title: WT_3

city: New York

first: Erika

last: Bach

state: NY

department: Biochemistry and Molecular Pharmacology

institute: NYU Grossman School of Medicine

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina Bcl2FastQ software
Sequencing reads were mapped to the reference genome (dm6/BDGP6) using the splice-aware STAR aligner
PCR duplicates were removed using the Picard toolkit
HTSeq package was used to generate counts for each gene based on how many aligned reads overlap its exon
The DESeq2 package in the R statistical programming environment was utilized to differential expression using negative binomial generalized linear models
The mean read insert sizes and their standard deviations were calculated using Picard tools
Genome_build: dm6/BDGP6
Supplementary_files_format_and_content: CSV file containing normalized matrix of read counts which includes values for all features and all samples

source_name: adult testes

growth_protocol: We crossed tj-Gal4,UAS-GFPnls/CyO flies to UAS-GFPnls flies (for WT samples), to UAS-Ci5Ncm5, UAS-Ci5m30/TM6B, Tb flies (for Ci samples), to UAS-Upd/CyO; UAS-GFP flies (for Upd samples). We crossed tj-Gal4,UAS-GFPnls/CyO; UAS-dcr2 flies to UAS-Chinmo RNAi flies (for Chinmo RNAi samples). We crossed tj-Gal4,UAS-GFPnls/CyO; tub-Gal80TS flies to UAS-5’UTR-chinmo-3’UTR/CyO flies (for Chinmo samples). We dissect testes from adult males at the indicated timepoint for each genotype. For each sample, we dissected between 50-100 flies and obtained between 100-200 testes.

extract_protocol:
Testes were dissociated by enzymatic digestion and vigorous agitation. GFP-expressing somatic cells were purified by FACS using a Sony SY3200 highly automated parallel sorting (HAPS) cell sorter into 750 µL TRIzol LS (Thermo Fisher). RNA was isolated and precipitated according to manufacturer’s instructions. RNA extracts were cleaned using RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity were determined using the Agilent 1200 Bioanalyzer.
The RNA sequencing was performed by the Genome Technology Center at the NYU Langone Medical Center using Illumina HiSeq2500 Paired-End 50 Cycle Flow Cell.

tag: expression domain

value: FACS-sorted cells from the tj-Gal4 expression domain

tag: developmental stage

value: 10 days after eclosion

value: w/Y; tj-Gal4,UAS-GFPnls/UAS-GFPnls; +/+


title: WT_2

status: Public on Mar 28 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Drosophila melanogaster

tag: genotype


title: H1_0051

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

description: Human skin cell

data_processing:
The sequencing fregments were aligned to the GRCh38 genome assembly using STAR.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include "Read counts" and RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Human skin

extract_protocol:
Libraries generated for sequencing was carried out on Illumina sequencer based on Smart-seq2 protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Male

tag: age

tag: wound type

value: Skin


title: H1_0047

description: Human skin cell


title: H1_0045

description: Human skin cell


title: H1_0044

description: Human skin cell


title: H1_0061

description: Human skin cell


title: WT_1


title: Chinmo_RNAi_3

value: 2 or 3 days after eclosion

value: w/Y; tj-Gal4,UAS-GFPnls/+; UAS-chinmoRNAi (HMS00036)/UAS-dcr2


title: H1_0042

description: Human skin cell


title: H1_0041

description: Human skin cell


title: H1_0054

description: Human skin cell


title: Chinmo_RNAi_2


title: Chinmo_RNAi_1


title: Upd_3


title: Upd_1


title: H1_0040

description: Human skin cell


title: Ci_3

value: w/Y; tj-Gal4,UAS-GFPnls/+; UAS-Ci5Ncm5, UAS-Ci5m30/+


title: Ci_1


title: H1_0039

description: Human skin cell


title: H1_0037

description: Human skin cell


title: Chinmo_3


title: Ci_2


title: H1_0035

description: Human skin cell


title: H1_0036

description: Human skin cell


title: Chinmo_2


title: H1_0034

description: Human skin cell


title: Chinmo_1


title: H1_0102

description: Human skin cell

value: Acute wound


title: H1_0043

description: Human skin cell


title: H1_0031

description: Human skin cell


title: H1_0032

description: Human skin cell


title: H1_0030

description: Human skin cell


title: starrseq-lncap-etoh-2

city: Vancouver

first: Nathan

middle: A

last: Lack

state: BC

address: 2260 Oak St

department: Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

description: STAR Seq etoh sample 2

data_processing:
Library strategy: STARRseq
starrseq files were mapped with bwa mem (version 0.7.17)
reads with insertion/deletions and mapq 60 were removed from the bam files.
bigwig files were generated with bamCoverage with following arguments
--samFlagInclude 64 --extendReads --normalizeUsing RPKM --blacklist (ENCODE:ENCFF001TDO.bed)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig - starrseq intensity values.

source_name: Prostate Cancer Immortilized Cell line

growth_protocol: LNCaP cells were routinely grown in RPMI 1640 media with 1% Penicillin-Streptomycin and 10% FBS. After transfection and overnight recovery, the culture media was changed to RPMI 1640 media supplemented with 5% CSS and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNA was extracted and the mRNA was isolated using the Oligo (dT)25 Dynabeads. The isolated mRNA samples were synthesized into cDNA using the the gene-specific primer, and were PCR-amplified with the junction PCR primers. The ARBS STARRseq capture library was separately PCR-amplified with DNA specific junction PCR primers
ARBS STARRseq library was generated for sequencing by PCR amplification using standard Illumina protocols.

treatment_protocol: Approximately 72 hours after transfection, LNCaP cells transfected with ARBS STARRseq capture library were treated with 10nM DHT or 100% EtOH for 4 hours .

tag: tissue

value: Prostate Cancer Immortilized Cell line

tag: cell line

value: LNCaP

tag: treatment

value: ETOH

tag: dht concentrations and etoh %


title: Upd_2


title: H1_0028

description: Human skin cell


title: starrseq-lncap-etoh-1

description: STAR Seq etoh sample 1


title: H1_0038

description: Human skin cell


title: H1_0027

description: Human skin cell


title: H1_0029

description: Human skin cell


title: starrseq-lncap-dht-2

description: STAR Seq dht sample 2

value: DHT


title: H1_0026

description: Human skin cell


title: starrseq-lncap-dht-1

description: STAR Seq dht sample 1


title: H1_0025

description: Human skin cell


title: Methyl-seq_iN_CONTROL3-2

city: Palo Alto

first: Siming

last: Zhang

address: 3165 Porter Drive

institute: Stanford University

library_source: genomic

data_processing:
RNA-Seq data: Cutadapt (Version 1.8.1) was used to trim Illumina TruSeq adapters and low-quality ends from the raw reads. Tophat (Version 2.0.13) was used to align the trimmed reads to the RefSeq transcriptome (GRCh38.p10). DESeq2 (Version 1.12.4) was used to perform differential expression analysis between cell types as well as between patients and controls within each cell type.
Methyl-seq data: Cutadapt (Version 1.8.1) was used to trim Illumina adapters and low-quality ends from the raw reads. The trimmed reads were mapped to human RefSeq genome (GRCh38.p10) using Bismark (Version 0.16.3). Duplicates were removed by the deduplicate_bismark script in Bismark. Methylation ratios for each CpG was extracted by the bismark_methylation_extractor script in Bismark. Differentially methylated regions (DMRs) were identified between patients and controls by metilene (Version 0.2-6).
ATAC-seq data: Bowtie2 (Version 2.2.6) was used to map reads to RefSeq genome (GRCh38.p10). Reads with low quality (MAPQ < 30) or mapping to mitochondrial DNA were filtered out. Peaks for each sample were called using MACS2 (Version 2.1.1). Diffbind (Version 2.0.9) was used to normalize peak reads from each sample to the total number of aligned reads and perform differential peak analysis.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: RNA-Seq data: gene name, read count
Supplementary_files_format_and_content: Methylation data: chromosome, CpG position, CpG methylation ratio
Supplementary_files_format_and_content: ATAC-seq data: chromosome, start position, end poisition, peak width, strand, mean log reads across all samples, mean log reads across first group, mean log reads across second group, fold difference between first and second group, p-value, FDR, read count

molecule: genomic DNA

source_name: induced neuron

growth_protocol: iPSCs were grown in mTeSR1 media. To generate iNs, cells were infected on day 1 with the lentivirus vectors FUW-rtTA and pTet-O-Ngn2-puro. On day 2, the culture medium was replaced with DMEM/F12 mixed with N2 supplement, penicillin-streptomycin, and doxycycline to induce TetO expression. Starting on day 3, puromycin was added to the media to select for cells expressing Ngn2. On day 6, early stage induced neurons (iNs) were collected for downstream analysis.

extract_protocol:
Genomic DNA was extracted using the Quick-DNA Universal Ki (Zymo Research).  Total RNA was extracted using the Direct-zol RNA MiniPrep Kit (Zymo Research). For ATAC-seq, 50,000 cells were lysed, transposed, and PCR amplified as previously described (Buenrostro et al, 2013).
For RNA-seq, library construction was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s instructions. Libraries were sequenced on the Illumina NextSeq 500 using 2x150 bp paired-end runs. For Methyl-seq, libraries were prepared using the SeqCap Epi System from Roche, which captures 5.5 million CpGs in the human genome. Libraries were multiplexed and sequenced on the Illumina HiSeq 4000 using 2x150 bp paired-end runs and 30% PhiX spike-in. For ATAC-seq, libraries were prepared using the Illumina Nextera DNA kit and multiplexed and sequenced on the Illumina NextSeq 500 using 2x75 bp paired-end runs and 1% PhiX spike-in.
RNA-seq, Capture-base Bisulfite Sequencing, ATAC-seq

tag: cell type

value: induced neuron

value: control


title: OSW rep4

city: Graz

first: Leila

last: Taher

address: Stremayrgasse 16/I

country: Austria

institute: Graz University of Technology

data_processing:
Bases were called with Illumina Casava bcl2fastq (version 2.15.0.4).
The reads were mapped to the canine genome (Broad CanFam3.1/canFam3, Sep. 2011) using BWA. Duplicate reads and low quality mappings were removed using Picard (http://broadinstitute.github.io/picard) and samtools. Raw read counts for each of the Ensembl (release 815, fpt://ftp.ensembl.org/pub/releas-815/gtf/canis_familiaris) genes were obtained using the Python package HTSeq (version 0.6.1). Quality control was assessed using FastQC.
Genome_build: CanFam 3.1
Supplementary_files_format_and_content: Tab-delimited text files that include counts for each Ensembl gene.

