastq v2.20. Both tasks were carried out by the UCSD IGM Genomics Center.
RNA-seq read pairs were aligned to the GRCm38 reference genome using STAR aligner version 2.7.3a (Dobin A et al 2013). The genome index was built using primary assembly annotations from ENSEMBL release 100. Default parameters were used to run STAR, except for the following relevant settings: --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3
The gene counts output by STAR (see processed data files) were used as input to DESeq2 for gene expression quantification and analysis. Differential expression analysis was done using the standard DESeq2 pipeline with no independent filtering of genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: gene counts

growth_protocol: Neuro2a cells were grown in EMEM supplemented with 10% fetal bovine serum (FBS) and 1% Antibiotic-Antimycotic (Thermo Fisher Scientific) in an incubator at 37°C and 5% CO2 atmosphere.

extract_protocol:
RNA from Neuro2a cells was extracted using RNeasy Kit (QIAGEN; 74104)
Libraries were constructed using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB; E7103S)
NovaSeq 6000; Flowcell S4

treatment_protocol: One day prior to transfection, Neuro2a cells were seeded in a 24-well plate at a cell density of 1 or 2E+5 cells per well. 0.5 μg of each plasmid was added to 25 μL of Opti-MEM medium, followed by addition of 25 μL of Opti-MEM containing 2 μL of Lipofectamine 2000. The mixture was incubated at room temperature for 15 min. The entire solution was then added to the cells in a 24-well plate and mixed by gently swirling the plate. Media was changed after 24 h, and the plate was incubated at 37°C for 72 h in a 5% CO2 incubator. Cells were harvested, spun down, and frozen at 80°C.

tag: cell line

value: Plasmid transfection (ZF-SCN9A)

value: wild-type


title: L01_AE04_141_gasoline_1

description:
L01_AE04
Hepatocyte_normcounts.csv

value: NAPTHA


title: human atria, tachycardia, 20B

description: HA TC6 20B

value: tachycardia


title: GA Muscle 122 EV3

city: SANDIEGO

first: XIANHUI

last: RUAN

address: 9500 Gilman Dr (#0612), La Jolla

department: PATHOLOGY

institute: UCSD

data_processing:
RNA-seq and data processing were performed by Novogene Co., Ltd. Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene's wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file including FPKM values for each sample.

source_name: Muscle

growth_protocol: Female NOD scid gamma (NSG) mice were maintained in a standard mouse facility in sterile conditions.

extract_protocol:
Homogenized GA tissue (~20 mg) was used to extract RNA by using 1 ml of Trizol reagent (Invitrogen). The RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Co., Ltd.
mRNA is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by addition of fragmentation buffer.

treatment_protocol: Mice received tail-vein injections of EVs twice a week for 5 weeks (~10 ug EV per injection). Two days after the last injection, GA muscle was collected for immediate RNA extraction.

value: NSG

value: GA Muscle

value: week 12

value: Wild Type

value: MCF-10A/miR122 EV


title: L01_AD09_093_petrolatum_1

description:
L01_AD09
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: Nuero2a-mCherry_rep1

value: Plasmid transfection (mCherry)


title: Neuro2a-ZF-SCN9A_rep1


title: L01_AD08_103_gasoline_1

description:
L01_AD08
Hepatocyte_normcounts.csv


title: Neuro2a-mCherry_rep2


title: L01_AD07_008_HFO_1

description:
L01_AD07
Hepatocyte_normcounts.csv

value: HFO


title: fusiontg_CD4_2

value: FVB/NJ

value: Lymph node


title: Neuro2a-dCas9-SCN9A_rep2

value: Plasmid transfection (dCas9-SCN9A)


title: Neuro2a-dCas9-SCN9A_rep1


title: WT_CD4_1

value: wildtype


title: Neuro2a-dCas9-SCN9A_rep3


title: human atria, tachycardia control, 8A

description: HA CTL6 8A

value: tachycardia control

value: atrial appendage


title: human atria, tachycardia control, 13B

description: HA CTL6 13B


title: L01_AD06_MethodBlank_0

description:
L01_AD06
Hepatocyte_normcounts.csv


title: human atria, tachycardia control, 20A

description: HA CTL6 20A


title: human atria, stretch,  13A_13B

description: HA STR6 13A+B

value: stretch


title: Neuro2a-dCas9-empty_rep2

value: Plasmid transfection (dCas9-empty)

value: wild-type


title: Neuro2a-dCas9-empty_rep3


title: Neuro2a-dCas9-empty_rep1


title: L01_AD05_074_OLBO_1

description:
L01_AD05
Hepatocyte_normcounts.csv

value: BO


title: human atria, stretch,  11A

description: HA STR6 11A


title: LSD1_MidK_chrX

city: Tsukuba, Ibaraki

first: Ken

last: Nishimura

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly by bwa
Valiantcall was performed using bcftools mpileup
Genome_build: mm10
Supplementary_files_format_and_content: variantcall file in csv format

source_name: MEF+SeVdp(fKOSMaB)+Shield1 30 nM; Day20

growth_protocol: MEF, and cells reprogrammed by SeVdp(fKOSMaB) with or without 30 nM Shield1 for 20 days

extract_protocol:
Lysates were clarified from sonicated chromatins and LSD1-DNA complexes were isolated with antibody.
Libraries were prepared using KAPA HyperPlus Kit (Roche) according to the manufacturer’s instructions. Briefly, 10 ng of ChIP DNA was used for library preparation with unique dual index adaptor from IDT for Illumina TruSeq DNA UD Indexes (Illumina). The libraries were quantified using Qubit 4 Fluorometer (Thermo Fisher Scientific) and analyzed for size distribution using MultiNA (Shimdzu) or TapeStation 2200 (Agilent Technologies).

value: reprogramming cell

value: LSD1 (ab17721, abcam)

tag: time point

value: Day 20


title: L01_AD02_127_slackwax_1

description:
L01_AD02
Hepatocyte_normcounts.csv

value: WAX


title: LSD1_MEF_chrX

source_name: Mouse embryonic fibroblast

value: somatic cell

value: Day 0


title: LSD1_LowK_chrX

source_name: MEF+SeVdp(fKOSMaB); Day20


title: macrophages, siTet2_IFNγ

city: hangzhou

first: xu

last: li

state: zhejiang province

address: shilongshan street 18#

institute: westlake university

data_processing:
Basecalls performed using CASAVA
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5 with reference genome and gene model annotation files were downloaded from genome website directly and index of the reference genome was built using Hisat2 v2.0.5
The reads numbers mapped to each gene were counted using featureCounts v1.5.0-p3, and FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file contains abundance measurements of different genes

source_name: macrophage

growth_protocol: PMs were generated on DMEM medium supplemented with 10% Gibico FBS and Penicillin-Streptomycin

extract_protocol:
Peritoneal perfusion to collect mice PMs,and RNA was harvested by using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: macrophage

value: 6-8 weeks

value: wild type

value: si-Tet2 followed by 12 h IFN-γ stimulation


title: L01_AD01_081_OLBO_1

description:
L01_AD01
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: macrophages, IFNγ

