title: U87MG_SC_2-1-10F_3-1-8G_20190922-Plate1-8B

value: U87MG likely glioblastoma cell line


title: YBEY KO #2

status: Public on Feb 26 2020

type: SRA

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
KO_rep2_sort
mtDNA
processed data file: counts_stranded.txt

library_source: transcriptomic

data_processing:
Reads libraries were converted from bam format to fastq format with the bamtofastq version v2.26.0 from the bedtools package. Adapters were trimmed with cutadapt version 1.15. Reads were then mapped to the Mitochondrion genome Genbank accession J01415.2 using Segemehl version 0.1.7 with -q and -p options for paired reads. The generated sam files were converted to bam files using samtools version 1.4 with qview and -bS options.
Feature quantification was done using featureCounts version v1.4.6 from the Subread package with the following options -T (10) -p -t (exon) -0 -g (gene_id) -s 1 with a manually curated mitochondrion genome annotation provided in appendix.
Differential analysis was done with the DeSeq2 package version 1.16.1 in R version 3.4.4. All conditions were compared.
Genome_build: Homo sapiens mitochondrion, complete genome GenBank version: J01415.2.
Supplementary_files_format_and_content: counts_stranded.txt: Tab-delimited text file.

molecule: total RNA

organism: Homo sapiens

source_name: HEK293T-REx cells

extract_protocol:
RNA was extracted from isolated mitochondria with Trizol.
Standard stranded RNA-seq protocol without any enrichment.
Paired-end RNA-seq; HiSeqV4 PE50.

tag: cell line

tag: genotype

value: YBEY KO


title: Brain_10cell_Cereb-NeuNpos_20190321-Plate2-9A

city: La Jolla

first: Christopher

middle: Jen-Yue

last: Wei

state: CA

address: 9500 Gilman Dr

department: Bioengineering

country: USA

institute: University of California, San Diego

library_source: genomic

data_processing:
base-callingwith bcl2fastq with barcode-mismatch=0
methylpy on paired-end reads with min-qual-score=30
Genome_build: hg19
Supplementary_files_format_and_content: methylpy tsv file output (column 1=chromosome; column 2=position; column 3=strand; column 4=sequence context; column 5=number methylated reads; column 6=read coverage)

molecule: genomic DNA

source_name: Adult human post-mortem brain tissue

extract_protocol:
SDS cell lysis
RETrace methylation post-processing

tag: cell type

value: Human NeuN+ nuclei derived from cerebellum


title: Brain_100cell_Hipp-NeuNneg_20190321-Plate2-11A

value: Human NueN- nuclei derived from hippocampus


title: Brain_100cell_Hipp-NeuNpos_20190321-Plate2-2A

value: Human NeuN+ nuclei derived from hippocampus


title: p53 wt cell treated with belinostat (0.1uM) + 10uM Cisplatin

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description:
Calu-1 lung cancer cell line with p53 WT treated with Belinostat and Cisplatin
IonXpress_012

data_processing:
For AmpliSeq, fastq files was analyzed with the ampliSeqRNA plugin available for Ion Torrent sequencing platforms that used the Torrent Mapping Alignment Program (TMAP). TMAP first identify a list of Candidate Mapping Locations (CMLs) and aligned with Smith Waterman algorithm for specific and sensitive mapping.
Genome_build: hg19
Supplementary_files_format_and_content: RPM normalization values for each samples

source_name: Cell Line

growth_protocol: Cell lines were obtained directly from the American Type Culture Collection (ATCC), and were maintained in a humidified 37°C incubator, in culture medium (RPMI for Calu-1 and H2170; EMEM for MRC-5) supplemented with 10% fetal bovine serum, 2mM L-glutamine, 100 μg/mL streptomycin and 100 U/mL penicillin.

extract_protocol:
Cells were treated with the indicated treatment for 48hours, and RNA was extracted using Qiagen RNAeasy kit.
For Ion AmpliSeq Transcriptome Human Gene Expression (Thermo Fisher), 10 ng RNA was used for barcoded cDNA library preparation using PCR-based targeted-amplicon amplification according to manufacturer’s protocol. Pooled libraries were amplified emulsion PCR on Ion Torrent OneTouch2 instruments (OT2) and sequenced on Ion Torrent Proton sequencing system.

treatment_protocol: Cell lines were cultured in petri dishes and treated with either 0.01% DMSO or 0.1uM belinostat with 10uM cisplatin for 48 hours

tag: genotype/variation

value: p53 wild type

tag: treatment

value: belinostat (0.1µM) + 10µM Cisplatin


title: p53 wt cell treated with DMSO

description:
Calu-1 lung cancer cell line with p53 WT treated with DMSO
IonXpress_011

value: DMSO


title: YBEY KO #1

description:
KO_rep1_sort
mtDNA
processed data file: counts_stranded.txt


title: Brain_100cell_Cortex2-NeuNpos_20190321-Plate1-2A

value: Human NeuN+ nuclei derived from cortex


title: Brain_100cell_Cortex1-NeuNpos_20190321-Plate1-8A


title: Brain_100cell_Cortex1-NeuNneg_20190321-Plate1-11A

value: Human NeuN- nuclei derived from cortex


title: Brain_100cell_Cereb-NeuNpos_20190321-Plate2-8A


title: Hela_2 [miRNA-seq]

city: Hangzhou

first: lin

last: yinuo

address: Jiefang Road NO.88

country: China

institute: Second Affiliated Hospital of Zhejiang University

description:
IonXpressRNA_015_R_2016_12_09_16_20_44_sn247770157_NOV-436-LYN-SRNA_LYN-SRNA-ra
IonXpressRNA_015_R_2016_12_16_11_50_22_sn247770157_NOV-437-LYN2-SRNA_LYN2-SRNA-ra

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and Homo sapiens genome.
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: HeLa exosome

growth_protocol: HeLa cells and Hcer cell were cultured in RPMI1640 and high glocose DMEM respectively,supplemented with exosome-depleted FBS for 48 h and supernatents were collected for exosome isolation

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
miRNA Library Construction and RNA Sequencing:  The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA library had been size selected by PAGE Gel electrophoresis for miRNA sequencing. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

value: HeLa

value: human cervical carcinoma


title: Hela_3 [miRNA-seq]

description:
IonXpressRNA_016_R_2016_12_09_16_20_44_sn247770157_NOV-436-LYN-SRNA_LYN-SRNA-ra
IonXpressRNA_016_R_2016_12_16_11_50_22_sn247770157_NOV-437-LYN2-SRNA_LYN2-SRNA-ra


title: YBEY+ #1

description:
HT_rep1_sort
mtDNA
processed data file: counts_stranded.txt

value: YBEY+


title: Brain_1000cell_Hipp-NeuNpos_20190321-Plate2-1A


title: Brain_1000cell_Hipp-NeuNneg_20190321-Plate2-10A


title: ELP1-/- rep3

city: Trondheim

first: Nicola

middle: Pietro

last: Montaldo

address: Erling Skjalgssons gt 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: NTNU

description: knockout generated using SgRNA specific for ELP1 in combination with CRISPRCas9 system

data_processing:
Illumina 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 release 80 whole genome using STAR v2.4.2a with parameters --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Counting was performed using featureCounts in Bioconductor (3.2) package Rsubread (1.20.6) with the following settings: strandMode  antisense, featureLevel gene, countNonredundant TRUE, minFeatureOverlap 10, countTrimmedTranscripts  FALSE, trimmedMaxLength  200, minMapQuality 10, keepMultiHits TRUE
Data normalization and differential expression analysis was performed using DESeq2 v1.10.0 (Love et al. 2014 Genome Biology), in R v 3.2.2, with settings: featureLevel gene, grouping Group, and sampleGround WT, refGroup AAG-/- or ELP1-/-.
Genome_build: GRCh37 ensembl release 80
Supplementary_files_format_and_content: tab-delimited text files normalized read counts (DESeq2) for each sample (see settings detailed above).

growth_protocol: HEK293T cells were cultured in  Dulbecco’s modified Eagle Medium (DMEM) (Sigma Aldrich) supplemented with  Penicillin-Streptomycin (1% v/v Gibco, Invitrogen) and Fetal Bovine Serum (FBS) (10% v/v, Sigma-Aldrich) at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted from the pellets using RNAEasy Mini Kit (Qiagen, #74104).
RNA libraries were prepared for sequencing using standard Illumina protocols; TruSeq RNA Stranded (polyA)

tag: tissue

value: Human embryonic kidney 293 cells expressing a mutant version of the SV40 large T antigen


title: Hela_1 [miRNA-seq]

description:
IonXpressRNA_014_R_2016_12_09_16_20_44_sn247770157_NOV-436-LYN-SRNA_LYN-SRNA-ra
IonXpressRNA_014_R_2016_12_16_11_50_22_sn247770157_NOV-437-LYN2-SRNA_LYN2-SRNA-ra


title: Brain_1000cell_Cortex2-NeuNpos_20190321-Plate1-4A


title: Brain_1000cell_Cortex2-NeuNpos_20190321-Plate1-1A


title: ELP1-/- rep2


title: Hcer_3 [miRNA-seq]

description:
IonXpressRNA_013_R_2016_12_09_16_20_44_sn247770157_NOV-436-LYN-SRNA_LYN-SRNA-ra
IonXpressRNA_013_R_2016_12_16_11_50_22_sn247770157_NOV-437-LYN2-SRNA_LYN2-SRNA-ra

source_name: Human cervical epithelial cell exosome

value: HCER

value: normal human cervical epithelial cell line


title: Hcer_2 [miRNA-seq]

description:
IonXpressRNA_012_R_2016_12_09_16_20_44_sn247770157_NOV-436-LYN-SRNA_LYN-SRNA-ra
IonXpressRNA_012_R_2016_12_16_11_50_22_sn247770157_NOV-437-LYN2-SRNA_LYN2-SRNA-ra


title: ELP1-/- rep1


title: Brain_1000cell_Cortex2-NeuNneg_20190321-Plate2-4A


title: Brain_100cell_Cortex2-NeuNpos_20190321-Plate1-5A


title: Brain_1000cell_Cortex1-NeuNpos_20190321-Plate1-7A


title: Brain_100cell_Cortex2-NeuNneg_20190321-Plate2-5A


title: YBEY+ #3

description:
HT_rep3_sort
mtDNA
processed data file: counts_stranded.txt


title: AAG-/- rep3

description: knockout generated using SgRNA specific for AAG in combination with CRISPRCas9 system

value: AAG-/-


title: Brain_1000cell_Cereb-NeuNpos_20190321-Plate2-7A


title: HUVEC+HeLa exo_exo3

description:
IonXpressRNA_016_R_2017_03_14_11_58_50_sn247770157_NOV-485-LYN_Auto_sn247770157_NOV-485-LYN_535
IonXpressRNA_016_R_2017_03_15_11_28_03_sn247770157_NOV-487-LYN2_Auto_sn247770157_NOV-487-LYN2_537

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
MapSplice mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: HUVEC+HeLa exo

growth_protocol: Cells were isolated from umbilical vein by digestion using 1 mg/ml collagenase I (Gibco, USA) for 30 min. cells were cultured in EGM2 supplemented with 10% FBS, cells at 6th passage were used for sequencing

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction:  The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: 6th passage HUVECs were treated with 10μg/ml HeLa exosome or 10μg/ml Hcer exosome for 48 h，and total RNA was then extracted for RNA sequencing.