organism: Canis lupus familiaris

source_name: Cell line derived from canine T-cell lymphoma

extract_protocol:
RNA was isolated from primary lymphoma samples and lymphoid cell lines using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: classification

value: Classified by flow cytometry as T cell lymphoma derived


title: OSW rep2


title: OSW rep3


title: H1_0023

description: Human skin cell


title: H1_0024

description: Human skin cell


title: Methyl-seq_iN_CONTROL3-1


title: OSW rep1


title: starrseq-lncap-lib

description: STAR Seq library sample

value: NO TREATMENT


title: control rep4


title: H1_0022

description: Human skin cell


title: H1_0033

description: Human skin cell


title: Methyl-seq_iN_CONTROL2-2


title: B-cell lymphoma rep12

source_name: Primary B-cell lymphoma sample


title: control rep3

source_name: Canine non-neoplastic lymph node


title: starrseq-lncap-etoh-3

description: STAR Seq etoh sample 3


title: Methyl-seq_iN_CONTROL2-1


title: H1_0021

description: Human skin cell


title: B-cell lymphoma rep11

value: Classified by flow cytometry as B cell lymphoma


title: Methyl-seq_iN_CONTROL1-2


title: H1_0020

description: Human skin cell


title: Methyl-seq_iN_CONTROL1-1


title: H1_0019

description: Human skin cell


title: B-cell lymphoma rep6

value: non-neoplastic reference tissue


title: B-cell lymphoma rep9


title: control rep2


title: B-cell lymphoma rep10


title: T-cell rep1

source_name: Primary T-cell lymphoma sample


title: B-cell lymphoma rep5


title: H1_0018

description: Human skin cell


title: B-cell lymphoma rep4


title: Methyl-seq_iN_DEL3-1

value: 15q13.3 deletion


title: Methyl-seq_iN_DEL3-2


title: H1_0017

description: Human skin cell

value: Male


title: Methyl-seq_iN_DEL2-2


title: B-cell lymphoma rep7


title: intestinal lymphoma rep2

source_name: Primary lymphoma sample unclassifiable by flow cytometry


title: B-cell lymphoma rep3

value: Unclassifiable by flow cytometry as B or T cell lymphoma


title: H1_0016

description: Human skin cell

value: Skin


title: intestinal lymphoma rep3


title: Methyl-seq_iN_DEL2-1


title: starrseq-lncap-dht-3

description: STAR Seq dht sample 3


title: Methyl-seq_iN_DEL1-2


title: control rep1

value: Classified by flow cytometry as T cell lymphoma


title: H1_0014

description: Human skin cell


title: B-cell lymphoma rep8


title: B-cell lymphoma rep2


title: CLBL-1 rep5

source_name: Cell line derived from canine Defuse Large B-cell lymphoma


title: GL-1 rep1

source_name: Cell line derived from canine B-cell lymphoma


title: intestinal lymphoma rep1


title: Methyl-seq_iN_DEL1-1


title: Methyl-seq_iPSC_CONTROL3-2

source_name: iPSC

value: iPSC


title: H1_0012

description: Human skin cell


title: H1_0013

description: Human skin cell


title: Methyl-seq_iPSC_CONTROL2-1


title: CLBL-1 rep3

value: Classified by flow cytometry as B cell lymphoma derived


title: CLBL-1 rep4


title: Hetero sample 2 [J-HET2]

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

country: South Korea

institute: Korea University College of Medicine

data_processing:
Transcript abundance was estimated with Salmon(v0.11.2) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.0) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.19.11).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit  (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Guide)

tag: strain

value: Prefrontal cortex

value: Juvenile (P28)

value: Cyfip2 mutant


title: CLBL-1 rep2


title: H1_0009

description: Human skin cell


title: Hetero sample 3 [J-HET3]


title: H1_0015

description: Human skin cell


title: Methyl-seq_iPSC_CONTROL1-2


title: Methyl-seq_iPSC_CONTROL2-2


title: H1_0010

description: Human skin cell


title: Methyl-seq_iPSC_CONTROL3-1


title: H1_0008

description: Human skin cell


title: H1_0011

description: Human skin cell


title: Methyl-seq_iPSC_DEL3-2


title: H1_0006

description: Human skin cell


title: CLBL-1 rep1


title: H1_0007

description: Human skin cell


title: Wild-type sample 2 [J-WT2]

value: WT


title: Methyl-seq_iPSC_CONTROL1-1


title: H1_0067

description: Human skin cell


title: CLBL-1M rep5

source_name: Cell line derived from canine B-cell lymphoma CLBL1 xenograft tumour


title: Wild-type sample 1 [J-WT1]


title: Hetero sample 1 [J-HET1]


title: Methyl-seq_iPSC_DEL3-1


title: CLBL-1M rep4


title: H1_0004

description: Human skin cell


title: Methyl-seq_iPSC_DEL2-2


title: H1_0005

description: Human skin cell


title: B-cell lymphoma rep1


title: Wild-type sample 3 [J-WT3]


title: Wild-type sample 3 [A-WT3]

description:
A-WT3
processed data file: processed_data_DESeq_count.txt

data_processing:
Transcript abundance was estimated with Salmon (v0.11.2) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.0) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.19.11).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: processed_data_DESeq_count.txt: Tab-delimited text file includes normalized read count matrix calculated by using DESeq2.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Guide).

tag: strain/background

tag: genotype/variation

value: Adult (P56)


title: Methyl-seq_iPSC_DEL2-1


title: H1_0003

description: Human skin cell


title: Hetero sample 2 [A-HET2]

description:
A-HET2
Cyfip2 mutant
processed data file: processed_data_DESeq_count.txt

value: CYFIP2 heterozygote


title: Hetero sample 3 [A-HET3]

description:
A-HET3
Cyfip2 mutant
processed data file: processed_data_DESeq_count.txt


title: CLBL-1M rep2


title: CLBL-1M rep1


title: Methyl-seq_iPSC_DEL1-2


title: Wild-type sample 2 [A-WT2]

description:
A-WT2
processed data file: processed_data_DESeq_count.txt


title: CL-1 rep2


title: Methyl-seq_iPSC_DEL1-1


title: H1_0001

description: Human skin cell


title: CL-1 rep1


title: CLBL-1M rep3


title: Wild-type sample 1 [A-WT1]

description:
A-WT1
processed data file: processed_data_DESeq_count.txt


title: PEA2_rep3 (RNA-seq)

status: Public on Mar 27 2021

city: London

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Imperial College London

description: rRNA-depleted

data_processing:
Reads were aligned to hg19 using Bowtie2
Using the featurecounts function from the RSubread package in R, aligned reads were assigned to genes as counts, using a reference file of all known genes on the hg19 genome assembly obtained from the University of California Santa Cruz Genome Browser
RPKM values were calculated using the rpkm function from the limma package
Genome_build: hg19
Supplementary_files_format_and_content: normCounts.txt file contains normalized read-counts for genes

source_name: PEA2 ovarian cancer cells

growth_protocol: All cell lines were grown in RPMI-1640 (Sigma Aldrich) supplemented with glutamine (2 mM) (Gibco) and 10% fetal bovine serum (First Link)

extract_protocol:
Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), according to the manufacturer’s instructions
Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), according to the manufacturer’s instructions

tag: clinical platinum sensitivity

value: resistant


title: Hetero sample 1 [A-HET1]

description:
A-HET1
Cyfip2 mutant
processed data file: processed_data_DESeq_count.txt


title: H1_0002

description: Human skin cell


title: PEA2_rep2 (RNA-seq)

description: rRNA-depleted


title: PEA1_rep3 (RNA-seq)

description: rRNA-depleted

source_name: PEA1 ovarian cancer cells

value: sensitive


title: PEO1_rep1 (RNA-seq)

description: rRNA-depleted

source_name: PEO1 ovarian cancer cells


title: PEA2_rep1 (RNA-seq)

description: rRNA-depleted


title: PEA1_rep2 (RNA-seq)

description: rRNA-depleted


title: PEA1_rep1 (RNA-seq)

description: rRNA-depleted


title: T19

city: Shanghai

first: Jing

last: Yang

state: Shanghai

address: No. 1508 Longhang Road  Jinshan District

department: Pediatrics

country: China

institute: Jinshan Hospital of Fudan University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10/hg19 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: Genome_build: mm10/hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

source_name: liver

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

value: 6 years

value: Zfyve19 mutant


title: PEO4_rep2 (RNA-seq)

description: rRNA-depleted

source_name: PEO4 ovarian cancer cells


title: T65_miRNA

value: 2 years


title: T19_miRNA


title: T35

value: 11 years


title: CP70_rep1 (RNA-seq)

description: rRNA-depleted

source_name: CP70 platinum-resistant endometrial/ovarian cancer cells


title: T65


title: T35_miRNA


title: A2780_rep2 (RNA-seq)

description: rRNA-depleted

source_name: A2780 endometrial/ovarian cancer cells


title: A2780_rep1 (RNA-seq)

description: rRNA-depleted


title: EMLO day 16 scRNA-seq

city: Albany

first: Janet

middle: L

last: Paluh

address: CNSE, Nanofab East, 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

description: Human EMLO Gastruloid

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 4.0.0 mkfastq with Bcl2Fastq 2.20.0.422
Cellranger 4.0.0 Count against mm10 genome to produce count matrix
Cellranger Loupe Browser
Genome_build: GRCh38

source_name: Human iPSC  line H3.3.1 passage

growth_protocol: hiPSC in 2D grown in mTeSR Plus medium were induced by dual SMAD CHIR/FGF then 2D colonies dissociated and ROCK inhibitor added, cells transitioned to orbital shaking culture an maturation

extract_protocol:
Chromimum Single Cell 3' v2 (10x Genomics)
TruSeq Stranded RNA (illumina)

tag: ethnicity

value: Hispanic-Latino self designation

value: elongating multilineage organized (EMLO) gastruloid

value: Day 16


title: PEO4_rep3 (RNA-seq)

description: rRNA-depleted


title: PEO4_rep1 (RNA-seq)

description: rRNA-depleted


title: PEO1_rep3 (RNA-seq)

description: rRNA-depleted


title: PEA1_rep3 (ATAC-seq)

description: Tn5 ATAC-seq

data_processing:
Reads were aligned to the genome using Bowtie2 with the parameters -X2000 and -m1. This ensured that fragments up to 2 kb were allowed to align (-X2000) and that only uniquely aligning reads were collected (-m1)
Reads were filtered against genomic blacklist regions, including mitochondrial sequences, defined by The ENCODE Project Consortium
Duplicate reads were removed using the MarkDuplicates tool from the Picard tools suite (https://github.com/broadinstitute/picard)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM.txt file contains normalized read-counts for 1kb windows across the genome, filtered by requiring a depth >1 RPKM and < 1 SD above the median depth for all windows analysed

extract_protocol:
Chromatin was extracted and digested as described in Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015;109:21 9 1-9
Libraries were prepared as described in Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015;109:21 9 1-9


title: PEO1_rep2 (RNA-seq)

description: rRNA-depleted


title: CP70_rep2 (RNA-seq)

description: rRNA-depleted


title: CP70_rep3 (RNA-seq)

description: rRNA-depleted


title: PEA2_rep3 (ATAC-seq)

description: Tn5 ATAC-seq


title: A2780_rep3 (RNA-seq)

description: rRNA-depleted


title: PEA2_rep2 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEO1_rep3 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEO1_rep1 (ATAC-seq)

description: Tn5 ATAC-seq


title: CP70_rep3 (ATAC-seq)

description: Tn5 ATAC-seq


title: A2780_rep2 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEO4_32uM_rep3 (Exo-seq)

description: exonuclease-digested DNA

data_processing:
adapter trimming with BBDuK
alignment to the hg19 genome assembly using bowtie2
Reads were filtered against genomic blacklist regions, including mitochondrial sequences, defined by The ENCODE Project Consortium
Duplicate reads were removed using the MarkDuplicates tool from the Picard tools suite (https://github.com/broadinstitute/picard)
Genome_build: hg19
Supplementary_files_format_and_content: Counts file contains read-counts for 1kb windows across the genome

extract_protocol:
DNA was isolated from cells using the Gentra PureGene kit (Qiagen). 1µg purified DNA was sheared using Bioruptor Pico (Diagenode) to sizes of ~ 150 bp. Fragment sizes were confirmed using TapeStation (Agilent) .  Fragmented DNA was then incubated at 30˚C for 30 mins, with dNTPs, ATP, T4 DNA polymerase, Polynucleotide Kinase and DNA Polymerase 1 (Klenow fragment) to generate blunt ends before the reaction was stopped by incubation at 75˚C for 20 mins.
Fragments were then incubated with the annealed P7 adapters along with ATP, and the T4 DNA ligase. Adapter ligated fragments were purified and incubated with the phi29 DNA polymerase, along with dNTPs, to allow the overhang between the fragment end and the adapter to be filled in. Adapter ligated DNA was incubated with Lambda exonuclease for 1h at 37˚C. After DNA purification, RecJF and single stranded DNA binding protein (SSB) were added with Lambda exonuclease to maximise digestion efficiency. The platinum molecules which were still present in the fragment, adapter ligated, digested DNA were then displaced by incubation with sodium cyanide at 65˚C for 2h. Complementary strand synthesis was carried out using adapters complementary to the P7 adapter sequence, along with the phi29 DNA polymerase and dNTPs. Finally, the P5 adapter was ligated to the purified, double stranded DNA by incubation for 60 min at 25°C and then 10 min at 65°C to inactivate the enzymes. Purified libraries were then amplified by PCR.