description: IFNG

value: si-NC followed by 12 h IFN-γ stimulation


title: macrophages, control

description: Control

value: control


title: macrophages, NC_LM

value: si-NC followed by 12 h LM infection


title: macrophages, siTet2_LM

value: si-Tet2 followed by 12 h LM infection


title: human atria, stretch, 4B

description: HA STR6 4B

value: stretch

value: atrial appendage


title: L01_AC06_MethodBlank_0

description:
L01_AC06
Hepatocyte_normcounts.csv


title: human atria, stretch, 5A

description: HA STR6 5A


title: L01_AB11_063_P_Hwax_1

description:
L01_AB11
Hepatocyte_normcounts.csv


title: human atria, stretch control, 13A_13B

description: HA NS6 13A+B

value: stretch control


title: drerio_P8

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


title: L01_AB10_083_UATO_1

description:
L01_AB10
Hepatocyte_normcounts.csv

value: UATO


title: drerio_P9

description: drerio.loom


title: drerio_P6

description: drerio.loom


title: L01_AB09_187_1__OGO_1

description:
L01_AB09
Hepatocyte_normcounts.csv

value: OGO


title: drerio_P5

description: drerio.loom


title: L01_AB08_080_HFO_1

description:
L01_AB08
Hepatocyte_normcounts.csv

value: HFO


title: drerio_P4

description: drerio.loom


title: drerio_P3

description: drerio.loom


title: DSC_hypoxia_B_input

city: West Haven

first: Kalle

middle: T

last: Rytkönen

state: CT

address: 840 West Campus Drive

department: EEB, Systems Biology institute

institute: Yale University

description: DSC_hypoxia_H3K4me3_vs_Input_peaks_merged_broadPeak.txt

data_processing:
Basecalls performed using CASAVA version 1.4
Sequence reads were aligned to the Homo Sapiens reference genome (hg19) using using the ultra-fast short DNA sequence aligner Bowtie2
Two biological samples for both H3K4me3 and input for each condition were sequenced at Yale Center for Genome Analysis using Illumina Genome Analyzer II platform. For each sample at least 35 million reads were acquired and basic quality parameters checked with FASTQC. Sequence reads were aligned to the human reference genome (hg19) using DNA sequence aligner Bowtie2 with option “very-sensitive”.
Peak calling was done using MACS2, with broadPeak option. From the resulting MACS2 peaks only the peaks outside ENCODE blacklist regions (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz) were kept.
Genome_build: GRCh37.69
Supplementary_files_format_and_content: ESF_normoxia_H3K4me3_vs_Input_peaks.merged.broadPeak is a text file that contains the ESF normoxic H3K4me3 ChIP-Seq peak coordinates after MACS2 run and filtering
Supplementary_files_format_and_content: ESF_hypoxia_H3K4me3_vs_Input_peaks.merged.broadPeak is a text file that contains ESF hypoxic H3K4me3 ChIP-Seq peak coordinates after MACS2 run and filtering
Supplementary_files_format_and_content: DSC_hypoxia_H3K4me3_vs_Input_peaks.merged.broadPeak is a text file that contains ESF hypoxic H3K4me3 ChIP-Seq peak coordinates after MACS2 run and filtering

source_name: decidual stromal cells

growth_protocol: Human endometrial stromal fibroblasts (ESF) (T HESC, ATCC CRL-4003) were grown with DMEM (Sigma-Aldrich, D2906), supplemented with 10% charcoal stripped calf-serum (Hyclone), 1% antibiotic/antimycotic (ABAM; Gibco), 1nM sodium pyruvate (Gibco), 0.1% Insulin-Transferrin-Selenium (ITS premix, BD Biosciences), and 0.12% sodium bicarbonate. Cells were in vitro decidualized for 2 days by addition of 0.5 mM 8-Br-cAMP (Sigma) and 0.5 μM of synthetic progestin medroxyprogesterone acetate (MPA) in DMEM supplemented with 2% charcoal-stripped calf-serum.

extract_protocol:
Cells were harvested, resuspended and chemically cross-linked in suspension by the addition of 1% fresh formaldehyde with 10 minutes incubation at room temperature on a rotator. Cross-linking was quenched and cells were harvested by centrifugation and washed twice in cold PBS. Nuclei were extracted and sonication was performed using a Misonix S4000 sonicator.  Fragment size between 200bp and 600bp was obtained and confirmed by gel electrophoresis and Bionalyzer. For each H3K4Me3 ChIP sample also an input chromatin sample was sequenced.
DNA library preparation and high-throughput sequencing were performed on an Illumina Genome Analyzer II following the protocol recommended by Illumina with a 75bp readleght at the Yale Center for Genome Analysis.

value: 2 days in vitro decidualized endometrial stromal fibroblast

value: hypoxia

value: ATCC CRL-4003

tag: antibody


title: drerio_P24

description: drerio.loom


title: L01_AB07_129_HFO_1

description:
L01_AB07
Hepatocyte_normcounts.csv


title: human atria, stretch control, 9B

description: HA NS6 9B


title: drerio_P23

description: drerio.loom


title: human atria, stretch control, 4B

description: HA NS6 4B


title: human atria, stretch control, 5A

description: HA NS6 5A


title: Pla2g2a+/+_small intestine

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

institute: The University of Tokyo

description: Gene expression in small intestine tissue sample pooled from three mice

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit and hybridized with a Whole Mouse Genome Microarray (4x44K, Agilent Technologies). Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: The slides were scanned  immediately after washing on SureScan Microarray Scanner (Agilent Technologies) using one color scan setting for 4x44k array slides (Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: Small intestine

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: All mice were housed in climate-controlled (23 oC) specific pathogenfree facilities with a 12-h light-dark cycle, with free access to standard diet CE2 (CLEA Japan) and water.

extract_protocol: Total RNA was extracted from mouse tissues was purified using the RNeasy Mini Kit (Qiagen), and the quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mouse small intestine lysate was prepared by homogenization using lylysis and homogenization system (Precellys, M&S Instruments)

tag: Sex

value: Male

value: BALB/c

value: wild-type

value: Small intestine


title: L01_AB06_MethodBlank_0

description:
L01_AB06
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: drerio_P22

description: drerio.loom


title: drerio_P20

description: drerio.loom


title: drerio_P7

description: drerio.loom


title: human atria, stretch, 9B

description: HA STR6 9B


title: drerio_P2

description: drerio.loom


title: L01_AB05_059_dieselfuel_1

description:
L01_AB05
Hepatocyte_normcounts.csv

value: KER


title: GA Muscle 122 EV2

value: NSG

value: GA Muscle

value: week 12

value: Wild Type

value: MCF-10A/miR122 EV


title: human atria, stretch control, 11A_11B

description: HA NS6 11A+B

value: stretch control

value: atrial appendage


title: DSC_hypoxia_A_input


title: ESF_hypoxia_A_input

description: ESF_hypoxia_H3K4me3_vs_Input_peaks_merged_broadPeak.txt

source_name: endometrial stromal fibroblasts

value: endometrial stromal fibroblast


title: drerio_P19

description: drerio.loom

value: spinal cord


title: L01_AB04_155_HFO_1

description:
L01_AB04
Hepatocyte_normcounts.csv

value: HFO


title: ESF_hypoxia_B_input

value: hypoxia

value: ATCC CRL-4003


title: drerio_P17

description: drerio.loom


title: drerio_P18

description: drerio.loom


title: DSC_hypoxia_B_h3k4me3

value: 2 days in vitro decidualized endometrial stromal fibroblast


title: L01_AB03_184_VHGO_1

description:
L01_AB03
Hepatocyte_normcounts.csv

value: VHGO


title: drerio_P16

description: drerio.loom


title: DSC_hypoxia_A_h3k4me3


title: Pla2g2a–/–_small intestine

value: Male

value: BALB/c

value: Small intestine


title: L01_AB02_009_gasoline_1

description:
L01_AB02
Hepatocyte_normcounts.csv

value: iCell Hepatocytes

value: NAPTHA


title: drerio_P15

description: drerio.loom


title: ESF_hypoxia_B_h3k4me3

value: endometrial stromal fibroblasts


title: drerio_P14

description: drerio.loom


title: drerio_P21

description: drerio.loom


title: drerio_P12

description: drerio.loom


title: L01_AB01_041_CGO_1

description:
L01_AB01
Hepatocyte_normcounts.csv

value: CGO


title: drerio_P13

description: drerio.loom


title: drerio_P11

description: drerio.loom


title: drerio_P10

description: drerio.loom


title: ESF_normoxia_B_input

description: ESF_normoxia_H3K4me3_vs_Input_peaks_merged_broadPeak.txt

value: normoxia


title: drerio_O9

description: drerio.loom


title: L01_AA10_180_VHGO_1

description:
L01_AA10
Hepatocyte_normcounts.csv


title: L01_AA08_006_HFO_1

description:
L01_AA08
Hepatocyte_normcounts.csv


title: L01_AA09_082_UATO_1

description:
L01_AA09
Hepatocyte_normcounts.csv

value: UATO


title: drerio_P1

description: drerio.loom


title: drerio_O8

description: drerio.loom


title: drerio_O6

description: drerio.loom


title: ESF_normoxia_A_input


title: ESF_normoxia_A_h3k4me3


title: L01_AA06_MethodBlank_0

description:
L01_AA06
Hepatocyte_normcounts.csv


title: drerio_O4

description: drerio.loom


title: L01_AA05_151_OLBO_1

description:
L01_AA05
Hepatocyte_normcounts.csv

value: BO


title: drerio_O3

description: drerio.loom


title: drerio_O5

description: drerio.loom


title: drerio_O24

description: drerio.loom


title: L01_AA03_043_kerosine_1

description:
L01_AA03
Hepatocyte_normcounts.csv

value: KER


title: drerio_O23

description: drerio.loom

value: spinal cord


title: L01_AA01_016_kerosine_1

description:
L01_AA01
Hepatocyte_normcounts.csv


title: ESF_hypoxia_A_h3k4me3


title: drerio_O21

description: drerio.loom


title: drerio_O22

description: drerio.loom


title: lib44587

city: Seattle

first: Kimberly

middle: A

last: Dill-McFarland

state: WA

address: 750 Republican St

department: Allergy and Infectious Diseases

institute: University of Washington

data_processing:
Reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of 30 (Galaxy FASTQ Trimmer tool v1.0.0). FastqMcf (v1.1.2) was used to remove adapter sequences.
Reads were aligned using the STAR aligner (v2.4.2) with the GRCh38 reference genome and gene annotations from ensembl release 91.
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), Samtools (v1.2), and HTSeq-count (v0.4.1).
Libraries were quality filtered by median coefficient of variation (CV) coverage < 0.84, duplicate mapped reads > 0.87, total aligned sequences > 188,000, and the first two principal components
Counts were normalized for RNA composition using the trimmed mean of M-values normalization method, filtered to protein coding genes with at least 1 count per million (CPM) in at least 3 samples, and converted to log2 CPM with quality weights using voom in R (v4.0.0)
Genome_build: hg38
Supplementary_files_format_and_content: CSV: normalized counts in genes (ENSEMBL ID) for each sample (library ID)

growth_protocol: pDC and eosinophils were obtained from leukocyte-enriched blood samples from a local blood bank. pDC were also obtained from blood samples from participants with allergic asthma (treated versus non-treated with anti-IL-5/5Rα therapy). For pDC purification, peripheral blood mononuclear cells (PBMCs) were isolated by density centrifugation and pDCs subsequently purified from PBMCs by negative selection using antibody-coated magnetic beads. For eosinophil purification, a nucleated cell suspension was obtained using HetaSep to sediment red blood cells, and eosinophils were purified from the nucleated cell suspension by negative selection using antibody-coated magnetic beads.