value: HUVEC

value: human umbilical vein endothelial cell

tag: passage

value: 10μg/ml HeLa exosome


title: Hcer_1 [miRNA-seq]

description:
IonXpressRNA_010_R_2016_12_09_16_20_44_sn247770157_NOV-436-LYN-SRNA_LYN-SRNA-ra
IonXpressRNA_010_R_2016_12_16_11_50_22_sn247770157_NOV-437-LYN2-SRNA_LYN2-SRNA-ra


title: R474-15-P3759

city: Houston

first: Christine

middle: B.

last: Peterson

state: TX

address: 1400 Pressler St.

department: Biostatistics

institute: University of Texas MD Anderson Cancer Center

data_processing:
The sequencing reads were aligned to mouse reference genome (mm10) with tophat2
Gene-based read counts were generated by HTSeq
The raw counts were normalized with R package DESeq
Genome_build: mm10
Supplementary_files_format_and_content: csv (comma separated value) file with normalized gene expression values

organism: Mus musculus

source_name: Tumors of Pbrm1 KO #18 cells

growth_protocol: Four to six week-old-female Balb/c mice were purchased from TACONIC. 5X105 Renca cells were suspended in 100 µl Matrigel Matrix (Corning, 354234) diluted with PBS at 1:1, and subcutaneously injected into the backs of mice.

extract_protocol: Mice were sacrificed once the tumors reached 1000mm3, ulceration occurred, or animals showed signs of distress. Tumors were fixed in RNA stabilization reagent for RNA extraction or in 10% buffered formalin phosphate for IHC or Opal staining.

treatment_protocol: Mice were left untreated or treated with PD-1 antibody (100 µg/mouse/3 days) via intraperitoneal injection (I.P.) for 3 times every third day. After the tumors were palpable (i.e., tumor volume reached around100 mm3), tumors were measured every day with caliper, and volume calculations were obtained using the formula V = (W2 × L)/2.

value: Pbrm1 KO #18


title: R474-14-P3758


title: YBEY+ #2

description:
HT_rep2_sort
mtDNA
processed data file: counts_stranded.txt


title: R474-13-P3757


title: AAG-/- rep2


title: HUVEC+HeLa exo_exo2

description:
IonXpressRNA_015_R_2017_03_14_11_58_50_sn247770157_NOV-485-LYN_Auto_sn247770157_NOV-485-LYN_535
IonXpressRNA_015_R_2017_03_15_11_28_03_sn247770157_NOV-487-LYN2_Auto_sn247770157_NOV-487-LYN2_537


title: R474-12-P3756


title: R474-10-P3754

source_name: Tumors of Pbrm1 KO #4 cells

value: Pbrm1 KO #4


title: Brain_10cell_Cortex2-NeuNneg_20190321-Plate2-6A


title: AAG-/- rep1


title: WT rep3

description: generated using CRISPR Cas9 system without any SgRNA

value: wild type


title: R474-9-P3753


title: R474-8-P3752


title: KO_Light_3

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: Mouse brown adipocytes  RNA-seq by Illumina HiSeq 2500

data_processing:
Paired-end sequencing reads from HiSeq 2500 were subjected to adaptor-trimming using cutadapt Version 1.1 , and quality-trimmed using Trimmomatic Version 0.32.
TopHat (version 2.0.14) was used with the default parameters to map the reads to the reference genome (GRCm38, mm10).
Counts were calculated using Cufflinks (version2.2.1) with a transcriptome reference (Ensembl Mouse Transcript).
Genome_build: GRCm38, mm10
Supplementary_files_format_and_content: CSV file contains read counts.

source_name: Brown adipocytes

extract_protocol:
Total RNA was extracted from cells using the spin column kit (Zymo Research).
The Illumina TruSeq Stranded mRNA protocol was used for the preparation of RNA sequencing (RNA-Seq) libraries.

value: KO

tag: light condition

value: Light


title: Brain_1000cell_Cortex1-NeuNneg_20190321-Plate1-10A


title: HUVEC+Hcer exo_CTL3

description:
IonXpressRNA_010_R_2017_03_14_11_58_50_sn247770157_NOV-485-LYN_Auto_sn247770157_NOV-485-LYN_535
IonXpressRNA_010_R_2017_03_15_11_28_03_sn247770157_NOV-487-LYN2_Auto_sn247770157_NOV-487-LYN2_537

source_name: HUVEC+Hcer exo

value: 10μg/ml Hcer exosome


title: R474-7-P3751


title: WT rep2


title: R474-6-P3750


title: WT rep1


title: HUVEC+Hcer exo_CTL1

description:
IonXpressRNA_008_R_2017_03_14_11_58_50_sn247770157_NOV-485-LYN_Auto_sn247770157_NOV-485-LYN_535
IonXpressRNA_008_R_2017_03_15_11_28_03_sn247770157_NOV-487-LYN2_Auto_sn247770157_NOV-487-LYN2_537


title: R474-5-R3749

source_name: Tumors of Renca parental cells

value: Renca


title: R474-2-R3746


title: HH gr8i Day16

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

data_processing:
Alignment software: STAR version 2.3.0ewith default parameters and annotated genome with UCSC hg19 gtf
Sam to BAM and sorting: sambamba version 0.6.7
Read counts: Rsubread version 1.30.9 with in built annotation hg19 and default parameters
Count normalization: DESeq2 version 1.20.0 function "counts" with normalization parameter=TRUE
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix of normalized counts with the DESeq2 function "counts" and normalization parameter = TRUE

source_name: gr8i Day16

growth_protocol: Human PSC (H1, HERVH, D2#2, D2#4) were maintained in conventional primed conditions, specifically, by culture on growth factor-reduced phenol red-free matrigel (BD Biosciences #356231) with mTeSR (Stem Cell Technologies). Cultures were passage every 5-7 days manually using either 2mg/ml dispase (Gibco), 0,5 μM EDTA/1xPBS, or accutase (Gibco).

extract_protocol:
Total RNA was extracted from cells on column by RNeasy kit with DNA digestion following provider’s recommendations (Qiagen #74104, #79254),
total RNA with RIN numbers in the range 9.0 to 10 (Agilent 2100 Bioanalyzer), were used. For library construction 10 ng of total RNA samples were processed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) by following manufacturer instructions. Resulting cDNA was sheared on a S220 Focused-ultrasonicator (Covaris) and subsequently processed with the ""NEBNext Ultra II DNA Library Prep Kit for Illumina"" (NEB #E7645). Briefly, oligo(dT)-primed reverse transcription was performed in presence of a template switching oligonucleotide, double stranded cDNA was produced by 11 cycles of PCR and submitted to acoustic shearing. Fragments were processed through subsequent enzymatic treatments of end repair, dA-tailing, and ligation to Illumina adapters. Adapter-ligated libraries were completed by limited-cycle PCR (8 cycles). The resulting directional cDNA libraries were sequenced for 50 bases in a single-read format, instrument: Illumina HiSeq2500. Primary data processing: Image analysis, per-cycle base-calling and quality score assignment was performed with Illumina Real Time Analysis software.

treatment_protocol: Human PSC were cultured in three media conditions. Standard primed conditions ("Primed" = mTeSR media with FGF2 and TGFb1, feeder-free, on matrigel); or, including additional media supplementation with recombinant human LIF (10 mg/ml) and CDK8/19-small molecule inhibitor at 0,4 mM (= "CDK8/19i" or "8i"); or, for the "gr8i" condition: recombinant human LIF (10 mg/ml), CDK8/19-small molecule inhibitor at 0,4 mM, GSK3-inhibitor CHIR99021 at 1 mM, plus IWR1 at 5 mM.

value: Pluripotent stem cells (PSCs)

tag: condition

value: gr8i Day16

value: HH


title: R474-3-R3747


title: R474-1-R3745


title: R474-4-R3748


title: Villi_Prdm16 KO 3

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: Smilow Center for Translational Research, 12th Floor 3400 Civic Center Blvd. Bldg 421

department: Institute for Diabetes, Obesity & Metabolism

institute: University of Pennsylvania

data_processing:
RNA-seq was performed by the University of Pennsylvania Next Gen Sequencing Core using a HiSeq 2000 high output sequencer.  Differential expression was determined using the EdgeR software package using log2 fold change of KO divided by WT. 0-1 False Discovery Rates were calculated from the p-value using a Benjamini-Hochberg correction
Genome_build: mm9
Supplementary_files_format_and_content: log2 fold change spreadsheet

source_name: Prdm16 KO Villi 3 days

extract_protocol:
Total RNA was extracted from isolated villi using TRIzol (Invitrogen) combined with Purelink RNA Mini columns (Fisher).
RNA-seq libraries were generated using  a Truseq RNA Sample Preparation kit (Version 2, Illumina, RS-122-2001).

treatment_protocol: RNA was isolated from duodenal villi of WT (Prdm16loxP/loxP) or KO (Rosa26CreERT2; Prdm16loxP/loxP ) mice 3 days after tamoxifen injection.

value: Rosa26CreERT2; Prdm16loxP/loxP


title: R474-11-P3755


title: H1 Primed

source_name: Primed

value: Primed


title: D2#4 Primed


title: Ws rep 2 (RNA-Seq)

city: Knoxville

first: Sarbottam

last: Piya

state: Tennessee

address: 2431 Joe Johnson Dr.

department: Plant Science

institute: University of Tennessee

data_processing:
Low quality reads were removed using Trimmomatic.
TopHat v2.0.14 was used to map the reads to the Arabidopsis reference genome (TAIR10).
Number of reads mapped to each annotated Arabidopsis gene were counted using HTSeq.
Diferentially expressed genes were identified using the R package DESeq2
Genome_build: Arabidopsis reference genome (TAIR10).
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each sample.

organism: Arabidopsis thaliana

source_name: Whole plant

growth_protocol: Seeds of 35S:GRF1-GFP, 35S:GRF3-GFP, grf1/grf2/grf3, and WS were planted on MS medium in a randomized complete-block design with three replications. Two-week-old plants were collected, frozen in liquid nitrogen and grounded into fine powder.

extract_protocol:
mRNA was isolated using magnetic mRNA isolation kit (NEB) following manufacturer’s protocol.
RNA-seq libraries were prepared from 250 ng of mRNA using NEBnext mRNA library prep master mix (NEB) following manufacturer’s protocol.

tag: strain

value: Ws

value: Whole plant

tag: age

value: 14 days


title: Villi_Prdm16 KO 2


title: Villi_Prdm16 KO 1


title: HUVEC+HeLa exo_exo1

description:
IonXpressRNA_014_R_2017_03_14_11_58_50_sn247770157_NOV-485-LYN_Auto_sn247770157_NOV-485-LYN_535
IonXpressRNA_014_R_2017_03_15_11_28_03_sn247770157_NOV-487-LYN2_Auto_sn247770157_NOV-487-LYN2_537

value: HUVEC

value: human umbilical vein endothelial cell


title: Villi_Control 2

source_name: Control Villi


title: Villi_Control 3


title: Ws rep 1 (RNA-Seq)


title: D2#4 8i Day16

source_name: 8i Day16

value: 8i Day16


title: Prdm16 KO 3

data_processing:
RNA-seq was performed by the University of Pennsylvania Next Gen Sequencing Core using a HiSeq 2000 high output sequencer.  Differential expression was determined using the EdgeR software package using log2 fold change of KO divided by WT. 0-1 False Discovery Rates were calculated from the p-value using a Benjamini-Hochberg correction
Genome_build: mm9
Supplementary_files_format_and_content: [Log2_FC_Prdm16_KO_vs_WT.txt]  log2 fold change spreadsheet; log2 transformed quantile normalized read counts (columns H-M); raw read counts (columns N-S)

source_name: Prdm16 KO crypts 3 days

extract_protocol:
Total RNA was extracted from isolated crypts using TRIzol (Invitrogen) combined with Purelink RNA Mini columns (Fisher).
RNA-seq libraries were generated using  a Truseq RNA Sample Preparation kit (Version 2, Illumina, RS-122-2001).