treatment_protocol: treatment with cisplatin

value: cisplatin

tag: treatment dose (um)


title: A2780_rep1 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEA2_rep1 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEA1_rep2 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEO4_16uM_rep3 (Exo-seq)

description: exonuclease-digested DNA


title: PEO4_UT_rep3 (Exo-seq)

description: exonuclease-digested DNA

value: untreated


title: PEA1_rep1 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEO4_rep3 (ATAC-seq)

description: Tn5 ATAC-seq


title: CP70_rep1 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEO4_rep2 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEO1_UT_rep2 (Exo-seq)

description: exonuclease-digested DNA


title: PEO1_UT_rep1 (Exo-seq)

description: exonuclease-digested DNA


title: A2780_rep3 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEO4_32uM_rep2 (Exo-seq)

description: exonuclease-digested DNA


title: CP70_rep2 (ATAC-seq)

description: Tn5 ATAC-seq


title: PEO4_16uM_rep2 (Exo-seq)

description: exonuclease-digested DNA


title: PEO4_16uM_rep1 (Exo-seq)

description: exonuclease-digested DNA


title: dbdb NFD rep2

city: Xi'an

first: Ke

last: Cao

state: Shannxi

address: 28# West Xianning Road

institute: Xi'an Jiaotong University

data_processing:
bsmap(V2.74) software was used for alignment with parameters -u -v 0.1 -z 33 -p 4 -n 1 -w 40 -s 16 -f 20 -L 150.
A bioruptor (Covaris S220, Woburn, MA, USA) was used to fragment genomic DNA to a mean size of approximately 150 bp. After fragmentation, DNA fragments were blunt-ended, added dA at the 3’-ends, and then added adapters. The procedure was carried out in strict accordance with the Illumina manufacturer instructions. Adapters-added DNA was given a bisulfite conversion step, and the bisulfite-treated DNA was PCR amplified and then sequenced using Illumina HiSeq 4000.
Reads yielded from BS-seq were mapped to reference genome (ensembl V81 Mus_musculus.GRCm38.81). Only one mismatch is permitted in the “seed” (the high quality end of the read, default is 16 bases) while aligning. Other parameters were set as default. Every reported cytosine site, with four or more covered reads was used to produce cytosine report.
Genome_build: ensembl V81 Mus_musculus.GRCm38.81
Supplementary_files_format_and_content: Wig files include CG, CHG and CHH for each sample.

source_name: Liver

extract_protocol:
Mitochondrial DNA was extracted using a commercial kit according to the manufacturer’s protocols (Biovision, Sanfrancisco, USA) followed by Exonuclease V (NEB, Beijing, China) and Ampure beads (Beckam Coulter, USA) treatments.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: 19-week old

value: leptin-receptor -/-

tag: diet

value: normal diet


title: C57 HFD rep2

tag: genotype

value: wild type

value: high fat diet


title: C57 HFD rep4


title: PEO4_UT_rep1 (Exo-seq)

description: exonuclease-digested DNA

value: resistant


title: PEO1_16uM_rep3 (Exo-seq)

description: exonuclease-digested DNA

value: sensitive


title: PEO1_16uM_rep1 (Exo-seq)

description: exonuclease-digested DNA


title: PEO1_16uM_rep2 (Exo-seq)

description: exonuclease-digested DNA


title: PEO1_UT_rep3 (Exo-seq)

description: exonuclease-digested DNA


title: PEO4_UT_rep2 (Exo-seq)

description: exonuclease-digested DNA


title: PEO4_rep1 (ATAC-seq)

description: Tn5 ATAC-seq


title: dbdb NFD rep4


title: C57 NFD rep3


title: C57 NFD rep4


title: C57 NFD rep5


title: PEO1_rep2 (ATAC-seq)

description: Tn5 ATAC-seq


title: C57 NFD rep2


title: dbdb NFD rep1


title: C57 HFD rep3


title: C57 HFD rep1


title: PEO4_32uM_rep1 (Exo-seq)

description: exonuclease-digested DNA


title: C57 NFD rep8


title: siP_Con4

city: ATLANTA

first: Elena

last: Dolmatova

state: GA

address: 100 Woodruff cir NE #1013 # 1013

institute: Emory University

description:
siPlodip2 + PBS
siP_ConvssiC_Con.DEG.txt
siP_TNFvssiP_Con.DEG.txt

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data.
Genome_build: Homo sapiens GRCh38/hg38
Supplementary_files_format_and_content: *.DEG.txt: Tab-delimited text files with differential expression analysis between the two groups (n=3).

source_name: Human lung microvascular endothelial cells

growth_protocol: EBM-2 media (Lonza) supplemented with EGMTM -2 MV Microvascular Endothelial Cell Growth Medium-2 BulletKitTM.

extract_protocol:
Cells were lysed with Qiazol and RNA was extracted with RNeasy kit (QIAGEN).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: siControl/siPoldip2 -> 48 hrs later 10ng/ml human TNF-alpha for 6 hrs.

value: Lung microvascular endothelial cells

tag: sirna

value: PBS


title: siC_Con4

description:
siControl + PBS
siC_TNFvssiC_Con.DEG.txt
siP_ConvssiC_Con.DEG.txt
siP_TNFvssiC_Con.DEG.txt

value: siControl


title: C57 NFD rep7

tag: age


title: siP_Con1


title: siC_TNF1

description:
siControl+ TNF-alpha
siC_TNFvssiC_Con.DEG.txt
siP_TNFvssiC_TNF.DEG.txt

value: TNF-alpha


title: siP_TNF4

description:
siPoldip2 + TNF-alpha
siP_TNFvssiC_Con.DEG.txt
siP_TNFvssiC_TNF.DEG.txt
siP_TNFvssiP_Con.DEG.txt


title: C57 NFD rep1


title: siC_Con1


title: dbdb NFD rep3


title: HeLa RNAseq

city: Boulder

first: Gabrijela

last: Dumbovic

state: Colorado

address: 3415 Colorado avenue

department: BioFrontiers

institute: University of Colorado

description: No quantified processed data produced for this sample. The bam file was used to identify intron rention in two genes.

data_processing:
Raw reads of U-2 OS and HeLa samples were mapped to GRCm38 using the NF-CORE RNA-seq pipeline (v1.4.2)
Raw RNA-seq reads were processed for alternative splicing and expression analysis using vast-tools, version 2.2.2 (Tapial et al., (2017)), which is available on github (https://github.com/vastgroup/vast-tools), in combination with the Mm2 and Hs2 VastDB versions released on Dec. 20, 2019.
From primary vast-tools output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW for cassette exon [CE], microexon [MIC] and alternative 5'/3'-ss events or coverage less than 15 reads for intron retention [IR] events; score 4 other than OK/B1 for CE and MIC events or less than 0.05 for IR events). Each event was required to pass filtering in at least 50% of replicates.
Genome_build: Human (GRCm38) (HeLa, U-2 OS)
Supplementary_files_format_and_content: INCLUSION_LEVELS_FULL-Hs23.tab.gz and INCLUSION_LEVELS_FULL-Mm25.tab.gz are primary vast-tools output files for human and mouse samples in tab-delimited format, respectively. See https://github.com/vastgroup/vast-tools#combine-output-format.

source_name: HeLa

growth_protocol: Cell lines were cultured under recommended culturing conditions.

extract_protocol:
RNA was extracted with Maxwell LEV Simply RNA isolation kit. RNA quality was assessed with BioAnalyzer.
Poly(A) RNA enrichment and library preparation was performed with TruSeq kit v2 according to manufacturer’s instructions and sequenced on HiSeq4000, paired end 150 bp.

value: cervix

tag: disease

value: adenocarcinoma

value: epithelial


title: U-2 OS RNAseq

source_name: U-2 OS

extract_protocol:
RNA was extracted with Maxwell LEV Simply RNA isolation kit. RNA quality was assessed with BioAnalyzer.
Poly(A) RNA enrichment and library preparation was performed with NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext® Ultra RNA Library Prep Kit for Illumina® (E7530), and sequenced on the HiSeq4000, paired end 150 bp.

tag: tissue

value: bone

value: osteosarcoma

value: epithelial-like morphology


title: siC_TNF3


title: no.bacteria_expB_rep1 (SSC022)

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

data_processing:
Illumina bcl2fastq v2.20.0 was used for basecalling
Quality assessment of the sequencing reads was performed using FastQC
Trimmomatic was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Arabidopsis thaliana TAIR10 genome using HISAT2
The featureCounts function from the subread package was used to count reads that mapped to protein-coding genes
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Arabidopsis seeds were germinated on Johnson medium solidified with 1% bacto-agar. Plates were kept in the vertical position for seven days in a growth chamber under a 16-hour light/8-hour dark regime at 21oC day/18oC night. The resulting seedlings were then submitted to the treatments.

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings according to Logemann, J. et al. Anal. Biochem. 163, 16–20 (1987). PMID: 2441623.
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare non-stranded Illumina RNA-seq libraries. Following library preparation, quality control and quantification were performed using a 2100 Bioanalyzer instrument (Agilent) and the Quant-iT PicoGreen dsDNA Reagent (Invitrogen), respectively.

treatment_protocol: Seven-day old seedlings were transferred to Johnson medium in the presence of SynCom5-S1 (10E5 cfu/mL of each strain), SynCom5-NS1 (10E5 cfu/mL of each strain) or no bacteria. Plates were kept in a growth chamber under a 9-hour light/15-hour dark regime at 21oC day/18oC night. Whole seedlings were harvested for RNA extraction 12 days after the transfer to the treatment plates.

tag: bacteria presence

value: No bacteria

tag: experiment

value: B


title: siP_TNF3

tag: treatment


title: C57 NFD rep6

value: Liver

value: 19-week old

value: normal diet


title: no.bacteria_expB_rep3 (SSC024)


title: siP_Con3

tag: cell type


title: siC_Con3


title: siP_TNF1


title: SynCom5-S1_expB_rep1 (SSC013)

value: SynCom5-S1 (suppressors)


title: SynCom5-NS1_expB_rep2 (SSC017)

value: SynCom5-NS1 (non-suppressors)


title: SynCom5-S1_expB_rep2 (SSC014)


title: SynCom5-NS1_expB_rep1 (SSC016)


title: SynCom5-NS1_expB_rep3 (SSC018)


title: no.bacteria_expB_rep2 (SSC023)


title: SynCom5-S1_expB_rep3 (SSC015)


title: no.bacteria_ExpA_rep3 (SSC012)

value: A


title: no.bacteria_ExpA_rep2 (SSC011)


title: SynCom5-NS1_expA_rep1 (SSC004)


title: SynCom5-NS1_expA_rep2 (SSC005)


title: SynCom5-S1_expA_rep3 (SSC003)


title: SynCom5-S1_expA_rep2 (SSC002)


title: SynCom5-S1_expA_rep1 (SSC001)


title: SynCom5-NS1_expA_rep3 (SSC006)


title: NoBact_Root_T1_flg22_e3-rep1

source_name: roots

treatment_protocol: Seven-day old seedlings were transferred to Johnson medium with or without 1 µM of flg22 (in the presence or not of SynCom35; 10e5 cfu/mL of each strain). A control condition in which plants were exposed to the dead SynCom35 was included in the experiment by heating the bacteria at 100oC for 2h in an oven immediately before inoculating them into the medium at the same concentration as the SynCom35 alive. Plates were kept in a growth chamber under a 9-hour light/15-hour dark regime at 21oC day/18oC night. The entire root system of the seedlings was harvested for RNA extraction at two time-points: 1 and 12 days after the transfer to the treatment plates.