extract_protocol:
Quick-RNA MicroPrep kit (Zymo Research)
SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit

treatment_protocol: Eosinophils were cultured for 24 hours in complete RPMI 1640 medium containing IL-3 and supernatants harvested. pDCs were cultured for 24 hours in complete RPMI 1640 medium containing IL-in the presence or absence of supernatants generated from eosinophil cultures in previous experiments and stimulated with rhinovirus (RV).

value: plasmacytoid dendritic cells

tag: virus

value: RV

tag: disease state

value: asthma

tag: donor

tag: pass-filter

value: TRUE


title: 1676 sponge_miR-26_+IL-7_rep2

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

institute: Medical University of Innsbruck, Biocenter

description: gene expression in the presence of IL-7

hyb_protocol: 1.65 µg of each Cy3-labeled cRNA was fragmented and prepared for one-color based hybridisation (Gene Expression Hybridisation Kit, Agilent Technologies). cRNA samples were hybridized for 17 hours at 65°C on a Sureprint G3 Mouse Gene Expression Microarray (Agilent Technologies, AMADID 028005). Afterwards, microarrays were washed with increasing stringency using Geene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitril.

scan_protocol: Fluorescent signal intensities were detected with Scan Control 8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner.

data_processing: Raw data were extracted from images using Feature Extraction 10.7.1.1 Software (Agilent Technologies). Data analysis was performed using the Subio software package (Subio, Japan).

source_name: mouse pre-B cell line, expression of sponge sequestering miR-26 family members, +IL7, replicate 2

label_protocol: 100 ng total RNA per sample were used for an RT-IVT reaction. Total RNA was reverse transcribed into cDNA and then converted into labelled cRNA by in-vitro transcription (Low Input Quick-Amp Labeling Kit One-Color; Agilent Technologies) incorporating Cyanine-3-CTP according to the manufacturer's instructions. RNA absorbance ratio, cRNA concentration and Cy3 dye concentration were checked with the NanoDrop ND-1000 UV-VIS spectrophotometer. Furthermore, the quality of labeled non-fragmented cRNA was analyzed with the 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: 1676 cells were cultured in Iscove’s medium containing 7.5% FCS (Biochrom Superior), 100 U/ml penicillin, 100 U/ml streptomycin (PAN) and 50 µM 2-ME supplemented with excessive IL-7 obtained as a supernatant of IL-7-expressing J558L cells. Following infection with retroviral vectors, transduced cells were selected with puromycin at a concentration of 1 µg/ml for 3-4 days.

extract_protocol: Total RNA was prepared using the RNeasy RNA Purification kit (Qiagen) including on-column DNase digestion according to the manufacturer's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer (Peqlab) and integrity was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 1676 cells selected for expression of a control vector or a vector encoding the designated constructs were cultured in excessive IL-7 or without IL-7 for 24 hours to induce pre-B cell differentiation.

value: pre-B cell

tag: over-expression

value: miR-26 sponge


title: drerio_O2

description: drerio.loom


title: lib44586

tag: treatment


title: drerio_O16

description: drerio.loom

tag: tissue


title: ESF_normoxia_B_h3k4me3

value: ATCC CRL-4003


title: drerio_O17

description: drerio.loom


title: drerio_O19

description: drerio.loom


title: lib44585


title: lib44582


title: drerio_O7

description: drerio.loom


title: drerio_O15

description: drerio.loom


title: 1676 miR-26a_+IL-7_rep2

description: gene expression in the presence of IL-7

source_name: mouse pre-B cell line, expression of hsa-miR-26a-2, +IL7, replicate 2

tag: genotype


title: drerio_O14

description: drerio.loom


title: drerio_O18

description: drerio.loom


title: lib44581


title: 1676 miR-26a_+IL-7_rep1

description: gene expression in the presence of IL-7

source_name: mouse pre-B cell line, expression of hsa-miR-26a-2, +IL7, replicate 1


title: drerio_O13

description: drerio.loom


title: drerio_O12

description: drerio.loom


title: drerio_O20

description: drerio.loom


title: drerio_O11

description: drerio.loom


title: 1676 sponge_miR-26_+IL-7_rep1

description: gene expression in the presence of IL-7

source_name: mouse pre-B cell line, expression of sponge sequestering miR-26 family members, +IL7, replicate 1


title: lib44580


title: drerio_O10

description: drerio.loom


title: drerio_O1

description: drerio.loom


title: drerio_N9

description: drerio.loom


title: lib44559


title: lib44558


title: drerio_N7

description: drerio.loom


title: drerio_N5

description: drerio.loom


title: lib44557


title: drerio_N4

description: drerio.loom


title: lib44554


title: lib44553


title: drerio_N24

description: drerio.loom


title: drerio_N23

description: drerio.loom


title: Lpcat1 KO retina_rep4

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 retina

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, Retina, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 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: whole retina

value: Lpcat1 KO


title: drerio_N22

description: drerio.loom


title: drerio_N20

description: drerio.loom


title: drerio_N21

description: drerio.loom


title: lib44552


title: lib44549


title: drerio_N8

description: drerio.loom


title: drerio_N6

description: drerio.loom


title: drerio_N2

description: drerio.loom


title: GSM1463279 (1676 control_+IL-7_rep1)

description: gene expression in the presence of IL-7

source_name: mouse pre-B cell line, control vector, +IL7, replicate 1

value: control vector


title: Lpcat1 KO retina_rep2

description: Gene expression in Lpcat1 KO retina

source_name: Lpcat1 KO, Retina, replicate 2


title: Lpcat1 KO retina_rep3

description: Gene expression in Lpcat1 KO retina

source_name: Lpcat1 KO, Retina, replicate 3


title: drerio_N19

description: drerio.loom


title: lib44548


title: drerio_N3

description: drerio.loom


title: drerio_N18

description: drerio.loom


title: GSM1463280 (1676 control_+IL-7_rep2)

description: gene expression in the presence of IL-7

source_name: mouse pre-B cell line, control vector, +IL7, replicate 2


title: Lpcat1 KO retina_rep1

description: Gene expression in Lpcat1 KO retina

source_name: Lpcat1 KO, Retina, replicate 1


title: Lpcat1 WT retina_rep3

description: Gene expression in Lpcat1 WT retina

source_name: Lpcat1 WT, Retina, replicate 3

value: Lpcat1 WT


title: Lpcat1 WT retina_rep4

description: Gene expression in Lpcat1 WT retina

source_name: Lpcat1 WT, Retina, replicate 4


title: Lpcat1 WT retina_rep1

description: Gene expression in Lpcat1 WT retina

source_name: Lpcat1 WT, Retina, replicate 1


title: Lpcat1 WT retina_rep2

description: Gene expression in Lpcat1 WT retina

source_name: Lpcat1 WT, Retina, replicate 2


title: lib44547


title: drerio_N16

description: drerio.loom

source_name: Zebrafish spinal cord


title: drerio_N14

description: drerio.loom


title: drerio_N15

description: drerio.loom


title: drerio_N13

description: drerio.loom


title: lib44010


title: drerio_N12

description: drerio.loom


title: lib44009


title: drerio_N17

description: drerio.loom


title: drerio_N10

description: drerio.loom


title: lib44008


title: drerio_N1

description: drerio.loom


title: lib44005


title: drerio_N11

description: drerio.loom


title: drerio_M8

description: drerio.loom


title: lib44004


title: drerio_M7

description: drerio.loom


title: drerio_M9

description: drerio.loom


title: drerio_M6

description: drerio.loom


title: drerio_M5

description: drerio.loom


title: drerio_M4

description: drerio.loom


title: drerio_M24

description: drerio.loom


title: lib44003


title: drerio_M23

description: drerio.loom


title: drerio_M22

description: drerio.loom


title: lib43988

value: FALSE


title: lib43986


title: drerio_M21

description: drerio.loom


title: drerio_M20

description: drerio.loom


title: drerio_M2

description: drerio.loom


title: lib43983


title: Susceptible_24 h_Rep2

city: Amarillo

first: Shuyu

state: Texas

address: 6500 Amarillo Blvd West

department: Texas A&M AgriLife Research

institute: Texas A&M University System

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Triticum aestivum

source_name: Leaf tissue

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: Plants were grown in greenhouse conditions