treatment_protocol: RNA was isolated from duodenal crypts of WT (Prdm16loxP/loxP) or KO (Rosa26CreERT2; Prdm16loxP/loxP ) mice 3 days after tamoxifen injection.

value: Prdm16 KO

value: Duodenal crypts


title: grf1/grf2/grf3 rep3 (RNA-Seq)

value: grf1/grf2/grf3 mutant


title: HUVEC+Hcer exo_CTL2

description:
IonXpressRNA_009_R_2017_03_14_11_58_50_sn247770157_NOV-485-LYN_Auto_sn247770157_NOV-485-LYN_535
IonXpressRNA_009_R_2017_03_15_11_28_03_sn247770157_NOV-487-LYN2_Auto_sn247770157_NOV-487-LYN2_537


title: Prdm16 KO 2


title: H1 gr8i Day16


title: D2#2 gr8i Day16


title: grf1/grf2/grf3 rep2 (RNA-Seq)


title: Prdm16 KO 1


title: grf1/grf2/grf3 rep1 (RNA-Seq)


title: Ws rep 3 (RNA-Seq)

value: wild type


title: Control 3

source_name: Control crypts

value: control


title: D2#4 gr8i Day16


title: Control 2


title: KO Input

data_processing:
Sequencing reads were aligned to mm9 using bowtie
Peaks from WT and KO were pooled to make a master peak set and overlapping peaks were merged if their center distance is < 100bp.
H3K27ac signal was measured for WT and KO in RPM scale within 2kb windows centering around the center of the master peaks. These signals were further normalized using 'normalize.loess' in affy, R package.
Differential H3K27ac peaks were defined by 1.5 fold-change cut off after adding a pseudo value 1.
All the bigwig files for ChIP-seq data were generated using Homer and bedGraphToBigWig command in RPM scale
Genome_build: mm9
Supplementary_files_format_and_content: .bw files; bed files of called peaks that results from the comparison between .bw files.

source_name: Duodenal crypts

extract_protocol: Wt and KO Crypts were isolated from 3 mice each, pooled, and fixed with 1.l% formaldehyde for 15 min at room temperature and then quenched  with 2.5 M glycine for 5 mins at room temperature. Samples were washed with PBS, pelleted and resuspended in ChIP lysis buffer (0.6% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris at pH 8) with protease inhibitors (Roche) and 1 mM PMSF. Crypts were sonicated to shear chromatin using an Active Motif EpiShear platform (8 minutes active time, 30 sec on, 20 sec off, amplitude 25%). To a achieve a final concentration of 0.1% SDS, chromatin was diluted 1:6 with ChIP dilution buffer (1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris at pH 8).  Inputs were removed.  Chromatin was split into  primary antibodies were added for overnight incubation at 4°C with rotation with 3ug anti H3K27Ac (Active Motif, 39133). Protein A Sepharose beads (GE healthcare) were then added for 4 hours at 4°C. Samples were washed twice with wash buffer 1 (0.1% SDS, 0.1% NaDOC, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris at pH 8), once with wash buffer 2 (0.1% SDS, 0.1% NaDOC, 1% Triton X-100, 0.5 M NaCl, 1 mM EDTA, 20 mM Tris at pH 8), once with wash buffer 3 (0.25 M LiCl, 0.5% NaDOC, 0.5% NP-40, 1 mM EDTA, 20 mM Tris at pH 8), and twice with wash buffer 4 (1 mM EDTA, 20 mM Tris at pH 8).  Samples were then eluted from beads with warm 100 mM NaHCO3/1% SDS buffer. Samples were reverse cross-linked overnight at 65°C with RNase A and then treated with proteinase K and column purified (Clontech NucleoSpin). ChIP enrichment was calculated as percent of input. H3K27 ChIP WT and KO samples were prepared as ChIPseq libraries and sequenced using a HiSeq 2000 high output sequencer.

treatment_protocol: Control and R26R-CreERT2; Prdm16 loxp/loxp mice were injected with tamoxifen 3 days before crypt extraction

tag: chip antibody


title: Control Input


title: GRF3 rep2 (RNA-Seq)

value: GRF3 overexpression


title: Villi_Control 1


title: HH 8i Day16

value: Pluripotent stem cells (PSCs)


title: D2#2 Primed


title: Control 1


title: GRF3 rep3 (RNA-Seq)


title: GRF3 rep1 (RNA-Seq)


title: Prdm16 KO  H3K27ac ChipSeq

value: H3K27Ac (Active Motif, 39133)


title: HH Primed

value: HH


title: D2#2 8i Day16


title: H1 8i Day16


title: GRF1 rep1 (RNA-Seq)

value: GRF1 overexpression


title: GRF1 rep2 (RNA-Seq)


title: 35S:GRF3-GFP Rep 3 (ChIP-Seq)

data_processing:
Quality was assessed using FastQC
Low-quality reads were trimmed using Trimmomatic
Reads were mapped using Bowtie2
Binding peaks were called using MACS2
Regulatory Sequence Analysis Tools suite was used to identify the cis-binding motifs
Genome_build: Ws genome constructed by replacing Ws SNPs from the 1,001 genome projects into the Columbia genome (TAIR10)
Supplementary_files_format_and_content: narrowPeak

growth_protocol: Seeds of 35S:GFP, 35S:GRF1-GFP, and 35S:GRF3-GFP were planted on MS medium in a randomized complete-block design with three replications. Two-week-old plants were collected, frozen in liquid nitrogen and grounded into fine powder.

extract_protocol: The ChIP-seq libraries were prepared from the purified ChIP-DNA using NEBNext Ultra II DNA Library Prep Kit (NEB E7645, Illumina) following manufacturer’s instructions

value: anti-GFP antibody (5 mg/ml, Abcam)


title: Restricted DO_Late-log Phase_Run3

type: RNA

city: Bethesda

first: Ashish

middle: K

last: Sharma

state: MD

address: 14 Service Rd West Building 14A Room 176 MS-5522

department: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

institute: National Institute of Health

description: Gene expression data from culture sample in late-log phase at restricted DO

hyb_protocol: Fragmented and Biotin labeled ds-cDNA were hybridized to array at final concentration 55ng/ul at 45 degree for 16 hours in AffyMetrix Hybridization oven. Then array were washed/stained with AffyMetrix Fluidic Station using protocol FS450_0006 according to manufacturer suggested.

scan_protocol: Stained array were scanned using AffyMetrix GeneChip Scanner GCS3000 System, data were generated in AffyMetreix GeneChip Command Console.

data_processing: The data were analyzed using the Partek Genomics Suite. The following parameters were used-- Algorithm: RMA; Background Correction: RMA Background Correction; Normalization: Quantile Normalization; Log Probes using Base: 2; Probeset Summarization: Median Polish.

label: Biotin

organism: Escherichia coli

source_name: sample collected at late-log phase

label_protocol: 50ng of total RNA were used for target preparation. RNA was amplified, fragmented and labeled with Biotin using manufacturer standard protocol.

growth_protocol: Modified Terrific Broth (TB) media was used throughout the growth experiments: 24 g/L yeast extract, 12 g/L  Tryptone, 12.4 g/L  K2HPO4,  2.35 g/L KH2PO4, 0.5 g/L MgSO4·7H2O, 1 ml/L of trace element solution (27 g/L FeCl3·6H2O,  2 g/L ZnCl2·4 H2O, 2 g/L CoCl2·6H2O, 2 g/L NaMoO4·2H2O, 1 g/L CaCl2·2H2O, 1 g/L CuCl2, 0.5 g/L H3BO3, 100 ml/L HCl  concentrated [75], and 25 mg/L kanamycin, supplemented with 15 g/L glycerol as indicated.

extract_protocol: Total RNA was extracted using hot phenol method.

treatment_protocol: The unrestricted DO (30%) condition was maintained with a constant supply of 2 vvm air cascaded to agitation, and the restricted DO conditions were supplied with 2 vvm air and a fixed agitation of 650 rpm. pH was controlled at 7.0 by addition of 2M NaOH and 10% H2CO3.

tag: phase

value: Late-log

tag: dissolved oxygen

value: restricted


title: Restricted DO_Late-log Phase_Run1


title: Restricted DO_Late-log Phase_Run2


title: Restricted DO_Log Phase_Run3

description: Gene expression data from culture sample in log phase at restricted DO

source_name: sample collected at log phase

value: Log


title: 35S:GRF3-GFP Rep 2 (ChIP-Seq)

value: Whole plant

value: Ws


title: Control H3K27ac ChipSeq


title: 35S:GRF3-GFP Rep 1 (ChIP-Seq)


title: GRF1 rep3 (RNA-Seq)

value: 14 days


title: 35S:GRF1-GFP Rep 3 (ChIP-Seq)


title: Restricted DO_Log Phase_Run2


title: Restricted DO_Log Phase_Run1


title: 35S:GRF1-GFP Rep 2 (ChIP-Seq)


title: 35S:GRF1-GFP Rep 1 (ChIP-Seq)


title: Unrestricted DO_Late-log Phase_Run3

description: Gene expression data from culture sample in late-log phase at unrestricted DO

value: unrestricted


title: Unrestricted DO_Late-log Phase_Run2


title: Unrestricted DO_Log Phase_Run3

description: Gene expression data from culture sample in log phase at unrestricted DO


title: Unrestricted DO_Late-log Phase_Run1


title: 35S:GFP Rep 3 (ChIP-Seq)


title: Unrestricted DO_Log Phase_Run1


title: Unrestricted DO_Log Phase_Run2


title: NC-2F: lung_control

city: Lanzhou

first: Dongmei

last: Chen

address: No. 35 Dingxi east road, chengguan district, Lanzhou, Gansu province

institute: Gansu University of Chinese Medicine

description: Gene expression in control group

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy5-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: we established the aging mice model, and used the traditional Chinese medicine Codonopsis pilosula to intervene. Then total RNA was extracted from lung tissues in the control group, the model group and high dose Codonopsis pilosula intervention group (n=3 mice).

value: lung

tag: gender

value: female


title: 35S:GFP Rep 2 (ChIP-Seq)


title: NX-1F: lung_control

description: Gene expression in control group

value: male


title: NC-1F: lung_control

description: Gene expression in control group


title: Naive_KO [15]

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

description:
Not DSS treated
sample name:
15

hyb_protocol: RNA was hybridised to Illumina MouseWG6_V2_0_R3_11278593_A arrays

scan_protocol: Scanning was performed using standard Illumina procedures.

data_processing:
Raw scanner output was processed in R/Bioconductor using the lumi package.  Features with probe detection values greater than zero were retained, background corrected, and normalised with rst and vsn algorithms in the lumi package.  Pair-wise group comparisons were performed using the limma package from Bioconductor.
The raw data matrix contains all raw output values in a full and un-normalised format.  The normalised matrix contains the normalised values for the detected probes, as described above.