tag: ecotype

tag: time


title: SynCom35_Root_T12_flg22_e3-rep3


title: NoBact_Root_T12_flg22_e3-rep1


title: HK-SynCom35_Root_T12_flg22_e3-rep1

value: Heat-killed SynCom35


title: HK-SynCom35_Root_T12_flg22_e3-rep2


title: NoBact_Root_T12_flg22_e3-rep3


title: HK-SynCom35_Root_T1_flg22_e3-rep3


title: HK-SynCom35_Root_T12_flg22_e3-rep3


title: NoBact_Root_T1_flg22_e3-rep2


title: NoBact_Root_T12_flg22_e3-rep2


title: HK-SynCom35_Root_T1_flg22_e3-rep2


title: no.bacteria_ExpA_rep1 (SSC010)


title: siC_TNF4

value: Lung microvascular endothelial cells

value: siControl


title: SynCom35_Root_T1_flg22_e3-rep3


title: SynCom35_Root_T12_flg22_e3-rep2


title: NoBact_Root_T1_flg22_e3-rep3


title: SynCom35_Root_T1_flg22_e3-rep2


title: SynCom35_Root_T1_flg22_e3-rep1


title: HK-SynCom35_Root_T1_Mock_e3-rep2

value: Mock


title: HK-SynCom35_Root_T1_Mock_e3-rep1


title: NoBact_Root_T1_Mock_e3-rep2


title: HK-SynCom35_Root_T1_Mock_e3-rep3


title: NoBact_Root_T12_Mock_e3-rep3


title: NoBact_Root_T1_Mock_e3-rep3


title: NoBact_Root_T12_Mock_e3-rep1


title: HK-SynCom35_Root_T12_Mock_e3-rep3


title: HK-SynCom35_Root_T12_Mock_e3-rep2


title: HK-SynCom35_Root_T12_flg22_e2-rep3


title: SynCom35_Root_T1_Mock_e3-rep2


title: HK-SynCom35_Root_T1_flg22_e2-rep3


title: SynCom35_Root_T12_Mock_e3-rep1


title: HK-SynCom35_Root_T12_flg22_e2-rep2


title: SynCom35_Root_T12_Mock_e3-rep3


title: HK-SynCom35_Root_T12_Mock_e3-rep1


title: SynCom35_Root_T12_Mock_e3-rep2


title: NoBact_Root_T1_flg22_e2-rep3


title: NoBact_Root_T12_flg22_e2-rep2


title: NoBact_Root_T12_flg22_e2-rep3


title: SynCom35_Root_T1_Mock_e3-rep3


title: HK-SynCom35_Root_T12_flg22_e2-rep1


title: SynCom35_Root_T12_flg22_e2-rep1


title: NoBact_Root_T1_flg22_e2-rep2


title: SynCom35_Root_T12_flg22_e2-rep2


title: NoBact_Root_T12_flg22_e2-rep1


title: SynCom35_Root_T12_flg22_e2-rep3


title: SynCom35_Root_T1_flg22_e2-rep3


title: SynCom35_Root_T12_flg22_e3-rep1


title: HK-SynCom35_Root_T12_Mock_e2-rep2


title: HK-SynCom35_Root_T12_Mock_e2-rep3


title: SynCom35_Root_T1_flg22_e2-rep1


title: SynCom35_Root_T1_flg22_e2-rep2


title: HK-SynCom35_Root_T12_Mock_e2-rep1


title: HK-SynCom35_Root_T1_Mock_e2-rep3


title: HK-SynCom35_Root_T1_Mock_e2-rep2


title: HK-SynCom35_Root_T1_Mock_e2-rep1


title: NoBact_Root_T1_flg22_e2-rep1


title: HK-SynCom35_Root_T1_flg22_e2-rep2


title: NoBact_Root_T12_Mock_e2-rep1


title: SynCom35_Root_T12_Mock_e2-rep2


title: NoBact_Root_T1_Mock_e2-rep1


title: NoBact_Root_T1_Mock_e2-rep2


title: HK-SynCom35_Root_T1_flg22_e1-rep2


title: HK-SynCom35_Root_T1_flg22_e1-rep3


title: SynCom35_Root_T12_Mock_e2-rep1


title: SynCom35_Root_T1_Mock_e2-rep2


title: NoBact_Root_T12_flg22_e1-rep2


title: NoBact_Root_T12_flg22_e1-rep3


title: SynCom35_Root_T12_Mock_e2-rep3


title: NoBact_Root_T1_Mock_e2-rep3


title: NoBact_Root_T1_flg22_e1-rep3


title: NoBact_Root_T1_flg22_e1-rep2


title: NoBact_Root_T12_flg22_e1-rep1


title: SynCom35_Root_T1_Mock_e2-rep1


title: SynCom35_Root_T12_flg22_e1-rep3


title: NoBact_Root_T12_Mock_e2-rep2


title: SynCom35_Root_T1_flg22_e1-rep1


title: SynCom35_Root_T1_flg22_e1-rep2


title: SynCom35_Root_T12_flg22_e1-rep2


title: HK-SynCom35_Root_T12_flg22_e1-rep3


title: SynCom35_Root_T1_flg22_e1-rep3


title: HK-SynCom35_Root_T12_flg22_e1-rep1


title: HK-SynCom35_Root_T12_Mock_e1-rep1


title: HK-SynCom35_Root_T12_Mock_e1-rep3


title: HK-SynCom35_Root_T12_Mock_e1-rep2


title: HK-SynCom35_Root_T1_Mock_e1-rep3


title: HK-SynCom35_Root_T1_Mock_e1-rep2


title: HK-SynCom35_Root_T12_flg22_e1-rep2


title: NoBact_Root_T1_flg22_e1-rep1


title: SynCom35_Root_T12_flg22_e1-rep1


title: NoBact_Root_T12_Mock_e1-rep1


title: NoBact_Root_T12_Mock_e1-rep3


title: NoBact_Root_T1_Mock_e1-rep3


title: SynCom35_Root_T1_Mock_e1-rep3


title: SynCom35_Root_T12_Mock_e1-rep1


title: NoBact_Root_T1_Mock_e1-rep1


title: SynCom35_Root_T12_Mock_e1-rep3


title: SynCom35_Root_T1_Mock_e1-rep2


title: SynCom35_Root_T1_Mock_e1-rep1


title: SynCom35_Root_T12_Mock_e1-rep2


title: SynCom35_Mock_rep3 (MAE711)

source_name: Seedlings

treatment_protocol: Seven-day old seedlings were transferred to Johnson medium with or without 1 µM of flg22 (in the presence of a commensal strain; 10e5 cfu/mL). Plates were kept in a growth chamber under a 9-hour light/15-hour dark regime at 21oC day/18oC night. The entire eedlings was harvested for RNA extraction 12 days after the transfer to the treatment plates.


title: HK-SynCom35_flg22_rep2 (MAE719)


title: HK-SynCom35_Mock_rep3 (MAE717)


title: SynCom35_flg22_rep2 (MAE713)


title: SynCom35_flg22_rep3 (MAE714)


title: HK-SynCom35_flg22_rep3 (MAE720)


title: SynCom35_Mock_rep2 (MAE710)


title: HK-SynCom35_Mock_rep1 (MAE715)


title: SynCom35_flg22_rep1 (MAE712)


title: HK-SynCom35_flg22_rep1 (MAE718)


title: SynCom35_Mock_rep1 (MAE709)


title: HK-SynCom35_Root_T1_Mock_e1-rep1


title: NoBact_flg22_rep3 (MAE708)


title: NoBact_flg22_rep1 (MAE706)


title: NoBact_flg22_rep2 (MAE707)


title: NoBact_Mock_rep3 (MAE705)


title: NoBact_Mock_rep2 (MAE704)


title: NoBact_Mock_rep1 (MAE703)


title: NoBact_Root_T12_Mock_e1-rep2


title: e.coli_flg22_rep3 (MAE702)


title: NoBact_Root_T1_Mock_e1-rep2


title: e.coli_flg22_rep2 (MAE701)


title: HK-SynCom35_Mock_rep2 (MAE716)


title: e.coli_flg22_rep1 (MAE700)


title: e.coli_Mock_rep3 (MAE699)


title: e.coli_Mock_rep2 (MAE698)


title: cl69_flg22_rep3 (MAE696)


title: e.coli_Mock_rep1 (MAE697)


title: cl69_flg22_rep1 (MAE694)


title: cl69_flg22_rep2 (MAE695)


title: cl69_Mock_rep1 (MAE691)


title: cl21_Mock_rep3 (MAE687)


title: cl69_Mock_rep3 (MAE693)


title: cl14_flg22_rep3 (MAE678)


title: cl18_flg22_rep1 (MAE682)


title: cl21_Mock_rep1 (MAE685)


title: cl18_flg22_rep2 (MAE683)


title: cl18_Mock_rep2 (MAE680)


title: cl18_Mock_rep1 (MAE679)


title: cl14_Mock_rep3 (MAE675)


title: cl14_flg22_rep1 (MAE676)


title: cl69_Mock_rep2 (MAE692)


title: cl21_flg22_rep3 (MAE690)


title: cl21_flg22_rep2 (MAE689)


title: cl21_flg22_rep1 (MAE688)


title: cl21_Mock_rep2 (MAE686)


title: cl14_Mock_rep2 (MAE674)


title: cl18_Mock_rep3 (MAE681)


title: cl18_flg22_rep3 (MAE684)


title: cl14_Mock_rep1 (MAE673)


title: MF376_flg22_rep2 (MAE671)


title: cl14_flg22_rep2 (MAE677)


title: MF376_flg22_rep1 (MAE670)


title: MF376_Mock_rep2 (MAE668)


title: MF376_flg22_rep3 (MAE672)


title: MF376_Mock_rep1 (MAE667)


title: MF374_flg22_rep1 (MAE664)


title: MF376_Mock_rep3 (MAE669)


title: MF370_flg22_rep3 (MAE660)


title: MF374_Mock_rep2 (MAE662)


title: MF370_flg22_rep1 (MAE658)


title: MF370_Mock_rep3 (MAE657)


title: MF374_Mock_rep3 (MAE663)


title: MF362_Mock_rep2 (MAE650)


title: MF370_Mock_rep1 (MAE655)


title: MF362_flg22_rep3 (MAE654)


title: MF374_flg22_rep2 (MAE665)


title: MF370_Mock_rep2 (MAE656)


title: MF362_Mock_rep3 (MAE651)


title: MF374_Mock_rep1 (MAE661)


title: MF362_Mock_rep1 (MAE649)


title: MF360_flg22_rep1 (MAE646)


title: MF360_flg22_rep3 (MAE648)


title: MF370_flg22_rep2 (MAE659)


title: MF360_Mock_rep3 (MAE645)


title: MF360_flg22_rep2 (MAE647)


title: MF362_flg22_rep2 (MAE653)


title: MF360_Mock_rep2 (MAE644)


title: MF374_flg22_rep3 (MAE666)


title: MF345_flg22_rep2 (MAE641)


title: MF362_flg22_rep1 (MAE652)


title: MF345_flg22_rep3 (MAE642)


title: MF345_flg22_rep1 (MAE640)


title: MF360_Mock_rep1 (MAE643)


title: MF339_Mock_rep3 (MAE633)


title: MF339_flg22_rep2 (MAE635)


title: MF339_flg22_rep3 (MAE636)


title: MF339_flg22_rep1 (MAE634)


title: MF327_flg22_rep3 (MAE630)


title: MF327_flg22_rep2 (MAE629)


title: MF327_flg22_rep1 (MAE628)


title: MF327_Mock_rep3 (MAE627)


title: MF339_Mock_rep1 (MAE631)


title: MF345_Mock_rep1 (MAE637)


title: MF327_Mock_rep2 (MAE626)


title: MF314_Mock_rep1 (MAE619)


title: MF314_flg22_rep3 (MAE624)


title: MF327_Mock_rep1 (MAE625)


title: MF314_Mock_rep3 (MAE621)


title: MF345_Mock_rep2 (MAE638)


title: MF303_Mock_rep3 (MAE615)


title: MF345_Mock_rep3 (MAE639)


title: MF302_flg22_rep3 (MAE612)


title: MF314_Mock_rep2 (MAE620)


title: MF303_Mock_rep1 (MAE613)


title: MF303_flg22_rep2 (MAE617)


title: MF303_flg22_rep3 (MAE618)


title: MF303_flg22_rep1 (MAE616)


title: MF303_Mock_rep2 (MAE614)


title: MF339_Mock_rep2 (MAE632)


title: MF314_flg22_rep2 (MAE623)


title: MF302_flg22_rep2 (MAE611)


title: MF302_Mock_rep2 (MAE608)


title: MF302_flg22_rep1 (MAE610)


title: MF314_flg22_rep1 (MAE622)


title: MF299_flg22_rep2 (MAE605)


title: MF299_flg22_rep1 (MAE604)