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

treatment_protocol: Plants were infested with greenbug biotype E and leaf samples were collected at 0, 24, and 48 hours after infestation from resistant and susceptible plants.

value: Greenbug aphid infestation

value: leaf

value: 3 leaf stage

tag: time (h)


title: Susceptible_48 h_Rep3


title: Susceptible_0 h_Rep3

value: control


title: Susceptible_24 h_Rep3


title: lib43982

tag: cell type


title: Susceptible_48 h_Rep1


title: Susceptible_24 h_Rep1


title: drerio_M19

description: drerio.loom

value: spinal cord

tag: strain


title: drerio_M18

description: drerio.loom


title: Resistant_48 h_Rep2


title: Resistant_48 h_Rep1


title: Susceptible_0 h_Rep2


title: drerio_M3

description: drerio.loom


title: Susceptible_48 h_Rep2


title: lib43987

value: plasmacytoid dendritic cells


title: drerio_M17

description: drerio.loom


title: drerio_M14

description: drerio.loom


title: drerio_M13

description: drerio.loom


title: drerio_M16

description: drerio.loom


title: Resistant_24 h_Rep2


title: drerio_M15

description: drerio.loom


title: lib28544

value: RV

value: healthy


title: lib43981

value: asthma


title: Susceptible_0 h_Rep1


title: lib28545

value: TRUE


title: drerio_M12

description: drerio.loom


title: Resistant_48 h_Rep3


title: drerio_M10

description: drerio.loom


title: lib28543


title: drerio_M1

description: drerio.loom


title: lib28538


title: drerio_L9

description: drerio.loom


title: drerio_M11

description: drerio.loom


title: drerio_L7

description: drerio.loom


title: drerio_L6

description: drerio.loom


title: drerio_L5

description: drerio.loom


title: drerio_L4

description: drerio.loom


title: drerio_L3

description: drerio.loom


title: drerio_L24

description: drerio.loom


title: drerio_L8

description: drerio.loom


title: drerio_L23

description: drerio.loom


title: Resistant_24 h_Rep3


title: drerio_L22

description: drerio.loom


title: drerio_L21

description: drerio.loom


title: lib28535


title: lib28536


title: lib28530


title: lib28531


title: lib28537


title: Resistant_0 h_Rep1


title: Resistant_24 h_Rep1


title: Resistant_0 h_Rep3


title: Resistant_0 h_Rep2


title: drerio_L20

description: drerio.loom


title: drerio_L19

description: drerio.loom


title: lib28529


title: drerio_L17

description: drerio.loom


title: TAM 112_Grain Filling_Wet_Rep2

description: Expression data from flag leaves in wheat in reponse to water-deficit stress

source_name: Flag leaves

treatment_protocol: Plants were subjected to two water treatments; 90% and 50 % field capacity

value: Grain Filling

value: TAM 112

value: Wet

value: flag leaf


title: TAM 112_Grain Filling_Dry_Rep3

value: Dry


title: TAM 112_Grain Filling_Wet_Rep3


title: TAM 112_Grain Filling_Dry_Rep2


title: TAM 112_Grain Filling_Wet_Rep1


title: lib28524


title: TAM 112_Grain Filling_Dry_Rep1


title: TAM 111_Grain Filling_Dry_Rep3

value: TAM 111


title: drerio_L15

description: drerio.loom


title: TAM 111_Grain Filling_Dry_Rep2


title: drerio_L11

description: drerio.loom


title: drerio_L12

description: drerio.loom


title: drerio_L18

description: drerio.loom


title: drerio_L13

description: drerio.loom


title: lib28521


title: drerio_L16

description: drerio.loom


title: lib28523


title: drerio_L10

description: drerio.loom


title: drerio_L2

description: drerio.loom


title: lib28522


title: drerio_L14

description: drerio.loom


title: lib28528


title: TAM 111_Grain Filling_Dry_Rep1


title: BC_DC_Tum_1

city: Paris

first: Floriane

last: Noël

address: 1 avenue Claude Vellefaux

country: France

institute: INSERM

description: gene expression

data_processing:
FASTQ files were processed using the CellRanger pipeline (10X Genomics; V3 for HNSCC samples and V2 for Breast cancer sample), and reads were aligned to the human genome hg38. True cells are distinguished from empty droplets in the Cell Ranger pipeline; additionally, they were also excluded by Dropletutils R package: the intersection of both was used. Cells with a high fraction of mitochondrial genes were filtered (> 10% HNSCC:  > 20% Breast); and potential doublets cells were excluded by filtering cells with too high library complexity were filtered (cells that expressed more than 4000 genes (HNSCC) or 5000 genes (Breast): this threshold was based on the distribution of the number of cells per gene expression).
CITE-seq features were detected using CITE-seq Count (Roelli et al., 2019)
Genome_build: GRCh38
Supplementary_files_format_and_content: output files from CellRanger (filtered gene matrices :barcodes, features and matrix) for each scRNA-seq sample. output files from CITE-seq Count (barcodes, features and matrix) for each ADT sample.

source_name: BC infiltrating dendtritic cells

extract_protocol:
For HNSCC patient 1 (Pt1), there was single-cell suspensions from a juxtatumor sample and from a tumor sample. The 2 samples were stained with antibodies for cell sorting for 15 min at 4°C (Table 30). The samples were washed, and DAPI was added just before sorting. After sort, the different cell populations sorted were merged in defined proportions as detailed below for each of the 2 samples. The samples were stained with CITEseq antibodies (Table 30) at 4°C for 30min according to manufacturer’s recommendations (Biolegend). Cells were washed, and the tumor sample was split in 2. In one of the samples, the primer specific for ADT was not added, to avoid the expansion by PCR of ADTs. This separation of the tumor sample in two was done to allow for comparison of tumor samples with or without ADT, because this was a new technology. We did not find any relevant difference between the samples with and without ADT, validating the absence of bias induced by this technological approach. Samples were then processed as recommended in 10X Genomics protocols.  For HNSCC patient 2 (Pt2), there was only one tumor sample available. Staining with antibodies for sort and with CITEseq antibodies were done simultaneously for 30 min at 4°C, before wash, DAPI staining and sorting. Sorting was performed using the purity and low-pressure mode, and a 100-μm nozzle on a BD FACS Aria III flow sorter for all samples.  The gating strategy is displayed in Fig S8. We excluded debris and doublets by FSC, SSC gating; dead cells by DAPI gating; red blood cells by CD235a staining (Pt2 only). All remaining cells were sorted in one of the 5 final population groups. Group 1 included CD45+CD3+ T cells; Group 2 included non-immune CD45- cells; Group 3 included MMAC and CD14+DC gated as CD45+CD3-CD19-CD56-CD11c+HLA-DR+CD14+; Group 4 included cDC1 and cDC2 gated as CD45+CD3-CD19-CD56-CD11c+HLA-DR+CD14- and was merged with pDC gated as CD45+CD3-CD19-CD56-CD11c-HLA-DR+CD123+; Group 5 included all remaining cells: CD45+CD3-CD19+ and/or CD56+, CD45+CD3-CD19-CD56-CD11c-HLA-DR+CD123-, and CD45+CD3-CD19-CD56-HLA-DR-.  The count provided by the flow sorter was used for subsequent processing. The population with the highest number of cells was also counted by trypan blue to ensure accuracy of the flow sorter counts. The final sample used for chip loading ScRNAseq contained 18000 (Pt1) or 16000 (Pt2) cells obtained by combining 3600 (Pt1) or 3200 (Pt2) cells from each of the 5 groups. The only exception was for the juxtatumor sample of Pt1, in which only 857 cells were available for the Group 4 of cells.   For the luminal breast cancer sample, the single-cell suspension from the tumor sample was stained with antibodies for cell sorting for 15 min at 4°C (Table 30). The sample was washed, and DAPI was added just before sorting. The gating strategy for DC included the following steps: (i) exclusion of debris and doublets by FSC, SSC gating; (ii) exclusion of dead cells by DAPI gating; (iii) selection of cells positive in CD45 BV570; (iv) exclusion of T cells, identified as CD3+ APC and CD19- Alexa700 and CD56- Alexa700; (v) exclusion of CD19+ Alexa700 and CD56+ Alexa700 cells; (vi) selection of CD11c- PECy5 cells, among which cells CD123+ BV650 and HLA-DR+ eFluor760 double positive were sorted as pDC; besides, selection of CD11c+ PECy5 and HLA-DR+ eFluor760 double positive cells, among which cells were classified according to CD1C PE and CD14 FITC: MMAC defined as CD1C- and CD14+ were excluded and all the other cells were sorted as cDC. Eventually, the DC sample used for ScRNA-seq included the pDC and the cDC. The CD45- cells, CD3+ cells, the MMAC and a mixed group of CD45+CD3- cells were also sorted independently but were not analyzed in the present study.
Single-cell sequencing of final samples was performed using Single Cell 3’ kit V1 (Breast cancer sample), v2 (HNSCC Pt1) and v3 (HNSCC Pt2) (10X Genomics), according to the manufacturer protocol (10X Genomics), including the CITE-seq libraries (HNSCC samples). Sample quality was checked with Bioanalyzer Agilent 2100 using a HighSensitivity DNA chip (Agilent Genomics). Samples were sequenced on an Illumina HiSeq (Breast cancer sample) and Novaseq (HNSCC samples) with a depth of sequencing of 50000 reads/cells (Breast cancer) and 100000 reads/cells (HNSCC samples).