source_name: Colon epithelium (FACS sorted)

label_protocol: RNA quality and integrity was determined using Agilent RNA 6000 Nano Kit. RNA integrity number >9 was used for downstream processing. RNA was labelled using TotalPrep RNA amplification kits (Life Technologies)

extract_protocol: Total RNA was purified using RNeasy mini kits (Qiagen).

value: Colon epithelium


title: DSS_KO [5R]

description:
2% DSS treated
sample name:
5R


title: 35S:GFP Rep 1 (ChIP-Seq)


title: Naive_KO [13]

description:
Not DSS treated
sample name:
13


title: PC-3F: lung_D-galactose,sodium nitrite_42d

description: Gene expression in aging mice

source_name: lung_D-galactose,sodium nitrite_42d


title: Naive_KO [14]

description:
Not DSS treated
sample name:
14


title: PC-2F: lung_D-galactose,sodium nitrite_42d

description: Gene expression in aging mice


title: siKDM3A_2

city: Jerusalem

first: Maayan

last: Salton

address: Ein-Kerem Canpus

country: Israel

institute: Hebrew University

data_processing:
Illumina bcl2fastq, v2.17.1.14, was used for transforming basecalls to fastq files, using default parameters, for both sequencing runs.
Expression processing: Raw reads were quality trimmed at both ends with PHRED score threshold of 32, adapter sequences were trimmed with cutadapt, v1.12, leaving only reads of length 15 and above after trimming, and filtered for low-quality reads with the FASTX package, v0.0.14, with parameters -p 90 and -q 20. The remaining reads were then paired again to produce proper paired R1 and R2 files and a single file for single-reads. Alignment was done with TopHat, v2.0.14, with parameters -N 3 --read-gap-length 5 --read-edit-dist 8 --segment-length 20 --read-realign-edit-dist 3 --no-coverage-search --library-type fr-firststrand, given the Ensembl release 84 GTF file (-G), the GRCh38 genome index and the paired- and single-reads as input. Counts were calculated for each sequencing run with htseq-count, version 0.6.0, using parameters -s reverse and a GTF file masked for genes of type IG, TR, Mt, rRNA, tRNA, miRNA, misc_RNA, scRNA, snRNA, snoRNA, sRNA, scaRNA, piRNA, vaultRNA, ribozyme, artifact and LRG_gene. The counts from both runs were summed to give the final counts per gene per sample. Differential expression was done with DESeq2, v1.12.4, using default parameters, except for a more stringent significance threshold of padj<0.05. The design included the siRNA factor, as well as a batch factor for the day of preparation.
Alternative splicing processing: Reads of the longer sequencing run were processed as for expression analysis, but only reads of length at least 70 were kept, then trimmed to length 70 with the FASTX package. Only paired-reads were used for alignment, with the same parameters as for the expression analysis. Uniquely mapped reads, where both reads of the pair mapped to the same chromosome were taken for further analysis. Alternative splicing was calculated with rMATS, v3.2.5, using parameters -t paired -len 70 -c 0.05 -analysis P -libType fr-firststrand -novelSS 1, and giving the Ensembl release 84 GTF file (-gtf). In addition, reads from the short sequencing run were processed similarly, leaving reads of length 38, then aligned with similar parameters except for --segment-length 18. The BAM files of that alignment were merged with an alignment result for the reads of the long sequencing run, after trimming those also to a length of 38 nucleotides, and the merged BAM files were used as input for rMATS. New alternative splicing events from this analysis were added to the results obtained for the reads of the long sequencing run alone.
see GSE109957 for siNT
Genome_build: GRCh38
Supplementary_files_format_and_content: An Excel file with sheets for the expression analysis and the alternative splicing analysis results. The expression results include general gene details, raw counts, normalized counts, the results of differential expression testing, a column indicating significance (padj<0.05) and a column indicating significance and an absolute log2-fold-change greater than 0.6. Results of the alternative splicing analysis include a sheet for each splicing event type, separated to up- or down-regulated. Each sheet contains general gene details, the rMATS results, and columns for indicating significance in the junction-and-exon analysis (JnR) and junction-only analysis (JO), where significance is taken as padj<0.05 and a minimal average counts (>10 for JnR and >3 for JO). Multiple data is separated by semicolon. Missing data is represented by a question mark.

source_name: MCF7 cell line

growth_protocol: MCF7 (ATCC Number: HTB-22) cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum; cell lines were maintained at 37°C and 5% CO2 atmosphere.

extract_protocol:
RNA was isolated from cells using the GENEzol TriRNA Pure Kit (GeneAid).
RNA ScreenTape kit (catalog #5067-5576; Agilent Technologies, Santa Clara, CA), D1000 ScreenTape kit (catalog #5067-5582; Agilent Technologies), Qubit® RNA HS Assay kit (catalog # Q32852; Invitrogen, Carlsbad, CA) and Qubit® DNA HS Assay kit (catalog #32854; Invitrogen) were used for each specific step for quality control and quantity determination of RNA and library preparation. For mRNA library preparation: TruSeq RNA Library Prep Kit v2 was used (Illumina). In brief, 1 g was used for the library construction; library was eluted in 20 l of elution buffer. Libraries were adjusted to 10 mM, then 10 l (50%) from each sample was collected and pooled in one tube. Multiplex sample pool (1.5 pM including PhiX 1.5%) was loaded in NextSeq 500/550 High Output v2 kit (75 cycles cartridge and 150 cycles cartridge; Illumina, San Diego, CA). Run conditions were in paired end (43X43bp and 80X80 bp, respectively) and loaded on NextSeq 500 System machine (Illumina).

treatment_protocol: Cells were transfected with TransIT-X2 Transfection Reagent (Roche) following the manufacturer’s instructions. After 72 h in culture, RNA was extracted from siRNA transfected cells.

value: Experiment

tag: transfection


title: Naive_WT [12]

description:
Not DSS treated
sample name:
12


title: PC-1F: lung_D-galactose,sodium nitrite_42d

description: Gene expression in aging mice


title: Naive_KO [16]

description:
Not DSS treated
sample name:
16


title: GC-4F: lung_Codonopsis pilosula(15 g•kg-1)_30d

description: Gene expression after intervention of Codonopsis pilosula

source_name: lung_Codonopsis pilosula(15 g•kg-1)_30d


title: siKDM3A_1


title: GX-2F: lung_Codonopsis pilosula(15 g•kg-1)_30d


title: DSS_WT [4R]

description:
2% DSS treated
sample name:
4R

value: WT


title: NC-1F_miRNA: lung_control

description: Gene expression in control group

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: we established the aging mice model, and used the traditional Chinese medicine Codonopsis pilosula to intervene. Then miRNA was extracted from lung tissues in the control group, the model group and high dose Codonopsis pilosula intervention group (n=3 mice).


title: NC-2F_miRNA: lung_control

description: Gene expression in control group


title: Naive_WT [11]

description:
Not DSS treated
sample name:
11


title: NX-1F_miRNA: lung_control

description: Gene expression in control group


title: DSS_KO [7]

description:
2% DSS treated
sample name:
7


title: DSS_KO [8]

description:
2% DSS treated
sample name:
8


title: DSS_KO [5]

description:
2% DSS treated
sample name:
5


title: Naive_WT [10]

description:
Not DSS treated
sample name:
10


title: PC-3F_miRNA: lung_D-galactose,sodium nitrite_42d

description: Gene expression in aging mice


title: DSS_WT [4]

description:
2% DSS treated
sample name:
4


title: grhZwt_stage6_rep3

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

data_processing:
To remove adapter and low-quality sequences, raw ATAC-seq reads were trimmed using Trimmomatic v0.36 (Bolger et al., 2014).
Reads from single and paired-end libraries were aligned to the BDGP D. melanogaster genome release 6 (dm6) using bowtie 2 (Langmead et al., 2012). Single end libraries were aligned using default parameters, paired-end used parameters: -dovetail -k 2 -p 4 -N 1 -R 3
Reads that were unmapped, multiply aligning, aligned to mitochondia, and aligned to scaffolds were discarded.
MACS version 2 (Zhang, et al., 2008) was used with default parameters to identify any regions of open chromatin in all datasets, grouping replicates when available.
Bedtools genomecov (Quinlan and Hall, 2010) was used to generage bedgraphs.
Genome_build: dm6
Supplementary_files_format_and_content: BEDGRAPH, TEXT

organism: Drosophila melanogaster

growth_protocol: All stocks were grown on molasses food at 25°C

extract_protocol:
After collection, dechorionation, and staging embryos were homogenized in ATAC lysis buffer as described in Blythe and Wieschaus (2016).
Library preparation was performed using the Illumina Nextera DNA library preperation kit according to manufacturer instructions. Resultant tagmented DNA was purified with a Qiagen Minelute Cleanup Kit. Libraries were size-selected using a 1.2x ratio of Axygen Axyprep Mag PCR Cleanup beads.

treatment_protocol: Maternal depletion embryos were examined under a fluorescence microsocope to identify embryos depleted of maternal GRH and wild-type siblings. These embryos were then dechorionated. Zygotic depletion embryos were first dechorionated, then examined under a fluorescence microscope to identify embryos depleted of zygotic GRH and wild-type siblings. After separation of embryos and dechorionation, embryos were precisely staged under a light microscope

tag: developmental stage

value: Embryonic stage 6


title: GX-1F: lung_Codonopsis pilosula(15 g•kg-1)_30d


title: DSS_WT [1]

description:
2% DSS treated
sample name:
1


title: DSS_WT [3]

description:
2% DSS treated
sample name:
3


title: DSS_KO [6]

description:
2% DSS treated
sample name:
6


title: DSS_WT [2]

description:
2% DSS treated
sample name:
2


title: PC-1F_miRNA: lung_D-galactose,sodium nitrite_42d

description: Gene expression in aging mice


title: Naive_WT [9]

description:
Not DSS treated
sample name:
9


title: Mbd2KO_CD11bnegDC_Colon [28]

description:
2% DSS treated
sample name:
28

value: Colon


title: Mbd2KO_CD4plusTcell_Spleen [35]

description:
6 weeks post T cell transfer model of colitis
sample name:
35

value: Spleen


title: grhZwt_stage6_rep2


title: Mbd2KO_CD11bnegDC_Colon [30]

description:
2% DSS treated
sample name:
30


title: Mbd2KO_Macrophage_Colon [16]

description:
2% DSS treated
sample name:
16

source_name: Macrophage

value: Macrophage


title: WT_Macrophage_Colon [14]

description:
2% DSS treated
sample name:
14


title: Mbd2KO_Macrophage_Colon [18]

description:
2% DSS treated
sample name:
18


title: grhZwt_stage6_rep1


title: GC-4F_miRNA: lung_Codonopsis pilosula(15 g•kg-1)_30d


title: Control  rep 3

city: Chongqing

first: Cong

last: Lan

state: Chognqing

address: 10 Changjiangzhilu Road

department: Department of Cardiology

institute: Daping Hospital, The Third Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Rattus_norvegicus_ensemble_98
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Rattus norvegicus

source_name: primary cardiomyocytes

growth_protocol: We isolated  cardiomyocytes using 7-day-old SD rats and  cultured in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum at 37℃ in atmosphere with 5% CO2.