title: MF299_Mock_rep3 (MAE603)


title: MF299_flg22_rep3 (MAE606)


title: MF302_Mock_rep3 (MAE609)


title: MF299_Mock_rep2 (MAE602)


title: MF273_flg22_rep3 (MAE600)


title: MF299_Mock_rep1 (MAE601)


title: MF273_flg22_rep2 (MAE599)


title: MF273_Mock_rep2 (MAE596)


title: MF273_Mock_rep1 (MAE595)


title: MF181_flg22_rep3 (MAE594)


title: MF273_flg22_rep1 (MAE598)


title: MF181_flg22_rep1 (MAE592)


title: MF181_flg22_rep2 (MAE593)


title: MF181_Mock_rep3 (MAE591)


title: MF273_Mock_rep3 (MAE597)


title: MF161_flg22_rep3 (MAE588)


title: MF302_Mock_rep1 (MAE607)


title: MF161_flg22_rep1 (MAE586)


title: MF181_Mock_rep2 (MAE590)


title: MF138_flg22_rep3 (MAE582)


title: MF161_Mock_rep3 (MAE585)


title: MF138_flg22_rep2 (MAE581)


title: MF161_Mock_rep2 (MAE584)


title: MF138_flg22_rep1 (MAE580)


title: MF161_Mock_rep1 (MAE583)


title: MF136_flg22_rep3 (MAE576)


title: MF136_flg22_rep1 (MAE574)


title: MF136_flg22_rep2 (MAE575)


title: MF138_Mock_rep3 (MAE579)


title: MF138_Mock_rep2 (MAE578)


title: MF138_Mock_rep1 (MAE577)


title: MF136_Mock_rep1 (MAE571)


title: MF136_Mock_rep3 (MAE573)


title: MF125_flg22_rep3 (MAE570)


title: MF125_Mock_rep2 (MAE566)


title: MF125_Mock_rep3 (MAE567)


title: MF109_flg22_rep3 (MAE564)


title: MF161_flg22_rep2 (MAE587)


title: MF109_flg22_rep2 (MAE563)


title: MF109_flg22_rep1 (MAE562)


title: MF181_Mock_rep1 (MAE589)


title: MF125_Mock_rep1 (MAE565)


title: MF109_Mock_rep2 (MAE560)


title: MF105_flg22_rep3 (MAE558)


title: MF109_Mock_rep1 (MAE559)


title: MF79_flg22_rep2 (MAE551)


title: MF105_Mock_rep2 (MAE554)


title: MF105_Mock_rep3 (MAE555)


title: MF79_Mock_rep2 (MAE548)


title: MF79_Mock_rep3 (MAE549)


title: MF105_flg22_rep2 (MAE557)


title: MF79_flg22_rep1 (MAE550)


title: MF105_Mock_rep1 (MAE553)


title: MF79_flg22_rep3 (MAE552)


title: MF136_Mock_rep2 (MAE572)


title: MF50_flg22_rep3 (MAE546)


title: MF125_flg22_rep2 (MAE569)


title: MF125_flg22_rep1 (MAE568)


title: MF79_Mock_rep1 (MAE547)


title: MF50_flg22_rep2 (MAE545)


title: MF50_Mock_rep3 (MAE543)


title: MF50_flg22_rep1 (MAE544)


title: MF50_Mock_rep2 (MAE542)


title: MF47_flg22_rep3 (MAE540)


title: MF109_Mock_rep3 (MAE561)


title: MF47_flg22_rep2 (MAE539)


title: MF47_Mock_rep2 (MAE536)


title: MF47_flg22_rep1 (MAE538)


title: MF50_Mock_rep1 (MAE541)


title: MF105_flg22_rep1 (MAE556)


title: MF47_Mock_rep1 (MAE535)


title: MF41_Mock_rep3 (MAE531)


title: MF41_flg22_rep1 (MAE532)


title: MF40_flg22_rep1 (MAE526)


title: MF40_Mock_rep2 (MAE524)


title: MF40_flg22_rep2 (MAE527)


title: MF41_Mock_rep1 (MAE529)


title: MF41_Mock_rep2 (MAE530)


title: MF33_flg22_rep3 (MAE522)


title: MF41_flg22_rep2 (MAE534)


title: MF33_Mock_rep3 (MAE519)


title: MF40_Mock_rep3 (MAE525)


title: MF33_flg22_rep1 (MAE520)


title: MF33_Mock_rep1 (MAE517)


title: MF33_Mock_rep2 (MAE518)


title: MF40_Mock_rep1 (MAE523)


title: MF33_flg22_rep2 (MAE521)


title: MF29_flg22_rep2 (MAE515)


title: MF29_Mock_rep3 (MAE513)


title: MF29_flg22_rep3 (MAE516)


title: MF29_Mock_rep2 (MAE512)


title: MF29_Mock_rep1 (MAE511)


title: MF29_flg22_rep1 (MAE514)


title: MF47_Mock_rep3 (MAE537)


title: MF27_flg22_rep2 (MAE509)


title: MF27_Mock_rep3 (MAE507)


title: MF27_flg22_rep1 (MAE508)


title: MF27_flg22_rep3 (MAE510)


title: MF27_Mock_rep2 (MAE506)


title: MF27_Mock_rep1 (MAE505)


title: MF8_flg22_rep3 (MAE504)


title: MF8_flg22_rep2 (MAE503)


title: MF8_Mock_rep3 (MAE501)


title: MF2_flg22_rep3 (MAE498)


title: MF8_Mock_rep1 (MAE499)


title: MF8_flg22_rep1 (MAE502)


title: MF2_flg22_rep1 (MAE496)


title: MF2_flg22_rep2 (MAE497)


title: HK-SynCom35_flg22_rep1 (MAE472)


title: HK-SynCom35_flg22_rep2 (MAE473)


title: MF2_Mock_rep3 (MAE495)


title: HK-SynCom35_Mock_rep2 (MAE470)


title: HK-SynCom35_Mock_rep1 (MAE469)


title: SynCom35_Mock_rep3 (MAE465)


title: HK-SynCom35_Mock_rep3 (MAE471)


title: SynCom35_Mock_rep2 (MAE464)


title: SynCom35_Mock_rep1 (MAE463)


title: NoBact_flg22_rep3 (MAE462)


title: NoBact_flg22_rep2 (MAE461)


title: NoBact_flg22_rep3 (MAE460)


title: NoBact_Mock_rep2 (MAE459)


title: NoBact_Mock_rep1 (MAE458)


title: e.coli_flg22_rep2 (MAE455)


title: e.coli_flg22_rep1 (MAE454)


title: MF8_Mock_rep2 (MAE500)


title: e.coli_Mock_rep2 (MAE452)


title: e.coli_Mock_rep3 (MAE453)


title: e.coli_Mock_rep1 (MAE451)


title: MF2_Mock_rep2 (MAE494)


title: cl69_flg22_rep1 (MAE448)


title: cl69_Mock_rep3 (MAE447)


title: MF2_Mock_rep1 (MAE493)


title: cl69_flg22_rep2 (MAE449)


title: SynCom35_flg22_rep2 (MAE467)


title: cl69_flg22_rep3 (MAE450)


title: cl21_flg22_rep2 (MAE443)


title: cl69_Mock_rep2 (MAE446)


title: cl21_Mock_rep3 (MAE441)


title: cl69_Mock_rep1 (MAE445)


title: cl21_flg22_rep3 (MAE444)


title: cl21_flg22_rep1 (MAE442)


title: cl21_Mock_rep2 (MAE440)


title: cl21_Mock_rep1 (MAE439)


title: cl18_flg22_rep2 (MAE437)


title: cl18_flg22_rep3 (MAE438)


title: cl18_flg22_rep1 (MAE436)


title: cl18_Mock_rep2 (MAE434)


title: cl18_Mock_rep3 (MAE435)


title: e.coli_flg22_rep3 (MAE456)


title: cl18_Mock_rep1 (MAE433)


title: cl14_flg22_rep3 (MAE432)


title: cl14_Mock_rep2 (MAE428)


title: cl14_flg22_rep1 (MAE430)


title: cl14_flg22_rep2 (MAE431)


title: cl14_Mock_rep3 (MAE429)


title: MF376_flg22_rep2 (MAE425)


title: cl14_Mock_rep1 (MAE427)


title: MF376_flg22_rep3 (MAE426)


title: MF374_flg22_rep2 (MAE419)


title: MF376_Mock_rep3 (MAE423)


title: MF374_flg22_rep3 (MAE420)


title: MF374_Mock_rep1 (MAE415)


title: MF370_flg22_rep3 (MAE414)


title: MF374_flg22_rep1 (MAE418)


title: MF374_Mock_rep3 (MAE417)


title: MF376_Mock_rep2 (MAE422)


title: MF370_Mock_rep2 (MAE410)


title: SynCom35_flg22_rep1 (MAE466)


title: MF370_Mock_rep3 (MAE411)


title: MF362_flg22_rep1 (MAE406)


title: MF362_flg22_rep2 (MAE407)


title: MF374_Mock_rep2 (MAE416)


title: MF362_Mock_rep3 (MAE405)


title: MF362_Mock_rep1 (MAE403)


title: MF360_flg22_rep2 (MAE401)


title: MF360_flg22_rep3 (MAE402)


title: MF376_Mock_rep1 (MAE421)


title: MF376_flg22_rep1 (MAE424)


title: MF370_flg22_rep2 (MAE413)


title: MF370_flg22_rep1 (MAE412)


title: MF370_Mock_rep1 (MAE409)


title: MF362_flg22_rep3 (MAE408)


title: MF362_Mock_rep2 (MAE404)


title: MF339_flg22_rep3 (MAE390)


title: MF360_Mock_rep1 (MAE397)


title: MF360_Mock_rep2 (MAE398)


title: MF345_Mock_rep1 (MAE391)


title: MF360_Mock_rep3 (MAE399)


title: MF339_flg22_rep1 (MAE388)


title: MF360_flg22_rep1 (MAE400)


title: MF345_Mock_rep3 (MAE393)


title: MF345_Mock_rep2 (MAE392)


title: MF345_flg22_rep2 (MAE395)


title: MF339_Mock_rep3 (MAE387)


title: MF327_Mock_rep2 (MAE380)


title: MF327_flg22_rep2 (MAE383)


title: MF345_flg22_rep3 (MAE396)


title: MF314_flg22_rep2 (MAE377)


title: MF327_flg22_rep3 (MAE384)


title: MF314_flg22_rep1 (MAE376)


title: MF327_Mock_rep3 (MAE381)


title: MF345_flg22_rep1 (MAE394)


title: MF339_Mock_rep2 (MAE386)


title: MF327_flg22_rep1 (MAE382)


title: MF314_Mock_rep3 (MAE375)


title: MF339_Mock_rep1 (MAE385)


title: MF314_Mock_rep2 (MAE374)


title: MF327_Mock_rep1 (MAE379)


title: MF339_flg22_rep2 (MAE389)


title: MF314_Mock_rep1 (MAE373)


title: MF303_flg22_rep3 (MAE372)


title: MF303_flg22_rep2 (MAE371)


title: MF314_flg22_rep3 (MAE378)


title: MF302_flg22_rep3 (MAE366)


title: MF299_Mock_rep3 (MAE357)


title: MF299_flg22_rep2 (MAE360)


title: MF299_Mock_rep1 (MAE355)


title: MF299_flg22_rep1 (MAE358)


title: MF303_Mock_rep2 (MAE368)


title: MF303_flg22_rep1 (MAE370)


title: MF273_flg22_rep1 (MAE352)


title: MF302_flg22_rep1 (MAE364)


title: MF302_Mock_rep3 (MAE363)


title: MF273_Mock_rep2 (MAE350)


title: MF303_Mock_rep3 (MAE369)


title: MF303_Mock_rep1 (MAE367)


title: MF302_Mock_rep1 (MAE361)


title: MF273_Mock_rep1 (MAE349)


title: MF299_Mock_rep2 (MAE356)


title: MF302_Mock_rep2 (MAE362)


title: MF273_flg22_rep3 (MAE354)


title: MF302_flg22_rep2 (MAE365)


title: MF181_flg22_rep3 (MAE348)