value: Breast tumor

value: BC Patient 1

tag: hpv status

tag: age

tag: molecule subtype

value: cDNA


title: drerio_K9

description: drerio.loom

tag: developmental stage


title: drerio_L1

description: drerio.loom


title: drerio_K7

description: drerio.loom


title: drerio_K8

description: drerio.loom


title: drerio_K6

description: drerio.loom


title: drerio_K5

description: drerio.loom


title: TAM 112_Heading_Dry_Rep3

value: Heading


title: HNC_B_BDCA1posDC_D9_3

data_processing:
Sequencing was performed in a single batch with Illumina HiSeq 2500 using an average depth of 15 million reads
Reads were mapped to the human genome reference (hg19/GRCh37) using Tophat2 version 2.0.14.
Gene expression values were quantified as read counts using HTSeq-count version 0.6.1.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BDCA1+ DC from blood of head and neck cancer patient - A308-A309U38

extract_protocol:
Single Cell RNA Purification Kit (Norgen Bioteck) was used for RNA extraction, including on-column DNase digestion (Qiagen), as described by the manufacturer's protocol.
cDNA was generated with SMARTer Ultra Low input RNA for Illumina Sequencing-HV (Clontech), following manufacturer’s protocol with 14 cycles for amplification. Quality controls were performed with Qubit dsDNA high sensitivity (Thermofisher) and an Agilent RNA 6000 Nano Kit (Agilent Technologies). Multiplexed paired-end libraries 50nt in length were obtained using Nextera XT kit (Clontech).

value: blood of head and neck cancer patient

value: BDCA1+ DC

tag: disease stage

tag: gender

value: F

value: untreated


title: HNC_B_BDCA1posDC_D10_3

source_name: BDCA1+ DC from blood of head and neck cancer patient - A308-A309U37

value: M


title: TAM 111_Grain Filling_Wet_Rep1


title: TAM 111_Grain Filling_Wet_Rep3


title: TAM 111_Grain Filling_Wet_Rep2


title: drerio_K4

description: drerio.loom

value: spinal cord


title: HNC_B_BDCA1posDC_D7_3

source_name: BDCA1+ DC from blood of head and neck cancer patient - A308-A309U36


title: drerio_K3

description: drerio.loom


title: drerio_K23

description: drerio.loom


title: drerio_K21

description: drerio.loom


title: TAM 112_Heading_Dry_Rep1


title: HNC_T_BDCA1posDC_D9_3

source_name: BDCA1+ DC from primary head and neck tumor - A308-A309U34

value: from primary head and neck tumor


title: drerio_K22

description: drerio.loom


title: HNC_T_MMAC_D9_3

source_name: MMAC from primary head and neck tumor - A308-A309U35

value: MMAC


title: HNC_T_pDC_D9_3

source_name: pDC from primary head and neck tumor - A308-A309U33

value: pDC


title: HNC_T_MMAC_D8_3

source_name: MMAC from primary head and neck tumor - A308-A309U32


title: drerio_K18

description: drerio.loom


title: TAM 112_Heading_Wet_Rep3

value: TAM 112

value: Wet


title: drerio_K24

description: drerio.loom


title: drerio_K17

description: drerio.loom


title: TAM 112_Heading_Dry_Rep2

value: Dry

value: flag leaf


title: drerio_K16

description: drerio.loom


title: drerio_K19

description: drerio.loom


title: HNC_T_BDCA1posDC_D8_3

source_name: BDCA1+ DC from primary head and neck tumor - A308-A309U30


title: drerio_K2

description: drerio.loom


title: drerio_K15

description: drerio.loom


title: HNC_T_CD14posDC_D8_3

source_name: CD14+ DC from primary head and neck tumor - A308-A309U31

value: CD14+ DC


title: drerio_K13

description: drerio.loom


title: drerio_K10

description: drerio.loom


title: drerio_K11

description: drerio.loom


title: drerio_K12

description: drerio.loom


title: HNC_T_MMAC_D7_3

source_name: MMAC from primary head and neck tumor - A308-A309U28


title: HNC_T_pDC_D8_3

source_name: pDC from primary head and neck tumor - A308-A309U29


title: drerio_K1

description: drerio.loom


title: HNC_T_CD14posDC_D7_3

source_name: CD14+ DC from primary head and neck tumor - A308-A309U27


title: HNC_T_BDCA1posDC_D7_3

source_name: BDCA1+ DC from primary head and neck tumor - A308-A309U26


title: drerio_J7

description: drerio.loom

source_name: Zebrafish spinal cord


title: drerio_J8

description: drerio.loom


title: TAM 111_Heading_Dryt_Rep1

value: TAM 111


title: TAM 112_Heading_Wet_Rep2


title: HNC_T_pDC_D7_3

source_name: pDC from primary head and neck tumor - A308-A309U25


title: TAM 112_Heading_Wet_Rep1

source_name: Flag leaves


title: drerio_J6

description: drerio.loom


title: drerio_J5

description: drerio.loom


title: drerio_K14

description: drerio.loom


title: TAM 111_Heading_Wet_Rep3


title: HNC_T_MMAC_D6_3

source_name: MMAC from primary head and neck tumor - A308-A309U24


title: TAM 111_Heading_Dryt_Rep2


title: drerio_J3

description: drerio.loom


title: TAM 111_Heading_Dryt_Rep3


title: TAM 111_Heading_Wet_Rep1


title: drerio_J4

description: drerio.loom


title: drerio_J24

description: drerio.loom


title: HNC_T_BDCA1posDC_D6_3

source_name: BDCA1+ DC from primary head and neck tumor - A308-A309U23


title: drerio_J21

description: drerio.loom


title: TAM 111_Heading_Wet_Rep2


title: drerio_J9

description: drerio.loom


title: drerio_J22

description: drerio.loom


title: drerio_J19

description: drerio.loom


title: drerio_J23

description: drerio.loom


title: drerio_J2

description: drerio.loom


title: HNC_T_MMAC_D5_3

source_name: MMAC from primary head and neck tumor - A308-A309U21


title: drerio_J16

description: drerio.loom


title: drerio_J20

description: drerio.loom


title: drerio_J17

description: drerio.loom


title: HNC_T_CD14posDC_D5_3

source_name: CD14+ DC from primary head and neck tumor - A308-A309U20


title: drerio_J18

description: drerio.loom


title: HNC_T_pDC_D6_3

source_name: pDC from primary head and neck tumor - A308-A309U22


title: HNC_T_BDCA1posDC_D5_3

source_name: BDCA1+ DC from primary head and neck tumor - A308-A309U19


title: drerio_J15

description: drerio.loom


title: drerio_J14

description: drerio.loom


title: HNC_T_MMAC_D4_3

source_name: MMAC from primary head and neck tumor - A308-A309U18


title: drerio_J13

description: drerio.loom


title: HNC_T_CD14posDC_D4_3

source_name: CD14+ DC from primary head and neck tumor - A308-A309U17


title: drerio_J12

description: drerio.loom


title: drerio_J11

description: drerio.loom


title: HNC_T_BDCA1posDC_D4_3

source_name: BDCA1+ DC from primary head and neck tumor - A308-A309U16


title: drerio_J10

description: drerio.loom


title: drerio_J1

description: drerio.loom


title: drerio_I9

description: drerio.loom


title: drerio_I8

description: drerio.loom


title: drerio_I7

description: drerio.loom


title: nmPos

first: Shuo

address: 94 Weijin Road

institute: Nankai University

data_processing:
1.Eliminate the low-quality reads,adaptors and other contaminants to get clean reads
2.Summarize the length distribution of the clean tags, common and specific sequences between samples
3.Annotate the clean tags into different categories
4.Predict the novel miRNA and function annotation of known miRNAs
5.Comparison the expression of miRNA in different groups
Supplementary_files_format_and_content: predicted_miRNA.txt

source_name: Non-metastasis Post-operation

extract_protocol:
Exosomal miRNA was extracted using RNeasy mini spin columns (QIAGEN) following the manufacturer’s recommendations. Small RNA samples were tested the integrity and concentration using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pooled male and female

tag: subject status

value: Non-metastasis Post-operation

value: Plasma

tag: sample type

value: exosomes

tag: molecule type

value: Small RNAs


title: drerio_I6

description: drerio.loom


title: HNC_T_pDC_D4_3

source_name: pDC from primary head and neck tumor - A308-A309U15

value: untreated


title: nmPre

source_name: Non-metastasis Pre-operation

value: Non-metastasis Pre-operation


title: drerio_I5

description: drerio.loom

value: spinal cord


title: drerio_I4

description: drerio.loom


title: WT_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 splenic B lymphocytes

hyb_protocol: Hybridization and washing were done using Agilent Gene Expression Hybridization Kit (Agilent, 5188-5242) and Agilent Wash Buffer Kit (Agilent, 5188-5327) according to manufacturer’s protocols (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.5, May 2012).