extract_protocol:
Cells were collected and Total RNA was extracted using Trizol reagent and mRNA was enriched and Illumina TruSeq RNA Sample Prep Kit  was for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We treated cells with control vehicle (control) or progesterone (10-7 M) (progesterone)  for 24 hours to prepare sample (three biological replicates for each group)

value: Sprague-Dawley (SD) rats

value: heart

value: postnatal day 7

value: primary cardiomyocytes


title: Progesterone  rep 1


title: Progesterone  rep 3


title: grhZ-_stage6_rep3


title: GX-2F_miRNA: lung_Codonopsis pilosula(15 g•kg-1)_30d


title: Mbd2KO_Macrophage_Colon [17]

description:
2% DSS treated
sample name:
17


title: Control rep 1


title: grhZ-_stage6_rep2


title: OA

city: Guangzhou

first: Hao

last: Sun

state: Guangdong

address: Zhongshan 2nd Road

department: Joint surgery

institute: First Affiliated Hospital of Sun Yat-sen University,

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: degenerated human meniscus cells

extract_protocol:
Human meniscus tissues were dissected away from the synovium, and then cut into small pieces. Next, these small pieces were digested by 4 mg/mL protease for 1 hour and 0.25 mg/mL collagenase P for 4 to 6 hours.
RNA libraries were generated by BD Rhapsody singel cell RNA-seq and prepared for sequencing using standard Illumina protocols

value: degenerated


title: Control rep 2


title: GX-1F_miRNA: lung_Codonopsis pilosula(15 g•kg-1)_30d


title: grhMwt_stage6_rep3

value: grhMaternal+


source_name: healthy human meniscus cells

value: healthy


title: grhMwt_stage6_rep2


title: dn LPS plus TNF 441

city: Los Angeles

first: Suhas

middle: G

last: Kallapur

address: 10833 Le Conte Avenue

institute: UCLA

data_processing:
The reads were mapped with STAR 2.5.3a to the Macaca mulatta genome (Mmul 8.0.1).
The counts for each gene were obtained by using quantMode GeneCounts in the STAR commands, and only counts for the featured genes were reserved.
Differential expression analyses were carried out using DESeq2.
The normalized counts were obtained from the DESeq2 analysis. Principal Component Analysis (PCA) were performed on the normalized counts using the open-source software AltAnalyze (http://www.altanalyze.org/).
Volcano plots were made for the results from the differential expression analyses.
Genome_build: mmul 8.0.1
Supplementary_files_format_and_content: Deseq2 normalized count: normalize counts_txt
Supplementary_files_format_and_content: Raw counts: raw_counts_2.txt

organism: Macaca mulatta

source_name: FACS-sorted chorio-decidua neutrophils

extract_protocol: 10 to 50 ng of starting material were used as input material for the NEBNext rRNA Depletion kit (cat# E6350). RNA libraries were then prepared using the NEBNext Ultra II RNA kit (cat# E7765). Quality control for each final library was performed using a D1000 ScreenTape (TapeStation 2200 - Agilent Technologies) and quantified using a Qubit dsDNA BR Assay (Life Technologies). Diluted libraries were pooled and sequenced 50 single-end on a HiSeq3000 (Illumina).

treatment_protocol: intra-amniotic saline (ctrl)

value: chorio-decidua neutrophils


title: dn LPS plus TNF 443


title: Mbd2KO_Macrophage_Colon [20]

description:
2% DSS treated
sample name:
20


title: grhMwt_stage6_rep1


title: dn LPS plus TNF 439


title: dn LPS plus TNF 431


title: grhMwt_stage5_rep3

value: Embryonic stage 5


title: dn LPS 442


title: Mbd2KO_CD11bnegDC_Colon [27]

description:
2% DSS treated
sample name:
27


title: grhZ-_stage6_rep1


title: WT_Macrophage_Colon [12]

description:
2% DSS treated
sample name:
12


title: grhMwt_stage5_rep2


title: grhMwt_stage5_rep1


title: grhM-_stage6_rep3

value: grhMaternal-


title: WT_Macrophage_Colon [11]

description:
2% DSS treated
sample name:
11


title: Mbd2KO_Macrophage_Colon [19]

description:
2% DSS treated
sample name:
19


title: WT_CD11bnegDC_Colon [26]

description:
2% DSS treated
sample name:
26


title: Mbd2KO_Monocyte_Colon [8]

description:
2% DSS treated
sample name:
8

source_name: Monocyte

value: Monocyte


title: grhM-_stage6_rep2


title: WT_Macrophage_Colon [13]

description:
2% DSS treated
sample name:
13


title: dn LPS 436


title: Progesterone  rep 2


title: dn LPS 437


title: grhM-_stage6_rep1


title: grhM-_stage5_rep3


title: dn LPS 429


title: WT_Monocyte_Colon [5]

description:
2% DSS treated
sample name:
5


title: dn LPS 440


title: Mbd2KO_Monocyte_Colon [7]

description:
2% DSS treated
sample name:
7


title: dn ctrl 430


title: WT_CD11bnegDC_Colon [23]

description:
2% DSS treated
sample name:
23


title: grhM-_stage5_rep2


title: dn ctrl 427


title: Mbd2KO_Monocyte_Colon [6]

description:
2% DSS treated
sample name:
6


title: grhM-_stage5_rep1


title: miR-205 induced with Doxycycline 3

city: Boulder

first: Glen

last: Bjerke

state: CO

address: 347 UCB

department: MCDB

institute: University of Colorado

data_processing:
Aligned with Bowtie2
Genes counted with Htseq against mm10
For miR-200 samples the Hiseq and Miseq counts were combined
Htseq was loaded into DESeq2 for differential analysis using the default settings
Genome_build: mm10
Supplementary_files_format_and_content: Htseq count files and DESeq output for each experiment

source_name: Keratinocytes

extract_protocol:
RNA extracted with Trizol
Poly A selected and then NEB Next Ultra Directional kit

treatment_protocol: Treated with vehicle or 3 ug/ml doxycycline

tag: agent

value: Doxycycline

value: Keratinocytes


title: miR-205 induced with Doxycycline 2


title: bn LPS plus TNF 439

source_name: bead-sorted maternal blood neutrophils

value: maternal blood neutrophils


title: bn LPS plus TNF 443


title: Mycelium, W-FA-2

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

description: 2h incubation on Ferulic acid

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-quality sequence, then mapped to Aspergillus niger NRRL3  whole genome using Bowtie2 (Langmead B et al., Genome Biology, 2009) and HISAT software (Kim D, Langmead B and Salzberg SL, Nature Methods, 2015).
“Fragments per kilobase of exon model per million mapped reads” (FPKM) was calculated using RSEM tool (Li B & Dewey CN, BMC bioinformatics, 2011).
Genome_build: Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Aspergillus niger

source_name: Mycelium sample

growth_protocol: Strains were grown at 30 °C in Minimal Medium (MM) or Compete Medium (CM) prepared as described previously. All liquid cultures were incubated in the rotary shaker at 250 rpm. In transfer experiment, freshly harvested spores were pre-grown for 16h in CM with 2% (w/v) glucose. The mycelium was then harvested by filtration over sterile cheesecloth, washed with MM andwas transferred to 50 mL MM with 0.02 % (w/v) aromatic compound. After 2h of incubation, the mycelium was harvested by vacuum filtration, dried between two sheets of paper and frozen in liquid nitrogen. The culture filtrate was harvested, centrifuged and frozen. All samples were stored in -20°C until being processed.

extract_protocol:
RNA was extracted from ground mycelia using TRIzol® reagent (Invitrogen, Breda, the Netherlands) and purified with NucleoSpin® RNA II Clean-up kit (Macherey-Nagel) with rDNase treatment. The RNA quantity and quality was checked with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype

value: Ferulic acid

tag: sampling time

value: Mycelium sample


title: miR-205 induced with Doxycycline 1

tag: cell type


title: dn ctrl 432


title: miR-205 Control 3 - Vehicle

value: Vehicle


title: TbRAP1∆Myb rep 1

city: CLEVELAND

first: Bibo

last: Li

state: OH

address: 2121 Euclid Avenue

department: Center for Gene Regulation in Health and Disease

institute: CLEVELAND STATE University

data_processing:
Base-calling using NovaSeq 6000 for Illumina sequencing
Raw reads were first processed with Novogene Perl Scripts (removing reads with low quality,  with adapters, and containing poly-N; calculating Q20, Q30 and GC contents).
Clean reads were mapped to T. brucei Lister 427 genome TriTrypDB-45_TbruceiLister427_2018_Genome.fasta and its annotation TriTrypDB-45_TbruceiLister427_2018.gff Idownloaded from the TriTryp DB) using HISAT2.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq R package (1.18.0)

molecule: polyA RNA

organism: Trypanosoma brucei brucei

source_name: cultured cells

growth_protocol: bloodstream T. brucei cells were cultured in HMI9 medium with 10% FBS. Both cells were maintained with medium containing 2 µg/ml G418, 4 µg/ml Hygromycin, 2 µg/ml of Phleomycin, 5 µg/ml blasticidin. The TbRAP1 F/F2H-∆myb cells are also selected with 0.1 µg/ml Puromycin. At the time of adding 100 ng/ml doxycycline, Hygromycin and blasticidin were removed by washing cells 3 times.

extract_protocol:
Total RNA was isolated and purified through RNeasy columns (Qiagen). RNA samples were run on a BioAnalyzer 2100 (Agilent Technologies) using the Agilent RNA 6000 nano kit to verify the RNA quality before sent to Novogene, where RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) using 1 μg poly(A) RNA according to manufacturer’s protocol and index codes were added to attribute sequences to each sample.

treatment_protocol: 100 ng/ml doxycycline (to induce Cre expression) for 30 hrs

value: TbRAP1 F/F2H-deltaMyb

tag: treatment

value: +Cre 30 hrs


title: TbRAP1∆Myb rep 2


title: TbRAP1∆Myb rep 3


title: bn LPS 442


title: miR-205 Control 2 - Vehicle


title: Mycelium, W-FA-1

description: 2h incubation on Ferulic acid

tag: tissue


title: Mycelium, F-NC-2

description: 2h incubation, no carbon source

value: no carbon source


title: Mbd2KO_Monocyte_Colon [9]

description:
2% DSS treated
sample name:
9

value: Colon


title: TbRAP1 CSKO rep 3

value: TbRAP1 F/+


title: Mbd2KO_Monocyte_Colon [10]

description:
2% DSS treated
sample name:
10


title: bn LPS plus TNF 431


title: bn LPS 440


title: Mycelium, F-NC-1

description: 2h incubation, no carbon source


title: WT_Monocyte_Colon [1]

description:
2% DSS treated
sample name:
1

value: WT


title: miR-205 Control 1 - Vehicle


title: WT_Monocyte_Colon [3]

description:
2% DSS treated
sample name:
3


title: WT_Monocyte_Colon [4]

description:
2% DSS treated
sample name:
4


title: WT_Monocyte_Colon [2]

description:
2% DSS treated
sample name:
2


title: Mycelium, F-FA-2

description: 2h incubation on Ferulic acid


title: TbRAP1 CSKO rep 2


title: bn LPS 436


title: Mycelium, F-FA-1

description: 2h incubation on Ferulic acid


title: TbRAP1 CSKO rep 1


title: Ileum_Crypts_Rep3

description:
Jejunum_v_Ileum_ForGEO.xslx
Duodenum_v_Ileum_ForGEO.xslx

data_processing:
Sequenced reads were mapped to mm10 whole genome using STAR v2.5.2a with parameters --outFilterMultimapNmax 1 --quantmode Genecounts
Raw genecounts were analyzed for differential expression via DeSeq2 in R 3.5.1
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 analysis of differential expression in all pairwise comparisons of Duodenum, Jejunum, and Ileum crypts

source_name: Ileum

extract_protocol:
Total RNA was extracted from isolated crypts using TRIzol (Invitrogen) combined with Purelink RNA Mini columns (Fisher).
Novogene Paired End Protocol "fter the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment."