title: MF181_flg22_rep2 (MAE347)


title: MF181_flg22_rep1 (MAE346)


title: MF181_Mock_rep3 (MAE345)


title: MF181_Mock_rep2 (MAE344)


title: MF181_Mock_rep1 (MAE343)


title: MF161_flg22_rep3 (MAE342)


title: MF161_flg22_rep2 (MAE341)


title: MF273_Mock_rep3 (MAE351)


title: MF273_flg22_rep2 (MAE353)


title: MF161_flg22_rep1 (MAE340)


title: MF161_Mock_rep2 (MAE338)


title: MF136_flg22_rep1 (MAE328)


title: MF138_Mock_rep2 (MAE332)


title: MF161_Mock_rep3 (MAE339)


title: MF138_flg22_rep1 (MAE334)


title: MF138_Mock_rep1 (MAE331)


title: MF138_Mock_rep3 (MAE333)


title: MF136_flg22_rep3 (MAE330)


title: MF138_flg22_rep3 (MAE336)


title: MF125_flg22_rep1 (MAE323)


title: MF138_flg22_rep2 (MAE335)


title: MF125_Mock_rep3 (MAE321)


title: MF125_flg22_rep2 (MAE324)


title: MF136_Mock_rep2 (MAE326)


title: MF136_flg22_rep2 (MAE329)


title: MF136_Mock_rep1 (MAE325)


title: MF125_Mock_rep1 (MAE319)


title: MF125_Mock_rep2 (MAE320)


title: MF109_flg22_rep2 (MAE317)


title: MF109_flg22_rep1 (MAE316)


title: MF109_Mock_rep1 (MAE313)


title: MF109_Mock_rep2 (MAE314)


title: MF109_Mock_rep3 (MAE315)


title: MF109_flg22_rep3 (MAE318)


title: MF105_flg22_rep2 (MAE311)


title: MF105_Mock_rep3 (MAE309)


title: MF105_flg22_rep1 (MAE310)


title: MF105_Mock_rep2 (MAE308)


title: MF136_Mock_rep3 (MAE327)


title: MF161_Mock_rep1 (MAE337)


title: MF79_flg22_rep1 (MAE304)


title: MF105_Mock_rep1 (MAE307)


title: MF79_Mock_rep3 (MAE303)


title: MF79_Mock_rep2 (MAE302)


title: MF79_flg22_rep2 (MAE305)


title: MF50_flg22_rep1 (MAE298)


title: MF79_flg22_rep3 (MAE306)


title: MF50_Mock_rep2 (MAE296)


title: MF50_Mock_rep1 (MAE295)


title: MF79_Mock_rep1 (MAE301)


title: MF50_Mock_rep3 (MAE297)


title: MF47_flg22_rep1 (MAE292)


title: MF50_flg22_rep2 (MAE299)


title: MF47_Mock_rep3 (MAE291)


title: MF47_Mock_rep2 (MAE290)


title: MF47_flg22_rep3 (MAE294)


title: MF41_flg22_rep1 (MAE286)


title: MF41_Mock_rep3 (MAE285)


title: MF41_flg22_rep2 (MAE287)


title: MF47_Mock_rep1 (MAE289)


title: MF41_Mock_rep2 (MAE284)


title: MF50_flg22_rep3 (MAE300)


title: MF40_flg22_rep3 (MAE282)


title: MF47_flg22_rep2 (MAE293)


title: MF40_flg22_rep2 (MAE281)


title: MF40_flg22_rep1 (MAE280)


title: MF41_Mock_rep1 (MAE283)


title: MF40_Mock_rep3 (MAE279)


title: MF40_Mock_rep2 (MAE278)


title: MF33_flg22_rep3 (MAE276)


title: MF40_Mock_rep1 (MAE277)


title: MF33_flg22_rep2 (MAE275)


title: MF29_flg22_rep3 (MAE270)


title: MF33_Mock_rep2 (MAE272)


title: MF33_Mock_rep3 (MAE273)


title: MF29_Mock_rep3 (MAE267)


title: MF29_flg22_rep1 (MAE268)


title: MF27_flg22_rep3 (MAE264)


title: MF27_flg22_rep2 (MAE263)


title: MF29_Mock_rep1 (MAE265)


title: MF27_Mock_rep3 (MAE261)


title: MF27_Mock_rep1 (MAE259)


title: MF27_Mock_rep2 (MAE260)


title: MF8_flg22_rep3 (MAE258)


title: MF8_flg22_rep2 (MAE257)


title: MF8_Mock_rep3 (MAE255)


title: MF8_flg22_rep1 (MAE256)


title: MF8_Mock_rep2 (MAE254)


title: MF8_Mock_rep1 (MAE253)


title: MF2_flg22_rep3 (MAE252)


title: MF2_flg22_rep2 (MAE251)


title: MF2_flg22_rep1 (MAE250)


title: MF2_Mock_rep3 (MAE249)


title: MF33_flg22_rep1 (MAE274)


title: MF29_flg22_rep2 (MAE269)


title: MF2_Mock_rep1 (MAE247)


title: MF33_Mock_rep1 (MAE271)


title: MF29_Mock_rep2 (MAE266)


title: MF41_flg22_rep3 (MAE288)


title: SynCom35_flg22_rep3 (MAE222)


title: SynCom35_flg22_rep1 (MAE220)


title: SynCom35_flg22_rep2 (MAE221)


title: SynCom35_Mock_rep3 (MAE219)


title: MF27_flg22_rep1 (MAE262)


title: NoBact_flg22_rep2 (MAE215)


title: NoBact_Mock_rep1 (MAE211)


title: NoBact_flg22_rep1 (MAE214)


title: NoBact_Mock_rep3 (MAE213)


title: NoBact_flg22_rep3 (MAE216)


title: NoBact_Mock_rep2 (MAE212)


title: e.coli_flg22_rep3 (MAE210)


title: e.coli_flg22_rep2 (MAE209)


title: e.coli_flg22_rep1 (MAE208)


title: e.coli_Mock_rep3 (MAE207)


title: e.coli_Mock_rep1 (MAE205)


title: e.coli_Mock_rep2 (MAE206)


title: MF2_Mock_rep2 (MAE248)


title: cl69_Mock_rep3 (MAE201)


title: cl69_flg22_rep1 (MAE202)


title: cl69_flg22_rep2 (MAE203)


title: cl69_Mock_rep2 (MAE200)


title: SynCom35_Mock_rep2 (MAE218)


title: cl21_flg22_rep3 (MAE198)


title: cl21_flg22_rep1 (MAE196)


title: cl21_Mock_rep3 (MAE195)


title: cl69_Mock_rep1 (MAE199)


title: cl21_flg22_rep2 (MAE197)


title: cl21_Mock_rep2 (MAE194)


title: SynCom35_Mock_rep1 (MAE217)


title: cl18_flg22_rep2 (MAE191)


title: cl69_flg22_rep3 (MAE204)


title: cl18_flg22_rep3 (MAE192)


title: cl18_flg22_rep1 (MAE190)


title: cl18_Mock_rep3 (MAE189)


title: cl14_flg22_rep2 (MAE185)


title: cl14_flg22_rep1 (MAE184)


title: cl18_Mock_rep1 (MAE187)


title: cl14_flg22_rep3 (MAE186)


title: cl14_Mock_rep3 (MAE183)


title: cl18_Mock_rep2 (MAE188)


title: cl14_Mock_rep1 (MAE181)


title: MF376_flg22_rep2 (MAE179)


title: MF376_flg22_rep1 (MAE178)


title: MF376_Mock_rep3 (MAE177)


title: MF376_flg22_rep3 (MAE180)


title: MF376_Mock_rep2 (MAE176)


title: cl21_Mock_rep1 (MAE193)


title: MF374_flg22_rep1 (MAE172)


title: MF374_flg22_rep2 (MAE173)


title: MF374_Mock_rep2 (MAE170)


title: MF370_flg22_rep1 (MAE166)


title: MF370_flg22_rep3 (MAE168)


title: MF374_flg22_rep3 (MAE174)


title: MF370_Mock_rep3 (MAE165)


title: MF374_Mock_rep3 (MAE171)


title: MF374_Mock_rep1 (MAE169)


title: MF370_Mock_rep1 (MAE163)


title: MF370_flg22_rep2 (MAE167)


title: cl14_Mock_rep2 (MAE182)


title: MF362_flg22_rep2 (MAE161)


title: MF362_Mock_rep2 (MAE158)


title: MF362_Mock_rep3 (MAE159)


title: MF362_Mock_rep1 (MAE157)


title: MF360_flg22_rep3 (MAE156)


title: MF360_flg22_rep1 (MAE154)


title: MF362_flg22_rep1 (MAE160)


title: MF360_flg22_rep2 (MAE155)


title: MF376_Mock_rep1 (MAE175)


title: MF360_Mock_rep1 (MAE151)


title: MF360_Mock_rep2 (MAE152)


title: MF360_Mock_rep3 (MAE153)


title: MF345_flg22_rep3 (MAE150)


title: MF345_flg22_rep2 (MAE149)


title: MF345_flg22_rep1 (MAE148)


title: MF362_flg22_rep3 (MAE162)


title: MF345_Mock_rep1 (MAE145)


title: MF345_Mock_rep2 (MAE146)


title: MF370_Mock_rep2 (MAE164)


title: MF345_Mock_rep3 (MAE147)


title: MF339_flg22_rep3 (MAE144)


title: MF339_flg22_rep2 (MAE143)


title: MF339_Mock_rep3 (MAE141)


title: MF339_Mock_rep2 (MAE140)


title: MF339_flg22_rep1 (MAE142)


title: MF339_Mock_rep1 (MAE139)


title: MF327_flg22_rep3 (MAE138)


title: MF327_Mock_rep3 (MAE135)


title: MF327_flg22_rep1 (MAE136)


title: MF327_flg22_rep2 (MAE137)


title: MF327_Mock_rep2 (MAE134)


title: MF327_Mock_rep1 (MAE133)


title: MF314_flg22_rep3 (MAE132)


title: MF314_flg22_rep2 (MAE131)


title: MF314_flg22_rep1 (MAE130)


title: MF314_Mock_rep3 (MAE129)


title: MF314_Mock_rep2 (MAE128)


title: Ets1/2 null EC, biological rep1

type: RNA

city: Charleston

first: Michael

middle: C

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description: Gene expression data from EC with Ets1/2 deletion

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the mouse chip 430A.2. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: RMA method was applied to the primary data to correct the technical bias and summarize gene expression values over probe-sets

label: biotin

source_name: Aortic EC isolated from mouse infected with lentivirus-egfp-Cre

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: EC were isolated from mouse aorta

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

treatment_protocol: EC were grown in complete EC media (DMEM-F12+20% FBS+heparin+ECGS+PS) in a 37º incubator with 5% CO2.

value: 4 Weeks

value: Aorta

value: Endothelial Cells

value: Ets1-/-; Ets2fl/fl + lentiviral-egfp-Cre


title: Ets1/2 null EC, biological rep2


title: MF314_Mock_rep1 (MAE127)


title: Ets1/2 null EC, biological rep3


title: Ets1/2 Wild type EC, biological rep3

description: Gene expression data from EC with wild type Ets1/2

source_name: Aortic EC isolated from mouse infected with lentivirus-egfp

value: Ets1+/+; Ets2+/+ + lentiviral-egfp


title: Ets1 null EC, biological rep2

description: Gene expression data from EC with wild type Ets1

value: Ets1-/-; Ets2fl/fl+ lentiviral-egfp


title: Ets1 null EC, biological rep1


title: sample6_RAG2-2-deficient 2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
STAR_2.4.0a paired-end mapping versus mm10.
FeatureCounts transcripts quantification (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: feature counts

source_name: Femoral B-cells

growth_protocol: Femoral B cells were directly RNA extracted after recovery. CD43- splenocytes were obtained from KOKI mice and BLACK-6 control mice and stimulated 2 days (1x10^6 cells/ml in RPMI 1640 with 10% FCS) with 5µg/ml LPS and 20 ng/ml IL4.

extract_protocol:
RNA was extracted using miRNeasy kit from QIAGEN, according to the manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA was used with 500 ng of total RNA for the construction of sequencing libraries.