scan_protocol: Slides were scanned (after washing) on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 4x 44k array slides (Profile: AgilentHD_GX1col, resolution: 5 μm).

data_processing: The scanned images were analyzed with Feature Extraction Software using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Further data processing was done using GeneSpring GX Software v12.0.  The data processed with the GeneSpring GX Software v12.0 are not available. The sample data tables contain the gProcessed signal.

source_name: WT Bcell after 6 days of malaria infection replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to manufacturer’s instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.5, May 2012), followed by RNAeasy column purification (Qiagen, 4106).

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

extract_protocol: RNA was extracted by using the miRMeasy kit (Qiagen, 217004), following the manufacturer’s protocol. Additional on-column DNase digestion was performed. The total RNA was quatified by a NanoDrop-1000 spectrophotometer and RNA quality was established by an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Resting conventional B lymphocytes were purified from the spleens of infected WT and miR-155 KO mice on the 0, 3rd and 6th day of P. berghei ANKA infection according to the manufacture’s recommended method with the BD IMag mouse B lymphocyte enrichment kit (BD Biosciences Pharmingen).

value: spleen

value: Splenic B lymphocytes

value: female

value: post natal week 8

tag: genotype/variation

value: WT


title: KO_2_rep2

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

value: miR-155 KO


title: KO_1_rep1

source_name: miR-155 KO Bcell after 3 days of malaria infection replicate1


title: drerio_I3

description: drerio.loom

source_name: Zebrafish spinal cord


title: WT_2_rep1

source_name: WT Bcell after 6 days of malaria infection replicate1


title: WT_1_rep2

source_name: WT Bcell after 3 days of malaria infection replicate2


title: KO_1_rep2

source_name: miR-155 KO Bcell after 3 days of malaria infection replicate2


title: mPre

source_name: Metastasis Pre-operation

value: Metastasis Pre-operation


title: KO_2_rep1

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


title: drerio_I23

description: drerio.loom


title: KO_0_rep2

source_name: miR-155 KO Bcell without infection replicate2


title: drerio_I22

description: drerio.loom


title: KO_0_rep1

source_name: miR-155 KO Bcell without infection replicate1


title: Health

source_name: Health

value: Healthy


title: WT_1_rep1

source_name: WT Bcell after 3 days of malaria infection replicate1


title: drerio_I21

description: drerio.loom


title: WT_0_rep2

source_name: WT Bcell without infection replicate2


title: WT_0_rep1

source_name: WT Bcell without infection replicate1


title: NC-3

city: Nanjing

first: Ling

last: Zhang

address: Hankou road

institute: Nanjing University

description:
NC-3 is z0920-4
piRNA

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, then mapped to GENCODE,GRCH38 whole genome using bowtie v1.1.2
The sequences that correspond to known piRNAs were determined by perfect sequence matching to the pirnabank database (http://pirnabank.ibab.ac.in/).
Genome_build: GRCH38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: matched normal adjacent prostate tissues

extract_protocol:
Total RNA was extracted from 3 pairs of tumor tissues and their adjacent normal tissues using Trizol reagent (Invitrogen, Shanghai, China) according to the manufacturer’s instructions. After purification of RNA molecules smaller than 45 nt by polyacrylamide gel electrophoresis
RNA libraries were prepared for sequencing using standard Illumina protocols


title: drerio_I2

description: drerio.loom


title: mPos

source_name: Metastasis Post-operation

value: Metastasis Post-operation


title: drerio_I19

description: drerio.loom


title: drerio_I18

description: drerio.loom


title: drerio_I24

description: drerio.loom


title: NC-2

description:
NC-2 is z0920-3
piRNA

value: matched normal adjacent prostate tissues


title: drerio_I16

description: drerio.loom


title: NC-1

description:
NC-1 is z0903-2
piRNA


title: Pca-3

description:
PCa-3 is z0903-1
piRNA

source_name: prostate cancer tissue

value: prostate cancer tissue


title: drerio_I17

description: drerio.loom


title: 72 h_vehicle_mouse kidney, biological rep2

city: Yonago

first: Fumiko

last: Obata

state: Tottori

address: 86 Nichicho

department: Bacteriology

institute: Tottori University

description: Gene expression data from 72 h after PBS injection, 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

source_name: 72 h after PBS (vehicle) injection, mouse kidney

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 PBS-injected mouse

value: C57BL/6 (wild type)

tag: weight


title: 72 h_vehicle_mouse kidney, biological rep3


title: drerio_I14

description: drerio.loom


title: drerio_I15

description: drerio.loom


title: drerio_I13

description: drerio.loom


title: drerio_I20

description: drerio.loom


title: Pca-2

description:
PCa-2 is z0920-1
piRNA


title: 72 h_vehicle_mouse kidney, biological rep1


title: drerio_I11

description: drerio.loom


title: Pca-1

description:
PCa-1 is z1018-1
piRNA


title: drerio_I10

description: drerio.loom


title: drerio_I1

description: drerio.loom


title: V1012

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"

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: non-Pseudomonas aeruginosa colonization

tag: disease state

value: bronchiectasis patients in stable stage

tag: Sex

value: male


title: drerio_H9

description: drerio.loom

source_name: Zebrafish spinal cord

tag: tissue

value: spinal cord


title: 72 h_Stx2_mouse kidney, biological rep1

description: Gene expression data from 72 h after Stx2 injection, mouse kidney

source_name: 72 h after Stx2 injection, mouse kidney

value: kidney from Stx2-injected mouse

tag: genotype


title: 72 h_Stx2_mouse kidney, biological rep3


title: 72 h_Stx2_mouse kidney, biological rep2


title: 48 h_Stx2_mouse kidney, biological rep3

description: Gene expression data from 48 h after Stx2 injection, mouse kidney

source_name: 48 h after Stx2 injection, mouse kidney


title: V297

value: female


title: 48 h_Stx2_mouse kidney, biological rep2


title: H3.3-G34R rep 5

city: Ann Arbor

first: Margaret

last: Hartlage

state: MI

address: 1150 W Medical Center Dr.

department: Neurosurgery

institute: University of Michigan

data_processing:
Indexing using kallisto version 0.45.1 on Ensembl v96 Homo sapeins transcriptome.
Quantification using kallisto version 0.45.1 with 100 bootstrap samples.
Estimated counts used for further analysis.
Genome_build: Ensembl v96 Mus Musculus
Supplementary_files_format_and_content: counts (gene x sample)

source_name: Mouse neurosphere cells derived from a Sleeping beauty-based genetically engenieered high grade glioma (HGG) mouse model encoding for H3.3-G34R

growth_protocol: Primary glioma neurospheres (NS) (H3.3-G34R NS and H3.3-WT NS) were generated from our SB transposase HGG model. Briefly, tumors were harvested at the time of euthanasia by transcardial perfusion with Tyrode’s solution. The brains were excised and the tumors were identified by GFP or by GFP/Katushka expression under an epi-fluorescence stereo microscopes at the time of resection. The tumor mass was dissociated using non-enzymatic cell dissociation buffer, filtered through a 70 μm strainer and maintained in neurosphere cell medium (DMEM/F12 with L-Glutamine, B-27 supplement, N-2 supplement, penicillin-streptomycin, and Normocin 1X) at 37 °C, 5% CO2. hFGF and hEGF were added twice weekly at 1 μL (20 ng/μL each stock, 1000x formulation) per 1 mL medium. Primary cell cultures used in this study were generated from female mice.

extract_protocol:
RNeasy Plus Mini Kit (Qiagen, Cat #74134)
RNA quality was assessed using a TapeStation (Agilent Technologies) following the manufacturer's recommended protocol. RNA sequencing libraries were prepared according to the TruSeq Stranded Total RNA Human/Mouse/Rat (Illumina) and were sequenced on the HiSeq 2000 platform.