value: 6-8 weeks old

value: C57BL/6 mice

value: Ileum


title: Ileum_Crypts_Rep2


title: Ileum_Crypts_Rep1


title: Mycelium, F-PC-2

description: 2h incubation on p-coumaric acid

value: p-coumaric acid


title: bn ctrl 432


title: Sample 6_ES-3_THY_raw

first: Priyanka

last: Kachroo

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

description:
MGAS2221 was streaked from a freezer stock onto a blood agar plate for O/N growth.  From the blood agar plates, a loop full of bacterial colonies were grown in THY browth for 10-11 h overnight. Overnight culture was inoculated into fresh pre-warmed THY broth and grown to appropriate OD.
processed data: 'GAS_sections_combined' spreadsheet in the 'processed_data.xlsx'

data_processing:
Multiplexed single-end (SE) libraries were sequenced on an Illumina Illumina NextSeq500/550 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files.
RNA-seq reads from strains grown in vitro were mapped to reference strain MGAS2221 (GenBank accession number CP043530), and MGAS5005 (accession number NC_007297) using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes), and CLC Genomics workbench.
Sequencing read quality was evaluated with FASTQC software
Adapter contamination and read quality filtering was performed with Trimmomatic.
Reads were mapped to the genome of Macaca fascicularis (5.0, release-95, Ensembl (http://useast.ensembl.org/Macaca_fascicularis/Info/Annotation) using STAR. Reads mapping to the NHP genome were subsequently mapped to the GAS genome (MGAS2221, Genbank ID CP043530).
Cross-mapping reads were identified and excluded with SeqFilter (https://github.com/BioInf-Wuerzburg/SeqFilter/blob/master/README.org). Filtered reads were mapped to the genome of reference GAS strain MGAS2221 using EDGE-pro (http://ccb.jhu.edu/software/EDGE-pro/). Differential expression analysis was performed using DESeq2 version 1.16.1, or expression levels were normalized as RPKM (reads per kilobase of exon model per million reads) using CLC Genomics workbench.
Genome_build: Macaca fascicularis (5.0, release-95, Ensembl (http://useast.ensembl.org/Macaca_fascicularis/Info/Annotation)
Supplementary_files_format_and_content: Raw reads were normalized as a part of DESeq2 pipeline, as a part of CLC Genomics workbench, or using TPM are provided along with raw data.

organism: Streptococcus pyogenes

source_name: cell pellet

growth_protocol: For in vitro growth, cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37° C in atmosphere supplemented with 5% CO2. For in vivo growth, cells were inoculated in the quadriceps muscle of three NHPs, and 24 h after infection the muscle was removed en bloc, and sections corresponding to the infection site were collected.

extract_protocol:
In vitro grown pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Illumina). The tissue (80-100 mg) corresponding to the in vivo samples was washed in PBS, homogenized, and mechanically disrupted using 0.1 mm and 0.5 mm beads. RNA was extracted (MasterPure Complete DNA and RNA purification kit, Lucigen), subjected to three consecutive DNase treatments with Turbo DNA-free (Ambion), and depletion of ribosomal RNA was performed with the Ribo-Zero Gold rRNA Removal Kit, Epidemiology (Illumina).
Resultant RNA from dahA mutant and parental wild-type samples was reverse transcribed to cDNA and sequencing libraries were generated using ScriptSeq RNA-seq preparation kit (Epicentre). cDNA libraries from in vivo samples were generated from rRNA depleted RNA using a NEBNext Ultra II Directional RNA Library Preparation kit for Illumina (NEB).

treatment_protocol: At the desired growth stage, mid-exponential (OD 600nm 0.5) or early-stationary (OD 600nm 1.55), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation. For the in vivo growth the excised tissue sections were submerged in RNAShield and frozen at -80°C until processed.

value: MGAS2221 (THY)

tag: growth condition

value: In vitro

tag: replicates

value: replicate 3 for in vitro growth_ES

tag: growth condition/time of isolation

value: Early-stationary (ES, OD600nm=1.5)


title: bn LPS 437

value: maternal blood neutrophils


title: Sample 5_ES-2_THY_raw

tag: strain

value: replicate 2 for in vitro growth_ES


title: Jejunum_Crypts_Rep3

description:
Jejunum_v_Ileum_ForGEO.xslx
Duodenum_v_Jejunum_ForGEO.xslx

source_name: Jejunum

tag: age

value: Jejunum


title: bn ctrl 430


title: Sample 4_ES-1_THY_raw

value: replicate 1 for in vitro growth_ES


title: Jejunum_Crypts_Rep2


title: bn ctrl 427


title: Sample 3_ME-3_THY_raw

value: replicate 3 for in vitro growth_ME

value: Mid-exponential (ME, OD600nm=0.5)


title: Jejunum_Crypts_Rep1


title: Sample 1_ME-1_THY_raw

value: replicate 1 for in vitro growth_ME


title: Sample 2_ME-2_THY_raw

value: replicate 2 for in vitro growth_ME


title: Duodenum Crypts_Rep3

description:
Duodenum_v_Ileum_ForGEO.xslx
Duodenum_v_Jejunum_ForGEO.xslx

source_name: Duodenum

value: Duodenum


title: Mycelium, W PR 2

description: 2h incubation on protocatechuic acid

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and removed for low-quality sequence, then mapped to Aspergillus niger NRRL3 whole genome using Bowtie2 (Langmead B et al., Genome Biology, 2009) and HISAT software (Kim D, Langmead B and Salzberg SL, Nature Methods, 2015).
“Fragments per kilobase of exon model per million mapped reads” (FPKM) was calculated using RSEM tool (Li B & Dewey CN, BMC bioinformatics, 2011).
Genome_build: Aspergillus niger NRRL3 (http://genome.jgi.doe.gov/Aspni_NRRL3_1)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was extracted from ground mycelia using TRIzol® reagent (Invitrogen, Breda, the Netherlands) and purified with NucleoSpin® RNA II Clean-up kit (Macherey-Nagel) with rDNase treatment. The RNA quantity and quality was checked with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: protocatechuic acid

value: Mycelium sample


title: bn LPS 429


title: Mycelium, W PR 1

description: 2h incubation on protocatechuic acid


title: Mycelium, W NC 1

description: 2h incubation, no carbon source

value: no carbon source


title: NI_BMDMs_RNAseq_2

city: Porto

first: Ana

middle: Raquel

last: Maceiras

address: Rua Alfredo Allen, 208

country: Portugal

description: processed data file: MSaraiva_16-11-2018_ChipA_torrent-server_2705.bcmatrix.xls

data_processing:
Run metrics on technical reproducibility, read alignment, and detection of on-target transcripts was performed using Torrent Suite Software, producing a raw count matrix as output.
Genome_build: Not provided
Supplementary_files_format_and_content: MSaraiva_16-11-2018_ChipA_torrent-server_2705.bcmatrix.xls: Excel file includes raw counts.

source_name: Bone Marrow-Derived Macrophages

growth_protocol: Bone marrow cells were cultured in complete DMEM supplemented with 20% of LCCM for 7 days to obtain bone marrow-derived macrophages (BMDMs).

extract_protocol:
Total RNA from infected cells was extracted with TRIzol Reagent according to the manufacturer’s instructions. Samples were then treated with Turbo DNA-free kit also according to the manufacturer’s instructions.
Sequencing library was obtained using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit.

treatment_protocol: Fully differentiated BMDMs were harvested, counted, plated in 24 well plates and infected with Mtb for 6h.

tag: infection

value: NI control

tag: duration of infection

value: Bone marrow-derived macrophages


title: Duodenum Crypts_Rep2

value: 6-8 weeks old

value: C57BL/6 mice


title: 6C4_BMDMs_RNAseq_3

value: 6C4 M. tuberculosis


title: Mycelium, W PH 2

description: 2h incubation on p-hydroxybenzoic acid

value: p-hydroxybenzoic acid


title: Mycelium, F-PC-1

description: 2h incubation on p-coumaric acid

value: p-coumaric acid


title: 6C4_BMDMs_RNAseq_2


title: Mycelium, W NC 2

description: 2h incubation, no carbon source


title: Duodenum Crypts_Rep1


title: Mycelium, W PH 1

description: 2h incubation on p-hydroxybenzoic acid


title: 6C4_BMDMs_RNAseq_1


title: NI_BMDMs_RNAseq_1


title: WT_CD4plusTcell_Spleen [34]

description:
6 weeks post T cell transfer model of colitis
sample name:
34

value: Spleen

value: WT


title: Mycelium, W CA2

description: 2h incubation on caffeic acid

value: caffeic acid


title: Mycelium, W CA 1

description: 2h incubation on caffeic acid


title: 4I2_BMDMs_RNAseq_2

value: 4I2 M. tuberculosis


title: 4I2_BMDMs_RNAseq_3


title: 4I2_BMDMs_RNAseq_1


title: Mycelium, W PC 2

description: 2h incubation on p-coumaric acid


title: Patient 8 mUM 004

city: Liverpool

first: Carlos

middle: Rogerio

last: De Figueiredo

state: Merseyside

address: 6 West Derby Street

department: Molecular and Clinical Cancer Medicine

institute: University of Liverpool

hyb_protocol: Sample hybridization was performed using CodeSet and Capture ProbeSet reagents. Aliquots were used to perform a master mix by adding 70 μL of hybridization buffer to the tube containing the Reporter CodeSet. RNase-free water was added to this mix that the volume of the individual RNA samples was less than 5 μL. 8 μL of master mix was added to each of the 11 tubes. 5 μl of sample was added to each tube. 2 μL of Capture ProbeSet was added to each tube immediately before placing at 65°C. Reactions was performed for at least 16 hours, further stopped at 4°C and processed in the following day.

scan_protocol: After hybridization, excess probes are washed away and the Capture Probes and Target/Probe Complexes are eluted off of the beads and are then hybridized to magnetic beads complementary to the Reporter Probe. Wash steps are performed and excess Capture Probes are washed away. Finally, the purified Target/Probe Complexes are eluted off and are immobilized in the cartridge for data collection. Data collection is carried out in the nCounter® Digital Analyzer. Fields of view (FOV) are collected per sample using a microscope objective and a CCD camera yielding data of hundreds of thousands of target molecule counts. Digital images are processed on the Digital Analyzer and the barcode counts are then tabulated and displayed.

data_processing:
The NanoString nSolver 2.6 software was used for normalization of expression counts using housekeeping genes following the manufacturer’s recommendations (NanoString). normalized within each immune category (e.g. CTLs suppression, M2 macrophages regulation and Immune checkpoint regulators).
Normalized signal intensity. Data are displayed in expression count units of individual gene per patient and normal liver sample.

label: Molecular barcode on reporter probe

source_name: metastatic Uveal Melanoma Tumor

label_protocol: NanoString protocol

extract_protocol: Formalin fixed paraffin embedded (FFPE) samples were used for total RNA immune gene expression analysis. The tumor areas were selected for RNA extraction, or the entire normal liver tissue. Tissue dissociation, RNA extraction and purification was performed using the RNeasy FFPE Kit (Qiagen) according to manufactures instructions (Qiagen). At least 4 FFPE sections were vortexed in 1ml xylene to remove paraffin wax. Tissues were digested using proteinase K for 15 min at 56 °C and then 15 min at 80 °C. RNA was precipitated and further purified in a RNeasy MinElute spin columns. RNA concentrations were determined using a Qubit® RNA Broad-Range assay. The expression of ~730 immune-related genes were assessed using the NanoString PanCancer Immune Profiling gene set.