treatment_protocol: Some samples were treated with 200 ng/ml of SAHA (an HDAC inhibitor) at the start of the culture.

tag: strain background

value: 8-10 weeks animals

value: Femoral B-cells


title: sample10_wt_6_et_8_LPS_IL4_200nM_SAHA

source_name: Splenic-B cells

value: Splenic-B cells

value: 5µg/ml LPS ± 200 ng/ml SAHA


title: sample8_wt_4_et_7_LPS_IL4_200nM_SAHA


title: sample9_wt_6_et_8_LPS_IL4


title: Ets1/2 Wild type EC, biological rep2


title: sample4_ΔEµ7

tag: genotype/variation


title: MF303_flg22_rep2 (MAE125)


title: MF303_flg22_rep3 (MAE126)


title: sample3_ΔEµ5


title: Ets2 null EC, biological rep2

description: Gene expression data from EC with wild type Ets2

value: Ets1+/+; Ets2fl/fl + lentiviral-egfp-Cre


title: Ets2 null EC, biological rep1


title: Ets2 null EC, biological rep3


title: Ets1/2 Wild type EC, biological rep1


title: Ets1 null EC, biological rep3

value: Ets1-/-; Ets2fl/fl + lentiviral-egfp


title: sample7_wt_4_et_7 LPS_IL4


title: MF303_Mock_rep3 (MAE123)


title: sample5_RAG-2-deficient 1


title: sample1_2KO1


title: sample10_KOKI 2 LPS

source_name: Splenic B cells

growth_protocol: Femoral B cells were directly RNA extracted after recovery. CD43- splenocytes were obtained from KOKI mice and BLACK-6 control mice and stimulated 2 days (1x106 cells/ml in RPMI 1640 with 10% FCS) with 5µg/ml LPS.

value: KOKI mice

value: Stimulation with LPS + SAHA

tag: tissue/cell type

value: Splenic B cells


title: sample2_2KO3


title: MF303_Mock_rep2 (MAE122)


title: sample9_KOKI 1 LPS


title: sample8_WT2 LPS + SAHA

value: Wt mice


title: sample7_WT 2 + LPS

value: Stimulation with LPS


title: MF303_Mock_rep1 (MAE121)

value: Mock


title: MF302_flg22_rep2 (MAE119)


title: sample6_WT 1 LPS + SAHA

value: Stmulation with LPS + SAHA


title: sample4_RAG KOKI mice

source_name: Femoral B cells

value: KOKI mice in a background deficient for RAG2

value: Femoral B cells


title: sample5_WT 1 LPS


title: MF302_Mock_rep3 (MAE117)


title: sample3_RAG gamma C KOKI mice

value: KOKI mice in a background deficient for RAG2 and gamma C


title: MF302_Mock_rep2 (MAE116)


title: MF303_flg22_rep1 (MAE124)


title: sample2_RAG Gamma C KO mice 2

value: RAG2-deficient and Gamma C-deficient


title: MF299_flg22_rep2 (MAE113)


title: MF299_flg22_rep1 (MAE112)


title: MF299_Mock_rep3 (MAE111)


title: MF299_Mock_rep2 (MAE110)


title: tumor_78_a

city: Boston

first: Rakesh

last: Jain

state: MA

address: 100 Blossom Street, Cox-7

institute: Massachusetts General Hospital

data_processing:
Base calls were converted to FASTQs using Illumina bcl2fastq2
Reads were aligned using Tophat2
Gene expression pseudocounts and transcripts per million were calculated using Rsem
Genome_build: mm10
Supplementary_files_format_and_content: tpm_matrix_correct.txt, metadata.txt

source_name: brain; tumor

extract_protocol:
Samples were prepared by harvesting (1) CT2A tumors from the forebrain of mice , or (2) spleen. After single-cell preparation, cells were stained with TCR, CD4, C8, CD25, CD127. Cells were sorted on Aria 4 into 96-well plates containing RLT buffer + 1% BME. TCR+CD8+ cells were assigned to a dump channel in flow cytometry to avoid CD8 T cell contamination. TCR+CD4+CD25hi CD127lo cells were sorted as Tregs. A fraction of cells were tested for FoxP3 positivity to double-check and were all FoxP3. RNA was extracted from RLT bufffer using 2.2x SPRI bead wash.
RNA was converted to cDNA,amplified, and prepared for sequencing  using the SmartSeq2 protocol (Trombetta et al., Current Protocols in Molecular Biology, 2014, 107:II:4:22).

treatment_protocol: Treatment: After tumors reach a size of 2mm^3, mice were randomly assigned to treatment groups. Two groups were IgG (control) or aPD1+aGITR therapy. Mice received 4 treatment (250ug/mice ) every 3 days. Two days after last dose tumors or spleens were harvested

value: tumor biopsy

value: control

value: CD4+ T regulatory cells


title: tumor_77_a


title: tumor_80_a

value: aGITR+aPD1 treated


title: MF299_Mock_rep1 (MAE109)


title: tumor_79_a


title: MF273_flg22_rep3 (MAE108)


title: tumor_76_a


title: MF302_flg22_rep1 (MAE118)


title: MF302_flg22_rep3 (MAE120)


title: tumor_73_b


title: MF273_Mock_rep3 (MAE105)


title: tumor_73_a


title: MF273_flg22_rep2 (MAE107)


title: MF273_Mock_rep1 (MAE103)


title: MF299_flg22_rep3 (MAE114)


title: tumor_70_a


title: MF273_Mock_rep2 (MAE104)


title: MF273_flg22_rep1 (MAE106)


title: MF181_flg22_rep2 (MAE102)


title: tumor_70_b


title: tumor_369_a


title: sample1_RAG Gamma C KO mice 1


title: spleen_80_a

source_name: spleen

value: spleen


title: MF302_Mock_rep1 (MAE115)


title: MF181_Mock_rep3 (MAE099)


title: tumor_74_a


title: MF181_Mock_rep2 (MAE098)


title: spleen_79_a


title: MF181_Mock_rep1 (MAE097)


title: spleen_77_a


title: spleen_79_c


title: MF161_flg22_rep3 (MAE096)


title: spleen_79_b


title: tumor_72_a


title: MF161_Mock_rep3 (MAE093)


title: spleen_76_a


title: spleen_74_a


title: MF161_flg22_rep2 (MAE095)


title: MF161_Mock_rep2 (MAE092)


title: spleen_73_a


title: spleen_72_c


title: MF181_flg22_rep1 (MAE101)


title: spleen_72_b


title: MF138_flg22_rep2 (MAE089)


title: MF138_flg22_rep3 (MAE090)


title: spleen_79_d


title: MF138_Mock_rep3 (MAE087)


title: spleen_70_c


title: MF161_Mock_rep1 (MAE091)


title: MF138_Mock_rep2 (MAE086)


title: spleen_72_a


title: spleen_70_a


title: MF138_Mock_rep1 (MAE085)


title: spleen_70_b


title: spleen_369_a


title: MF136_flg22_rep3 (MAE084)


title: mES RNAseq - rep3

source_name: mES

extract_protocol:
RNA was extracted with Maxwell LEV Simply RNA isolation kit. RNA quality was assessed with BioAnalyzer.
Poly(A) RNA enrichment and library preparation was performed with TruSeq kit v2 according to manufacturer’s instructions and sequenced on HiSeq2500, paired end 75 bp.

value: embryonic

value: embryonic stem cell


title: MF136_flg22_rep1 (MAE082)


title: mES RNAseq - rep2


title: mES RNAseq - rep1


title: MF136_Mock_rep3 (MAE081)


title: MF136_flg22_rep2 (MAE083)


title: MF136_Mock_rep2 (MAE080)


title: 150_RSS31_JoDo01_D3_F_pos_N723_S508

city: La Jolla

first: Joseph

middle: S.

last: Dolina

state: California

address: 9420 Athena Circle

department: Division of Developmental Immunology

institute: La Jolla Institute for Immunology

description:
High dose day 3 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen
High dose day 3 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr).
Filtered reads were mapped against the UCSC mouse mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand).
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4).
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed.
Genome_build: mm10
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

source_name: CD4+eGFP+ (Treg)

growth_protocol: Listeria monocytogenes (Lm) derived from the wild type 10403S background deficient in the actin assembly-inducing protein alone (Lm ΔactA) or expressing ovalbumin (Lm ΔactA-Ova) were obtained from the laboratory of Daniel A. Portnoy (University of California, Berkeley, CA). Bacteria were cultured in BBL brain heart infusion medium (Becton, Dickinson and Company, Sparks, MD) at 37°C, back-diluted to log-phase (OD600 0.075-0.100), washed, and re-suspended in 1×PBS.

extract_protocol:
Total RNA was purified using the Direct-zol RNA MiniPrep Plus and RNA Clean & Concentrator-25 kits (Zymo Research, Irvine, CA). RNA quality and quantity was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA) resulting in all samples producing RIN scores above 9.0. 5 ng of total RNA was then amplified using the Smart-seq2 protocol.
A 1:1 ratio of Agencourt AMPure XP beads (Beckman Coulter Inc., Brea, CA) were used to purify resulting cDNA, and 1 ng cDNA was subsequently used to prepare a sequencing library with the Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA). Both whole-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included to determine total RNA quality and quantity, the optimal number of PCR pre-amplification cycles, and fragment size selection.
The resulting libraries were deep sequenced on the HiSeq 2500 System in Rapid Run mode (Illumina) using 50-bp single-end reads (~6.0×10^6 reads per condition).

treatment_protocol: Primary infections were conducted via intravenous (IV) injection of HD; 1×106 CFU Lm in the caudal vein.

tag: strain

value: Foxp3eGFP (C57BL/6 background)

tag: agent

value: Listeria deltaactA-Ova

tag: time point

value: Day 3


title: 154_RSS31_JoDo01_D7_F_pos_N724_S503

description:
Day 7 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen
Day 7 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen

value: Day 7


title: MF138_flg22_rep1 (MAE088)


title: 142_RSS31_JoDo01_Naive_F_pos_N722_S508

description:
Naïve Foxp3-eGFP mouse spleen
Naïve Foxp3-eGFP mouse spleen


title: MF125_flg22_rep3 (MAE078)


title: 146_RSS31_JoDo01_D1_F_pos_N723_S503

description:
Day 1 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen
Day 1 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen

value: Day 1


title: MF125_flg22_rep2 (MAE077)


title: MF125_flg22_rep1 (MAE076)


title: MF125_Mock_rep3 (MAE075)

value: Mock


title: 014_D7_2_GFPpos


title: MF161_flg22_rep1 (MAE094)


title: MF125_Mock_rep2 (MAE074)


title: MF125_Mock_rep1 (MAE073)


title: 010_D3_2_GFPpos

description:
Day 3 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen
Day 3 Listeria ΔactA-Ova infected Foxp3-eGFP mouse spleen


title: 009_D3_1_GFPpos


title: 006_D1_2_GFPpos

description:
Day 1 Listeria ΔactA-Ova infected
Day 1 Listeria ΔactA-Ova infected


title: 005_D1_1_GFPpos

description:
Day 1 Listeria deltaactA-Ova infected
Foxp3-eGFP mouse spleen


title: MF109_flg22_rep3 (MAE072)


title: MF109_flg22_rep2 (MAE071)


title: 002_Naive_2_GFPpos


title: 001_Naive_1_GFPpos


title: MF136_Mock_rep1 (MAE079)


title: 4_miRNA

source_name: liver

value: 8.71 weeks

value: wild type


title: MF109_Mock_rep1 (MAE067)


title: 3_miRNA


title: MF109_Mock_rep2 (MAE068)


title: MF109_flg22_rep1 (MAE070)


title: MF109_Mock_rep3 (MAE069)


title: 013_D7_1_GFPpos


title: 1_miRNA


title: 173_miRNA

value: 11.29 weeks


title: 170_miRNA


title: MF105_flg22_rep2 (MAE066)


title: MF105_flg22_rep1 (MAE064)


title: MF105_Mock_rep2 (MAE062)


title: MF105_Mock_rep3 (MAE063)


title: Cortex from wildtype Mice - WT rep1

city: Changsha

first: Cong

last: Liu

address: No.110 Xiangya road

institute: Central South University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set
Expression level of gene was calculated by RSEM (v1.2.12)
Differentially expressed genes were identified using DESeq2.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: Matrix table with fpkm for every gene and every sample.