treatment_protocol: For mouse pHGG cells, 5 cell cultures derived from 5 different H3.3-Wt de novo generated tumors, and 5 cell cultures derived from 5 different H3.3-Wt de novo generated tumors were used.Biological replicates were grown in T25 flasks, and 2 million cells were used for RNA purification. RNA extraction was performed using RNeasy Plus Mini Kit (Qiagen, Cat #74134) following the manufacturer instructions.

value: brain tumor cells

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX + overexpression of mutated histone H3.3 G34R


title: drerio_H6

description: drerio.loom

tag: strain


title: drerio_K20

description: drerio.loom


title: 48 h_Stx2_mouse kidney, biological rep1


title: drerio_H7

description: drerio.loom


title: V292


title: H3.3-G34R rep 4


title: V294

value: Pseudomonas aeruginosa colonization


title: V289


title: H3.3-G34R rep 3


title: drerio_H4

description: drerio.loom


title: drerio_H5

description: drerio.loom


title: V288


title: H3.3-G34R rep 2


title: 12 h_Stx2_mouse kidney, biological rep3

description: Gene expression data from 12 h after Stx2 injection, mouse kidney

source_name: 12 h after Stx2 injection, mouse kidney


title: drerio_H3

description: drerio.loom


title: H3.3-G34R rep 1


title: 24 h_Stx2_mouse kidney, biological rep1

description: Gene expression data from 24 h after Stx2 injection, mouse kidney

source_name: 24 h after Stx2 injection, mouse kidney


title: drerio_H8

description: drerio.loom


title: V286


title: drerio_H24

description: drerio.loom


title: H3.3-Wt rep 5

source_name: Mouse neurosphere cells derived from a Sleeping beauty-based genetically engenieered high grade glioma (HGG) mouse model encoding for H3.3-WT

value: overexpression of NRASG12V + short hairpin for TP53 + short hairpin for ATRX


title: drerio_H23

description: drerio.loom


title: drerio_H22

description: drerio.loom


title: V284


title: H3.3-Wt rep 4


title: V279


title: V280


title: 24 h_Stx2_mouse kidney, biological rep2


title: 24 h_Stx2_mouse kidney, biological rep3


title: 8 h_Stx2_mouse kidney, biological rep3

description: Gene expression data from 8 h after Stx2 injection, mouse kidney

source_name: 8 h after Stx2 injection, mouse kidney


title: 12 h_Stx2_mouse kidney, biological rep2


title: drerio_I12

description: drerio.loom


title: H3.3-Wt rep 1


title: H3.3-Wt rep 2


title: drerio_H20

description: drerio.loom


title: drerio_H2

description: drerio.loom


title: V275


title: 8 h_Stx2_mouse kidney, biological rep1


title: ESC-WT-rep3

city: Guangzhou

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

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, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

source_name: Wild Type ESCs

growth_protocol: Cells were culture in mES+2i medium.

extract_protocol:
Cells were collected, and RNA was harvested using Trizol reagent. VAHTS® Stranded mRNA-seq Library Prep Kit for Illumina V2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: E3.5 embryo

value: Wild Type

tag: cell type

value: embryonic stem cells


title: V273

tag: age


title: drerio_H19

description: drerio.loom


title: H3.3-Wt rep 3


title: ESC-WT-rep2


title: V270


title: ESC-WT-rep1


title: V268


title: drerio_H17

description: drerio.loom


title: drerio_H18

description: drerio.loom


title: V266


title: drerio_H21

description: drerio.loom


title: V278


title: drerio_H16

description: drerio.loom


title: ESC-KO-Hoxd12-rep3

source_name: Hoxd12-/- ESCs


title: 8 h_Stx2_mouse kidney, biological rep2


title: drerio_H15

description: drerio.loom


title: ESC-KO-Hoxd12-rep2


title: V265


title: ESC-KO-Hoxd12-rep1


title: V264


title: 4 h_Stx2_mouse kidney, biological rep3

description: Gene expression data from 4 h after Stx2 injection, mouse kidney

source_name: 4 h after Stx2 injection, mouse kidney


title: drerio_H14

description: drerio.loom


title: V263


title: 6 h_Stx2_mouse kidney, biological rep1

description: Gene expression data from 6 h after Stx2 injection, mouse kidney

source_name: 6 h after Stx2 injection, mouse kidney


title: 12 h_Stx2_mouse kidney, biological rep1


title: drerio_H13

description: drerio.loom


title: 4 h_Stx2_mouse kidney, biological rep2


title: 6 h_Stx2_mouse kidney, biological rep3


title: 4 h_Stx2_mouse kidney, biological rep1


title: 2 h_Stx2_mouse kidney, biological rep3

description: Gene expression data from 2 h after Stx2 injection, mouse kidney

source_name: 2 h after Stx2 injection, mouse kidney


title: drerio_H12

description: drerio.loom


title: V259


title: 2 h_Stx2_mouse kidney, biological rep2


title: 6 h_Stx2_mouse kidney, biological rep2


title: drerio_H11

description: drerio.loom


title: drerio_H10

description: drerio.loom


title: Stationary phase (14h), replicate 3

first: Dmitry

last: Sutormin

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Total RNA was extracted and sequenced from E. coli DY330 culture growing in LB medium for 14 h after the starter culture inoculation in a fresh LB (OD600~10, stationary phase culture). Total RNA was extracted from 2 mL of culture using ExtractRNA reagent (Evrogen). RNA sample was treated with DNAse I and sequencing library was prepared without rRNA depletion using NEBNext Ultra II Directional RNA Library kit (NEB). Library was sequenced using HiSeq4000 (Illumina, USA) with 50 bp single-end reads protocol. Biological replicate 3.

data_processing:
Raw reads were trimmed and filtered using Trimmomatic (ILLUMINACLIP:2:30:10 LEADING:0 TRAILING:0 SLIDINGWINDOW:4:0 MINLEN:30).
Processed reads were aligned to the E. coli w3110 MuSGS genome with BWA MEM (default settings).
Resulting sam files were converted to bam and sorted using samtools.
FPKM values for transcription units annotation were calculated using FPKM_count.py (RSeQC v3.0.0) with read mapping quality -q 25.
Sequencing coverage depth was calculated from bam file using samtools and converted to wig format using custom script.
Genome_build: NC_007779.1_w3110_Mu (custom build, fasta and genome annotation are provided as supplementary files)
Supplementary_files_format_and_content: wig files with sequencing coverage depth.
Supplementary_files_format_and_content: tab-delimeted files with FPKM values assigned to annotated transcription units.

organism: Escherichia coli

source_name: Escherichia coli DY330 topA-SPA

growth_protocol: For starters culture, a single colony of E. coli DY330 topA-SPA was inoculated in 5 mL of LB supplemented with 50 mkg/ml kanamycin. The starter was grown overnight at 37C with shaking 180 rpm. 0.5 mL of the starter culture was inoculated in 50 mL of fresh LB and the culture was cultivated at 37C with shaking 180 rpm. 2 mL aliquot of the culture was collected after 14 h (OD600~10, stationary phase culture) upon the starter inoculation. Cells were harvested by centrifugation at 3000 g, 10 min, 4C. Cells pellets were snap-freezed in liquid nitrogen and stored at -80C until further processing.

extract_protocol:
Total RNA was extracted using ExtractRNA reagent (Evrogen) according to the manufacturer's protocol. RNA sample was treated with DNAse I (ThermoFisher Scientific) and purified with RNAClean XP beads (Beckman Coulter).
Sequencing libraries were prepared without rRNA depletion using NEBNext Ultra II Directional RNA Library kit (NEB) with the following modifications: 10 minutes of fragmentation instead of 15 and 10 PCR cycles. Then they were quantified using qPCR, pooled in equal amounts, diluted to 2 nM and sequenced on HiSeq4000 instrument (Illumina, USA) with 50 bp single-end reads protocol. Libraries preparation and sequencing were performed at Skoltech Sequencing Core Facilities.

tag: growth phase

value: Stationary phase

tag: time-point

tag: optical density at 600 nm

value: DY330 topA-SPA


title: V256


title: drerio_H1

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.

tag: developmental stage


title: V262


title: V255


title: Stationary phase (14h), replicate 2

description: Total RNA was extracted and sequenced from E. coli DY330 culture growing in LB medium for 14 h after the starter culture inoculation in a fresh LB (OD600~10, stationary phase culture). Total RNA was extracted from 2 mL of culture using ExtractRNA reagent (Evrogen). RNA sample was treated with DNAse I and sequencing library was prepared without rRNA depletion using NEBNext Ultra II Directional RNA Library kit (NEB). Library was sequenced using HiSeq4000 (Illumina, USA) with 50 bp single-end reads protocol. Biological replicate 2.