tag: individual

value: Patient 8

value: metastatic Uveal Melanoma Tumor


title: Patient 9 mUM 005

value: Patient 9


title: Patient 11 Normal Liver

value: Patient 11

value: Normal Liver


title: Mycelium, W PC 1

description: 2h incubation on p-coumaric acid

value: Mycelium sample


title: Patient 7 mUM 003

value: Patient 7


title: Patient 10 mUM 006

value: Patient 10


title: Sample 42_nhp3_mock_raw

city: Houston

description:
The same volume of PBS, compared to the infected samples, was inoculated in the skeletal muscle and tissue excised 24 h later
processed data: mock-infected host combined section data in 'NHP(host)_Sections_combined' spreadsheet in the 'processed_data.xlsx'

organism: Macaca fascicularis

source_name: Combined skeletal muscle mock-infected tissue sections

value: None (Mock-infected NHP skeletal muscle tissue)

value: In vivo

tag: replictaes

value: in vivo mock-infected NHP 3-Pooled sections

value: Collected 24 h post-mock-inoculation


title: Patient 6 mUM 002

value: Patient 6


title: AO rep2

city: Kongens Lyngby

first: Xiaobo

address: Kemitorvet

country: Denmark

institute: Technical University of Denmark

data_processing:
Basecalling online_YX BasecallVersion0.5.6.153
Sequenced reads were filtered by removing adaptor sequences and low-quality reads
Sequenced reads were mapped to reference sequence S.erythraea NRRL2338 (Genbank accession number: NC_009142) using Geneious Prime version 2019.1.3.
Genome_build: S.erythraea NRRL2338 (NC_009142)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Saccharopolyspora erythraea

source_name: engineered strain, the end of exponential phase

growth_protocol: Modified minimal liquid medium was used for liquid culture of S.erythraea. Cells were harvested at two time points, i.e. 10 h in the early exponential phase and 48 h at the end of exponential phase, namely, the onset point of erythromycin biosynthesis, for total RNA extraction.

extract_protocol:
Total RNA was extracted with an RNAeasy Plus Mini kit (Qiagen, Germany) using glass beads to mechanically disrupting cells with a FastPrep (30 s ×4; M.P. Biomedical, USA). DNase treatment by RNase-Free DNase Set (Qiagen, Germany) aided to digest DNA in samples.
rRNA was removed with Illumina Ribo-zero rRNA removal kit(bacteria) after total RNA was collected. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamer-primer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dATPs,dGTPs,dCTPs,dUTPs, RNase H and DNA polymerase I respectively after removing dNTPs. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adapters. Then, the UNG enzyme was used to degrade the second-strand cDNA, and the product was purified by MiniElute PCR Purification Kit before PCR amplification.

treatment_protocol: The  cells were harvested and resuspended in 2 mL RNAlaterTM solution (Invitrogen, USA).

value: EA

tag: growth phase

value: the end of exponential phase


title: AO rep1


title: Sample 41_nhp2_mock_raw

value: in vivo mock-infected NHP 2-Pooled sections


title: Sample 40_nhp1_mock_raw

value: in vivo mock-infected NHP 1-Pooled sections


title: Patient 4 pUM 004

source_name: primary Uveal Melanoma Tumor

value: Patient 4

value: primary Uveal Melanoma Tumor


title: Patient 5 mUM 001

value: Patient 5

value: metastatic Uveal Melanoma Tumor


title: Trunk - 27 hpf - Replicate 1

city: Syracuse

first: Samantha

middle: Jane

last: England

state: NY

address: 107 College Place

department: Biology

institute: Syracuse University

hyb_protocol: The amplified RNA was hybridized to the Affymetrix GeneChip Zebrafish Genome Array according to the manufacturer's instructions.  Affymetrix GeneChip Hybridization Control RNAs were always included.

scan_protocol: Slides were scanned immediately after washing on the Affymetrix GeneChip Scanner 3000 7G, according to the manufacturer's instructions.

data_processing: The scanned images were analyzed with Affymetrix Expression Console software and the following critical metrics determined: background, noise, probe cell intensity, scaling factor and the percent of probe sets called present or absent.  Once satisfied that all of our hybridizations were successful and as consistent as could be expected, the data were subjected to an analysis pipeline incorporating background correction using the Robust Multi-chip Algorithm (RMA) and quantiles normalization. This was performed using the T-rex utility at the Gene Expression Profile Analysis Suite (GEPAS; www.gepas.org, Montagner et al., 2006 - now incorporated in to Babelomics 5; http://babelomics.bioinfo.cipf.es, Alonso et al., 2015). Subsequently in T-rex, a multi-class ANOVA test was performed to calculate differential expression.  P-values were corrected for multiple testing using the Benjamini & Hochberg (BH) method.

organism: Danio rerio

source_name: All trunk cells, 27 hpf

label_protocol: As per the manufacturer's instructions, total RNA extracted from FAC-sorted cells was subjected to two rounds of amplification before labelling using the Affymetrix Two-Cycle Target Labeling and Control Reagents Kit (Affymetrix, 900494).  As recommended by the manufacturer, Affymetrix GeneChip spike-in polyadenylated prokaryotic RNA controls were included as amplification controls.

growth_protocol: Embryos were raised at 28.5oC until 10 hours post fertilisation (hpf), and then incubated at 32oC until they reached 27 hpf.  Developmental stage was confirmed by prim-staging.

extract_protocol: Total RNA was extracted from FAC-sorted cells using the Ambion RNaqueous-Micro Total RNA Extraction Kit (Thermo Fisher Scientific, AM1931), following the manufacturer's instructions.  The optional DNase-treatment step was not performed.  Extracted total RNA was eluted in 20 µl of nuclease-free water (two 10 µl elution volumes subsequently combined).  RNA integrity was analyzed using the Agilent RNA 6000 Pico Kit (Agilent, 5067-1513) on the Agilent 2100 Bioanalyzer.  Total RNA concentration was subsequently quantified using the Quant-IT RiboGreen RNA Assay Kit (Thermo Fisher Scientific, R11490) and a Mx3000P qPCR machine (Stratagene).  A triplicate series containing 0, 0.1, 0.2, 0.5, 1, 2, 3, 4, 5 and 10 ng of the ribosomal RNA standard provided in the kit was used to construct a standard curve of fluorescence versus RNA quantity from which the concentration of 0.5 µl aliquots of each experimental RNA sample was inferred.

treatment_protocol: Prior to fluorescence activated cell sorting (FACS), prim-staged embryos were manually deyolked by gently pipetting them up and down in ice-cold Ringer's Solution (116 mM NaCl, 2.9 mM KCl, 1.8 mM CaCl2, 5 mM HEPES, pH7.2).  Using a glass pipette coated with foetal bovine serum, deyolked embryos were transferred to a petri dish containing fresh ice-cold Ringer's Solution.  The spinal cord region immediately above the yolk extension was dissected.  For the CiA (V1) samples (collected from the Tg(pax2a:GFP) line), the pronephros region was removed to prevent contamination during FACS.  The dissected tissue was then dissociated using the Worthington Papain Dissociation System (Worthington Biochemical Corporation, LK003150).  Dissociated cells were resuspended in 0.5 ml Leibovitz's L-15 Medium (Thermo Fisher Scientific, 11415064) + 0.5% foetal bovine serum.  All FAC-sorting was performed within four hours of commencing the spinal cord dissections.  Cell suspensions were filtered to remove cellular aggregates using 35 µm Cell Strainer Cap Tubes (BD Falcon, 352235) and then FAC-sorted using a Beckman Coulter 3-laser MoFlo cytometer.  Cells were sorted directly in to 100 µl of RNA extraction lysis buffer from the Ambion RNaqueous-Micro Total RNA Extraction kit (Thermo Fisher Scientific, AM1931)  and immediately stored at -80oC.

value: Trunk cells (spinal cord and other tissues)

tag: transgenic line

value: None used

value: 27 hpf


title: Trunk - 27 hpf - Replicate 3


title: Trunk - 27 hpf - Replicate 4


title: AE rep2

source_name: engineered strain, early exponential phase

value: early exponential phase


title: Trunk - 27 hpf - Replicate 2


title: Patient 3 pUM 003

value: Patient 3


title: CiA - 27 hpf - Replicate 6

source_name: CiA (V1) interneurons, 27 hpf

value: CiA (V1) spinal interneurons


title: Sample 39_nhp3_5_mock_raw

description: The same volume of PBS, compared to the infected samples, was inoculated in the skeletal muscle and tissue excised 24 h later

source_name: Skeletal muscle mock-infected tissue section

value: None (Mock-infected NHP skeletal muscle tissue)

value: In vivo

value: in vivo mock-infected NHP 3-Section 5


title: AE rep1

value: EA


title: Sample 38_nhp3_4_mock_raw

value: in vivo mock-infected NHP 3-Section 4

value: Collected 24 h post-mock-inoculation


title: EO rep2

source_name: parental strain, the end of exponential phase

value: the end of exponential phase


title: Sample 37_nhp3_3_mock_raw

value: in vivo mock-infected NHP 3-Section 3


title: EO rep1


title: Patient 1 pUM 001

value: Patient 1

value: primary Uveal Melanoma Tumor


title: Sample 36_nhp3_2_mock_raw

value: in vivo mock-infected NHP 3-Section 2


title: EE rep2

source_name: parental strain, early exponential phase


title: CiA - 27 hpf - Replicate 3


title: Sample 53_WT-3-05

description:
MGAS2221 was streaked from a freezer stock onto a blood agar plate for O/N growth, and grown for 10-11 h O/N before sampling
processed data: 'dahA-mutant_and_wild-type' spreadsheet in the 'processed_data.xlsx'

value: MGAS2221 (parental wild-type)

value: In vitro

value: replicate 3 for in vitro growth_ME

value: Mid-exponential (ME, OD600nm=0.5)


title: Sample 52_WT-2-15

value: replicate 2 for in vitro growth_ES

value: Early-stationary (ES, OD600nm=1.5)


title: EE rep1

value: early exponential phase


title: Sample 51_WT-2-05

value: replicate 2 for in vitro growth_ME


title: MPG-/- rep1

city: Trondheim

first: Nicola

last: Montaldo

address: Erling Skjalgssons gt 1

institute: NTNU

data_processing:
Adatper trimming,remove reads in which uknown bases are more than 10%, and remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5) - custom pipeline by BGI
Bowtie2 used to map clean reads to reference transcriptome -q --phred64 -- sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
BWA use to map to reference genome -o1-e50-i50-L-k2-l31-t4-q10
Gene Quantification done using RSEM (Li and Dewey et al., 2011 BMC Bioinformatics) which calculates FPKM
DEGs screened using Poisson Distribution Method, performed using custom BGI pipelines (sequencing and analysis by BGI)
Genome_build: hg18 Entrez Gene annotations
Supplementary_files_format_and_content: Normalized abundance measurements (FPKM) generated with RSEM (as described above).

growth_protocol: HAP1 cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (Sigma Aldrich) supplemented with amphotericin B (2.5 μg/mL, Sigma-Aldrich), gentamicin (0.1 mg/mL, Life Technologies), L-glutamine (8 mM, Sigma-Aldrich) and Fetal Bovine Serum (FBS) (10% v/v, Sigma-Aldrich) at 37 °C and 5% CO2.