source_name: cortex

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4℃, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4℃. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4℃. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4℃ to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: cortex


title: Cortex from wildtype Mice - WT rep2


title: Cortex from Stxbp6-null Mice - KO rep1


title: Cortex from Stxbp6-null Mice - KO rep3


title: Cortex from wildtype Mice - WT rep3


title: 11_miRNA


title: 10_miRNA


title: Cortex from Stxbp6-null Mice - KO rep2


title: MF79_flg22_rep3 (MAE060)


title: 12_miRNA


title: 159_miRNA


title: MF79_flg22_rep2 (MAE059)


title: Horse 8, timepoint 0 h

city: Aberystwyth

first: Maithe

middle: Monteiro

last: Rocha Monteiro de Barros

state: Ceredigion

address: Penglais Campus

institute: Aberystwyth University

data_processing:
Illumina Hiseq pair-end reads were trimmed and clipped for quality control in Trimommatic v0.33
Trimming: Illuminaclip; leading or trailing = 30; slidingwindow 4:30; minlen = 100; headcrop = 10
Read quality was checked for each sample using FastQC v0.11.2
Trimmed reads were mapped to the reference genome using Bowtie v2.2.3 and TopHat v2.0.14 for aligment into BAM files
The number of reads/fragments assigned to genomic features for each sample was
BAM files were imported to R and differentially expressed genes were identified using DESeq2 R/Bioconductor v1.28.1
Genome_build: EquCab3.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Equus caballus

source_name: Endometrium

growth_protocol: Explants were cultured for 24h, 48 and 72h in supplemented William's Liquied E Medium  (William’s phenol red free, 500 mL, A12176-01, Life Technologies, UK) with 0.01 µg/mL epidermal growth factor (EGF) (Recombinant Human Protein, 10605-HNAE-250, Life Technologies, UK) (Appendix 3.2), 0.1 mg/mL neomycin (N6386, Sigma, UK) and streptomycin (S6501, Sigma, UK) solution (Appendix 3.2), 2 miliMolar (mM) of L-Glutamine (25030-032, Life Technologies, UK), 2.5 µg/mL amphotericin B (A2942-20ML, Sigma, UK), 5 mL of insulin-transferrin-selenium (ITS) (Gibco, 100X, 10524233, Fisher, UK) and 50 mL of batch tested foetal bovine serum (FBS) (Invitrogen FBS Heat Inactivated 500 mL, 10695023, Fisher, UK).

extract_protocol:
Biopsies at 0 h were taken in duplicate (per animal) from the uterine horn bifurcation at the abattoir, placed into 1.5 mL of RNALater (10437114, Fisher, UK) in RNAse/DNAse free tubes, kept at 4 °C for 24 h. RNALater was removed from the tubes and tissues were stored at -80 °C until extraction. The explant culture was performed in triplicate for timepoint per animal. After periods of 24, 48 and 72 h explants were removed from the well and stored in 1.5 mL of RNALater for a 24 h period at 4 °C, RNALater removed and explants stored at -80 °C for future RNA extraction. Total RNA was extracted from endometrial samples using the GeneJET RNA Purification kit (Thermo Scientific, UK) following the manufacturer's instructions.
cDNA synthesis, fragmentation and library preparation were performed using the Illumina TruSeq Stranded mRNA kit #20020594 according to the manufacturer's instructoins to prepare the dual-indexed next-generation sequencing libraries

treatment_protocol: No treatment

value: 0 h


title: Horse 8, timepoint 24 h


title: MF79_flg22_rep1 (MAE058)


title: Horse 8, timepoint 48 h


title: 151_miRNA


title: Horse 8, timepoint 72 h


title: Horse 7, timepoint 72 h


title: 149_miRNA


title: Horse 7, timepoint 24 h


title: Horse 7 timepoint 0 h


title: MF79_Mock_rep3 (MAE057)


title: Horse 7, timepoint 48 h


title: 199_miRNA


title: Horse 6, timepoint 72 h


title: Horse 6, timepoint 48 h


title: Horse 6, timepoint 24 h


title: MF105_Mock_rep1 (MAE061)


title: Horse 6, timepoint 0 h


title: 198_miRNA


title: MF79_Mock_rep2 (MAE056)


title: MF79_Mock_rep1 (MAE055)


title: MF50_flg22_rep3 (MAE054)


title: 166_miRNA


title: Horse 5, timepoint 48 h


title: Horse 5, timepoint 0 h


title: Horse 5, timepoint 24 h


title: 163_miRNA


title: Horse 5, timepoint 72 h


title: MF50_flg22_rep2 (MAE053)


title: Horse 4, timepoint 72 h


title: Horse 4, timepoint 48 h


title: 162_miRNA


title: MF50_flg22_rep1 (MAE052)


title: Horse 4, timepoint 0 h


title: Horse 4, timepoint 24 h


title: 7_miRNA


title: Horse 3, timepoint 24 h


title: 9_miRNA


title: Horse 3, timepoint 72 h


title: MF50_Mock_rep3 (MAE051)


title: Horse 3, timepoint 0 h


title: Horse 3, timepoint 48 h


title: MF50_Mock_rep2 (MAE050)


title: 6_miRNA


title: Horse 2, timepoint 72 h


title: 158_miRNA

value: 11.14 weeks


title: MF50_Mock_rep1 (MAE049)


title: MF47_flg22_rep3 (MAE048)


title: Horse 2, timepoint 24 h


title: 156_miRNA


title: Horse 2, timepoint 48 h


title: Horse 1, timepoint 72 h


title: MF47_flg22_rep2 (MAE047)


title: Horse 2, timepoint 0 h


title: MF47_flg22_rep1 (MAE046)


title: Horse 1, timepoint 48 h


title: Horse 1, timepoint 0 h


title: Horse 1, timepoint 24 h


title: 146_miRNA


title: 4


title: MII NSN rep3

city: Beijing

first: Ting

last: WANG

address: Qinghuayuan Street

institute: Tsinghua University

data_processing:
Adapter sequences were trimmed using TrimGalore (v0.4.4).
Clean reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.5) software with Ensembl Annotation. Read counts and Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated by RSEM (v1.2.28).
Differential expressed genes were analyzed by DESeq2 package (v1.20.0).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-seperated files include read counts or FPKM values for all samples.

source_name: single oocyte

growth_protocol: Oocytes  were cultured in IVM medium at 37.5℃ in 5% CO2 incubator.

extract_protocol:
After removing the zona pellucida, oocytes were lysed in lysis buffer.
For RNA-seq, cDNA was generated using the SMART-seq2 protocol. Then cDNA was fragmented by Tn5 enzyme and subjected to Illumina Nextera library preparation. All libraries were sequenced on Illumina HiSeq X-10 according to the manufacturer’s instruction.

treatment_protocol: Oocytes were injected with FBL-GFP mRNA, treated with Cilostamide for 6 hrs, then classified according to FBL-GFP marked nucleolus pattern, then released and cultured to specific maturation stages in 37.5℃ and 5% CO2 incubator.

value: oocyte


title: 3

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.


title: MII NSN rep1


title: MII SN rep4


title: MF47_Mock_rep1 (MAE043)


title: MII SN rep3


title: MF47_Mock_rep2 (MAE044)


title: 1


title: MII SN rep2


title: GV NSN rep3


title: MII SN rep1


title: 170


title: 173


title: MF41_flg22_rep2 (MAE041)


title: 12


title: MF41_flg22_rep1 (MAE040)


title: 11


title: LDHA-KO Th17 cell (CD44Low CD62LHi) rep2

city: New York

first: Sagar

last: Chhangawala

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

data_processing:
Raw fastq files were first QC’d using FASTQC to ensure read qualities were greater than phred score of 30. Paired-end reads were then aligned using STAR v2.3 to mouse genome (mm10). The mapped reads were counted against gene models from Ensembl transcriptome (v90) using htseq-count (v0.6.0, parameters -t exon).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited counts file

source_name: draining lymph nodes

extract_protocol:
In the experimental autoimmune encephalomyelitis model, WT CD44HiCD62LLo, WT CD44LoCD62LHi and KO CD44LoCD62LHi 2D2 T cells were isolated from the draining lymph nodes of recipient mice on day 9 post-immunization by fluorescence-activated cell sorting. Total RNA was extracted with RNeasy kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell types

value: primary mouse CD4 2D2 T cells

tag: genotype

value: LDHA knockout


title: GV NSN rep1


title: MF47_Mock_rep3 (MAE045)


title: GV SN rep3


title: 10

tag: age


title: LDHA-KO Th17 cell (CD44Low CD62LHi) rep1


title: MII NSN rep2


title: WT Th17 cell (CD44Low CD62LHi) rep2


title: MF41_Mock_rep2 (MAE038)


title: MF41_Mock_rep1 (MAE037)


title: MF41_flg22_rep3 (MAE042)


title: GV SN rep1


title: MF40_flg22_rep3 (MAE036)


title: 151


title: 159


title: GV SN rep2


title: GV NSN rep2


title: 149


title: MF40_flg22_rep2 (MAE035)


title: WT Th17 cell (CD44Hi CD62LLow) rep1


title: ETS2

data_processing:
Basecalls performed using CASAVA version 1.8
ChIPseq reads were aligned to mm9 using bowtie2 software
Peaks were called using peak caller algorithm in HOMER suite using fdr cut off of 0.01
Peak.txt files were converted to bed format
Genome_build: mm10
Supplementary_files_format_and_content: peaks files in .bed format

source_name: endothelial cell

extract_protocol:
10 µg of either ETS1 or ETS2 antibody was used to immunoprecipitate soluble chromatin from 15 million aortic endothelila cells. After wash and elution aproximately 5-10 ng of the chromatin immunoprecipitate was used for library construction
Illumina single end ChIP-seq protocol was used to construct the library.

value: aortic endothelial cell


title: MF40_flg22_rep1 (MAE034)

source_name: Seedlings


title: MF41_Mock_rep3 (MAE039)


title: HMJ5-380

city: Huntington

first: Sandrine

last: Pierre

state: West Virginia

address: 1676 Third Avenue

department: MIIR

institute: Marshall University

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data.
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, 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 includes log2FoldChange, padj, gene name
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted from cardiac tissue using Trizol® reagent (Life Technologies, Carlsbad, CA, USA) and the RNeasy Midi Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
RNA-seq was performed by Novogene (Sacramento, CA, USA) using the Illumina NovaSeq 6000 system.

value: Na/K-ATPase a1s/sa2s/s (sensitive)

value: 3 months

value: Heart


title: 166

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10/hg19 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: Genome_build: mm10/hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample


title: HMJ5-370

value: Na/K-ATPase a1r/ra2s/s (resistant)


title: MF40_Mock_rep2 (MAE032)


title: MF40_Mock_rep3 (MAE033)


title: 163


title: ETS1


title: 198


title: HMJ5-369


title: S3_S_3 (bicolor leaf development)

city: Shenyang City

first: jie

last: ren

address: Dongling Road NO.120

institute: Shenyang Agricultural University

description: Bicolor leaf during development proceeded as follows: S1, leaves are red; S2, red appears at the leaf center, although the margins are green; and S3, the leaf center is red while the margins are green. Samples of the green margin at S3.

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 brassica_oleracea ensemble v38 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM. estimate the expression levels of all transcripts. software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: brassica_oleracea ensembl v38 (ftp://ftp.ensemblgenomes.org/pub/release-38/plants/genbank/brassica_oleracea/)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Brassica oleracea

source_name: Brassica oleracea L. var. acephala

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: leaf

tag: leaf developmental stage

value: the green margin at S3


title: WT Th17 cell (CD44Hi CD62LLow) rep2


title: WT Th17 cell (CD44Low CD62LHi) rep1


title: HMJ5-381

tag: tissue


title: S3_S_2 (bicolor leaf development)


title: HMJ5-368


title: 162


title: S3_S_1 (bicolor leaf development)


title: 9