title: V254


title: drerio_G9

description: drerio.loom


title: MII oocytes, TubA rep5

city: Changchun

first: Liyan

last: Sui

address: Xinzhu street 1977

institute: Jilin University

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, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

source_name: oocytes

growth_protocol: Fully grown, germinal vesicle (GV)-intact oocytes were collected using an 18-chanel needle from ovaries, and placed in M2 medium (Sigma, M7167). After washing three times, the oocytes were cultured in M16 medium (Sigma, M7292) under liquid paraffin oil at 37 °C in an atmosphere of 5% CO2 incubator for in vitro maturation.  metaphase II (MII) oocytes were collected after further 16 h culture for subsequent analysis.

extract_protocol:
Single cell sample was amplified directly with the Smart-Seq2 method according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 0.1μg/mL TubA were used to treat GV oocytes for 16hours

value: ICR

value: ovary

value: 6-8 weeks old

value: oocytes

tag: agent

value: TubA


title: drerio_G8

first: Henrik

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

institute: Uppsala University

description: drerio.loom

value: spinal cord


title: MII oocytes, TubA rep4


title: Stationary phase (14h), replicate 1

description: Total RNA was extracted and sequenced from E. coli DY330 culture growing in LB medium for 14 h after the starter culture inoculation in a fresh LB (OD600~10, stationary phase culture). Total RNA was extracted from 2 mL of culture using ExtractRNA reagent (Evrogen). RNA sample was treated with DNAse I and sequencing library was prepared without rRNA depletion using NEBNext Ultra II Directional RNA Library kit (NEB). Library was sequenced using HiSeq4000 (Illumina, USA) with 50 bp single-end reads protocol. Biological replicate 1.


title: Exponential-to-stationary phase transition (6h), replicate 3

description: Total RNA was extracted and sequenced from E. coli DY330 culture growing in LB medium for 6 h after the starter culture inoculation in a fresh LB (OD600~6, exponential-to-stationary phase transition culture). Total RNA was extracted from 2 mL of culture using ExtractRNA reagent (Evrogen). RNA sample was treated with DNAse I and sequencing library was prepared without rRNA depletion using NEBNext Ultra II Directional RNA Library kit (NEB). Library was sequenced using HiSeq4000 (Illumina, USA) with 50 bp single-end reads protocol. Biological replicate 3.

growth_protocol: For starter culture, a single colony of E. coli DY330 topA-SPA was inoculated in 5 mL of LB supplemented with 50 mkg/ml kanamycin. The starter was grown overnight at 37C with shaking 180 rpm. 0.5 mL of the starter culture was inoculated in 50 mL of fresh LB and the culture was cultivated at 37C with shaking 180 rpm. 2 mL aliquote of the culture was collected after 6 h (OD600~6, exponential-to-stationary phase transition culture) upon the starter inoculation. Cells were harvested by centrifugation at 3000 g, 10 min, 4C. Cells pellets were snap-freezed in liquid nitrogen and stored at -80C until further processing.

value: 6 h


title: V250

value: sputum

value: bronchiectasis patients in stable stage

value: female


title: V253

value: Pseudomonas aeruginosa colonization

value: male


title: drerio_G7

description: drerio.loom


title: Exponential-to-stationary phase transition (6h), replicate 2

description: Total RNA was extracted and sequenced from E. coli DY330 culture growing in LB medium for 6 h after the starter culture inoculation in a fresh LB (OD600~6, exponential-to-stationary phase transition culture). Total RNA was extracted from 2 mL of culture using ExtractRNA reagent (Evrogen). RNA sample was treated with DNAse I and sequencing library was prepared without rRNA depletion using NEBNext Ultra II Directional RNA Library kit (NEB). Library was sequenced using HiSeq4000 (Illumina, USA) with 50 bp single-end reads protocol. Biological replicate 2.


title: drerio_G6

description: drerio.loom


title: MII oocytes, TubA rep3


title: V248

value: non-Pseudomonas aeruginosa colonization


title: MII oocytes, TubA rep2


title: 2 h_Stx2_mouse kidney, biological rep1

value: kidney from Stx2-injected mouse

value: C57BL/6 (wild type)


title: drerio_G5

description: drerio.loom


title: Exponential-to-stationary phase transition (6h), replicate 1

description: Total RNA was extracted and sequenced from E. coli DY330 culture growing in LB medium for 6 h after the starter culture inoculation in a fresh LB (OD600~6, exponential-to-stationary phase transition culture). Total RNA was extracted from 2 mL of culture using ExtractRNA reagent (Evrogen). RNA sample was treated with DNAse I and sequencing library was prepared without rRNA depletion using NEBNext Ultra II Directional RNA Library kit (NEB). Library was sequenced using HiSeq4000 (Illumina, USA) with 50 bp single-end reads protocol. Biological replicate 1.


title: V243


title: Exponential phase (2h), replicate 3

description: Total RNA was extracted and sequenced from E. coli DY330 culture growing in LB medium for 2 h after the starter culture inoculation in a fresh LB (OD600~0.6, exponential phase culture). Total RNA was extracted from 2 mL of culture using ExtractRNA reagent (Evrogen). RNA sample was treated with DNAse I and sequencing library was prepared without rRNA depletion using NEBNext Ultra II Directional RNA Library kit (NEB). Library was sequenced using HiSeq4000 (Illumina, USA) with 50 bp single-end reads protocol. Biological replicate 3.

growth_protocol: For starter culture, a single colony of E. coli DY330 topA-SPA was inoculated in 5 mL of LB supplemented with 50 mkg/ml kanamycin. The starter was grown overnight at 37C with shaking 180 rpm. 0.5 mL of the starter culture was inoculated in 50 mL of fresh LB and the culture was cultivated at 37C with shaking 180 rpm. 2 mL aliquot of the culture was collected after 2 h (OD600~0.6, exponential phase culture) upon the starter inoculation. Cells were harvested by centrifugation at 3000 g, 10 min, 4C. Cells pellets were snap-freezed in liquid nitrogen and stored at -80C until further processing.

value: Exponential phase

value: 2 h


title: V238


title: drerio_G4

description: drerio.loom


title: Exponential phase (2h), replicate 2

description: Total RNA was extracted and sequenced from E. coli DY330 culture growing in LB medium for 2 h after the starter culture inoculation in a fresh LB (OD600~0.6, exponential phase culture). Total RNA was extracted from 2 mL of culture using ExtractRNA reagent (Evrogen). RNA sample was treated with DNAse I and sequencing library was prepared without rRNA depletion using NEBNext Ultra II Directional RNA Library kit (NEB). Library was sequenced using HiSeq4000 (Illumina, USA) with 50 bp single-end reads protocol. Biological replicate 2.

value: DY330 topA-SPA


title: MII oocytes, control rep5

value: ICR

value: ovary

value: control


title: 0 h (no Stx2) mouse kidney, biological rep2

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

value: kidney from naive mouse


title: MII oocytes, TubA rep1

value: 6-8 weeks old

value: oocytes

value: TubA


title: drerio_G3

description: drerio.loom

value: spinal cord


title: 0 h (no Stx2) mouse kidney, biological rep1

source_name: 0 h (not treated with Stx2) mouse kidney


title: Exponential phase (2h), replicate 1

description: Total RNA was extracted and sequenced from E. coli DY330 culture growing in LB medium for 2 h after the starter culture inoculation in a fresh LB (OD600~0.6, exponential phase culture). Total RNA was extracted from 2 mL of culture using ExtractRNA reagent (Evrogen). RNA sample was treated with DNAse I and sequencing library was prepared without rRNA depletion using NEBNext Ultra II Directional RNA Library kit (NEB). Library was sequenced using HiSeq4000 (Illumina, USA) with 50 bp single-end reads protocol. Biological replicate 1.


title: V237

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

source_name: sputum

value: sputum

value: bronchiectasis patients in stable stage

value: female


title: V236

value: Pseudomonas aeruginosa colonization


title: MII oocytes, control rep4


title: drerio_G24

description: drerio.loom

source_name: Zebrafish spinal cord


title: MII oocytes, control rep3


title: drerio_G23

description: drerio.loom


title: Root sample_NPK_7_9

city: Taian

first: Nana

last: Ma

address: No 61 Daizong Street No 61

institute: Shandong Agricultural University

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

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

value: root

tag: treatment

value: normal N, P, and K level


title: V235

value: male


title: Root sample_NPK_4_6


title: drerio_G22

description: drerio.loom


title: MII oocytes, control rep1


title: Root sample_NPK_1_3


title: V234


title: MII oocytes, control rep2


title: drerio_G21

description: drerio.loom


title: V227

value: non-Pseudomonas aeruginosa colonization


title: V226


title: Root sample_P_4_6

value: phosphorus deficiency


title: V224


title: drerio_G2

description: drerio.loom


title: Root sample_P_1_3