extract_protocol:
Cells were harvested 0 and 48 hours after treatment, pelleted and snap frozen. RNA was extracted from the pellets using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, #80004).
RNA libraries were prepared for sequencing using standard Complete Genomics protocols

treatment_protocol: Cells were incubated for one hour in medium containing 0.25 mM methyl methanesulfonate (MMS) and further incubated in fresh medium before harvest.

tag: cell line

value: HAP1 cell line, near-haploid fibroblast-like cells derived from Male Chronic Myelogenous Leukemia (CML) cell line KBM-7

value: MPG-/-


title: CiA - 27 hpf - Replicate 4

value: CiA (V1) spinal interneurons

value: 27 hpf


title: Sample 33_nhp2_4_mock_raw

value: None (Mock-infected NHP skeletal muscle tissue)

value: In vivo

value: in vivo mock-infected NHP 2-Section 4

value: Collected 24 h post-mock-inoculation


title: Sample 50_WT-1-15

value: replicate 1 for in vitro growth_ES


title: CiA - 27 hpf - Replicate 2


title: Patient 2 pUM 002

value: Patient 2

value: primary Uveal Melanoma Tumor


title: WT rep1

tag: genotype

value: wild type


title: Sample 32_nhp2_3_mock_raw

value: in vivo mock-infected NHP 2-Section 3


title: CiA - 27 hpf - Replicate 5


title: Sample 49_WT-1-05

value: MGAS2221 (parental wild-type)

value: In vitro

value: replicate 1 for in vitro growth_ME

value: Mid-exponential (ME, OD600nm=0.5)


title: All Spinal Neurons - 27 hpf - Replicate 5

source_name: All spinal neurons, 27 hpf

value: All spinal neurons


title: CiA - 27 hpf - Replicate 1


title: Sample 31_nhp2_2_mock_raw

value: in vivo mock-infected NHP 2-Section 2


title: Sample 35_nhp3_1_mock_raw

value: in vivo mock-infected NHP 3-Section 1


title: Sample 48_JE84-3-15

description:
dahA mutant  was streaked from a freezer stock onto a blood agar plate for O/N growth, and grown for 10-11 h O/N before sampling
processed data: 'dahA-mutant_and_wild-type' spreadsheet in the 'processed_data.xlsx'

value: MGAS2221 dahA  mutant

value: replicate 3 for in vitro growth_ES

value: Early-stationary (ES, OD600nm=1.5)


title: stage 12 ectodermal explant rep3

city: Philadelphia

first: Peter

middle: S

last: Klein

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania School of Medicine

description:
5_12
Animal caps dissected at stage 9 and cultured to stage 12.
Tn5 digested and amplified.
processed data file: s12_sort.bed

data_processing:
Fastq files were generated and demultiplexed with bcl2fastq v2.20 (Illumina).
Fastq files for each stage-specific replicate set were processed with the ENCODE ATAC-seq pipeline (v1.4.2, https://github.com/ENCODE-DCC/atac-seq-pipeline).
Genome_build: XenLae2 (Xenopus laevis) sourced from UCSC.
Supplementary_files_format_and_content: *_sort.bed.gz: Called, IQR-passed, ATAC-seq peaks for stage 10 and stage 12 replicate sets.

organism: Xenopus laevis

source_name: ectodermal explant--late gastrula (stage 12)

growth_protocol: Xenopus embryos were cultured in 0.1XMMR until the blastula stage. Ectoderm was explanted at the late blastula stage and cultured in 0.5XMMR until either early gastrula (stage 10) or late gastrula (stage 12).

extract_protocol:
Xenopus laevis ectodermal explants (animal caps) were dissected at the blastula stage and collected at the onset of gastrulation (stage 10) or at the end of gastrulation (stage 12). Two explants per replicate were washed twice in 1 ml cold PBS, resuspended in 50 µl RSB (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2) with 0.1% (v/v) Igepal CA-630 at 4ºC and dispersed by pipetting. Samples were centrifuged at 500xg for 10 minutes at 4ºC, and pellets were resuspended in 1X TD buffer (10mM Tris pH 7.6, 5 mM MgCl2, and 10% dimethylformamide) and 2.5µL of Tn5 (3µM) was added. Samples were incubated at 37ºC for 1 hour with constant shaking and digested with protease K overnight. DNA was purified with 1.8 volumes of Ampure XP Beads (Beckman Coulter), eluted in 40 µl, amplified by PCR with barcoded primers as described (Buenrostro et al., 2013), purified by AMPure XP beads (Thermo-Fisher) to remove adaptors, and submitted in triplicate for sequencing on a HiSeq 4000 with 100 nucleotide paired-end reads.
Libraries were constructed using the Illumina Nextera Library Prep kit (cat#15028212) with modifications described above.

value: Ectodermal explant

tag: developmental stage

value: Late gastrula (stage 12)


title: All Spinal Neurons - 27 hpf - Replicate 2

tag: cell type

value: 27 hpf


title: All Spinal Neurons - 27 hpf - Replicate 3


title: All Spinal Neurons - 27 hpf - Replicate 4


title: stage 12 ectodermal explant rep2

description:
4_12
Animal caps dissected at stage 9 and cultured to stage 12.
Tn5 digested and amplified.
processed data file: s12_sort.bed


title: Sample 30_nhp2_1_mock_raw

value: None (Mock-infected NHP skeletal muscle tissue)

value: In vivo

value: in vivo mock-infected NHP 2-Section 1

value: Collected 24 h post-mock-inoculation


title: All Spinal Neurons - 27 hpf - Replicate 1


title: Sample 47_JE84-3-05

value: replicate 3 for in vitro growth_ME


title: Sample 22_nhp1_inf_raw

description:
1 x 108 CFU/kg serotype M1 strain MGAS2221 were inoculated in the skeletal muscle and tissue excised 24 h later
processed data: 'GAS_sections_combined' spreadsheet in the 'processed_data.xlsx'

organism:
Streptococcus pyogenes
Macaca fascicularis

source_name: Combined skeletal muscle infected tissue sections

value: MGAS2221 (infected NHP skeletal muscle tissue)

value: in vivo infected NHP 1-Pooled sections

value: Collected 24 h post-inoculation


title: stage 12 ectodermal explant rep1

description:
2_12
Animal caps dissected at stage 9 and cultured to stage 12.
Tn5 digested and amplified.
processed data file: s12_sort.bed


title: Sample 46_JE84-2-15

source_name: cell pellet

value: In vitro

value: replicate 2 for in vitro growth_ES


title: Sample 21_nhp3_5_inf_raw

description:
1 x 108 CFU/kg serotype M1 strain MGAS2221 were inoculated in the skeletal muscle and tissue excised 24 h later
processed data: 'GAS_sections' spreadsheet in the 'processed_data.xlsx'

source_name: Skeletal muscle infected tissue section

value: in vivo infected NHP 3-Section 5


title: Sample 24_nhp3_inf_raw

value: in vivo infected NHP 3-Pooled sections


title: Sample 45_JE84-2-05

value: MGAS2221 dahA  mutant

value: replicate 2 for in vitro growth_ME

value: Mid-exponential (ME, OD600nm=0.5)


title: Sample 28_nhp1_4_mock_raw

value: in vivo mock-infected NHP 1-Section 4


title: Sample 20_nhp3_4_inf_raw

value: in vivo infected NHP 3-Section 4


title: PC-2F_miRNA: lung_D-galactose,sodium nitrite_42d

city: Lanzhou

first: Dongmei

address: No. 35 Dingxi east road, chengguan district, Lanzhou, Gansu province

description: Gene expression in aging mice

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: lung_D-galactose,sodium nitrite_42d

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: lung

tag: gender

value: female


title: stage 10 ectodermal explant rep2

description:
4_10
Animal caps dissected at stage 9 and cultured to stage 10.
Tn5 digested and amplified.
processed data file: s10_sort.bed

source_name: ectodermal explant--early gastrula (stage 10)

tag: tissue

value: Ectodermal explant

value: Early gastrula (stage 10)


title: Sample 44_JE84-1-15

tag: growth condition

value: replicate 1 for in vitro growth_ES

value: Early-stationary (ES, OD600nm=1.5)


title: Sample 19_nhp3_3_inf_raw

value: MGAS2221 (infected NHP skeletal muscle tissue)

value: In vivo

value: in vivo infected NHP 3-Section 3


title: Sample 23_nhp2_inf_raw

value: in vivo infected NHP 2-Pooled sections

value: Collected 24 h post-inoculation


title: stage 10 ectodermal explant rep1

description:
3_10
Animal caps dissected at stage 9 and cultured to stage 10.
Tn5 digested and amplified.
processed data file: s10_sort.bed


title: Sample 26_nhp1_2_mock_raw

value: None (Mock-infected NHP skeletal muscle tissue)

value: in vivo mock-infected NHP 1-Section 2

value: Collected 24 h post-mock-inoculation


title: Sample 43_JE84-1-05

value: MGAS2221 dahA  mutant

value: In vitro

tag: replicates

value: replicate 1 for in vitro growth_ME

value: Mid-exponential (ME, OD600nm=0.5)


title: Sample 25_nhp1_1_mock_raw

value: in vivo mock-infected NHP 1-Section 1

tag: growth condition/time of isolation


title: Sample 18_nhp3_2_inf_raw

tag: strain

value: in vivo infected NHP 3-Section 2


title: Sample 17_nhp3_1_inf_raw

value: in vivo infected NHP 3-Section 1


title: V_2

city: nanjing

first: liu

last: qingtao

state: jiangsu

address: zhongling road NO. 50

department: Institute of veterinary medicine

institute: jiangsu academy of agricultural sciences

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2 mapping to reference genome
count counting
Genome_build: Gallus-5.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Gallus gallus

source_name: H9N2 AIV infected chicken DCs

growth_protocol: bone marrow monocytes were cultured in 6-well plates at a concentration of 5 × 106/ml in RPMI-1640 (Wisent) complete medium containing 5% FBS (Wisent), 100 U/ml penicillin and 100 µg/ml streptomycin for 6 hours at 41°C in 5% CO2, and then non-adherent cells were removed by replacing with fresh complete medium containing 50 ng/ml chicken GM-CSF (Abcam, USA), and 10 ng/ml IL-4 (Kingfisher, USA). Half of the medium was replaced with pre-warmed complete medium containing GM-CSF and IL-4 on every second day until day 6. At day 7, BM-DCs were used for the infection of H9N2 AIV

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction:  The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: The H9N2 influenza virus infected and mock infected cells were collected for RNA sequencing at 6 h post infection.

value: Bone marrow derived DCs

value: H9N2 AIV infection


title: Sample 29_nhp1_5_mock_raw

value: in vivo mock-infected NHP 1-Section 5


title: V_1


title: V_3


title: Sample 15_nhp2_4_inf_raw

value: MGAS2221 (infected NHP skeletal muscle tissue)

value: In vivo

value: in vivo infected NHP 2-Section 4


title: stage 10 ectodermal explant rep3

description:
5_10
Animal caps dissected at stage 9 and cultured to stage 10.
Tn5 digested and amplified.
processed data file: s10_sort.bed

value: Ectodermal explant

value: Early gastrula (stage 10)


title: Sample 14_nhp2_3_inf_raw

value: in vivo infected NHP 2-Section 3

value: Collected 24 h post-inoculation